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Sample records for 2d pattern evolution

  1. 2D pattern evolution constrained by complex network dynamics

    da Rocha, L. E. C.; Costa, L. da F.

    2007-03-01

    Complex networks have established themselves in recent years as being particularly suitable and flexible for representing and modelling several complex natural and artificial systems. In the same time in which the structural intricacies of such networks are being revealed and understood, efforts have also been directed at investigating how such connectivity properties define and constrain the dynamics of systems unfolding on such structures. However, less attention has been focused on hybrid systems, i.e. involving more than one type of network and/or dynamics. Several real systems present such an organization, e.g. the dynamics of a disease coexisting with the dynamics of the immune system. The current paper investigates a specific system involving diffusive (linear and nonlinear) dynamics taking place in a regular network while interacting with a complex network of defensive agents following Erdös Rényi (ER) and Barabási Albert (BA) graph models with moveable nodes. More specifically, the complex network is expected to control, and if possible, to extinguish the diffusion of some given unwanted process (e.g. fire, oil spilling, pest dissemination, and virus or bacteria reproduction during an infection). Two types of pattern evolution are considered: Fick and Gray Scott. The nodes of the defensive network then interact with the diffusing patterns and communicate between themselves in order to control the diffusion. The main findings include the identification of higher efficiency for the BA control networks and the presence of relapses in the case of the ER model.

  2. Planar maps, circle patterns and 2d gravity

    David, Francois

    2013-01-01

    Via circle pattern techniques, random planar triangulations (with angle variables) are mapped onto Delaunay triangulations in the complex plane. The uniform measure on triangulations is mapped onto a conformally invariant spatial point process. We show that this measure can be expressed as: (1) a sum over 3-spanning-trees partitions of the edges of the Delaunay triangulations; (2) the volume form of a K\\"ahler metric over the space of Delaunay triangulations, whose prepotential has a simple formulation in term of ideal tessellations of the 3d hyperbolic space; (3) a discretized version (involving finite difference complex derivative operators) of Polyakov's conformal Fadeev-Popov determinant in 2d gravity; (4) a combination of Chern classes, thus also establishing a link with topological 2d gravity.

  3. Contributions to statistical image segmentation and 2D pattern Recognition

    Derrode, Stéphane

    2008-01-01

    This dissertation follows 9 years of my research activities, including 7 years as an assistant professor at the École Centrale Marseille and as a researcher into the Multidimensional Signal Processing Group of Institut Fresnel (CNRS UMR 6133). Works which I present explore some aspects of the statistical segmentation of images for applications in space imagery and the invariant description of 2D shapes for object recognition in video imagery. More precisely, the first part of the manuscript s...

  4. 2-D traveling-wave patterns in binary fluid convection

    Surko, C.M.; Porta, A.L. [Univ. of California, La Jolla, CA (United States)

    1996-12-31

    An overview is presented of recent experiments designed to study two-dimensional traveling-wave convection in binary fluid convection in a large aspect ratio container. Disordered patterns are observed when convection is initiated. As time proceeds, they evolve to more ordered patterns, consisting of several domains of traveling-waves separated by well-defined domain boundaries. The detailed character of the patterns depends sensitively on the Rayleigh number. Numerical techniques are described which were developed to provide a quantitative characterization of the traveling-wave patterns. Applications of complex demodulation techniques are also described, which make a detailed study of the structure and dynamics of the domain boundaries possible.

  5. Layout decomposition of self-aligned double patterning for 2D random logic patterning

    Ban, Yongchan; Miloslavsky, Alex; Lucas, Kevin; Choi, Soo-Han; Park, Chul-Hong; Pan, David Z.

    2011-04-01

    Self-aligned double pattering (SADP) has been adapted as a promising solution for sub-30nm technology nodes due to its lower overlay problem and better process tolerance. SADP is in production use for 1D dense patterns with good pitch control such as NAND Flash memory applications, but it is still challenging to apply SADP to 2D random logic patterns. The favored type of SADP for complex logic interconnects is a two mask approach using a core mask and a trim mask. In this paper, we first describe layout decomposition methods of spacer-type double patterning lithography, then report a type of SADP compliant layouts, and finally report SADP applications on Samsung 22nm SRAM layout. For SADP decomposition, we propose several SADP-aware layout coloring algorithms and a method of generating lithography-friendly core mask patterns. Experimental results on 22nm node designs show that our proposed layout decomposition for SADP effectively decomposes any given layouts.

  6. Short local descriptors from 2D connected pattern spectra

    Bosilj, Petra; Kijak, Ewa; Wilkinson, Michael H. F.; Lefèvre, Sebastien

    2015-01-01

    We propose a local region descriptor based on connected pattern spectra, and combined with normalized central moments. The descriptors are calculated for MSER regions of the image, and their performance compared against SIFT. The MSER regions were chosen because they can be efficiently selected by c

  7. Tooth patterning and evolution.

    Salazar-Ciudad, Isaac

    2012-12-01

    Teeth are a good system for studying development and evolution. Tooth development is largely independent of the rest of the body and teeth can be grown in culture to attain almost normal morphology. Their development is not affected by the patterns of movement or sensorial perception in the embryo. Teeth are hard and easily preserved. Thus, there is plenty of easily accessible information about the patterns of morphological variation occurring between and within species. This review summarises recent work and describes how tooth development can be understood as the coupling between a reaction-diffusion system and differential growth produced by diffusible growth factors: which growth factors are involved, how they affect each other's expression and how they affect the spatial patterns of proliferation that lead to final morphology. There are some aspects of tooth development, however, that do not conform to some common assumptions in many reaction-diffusion models. Those are discussed here since they provide clues about how reaction-diffusion systems may work in actual developmental systems. Mathematical models implementing what we know about tooth development are discussed. PMID:23266218

  8. Groupware requirements evolution patterns

    Pumareja, Dulce Trinidad

    2013-01-01

    Requirements evolution is a generally known problem in software development. Requirements are known to change all throughout a system's lifecycle. Nevertheless, requirements evolution is a poorly understood phenomenon. Most studies on requirements evolution focus on changes to written specifications

  9. Self-similar evolution of 2D aquatic dunes over an erodible bed

    Doppler, Delphine; Lagrée, Pierre Yves; Gondret, Philippe; Rabaud, Marc

    2015-11-01

    Scale invariance of shape is a common feature of erosion patterns, such as barchan dunes, sand ripples under shoaling waves or scour holes. Due to their universal and fascinating crescentic shape, barchans dunes have received much attention and scaling laws have been deduced from field observations, satellite images and laboratory experiments. On the other hand, the dynamical long term evolution of ripples and dunes formed over an erodible bed has been far less studied while the temporal behavior of erosion patterns contains substantial information on the physical processes involved. Here, we present experimental results obtained in a linear, quasi-2D closed water channel. When a granular bed is submitted to a uniform shear flow, periodic sand ripples appear all along the channel. We found that the first ripple near the channel inlet exhibit unreported long-term scale-invariant growth. The self-similar dune shape and power-law growth exponent are extracted by image processing for several flow velocity. A simple linear model is built using mass conservation and a granular flux law, so that the bed form is described by a self-similar order 2 linear system. Experimental data fit nicely with the model results.

  10. Groupware requirements evolution patterns

    Pumareja, Dulce Trinidad

    2013-01-01

    Requirements evolution is a generally known problem in software development. Requirements are known to change all throughout a system's lifecycle. Nevertheless, requirements evolution is a poorly understood phenomenon. Most studies on requirements evolution focus on changes to written specifications and on software architecture and design. Usually, the focus is when the software is under development. Little is known about how requirements evolve when software is put into use. Groupware is an ...

  11. Fast Computation of Wideband Beam Pattern for Designing Large-Scale 2-D Arrays.

    Chi, Cheng; Li, Zhaohui

    2016-06-01

    For real-time and high-resolution 3-D ultrasound imaging, the design of sparse distribution and weights of elements of a large-scale wideband 2-D array is needed to reduce hardware cost and achieve better directivity. However, due to the high time consumption of computing the wideband beam pattern, the design methods that need massive iterations have rarely been applied to design large-scale wideband 2-D arrays by directly computing the wideband beam pattern. In this paper, a fast method is proposed to realize the computation of a wideband beam pattern of arbitrary 2-D arrays in the far field in order to design large-scale wideband 2-D arrays. The proposed fast method exploits two important techniques: 1) nonuniform fast Fourier transform (FFT) and 2) short inverse FFT. Compared with the commonly used ultrasound simulator Field II, two orders of magnitude improvement in computation speed is achieved with comparable accuracy. The proposed fast method enables massive iterations of direct wideband beam pattern computation of arbitrary large-scale 2-D arrays. A design example in this paper demonstrates that the proposed fast method can help achieve better performance in designing large-scale wideband 2-D arrays. PMID:27046870

  12. DRCPlus in a router: automatic elimination of lithography hotspots using 2D pattern detection and correction

    Yang, Jie; Rodriguez, Norma; Omedes, Olivier; Gennari, Frank; Lai, Ya-Chieh; Mankad, Viral

    2010-03-01

    As technology processes continue to shrink, standard design rule checking (DRC) has become insufficient to guarantee design manufacturability. DRCPlus is a powerful technique for capturing yield detractors related to complex 2D situations1,2. DRCPlus is a pattern-based 2D design rule check beyond traditional width and space DRC that can identify problematic 2D configurations which are difficult to manufacture. This paper describes a new approach for applying DRCPlus in a router, enabling an automated approach to detecting and fixing known lithography hotspots using an integrated fast 2D pattern matching engine. A simple pass/no-pass criterion associated with each pattern offers designers guidance on how to fix these problematic patterns. Since it does not rely on compute intensive simulations, DRCPlus can be applied on fairly large design blocks and enforced in conjunction with standard DRC in the early stages of the design flow. By embedding this capability into the router, 2D yield detractors can be identified and fixed by designers in a push-button manner without losing design connectivity. More robust designs can be achieved and the impact on parasitics can be easily assessed. This paper will describe a flow using a fast 2D pattern matching engine integrated into the router in order to enforce DRCPlus rules. An integrated approach allows for rapid identification of hotspot patterns and, more importantly, allows for rapid fixing and verification of these hotspots by a tool that understands design intent and constraints. The overall flow is illustrated in Figure 1. An inexact search pattern is passed to the integrated pattern matcher. The match locations are filtered by the router through application of a DRC constraint (typically a recommended rule). Matches that fail this constraint are automatically fixed by the router, with the modified regions incrementally re-checked to ensure no additional DRCPlus violations are introduced.

  13. EVOLUTION OF A 2-D DISTURBANCE IN A SUPERSONIC BOUNDARY LAYER AND THE GENERATION OF SHOCKLETS

    黄章峰; 周恒

    2004-01-01

    Through direct numerical simulation, the evolution of a 2-D disturbance in a supersonic boundary layer has been investigated. At a chosen location, a small amplitude T-S wave was fed into the boundary layer to investigate its evolution. Characteristics of nonlinear evolution have been found. Two methods were applied for the detection of shocklets ,and it was found that when the amplitude of the disturbance reached a certain value,shocklets would be generated, which should be taken into consideration when nonlinear theory of hydrodynamic stability for compressible flows is to be established.

  14. 2D pattern evolution constrained by complex network dynamics

    Rocha, L E C; Costa, Luciano da Fontoura; Rocha, Luis Enrique Correa da

    2006-01-01

    Complex networks have established themselves along the last years as being particularly suitable and flexible for representing and modeling several complex natural and human-made systems. At the same time in which the structural intricacies of such networks are being revealed and understood, efforts have also been directed at investigating how such connectivity properties define and constrain the dynamics of systems unfolding on such structures. However, lesser attention has been focused on hybrid systems, \\textit{i.e.} involving more than one type of network and/or dynamics. Because several real systems present such an organization (\\textit{e.g.} the dynamics of a disease coexisting with the dynamics of the immune system), it becomes important to address such hybrid systems. The current paper investigates a specific system involving a diffusive (linear and non-linear) dynamics taking place in a regular network while interacting with a complex network of defensive agents following Erd\\"os-R\\'enyi and Barab\\'a...

  15. 2 D patterns of soil gas diffusivity , soil respiration, and methane oxidation in a soil profile

    Maier, Martin; Schack-Kirchner, Helmer; Lang, Friederike

    2015-04-01

    The apparent gas diffusion coefficient in soil (DS) is an important parameter describing soil aeration, which makes it a key parameter for root growth and gas production and consumption. Horizontal homogeneity in soil profiles is assumed in most studies for soil properties - including DS. This assumption, however, is not valid, even in apparently homogeneous soils, as we know from studies using destructive sampling methods. Using destructive methods may allow catching a glimpse, but a large uncertainty remains, since locations between the sampling positions cannot be analyzed, and measurements cannot be repeated. We developed a new method to determine in situ the apparent soil gas diffusion coefficient in order to examine 2 D pattern of DS and methane oxidation in a soil profile. Different tracer gases (SF6, CF4, C2H6) were injected continuously into the subsoil and measured at several locations in the soil profile. These data allow for modelling inversely the 2 D patterns of DS using Finite Element Modeling. The 2D DS patterns were then combined with naturally occurring CH4 and CO2 concentrations sampled at the same locations to derive the 2D pattern of soil respiration and methane oxidation in the soil profile. We show that methane oxidation and soil respiration zones shift within the soil profile while the gas fluxes at the surface remain rather stable during a the 3 week campaign.

  16. Stochastic 2-D Models of Galaxy Disk Evolution. The Galaxy M33

    Mineikis, Tadas; Vansevičius, Vladas

    2015-01-01

    We have developed a fast numerical 2-D model of galaxy disk evolution (resolved along the galaxy radius and azimuth) by adopting a scheme of parameterized stochastic self-propagating star formation. We explore the parameter space of the model and demonstrate its capability to reproduce 1-D radial profiles of the galaxy M33: gas surface density, surface brightness in the i and GALEX FUV passbands, and metallicity.

  17. Small-amplitude 2D patterns with nontrivial symmetry in a simple nonlinear field model

    Quasiperiodic (QP) small-amplitude patterns are studied in a scalar field theory with quadratic nonlinearity. QP solutions of the class in interest are found as a projection of strictly periodic solutions of an associated 4D problem onto an 'irrationally oriented' 2D subspace. The periodic solutions of the 4D problem are constructed using a version of the method of asymptotic expansions. The analysis reveals complex patterns. In particular, there exists a one-parametric QP pattern with strict 12-fold symmetry, which contains infinitely many local patches with approximate 5-fold symmetry. In limit cases, the complex patterns transform into a simple pattern: a close pack of hexagonal cells. In certain resonance cases there exist patterns consisting of alternating pieces of close cell packs with either hexagonal or quadrangular symmetry. The relation between the 12-fold and 5-fold approximate symmetries is discussed. (author)

  18. Self-assembled nano-patterns in strained 2D metalic alloys: stripes vs. islands

    Kotrla, Miroslav; Weber, S.; Much, F.; Biehl, M.; Kinzel, W.

    2007-01-01

    Roč. 13, - (2007), s. 70-75. ISSN 1335-1532 Grant ostatní: European Community(XE) NMP3-CT-2006-016447 MagDot; NSF DMR Award(DE) 0502737 Institutional research plan: CEZ:AV0Z10100520 Keywords : nanoscale pattern formation * selfassembly * coarsening of 2D islands * metalic alloys * misfit-induced strain * computer modeling and simulation. Subject RIV: BM - Solid Matter Physics ; Magnetism

  19. Optical properties of 2D fractional Talbot patterns under coherent EUV illumination

    We investigate optical properties of (2D) fractional Talbot patterns under illumination with EUV laser light. The fractional Talbot effect, due to spatial frequency multiplication, can enable patterning of micro and nano-structures with various feature sizes using a micro-scale pitch mask. The experiment is performed with a free-standing mask fabricated by focused ion beam milling and a highly coherent illumination at 46.9 nm wavelength generated by a compact capillary discharge Ne-like Argon laser. As a result of spatial frequency multiplication, structure density of a square array of apertures in the mask was increased by a factor of up to 9 at the recording plane. The depth of field of the fractional Talbot images has been investigated using Fresnel diffraction analysis. Added field distribution complexity caused by asymmetry of the 2D arrays was observed both in simulation and in the experiment. This approach could be useful for sub-micron structuring of 2D patterns for various applications including among others the fabrication of photonic crystals, quantum dots, and also of submicron-electronic devices. (paper)

  20. Studies of a suitable mask error enhancement factor for 2D patterns

    Wei, Chih I.; Cheng, Yung Feng; Chen, Ming Jui

    2013-04-01

    In advanced 20nm and below technology nodes, the mask enhanced error factor (MEEF) plays an important rule due to the request of stable process control and quality of mask manufacture. It provides us an effective parameter to analyze the process window for lithography. In advanced nodes, MEEF criterion becomes more important than previous nodes because very tight process tolerance is requested, especially in OPC and mask capability control. Therefore, we have to do further studies on this topic. In the simple line/trench design layers (for example: Active and poly), the MEEF is easy to be defined because mask bias is isotropic. However, in the complicated two-dimensional (2D) design layers (for example: Contact and Mvia), they are hard to be defined a suitable definition of MEEF. In the first part, we used the global bias to calculate the MEEF on all patterns. It makes calculation easier to compare with other patterns which are different shapes. However, when we inspected the 2D line-end patterns on the wafer, we found the significant differences between the MEEF of wafer data and aerial simulation. In order to clarify this issue, we perform series simulation studies of the line-end MEEF. Then we knew that it came from the different bias strategies. Furthermore, the simulation studies show that the line-end MEEF of non-preferable orientation is very sensitive to mask X/Y ratio bias due to strong OAI optical behavior by the SMO source. As a result, a new point of view of 2D MEEF is suggested according to physical mask CD error measurement data. In this study, we would find a better description of the MEEF than traditional one for lithographic process development on 2D region.

  1. Film flows and self-organized patterns of 2D-localized structures

    Frenkel, A.L. [Univ. of Alabama, Tuscaloosa, AL (United States)

    1996-12-31

    Films flowing down an inclined plane are considered. An unconventional perturbation approach is discussed. It yields the most general evolution equation for film thickness and the least restrictive conditions for its validity. Results of numerical simulations of the dissipative-dispersive evolution equation indicate that novel, more complex type of spatiotemporal patterns can exist for strange attractors of nonequilibrium systems. It is suggested that real-life experiments satisfying the validity conditions of this theory are possible.

  2. 2D cellular automaton model for the evolution of active region coronal plasmas

    Fuentes, Marcelo López

    2016-01-01

    We study a 2D cellular automaton (CA) model for the evolution of coronal loop plasmas. The model is based on the idea that coronal loops are made of elementary magnetic strands that are tangled and stressed by the displacement of their footpoints by photospheric motions. The magnetic stress accumulated between neighbor strands is released in sudden reconnection events or nanoflares that heat the plasma. We combine the CA model with the Enthalpy Based Thermal Evolution of Loops (EBTEL) model to compute the response of the plasma to the heating events. Using the known response of the XRT telescope on board Hinode we also obtain synthetic data. The model obeys easy to understand scaling laws relating the output (nanoflare energy, temperature, density, intensity) to the input parameters (field strength, strand length, critical misalignment angle). The nanoflares have a power-law distribution with a universal slope of -2.5, independent of the input parameters. The repetition frequency of nanoflares, expressed in t...

  3. Patterned Peeling 2D MoS2 off the Substrate.

    Zhao, Jing; Yu, Hua; Chen, Wei; Yang, Rong; Zhu, Jianqi; Liao, Mengzhou; Shi, Dongxia; Zhang, Guangyu

    2016-07-01

    The performance of two-dimensional (2D) MoS2 devices depends largely on the quality of the MoS2 itself. Existing fabrication process for 2D MoS2 relies on lithography and etching. However, it is extremely difficult to achieve clean patterns without any contaminations or passivations. Here we report a peel-off pattering of MoS2 films on substrates based on a proper interface engineering. The peel-off process utilizes the strong adhesion between gold and MoS2 and removes the MoS2 film contact with gold directly, leading to clean MoS2 pattern generation without residuals. Significantly improved electrical performances including high mobility ∼17.1 ± 8.3 cm(2)/(V s) and on/off ratio ∼5.6 ± 3.6 × 10(6) were achieved. Such clean fabrication technique paves a way to high quality MoS2 devices for various electrical and optical applications. PMID:27314173

  4. 2D Transition-Metal-Dichalcogenide-Nanosheet-Based Composites for Photocatalytic and Electrocatalytic Hydrogen Evolution Reactions.

    Lu, Qipeng; Yu, Yifu; Ma, Qinglang; Chen, Bo; Zhang, Hua

    2016-03-01

    Hydrogen (H2) is one of the most important clean and renewable energy sources for future energy sustainability. Nowadays, photocatalytic and electrocatalytic hydrogen evolution reactions (HERs) from water splitting are considered as two of the most efficient methods to convert sustainable energy to the clean energy carrier, H2. Catalysts based on transition metal dichalcogenides (TMDs) are recognized as greatly promising substitutes for noble-metal-based catalysts for HER. The photocatalytic and electrocatalytic activities of TMD nanosheets for the HER can be further improved after hybridization with many kinds of nanomaterials, such as metals, oxides, sulfides, and carbon materials, through different methods including the in situ reduction method, the hot-injection method, the heating-up method, the hydro(solvo)thermal method, chemical vapor deposition (CVD), and thermal annealing. Here, recent progress in photocatalytic and electrocatalytic HERs using 2D TMD-based composites as catalysts is discussed. PMID:26676800

  5. Estimation of strength of source in a 2D participating media using the differential evolution algorithm

    A numerical model is developed to estimate the time varying strength of a heat source without prior information about the unknown function. The medium is considered to be gray, absorbing and emitting and the heat transfer is assumed to take place by both radiation and conduction. All the boundaries of the 2-D enclosure are considered to be black with known temperature. The finite-volume method is used for discretization of the energy as well as the radiative transfer equation. This inverse radiation-conduction problem is solved with the minimization of a performance function, which is expressed by the sum of square residuals between calculated and observed temperature, utilizing the differential evolution algorithm. The prediction of the strength of the source by the present algorithm is found to be quite reasonable.

  6. 2D-patterning of self-assembled silver nanoisland films.

    Chervinskii, Semen; Reduto, Igor; Kamenskii, Alexander; Mukhin, Ivan S; Lipovskii, Andrey A

    2016-04-12

    The paper is dedicated to the recently developed by the authors technique of silver nanoisland growth, allowing self-arrangement of 2D-patterns of nanoislands. The technique employs silver out-diffusion from ion-exchanged glass in the course of annealing in hydrogen. To modify the silver ion distribution in the exchanged soda-lime glass we included the thermal poling of the ion-exchanged glass with a profiled electrode as an intermediate stage of the process. The resulting consequence consists of three steps: (i) during the ion exchange of the glass in the AgxNa1-xNO3 (x = 0.01-0.15) melt we enrich the subsurface layer of the glass with silver ions; (ii) under the thermal poling, the electric field displaces these ions deeper into the glass under the 2D profiled anodic electrode, the displacement is smaller under the hollows in the electrode where the intensity of the field is minimal; (iii) annealing in a reducing atmosphere of hydrogen results in silver out-diffusion only in the regions corresponding to the electrode hollows, as a result silver forms nanoislands following the shape of the electrode. Varying the electrode and mode of processing allows governing the nanoisland size distribution and self-arrangement of the isolated single nanoislands, pairs, triples or groups of several nanoislands-so-called plasmonic molecules. PMID:26765367

  7. Study of 2D interpolating readout for a micro-pattern gaseous detector

    The two-dimensional interpolating readout, a new readout concept based on resistive anode structure, was studied for the micro-pattern gaseous detector. Within its high spatial resolution, the interpolating resistive readout structure leads to an enormous reduction of electronic channels compared with pure pixel devices, and also makes the detector more reliable and robust, which is attributed to its resistive anode relieving discharge. A GEM (gaseous electron multiplier) detector with 2D interpolating resistive readout structure was set up and the performance of the detector was studied with 55Fe 5.9 keV X-ray. The detector worked stably at the gain up to 3.5×104 without any discharge. An energy resolution of about 19%, and a spatial resolution of about 219 μm (FWHM) were reached, and good imaging performance was also obtained. (authors)

  8. Non-linear evolution of the diocotron instability in a pulsar electrosphere: 2D PIC simulations

    Petri, J

    2009-01-01

    (abridged) The physics of the pulsar magnetosphere near the neutron star surface remains poorly constrained by observations. Nevertheless it is believed that large vacuum gaps exist in the magnetosphere, and a non-neutral plasma partially fills the neutron star surroundings to form an electrosphere. The equatorial disk in this electrosphere is diocotron and magnetron unstable. To better assess the long term evolution of these instabilities, we study the behavior of the non-neutral plasma with help on particle simulations. We designed a 2D electrostatic PIC code. In the diocotron regime, the equation of motion for particles obeys the electric drift approximation. The plasma is confined between two conducting walls. Moreover, in order to simulate a pair cascade in the gaps, we add a source term feeding the plasma with charged particles. We consider the long term non-linear evolution of the diocotron instability. We found that particles tend to attract together to form small vortex of high charge density rotatin...

  9. Design and testing of the first 2D Prototype Vertically Integrated Pattern Recognition Associative Memory

    Liu, T.; Deptuch, G.; Hoff, J.; Jindariani, S.; Joshi, S.; Olsen, J.; Tran, N.; Trimpl, M.

    2015-02-01

    An associative memory-based track finding approach has been proposed for a Level 1 tracking trigger to cope with increasing luminosities at the LHC. The associative memory uses a massively parallel architecture to tackle the intrinsically complex combinatorics of track finding algorithms, thus avoiding the typical power law dependence of execution time on occupancy and solving the pattern recognition in times roughly proportional to the number of hits. This is of crucial importance given the large occupancies typical of hadronic collisions. The design of an associative memory system capable of dealing with the complexity of HL-LHC collisions and with the short latency required by Level 1 triggering poses significant, as yet unsolved, technical challenges. For this reason, an aggressive R&D program has been launched at Fermilab to advance state of-the-art associative memory technology, the so called VIPRAM (Vertically Integrated Pattern Recognition Associative Memory) project. The VIPRAM leverages emerging 3D vertical integration technology to build faster and denser Associative Memory devices. The first step is to implement in conventional VLSI the associative memory building blocks that can be used in 3D stacking, in other words, the building blocks are laid out as if it is a 3D design. In this paper, we report on the first successful implementation of a 2D VIPRAM demonstrator chip (protoVIPRAM00). The results show that these building blocks are ready for 3D stacking.

