bluuebunny/crossref_metadata_2025 huggingface dataset:
Image irradiance harmonics: a phenomenological model of image irradiance of arbitrary surface reflectance
Authors: Elhabian Shireen Y. , Farag Aly A.
Published: February 2014

Phenomenological appearance models capture surface appearance through mathematical modelling of the reflection process. Theoretically, the space of all possible images of a fixed‐pose object under all possible illumination conditions is infinite dimensional. Nonetheless, because of their low‐frequency nature, irradiance signals can be represented using low‐order basis functions. Discounting subsurface scattering and surface emittance, this work seeks to address the question; how to compactly and accurately represent image irradiance under unknown general illumination, given that a surface point sees its surrounding world through the local upper hemisphere oriented by the surface normal at this point. In this study, we formulate the image formation process of isotropic surface reflectance under arbitrary distant illumination in the frequency space while addressing the physical compliance of hemispherical basis for representing surface reflectance, for example, Helmholtz reciprocity and isotropy. The term ‘irradiance harmonics’ is also defined which enables decoupling illumination and reflectance from the underlying geometry and pose. We provide a closed form of the energy content being maintained by different reflectance modes of the proposed irradiance harmonics. Since specular materials tend to require more basis functions when compared with diffuse ones, the presented harmonics captures same cumulative energy content, by providing larger number of orthogonal irradiance basis, at lower illumination orders when compared to similar basis in literature.
Artificial neural network model of photovoltaic generator for power flow analysis in PSS®SINCAL
Authors: Xu Travis , Venkatesh Bala , Opathella Chandrabhanu , Singh Birendra N.
Published: February 2014

Output of a three‐phase photovoltaic generator (PVG) is a function of sunlight irradiance, temperature, and three‐phase terminal voltage phasors. Three‐phase PVGs are largely connected to rural distribution systems feeders that are predominantly unbalanced. Models of PVGs that are only a function of sunlight irradiance and temperature disregarding unbalanced three‐phase terminal voltages phasors are simple to use with three‐phase power flow analysis but yield inaccurate solutions. Detailed three‐phase PVG models are complex and non‐linear, hence unsuitable for power flow analysis applications. This study proposes an artificial neural network (ANN) model to represent a PVG comprising photovoltaic panels, a boost chopper and a three‐phase inverter. Main advantages of the ANN model are that it can be readily used to model a PVG of any size and type, mathematical simplicity, high accuracy with unbalanced systems and computational speed. The model was tested with the unbalanced distribution system feeder from a Canadian utility. The results show that the ANN model of a PVG is computationally fast and more accurate than simple model that ignores unbalanced three‐phase terminal voltage phasors. In addition, simplicity of the proposed ANN model of PVG allows easy integration into commercial software packages such as PSS® SINCAL as reported in this study.
Fault section estimation in power distribution network using impedance‐based fault distance calculation and frequency spectrum analysis
Authors: Dashti Rahman , Sadeh Javad
Published: February 2014

In this study, a practical method is proposed for determining the distance and the section of fault in power distribution system (PDS). In the suggested method, at first the possible fault points are determined using a novel impedance‐based fault location method. Since the number of these points may be more than one, thus two methods are proposed for determining the real location of fault. In the first method, the measured and recorded samples of voltages at the beginning of feeder for actual fault are compared with the stored samples of voltages which are obtained from simulating of fault at the possible fault points. The one with highest matching is the real location of fault. In the second method, frequency spectrum (FS) of voltage is defined as a suitable criterion for this purpose. Therefore the real fault point is determined by comparing and matching the FS of voltages obtained from the simulated faults and the recorded voltage for actual fault. The performance of the proposed method is evaluated in a real feeder in distribution network of Iran considering different types of faults, fault resistances, fault inception angles, real instrument transformer models and X/R ratio changes of upstream PDS network. The obtained results show that the performance of the proposed method is quite satisfactory and its accuracy is very high.
Monovision‐based vehicle detection, distance and relative speed measurement in urban traffic
Authors: Arenado Manuel Ibarra , Oria Juan Maria Pérez , Torre‐Ferrero Carlos , Rentería Luciano Alonso
Published: February 2014

This study presents a monovision‐based system for on‐road vehicle detection and computation of distance and relative speed in urban traffic. Many works have dealt with monovision vehicle detection, but only a few of them provide the distance to the vehicle which is essential for the control of an intelligent transportation system. The system proposed integrates a single camera reducing the monetary cost of stereovision and RADAR‐based technologies. The algorithm is divided in three major stages. For vehicle detection, the authors use a combination of two features: the shadow underneath the vehicle and horizontal edges. They propose a new method for shadow thresholding based on the grey‐scale histogram assessment of a region of interest on the road. In the second and third stages, the vehicle hypothesis verification and the distance are obtained by means of its number plate whose dimensions and shape are standardised in each country. The analysis of consecutive frames is employed to calculate the relative speed of the vehicle detected. Experimental results showed excellent performance in both vehicle and number plate detections and in the distance measurement, in terms of accuracy and robustness in complex traffic scenarios and under different lighting conditions.
Robust technique based on transition matrix method to electromagnetic characterisation of anisotropic material
Authors: Zarifi Davoud , Soleimani Mohammad , Abdolali Ali , Oraizi Homayoon
Published: February 2014

