bluuebunny/crossref_metadata_2025 huggingface dataset:
Coordinate logic order statistics filters: new approach for real‐time image processing
Authors: Kostas Tsirikolias
Published: May 2014

A new approach regarding real‐time low‐level image and signal processing is presented. This new approach deals with the philosophy of finding a method for designing and executing algorithms (filters), using the most minimum possible complexity. The proposed method is based on a special formation of coordinate logic filters (CLFs), the coordinate logic order statistics (CL‐OS) filters. CL‐OS introduces a minimalistic approach in filter design followed by the greatest possible efficiency in terms of speed, quality, complexity and energy consumption. Moreover CL‐OS reveals new signal information; this information gives a different interpretation of the original signal, it could be said that it acts like a function applying a nonlinear quantisation in order to approximate the desired output.
Adaptive CU splitting and pruning method for HEVC intra coding
Authors: Kim Gaewon , Yim Changhoon
Published: May 2014

Coding unit (CU) splitting and pruning for complexity reduction in high‐efficiency video coding (HEVC) intra coding is dealt with. Adaptive determination of the threshold values for splitting and pruning in each CU is proposed based on the depth level information of neighbour CUs, whose values are determined from a fixed parameter in the previous method. Simple preconditions for splitting and pruning are also proposed to improve coding efficiency. Simulation results show that the proposed method gives significant improvement of computational complexity with much smaller reduction of coding efficiency compared with the previous method.
Compact microstrip lowpass filter with sharp roll‐off using radial resonator
Authors: Hayati M. , Naderi S. , Jafari F.
Published: May 2014

A compact microstrip lowpass filter (LPF) with sharp roll‐off is presented. The proposed filter consists of radial resonator, triangular patch and open stub. The proposed filter has good specifications such as low insertion loss <0.1 dB, high return loss of −20 dB, wide stopband from 4.37 to 19 GHz with −20 dB attenuation level and compact size. The LPF filter has a cut‐off frequency of 3 dB at 4.24 GHz and a high roll‐off rate of 130.7 and finally a high figure‐of‐merit of 23526.
Design and fabrication of cost‐effective side‐stem micromechanical disk resonator with large capacitive gap
Authors: Phamvan Huan , Seok Jongwon , Choi Hae‐Jin
Published: May 2014

A high‐performance micromechanical disk resonator is developed for use in mass detection biosensors. The resonator is designed to facilitate easy and cost‐effective fabrication by anchoring the disk on the side stems and increasing the capacitive gap size up to 4.75 µm. The designed disk resonator operates in an elliptic contour‐mode at a resonance frequency of 5.971 MHz with a quality factor of 4272 in ambient air condition and 17 221 in a 600 Torr vacuum environment.
2.8 dB conversion gain broadband HBT–HEMT balanced frequency tripler with high harmonic suppression
Authors: Chen Guan‐Yu , Chang Hong‐Yeh , Weng Shou‐Hsien , Hsin Yue‐Ming , Wang Yu‐Chi
Published: May 2014

A 10.2–12.6 GHz balanced heterojunction bipolar transistor (HBT)–high electron mobility transistor (HEMT) frequency tripler is presented. A pair of common‐base/common‐emitter HBTs is used to generate in‐phase and out‐of‐phase harmonics. Two bandpass filters are utilised as matching networks to enhance the harmonic suppression. A common‐gate/common‐source HEMT active balun is employed to combine the third harmonic in‐phase and provide conversion gain. The proposed frequency tripler shows a conversion gain of 2.8 dB, a fractional bandwidth of 21.2% and a fundamental suppression higher than 47 dB.
Highly stable operations of transverse‐coupled cavity VCSELs with enhanced modulation bandwidth
Authors: Dalir H. , Koyama F.
Published: May 2014

The highly stable operation of 980 nm transverse coupled cavity vertical cavity surface emitting lasers (VCSELs) with enhanced modulation bandwidth for high‐speed optical interconnects is reported. The device operates at 25 Gbit/s from 0 to 60°C with fixed driving conditions. In addition, the stability of driving currents into the VCSEL is explored, exhibiting that the bandwidth enhancement is not sensitive to the current. The ultra‐compact inplane coupled cavity VCSEL can boost the modulation speed beyond the relaxation oscillation frequency because of the to photon–photon resonance, which makes it useful in next‐generation computing and data centre networking.
Simultaneous correlation architecture for multilevel complementary sequences
Authors: Hadad M.N. , Funes M.A. , Donato P.G. , Carrica D.O.
Published: May 2014

Complementary sequences are being widely used in applications ranging from communication to radar and sonar systems. The properties of these sequences render them suitable for applications requiring signal detection in noisy environments and/or multi‐user systems. The use of complementary sequences in practical applications with reduced hardware resources has promoted the development of efficient architectures that reduce the computational requirements for the generation and correlation of the sequences. An optimised architecture for the simultaneous correlation of pairs of multilevel complementary sequences is presented, which achieves that reduction by removing redundant operations. The proposal has an impact also on the correlation of binary complementary pairs of sequences of lengths of a power of 10 and 26 that use the multilevel architecture to generate the kernels.
Adaptive controller design for mobile robots
Authors: Lu Cheng‐Kai , Huang Yi‐Che , Lee Cheng‐Jung , Yang Zhijun
Published: May 2014