  10. Improved 2D Intelligent Driver Model simulating synchronized flow and evolution concavity in traffic flow

    Tian, Junfang; Li, Geng; Treiber, Martin; Zhu, Chenqiang; Jia, Bin

    2016-01-01

    This paper firstly show that 2 Dimensional Intelligent Driver Model (Jiang et al., PloS one, 9(4), e94351, 2014) is not able to replicate the synchronized traffic flow. Then we propose an improved model by considering the difference between the driving behaviors at high speeds and that at low speeds. Simulations show that the improved model can reproduce the phase transition from synchronized flow to wide moving jams, the spatiotemporal patterns of traffic flow induced by traffic bottleneck, and the evolution concavity of traffic oscillations (i.e. the standard deviation of the velocities of vehicles increases in a concave/linear way along the platoon). Validating results show that the empirical time series of traffic speed obtained from Floating Car Data can be well simulated as well.

  11. Bottom-up design of 2D organic photocatalysts for visible-light driven hydrogen evolution

    Wang, Peng; Jiang, Xue; Zhao, Jijun

    2016-01-01

    To design two-dimensional (2D) organocatalysts, three series of covalent organic frameworks (COFs) are constructed using bottom-up strategies, i.e. molecular selection, tunable linkage, and functionalization. First-principles calculations are performed to confirm their photocatalytic activity under visible light. Two of our constructed 2D COF models (B1 and C3) are identified as a sufficiently efficient organocatalyst for visible light water splitting. The controllable construction of such COFs from suitable organic subunit, linkage, and functional groups paves the way for correlating band edge alignments and geometry parameters of 2D organic materials. Our theoretical prediction not only provides essential insights into designing 2D-COF photocatalysts for water splitting, but also sparks other technological applications for 2D organic materials.

  12. Bottom-up design of 2D organic photocatalysts for visible-light driven hydrogen evolution

    To design two-dimensional (2D) organocatalysts, three series of covalent organic frameworks (COFs) are constructed using bottom-up strategies, i.e. molecular selection, tunable linkage, and functionalization. First-principles calculations are performed to confirm their photocatalytic activity under visible light. Two of our constructed 2D COF models (B1 and C3) are identified as a sufficiently efficient organocatalyst for visible light water splitting. The controllable construction of such COFs from suitable organic subunit, linkage, and functional groups paves the way for correlating band edge alignments and geometry parameters of 2D organic materials. Our theoretical prediction not only provides essential insights into designing 2D-COF photocatalysts for water splitting, but also sparks other technological applications for 2D organic materials. (paper)

  13. High Luminescence White LEDs Prepared with 2D Island-Pattern of Quantum Dots Dispersed Photopolymer Films

    Hyun-Guk Hong

    2015-01-01

    Full Text Available Since the reabsorption loss among different size quantum dots (QDs is a critical issue in the QD based white LEDs, we proposed and fabricated new film structure of 2D island-patterns consisting of separate green and red QDs dispersed photopolymer patterns in a zigzag form. A small air-gap such as 60 μm between QD islands helps to control the optical path at the interface to reduce the lateral reabsorption loss to enhance the optical efficiency of white LED. The 2D island-patterns of QD phosphor film were fabricated using a UV imprinting process and compared the optical efficiency with the other QD film structure prepared with same QD concentrations and thicknesses such as a mixed and separately layered QD structure. Experimental and simulation analysis were performed to confirm the better optical efficiency from the 2D island-patterns of QD films due to the reduced reabsorption loss. High luminescence white LED was finally realized with 2D island-patterns of QD film, resulting in a luminous efficiency of 62.2 lm/W and CRI of 83 with CCT of 4537 K at the operation current of 60 mA.

  14. 2D nanosheet molybdenum disulphide (MoS2) modified electrodes explored towards the hydrogen evolution reaction

    Rowley-Neale, Samuel J.; Brownson, Dale A. C.; Smith, Graham C.; Sawtell, David A. G.; Kelly, Peter J.; Banks, Craig E.

    2015-10-01

    We explore the use of two-dimensional (2D) MoS2 nanosheets as an electrocatalyst for the Hydrogen Evolution Reaction (HER). Using four commonly employed commercially available carbon based electrode support materials, namely edge plane pyrolytic graphite (EPPG), glassy carbon (GC), boron-doped diamond (BDD) and screen-printed graphite electrodes (SPE), we critically evaluate the reported electrocatalytic performance of unmodified and MoS2 modified electrodes towards the HER. Surprisingly, current literature focuses almost exclusively on the use of GC as an underlying support electrode upon which HER materials are immobilised. 2D MoS2 nanosheet modified electrodes are found to exhibit a coverage dependant electrocatalytic effect towards the HER. Modification of the supporting electrode surface with an optimal mass of 2D MoS2 nanosheets results in a lowering of the HER onset potential by ca. 0.33, 0.57, 0.29 and 0.31 V at EPPG, GC, SPE and BDD electrodes compared to their unmodified counterparts respectively. The lowering of the HER onset potential is associated with each supporting electrode's individual electron transfer kinetics/properties and is thus distinct. The effect of MoS2 coverage is also explored. We reveal that its ability to catalyse the HER is dependent on the mass deposited until a critical mass of 2D MoS2 nanosheets is achieved, after which its electrocatalytic benefits and/or surface stability curtail. The active surface site density and turn over frequency for the 2D MoS2 nanosheets is determined, characterised and found to be dependent on both the coverage of 2D MoS2 nanosheets and the underlying/supporting substrate. This work is essential for those designing, fabricating and consequently electrochemically testing 2D nanosheet materials for the HER.We explore the use of two-dimensional (2D) MoS2 nanosheets as an electrocatalyst for the Hydrogen Evolution Reaction (HER). Using four commonly employed commercially available carbon based electrode

  15. EXPRESSION PATTERN OF LUNG CANCER RELATED GENES IN MALIGNANT TRANSFORMATION OF BEP2D

    范保星; 张开泰; 李刚; 谢玲; 马淑华; 葛世丽; 项小琼; 胡迎春; 王升启; 周平坤; 吴德昌

    2002-01-01

    Objective: To detect the expression difference of 60 lung cancer associated genes in human bronchial epithelial malignant transformation cell model (BEP2D) induced by alpha-particles. Methods: 60 lung cancer associated genes were collected and micro-arrayed onto the microscope slides using Cartesian PixSys5500 cDNA Microarray machine. Total RNA from BEP2D cells and passage 20 (Rl5H-20), passage 35 (R15H-35) cells derived from BEP2D following 1.5 Gy alpha-particles was extracted and labeled by fluorescent dye. The labeled probe was then hybridized with the cDNA. Results: 40, 47, 20 genes were detected in BEP2D, R15H-20 and R15H-35 respectively. The expression level of tumor suppressor genes decreased greatly in the transformed R15H-35. Most oncogenes decreased slightly in R15H-20. Most growth factors expressed only in R15H-20. Conclusion: In human bronchial epithelial malignant transformed cell model generated by alpha-particles, the loss-function of tumor suppressor genes at initiation stage was dominant, some related oncogenes and growth factors promoted the malignant transformation.

  16. A physical pattern recognition approach for 2D electromagnetic induction studies

    D. Patella

    2000-06-01

    Full Text Available We present a new tomographic procedure for the analysis of natural source electromagnetic (EM induction field data collected over any complex 2D buried structure beneath a flat air-earth boundary. The tomography is developed in a pure physical context and the primary goal is the depiction of the space distribution of two occurrence probability functions for the induced electrical charge accumulations on resistivity discontinuities and current channelling inside conductive bodies, respectively. The procedure to obtain tomographic image consists of a scanning operation governed analytically by a set of multiple interference cross-correlations between the observed EM components and the corresponding synthetic components of a pair of elementary charge and dipole. To show the potentiality of the proposed physical tomography, we discuss the results from three 2D synthetic examples.

  17. A physical pattern recognition approach for 2D electromagnetic induction studies

    D. PATELLA; P. Mauriello

    2000-01-01

    We present a new tomographic procedure for the analysis of natural source electromagnetic (EM) induction field data collected over any complex 2D buried structure beneath a flat air-earth boundary. The tomography is developed in a pure physical context and the primary goal is the depiction of the space distribution of two occurrence probability functions for the induced electrical charge accumulations on resistivity discontinuities and current channelling inside conductive bodies, respectivel...

  18. Phenols content and 2-D electrophoresis protein pattern: a promising tool to monitor Posidonia meadows health state

    Randazzo Davide

    2007-07-01

    Full Text Available Abstract Background The endemic seagrass Posidonia oceanica (L. Delile colonizes soft bottoms producing highly productive meadows that play a crucial role in coastal ecosystems dynamics. Human activities and natural events are responsible for a widespread meadows regression; to date the identification of "diagnostic" tools to monitor conservation status is a critical issue. In this study the feasibility of a novel tool to evaluate ecological impacts on Posidonia meadows has been tested. Quantification of a putative stress indicator, i.e. phenols content, has been coupled to 2-D electrophoretic protein analysis of rhizome samples. Results The overall expression pattern from Posidonia rhizome was determined using a preliminary proteomic approach, 437 protein spots were characterized by pI and molecular weight. We found that protein expression differs in samples belonging to sites with high or low phenols: 22 unique protein spots are peculiar of "low phenols" and 27 other spots characterize "high phenols" samples. Conclusion Posidonia showed phenols variations within the meadow, that probably reflect the heterogeneity of environmental pressures. In addition, comparison of the 2-D electrophoresis patterns allowed to highlight qualitative protein expression differences in response to these pressures. These differences may account for changes in metabolic/physiological pathways as adaptation to stress. A combined approach, based on phenols content determination and 2-D electrophoresis protein pattern, seems a promising tool to monitor Posidonia meadows health state.

  19. NUMERICAL TESTS ON PATTERN FORMATION IN 2D HETEROGENEOUS MEDIUMS: AN APPROACH USING THE SCHNAKENBERG MODEL

    Diego A. Garzón-Alvarado; CARLOS GALEANO; JUAN MANTILLA

    2012-01-01

    Este articulo presenta distintas pruebas numéricas en dominios que presenta variación de parámetros, de forma espacial, de la ecuación de reacción- difusión en el espacio de Turing. Las pruebas son desarrolladas en cuadrados de lado unitario 2D en el cual se realizan subdivisiones (subdominios). En cada subdomminio se ingresan parámetros que corresponden a los diferentes números de onda, por lo tanto presentan un medio heterogéneo. Cada número de onda fue predicho mediante la teoría lineal de...

  20. Novel hybrid organic/inorganic 2D quasiperiodic PC: from diffraction pattern to vertical light extraction

    Zhou Jun

    2011-01-01

    Full Text Available Abstract Recently, important efforts have been dedicated to the realization of a fascinating class of new photonic materials or metamaterials, known as photonic quasicrystals (PQCs, in which the lack of the translational symmetry is compensated by rotational symmetries not achievable by the conventional periodic crystals. As ever, more advanced functionality is demanded and one strategy is the introduction of non-linear and/or active functionality in photonic materials. In this view, core/shell nanorods (NRs are a promising active material for light-emitting applications. In this article a two-dimensional (2D hybrid a 2D octagonal PQC which consists of air rods in an organic/inorganic nanocomposite is proposed and experimentally demonstrated. The nanocomposite was prepared by incorporating CdSe/CdS core/shell NRs into a polymer matrix. The PQC was realized by electron beam lithography (EBL technique. Scanning electron microscopy, far field diffraction and spectra measurements are used to characterize the experimental structure. The vertical extraction of the light, by the coupling of the modes guided by the PQC slab to the free radiation via Bragg scattering, consists of a narrow red emissions band at 690 nm with a full width at half-maximum (FWHM of 21.5 nm. The original characteristics of hybrid materials based on polymers and colloidal NRs, able to combine the unique optical properties of the inorganic moiety with the processability of the host matrix, are extremely appealing in view of their technological impact on the development of new high performing optical devices such as organic light-emitting diodes, ultra-low threshold lasers, and non-linear devices. PACS: 81.07.Pr Organic-inorganic hybrid nanostructures, 81.16.-c Methods of nanofabrication and processing, 42.70.Qs Photonic band-gap materials.

  1. Multilevel image thresholding based on 2D histogram and maximum Tsallis entropy--a differential evolution approach.

    Sarkar, Soham; Das, Swagatam

    2013-12-01

    Multilevel thresholding amounts to segmenting a gray-level image into several distinct regions. This paper presents a 2D histogram based multilevel thresholding approach to improve the separation between objects. Recent studies indicate that the results obtained with 2D histogram oriented approaches are superior to those obtained with 1D histogram based techniques in the context of bi-level thresholding. Here, a method to incorporate 2D histogram related information for generalized multilevel thresholding is proposed using the maximum Tsallis entropy. Differential evolution (DE), a simple yet efficient evolutionary algorithm of current interest, is employed to improve the computational efficiency of the proposed method. The performance of DE is investigated extensively through comparison with other well-known nature inspired global optimization techniques such as genetic algorithm, particle swarm optimization, artificial bee colony, and simulated annealing. In addition, the outcome of the proposed method is evaluated using a well known benchmark--the Berkley segmentation data set (BSDS300) with 300 distinct images. PMID:23955760

  2. Areal (2-D) Simulation of Water Flood Process in Unite Well Pattern

    Wei Wan; Shengbo Wang

    2013-01-01

    In this project, the partialdifferential equations governing a water flood in a unit well pattern weresolved numerically and then the numerical solutions were used to construct thecontour and surface plots of reservoir pressure and water saturation. Thereservoir pressure and water saturation at a given location in the reservoir asa function of injection time were also simulated. The simulation results showthat the reservoir pressure and water saturation gradually decreases with increasingthe ...

  3. 2dF-SDSS LRG and QSO (2SLAQ) Survey: Evolution of the Most Massive Galaxies

    Nichol, R; Roseboom, I; Wake, D; Nichol, Robert; Cannon, Russell; Roseboom, Isaac; Wake, David

    2006-01-01

    The 2dF-SDSS LRG and QSO (2SLAQ) survey is a new survey of distant Luminous Red Galaxies (LRGs) and faint quasars selected from the Sloan Digital Sky Survey (SDSS) multi-color photometric data and spectroscopically observed using the 2dF instrument on the Anglo-Australian Telescope (AAT). In total, the 2SLAQ survey has measured over 11000 LRG redshifts, covering 180deg^2 of SDSS imaging data, from 87 allocated nights of AAT time. Over 90% of these galaxies are within the range 0.45=3L*. When combined with the lower redshift SDSS LRGs, the evolution in the luminosity function of these LRGs is fully consistent with that expected from a simple passive (luminosity) evolution model. This observation suggests that at least half of the LRGs seen at z~0.2 must already have more than half their stellar mass in place by z~0.6, i.e., our observations are inconsistent with a majority of LRGs experiencing a major merger in the last 6 Gyrs. However, some "frosting" (i.e., minor mergers) has taken place with ~5% of LRGs sho...

  4. Modelling of the nonlinear evolution of 2D waves and vortices in plasmas

    In this report an antisymmetric lattice formed by standing waves of vorticity is considered. For small but finite amplitudes multiple-time-scale analysis is performed, higher harmonics generation and frequency shifts are evaluated analytically and critical amplitude for perturbation theory is determined. For amplitudes bigger than critical numerical simulations are carried out taking into account vortex nonlinearity, drift and dispersion effects. Numerical code is developed which allows to study long-term evolution of two-dimensional spatially periodic waves and vortex structures

  5. Development for 2D pattern quantification method on mask and wafer

    Matsuoka, Ryoichi; Mito, Hiroaki; Toyoda, Yasutaka; Wang, Zhigang

    2010-03-01

    We have developed the effective method of mask and silicon 2-dimensional metrology. The aim of this method is evaluating the performance of the silicon corresponding to Hotspot on a mask. The method adopts a metrology management system based on DBM (Design Based Metrology). This is the high accurate contouring created by an edge detection algorithm used in mask CD-SEM and silicon CD-SEM. Currently, as semiconductor manufacture moves towards even smaller feature size, this necessitates more aggressive optical proximity correction (OPC) to drive the super-resolution technology (RET). In other words, there is a trade-off between highly precise RET and mask manufacture, and this has a big impact on the semiconductor market that centers on the mask business. 2-dimensional Shape quantification is important as optimal solution over these problems. Although 1-dimensional shape measurement has been performed by the conventional technique, 2-dimensional shape management is needed in the mass production line under the influence of RET. We developed the technique of analyzing distribution of shape edge performance as the shape management technique. On the other hand, there is roughness in the silicon shape made from a mass-production line. Moreover, there is variation in the silicon shape. For this reason, quantification of silicon shape is important, in order to estimate the performance of a pattern. In order to quantify, the same shape is equalized in two dimensions. And the method of evaluating based on the shape is popular. In this study, we conducted experiments for averaging method of the pattern (Measurement Based Contouring) as two-dimensional mask and silicon evaluation technique. That is, observation of the identical position of a mask and a silicon was considered. It is possible to analyze variability of the edge of the same position with high precision. The result proved its detection accuracy and reliability of variability on two-dimensional pattern (mask and

  6. Topological evolution during coupled grain growth and Ostwald ripening in volume-conserved 2-D two-phase polycrystals

    The topological evolution during coupled grain growth and Ostwald ripening in volume-conserved two-phase polycrystalline systems was studied in two dimensions (2-D), employing computer simulations based on a continuum diffuse-interface field model. The topological distributions were found to scale with time, but dependent on the ratios of grain boundary energies to the interphase boundary energy, the volume fractions and the initial microstructures. The correlations between topological class and grain size, as well as the topological correlations of grains with their neighbor grains were observed. The differences in topological features between volume-conserved two-phase systems and single-phase systems are discussed for ZrO2 and Al2O3 phases

  7. Novel patterns of cancer genome evolution

    Xia Zhang; Xiaodi Deng; Yu Zhang; Zhiguang Li

    2015-01-01

    Cells usually undergo a long journey of evolution during the progression from normal to precancerous cells and finally to full-fledged cancer cells. Multiple genomic aberrations are acquired during this journey that could either act as drivers to confer significant growth advantages or act as passengers with little effect on the tumor growth. Recent advances in sequencing technology have made it feasible to decipher the evolutionary course of a cancer cell on a genome-wide level by evaluating the relative number of mutated alleles. Novel terms such as chromothripsis and chromoplexy have been introduced to describe the newly identified patterns of cancer genome evolution. These new insights have greatly expanded our understanding of the initiation and progression of cancers, which should aid in improving the efficiency of cancer management and treatment.

  8. Does the Medication Pattern Reflect the CYP2D6 Genotype in Patients With Diagnoses Within the Schizophrenic Spectrum?

    Jürgens, Gesche; Rasmussen, Henrik B; Werge, Thomas;

    2012-01-01

    Cytochrome P450 2D6 enzyme (CYP2D6) is an important metabolic pathway for many antipsychotics. Its genetic polymorphism causes pharmacokinetic variability that might lead to adverse drug reactions or treatment failure unless countered by appropriate dose adjustments or shift to CYP2D6-independent...

  9. The Evolution of Trilobite Body Patterning

    Hughes, Nigel C.

    2007-05-01

    The good fossil record of trilobite exoskeletal anatomy and ontogeny, coupled with information on their nonbiomineralized tissues, permits analysis of how the trilobite body was organized and developed, and the various evolutionary modifications of such patterning within the group. In several respects trilobite development and form appears comparable with that which may have characterized the ancestor of most or all euarthropods, giving studies of trilobite body organization special relevance in the light of recent advances in the understanding of arthropod evolution and development. The Cambrian diversification of trilobites displayed modifications in the patterning of the trunk region comparable with those seen among the closest relatives of Trilobita. In contrast, the Ordovician diversification of trilobites, although contributing greatly to the overall diversity within the clade, did so within a narrower range of trunk conditions. Trilobite evolution is consistent with an increased premium on effective enrollment and protective strategies, and with an evolutionary trade-off between the flexibility to vary the number of trunk segments and the ability to regionalize portions of the trunk.

  10. Orbital evolution of colliding star and pulsar winds in 2D and 3D: dimensionality, resolution, and grid size effects

    Bosch-Ramon, V; Perucho, M

    2014-01-01

    The structure formed by the shocked winds of a massive star and a non-accreting pulsar in a binary system suffers periodic and random variations of orbital and non-linear dynamical origin. The characterization of the evolution of the two-wind interaction region is necessary to understand the non-thermal emission from radio to gamma rays. For the first time, we simulate in 3D the interaction of isotropic stellar and relativistic pulsar winds along one full orbit, on scales well beyond the binary size. We also investigate the impact of grid resolution and size. We carry out, with the code PLUTO, relativistic hydrodynamical simulations in 2 and 3D of the interaction of a slow dense wind and a mildly relativistic wind along one full orbit, up to ~100 times the binary size. The 2-dimensional simulations are carried out with equal and larger grid resolution and size than in 3D. The simulations in 3D confirm previous results in 2D, showing a strong shock induced by Coriolis forces that terminates the pulsar wind in ...

  11. Global patterns of sequence evolution in Drosophila

    Marín Ignacio

    2007-11-01

    Full Text Available Abstract Background Sequencing of the genomes of several Drosophila allows for the first precise analyses of how global sequence patterns change among multiple, closely related animal species. A basic question is whether there are characteristic features that differentiate chromosomes within a species or between different species. Results We explored the euchromatin of the chromosomes of seven Drosophila species to establish their global patterns of DNA sequence diversity. Between species, differences in the types and amounts of simple sequence repeats were found. Within each species, the autosomes have almost identical oligonucleotide profiles. However, X chromosomes and autosomes have, in all species, a qualitatively different composition. The X chromosomes are less complex than the autosomes, containing both a higher amount of simple DNA sequences and, in several cases, chromosome-specific repetitive sequences. Moreover, we show that the right arm of the X chromosome of Drosophila pseudoobscura, which evolved from an autosome 10 – 18 millions of years ago, has a composition which is identical to that of the original, left arm of the X chromosome. Conclusion The consistent differences among species, differences among X chromosomes and autosomes and the convergent evolution of X and neo-X chromosomes demonstrate that strong forces are acting on drosophilid genomes to generate peculiar chromosomal landscapes. We discuss the relationships of the patterns observed with differential recombination and mutation rates and with the process of dosage compensation.

  12. Left Right Patterning, Evolution and Cardiac Development

    Iain M. Dykes

    2014-04-01

    Full Text Available Many aspects of heart development are determined by the left right axis and as a result several congenital diseases have their origins in aberrant left-right patterning. Establishment of this axis occurs early in embryogenesis before formation of the linear heart tube yet impacts upon much later morphogenetic events. In this review I discuss the differing mechanisms by which left-right polarity is achieved in the mouse and chick embryos and comment on the evolution of this system. I then discus three major classes of cardiovascular defect associated with aberrant left-right patterning seen in mouse mutants and human disease. I describe phenotypes associated with the determination of atrial identity and venous connections, looping morphogenesis of the heart tube and finally the asymmetric remodelling of the embryonic branchial arch arterial system to form the leftward looped arch of aorta and associated great arteries. Where appropriate, I consider left right patterning defects from an evolutionary perspective, demonstrating how developmental processes have been modified in species over time and illustrating how comparative embryology can aide in our understanding of congenital heart disease.

  13. Warm ionized gas in CALIFA early-type galaxies. 2D emission-line patterns and kinematics for 32 galaxies

    Gomes, J. M.; Papaderos, P.; Kehrig, C.; Vílchez, J. M.; Lehnert, M. D.; Sánchez, S. F.; Ziegler, B.; Breda, I.; Dos Reis, S. N.; Iglesias-Páramo, J.; Bland-Hawthorn, J.; Galbany, L.; Bomans, D. J.; Rosales-Ortega, F. F.; Cid Fernandes, R.; Walcher, C. J.; Falcón-Barroso, J.; García-Benito, R.; Márquez, I.; Del Olmo, A.; Masegosa, J.; Mollá, M.; Marino, R. A.; González Delgado, R. M.; López-Sánchez, Á. R.; Califa Collaboration

    2016-04-01

    traces of localized star formation in the extranuclear component of several of our sample galaxies points to a non-negligible contribution by OB stars to the global ionizing photon budget in ETGs. Additionally, our data again highlight the diversity of ETGs in their gaseous and stellar kinematics. While in one half of our sample, gas and stars show similar (yet not necessarily identical) velocity patterns that are both dominated by rotation along the major galaxy axis, our analysis also documents several cases of kinematical decoupling between gas and stars, or rotation along the minor galaxy axis. We point out that the generally very low (≲1 Å) EW(Hα) of ETGs requires a careful quantitative assessment of potential observational and analysis biases in studies of their wim. With standard emission-line fitting tools, Balmer emission lines become progressively difficult to detect below an EW(Hα) ~ 3 Å, therefore our current understanding of the presence and 2D emission patterns and kinematics of the diffuse wim ETGs may be severely incomplete. We demonstrate that at the typical emission-line detection threshold of ~2 Å in previous studies, most of the extranuclear wim emission in an ETG may evade detection, which could in turn cause ETGs to be classified as entirely gas-devoid systems. Conclusions: This study adds further observational evidence for a considerable heterogeneity among ETGs with regard to the physical properties and 2D kinematics of their extended wim component, and it clearly shows that a comprehensive understanding of these systems requires IFS studies over their entire optical extent.

