bluuebunny/crossref_metadata_2025 huggingface dataset:
The Stochastic Gravitational Wave Background Generated by Cosmic String Networks
Authors: Sousa L. , Avelino P. P.
Published: July 2015

Cosmic string interactions often result in the formation of cosmic string loops that detach from the long string network and radiate their energy in the form of gravitational waves. Loop production occurs copiously throughout the cosmological evolution of a cosmic string network and the superimposition of their emissions gives rise to a stochastic gravitational In this essay, we briefly review our recent work on the stochastic gravitational wave background generated by cosmic string networks and introduce a set of numerical and analytical tools for the computation of this background.
Photometric typing of normal and peculiar type Ia supernovae
Authors: González-Gaitán Santiago , Bufano Filomena
Published: July 2015

We present a new photometric typing technique for normal type Ia supernovae (SNe~Ia) and peculiar SNe~Ia such as SN~1991bg-like, type Iax and super-Chandrasekhar SNe~Ia. This photometric classifier allows the identification of exclusively normal SNe~Ia (with a purity above 99% and an efficiency greater than 80%) in current and future large wide field surveys for cosmological studies.
Application of Statistical Methods on Automated Recognition of Solar Activity Phenomena and Analysis of Their Correlation
Authors: Lin Ganghua
Published: July 2015

The recent immense volume of observation data has urged us to recognize solar features and to analyze their correlation with automation methods, and many of these automation methods are closely related to statistical methods. Author investigations the extensive literatures to sum up the function of statistical methods and their advantages in recognizing automatically solar features and analyzing their correlation. The review lists the results and summarizes conclusions of the investigations. The results and conclusions will be helpful to promote the further automation processing.
Improved KPCA for supernova photometric classification
Authors: Ishida Emille E. O. , Abdalla Filipe B. , de Souza Rafael S.
Published: July 2015

The problem of supernova photometric identification is still an open issue faced by large photometric surveys. In a previous investigation, we showed how combining Kernel Principal Component Analysis and Nearest Neighbour algorithms enable us to photometrically classify supernovae with a high rate of success. In the present work, we demonstrate that the introduction of Gaussian Process Regression (GPR) in determining each light curve highly improves the efficiency and purity rates. We present detailed comparison with results from the literature, based on the same simulated data set. The method proved to be satisfactorily efficient, providing high purity (⩽ 96%) rates when compared with standard algorithms, without demanding any information on astrophysical properties of the local environment, host galaxy or redshift.
Entropy in universes evolving from initial to final de Sitter eras
Authors: Mimoso José P. , Pavón Diego
Published: July 2015

This work studies the behavior of entropy in recent cosmological models that start with an initial de Sitter expansion phase, go through the conventional radiation and matter dominated eras to be followed by a final de Sitter epoch. In spite of their seemingly similarities (observationally they are close to the Λ-CDM model), different models deeply differ in their physics. The second law of thermodynamics encapsulates the underlying microscopic, statistical description, and hence we investigate it in the present work. Our study reveals that the entropy of the apparent horizon plus that of matter and radiation inside it, increases and is a concave function of the scale factor. Thus thermodynamic equilibrium is approached in the last de Sitter era, and this class of models is thermodynamically correct. Cosmological models that do not approach equilibrium appear in conflict with the second law of thermodynamics. (Based on Mimoso & Pavon 2013)
Testing the Equivalence Principle in space with MICROSCOPE: the data analysis challenge
Authors: Bergé Joel , Baghi Quentin , Pires Sandrine
Published: July 2015

Theories beyond the Standard Model and General Relativity predict a violation of the Weak Equivalence Principle (WEP) just below the current best experimental upper limits. MICROSCOPE (Micro-Satellite à traînée Compensée pour l'Observation du Principe d'Equivalence) will allow us to lower them by two orders of magnitude, and maybe to detect a WEP violation. However, analyzing the MICROSCOPE data will be challenging, mostly because of missing data and a colored noise burrying the signal of interest. In this communication, we apply an inpainting technique to simulated MICROSCOPE data and show that inpainting will help detect a WEP violation signal.
Density reconstruction from 3D lensing: Application to galaxy clusters
Authors: Lanusse François , Leonard Adrienne , Starck Jean-Luc
Published: July 2015

Using the 3D information provided by photometric or spectroscopic weak lensing surveys, it has become possible in the last few years to address the problem of mapping the matter density contrast in three dimensions from gravitational lensing. We recently proposed a new non linear sparsity based reconstruction method allowing for high resolution reconstruction of the over-density. This new technique represents a significant improvement over previous linear methods and opens the way to new applications of 3D weak lensing density reconstruction. In particular, we demonstrate that for the first time reconstructed over-density maps can be used to detect and characterise galaxy clusters in mass and redshift.
How well can the evolution of the scale factor be reconstructed by the current data?
Authors: Vitenti Sandro D. P. , Penna-Lima Mariana
Published: July 2015

