bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of polymorphisms in MALAT1 with the risk of endometriosis in Southern Chinese women
Authors: Chen Guange , Zhang Mingyao , Liang Zongwen , Chen Sailing , Chen Feng , Zhu Jiawei , Zhao Manman , Xu Chaoyi , He Jing , Hua Wenfeng , Duan Ping
Published: December 2019

Endometriosis is a common estrogen-dependent inflammatory disease characterized by the presence of endometrial-like tissue outside the uterine cavity, which causes infertility and pelvic pain. Polymorphisms in MALAT1 have been demonstrated to play crucial roles in many diseases. However, the roles of MALAT1 polymorphisms in the etiology of endometriosis have not been well documented. We genotyped three MALAT1 polymorphisms in 555 endometriosis patients and 535 female control participants using quantitative polymerase chain reaction with TaqMan probes. To estimate the associations between MALAT1 polymorphisms and endometriosis risk, an unconditional logistic regression model was conducted to calculate an odds ratio (OR) and the 95% confidence interval (CI), adjusting for age, abortion history, number of deliveries, Body Mass Index (BMI), and The International Federation of Gynecology and Obstetrics (FIGO) stage. We found that the MALAT1 rs591291 C > T polymorphism significantly enhanced endometriosis risk (heterogeneous: adjusted OR = 1.36, 95% CI = 1.00–1.85, P = 0.050; homogenous: adjusted OR = 1.55, 95% CI = 1.03–2.33, P = 0.037; dominant: adjusted OR = 1.41, 95% CI = 1.05–1.88, P = 0.021). In stratification analyses, these associations were more predominant in the patients younger than 35 years old, with a relatively high number of deliveries and with a BMI between 25 and 29.9. Compared with wild-type CCG haplotype carriers, individuals with TCC haplotypes had a higher risk of developing endometriosis. The MALAT1 rs591291 C > T polymorphism was associated with a significant increase in endometriosis risk.
Loss of Dmrt5 Affects the Formation of the Subplate and Early Corticogenesis
Authors: Ratié Leslie , Desmaris Elodie , García-Moreno Fernando , Hoerder-Suabedissen Anna , Kelman Alexandra , Theil Thomas , Bellefroid Eric J , Molnár Zoltán
Published: December 2019

Dmrt5 (Dmrta2) and Dmrt3 are key regulators of cortical patterning and progenitor proliferation and differentiation. In this study, we show an altered apical to intermediate progenitor transition, with a delay in SP neurogenesis and premature birth of Ctip2+ cortical neurons in Dmrt5−/− mice. In addition to the cortical progenitors, DMRT5 protein appears present in postmitotic subplate (SP) and marginal zone neurons together with some migrating cortical neurons. We observed the altered split of preplate and the reduced SP and disturbed radial migration of cortical neurons into cortical plate in Dmrt5−/− brains and demonstrated an increase in the proportion of multipolar cells in primary neuronal cultures from Dmrt5−/− embryonic brains. Dmrt5 affects cortical development with specific time sensitivity that we described in two conditional mice with slightly different deletion time. We only observed a transient SP phenotype at E15.5, but not by E18.5 after early (Dmrt5lox/lox;Emx1Cre), but not late (Dmrt5lox/lox;NestinCre) deletion of Dmrt5. SP was less disturbed in Dmrt5lox/lox;Emx1Cre and Dmrt3−/− brains than in Dmrt5−/− and affects dorsomedial cortex more than lateral and caudal cortex. Our study demonstrates a novel function of Dmrt5 in the regulation of early SP formation and radial cortical neuron migration.

Summary Statement

Our study demonstrates a novel function of Dmrt5 in regulating marginal zone and subplate formation and migration of cortical neurons to cortical plate.
Salt Fish Girl and “Hopeful Monsters”: Using Monstrous Reproduction to Disrupt Science Fiction’s Colonial Fantasies
Authors: Sharp Sabine Ruth
Published: December 2019