  14. Chromosome differentiation patterns during cichlid fish evolution

    Nirchio Mauro

    2010-06-01

    Full Text Available Abstract Background Cichlid fishes have been the subject of increasing scientific interest because of their rapid adaptive radiation which has led to an extensive ecological diversity and their enormous importance to tropical and subtropical aquaculture. To increase our understanding of chromosome evolution among cichlid species, karyotypes of one Asian, 22 African, and 30 South American cichlid species were investigated, and chromosomal data of the family was reviewed. Results Although there is extensive variation in the karyotypes of cichlid fishes (from 2n = 32 to 2n = 60 chromosomes, the modal chromosome number for South American species was 2n = 48 and the modal number for the African ones was 2n = 44. The only Asian species analyzed, Etroplus maculatus, was observed to have 46 chromosomes. The presence of one or two macro B chromosomes was detected in two African species. The cytogenetic mapping of 18S ribosomal RNA (18S rRNA gene revealed a variable number of clusters among species varying from two to six. Conclusions The karyotype diversification of cichlids seems to have occurred through several chromosomal rearrangements involving fissions, fusions and inversions. It was possible to identify karyotype markers for the subfamilies Pseudocrenilabrinae (African and Cichlinae (American. The karyotype analyses did not clarify the phylogenetic relationship among the Cichlinae tribes. On the other hand, the two major groups of Pseudocrenilabrinae (tilapiine and haplochromine were clearly discriminated based on the characteristics of their karyotypes. The cytogenetic mapping of 18S ribosomal RNA (18S rRNA gene did not follow the chromosome diversification in the family. The dynamic evolution of the repeated units of rRNA genes generates patterns of chromosomal distribution that do not help follows the phylogenetic relationships among taxa. The presence of B chromosomes in cichlids is of particular interest because they may not be represented in

  15. PSEMA: An Algorithm for Pattern Stimulated Evolution of Music

    Mavrogianni, A. N.; Vlachos, D. S.; Harvalias, G.

    2008-11-01

    An algorithm for pattern stimulating evolution of music is presented in this work (PSEMA). The system combines a pattern with a genetic algorithm for automatic music composition in order to create a musical phrase uniquely characterizing the pattern. As an example a musical portrait is presented. The initialization of the musical phrases is done with a Markov Chain process. The evolution is dominated by an arbitrary correspondence between the pattern (feature extraction of the pattern may be used in this step) and the esthetic result of the musical phrase.

  16. Centimeter Scale Patterned Growth of Vertically Stacked Few Layer Only 2D MoS2/WS2 van der Waals Heterostructure.

    Choudhary, Nitin; Park, Juhong; Hwang, Jun Yeon; Chung, Hee-Suk; Dumas, Kenneth H; Khondaker, Saiful I; Choi, Wonbong; Jung, Yeonwoong

    2016-01-01

    Two-dimensional (2D) van der Waal (vdW) heterostructures composed of vertically-stacked multiple transition metal dichalcogenides (TMDs) such as molybdenum disulfide (MoS2) and tungsten disulfide (WS2) are envisioned to present unprecedented materials properties unobtainable from any other material systems. Conventional fabrications of these hybrid materials have relied on the low-yield manual exfoliation and stacking of individual 2D TMD layers, which remain impractical for scaled-up applications. Attempts to chemically synthesize these materials have been recently pursued, which are presently limited to randomly and scarcely grown 2D layers with uncontrolled layer numbers on very small areas. Here, we report the chemical vapor deposition (CVD) growth of large-area (>2 cm(2)) patterned 2D vdW heterostructures composed of few layer, vertically-stacked MoS2 and WS2. Detailed structural characterizations by Raman spectroscopy and high-resolution/scanning transmission electron microscopy (HRTEM/STEM) directly evidence the structural integrity of two distinct 2D TMD layers with atomically sharp vdW heterointerfaces. Electrical transport measurements of these materials reveal diode-like behavior with clear current rectification, further confirming the formation of high-quality heterointerfaces. The intrinsic scalability and controllability of the CVD method presented in this study opens up a wide range of opportunities for emerging applications based on the unconventional functionalities of these uniquely structured materials. PMID:27147503

  17. Centimeter Scale Patterned Growth of Vertically Stacked Few Layer Only 2D MoS2/WS2 van der Waals Heterostructure

    Choudhary, Nitin; Park, Juhong; Hwang, Jun Yeon; Chung, Hee-Suk; Dumas, Kenneth H.; Khondaker, Saiful I.; Choi, Wonbong; Jung, Yeonwoong

    2016-05-01

    Two-dimensional (2D) van der Waal (vdW) heterostructures composed of vertically-stacked multiple transition metal dichalcogenides (TMDs) such as molybdenum disulfide (MoS2) and tungsten disulfide (WS2) are envisioned to present unprecedented materials properties unobtainable from any other material systems. Conventional fabrications of these hybrid materials have relied on the low-yield manual exfoliation and stacking of individual 2D TMD layers, which remain impractical for scaled-up applications. Attempts to chemically synthesize these materials have been recently pursued, which are presently limited to randomly and scarcely grown 2D layers with uncontrolled layer numbers on very small areas. Here, we report the chemical vapor deposition (CVD) growth of large-area (>2 cm2) patterned 2D vdW heterostructures composed of few layer, vertically-stacked MoS2 and WS2. Detailed structural characterizations by Raman spectroscopy and high-resolution/scanning transmission electron microscopy (HRTEM/STEM) directly evidence the structural integrity of two distinct 2D TMD layers with atomically sharp vdW heterointerfaces. Electrical transport measurements of these materials reveal diode-like behavior with clear current rectification, further confirming the formation of high-quality heterointerfaces. The intrinsic scalability and controllability of the CVD method presented in this study opens up a wide range of opportunities for emerging applications based on the unconventional functionalities of these uniquely structured materials.

  18. Exploring the evolution of investment pattern on advanced manufacturing technology

    Yang, Cheng; Matthiesen, Rikke Vestergaard; Johansen, John

    2014-01-01

    This paper explores the evolution of investment pattern on advanced manufacturing technology in a manner that builds on a longitudinal perspective. Based on the data of investments in AMTs from 567 manufacturing companies this paper develops a longitudinal taxonomy defined by the evolution of...

  19. EVOLUTIVE PATTERN FOR THE ECONOMIC GLOBALIZATION

    SILVIU-MARIUS ŞEITAN

    2014-06-01

    Full Text Available The necessity to identify and implement a solution for the region subject to the process globalization appeared due to the following reasons: during the stage of evolution of the process of globalization, there is no kind of coordination of this process towards the accomplishment of its goals, the character of this process being determined by the multitude of microeconomic processual elements coordinated from particular levels; therefore, the only objectives to be achieved are microeconomic by their nature, and there is a risk that adverse effects appear at the macroeconomic levels in relation with the specific objectives of the microeconomic level; the possible configuration of a global system of process administration is outrun temporally by the evolution of the global real economy. This entire period, represented by the stage of evolution of the process of globalization, is characterized by the lack of risk management capacity, the only such capacities, possibly to be activated, being those at the local level, but they have a low efficacy compared to the global nature of the risk and effects.

  20. A numerical investigation of the evolution of 2-D disturbances in hypersonic boundary layers and the effect on the flow structure due to the existence of shocklets

    CAO; Wei; ZHOU; Heng

    2004-01-01

    The evolution of 2-D disturbances in hypersonic boundary layer with Mach number 6,8, and 10 was investigated numerically by three different numerical schemes.At the entrance, second mode T-S waves with different amplitudes were introduced, and the relation between the Mach number and the amplitude of the disturbance when shocklets started to appear was investigated. By comparing the disturbance velocity profiles with those provided by linear stability theory, the effects of shocklets on flow structures were also investigated.

  1. A psychosocial model for the evolution of aesthetic patterns

    Souza, T.; Kalganova, T

    2002-01-01

    This paper describes an original attempt to evolve aesthetic patterns by integrating the rules of colour psychology into a multi-agent evolutionary model. The system uses the principles of evolution to determine social relationships between agents. Communication plays an important role in the evolution of social behaviour. In our case the exchange of information between agents determines their behavioural characteristics. The interaction between agents and their social behaviour may be contro...

  2. A coupled 2$\\times$2D Babcock-Leighton solar dynamo model. I. Surface magnetic flux evolution

    Lemerle, Alexandre; Carignan-Dugas, Arnaud

    2015-01-01

    The need for reliable predictions of the solar activity cycle motivates the development of dynamo models incorporating a representation of surface processes sufficiently detailed to allow assimilation of magnetographic data. In this series of papers we present one such dynamo model, and document its behavior and properties. This first paper focuses on one of the model's key components, namely surface magnetic flux evolution. Using a genetic algorithm, we obtain best-fit parameters of the transport model by least-squares minimization of the differences between the associated synthetic synoptic magnetogram and real magnetographic data for activity cycle 21. Our fitting procedure also returns Monte Carlo-like error estimates. We show that the range of acceptable surface meridional flow profiles is in good agreement with Doppler measurements, even though the latter are not used in the fitting process. Using a synthetic database of bipolar magnetic region (BMR) emergences reproducing the statistical properties of ...

  3. Characteristics of surface plasmon-polariton waves excited on 2D periodically patterned columnar thin films of silver.

    Dutta, Jhuma; Anantha Ramakrishna, S; Lakhtakia, Akhlesh

    2016-09-01

    Periodically patterned thin films of slanted silver nanocolumns were deposited by directing a collimated vapor flux of silver toward square and hexagonal gratings of photoresist on glass substrates. Angle-resolved specular-transmittance measurements in the visible and near-infrared wavelength bands on these periodically patterned columnar thin films (CTFs) were carried out to investigate the excitation of surface plasmon-polariton (SPP) waves bound tightly to either the air/CTF or the photoresist/CTF interfaces. The orientation of the propagation vector of the incident p-polarized plane wave with respect to the morphologically significant plane of the CTFs was varied to reveal asymmetric (unidirectional) coupling of Floquet modes to SPP waves. The asymmetric coupling is maximal when the propagation vector of the incident plane wave lies wholly in the morphologically significant plane. Theoretical understanding based on the Bruggeman formalism to homogenize the silver CTFs into hyperbolic biaxial continua is able to explain the experimental observations very well. PMID:27607490

  4. Pattern evolution during ion beam sputtering; reductionistic view

    Kim, J.-H.; Kim, J.-S.

    2016-09-01

    The development of the ripple pattern during the ion beam sputtering (IBS) is expounded via the evolution of its constituent ripples. For that purpose, we perform numerical simulation of the ripple evolution that is based on Bradley-Harper model and its non-linear extension. The ripples are found to evolve via various well-defined processes such as ripening, averaging, bifurcation and their combinations, depending on their neighboring ripples. Those information on the growth kinetics of each ripple allow the detailed description of the pattern development in real space that the instability argument and the diffraction study both made in k-space cannot provide.

  5. 2D x-ray imaging using a micro-pattern gas detector 'micro pixel chamber (μ-PIC)'

    The micro-pattern gas detector (MPGD) has a fine electrode structure, and it can obtain much higher positional resolution compared to that of the conventional gas detector based on the multi-wire proportional chamber. The 'Micro Pixel Chamber (μ-PIC)' is a new MPGD developed at Kyoto University. It has been applied not only to X-ray crystallographic analysis, but also particle and nuclear physics. In the present study, some experiments were conducted in order to evaluate the capability of μ-PIC in X-ray analysis. The gas gain of 3000 and linearity up to 200 kcps were obtained. Effect of parallax was examined, showing the image distortion within the theoretical estimate. Small angle X-ray scattering experiment using a collagen sample was also conducted, having demonstrated good X-ray imaging performance of μ-PIC. (author)

  6. The evolution of host mass and black hole mass in QSOs from the 2dF QSO Redshift Survey

    Fine, S; Miller, L; Babic, A; Moore, D; Brewer, B; Sharp, R G; Boyle, B J; Shanks, T; Smith, R J; Outram, P J; Loaring, N S

    2006-01-01

    We investigate the relation between the mass of super-massive black holes (Mbh) in QSOs and the mass of the dark matter halos hosting them (Mdh). We measure the widths of broad emission lines (Mgii lambda 2798, Civ lambda 1549) from QSO composite spectra as a function of redshift. These widths are then used to determine virial black hole mass estimates. We compare our virial black hole mass estimates to dark matter halo masses for QSO hosts derived by Croom et al. (2005) based on measurements of QSO clustering. This enables us to trace the Mbh-Mdh relation over the redshift range z=0.5 to 2.5. We calculate the mean zero-point of the Mbh-Mdh relation to be Mbh=10^(8.4+/-0.2)Msun for an Mdh=10^(12.5)Msun. These data are then compared with several models connecting Mbh and Mdh as well as recent hydrodynamical simulations of galaxy evolution. We note that the flux limited nature of QSO samples can cause a Malmquist-type bias in the measured zero-point of the Mbh-Mdh relation. The magnitude of this bias depends on...

  7. Influence of anisotropic grain boundary properties on the evolution of grain boundary character distribution during grain growth—a 2D level set study

    The present study elaborates on a 2D level set model of polycrystal microstructures that was recently established by adding the influence of anisotropic grain boundary energy and mobility on microstructure evolution. The new model is used to trace the evolution of grain boundary character distribution during grain growth. The employed level set formulation conveniently allows the grain boundary characteristics to be quantified in terms of coincidence site lattice (CSL) type per unit of grain boundary length, providing a measure of the distribution of such boundaries. In the model, both the mobility and energy of the grain boundaries are allowed to vary with misorientation. In addition, the influence of initial polycrystal texture is studied by comparing results obtained from a polycrystal with random initial texture against results from a polycrystal that initially has a cube texture. It is shown that the proposed level set formulation can readily incorporate anisotropic grain boundary properties and the simulation results further show that anisotropic grain boundary properties only have a minor influence on the evolution of CSL boundary distribution during grain growth. As anisotropic boundary properties are considered, the most prominent changes in the CSL distributions are an increase of general low-angle Σ1 boundaries as well as a more stable presence of Σ3 boundaries. The observations also hold for the case of an initially cube-textured polycrystal. The presence of this kind of texture has little influence over the evolution of the CSL distribution. Taking into consideration the anisotropy of grain boundary properties, grain growth alone does not seem to be sufficient to promote any significantly increased overall presence of CSL boundaries. (paper)

  8. 2D solar modeling

    Ventura, P; Li, L; Sofia, S; Basu, S; Demarque, P

    2009-01-01

    Understanding the reasons of the cyclic variation of the total solar irradiance is one of the most challenging targets of modern astrophysics. These studies prove to be essential also for a more climatologic issue, associated to the global warming. Any attempt to determine the solar components of this phenomenon must include the effects of the magnetic field, whose strength and shape in the solar interior are far from being completely known. Modelling the presence and the effects of a magnetic field requires a 2D approach, since the assumption of radial symmetry is too limiting for this topic. We present the structure of a 2D evolution code that was purposely designed for this scope; rotation, magnetic field and turbulence can be taken into account. Some preliminary results are presented and commented.

  9. Characterization of Muscat wines aroma evolution using comprehensive gas chromatography followed by a post-analytic approach to 2D contour plots comparison.

    Bordiga, Matteo; Rinaldi, Maurizio; Locatelli, Monica; Piana, Gianluca; Travaglia, Fabiano; Coïsson, Jean Daniel; Arlorio, Marco

    2013-09-01

    This study presents the application of a headspace solid-phase microextraction (HS-SPME) method on the analysis of Muscat-based wines volatiles by comprehensive two-dimensional gas chromatography (GC×GC) and Time-Of-Flight mass spectrometry (TOF-MS). The aroma patterns were established for different samples of Asti Spumante and Moscato d'Asti wines, stored in bottles for 6 months at different temperatures. Wines stored at 5 °C for 6 months did not show significant changes in flavor; otherwise, the samples stored at 15 and 25 °C, showed a significant decrease in linalool, β-damascenone, ethyl hexanoate, and ethyl octanoate levels. In these last samples, α-terpineol, hotrienol, nerol oxide, furanic linalool oxides A/B and rose oxide concentrations significantly increased. A mathematical approach was developed and applied to raw data exported after the chromatographic course, in order (i) to normalise different 2D chromatograms, permitting their direct comparison and (ii) to automatically identify and calculate from pixel-to-pixel re-designed 2D chromatograms any differences among key volatile compounds. PMID:23578615

  10. Investigating the evolution of gravel bar at river confluence during flood events using a 2D many-fraction river morphodynamic model

    Chen, Y.; Wu, F.; Ecohydraulics Lab.

    2010-12-01

    The knowledge of river morphology is fundamental and useful information for engineering and habitat restoration purposes. Many interesting phenomena such as armoring and downstream fining significantly affect the quality of riverine habitats. These phenomena could be even more devastating when they occur during the extreme flood events. Therefore, the development of meso-scale bedforms during flood events and the change in their sediment composition have become important topics of study. However, the complex interactions between flood flow, nonuniform particles and sediment transport make these problems difficult to tackle. In this study, we develop a 2D (two-dimensional) many-fraction FE (finite element) morphodynamic model to investigate the evolution of gravel bar during flood events. The proposed model adopts the characteristic dissipative Galerkin (CDG) scheme such that the convection-dominated bar evolution can be computed without numerical instabilities. A two-year record of DEM (digital elevation model) is obtained by airborne Lidar at the confluence of the Xin-Dian River (Taiwan), which is used to verify the model results. The proposed model is further applied to determine the best operation scheme of the Feitsui reservoir for mitigating blockage of river confluence by the gravel bar and sustaining the bed composition favorable to the river biota.

  11. PHREEQC modelling of concrete/clay interactions in a 2D geometry with explicit effect of porosity evolution on transport properties due to mineralogical changes

    Document available in extended abstract form only. In the context of deep repository for radioactive waste, significant use of concrete will be made. This material constitutes a compromise between properties, technical uses and costs. Within the French concepts, concrete will be used to build access structures, drifts as well as waste disposal cells and waste packages for Intermediate Level Wastes (ILW). With this design, concrete will be at the interface with either/both the host rock, Callovo-Oxfordian argillites in our case, and/or the clay plug built with swelling clay such as bentonite. Due to the chemical disequilibrium between concrete and clay, chemical reactions can modify both chemical and physical properties of these materials (e.g. mineralogical composition, diffusion coefficient...). In order to assess the long term behaviour of concrete/clay interfaces and the evolution of their properties with time, predictive modelling have to be performed. The high chemical contrast (e.g. pH or pe at the interface) often leads to problems of numerical convergence. Our own experience showed that PHREEQC is very successful in handling such difficulties in 1D geometry. PHREEQC is also able to handle 2D geometries as presented hereafter thanks to the MIX option as well as feedback on porosity thanks to the MCD option (multi component diffusion). Indeed, 2D simulation of a drift sealing concept developed by Andra was attempted using PHREEQC with the MIX option which allows the use of different transport properties in the different cells. A basic program was developed to generate this complex 2D mesh and another one to treat the outputs under TECPLOTR. The mesh is composed of 3081 cells with a refinement of 3 cm at each interface. Such a simulation was already conducted under ALLIANCES geochemistry transport tools, but in our cases the mesh refinement and the chemistry of the system are extended and the feedback on porosity is now considered. Furthermore, the new multi

  12. Instabilities and pattern evolution in a vertically heated annulus

    Wang, BoFu; Guo, ZhiWei; Ma, DongJun; Sun, DeJun

    2013-02-01

    The convection in an annular container with heated bottom, cooled top and insulated side walls are studied by both linear instability analysis and direct numerical simulation. The onset of convection is investigated by linear stability analysis and corresponding pattern selection mechanisms are discussed. The nonlinear evolution of different flow patterns and the convective heat transfer are simulated. The transition to oscillatory flow is also given by stability analysis where the base flow is a steady three dimensional flow. The stability predictions are in good agreement with the numerical simulations, including both the growth rate and the dimensionless frequency.

  13. Sample Optimization and Identification of Signal Patterns of Amino Acid Side Chains in 2D RFDR Spectra of the α-Spectrin SH3 Domain

    Pauli, Jutta; van Rossum, Barth; Förster, Hans; de Groot, Huub J. M.; Oschkinat, Hartmut

    2000-04-01

    Future structural investigations of proteins by solid-state CPMAS NMR will rely on uniformly labeled protein samples showing spectra with an excellent resolution. NMR samples of the solid α-spectrin SH3 domain were generated in four different ways, and their 13C CPMAS spectra were compared. The spectrum of a [u-13C, 15N]-labeled sample generated by precipitation shows very narrow 13C signals and resolved scalar carbon-carbon couplings. Linewidths of 16-19 Hz were found for the three alanine Cβ signals of a selectively labeled [70% 3-13C]alanine-enriched SH3 sample. The signal pattern of the isoleucine, of all prolines, valines, alanines, and serines, and of three of the four threonines were identified in 2D 13C-13C RFDR spectra of the [u-13C,15N]-labeled SH3 sample. A comparison of the 13C chemical shifts of the found signal patterns with the 13C assignment obtained in solution shows an intriguing match.

  14. Theory and realization of a 2D high resolution and high sensitivity SPECT system with an angle-encoding attenuator pattern

    Feng, Tao; Wang, Jizhe; Tsui, Benjamin M. W.

    2016-04-01

    The camera of the conventional SPECT system requires a collimator to allow incoming photons from a specific range of incident angle to reach the detector. It is the major factor that determines the spatial resolution of the camera. Moreover, it also greatly reduces the number of detected photons and hence increases statistical fluctuations in the acquired image data. The goal of this paper is to propose a theory and design for a novel high resolution and high sensitivity SPECT system without conventional collimators. The key is to resolve the incident photons from all directional angles and detected by every detector bin. Special ‘attenuators’ were designed to ‘encode’ the incoming photons from different directions similar to coded aperture to form projection data for image reconstruction. Each encoded angular pattern of detected photons was recorded as one measurement. Different angular patterns were achieved by changing the configurations of the attenuators so that angular pattern of different measurements or measurement matrix (MM) is invertible, which guarantee a unique reconstructed image. In simulation, the attenuators were fitted on a virtual full-ring gamma camera, as an alternative to the collimators in conventional SPECT systems. To evaluate the performance of the new SPECT system, analytical simulated projection data in 2D scenario were generated from the XCAT phantom. Noisy simulation using 100 noise realizations suggests that the new attenuator design provides much improved image quality in terms of contrast-noise trade-offs (~30% improvement). The results suggest that the new design of using attenuators to replace collimator is feasible and could potentially improve sensitivity without sacrificing resolution in today’s SPECT systems.

  15. Discrete model for the interface evolution in a 2d space with some well-defined set of annihilation-creation rules

    A simple discrete model for the evolution of the interface (or front) in a 2d (square) lattice, based on a complete as well as natural set of a few stochastic rules, has been examined. The interface is initially assumed to be a vertical straight-line which is made of elementary unit pieces called further particles. Once one of the particles is chosen at random it is pushed either left or right, drawing two new horizontal units (particles). Then the process continues to proceed into both main directions, following the rules (reversible and irreversible) that generally rely on creating and annihilating at random the vertical as well as horizontal particles. The scaling properties of the system have been analyzed, recognizing the front as a subdiffusive (anomalous) macromolecular chain or ''lattice animal'', with a few residual parts, on the one hand, and as a rough surface with overhangs in a 1+1- space, on the other. In the former, it turns out that the current length of the front scales more or less like a polymeric chain under an attractive (qualitatively: ''suppressing'') potential field, while in the latter it seems at a first glance that the problem may fall into an universality class characteristic of the nonlinear nonconservative dynamics with possibly nonconservative noise, exemplified by some dynamics of rough surfaces or interfaces. (author)

  16. Evolution of crustal stress, pressure and temperature around shear zones during orogenic wedge formation: a 2D thermo-mechanical numerical study

    Markus Schmalholz, Stefan; Jaquet, Yoann

    2016-04-01

    We study the formation of an orogenic wedge during lithospheric shortening with 2D numerical simulations. We consider a viscoelastoplastic rheology, thermo-mechanical coupling by shear heating and temperature-dependent viscosities, gravity and erosion. In the initial model configuration there is either a lateral temperature variation at the model base or a lateral variation in crustal thickness to generate slight stress variations during lithospheric shortening. These stress variations can trigger the formation of shear zones which are caused by thermal softening associated with shear heating. We do not apply any kind of strain softening, such as reduction of friction angle with progressive plastic strain. The first major shear zone that appears during shortening crosscuts the entire crust and initiates the asymmetric subduction/underthrusting of mainly the mechanically strong lower crust. After some deformation, the first shear zone in the upper crust is abandoned, the deformation propagates towards the foreland and a new shear zone forms only in the upper crust. The shear zone propagation occurs several times where new shear zones form in the upper crust and the mechanically strong top of the lower crust acts as detachment horizon. We calculate the magnitudes of the maximal and minimal principal stresses and of the mean stress (or dynamic pressure), and we record also the temperature for several marker points in the upper and lower crust. We analyse the evolution of stresses and temperature with burial depth and time. Deviatoric stresses (half the differential stress) in the upper crust are up to 200 MPa and associated shear heating in shear zones ranges between 40 - 80 °C. Lower crustal rocks remain either at the base of the orogenic wedge at depths of around 50 km or are subducted to depths of up to 120 km, depending on their position when the first shear zone formed. Largest deviatotric stresses in the strong part of the lower crust are about 1000 MPa and

  17. A pattern language for the evolution of component-based software architectures

    Ahmad, Aakash; Jamshidi, Pooyan; Pahl, Claus; Khaliq, Fawad

    2014-01-01

    Architecture-centric software evolution enables change in a system’s structure and behaviour while maintaining a global view of the software to address evolution-centric trade-offs. The existing solutions for architectural maintenance and evolution fall short of exploiting generic and reusable expertise to address recurring evolution problems. We present a pattern language as a collection of interconnected change patterns that enable reuse-driven and consistent evolution of component-based so...

  18. Pattern recognition of structural boundaries from aeromagnetic data using the 2-D continuous wavelet transform and the 3-D analytic signal

    Ouadfeul, S.-A.; Aliouane, L.

    2013-01-01

    The main goal of this paper is to use the 2-D continuous wavelet transform (CWT) combined with the 3-D analytic signal (AS) for structural boundaries delimitation from aeromagnetic data. The basic idea is based on the mapping of the maxima of the modulus of the 2-D CWT of the amplitude of the 3-D analytic signal (AS) for the full range of scales used to calculate the 2-D CWT. The proposed idea is applied to the synthetic data of a prism and a cylinder; obtained results show ...

