bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential regulation of OCT4 targets facilitates reacquisition of pluripotency
Authors: Thakurela Sudhir , Sindhu Camille , Yurkovsky Evgeny , Riemenschneider Christina , Smith Zachary D. , Nachman Iftach , Meissner Alexander 
Published: September 2019

AbstractEctopic transcription factor expression enables reprogramming of somatic cells to pluripotency, albeit with generally low efficiency. Despite steady progress in the field, the exact molecular mechanisms that coordinate this remarkable transition still remain largely elusive. To better characterize the final steps of pluripotency induction, we optimized an experimental system where pluripotent stem cells are differentiated for set intervals before being reintroduced to pluripotency-supporting conditions. Using this approach, we identify a transient period of high-efficiency reprogramming where ectopic transcription factors, but not serum/LIF alone, rapidly revert cells to pluripotency with near 100% efficiency. After this period, cells reprogram with somatic-like kinetics and efficiencies. We identify a set of OCT4 boundcis-regulatory elements that are dynamically regulated during this transient phase and appear central to facilitating reprogramming. Interestingly, these regions remain hypomethylated during in vitro and in vivo differentiation, which may allow them to act as primary targets of ectopically induced factors during somatic cell reprogramming.
Constitutive XBP-1s-mediated activation of the endoplasmic reticulum unfolded protein response protects against pathological tau
Authors: Waldherr Sarah M. , Strovas Timothy J. , Vadset Taylor A. , Liachko Nicole F. , Kraemer Brian C. 
Published: September 2019

AbstractTo endure over the organismal lifespan, neurons utilize multiple strategies to achieve protein homeostasis (proteostasis). Some homeostatic mechanisms act in a subcellular compartment-specific manner, but others exhibit trans-compartmental mechanisms of proteostasis. To identify pathways protecting neurons from pathological tau protein, we employed a transgenic Caenorhabditis elegans model of human tauopathy exhibiting proteostatic disruption. We show normal functioning of the endoplasmic reticulum unfolded protein response (UPRER) promotes clearance of pathological tau, and loss of the three UPRER branches differentially affects tauopathy phenotypes. Loss of function of xbp-1 and atf-6 genes, the two main UPRER transcription factors, exacerbates tau toxicity. Furthermore, constitutive activation of master transcription factor XBP-1 ameliorates tauopathy phenotypes. However, both ATF6 and PERK branches of the UPRER participate in amelioration of tauopathy by constitutively active XBP-1, possibly through endoplasmic reticulum-associated protein degradation (ERAD). Understanding how the UPRER modulates pathological tau accumulation will inform neurodegenerative disease mechanisms.
Abl family tyrosine kinases govern IgG extravasation in the skin in a murine pemphigus model
Authors: Ono Sachiko , Egawa Gyohei , Nomura Takashi , Kitoh Akihiko , Dainichi Teruki , Otsuka Atsushi , Nakajima Saeko , Amagai Masayuki , Matsumoto Fumi , Yamamoto Mami , Kubota Yoshiaki , Takai Toshiyuki , Honda Tetsuya , Kabashima Kenji 
Published: September 2019