The revival of the Frankenstein origin myth has left science fiction’s relationship to colonialism undertheorized. More recent creative interventions have, however, challenged the genre’s colonialist legacy: two works that achieve this are Larissa Lai’s novel Salt Fish Girl (2002) and Hiromi Goto’s short story “Hopeful Monsters” (2004). Using different forms of unruly reproduction—strange births, recurring histories, and eclectic intertextuality—these texts unravel the tangled histories of science fiction and colonialism. Using tropes of repetition and mutation, Lai and Goto trace not a myth of origins but the texture of interwoven histories of gendered and racialized oppression. Monstrous patchworks of texts, these works interrogate the boundaries between science fiction, myth, folklore, and fantasy, showing these generic distinctions to have been buttressed by colonialist discourses.
Language and Reading Progress of Young Deaf and Hard-of-Hearing Children
Authors: Antia Shirin D , Lederberg Amy R , Easterbrooks Susan , Schick Brenda , Branum-Martin Lee , Connor Carol M , Webb Mi-Young
Published: December 2019

We examined the language and reading progress of 336 young DHH children in kindergarten, first and second grades. Trained assessors tested children’s language, reading, and spoken and fingerspelled phonological awareness in the fall and spring of the school year. Children were divided into groups based on their auditory access and classroom communication: a spoken-only group (n = 101), a sign-only group (n = 131), and a bimodal group (n = 104). Overall, children showed delays in language and reading compared to norms established for hearing children. For language, vocabulary standard scores were higher than for English syntax. Although delayed in language, children made expected gains based on hearing norms from kindergarten to second grade. Reading scores declined from kindergarten to second grade. Spoken-only and bimodal children had similar word reading and reading comprehension abilities and higher scores than sign-only children. Spoken-only children had better spoken phonological awareness and nonword reading skills than the other two groups. The sign-only and bimodal groups made similar and significant gains in ASL syntax and fingerspelling phonological awareness.
Circulating stem cells and cardiovascular outcomes: from basic science to the clinic
Authors: Fadini Gian Paolo , Mehta Anurag , Dhindsa Devinder Singh , Bonora Benedetta Maria , Sreejit Gopalkrishna , Nagareddy Prabhakara , Quyyumi Arshed Ali
Published: December 2019

The cardiovascular and haematopoietic systems have fundamental inter-relationships during development, as well as in health and disease of the adult organism. Although haematopoietic stem cells (HSCs) emerge from a specialized haemogenic endothelium in the embryo, persistence of haemangioblasts in adulthood is debated. Rather, the vast majority of circulating stem cells (CSCs) is composed of bone marrow-derived HSCs and the downstream haematopoietic stem/progenitors (HSPCs). A fraction of these cells, known as endothelial progenitor cells (EPCs), has endothelial specification and vascular tropism. In general, the levels of HSCs, HSPCs, and EPCs are considered indicative of the endogenous regenerative capacity of the organism as a whole and, particularly, of the cardiovascular system. In the last two decades, the research on CSCs has focused on their physiologic role in tissue/organ homoeostasis, their potential application in cell therapies, and their use as clinical biomarkers. In this review, we provide background information on the biology of CSCs and discuss in detail the clinical implications of changing CSC levels in patients with cardiovascular risk factors or established cardiovascular disease. Of particular interest is the mounting evidence available in the literature on the close relationships between reduced levels of CSCs and adverse cardiovascular outcomes in different cohorts of patients. We also discuss potential mechanisms that explain this association. Beyond CSCs’ ability to participate in cardiovascular repair, levels of CSCs need to be interpreted in the context of the broader connections between haematopoiesis and cardiovascular function, including the role of clonal haematopoiesis and inflammatory myelopoiesis.
The influence of scar on the spatio-temporal relationship between electrical and mechanical activation in heart failure patients
Authors: Maffessanti Francesco , Jadczyk Tomasz , Kurzelowski Radosław , Regoli François , Caputo Maria Luce , Conte Giulio , Gołba Krzysztof S , Biernat Jolanta , Wilczek Jacek , Dąbrowska Magdalena , Pezzuto Simone , Moccetti Tiziano , Krause Rolf , Wojakowski Wojciech , Prinzen Frits W , Auricchio Angelo
Published: December 2019

Aims

The aim of this study was to determine the relationship between electrical and mechanical activation in heart failure (HF) patients and whether electromechanical coupling is affected by scar.

