bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Studies of the Dust around Red Supergiant and Oxygen-Rich Asymptotic Giant Branch Stars in the Local Universe
Authors: Sargent B. A. , Srinivasan S. , Speck A. , Volk K. , Kemper F. , Reach W. , Lagadec E. , Bernard J.-P. , McDonald I. , Meixner M. , Sloan G. C. , Jones O.
Published: October 2016

We analyze the dust emission features seen in Spitzer Space Telescope Infrared Spectrograph (IRS) spectra of red supergiant (RSG) and oxygen-rich asymptotic giant branch (AGB) stars in the Large Magellanic Cloud and Small Magellanic Cloud galaxies and in various Milky Way globular clusters. The spectra come from the Spitzer Legacy program SAGE-Spectroscopy (PI: F. Kemper), the Spitzer program SMC-Spec (PI: G. Sloan), and other archival Spitzer-IRS programs. The broad 10 and 20 micron emission features attributed to amorphous dust of silicate composition seen in the spectra show evidence for systematic differences in the centroid of both emission features between O-rich AGB and RSG populations. Radiative transfer modeling using the GRAMS grid of models of AGB and RSG stars suggests that the centroid differences are due to differences in dust properties. We investigate differences in dust composition, size, shape, etc that might be responsible for these spectral differences. We explore how these differences may arise from the different circumstellar environments around RSG and O-rich AGB stars and assess effects of varying metallicity (LMC versus SMC versus Milky Way globular cluster) and other properties (mass-loss rate, luminosity, etc.) on the dust originating from these stars. BAS acknowledges funding from NASA ADAP grant NNX13AD54G.
Revisiting the red supergiant progenitors of core-collapse supernovae
Authors: Van Dyk Schuyler D.
Published: October 2016

I will present a reanalysis of the properties of the red supergiant (RSG) progenitors of several extragalactic core-collapse, Type II-Plateau supernovae, including SN 2012aw, SN 2013ej, SN 2004et, and SN 2008bk. The observed spectral energy distributions (SEDs) for these stars, from the optical to the infrared, are compared with model SEDs for Galactic RSGs, as well as with the observed SEDs of analogous RSGs in Local Group galaxies. As a result, new estimates of the stellar temperatures and luminosities for the progenitors are obtained, and through comparison with recent massive stellar evolutionary tracks, new inferences are made for the progenitors initial masses. I will place these in the context of the RSG SN progenitor mass spectrum and of the so-called “red supergiant problem.”
Cool Stars in the Hertzsprung–Russell Diagram
Authors: van Loon Jacco Th.
Published: October 2016

As the opening review to the focus meeting “Stellar Behemoths: Red Supergiants across the Local Universe”, I here provide a brief introduction to red supergiants, setting the stage for subsequent contributions. I highlight some recent activity in the field, and identify areas of progress, areas where progress is needed, and how such progress might be achieved.
The Kepler field of view covered with the LAMOST spectroscopic observations
Authors: Molenda-Żakowicz Joanna , De Cat Peter , Fu Jian-Ning , Ren An-Bing , Frasca Antonio , Catanzaro Giovanni
Published: October 2016

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) at the Xinglong observatory in China is a 4-m telescope equipped with 4,000 optical fibres. In 2010, we initiated the LAMOST-Kepler project which aimed at collecting low-resolution spectra of stars from the Kepler Input Catalog covering uniformly the Kepler field of view. The first round of the LAMOST-Kepler project has been completed in September 2014 resulting in more than 100,000 low-resolution spectra. We used those data to derive the effective temperature, the surface gravity, and the mean metallicity of our targets, as well as to detect fast rotators, and to identify emission-line stars. Our results are consistent with those reported in the literature and derived from high-resolution spectroscopy. The second round of the LAMOST-Kepler project will allow to improve the coverage of the Kepler field and to repeat observations of selected targets.
Theory of stellar convection: removing the mixing-length parameter
Authors: Pasetto Stefano , Chiosi Cesare , Cropper Mark , Grebel Eva K.
Published: October 2016

Stellar convection is customarily described by the mixing-length theory, which makes use of the mixing-length scale to express the convective flux, velocity, and temperature gradients of the convective elements and stellar medium. The mixing-length scale is taken to be proportional to the local pressure scale height, and the proportionality factor (the mixing-length parameter) must be determined by comparing the stellar models to some calibrator, usually the Sun. No strong arguments exist to suggest that the mixing-length parameter is the same in all stars and all evolutionary phases. Because of this, all stellar models in the literature are hampered by this basic uncertainty.

In a recent paper (Pasettoet al.2014) we presented a new theory that does not require the mixing length parameter. Our self-consistent analytical formulation of stellar convection determines all the properties of stellar convection as a function of the physical behaviour of the convective elements themselves and the surrounding medium. The new theory of stellar convection is formulated starting from a conventional solution of the Navier-Stokes/Euler equations, i.e. the Bernoulli equation for a perfect fluid, but expressed in a non-inertial reference frame co-moving with the convective elements. In our formalism, the motion of stellar convective cells inside convective-unstable layers is fully determined by a new system of equations for convection in a non-local and time-dependent formalism.