  19. Centimeter Scale Patterned Growth of Vertically Stacked Few Layer Only 2D MoS2/WS2 van der Waals Heterostructure

    Nitin Choudhary; Juhong Park; Jun Yeon Hwang; Hee-Suk Chung; Dumas, Kenneth H.; Saiful I. Khondaker; Wonbong Choi; Yeonwoong Jung

    2016-01-01

    Two-dimensional (2D) van der Waal (vdW) heterostructures composed of vertically-stacked multiple transition metal dichalcogenides (TMDs) such as molybdenum disulfide (MoS2) and tungsten disulfide (WS2) are envisioned to present unprecedented materials properties unobtainable from any other material systems. Conventional fabrications of these hybrid materials have relied on the low-yield manual exfoliation and stacking of individual 2D TMD layers, which remain impractical for scaled-up applica...

  20. Evolution of differentiated expression patterns in digital organisms

    Ofria, C A; Collier, T C; Hsu, G K; Ofria, Charles; Adami, Christoph; Collier, Travis C.; Hsu, Grace K.

    2000-01-01

    We investigate the evolutionary processes behind the development andoptimization of multiple threads of execution in digital organisms using theavida platform, a software package that implements Darwinian evolution onpopulations of self-replicating computer programs. The system is seeded with alinearly executed ancestor capable only of reproducing its own genome, whereasits underlying language has the capacity for multiple threads of execution(i.e., simultaneous expression of sections of the genome.) We witness theevolution to multi-threaded organisms and track the development of distinctexpression patterns. Additionally, we examine both the evolvability ofmulti-threaded organisms and the level of thread differentiation as a functionof environmental complexity, and find that differentiation is more pronouncedin complex environments.

  1. Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution.

    Zanno, Lindsay E; Makovicky, Peter J

    2011-01-01

    Interpreting key ecological parameters, such as diet, of extinct organisms without the benefit of direct observation or explicit fossil evidence poses a formidable challenge for paleobiological studies. To date, dietary categorizations of extinct taxa are largely generated by means of modern analogs; however, for many species the method is subject to considerable ambiguity. Here we present a refined approach for assessing trophic habits in fossil taxa and apply the method to coelurosaurian dinosaurs--a clade for which diet is particularly controversial. Our findings detect 21 morphological features that exhibit statistically significant correlations with extrinsic fossil evidence of coelurosaurian herbivory, such as stomach contents and a gastric mill. These traits represent quantitative, extrinsically founded proxies for identifying herbivorous ecomorphology in fossils and are robust despite uncertainty in phylogenetic relationships among major coelurosaurian subclades. The distribution of these features suggests that herbivory was widespread among coelurosaurians, with six major subclades displaying morphological evidence of the diet, and that contrary to previous thought, hypercarnivory was relatively rare and potentially secondarily derived. Given the potential for repeated, independent evolution of herbivory in Coelurosauria, we also test for repetitive patterns in the appearance of herbivorous traits within sublineages using rank concordance analysis. We find evidence for a common succession of increasing specialization to herbivory in the subclades Ornithomimosauria and Oviraptorosauria, perhaps underlain by intrinsic functional and/or developmental constraints, as well as evidence indicating that the early evolution of a beak in coelurosaurians correlates with an herbivorous diet. PMID:21173263

  2. A simple model for research interest evolution patterns

    Jia, Tao; Wang, Dashun; Szymanski, Boleslaw

    Sir Isaac Newton supposedly remarked that in his scientific career he was like ``...a boy playing on the sea-shore ...finding a smoother pebble or a prettier shell than ordinary''. His remarkable modesty and famous understatement motivate us to seek regularities in how scientists shift their research focus as the career develops. Indeed, despite intensive investigations on how microscopic factors, such as incentives and risks, would influence a scientist's choice of research agenda, little is known on the macroscopic patterns in the research interest change undertaken by individual scientists throughout their careers. Here we make use of over 14,000 authors' publication records in physics. By quantifying statistical characteristics in the interest evolution, we model scientific research as a random walk, which reproduces patterns in individuals' careers observed empirically. Despite myriad of factors that shape and influence individual choices of research subjects, we identified regularities in this dynamical process that are well captured by a simple statistical model. The results advance our understanding of scientists' behaviors during their careers and open up avenues for future studies in the science of science.

  3. Evolution of the shell structure in medium-mass nuclei: search for the 2d5/2 neutron orbital in 69Ni

    The harmonic oscillator shell closure at N=40 in 68Ni is weak and loses its strength when removing (or adding) pair of protons. Calculations performed in this mass region predict a new island of inversion at N=40 similar to the one at N=20. Using a large valence space, the neutron orbital 2d(5/2) is shown to be a crucial ingredient for the interpretation of the nuclear structure at N ∼40. The neutron 1g(9/2) -2d(5/2) energy difference has been determined in 69Ni beam at 25.14 MeV/u separated by the LISE3 spectrometer was impinging a CD2 target of 2.6 mg/cm2 thickness. The experimental setup consisted of CATS/MUST2-S1/EXOGAM detectors coupled to an ionization chamber and a plastic scintillator. The angular moment and spectroscopic factors of the ground state (Jπ=9/2+) and a doublet of states (Jπ=5/2+) around 2.48 MeV corresponding to the population of the 1g(9/2) and the 2d(5/2) orbitals, were obtained from the comparison between the experimental cross-sections as a function of the proton detection angle and ADWA calculations. The spins of the observed states were assigned by comparison to large scale Shell-Model calculations. The position of the 2d(5/2) orbital in 69Ni has been established for the first time. Our measurements support the hypothesis of a low-lying 2d(5/2) orbital (∼2.5 MeV) with respect to the 1g(9/2) neutron orbital and thus its major role in the structure of the nuclei around N=40. (author)

  4. Overlapping patterns of brain activation to food and cocaine cues in cocaine abusers: association to striatal D2/D3 receptors

    Tomasi, Dardo; Wang, Gene-Jack; Wang, Ruiliang; Caparelli, Elisabeth C.; Logan, Jean; Volkow, Nora D.

    2014-01-01

    Cocaine, through its activation of dopamine (DA) signaling, usurps pathways that process natural rewards. However, the extent to which there is overlap between the networks that process natural and drug rewards and whether DA signaling associated with cocaine abuse influences these networks have not been investigated in humans. We measured brain activation responses to food and cocaine cues with fMRI, and D2/D3 receptors in the striatum with [11C]raclopride and PET in 20 active cocaine abuser...

  5. A Pattern Language for the Evolution of Component-based Software Architectures

    Ahmad, Aakash; Jamshidi, Pooyan; Pahl, Claus;

    2013-01-01

    Modern software systems are prone to a continuous evolution under frequently varying requirements. Architecture-centric software evolution enables change in system’s structure and behavior while maintaining a global view of the software to address evolution-centric tradeoffs. Lehman’s law of...... continuing change demands for long-living and continuously evolving architectures to prolong the productive life and economic value of deployed software. However, existing solutions for architectural maintenance and evolution fall short of exploiting generic and reusable expertise to address recurring...... enable reuse-driven and consistent evolution in component-based software architectures. Pattern interconnections represent possible relationships among patterns (such as variants or related patterns) in the language. In general, we introduce architecture change mining (pattern language development) as a...

  6. Calculation of the spatial distribution of photovoltaic field by arbitrary 2D ilumination patterns en LiNbO3; application to photovoltaic particle trapping.

    Arregui Hernández, Cándido; Alcazar de Velasco Rico, Angel Manuel; Ramiro Diaz, Jose Bruno; Mendez Jaque, Angel; Villarroel, J.; García Cabañes, A.; Carrascosa, M.

    2013-01-01

    Patterns of evanescent photovoltaic field induced by illumination on a surface of lithium niobate (LN) have been calculated and compared with the experimental patterns of nano- and microparticles trapped by dielectrophoretic forces. A tool for this calculation has been developed. Calculo de distribución espacial de campo por efecto fotovoltaico con patrones arbitrarios de iluminación, en LiNbO3

  7. The evolution of host mass and black hole mass in quasi-stellar objects from the 2dF QSO Redshift Survey

    Fine, S.; Croom, S. M.; Miller, L.; Babic, A.; Moore, D.; Brewer, B.; Sharp, R. G.; Boyle, B. J.; Shanks, T.; Smith, R. J.; Outram, P. J.; Loaring, N. S.

    2006-12-01

    We investigate the relation between the mass of supermassive black holes (MBH) in quasi-stellar objects (QSOs) and the mass of the dark matter haloes hosting them (MDH). We measure the widths of broad emission lines (MgII λ2798, CIV λ1549) from QSO composite spectra as a function of redshift. These widths are then used to determine virial black hole mass estimates. We compare our virial black hole mass estimates to dark matter halo masses for QSO hosts derived by Croom et al. based on measurements of QSO clustering. This enables us to trace the MBH-MDH relation over the redshift range z = 0.5-2.5. We calculate the mean zero-point of the MBH-MDH relation to be MBH = 108.4+/-0.2Msolar for an MDH = 1012.5Msolar. These data are then compared with several models connecting MBH and MDH as well as recent hydrodynamical simulations of galaxy evolution. We note that the flux-limited nature of QSO samples can cause a Malmquist-type bias in the measured zero-point of the MBH-MDH relation. The magnitude of this bias depends on the scatter in the MBH-MDH relation, and we re-evaluate the zero-point assuming three published values for this scatter. We create a subsample of our data defined by a constant magnitude interval around L* and find (1 + z)3.3+/-1.3 evolution in MBH between z ~ 0.5 and 2.5 for typical, L* QSOs. We also determine the Eddington ratios (L/LEdd) for the same subsample and find no significant evolution: (1 + z)-0.4+/-1.1. Taken at face value, our data suggest that a decrease in active black hole mass since z ~ 2.5 is the driving force behind luminosity evolution of typical, L*, optically selected QSOs. However, we note that our data are also consistent with a picture in which reductions in both black hole mass and accretion rate contribute equally to luminosity evolution. In addition, we find that these evolution results are strongly affected by the virial black hole mass estimators used. Changes to the calibration of these have a significant effect on the

  8. The warm ionized gas in CALIFA early-type galaxies: 2D emission-line patterns and kinematics for 32 galaxies

    Gomes, J M; Kehrig, C; Vílchez, J M; Lehnert, M D; Sánchez, S F; Ziegler, B; Breda, I; Reis, S N dos; Iglesias-Páramo, J; Bland-Hawthorn, J; Galbany, L; Bomans, D J; Rosales-Ortega, F F; Fernandes, R Cid; Walcher, C J; Falcón-Barroso, J; García-Benito, R; Márquez, I; del Olmo, A; Masegosa, J; Mollá, M; Marino, R A; Delgado, R M González; López-Sánchez, Á R

    2015-01-01

    The morphological, spectroscopic and kinematical properties of the warm interstellar medium (wim) in early-type galaxies (ETGs) hold key observational constraints to nuclear activity and the buildup history of these massive, quiescent systems. High-quality integral field spectroscopy (IFS) data with a wide spectral and spatial coverage, such as those from the CALIFA survey, offer an unprecedented opportunity for advancing our understanding of the wim in ETGs. This article centers on a 2D investigation of the wim component in 32 nearby (<~150Mpc) ETGs from CALIFA, complementing a previous 1D analysis of the same sample (Papaderos et al. 2013; P13). We include here H\\alpha\\ intensity and equivalent width (EW) maps and radial profiles, diagnostic emission-line ratios, besides ionized-gas and stellar kinematics. This study is supplemented by \\tau-ratio maps as an efficient means to quantify the role of photoionization by pAGB stars, as compared to other mechanisms (e.g., AGN, low-level star formation). Additio...

  9. Time evolution of the phonon and ionized impurity limited 2D hot carrier distribution function in a n-GaAs square quantum well (QW)

    Zandler, G.; Vass, E.

    1988-10-01

    The time evolution of the distribution function of hot electrons interacting with ionized impurities, acoustic and polar optical phonons is studied in terms of the Boltzmann integral equation. The calculated distribution functions are used to determine the charge carrier drift velocity, the average energy as well as the average momentum and energy loss rates as a function of time at constant values of the lattice temperature and charge carrier density. The stationary non-equilibrium values of these quantities are found to be established after 3-4 ps.

  10. Justification of the Nonlinear Schrödinger Equation for the Evolution of Gravity Driven 2D Surface Water Waves in a Canal of Finite Depth

    Düll, Wolf-Patrick; Schneider, Guido; Wayne, C. Eugene

    2016-05-01

    In 1968 V.E. Zakharov derived the Nonlinear Schrödinger equation for the two-dimensional water wave problem in the absence of surface tension, that is, for the evolution of gravity driven surface water waves, in order to describe slow temporal and spatial modulations of a spatially and temporarily oscillating wave packet. In this paper we give a rigorous proof that the wave packets in the two-dimensional water wave problem in a canal of finite depth can be approximated over a physically relevant timespan by solutions of the Nonlinear Schrödinger equation.

  11. Patterns of technological innovation and evolution in the energy sector: A patent-based approach

    Given the ever-increasing pace and complexity of technological innovation in the energy sector, monitoring technological changes has become of strategic importance. One of the most common techniques for technology monitoring is patent analysis, which enables the identification of technological trends over time. However, few previous studies have carried out patent analysis in the energy sector. This study aims to explore patterns of innovation and of evolution in energy technologies, particularly focusing on similarities and differences across technologies. For this purpose, we first defined the relevant energy technologies and extracted the associated patent data from the United States Patents and Trademark Office (USPTO) and then adopted six patent indices and developed six patent maps to analyze their innovation characteristics. We then clustered energy technologies with similar characteristics, so defining innovation categories, and analyzed the changes in these characteristics over time to define their evolution categories. As one of the few attempts to investigate the overall trends in the energy sector's innovation and evolution, this study is expected to help develop an in-depth understanding of the energy industry, which will be useful in establishing technology strategies and policy in this rapidly changing sector. - Highlights: • We examined the patterns of innovation and evolution of energy technologies. • Six types of innovation patterns such as “competitive” or “mature” were identified. • Six types of evolution patterns such as “towards closed innovation” were identified. • The patterns of evolution were related to the patterns of innovation

  12. Binary Bell Polynomials, Bilinear Approach to Exact Periodic Wave Solutions of (2 d- 1)-Dimensional Nonlinear Evolution Equations

    王云虎; 陈勇

    2011-01-01

    In the present letter, we get the appropriate bilinear forms of (2 + 1)-dimensional KdV equation, extended (2 + 1)-dimensional shallow water wave equation and (2 + 1)-dimensional Sawada -Kotera equation in a quick and natural manner, namely by appling the binary Bell polynomials. Then the Hirota direct method and Riemann theta function are combined to construct the periodic wave solutions of the three types nonlinear evolution equations. And the corresponding figures of the periodic wave solutions are given. Furthermore, the asymptotic properties of the periodic wave solutions indicate that the soliton solutions can be derived from the periodic wave solutions.

  13. Tomographic analysis of data from the JET neutron profile monitor to deduce the 2-D spatial and temporal evolution of neutron emissivity

    Measurements from the JET neutron profile monitor are analyzed tomographically to deduce the two-dimensional spatial distribution of neutron emissivity and its temporal evolution. The most dramatic change in the emissivity profile is produced by a sawtooth crash. The profiles before and after a sawtooth crash are determined and changes in their characteristics, such as width and amplitude, are compared to those deduced from other diagnostics, including soft X-rays, electron density interferometers and electron cyclotron emission. The drop in the central neutron emissivity can be much larger than that obtained from the integrated global neutron emission, and hollow emissivity profiles are produced. The observed inversion radius is the same on neutron, soft X-ray, and electron temperature profiles. This hollow profile can be understood by observations of the soft X-ray emissivity on the fastest time-scale. A major theme of this paper is that much more information and understanding can be gained if several diagnostics are used together, with their different resolutions, time-scales and physical properties measured. (author). 12 refs, 5 figs

  14. A layered framework for pattern-based ontology evolution

    Javed, Muhammad; M. Abgaz, Yalemisew; Pahl, Claus

    2011-01-01

    The challenge of ontology-driven modelling of information components is well known in both academia and industry. In this paper, we present a novel approach to deal with customisation and abstraction of ontology-based model evolution. As a result of an empirical study, we identify a layered change operator framework based on the granularity, domain-specificity and abstraction of changes. The implementation of the operator framework is supported through layered change logs. Layered change...

  15. Adaptive evolution of facial colour patterns in Neotropical primates

    Santana, Sharlene E.; Lynch Alfaro, Jessica; Alfaro, Michael E.

    2012-01-01

    The rich diversity of primate faces has interested naturalists for over a century. Researchers have long proposed that social behaviours have shaped the evolution of primate facial diversity. However, the primate face constitutes a unique structure where the diverse and potentially competing functions of communication, ecology and physiology intersect, and the major determinants of facial diversity remain poorly understood. Here, we provide the first evidence for an adaptive role of facial co...

  16. Contrasting patterns of karyotype and sex chromosome evolution in Lepidoptera

    Šíchová, Jindra

    2016-01-01

    It is known that chromosomal rearrangements play an important role in speciation by limiting gene flow within and between species. Furthermore, this effect may be enhanced by involvement of sex chromosomes that are known to undergo fast evolution compared to autosomes and play a special role in speciation due to their engagement in postzygotic reproductive isolation. The work presented in this study uses various molecular-genetic and cytogenetic techniques to describe karyotype and sex chromo...

  17. Patterns of Finance: Revolution, Evolution, or More of the Same?

    Johnstone, D. Bruce

    1998-01-01

    Examines the prospects for change in the financing of American higher education in the next decade, looking at current patterns of financing along three dimensions (total resources, cost per unit, apportionment of costs) that may or may not change profoundly and how they may do so. Considers the likelihood that such shifts will be evolutionary or…

  18. Vertical 2D Heterostructures

    Lotsch, Bettina V.

    2015-07-01

    Graphene's legacy has become an integral part of today's condensed matter science and has equipped a whole generation of scientists with an armory of concepts and techniques that open up new perspectives for the postgraphene area. In particular, the judicious combination of 2D building blocks into vertical heterostructures has recently been identified as a promising route to rationally engineer complex multilayer systems and artificial solids with intriguing properties. The present review highlights recent developments in the rapidly emerging field of 2D nanoarchitectonics from a materials chemistry perspective, with a focus on the types of heterostructures available, their assembly strategies, and their emerging properties. This overview is intended to bridge the gap between two major—yet largely disjunct—developments in 2D heterostructures, which are firmly rooted in solid-state chemistry or physics. Although the underlying types of heterostructures differ with respect to their dimensions, layer alignment, and interfacial quality, there is common ground, and future synergies between the various assembly strategies are to be expected.

  19. Mosaic evolution and the pattern of transitions in the hominin lineage.

    Foley, Robert A

    2016-07-01

    Humans are uniquely unique, in terms of the extreme differences between them and other living organisms, and the impact they are having on the biosphere. The evolution of humans can be seen, as has been proposed, as one of the major transitions in evolution, on a par with the origins of multicellular organisms or the eukaryotic cell (Maynard Smith & Szathmáry 1997 Major transitions in evolution). Major transitions require the evolution of greater complexity and the emergence of new evolutionary levels or processes. Does human evolution meet these conditions? I explore the diversity of evidence on the nature of transitions in human evolution. Four levels of transition are proposed-baseline, novel taxa, novel adaptive zones and major transitions-and the pattern of human evolution considered in the light of these. The primary conclusions are that changes in human evolution occur continuously and cumulatively; that novel taxa and the appearance of new adaptations are not clustered very tightly in particular periods, although there are three broad transitional phases (Pliocene, Plio-Pleistocene and later Quaternary). Each phase is distinctive, with the first based on ranging and energetics, the second on technology and niche expansion, and the third on cognition and cultural processes. I discuss whether this constitutes a 'major transition' in the context of the evolutionary processes more broadly; the role of behaviour in evolution; and the opportunity provided by the rich genetic, phenotypic (fossil morphology) and behavioural (archaeological) record to examine in detail major transitions and the microevolutionary patterns underlying macroevolutionary change. It is suggested that the evolution of the hominin lineage is consistent with a mosaic pattern of change.This article is part of the themed issue 'Major transitions in human evolution'. PMID:27298474

  20. Phenotypic Evolution in Fossil Species: Pattern and Process

    Hunt, Gene; Rabosky, Daniel L.

    2014-05-01

    Since Darwin, scientists have looked to the fossil record with the hope of using it to document how the phenotypes of species change over substantial periods of time. How best to interpret this record has been controversial, but empirical and methodological advances have resolved at least two issues about pattern: (a) directional transformations are seldom sustained over geological timescales, and (b) net rates of morphological change in fossil species are usually quite slow. Considerable uncertainty remains, however, about the processes responsible for these patterns, but most fruitful explanations use the framework of adaptive landscapes to consider the role of natural selection and other processes. An additional, unresolved issue is the claim that most phenotypic change is associated with speciation. A variety of methods, using data from both fossil and extant species, have supported such a link, at least in some clades and traits, but its prevalence and underlying mechanism remain unresolved.

  1. Quantitative patterns of stylistic influence in the evolution of literature.

    Hughes, James M; Foti, Nicholas J; Krakauer, David C; Rockmore, Daniel N

    2012-05-15

    Literature is a form of expression whose temporal structure, both in content and style, provides a historical record of the evolution of culture. In this work we take on a quantitative analysis of literary style and conduct the first large-scale temporal stylometric study of literature by using the vast holdings in the Project Gutenberg Digital Library corpus. We find temporal stylistic localization among authors through the analysis of the similarity structure in feature vectors derived from content-free word usage, nonhomogeneous decay rates of stylistic influence, and an accelerating rate of decay of influence among modern authors. Within a given time period we also find evidence for stylistic coherence with a given literary topic, such that writers in different fields adopt different literary styles. This study gives quantitative support to the notion of a literary "style of a time" with a strong trend toward increasingly contemporaneous stylistic influence. PMID:22547796

  2. Dental patterning in the earliest sharks: Implications for tooth evolution.

    Maisey, John G; Turner, Susan; Naylor, Gavin J P; Miller, Randall F

    2014-05-01

    Doliodus problematicus is the oldest known fossil shark-like fish with an almost intact dentition (Emsian, Lower Devonian, c. 397Ma). We provide a detailed description of the teeth and dentition in D. problematicus, based on tomographic analysis of NBMG 10127 (New Brunswick Museum, Canada). Comparisons with modern shark dentitions suggest that Doliodus was a ram-feeding predator with a dentition adapted to seizing and disabling prey. Doliodus provides several clues about the early evolution of the "shark-like" dentition in chondrichthyans and also raises new questions about the evolution of oral teeth in jawed vertebrates. As in modern sharks, teeth in Doliodus were replaced in a linguo-labial sequence within tooth families at fixed positions along the jaws (12-14 tooth families per jaw quadrant in NBMG 10127). Doliodus teeth were replaced much more slowly than in modern sharks. Nevertheless, its tooth formation was apparently as highly organized as in modern elasmobranchs, in which future tooth positions are indicated by synchronized expression of shh at fixed loci within the dental epithelium. Comparable dental arrays are absent in osteichthyans, placoderms, and many "acanthodians"; a "shark-like" dentition, therefore, may be a synapomorphy of chondrichthyans and gnathostomes such as Ptomacanthus. The upper anterior teeth in Doliodus were not attached to the palatoquadrates, but were instead supported by the ethmoid region of the prechordal basicranium, as in some other Paleozoic taxa (e.g., Triodus, Ptomacanthus). This suggests that the chondrichthyan dental lamina was originally associated with prechordal basicranial cartilage as well as jaw cartilage, and that the modern elasmobranch condition (in which the oral dentition is confined to the jaws) is phylogenetically advanced. Thus, oral tooth development in modern elasmobranchs does not provide a complete developmental model for chondrichthyans or gnathostomes. PMID:24347366

  3. Evolution of Simple Behavior Patterns for Autonomous Robotic Agent

    Neruda, Roman; Slušný, Stanislav; Vidnerová, Petra

    -: WSEAS Press, 2007 - (Revetria, R.; Cecchi, A.; Schenone, M.; Mladenov, V.; Zemiak, A.), s. 411-417. (Electrical and Computer Engineering Series). ISBN 978-960-6766-14-5. [ICOSSSE'07. WSEAS International Conference on System Science and Simulation in Engineering /6./. Venice (IT), 21.11.2007-23.11.2007] R&D Projects: GA MŠk(CZ) 1M0567 Grant ostatní: HPC-Europa(EU) RII3-CT-2003-506079 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary robotics * neural networks * behavior patterns Subject RIV: IN - Informatics, Computer Science

  4. Evolution at Two Levels in Fire Ants: The Relationship between Patterns of Gene Expression and Protein Sequence Evolution

    Hunt, B. G.; Ometto, L.; Keller, L.; Goodisman, M. A. D.

    2013-01-01

    Variation in protein sequence and gene expression each contribute to phenotypic diversity, and may be subject to similar selective pressures. Eusocial insects are particularly useful for investigating the evolutionary link between protein sequence and condition-dependent patterns of gene expression because gene expression plays a central role in determining differences between eusocial insect sexes and castes. We investigated the relationship between protein coding sequence evolution and gene...

  5. Dorsoventral patterning in hemichordates: insights into early chordate evolution.

    Christopher J Lowe

    2006-09-01

    Full Text Available We have compared the dorsoventral development of hemichordates and chordates to deduce the organization of their common ancestor, and hence to identify the evolutionary modifications of the chordate body axis after the lineages split. In the hemichordate embryo, genes encoding bone morphogenetic proteins (Bmp 2/4 and 5/8, as well as several genes for modulators of Bmp activity, are expressed in a thin stripe of ectoderm on one midline, historically called "dorsal." On the opposite midline, the genes encoding Chordin and Anti-dorsalizing morphogenetic protein (Admp are expressed. Thus, we find a Bmp-Chordin developmental axis preceding and underlying the anatomical dorsoventral axis of hemichordates, adding to the evidence from Drosophila and chordates that this axis may be at least as ancient as the first bilateral animals. Numerous genes encoding transcription factors and signaling ligands are expressed in the three germ layers of hemichordate embryos in distinct dorsoventral domains, such as pox neuro, pituitary homeobox, distalless, and tbx2/3 on the Bmp side and netrin, mnx, mox, and single-minded on the Chordin-Admp side. When we expose the embryo to excess Bmp protein, or when we deplete endogenous Bmp by small interfering RNA injections, these expression domains expand or contract, reflecting their activation or repression by Bmp, and the embryos develop as dorsalized or ventralized limit forms. Dorsoventral patterning is independent of anterior/posterior patterning, as in Drosophila but not chordates. Unlike both chordates and Drosophila, neural gene expression in hemichordates is not repressed by high Bmp levels, consistent with their development of a diffuse rather than centralized nervous system. We suggest that the common ancestor of hemichordates and chordates did not use its Bmp-Chordin axis to segregate epidermal and neural ectoderm but to pattern many other dorsoventral aspects of the germ layers, including neural cell fates

  6. Climate-linked temporal and spatial patterns in the evolution of African bovidae

    Schikora, Tim F. (Dr. phil. nat.)