A simple yet effective method to reduce the dimensions of the input variables and is adaptive to various users for intelligent controllers is proposed. The method has been developed specifically to address the challenge due to fuzziness in the system inputs, especially when studying the relationship of a large mapping between input variables and system response outputs. The proposed method exploits the principal components analysis to reduce the number of inputs and uses a fuzzy c‐means technique to cluster them. The objective is to extract significant principal components for adaptive neural fuzzy inference systems (ANFIS) learning. The method has been applied to a robotic walker system for elderly movement assistance. Experimental results demonstrate the feasibility of the proposed method.
Experimental investigation of bias current and load modulation effects in phase distortion of GaN HEMTs
Authors: Quaglia R. , Piazzon L. , Camarchia V. , Giofrè R. , Pirola M. , Colantonio P. , Ghione G. , Giannini F.
Published: May 2014

The relationships between phase distortion, bias point and load modulation in power amplifiers are experimentally evaluated for two different GaN HEMT technologies. Measurements on devices with fixed and modulated load, to emulate the dynamic working conditions of the main stage of a Doherty amplifier, have been carried out through an advanced source/load‐pull setup. Almost flat phase distortion against output power can be obtained by the proper bias point when the load remains constant, whereas it is shown that this possibility is not compatible with load modulation, inherently present in Doherty power amplifiers.
Double‐sampled wideband delta–sigma ADCs with shifted loop delays
Authors: Meng X. , Temes G.C.
Published: May 2014

A novel double‐sampled wideband delta–sigma modulator topology with shifted loop delays is proposed. Compared with the conventional double‐sampled modulator, this analogue‐to‐digital converter (ADC) implements the inherent quantisation delay by shifting one loop delay from the last integrator to the quantiser, and it relaxes the critical timing for dynamic element matching (DEM) by shifting the loop delay from the first integrator to the feedback path. In addition, by inserting one more delay in the signal path, the proposed modulator retains the low‐distortion property. To verify the effectiveness of the proposed topology, a second‐order double‐sampled delta–sigma modulator is analysed and simulated.
Frequency‐modulated magneto‐acoustic detection and imaging
Authors: Aliroteh M.S. , Scott G. , Arbabian A.
Published: May 2014

Magneto‐acoustic (MA) tomography combines near‐field RF and ultrasound for the goal of a safe, high‐resolution, high‐contrast bimodal imaging technique. Coherency between RF excitation and the resulting ultrasound generation through Lorentz force interactions is established. This allows for continuous‐wave (CW) imaging techniques to replace conventional pulsed‐based approaches, easing system design and improving signal‐to‐noise ratio (SNR) while reducing the peak‐to‐average excitation power ratio, for the same averaging time, sensitivity and gain. This is the first successful demonstration of MA detection using step frequency CW (SFCW) as well as frequency‐modulated CW (FMCW) approaches with up to 36 dB SNR improvement.
Modelling, analysis and control of stand‐alone self‐excited induction generator‐pulse width modulation rectifier systems feeding constant DC voltage applications
Authors: Senthil Kumar Subramaniam , Kumaresan Natarajan , Subbiah Muthiah , Rageeru Mahendhar
Published: May 2014

An analogue‐based pulse width modulation (PWM) hysteresis current mode controller has been developed for the stand‐alone operation of self‐excited induction generator (SEIG)‐PWM rectifier systems for constant DC voltage applications. The configuration and implementation of the control scheme have been fully described. A method for predetermining the steady‐state performance of the system for a given rectifier DC output has been explained with relevant analytical expressions derived for suitably reflecting the DC load resistance on the generator terminals. An ‘abc‐dq’ axis model has also been formulated for the study of transient behaviour of the system for step changes in the driving speed and DC load on the system. A prototype system consisting of an SEIG, rectifier and the associated control circuits has been built in the laboratory and its satisfactory working has been demonstrated experimentally, for the different loading patterns and the corresponding predetermined results are also provided.
Optimal configuration of underground cables to maximise total ampacity considering current harmonics
Authors: Zarchi Davoud Abootorabi , Vahidi Behrooz , Haji Moosa Moghimi
Published: May 2014

This study presents an efficient algorithm to find optimal underground cable configuration with maximum ampacity in a concrete duct bank. The current's harmonics and its effects on the sheath losses are considered in the proposed algorithm. To find the optimal configuration of the cables in the duct bank, two heuristic optimisation methods are applied: the first algorithm is the well‐known particle swarm optimisation (PSO), and the second one is the shuffled frog‐leaping algorithm (SFLA) which has attracted considerable attraction in recent years. The objective function of these methods which has to be optimised is total ampacity. Calculating the total ampacity for a required configuration by using PSO/SFLA is a convex optimisation problem. The interior point method is utilised to solve this problem. The proposed method has been implemented on four test cases to show the importance of considering the current harmonics in determining the optimal configuration. To evaluate the performance of the PSO and the SFLA, the obtained results are compared in different test cases.
Non‐coherent squaring detector and its application to bi‐phased signals
Authors: Borio Daniele
Published: May 2014

