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  • 1
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    Crystal structure of a Xenopus laevis skin proto-type galectin, close to but distinct from galectin-1 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-04
    Description: Xenopus laevis (African clawed frog) has two types of proto-type galectins that are similar to mammalian galectin-1 in amino acid sequence. One type, comprising xgalectin-Ia and -Ib, is regarded as being equivalent to galectin-1, and the other type, comprising xgalectin-Va and -Vb, is expected to be a unique galectin subgroup. The latter is considerably abundant in frog skin; however, its biological function remains unclear. We determined the crystal structures of two proto-type galectins, xgalectin-Ib and -Va. The structures showed that both galectins formed a mammalian galectin-1-like homodimer, and furthermore, xgalectin-Va formed a homotetramer. This tetramer structure has not been reported for other galectins. Gel filtration and other experiments indicated that xgalectin-Va was in a dimer–tetramer equilibrium in solution, and lactose binding enhanced the tetramer formation. The residues involved in the dimer–dimer association were conserved in xgalectin-Va and -Vb, and one of the Xenopus (Silurana) tropicalis proto-type galectins, but not in xgalectin-Ia and -Ib, and other galectin-1-equivalent proteins. Xgalectin-Va preferred Galβ1-3GalNAc and not Galβ1-4GlcNAc, while xgalectin-Ib preferred Galβ1-4GlcNAc as well as human galectin-1. Xgalectin-Va/Vb would have diverged from the galectin-1 group with accompanying acquisition of the higher oligomer formation and altered ligand selectivity.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    Nebular line emission from z 〉 7 galaxies in a cosmological simulation: rest-frame UV to optical lines (2016)
    Oxford University Press
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    Publication Date: 2016-07-22
    Description: We have performed very large and high-resolution cosmological hydrodynamic simulations in order to investigate detectability of nebular lines in the rest-frame ultraviolet (UV) to optical wavelength range from galaxies at z 〉 7. We find that the expected line fluxes are very well correlated with the apparent UV magnitudes. The C  iv 1549 Å and C  iii ] 1909 Å lines of galaxies brighter than 26 AB magnitudes are detectable with current facilities such as the Very Large Telescope (VLT) XShooter and the Keck Multi-Object Spectrometer for Infra-Red Exploration (MOSFIRE). Metal lines such as C  iv 1549 Å, C  iii ] 1909 Å, [O  ii ] 3727 Å and [O  iii ] 4959/5007 Å are good targets for spectroscopic observation with the Thirty-Metre Telescope ( TMT ), European Extremely Large Telescope ( E-ELT ), Giant Magellan Telescope ( GMT ) and James Webb Space Telescope ( JWST ). We also expect Hα and Hβ lines to be detectable with these telescopes. Additionally, we predict the detectability of nebular lines for z 〉 10 galaxies, which will be found with JWST , the Wide-Field Infrared Survey Telescope ( WFIRST ) and First Light And Reionization Explorer ( FLARE ) (11 ≤ z ≤ 15). We conclude that the C  iv 1549 Å, C  iii ] 1909 Å, [O  iii ] 4959/5007 Å and Hβ lines from even z ~15 galaxies could be strong targets for TMT , E-ELT and JWST . We also find that magnification by gravitational lensing is of great help in detecting such high- z galaxies. According to our model, the C  iii ] 1909 Å line in z 〉 9 galaxy candidates is detectable even using current facilities.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Formation of primordial supermassive stars by burst accretion (2015)
    Oxford University Press
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    Publication Date: 2015-07-10
    Description: Recent observations show that supermassive black holes (BHs) with ~10 9 M exist at redshift z   6. A promising formation channel is the so-called direct collapse model, which posits that a massive seed BH forms through gravitational collapse of a ~10 5 M supermassive star (SMS). We study the evolution of such an SMS growing by rapid mass accretion. In particular, we examine the impact of time-dependent mass accretion of repeating burst and quiescent phases expected to occur with a self-gravitating circumstellar disc. We show that protostars growing via episodic accretion can substantially contract during the quiescent phases, in contrast to the case of constant mass accretion, whereby the star expands roughly monotonically. The stellar effective temperature and ionizing photon emissivity increase accordingly, which can cause strong ionizing feedback and halt the mass accretion. With a fixed duration of the quiescent phase t q , this contraction occurs in early evolutionary phases, i.e. for M *   10 3 M with t q ~= 10 3  yr. For later epochs and larger masses but the same t q , contraction is negligible even during quiescent phases. With larger t q , however, the star continues to contract during quiescent phases even for the higher stellar masses. We show that this behaviour is well understood by comparing the interval time and the thermal relaxation time for a bloated surface layer. We conclude that the feedback becomes effective, if t q   10 3 yr, which is possible in an accretion disc forming in the direct collapse model.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Physical properties of UDF12 galaxies in cosmological simulations (2014)
    Oxford University Press
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    Publication Date: 2014-04-02