This study presents a parameter retrieval technique based on the state space approach for the electromagnetic characterisation of biaxial anisotropic structures. First, the formulation of a 4 × 4 transition matrix method for the analysis of forward scattering problems is reviewed; then a procedure for the extraction of the constitutive tensor parameters of a biaxial anisotropic medium from the knowledge of reflection and transmission coefficients is implemented. In the proposed retrieval method, scattering parameters are employed for a plane wave incident normally and obliquely on a biaxial anisotropic slab. This characterisation algorithm is based on the state transition matrix and its properties in the biaxial anisotropic layers are presented as two theorems. In this method, it is not necessary to solve directly the wave equation in complex media and then apply the boundary conditions. To demonstrate the validity of the proposed method, the constitutive parameters of two non‐dispersive and dispersive biaxial anisotropic slabs at microwave frequencies are retrieved. From the numerical results, one can find out that when the scattering parameters are combined with the properties of a state transition matrix, a robust technique is provided for the parameter retrieval of the anisotropic structures.
Study of gene transfection enhancement and parameters optimisation using electroporation microchip
Authors: Chung Yung‐Chiang , Liao Wei‐Jie , Huang Yu‐Tzu , Wu Cheng‐Yuan
Published: February 2014

A design for improving gene transfection efficiency, which provides simple fabrication, low voltage and power consumptions, and easy implementation is developed; this design entails combining high and low electric fields, adjusting the voltage, using different numbers of pulses with varying durations, and different types of buffers with differing conductivities. The human embryonic kidney 293 (293T) cells were used. It was shown that a combination of two units of high electric field (1600 V/cm) for 0.6 ms and three units of low electric field (800 V/cm) for 1.2 ms is the optimum combination. This combination yielded a survival rate greater than 70% and a transfection rate of approximately 45%. The transfection rate of this combination was 80–100% greater than that obtained using two pulses, and the transfection rate obtained using two pulses was 40–50% greater than that obtained using single pulses. However, the survival rate decreases when the pulse duration is considerably long, even for low electric fields; therefore the number of pulses and their durations should be limited. The hypoosmolar buffer yielded the largest transfection rate. It was shown that the conductivity of the buffer solution is an important parameter, with the appropriate value ranging within 1.0–3.6 mS/cm. The transfection rate of the 293T cells using a cytoporation buffer could be enhanced by adding potassium ions in concentration lower than 2 μg/ml.
Formation and characterisation of nanoporous TiO2 layers on microroughened titanium surfaces by electrochemical anodisation
Authors: Dikici Tuncay , Guzelaydin Abdurrahman Halis , Toparli Mustafa
Published: February 2014

Nanoporous titanium dioxide (TiO2) layers were successfully formed by an electrochemical anodisation method on microroughened titanium (Ti) surfaces in ﬂuoride containing aqueous electrolyte. Microroughened Ti surfaces were produced by sandblasting with Al2O3 particles of 50 μm in diameter and acid‐etching in a blend of HCl/H2SO4 solution. The surface morphology, topography and chemical composition of the specimens were analysed by scanning electron microscopy, atomic force microscopy and X‐ray photoelectron spectroscopy. The surface roughness and the wettability of treated Ti surfaces were measured using profilometry and a contact angle measurement system, respectively. With anodising of sandblasted‐/acid etched surfaces, micrometre‐ and nanometre‐scale textures on titanium specimens were created. Results showed that these developed nanoporous‐microroughened surfaces exhibited lower contact angle values than the other treated Ti surfaces. The sandblasted/acid‐etched/anodised Ti specimen had a surface morphology with distinctively formed hills and valleys and higher surface roughness than the other anodised specimens. This study indicated that nanoporous TiO2 structures fabricated on microroughened Ti can be an effective way to modify the titanium surfaces for the future development of implant applications.
Instability of the Vertebrae Remains following Balloon Kyphoplasty
Authors: Tarukado Kiyoshi , Tono Osamu , Ikuta Ko , Harimaya Katsumi , Matsumoto Yoshihiro , Okada Seiji , Hayashida Mitsumasa , Iwamoto Yukihide , Doi Toshio
Published: February 2014

Study Design

Retrospective cohort study.

Objectives

The mechanism underlying the pain relief observed following balloon kyphoplasty (BKP) to vertebral compression fractures is reported to involve stabilization of the fractured vertebrae. However, whether fixation of the vertebrae was achieved immediately after BKP has not been investigated. The purpose of this study was to assess fixation of the vertebrae immediately after BKP and whether the instability was related to visual analog scale (VAS) scores.