Methods and results

Seventy HF patients referred for cardiac resynchronization therapy or biological therapy underwent endocardial anatomo-electromechanical mapping (AEMM) and delayed-enhancement magnetic resonance (CMR) scans. Area strain and activation times were derived from AEMM data, allowing to correlate mechanical and electrical activation in time and space with unprecedented accuracy. Special attention was paid to the effect of presence of CMR-evidenced scar. Patients were divided into a scar (n = 43) and a non-scar group (n–27). Correlation between time of electrical and mechanical activation was stronger in the non-scar compared to the scar group [R = 0.84 (0.72–0.89) vs. 0.74 (0.52–0.88), respectively; P = 0.01]. The overlap between latest electrical and mechanical activation areas was larger in the absence than in presence of scar [72% (54–81) vs. 56% (36–73), respectively; P = 0.02], with smaller distance between the centroids of the two regions [10.7 (4.9–17.4) vs. 20.3 (6.9–29.4) % of left ventricular radius, P = 0.02].

Conclusion

Scar decreases the association between electrical and mechanical activation, even when scar is remote from late activated regions.
The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging
Authors: Barrera-Vázquez Oscar Salvador , Gomez-Verjan Juan Carlos
Published: December 2019

In the last decades, improvements in different aspects of sanitation, medical care, and nutrition, among others, have permitted an increase in the average lifespan of human population around the world. These advances have stimulated an increased interest in the study of the aging process and age-sensitive characteristics, such as the microbial community that colonizes the human body (microbiome). The human microbiome is composed of bacteria (bacteriome), archaea (archaeome), fungi (mycobiome), and viruses (virome). To date, research has mainly been centered on the composition of the bacteriome, with other members remain poorly studied. Interestingly, changes in the composition of the microbiome have been implicated in aging and age-related diseases. Therefore, in the present perspective, we suggest expanding the scope to research to include the role and the possible associations that the other members of the microbiome could have in the aging organism. An expanded view of the microbiome would increase our knowledge of the physiology of aging and may be particularly valuable for the treatment and diagnosis of age-related diseases.
New Directions to Advance Family Caregiving Research
Authors: Hepburn Ken , Siegel Elena O
Published: December 2019

This supplement describes the content, processes, and outcomes of the Research Priorities in Caregiving Summit convened by the Family Caregiving Institute (FCI) at the Betty Irene Moore School of Nursing at UC Davis in March 2018. As described in the editorial introduction and the supplement’s four papers, the summit sought to integrate and cross-pollenate the already compendious work on family caregiving to describe ways forward in the field. Thought-provoking commissioned synthesizing papers on issues of heterogeneity and trajectories of caregiving and its cultural embeddedness and on the potential of technology to shape and enhance caregiving interventions set the stage for a highly disciplined, multistaged process that resulted in the drafting of a set of research themes and priorities that were later finalized by faculty at the FCI.
Denoising ambient seismic field correlation functions with convolutional autoencoders
Authors: Viens Loïc , Van Houtte Chris
Published: December 2019

Seismic interferometry is an established method for monitoring the temporal evolution of the Earth’s physical properties. We introduce a new technique to improve the precision and temporal resolution of seismic monitoring studies based on deep learning. Our method uses a convolutional denoising autoencoder, called ConvDeNoise, to denoise ambient seismic field correlation functions. The technique can be applied to traditional two-station cross-correlation functions but this study focuses on single-station cross-correlation (SC) functions. SC functions are computed by cross correlating the different components of a single seismic station and can be used to monitor the temporal evolution of the Earth’s near surface. We train and apply our algorithm to SC functions computed with a time resolution of 20 min at seismic stations in the Tokyo metropolitan area, Japan. We show that the relative seismic velocity change [dv/v(t)] computed from SC functions denoised with ConvDeNoise has less variability than that calculated from raw SC functions. Compared to other denoising methods such as the SVD-based Wiener Filter method developed by Moreau et al., the dv/v results obtained after using our algorithm have similar precision. The advantage of our technique is that once the algorithm is trained, it can be apply to denoise near-real-time SC functions. The near-real-time aspect of our denoising algorithm may be useful for operational hazard forecasting models, for example when applying seismic interferometry at an active volcano.
How Scary Are Threat Appeals? Evaluating the Intensity of Fear in Experimental Research
Authors: Dillard James Price , Li Shu Scott
Published: December 2019