We obtained an analytical, non-local, time-dependent solution for the convective energy transport that does not depend on any free parameter. The predictions of the new theory are compared with those from the standard mixing-length paradigm with positive results for atmosphere models of the Sun and all the stars in the Hertzsprung-Russell diagram.
Frequency shifts of resonant modes of the Sun due to near-surface convective scattering
Authors: Bhattacharya J. , Hanasoge S. M. , Antia H. M.
Published: October 2016

Measurements of oscillation frequencies of the Sun and stars can provide important independent constraints on their internal structure and dynamics. Seismic models of these oscillations are used to connect structure and rotation of the star to its resonant frequencies, which are then compared with observations, the goal being that of minimizing the difference between the two. Even in the case of the Sun, for which structure models are highly tuned, observed frequencies show systematic deviations from modeled frequencies, a phenomenon referred to as the “surface term.” The dominant source of this systematic effect is thought to be vigorous near-surface convection, which is not well accounted for in both stellar modeling and mode-oscillation physics. Here we bring to bear the method of homogenization, applicable in the asymptotic limit of large wavelengths (in comparison to the correlation scale of convection), to characterize the effect of small-scale surface convection on resonant-mode frequencies in the Sun. We show that the full oscillation equations, in the presence of temporally stationary 3D flows, can be reduced to an effective “quiet-Sun” wave equation with altered sound speed, Brünt–Väisäla frequency, and Lamb frequency. We derive the modified equation and relations for the appropriate averaging of 3D flows and thermal quantities to obtain the properties of this effective medium. Using flows obtained from 3D numerical simulations of near-surface convection, we quantify their effect on solar oscillation frequencies and find that they are shifted systematically and substantially. We argue therefore that consistent interpretations of resonant frequencies must include modifications to the wave equation that effectively capture the impact of vigorous hydrodynamic convection.
Cosmic Bulk Flow and the Local motions from CosmicFlows-2 dataset
Authors: Courtois H. M.
Published: October 2016

Using the largest and most accurate ever catalog of galaxy peculiar velocities Cosmicflows-2, the large scale structure has been reconstructed by means of the Wiener filter and constrained realizations assuming as a Bayesian prior model the LCDM standard model of cosmology. Our main result is that the estimated bulk flow is consistent with the LCDM model with the WMAP inferred cosmological parameters. At R=50 (150)Mpc/h the estimated bulk velocity is 250 ± 21 (239 ± 38) km/s. The SGX and SGY components of the CMB dipole velocity are recovered by the Wiener Filter (WF) velocity field down to a very few km/s. The SGZ component of the estimated velocity, the one that is most affected by the Zone of Avoidance, is off by 126 km/s (an almost 2 sigma discrepancy).
Filament Formation in Molecular Clouds as a Scale-Free Process
Authors: Vázquez-Semadeni Enrique , Gómez Gilberto
Published: October 2016

We discuss the formation of filaments in molecular clouds (MCs) as the result of large-scale collapse in the clouds. We first give arguments suggesting that self-gravity dominates the nonthermal motions, and then briefly describe the resulting structure, similar to that found in molecular-line and dust observations of the filaments in the clouds. The filaments exhibit a hierarchical structure in both density and velocity, suggesting a scale-free nature, similar to that of the cosmic web, resulting from the domination of self-gravity from the MC down to the core scale.
The linewidth-size scaling law of molecular gas revisited
Authors: Falgarone Edith , McKee Christopher F.
Published: October 2016

The origin of the linewidth-size (LWS) scaling law, first noticed by Larson three decades ago and ascribed to turbulence, is still a highly debated issue. Not unexpectedly, its properties depend on the environment and on the line tracer used. When the optically thick 12CO (J=1-0) line is used, a specific medium is sampled: the translucent molecular gas of moderate density that builds up the bulk of the molecular interstellar medium in galaxies like the Milky Way. The sensitivity of the 12CO line to this gas is such that the LWS is found to hold over almost five orders of magnitude in lengthscale, although with a considerable scatter (± 0.5 dex). It also appears to split into two regimes, depending on the gas mass surface density: below a given threshold that is proposed to be linked to the galactic structure, it bears the signature of a turbulent cascade, while above it, the scaling law is ascribed to virial balance. Large deviations from the LWS scaling law are observed at small scales where signatures of turbulent intermittency appear. The mass-size scaling law built with the 12CO (J=1-0) line also splits into two regimes. The mass surface density is uniform (also with a large scatter) above lengthscales ~ 10pc and increases with size at smaller scales, following turbulence predictions. The two thresholds define an average gas density nH ~ 300 cm−3.
A Self-Critique of Self-Organized Criticality in Astrophysics
Authors: Aschwanden Markus J.
Published: October 2016

The concept of “self-organized criticality” (SOC) was originally proposed as an explanation of 1/f-noise by Bak, Tang, and Wiesenfeld (1987), but turned out to have a far broader significance for scale-free nonlinear energy dissipation processes occurring in the entire universe. Over the last 30 years, an inspiring cross-fertilization from complexity theory to solar and astrophysics took place, where the SOC concept was initially applied to solar flares, stellar flares, and magnetospheric substorms, and later extended to the radiation belt, the heliosphere, lunar craters, the asteroid belt, the Saturn ring, pulsar glitches, soft X-ray repeaters, blazars, black-hole objects, cosmic rays, and boson clouds. The application of SOC concepts has been performed by numerical cellular automaton simulations, by analytical calculations of statistical (powerlaw-like) distributions based on physical scaling laws, and by observational tests of theoretically predicted size distributions and waiting time distributions. Attempts have been undertaken to import physical models into numerical SOC toy models. The novel applications stimulated also vigorous debates about the discrimination between SOC-related and non-SOC processes, such as phase transitions, turbulence, random-walk diffusion, percolation, branching processes, network theory, chaos theory, fractality, multi-scale, and other complexity phenomena. We review SOC models applied to astrophysical observations, attempt to describe what physics can be captured by SOC models, and offer a critique of weaknesses and strengths in existing SOC models.
A Spatial Study of X-ray Properties in Superbubble 30 Dor C with XMM-Newton
Authors: Babazaki Y. , Mitsuishi I. , Sano H. , Yoshiike S. , Fukuda T. , Maruyama S. , Fujii K. , Fukui Y. , Tawara Y. , Matsumoto H
Published: October 2016