Methods

Thirty-eight patients with vertebrae that were evaluated on lateral roentgenkymography within 1 week after BKP were recruited. Instability was defined as a cleft observed between the cement and end plate of the vertebra in the supine position that disappeared in the sitting position, and the posterior wall height of the vertebra was reduced in the sitting position.

Results

Instability of the vertebrae immediately after BKP was observed in 17 cases. VAS scores improved in all cases, and no significant differences were observed with or without instability.

Conclusions

The mechanism of rapid pain relief following BKP was not strong fixation but some degree of stabilization or other factors. We suggest that more research is needed about the mechanism of pain relief following BKP in the future.
Velocity profiles in strongly turbulent Taylor-Couette flow
Authors: Grossmann Siegfried , Lohse Detlef , Sun Chao
Published: February 2014

We derive the velocity profiles in strongly turbulent Taylor-Couette flow for the general case of independently rotating cylinders. The theory is based on the Navier-Stokes equations in the appropriate (cylinder) geometry. In particular, we derive the axial and the angular velocity profiles as functions of distance from the cylinder walls and find that both follow a logarithmic profile, with downwards-bending curvature corrections, which are more pronounced for the angular velocity profile as compared to the axial velocity profile, and which strongly increase with decreasing ratio η between inner and outer cylinder radius. In contrast, the azimuthal velocity does not follow a log-law. We then compare the angular and azimuthal velocity profiles with the recently measured profiles in the ultimate state of (very) large Taylor numbers. Though the qualitative trends are the same – down-bending for large wall distances and the (properly shifted and non-dimensionalized) angular velocity profile ω+(r) being closer to a log-law than the (properly shifted and non-dimensionalized) azimuthal velocity profile \documentclass[12pt]{minimal}\begin{document}$u^+_{\varphi }(r)$\end{document}uφ+(r) – quantitativedeviations are found for large wall distances. We attribute these differences to the nonlinear dependence of the turbulent ω-diffusivity on the wall distance and partly also to the Taylor rolls and the axial dependence of the profiles, neither of which are considered in the theoretical approach. Assuming that the first origin is the most relevant one, we calculate from the experimental profile data how the turbulent ω-diffusivity depends on the wall distance and find a linear behavior for small wall distances as assumed and a saturation behavior for very large distances, reflecting the finite gap width: But in between the ω-diffusivity increases stronger than linearly, reflecting that more eddies can contribute to the turbulent transport (or they contribute more efficiently) as compared to the plane wall case.
A bridge-functional-based classical mapping method for predicting the correlation functions of uniform electron gases at finite temperature
Authors: Liu Yu , Wu Jianzhong
Published: February 2014

Efficient and accurate prediction of the correlation functions of uniform electron gases is of great importance for both practical and theoretical applications. This paper presents a bridge-functional-based classical mapping method for calculating the correlation functions of uniform spin-unpolarized electron gases at finite temperature. The bridge functional is formulated by following Rosenfeld's universality ansatz in combination with the modified fundamental measure theory. The theoretical predictions are in good agreement with recent quantum Monte Carlo results but with negligible computational cost, and the accuracy is better than a previous attempt based on the hypernetted-chain approximation. We find that the classical mapping method is most accurate if the effective mass of electrons increases as the density falls.
Decay of the supersonic turbulent wakes from micro-ramps
Authors: Sun Z. , Schrijer F. F. J. , Scarano F. , van Oudheusden B. W.
Published: February 2014

The wakes resulting from micro-ramps immersed in a supersonic turbulent boundary layer at Ma = 2.0 are investigated by means of particle image velocimetry. Two micro-ramps are investigated with height of 60% and 80% of the undisturbed boundary layer, respectively. The measurement domain is placed at the symmetry plane of the ramp and encompasses the range from 10 to 32 ramp heights downstream of the ramp. The decay of the flow field properties is evaluated in terms of time-averaged and root-mean-square (RMS) statistics. In the time-averaged flow field, the recovery from the imparted momentum deficit and the decay of upwash motion are analyzed. The RMS fluctuations of the velocity components exhibit strong anisotropy at the most upstream location and develop into a more isotropic regime downstream. The self-similarity properties of velocity components and fluctuation components along wall-normal direction are followed. The investigation of the unsteady large scale motion is carried out by means of snapshot analysis and by a statistical approach based on the spatial auto-correlation function. The Kelvin-Helmholtz (K-H) instability at the upper shear layer is observed to develop further with the onset of vortex pairing. The average distance between vortices is statistically estimated using the spatial auto-correlation. A marked transition with the wavelength increase is observed across the pairing regime. The K-H instability, initially observed only at the upper shear layer also begins to appear in the lower shear layer as soon as the wake is elevated sufficiently off the wall. The auto-correlation statistics confirm the coherence of counter-rotating vortices from the upper and lower sides, indicating the formation of vortex rings downstream of the pairing region.
Origami-enabled deformable silicon solar cells
Authors: Tang Rui , Huang Hai , Tu Hongen , Liang Hanshuang , Liang Mengbing , Song Zeming , Xu Yong , Jiang Hanqing , Yu Hongyu
Published: February 2014