Distance measurements are currently the most powerful tool to study the expansion history of the universe without assuming its matter content nor any theory of gravitation. In general, the reconstruction of the scale factor derivatives, such as the deceleration parameter q(z), is computed using two different methods: fixing the functional form of q(z), which yields potentially biased estimates, or approximating q(z) by a piecewise nth-order polynomial function, whose variance is large. In this work, we address these two methods by reconstructing q(z) assuming only an isotropic and homogeneous universe. For this, we approximate q(z) by a piecewise cubic spline function and, then, we add to the likelihood function a penalty factor, with scatter given by σrel. This factor allows us to vary continuously between the full n knots spline, σrel → ∞, and a single linear function, σrel → 0. We estimate the coefficients of q(z) using the Monte Carlo approach, where the realizations are generated considering ΛCDM as a fiducial model. We apply this procedure in two different cases and assuming four values of σrel to find the best balance between variance and bias. First, we use only the Supernova Legacy Survey 3-year (SNLS3) sample and, in the second analysis, we combine the type Ia supernova (SNeIa) likelihood with those of baryonic acoustic oscillations (BAO) and Hubble function measurements. In both cases we fit simultaneously q(z) and 4 nuisance parameters of the supernovae, namely, the magnitudes $\mathcal{M}$1 and $\mathcal{M}$2 and the light curve parameters α and β.
Cosmic infrared background measurements and star formation history from Planck
Authors: Serra Paolo ,   on behalf of the Planck Collaboration
Published: July 2015

We present new measurements of Cosmic Infrared Background (CIB) anisotropies using Planck. Combining HFI data with IRAS, the angular auto- and cross-frequency power spectrum is measured from 143 to 3000 GHz. After careful removal of the contaminants (cosmic microwave background anisotropies, Galactic dust and Sunyaev-Zeldovich emission), and a complete study of systematics, the CIB power spectrum is measured with unprecedented signal to noise ratio from angular multipoles ℓ ~ 150 to 2500. The interpretation based on the halo model is able to associate star-forming galaxies with dark matter halos and their subhalos, using a parametrized relation between the dust-processed infrared luminosity and (sub-)halo mass, and it allows to simultaneously fit all auto- and cross- power spectra very well. We find that the star formation history is well constrained up to redshifts around 2, and agrees with recent estimates of the obscured star-formation density using Spitzer and Herschel. However, at higher redshift, the accuracy of the star formation history measurement is strongly degraded by the uncertainty in the spectral energy distribution of CIB galaxies. We also find that the mean halo mass which is most efficient at hosting star formation is log(Meff/M⊙) = 12.6 and that CIB galaxies have warmer temperatures as redshift increases.
On spin scale-discretised wavelets on the sphere for the analysis of CMB polarisation
Authors: McEwen Jason D. , Büttner Martin , Leistedt Boris , Peiris Hiranya V. , Vandergheynst Pierre , Wiaux Yves
Published: July 2015

A new spin wavelet transform on the sphere is proposed to analyse the polarisation of the cosmic microwave background (CMB), a spin ± 2 signal observed on the celestial sphere. The scalar directional scale-discretised wavelet transform on the sphere is extended to analyse signals of arbitrary spin. The resulting spin scale-discretised wavelet transform probes the directional intensity of spin signals. A procedure is presented using this new spin wavelet transform to recover E- and B-mode signals from partial-sky observations of CMB polarisation.
Data-mining Based Expert Platform for the Spectral Inspection
Authors: Tian Haijun , Xu Yang , Tu Yang , Zhang Yanxia , Zhao Yongheng , Lei Guohong , He Boliang , Cui Chenzhou , Chen Xuelei
Published: July 2015

We propose and preliminarily implement a data-mining based platform to assist experts to inspect the increasing amount of spectra with low signal to noise ratio (SNR) generated by large sky surveys. The platform includes three layers: data-mining layer, data-node layer and expert layer. It is similar to the GalaxyZoo project and it is VO-compatible. The preliminary experiment suggests that this platform can play an effective role in managing the spectra and assisting the experts to inspect a large number of spectra with low SNR.
Bayesian CMB foreground separation with a correlated log-normal model
Authors: Oppermann Niels , Enßlin Torsten A.
Published: July 2015

The extraction of foreground and CMB maps from multi-frequency observations relies mostly on the different frequency behavior of the different components. Existing Bayesian methods additionally make use of a Gaussian prior for the CMB whose correlation structure is described by an unknown angular power spectrum. We argue for the natural extension of this by using non-trivial priors also for the foreground components. Focusing on diffuse Galactic foregrounds, we propose a log-normal model including unknown spatial correlations within each component and cross-correlations between the different foreground components. We present case studies at low resolution that demonstrate the superior performance of this model when compared to an analysis with flat priors for all components.
Detecting Particle Dark Matter Signatures via Cross-Correlation of Gamma-Ray Anisotropies and Cosmic Shear
Authors: Camera Stefano
Published: July 2015

Similarly to gravitational lensing effects like cosmic shear, cosmological γ-ray emission too is to some extent a tracer of the distribution of dark matter (DM) in the Universe. Intervening DM structures source gravitational lensing distortions of distant galaxy images, and those same galaxies can emit γ rays, either because they host astrophysical sources, or directly by particle DM annihilations or decays occurring in the galactic halo. If such γ rays exhibit correlation with the cosmic shear signal, this will provide novel information on the composition of the extragalactic γ-ray background.
Transformed Auto-correlation
Authors: Zhou Jianfeng , Gao Yang
Published: July 2015