The superbubble (SB) 30 Dor C with the strong non-thermal X-ray emission is one of the best targets for study of the cosmic-ray (CR) acceleration. We investigated X-ray spectral properties of the SB with a high spatial resolution of ~10 pc. Consequently, the spectra in the east regions can be described with a combination of absorbed thermal and non-thermal models while the spectra in the west regions can be fitted with an absorbed non-thermal model. We found that the observed photon index and intensity in 2-10 keV show variations of 2.0-3.5 and (0.6-8.0) × 10−7 erg s−1 cm−2 str−1, respectively. The results are possibly caused by the spatial variation of the CR acceleration efficiency and/or the circumstellar environment.
Transonic galactic outflows in a dark matter halo with a central black hole
Authors: Igarashi Asuka , Mori Masao , Nitta Shin-ya
Published: October 2016

We study fundamental properties of transonic galactic outflows in the gravitational potential of a cold dark matter halo (DMH) with a central super-massive black hole (SMBH) assuming an isothermal, steady and spherically symmetric state. Transonic solutions of galactic outflows are classified according to their topological features. As result, we find two types of transonic solutions distinguished by a magnitude relationship between the gravity of DMH and that of SMBH. The loci of transonic points for two types are different; one transonic point is formed at a central region (< 0.01kpc) and another is at a very distant region (> 100kpc). Also, mass fluxes and outflow velocities are different for two solutions. Thus, these solutions may differently influence the evolution of galaxies and the release of metals into the intergalactic space.

Furthermore, we apply our model to the Sombrero galaxy. In this galaxy, the wide-spread hot gas is detected as the trace of galactic outflows while the star-formation rate is low, and the observed gas density distribution is similar to the hydrostatic state (Li et al. 2011). To solve this discrepancy, we propose a solution that this galaxy has a slowly accelerating outflow; the transonic point forms in a very distant region (~ 120 kpc) and the wide subsonic region spreads across the stellar distribution. Thus, the gas density distribution in the observed region is similar to the hydrostatic state. Such slowly accelerating outflows are different from high-velocity outflows conventionally studied (Igarashi et al. 2014).

However, this isothermal model requires an unrealistically large mass flux. Then, we apply the polytropic model to this galaxy incorporating mass flux supplied by stellar components. We find that it can reproduce the observed gas density and the temperature distributions with the realistic mass flux. Thus, our polytropic model successfully demonstrates the existence of the slowly accelerating outflow in the Sombrero galaxy (Igarashi et al. 2015).
A novel approach to gravitation from fluid theory: Titius-Bode structures, flat rotation rate of galaxies, and other predictions
Authors: Munera Hector A.
Published: October 2016

Following the discovery of quantum phenomena at laboratory scale (Couder & Fort 2006), de Broglie pilot wave theory (De Broglie 1962) has been revived under a hydrodynamic guise (Bush 2015). Theoretically, it boils down to solving the transport equations for the energy and linear momentum densities of a postulated fundamental fluid in terms of classical wave equations, which inherently are Lorentz-invariant and scale-invariant. Instead of the conventional harmonic solutions, for astronomical and gravitational problems the novel solutions for the homogeneous wave equation in spherical coordinates are more suitable (Munera et al. 1995, Munera & Guzman 1997, and Munera 2000). Two groups of solutions are particularly relevant: (a) The inherently-quantized helicoidal solutions that may be applicable to describe spiral galaxies, and (b) The non-harmonic solutions with time (t) and distance (r) entangled in the single variable q = Ct/r (C is the two-way local electromagnetic speed). When these functions are plotted against 1/q they manifestly depict quantum effects in the near field, and Newtonian-like gravity in the far-field. The near-field predicts quantized effects similar to ring structures and to Titius-Bode structures, both in our own solar system and in exoplanets, the correlation between predicted and observed structures being typically larger than 99 per cent. In the far-field, some non-harmonic functions have a rate of decrement with distance slower than inverse-square thus explaining the flat rotation rate of galaxies. Additional implications for Trojan orbits, and quantized effects in photon deflection were also noted.
Scale-free convection theory
Authors: Pasetto Stefano , Chiosi Cesare , Cropper Mark , Grebel Eva K.
Published: October 2016