Deformable electronics have found various applications and elastomeric materials have been widely used to reach flexibility and stretchability. In this Letter, we report an alternative approach to enable deformability through origami. In this approach, the deformability is achieved through folding and unfolding at the creases while the functional devices do not experience strain. We have demonstrated an example of origami-enabled silicon solar cells and showed that this solar cell can reach up to 644% areal compactness while maintaining reasonable good performance upon cyclic folding/unfolding. This approach opens an alternative direction of producing flexible, stretchable, and deformable electronics.
Extension of the quantum-kinetic model to lunar and Mars return physics
Authors: Liechty D. S. , Lewis M. J.
Published: February 2014

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high-mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. A recently introduced molecular-level chemistry model, the quantum-kinetic, or Q-K, model that predicts reaction rates for gases in thermal equilibrium and non-equilibrium using only kinetic theory and fundamental molecular properties, is extended in the current work to include electronic energy level transitions and reactions involving charged particles. Like the Q-K procedures for neutral species chemical reactions, these new models are phenomenological procedures that aim to reproduce the reaction/transition rates but do not necessarily capture the exact physics. These engineering models are necessarily efficient due to the requirement to compute billions of simulated collisions in direct simulation Monte Carlo (DSMC) simulations. The new models are shown to generally agree within the spread of reported transition and reaction rates from the literature for near equilibrium conditions.
Polariton lasing in a ZnO microwire above 450 K
Authors: Xu Dan , Xie Wei , Liu Wenhui , Wang Jian , Zhang Long , Wang Yinglei , Zhang Saifeng , Sun Liaoxin , Shen Xuechu , Chen Zhanghai
Published: February 2014

Exciton-polariton lasing in a one-dimensional ZnO microcavity is demonstrated at high temperature of 455 K. The massive occupation of the polariton ground state above a distinct pump power threshold is clearly demonstrated by using the angular resolved spectroscopy under non-resonant excitation. The temperature dependence of the polariton lasing threshold is well interpreted by two competing mechanisms, i.e., the thermodynamic and kinetic mechanisms. Michelson interference measurements are performed to investigate the temporal and spatial coherence of polariton laser, with the coherence time and coherence length being τc∼0.97 ps and rc∼0.72μm at 440 K and 400 K, respectively.
Distribution of critical current density for magnetic domain wall motion
Authors: Fukami S. , Yamanouchi M. , Nakatani Y. , Kim K.-J. , Koyama T. , Chiba D. , Ikeda S. , Kasai N. , Ono T. , Ohno H.
Published: February 2014

The bit-to-bit distribution of a critical current density for magnetic domain wall (DW) motion is studied using Co/Ni wires with various wire widths (ws). The distribution inherently decreases with the w, and the ratio of standard deviation to average is 9.8% for wires with w = 40 nm. It is found that a self-distribution within one device, which is evaluated through repeated measurement, is a dominant factor in the bit-to-bit distribution. Micromagnetic simulation reveals that the distribution originates from DW configuration, which varies with device size.
Characteristics of the viscous superlayer in shear free turbulence and in planar turbulent jets
Authors: Taveira Rodrigo R. , da Silva Carlos B.
Published: February 2014

Direct numerical simulations of a planar jet and of shear free turbulence at Reλ = 115–140 using very fine resolutions allow the first direct identification and characterisation of the viscous superlayer (VSL) that exists at the edges of mixing layers, wakes, jets, and boundary layers, adjacent to the turbulent/non-turbulent interface. For both flows the VSL is continuous with higher local thicknesses forming near the larger intense vorticity structures. The mean thickness of the VSL is of the order of the Kolmogorov micro-scale and agrees well with an estimate based on the Burgers vortex model.
Solid phase microextraction speciation analysis of triclosan in aqueous media containing sorbing nanoparticles
Authors: Zielińska Katarzyna
Published: February 2014

