bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrodynamical interaction of stellar and planetary winds: effects of charge exchange and radiation pressure on the observed Ly α absorption
Authors: Esquivel A , Schneiter M , Villarreal D’Angelo C , Sgró M A , Krapp L 
Published: June 2019

ABSTRACT
Lyman α observations of the transiting exoplanet HD 209458b enable the study of exoplanet exospheres exposed to stellar extreme ultraviolet (EUV) fluxes, as well as the interacting stellar wind properties. In this study we present 3D hydrodynamical models for the stellar–planetary wind interaction including radiation pressure and charge exchange, together with photoionization, recombination, and collisional ionization processes. Our models explore the contribution of the radiation pressure and charge exchange to the Ly α absorption profile in a hydrodynamical framework, and for a single set of stellar wind parameters appropriate for HD 209458. We find that most of the absorption is produced by the material from the planet, with a secondary contribution of neutralized stellar ions by charge exchange. At the same time, the hydrodynamic shock heats up the planetary material, resulting in a broad thermal profile. Meanwhile, the radiation pressure yields a small velocity shift of the absorbing material. While neither charge exchange nor radiation pressure provides enough neutrals at the velocity needed to explain the observations at −100 km s−1 individually, we find that the two effects combined with the broad thermal profile are able to explain the observations.
Modelling decretion discs in Be/X-ray binaries
Authors: Brown R O , Coe M J , Ho W C G , Okazaki A T 
Published: June 2019

Abstract
As the largest population of high mass X-ray binaries, Be/X-ray binaries provide an excellent laboratory to investigate the extreme physics of neutron stars. It is generally accepted that Be stars possess a circumstellar disc, providing an additional source of accretion to the stellar winds present around young hot stars. Interaction between the neutron star and the disc is often the dominant accretion mechanism. A large amount of work has gone into modelling the properties of these circumstellar discs, allowing for the explanation of a number of observable phenomena. In this paper, smoothed particle hydroynamics simulations are performed whilst varying the model parameters (orbital period, eccentricity, the mass ejection rate of the Be star and the viscosity and orientation of the disc). The relationships between the model parameters and the disc’s characteristics (base gas density, the accretion rate of the neutron star and the disc’s size) are presented. The observational evidence for a dependency of the size of the Be star’s circumstellar disc on the orbital period (and semi-major axis) is supported by the simulations.
Spectro-timing analysis of MAXI J1535–571 using AstroSat
Authors: Bhargava Yash , Belloni Tomaso , Bhattacharya Dipankar , Misra Ranjeev 
Published: June 2019

Abstract
We report the results of the analysis of an AstroSat observation of the black hole candidate MAXI J1535–571 during its hard-intermediate state. We studied the evolution of the spectral and timing parameters of the source during the observation. The observation covered a period of ∼5 d and consisted of 66 continuous segments, corresponding to individual spacecraft orbits. Each segment was analysed independently. The source count rate increased roughly linearly by ∼30 per cent. We modelled the spectra as a combination of radiation from a thermal disc component and a power law. The timing analysis revealed the presence of strong quasi-periodic oscillations with centroid frequency νQPO fluctuating in the range of 1.7–3.0 Hz. We found a tight correlation between the QPO centroid frequency νQPO and the power-law spectral index Γ, while νQPO appeared not to be correlated with the linearly increasing flux itself. We discuss the implications of these results on physical models of accretion.
A comprehensive examination of the optical morphologies of 719 isolated galaxies in the AMIGA sample
Authors: Buta Ronald J , Verdes-Montenegro Lourdes , Damas-Segovia Ancor , Jones Michael , Blasco Javier , Fernández-Lorenzo Mirian , Sanchez Susana , Garrido Julian , Ramirez-Moreta Pablo , Sulentic Jack W 
Published: June 2019