    2012-01-01

    Climate and subsequent environmental changes are regarded as one driver of species evolution. Against this background the present study investigates the evolutionary history of the mammalian family Bovidae (Cetartiodactyla, Mammalia), today the most species-rich family of large herbivores on the African continent. Temporal and spatial patterns in that group’s evolution are the focus of the present study and were investigated using methods and data deriving from multiple disciplines (palaeonto...

  7. Patterning and evolution of floral structures - marking time.

    McKim, Sarah; Hay, Angela

    2010-08-01

    The diversity of flowering structures dazzles the eye, dominates the landscape, and invites evolutionary questions regarding the development of such variety. Comparative work in a number of genetically tractable plant species has addressed how diverse floral architectures develop, and started to reveal the balance between conservation and divergence of the patterning mechanisms responsible for when and where flowers form on a plant. We highlight findings from Petunia where conserved LFY/UFO function is under species-specific regulation, and a novel mechanism involving WOX homeodomain proteins for modulating cyme development in diverse nightshades. We also draw attention to recent findings in Arabidopsis of miRNA and chromatin-based timing mechanisms controlling floral development, and illustrate how genetic studies in Arabidopsis relatives can reveal how evolutionary changes in such mechanisms generate diversity in form. PMID:20452201

  8. 2D numerical modelling of meandering channel formation

    Y Xiao; G Zhou; F S Yang

    2016-03-01

    A 2D depth-averaged model for hydrodynamic sediment transport and river morphological adjustment was established. The sediment transport submodel takes into account the influence of non-uniform sediment with bed surface armoring and considers the impact of secondary flow in the direction of bed-loadtransport and transverse slope of the river bed. The bank erosion submodel incorporates a simple simulation method for updating bank geometry during either degradational or aggradational bed evolution. Comparison of the results obtained by the extended model with experimental and field data, and numericalpredictions validate that the proposed model can simulate grain sorting in river bends and duplicate the characteristics of meandering river and its development. The results illustrate that by using its control factors, the improved numerical model can be applied to simulate channel evolution under differentscenarios and improve understanding of patterning processes.

  9. 2D numerical modelling of meandering channel formation

    XIAO, Y.; ZHOU, G.; YANG, F. S.

    2016-03-01

    A 2D depth-averaged model for hydrodynamic sediment transport and river morphological adjustment was established. The sediment transport submodel takes into account the influence of non-uniform sediment with bed surface armoring and considers the impact of secondary flow in the direction of bed-load transport and transverse slope of the river bed. The bank erosion submodel incorporates a simple simulation method for updating bank geometry during either degradational or aggradational bed evolution. Comparison of the results obtained by the extended model with experimental and field data, and numerical predictions validate that the proposed model can simulate grain sorting in river bends and duplicate the characteristics of meandering river and its development. The results illustrate that by using its control factors, the improved numerical model can be applied to simulate channel evolution under different scenarios and improve understanding of patterning processes.

  10. Evolution patterns and parameter regimes in edge localized modes on the National Spherical Torus Experiment

    Smith, D. R.; Fonck, R. J.; McKee, G. R.; Diallo, A.; Kaye, S. M.; LeBlanc, B. P.; Sabbagh, S. A.

    2016-04-01

    We implement unsupervised machine learning techniques to identify characteristic evolution patterns and associated parameter regimes in edge localized mode (ELM) events observed on the National Spherical Torus Experiment. Multi-channel, localized measurements spanning the pedestal region capture the complex evolution patterns of ELM events on Alfvén timescales. Some ELM events are active for less than 100 μs, but others persist for up to 1 ms. Also, some ELM events exhibit a single dominant perturbation, but others are oscillatory. Clustering calculations with time-series similarity metrics indicate the ELM database contains at least two and possibly three groups of ELMs with similar evolution patterns. The identified ELM groups trigger similar stored energy loss, but the groups occupy distinct parameter regimes for ELM-relevant quantities like plasma current, triangularity, and pedestal height. Notably, the pedestal electron pressure gradient is not an effective parameter for distinguishing the ELM groups, but the ELM groups segregate in terms of electron density gradient and electron temperature gradient. The ELM evolution patterns and corresponding parameter regimes can shape the formulation or validation of nonlinear ELM models. Finally, the techniques and results demonstrate an application of unsupervised machine learning at a data-rich fusion facility.

  11. Activated sludge model No. 2d, ASM2d

    Henze, M.

    1999-01-01

    The Activated Sludge Model No. 2d (ASM2d) presents a model for biological phosphorus removal with simultaneous nitrification-denitrification in activated sludge systems. ASM2d is based on ASM2 and is expanded to include the denitrifying activity of the phosphorus accumulating organisms (PAOs...

  12. Patterns of evolution of research strands in the hydrologic sciences

    Schwartz, F. W.; Fang, Y. C.; Parthasarathy, S.

    2005-03-01

    This paper examines issues of impact and innovation in groundwater research by using bibliometric data and citation analysis.The analysis is based on 3120 papers from the journal Water Resources Research with full contents and their citation data from the ISI Web of Science. The research is designed to develop a better understanding of the way citation numbers can be interpreted by scientists. Not surprisingly, the most highly cited papers appear to be pioneers in the field with papers departing significantly from what has come before and to be effective in creating similar, follow-on papers. Papers that are early contributions to a new research strand that is highly influential will be on average highly cited. However, the importance of a research strand as measured by citations seems to fall with time. The citation patterns of some classic papers show that the activity in the topical area and impact of follow-on papers gradually decline with time, which has similarities with Kuhn's ideas of revolutionary and normal science. The results of this study reinforce the importance of being a pioneer in a research strand, strategically shifting research strands, adopting strategies that can facilitate really major research breakthroughs. L'article examine les problèmes d'impact et d'innovation dans la recherche des eaux souterraines en utilisant les données bibliométriques et l'analyse des citations. L'analyse a été faite sur 3120 articles parus dans Water Resources Research en tenant compte de leur texte complet et de toutes citations parues dans l' ISI Web de la Science. Le but de la recherche a été de mieux comprendre comment le nombre des citations peut être interprété par les scientifiques. Ce n'est pas une surprise que les plus cités articles soient les articles-pionniers dans leurs domaines, qui s'écartent d'une manière significative de ce qui a été écrit auparavant et qui ont été suivi par des nouveaux articles. Les articles qui présentent une

  13. Patterns of evolution of research strands in the hydrologic sciences

    Schwartz, F. W.; Fang, Y. C.; Parthasarathy, S.

    2005-03-01

    This paper examines issues of impact and innovation in groundwater research by using bibliometric data and citation analysis.The analysis is based on 3120 papers from the journal Water Resources Research with full contents and their citation data from the ISI Web of Science. The research is designed to develop a better understanding of the way citation numbers can be interpreted by scientists. Not surprisingly, the most highly cited papers appear to be pioneers in the field with papers departing significantly from what has come before and to be effective in creating similar, follow-on papers. Papers that are early contributions to a new research strand that is highly influential will be on average highly cited. However, the importance of a research strand as measured by citations seems to fall with time. The citation patterns of some classic papers show that the activity in the topical area and impact of follow-on papers gradually decline with time, which has similarities with Kuhn's ideas of revolutionary and normal science. The results of this study reinforce the importance of being a pioneer in a research strand, strategically shifting research strands, adopting strategies that can facilitate really major research breakthroughs. L'article examine les problèmes d'impact et d'innovation dans la recherche des eaux souterraines en utilisant les données bibliométriques et l'analyse des citations. L'analyse a été faite sur 3120 articles parus dans Water Resources Research en tenant compte de leur texte complet et de toutes citations parues dans l' ISI Web de la Science. Le but de la recherche a été de mieux comprendre comment le nombre des citations peut être interprété par les scientifiques. Ce n'est pas une surprise que les plus cités articles soient les articles-pionniers dans leurs domaines, qui s'écartent d'une manière significative de ce qui a été écrit auparavant et qui ont été suivi par des nouveaux articles. Les articles qui présentent une

  14. Temporal evolution of the chemical structure during the pattern transfer by ion-beam sputtering

    Ha, N.-B.; Jeong, S.; Yu, S.; Ihm, H.-I.; Kim, J.-S.

    2015-01-01

    Highlights: • Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution were performed. • Degradation of the transferred pattern starts before the overlayer is fully removed. • The chemical analysis reveals the severe reduction of the sputter yield of the material forming the overlayer near the interface due to the compound formation, requesting caution in the practice of the pattern transfer. - Abstract: Ru films patterned by ion-beam sputtering (IBS) serve as sacrificial masks for the transfer of the patterns to Si(1 0 0) and metallic glass substrates by continued IBS. Under the same sputter condition, however, both bare substrates remain featureless. Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution reveal that the pattern transfer, despite its apparent success, suffers from premature degradation before the mask is fully removed by IBS. Moreover, the residue of the mask or Ru atoms stubbornly remains near the surface, resulting in unintended doping or alloying of both patterned substrates.

  15. Temporal evolution of the chemical structure during the pattern transfer by ion-beam sputtering

    Highlights: • Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution were performed. • Degradation of the transferred pattern starts before the overlayer is fully removed. • The chemical analysis reveals the severe reduction of the sputter yield of the material forming the overlayer near the interface due to the compound formation, requesting caution in the practice of the pattern transfer. - Abstract: Ru films patterned by ion-beam sputtering (IBS) serve as sacrificial masks for the transfer of the patterns to Si(1 0 0) and metallic glass substrates by continued IBS. Under the same sputter condition, however, both bare substrates remain featureless. Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution reveal that the pattern transfer, despite its apparent success, suffers from premature degradation before the mask is fully removed by IBS. Moreover, the residue of the mask or Ru atoms stubbornly remains near the surface, resulting in unintended doping or alloying of both patterned substrates

  16. Derivation of a Differential Equation Exhibiting Replicative Time-Evolution Patterns by Inverse Ultra-Discretization

    Tanaka, Hiroshi; Nakajima, Asumi; Nishiyama, Akinobu; Tokihiro, Tetsuji

    2009-03-01

    A differential equation exhibiting replicative time-evolution patterns is derived by inverse ultradiscretizatrion of Fredkin’s game, which is one of the simplest replicative cellular automaton (CA) in two dimensions. This is achieved by employing a certain filter and a clock function in the equation. These techniques are applicable to the inverse ultra-discretization (IUD) of other CA and stabilize the time-evolution of the obtained differential equation. Application to the game of life, another CA in two dimensions, is also presented.

  17. Characteristics of pattern formation and evolution in approximations of Physarum transport networks.

    Jones, Jeff

    2010-01-01

    Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation. PMID:20067403

  18. Time Curves: Folding Time to Visualize Patterns of Temporal Evolution in Data.

    Bach, Benjamin; Shi, Conglei; Heulot, Nicolas; Madhyastha, Tara; Grabowski, Tom; Dragicevic, Pierre

    2016-01-01

    We introduce time curves as a general approach for visualizing patterns of evolution in temporal data. Examples of such patterns include slow and regular progressions, large sudden changes, and reversals to previous states. These patterns can be of interest in a range of domains, such as collaborative document editing, dynamic network analysis, and video analysis. Time curves employ the metaphor of folding a timeline visualization into itself so as to bring similar time points close to each other. This metaphor can be applied to any dataset where a similarity metric between temporal snapshots can be defined, thus it is largely datatype-agnostic. We illustrate how time curves can visually reveal informative patterns in a range of different datasets. PMID:26529718

  19. Phylomemetic patterns in science evolution--the rise and fall of scientific fields.

    Chavalarias, David; Cointet, Jean-Philippe

    2013-01-01

    We introduce an automated method for the bottom-up reconstruction of the cognitive evolution of science, based on big-data issued from digital libraries, and modeled as lineage relationships between scientific fields. We refer to these dynamic structures as phylomemetic networks or phylomemies, by analogy with biological evolution; and we show that they exhibit strong regularities, with clearly identifiable phylomemetic patterns. Some structural properties of the scientific fields - in particular their density -, which are defined independently of the phylomemy reconstruction, are clearly correlated with their status and their fate in the phylomemy (like their age or their short term survival). Within the framework of a quantitative epistemology, this approach raises the question of predictibility for science evolution, and sketches a prototypical life cycle of the scientific fields: an increase of their cohesion after their emergence, the renewal of their conceptual background through branching or merging events, before decaying when their density is getting too low. PMID:23408947

  20. Phylomemetic patterns in science evolution--the rise and fall of scientific fields.

    David Chavalarias

    Full Text Available We introduce an automated method for the bottom-up reconstruction of the cognitive evolution of science, based on big-data issued from digital libraries, and modeled as lineage relationships between scientific fields. We refer to these dynamic structures as phylomemetic networks or phylomemies, by analogy with biological evolution; and we show that they exhibit strong regularities, with clearly identifiable phylomemetic patterns. Some structural properties of the scientific fields - in particular their density -, which are defined independently of the phylomemy reconstruction, are clearly correlated with their status and their fate in the phylomemy (like their age or their short term survival. Within the framework of a quantitative epistemology, this approach raises the question of predictibility for science evolution, and sketches a prototypical life cycle of the scientific fields: an increase of their cohesion after their emergence, the renewal of their conceptual background through branching or merging events, before decaying when their density is getting too low.

  1. A comparative approach reveals differences in patterns of numt insertion during hominoid evolution

    Jensen-Seaman, M.I.; Wildschutte, J.H.; Soto-Calderón, I.D.; Anthony, N. M.

    2009-01-01

    Nuclear integrations of mitochondrial DNA (numts) are widespread among eukaryotes although their prevalence differs greatly among taxa. Most knowledge of numt evolution comes from analyses of whole genome sequences of single species, or more recently from genomic comparisons across vast phylogenetic distances. Here, we employ a comparative approach using human and chimpanzee genome sequence data to infer differences in the patterns and processes underlying numt integrations. We identified 66 ...

  2. On the Evolution of Corruption Patterns in the Post-Communist Countries

    Andrzej Cieslik; Lukasz Goczek

    2015-01-01

    In this paper, we study the evolution of corruption patterns in 27 post-communist countries during the period 1996-2012 using the Control of Corruption Index and the corruption category Markov transition probability matrix. This method allows us to generate the long-run distribution of corruption among the post-communist countries. Our empirical findings suggest that corruption in the post-communist countries is a very persistent phenomenon that does not change much over time. Several theoret...

  3. Post-orogenic evolution of the Sierras Septentrionales and the Sierras Australes and links to the evolution of the eastern Argentina South Atlantic passive continental margin constrained by low temperature thermochronometry and 2D thermokinematic modeling

    Kollenz, Sebastian; Glasmacher, Ulrich Anton; Rossello, Eduardo A.

    2013-04-01

    The eastern Argentina South Atlantic passive continental margin is distinguished by a very flat topography. Out of the so called Pampean flat two mountain ranges are arising. These mountain ranges, the Sierras Australes and the Sierras Septentrionales, are located in the State of Buenos Aires south of the capital Buenos Aires. North of the Sierras Septentrionales the Salado basin is located. The Sierras Septentrionales and the Sierras Australes are also divided by a smaller intracratonic basin. Further in the South the Colorado basin is located. The Sierras Australes is a variscian fold belt originated by strong phases of metamorphosis, but till now it is unclear by how many tectonic phases the area was influenced (Tomezzoli & Vilas, 1999). It consists of Proterozoic to Paleozoic rocks. The Sierras Septentrionales consists mainly of Precambrian crystalline rocks. The Precambrian sequences are overlain by younger Sediments (Cingolani, 2010). The aim is to understand the long-term landscape evolution of the area by quantifiying erosion- and exhumation-rates and by dating ancient rock-uplift-events. Another goal is to find out how the opening of the south atlantic took effect on this region. To fulfill this goal, thermochronological techniques, such as fission-track dating and (U-Th-Sm)/He dating has been applied to samples from the region. Because there was no low-temperature thermochronology done in this area, both techniques were applied on apatites and zircons. Furthermore, numerical modeling of the cooling history has provided the data base for the quantification of the exhumation rates. The first data-set shows clusters of different ages which can be linked to tectonic activities during late Paleozoic times. Also the thermokinematic modeling is leading to new insights of the evolution of both mountain ranges. References: Renata Nela Tomezzoli and Juan Francisco Vilas (1999): Palaeomagnetic constraints on the age of deformation of the Sierras Australes thrust and

  4. Temporal evolution of ripple pattern on silicon surface: An ion induced solid flow approach

    Highlights: • This paper deals with study of 500 eV Ar-ion induced temporal evolution of ripple morphology on p-Si (1 0 0) at room temperature. • An angular window of 51°–72.5°, in terms of ion incidence angle, was chosen for this study. • Temporal evolution of parallel-mode ripples fits well in the framework of ion induced solid flow model over this entire angular window. • We show that the experimentally determined reference timescale (corresponding to the reference angle of 60°) can be used to predict the intrinsic timescales (below which ripple evolution remains in the linear regime) at all other angles. • Our approach reveals that calculation of the ion induced stress can be avoided for calculation of the intrinsic timescales. - Abstract: In this paper, we study temporal evolution of low energy ion-beam induced parallel-mode ripple patterns and explore the possibility of applying ion induced solid flow model on our experimental data. Experiments were performed by using 500 eV argon ions at a fixed ion flux over an angular window of 51° to 72.5°—where parallel-mode ripple patterns evolve. It is observed that evolution of ripples at all angles remains in the linear regime (where the ripple wavelength remains constant and the roughness evolution follows an exponential growth) up to a certain crossover time beyond which the non-linear effects get into the act (in the form of ripple coarsening at lower incidence angles and faceting at higher ones). The intrinsic timescale, beyond which transition from the linear to the non-linear regime takes place at all angles, matches quite well with those predicted by the solid flow model. It is also observed that the non-linear regime sets in quickly at higher incidence angles

  5. Temporal evolution of ripple pattern on silicon surface: An ion induced solid flow approach

    Basu, Tanmoy, E-mail: tanmoy@iopb.res.in; Som, T., E-mail: tsom@iopb.res.in

    2014-08-15

    Highlights: • This paper deals with study of 500 eV Ar-ion induced temporal evolution of ripple morphology on p-Si (1 0 0) at room temperature. • An angular window of 51°–72.5°, in terms of ion incidence angle, was chosen for this study. • Temporal evolution of parallel-mode ripples fits well in the framework of ion induced solid flow model over this entire angular window. • We show that the experimentally determined reference timescale (corresponding to the reference angle of 60°) can be used to predict the intrinsic timescales (below which ripple evolution remains in the linear regime) at all other angles. • Our approach reveals that calculation of the ion induced stress can be avoided for calculation of the intrinsic timescales. - Abstract: In this paper, we study temporal evolution of low energy ion-beam induced parallel-mode ripple patterns and explore the possibility of applying ion induced solid flow model on our experimental data. Experiments were performed by using 500 eV argon ions at a fixed ion flux over an angular window of 51° to 72.5°—where parallel-mode ripple patterns evolve. It is observed that evolution of ripples at all angles remains in the linear regime (where the ripple wavelength remains constant and the roughness evolution follows an exponential growth) up to a certain crossover time beyond which the non-linear effects get into the act (in the form of ripple coarsening at lower incidence angles and faceting at higher ones). The intrinsic timescale, beyond which transition from the linear to the non-linear regime takes place at all angles, matches quite well with those predicted by the solid flow model. It is also observed that the non-linear regime sets in quickly at higher incidence angles.

  6. Correlated evolution of short wavelength sensitive photoreceptor sensitivity and color pattern in Lake Malawi cichlids

    Michael J. Pauers

    2016-02-01

    Full Text Available For evolutionary ecologists, the holy grail of visual ecology is to establish an unambiguous link between photoreceptor sensitivity, the spectral environment, and the perception of specific visual stimuli (e.g., mates, food, predators, etc.. Due to the bright nuptial colors of the males, and the role female mate choice plays in their evolution, the haplochromine cichlid fishes of the African great lakes are favorite research subjects for such investigations. Despite this attention, current evidence is equivocal; while distinct correlations among photoreceptor sensitivity, photic environment, and male coloration exist in Lake Victorian haplochromines, attempts to find such correlations in Lake Malawian cichlids have failed. Lake Malawi haplochromines have a wide variability in their short-wavelength-sensitive photoreceptors, especially compared to their mid- and long-wavelength-sensitive photoreceptors; these cichlids also vary in the degree to which they express one of three basic color patterns (vertical bars, horizontal stripes, and solid patches of colors, each of which is likely used in a different form of communication. Thus, we hypothesize that, in these fishes, spectral sensitivity and color pattern have evolved in a correlated fashion to maximize visual communication; specifically, ultraviolet sensitivity should be found in vertically-barred species to promote ‘private’ communication, while striped species should be less likely to have ultraviolet sensitivity, since their color pattern carries ‘public’ information. Using phylogenetic independent contrasts, we found that barred species had strong sensitivity to ultraviolet wavelengths, but that striped species typically lacked sensitivity to ultraviolet light. Further, the only variable, even when environmental variables were simultaneously considered, that could predict ultraviolet sensitivity was color pattern. We also found that, using models of correlated evolution, color

  7. Refractory nonconvulsive status epilepticus in coma: analysis of the evolution of ictal patterns

    Paulo Breno Noronha Liberalesso

    2012-07-01

    Full Text Available OBJECTIVE: Nonconvulsive status epilepticus (NCSE is currently considered as one of the most frequent types of status epilepticus (SE. The objective of the present study was to identify the natural history of the electrographical evolution of refractory NCSE and to establish the relationship between ictal patterns and prognosis. METHODS: We analyzed, retrospectively, 14 patients with loss of consciousness and NCSE. The ictal patterns were classified as discrete seizures (DS, merging seizures (MS, continuous ictal discharges (CID, continuous ictal discharges with flat periods (CID-F, and periodic lateralized epileptiform discharges (PLEDs. RESULTS: The ictal patterns were DS (n=7; 50.0%, PLEDs (n=3; 1.4%, CID (n=2; 14.3%, MS (n=1; 7.1%, and CID-F (n=1; 7.1%. CONCLUSIONS: NCSE electrographic findings are heterogeneous and do not follow a stereotyped sequence. PLEDs were related to a higher probability of neurological morbidity and mortality.

  8. Comparison patterns of 4 T1 antigens recognized by humoral immune response mediated by IgG and IgM antibodies in female and male mice with breast cancer using 2D-immnunoblots.

    Díaz-Zaragoza, Mariana; Hernández-Ávila, Ricardo; Govezensky, Tzipe; Mendoza, Luis; Meneses-Ruíz, Dulce María; Ostoa-Saloma, Pedro

    2015-09-01

    The early detection of cancer is one of the most promising approaches to reduce its growing burden and develop a curative treatment before the tumor is established. The early diagnosis of breast cancer is the most demanding of all tumors, because it is the most common cancer in women worldwide. We have described a new approach to analyze humoral immune reactions against 4 T1 cell antigens in female mice, reporting that the IgG and IgM responses differed and varied over time and between individuals. In this study, we compared and analyzed the detection of tumor antigens with IgG and IgM from the sera of male mice that were injected with 4 T1 cells into the mammary gland nipple in 2D immunoblot images. The variability in IgM and IgG responses in female and male mice with breast cancer at various stages of disease was characterized, and the properties with regard to antigen recognition were correlated statistically with variables that were associated with the individuals and tumors. The ensuing IgG and IgM responses differed. Only the IgG response decreased over time in female mice--not in male mice. The IgM response was maintained during tumor development in both sexes. Each mouse had a specific pattern of antigen recognition--ie, an immunological signature--represented by a unique set of antigen spots that were recognized by IgM or IgG. These data would support that rationale IgM is a better tool for early diagnosis, because it is not subject to immunosuppression like IgG in female mice with breast cancer. PMID:26026196

  9. Electrodeposition modeling and optimization to improve thin film patterning with orchestrated structure evolution

    Abbasi, Shaghayegh; Kitayaporn, Sathana; Siedlik, Michael J.; Schwartz, Daniel T.; Böhringer, Karl F.

    2012-08-01

    Orchestrated structure evolution is an alternative nanomanufacturing approach that combines the advantages of top-down patterning and bottom-up self-organizing growth. It relies upon tool-directed patterning to create ‘seed’ locations on a surface from which a subsequent deposition process produces the final, merged film. Despite its demonstrated ability to reduce patterning time by orders of magnitude, our prior reliance on mass transfer limited deposition and square seed arrays resulted in extraneous film growth along pattern edges, thereby limiting the pattern quality of the final film. Here, quality improvements are demonstrated by modeling and tuning the growth mechanism of the deposition step to include charge transfer effects. In addition, a seed positioning optimization technique derived from simulated annealing is introduced as a method for relocating the seeds to minimize film overgrowth at the pattern edges. These improvements enable OSE to maintain geometric quality while substantially reducing the time and cost compared to traditional direct-write manufacturing methods.