Environmental context Speciation analysis of organic compounds in aquatic media is often performed using solid phase microextraction with the assumption that only the free organic form is accumulated. We show that in the presence of silica nanoparticles, this interpretation is confounded by partitioning of nanoparticulate-bound compounds between water and the solid phase, as well as their aggregation at solid–bulk medium interfaces. Equilibrium measurement of the target analyte is feasible if the solid phase is protected by a suitable membrane. Abstract Solid phase microextraction (SPME) is applied in the speciation analysis of the hydrophobic compound triclosan in an aqueous medium containing sorbing SiO2 nanoparticles (NPs). It is found that these NPs, as well as their complexes with triclosan, partition between the bulk medium and the solid phase poly(dimethylsiloxane) (PDMS). Furthermore, they appear to aggregate at the PDMS–water interface. The total triclosan concentration in the solid phase thus includes both the free and the NP-bound forms. Proper computation of the analyte concentration in the sample medium requires (i) consideration of the speciation of triclosan inside the solid phase and (ii) elimination of the effects of aggregation of NP complexes at the solid phase–bulk medium interface. Possible solutions include application of a protective membrane with pore size smaller than the NP diameter. This allows measurement of the free triclosan concentration, albeit at the cost of longer accumulation times and loss of kinetic information on the triclosan–NP complex.
Physiological, proteomic and transcriptional responses of wheat to combination of drought or waterlogging with late spring low temperature
Authors: Li Xiangnan , Cai Jian , Liu Fulai , Dai Tingbo , Cao Weixing , Jiang Dong
Published: February 2014

Spring low temperature events affect winter wheat (Triticum aestivum L.) during late vegetative or reproductive development, exposing plants to a subzero low temperature stress when winter hardening is lost. The increased climatic variability results in wheat being exposed to more frequent adverse impacts of combined low temperature and water stress, including drought and waterlogging. The responses of potted wheat plants cultivated in climatic chambers to these environmental perturbations were investigated at physiological, proteomic and transcriptional levels. At the physiological level, the depressed carbon (C) assimilation induced by the combined stresses was due mainly to stomatal closure and damage of photosynthetic electron transport. Biochemically, the adaptive effects of early moderate drought or waterlogging stress were associated with the activation of antioxidant enzyme system in chloroplasts and mitochondria of leaf under low temperature. Further proteomic analysis revealed that the oxidative stress defence, C metabolism and photosynthesis related proteins were modulated by the combined low temperature and water stress. Collectively, the results indicate that impairment of photosynthesis and C metabolism was responsible for the grain yield loss in winter wheat under low temperature in combination with severe drought or waterlogging stress. In addition, prior mild drought or waterlogging contributed to the homeostasis of oxidative metabolism and relatively better photosynthesis, and hence to less grain yield loss under later spring low temperature stress.
Selection of pre- versus postpubertal pig oocytes for parthenogenetic activation and somatic cell nuclear transfer
Authors: Pedersen H. S. , Liu Y. , Li R. , Purup S. , Løvendahl P. , Holm P. , Hyttel P. , Callesen H.
Published: February 2014

Pig oocytes have been used increasingly for in vitro production techniques in recent years. The slaughterhouse-derived oocytes that are often used are mostly of prepubertal origin. The aims of the present study were to compare the developmental competence between pre- and postpubertal pig oocytes, and to develop a simple and practical method for the selection of prepubertal pig oocytes for parthenogenetic activation (PA) and somatic cell nuclear transfer (SCNT) based on oocyte morphology after IVM and oocyte inside zona pellucida (ZP) diameter (‘small’ ≤110 µm; ‘medium’ >110 µm; ‘large’ ≥120 µm). Meiotic competence and blastocyst rates after PA and SCNT of prepubertal oocytes increased with oocyte size, with the large prepubertal oocytes reaching a level similar to postpubertal oocytes after SCNT. Blastocyst cell number was not related to oocyte inside ZP diameter and oocyte donor to the same extent as blastocyst rate. Very low blastocyst rates were obtained after PA of morphologically bad pre- and postpubertal oocytes. In conclusion, measurement of inside ZP diameter combined with morphological selection is useful to remove incompetent oocytes. Further studies are needed to clarify the relative importance of cytoplasmic volume and stage in oocyte growth phase.
How fragmentation and corridors affect wind dynamics and seed dispersal in open habitats
Authors: Damschen Ellen I. , Baker Dirk V. , Bohrer Gil , Nathan Ran , Orrock John L. , Turner Jay R. , Brudvig Lars A. , Haddad Nick M. , Levey Douglas J. , Tewksbury Joshua J.
Published: February 2014

Significance

Understanding how widespread human-induced global changes are affecting the movement and dispersal of organisms is critical for maintaining species diversity and making sound land management decisions. In contrast with animal-dispersed species, little is known about how wind-dispersed species are affected by conservation strategies such as corridors. We use a combination of mechanistic models and field data to show that habitat corridors alter wind dynamics in a way that promotes seed dispersal and appears to increase plant diversity. Wind direction also interacts with landscape orientation to determine when corridors can provide connectivity.
Designer receptor manipulations reveal a role of the locus coeruleus noradrenergic system in isoflurane general anesthesia
Authors: Vazey Elena M. , Aston-Jones Gary
Published: February 2014