The non‐coherent squaring detector (NSD) has been recently derived from the generalised likelihood ratio test (GLRT) as the linear combination of the non‐coherent and squaring detectors. The statistical properties of the NSD are investigated and a simple criterion for fixing the decision threshold is provided. In particular, approximations for the false alarm and detection probabilities are derived and used to characterise the performance of the NSD. The application of the NSD to the detection of pulsed bi‐phased signals is then considered. The validity of the theoretical findings is supported by real data analysis and Monte Carlo simulations.
Formation en Nanosciences et Nanotechnologies : Un pas vers une
«vraie » interdisciplinarité
Authors: Sellier H. , Planus E. , Dubois F. , Lévy L. , Gautier-Luneau I. , Peyla Ph. , Marchi F.
Published: May 2014

En 2011, l’Université Joseph Fourier (UJF), s'appuyant sur la force de la recherche
interdisciplinaire des laboratoires grenoblois dans les Nanosciences et Nanotechnologies, a
ouvert deux majeures : un M1 « Physique fondamentale et Nanosciences » et un M1 « Chimie
et Nanosciences ». Dans ce cadre, des Travaux Pratiques interdisciplinaires et interplateformes
ont été mis en place afin d’illustrer de manière concrète la convergence de la
physique, de la chimie et de la biologie à l’échelle micro/nanométrique qui s’appuie sur les
micro et nanotechnologies. Cet article décrit en détail ces TP et expose leur intérêt
pédagogique pour la formation des étudiants ainsi que pour des enseignants-chercheurs.
Vectorial Kerr magnetometer for simultaneous and quantitative measurements of the in-plane magnetization components
Authors: Jiménez E. , Mikuszeit N. , Cuñado J. L. F. , Perna P. , Pedrosa J. , Maccariello D. , Rodrigo C. , Niño M. A. , Bollero A. , Camarero J. , Miranda R.
Published: May 2014

A vectorial magneto-optic Kerr effect (v-MOKE) setup with simultaneous and quantitative determination of the two in-plane magnetization components is described. The setup provides both polarization rotations and reflectivity changes at the same time for a given sample orientation with respect to a variable external magnetic field, as well as allowing full angular studies. A classical description based on the Jones formalism is used to calculate the setup's properties. The use of different incoming light polarizations and/or MOKE geometries, as well as the errors due to misalignment and solutions are discussed. To illustrate the capabilities of the setup a detailed study of a model four-fold anisotropy system is presented. Among others, the setup allows to study the angular dependence of the hysteresis phenomena, remanences, critical fields, and magnetization reversal processes, as well as the accurate determination of the easy and hard magnetization directions, domain wall orientations, and magnetic anisotropies.
Effect of entropy on anomalous transport in electron-temperature-gradient-modes
Authors: Yaqub Khan M. , Iqbal J. , ul Haq A.
Published: May 2014

Due to the interconnection of entropy with temperature and density of plasma, it would be interesting to investigate plasma related phenomena with respect to entropy. By employing Braginskii transport equations, it is proved that entropy is proportional to a function of potential and distribution function of entropy is re-defined, ∇S–drift in obtained. New dispersion relation is derived; it is found that the anomalous transport depends on the gradient of the entropy.
The effect of structural changes on charge transfer states in a light-harvesting carotenoid-diaryl-porphyrin-C60 molecular triad
Authors: Olguin Marco , Basurto Luis , Zope Rajendra R. , Baruah Tunna
Published: May 2014

We present a detailed study of charge transfer (CT) excited states for a large number of configurations in a light-harvesting Carotenoid-diaryl-Porphyrin-C60 (CPC60) molecular triad. The chain-like molecular triad undergoes photoinduced charge transfer process exhibiting a large excited state dipole moment, making it suitable for application to molecular-scale opto-electronic devices. An important consideration is that the structural flexibility of the CPC60 triad impacts its dynamics in solvents. Since experimentally measured dipole moments for the triad of ∼110 D and ∼160 D strongly indicate a range in structural variability in the excited state, studying the effect of structural changes on the CT excited state energetics furthers the understanding of its charge transfer states. We have calculated the variation in the lowest CT excited state energies by performing a scan of possible variation in the structure of the triad. Some of these configurations were generated by incrementally scanning a 360° torsional (dihedral) twist at the C60-porhyrin linkage and the porphyrin-carotenoid linkage. Additionally, five different CPC60 conformations were studied to determine the effect of pi-conjugation and particle-hole Coulombic attraction on the CT excitation energies. Our calculations show that configurational changes in the triad induces a variation of ∼0.6 eV in CT excited state energies in the gas-phase. The corresponding calculated excited state dipoles show a range of 47 D–188 D. The absorption spectra and density of states of these structures show little variation except for the structures where the porphyrin and aryl conjugation is changed.
Melting transition of Lennard-Jones fluid in cylindrical pores
Authors: Das Chandan K. , Singh Jayant K.
Published: May 2014

