bluuebunny/crossref_metadata_2025 huggingface dataset:
Variation in pre-harvest sprouting resistance, seed germination and changes in abscisic acid levels during grain development in diverse rice genetic resources
Authors: Lee Gi-An , Jeon Young-Ah , Lee Ho-Sun , Hyun Do-Yun , Lee Jung-Ro , Lee Myung-Chul , Lee Sok-young , Ma Kyung-Ho , Koh Hee-Jong
Published: October 2016

Among domesticated traits, pre-harvest sprouting (PHS) caused by the early breakage of dormancy leads to severe economic losses. Therefore, regulating PHS is important for cereal crop improvement against changes in climate. In this study, we surveyed naturally occurring variations in seed germination in diverse rice germplasm for the available resources of this trait, and investigated the changes of abscisic acid (ABA) levels during grain development by the distinguished PHS-resistant groups. We discovered wide variations in germination among the 205 rice accessions examined and found that 90 accessions are resistant (germination <20%) to PHS. Tropical and subtropical accessions, which are subjected to long wet periods, are more resistant to PHS than the other accessions. We detected an increase in germination of detached seeds from the panicle compared with intact seeds in panicle at harvesting time. This might be attributed to a weakening of the mechanical barrier that prevents water imbibition and radical emergence. ABA levels were maximal at 10 d after flowering and decreased thereafter. Interestingly, PHS-susceptible accessions maintained higher or similar ABA levels compared with PHS-resistant accessions, suggesting that the key factors for seed dormancy and its breakage are ABA perception and signal transduction rather than total ABA content. The diversity of germination ability detected in this study could be sustainably used for crop improvement and to help unveil the genetic and physiological basis of this quantitative trait.
Improved correction of VIPERS angular selection effects in clustering measurements
Authors: Pezzotta A. , Granett B.R. , Bel J. , Guzzo L. , de la Torre S. ,   and VIPERS team
Published: October 2016

Clustering estimates in galaxy redshift surveys need to account and correct for the way targets are selected from the general population, as to avoid biasing the measured values of cosmological parameters. The VIMOS Public Extragalactic Redshift Survey (VIPERS) is no exception to this, involving slit collisions and masking effects. Pushed by the increasing precision of the measurements, e.g. of the growth rate f, we have been re-assessing these effects in detail. We present here an improved correction for the two-point correlation function, capable to recover the amplitude of the monopole of the two-point correlation function ξ(r) above 1 h-1 Mpc to better than 2.
Measuring the VIPERS galaxy power spectrum at $z\sim1$
Authors: Rota Stefano , Bel Julien , Granett Ben , Guzzo Luigi
Published: October 2016

The VIMOS Public Extragalactic Redshift Survey [VIPERS, Guzzo et al. 2014] is using the VIMOS spectrograph at the ESO VLT to measure redshifts for ∼ 100,000 galaxies with IAB < 22.5 and 0.5 < z < 1.2, over an area of 24 deg2 (split over the W1 and W4 fields of CFHTLS). VIPERS currently provides, at such redshifts, the best compromise between volume, number of galaxies and dense spatial sampling. We present here the first estimate of the power spectrum of the galaxy distribution, P(k), at redshifts z ∼ 0.75 and z ∼ 1, obtained from the ∼ 55,000 redshifts of the PDR-1 data release. We discuss first constraints on cosmological quantities, as the matter density and the baryonic fraction, obtained for the first time at an epoch when the Universe was about half its current age.
3D structure of nearby groups of galaxies
Authors: Makarova L. , Makarov D. , Klypin A. , Gottlöber S.
Published: October 2016

Using high accuracy distance estimates, we study the three-dimensional distribution of galaxies in five galaxy groups at a distance less than 5 Mpc from the Milky Way. Due to proximity of these groups our sample of galaxies is nearly complete down to extremely small dwarf galaxies with absolute magnitudes MB = -12. We find that the average number-density profile of the groups shows a steep power-law decline dn/dV ∼ R-3 at distances R=(100–500) kpc consistent with predictions of the standard cosmological model. We also find that there is no indication of a truncation or a cutoff in the density at the expected virial radius: the density profile extends at least to 1.5 Mpc. Vast majority of galaxies within 1.5 Mpc radius around group centres are gas-rich star-forming galaxies. Early-type galaxies are found only in the central ∼ 300 kpc region. Lack of dwarf spheroidal and dwarf elliptical galaxies in the field and in the outskirts of large groups is a clear indication that these galaxies experienced morphological transformation when they came close to the central region of forming galaxy group.
Galaxy and Mass Assembly (GAMA): Selection of the Most Massive Clusters
Authors: Ibarra-Medel Héctor J. , Lara-López Maritza , López-Cruz Omar
Published: October 2016

We have developed a galaxy cluster finding technique based on the Delaunay Tessellation Field Estimator (DTFE) combined with caustic analysis. Our method allows us to recover clusters of galaxies within the mass range of $10^{12}$ to $10^{16}\ \mathcal{M}_{\odot}$. We have found a total of 113 galaxy clusters in the Galaxy and Mass Assembly survey (GAMA). In the corresponding mass range, the density of clusters found in this work is comparable to the density traced by clusters selected by the thermal Sunyaev Zel'dovich Effect; however, we are able to cover a wider mass range. We present the analysis of the two-point correlation function for our cluster sample.
Big Data of the Cosmic Web
Authors: Kitaura Francisco-Shu
Published: October 2016

One of the main goals in cosmology is to understand how the Universe evolves, how it forms structures, why it expands, and what is the nature of dark matter and dark energy. Next decade large and expensive observational projects will bring information on the structure and the distribution of many millions of galaxies at different redshifts enabling us to make great progress in answering these questions. However, these data require a very special and complex set of analysis tools to extract the maximum valuable information. Statistical inference techniques are being developed, bridging the gaps between theory, simulations, and observations. In particular, we discuss the efforts to address the question: What is the underlying nonlinear matter distribution and dynamics at any cosmic time corresponding to a set of observed galaxies in redshift space?