A transformed auto-correlation method is presented here, where a received signal is transformed based on a priori reflecting model, and then the transformed signal is cross-correlated to its original one. If the model is correct, after transformation, the reflected signal will be coherent to the transmitted signal, with zero delay. A map of transformed auto-correlation function with zero delay can be generated in a given parametric space. The significant peaks in the map may indicate the possible reflectors nearby the central transmitter. The true values of the parameters of reflectors can be estimated at the same time.
Cross-correlation between cosmological and astrophysical datasets: the Planck and Herschel case
Authors: Bianchini Federico , Lapi Andrea
Published: July 2015

We present the first measurement of the correlation between the map of the CMB lensing potential derived from the Planck nominal mission data and z ≳ 1.5 galaxies detected by Herschel-ATLAS (H-ATLAS) survey covering about 550 deg2. We detect the cross-power spectrum with a significance of ∼ 8.5σ, ruling out the absence of correlation at 9σ. We check detection with a number of null tests. The amplitude of cross-correlation and the galaxy bias are estimated using joint analysis of the cross-power spectrum and the galaxy survey auto-spectrum, which allows to break degeneracy between these parameters. The estimated galaxy bias is consistent with previous estimates of the bias for the H-ATLAS data, while the cross-correlation amplitude is higher than expected for a ΛCDM model. The content of this work is to appear in a forthcoming paper Bianchini, et al. (2014).
Machine-learning in astronomy
Authors: Hobson Michael , Graff Philip , Feroz Farhan , Lasenby Anthony
Published: July 2015

Machine-learning methods may be used to perform many tasks required in the analysis of astronomical data, including: data description and interpretation, pattern recognition, prediction, classification, compression, inference and many more. An intuitive and well-established approach to machine learning is the use of artificial neural networks (NNs), which consist of a group of interconnected nodes, each of which processes information that it receives and then passes this product on to other nodes via weighted connections. In particular, I discuss the first public release of the generic neural network training algorithm, calledSkyNet, and demonstrate its application to astronomical problems focusing on its use in the BAMBI package for accelerated Bayesian inference in cosmology, and the identification of gamma-ray bursters. TheSkyNetand BAMBI packages, which are fully parallelised using MPI, are available athttp://www.mrao.cam.ac.uk/software/.
Adapting Predictive Models for Cepheid Variable Star Classification Using Linear Regression and Maximum Likelihood
Authors: Gupta Kinjal Dhar , Vilalta Ricardo , Asadourian Vicken , Macri Lucas
Published: July 2015

We describe an approach to automate the classification of Cepheid variable stars into two subtypes according to their pulsation mode. Automating such classification is relevant to obtain a precise determination of distances to nearby galaxies, which in addition helps reduce the uncertainty in the current expansion of the universe. One main difficulty lies in the compatibility of models trained using different galaxy datasets; a model trained using a training dataset may be ineffectual on a testing set. A solution to such difficulty is to adapt predictive models across domains; this is necessary when the training and testing sets do not follow the same distribution. The gist of our methodology is to train a predictive model on a nearby galaxy (e.g., Large Magellanic Cloud), followed by a model-adaptation step to make the model operable on other nearby galaxies. We follow a parametric approach to density estimation by modeling the training data (anchor galaxy) using a mixture of linear models. We then use maximum likelihood to compute the right amount of variable displacement, until the testing data closely overlaps the training data. At that point, the model can be directly used in the testing data (target galaxy).
Bayesian Inference for Radio Observations - Going beyond deconvolution
Authors: Lochner Michelle , Bassett Bruce , Kunz Martin , Natarajan Iniyan , Oozeer Nadeem , Smirnov Oleg , Zwart Jonathan
Published: July 2015

Radio interferometers suffer from the problem of missing information in their data, due to the gaps between the antennae. This results in artifacts, such as bright rings around sources, in the images obtained. Multiple deconvolution algorithms have been proposed to solve this problem and produce cleaner radio images. However, these algorithms are unable to correctly estimate uncertainties in derived scientific parameters or to always include the effects of instrumental errors. We propose an alternative technique called Bayesian Inference for Radio Observations (BIRO) which uses a Bayesian statistical framework to determine the scientific parameters and instrumental errors simultaneously directly from the raw data, without making an image. We use a simple simulation of Westerbork Synthesis Radio Telescope data including pointing errors and beam parameters as instrumental effects, to demonstrate the use of BIRO.
Constraints on Growth Index from LSS
Authors: Pouri Athina , Basilakos Spyros , Plionis Manolis
Published: July 2015

We utilize the clustering properties of the Luminous Red Galaxies (LRGs) and the growth rate data in order to constrain the growth index (γ) of the linear matter fluctuations based on a standard χ2joint likelihood analysis between theoretical expectations and data. We find a value of γ=0.56± 0.05, perfectly consistent with the expectations of the ΛCDM model, and Ωm0=0.29± 0.02, in very good agreement with the latest Planck results. Our analysis provides significantly more stringent growth index constraints with respect to previous studies as indicated by the fact that the corresponding uncertainty is only ∼ 0.09 γ.
Statistical analysis of cross-correlation sample of 3XMM-DR4 with SDSS-DR10 and UKIDSS-DR9
Authors: Zhang Yan-Xia , Zhao Yong-Heng , Wu Xue-Bing , Tian Hai-Jun
Published: July 2015