Three-stage pseudo-supercritical transformation path and multiple-histogram reweighting technique are employed for the determination of solid-liquid coexistence of the Lennard-Jones (12-6) fluid, in a structureless cylindrical pore of radius, R, ranging from 4 to 20 molecular diameters. The Gibbs free energy difference is evaluated using thermodynamic integration method by connecting solid and liquid phases under confinement via one or more intermediate states without any first order phase transition among them. The thermodynamic melting temperature, Tm, is found to oscillate for pore size, R < 8, which is in agreement with the behavior observed for the melting temperature in slit pores. However, Tm for almost all pore sizes is less than the bulk case, which is contrary to the behavior seen for the slit pore. The oscillation in Tm decays at around pore radius R = 8, and beyond that shift in the melting temperature with respect to the bulk case is in line with the prediction of the Gibbs-Thomson equation.
A fast non-Fourier method for Landau-fluid operators
Authors: Dimits A. M. , Joseph I. , Umansky M. V.
Published: May 2014

An efficient and versatile non-Fourier method for the computation of Landau-fluid (LF) closure operators [Hammett and Perkins, Phys. Rev. Lett. 64, 3019 (1990)] is presented, based on an approximation by a sum of modified-Helmholtz-equation solves (SMHS) in configuration space. This method can yield fast-Fourier-like scaling of the computational time requirements and also provides a very compact data representation of these operators, even for plasmas with large spatial nonuniformity. As a result, the method can give significant savings compared with direct application of “delocalization kernels” [e.g., Schurtz et al., Phys. Plasmas 7, 4238 (2000)], both in terms of computational cost and memory requirements. The method is of interest for the implementation of Landau-fluid models in situations where the spatial nonuniformity, particular geometry, or boundary conditions render a Fourier implementation difficult or impossible. Systematic procedures have been developed to optimize the resulting operators for accuracy and computational cost. The four-moment Landau-fluid model of Hammett and Perkins has been implemented in the BOUT++ code using the SMHS method for LF closure. Excellent agreement has been obtained for the one-dimensional plasma density response function between driven initial-value calculations using this BOUT++ implementation and matrix eigenvalue calculations using both Fourier and SMHS non-Fourier implementations of the LF closures. The SMHS method also forms the basis for the implementation, which has been carried out in the BOUT++ code, of the parallel and toroidal drift-resonance LF closures. The method is a key enabling tool for the extension of gyro-Landau-fluid models [e.g., Beer and Hammett, Phys. Plasmas 3, 4046 (1996)] to codes that treat regions with strong profile variation, such as the tokamak edge and scrapeoff-layer.
A hydrodynamic microchip for formation of continuous cell chains
Authors: Khoshmanesh Khashayar , Zhang Wei , Tang Shi-Yang , Nasabi Mahyar , Soffe Rebecca , Tovar-Lopez Francisco J. , Rajadas Jayakumar , Mitchell Arnan
Published: May 2014

Here, we demonstrate the unique features of a hydrodynamic based microchip for creating continuous chains of model yeast cells. The system consists of a disk shaped microfluidic structure, containing narrow orifices that connect the main channel to an array of spoke channels. Negative pressure provided by a syringe pump draws fluid from the main channel through the narrow orifices. After cleaning process, a thin layer of water is left between the glass substrate and the polydimethylsiloxane microchip, enabling leakage beneath the channel walls. A mechanical clamp is used to adjust the operation of the microchip. Relaxing the clamp allows leakage of liquid beneath the walls in a controllable fashion, leading to formation of a long cell chain evenly distributed along the channel wall. The unique features of the microchip are demonstrated by creating long chains of yeast cells and model 15 μm polystyrene particles along the side wall and analysing the hydrogen peroxide induced death of patterned cells.
Optical bandgap of ultra-thin amorphous silicon films deposited on crystalline silicon by PECVD
Authors: Abdulraheem Yaser , Gordon Ivan , Bearda Twan , Meddeb Hosny , Poortmans Jozef
Published: May 2014

An optical study based on spectroscopic ellipsometry, performed on ultrathin hydrogenated amorphous silicon (a-Si:H) layers, is presented in this work. Ultrathin layers of intrinsic amorphous silicon have been deposited on n-type mono-crystalline silicon (c-Si) wafers by plasma enhanced chemical vapor deposition (PECVD). The layer thicknesses along with their optical properties –including their refractive index and optical loss- were characterized by spectroscopic ellipsometry (SE) in a wavelength range from 250 nm to 850 nm. The data was fitted to a Tauc-Lorentz optical model and the fitting parameters were extracted and used to compute the refractive index, extinction coefficient and optical bandgap. Furthermore, the a-Si:H film grown on silicon was etched at a controlled rate using a TMAH solution prepared at room temperature. The optical properties along with the Tauc-Lorentz fitting parameters were extracted from the model as the film thickness was reduced. The etch rate for ultrathin a-Si:H layers in TMAH at room temperature was found to slow down drastically as the c-Si interface is approached. From the Tauc-Lorentz parameters obtained from SE, it was found that the a-Si film exhibited properties that evolved with thickness suggesting that the deposited film is non-homogeneous across its depth. It was also found that the degree of crystallinity and optical (Tauc) bandgap increased as the layers were reduced in thickness and coming closer to the c-Si substrate interface, suggesting the presence of nano-structured clusters mixed into the amorphous phase for the region close to the crystalline silicon substrate. Further results from Atomic Force Microscopy and Transmission Electron Microscopy confirmed the presence of an interfacial transitional layer between the amorphous film and the underlying substrate showing silicon nano-crystalline enclosures that can lead to quantum confinement effects. Quantum confinement is suggested to be the cause of the observed increase in the optical bandgap of a-Si:H films close to the a-Si:H/cSi interface.
Visible magnetic circular dichroism spectroscopy of the Pr0.8Sr0.2MnO3 and Pr0.6Sr0.4MnO3 thin films
Authors: Edelman I. , Greben'kova Yu. , Sokolov A. , Molokeev M. , Aleksandrovskiy A. , Chichkov V. , Andreev N. , Mukovskii Y.
Published: May 2014