One long-standing concern holds that much is unknown about the operation of threat appeals because practical and ethical matters preclude the use of seriously frightening messages. This project compared the intensity of fear produced by experimental messages with that produced by adverse events, such as wars and hurricanes. Results showed that threat appeals (k = 80; N = 6,738; Δ = 2.15) have been effective at inducing levels of fear that are on par with the fear induced by real-world occurrences (k = 19, N = 4,928, Δ = 2.01). Thus, the positive, linear association between threat (X) and persuasion (Y) observed in previous meta-analyses is probably an accurate characterization of the X-Y association: a finding that is inconsistent with inverted-U theories. The distribution of fear values produced by the experimental messages provides empirical benchmarks for future research.
Insights into the genetic basis of retinal detachment
Authors: Boutin Thibaud S , Charteris David G , Chandra Aman , Campbell Susan , Hayward Caroline , Campbell Archie ,   UK Biobank Eye & Vision Consortium, Nandakumar Priyanka , Hinds David ,   23andMe Research Team, Mitry Danny , Vitart Veronique , Agee Michelle , Alipanahi Babak , Auton Adam , Bell Robert K , Bryc Katarzyna , Elson Sarah L , Fontanillas Pierre , Furlotte Nicholas A , Hicks Barry , Huber Karen E , Jewett Ethan M , Jiang Yunxuan , Kleinman Aaron , Lin Keng-Han , Litterman Nadia K , McIntyre Matthew H , McManus Kimberly F , Mountain Joanna L , Noblin Elizabeth S , Northover Carrie A M , Pitts Steven J , Poznik G David , Sathirapongsasuti J Fah , Shelton Janie F , Shringarpure Suyash , Tian Chao , Tung Joyce Y , Vacic Vladimir , Wang Xin , Wilson Catherine H
Published: December 2019

Retinal detachment (RD) is a serious and common condition, but genetic studies to date have been hampered by the small size of the assembled cohorts. In the UK Biobank data set, where RD was ascertained by self-report or hospital records, genetic correlations between RD and high myopia or cataract operation were, respectively, 0.46 (SE = 0.08) and 0.44 (SE = 0.07). These correlations are consistent with known epidemiological associations. Through meta-analysis of genome-wide association studies using UK Biobank RD cases (N = 3 977) and two cohorts, each comprising ~1 000 clinically ascertained rhegmatogenous RD patients, we uncovered 11 genome-wide significant association signals. These are near or within ZC3H11B, BMP3, COL22A1, DLG5, PLCE1, EFEMP2, TYR, FAT3, TRIM29, COL2A1 and LOXL1. Replication in the 23andMe data set, where RD is self-reported by participants, firmly establishes six RD risk loci: FAT3, COL22A1, TYR, BMP3, ZC3H11B and PLCE1. Based on the genetic associations with eye traits described to date, the first two specifically impact risk of a RD, whereas the last four point to shared aetiologies with macular condition, myopia and glaucoma. Fine-mapping prioritized the lead common missense variant (TYR S192Y) as causal variant at the TYR locus and a small set of credible causal variants at the FAT3 locus. The larger study size presented here, enabled by resources linked to health records or self-report, provides novel insights into RD aetiology and underlying pathological pathways.
Berry–Esseen Type Estimate and Return Sequence for Parabolic Iteration in the Upper Half-Plane
Authors: Arizmendi Octavio , Salazar Mauricio , Wang Jiun-Chau
Published: December 2019

We prove a Berry–Esseen type theorem for the convergence rate in the monotone central limit theorem. When the underlying measure is singular relative to Lebesgue measure, this central limit process is viewed as an infinite measure-preserving dynamical system and we prove that it has a regularly varying return sequence of index $1/2$.
Elimination or Resurgence: Modelling Lymphatic Filariasis After Reaching the 1% Microfilaremia Prevalence Threshold
Authors: Prada Joaquin M , Davis Emma L , Touloupou Panayiota , Stolk Wilma A , Kontoroupis Periklis , Smith Morgan E , Sharma Swarnali , Michael Edwin , de Vlas Sake J , Hollingsworth T Déirdre
Published: December 2019