    Description: We have performed a large cosmological hydrodynamics simulation tailored to the deep survey with the Hubble Space Telescope made in 2012, the so-called UDF12 campaign. After making a light-cone output, we have applied the same colour-selection criteria as the UDF12 campaign to select galaxies from our simulation, and then, have examined the physical properties of them as a proxy of the real observed UDF12 galaxies at z  〉 7. As a result, we find that the halo mass is almost linearly proportional to the observed ultraviolet (UV) luminosity (4 10 11 M at M UV  = –21). The dust attenuation and UV slope β well correlates with the observed UV luminosity, which is consistent with observations quantitatively. The star formation rate (SFR) is also linearly proportional to the stellar mass and the specific SFR shows only a weak dependence on the mass. We also find an increasing star formation history with a time-scale of ~100 Myr in the high- z galaxies. An average metallicity weighted by the Lyman continuum luminosity reaches up to 〉0.1 Solar even at z  ~ 10, suggesting a rapid metal enrichment. We also expect ≥0.1 mJy at 350 GHz of the dust thermal emission from the galaxies with H 160  ≤ 27, which can be detectable with the Atacama Large Millimetre-sub-millimetre Array. The galaxies selected by the UDF12 survey contribute to only 52–12 per cent of the cosmic SFR density from z  ~ 7 to z  ~ 10, respectively. The James Webb Space Telescope will push the detection fraction up to 77–72 per cent.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Supernova dust formation and the grain growth in the early universe: the critical metallicity for low-mass star formation (2014)
    Oxford University Press
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    Publication Date: 2014-12-03
    Description: We investigate the condition for the formation of low-mass second-generation stars in the early Universe. It has been proposed that gas cooling by dust thermal emission can trigger fragmentation of a low-metallicity star-forming gas cloud. In order to determine the critical condition in which dust cooling induces the formation of low-mass stars, we follow the thermal evolution of a collapsing cloud by a one-zone semi-analytic collapse model. Earlier studies assume the dust amount in the local Universe, where all refractory elements are depleted on to grains, and/or assume the constant dust amount during gas collapse. In this paper, we employ the models of dust formation and destruction in early supernovae to derive the realistic dust compositions and size distributions for multiple species as the initial conditions of our collapse calculations. We also follow accretion of heavy elements in the gas phase on to dust grains, i.e. grain growth, during gas contraction. We find that grain growth well alters the fragmentation property of the clouds. The critical conditions can be written by the gas metallicity Z cr and the initial depletion efficiency f dep,0 of gas-phase metal on to grains, or dust-to-metal mass ratio, as ( Z cr /10 –5.5 Z ) = ( f dep,0 /0.18) –0.44 with small scatters in the range of Z cr  = [0.06–3.2] 10 –5 Z . We also show that the initial dust composition and size distribution are important to determine Z cr .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Supermassive star formation via episodic accretion: protostellar disc instability and radiative feedback efficiency (2016)
    Oxford University Press
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    Publication Date: 2016-04-23
    Description: The formation of supermassive stars (SMSs) is a potential pathway to seed supermassive black holes in the early universe. A critical issue for forming SMSs is stellar UV feedback, which may limit the stellar mass growth via accretion. In this paper, we study the evolution of an accreting SMS and its UV emissivity with realistic variable accretion from a circumstellar disc. First we conduct a 2D hydrodynamical simulation to follow the protostellar accretion until the stellar mass exceeds 10 4 M . The disc fragments by gravitational instability, creating many clumps that migrate inward to fall on to the star. The resulting accretion history is highly time-dependent: short episodic accretion bursts are followed by longer quiescent phases. We show that the disc for the direct collapse model is more unstable and generates greater variability than normal Pop III cases. Next, we conduct a stellar evolution calculation using the obtained accretion history. Our results show that, regardless of the variable accretion, the stellar radius monotonically increases with almost constant effective temperature at T eff ~= 5000 K as the stellar mass increases. The resulting UV feedback is too weak to hinder accretion due to the low flux of stellar UV photons. The insensitivity of stellar evolution to variable accretion is attributed to the fact that time-scales of variability, 10 3 yr, are too short to affect the stellar structure. We argue that this evolution will continue until the SMS collapses to produce a black hole by the general relativistic instability after the mass reaches 10 5 M .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    Modelling colour-dependent galaxy clustering in cosmological simulations (2013)
    Oxford University Press
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    Publication Date: 2013-11-17
    Description: We extend the subhalo abundance matching method to assign galaxy colour to subhaloes. We separate a luminosity-binned subhalo sample into two groups by a secondary subhalo property which is presumed to be correlated with galaxy colour. The two subsamples then represent red and blue galaxy populations. We explore two models for the secondary property, namely subhalo assembly time and local dark matter density around each subhalo. The model predictions for the galaxy two-point correlation functions are compared with the recent results from the Sloan Digital Sky Survey. We show that the observed colour dependence of galaxy clustering can be reproduced well by our method applied to cosmological N -body simulations without baryonic processes. We then compare the model predictions for the colour-dependent galaxy-mass cross-correlation functions with the results from gravitational lensing observations. The comparison allows us to distinguish the models, and also to discuss