Visible magnetic circular dichroism (MCD) in Pr1-xSrxMnO3 with x = 0.2 and 0.4 was investigated for the first time. Samples for the investigation – polycrystalline films with thickness from 20 to 150 nm were prepared with the dc magnetron sputtering. MCD spectra obtained in the energy interval 1–4 eV at temperatures 100–300 K consist of several maxima with different intensities: very strong one near 3.25–3.4 eV and a broad essentially weaker band near 2 eV. An additional maximum of opposite sign arises in the samples with x = 0.4MCD spectrum at 2.33 eV. Experimental spectra were decomposed to several Gaussian components, and their amplitudes temperature dependences were analyzed. In the case of x = 0.2, all four Gaussian components are characterized by the identical temperature dependence of their amplitudes. In the case of x = 0.4, maxima observed in different spectral intervals demonstrate different temperature dependences of their amplitudes. One more unexpected phenomenon is associated with the different MCD value change in different spectral intervals when coming from x = 0.2 to x = 0.4: high-energy maximum increases more than twice while low-energy maxima intensity stays at that, practically, unchanged.
The sociophonetic orientation of the language learner
Authors: Labov William
Published: May 2014

This paper is an effort to define the phonetic target of the language learner: what are the data that the child focuses on in becoming a native speaker? A number of studies are reviewed to show that children reject the idiosyncratic features of their parents’ phonetic system if they do not match the pattern of the larger speech community:  in the acquisition of the Philadelphia and New York City dialects;  the formation of a new dialect in Milton Keynes; the spread of the low back merger in eastern New England; the reduction of the future marker in Tok Pisin. The end result is a high degree of uniformity in both the categorical and variable aspects of language, where individual variation is reduced below the level of linguistic significance.
Where and what is (t, d)?
Authors: Temple Rosalind
Published: May 2014

The variable deletion of /t,d/ in word-final clusters in English has garnered much attention from sociolinguists and, more recently, phonologists, most of whom model it as a binary variable phonological rule. This paper examines in detail some (t,d) clusters in York English and compares them with other word-final singleton and cluster consonants. In the light of the general literature on English, it explores an alternative view, that in at least one variety of British English “-t,d deletion” is in fact one of the common connected speech processes which apply at the boundaries between words. It thus underlines the importance for advances in sociophonetics of taking a step back to examine critically the basic units of analysis of variable rules.
On the Pathology of the Enthymeme: Accounting for Hidden Visual Premises in Advertising Discourse
Authors: Rossolatos George
Published: May 2014

One of the key reasons that have been put forward for justifying the superior argumentative force of visuals over verbal arguments in advertising discourse is their immediacy. The immediate resonance of visuals and their forceful appeal bear considerable resemblance to the argumentative force of enthymemes as hidden premises in informal rhetorical argumentation. In this article an attempt is made at bridging the logical and pathemic appeals of enthymemes under the aegis of what may be called the pathology of the enthymeme, while demonstrating that what has been pejoratively tagged, since Freudian psychoanalytic discourse, as “the psychopathology of everyday life” in fact constitutes the very underpinning of enthymematic structures and a system of topoi of which such structures constitute an integral part. By assuming as the point of departure of this genealogico-pathological tracing Heidegger’s opening up of the meaning of logos and as destination Heidegger’s ontological reading of everydayness, the enthymematic embeddedness of cultural topoi is depathologized, while being reinserted in its “proper” pathological dimension. The exemplification of how visual enthymemes function and may be translated as hidden premises in advertising discourse seeks to demonstrate the pathology of the enthymeme as “unquestionable” major premises that underpin visual arguments.
Converting Knights: A Semiotic Reading of Spiritual Change in Four Italian Chivalric Poems
Authors: Leone Massimo
Published: May 2014

This essay compares representations of religious conversion in four Italian chivalric poems: Luigi Pulci’s Morgante, Matteo Maria Boiardo’s Orlando innamorato, Ludovico Ariosto’s Orlando furioso, and Torquato Tasso’s Gerusalemme liberata. Semiotically read, they cast new light on the Catholic idea of the religious self in its development from the late Middle Ages throughout the early modern era. In this evolution, the Council of Trent represents a fundamental watershed.
Identification of a large protein network involved in epigenetic transmission in replicating DNA of embryonic stem cells
Authors: Aranda Sergi , Rutishauser Dorothea , Ernfors Patrik
Published: May 2014