  10. Electrodeposition modeling and optimization to improve thin film patterning with orchestrated structure evolution

    Orchestrated structure evolution is an alternative nanomanufacturing approach that combines the advantages of top-down patterning and bottom-up self-organizing growth. It relies upon tool-directed patterning to create ‘seed’ locations on a surface from which a subsequent deposition process produces the final, merged film. Despite its demonstrated ability to reduce patterning time by orders of magnitude, our prior reliance on mass transfer limited deposition and square seed arrays resulted in extraneous film growth along pattern edges, thereby limiting the pattern quality of the final film. Here, quality improvements are demonstrated by modeling and tuning the growth mechanism of the deposition step to include charge transfer effects. In addition, a seed positioning optimization technique derived from simulated annealing is introduced as a method for relocating the seeds to minimize film overgrowth at the pattern edges. These improvements enable OSE to maintain geometric quality while substantially reducing the time and cost compared to traditional direct-write manufacturing methods. (paper)

  11. Competition, transmission and pattern evolution: A network analysis of global oil trade

    This paper studies the competition among oil importers using complex network theory, combined with several alternative measures of competition intensity, to analyze the evolution of the pattern and transmission of oil-trading competition. The results indicate that oil trade has formed a global competition pattern and that the role played by the Asian-Pacific region in the evolution of this competition pattern is becoming increasingly prominent. In addition, global competition intensity has continued to rise, and non-OECD countries have become the main driving force for this increase in global competition intensity. The large oil importers are the most significant parts of the global oil-trading competition pattern. They are not only the major participants in the competition for oil resources but also play important roles in the transmission of oil-trading competition. China and the United States especially display the feature of globalization, whose impacts of transmission reach across the whole oil-trading competition network. Finally, a “5C” (changeability, contestability, cooperation, commitment and circumstances) policy framework is put forward to maintain the stability of oil trade and improve the energy security of oil importers in various aspects. - Highlights: • An oil-trading competition network is constructed using complex network theory. • Oil trade has formed a global competition pattern and its intensity has kept rising. • The status of the Asian-Pacific region in the competition pattern becomes prominent. • Large oil importers play important roles in transmitting the trading competition. • A “5C” policy framework is put forward to cope with the intensive competition

  12. Lectures on 2D gravity and 2D string theory

    This report the following topics: loops and states in conformal field theory; brief review of the Liouville theory; 2D Euclidean quantum gravity I: path integral approach; 2D Euclidean quantum gravity II: canonical approach; states in 2D string theory; matrix model technology I: method of orthogonal polynomials; matrix model technology II: loops on the lattice; matrix model technology III: free fermions from the lattice; loops and states in matrix model quantum gravity; loops and states in the C=1 matrix model; 6V model fermi sea dynamics and collective field theory; and string scattering in two spacetime dimensions

  13. The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

    Wolf Yuri I

    2009-09-01

    Full Text Available Abstract Background The elucidation of the dominant role of horizontal gene transfer (HGT in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL concept and intense debates on this subject. Concept Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns and processes of evolution. We posit that replication of the genetic material is the singular fundamental biological process and that replication with an error rate below a certain threshold both enables and necessitates evolution by drift and selection. Starting from this proposition, we outline a general concept of evolution that consists of three major precepts. 1. The primary agency of evolution consists of Fundamental Units of Evolution (FUEs, that is, units of genetic material that possess a substantial degree of evolutionary independence. The FUEs include both bona fide selfish elements such as viruses, viroids, transposons, and plasmids, which encode some of the information required for their own replication, and regular genes that possess quasi-independence owing to their distinct selective value that provides for their transfer between ensembles of FUEs (genomes and preferential replication along with the rest of the recipient genome. 2. The history of replication of a genetic element without recombination is isomorphously represented by a directed tree graph (an arborescence, in the graph theory language. Recombination within a FUE is common between very closely related sequences where homologous recombination is feasible but becomes negligible for longer evolutionary distances. In contrast, shuffling of FUEs occurs at all evolutionary distances. Thus, a tree is a natural representation of the evolution of an individual FUE on the macro scale, but not of an ensemble of FUEs such as a genome. 3. The history of life is properly represented by the "forest" of evolutionary trees for individual FUEs (Forest of Life, or

  14. Cell state switching factors and dynamical patterning modules: complementary mediators of plasticity in development and evolution

    Stuart A Newman; Ramray Bhat; Nadejda V Mezentseva

    2009-10-01

    Ancient metazoan organisms arose from unicellular eukaryotes that had billions of years of genetic evolution behind them. The transcription factor networks present in single-celled ancestors at the origin of the Metazoa (multicellular animals) were already capable of mediating the switching of the unicellular phenotype among alternative states of gene activity in response to environmental conditions. Cell differentiation, therefore, had its roots in phenotypic plasticity, with the ancient regulatory proteins acquiring new targets over time and evolving into the ``developmental transcription factors” (DTFs) of the ``developmental-genetic toolkit.” In contrast, the emergence of pattern formation and morphogenesis in the Metazoa had a different trajectory. Aggregation of unicellular metazoan ancestors changed the organisms’ spatial scale, leading to the first ``dynamical patterning module” (DPM): cell-cell adhesion. Following this, other DPMs (defined as physical forces and processes pertinent to the scale of the aggregates mobilized by a set of toolkit gene products distinct from the DTFs), transformed simple cell aggregates into hollow, multilayered, segmented, differentiated and additional complex structures, with minimal evolution of constituent genes. Like cell differentiation, therefore, metazoan morphologies also originated from plastic responses of cells and tissues. Here we describe examples of DTFs and most of the important DPMs, discussing their complementary roles in the evolution of developmental mechanisms. We also provide recently characterized examples of DTFs in cell type switching and DPMs in morphogenesis of avian limb bud mesenchyme, an embryo-derived tissue that retains a high degree of developmental plasticity.

  15. Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses

    Guillaume Castel

    2014-03-01

    Full Text Available In the last 50 years, hantaviruses have significantly affected public health worldwide, but the exact extent of the distribution of hantavirus diseases, species and lineages and the risk of their emergence into new geographic areas are still poorly known. In particular, the determinants of molecular evolution of hantaviruses circulating in different geographical areas or different host species are poorly documented. Yet, this understanding is essential for the establishment of more accurate scenarios of hantavirus emergence under different climatic and environmental constraints. In this study, we focused on Murinae-associated hantaviruses (mainly Seoul Dobrava and Hantaan virus using sequences available in GenBank and conducted several complementary phylogenetic inferences. We sought for signatures of selection and changes in patterns and rates of diversification in order to characterize hantaviruses’ molecular evolution at different geographical scales (global and local. We then investigated whether these events were localized in particular geographic areas. Our phylogenetic analyses supported the assumption that RNA virus molecular variations were under strong evolutionary constraints and revealed changes in patterns of diversification during the evolutionary history of hantaviruses. These analyses provide new knowledge on the molecular evolution of hantaviruses at different scales of time and space.

  16. Changes in diversification patterns and signatures of selection during the evolution of murinae-associated hantaviruses.

    Castel, Guillaume; Razzauti, Maria; Jousselin, Emmanuelle; Kergoat, Gael J; Cosson, Jean-François

    2014-01-01

    In the last 50 years, hantaviruses have significantly affected public health worldwide, but the exact extent of the distribution of hantavirus diseases, species and lineages and the risk of their emergence into new geographic areas are still poorly known. In particular, the determinants of molecular evolution of hantaviruses circulating in different geographical areas or different host species are poorly documented. Yet, this understanding is essential for the establishment of more accurate scenarios of hantavirus emergence under different climatic and environmental constraints. In this study, we focused on Murinae-associated hantaviruses (mainly Seoul Dobrava and Hantaan virus) using sequences available in GenBank and conducted several complementary phylogenetic inferences. We sought for signatures of selection and changes in patterns and rates of diversification in order to characterize hantaviruses' molecular evolution at different geographical scales (global and local). We then investigated whether these events were localized in particular geographic areas. Our phylogenetic analyses supported the assumption that RNA virus molecular variations were under strong evolutionary constraints and revealed changes in patterns of diversification during the evolutionary history of hantaviruses. These analyses provide new knowledge on the molecular evolution of hantaviruses at different scales of time and space. PMID:24618811

  17. Distinctive patterns of evolution of the δ-globin gene (HBD in primates.

    Ana Moleirinho

    Full Text Available In most vertebrates, hemoglobin (Hb is a heterotetramer composed of two dissimilar globin chains, which change during development according to the patterns of expression of α- and β-globin family members. In placental mammals, the β-globin cluster includes three early-expressed genes, ε(HBE-γ(HBG-ψβ(HBBP1, and the late expressed genes, δ (HBD and β (HBB. While HBB encodes the major adult β-globin chain, HBD is weakly expressed or totally silent. Paradoxically, in human populations HBD shows high levels of conservation typical of genes under strong evolutionary constraints, possibly due to a regulatory role in the fetal-to-adult switch unique of Anthropoid primates. In this study, we have performed a comprehensive phylogenetic and comparative analysis of the two adult β-like globin genes in a set of diverse mammalian taxa, focusing on the evolution and functional divergence of HBD in primates. Our analysis revealed that anthropoids are an exception to a general pattern of concerted evolution in placental mammals, showing a high level of sequence conservation at HBD, less frequent and shorter gene conversion events. Moreover, this lineage is unique in the retention of a functional GATA-1 motif, known to be involved in the control of the developmental expression of the β-like globin genes. We further show that not only the mode but also the rate of evolution of the δ-globin gene in higher primates are strictly associated with the fetal/adult β-cluster developmental switch. To gain further insight into the possible functional constraints that have been shaping the evolutionary history of HBD in primates, we calculated dN/dS (ω ratios under alternative models of gene evolution. Although our results indicate that HBD might have experienced different selective pressures throughout primate evolution, as shown by different ω values between apes and Old World Monkeys + New World Monkeys (0.06 versus 0.43, respectively, these estimates

  18. Axial segregation of granular media rotated in a drum mixer: Pattern evolution

    In the traditional axial segregation effect, a homogeneous mixture of different types of granular material rotated in a drum mixer segregates into surface bands of relatively pure single concentrations along the axis of rotation. This effect primarily has been studied with respect to the initial segregation. However, the initial pattern is not stable, but evolves in time with continued rotation through metastable states of fewer and fewer bands. We describe two experimental studies of this evolution that provide a more complete picture of the dynamics involved in the pattern progression. The use of a charge coupled device camera in conjunction with digital analysis techniques provides a quantitative measure of the state of the surface as a function of time, while magnetic resonance imaging techniques provide a noninvasive method for studying the segregation beneath the surface. These methods indicate that the underlying mechanisms for the pattern evolution may originate in the bulk of the material, beneath the avalanching surface. copyright 1997 The American Physical Society

  19. 2D-hahmoanimaation toteuttamistekniikat

    Smolander, Aku

    2009-01-01

    Opinnäytetyössä tutkitaan erilaisia 2D-hahmoanimaation toteuttamistekniikoita. Aluksi luodaan yleiskatsaus animoinnin historiaan ja tekniikoihin piirtämisestä mallintamiseen. Alkukatsauksen jälkeen tutkitaan 2D-hahmon suunnittelua ja liikkeitä koskevia sääntöjä. Hahmoanimaation liikkeissä huomionarvoisia asioita ovat muun muassa ajastus, liioittelu, ennakointi ja painovoima. Seuraavaksi perehdytään itse 2D-hahmoanimaation toteuttamistekniikoihin. Tavoitteena on selvittää, tutkia ja vertailla ...

  20. Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures.

    Kohsokabe, Takahiro; Kaneko, Kunihiko

    2016-01-01

    Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. PMID:26678220

  1. Differential evolution of MAGE genes based on expression pattern and selection pressure.

    Qi Zhao

    Full Text Available Starting from publicly-accessible datasets, we have utilized comparative and phylogenetic genome analyses to characterize the evolution of the human MAGE gene family. Our characterization of genomic structures in representative genomes of primates, rodents, carnivora, and macroscelidea indicates that both Type I and Type II MAGE genes have undergone lineage-specific evolution. The restricted expression pattern in germ cells of Type I MAGE orthologs is observed throughout evolutionary history. Unlike Type II MAGEs that have conserved promoter sequences, Type I MAGEs lack promoter conservation, suggesting that epigenetic regulation is a central mechanism for controlling their expression. Codon analysis shows that Type I but not Type II MAGE genes have been under positive selection. The combination of genomic and expression analysis suggests that Type 1 MAGE promoters and genes continue to evolve in the hominin lineage, perhaps towards functional diversification or acquiring additional specific functions, and that selection pressure at codon level is associated with expression spectrum.

  2. The Formation, Movement and Evolution Pattern of Jurassic Terrestrial Deposit Basin in Daqingshan Region

    PENG Xiangdong; XU Zhongyuan; LIU Zhenghong

    2001-01-01

    The authors have reconstructed the original shape of Jurassic basin in Daqingshan region and discussed the movement and evolution pattern of the basin. The basin developed between Paleozoic strata sliver and metamorphic rock sliver in late stage of Early Jurassic and extended in latitude direction. The palco - terrene of the basin is higher in north and west than south and east. The boundary of basin is largest in Changhangou stage of Middle Jurassic. After middle Jurassic, the region took place Yenshan movement, and then the basin changed obviously from weakly extending environment of Early and Middle Jurassic to extruding environment of late Jurassic, and the paleoclimate of the basin changed from warmth and wetness to dry. The basin finished the evolution history in the late stage of Late Jurassic with the development of thrust.

  3. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata.

    Maurer-Alcalá, Xyrus X; Katz, Laura A

    2016-01-01

    The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a "heteromeric" macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into "gene-sized" chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a "gene bank" that facilitates rapid changes in expression of genes required only in specific life history stages. By using "nonmodel" organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features. PMID:27189988

  4. Phylogeographic patterns and evolution of the mitochondrial DNA control region in two neotropical cats (Mammalia, felidae).

    Eizirik, E; Bonatto, S L; Johnson, W E; Crawshaw, P G; Vié, J C; Brousset, D M; O'Brien, S J; Salzano, F M

    1998-11-01

    The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation of the Panamanian land bridge 3-5 million years ago. Patterns of population genetic divergence of each species were studied by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed, identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography, population genetic structure, and demographic history were used to formulate conservation recommendations for these species. In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region in closely related felids. PMID:9797412

  5. Exploring the patterns and evolution of self-organized urban street networks through modeling

    Rui, Yikang; Ban, Yifang; Wang, Jiechen; Haas, Jan

    2013-03-01

    As one of the most important subsystems in cities, urban street networks have recently been well studied by using the approach of complex networks. This paper proposes a growing model for self-organized urban street networks. The model involves a competition among new centers with different values of attraction radius and a local optimal principle of both geometrical and topological factors. We find that with the model growth, the local optimization in the connection process and appropriate probability for the loop construction well reflect the evolution strategy in real-world cities. Moreover, different values of attraction radius in centers competition process lead to morphological change in patterns including urban network, polycentric and monocentric structures. The model succeeds in reproducing a large diversity of road network patterns by varying parameters. The similarity between the properties of our model and empirical results implies that a simple universal growth mechanism exists in self-organized cities.

  6. An evolution from 3D face-centered-cubic ZnSnO3 nanocubes to 2D orthorhombic ZnSnO3 nanosheets with excellent gas sensing performance

    We have successfully observed the development of three-dimensional (3D) face-centered-cubic ZnSnO3 into two-dimensional (2D) orthorhombic ZnSnO3 nanosheets, which is the first observation of 2D ZnSnO3 nanostructures to date. The synthesis from 3D to 2D nanostructures is realized by the dual-hydrolysis-assisted liquid precipitation reaction and subsequent hydrothermal treatment. The time-dependent morphology indicates the transformation via a ‘dissolution–recrystallization’ mechanism, accompanied by a ‘further growth’ process. Furthermore, the 2D ZnSnO3 nanosheets consist of smaller sized nanoflakes. This further increases the special specific surface area and facilitates their application in gas sensing. The 2D ZnSnO3 nanosheets exhibit excellent gas sensing properties, especially through their ultra-fast response and recovery. When exposed to ethanol and acetone, the response rate is as fast as 0.26 s and 0.18 s, respectively, and the concentration limit can reach as low as 50 ppb of ethanol. All these results are much better than those reported so far. Our experimental results indicate an efficient approach to realize high-performance gas sensors. (paper)

  7. Numerical study of IP3-induced Ca2+ spiral pattern evolution

    Tang Jun; Ma Jun; Yi Ming; Jia Ya

    2008-01-01

    The effect of change in concentration of messenger molecule inositol 1,4,5-trisphosphate (IP3) on intracellular Ca2+spiral pattern evolution is studied numerically.The results indicate that when the IP3 concentration decreases from 0.27μM,a physiologically reasonable value,to different values,the spiral centre drifts to the edge of the medium and disappears for a small enough IP3 concentration.The instability of spiral pattern can be understood in terms of excitability-change controlled by the IP3 concentration.On the other hand,when the IP3 concentration increases from 0.27μM,a homogeneous area with a high Ca2+ concentration emerges and competes with the spiral pattern.A high enough IP3 concentration can lead the homogeneous area to occupy the whole medium.The instability of spiral pattern is ascribed to the change in stability of a stationary state with a high Ca2+ concentration.

  8. Rapid identification of amino acid types in proteins using phase modulated 2D HN(CACB) and 2D HN(COCACB)

    Dubey, Abhinav; Mondal, Somnath; Chandra, Kousik; Atreya, Hanudatta S.

    2016-06-01

    We present a simple approach to rapidly identify amino acid types in proteins from a 2D spectrum. The method is based on the fact that 13Cβ chemical shifts of different amino acid types fall in distinct spectral regions. By evolving the 13C chemical shifts in the conventional HNCACB or HN(CO)CACB type experiment for a single specified delay period, the phase of the cross peaks of different amino acid residues are modulated depending on their 13Cβ shift values. Following this specified evolution period, the 2D HN projections of these experiments are acquired. The 13C evolution period can be chosen such that all residues belonging to a given set of amino acid types have the same phase pattern (positive or negative) facilitating their identification. This approach does not require the preparation of any additional samples, involves the analysis of 2D [15N-1H] HSQC-type spectra obtained from the routinely used triple resonance experiments with minor modifications, and is applicable to deuterated proteins. The method will be useful for quick assignment of signals that shift during ligand binding or in combination with selective labeling/unlabeling approaches for identification of amino acid types to aid the sequential assignment process.

  9. Holocene denudation pattern across the South-Eastern Australian Escarpment and implications for its evolution

    Godard, Vincent; Dosseto, Anthony; Bellier, Olivier; Bourlès, Didier; Fleury, Jules; Aster Team

    2016-04-01

    Developing a process based understanding of continental relief evolution requires to quantify rates of denudation and to compare their distribution with the evolution of geomorphic parameters. The analysis of denudation and exhumation spatial patterns based from cosmogenic nuclides and low temperature thermochronology are routinely used to document the processes associated with the geomorphic evolution of continental relief over various timescales. Passive margin escarpments are among some of the most salient continental geomorphic features outside of orogenic areas. Their evolution have been studied intensively over the long-term (several Ma to tens of Ma), using for example low-temperature thermochronology. However, datasets documenting their shorter-term (1-10 ka) dynamics are scarcer, and only a limited number of case studies have used quantitative techniques such as cosmogenic nuclides to document the denudation pattern across such escarpments. The South Eastern Australian Escarpment is such a place where cosmogenic nuclides have been intensively used over the last two decades to constrain processes of landscape evolution over short wavelength, with, for example the calibration of the soil production function. Such existing data and constraints provide an ideal setting to carry on further long-wavelength exploration of the dynamics of the whole escarpment. We have sampled 17 catchments across the South Eastern Australian Escarpment, starting from the coastal plain and moving westward up to the low relief plateau surface. The observed landscape denudation rates are 10-20 mm/ka in the coastal area and progressively increases up to ~60 mm/ka toward the edge of the escarpment. In the low-relief areas located west of the continental drainage divide denudation rates fall back to 10-20 mm/ka. This nearly four-fold contrast in denudation across the divide is characteristic of a major disequilibrium in the dynamics of the river network associated with a progressive

  10. Optoelectronics with 2D semiconductors

    Mueller, Thomas

    2015-03-01

    Two-dimensional (2D) atomic crystals, such as graphene and layered transition-metal dichalcogenides, are currently receiving a lot of attention for applications in electronics and optoelectronics. In this talk, I will review our research activities on electrically driven light emission, photovoltaic energy conversion and photodetection in 2D semiconductors. In particular, WSe2 monolayer p-n junctions formed by electrostatic doping using a pair of split gate electrodes, type-II heterojunctions based on MoS2/WSe2 and MoS2/phosphorene van der Waals stacks, 2D multi-junction solar cells, and 3D/2D semiconductor interfaces will be presented. Upon optical illumination, conversion of light into electrical energy occurs in these devices. If an electrical current is driven, efficient electroluminescence is obtained. I will present measurements of the electrical characteristics, the optical properties, and the gate voltage dependence of the device response. In the second part of my talk, I will discuss photoconductivity studies of MoS2 field-effect transistors. We identify photovoltaic and photoconductive effects, which both show strong photoconductive gain. A model will be presented that reproduces our experimental findings, such as the dependence on optical power and gate voltage. We envision that the efficient photon conversion and light emission, combined with the advantages of 2D semiconductors, such as flexibility, high mechanical stability and low costs of production, could lead to new optoelectronic technologies.

  11. Accretion Disks Phase Transitions 2-D or not 2-D?

    Abramowicz, M A; Igumenshchev, I V; Abramowicz, Marek Artur; Bjornsson, Gunnlaugur; Igumenshchev, Igor V.

    2000-01-01

    We argue that the proper way to treat thin-thick accretion-disk transitions should take into account the 2-D nature of the problem. We illustrate the physical inconsistency of the 1-D vertically integrated approach by discussing a particular example of the convective transport of energy.

  12. DESIGN METHODOLOGY OF NETWORKED SOFTWARE EVOLUTION GROWTH BASED ON SOFTWARE PATTERNS

    Keqing HE; Rong PENG; Jing LIU; Fei HE; Peng LIANG; Bing LI

    2006-01-01

    Recently, some new characteristics of complex networks attract the attentions of scientists in different fields, and lead to many kinds of emerging research directions. So far, most of the research work has been limited in discovery of complex network characteristics by structure analysis in large-scale software systems. This paper presents the theoretical basis, design method, algorithms and experiment results of the research. It firstly emphasizes the significance of design method of evolution growth for network topology of Object Oriented (OO) software systems, and argues that the selection and modulation of network models with various topology characteristics will bring un-ignorable effect on the process of design and implementation of OO software systems. Then we analyze the similar discipline of "negation of negation and compromise" between the evolution of network models with different topology characteristics and the development of software modelling methods. According to the analysis of the growth features of software patterns, we propose an object-oriented software network evolution growth method and its algorithms in succession. In addition, we also propose the parameter systems for Oosoftware system metrics based on complex network theory. Based on these parameter systems, it can analyze the features of various nodes, links and local-world, modulate the network topology and guide the software metrics. All these can be helpful to the detailed design, implementation and performance analysis. Finally, we focus on the application of the evolution algorithms and demonstrate it by a case study.Comparing the results from our early experiments with methodologies in empirical software engineering, we believe that the proposed software engineering design method is a computational software engineering approach based on complex network theory. We argue that this method should be greatly beneficial for the design, implementation, modulation and metrics of

  13. Patterns of evolution of MHC class II genes of crows (Corvus suggest trans-species polymorphism

    John A. Eimes

    2015-03-01

    Full Text Available A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP, in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis American crows (C. brachyrhynchos and carrion crows (C. corone orientalis. Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed using non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While

  14. Evolution of large amplitude 3D fold patterns: A FEM study

    Schmid, D. W.; Dabrowski, M.; Krotkiewski, M.

    2008-12-01

    The numerical study of three-dimensional (3D) fold patterns formation in randomly perturbed layers requires large numbers of degrees of freedom (≥100,000,000). We have developed BILAMIN, an unstructured (geometry fitted) mesh implementation of the finite element method for incompressible Stokes flow that is capable of solving such systems. All repetitive and computationally intensive steps are fully parallelized. One of the main components is the iterative solver. We chose the minimum residual method (MINRES) because it allows operating directly on the indefinite systems resulting from the incompressibility condition. We use BILAMIN in a case study of fold pattern evolution. Folds are ubiquitous in nature, and contain both mechanical and kinematic information that can be deciphered with appropriate tools. Our results show that there is a relationship between fold aspect ratio and in-plane loading conditions. We propose that this finding can be used to determine the complete parameter set potentially contained in the geometry of three-dimensional folds: mechanical properties of natural rocks, maximum strain, and relative strength of the in-plane far-field load components. Furthermore, we show how folds in 3D amplify and that there is a second deformation mode, besides continuous amplification, where compression leads to a lateral rearrangement of blocks of folds. Finally, we demonstrate that the textbook prediction of egg carton-shaped dome and basin structures resulting from folding instabilities in constriction is largely oversimplified. The fold patterns resulting in this setting are curved, elongated folds with random orientation.