Convection is one of the fundamental mechanisms to transport energy, e.g., in planetology, oceanography, as well as in astrophysics where stellar structure is customarily described by the mixing-length theory, which makes use of the mixing-length scale parameter to express the convective flux, velocity, and temperature gradients of the convective elements and stellar medium. The mixing-length scale is taken to be proportional to the local pressure scale height of the star, and the proportionality factor (the mixing-length parameter) must be determined by comparing the stellar models to some calibrator, usually the Sun. No strong arguments exist to claim that the mixing-length parameter is the same in all stars and all evolutionary phases. Because of this, all stellar models in the literature are hampered by this basic uncertainty. In a recent paper (Pasetto et al. 2014) we presented the first fully analytical scale-free theory of convection that does not require the mixing-length parameter. Our self-consistent analytical formulation of convection determines all the properties of convection as a function of the physical behaviour of the convective elements themselves and the surrounding medium (be it a star, an ocean, or a primordial planet). The new theory of convection is formulated starting from a conventional solution of the Navier-Stokes/Euler equations, i.e. the Bernoulli equation for a perfect fluid, but expressed in a non-inertial reference frame co-moving with the convective elements. In our formalism, the motion of convective cells inside convective-unstable layers is fully determined by a new system of equations for convection in a non-local and time dependent formalism. We obtained an analytical, non-local, time-dependent solution for the convective energy transport that does not depend on any free parameter. The predictions of the new theory in astrophysical environment are compared with those from the standard mixing-length paradigm in stars with exceptional results for atmosphere models of the Sun and all the stars in the Hertzsprung-Russell diagram.
X-raying the Hubble Frontier Fields cluster Abell 2744
Authors: Eckert Dominique
Published: October 2016

Abell 2744 was the first HFF cluster completed. It displays a fascinating complexity in its distribution of dark and luminous matter, which led to its nickname of the Pandora cluster. In late 2014 we obtained a deep (110 ks) observation of this cluster with XMM-Newton, with the aim of making a detailed comparison between the optical, X-ray and lensing properties of this system. The new X-ray observation unveiled the presence of three hot gas filaments extending on scales of several Mpc and connected to the cluster core. The X-ray structures coincide spatially with the distribution of galaxies and dark matter and provide strong evidence for the existence of the elusive warm-hot intergalactic medium (WHIM). The new observation also reveals the complexity of the thermodynamic structure of the cluster core and a probable shock front associated with the radio relic located 1 Mpc NW of the cluster core.
The MUSE view of the Frontier Field clusters
Authors: Richard Johan , Mahler Guillaume , Clément Benjamin , Lagattuta David , Patriício Vera , Pelló Roser , Bina David ,   the MUSE consortium
Published: October 2016

Strong gravitational magnification in the core of lensing clusters allows to probe the faint-end of the galaxy luminosity function up to very high redshift. In particular, the Frontier Fields have allowed us to identify a large number of faint dropouts and constrain the Lyman-break luminosity function at z~5-7. I present here the results of an ongoing program with MUSE, a new integral field spectrograph on the Very Large Telescope having a large field of view (1 arcmin2), to confirm these candidate high redshift dropouts through Lyman-α emission and identify additional emitters with high equivalent width, fainter than the depth of the Frontier Fields Hubble images. Combined with similar deep exposures taken with MUSE in blank fields, this gives us the best opportunity to probe the Lyman-α luminosity function over a wide range in luminosity.
Automatic Selection of Multiple Images in the Frontier Field Clusters
Authors: Mahler Guillaume , Richard Johan , Clément Benjamin , Lagattuta David , Patricio Vera
Published: October 2016

Probing the central mass distribution of massive galaxy clusters is an important step towards mapping the overall distribution of their dark matter content. Thanks to gravitational lensing and the appearance of multiple images, we can constrain the inner region of galaxy clusters with a high precision. The Frontier Fields (FF) provide us with the deepest HST data ever in such clusters. Currently, most multiple-image systems are found by eye, yet in the FF, we expect hundreds to exist. Thus, in order to deal with such huge amounts of data, we need to develop an automated detection method. I present a new tool to perform this task, MISE (Multiple Image SEarcher), a program which identifies multiple images by combining their specific properties. MISE allows us to confirm or reject multiple images identified visually, but also detect new multiple-image candidates in MACS0416 and A2744, giving us additional constraints on the mass distribution in these clusters. A spectroscopic follow-up of these candidates is currently underway with MUSE.
Strong Lensing Mass Reconstruction: from Frontier Fields to the Typical Lensing Clusters of Future Surveys
Authors: Sharon Keren , Gladders Michael D. , Rigby Jane R. , Bayliss Matthew B. , Wuyts Eva , Dahle Håkon , Johnson Traci L. , Florian Michael K. , Dunham Samuel , Murray Katherine , Whitaker Kate , Li Nan
Published: October 2016

Driven by the unprecedented wealth of high quality data that is accumulating for the Frontier Fields, they are becoming some of the best-studied strong lensing clusters to date, and probably the next few years. As will be discussed intensively in this focus meeting, the FF prove transformative for many fields: from studies of the high redshift Universe, to the assembly and structure of the clusters themselves. The FF data and the extensive collaborative effort around this program will also allow us to examine and improve upon current lens modeling techniques. Strong lensing is a powerful tool for mass reconstruction of the cores of galaxy clusters of all scales, providing an estimate of the total (dark and seen) projected mass density distribution out to 0.5 Mpc. Though SL mass may be biased by contribution from structures along the line of sight, its strength is that it is relatively insensitive to assumptions on cluster baryon astrophysics and dynamical state. Like the Frontier Fields clusters, the most “famous” strong lensing clusters are at the high mass end; they lens dozens of background sources into multiple images, providing ample lensing constraints. In this talk, I will focus on how we can leverage what we learn from modeling the FF clusters in strong lensing studies of the hundreds of clusters that will be discovered in upcoming surveys. In typical clusters, unlike the Frontier Fields, the Bullet Cluster and A1689, we observe only one to a handful of background sources, and have limited lensing constraints. I will describe the limitations that such a configuration imposes on strong lens modeling, highlight measurements that are robust to the richness of lensing evidence, and address the sources of uncertainty and what sort of information can help reduce those uncertainties. This category of lensing clusters is most relevant to the wide cluster surveys of the future.
Substructure in the Frontier Fields from weak lensing flexion
Authors: Rexroth Markus
Published: October 2016