Abstract
Using images from Sloan Digital Sky Survey Data Release 8, we have re-examined the morphology of 719 galaxies from the Analysis of the interstellar Medium in Isolated GAlaxies (AMIGA) project, a sample consisting of the most isolated galaxies that have yet been identified. The goal is to further improve the classifications of these galaxies by examining them in the context of the Comprehensive de Vaucouleurs revised Hubble-Sandage (CVRHS) system, which includes recognition of features that go beyond the original de Vaucouleurs point of view. Our results confirm previous findings that isolated galaxies are found across the complete revised Hubble sequence, with intermediate- to late-type (Sb-Sc) spirals being relatively more common. Elmegreen Arm Classifications are also presented, and show that more than 50 per cent of the 514 spirals in the sample for which an arm class (AC) could be judged are grand design (AC 8,9,12). The visual bar fraction for the sample is ≈50 per cent, but only 16 per cent are classified as strongly barred (SB). The dominant family classification is SA (non-barred), the dominant inner variety classification is (s) (pure spiral), and the dominant outer variety classification is no outer ring, pseudo-ring, or lens. The Kolmogorov–Smirnov test is used to check for potential biases in the morphological interpretations, and for any possible relation between rings, bars, and ACs with local environment and far-infrared excess. The connection between morphology and stellar mass is also examined for a subset of the sample.
Parallel Evolution of HIV-1 in a Long-Term Experiment
Authors: Bertels Frederic , Leemann Christine , Metzner Karin J , Regoes Roland R 
Published: June 2019

AbstractOne of the most intriguing puzzles in biology is the degree to which evolution is repeatable. The repeatability of evolution, or parallel evolution, has been studied in a variety of model systems, but has rarely been investigated with clinically relevant viruses. To investigate parallel evolution of HIV-1, we passaged two replicate HIV-1 populations for almost 1 year in each of two human T-cell lines. For each of the four evolution lines, we determined the genetic composition of the viral population at nine time points by deep sequencing the entire genome. Mutations that were carried by the majority of the viral population accumulated continuously over 1 year in each evolution line. Many majority mutations appeared in more than one evolution line, that is, our experiments showed an extreme degree of parallel evolution. In one of the evolution lines, 62% of the majority mutations also occur in another line. The parallelism impairs our ability to reconstruct the evolutionary history by phylogenetic methods. We show that one can infer the correct phylogenetic topology by including minority mutations in our analysis. We also find that mutation diversity at the beginning of the experiment is predictive of the frequency of majority mutations at the end of the experiment.
Meta-Omics Reveals Genetic Flexibility of Diatom Nitrogen Transporters in Response to Environmental Changes
Authors: Busseni Greta , Rocha Jimenez Vieira Fabio , Amato Alberto , Pelletier Eric , Pierella Karlusich Juan J , Ferrante Maria I , Wincker Patrick , Rogato Alessandra , Bowler Chris , Sanges Remo , Maiorano Luigi , Chiurazzi Maurizio , Ribera d’Alcalà Maurizio , Caputi Luigi , Iudicone Daniele 
Published: June 2019

Abstract
Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution, and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate, and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.
Prevalence and correlates of fatigue in patients with meningioma before and after surgery
Authors: van der Linden Sophie D , Gehring Karin , Rutten Geert-Jan M , Kop Willem J , Sitskoorn Margriet M 
Published: June 2019