  15. Patterns of evolution and host gene mimicry in influenza and other RNA viruses.

    Benjamin D Greenbaum

    2008-06-01

    Full Text Available It is well known that the dinucleotide CpG is under-represented in the genomic DNA of many vertebrates. This is commonly thought to be due to the methylation of cytosine residues in this dinucleotide and the corresponding high rate of deamination of 5-methycytosine, which lowers the frequency of this dinucleotide in DNA. Surprisingly, many single-stranded RNA viruses that replicate in these vertebrate hosts also have a very low presence of CpG dinucleotides in their genomes. Viruses are obligate intracellular parasites and the evolution of a virus is inexorably linked to the nature and fate of its host. One therefore expects that virus and host genomes should have common features. In this work, we compare evolutionary patterns in the genomes of ssRNA viruses and their hosts. In particular, we have analyzed dinucleotide patterns and found that the same patterns are pervasively over- or under-represented in many RNA viruses and their hosts suggesting that many RNA viruses evolve by mimicking some of the features of their host's genes (DNA and likely also their corresponding mRNAs. When a virus crosses a species barrier into a different host, the pressure to replicate, survive and adapt, leaves a footprint in dinucleotide frequencies. For instance, since human genes seem to be under higher pressure to eliminate CpG dinucleotide motifs than avian genes, this pressure might be reflected in the genomes of human viruses (DNA and RNA viruses when compared to those of the same viruses replicating in avian hosts. To test this idea we have analyzed the evolution of the influenza virus since 1918. We find that the influenza A virus, which originated from an avian reservoir and has been replicating in humans over many generations, evolves in a direction strongly selected to reduce the frequency of CpG dinucleotides in its genome. Consistent with this observation, we find that the influenza B virus, which has spent much more time in the human population, has

  16. SES2D user's manual

    SES2D is an interactive graphics code designed to generate plots of equation of state data from the Los Alamos National Laboratory Group T-4 computer libraries. This manual discusses the capabilities of the code. It describes the prompts and commands and illustrates their use with a sample run

  17. 2D-Oide effect

    Blanco, O R; Bambade, P

    2015-01-01

    The Oide effect considers the synchrotron radiation in the final focusing quadrupole and it sets a lower limit on the vertical beam size at the Interaction Point, particularly relevant for high energy linear colliders. The theory of the Oide effect was derived considering only the radiation in the focusing plane of the magnet. This article addresses the theoretical calculation of the radiation effect on the beam size consider- ing both focusing and defocusing planes of the quadrupole, refered to as 2D-Oide. The CLIC 3 TeV final quadrupole (QD0) and beam parameters are used to compare the theoretical results from the Oide effect and the 2D-Oide effect with particle tracking in PLACET. The 2D-oide demonstrates to be important as it increases by 17% the contribution to the beam size. Further insight into the aberrations induced by the synchrotron radiation opens the possibility to partially correct the 2D-Oide effect with octupole magn

  18. Excitation of 2D plasmons in Cs/W(110)

    Benemanskaya, G V; Frank-Kamenetskaya, G E

    2001-01-01

    One studied the evolution of surface photoemission spectra for Cs/W(110) system at metastable Cs coatings exceeding monolayer. One showed possibility to observe 2D plasmons by means of threshold photoemission spectroscopy. One detected three photoemission peaks characterized by complicated behavior depending on Cd adsorption dose. The nature of peaks may be related to plasmon photoinduced excitation in quasi-2D Cs clusters, surface Cs plasmon and interface Cs-W plasmon

  19. Nonlinear Amplitude Evolution During Spontaneous Patterning of Ion-Bombarded Si(001)

    Chason, Eric; Erlebacher, Jonah, Aziz, Michael J.; Floro, Jerold A.; Sinclair, Michael B.

    1999-05-05

    The time evolution of the amplitude of periodic nanoscale ripple patterns formed on Ar+ sputtered Si(OOl ) surfaces was examined using a recently developed in situ spectroscopic technique. At sufficiently long times, we find that the amplitude does not continue to grow exponentially as predicted by the standard Bradley-Harper sputter rippling model. In accounting for this discrepancy, we rule out effects related to the concentration of mobile species, high surface curvature, surface energy anisotropy, and ion-surface interactions. We observe that for all wavelengths the amplitude ceases to grow when the width of the topmost terrace of the ripples is reduced to approximately 25 nm. This observation suggests that a short circuit relaxation mechanism limits amplitude . growth. A strategy for influencing the ultimate ripple amplitude is discussed.

  20. Nonlinear Amplitude Evolution During Spontaneous Patterning of Ion-Bombarded Si(001)

    The time evolution of the amplitude of periodic nanoscale ripple patterns formed on Ar+ sputtered Si(OOl ) surfaces was examined using a recently developed in situ spectroscopic technique. At sufficiently long times, we find that the amplitude does not continue to grow exponentially as predicted by the standard Bradley-Harper sputter rippling model. In accounting for this discrepancy, we rule out effects related to the concentration of mobile species, high surface curvature, surface energy anisotropy, and ion-surface interactions. We observe that for all wavelengths the amplitude ceases to grow when the width of the topmost terrace of the ripples is reduced to approximately 25 nm. This observation suggests that a short circuit relaxation mechanism limits amplitude . growth. A strategy for influencing the ultimate ripple amplitude is discussed

  1. Experimental Evolution under Fluctuating Thermal Conditions Does Not Reproduce Patterns of Adaptive Clinal Differentiation in Drosophila melanogaster.

    Kellermann, Vanessa; Hoffmann, Ary A; Kristensen, Torsten Nygaard; Moghadam, Neda Nasiri; Loeschcke, Volker

    2015-11-01

    Experimental evolution can be a useful tool for testing the impact of environmental factors on adaptive changes in populations, and this approach is being increasingly used to understand the potential for evolutionary responses in populations under changing climates. However, selective factors will often be more complex in natural populations than in laboratory environments and produce different patterns of adaptive differentiation. Here we test the ability of laboratory experimental evolution under different temperature cycles to reproduce well-known patterns of clinal variation in Drosophila melanogaster. Six fluctuating thermal regimes mimicking the natural temperature conditions along the east coast of Australia were initiated. Contrary to expectations, on the basis of field patterns there was no evidence for adaptation to thermal regimes as reflected by changes in cold and heat resistance after 1-3 years of laboratory natural selection. While laboratory evolution led to changes in starvation resistance, development time, and body size, patterns were not consistent with those seen in natural populations. These findings highlight the complexity of factors affecting trait evolution in natural populations and indicate that caution is required when inferring likely evolutionary responses from the outcome of experimental evolution studies. PMID:26655772

  2. Controllable synthesis of Cu2O petalody octahedral microcrystals and multi-patterned evolution.

    Ding, Yanbo; Ge, Dengteng; Yang, Lili; Li, Zhenyu; Xin, Wuhong; Li, Yao; Wu, Xiaohong; Zhao, Jiupeng

    2013-02-15

    The fabrication of cuprous oxide (Cu(2)O) with various morphologies has attracted extensive interest due to its applications in solar energy conversion, electrode materials, sensors, and catalysts. Herein, we report a facile controllable route for Cu(2)O microcrystals with various architectures via a hydrothermal method without using templates or surfactants. Six types of Cu(2)O microcrystals including petalody octahedral, concave truncated octahedron, truncated octahedron, octahedron, sphere-like, and sphere are obtained accompanying with Cu precipitation or urchin-like CuO particles due to the modifying of pH values. The petalody octahedral pattern of Cu(2)O is for the first time found here under the condition of pH 7-8. Additionally, possible growth mechanism for multi-patterned Cu(2)O and compositional evolution is discussed via preferential growths induced by selective absorption of acrylic acid and decomposition of lactic acid in the present reaction system. These experimental results prove a versatile and facile strategy for Cu(2)O microcrystals with special and complex architectures, which may highlights their potential applications due to the improved surface activity, catalytic, or photoelectric performance. PMID:23127874

  3. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    Sen, Lin

    2011-06-03

    mutations put forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities. Reviewers This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier.

  4. Flow pattern and lift evolution of hydrofoil with control of electro-magnetic forces

    CHEN YaoHui; FAN BaoChun; CHEN ZhiHua; LI HongZhi

    2009-01-01

    The Initial responses and evolutions of the flow pattern and lift coefficient of a hydrofoil under the ac-tion of electro-magnetic (Lorentz) force have been studied experimentally and numerically,and trace particle methods are employed for them.With the introduction of BVF (boundary vortex flux),the quantitative relation among Lorentz forces,BVF and lifts is deduced.The influences of flow patterns on the hydrofoil lift coefficient have been discussed based on the BVF distribution,and the flow control mechanism of Lorentz force for a hydrofoil has been elucidated.Our results show that the flow pattern and lift of the hydrofoil vary periodically without any force.However,with the action of streamwise Lorentz forces,the separation point on the hydrofoil surface moves backward with a certain velocity,which makes the flow field steady finally.The streamwise Lorentz force raises the foil lift due to the Increase of BVF intensity.On the other hand,Lorentz force also increases the hydrofoil surface pres-sure,which makes the lift decrease.However,the factor leading to the lift enhancement is determinant,therefore,the Lorentz force on the suction side can increase the lift,and the stronger the Lorentz force,the larger the lift enhancement.Our results also show that the localized Lorentz force can also both suppress the flow separation and increase the hydrofoil lift coefficient,furthermore,the Lorentz force located on the tail acts better than that located on the front.

  5. Dynamical patterning modules: physico-genetic determinants of morphological development and evolution

    Newman, Stuart A.; Bhat, Ramray

    2008-03-01

    The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved 'developmental-genetic toolkit', the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of 'dynamical patterning modules' (DPMs), units consisting of one or more products of the 'toolkit' genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a 'pattern language' capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent 'molecular homology-analogy paradox', whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo

  6. Dynamical patterning modules: physico-genetic determinants of morphological development and evolution

    The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved 'developmental-genetic toolkit', the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of 'dynamical patterning modules' (DPMs), units consisting of one or more products of the 'toolkit' genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a 'pattern language' capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent 'molecular homology-analogy paradox', whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo

  7. Multienzyme Inkjet Printed 2D Arrays.

    Gdor, Efrat; Shemesh, Shay; Magdassi, Shlomo; Mandler, Daniel

    2015-08-19

    The use of printing to produce 2D arrays is well established, and should be relatively facile to adapt for the purpose of printing biomaterials; however, very few studies have been published using enzyme solutions as inks. Among the printing technologies, inkjet printing is highly suitable for printing biomaterials and specifically enzymes, as it offers many advantages. Formulation of the inkjet inks is relatively simple and can be adjusted to a variety of biomaterials, while providing nonharmful environment to the enzymes. Here we demonstrate the applicability of inkjet printing for patterning multiple enzymes in a predefined array in a very straightforward, noncontact method. Specifically, various arrays of the enzymes glucose oxidase (GOx), invertase (INV) and horseradish peroxidase (HP) were printed on aminated glass surfaces, followed by immobilization using glutardialdehyde after printing. Scanning electrochemical microscopy (SECM) was used for imaging the printed patterns and to ascertain the enzyme activity. The successful formation of 2D arrays consisting of enzymes was explored as a means of developing the first surface confined enzyme based logic gates. Principally, XOR and AND gates, each consisting of two enzymes as the Boolean operators, were assembled, and their operation was studied by SECM. PMID:26214072

  8. R2d2 Drives Selfish Sweeps in the House Mouse.

    Didion, John P; Morgan, Andrew P; Yadgary, Liran; Bell, Timothy A; McMullan, Rachel C; Ortiz de Solorzano, Lydia; Britton-Davidian, Janice; Bult, Carol J; Campbell, Karl J; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J; Crowley, James J; Chesler, Elissa J; Förster, Daniel W; French, John E; Gabriel, Sofia I; Gatti, Daniel M; Garland, Theodore; Giagia-Athanasopoulou, Eva B; Giménez, Mabel D; Grize, Sofia A; Gündüz, İslam; Holmes, Andrew; Hauffe, Heidi C; Herman, Jeremy S; Holt, James M; Hua, Kunjie; Jolley, Wesley J; Lindholm, Anna K; López-Fuster, María J; Mitsainas, George; da Luz Mathias, Maria; McMillan, Leonard; Ramalhinho, Maria da Graça Morgado; Rehermann, Barbara; Rosshart, Stephan P; Searle, Jeremy B; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L; Thomas-Laemont, Patricia; Threadgill, David W; Ventura, Jacint; Weinstock, George M; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando

    2016-06-01

    A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether "selfish" genes are capable of fixation-thereby leaving signatures identical to classical selective sweeps-despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2(HC)) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2(HC) rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2(HC) is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. PMID:26882987

  9. Patterns of Chromosomal Evolution in Sigmodon, Evidence from Whole Chromosome Paints

    Swier, V.J.; Bradley, R.D.; Rens, W.; Elder, F.F.B.; Baker, R.J.

    2009-01-01

    Of the superfamily Muroidea (31 genera, 1578 species), the Sigmodontinae (74 genera, 377 species) is the second largest subfamily in number of species and represents a significant radiation of rodent biodiversity. Only 2 of the 74 genera are found in both North and South America (Sigmodon and Oryzomys) and the remainder are exclusively from South America. In recent molecular studies, the genus Sigmodon (Cricetidae, Sigmodontinae) has been considered sister to many other South American Sigmodontines [Steppan et al., 2004]. We examine the chromosomal evolution of 9 species of Sigmodon utilizing chromosomal paints isolated from S. hispidus, proposed to be similar to the ancestral karyotype [Elder, 1980]. Utilizing a phylogenetic hypothesis of a molecular phylogeny of Sigmodon [Henson and Bradley, 2009], we mapped shared chromosomal rearrangements of taxa on a molecular tree to estimate the evolutionary position of each rearrangement. For several species (S. hirsutus, S. leucotis, S. ochrognathus, S. peruanus, and S. toltecus), the karyotype accumulated few or no changes, but in three species (S. arizonae, S. fulviventer, and S. mascotensis) numerous karyotype rearrangements were observed. These rearrangements involved heterochromatic additions, centric fusions, tandem fusions, pericentric inversions, as well as the addition of interstitial DNA not identified by chromosome paints or C-banding. The hypothesis that the ancestral karyotype for this complex had a diploid number of 52, a fundamental number of 52, and a G-band pattern of which most, if not all are similar to that present in modern day S. hispidus fails to be rejected. This hypothesis remains viable as an explanation of chromosomal evolution in Sigmodontine rodents. PMID:19617697

  10. 2D-animaatiotuotannon optimointi

    Saturo, Reetta

    2015-01-01

    Tämän opinnäytetyön tavoitteena on tutkia 2D-animaatiotuotannon optimoinnin mahdollisuuksia tiukan tuotantoaikataulun vaatimuksissa. Tutkielmassa tarkastellaan kahta asiakasprojektia, jotka on toteutettu pienellä tuotantotiimillä. Työkaluna animaatioissa on käytetty pääosin Adoben After Effects -ohjelmistoa. Tutkielman alussa esitellään animaatiotuotannot, joiden tuloksena syntyi kaksi lyhyttä mainoselokuvaa. Sen jälkeen käydään läpi animaatioelokuvan tuotantoprosessia vaiheittain ja tark...

  11. Head First 2D Geometry

    Fallow), Stray

    2009-01-01

    Having trouble with geometry? Do Pi, The Pythagorean Theorem, and angle calculations just make your head spin? Relax. With Head First 2D Geometry, you'll master everything from triangles, quads and polygons to the time-saving secrets of similar and congruent angles -- and it'll be quick, painless, and fun. Through entertaining stories and practical examples from the world around you, this book takes you beyond boring problems. You'll actually use what you learn to make real-life decisions, like using angles and parallel lines to crack a mysterious CSI case. Put geometry to work for you, and

  12. [Spatial pattern evolution of carbon emission intensity from energy consumption in China].

    Zhao, Yun-Tai; Huang, Xian-Jin; Zhong, Tai-Yang; Peng, Jia-Wen

    2011-11-01

    Using Theil index and spatial autocorrelation analysis methods, the characteristics, regional disparity and spatial pattern evolution of carbon emission intensity from energy consumption were analyzed on national, regional and provincial level from 1999 to 2007 in China. The results indicate that: (1) total energy carbon emission in China has increased from 0.91Gt in 1999 to 1.83Gt in 2007, while carbon emission intensity has decreased from 0.83 t x (10(4) yuan) (-1) to 0.79 t x (10(4) yuan) (-1); (2) carbon emission intensity of eight major economic blocks showed the trend of three-level differentiation, with that of northeast regions, the middle reaches of Yellow River regions and northwest regions above 1.0 t x (10(4) yuan)(-1); northern coastal regions, the middle reaches of Yangtze River regions and southwest regions 0.7-1.0 t x (10(4) yuan) (-1); eastern and northern regions 0.32-0.51 t x (10(4) yuan) (-1); (3) Theil index analysis indicates that the within-region carbon emission intensities were similar, and the expanding total disparity of carbon emission intensity was primarily due to between-region inequalities. (4) spatial autocorrelation analysis shows that Global Moran's I has increased from 0.19 to 0.25, indicating that there were positive spatial correlations among provincial regions in China, and regions of similar carbon emission intensity agglomerated in space. The "cold spot" areas of carbon emission intensity were relatively stable, while the "hot spot" areas has gradually shifted from northwest regions to the middle reaches of Yellow River regions and northeast regions. (5) spatial disparity of carbon emission intensity is closely related to factors such as regional resources endowment, economic development, industrial structure and energy utilization efficiency. The study of regional disparity and spatial autocorrelation provides insight into spatial heterogeneity and spatial pattern evolution of carbon emission intensity in China, and also

  13. Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI from the Class Arachnida.

    Monica R Young

    Full Text Available Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625. It examines divergences at three taxonomic levels-among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10-0.39, while the mean of the Family Distances for the ten orders ranges fivefold (0.07-0.35. BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is 'locked down' in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in 'locked down' taxa.

  14. Orchestrated structure evolution: accelerating direct-write nanomanufacturing by combining top-down patterning with bottom-up growth

    Direct-write nanomanufacturing with scanning beams and probes is flexible and can produce high quality products, but it is normally slow and expensive to raster point-by-point over a pattern. We demonstrate the use of an accelerated direct-write nanomanufacturing method called 'orchestrated structure evolution' (OSE), where a direct-write tool patterns a small number of growth 'seeds' that subsequently grow into the final thin film pattern. Through control of seed size and spacing, it is possible to vary the ratio of 'top-down' to 'bottom-up' character of the patterning processes, ranging from conventional top-down raster patterning to nearly pure bottom-up space-filling via seed growth. Electron beam lithography (EBL) and copper electrodeposition were used to demonstrate trade-offs between process time and product quality over nano- to microlength scales. OSE can reduce process times for high-cost EBL patterning by orders of magnitude, at the expense of longer (but inexpensive) copper electrodeposition processing times. We quantify the degradation of pattern quality that accompanies fast OSE patterning by measuring deviations from the desired patterned area and perimeter. We also show that the density of OSE-induced grain boundaries depends upon the seed separation and size. As the seed size is reduced, the uniformity of an OSE film becomes more dependent on details of seed nucleation processes than normally seen for conventionally patterned films.

  15. Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome

    Sreepriya Pramod; Andy D. Perkins; Mark E. Welch

    2014-08-01

    The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly 5′UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli.

  16. Computational Experiment Approach to Controlled Evolution of Procurement Pattern in Cluster Supply Chain

    Xiao Xue

    2015-01-01

    Full Text Available Companies have been aware of the benefits of developing Cluster Supply Chains (CSCs, and they are spending a great deal of time and money attempting to develop the new business pattern. Yet, the traditional techniques for identifying CSCs have strong theoretical antecedents, but seem to have little traction in the field. We believe this is because the standard techniques fail to capture evolution over time, nor provide useful intervention measures to reach goals. To address these problems, we introduce an agent-based modeling approach to evaluate CSCs. Taking collaborative procurement as research object, our approach is composed of three parts: model construction, model instantiation, and computational experiment. We use the approach to explore the service charging policy problem in collaborative procurement. Three kinds of service charging polices are compared in the same experiment environment. Finally, “Fixed Cost” is identified as the optimal policy under the stable market environment. The case study can help us to understand the workflow of applying the approach, and provide valuable decision support applications to industry.

  17. 2D SIMPLIFIED SERVO VALVE

    2003-01-01

    A novel pilot stage valve called simplified 2D valve, which utilizes both rotary and linear motions of a single spool, is presented.The rotary motion of the spool incorporating hydraulic resistance bridge, formed by a damper groove and a crescent overlap opening, is utilized as pilot to actuate linear motion of the spool.A criterion for stability is derived from the linear analysis of the valve.Special experiments are designed to acquire the mechanical stiffness, the pilot leakage and the step response.It is shown that the sectional size of the spiral groove affects the dynamic response and the stiffness contradictorily and is also very sensitive to the pilot leakage.Therefore, it is necessary to establish a balance between the static and dynamic characteristics in deciding the structural parameters.Nevertheless, it is possible to sustain the dynamic response at a fairly high level, while keeping the leakage of the pilot stage at an acceptable level.

  18. Personalized 2D color maps

    Waldin, Nicholas

    2016-06-24

    2D color maps are often used to visually encode complex data characteristics such as heat or height. The comprehension of color maps in visualization is affected by the display (e.g., a monitor) and the perceptual abilities of the viewer. In this paper we present a novel method to measure a user\\'s ability to distinguish colors of a two-dimensional color map on a given monitor. We show how to adapt the color map to the user and display to optimally compensate for the measured deficiencies. Furthermore, we improve user acceptance of the calibration procedure by transforming the calibration into a game. The user has to sort colors along a line in a 3D color space in a competitive fashion. The errors the user makes in sorting these lines are used to adapt the color map to his perceptual capabilities.

  19. The evolution of pattern camouflage strategies in waterfowl and game birds

    Marshall, Kate L A; Gluckman, Thanh-Lan

    2015-01-01

    Visual patterns are common in animals. A broad survey of the literature has revealed that different patterns have distinct functions. Irregular patterns (e.g., stipples) typically function in static camouflage, whereas regular patterns (e.g., stripes) have a dual function in both motion camouflage and communication. Moreover, irregular and regular patterns located on different body regions (?bimodal? patterning) can provide an effective compromise between camouflage and communication and/or e...

  20. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera.

    Lewis, James J; van der Burg, Karin R L; Mazo-Vargas, Anyi; Reed, Robert D

    2016-09-13

    Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution. PMID:27626657

  1. Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses

    Ghose Chandrabali

    2006-01-01

    Full Text Available Abstract Background Virus taxonomy is based on morphologic characteristics, as there are no widely used non-phenotypic measures for comparison among virus families. We examined whether there is phylogenetic signal in virus nucleotide usage patterns that can be used to determine ancestral relationships. The well-studied model of tail morphology in bacteriophage classification was used for comparison with nucleotide usage patterns. Tetranucleotide usage deviation (TUD patterns were chosen since they have previously been shown to contain phylogenetic signal similar to that of 16S rRNA. Results We found that bacteriophages have unique TUD patterns, representing genomic signatures that are relatively conserved among those with similar host range. Analysis of TUD-based phylogeny indicates that host influences are important in bacteriophage evolution, and phylogenies containing both phages and their hosts support their co-evolution. TUD-based phylogeny of eukaryotic viruses indicates that they cluster largely based on nucleic acid type and genome size. Similarities between eukaryotic virus phylogenies based on TUD and gene content substantiate the TUD methodology. Conclusion Differences between phenotypic and TUD analysis may provide clues to virus ancestry not previously inferred. As such, TUD analysis provides a complementary approach to morphology-based systems in analysis of virus evolution.

  2. SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in Warblers

    Bloch, Natasha I.; Morrow, James M; Chang, Belinda S. W.; Price, Trevor D

    2015-01-01

    Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors – historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between ...

  3. Bone remodelling after hip prostheses surgery: normal evolution patterns by bone scintigraphy

    Evaluation of hip prostheses is a common task in nuclear medicine practice. Physicians usually have problems to differentiate between changes in bone remodelling related to surgical procedures and complications like infection or loosening. Aim: To assess changes in bone remodelling after hip prostheses surgery by bone scintigraphy, and to determine normal evolution patterns of tracer uptake. To relate changes in bone remodelling with type of prostheses and clinical outcome. Materials and Methods: We studied 18 patients (6 males, mean age 68±10 years) who receipt a hip prostheses. Every patient underwent 3 bone scintigraphies, at 3 months, 1 year and 2 years after surgical implant of hip prostheses. Twelve prostheses were non-cemented, 3 were cemented and 3 hybrids. A semi-quantification of tracer uptake was performed, obtaining an uptake index from the average counts per pixel of regions of interest (ROIs) drawn around sacroiliac joints, acetabulum, greater trochanter, calcar, femur shaft, tip, and opposite normal femur. Sacroiliac joints and opposite normal femur were selected as reference areas. The uptake index was calculated by the formula: (ROI-reference)/reference. Clinical follow-up was performed at 3 months, 6 months, 1 year and 2 years. Results: While tracer uptake indexes of non-cemented prostheses decreased significantly in greater trochanter, calcar, femur shaft, and tip between 3 months-1 year studies, 1 year-2 years studies and between 3 months and 2 years studies (t-student, p<0.05), tracer uptake indexes did not decrease in acetabulum, opposite normal femur, and sacroiliac joint. On the contrary, cemented and hybrid prostheses did not show any significant difference in studied areas during the follow-up. All patients presented good clinical outcome, without pain and with correct mobility of the leg. Conclusion: These preliminary results indicate that, when non-cemented hip prostheses are implanted, there are important bone remodelling changes at 3

  4. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

    Lapidus, Alla; Kettler, Gregory C.; Martiny, Adam C.; Huang, Katherine; Zucker, Jeremy; Coleman, Maureen L.; Rodrigue, Sebastien; Chen, Feng; Lapidus, Alla; Ferriera, Steven; Johnson, Justin; Steglich, Claudia; Church, George M.; Richardson, Paul; Chisholm, Sallie W.

    2007-07-30

    Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolatesfrom diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3percent, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer

  5. A pattern language for evolution in component-based software architectures

    Ahmad, Aakash; Jamshidi, Pooyan; Pahl, Claus; Khaliq, Fawad

    2013-01-01

    peer-reviewed Modern software systems are prone to a continuous evolution under frequently varying requirements. Architecture-centric software evolution enables change in system structure and behavior while maintaining a global view of software to address evolution-centric tradeoffs. The Lehman???s law of continuing change demands for long-living and continuously evolving architectures to prolong the productive life and economic value of deployed software. However, the existing solutions f...

  6. PatEvol – A pattern language for evolution in component-based software architectures

    Aakash, Ahmad; Jamshidi, Pooyan; Pahl, Claus; Khaliq, Fawad

    2013-01-01

    Modern software systems are prone to a continuous evolution under frequently varying requirements. Architecture-centric software evolution (ACSE) enables change in system structure and behavior while maintaining a global view of software to address evolution-centric tradeoffs. Lehman’s law of continuing change demands for long-living and continuously evolving architectures to prolong the productive life and economic value of software systems. To support a continuous change, the existing solut...

  7. A pattern language for evolution reuse in component-based software architectures

    Abbasi, Aakash Ahmad

    2015-01-01

    Context: Modern software systems are prone to a continuous evolution under frequently varying requirements and changes in operational environments. Architecture-Centric Software Evolution (ACSE) enables changes in a system’s structure and behaviour while maintaining a global view of the software to address evolution-centric trade-offs. Lehman’s law of continuing change demands for long-living and continuously evolving architectures to prolong the productive life and economic value of software...