An accurate reconstruction of the initial conditions encodes the full phase-space information at any later cosmic time (given a particular structure formation model and a set of cosmological parameters). We present advances to solve this problem in a self-consistent way with Big Data techniques of the Cosmic Web.
Galaxy and Mass Assembly (GAMA): galaxy pairwise velocity dispersion
Authors: Loveday Jon , Christodoulou Leonidas ,   the GAMA team
Published: October 2016

We describe preliminary measurements of the pairwise velocity dispersion (PVD) of galaxies in the Galaxy and Mass Assembly (GAMA) survey as a function of projected separation and galaxy luminosity. Due to the faint magnitude limit (r < 19.8) and highly-complete spectroscopic sampling of the GAMA survey, we are able to measure the PVD to smaller scales and for lower-luminosity galaxies than previous SDSS-based work. We see no strong scale-dependence at most luminosities in the quasi-linear regime. We observe an apparent drop in PVD towards very small scales (below ≈ 0.1h−1 Mpc), but this could in part be due to a restriction of the streaming model employed. At intermediate scales, the PVD is highest (~ 500 km/s) at intermediate luminosities, dropping at both fainter and brighter luminosities.
Large-scale peculiar velocities through the galaxy luminosity function at z ~ 0.1
Authors: Feix Martin , Nusser Adi , Branchini Enzo
Published: October 2016

Peculiar motion introduces systematic variations in the observed luminosity distribution of galaxies. This allows one to constrain the cosmic peculiar velocity field from large galaxy redshift surveys. Using around half a million galaxies from the SDSS Data Release 7 at z ~ 0.1, we demonstrate the applicability of this approach to large datasets and obtain bounds on peculiar velocity moments and σ8, the amplitude of the linear matter power spectrum. Our results are in good agreement with the ΛCDM model and consistent with the previously reported ~ 1% zero-point tilt in the SDSS photometry. Finally, we discuss the prospects of constraining the growth rate of density perturbations by reconstructing the full linear velocity field from the observed galaxy clustering in redshift space.
The intergalactic medium in the cosmic web
Authors: Tejos Nicolas
Published: October 2016

The intergalactic medium (IGM) accounts for ≳ 90% of baryons at all epochs and yet its three dimensional distribution in the cosmic web remains mostly unknown. This is so because the only feasible way to observe the bulk of the IGM is through intervening absorption line systems in the spectra of bright background sources, which limits its characterization to being one-dimensional. Still, an averaged three dimensional picture can be obtained by combining and cross-matching multiple one-dimensional IGM information with three-dimensional galaxy surveys. Here, we present our recent and current efforts to map and characterize the IGM in the cosmic web using galaxies as tracers of the underlying mass distribution. In particular, we summarize our results on: (i) IGM around star-forming and non-star-forming galaxies; (ii) IGM within and around galaxy voids; and (iii) IGM in intercluster filaments. With these datasets, we can directly test the modern paradigm of structure formation and evolution of baryonic matter in the Universe.
Gas accretion from the cosmic web in the local Universe
Authors: Almeida J. Sánchez , Elmegreen B. G. , Muñoz-Tuñnón C. , Elmegreen D. M.
Published: October 2016

Numerical simulations predict that gas accretion from the cosmic web drives star formation in disks galaxies. The process is important in low mass haloes (< 1012M⊙), therefore, in the early universe when galaxies were low mass, but also in dwarf galaxies of the local universe. The gas that falls in is predicted to be tenuous, patchy, partly ionized, multi-temperature, and large-scale; therefore, hard to show in a single observation. One of the most compelling cases for gas accretion at work in the local universe comes from the extremely metal poor (XMP) galaxies. They show metallicity inhomogeneities associated with star-forming regions, so that large starbursts have lower metallicity than the underlying galaxy. Here we put forward the case for gas accretion from the web posed by XMP galaxies. Two other observational results are discussed too, namely, the fact that the gas consumption time-scale is shorter than most stellar ages, and the systematic morphological distortions of the HI around galaxies.
The different lives of galaxies at different environment density levels
Authors: Tamm Antti , Liivamägi Lauri Juhan , Tempel Elmo
Published: October 2016

We take a closer look at the dependence of the galactic colour histogram on the environment density using a volume-limited sample of SDSS galaxies. We find that the strongest changes with environment are taking place with spiral galaxies. In dense environment, discs become considerably redder, apparently due to the shortage of gas, and less concentrated. Contrary to expectation, the mean Sérsic index of luminous elliptical galaxies decreases in denser environments.
Why do galactic spins flip in the cosmic web? A Theory of Tidal Torques near saddles
Authors: Pichon Christophe , Codis Sandrine , Pogosyan Dmitry , Dubois Yohan , Desjacques Vincent , Devriendt Julien
Published: October 2016