AbstractBackgroundFatigue is a common symptom in patients with brain tumors, but comprehensive studies on fatigue in patients with meningioma specifically are lacking. This study examined the prevalence and correlates of fatigue in meningioma patients.MethodsPatients with grade I meningioma completed the Multidimensional Fatigue Inventory (MFI-20) before and 1 year after neurosurgery. The MFI consists of 5 subscales: General Fatigue, Physical Fatigue, Mental Fatigue, Reduced Motivation, and Reduced Activity. Patients’ scores were compared with normative data. Preoperative fatigue was compared with postoperative fatigue. Correlations with sex, age, education, tumor hemisphere, preoperative tumor volume, antiepileptic drugs (AEDs), symptoms of anxiety/depression, and self-reported cognitive complaints were explored.ResultsQuestionnaires were completed by 65 patients preoperatively, and 53 patients postoperatively. Of 34 patients, data from both time points were available. Patients had significantly higher fatigue levels on all subscales compared to normative values at both time points. Mean scores on General Fatigue, Physical Fatigue, and Mental Fatigue remained stable over time and improvements were observed on Reduced Motivation and Reduced Activity. Preoperatively, the prevalence of high fatigue (Z-score ≥ 1.3) varied between 34% for Reduced Motivation and 43% for General Fatigue/Mental Fatigue. The postoperative prevalence ranged from 19% for Reduced Activity to 49% on Mental Fatigue. Fatigue was associated with cognitive complaints, anxiety and depression, but not with education, tumor lateralization, tumor volume, or AEDs.ConclusionFatigue is a common and persistent symptom in patients with meningioma undergoing neurosurgery. Findings emphasize the need for more research and appropriate care targeting fatigue for meningioma patients.
Lymphocyte Hydrogen Sulfide Production Predicts Coronary Artery Lesions in Children with Kawasaki Disease: A Preliminary, Single-Center Study
Authors: Lin Jing , Zhao Huacai , Jiao Fuyong , Ma Lei , Wang Weiqing , Ma Le 
Published: June 2019

AbstractTo identify whether lymphocyte hydrogen sulfide production is a potential biomarker for predicting coronary artery lesions (CAL) in children with Kawasaki disease (KD). Eighty-six children with KD, 33 normal children and 43 children with fever from June 2016 to January 2019 in Shaanxi Provincial People's Hospital were enrolled. Of 86 KD patients, 16 patients exhibited CAL. Lymphocyte hydrogen sulfide production was significantly greater in KD patients (13.7 ± 2.7) nmol/min/108 lymphocytes than in the controls (9.26 ± 3.33) nmol/min/108 lymphocytes and the fever group (8.21 ± 2.77) nmol/min/108 lymphocytes. The lymphocyte hydrogen sulfide production was greater in CAL patients than the non-CAL patients [(16.24 ± 1.81) vs. (13.12 ± 2.58), p &lt; 0.001]. Receiver operating characteristic curve indicated when the lymphocyte hydrogen sulfide production was &gt;15.285 nmol/min/108 lymphocytes, the sensitivity and specificity for predicting CAL at convalescence were 87.5% and 82.9%, respectively. Lymphocyte hydrogen sulfide production in the acute period is a potentially useful biomarker for predicting CAL in KD children.
SynGAP Splice Variants Display Heterogeneous Spatio-Temporal Expression And Subcellular Distribution In The Developing Mammalian Brain
Authors: Gou Gemma , Roca-Fernandez Adriana , Kilinc Murat , Serrano Elena , Reig-Viader Rita , Araki Yoichi , Huganir Richard L. , de Quintana-Schmidt Cristian , Rumbaugh Gavin , Bayés Àlex 
Published: June 2019

AbstractThe Syngap1 gene is a major regulator of synapse biology and neural circuit function. Genetic variants linked to epilepsy and intellectual disability disrupt synaptic function and neural excitability. The SynGAP protein has been involved in multiple signaling pathways and can regulate small GTPases with very different functions. Yet, the molecular bases behind this pleiotropy are poorly understood. We hypothesize that different SynGAP isoforms will mediate different sets of functions and that deciphering their spatio-temporal expression and subcellular localization will accelerate our understanding of the multiple functions performed by SynGAP. Using antibodies that detect all isoforms of SynGAP, we found that its subcellular localization changed throughout postnatal development. Consistent with previous reports, SynGAP was enriched in the postsynaptic density in the mature forebrain. However, this was age-dependent and SynGAP was predominantly found in non-synaptic locations in a period of postnatal development highly sensitive to SynGAP levels. Furthermore, we identified different expression patterns in the spatial and temporal axes for different SynGAP isoforms. Particularly noticeable was the delayed expression of SynGAP α1 isoforms, which bind to PSD-95 at the postsynaptic density, in cortex and hippocampus during the first two weeks of postnatal development. The subcellular localization of SynGAP was also isoform-dependent. While, α1 isoforms were highly enriched in the postsynaptic density, other C-terminal isoforms were less enriched or even more abundant in non-synaptic locations, particularly during the postnatal period. Thus, the regulation of expression and subcellular distribution of SynGAP isoforms may contribute to isoform-specific regulation of small GTPases, explaining SynGAP pleiotropy.
Quantitation of vector uptake reveals non-Poissonian transfection dynamics in Plasmodium falciparum
Authors: Carrasquilla Manuela , Sanderson Theo , Montandon Ruddy , Rayner Julian , Pance Alena , Lee Marcus 
Published: June 2019