We match the XMM-Newton 3XMMi-DR4 catalog with the Sloan Digital Sky Survey (SDSS) Data Release 10 and the United Kingdom Infrared Deep Sky Survey (UKIDSS) Data Release 9. Based on this X-ray/optical/infrared catalog, we probe the distribution of various types of X-ray emitters in the multidimensional parameter space. It is found that quasars, galaxies and stars have some kind distribution rule, especially for stars. The result shows that only using the X-ray/optical features, stars are difficult to discriminate from galaxies and quasars, the added information from infrared band is very helpful to improve the classification result of any classifier. Comparing the classification accuracy of random forests with that of rotation forests, rotation forests show better performance.
What are ‘property rights’, and why do they matter? A comment on Hodgson's article
Authors: BARZEL YORAM
Published: July 2015

This comment divides ‘property rights’ into ‘legal rights’ and ‘economic rights’ in order to distinguish between two very different concepts that are often confounded in the literature. Because of transaction costs, neither kind of rights is ever complete. These are useful in economic analysis as maximizing individuals constantly expand and shrink them. Unlike Hodgson’s, both notions of rights adopted here are positive, useful in analyzing behavior, and not normative as Hodgson (2015) claims them to be. As used by me, they do not devalue property rights as Hodgson claims.
Die Spontaneous Use of Imagery Scale (SUIS)–Entwicklung und teststatistische Prüfung einer deutschen Adaption
Authors: Görgen Stefanie Maria , Hiller Wolfgang , Witthöft Michael
Published: July 2015

Zusammenfassung. Mentale Vorstellungsbilder spielen bei zahlreichen kognitiven, motorischen und emotionalen Prozessen eine bedeutende Rolle. Die Spontaneous Use of Imagery Scale (SUIS; Kosslyn, Chabris, Shephard & Thompson, 1998 ) ist ein Selbstbeurteilungsinstrument zur Erfassung von interindividuellen Unterschieden hinsichtlich des alltäglichen Gebrauchs mentaler Vorstellungsbilder. In zwei Studien wurde eine deutsche Adaption der SUIS entwickelt und psychometrisch erprobt. Mittels konfirmatorischer Faktorenanalyse wurde in beiden Studien die Eindimensionalität der Skala nachgewiesen. Erste Validitätshinweise ergeben sich aus Beziehungen der SUIS zu Maßen von bildhaften (visuell-imaginativen) sowie verbal-gedanklichen kognitiven Stilen (Studie 1, N = 216). Mit der deutschen Version konnten auch positive Zusammenhänge mit Hypomanie repliziert werden. In der zweiten Studie (N = 447) konnte die interne Konsistenz der deutschen Version durch eine Erweiterung der Skala deutlich verbessert werden. Mit der erweiterten Version der SUIS liegt nun erstmalig für den deutschsprachigen Raum ein Instrument vor, das die Imaginationsneigung reliabel erfassen kann.
Konstruktvalidität und Faktorenstruktur des deutschsprachigen Youth Psychopathic Traits Inventory (YPI) in einer repräsentativen Schulstichprobe
Authors: Stadlin Christina , Pérez Tania , Schmeck Klaus , Gallo Alain Di , Schmid Marc
Published: July 2015

Zusammenfassung. Die vorliegende Studie untersucht die Konstruktvalidität und Faktorenstruktur der deutschen Version des Youth Psychopathic Traits Inventory (YPI), einem Selbstbeurteilungsverfahren, welches psychopathische Persönlichkeitseigenschaften effizient erfasst. Die Verteilung psychopathischer Persönlichkeitseigenschaften und deren Korrelation mit der selbstberichteten Delinquenz wird in einer repräsentativen Schulstichprobe (N = 840) untersucht. Das YPI zeigte in der deutschsprachigen Version eine gute interne Konsistenz (α = .92). Die Jungen erreichten signifikant höhere Werte als die Mädchen. Die drei Faktoren (interpersonaler, affektiver und behavioraler Faktor) der Originalversion wurden sowohl für Jungen als auch für Mädchen bestätigt. Außerdem korrelierten alle drei Faktoren mit der selbstberichteten Delinquenz. Mit der deutschsprachigen Version des YPI sind psychopathische Persönlichkeitseigenschaften im Selbsturteil reliabel und valide erfassbar.
Differential effects of ischemic vascular disease and Alzheimer’s disease on brain atrophy and cognition
Authors: Zheng Ling , Vinters Harry V , Mack Wendy J , Weiner Michael W , Chui Helena C ,   for the IVD program project
Published: July 2015