AbstractThe pathway of homeostatic IgG extravasation is not fully understood, in spite of its importance for the maintenance of host immunity, the management of autoantibody-mediated disorders, and the use of antibody-based biologics. Here we show in a murine model of pemphigus, a prototypic cutaneous autoantibody-mediated disorder, that blood-circulating IgG extravasates into the skin in a time- and dose-dependent manner under homeostatic conditions. This IgG extravasation is unaffected by depletion of Fcγ receptors, but is largely attenuated by specific ablation of dynamin-dependent endocytic vesicle formation in blood endothelial cells (BECs). Among dynamin-dependent endocytic vesicles, IgG co-localizes well with caveolae in cultured BECs. An Abl family tyrosine kinase inhibitor imatinib, which reduces caveolae-mediated endocytosis, impairs IgG extravasation in the skin and attenuates the murine pemphigus manifestations. Our study highlights the kinetics of IgG extravasation in vivo, which might be a clue to understand the pathological mechanism of autoantibody-mediated autoimmune disorders.
The bracteatus pineapple genome and domestication of clonally propagated crops
Authors: Chen Li-Yu , VanBuren Robert , Paris Margot , Zhou Hongye , Zhang Xingtan , Wai Ching Man , Yan Hansong , Chen Shuai , Alonge Michael , Ramakrishnan Srividya , Liao Zhenyang , Liu Juan , Lin Jishan , Yue Jingjing , Fatima Mahpara , Lin Zhicong , Zhang Jisen , Huang Lixian , Wang Hao , Hwa Teh-Yang , Kao Shu-Min , Choi Jae Young , Sharma Anupma , Song Jian , Wang Lulu , Yim Won C. , Cushman John C. , Paull Robert E. , Matsumoto Tracie , Qin Yuan , Wu Qingsong , Wang Jianping , Yu Qingyi , Wu Jun , Zhang Shaoling , Boches Peter , Tung Chih-Wei , Wang Ming-Li , Coppens d’Eeckenbrugge Geo , Sanewski Garth M. , Purugganan Michael D. , Schatz Michael C. , Bennetzen Jeffrey L. , Lexer Christian , Ming Ray 
Published: September 2019

AbstractDomestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome ofAnanas comosusvar.bracteatusCB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89Ananasgenomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.
Physical parameters of red supergiants in dwarf irregular galaxies in the Local Group
Authors: Britavskiy N. E. , Bonanos A. Z. , Herrero A. , Cerviño M. , García-Álvarez D. , Boyer M. L. , Masseron T. , Mehner A. , McQuinn K. B. W. 
Published: September 2019

Context. Increasing the statistics of evolved massive stars in the Local Group enables investigating their evolution at different metallicities. During the late stages of stellar evolution, the physics of some phenomena, such as episodic and systematic mass loss, are not well constrained. For example, the physical properties of red supergiants (RSGs) in different metallicity regimes remain poorly understood. Thus, we initiated a systematic study of RSGs in dwarf irregular galaxies (dIrrs) in the Local Group.
Aims. We aim to derive the fundamental physical parameters of RSGs and characterize the RSG population in nearby dIrrs.
Methods. The target selection is based on 3.6 μm and 4.5 μm photometry from archival Spitzer Space Telescope images of nearby galaxies. We selected 46 targets in the dIrrs IC 10, IC 1613, Sextans B, and the Wolf-Lundmark-Melotte (WLM) galaxy that we observed with the GTC–OSIRIS and VLT–FORS2 instruments. We used several photometric techniques together with a spectral energy distribution analysis to derive the luminosities and effective temperatures of known and newly discovered RSGs.
Results. We identified and spectroscopically confirmed 4 new RSGs, 5 previously known RSGs, and 5 massive asymptotic giant branch (AGB) stars. We added known objects from previous observations. In total, we present spectral classification and fundamental physical parameters of 25 late-type massive stars in the following dIrrs: Sextans A, Sextans B, IC 10, IC 1613, Pegasus, Phoenix, and WLM. This includes 17 RSGs and 8 AGB stars that have been identified here and previously.
Conclusions. Based on our observational results and PARSEC evolutionary models, we draw the following conclusions: (i) a trend to higher minimum effective temperatures at lower metallicities and (ii) the maximum luminosity of RSGs appears to be constant at log(L/L⊙)≈5.5, independent of the metallicity of the host environment (up to [Fe/H] ≈ −1 dex).
A first quantification of the effects of absorption for H I intensity mapping experiments
Authors: Roychowdhury Sambit , Dickinson Clive , Browne Ian W. A. 
Published: September 2019