Filaments of the cosmic web drive spin acquisition of disc galaxies. The point process of filament-type saddle represent best this environment and can be used to revisit the Tidal Torque Theory in the context of an anisotropic peak (saddle) background split. The constrained misalignment between the tidal tensor and the Hessian of the density field generated in the vicinity of filament saddle points simply explains the corresponding transverse and longitudinal point-reflection symmetric geometry of spin distribution. It predicts in particular an azimuthal orientation of the spins of more massive galaxies and spin alignment with the filament for less massive galaxies. Its scale dependence also allows us to relate the transition mass corresponding to the alignment of dark matter halos' spin relative to the direction of their neighboring filament to this geometry, and to predict accordingly it's scaling with the mass of non linearity, as was measured in simulations.
The morphological types of galaxies in the Local Supercluster
Authors: Bajan K. , Flin P. , Godłowski W.
Published: October 2016

On the basis of the Hyper – Leda Catalogue HyperLeda 8293 galaxies with heliocentric radial velocities below 2500 km s-1 were selected; 4570 had known morphological types (4366 had calculated b/a ratio). We checked the frequency of the distribution of various types in the LSC, finding spirals and irregulars most numerous, in accordance with expectations. The axial ratio of galaxy diameters of various types was studied, and the dependence of this parameter on the morphological type was noted.
Structural decomposition of galaxies in the CALIFA survey
Authors: Kuutma Teet , Tamm Antti , Tempel Elmo
Published: October 2016

Several clues for understanding the nature and evolution of galaxies can be gained by studying galactic structures and their evolution with time and environment. However, even for nearby galaxies, detailed structural decomposition is not a straightforward task. Choosing the number of structural components and the limits placed on their parameters can have a large effect on the derived characteristics of galaxies. For distant galaxies, structural analysis is further hampered by the spatial resolution limits of the imaging. However, by using a relatively robust two-component bulge+disk modelling, galaxies in the nearby Universe can be compared to distant galaxies for tracing signs of evolution in the extracted structures. We start such a study by analysing first a well observed nearby sample of galaxies, using ∼600 targets from the CALIFA survey. We show that even in this small sample of nearby galaxies, the effects of environmental density are already well apparent.
Properties of satellite galaxies in nearby groups
Authors: Vennik Jaan
Published: October 2016

We studied the variation of stellar mass and various star-formation characteristics of satellite galaxies in a volume limited sample of nearby groups as a function of their group-centric distance and of their relative line-of-sight velocity in the group rest frame. We found clear radial dependencies, e.g. massive, red and passive satellites being distributed predominantly near the center of composite group. We also found some evidence of velocity modulation of star-forming properties of satellite galaxies near the group virial radius. We conclude that using kinematical data, it should be feasible to separate dynamical classes of bound, in-falling and 'backsplash' satellite galaxies.
The Direct Collapse of Supermassive Black Hole Seeds
Authors: Regan John A. , Johansson Peter H. , Wise John H.
Published: October 2016

The direct collapse model of supermassive black hole seed formation requires that the
gas cools predominantly via atomic hydrogen. To this end we simulate the effect of an
anisotropic radiation source on the collapse of a halo at high redshift. The radiation
source is placed at a distance of 3 kpc (physical) from the collapsing object and is set
to emit monochromatically in the center of the Lyman-Werner (LW) band. The LW radiation
emitted from the high redshift source is followed self-consistently using ray tracing
techniques. Due to self-shielding, a small amount of H2 is able to form at the very
center of the collapsing halo even under very strong LW radiation. Furthermore, we find that
a radiation source, emitting < 1054 (∼103 J21) photons per second is
required to cause the collapse of a clump of M ∼ 105 M⊙. The resulting
accretion rate onto the collapsing object is ∼ 0.25 M⊙ yr−1.
Our results display significant differences, compared to the isotropic radiation field case,
in terms of H2 fraction at an equivalent radius. These differences will significantly effect
the dynamics of the collapse. With the inclusion of a strong anisotropic radiation source, the
final mass of the collapsing object is found to be M ∼ 105 M⊙. This is consistent
with predictions for the formation of a supermassive star or quasi-star leading to a
supermassive black hole.
Voids and the Cosmic Web: cosmic depression & spatial complexity
Authors: van de Weygaert Rien
Published: October 2016

Voids form a prominent aspect of the Megaparsec distribution of galaxies and matter. Not only do they represent a key constituent of the Cosmic Web, they also are one of the cleanest probes and measures of global cosmological parameters. The shape and evolution of voids are highly sensitive to the nature of dark energy, while their substructure and galaxy population provides a direct key to the nature of dark matter. Also, the pristine environment of void interiors is an important testing ground for our understanding of environmental influences on galaxy formation and evolution. In this paper, we review the key aspects of the structure and dynamics of voids, with a particular focus on the hierarchical evolution of the void population. We demonstrate how the rich structural pattern of the Cosmic Web is related to the complex evolution and buildup of voids.
Universal void density profiles from simulation and SDSS
Authors: Nadathur S. , Hotchkiss S. , Diego J. M. , Iliev I. T. , Gottlöber S. , Watson W. A. , Yepes G.
Published: October 2016