Pluripotency of embryonic stem cells (ESCs) is maintained by transcriptional activities and chromatin modifying complexes highly organized within the chromatin. Although much effort has been focused on identifying genome-binding sites, little is known on their dynamic association with chromatin across cell divisions. Here, we used a modified version of the iPOND (isolation of proteins at nascent DNA) technology to identify a large protein network enriched at nascent DNA in ESCs. This comprehensive and unbiased proteomic characterization in ESCs reveals that, in addition to the core replication machinery, proteins relevant for pluripotency of ESCs are present at DNA replication sites. In particular, we show that the chromatin remodeller HDAC1–NuRD complex is enriched at nascent DNA. Interestingly, an acute block of HDAC1 in ESCs leads to increased acetylation of histone H3 lysine 9 at nascent DNA together with a concomitant loss of methylation. Consistently, in contrast to what has been described in tumour cell lines, these chromatin marks were found to be stable during cell cycle progression of ESCs. Our results are therefore compatible with a rapid deacetylation-coupled methylation mechanism during the replication of DNA in ESCs that may participate in the preservation of pluripotency of ESCs during replication.
Motions of the central objects in cD clusters of galaxies and transverse cooling flows
Authors: Inoue Hajime
Published: May 2014

We first study dynamical effects of dark matter sub-halos (optically observed as member galaxies) on the central object (optically observed as a cD galaxy) in a cD cluster of galaxies. The sub-halos come closest to the center in turn and cause the central object to be pulled to random directions.Thus, the central object tends to move with a velocity given from an equipartition of the kinetic energy of the central object with the averaged kinetic energy of the sub-halos. The dark matter particles in the halo around the central object, however, give the central object a drag force to suppress the motion. Under a balance between the energy input from the closest sub-halo and the output to the ambient dark matter halo, the average velocity of the central object is roughly estimated to be 107 cm s−1. We secondly investigate effects of radiative cooling on hot plasma when the central object moves relatively to the hot plasma. The current cooling flow hypothesis is based on the estimation that the radiative cooling time is sufficiently shorter than the age of the cluster of galaxies. In the present case, however, the cooling flow would be excited when the radiative cooling time is shorter than the plasma passage time across the central object. We perform such a time scale comparison in an approximate way, and find that only the plasma flowing to the central object with an impact parameter less than a critical one is trapped by the central object and falls on to the central object as the cooling flow. This transverse cooling flow scenario well explains several observational evidences which have been argued to be inconsistent with the current isotropic cooling flow hypothesis, when the relative velocity is ∼ 107 cm s−1.
A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
Authors: O’Geen Henriette , Henry Isabelle M. , Bhakta Mital S. , Meckler Joshua F. , Segal David J.
Published: May 2014

Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of their target site recognition. Most previous studies have examined predicted off-target binding sites that differ from the perfect target site by one to four mismatches, which represent only a subset of genomic regions. Here, we use ChIP-seq to examine genome-wide CRISPR binding specificity at gRNA-specific and gRNA-independent sites. For two guide RNAs targeting the murineSnurfgene promoter, we observed very high binding specificity at the intended target site while off-target binding was observed at 2- to 6-fold lower intensities. We also identified significant gRNA-independent off-target binding. Interestingly, we found that these regions are highly enriched in the PAM site, a sequence required for target site recognition by CRISPR. To determine the relationship between Cas9 binding and endonuclease activity, we used targeted sequence capture as a high-throughput approach to survey a large number of the potential off-target sites identified by ChIP-seq or computational prediction. A high frequency of indels was observed at both target sites and one off-target site, while no cleavage activity could be detected at other ChIP-bound regions. Our data is consistent with recent finding that most interactions between the CRISPR nuclease complex and genomic PAM sites are transient and do not lead to DNA cleavage. The interactions are stabilized by gRNAs with good matches to the target sequence adjacent to the PAM site, resulting in target cleavage activity.
Ten years of probabilistic estimates of biocrystal solvent content: new insightsvianonparametric kernel density estimate
Authors: Weichenberger Christian X. , Rupp Bernhard
Published: May 2014

The probabilistic estimate of the solvent content (Matthews probability) was first introduced in 2003. Given that the Matthews probability is based on prior information, revisiting the empirical foundation of this widely used solvent-content estimate is appropriate. The parameter set for the original Matthews probability distribution function employed inMATTPROBhas been updated after ten years of rapid PDB growth. A new nonparametric kernel density estimator has been implemented to calculate the Matthews probabilities directly from empirical solvent-content data, thus avoiding the need to revise the multiple parameters of the original binned empirical fit function. The influence and dependency of other possible parameters determining the solvent content of protein crystals have been examined. Detailed analysis showed that resolution is the primary and dominating model parameter correlated with solvent content. Modifications of protein specific density for low molecular weight have no practical effect, and there is no correlation with oligomerization state. A weak, and in practice irrelevant, dependency on symmetry and molecular weight is present, but cannot be satisfactorily explained by simple linear or categorical models. The Bayesian argument that the observed resolution represents only a lower limit for the true diffraction potential of the crystal is maintained. The new kernel density estimator is implemented as the primary option in theMATTPROBweb application at http://www.ruppweb.org/mattprob/.
In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27
Authors: Acosta-Reyes Francisco J. , Dardonville Christophe , de Koning Harry P. , Natto Manal , Subirana Juan A. , Campos J. Lourdes
Published: May 2014