Context. HI intensity mapping (IM) will be used to do precision cosmology, using many existing and upcoming radio observatories. It will measure the integrated HI 21 cm emission signal from “voxels” of the sky at different redshifts. The signal will be contaminated due to absorption, the largest component of which will be the flux absorbed by the HI emitting sources themselves from the potentially bright flux incident on them from background radio continuum sources.
Aims. We, for the first time, provide a quantitative estimate of the magnitude of the absorbed flux compared to the emitted HI flux. The ratio of the two fluxes was calculated for various voxels placed at redshifts between 0.1 and 2.5.
Methods. We used a cosmological sky simulation of the atomic HI emission line, and summed over the emitted and absorbed fluxes for all sources within voxels at different redshifts. In order to determine the absorbed flux, for each HI source the flux incident from background radio continuum sources was estimated by determining the numbers, sizes, and redshift distribution of radio continuum sources that lie behind it, based on existing observations and simulations. The amount of this incident flux that is absorbed by each HI source was calculated using a relation between integrated optical depth with HI column density determined using observations of damped Lyman-α systems (DLAs) and sub-DLAs.
Results. We find that for the same co-moving volume of sky, the HI emission decreases quickly with increasing redshift, while the absorption varies much less with redshift and follows the redshift distribution of faint sources that dominate the number counts of radio continuum sources. This results in the fraction of absorption compared to emission to be negligible in the nearby Universe (up to a redshift of ∼0.5), increases to about 10% at a redshift of one, and continues to increase to about 30% up to a redshift of 2.5. These numbers can vary significantly due to the uncertainty on the exact form of the following relations: firstly, the number counts of radio continuum sources at sub-mJy flux densities; secondly, the relation between integrated optical depth and HI column density of HI sources; and thirdly, the redshift distribution of radio continuum sources up to the highest redshifts.
Conclusions. Absorption of the flux incident from background radio continuum sources might become an important contaminant to HI IM signals beyond redshifts of 0.5. The impact of absorption needs to be quantified more accurately using inputs from upcoming deep surveys of radio continuum sources, H I absorption, and HI emission with the Square Kilometre Array and its precursors.
Asymmetric shocks in χ Cygni observed with linear spectropolarimetry
Authors: López Ariste A. , Tessore B. , Carlín E. S. , Mathias Ph. , Lèbre A. , Morin J. , Petit P. , Aurière M. , Gillet D. , Herpin F. 
Published: September 2019

Aims. We derive information about the dynamics of the stellar photosphere, including pulsation, from a coherent interpretation of the linear polarisation detected in the spectral lines of the Mira star χ Cyg.
Methods. From spectropolarimetric observations of χ Cyg, we performed a careful analysis of the polarisation signals observed in atomic and molecular lines, both in absorption and emission, using radiative transfer in the context of polarisation produced through two mechanisms: intrinsic polarisation and continuum depolarisation. We also explain the observed line doubling phenomenon in terms of an expanding shell in spherical geometry, which allows us to pinpoint the coordinates over the stellar disc with enhanced polarisation.
Results. We find that the polarised spectrum of χ Cyg is dominated by intrinsic polarisation and has a negligible continuum depolarisation. The observed polarised signals can only be explained by assuming that this polarisation is locally enhanced by velocity fields. During the pulsation, radial velocities are not homogeneous over the disc. We map these regions of enhanced velocities.
Conclusions. We set an algorithm to distinguish the origin of this polarisation in any stellar spectra of linear polarisation and to find a way to increase the signal by coherently adding many lines with an appropriated weight. Applied to the Mira star χ Cyg, we reached the unexpected result that during the pulsation, velocities are radial but not homogeneous over the disc. The reason for these local velocity enhancements are probably related to the interplay between the atmospheric pulsation dynamics and the underlying stellar convection.
Minimization of non-common path aberrations at the Palomar telescope using a self-coherent camera
Authors: Galicher R. , Baudoz P. , Delorme J.-R. , Mawet D. , Bottom M. , Wallace J. K. , Serabyn E. , Shelton C. 
Published: September 2019