We discuss the universality and self-similarity of void density profiles, for voids in realistic mock luminous red galaxy (LRG) catalogues from the Jubilee simulation, as well as in void catalogues constructed from the SDSS LRG and Main Galaxy samples. Voids are identified using a modified version of the ZOBOV watershed transform algorithm, with additional selection cuts. We find that voids in simulation areself-similar, meaning that their average rescaled profile does not depend on the void size, or – within the range of the simulated catalogue – on the redshift. Comparison of the profiles obtained from simulated and real voids shows an excellent match. The profiles of real voids also show auniversalbehaviour over a wide range of galaxy luminosities, number densities and redshifts. This points to a fundamental property of the voids found by the watershed algorithm, which can be exploited in future studies of voids.
On the universality of void density profiles
Authors: Ricciardelli E. , Quilis V. , Varela J.
Published: October 2016

The massive exploitation of cosmic voids for precision cosmology in the upcoming dark energy experiments, requires a robust understanding of their internal structure, particularly of their density profile. We show that the void density profile is insensitive to the void radius both in a catalogue of observed voids and in voids from a large cosmological simulation. However, the observed and simulated voids display remarkably different profile shapes, with the former having much steeper profiles than the latter. We ascribe such difference to the dependence of the observed profiles on the galaxy sample used to trace the matter distribution. Samples including low-mass galaxies lead to shallower profiles with respect to the samples where only massive galaxies are used, as faint galaxies live closer to the void centre. We argue that galaxies are biased tracers when used to probe the matter distribution within voids.
Glucocorticoid regulation of ATP release from spinal astrocytes underlies diurnal exacerbation of neuropathic mechanical allodynia
Authors: Koyanagi Satoru , Kusunose Naoki , Taniguchi Marie , Akamine Takahiro , Kanado Yuki , Ozono Yui , Masuda Takahiro , Kohro Yuta , Matsunaga Naoya , Tsuda Makoto , Salter Michael W. , Inoue Kazuhide , Ohdo Shigehiro
Published: October 2016

Diurnal variations in pain hypersensitivity are common in chronic pain disorders, but the underlying mechanisms are enigmatic. Here, we report that mechanical pain hypersensitivity in sciatic nerve-injured mice shows pronounced diurnal alterations, which critically depend on diurnal variations in glucocorticoids from the adrenal glands. Diurnal enhancement of pain hypersensitivity is mediated by glucocorticoid-induced enhancement of the extracellular release of ATP in the spinal cord, which stimulates purinergic receptors on microglia in the dorsal horn. We identify serum- and glucocorticoid-inducible kinase-1 (SGK-1) as the key molecule responsible for the glucocorticoid-enhanced release of ATP from astrocytes. SGK-1 protein levels in spinal astrocytes are increased in response to glucocorticoid stimuli and enhanced ATP release by opening the pannexin-1 hemichannels. Our findings reveal an unappreciated circadian machinery affecting pain hypersensitivity caused by peripheral nerve injury, thus opening up novel approaches to the management of chronic pain.
Boundaries steer the contraction of active gels
Authors: Schuppler Matthias , Keber Felix C. , Kröger Martin , Bausch Andreas R.
Published: October 2016

Cells set up contractile actin arrays to drive various shape changes and to exert forces to their environment. To understand their assembly process, we present here a reconstituted contractile system, comprising F-actin and myosin II filaments, where we can control the local activation of myosin by light. By stimulating different symmetries, we show that the force balancing at the boundaries determine the shape changes as well as the dynamics of the global contraction. Spatially anisotropic attachment of initially isotropic networks leads to a self-organization of highly aligned contractile fibres, being reminiscent of the order formation in muscles or stress fibres. The observed shape changes and dynamics are fully recovered by a minimal physical model.
Possible ground states and parallel magnetic-field-driven phase transitions of collinear antiferromagnets
Authors: Li Hai-Feng
Published: October 2016

Understanding the nature of all possible ground states and especially magnetic-field-driven phase transitions of antiferromagnets represents a major step towards unravelling the real nature of interesting phenomena such as superconductivity, multiferroicity or magnetoresistance in condensed-matter science. Here a consistent mean-field calculation endowed with antiferromagnetic (AFM) exchange interaction (J), easy axis anisotropy (γ), uniaxial single-ion anisotropy (D) and Zeeman coupling to a magnetic field parallel to the AFM easy axis consistently unifies the AFM state, spin-flop (SFO) and spin-flip transitions. We reveal some mathematically allowed exotic spin states and fluctuations depending on the relative coupling strength of (J, γ and D). We build the three-dimensional (J, γ and D) and two-dimensional (γ and D) phase diagrams clearly displaying the equilibrium phase conditions and discuss the origins of various magnetic states as well as their transitions in different couplings. Besides the traditional first-order type one, we unambiguously confirm an existence of a second-order type SFO transition. This study provides an integrated theoretical model for the magnetic states of collinear antiferromagnets with two interpenetrating sublattices and offers a practical approach as an alternative to the estimation of magnetic exchange parameters (J, γ and D), and the results may shed light on nontrivial magnetism-related properties of bulks, thin films and nanostructures of correlated electron systems.
A Paradoxical Evolutionary Mechanism in Stochastically Switching Environments
Authors: Cheong Kang Hao , Tan Zong Xuan , Xie Neng-gang , Jones Michael C.
Published: October 2016