The low prevalence levels associated with lymphatic filariasis elimination pose a challenge for effective disease surveillance. As more countries achieve the World Health Organization criteria for halting mass treatment and move on to surveillance, there is increasing reliance on the utility of transmission assessment surveys (TAS) to measure success. However, the long-term disease outcomes after passing TAS are largely untested. Using 3 well-established mathematical models, we show that low-level prevalence can be maintained for a long period after halting mass treatment and that true elimination (0% prevalence) is usually slow to achieve. The risk of resurgence after achieving current targets is low and is hard to predict using just current prevalence. Although resurgence is often quick (<5 years), it can still occur outside of the currently recommended postintervention surveillance period of 4–6 years. Our results highlight the need for ongoing and enhanced postintervention monitoring, beyond the scope of TAS, to ensure sustained success.
Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact
Authors: Mbunkah Herbert A , Bertagnolio Silvia , Hamers Raph L , Hunt Gillian , Inzaule Seth , Rinke De Wit Tobias F , Paredes Roger , Parkin Neil T , Jordan Michael R , Metzner Karin J ,   WHO HIVResNet Working Group
Published: December 2019

Background

The presence of high-abundance drug-resistant HIV-1 jeopardizes success of antiretroviral therapy (ART). Despite numerous investigations, the clinical impact of low-abundance drug-resistant HIV-1 variants (LA-DRVs) at levels <15%–25% of the virus population in antiretroviral (ARV) drug-naive individuals remains controversial.

Methods

We systematically reviewed 103 studies assessing prevalence, detection methods, technical and clinical detection cutoffs, and clinical significance of LA-DRVs in antiretroviral drug-naive adults.

Results

In total, 14 919 ARV drug-naive individuals were included. Prevalence of LA-DRVs (ie, proportion of individuals harboring LA-DRVs) was 0%–100%. Technical detection cutoffs showed a 4 log range (0.001%–10%); 42/103 (40.8%) studies investigating the impact of LA-DRVs on ART; 25 studies included only individuals on first-line nonnucleoside reverse transcriptase inhibitor-based ART regimens. Eleven of those 25 studies (44.0%) reported a significantly association between preexisting LA-DRVs and risk of virological failure whereas 14/25 (56.0%) did not.

Conclusions

Comparability of the 103 studies is hampered by high heterogeneity of the studies’ designs and use of different methods to detect LA-DRVs. Thus, evaluating clinical impact of LA-DRVs on first-line ART remains challenging. We, the WHO HIVResNet working group, defined central areas of future investigations to guide further efforts to implement ultrasensitive resistance testing in routine settings.
Large-scale genome mining allows identification of neutral polymorphisms and novel resistance mutations in genes involved in Candida albicans resistance to azoles and echinocandins
Authors: Sitterlé Emilie , Coste Alix T , Obadia Thomas , Maufrais Corinne , Chauvel Murielle , Sertour Natacha , Sanglard Dominique , Puel Anne , D’Enfert Christophe , Bougnoux Marie-Elisabeth
Published: December 2019

Background

The genome of Candida albicans displays significant polymorphism. Point mutations in genes involved in resistance to antifungals may either confer phenotypic resistance or be devoid of phenotypic consequences.

Objectives

To catalogue polymorphisms in azole and echinocandin resistance genes occurring in susceptible strains in order to rapidly pinpoint relevant mutations in resistant strains.

Methods

Genome sequences from 151 unrelated C. albicans strains susceptible to fluconazole and caspofungin were used to create a catalogue of non-synonymous polymorphisms in genes involved in resistance to azoles (ERG11, TAC1, MRR1 and UPC2) or echinocandins (FKS1). The potential of this catalogue to reveal putative resistance mutations was tested in 10 azole-resistant isolates, including 1 intermediate to caspofungin. Selected mutations were analysed by mutagenesis experiments or mutational prediction effect.

Results

In the susceptible strains, we identified 126 amino acid substitutions constituting the catalogue of phenotypically neutral polymorphisms. By excluding these neutral substitutions, we identified 22 additional substitutions in the 10 resistant strains. Among these substitutions, 10 had already been associated with resistance. The remaining 12 were in Tac1p (n = 6), Upc2p (n = 2) and Erg11p (n = 4). Four out of the six homozygous substitutions in Tac1p (H263Y, A790V, H839Y and P971S) conferred increases in azole MICs, while no effects were observed for those in Upc2p. Additionally, two homozygous substitutions (Y64H and P236S) had a predicted conformation effect on Erg11p.

