bluuebunny/crossref_metadata_2025_split huggingface dataset:
A young and obscured AGN embedded in the giant radio galaxy Mrk 1498
Authors: Hernández-García L , Panessa F , Bassani L , Bruni G , Ursini F , Chavushyan V , González-Martín O , Cazzoli S , Jiménez-Andrade E F , Arévalo P , Díaz Y , Bazzano A , Ubertini P 
Published: August 2019

Abstract
Mrk 1498 is part of a sample of galaxies with extended emission line regions (extended outwards up to a distance of ∼7 kpc) suggested to be photo-ionized by an AGN that has faded away or that is still active but heavily absorbed. Interestingly, the nucleus of Mrk 1498 is at the center of two giant radio lobes with a projected linear size of 1.1 Mpc. Our multi-wavelength analysis reveals a complex nuclear structure, with a young radio source (Giga-hertz Peaked Spectrum) surrounded by a strong X-ray nuclear absorption, a mid-infrared spectrum that is dominated by the torus emission, plus a circum-nuclear extended emission in the [OIII] image (with radius of ∼ 1 kpc), most likely related to the ionization of the AGN, aligned with the small and large scale radio jet and extended also at X-rays. In addition a large-scale extended emission (up to ∼ 10 kpc) is only visible in [OIII]. These data show conclusive evidence of a heavily absorbed nucleus and has recently restarted its nuclear activity. To explain its complexity, we propose that Mrk 1498 is the result of a merging event or secular processes, such as a minor interaction, that has triggered the nuclear activity and produced tidal streams. The large-scale extended emission that gives place to the actual morphology could either be explained by star formation or outflowing material from the AGN.
NuSTAR and XMM–Newton observations of SXP 59 during its 2017 giant outburst
Authors: Weng Shan-Shan , Ge Ming-Yu , Zhao Hai-Hui 
Published: August 2019

ABSTRACT
The Be X-ray pulsar (BeXRP) SXP 59 underwent a giant outburst in 2017 with a peak X-ray luminosity of 1.1 × 1038 erg s−1. We report on the X-ray behaviour of SXP 59 with the XMM–Newton and NuSTAR observations collected at the outburst peak, decay, and the low luminosity states. The pulse profiles are energy dependent, the pulse fraction increases with the photon energy and saturates at 65 per cent above 10 keV. It is difficult to constrain the change in the geometry of emitting region with the limited data. Nevertheless, because the pulse shape generally has a double-peaked profile at high luminosity and a single peak profile at low luminosity, we prefer the scenario that the source transited from the super-critical state to the sub-critical regime. This result would further imply that the neutron star (NS) in SXP 59 has a typical magnetic field. We confirm that the soft excess revealed below 2 keV is dominated by a cool thermal component. On the other hand, the NuSTAR spectra can be described as a combination of the non-thermal component from the accretion column, a hot blackbody emission, and an iron emission line. The temperature of the hot thermal component decreases with time, while its size remains constant (R ∼ 0.6 km). The existence of the hot blackbody at high luminosity cannot be explained with the present accretion theories for BeXRPs. It means that either more sophisticated spectral models are required to describe the X-ray spectra of luminous BeXRPs, or there is non-dipole magnetic field close to the NS surface.
Helium settling in F stars: constraining turbulent mixing using observed helium glitch signature
Authors: Verma Kuldeep , Silva Aguirre Víctor 
Published: August 2019

ABSTRACT
Recent developments in asteroseismology – due to space-based missions such as CoRoT and Kepler – provide handles on those properties of stars that were either completely inaccessible in the past or only poorly measured. Among several such properties is the surface helium abundance of F and G stars. We used the oscillatory signature introduced by the ionization of helium in the observed oscillation frequencies to constrain the amount of helium settling in F stars. For this purpose, we identified three promising F stars for which the standard models of atomic diffusion predict large settling (or complete depletion) of surface helium. Assuming turbulence at the base of envelope convection zone slows down settling of the helium and heavy elements, we found an envelope mixed mass of approximately 5 × 10−4 M⊙ necessary to reproduce the observed amplitude of helium signature for all the three stars. This is much larger than the mixed mass of the order of 10−6 M⊙ found in the previous studies performed using the measurements of the heavy element abundances. This demonstrates the potential of using the helium signature together with measurements of the heavy element abundances to identify the most important physical processes competing against atomic diffusion, allowing eventually to correctly interpret the observed surface abundances of hot stars, consistent use of atomic diffusion in modelling both hot and cool stars, and shed some light on the long-standing cosmological lithium problem.
Longitudinal wave instability due to rotating beam-plasma interaction in weakly turbulent astrophysical plasmas
Authors: Khorashadizadeh S M , Rostami Sh Abbasi , Niknam A R , Farahani S Vasheghani , Fallah R 
Published: August 2019