Organisms with environmental sensors that guide survival are considered more likely to be favored by natural selection if they possess more accurate sensors. In this paper, we develop a theoretical model which shows that under certain conditions of environmental stochasticity, selection actually favors sensors of lower accuracy. An analogy between this counter-intuitive phenomenon and the well-known Parrondo’s paradox is suggested.
Self-Other Distinction Enhanced Empathic Responses in Individuals with Alexithymia
Authors: Saito Natsuki , Yokoyama Takemasa , Ohira Hideki
Published: October 2016

Although empathy is important for social interactions, individuals with alexithymia have low empathic ability, particularly where advanced empathy is concerned (empathic concern, perspective taking). It has been argued that awareness of the self-other distinction enhances advanced empathy, and alexithymics are thought to inadequately distinguish the self from others. We therefore tested whether the self-other distinction increases advanced empathy in alexithymics. To this end, we presented painful hand images over participants’ own hands, and required participants to estimate felt pain intensity and their affective states. Half of the participants got specific instructions to distinct themselves from the other in the images. Felt pain intensity (perspective taking) and other-oriented affective responses (empathic concern) were increased by the instructions only when participants had high alexithymia scores as measured by questionnaire, although self-oriented affective responses (personal distress) were not affected by the instructions. These findings indicate that enhancing the self-other distinction enhances alexithymics’ ability to use advanced empathy, but not the primitive empathy.
Lipidomic Profiling of Lung Pleural Effusion Identifies Unique Metabotype for EGFR Mutants in Non-Small Cell Lung Cancer
Authors: Ho Ying Swan , Yip Lian Yee , Basri Nurhidayah , Chong Vivian Su Hui , Teo Chin Chye , Tan Eddy , Lim Kah Ling , Tan Gek San , Yang Xulei , Yeo Si Yong , Koh Mariko Si Yue , Devanand Anantham , Takano Angela , Tan Eng Huat , Tan Daniel Shao Weng , Lim Tony Kiat Hon
Published: October 2016

Cytology and histology forms the cornerstone for the diagnosis of non-small cell lung cancer (NSCLC) but obtaining sufficient tumour cells or tissue biopsies for these tests remains a challenge. We investigate the lipidome of lung pleural effusion (PE) for unique metabolic signatures to discriminate benign versus malignant PE and EGFR versus non-EGFR malignant subgroups to identify novel diagnostic markers that is independent of tumour cell availability. Using liquid chromatography mass spectrometry, we profiled the lipidomes of the PE of 30 benign and 41 malignant cases with or without EGFR mutation. Unsupervised principal component analysis revealed distinctive differences between the lipidomes of benign and malignant PE as well as between EGFR mutants and non-EGFR mutants. Docosapentaenoic acid and Docosahexaenoic acid gave superior sensitivity and specificity for detecting NSCLC when used singly. Additionally, several 20- and 22- carbon polyunsaturated fatty acids and phospholipid species were significantly elevated in the EGFR mutants compared to non-EGFR mutants. A 7-lipid panel showed great promise in the stratification of EGFR from non-EGFR malignant PE. Our data revealed novel lipid candidate markers in the non-cellular fraction of PE that holds potential to aid the diagnosis of benign, EGFR mutation positive and negative NSCLC.
Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites
Authors: Grijseels Sietske , Nielsen Jens Christian , Randelovic Milica , Nielsen Jens , Nielsen Kristian Fog , Workman Mhairi , Frisvad Jens Christian
Published: October 2016

A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311T = IBT 12289T). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species.
A Study of Drop-Microstructured Surface Interactions during Dropwise Condensation with Quartz Crystal Microbalance
Authors: Su Junwei , Charmchi Majid , Sun Hongwei
Published: October 2016

Dropwise condensation (DWC) on hydrophobic surfaces is attracting attention for its great potential in many industrial applications, such as steam power plants, water desalination, and de-icing of aerodynamic surfaces, to list a few. The direct dynamic characterization of liquid/solid interaction can significantly accelerate the progress toward a full understanding of the thermal and mass transport mechanisms during DWC processes. This work reports a novel Quartz Crystal Microbalance (QCM) based method that can quantitatively analyze the interaction between water droplets and micropillar surfaces during different condensation states such as filmwise, Wenzel, and partial Cassie states. A combined nanoimprinting lithography and chemical surface treatment approach was utilized to fabricate the micropillar based superhydrophobic and superhydrophilic surfaces on the QCM substrates. The normalized frequency shift of the QCM device together with the microscopic observation of the corresponding drop motion revealed the droplets growth and their coalescence processes and clearly demonstrated the differences between the three aforementioned condensation states. In addition, the transition between Cassie and Wenzel states was successfully captured by this method. The newly developed QCM system provides a valuable tool for the dynamic characterization of different condensation processes.
Multiparametric MRI-based differentiation of WHO grade II/III glioma and WHO grade IV glioblastoma
Authors: Wiestler Benedikt , Kluge Anne , Lukas Mathias , Gempt Jens , Ringel Florian , Schlegel Jürgen , Meyer Bernhard , Zimmer Claus , Förster Stefan , Pyka Thomas , Preibisch Christine
Published: October 2016