Flexion is the second order weak gravitational lensing effect responsible for the arclike appearance of sources. It is highly sensitive to dark matter substructure and can greatly increase the resolution of mass maps, but it is very hard to measure. We present an automated flexion measurement pipeline for Hubble Space Telescope data and a preliminary application to the Frontier Fields cluster MACSJ0416.1-2403.
Strong Lensing Cosmography in the Frontier Fields
Authors: Jullo Eric , Acebron Ana , Limousin Marceau , Giocoli Carlo , Despali Giulia , Bonamigo Mario ,   the CATS team
Published: October 2016

The wealth of strong lensing features observed in the Frontier Fields clusters offers insights on the nature of dark energy. The large number of multiple-images systems with redshifts allows to simultaneously estimate the lens model parameters and the cosmological parameters involved in the distances calculations. In particular for the ΛCDM model, it is possible to estimate the matter density Ωm and the dark energy equations parameters wX. In this talk, I will present recent analyses of systematic errors based on Frontier Fields observed and simulated data.
2016 AGU Election Statistics
Authors: Finn Carol , Brigham-Grette Julie , Carroll Mary , Lechner Hans , McCammon Catherine , Tiessen Holm , Tsoflias George , McEntee Chris , Enderlein Cheryl
Published: October 2016

The American Geophysical Union's Governance Committee recaps the timing, participation, and other details of the organization's recently completed 2016 leadership election.
Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor
Authors: Suzuki Kano , Mizutani Kenji , Maruyama Shintaro , Shimono Kazumi , Imai Fabiana L. , Muneyuki Eiro , Kakinuma Yoshimi , Ishizuka-Katsura Yoshiko , Shirouzu Mikako , Yokoyama Shigeyuki , Yamato Ichiro , Murata Takeshi
Published: October 2016

V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model.
Sulfur mass-independent fractionation in subsurface fracture waters indicates a long-standing sulfur cycle in Precambrian rocks
Authors: Li L. , Wing B. A. , Bui T. H. , McDermott J. M. , Slater G. F. , Wei S. , Lacrampe-Couloume G. , Lollar B. Sherwood
Published: October 2016

The discovery of hydrogen-rich waters preserved below the Earth’s surface in Precambrian rocks worldwide expands our understanding of the habitability of the terrestrial subsurface. Many deep microbial ecosystems in these waters survive by coupling hydrogen oxidation to sulfate reduction. Hydrogen originates from water–rock reactions including serpentinization and radiolytic decomposition of water induced by decay of radioactive elements in the host rocks. The origin of dissolved sulfate, however, remains unknown. Here we report, from anoxic saline fracture waters ∼2.4 km below surface in the Canadian Shield, a sulfur mass-independent fractionation signal in dissolved sulfate. We demonstrate that this sulfate most likely originates from oxidation of sulfide minerals in the Archaean host rocks through the action of dissolved oxidants (for example, HO·and H2O2) themselves derived from radiolysis of water, thereby providing a coherent long-term mechanism capable of supplying both an essential electron donor (H2) and a complementary acceptor (sulfate) for the deep biosphere.
Adaptive Intuitionistic Fuzzy Enhancement of Brain Tumor MR Images
Authors: Deng He , Deng Wankai , Sun Xianping , Ye Chaohui , Zhou Xin
Published: October 2016

Image enhancement techniques are able to improve the contrast and visual quality of magnetic resonance (MR) images. However, conventional methods cannot make up some deficiencies encountered by respective brain tumor MR imaging modes. In this paper, we propose an adaptive intuitionistic fuzzy sets-based scheme, called as AIFE, which takes information provided from different MR acquisitions and tries to enhance the normal and abnormal structural regions of the brain while displaying the enhanced results as a single image. The AIFE scheme firstly separates an input image into several sub images, then divides each sub image into object and background areas. After that, different novel fuzzification, hyperbolization and defuzzification operations are implemented on each object/background area, and finally an enhanced result is achieved via nonlinear fusion operators. The fuzzy implementations can be processed in parallel. Real data experiments demonstrate that the AIFE scheme is not only effectively useful to have information from images acquired with different MR sequences fused in a single image, but also has better enhancement performance when compared to conventional baseline algorithms. This indicates that the proposed AIFE scheme has potential for improving the detection and diagnosis of brain tumors.
Infantile Hemangioma Originates From A Dysregulated But Not Fully Transformed Multipotent Stem Cell
Authors: Harbi Shaghayegh , Wang Rong , Gregory Michael , Hanson Nicole , Kobylarz Keith , Ryan Kamilah , Deng Yan , Lopez Peter , Chiriboga Luis , Mignatti Paolo
Published: October 2016