AbstractThe recurrent emergence of drug resistance in Plasmodium falciparum increases the urgency to genetically validate drug resistance mechanisms and identify new targets. Reverse genetics have facilitated genome-scale knockout screens in Plasmodium berghei and Toxoplasma gondii, in which pooled transfections of multiple vectors were critical to increasing scale and throughput. These approaches have not yet been implemented in P. falciparum, mainly because the extent to which pooled transfections can be performed in this species still remains unknown. Here we use next-generation sequencing to quantitate uptake of a pool of 94 barcoded vectors. The distribution of vectors in different transfections allowed us to estimate the number of barcodes and DNA molecules taken up by the parasite population. Dilution cloning showed that single transfected parasites routinely carry as many as seven episomal barcodes, revealing an intake of multiple vectors in a highly non-uniform fashion. Transfection of non-overlapping fluorescent proteins, which allowed us to follow the dynamics of the process, confirmed the tendency for parasites to take up multiple vectors from the early stages of transfection. This finding has important implications for how reverse genetics can be scaled in P. falciparum.
Astrocytes Contribute to Remote Memory Formation by Modulating Hippocampal-Cortical Communication During Learning
Authors: Kol Adi , Adamsky Adar , Groysman Maya , Kreisel Tirzah , London Michael , Goshen Inbal 
Published: June 2019

ABSTRACTThe consolidation and retrieval of remote memories depend on the coordinated activity of the hippocampus and frontal cortices. However, the exact time at which these regions are recruited to support memory and the interactions between them are still debated. Astrocytes can sense and modify neuronal activity with great precision, but their role in cognitive function has not been extensively explored. To investigate the role of astrocytes in remote memory we expressed the Gi-coupled receptor hM4Di in CA1 astrocytes, allowing their manipulation by a designer drug. We discovered that astrocytic modulation during learning resulted in a specific impairment in remote, but not recent, memory recall, accompanied by decreased neuronal activity in the anterior cingulate cortex (ACC) during retrieval. We revealed a massive recruitment of ACC-projecting neurons in CA1 during memory acquisition, accompanied by activation of ACC neurons. Astrocytic Gi activation disrupted CA3 to CA1 communication in-vivo, and reduced the downstream response in the ACC. This same manipulation in behaving mice induced a projection-specific inhibition of ACC-projecting CA1 neurons during learning, consequently preventing the recruitment of the ACC. Our findings suggest that the foundation of remote memory is established in the ACC during acquisition, engaging a distinct process from the one supporting consolidation of recent memory. Furthermore, the mechanism underlying remote memory involves projection-specific functions of astrocytes in regulating neuronal activity.
Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses
Authors: O’Flanagan Ciara H , Campbell Kieran R , Zhang Allen W , Kabeer Farhia , Lim Jamie LP , Biele Justina , Eirew Peter , Lai Daniel , McPherson Andrew , Kong Esther , Bates Cherie , Borkowski Kelly , Wiens Matt , Hopkins James , Hewitson Brittany , Ceglia Nicholas , Moore Richard , Mungall Andy J , McAlpine Jessica N ,   The CRUK IMAXT Grand Challenge Team, Shah Sohrab P , Aparicio Samuel 
Published: June 2019