Conclusions

By establishing a catalogue of neutral polymorphisms occurring in genes involved in resistance to antifungal drugs, we provide a useful resource for rapid identification of mutations possibly responsible for phenotypic resistance in C. albicans.
The Role of Liquidity in Preventing Dis-investment in Crop Inputs: Evidence from Zambia
Authors: Kusunose Yoko , Mason-Wardell Nicole , Tembo Solomon
Published: December 2019

Despite the current focus on asset smoothing, very few studies consider how seasonal crop input decisions are affected by income shocks. If households cope with ‘bad’ harvests by cutting back on production inputs in the following seasons, they are likely to be slowing down their economic recovery. If such shocks increase in frequency, the ability to recover quickly becomes critical. This study posits that access to liquidity sources plays a role in determining a household’s investments in crop inputs following low-harvest years. Using nationally representative, household-level panel survey data from rural Zambia, we test for differential effects—by household liquidity level—of rainfall shocks on input investments in own-farm production. We estimate semi-elasticities, with respect to these shocks, of four maize inputs: basal fertilizer, top dressing fertilizer, improved maize seed and area planted to maize. Crucially, we allow the magnitude of these input adjustments to differ by household liquidity indicators, as measured by chickens, small livestock (sheep, goats, pigs), cattle, off-farm income and access to fertilizer subsidies. Our findings suggest that rainfall shocks negatively affect the use of some maize inputs. Importantly, households with cattle and access to the national fertilizer subsidy program show significantly smaller reductions in the use of mineral fertilizer. Curiously, we also observe that households with poultry and small livestock reduce their fertilizer use even more than those without.
An exact solution of cosmic ray modulation problem in a stationary composite heliosphere model
Authors: Kolesnyk Yuriy L , Shakhov Boris A , Bobik Pavol , Putis Marian
Published: December 2019

A new theoretical approach to describe the physical processes of energy particle propagation is proposed. This approach is based on the analytically iterative method for solving closed cosmic ray (CR) modulation problems, which was proposed by Shakhov and Kolesnyk. First, we have applied the approach on a simple model of the heliosphere, wherein the diffusion coefficients κ for each region of CR modulation are constants. This approach produced a very good matching of the obtained solution and also provided a numerical solution and an analytical solution. Finally, a modern problem of CR modulation in a stationary composite model of the heliosphere was considered. This model includes an environment that contains adjacent spherically symmetric regions with different modes of propagation of the solar wind (SW) speed for each layer. The CR scattering is due to different factors for each layer of the environment, as characterized by relevant κ values that simultaneously have dependence on the momentum of the particle p and the particle speed $\upsilon$, i.e. $\kappa \propto p\upsilon$. The local interstellar spectra (LISs) are given by a power-law unmodulated spectrum with the slope of the initial spectrum α, i.e. LIS ∝ p−α. An exact solution of the problem of CR modulation for low-energy particles and high-energy particles was first derived and qualitatively compared against the Voyager 1 data.
BALQSO spectra explained by shock disruption of galactic clouds
Authors: Zeilig-Hess Meir , Levinson Amir , Xu Xinfeng , Arav Nahum
Published: December 2019

Blue-shifted broad absorption lines (BALs) detected in quasar’s spectra are indicative of active galactic nuclei (AGN) outflows. We show, using 2D hydrodynamical simulations, that disruption of interstellar clouds by a fast AGN wind can lead to formation of cold, dense high-speed blobs that give rise to broad absorption features in the transmission spectrum of the AGN continuum source. For a wind velocity of 0.1c and sufficiently high cloud density (nc ≳ 104 cm−3; depending on size), absorption troughs with velocities up to about 3000 km s−1can be produced. For slower winds and/or lower cloud density, the anticipated velocity of the absorbing clouds should be smaller.
Simultaneous detection of an intrinsic absorber and a compact jet emission in the X-ray binary IGR J17091−3624 during a hard accretion state
Authors: Gatuzz E , Díaz Trigo M , Miller-Jones J C A , Migliari S
Published: December 2019