Infantile hemangioma (IH) is the most common tumor of infancy. Its cellular origin and biological signals for uncontrolled growth are poorly understood, and specific pharmacological treatment is unavailable. To understand the process of hemangioma-genesis we characterized the progenitor hemangioma-derived stem cell (HemSC) and its lineage and non-lineage derivatives. For this purpose we performed a high-throughput (HT) phenotypic and gene expression analysis of HemSCs, and analyzed HemSC-derived tumorspheres. We found that IH is characterized by high expression of genes involved in vasculogenesis, angiogenesis, tumorigenesis and associated signaling pathways. These results show that IH derives from a dysregulated stem cell that remains in an immature, arrested stage of development. The potential biomarkers we identified can afford the development of diagnostic tools and precision-medicine therapies to “rewire” or redirect cellular transitions at an early stage, such as signaling pathways or immune response modifiers.
Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa
Authors: Deng Zhaojie , Arsenault Sam , Caranica Cristian , Griffith James , Zhu Taotao , Al-Omari Ahmad , Schüttler Heinz-Bernd , Arnold Jonathan , Mao Leidong
Published: October 2016

The synchronization of stochastic coupled oscillators is a central problem in physics and an emerging problem in biology, particularly in the context of circadian rhythms. Most measurements on the biological clock are made at the macroscopic level of millions of cells. Here measurements are made on the oscillators in single cells of the model fungal system, Neurospora crassa, with droplet microfluidics and the use of a fluorescent recorder hooked up to a promoter on a clock controlled gene-2 (ccg-2). The oscillators of individual cells are stochastic with a period near 21 hours (h), and using a stochastic clock network ensemble fitted by Markov Chain Monte Carlo implemented on general-purpose graphical processing units (or GPGPUs) we estimated that >94% of the variation in ccg-2 expression was stochastic (as opposed to experimental error). To overcome this stochasticity at the macroscopic level, cells must synchronize their oscillators. Using a classic measure of similarity in cell trajectories within droplets, the intraclass correlation (ICC), the synchronization surface ICC is measured on >25,000 cells as a function of the number of neighboring cells within a droplet and of time. The synchronization surface provides evidence that cells communicate, and synchronization varies with genotype.
The robustness of ecosystems to the species loss of community
Authors: Cai Qing , Liu Jiming
Published: October 2016

To study the robustness of ecosystems is crucial to promote the sustainable development of human society. This paper aims to analyze the robustness of ecosystems from an interesting viewpoint of the species loss of community. Unlike the existing definitions, we first introduce the notion of a community as a population of species belonging to the same trophic level. We then put forward a novel multiobjective optimization model which can be utilized to discover community structures from arbitrary unipartite networks. Because an ecosystem is commonly represented as a multipartite network, we further introduce a mechanism of competition among species whereby a multipartite network is transformed into a unipartite signed network without loss of species interaction information. Finally, we examine three strategies to test the robustness of an ecosystem. Our experiments indicate that ecosystems are robust to random species loss of community but fragile to target ones. We also investigate the relationships between the robustness of an ecosystem and that of its community composed network both to species loss. Our experiments indicate that the robustness analysis of a large-scale ecosystem to species loss may be akin to that of its community composed network which is usually small in size.
The conformational dynamics of H2-H3n and S2-H6 in gating ligand entry into the buried binding cavity of vitamin D receptor
Authors: Tee Wei-Ven , Ripen Adiratna Mat , Mohamad Saharuddin Bin
Published: October 2016

Crystal structures of holo vitamin D receptor (VDR) revealed a canonical conformation in which the ligand is entrapped in a hydrophobic cavity buried in the ligand-binding domain (LBD). The mousetrap model postulates that helix 12 is positioned away from the domain to expose the interior cavity. However, the extended form of helix 12 is likely due to artifacts during crystallization. In this study, we set out to investigate conformational dynamics of apo VDR using molecular dynamics simulation on microsecond timescale. Here we show the neighboring backbones of helix 2-helix 3n and beta strand 2-helix 6 of LBD, instead of the helix 12, undergo large-scale motion, possibly gating the entrance of ligand to the ligand binding domain. Docking analysis to the simulated open structure of VDR with the estimated free energy of −37.0 kJ/mol, would emphasise the role of H2-H3n and S2-H6 in facilitating the entrance of calcitriol to the LBD of VDR.
Goblet Cell Hyperplasia Requires High Bicarbonate Transport To Support Mucin Release
Authors: Gorrieri Giulia , Scudieri Paolo , Caci Emanuela , Schiavon Marco , Tomati Valeria , Sirci Francesco , Napolitano Francesco , Carrella Diego , Gianotti Ambra , Musante Ilaria , Favia Maria , Casavola Valeria , Guerra Lorenzo , Rea Federico , Ravazzolo Roberto , Di Bernardo Diego , Galietta Luis J. V.
Published: October 2016