Significance

Thousands of people each day receive general anesthesia. Recovery from the anesthetic state is a passive process that can be variable and unpredictable. Identifying neural systems involved in recovery of consciousness after general anesthesia is fundamental to optimizing anesthetic safety and our knowledge of anesthetic action. We examined how norepinephrine from the nucleus locus coeruleus (LC) affects general anesthesia, and found that blocking the action of norepinephrine, particularly in the CNS, delayed recovery from general anesthesia. Using genetic tools to selectively activate only LC neurons, we found that LC activation was sufficient to alter EEG measurements of anesthetic depth and accelerate recovery of consciousness. Our data show that LC activity can alter the anesthetic state, and that noradrenergic medications may affect clinical responses to anesthetic agents.
Media-ted political oratory following terrorist events
Authors: McKenna Bernard , Waddell Neal
Published: February 2014

Using a computer-assisted content analysis, this study analyzes a 32,000 word corpus drawn from mediated political statements made in response to the July 2005 London bombing. This grounded research led to a focus on the deontic nature of these statements, and also revealed a relative absence of condoling. Although condemnatory, statements did not specifically attribute the ‘evil’ to particular people. Particularly mindful of Widdowson’s (2004) distinction between analysis (text) and interpretation (discourse), the paper first identifies the textual features, but then “hermeneutically” interprets their meaning within a wider context of international political discourse. The paper concludes that the statements performed a positive epideictic purpose, although it tended to occlude the compassionate element of public grieving.
Caveolae regulate the nanoscale organization of the plasma membrane to remotely control Ras signaling
Authors: Ariotti Nicholas , Fernández-Rojo Manuel A. , Zhou Yong , Hill Michelle M. , Rodkey Travis L. , Inder Kerry L. , Tanner Lukas B. , Wenk Markus R. , Hancock John F. , Parton Robert G.
Published: February 2014

The molecular mechanisms whereby caveolae exert control over cellular signaling have to date remained elusive. We have therefore explored the role caveolae play in modulating Ras signaling. Lipidomic and gene array analyses revealed that caveolin-1 (CAV1) deficiency results in altered cellular lipid composition, and plasma membrane (PM) phosphatidylserine distribution. These changes correlated with increased K-Ras expression and extensive isoform-specific perturbation of Ras spatial organization: in CAV1-deficient cells K-RasG12V nanoclustering and MAPK activation were enhanced, whereas GTP-dependent lateral segregation of H-Ras was abolished resulting in compromised signal output from H-RasG12V nanoclusters. These changes in Ras nanoclustering were phenocopied by the down-regulation of Cavin1, another crucial caveolar structural component, and by acute loss of caveolae in response to increased osmotic pressure. Thus, we postulate that caveolae remotely regulate Ras nanoclustering and signal transduction by controlling PM organization. Similarly, caveolae transduce mechanical stress into PM lipid alterations that, in turn, modulate Ras PM organization.
Commanding Legality
Authors: Kawar Leila
Published: February 2014

The emergence of constitutional review in France has attracted substantial attention from scholars of public law. Yet little has been written about the political implications of the expansion of rights-based review on the part of France’s highest administrative jurisdiction, the Conseil d’Etat. The argument is made in this article that repeat litigation by French lawyers defending the cause of immigrants is an important site for observing the symbolic power of legal forms. The analysis focuses on cases challenging immigration-related administrative regulations and shows how the process of repeatedly adjudicating these issues has focused attention away from litigants and their claims at the same time that it has reinforced the centrality of the Conseil d’Etat and its formalist jurisprudence in administrative governance. This detailed examination of the practical operation of France’s highest administrative jurisdiction leads to the surprising conclusion that this distinctly nonadversarial form of adjudication has contributed over the long term to institutionalizing a juridification of immigration-related administrative policy making.
Constraints on counterexamples to the Casas-Alvero conjecture and a verification in degree 12
Authors: Castryck Wouter , Laterveer Robert , Ounaïes Myriam
Published: February 2014

In the first (theoretical) part of this paper, we prove a number of constraints on hypothetical counterexamples to the Casas-Alvero conjecture, building on ideas of Graf von Bothmer, Labs, Schicho and van de Woestijne

that were recently reinterpreted by Draisma and de Jong in terms of

p
p

-adic valuations. In the second (computational) part, we present ideas improving upon Diaz-Toca and Gonzalez-Vega’s Gröbner basis approach to the Casas-Alvero conjecture. One application is an extension of the proof of Graf von Bothmer et al. to the cases

5

p
k

5p^k

,

6

p
k

6p^k

and

7

p
k

7p^k

(that is, for each of these cases, we determine the finite list of primes

p
p

to which their proof is not applicable). Finally, by combining both parts, we settle the Casas-Alvero conjecture in degree

12
12

(the smallest open case).
Discreteness of log discrepancies over log canonical triples on a fixed pair
Authors: Kawakita Masayuki
Published: February 2014

For a fixed pair and fixed exponents, we prove the discreteness of log discrepancies over all log canonical triples formed by attaching a product of ideals with given exponents.
Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model
Authors: Cao Yang , Li Lei
Published: February 2014

Motivation: Hydrophobic effect plays a pivotal role in most protein–ligand binding. State-of-the-art protein–ligand scoring methods usually treat hydrophobic free energy as surface tension, which is proportional to interfacial surface area for simplicity and efficiency. However, this treatment ignores the role of molecular shape, which has been found very important by either experimental or theoretical studies.

