bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quasi-simultaneous radio and X-ray observations of Aql X-1 : probing low luminosities
Authors: Gusinskaia N V , Hessels J W T , Degenaar N , Deller A T , Miller-Jones J C A , Archibald A M , Heinke C O , Moldón J , Patruno A , Tomsick J A , Wijnands R 
Published: December 2019

ABSTRACT
Aql X-1 is one of the best-studied neutron star low-mass X-ray binaries. It was previously targeted using quasi-simultaneous radio and X-ray observations during at least seven different accretion outbursts. Such observations allow us to probe the interplay between accretion inflow (X-ray) and jet outflow (radio). Thus far, these combined observations have only covered one order of magnitude in radio and X-ray luminosity range; this means that any potential radio–X-ray luminosity correlation, LR ∝ LXβ, is not well constrained (β ≈ 0.4–0.9, based on various studies) or understood. Here we present quasi-simultaneous Very Large Array and Swift-XRT observations of Aql X-1’s 2016 outburst, with which we probe one order of magnitude fainter in radio and X-ray luminosity compared to previous studies (6 × 1034 erg s−1 &lt; LX &lt;3 × 1035 erg s−1, i.e. the intermediate to low-luminosity regime between outburst peak and quiescence). The resulting radio non-detections indicate that Aql X-1’s radio emission decays more rapidly at low X-ray luminosities than previously assumed – at least during the 2016 outburst. Assuming similar behaviour between outbursts, and combining all available data in the hard X-ray state, this can be modelled as a steep β =$1.17^{+0.30}_{-0.21}$ power-law index or as a sharp radio cut-off at LX ≲ 5 × 1035 erg s−1 (given our deep radio upper limits at X-ray luminosities below this value). We discuss these results in the context of other similar studies.
Prospects for the characterization of the VHE emission from the Crab nebula and pulsar with the Cherenkov Telescope Array
Authors: Mestre E , de Oña Wilhelmi E , Zanin R , Torres D F , Tibaldo L 
Published: December 2019

ABSTRACT
The Cherenkov Telescope Array (CTA) will be the next generation instrument for the very high energy gamma-ray astrophysics domain. With its enhanced sensitivity in comparison with the current facilities, CTA is expected to shed light on a varied population of sources. In particular, we will achieve a deeper knowledge of the Crab nebula and pulsar, which are the best characterized pulsar wind nebula and rotation powered pulsar, respectively. We aim at studying the capabilities of CTA regarding these objects through simulations, using the main tools currently in development for the CTA future data analysis: gammapy and ctools. We conclude that, even using conservative Instrument Response Functions, CTA will be able to resolve many uncertainties regarding the spectrum and morphology of the pulsar and its nebula. The large energy range covered by CTA will allow us to disentangle the nebula spectral shape among different hypotheses, corresponding to different underlying emitting mechanisms. In addition, resolving internal structures (smaller than ∼0.02° in size) in the nebula and unveiling their location, would provide crucial information about the propagation of particles in the magnetized medium. We used a theoretical asymmetric model to characterize the morphology of the nebula and we showed that if predictions of such morphology exist, for instance as a result of hydrodynamical or magneto-hydrodynamical simulations, it can be directly compared with CTA results. We also tested the capability of CTA to detect periodic radiation from the Crab pulsar obtaining a precise measurement of different light curves shapes.
Implications of second-order resonance for the thermal and orbital evolution of Mimas
Authors: Tian ZhenLiang , Nimmo Francis 
Published: December 2019

ABSTRACT
Mimas’s current eccentricity is not being excited by any present-day resonance. We investigate whether its eccentricity could have been excited by passage through the set of resonances associated with the Mimas:Enceladus 3:2 commensurability, which occurred roughly 0.3 Gyr ago. Both the 3:2 e-Mimas resonance and the 6:4 mixed resonance can explain the present-day eccentricity without violating heat flux constraints imposed by the absence of relaxation of the Herschel impact basin. We favour the 6:4 mixed resonance because it occurs first and often prevents capture into the subsequent 3:2. During passage through the 6:4 the k2/Q of Mimas was less than $\rm 2\times 10^{-5}$, while that of Enceladus was $\lt \rm \sim 5\times 10^{-5}$. Mimas’s lack of dissipation can be explained by a cold, rigid ice shell and no subsurface ocean, while Enceladus must have subsequently become more dissipative, probably as a result of its capture into the 2:1 resonance with Dione.
A spider timing model: accounting for quadrupole deformations and relativity in close pulsar binaries
Authors: Voisin Guillaume , Breton René P , Summers Charlotte 
Published: December 2019