Goblet cell hyperplasia, a feature of asthma and other respiratory diseases, is driven by the Th-2 cytokines IL-4 and IL-13. In human bronchial epithelial cells, we find that IL-4 induces the expression of many genes coding for ion channels and transporters, including TMEM16A, SLC26A4, SLC12A2, and ATP12A. At the functional level, we find that IL-4 enhances calcium- and cAMP-activated chloride/bicarbonate secretion, resulting in high bicarbonate concentration and alkaline pH in the fluid covering the apical surface of epithelia. Importantly, mucin release, elicited by purinergic stimulation, requires the presence of bicarbonate in the basolateral solution and is defective in cells derived from cystic fibrosis patients. In conclusion, our results suggest that Th-2 cytokines induce a profound change in expression and function in multiple ion channels and transporters that results in enhanced bicarbonate transport ability. This change is required as an important mechanism to favor release and clearance of mucus.
Antioxidant and Antitumor Activity of a Bioactive Polyphenolic Fraction Isolated from the Brewing Process
Authors: Tatullo Marco , Simone Grazia Maria , Tarullo Franco , Irlandese Gianfranco , Vito Danila De , Marrelli Massimo , Santacroce Luigi , Cocco Tiziana , Ballini Andrea , Scacco Salvatore
Published: October 2016

There is increasing interest in identifying natural bioactive compounds that can improve mitochondrial functionality and regulate apoptosis. The brewery industry generates wastewater that could yield a natural extract containing bioactive phenolic compounds. Polyphenols act as antioxidants and have been documented to protect the human body from degenerative diseases such as cardiovascular diseases or cancer. The main aims of our research were to determine the phenolic profile of a crude extract obtained (at pilot scale) from a brewery waste stream and to evaluate the biochemical activity of this extract on the mitochondrial function of a cancer cell line (SH-SY5Y). This work is a basic translational pilot study. The total phenolic content was determined by the Folin–Ciocalteu assay, which revealed that 2.30% of the extract consisted of phenolic compounds. The polyphenols, identified and quantified by reverse-phase-high-performance liquid chromatography and mass spectrometry (RP-HPLC/MS), were mainly flavonoids. After cell culture, the tumoral cells treated with the polyphenolic extract showed enhanced mitochondrial oxidative function, which is likely related to a decrease in oxidative stress and an increase in mitochondrial biogenesis. This type of brewery waste stream, properly treated, may be a promising source of natural antioxidants to replace the synthetic antioxidants currently used in the food industry.
Prevalence of hemorrhagic fever with renal syndrome in Qingdao City, China, 2010–2014
Authors: Jiang Fachun , Zhang Zhentang , Dong Liyan , Hao Bi , Xue Zaifeng , Ma Dongqiang , Su Hang , Wen Hong-ling , Yu Hao , Yu Xue-jie
Published: October 2016

Hemorrhagic fever with renal syndrome (HFRS) was considered to be transmitted by Apodemus agrarius and Rattus norvegicus, the principal animal hosts of Hantaan virus and Seoul virus, respectively. The aim of this study is to determine the correlation of HFRS incidence with capture rate and hantavirus infection rate of rodent species in Qingdao City, China. We collected HFRS patients’ information and captured field and residential rodents in Qingdao City, China from 2010 to 2014. The correlations of HFRS incidence to rodent capture rate and hantavirus infection rate of rodents were analyzed statistically. The main findings of this study are that the high HFRS incidence (19.3/100,000) is correlated to the capture rate of field Mus musculus (p = 0.011, r = 0.037); but surprisingly it did not correlated to the capture rate of the principal rodent hosts Apodemus agrarius and Rattus norvegicus and the hantavirus infection rate of these rodent species in the field or residential area. These novel findings suggest that Mus musculus, a nontraditional animal host of hantavirus may play an important role in hantavirus transmission in Qingdao City.
Non-toxigenic environmental Vibrio cholerae O1 strain from Haiti provides evidence of pre-pandemic cholera in Hispaniola
Authors: Azarian Taj , Ali Afsar , Johnson Judith A. , Jubair Mohammad , Cella Eleonora , Ciccozzi Massimo , Nolan David J. , Farmerie William , Rashid Mohammad H. , Sinha-Ray Shrestha , Alam Meer T. , Morris J. Glenn , Salemi Marco
Published: October 2016

Vibrio cholerae is ubiquitous in aquatic environments, with environmental toxigenic V. cholerae O1 strains serving as a source for recurrent cholera epidemics and pandemic disease. However, a number of questions remain about long-term survival and evolution of V. cholerae strains within these aquatic environmental reservoirs. Through monitoring of the Haitian aquatic environment following the 2010 cholera epidemic, we isolated two novel non-toxigenic (ctxA/B-negative) Vibrio cholerae O1. These two isolates underwent whole-genome sequencing and were investigated through comparative genomics and Bayesian coalescent analysis. These isolates cluster in the evolutionary tree with strains responsible for clinical cholera, possessing genomic components of 6th and 7th pandemic lineages, and diverge from “modern” cholera strains around 1548 C.E. [95% HPD: 1532–1555]. Vibrio Pathogenicity Island (VPI)-1 was present; however, SXT/R391-family ICE and VPI-2 were absent. Rugose phenotype conversion and vibriophage resistance evidenced adaption for persistence in aquatic environments. The identification of V. cholerae O1 strains in the Haitian environment, which predate the first reported cholera pandemic in 1817, broadens our understanding of the history of pandemics. It also raises the possibility that these and similar environmental strains could acquire virulence genes from the 2010 Haitian epidemic clone, including the cholera toxin producing CTXϕ.
RSK1 protects P-glycoprotein/ABCB1 against ubiquitin–proteasomal degradation by downregulating the ubiquitin-conjugating enzyme E2 R1
Authors: Katayama Kazuhiro , Fujiwara Chiaki , Noguchi Kohji , Sugimoto Yoshikazu
Published: October 2016