Results: We propose a new empirical scoring function, named Cyscore. Cyscore improves the prediction accuracy by using a novel curvature-dependent surface-area model, which is able to distinguish convex, planar and concave surface in hydrophobic free energy calculation. Benchmark tests show that this model significantly improves the protein–ligand scoring and Cyscore outperforms a variety of well established scoring functions using PDBbind benchmark sets for binding affinity correlation and ranking tests. We expect the curvature-dependent surface-area model and Cyscore would contribute to the study of protein–ligand interactions.

Availability: Cyscore is available to non-commercial users at http://clab.labshare.cn/software/cyscore.html.

Contact:  cao@scu.edu.cn

Supplementary information:  Supplementary Data is available at Bioinformatics online.
Getting all information out of logbooks: estimating banana prawn fishable biomass, catchability, and fishing power increase, with a focus on natural mortality
Authors: Zhou Shijie , Buckworth Rik C. , Ellis Nick , Deng Roy A. , Pascoe Sean
Published: February 2014

Biomass, catchability, and natural mortality are key parameters in fish stock assessment. Yet, it is difficult to estimate these quantities, especially natural mortality, when only fishery data are available. Using a method of population depletion analysis, we estimated these population and biological quantities for the white banana prawn (Penaeus merguiensis) in Australia's valuable Northern Prawn Fishery. In addition, we directly included fishing power change over time. The models were implemented in a Bayesian framework by incorporating process error, observation error, and random variability for the underlying parameters. The posterior median initial fishable biomass ranged from ∼2000 to 7000 t year−1, and the median catchability varied from ∼3.8 × 10−4 to 7.3 × 10−4 boat-day−1, resulting in an average fishing power increase of 2.6% per year. An unexpected result is the estimate of exponential natural mortality rate of ∼0.03 week−1. This value is substantially lower than an earlier estimate of 0.05 week−1, which was based on a single year's fishery data in one stock region and has been widely used for over four decades without validation. We attribute this low natural mortality estimate mainly to prawn aggregation behaviour.
Chemistry integrated circuit: chemical system on a complementary metal oxide semiconductor integrated circuit
Authors: Nakazato Kazuo
Published: February 2014

By integrating chemical reactions on a large-scale integration (LSI) chip, new types of device can be created. For biomedical applications, monolithically integrated sensor arrays for potentiometric, amperometric and impedimetric sensing of biomolecules have been developed. The potentiometric sensor array detects pH and redox reaction as a statistical distribution of fluctuations in time and space. For the amperometric sensor array, a microelectrode structure for measuring multiple currents at high speed has been proposed. The impedimetric sensor array is designed to measure impedance up to 10 MHz. The multimodal sensor array will enable synthetic analysis and make it possible to standardize biosensor chips. Another approach is to create new functional devices by integrating molecular systems with LSI chips, for example image sensors that incorporate biological materials with a sensor array. The quantum yield of the photoelectric conversion of photosynthesis is 100%, which is extremely difficult to achieve by artificial means. In a recently developed process, a molecular wire is plugged directly into a biological photosynthetic system to efficiently conduct electrons to a gold electrode. A single photon can be detected at room temperature using such a system combined with a molecular single-electron transistor.
Terahertz real-time imaging uncooled array based on antenna- and cavity-coupled bolometers
Authors: Simoens François , Meilhan Jérôme
Published: February 2014

The development of terahertz (THz) applications is slowed down by the availability of affordable, easy-to-use and highly sensitive detectors. CEA-Leti took up this challenge by tailoring the mature infrared (IR) bolometer technology for optimized THz sensing. The key feature of these detectors relies on the separation between electromagnetic absorption and the thermometer. For each pixel, specific structures of antennas and a resonant quarter-wavelength cavity couple efficiently the THz radiation on a broadband range, while a central silicon microbridge bolometer resistance is read out by a complementary metal oxide semiconductor circuit. 320×240 pixel arrays have been designed and manufactured: a better than 30 pW power direct detection threshold per pixel has been demonstrated in the 2–4 THz range. Such performance is expected on the whole THz range by proper tailoring of the antennas while keeping the technological stack largely unchanged. This paper gives an overview of the developed bolometer-based technology. First, it describes the technology and reports the latest performance characterizations. Then imaging demonstrations are presented, such as real-time reflectance imaging of a large surface of hidden objects and THz time-domain spectroscopy beam two-dimensional profiling. Finally, perspectives of camera integration for scientific and industrial applications are discussed.
A new era of semiconductor genetics using ion-sensitive field-effect transistors: the gene-sensitive integrated cell
Authors: Toumazou Christofer , Thay Tan Sri Lim Kok , Georgiou Pantelis
Published: February 2014