We previously reported that pathologic measures of arteriosclerosis (AS), cerebral infarction, and Alzheimer’s disease (AD) are independently correlated with cortical gray matter (CGM) atrophy measured by in vivo magnetic resonance imaging (MRI). Here, we use path analyses to model the associations between these three pathology measures and cognitive impairment, as mediated by CGM atrophy, after controlling for age and education. In this sample of 116 elderly persons followed longitudinally to autopsy (ischemic vascular disease (IVD) program project), differential patterns were observed between AS and atrophy/cognition versus AD and atrophy/cognition. The total effect of AD pathology on global cognition ( β = −0.61, s.e. = 0.06) was four times stronger than that of AS ( β = −0.15, s.e. = 0.08). The effect of AS on cognition appears to occur through cerebral infarction and CGM atrophy ( β = −0.13, s.e. = 0.04). In contrast, the effects of AD pathology on global cognition ( β = −0.50, s.e. = 0.07) occur through a direct pathway that is five times stronger than the indirect pathway acting through CGM atrophy ( β = −0.09, s.e. = 0.03). The strength of this direct AD pathway was not significantly mitigated by adding hippocampal volume to the model. AD pathology affects cognition not only through brain atrophy, but also via an unmeasured pathway that could be related to synaptic dysfunction before the development of cortical atrophy.
A Rac/Cdc42 exchange factor complex promotes formation of lateral filopodia and blood vessel lumen morphogenesis
Authors: Abraham Sabu , Scarcia Margherita , Bagshaw Richard D. , McMahon Kathryn , Grant Gary , Harvey Tracey , Yeo Maggie , Esteves Filomena O.G. , Thygesen Helene H. , Jones Pamela F. , Speirs Valerie , Hanby Andrew M. , Selby Peter J. , Lorger Mihaela , Dear T. Neil , Pawson Tony , Marshall Christopher J. , Mavria Georgia
Published: July 2015

During angiogenesis, Rho-GTPases influence endothelial cell migration and cell–cell adhesion; however it is not known whether they control formation of vessel lumens, which are essential for blood flow. Here, using an organotypic system that recapitulates distinct stages of VEGF-dependent angiogenesis, we show that lumen formation requires early cytoskeletal remodelling and lateral cell–cell contacts, mediated through the RAC1 guanine nucleotide exchange factor (GEF) DOCK4 (dedicator of cytokinesis 4). DOCK4 signalling is necessary for lateral filopodial protrusions and tubule remodelling prior to lumen formation, whereas proximal, tip filopodia persist in the absence of DOCK4. VEGF-dependent Rac activation via DOCK4 is necessary for CDC42 activation to signal filopodia formation and depends on the activation of RHOG through the RHOG GEF, SGEF. VEGF promotes interaction of DOCK4 with the CDC42 GEF DOCK9. These studies identify a novel Rho-family GTPase activation cascade for the formation of endothelial cell filopodial protrusions necessary for tubule remodelling, thereby influencing subsequent stages of lumen morphogenesis.
Influencing the properties of dysprosium single-molecule magnets with phosphorus donor ligands
Authors: Pugh Thomas , Tuna Floriana , Ungur Liviu , Collison David , McInnes Eric J.L. , Chibotaru Liviu F. , Layfield Richard A.
Published: July 2015

Single-molecule magnets are a type of coordination compound that can retain magnetic information at low temperatures. Single-molecule magnets based on lanthanides have accounted for many important advances, including systems with very large energy barriers to reversal of the magnetization, and a di-terbium complex that displays magnetic hysteresis up to 14 K and shows strong coercivity. Ligand design is crucial for the development of new single-molecule magnets: organometallic chemistry presents possibilities for using unconventional ligands, particularly those with soft donor groups. Here we report dysprosium single-molecule magnets with neutral and anionic phosphorus donor ligands, and show that their properties change dramatically when varying the ligand from phosphine to phosphide to phosphinidene. A phosphide-ligated, trimetallic dysprosium single-molecule magnet relaxes via the second-excited Kramers' doublet, and, when doped into a diamagnetic matrix at the single-ion level, produces a large energy barrier of 256 cm−1 and magnetic hysteresis up to 4.4 K.
Electric-field-induced strong enhancement of electroluminescence in multilayer molybdenum disulfide
Authors: Li Dehui , Cheng Rui , Zhou Hailong , Wang Chen , Yin Anxiang , Chen Yu , Weiss Nathan O. , Huang Yu , Duan Xiangfeng
Published: July 2015

The layered transition metal dichalcogenides have attracted considerable interest for their unique electronic and optical properties. While the monolayer MoS2 exhibits a direct bandgap, the multilayer MoS2 is an indirect bandgap semiconductor and generally optically inactive. Here we report electric-field-induced strong electroluminescence in multilayer MoS2. We show that GaN–Al2O3–MoS2 and GaN–Al2O3–MoS2–Al2O3-graphene vertical heterojunctions can be created with excellent rectification behaviour. Electroluminescence studies demonstrate prominent direct bandgap excitonic emission in multilayer MoS2 over the entire vertical junction area. Importantly, the electroluminescence efficiency observed in multilayer MoS2 is comparable to or higher than that in monolayers. This strong electroluminescence can be attributed to electric-field-induced carrier redistribution from the lowest energy points (indirect bandgap) to higher energy points (direct bandgap) in k-space. The electric-field-induced electroluminescence is general for other layered materials including WSe2 and can open up a new pathway towards transition metal dichalcogenide-based optoelectronic devices.
The free energy of mechanically unstable phases
Authors: van de Walle A. , Hong Q. , Kadkhodaei S. , Sun R.
Published: July 2015