We present a detailed analysis of three XMM–Newton observations of the black hole low-mass X-ray binary IGR J17091−3624 taken during its 2016 outburst. Radio observations obtained with the Australia Telescope Compact Array indicate the presence of a compact jet during all observations. From the best X-ray data fit results, we concluded that the observations were taken during a transition from a hard accretion state to a hard-intermediate accretion state. For Observations 1 and 2, a local absorber can be identified in the EPIC-pn spectra but not in the RGS spectra, preventing us from distinguishing between absorption local to the source and that from the hot ISM component. For Observation 3, on the other hand, we have identified an intrinsic ionized static absorber in both EPIC-pn and RGS spectra. The absorber, observed simultaneously with a compact jet emission, is characterized by an ionization parameter of 1.96 < log ξ < 2.05 and traced mainly by Ne x, Mg xii, Si xiii, and Fe xviii.
The HASHTAG project I. A survey of CO(3–2) emission from the star forming disc of M31
Authors: Li Zongnan , Li Zhiyuan , Smith Matthew W L , Wilson Christine D , Gao Yu , Eales Stephen A , Ao Yiping , Bureau Martin , Chung Aeree , Davis Timothy A , de Grijs Richard , Eden David J , He Jinhua , Hughes Tom M , Jiang Xuejian , Kemper Francisca , Lamperti Isabella , Lee Bumhyun , Lee Chien-Hsiu , Michałowski Michał J , Parsons Harriet , Ragan Sarah , Scicluna Peter , Shi Yong , Tang Xindi , Tomičić Neven , Viaene Sebastien , Williams Thomas G , Zhu Ming
Published: December 2019

We present a CO(3–2) survey of selected regions in the M31 disc as part of the JCMT large programme, HARP and SCUBA-2 High-Resolution Terahertz Andromeda Galaxy Survey (HASHTAG). The 12 CO(3–2) fields in this survey cover a total area of 60 arcmin2, spanning a deprojected radial range of 2–14 kpc across the M31 disc. Combining these observations with existing IRAM 30 m CO(1–0) observations and JCMT CO(3–2) maps of the nuclear region of M31, as well as dust temperature and star formation rate surface density maps, we are able to explore the radial distribution of the CO(3–2)/CO(1–0) integrated intensity ratio (R31) and its relationship with dust temperature and star formation. We find that the value of R31 between 2 and 9 kpc galactocentric radius is 0.14, significantly lower than what is seen in the nuclear ring at 1 kpc (R31 ∼ 0.8), only to rise again to 0.27 for the fields centred on the 10 kpc star forming ring. We also found that R31 is positively correlated with dust temperature, with Spearman’s rank correlation coefficient ρ = 0.55. The correlation between star formation rate surface density and CO(3–2) intensity is much stronger than with CO(1–0), with ρ = 0.54 compared to –0.05, suggesting that the CO(3–2) line traces warmer and denser star forming gas better. We also find that R31 correlates well with star formation rate surface density, with ρ = 0.69.
Radio study of the extended TeV source VER J1907+062
Authors: Duvidovich L , Petriella A , Giacani E
Published: December 2019

This paper aims to provide new insights on the origin of the TeV source VER J1907+062 through new high-quality radio observations. We used the Karl G. Jansky Very Large Array (VLA) to observe the whole extension of VER J1907+062 at 1.5 GHz with a mosaicking technique and the PSR J1907+0602 in a single pointing at 6 GHz. These data were used together with 12CO and atomic hydrogen observations obtained from public surveys to investigate the interstellar medium in the direction of VER J1907+062. The new radio observations do not show any evidence of a pulsar wind nebula (PWN) driven by the pulsars present in the field and no radio counterpart to the proposed X-ray PWN powered by PSR J1907+0602 is seen in the new VLA image at 6 GHz down to a noise level of 10 $\mu$Jy beam−1. Molecular clouds were discovered over the eastern, southern, and western borders of the radio shell of G40.5−0.5, suggesting an association with this supernova remnant. We explored several scenarios for the origin of VER J1907+062. We propose as the most probable scenario one in which the TeV emission is produced by two separated γ-ray sources located at different distances: one of leptonic origin and associated with a PWN powered by PSR J1907+0602 at ∼3.2 kpc and another of hadronic origin and produced by the interaction between G40.5−0.5 and the surrounding molecular gas at ∼8.7 kpc.
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

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 < LX <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

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

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

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

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

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

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

Small 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

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

Staufen1 (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.