AbstractBackgroundSingle-cell RNA sequencing (scRNAseq) is a powerful tool for studying complex biological systems, such as tumour heterogeneity and tissue microenvironments. However, the sources of technical and biological variation in primary solid tumour tissues and patient-derived mouse xenografts for scRNAseq, are not well understood. Here, we used low temperature (6°C) protease and collagenase (37°C) to identify the transcriptional signatures associated with tissue dissociation across a diverse scRNAseq dataset comprising 128,481 cells from patient cancer tissues, patient-derived breast cancer xenografts and cancer cell lines.ResultsWe observe substantial variation in standard quality control (QC) metrics of cell viability across conditions and tissues. From FACS sorted populations gated for cell viability, we identify a sub-population of dead cells that would pass standard data filtering practices, and quantify the extent to which their transcriptomes differ from live cells. We identify a further subpopulation of transcriptomically “dying” cells that exhibit up-regulation of MHC class I transcripts, in contrast with live and fully dead cells. From the contrast between tissue protease dissociation at 37°C or 6°C, we observe that collagenase digestion results in a stress response. We derive a core gene set of 512 heat shock and stress response genes, includingFOSandJUN, induced by collagenase (37°C), which are minimized by dissociation with a cold active protease (6°C). While induction of these genes was highly conserved across all cell types, cell type-specific responses to collagenase digestion were observed in patient tissues. We observe that the yield of cancer and non-cancer cell types varies between tissues and dissociation methods.ConclusionsThe method and conditions of tumour dissociation influence cell yield and transcriptome state and are both tissue and cell type dependent. Interpretation of stress pathway expression differences in cancer single cell studies, including components of surface immune recognition such as MHC class I, may be especially confounded. We define a core set of 512 genes that can assist with identification of such effects in dissociated scRNA-seq experiments.
Dual Role of Cell-Cell Adhesion In Tumor Suppression and Proliferation Due to Collective Mechanosensing
Authors: Malmi-Kakkada Abdul N , Li Xin , Sinha Sumit , Thirumalai D. 
Published: June 2019

AbstractIt is known that mechanical interactions couple a cell to its neighbors, enabling a feedback loop to regulate tissue growth. However, the interplay between cell-cell adhesion strength, local cell density and force fluctuations in regulating cell proliferation is poorly understood. Here, we show that spatial variations in the tumor growth rates, which depend on the location of cells within tissue spheroids, are strongly influenced by cell-cell adhesion. As the strength of the cell-cell adhesion increases, intercellular pressure initially decreases, enabling dormant cells to more readily enter into a proliferative state. We identify an optimal cell-cell adhesion regime where pressure on a cell is a minimum, allowing for maximum proliferation. We use a theoretical model to validate this novel collective feedback mechanism coupling adhesion strength, local stress fluctuations and proliferation. Our results predict the existence of a non-monotonic proliferation behavior as a function of adhesion strength, consistent with experimental results. Several experimental implications of the proposed role of cell-cell adhesion in proliferation are quantified, making our model predictions amenable to further experimental scrutiny. We show that the mechanism of contact inhibition of proliferation, based on a pressure-adhesion feedback loop, serves as a unifying mechanism to understand the role of cell-cell adhesion in proliferation.
Inferring generation-interval distributions from contact-tracing data
Authors: Park Sang Woo , Champredon David , Dushoff Jonathan 
Published: June 2019

AbstractGeneration intervals, defined as the time between when an individual is infected and when that individual infects another person, link two key quantities that describe an epidemic: the reproductive number,, and the rate of exponential growth,r. Generation intervals are often measured through contact tracing by identifying who infected whom. We study how observed intervals differ from “intrinsic” intervals that could be estimated by tracing individual-level infectiousness, and identify both spatial and temporal effects, including censoring (due to observation time), and the effects of susceptible depletion at various spatial scales. Early in an epidemic, we expect the variation in the observed generation intervals to be mainly driven by the censoring and the population structure near the source of disease spread; therefore, we predict that correcting observed intervals for the effect of temporal censoring butnotfor spatial effects will provide a spatially informed “effective” generation-interval distribution, which will correctly linkrand. We develop and test statistical methods for temporal corrections of generation intervals, and confirm our prediction using individual-based simulations on an empirical network.