Non-invasive, imaging-based examination of glioma biology has received increasing attention in the past couple of years. To this end, the development and refinement of novel MRI techniques, reflecting underlying oncogenic processes such as hypoxia or angiogenesis, has greatly benefitted this research area. We have recently established a novel BOLD (blood oxygenation level dependent) based MRI method for the measurement of relative oxygen extraction fraction (rOEF) in glioma patients. In a set of 37 patients with newly diagnosed glioma, we assessed the performance of a machine learning model based on multiple MRI modalities including rOEF and perfusion imaging to predict WHO grade. An oblique random forest machine learning classifier using the entire feature vector as input yielded a five-fold cross-validated area under the curve of 0.944, with 34/37 patients correctly classified (accuracy 91.8%). The most important features in this classifier as per bootstrapped feature importance scores consisted of standard deviation of T1-weighted contrast enhanced signal, maximum rOEF value and cerebral blood volume (CBV) standard deviation. This study suggests that multimodal MRI information reflects underlying tumor biology, which is non-invasively detectable through integrative data analysis, and thus highlights the potential of such integrative approaches in the field of radiogenomics.
Senescence Mediated by p16INK4a Impedes Reprogramming of Human Corneal Endothelial Cells into Neural Crest Progenitors
Authors: Lu Wen-Juan , Tseng Scheffer C. G. , Chen Shuangling , Tighe Sean , Zhang Yuan , Liu Xin , Chen Szu-Yu , Su Chen-Wei , Zhu Ying-Ting
Published: October 2016

Human corneal endothelial cells (HCECs) have limited proliferative capacity due to “contact-inhibition” at G1 phase. Such contact-inhibition can be delayed from Day 21 to Day 42 by switching EGF-containing SHEM to LIF/bFGF-containing MESCM through transient activation of LIF-JAK1-STAT3 signaling that delays eventual nuclear translocation of p16INK4a. Using the latter system, we have reported a novel tissue engineering technique by implementing 5 weekly knockdowns with p120 catenin (p120) and Kaiso siRNAs since Day 7 to achieve effective expansion of HCEC monolayers to a transplantable size with a normal HCEC density, through reprogramming of HCECs into neural crest progenitors by activating p120-Kaiso-RhoA-ROCK-canonical BMP signaling. Herein, we noted that a single knockdown with p120-Kaiso siRNAs at Day 42 failed to achieve such reprogramming when contact inhibition transitioned to senescence with nuclear translocation of p16INK4a. In contrast, 5 weekly knockdowns with p120-Kaiso siRNAs since Day 7 precluded senescence mediated by p16INK4a by inducing nuclear translocation of Bmi1 because of sustained activation of JAK2-STAT3 signaling downstream of p120-Kaiso-RhoA-ROCK signaling. STAT3 or Bmi1 siRNA impeded nuclear exclusion of p16INK4a and suppressed the reprogramming induced by p120-Kaiso siRNAs, suggesting that another important engineering strategy of HCEC lies in prevention of senescence mediated by nuclear translocation of p16INK4a.
Multimodal imaging of a humanized orthotopic model of hepatocellular carcinoma in immunodeficient mice
Authors: Wu Tao , Heuillard Emilie , Lindner Véronique , Bou About Ghina , Ignat Mihaela , Dillenseger Jean-Philippe , Anton Nicolas , Dalimier Eugénie , Gossé Francine , Fouré Gael , Blindauer Franck , Giraudeau Céline , El-Saghire Hussein , Bouhadjar Mourad , Calligaro Cynthia , Sorg Tania , Choquet Philippe , Vandamme Thierry , Ferrand Christophe , Marescaux Jacques , Baumert Thomas F. , Diana Michele , Pessaux Patrick , Robinet Eric
Published: October 2016

The development of multimodal strategies for the treatment of hepatocellular carcinoma requires tractable animal models allowing for advanced in vivo imaging. Here, we characterize an orthotopic hepatocellular carcinoma model based on the injection of luciferase-expressing human hepatoma Huh-7 (Huh-7-Luc) cells in immunodeficient mice. Luciferase allows for an easy repeated monitoring of tumor growth by in vivo bioluminescence. The intrahepatic injection was more efficient than intrasplenic or intraportal injection in terms of survival, rate of orthotopic engraftment, and easiness. A positive correlation between luciferase activity and tumor size, evaluated by Magnetic Resonance Imaging, allowed to define the endpoint value for animal experimentation with this model. Response to standard of care, sorafenib or doxorubicin, were similar to those previously reported in the literature, with however a strong toxicity of doxorubicin. Tumor vascularization was visible by histology seven days after Huh-7-Luc transplantation and robustly developed at day 14 and day 21. The model was used to explore different imaging modalities, including microtomography, probe-based confocal laser endomicroscopy, full-field optical coherence tomography, and ultrasound imaging. Tumor engraftment was similar after echo-guided intrahepatic injection as after laparotomy. Collectively, this orthotopic hepatocellular carcinoma model enables the in vivo evaluation of chemotherapeutic and surgical approaches using multimodal imaging.
A new marseillevirus isolated in Southern Brazil from Limnoperna fortunei
Authors: dos Santos Raíssa Nunes , Campos Fabrício Souza , Medeiros de Albuquerque Nathalia Rammé , Finoketti Fernando , Côrrea Rayra Almeida , Cano-Ortiz Lucia , Assis Felipe Lopes , Arantes Thalita Souza , Roehe Paulo Michel , Franco Ana Cláudia
Published: October 2016