ABSTRACTThe aim of this study is to highlight the temporal evolution of the longitudinal wave instability due to the interaction between a rotating electron beam and the magnetoactive plasma region in space plasma structures. The plasma structure which could be either in the solar atmosphere or any active plasma region in space is considered weakly turbulent, where the quasi-linear theory is implemented to enable analytic insight on the wave–particle interaction in the course of the event. It is found that in a weakly turbulent plasma, quasi-linear saturation of the longitudinal wave is accompanied by a significant alteration in the distribution function in the resonant region. In case of a pure electrostatic wave, the wave amplitude experiences elevation due to the energy transfer from the plasma particles. This causes flattening of the bump on tail (BOT) in the electron distribution function. If the gradient of the distribution function is positive, the chance that the beam would excite the wave is probable. In such a situation a plateau on the distribution function (∂f/∂v ≈ 0) is formed that will stop the diffusion of beam particles in the velocity space. Evolution of the electron distribution function experiences a decreases of the instability of the longitudinal wave. It is deduced that the growth rate of the wave instability is inversely proportional to the wave energy. Regarding the Sun, in addition to creating micro-turbulence due to wave–particle interaction, as the wave elevates to higher altitudes it enters a saturated energy state before releasing energy that may be a candidate for the generation of radio bursts.
N-body simulations of terrestrial planet growth with resonant dynamical friction
Authors: Wallace Spencer C , Quinn Thomas R 
Published: August 2019

ABSTRACTWe investigate planetesimal accretion via a direct N-body simulation of an annulus at 1 au orbiting a 1 M$\odot$ star. The planetesimal ring, which initially contains N = 106 bodies is evolved into the oligarchic growth phase. Unlike previous lower resolution studies, we find that the mass distribution of planetesimals develops a bump at intermediate mass after the oligarchs form. This feature marks a boundary between growth modes. The smallest planetesimals are packed tightly enough together to populate mean motion resonances with the oligarchs, which heats the small bodies, enhancing their growth. If we depopulate most of the resonances by decreasing the width of the annulus, this effect becomes weaker. To clearly demonstrate the dynamics driving these growth modes, we also examine the evolution of a planetary embryo embedded in an annulus of collisionless planetesimals. In this case, we find that the resonances push planetesimals away from the embryo, decreasing the surface density of the bodies adjacent to the embryo. This effect only occurs when the annulus is wide enough and the mass resolution of the planetesimals is fine enough to populate the resonances. The bump we observe in the mass distribution resembles the 100 km power-law break seen in the size distribution of asteroid belt objects. Although the bump produced in our simulations occurs at a size larger than 100 km, we show that the bump location is sensitive to the initial planetesimal mass, which implies that this feature is potentially useful for constraining planetesimal formation models.
NUQA: Estimating Cancer Spatial and Temporal Heterogeneity and Evolution through Alignment-Free Methods
Authors: Roddy Aideen C , Jurek-Loughrey Anna , Souza Jose , Gilmore Alan , O’Reilly Paul G , Stupnikov Alexey , Gonzalez de Castro David , Prise Kevin M , Salto-Tellez Manuel , McArt Darragh G 
Published: August 2019

Abstract
Longitudinal next-generation sequencing of cancer patient samples has enhanced our understanding of the evolution and progression of various cancers. As a result, and due to our increasing knowledge of heterogeneity, such sampling is becoming increasingly common in research and clinical trial sample collections. Traditionally, the evolutionary analysis of these cohorts involves the use of an aligner followed by subsequent stringent downstream analyses. However, this can lead to large levels of information loss due to the vast mutational landscape that characterizes tumor samples.
Here, we propose an alignment-free approach for sequence comparison—a well-established approach in a range of biological applications including typical phylogenetic classification. Such methods could be used to compare information collated in raw sequence files to allow an unsupervised assessment of the evolutionary trajectory of patient genomic profiles.
In order to highlight this utility in cancer research we have applied our alignment-free approach using a previously established metric, Jensen–Shannon divergence, and a metric novel to this area, Hellinger distance, to two longitudinal cancer patient cohorts in glioma and clear cell renal cell carcinoma using our software, NUQA.
We hypothesize that this approach has the potential to reveal novel information about the heterogeneity and evolutionary trajectory of spatiotemporal tumor samples, potentially revealing early events in tumorigenesis and the origins of metastases and recurrences.
Key words: alignment-free, Hellinger distance, exome-seq, evolution, phylogenetics, longitudinal.
Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils
Authors: Patton Austin H , Margres Mark J , Stahlke Amanda R , Hendricks Sarah , Lewallen Kevin , Hamede Rodrigo K , Ruiz-Aravena Manuel , Ryder Oliver , McCallum Hamish I , Jones Menna E , Hohenlohe Paul A , Storfer Andrew 
Published: August 2019

AbstractReconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ∼300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species’ effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved
Authors: Ntountoumi Chrysa , Vlastaridis Panayotis , Mossialos Dimitris , Stathopoulos Constantinos , Iliopoulos Ioannis , Promponas Vasilios , Oliver Stephen G , Amoutzias Grigoris D 
Published: August 2019

Abstract
We provide the first high-throughput analysis of the properties and functional role of Low Complexity Regions (LCRs) in more than 1500 prokaryotic and phage proteomes. We observe that, contrary to a widespread belief based on older and sparse data, LCRs actually have a significant, persistent and highly conserved presence and role in many and diverse prokaryotes. Their specific amino acid content is linked to proteins with certain molecular functions, such as the binding of RNA, DNA, metal-ions and polysaccharides. In addition, LCRs have been repeatedly identified in very ancient, and usually highly expressed proteins of the translation machinery. At last, based on the amino acid content enriched in certain categories, we have developed a neural network web server to identify LCRs and accurately predict whether they can bind nucleic acids, metal-ions or are involved in chaperone functions. An evaluation of the tool showed that it is highly accurate for eukaryotic proteins as well.
Functional analysis of Cwc24 ZF-domain in 5′ splice site selection
Authors: Wu Nan-Ying , Cheng Soo-Chen 
Published: August 2019

AbstractThe essential splicing factor Cwc24 contains a zinc-finger (ZF) domain required for its function in splicing. Cwc24 binds over the 5′ splice site after the spliceosome is activated, and its binding prior to Prp2-mediated spliceosome remodeling is important for proper interactions of U5 and U6 with the 5′ splice site sequence and selection of the 5′ splice site. Here, we show that Cwc24 transiently interacts with the 5′ splice site in formation of the functional RNA catalytic core during spliceosome remodeling, and the ZF-motif is required for specific interaction of Cwc24 with the 5′ splice site. Deletion of the ZF domain or mutation of the conserved ZF residues greatly weakened the association of Cwc24 with the spliceosome, and lowered the affinity and specificity of its interaction with the 5′ splice site, resulting in atypical interactions of U5, U6 and Prp8 with the 5′ splice site, and aberrant cleavage at the 5′ splice site. Our results reveal a crucial role of the Cwc24 ZF-motif for defining 5′ splice site selection in the first splicing step.
Alternative ORFs and small ORFs: shedding light on the dark proteome
Authors: Orr Mona Wu , Mao Yuanhui , Storz Gisela , Qian Shu-Bing 
Published: August 2019

AbstractTraditional annotation of protein-encoding genes relied on assumptions, such as one open reading frame (ORF) encodes one protein and minimal lengths for translated proteins. With the serendipitous discoveries of translated ORFs encoded upstream and downstream of annotated ORFs, from alternative start sites nested within annotated ORFs and from RNAs previously considered noncoding, it is becoming clear that these initial assumptions are incorrect. The findings have led to the realization that genetic information is more densely coded and that the proteome is more complex than previously anticipated. As such, interest in the identification and characterization of the previously ignored ‘dark proteome’ is increasing, though we note that research in eukaryotes and bacteria has largely progressed in isolation. To bridge this gap and illustrate exciting findings emerging from studies of the dark proteome, we highlight recent advances in both eukaryotic and bacterial cells. We discuss progress in the detection of alternative ORFs as well as in the understanding of functions and the regulation of their expression and posit questions for future work.
Dietary fiber and its associations with depression and inflammation
Authors: Swann Olivia G , Kilpatrick Michelle , Breslin Monique , Oddy Wendy H 
Published: August 2019

AbstractDietary fiber is a crucial component of a healthy diet, with benefits that can be attributed to processes in the gut microbiota and the resulting by-products. Observational studies support associations between dietary fiber intake and depression and inflammation, but the potential mechanisms are poorly understood. This review examines evidence of the effects of dietary fiber on depression and inflammation and considers plausible mechanisms linking dietary fiber and depression, including microbiota-driven modification of gene expression and increased production of neurotransmitters. Additionally, inflammation may mediate the relationship between dietary fiber intake and depression. A high-fiber diet potentially lowers inflammation by modifying both the pH and the permeability of the gut. The resultant reduction in inflammatory compounds may alter neurotransmitter concentrations to reduce symptoms of depression. Further research into the link between dietary fiber intake and inflammation and depression is essential, as findings could potentially provide guidance for improvement in or prevention of inflammatory and depressive disorders.
A comprehensive classification of monetary policy frameworks in advanced and emerging economies
Authors: Cobham David 
Published: August 2019