what subhalo property should be used to assign colour to subhaloes accurately. We show that the extended abundance matching method using the local dark matter density as a colour proxy provides an accurate description of the galaxy populations in the local universe. We also study impacts of scatter on the local dark matter density–colour relations. Introducing scatter improves agreements of our model predictions with the observed red and blue galaxy clustering and is needed to explain observed correlation functions in finer colour bins. Finally, we study red galaxy fraction profiles in galaxy group- and cluster-sized haloes and find that the red fraction profiles have a relatively strong dependence on our model parameters. We argue that the red fraction profiles can be an important observational clue, in addition to galaxy clustering and galaxy–galaxy lensing, to explore the galaxy–(sub)halo connections.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Revealing the heterogeneous contamination process in metal nanoparticulate catalysts in CO gas without purification by in situ environmental transmission electron microscopy (2016)
    Oxford University Press
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    Publication Date: 2016-12-06
    Description: It is known that samples become contaminated in CO gas of high pressure unless care is taken with the gas supply line to an environmental transmission electron microscope. This technical note reveals the heterogeneous formation process of contamination in situ on a nanoparticulate catalyst sample. It is shown that the surface of metal nanoparticles is preferentially contaminated, while the surface of metal oxide supports remains uncontaminated. It is also demonstrated that the contamination is suppressed by introducing a gas purifier in a gas supply line.
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
    Published by Oxford University Press on behalf of The Japanese Electron Microscopy Society.
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  • 9
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    Probing cosmology with weak lensing selected clusters - I. Halo approach and all-sky simulations (2015)
    Oxford University Press
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    Publication Date: 2015-09-05
    Description: We explore a variety of statistics of clusters selected with cosmic shear measurement by utilizing both analytic models and large numerical simulations. We first develop a halo model to predict the abundance and the clustering of weak lensing selected clusters. Observational effects such as galaxy shape noise are included in our model. We then generate realistic mock weak lensing catalogues to test the accuracy of our analytic model. To this end, we perform full-sky ray-tracing simulations that allow us to have multiple realizations of a large continuous area. We model the masked regions on the sky using the actual positions of bright stars, and generate 200 mock weak lensing catalogues with sky coverage of ~1000 deg 2 . We show that our theoretical model agrees well with the ensemble average of statistics and their covariances calculated directly from the mock catalogues. With a typical selection threshold, ignoring shape noise correction causes overestimation of the clustering of weak lensing selected clusters with a level of about 10 per cent, and shape noise correction boosts the cluster abundance by a factor of a few. We calculate the cross-covariances using the halo model with accounting for the effective reduction of the survey area due to masks. The covariance of the cosmic shear auto power spectrum is affected by the mode-coupling effect that originates from sky masking. Our model and the results can be readily used for cosmological analysis with ongoing and future weak lensing surveys.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Primordial star formation under the influence of far ultraviolet radiation: 1540 cosmological haloes and the stellar mass distribution (2015)
    Oxford University Press
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    Publication Date: 2015-02-08
    Description: We perform a large set of cosmological simulations of early structure formation and follow the formation and evolution of 1540 star-forming gas clouds to derive the mass distribution of primordial stars. The star formation in our cosmological simulations is characterized by two distinct populations, the so-called Population III.1 stars and primordial stars formed under the influence of far-ultraviolet (FUV) radiation (Population III.2 D stars). In this work, we determine the stellar masses by using the dependences on the physical properties of star-forming cloud and/or the external photodissociating intensity from nearby primordial stars, which are derived from the results of 2D radiation hydrodynamic simulations of protostellar feedback. The characteristic mass of the Pop III stars is found to be a few hundred solar masses at z  ~ 25, and it gradually shifts to lower masses with decreasing redshift. At high redshifts z  〉 20, about half of the star-forming gas clouds are exposed to intense FUV radiation and thus give birth to massive Pop III.2 D stars. However, the local FUV radiation by nearby Pop III stars becomes weaker at lower redshifts, when typical Pop III stars have smaller masses and the mean physical separation between the stars becomes large owing to cosmic expansion. Therefore, at z  〈 20, a large fraction of the primordial gas clouds host Pop III.1 stars. At z   15, the Pop III.1 stars are formed in relatively cool gas clouds due to efficient radiative cooling by H 2 and HD molecules; such stars have masses of a few 10 M . Since the stellar evolution and the final fate are determined by the stellar mass, Pop III stars formed at different epochs play different roles in the early universe.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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