Phase diagrams provide ‘roadmaps’ to the possible states of matter. Their determination traditionally rests on the assumption that all phases, even unstable ones, have well-defined free energies under all conditions. However, this assumption is commonly violated in condensed phases due to mechanical instabilities. This long-standing problem impedes thermodynamic database development, as pragmatic attempts at solving this problem involve delicate extrapolations that are highly nonunique and that lack an underlying theoretical justification. Here we propose an efficient computational solution to this problem that has a simple interpretation, both as a topological partitioning of atomic configuration space and as a minimally constrained physical system. Our natural scheme smoothly extends the free energy of stable phases, without relying on extrapolation, thus enabling a formal assessment of widely used extrapolation schemes.
Scopolamine effects on functional brain connectivity: a pharmacological model of Alzheimer’s disease
Authors: Bajo R. , Pusil S. , López M. E. , Canuet L. , Pereda E. , Osipova D. , Maestú F. , Pekkonen E.
Published: July 2015

Scopolamine administration may be considered as a psychopharmacological model of Alzheimer’s disease (AD). Here, we studied a group of healthy elderly under scopolamine to test whether it elicits similar changes in brain connectivity as those observed in AD, thereby verifying a possible model of AD impairment. We did it by testing healthy elderly subjects in two experimental conditions: glycopyrrolate (placebo) and scopolamine administration. We then analyzed magnetoencephalographic (MEG) data corresponding to both conditions in resting-state with eyes closed. This analysis was performed in source space by combining a nonlinear frequency band-specific measure of functional connectivity (phase locking value, PLV) with network analysis methods. Under scopolamine, functional connectivity between several brain areas was significantly reduced as compared to placebo, in most frequency bands analyzed. Besides, regarding the two complex network indices studied (clustering and shortest path length), clustering significantly decreased in the alpha band while shortest path length significantly increased also in alpha band both after scopolamine administration. Overall our findings indicate that both PLV and graph analysis are suitable tools to measure brain connectivity changes induced by scopolamine, which causes alterations in brain connectivity apparently similar to those reported in AD.
Long-duration animal tracking in difficult lighting conditions
Authors: Stern Ulrich , Zhu Edward Y. , He Ruo , Yang Chung-Hui
Published: July 2015

High-throughput analysis of animal behavior requires software to analyze videos. Such software typically depends on the experiments’ being performed in good lighting conditions, but this ideal is difficult or impossible to achieve for certain classes of experiments. Here, we describe techniques that allow long-duration positional tracking in difficult lighting conditions with strong shadows or recurring “on”/“off” changes in lighting. The latter condition will likely become increasingly common, e.g., for Drosophila due to the advent of red-shifted channelrhodopsins. The techniques enabled tracking with good accuracy in three types of experiments with difficult lighting conditions in our lab. Our technique handling shadows relies on single-animal tracking and on shadows’ and flies’ being accurately distinguishable by distance to the center of the arena (or a similar geometric rule); the other techniques should be broadly applicable. We implemented the techniques as extensions of the widely-used tracking software Ctrax; however, they are relatively simple, not specific to Drosophila and could be added to other trackers as well.
Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies
Authors: Chen Jing , Shinde Sudhirkumar , Koch Markus-Hermann , Eisenacher Martin , Galozzi Sara , Lerari Thilo , Barkovits Katalin , Subedi Prabal , Krüger Rejko , Kuhlmann Katja , Sellergren Börje , Helling Stefan , Marcus Katrin
Published: July 2015

Phosphospecific enrichment techniques and mass spectrometry (MS) are essential tools for comprehending the cellular phosphoproteome. Here, we report a fast and simple approach for low sequence-bias phosphoserine (pS) peptide capture and enrichment that is compatible with low biological or clinical sample input. The approach exploits molecularly imprinted polymers (MIPs, “plastic antibodies”) featuring tight neutral binding sites for pS or pY that are capable of cross-reacting with phosphopeptides of protein proteolytic digests. The versatility of the resulting method was demonstrated with small samples of whole-cell lysate from human embryonic kidney (HEK) 293T cells, human neuroblastoma SH-SY5Y cells, mouse brain or human cerebrospinal fluid (CSF). Following pre-fractionation of trypsinized proteins by strong cation exchange (SCX) chromatography, pS-MIP enrichment led to the identification of 924 phosphopeptides in the HEK 293T whole-cell lysate, exceeding the number identified by TiO2-based enrichment (230). Moreover, the phosphopeptides were extracted with low sequence bias and showed no evidence for the characteristic preference of TiO2 for acidic amino acids (aspartic and glutamic acid). Applying the method to human CSF led to the discovery of 47 phosphopeptides belonging to 24 proteins and revealed three previously unknown phosphorylation sites.
RETRACTED ARTICLE: Large-Area Semiconducting Graphene Nanomesh Tailored by Interferometric Lithography
Authors: Kazemi Alireza , He Xiang , Alaie Seyedhamidreza , Ghasemi Javad , Dawson Noel Mayur , Cavallo Francesca , Habteyes Terefe G. , Brueck Steven R. J. , Krishna Sanjay
Published: July 2015