Semiconductor genetics is now disrupting the field of healthcare owing to the rapid parallelization and scaling of DNA sensing using ion-sensitive field-effect transistors (ISFETs) fabricated using commercial complementary metal -oxide semiconductor technology. The enabling concept of DNA reaction monitoring introduced by Toumazou has made this a reality and we are now seeing relentless scaling with Moore's law ultimately achieving the $100 genome. In this paper, we present the next evolution of this technology through the creation of the gene-sensitive integrated cell (GSIC) for label-free real-time analysis based on ISFETs. This device is derived from the traditional metal-oxide semiconductor field-effect transistor (MOSFET) and has electrical performance identical to that of a MOSFET in a standard semiconductor process, yet is capable of incorporating DNA reaction chemistries for applications in single nucleotide polymorphism microarrays and DNA sequencing. Just as application-specific integrated circuits, which are developed in much the same way, have shaped our consumer electronics industry and modern communications and memory technology, so, too, do GSICs based on a single underlying technology principle have the capacity to transform the life science and healthcare industries.
Actinoplanes lutulentus sp. nov., isolated from mucky soil in China
Authors: Gao Ruixia , Liu Chongxi , Zhao Junwei , Jia Feiyu , Li Chuang , Xing Jia , Wang Xiangjing , Xiang Wensheng
Published: February 2014

A novel actinomycete, designated strain NEAU-GRX6T, was isolated from mucky soil collected from a stream of Jinlong Mountain in Harbin, Heilongjiang Province, north China, and characterized using a polyphasic approach. The isolate formed irregular sporangia containing motile sporangiospores on the substrate mycelium. The whole-cell sugars were xylose, glucose and galactose. The predominant menaquinones were MK-9(H6), MK-10(H4) and MK-9(H4). The major fatty acids were C16 : 0, C15 : 0, C18 : 1ω9c, C17 : 1ω7c and C18 : 0. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 67 mol%. 16S rRNA gene sequence similarity studies showed that strain NEAU-GRX6T belonged to the genus

Actinoplanes

, being most closely related to

Actinoplanes palleronii

IFO 14916T (97.80 % similarity) and

Actinoplanes missouriensis

NBRC 102363T (97.76 %). However, the low observed levels of DNA–DNA relatedness allowed the isolate to be differentiated from the above-mentioned species of the genus

Actinoplanes

. Moreover, strain NEAU-GRX6T could also be distinguished from

A. palleronii

IFO 14916T and

A. missouriensis

NBRC 102363T by phenotypic characteristics. Therefore, it is proposed that strain NEAU-GRX6T represents a novel species of the genus

Actinoplanes

, for which the name Actinoplanes lutulentus sp. nov. is proposed. The type strain is strain NEAU-GRX6T ( = CGMCC 4.7090T = DSM 45883T).
Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat
Authors: Park Sooyeon , Park Ji-Min , Kang Chul-Hyung , Yoon Jung-Hoon
Published: February 2014

A Gram-stain-negative, non-motile, aerobic, curved-to-spiral-rod-shaped bacterium, designated AH-MY2T, was isolated from a tidal flat on Aphae island in the sea to the south-west of South Korea, and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain AH-MY2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain AH-MY2T clustered with the type strain of

Terasakiella pusilla

and that this cluster joined the clade comprising the type strains of species of the genus

Thalassospira

. Strain AH-MY2T exhibited 16S rRNA gene sequence similarity values of 90.6 % to the type strain of

Terasakiella pusilla

and of less than 91.0 % to the type strains of other species with validly published names. Strain AH-MY2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain AH-MY2T were phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids and one unidentified glycolipid. The DNA G+C content of strain AH-MY2T was 56.0 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain AH-MY2T represented a novel genus and species within the family

Rhodospirillaceae

of the class

Alphaproteobacteria

, for which the name Aestuariispira insulae gen. nov., sp. nov. is proposed. The type strain of Aestuariispira insulae is AH-MY2T ( = KCTC 32577T = CECT 8488T).
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data
Authors: Fiston-Lavier Anna-Sophie , Barrón Maite G. , Petrov Dmitri A. , González Josefa
Published: February 2014

Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic, and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing (NGS) data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online athttp://sourceforge.net/projects/tlex/.

Abbreviations

TE

transposable element

NGS

next-generation sequencing

LTR

long-terminal repeat

TSD

target site duplication

PTS

putative target site

PE

paired-end
Genetic drift suppresses bacterial conjugation in spatially structured populations
Authors: Freese Peter D. , Korolev Kirill S. , Jiménez José I. , Chen Irene A.
Published: February 2014

Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony ofEscherichia coligrowing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.