Members of the family Marseilleviridae are giant viruses that have the ability to infect amoebas. Such viruses were initially described in 2009. Since then, this family has grown, and diverse members have been found in different environments and geographic locations. Previous phylogenetic analyses suggested the existence of four marseillevirus lineages. A fourth lineage was described with the discovery of the Brazilian marseillevirus (BrMr), isolated from Pampulha Lake, Brazil. Here we describe the isolation and characterization of the Golden marseillevirus (GMar), a new marseillevirus isolated from golden mussels (Limnoperna fortunei) in South of Brazil. This new representative of Marseilleviridae has circular, double-stranded (dsDNA) that contains 360, 610 base pairs and encodes 483 open read frames (ORFs). The complete virus genome was sequenced and phylogenic analyses indicated clear differences between this virus and other marseilleviruses. In addition, this is the only marseillevirus so far that has been isolated from mussels, and this report expands the diversity of environments from which giant viruses could be recovered.
Serum YKL-40 as a marker of liver fibrosis in patients with non-alcoholic fatty liver disease
Authors: Kumagai Erina , Mano Yohei , Yoshio Sachiyo , Shoji Hirotaka , Sugiyama Masaya , Korenaga Masaaki , Ishida Tsuyoshi , Arai Taeang , Itokawa Norio , Atsukawa Masanori , Hyogo Hideyuki , Chayama Kazuaki , Ohashi Tomohiko , Ito Kiyoaki , Yoneda Masashi , Kawaguchi Takumi , Torimura Takuji , Nozaki Yuichi , Watanabe Sumio , Mizokami Masashi , Kanto Tatsuya
Published: October 2016

Non-alcoholic fatty liver disease (NAFLD) is a common cause of chronic non-viral liver disease. YKL-40, chitinase-like protein expressed in multiple tissues including liver, is involved in cell proliferation, inflammation and remodeling of the extracellular matrix. The aim of this study was to assess whether serum YKL-40 levels are associated with liver fibrosis in NAFLD patients. Serum YKL-40 levels were quantified in 111 NAFLD patients and 23 HCC patients with NAFLD. To identify the source of YKL-40, immunofluorescence staining of liver specimens from NAFLD patients was performed. Serum YKL-40 levels in NAFLD patients increased in accordance with the progression of liver fibrosis. Multivariate analysis revealed that YKL-40 was one of the independent factors significantly associated with severe fibrosis (F3-4). We established a new predictive model for fibrosis of NAFLD, using logistic regression analysis: YKL-40 based fibrosis score = −0.0545 + type IV collagen 7s * 0.3456 + YKL-40 * 0.0024. Serum YKL-40 levels of HCC patients with non-cirrhotic NAFLD were significantly higher than those without HCC. Immunofluorescence staining showed that YKL-40 was expressed by macrophages in liver tissue of NAFLD patients. In conclusion, macrophage-derived YKL-40 is a feasible biomarker of liver fibrosis in NAFLD patients.
Climate change and the ash dieback crisis
Authors: Goberville Eric , Hautekèete Nina-Coralie , Kirby Richard R. , Piquot Yves , Luczak Christophe , Beaugrand Grégory
Published: October 2016

Beyond the direct influence of climate change on species distribution and phenology, indirect effects may also arise from perturbations in species interactions. Infectious diseases are strong biotic forces that can precipitate population declines and lead to biodiversity loss. It has been shown in forest ecosystems worldwide that at least 10% of trees are vulnerable to extinction and pathogens are increasingly implicated. In Europe, the emerging ash dieback disease caused by the fungusHymenoscyphus fraxineus,commonly calledChalara fraxinea,is causing a severe mortality of common ash trees (Fraxinus excelsior); this is raising concerns for the persistence of this widespread tree, which is both a key component of forest ecosystems and economically important for timber production. Here, we show how the pathogen and climate change may interact to affect the future spatial distribution of the common ash. Using two presence-only models, seven General Circulation Models and four emission scenarios, we show that climate change, by affecting the host and the pathogen separately, may uncouple their spatial distribution to create a mismatch in species interaction and so a lowering of disease transmission. Consequently, as climate change expands the ranges of both species polewards it may alleviate the ash dieback crisis in southern and occidental regions at the same time.
The distribution of carotenoids in hens fed on biofortified maize is influenced by feed composition, absorption, resource allocation and storage
Authors: Moreno Jose Antonio , Díaz-Gómez Joana , Nogareda Carmina , Angulo Eduardo , Sandmann Gerhard , Portero-Otin Manuel , Serrano José C. E. , Twyman Richard M. , Capell Teresa , Zhu Changfu , Christou Paul
Published: October 2016