Graphene nanostructures are attracting a great deal of interest because of newly emerging properties originating from quantum confinement effects. We report on using interferometric lithography to fabricate uniform, chip-scale, semiconducting graphene nanomesh (GNM) with sub-10 nm neck widths (smallest edge-to-edge distance between two nanoholes). This approach is based on fast, low-cost and high-yield lithographic technologies and demonstrates the feasibility of cost-effective development of large-scale semiconducting graphene sheets and devices. The GNM is estimated to have a room temperature energy bandgap of ~30 meV. Raman studies showed that the G band of the GNM experiences a blue shift and broadening compared to pristine graphene, a change which was attributed to quantum confinement and localization effects. A single-layer GNM field effect transistor exhibited promising drive current of ~3.9 μA/μm and ON/OFF current ratios of ~35 at room temperature. The ON/OFF current ratio of the GNM-device displayed distinct temperature dependence with about 24-fold enhancement at 77 K.
Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes
Authors: Sello Mopeli Marshal , Jafta Norventia , Nelson David R , Chen Wanping , Yu Jae-Hyuk , Parvez Mohammad , Kgosiemang Ipeleng Kopano Rosinah , Monyaki Richie , Raselemane Seiso Caiphus , Qhanya Lehlohonolo Benedict , Mthakathi Ntsane Trevor , Sitheni Mashele Samson , Syed Khajamohiddin
Published: July 2015

Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins whose role as drug targets against pathogens, as well as in valuable chemical production and bioremediation, has been explored. In this study we performed comprehensive comparative analysis of P450s in 13 newly explored oomycete pathogens. Three hundred and fifty-six P450s were found in oomycetes. These P450s were grouped into 15 P450 families and 84 P450 subfamilies. Among these, nine P450 families and 31 P450 subfamilies were newly found in oomycetes. Research revealed that oomycetes belonging to different orders contain distinct P450 families and subfamilies in their genomes. Evolutionary analysis and sequence homology data revealed P450 family blooms in oomycetes. Tandem arrangement of a large number of P450s belonging to the same family indicated that P450 family blooming is possibly due to its members’ duplications. A unique combination of amino acid patterns was observed at EXXR and CXG motifs for the P450 families CYP5014, CYP5015 and CYP5017. A novel P450 fusion protein (CYP5619 family) with an N-terminal P450 domain fused to a heme peroxidase/dioxygenase domain was discovered in Saprolegnia declina. Oomycete P450 patterns suggested host influence in shaping their P450 content. This manuscript serves as reference for future P450 annotations in newly explored oomycetes.
Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films
Authors: Heon Kim Tae , Yoon Jong-Gul , Hyub Baek Seung , Park Woong-kyu , Mo Yang Sang , Yup Jang Seung , Min Taeyuun , Chung Jin-Seok , Eom Chang-Beom , Won Noh Tae
Published: July 2015

Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.
Highly homologous proteins exert opposite biological activities by using different interaction interfaces
Authors: Iosub Amir Anat , van Rosmalen Martijn , Mayer Guy , Lebendiker Mario , Danieli Tsafi , Friedler Assaf
Published: July 2015

We present a possible molecular basis for the opposite activity of two homologues proteins that bind similar ligands and show that this is achieved by fine-tuning of the interaction interface. The highly homologous ASPP proteins have opposite roles in regulating apoptosis: ASPP2 induces apoptosis while iASPP inhibits it. The ASPP proteins are regulated by an autoinhibitory interaction between their Ank-SH3 and Pro domains. We performed a detailed biophysical and molecular study of the Pro – Ank-SH3 interaction in iASPP and compared it to the interaction in ASPP2. We found that iASPP Pro is disordered and that the interaction sites are entirely different: iASPP Ank-SH3 binds iASPP Pro via its fourth Ank repeat and RT loop while ASPP2 Ank-SH3 binds ASPP2 Pro via its first Ank repeat and the n-src loop. It is possible that by using different moieties in the same interface, the proteins can have distinct and specific interactions resulting in differential regulation and ultimately different biological activities.
Molecular evolution of haemagglutinin (H) gene in measles virus
Authors: Kimura Hirokazu , Saitoh Mika , Kobayashi Miho , Ishii Haruyuki , Saraya Takeshi , Kurai Daisuke , Tsukagoshi Hiroyuki , Shirabe Komei , Nishina Atsuyoshi , Kozawa Kunihisa , Kuroda Makoto , Takeuchi Fumihiko , Sekizuka Tsuyoshi , Minakami Hisanori , Ryo Akihide , Takeda Makoto
Published: July 2015

We studied the molecular evolution of the haemagglutinin (H) gene (full length) in all genotypes (24 genotypes, 297 strains) of measles virus (MeV). The gene’s evolutionary timescale was estimated by the Bayesian Markov chain Monte Carlo (MCMC) method. We also analysed positive selection sites. The MCMC tree indicated that the MeV H gene diverged from the rinderpest virus (same genus) about 250 years ago and that 24 MeV genotypes formed 3 lineages dating back to a 1915 ancestor (95% highest posterior density [HPD] 1882–1941) with relatively rapid evolution (mean rate: 9.02 × 10−4 substitutions/site/year). The 3 lineages diverged in 1915 (lineage 1, 95% HPD 1882–1941), 1954 (lineage 2, 95% HPD 1937–1969) and 1940 (lineage 3, 95% HPD 1927–1952). These 24 genotypes may have diverged and emerged between the 1940s and 1990s. Selective pressure analysis identified many negative selection sites on the H protein but only a few positive selection sites, suggesting strongly operated structural and/or functional constraint of changes on the H protein. Based on the molecular evolution of H gene, an ancestor MeV of the 24 genotypes emerged about 100 years ago and the structure of H protein has been well conserved.
Late-glacial elevated dust deposition linked to westerly wind shifts in southern South America
Authors: Vanneste Heleen , De Vleeschouwer François , Martínez-Cortizas Antonio , von Scheffer Clemens , Piotrowska Natalia , Coronato Andrea , Le Roux Gaël
Published: July 2015