Context. The two main advantages of exoplanet imaging are the discovery of objects in the outer part of stellar systems, which constrains the models of planet formation, and its ability to spectrally characterize the planets to study their atmospheres. It is, however, challenging because exoplanets are up to 1010 times fainter than their stars and are separated by a fraction of an arcsecond. Current instruments like SPHERE-VLT or GPI-Gemini detect young and massive planets only because of non-common path aberrations (NCPA) that are not corrected by the adaptive optics system. To probe fainter exoplanets a new instruments capable of minimizing the NCPA is needed. One solution is the self-coherent camera (SCC) focal plane wavefront sensor which is able to attenuate the starlight by factors of up to several 108 in the laboratory in space-like conditions.
Aims. In this paper, we demonstrate the SCC on the sky for the first time.
Methods. We installed an SCC on the stellar double coronagraph instrument at the Hale telescope. We minimize the NCPA that limited the vortex coronagraph performance. We then compared this procedure to the standard procedure used at Palomar.
Results. On internal sources, we demonstrated that the SCC improves the coronagraphic detection limit by a factor of 4–20 between 1.5 and 5 λ/D. Using this SCC calibration, the on-sky contrast is improved by a factor of 5 between 2 and 4 λ/D. These results prove the ability of the SCC to be implemented in an existing instrument.
Conclusions. This paper highlights two interests of the self-coherent camera. First, the SCC can minimize the speckle intensity in the field of view, especially the ones that are very close to the star where many exoplanets are to be discovered. Then the SCC has a 100% efficiency with science time as each image can be used for both science and NCPA minimization.
Dust emissivity and absorption cross section in DustPedia late-type galaxies
Authors: Bianchi S. , Casasola V. , Baes M. , Clark C. J. R. , Corbelli E. , Davies J. I. , De Looze I. , De Vis P. , Dobbels W. , Galametz M. , Galliano F. , Jones A. P. , Madden S. C. , Magrini L. , Mosenkov A. , Nersesian A. , Viaene S. , Xilouris E. M. , Ysard N. 
Published: September 2019

Aims. We compare the far-infrared to sub-millimetre dust emission properties measured in high Galactic latitude cirrus with those determined in a sample of 204 late-type DustPedia galaxies. The aim is to verify if it is appropriate to use Milky Way dust properties to derive dust masses in external galaxies.
Methods. We used Herschel observations and atomic and molecular gas masses to estimate ϵ(250 μm), the disc-averaged dust emissivity at 250 μm, and from this, the absorption cross section per H atom σ(250 μm) and per dust mass κ(250 μm). The emissivity ϵ(250 μm) requires one assumption, which is the CO-to-H2 conversion factor, and the dust temperature is additionally required for σ(250 μm); yet another constraint on the dust-to-hydrogen ratio D/H, depending on metallicity, is required for κ(250 μm).
Results. We find ϵ(250 μm) = 0.82 ± 0.07 MJy sr−1 (1020 H cm−2)−1 for galaxies with 4 <  F(250 μm)/F(500 μm) < 5. This depends only weakly on the adopted CO-to-H2 conversion factor. The value is almost the same as that for the Milky Way at the same colour ratio. Instead, for F(250 μm)/F(500 μm) > 6, ϵ(250 μm) is lower than predicted by its dependence on the heating conditions. The reduction suggests a variation in dust emission properties for spirals of earlier type, higher metallicity, and with a higher fraction of molecular gas. When the standard emission properties of Galactic cirrus are used for these galaxies, their dust masses might be underestimated by up to a factor of two. Values for σ(250 μm) and κ(250 μm) at the Milky Way metallicity are also close to those of the cirrus. Mild trends of the absorption cross sections with metallicity are found, although the results depend on the assumptions made.
Role of the external drivers in the occurrence of low-latitude ionospheric scintillation revealed by multi-scale analysis
Authors: Spogli Luca , Piersanti Mirko , Cesaroni Claudio , Materassi Massimo , Cicone Antonio , Alfonsi Lucilla , Romano Vincenzo , Ezquer Rodolfo Gerardo 
Published: September 2019