Carotenoids are important dietary nutrients with health-promoting effects. The biofortification of staple foods with carotenoids provides an efficient delivery strategy but little is known about the fate and distribution of carotenoids supplied in this manner. The chicken provides a good model of human carotenoid metabolism so we supplemented the diets of laying hens using two biofortified maize varieties with distinct carotenoid profiles and compared the fate of the different carotenoids in terms of distribution in the feed, the hen’s livers and the eggs. We found that after a period of depletion, pro-vitamin A (PVA) carotenoids were preferentially diverted to the liver and relatively depleted in the eggs, whereas other carotenoids were transported to the eggs even when the liver remained depleted. When retinol was included in the diet, it accumulated more in the eggs than the livers, whereas PVA carotenoids showed the opposite profile. Our data suggest that a transport nexus from the intestinal lumen to the eggs introduces bottlenecks that cause chemically-distinct classes of carotenoids to be partitioned in different ways. This nexus model will allow us to optimize animal feed and human diets to ensure that the health benefits of carotenoids are delivered in the most effective manner.
Quantum Oscillations at Integer and Fractional Landau Level Indices in Single-Crystalline ZrTe5
Authors: Yu W. , Jiang Y. , Yang J. , Dun Z. L. , Zhou H. D. , Jiang Z. , Lu P. , Pan W.
Published: October 2016

A three-dimensional (3D) Dirac semimetal (DS) is an analogue of graphene, but with linear energy dispersion in all (three) momentum directions. 3D DSs have been a fertile playground in discovering novel quantum particles, for example Weyl fermions, in solid state systems. Many 3D DSs were theoretically predicted and experimentally confirmed. We report here the results in exfoliated ZrTe5 thin flakes from the studies of aberration-corrected scanning transmission electron microscopy and low temperature magneto-transport measurements. Several unique results were observed. First, a π Berry phase was obtained from the Landau fan diagram of the Shubnikov-de Haas oscillations in the longitudinal conductivity σxx. Second, the longitudinal resistivity ρxx shows a linear magnetic field dependence in the quantum limit regime. Most surprisingly, quantum oscillations were also observed at fractional Landau level indices N = 5/3 and 7/5, demonstrating strong electron-electron interaction effects in ZrTe5.
Ethylene and hydrogen peroxide are involved in brassinosteroid-induced salt tolerance in tomato
Authors: Zhu Tong , Deng Xingguang , Zhou Xue , Zhu Lisha , Zou Lijuan , Li Pengxu , Zhang Dawei , Lin Honghui
Published: October 2016

Crosstalk between phytohormone pathways is essential in plant growth, development and stress responses. Brassinosteroids (BRs) and ethylene are both pivotal plant growth regulators, and the interaction between these two phytohormones in the tomato response to salt stress is still unclear. Here, we explored the mechanism by which BRs affect ethylene biosynthesis and signaling in tomato seedlings under salt stress. The activity of 1-aminocyclopropane-1-carboxylate synthase (ACS), an ethylene synthesis enzyme, and the ethylene signaling pathway were activated in plants pretreated with BRs. Scavenging of ethylene production or silencing of ethylene signaling components inhibited BR-induced salt tolerance and blocked BR-induced activities of several antioxidant enzymes. Previous studies have reported that BRs can induce plant tolerance to a variety of environmental stimuli by triggering the generation of H2O2 as a signaling molecule. We also found that H2O2 might be involved in the crosstalk between BRs and ethylene in the tomato response to salt stress. Simultaneously, BR-induced ethylene production was partially blocked by pretreated with a reactive oxygen species scavenger or synthesis inhibitor. These results strongly demonstrated that ethylene and H2O2 play important roles in BR-dependent induction of plant salt stress tolerance. Furthermore, we also investigated the relationship between BR signaling and ethylene signaling pathways in plant processes responding to salt stress.
Facing the partner influences exchanges in force
Authors: Takagi Atsushi , Bagnato Carlo , Burdet Etienne
Published: October 2016

Many studies in psychology have documented how the behaviour of verbally communicating pairs is affected by social factors such as the partner’s gaze. However, few studies have examined whether physically interacting pairs are influenced by social factors. Here, we asked two partners to exchange forces with one another, where the goal was to accurately replicate the force back onto the other. We first measured an individual’s accuracy in reproducing a force from a robot. We then tested pairs who knowingly exchanged forces whilst separated by a curtain. These separated pairs exchanged forces as two independent individuals would, hence the force reproduction accuracy of partners is not affected by knowingly reproducing a force onto a nonvisible partner. On the other hand, pairs who exchanged forces whilst facing one another consistently under-reproduced the partner’s force in comparison to separated partners. Thus, the force reproduction accuracy of subjects is strongly biased by facing a partner.
Lithography Assisted Fiber-Drawing Nanomanufacturing
Authors: Gholipour Behrad , Bastock Paul , Cui Long , Craig Christopher , Khan Khouler , Hewak Daniel W. , Soci Cesare
Published: October 2016

We present a high-throughput and scalable technique for the production of metal nanowires embedded in glass fibres by taking advantage of thin film properties and patterning techniques commonly used in planar microfabrication. This hybrid process enables the fabrication of single nanowires and nanowire arrays encased in a preform material within a single fibre draw, providing an alternative to costly and time-consuming iterative fibre drawing. This method allows the combination of materials with different thermal properties to create functional optoelectronic nanostructures. As a proof of principle of the potential of this technique, centimetre long gold nanowires (bulk Tm = 1064 °C) embedded in silicate glass fibres (Tg = 567 °C) were drawn in a single step with high aspect ratios (>104); such nanowires can be released from the glass matrix and show relatively high electrical conductivity. Overall, this fabrication method could enable mass manufacturing of metallic nanowires for plasmonics and nonlinear optics applications, as well as the integration of functional multimaterial structures for completely fiberised optoelectronic devices.