P-glycoprotein (P-gp) is a critical determinant of multidrug resistance in cancer. We previously reported that MAPK inhibition downregulates P-gp expression and that P-gp undergoes ubiquitin–proteasomal degradation regulated by UBE2R1 and SCFFbx15. Here, we investigated the crosstalk between MAPK inhibition and the ubiquitin–proteasomal degradation of P-gp. Proteasome inhibitors or knockdown of FBXO15 and/or UBE2R1 cancelled MEK inhibitor-induced P-gp downregulation. RSK1 phosphorylated Thr162 on UBE2R1 but did not phosphorylate FBXO15. MEK and RSK inhibitors increased UBE2R1-WT but not UBE2R1-T162D and -T162A expression. UBE2R1-T162D showed higher self-ubiquitination and destabilisation than UBE2R1-WT and -T162A. Unlike UBE2R1-WT and -T162A, UBE2R1-T162D did not induce P-gp ubiquitination. UBE2R1-WT or -T162A downregulated P-gp expression and upregulated rhodamine 123 level and sensitivity to vincristine and doxorubicin. However, UBE2R1-T162D did not confer any change in P-gp expression, rhodamine 123 accumulation and sensitivity to the drugs. These results suggest that RSK1 protects P-gp against ubiquitination by reducing UBE2R1 stability.
Fully automated grey and white matter spinal cord segmentation
Authors: Prados Ferran , Cardoso M. Jorge , Yiannakas Marios C. , Hoy Luke R. , Tebaldi Elisa , Kearney Hugh , Liechti Martina D. , Miller David H. , Ciccarelli Olga , Wheeler-Kingshott Claudia A. M. Gandini , Ourselin Sebastien
Published: October 2016

Axonal loss in the spinal cord is one of the main contributing factors to irreversible clinical disability in multiple sclerosis (MS). In vivo axonal loss can be assessed indirectly by estimating a reduction in the cervical cross-sectional area (CSA) of the spinal cord over time, which is indicative of spinal cord atrophy, and such a measure may be obtained by means of image segmentation using magnetic resonance imaging (MRI). In this work, we propose a new fully automated spinal cord segmentation technique that incorporates two different multi-atlas segmentation propagation and fusion techniques: The Optimized PatchMatch Label fusion (OPAL) algorithm for localising and approximately segmenting the spinal cord, and the Similarity and Truth Estimation for Propagated Segmentations (STEPS) algorithm for segmenting white and grey matter simultaneously. In a retrospective analysis of MRI data, the proposed method facilitated CSA measurements with accuracy equivalent to the inter-rater variability, with a Dice score (DSC) of 0.967 at C2/C3 level. The segmentation performance for grey matter at C2/C3 level was close to inter-rater variability, reaching an accuracy (DSC) of 0.826 for healthy subjects and 0.835 people with clinically isolated syndrome MS.
Sustainable CNT-enabled lithium-ion battery manufacturing: evaluating the tradeoffs
Authors: Erbis Serkan , Kamarthi Sagar , Namin Amir Abdollahi , Hakimian Ali , Isaacs Jacqueline A.
Published: October 2016

A stochastic goal programming model is developed to aid decision making for CNT-enabled lithium-ion battery manufacturing production and capacity expansion, by considering the balance among economic growth, environmental and human health protection, and sustainability.
Hyperbranched polyesters by polycondensation of fatty acid-based ABn-type monomers
Authors: Testud Blandine , Pintori Didier , Grau Etienne , Taton Daniel , Cramail Henri
Published: October 2016

Widely available vegetable oils were readily derivatized into chemically pure ABn-type monomers (n = 2 or 3).
Matrix effects and mass bias caused by inorganic acids on boron isotope determination by multi-collector ICP-MS
Authors: Chen Xuefei , Zhang Le , Wei Gangjian , Ma Jinlong
Published: October 2016

Matrix effects and mass bias of inorganic acids on boron isotope measurement by MC-ICP-MS have been investigated.
Unusual surface and solution behaviour of keratin polypeptides
Authors: Lu Zhiming , Pan Fang , Wang Dong , Campana Mario , Xu Hai , Tucker Ian M. , Petkov Jordan T. , Webster John , Lu Jian R.
Published: October 2016

Intermediate filament-like aggregation from keratin polypeptides upon increasing [NaCl] as revealed by SANS.
Polyaniline–polystyrene membrane for simple and efficient retrieval of double-stranded DNA from aqueous media
Authors: Brandão Winnie Q. , Medina-Llamas Juan C. , Alcaraz-Espinoza José J. , Chávez-Guajardo Alicia E. , de Melo Celso P.
Published: October 2016

Extraction of nucleic acids from biological samples is a necessary step in almost all biotechnological procedures.
A simple and versatile solvothermal configuration to synthesize superparamagnetic iron oxide nanoparticles using a coaxial microwave antenna
Authors: Spepi Alessio , Duce Celia , Ferrari Carlo , González-Rivera José , Jagličić Zvonko , Domenici Valentina , Pineider Francesco , Tiné Maria Rosaria
Published: October 2016

Magnetic iron oxide nanoparticles (IONs) with controllable physicochemical and magnetic properties were synthesized by a fast and simple solvothermal microwave (MW) assisted approach.