We analyze the amplitude scintillation on L-band signals over San Miguel de Tucumán (Argentina), focusing on the multi-scale variability and speculating on the possible relationship between forcing factors from the geospace and the ionospheric response. The site is nominally located below the expected position of the southern crest of the Equatorial Ionospheric Anomaly (EIA). For this scope, we concentrate on the period 1–31 March 2011, during which one minor and one moderate storm characterize the first half of the month, while generally quiet conditions of the geospace stand for the second half.
By leveraging on the Adaptive Local Iterative Filtering (ALIF) signal decomposition technique, we investigate the multi-scale properties of Global Navigation Satellite Systems (GNSS) amplitude scintillation and helio-geophysical parameters, looking for possible cause-effect mechanisms relating the former to the latter. Namely, we identify resonant modes in the Akasofu (ε) parameter as likely related to the frequency components in the time evolution found for the amplitude scintillation index, hence modulating the scintillation itself.
The Location and Accessibility of the Second Mesiobuccal Canal in Maxillary First Molar
Authors: Tuncer Aysun Kara , Haznedaroglu Faruk , Sert Semih 
Published: September 2019

ABSTRACTObjective:The purpose of this study was to examine the location and accessibility of the second mesibuccal canal in maxillary first molar of a Turkish sub-population.Methods: Presence and accessibility of the MB2 canal in 110 extracted maxillary first molars was examined with unaided vision, dental loups and the DOM. To characterize the geometrical location of MB2 canals, photographs of pulp chambers were obtained.Results: With the unaided vision, 58 MB2 canal orifices and after evaluation with the dental loup, DOM an additional 28 MB2 canal orifices were detected. In 65 molars, the MB2 canal orifices was located 0.87 mm distally and 1.73 mm palatally to the main mesiobuccal canal and in the remaining 21 molars was 0.72 mm mesially and 1.86 mm palatally.Conclusion: Presence of second mesiobuccal canal was similar to the other studies but in a Turkish sub-population it originates mainly distal to the main MB canal. (Eur J Dent 2010;4:12-16)
Periapical Status and Quality of Root Fillings and Coronal Restorations in an Adult Turkish Subpopulation
Authors: Gencoglu Nimet , Pekiner Filiz Namdar , Gumru Birsay , Helvacioglu Dilek 
Published: September 2019

ABSTRACTObjectives: To investigate the quality of root fillings and coronal restorations and their association with periapical status in an adult Turkish subpopulation.Methods: A total of 400 subjects were examined. Panoramic radiographs of all participants and additional periapical radiographs of affected teeth were processed. The frequency of root canal treatment and the periapical status of all root filled teeth were evaluated. The relationship between the radiographic quality of root fillings and coronal restorations was examined by chi-squared statistical analysis.Results: A total of 9460 teeth were examined. The total number of root filled teeth was 890 (9.39%), and 658 (73.9%) had apical periodontitis (AP). There was a significant correlation between the presence of periapical pathology and inadequate root canal fillings (P <.05). Presence of AP in root filled teeth was associated with inadequate adaptation of the filling (OR=1.097; P=0.54), and with poor radiographic quality of the coronal restoration (OR=0.91; P=0.70), and with poor radiographic quality of the filling restoration (OR=0.97; P=0.92). Only 24.5% of the root fillings were adequate. The highest percentage of root fillings was found in maxillary right first molars (6.9%).Conclusions: The results demonstrate a low prevalence of root-filled teeth and poor quality of coronal restorations and root fillings consistent with a high prevalence of apical periodontitis in a Turkish subpopulation. (Eur J Dent 2010;4:17-22)
Prosthetic Rehabilitation of Velopharyngeal Insufficiency: Pharyngeal Obturator Prostheses with Different Retention Mechanisms
Authors: Tuna Suleyman Hakan , Pekkan Gurel , Gumus Hasan Onder , Aktas Alper 
Published: September 2019

ABSTRACTPharyngeal obturator prostheses restore the congenital or acquired defects of the soft palate and allow adequate closure of palatopharyngeal sphincter. Two patients with soft palate defect and subsequent velopharyngeal insufficiency were rehabilitated using pharyngeal obturator prostheses which had different retention mechanisms. Since it is necessary for swallowing and intelligible speech, the patients were examined in terms of adequate velopharyngeal closure after prosthetic treatment. The results were satisfying for both the patients and physicians. (Eur J Dent 2010;4:81-87)