ABSTRACT
Spider millisecond pulsars are, along with some eclipsing post-common envelope systems and cataclysmic variables, part of an expanding category of compact binaries with low-mass companions for which puzzling timing anomalies have been observed. The most prominent type of irregularities seen in them are orbital period variations, a phenomenon which has been proposed to originate from changes in the gravitational quadrupole moment of the companion star. A physically sound modelling of the timing of these systems is key to understanding their structure and evolution. In this paper we argue that a complete timing model must account for relativistic corrections as well as rotationally and tidally induced quadrupole distortions. We solve for the resulting orbital dynamics using perturbation theory and derive the corresponding timing model in the low eccentricity limit. We find that the expected strong quadrupole deformation of the companion star results in an effective minimum orbital eccentricity. It is accompanied by a fast periastron precession which, if not taken into account, averages out any measurement of the said eccentricity. We show that, with our model, detection of both eccentricity and precession is likely to be made in many if not all spider pulsar systems. Combined with optical light curves, this will allow us to measure the apsidal motion constant, connecting the quadrupole deformation to the internal structure, and thus opening a new window into probing the nature of their exotic stellar interiors. Moreover, more accurate timing may eventually lead spider pulsars to be used for high-precision timing experiments such as pulsar timing arrays.
Origins of Type Ibn SNe 2006jc/2015G in interacting binaries and implications for pre-SN eruptions
Authors: Sun Ning-Chen , Maund Jusytn R , Hirai Ryosuke , Crowther Paul A , Podsiadlowski Philipp 
Published: December 2019

ABSTRACT
Type Ibn supernovae (SNe Ibn) are intriguing stellar explosions whose spectra exhibit narrow helium lines with little hydrogen. They trace the presence of circumstellar material (CSM) formed via pre-SN eruptions of their stripped-envelope progenitors. Early work has generally assumed that SNe Ibn come from massive Wolf–Rayet (WR) stars via single-star evolution. In this paper, we report ultraviolet (UV) and optical observations of two nearby Type Ibn SNe 2006jc and 2015G conducted with the Hubble Space Telescope (HST) at late times. A point source is detected at the position of SN 2006jc, and we confirm the conclusion of Maund et al. that it is the progenitor’s binary companion. Its position on the Hertzsprung–Russell (HR) diagram corresponds to a star that has evolved off the main sequence (MS); further analysis implies a low initial mass for the companion star (M2 ≤ 12.3$^{+2.3}_{-1.5}$ M⊙) and a secondary-to-primary initial mass ratio very close to unity (q = M2/M1 ∼ 1); the SN progenitor’s hydrogen envelope had been stripped through binary interaction. We do not detect the binary companion of SN 2015G. For both SNe, the surrounding stellar populations have relatively old ages and argue against any massive WR stars as their progenitors. These results suggest that SNe Ibn may have lower mass origins in interacting binaries. As a result, they also provide evidence that the giant eruptions commonly seen in massive luminous blue variables (LBVs) can also occur in much lower mass, stripped-envelope stars just before core collapse.
Microlensing and photon bunching: the impact of decoherence
Authors: Lewis Geraint F , Tuthill Peter 
Published: December 2019

ABSTRACT
Gravitational microlensing within the Galaxy offers the prospect of probing the details of distant stellar sources, as well as revealing the distribution of compact (and potentially non-luminous) masses along the line of sight. Recently, it has been suggested that additional constraints on the lensing properties can be determined through the measurement of the time delay between images through the correlation of the bunching of photon arrival times; an application of the Hanbury–Brown Twiss effect. In this paper, we revisit this analysis, examining the impact of decoherence of the radiation from a spatially extended source along the multiple paths to an observer. The result is that, for physically reasonable situations, such decoherence completely erases any correlation that could otherwise be used to measure the gravitational lensing time delay. Indeed, the divergent light paths traverse extremely long effective baselines at the lens plane, corresponding to extremes of angular resolving power well beyond those attainable with any terrestrial technologies; the drawback being that few conceivable celestial objects would be sufficiently compact with high enough surface brightness to yield usable signals.
60S acidic ribosomal protein P1 (RPLP1) is elevated in human endometriotic tissue and in a murine model of endometriosis and is essential for endometriotic epithelial cell survival in vitro
Authors: Alali Zahraa , Graham Amanda , Swan Kimberly , Flyckt Rebecca , Falcone Tommaso , Cui Wei , Yang Xiaofang , Christianson Julie , Nothnick Warren B 
Published: December 2019