The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasitePlasmodium falciparumand the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact with the minor groove of DNA, some of which are used in medical practice. Previous studies have been performed almost exclusively with the AATT sequence. New features should be uncovered through the study of different DNA sequences. In this paper, the crystal structure of the complex of the DNA duplex d(AAAATTTT)2with the dicationic drug 4,4′-bis(imidazolinylamino)diphenylamine (CD27) is presented. The drug binds to the minor groove of DNA as expected, but it shows two new features that have not previously been described: (i) the drugs protrude from the DNA and interact with neighbouring molecules, so that they may act as cross-linking agents, and (ii) the drugs completely cover the whole minor groove of DNA and displace bound water. Thus, they may prevent the access to DNA of proteins such as AT-hook proteins. These features are also expected for other minor-groove binding drugs when associated with all-AT DNA. These findings allow a better understanding of this family of compounds and will help in the development of new, more effective drugs. New data on the biological interaction of CD27 with the causative agent of trichomoniasis,Trichomonas vaginalis, are also reported.
6-(Hex-5-enyloxy)naphthalene-2-carboxylic acid
Authors: Rahman Md. Lutfor , Srinivasa H. T. , Mohd. Yusoff Mashitah , Kwong Huey Chong , Quah Ching Kheng
Published: May 2014

The asymmetric unit of the title compound, C17H18O3, comprises three independent molecules with similar geometries. In each molecule, the carbonyl group is twisted away from the napthalene ring system, making dihedral angles of 1.0 (2), 1.05 (19)° and 1.5 (2)°. The butene group in all three molecules are disordered over two sets of sites, with a refined occupancy ratio of 0.664 (6):0.336 (6). In the crystal, molecules are oriented with respect to their carbonyl groups, forming head-to-head dimersviaO—H...O hydrogen bonds. Adjacent dimers are further interconnected by C—H...O hydrogen bonds into chains along thea-axis direction. The crystal structure is further stabilized by weak C—H...π interactions.
7,7-Dimethyl-2-methylamino-4-(4-methylphenyl)-3-nitro-7,8-dihydro-4H-chromen-5(6H)-one
Authors: Inglebert S. Antony , Kamalraja Jayabal , Sethusankar K. , Perumal Paramasivam T.
Published: May 2014

In the title compound, C19H22N2O4, the six-membered cyclohexenone ring of the chromene unit adopts an envelope conformation, with the dimethyl-substituted C atom as the flap, while the pyran ring has a boat conformation. These two mean planes are inclined to one another by 6.65 (13)°·The benzene ring is normal to the 4H-chromene moiety mean plane, making a dihedral angle of 89.18 (5)°. The methylamine and nitro groups are slightly twisted from the chromene moiety mean plane, with torsion angles C—N—C—O = 1.70 (18) and O—N—C—C = 0.15 (18)°. The molecular structure is characterized by an intramolecular N—H...O hydrogen bond, which generates anS(6) ring motif. In the crystal, molecules are linkedviapairs of weak C—H...O hydrogen bonds, forming inversion dimers. These dimers are connected by further C—H...O hydrogen bonds, forming sheets lying parallel to (10-1).
4-(Furan-2-carbonyl)piperazin-1-ium 3,5-dinitrobenzoate
Authors: Kavitha Channappa N. , Kaur Manpreet , Jasinski Jerry P. , Butcher Ray J. , Yathirajan H.S.
Published: May 2014

In the cation of the title salt, C9H13N2O2+·C7H3N2O6−, the piperazine ring adopts a slightly distorted chair conformation. Twofold rotational disorder is exhibited by the furan ring in a 0.430 (4):0.570 (4) ratio. In the crystal, N—H...O hydrogen bonds link the ions into chains along [010]. Additional weak C—H...O interactions are observed, leading to a supramolecular layer parallel to (011).
3-[3-(2-Fluorobenzoyl)thioureido]propionic acid
Authors: Ngah Nurziana , Mohamed Nor Azanita , Yamin Bohari M. , Mohd Zaki Hamizah
Published: May 2014

In the title compound, C10H11FN3O3S, the 2-fluorobenzoyl and proponic acid groups maintain atrans–cisconformation with respect to the thiono C=S bond across their C—N bonds. The propionic acid group adopts ananticonformation about the C—C bond, with an N—C—C—C torsion angle of 173.8 (2)°. The amino groups are involved in the formation of intramolecular N—H...O and N—H...F hydrogen bonds. In the crystal, pairs of O—H...O hydrogen bonds link molecules into inversion dimers.
3-Bromomethyl-4-methoxy-2-(2-nitrophenyl)-9-phenylsulfonyl-9H-carbazole
Authors: Gopinath S. , Sethusankar K. , Saravanan Velu , Mohanakrishnan Arasambattu K.
Published: May 2014