Abstract
The paper presents a new classification of monetary policy frameworks that it applies to advanced and emerging economies for the period since the end of the Bretton Woods international monetary system, with a focus on the monetary authorities’ objectives (domestic and external), and on pre-announced targets and actual performance. The classification (available at www.monetaryframeworks.org) also emphasizes the underlying monetary and financial infrastructure that conditions the instruments available to the authorities and, therefore, the coherence of different frameworks. It is constructed mainly from a close reading of IMF Article IV consultation reports. The two major changes revealed by the data are the trends over time towards a heavier focus on inflation, and towards more systematic and coherent monetary arrangements.
Type II Ice-Binding Proteins Isolated from an Arctic Microalga Are Similar to Adhesin-Like Proteins and Increase Freezing Tolerance in Transgenic Plants
Authors: Cho Sung Mi , Kim Sanghee , Cho Hojin , Lee Hyoungseok , Lee Jun Hyuck , Lee Horim , Park Hyun , Kang Seunghyun , Choi Han-Gu , Lee Jungeun 
Published: August 2019

AbstractMicroalgal ice-binding proteins (IBPs) in the polar region are poorly understood at the genome-wide level, although they are important for cold adaptation. Through the transcriptome study with the Arctic green alga Chloromonas sp. KNF0032, we identified six Chloromonas IBP genes (CmIBPs), homologous with the previously reported IBPs from Antarctic snow alga CCMP681 and Antarctic Chloromonas sp. They were organized with multiple exon/intron structures and low-temperature-responsive cis-elements in their promoters and abundantly expressed at low temperature. The biological functions of three representative CmIBPs (CmIBP1, CmIBP2 and CmIBP3) were tested using in vitro analysis and transgenic plant system. CmIBP1 had the most effective ice recrystallization inhibition (IRI) activities in both in vitro and transgenic plants, and CmIBP2 and CmIBP3 had followed. All transgenic plants grown under nonacclimated condition were freezing tolerant, and especially 35S::CmIBP1 plants were most effective. After cold acclimation, only 35S::CmIBP2 plants showed slightly increased freezing tolerance. Structurally, the CmIBPs were predicted to have β-solenoid forms with parallel β-sheets and repeated TXT motifs. The repeated TXT structure of CmIBPs appears similar to the AidA domain-containing adhesin-like proteins from methanogens. We have shown that the AidA domain has IRI activity as CmIBPs and phylogenetic analysis also supported that the AidA domains are monophyletic with ice-binding domain of CmIBPs, and these results suggest that CmIBPs are a type of modified adhesins.
The Impact of Childhood Emotional Abuse on Pain Interference Among People with Chronic Pain who Inject Drugs in Vancouver, Canada
Authors: Prangnell Amy , Shoveller Jean , Voon Pauline , Shulha Hennady , Grant Cameron , Milloy M -J , Kerr Thomas , Hayashi Kanna 
Published: August 2019

Abstract

Objective
High levels of chronic pain interference with daily activities are known to negatively impact quality of life. Although mental health conditions have been associated with pain interference and child abuse, research has been mixed regarding it acting as a mediator, with even less known among people who inject drugs. Therefore, we sought to explore childhood emotional abuse and pain interference among this population.

Methods
Data were derived from two prospective cohort studies of community-recruited people who inject drugs in Vancouver, Canada, between June 2014 and November 2016. We employed multivariable generalized estimating equations to examine the relationship between childhood emotional abuse and pain interference in the past six months. We also conducted a mediation analysis to examine whether mental health disorder diagnoses mediated this association.

Results
Among 822 eligible participants, 341 (41.5%) reported childhood emotional abuse. In a multivariable analysis, experiencing childhood emotional abuse remained independently associated with pain interference (adjusted odds ratio = 1.33, 95% confidence interval [CI] = 1.05–1.70) after adjusting for a range of confounders. Results from the mediation analysis yielded a statistically significant positive average causal mediation effect (β = 0.01, 95% CI = 0.001–0.02). Approximately 12% of the effect was due to mediation.

Conclusions
Our results demonstrate among people who inject drugs with chronic pain, those who experienced childhood emotional abuse were more likely to report pain interference, which was partially mediated by mental health disorder diagnosis history. These findings highlight the importance of incorporating screening and appropriate treatment for mental illness into chronic pain treatment.
Creating a Change Culture in a Police Service: The Role of Police Leadership
Authors: Dubord Neil , Griffiths Curt Taylor 
Published: August 2019

Abstract
Despite the increased emphasis on best practices and evidence-based policing, creating a change culture in police services has remained elusive. Few police agencies have developed the capacity to assess the effectiveness and efficiency of their operations, and there has often been a lack of innovative police leadership to lead reform efforts. This article presents a case study of a municipal police service that transformed the delivery of patrol services and, in so doing, altered the culture of the organization. The role played by an independent review of the department’s patrol division, the service delivery model that was developed, and the strategies used by senior management to secure buy-in from the membership via a department-wide collaborative process are discussed. The discussion concludes with the identification of key requirements for police leaders to create a change culture in their police services and, in so doing, improve the effectiveness and efficiency of the delivery of police services.