Abstract
Endometriosis is a female disease which is defined as the presence of ectopic endometrial tissue and is dependent on estrogen for its survival in these ectopic locations. Expression of the ribosomal protein large P1 (RPLP1) is associated with cell proliferation and invasion in several pathologies, but a role in the pathophysiology of endometriosis has not been explored. In this study, we aimed to evaluate the expression and function of RPLP1 with respect to endometriosis pathophysiology. RPLP1 protein was localised by immunohistochemistry (IHC) in eutopic and ectopic tissue from 28 subjects with confirmed endometriosis and from 20 women without signs or symptoms of the disease, while transcript levels were evaluated by qRT-PCR in 77 endometriotic lesions and 55 matched eutopic endometrial biopsies, and protein expression was evaluated using western blotting in 20 of these matched samples. To evaluate the mechanism for enhanced lesion expression of RPLP1, an experimental murine model of endometriosis was used and RPLP1 expression was localized using IHC. In vitro studies using an endometriosis cell line coupled with shRNA knockdown was used to demonstrate its role in cell survival. Expression of RPLP1 mRNA and protein were significantly higher in ectopic lesion tissue compared to paired eutopic endometrium and immunohistochemical localisation revealed predominant localisation to epithelial cells. This pattern of lesion RPLP1 was recapitulated in mice with experimentally induced endometriosis. Stable knockdown of RPLP1 protein resulted in a significant decrease in cell survival in vitro. These studies reveal that RPLP1 is associated with cell proliferation and/or survival and may play a role in the pathophysiology of endometriosis.
Functional diversity of small nucleolar RNAs
Authors: Bratkovič Tomaž , Božič Janja , Rogelj Boris 
Published: December 2019

AbstractSmall nucleolar RNAs (snoRNAs) are short non-protein-coding RNAs with a long-recognized role in tuning ribosomal and spliceosomal function by guiding ribose methylation and pseudouridylation at targeted nucleotide residues of ribosomal and small nuclear RNAs, respectively. SnoRNAs are increasingly being implicated in regulation of new types of post-transcriptional processes, for example rRNA acetylation, modulation of splicing patterns, control of mRNA abundance and translational efficiency, or they themselves are processed to shorter stable RNA species that seem to be the principal or alternative bioactive isoform. Intriguingly, some display unusual cellular localization under exogenous stimuli, or tissue-specific distribution. Here, we discuss the new and unforeseen roles attributed to snoRNAs, focusing on the presumed mechanisms of action. Furthermore, we review the experimental approaches to study snoRNA function, including high resolution RNA:protein and RNA:RNA interaction mapping, techniques for analyzing modifications on targeted RNAs, and cellular and animal models used in snoRNA biology research.
Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin
Authors: Spracklin George , Pradhan Sriharsa 
Published: December 2019

Abstract
In metazoan cell nuclei, heterochromatin constitutes large chromatin domains that are in close contact with the nuclear lamina. These heterochromatin/lamina-associated domains (LADs) domains are difficult to profile and warrants a simpler and direct method. Here we report a new method, Protect-seq, aimed at identifying regions of heterochromatin via resistance to nuclease degradation followed by next-generation sequencing (NGS). We performed Protect-seq on the human colon cancer cell line HCT-116 and observed overlap with previously curated LADs. We provide evidence that these protected regions are enriched for and can distinguish between the repressive histone modification H3K9me3, H3K9me2 and H3K27me3. Moreover, in human cells the loss of H3K9me3 leads to an increase in chromatin accessibility and loss of Protect-seq signal. For further validation, we performed Protect-seq in the fibrosarcoma cell line HT1080 and found a similar correlation with previously curated LADs and repressive histone modifications. In sum, Protect-seq is an efficient technique that allows rapid identification of nuclease resistant chromatin, which correlate with heterochromatin and radial positioning.
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition
Authors: Yadav Deepak Kumar , Zigáčková Dagmar , Zlobina Maria , Klumpler Tomáš , Beaumont Christelle , Kubíčková Monika , Vaňáčová Štěpánka , Lukavsky Peter J 
Published: December 2019