In the title compound, C26H19BrN2O5S, the carbazole tricycle is essentially planar, with the largest deviation being 0.126 (3) Å for the C atom connected to the nitrophenyl group. The carbazole moiety is almost orthogonal to the benzene rings of the adjacent phenylsulfonyl and nitrophenyl groups, making dihedral angles of 85.43 (15) and 88.62 (12)°, respectively. The molecular conformation is stabilized by two C—H...O hydrogen bonds involving the sulfone group, which form similar six-membered rings. In the crystal, molecules symmetrically related by a glide plane are linked inC(6) chains parallel to [001] by C—H...O hydrogen bonds formed with the participation of the nitro group. The chains are reinforced by additional C—H...π interactions.
catena-Poly[[silver(I)-μ-N-[(pyridin-2-yl)methyl]pyridine-3-amine-κ2N:N′] hexafluoridophosphate]
Authors: Moon Suk-Hee , Park Ki-Min
Published: May 2014

In the title polymeric complex, {[Ag(C11H11N3)]PF6}n, the AgIion is two-coordinated in a nearly linear coordination geometry [N—Ag—N = 175.98 (9)°] by two pyridine N atoms from two symmetry-relatedN-[(pyridine-2-yl)methyl]pyridine-3-amine ligands. Each AgIion is bridged by the ligands, forming a helical chain propagating along theb-axis direction. The right- and left-handed helical chains are alternately arrangedviaAg...Ag [3.2639 (5) Å] and π–π stacking interactions [centroid–centroid distance = 3.523 (1) Å], resulting in the formation of a two-dimensional supramolecular network extending parallel to (101). Weak Ag...F interactions [longest Ag...F interaction = 3.153 (2) Å], as well as N—H...F and C—H...F hydrogen-bonding interactions, occur between the helical chains and the anions.
2,5-Dibromo-3,6-dimethoxycyclohexa-2,5-diene-1,4-dione
Authors: Orhan Ersin , Garci Amine , Therrien Bruno
Published: May 2014

In the structure of the title compound, C8H6Br2O4, the complete molecule is generated by the application of a centre of inversion. The molecule is planar (r.m.s. deviation for all non-H atoms but methyl C = 0.0358 Å), with only the methyl groups being deviated from the plane [by ±0.321 (4) Å]. In the crystal packing, Br...O(methoxy) halogen bonds [3.2407 (19) Å] connect molecules into supramolecular layers parallel to (101).
Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study
Authors: Rajalakshmi Gnanasekaran , Hathwar Venkatesha R. , Kumaradhas Poomani
Published: May 2014

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max= 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods usingSHELXS97 and refined bySHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in theXDsoftware. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained fromCRYSTAL09at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.
Structural simplicity and complexity of compressed calcium: electronic origin
Authors: Degtyareva Valentina F.
Published: May 2014

A simple cubic structure with one atom in the unit cell found in compressed calcium is counterintuitive to the traditional view of a tendency towards densely packed structures with an increase in pressure. To understand this unusual transformation it is necessary to assume electron transfer from the outer core band to the valence band, and an increase of valence electron number for calcium from 2 to ∼ 3.5. This assumption is supported by the Fermi sphere–Brillouin zone interaction model that increases under compression. The recently found structure of Ca-VII with a tetragonal cell containing 32 atoms (tI32) is similar to that in the intermetallic compound In5Bi3with 3.75 valence electrons per atom. Structural relations are analyzed in terms of electronic structure resemblance. Correlations of structure and physical properties of Ca are discussed.
Temperature- and pressure-dependent structural study of {Fe(pmd)2[Ag(CN)2]2}nspin-crossover compound by neutron Laue diffraction
Authors: Rodríguez-Velamazán José Alberto , Cañadillas-Delgado Laura , Castro Miguel , McIntyre Garry J. , Real José Antonio
Published: May 2014

The effect of pressure (up to 0.17 GPa) on the spin-crossover compound {Fe(pmd)2[Ag(CN)2]2}n[orthorhombic isomer (II), pmd = pyrimidine] has been investigated by temperature- and pressure-dependent neutron Laue diffraction and magnetometry. The cooperative high-spin ↔ low-spin transition, centred atca180 K at ambient pressure, is shifted to higher temperatures as pressure is applied, showing a moderate sensitivity of the compound to pressure, since the spin transition is displaced byca140 K GPa−1. The space-group symmetry (orthorhombicPccn) remains unchanged over the pressure–temperature (P–T) range studied. The main structural consequence of the high-spin to low-spin transition is the contraction of the distorted octahedral [FeN6] chromophores, being more marked in the axial positions (occupied by the pmd units), than in the equatorial positions (occupied by four [Ag(CN)2]−bridging ligands).
Universal `bond valenceversusbond length' correlation curve for manganese–oxygen bonds
Authors: Sidey Vasyl
Published: May 2014

The oxidation-state independent `bond valence (s)versusbond length (r)' correlation curve for manganese–oxygen bonds has been closely approximated using the modified two-parameter Trömels=f(r) function [Trömel (1983).Acta Cryst.B39, 664–669],s= [(r0−l)/(r−l)]2, wherer0= 1.763 (2) Å andl= 1.148 (9) Å. Ther0andlrefinable parameters of the above function can be regarded as the alternative bond-valence parameters intended for use in the modern bond-valence model [Brown (2009).Chem. Rev.109, 6858–6919] in cases where the traditional bond-valence parameters (r0;n) and (r0;b) fail.