Atmospheric dust loadings play a crucial role in the global climate system. Southern South America is a key dust source, however, dust deposition rates remain poorly quantified since the last glacial termination (~17 kyr ago), an important timeframe to anticipate future climate changes. Here we use isotope and element geochemistry in a peat archive from Tierra del Fuego, to reconstruct atmospheric dust fluxes and associated environmental and westerly wind changes for the past 16.2 kyr. Dust depositions were elevated during the Antarctic Cold Reversal (ACR) and second half of the Younger Dryas (YD) stadial, originating from the glacial Beagle Channel valley. This increase was most probably associated with a strengthening of the westerlies during both periods as dust source areas were already available before the onset of the dust peaks and remained present throughout. Congruent with glacier advances across Patagonia, this dust record indicates an overall strengthening of the wind belt during the ACR. On the other hand, we argue that the YD dust peak is linked to strong and poleward shifted westerlies. The close interplay between dust fluxes and climatic changes demonstrates that atmospheric circulation was essential in generating and sustaining present-day interglacial conditions.
Quantum-confinement and Structural Anisotropy result in Electrically-Tunable Dirac Cone in Few-layer Black Phosphorous
Authors: Dolui Kapildeb , Quek Su Ying
Published: July 2015

Two-dimensional (2D) materials are well-known to exhibit interesting phenomena due to quantum confinement. Here, we show that quantum confinement, together with structural anisotropy, result in an electric-field-tunable Dirac cone in 2D black phosphorus. Using density functional theory calculations, we find that an electric field, Eext, applied normal to a 2D black phosphorus thin film, can reduce the direct band gap of few-layer black phosphorus, resulting in an insulator-to-metal transition at a critical field, Ec. Increasing Eext beyond Ec can induce a Dirac cone in the system, provided the black phosphorus film is sufficiently thin. The electric field strength can tune the position of the Dirac cone and the Dirac-Fermi velocities, the latter being similar in magnitude to that in graphene. We show that the Dirac cone arises from an anisotropic interaction term between the frontier orbitals that are spatially separated due to the applied field, on different halves of the 2D slab. When this interaction term becomes vanishingly small for thicker films, the Dirac cone can no longer be induced. Spin-orbit coupling can gap out the Dirac cone at certain electric fields; however, a further increase in field strength reduces the spin-orbit-induced gap, eventually resulting in a topological-insulator-to-Dirac-semimetal transition.
Beta-cell regeneration from vimentin+/MafB+ cells after STZ-induced extreme beta-cell ablation
Authors: Cheng Yu , Kang Hongjun , Shen Jing , Hao Haojie , Liu Jiejie , Guo Yelei , Mu Yiming , Han Weidong
Published: July 2015

Loss of functional beta-cells is fundamental in both type 1 and type 2 diabetes. In situ beta-cell regeneration therefore has garnered great interest as an approach to diabetes therapy. Here, after elimination of pre-existing beta cells by a single high-dose of streptozotocin (STZ), we demonstrated that a considerable amount of beta-like-cells was generated within 48 hrs. But the newly formed insulin producing cells failed to respond to glucose challenge at this time and diminished afterwards. Insulin treatment to normalize the glucose level protected the neogenic beta-like cells and the islet function was also gradually matured. Strikingly, intermediate cells lacking epithelial marker E-cadherin but expressing mesenchymal cell-specific marker vimentin appeared within 16 hrs following STZ exposure, which served as the major source of insulin-producing cells observed at 24 hrs. Moreover, these intermediate cells strongly expressed alpha-cell-specific marker MafB. In summary, the data presented here identified a novel intermediate cell type as beta-cell progenitors, showing mesenchymal cell feature as well as alpha-cell marker MafB. Our results might have important implications for efforts to stimulate beta-cell regeneration.
New Insulating Antiferromagnetic Quaternary Iridates MLa10Ir4O24 (M = Sr, Ba)
Authors: Zhao Qingbiao , Han Fei , Stoumpos Constantinos C. , Han Tian-Heng , Li Hao , Mitchell J. F.
Published: July 2015

Recently, oxides of Ir4+ have received renewed attention in the condensed matter physics community, as it has been reported that certain iridates have a strongly spin-orbital coupled (SOC) electronic state, Jeff = ½, that defines the electronic and magnetic properties. The canonical example is the Ruddlesden-Popper compound Sr2IrO4, which has been suggested as a potential route to a new class of high temperature superconductor due to the formal analogy between Jeff = ½ and the S = ½ state of the cuprate superconductors. The quest for other iridium oxides that present tests of the underlying SOC physics is underway. In this spirit, here we report the synthesis and physical properties of two new quaternary tetravalent iridates, MLa10Ir4O24 (M = Sr, Ba). The crystal structure of both compounds features isolated IrO6 octahedra in which the electronic configuration of Ir is d5. Both compounds order antiferromagnetically despite the lack of obvious superexchange pathways and resistivity measurement shows that SrLa10Ir4O24 is an insulator.