AbstractStaufen1 (STAU1) is a dsRNA binding protein mediating mRNA transport and localization, translational control and STAU1-mediated mRNA decay (SMD). The STAU1 binding site (SBS) within human ADP-ribosylation factor1 (ARF1) 3′UTR binds STAU1 and this downregulates ARF1 cytoplasmic mRNA levels by SMD. However, how STAU1 recognizes specific mRNA targets is still under debate. Our structure of the ARF1 SBS–STAU1 complex uncovers target recognition by STAU1. STAU1 dsRNA binding domain (dsRBD) 4 interacts with two pyrimidines and one purine from the minor groove side via helix α1, the β1–β2 loop anchors the dsRBD at the end of the dsRNA and lysines in helix α2 bind to the phosphodiester backbone from the major groove side. STAU1 dsRBD3 displays the same binding mode with specific recognition of one guanine base. Mutants disrupting minor groove recognition of ARF1 SBS affect in vitro binding and reduce SMD in vivo. Our data thus reveal how STAU1 recognizes minor groove features in dsRNA relevant for target selection.
APE1 senses DNA single-strand breaks for repair and signaling
Authors: Lin Yunfeng , Raj Jude , Li Jia , Ha Anh , Hossain Md Akram , Richardson Christine , Mukherjee Pinku , Yan Shan 
Published: December 2019

Abstract
DNA single-strand breaks (SSBs) represent the most abundant type of DNA damage. Unrepaired SSBs impair DNA replication and transcription, leading to cancer and neurodegenerative disorders. Although PARP1 and XRCC1 are implicated in the SSB repair pathway, it remains unclear how SSB repair and SSB signaling pathways are coordinated and regulated. Using Xenopus egg extract and in vitro reconstitution systems, here we show that SSBs are first sensed by APE1 to initiate 3′–5′ SSB end resection, followed by APE2 recruitment to continue SSB end resection. Notably, APE1’s exonuclease activity is critical for SSB repair and SSB signaling pathways. An APE1 exonuclease-deficient mutant identified in somatic tissue from a cancer patient highlighted the significance of APE1 exonuclease activity in cancer etiology. In addition, APE1 interacts with APE2 and PCNA, although PCNA is dispensable for APE1’s exonuclease activity. Taken together, we propose a two-step APE1/APE2-mediated mechanism for SSB end resection that couples DNA damage response with SSB repair in a eukaryotic system.
The SINEB1 element in the long non-coding RNA Malat1 is necessary for TDP-43 proteostasis
Authors: Nguyen Tuan M , Kabotyanski Elena B , Reineke Lucas C , Shao Jiaofang , Xiong Feng , Lee Joo-Hyung , Dubrulle Julien , Johnson Hannah , Stossi Fabio , Tsoi Phoebe S , Choi Kyoung-Jae , Ellis Alexander G , Zhao Na , Cao Jin , Adewunmi Oluwatoyosi , Ferreon Josephine C , Ferreon Allan Chris M , Neilson Joel R , Mancini Michael A , Chen Xi , Kim Jongchan , Ma Li , Li Wenbo , Rosen Jeffrey M 
Published: December 2019

Abstract
Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse nuclear speckles and is frequently translocated to the cytoplasm. SINE-deleted cells exhibit an activated unfolded protein response and PKR and markedly increased DNA damage and apoptosis caused by dysregulation of TDP-43 localization and formation of cytotoxic inclusions. TDP-43 binds stronger to Malat1 without the SINE and is likely ‘hijacked’ by cytoplasmic Malat1 to the cytoplasm, resulting in the depletion of nuclear TDP-43 and redistribution of TDP-43 binding to repetitive element transcripts and mRNAs encoding mitotic and nuclear-cytoplasmic regulators. The SINE promotes Malat1 nuclear retention by facilitating Malat1 binding to HNRNPK, a protein that drives RNA nuclear retention, potentially through direct interactions of the SINE with KHDRBS1 and TRA2A, which bind to HNRNPK. Losing these RNA–protein interactions due to the SINE deletion likely creates more available TDP-43 binding sites on Malat1 and subsequent TDP-43 aggregation. These results highlight the significance of lncRNA TEs in TDP-43 proteostasis with potential implications in both cancer and neurodegenerative diseases.
Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1
Authors: Nomura Yuichiro , Montemayor Eric J , Virta Johanna M , Hayes Samuel M , Butcher Samuel E 
Published: December 2019

Abstract
U6 snRNA undergoes post-transcriptional 3′ end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3′ end of U6 and, in humans, leaves a 2′,3′ cyclic phosphate that is recognized by the Lsm2–8 complex. Saccharomycescerevisiae Usb1 has additional 2′,3′ cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3′ phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5′-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n – 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.
Blunt and Non-Blunt Cannabis Use and Risk of Subsequent Combustible Tobacco Product Use Among Adolescents
Authors: Mayer Margaret E , Kong Grace , Barrington-Trimis Jessica L , McConnell Rob , Leventhal Adam M , Krishnan-Sarin Suchitra 
Published: December 2019

Abstract

Introduction
Cannabis—including blunts (cannabis rolled in tobacco-containing cigar casing) —is commonly the first substance used among adolescents and may increase the likelihood of subsequent initiation of combustible tobacco products.

Aims and Methods
Data were pooled from two prospective studies of adolescents in California and Connecticut (total N = 4594). Logistic regression models assessed the association of baseline ever blunt use and ever non-blunt cannabis use (vs. never cannabis use) with subsequent initiation of any combustible tobacco-only product (ie, cigarettes, cigars, or cigarillos) by 1-year follow-up after adjustment for demographic characteristics and other tobacco product use at baseline. We also assessed whether estimates differed by prior e-cigarette or hookah use at baseline.

Results
Among never combustible tobacco-only product users (N = 2973), 221 (7.4%) had ever used a blunt and 114 (3.8%) had ever used only non-blunt cannabis at baseline. Blunt use (adjusted odds ratio [AOR] = 1.98, 95% confidence interval [CI]: 1.30 to 3.01) and non-blunt cannabis use (AOR = 2.38, 95% CI: 1.41 to 4.00) were independently associated with greater odds of combustible tobacco-only product initiation by follow-up. Among those who had not tried e-cigarettes or who had not tried hookah, blunt use and non-blunt cannabis use were associated with significantly increased odds of combustible tobacco product initiation; among those who had tried e-cigarettes or hookah, the association was not significant.

Conclusions
We found blunt and non-blunt cannabis use to be associated with subsequent combustible tobacco-only product initiation, particularly among adolescents who had not also tried other products containing nicotine.

Implications
Adolescent-focused tobacco prevention efforts should consider incorporating cannabis products, including blunts. More research is needed to understand how blunt use and cannabis use more broadly are associated with initiation of tobacco products.
The plight of the skyscraper wean: public health and the Jeely Piece Song
Authors: Shaw David M 
Published: December 2019

Abstract
In this Chekhov's Corner article, I explore the public health lessons of a famous Scottish folk song. The Jeely Piece Song uses humour to highlight the health inequalities and other challenges facing children in one of Glasgow's new townships in the 1960s, some of which still persist today.
Complicated Diverticulitis
Authors: Mendez-Pastor Alvaro , Garcia-Henriquez Norbert 
Published: December 2019

CASE SUMMARY:
A 62-year-old previously healthy man presented with left lower quadrant pain and fever. Physical examination showed left lower quadrant peritonitis. Computed tomography scan showed a pelvic abscess with extraluminal air (Fig. 1). Intravenous antibiotics were started, and CT-guided percutaneous drainage was performed. The drain was removed 1 week after discharge. One week later, he presented with dysuria and pneumaturia and was started on antibiotics. Colonoscopy confirmed diverticulosis with no other mucosal abnormalities. He underwent a successful laparoscopic sigmoidectomy with colovesical fistula takedown.