  8. 2D-ACAR investigations of PPT aramid fibres

    2D-ACAR spectra of PPT (poly(p-phenylene terephthalamide)) fibres which contain structural elongated open spaces in the crystallographic unit cell show a p-Ps peak with an elliptical cross-section and side lobes. Peak broadening suggests dimensions of ∝14-17 by 7-9 A for the open spaces and indicates some penetration of Ps into the interlayer spacing. The side lobes can be related to projected reciprocal lattice points and indicate Ps delocalization. 2D-ACAR has also been used to study the evolution of water release from the open spaces. (orig.)

  9. Learn Unity for 2D game development

    Thorn, Alan

    2013-01-01

    The only Unity book specifically covering 2D game development Written by Alan Thorn, experience game developer and author of seven books on game programming Hands-on examples of all major aspects of 2D game development using Unity

  10. Modeling urban evolution by identifying spatiotemporal patterns and applying methods of artificial intelligence.Case study: Athens, Greece.

    Photis, Yorgos N.; Manetos, Panos; Grekoussis, George

    2003-01-01

    While during the past decades, urban areas experience constant slow population growth, the spatial patterns they form, by means of their limits and borders, are rapidly changing in a complex way. Furthermore, urban areas continue to expand to the expense of "rural” intensifying urban sprawl. The main aim of this paper is the definition of the evolution of urban areas and more specifically, the specification of an urban model, which deals simultaneously with the modification of population and ...

  11. Interactive Exploratory Visualization of 2D Vector Fields

    Isenberg, Tobias; Everts, Maarten H.; Grubert, Jens; Carpendale, Sheelagh

    2008-01-01

    In this paper we present several techniques to interactively explore representations of 2D vector fields. Through a set of simple hand postures used on large, touch-sensitive displays, our approach allows individuals to custom-design glyphs (arrows, lines, etc.) that best reveal patterns of the unde

  12. Three-dimensional shear-strain patterns induced by high-pressure torsion and their impact on hardness evolution

    Highlights: → Three-dimensional shear strain patterns were evaluated during high-pressure torsion. → Double-swirl patterns are visible on the top surfaces of discs in early stages of HPT. → Double-swirls ultimately evolve into a single swirl with increasing revolutions. → Microstructural evolution in HPT may deviate initially from rigid-body situation - Abstract: The shear strain imposed on austenite/ferrite duplex stainless steel discs at different stages of high-pressure torsion (HPT) processing was imaged in plan-view and cross-section using optical microscopy and scanning electron microscopy. The effect of the shear strain was correlated to the hardness evolution of the discs. The shear-strain patterns are complex and are different on the top and bottom surfaces of the discs. A double-swirl pattern emerged on the top surface in the early stages of HPT. These two centres of the swirl moved towards the centre of the disc as the numbers of HPT revolutions was increased and ultimately the double-swirl evolved into a single-swirl. Less regular shear-strain patterns were observed on the bottom surfaces of the discs. Multiple ring-like patterns with mirror symmetry over the central axes of the discs were visible from cross-sectional observations. Nanoindentation testing on the two surfaces and a cross-section of HPT discs showed that the hardness is insensitive to specific shear-strain patterns, but is closely related to the widths of the austenite and ferrite phase domains. Late in the deformation process, the hardness in the interior of an HPT disc may be higher than at either of the disc surfaces because of the development of finer microstructural phase distributions.

  13. 2D growth processes: SLE and Loewner chains

    Bauer, Michel [Service de Physique Theorique de Saclay, CE-Saclay, 91191 Gif-sur-Yvette (France) and Laboratoire de Physique Theorique, Ecole Normale Superieure, 24 rue Lhomond, 75005 Paris (France)]. E-mail: michel.bauer@cea.fr; Bernard, Denis [Service de Physique Theorique de Saclay, CE-Saclay, 91191 Gif-sur-Yvette (France) and Laboratoire de Physique Theorique, Ecole Normale Superieure, 24 rue Lhomond, 75005 Paris (France)]. E-mail: denis.bernard@cea.fr

    2006-10-15

    This review provides an introduction to two dimensional growth processes. Although it covers a variety of processes such as diffusion limited aggregation, it is mostly devoted to a detailed presentation of stochastic Schramm-Loewner evolutions (SLE) which are Markov processes describing interfaces in 2D critical systems. It starts with an informal discussion, using numerical simulations, of various examples of 2D growth processes and their connections with statistical mechanics. SLE is then introduced and Schramm's argument mapping conformally invariant interfaces to SLE is explained. A substantial part of the review is devoted to reveal the deep connections between statistical mechanics and processes, and more specifically to the present context, between 2D critical systems and SLE. Some of the remarkable properties of SLE are explained, together with the tools for computing with it. This review has been written with the aim of filling the gap between the mathematical and the physical literature on the subject.

  14. Patterns of Genome Evolution among the Microsporidian Parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi

    Corradi, Nicolas; Akiyoshi, Donna E.; Morrison, Hilary G; Feng, Xiaochuan; Weiss, Louis M.; Tzipori, Saul; Patrick J Keeling

    2007-01-01

    Background Microsporidia are intracellular parasites that are highly-derived relatives of fungi. They have compacted genomes and, despite a high rate of sequence evolution, distantly related species can share high levels of gene order conservation. To date, only two species have been analysed in detail, and data from one of these largely consists of short genomic fragments. It is therefore difficult to determine how conservation has been maintained through microsporidian evolution, and imposs...

  15. Explaining the Evolution of Domestic Nanotechnology Companies - Survival Patterns of a Young and Emerging Technology

    Funken, Melanie

    2012-01-01

    Nanotechnology (NT) is often considered to be the essential technology of the future. Since the economy shapes the competiveness of a country to a great extent, factors fostering or hindering the evolution of NT companies need to be disentangled. This thesis associates the evolution of domestic NT companies to several kinds of knowledge. It provides an empirical investigation using an industry-dynamic and a network-theoretic approach.

  16. A mechanistic description of the formation and evolution of vegetation patterns

    R. Foti; Ramírez, J. A.

    2013-01-01

    Vegetation patterns are a common and well-defined characteristic of many landscapes. In this paper we explore some of the physical mechanisms responsible for the establishment of self-organized, non-random vegetation patterns that arise at the hillslope scale in many areas of the world, especially in arid and semi-arid regions. In doing so, we provide a fundamental mechanistic understanding of the dynamics of vegetation pattern formation and development. Reciprocal effects of vegetation on th...

  17. Diversification of the expression patterns and developmental functions of the Dishevelled gene family during chordate evolution

    Gray, Ryan S.; Bayly, Robbie D.; Green, Stephen A.; Agarwala, Seema; Lowe, Christopher J.; Wallingford, John B.

    2009-01-01

    Dishevelled (Dvl) proteins are key transducers of Wnt signaling encoded by members of a multi-gene family in vertebrates. We report here the divergent, tissue-specific expression patterns for all three Dvl genes in Xenopus embryos, which contrast dramatically with their expression patterns in mice. Moreover, we find that the expression patterns of Dvl genes in the chick diverge significantly from those of Xenopus. In addition, in hemichordates, an outgroup to chordates, we find that the one D...

  18. A mechanistic description of the formation and evolution of vegetation patterns

    R. Foti

    2012-07-01

    Full Text Available Vegetation patterns are a common and well-defined characteristic of many landscapes. In this paper we explore some of the physical mechanisms responsible for the establishment of self-organized, non-random vegetation patterns that arise at the hillslope scale in many areas of the world, especially in arid and semi-arid regions. In doing so, we provide a fundamental mechanistic understanding of the dynamics of vegetation pattern formation and development. Reciprocal effects of vegetation on the hillslope thermodynamics, runoff production and run-on infiltration, root density, surface albedo and soil moisture content are analyzed. In particular, we: (1 present a physically based mechanistic description of processes leading to vegetation pattern formation; (2 quantify the relative impact of each process on pattern formation; and (3 describe the relationships between vegetation patterns and the climatic, hydraulic and topographic characteristics of the system. We validate the model by comparing simulations with observed natural patterns in the areas of Niger near Niamey and Somalia near Garoowe. Our analyses suggest that the phenomenon of pattern formation is primarily driven by run-on infiltration and mechanisms of facilitation/inhibition among adjacent vegetation groups mediated by vegetation effects on soil properties and controls on soil moisture and albedo. Nonetheless, even in presence of those mechanisms, patterns arise only when the climatic conditions, particularly annual precipitation and net radiation, are favorable.

  19. A mechanistic description of the formation and evolution of vegetation patterns

    R. Foti

    2013-01-01

    Full Text Available Vegetation patterns are a common and well-defined characteristic of many landscapes. In this paper we explore some of the physical mechanisms responsible for the establishment of self-organized, non-random vegetation patterns that arise at the hillslope scale in many areas of the world, especially in arid and semi-arid regions. In doing so, we provide a fundamental mechanistic understanding of the dynamics of vegetation pattern formation and development. Reciprocal effects of vegetation on the hillslope thermodynamics, runoff production and run-on infiltration, root density, surface albedo and soil moisture content are analyzed. In particular, we: (1 present a physically based mechanistic description of processes leading to vegetation pattern formation; (2 quantify the relative impact of each process on pattern formation; and (3 describe the relationships between vegetation patterns and the climatic, hydraulic and topographic characteristics of the system. We validate the model by comparing simulations with observed natural patterns in the areas of Niger near Niamey and Somalia near Garoowe. Our analyses suggest that the phenomenon of pattern formation is primarily driven by run-on infiltration and mechanisms of facilitation/inhibition among adjacent vegetation groups, mediated by vegetation effects on soil properties and controls on soil moisture and albedo. Nonetheless, even in presence of those mechanisms, patterns arise only when the climatic conditions, particularly annual precipitation and net radiation, are favorable.

  20. KOREAN MOBILE OPERATORS' VALUE MAP FOR LTE D2D

    Taisiya Kim

    2015-04-01

    Full Text Available Managing the wireless data traffic is a main concern for mobile network operators in Information of Things (IoT environment. Long Term Evolution Device to Device (LTE D2D is regarding as a solution for the spectrum problem. It will bring an impact on providers and the whole mobile environment. The main purpose of this study is to analyze the role of key players, who share spectrum with mobile operators, and to present the value map of relationship among Korean mobile operators and other key players in LTE D2D discovery (commercial channel, as complicated relationships of key players are expected. Then, this study suggests scenario for ‘Targeted Advertising’ service of LTE D2D. LTE D2D is early discussion stage and scenario has limitation of specific business model. However, results of this study are significant for the present stage and provide implications for future researches on strategies for LTE D2D environment.

  1. Surface modelling for 2D imagery

    Lieng, Henrik

    2014-01-01

    Vector graphics provides powerful tools for drawing scalable 2D imagery. With the rise of mobile computers, of different types of displays and image resolutions, vector graphics is receiving an increasing amount of attention. However, vector graphics is not the leading framework for creating and manipulating 2D imagery. The reason for this reluctance of employing vector graphical frameworks is that it is difficult to handle complex behaviour of colour across the 2D domain. ...

  2. Perspectives for spintronics in 2D materials

    Han, Wei

    2016-03-01

    The past decade has been especially creative for spintronics since the (re)discovery of various two dimensional (2D) materials. Due to the unusual physical characteristics, 2D materials have provided new platforms to probe the spin interaction with other degrees of freedom for electrons, as well as to be used for novel spintronics applications. This review briefly presents the most important recent and ongoing research for spintronics in 2D materials.

  3. Perspectives for spintronics in 2D materials

    Wei Han

    2016-03-01

    Full Text Available The past decade has been especially creative for spintronics since the (rediscovery of various two dimensional (2D materials. Due to the unusual physical characteristics, 2D materials have provided new platforms to probe the spin interaction with other degrees of freedom for electrons, as well as to be used for novel spintronics applications. This review briefly presents the most important recent and ongoing research for spintronics in 2D materials.

  4. 2D Barcode for DNA Encoding

    Elena Purcaru

    2011-09-01

    Full Text Available The paper presents a solution for endcoding/decoding DNA information in 2D barcodes. First part focuses on the existing techniques and symbologies in 2D barcodes field. The 2D barcode PDF417 is presented as starting point. The adaptations and optimizations on PDF417 and on DataMatrix lead to the solution – DNA2DBC – DeoxyriboNucleic Acid Two Dimensional Barcode. The second part shows the DNA2DBC encoding/decoding process step by step. In conclusions are enumerated the most important features of 2D barcode implementation for DNA.

  5. 2D Barcode for DNA Encoding

    Purcaru, Elena

    2012-01-01

    The paper presents a solution for endcoding/decoding DNA information in 2D barcodes. First part focuses on the existing techniques and symbologies in 2D barcodes field. The 2D barcode PDF417 is presented as starting point. The adaptations and optimizations on PDF417 and on DataMatrix lead to the solution - DNA2DBC - DeoxyriboNucleic Acid Two Dimensional Barcode. The second part shows the DNA2DBC encoding/decoding process step by step. In conclusions are enumerated the most important features of 2D barcode implementation for DNA.

  6. Bedform characterization through 2D spectral analysis

    Lefebvre, Alice; Ernstsen, Verner Brandbyge; Winter, Christian

    energetic peak of the 2D spectrum was found and its energy, frequency and direction were calculated. A power-law was fitted to the average of slices taken through the 2D spectrum; its slope and y-intercept were calculated. Using these results the test area was morphologically classified into 4 distinct...... characteristics using twodimensional (2D) spectral analysis is presented and tested on seabed elevation data from the Knudedyb tidal inlet in the Danish Wadden Sea, where large compound bedforms are found. The bathymetric data were divided into 20x20 m areas on which a 2D spectral analysis was applied. The most...

  7. UNITS IN $F_2D_{2p}$

    Kaur, Kuldeep; Khan, Manju

    2012-01-01

    Let $p$ be an odd prime, $D_{2p}$ be the dihedral group of order 2p, and $F_{2}$ be the finite field with two elements. If * denotes the canonical involution of the group algebra $F_2D_{2p}$, then bicyclic units are unitary units. In this note, we investigate the structure of the group $\\mathcal{B}(F_2D_{2p})$, generated by the bicyclic units of the group algebra $F_2D_{2p}$. Further, we obtain the structure of the unit group $\\mathcal{U}(F_2D_{2p})$ and the unitary subgroup $\\mathcal{U}_*(F_...

  8. Patterns of genome evolution among the microsporidian parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi.

    Nicolas Corradi

    Full Text Available BACKGROUND: Microsporidia are intracellular parasites that are highly-derived relatives of fungi. They have compacted genomes and, despite a high rate of sequence evolution, distantly related species can share high levels of gene order conservation. To date, only two species have been analysed in detail, and data from one of these largely consists of short genomic fragments. It is therefore difficult to determine how conservation has been maintained through microsporidian evolution, and impossible to identify whether certain regions are more prone to genomic stasis. PRINCIPAL FINDINGS: Here, we analyse three large fragments of the Enterocytozoon bieneusi genome (in total 429 kbp, a species of medical significance. A total of 296 ORFs were identified, annotated and their context compared with Encephalitozoon cuniculi and Antonospora locustae. Overall, a high degree of conservation was found between all three species, and interestingly the level of conservation was similar in all three pairwise comparisons, despite the fact that A. locustae is more distantly related to E. cuniculi and E. bieneusi than either are to each other. CONCLUSIONS/SIGNIFICANCE: Any two genes that are found together in any pair of genomes are more likely to be conserved in the third genome as well, suggesting that a core of genes tends to be conserved across the entire group. The mechanisms of rearrangments identified among microsporidian genomes were consistent with a very slow evolution of their architecture, as opposed to the very rapid sequence evolution reported for these parasites.

  9. Annotated Bibliography of EDGE2D Use

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables

  10. 2D NMR studies of biomolecules

    The work described in this thesis comprises two related subjects. The first part describes methods to derive high-resolution structures of proteins in solution using two-dimensional (2-D) NMR. The second part describes 2-D NMR studies on the interaction between proteins and DNA. (author). 261 refs.; 52 figs.; 23 tabs

  11. Applications of 2D helical vortex dynamics

    Okulov, Valery; Sørensen, Jens Nørkær

    In the paper, we show how the assumption of helical symmetry in the context of 2D helical vortices can be exploited to analyse and to model various cases of rotating flows. From theory, examples of three basic applications of 2D dynamics of helical vortices embedded in flows with helical symmetry...

  12. Annotated Bibliography of EDGE2D Use

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  13. Temporal and spatial evolution characteristics of gas-liquid two-phase flow pattern based on image texture spectrum descriptor

    ZHOU Xi-guo; JIN Ning-de; WANG Zhen-ya; ZHANG Wen-yin

    2009-01-01

    The dynamic image information of typical gas-liquid two-phase flow patterns in vertical upward pipe is captured by a high-speed dynamic camera. The texture spectrum descriptor is used to describe the texture characteristics of the processed images whose content is represented in the form of texture spectrum histogram, and four time-varying characteristic param-eter indexes which represent image texture structure of different flow patterns are extracted. The study results show that the amplitude fluctuation of texture characteristic parameter indexes of bubble flow is lowest and shows very random complex dynamic behavior; the amplitude fluctuation of slug flow is higher and shows intermittent motion behavior between gas slug and liquid slug, and the amplitude fluctuation of churn flow is the highest and shows better periodicity; the amplitude fluctuation of bubble-slug flow is from low to high and oscillating frequence is higher than that of slug flow, and includes the features of both slug flow and bubble flow; the slug-churn flow loses the periodicity of slug flow and churn flow, and the amplitude fluctuation is high. The results indicate that the image texture characteristic parameter indexes of different flow pattern can reflect the flow characteristics of gas-liquid two-phase flow, which provides a new approach to tmderstand the temporal and spatial evolution of flow pattern dynamics.

  14. Surface segregation of InGaAs films by the evolution of reflection high-energy electron diffraction patterns

    Zhou Xun; Luo Zi-Jiang; Guo Xiang; Zhang Bi-Chan; Shang Lin-Tao; Zhou Qing; Deng Chao-Yong; Ding Zhao

    2012-01-01

    Surface segregation is studied via the evolution of reflection high-energy electron diffraction (RHEED) patterns under different values of As4 BEP for InGaAs films.When the As4 BEP is set to be zero,the RHEED pattern keeps a 4×3/(n×3) structure with increasing temperature,and surface segregation takes place until 470 ℃.The RHEED pattern develops into a metal-rich (4×2) structure as temperature increases to 495 ℃.The reason for this is that surface segregation makes the In inside the InGaAs film climb to its surface.With the temperature increasing up to 515 ℃,the RHEED pattern turns into a GaAs(2×4) structure due to In desorption.While the As4 BEP comes up to a specific value (1.33×10-4 Pa-1.33×10-3 Pa),the surface temperature can delay the segregation and desorption.We find that As4 BEP has a big influence on surface desorption,while surface segregation is more strongly dependent on temperature than surface desorption.

  15. Surface segregation of InGaAs films by the evolution of reflection high-energy electron diffraction patterns

    Surface segregation is studied via the evolution of reflection high-energy electron diffraction (RHEED) patterns under different values of As4 BEP for InGaAs films. When the As4 BEP is set to be zero, the RHEED pattern keeps a 4×3/(n × 3) structure with increasing temperature, and surface segregation takes place until 470 °C. The RHEED pattern develops into a metal-rich (4 × 2) structure as temperature increases to 495 °C. The reason for this is that surface segregation makes the In inside the InGaAs film climb to its surface. With the temperature increasing up to 515 °C, the RHEED pattern turns into a GaAs(2 × 4) structure due to In desorption. While the As4 BEP comes up to a specific value (1.33 × 10-4 Pa−1.33 × 10-3 Pa), the surface temperature can delay the segregation and desorption. We find that As4 BEP has a big influence on surface desorption, while surface segregation is more strongly dependent on temperature than surface desorption. (condensed matter: structural, mechanical, and thermal properties)

  16. Modes of Knowledge Accumulation, Entry Regimes and Patterns of Industrial Evolution

    Giulio Bottazzi; Giovanni Dosi; Gaia Rocchetti

    2001-01-01

    In this work we explore the interplay between entry, selection and innovative learning as determinants of industrial evolution. We propose a model aimed to capture the essential features of learning and competition as drivers of the dynamics. Using both analytical and numerical techniques, we are able to disentangle possible generic properties which robustly hold for a wide range of parameterization. In particular, we identify different generic ``evolutionary archetypes'' in turn defined by c...

  17. Using experimental evolution to explore natural patterns between bacterial motility and resistance to bacteriophages

    Koskella, Britt; Taylor, Tiffany B; Bates, Jennifer; Buckling, Angus

    2011-01-01

    Resistance of bacteria to phages may be gained by alteration of surface proteins to which phages bind, a mechanism that is likely to be costly as these molecules typically have critical functions such as movement or nutrient uptake. To address this potential trade-off, we combine a systematic study of natural bacteria and phage populations with an experimental evolution approach. We compare motility, growth rate and susceptibility to local phages for 80 bacteria isolated from horse chestnut l...

  18. Hitting a BEC with a comb: Evolution of interference patterns inside a magnetic trap

    Müller, J. H.; Morsch, O.; Cristiani, M.; Ciampini, D.; Arimondo, E.

    2002-01-01

    We study the evolution inside a harmonic trap of Bose-Einstein condensates released from the periodic potential of an optical lattice. After a time-of-flight, harmonic motion of the interference peaks is observed as well as a breathing motion in the direction perpendicular to the optical lattice. We interpret these results in terms of a simple physical model and discuss the possibility of more detailed studies of such a system.

  19. Multi-Input Single Output SSSC based damping controller design by a hybrid Improved Differential Evolution-Pattern Search approach.

    Panda, Sidhartha; Yegireddy, Narendra Kumar

    2015-09-01

    In this paper, a hybrid Improved Differential Evolution and Pattern Search (hIDEPS) approach is proposed for the design of a PI-Type Multi-Input Single Output (MISO) Static Synchronous Series Compensator (SSSC) based damping controller. The improvement in Differential Evolution (DE) algorithm is introduced by a simple but effective scheme of changing two of its most important control parameters i.e. step size and crossover probability with an objective of achieving improved performance. Pattern Search (PS) is subsequently employed to fine tune the best solution provided by modified DE algorithm. The superiority of a proposed hIDEPS technique over DE and improved DE has also been demonstrated. At the outset, this concept is applied to a SSSC connected in a Single Machine Infinite Bus (SMIB) power system and then extended to a multi-machine power system. To show the effectiveness and robustness of the proposed design approach, simulation results are presented and compared with DE and Particle Swarm Optimization (PSO) optimized Single Input Single Output (SISO) SSSC based damping controllers. It is observed that the proposed approach yield superior damping performance compared to some approaches available in the literature. PMID:25864132

  20. DNA aneuploidy as a topographic malignant transformation pattern in a pleomorphic adenoma of long-term evolution: a case report

    Gallego Lorena

    2011-11-01

    Full Text Available Abstract Introduction We present a case of long-term evolution of a submandibular pleomorphic adenoma. There is little information about topographic malignant transformation patterns of pleomorphic adenomas. Case presentation We extensively analyze a giant submandibular mixed tumor of 25-year evolution in a 57-year-old Caucasian woman. Deoxyribonucleic acid ploidy was evaluated in different superficial and deep areas using flow cytometry analysis and correlated with pathological and immunohistochemical characteristics. Superficial areas exhibited a typical histological pleomorphic adenoma pattern and were deoxyribonucleic acid diploid. Deep samples showed deoxyribonucleic acid aneuploidy, atypical histological benign features and expression of markers involved at an early-stage of malignant transformation, such as tumor protein 53 and antigen Ki67. Conclusion These findings revealed that deep tumor compartments may be involved in the initial stages of malignant transformation. Deoxyribonucleic acid ploidy analysis may provide an additional diagnosis tool and indicate 'uncertain' areas that require careful study to avoid diagnostic errors. Larger studies are needed to confirm our results and to evaluate the usefulness of the technique.

  1. Clinicopathogenomic analysis of mismatch repair proficient colorectal adenocarcinoma uncovers novel prognostic subgroups with differing patterns of genetic evolution.

    Braxton, David R; Zhang, Ray; Morrissette, Jennifer D; Loaiza-Bonilla, Arturo; Furth, Emma E

    2016-10-01

    Cancer somatic genetic evolution is a direct contributor to heterogeneity at the clonal and molecular level in colorectal adenocarcinoma (COAD). We sought to determine the extent to which genetic evolution may be detected in COAD in routinely obtained single clinical specimens and establish clinical significance with regard to clinicopathologic and outcome data. One hundred and twenty three cases of routinely collected mismatch repair proficient COAD were sequenced on the Illumina Truseq Amplicon assay. Measures of intratumoral heterogeneity and the preferential timing of mutational events were assessed and compared to clinicopathologic data. Survival subanalysis was performed on 55 patients. Patient age (p = 0.013) and specimen percent tumor (p = 0.033) was associated with clonal diversity, and biopsy (p = 0.044) and metastasis (p = 0.044) returned fewer mutations per case. APC and TP53 mutations preferentially occurred early while alterations in FBXW7, FLT3, SMAD4, GNAS and PTEN preferentially occurred as late events. Temporal heterogeneity was evident in KRAS and PIK3CA mutations. Hierarchical clustering revealed a TP53 mutant subtype and a MAPK-PIK3CA subtype with differing patterns of late mutational events. Survival subanalysis showed a decreased median progression free survival for the MAPK-PIK3CA subtype (8 months vs. 13 months; univariate logrank p = 0.0380, cox model p= 0.018). Neoadjuvant therapy associated mutations were found for ERBB2 (p = 0.0481) and FBXW7 (p = 0.015). Our data indicate novel molecular subtypes of mismatch repair proficient COAD display differing patterns of genetic evolution which correlate with clinical outcomes. Furthermore, we report treatment acquired and/or selected mutations in ERBB2 and FBXW7. PMID:27194209

  2. Inertial solvation in femtosecond 2D spectra

    Hybl, John; Albrecht Ferro, Allison; Farrow, Darcie; Jonas, David

    2001-03-01

    We have used 2D Fourier transform spectroscopy to investigate polar solvation. 2D spectroscopy can reveal molecular lineshapes beneath ensemble averaged spectra and freeze molecular motions to give an undistorted picture of the microscopic dynamics of polar solvation. The transition from "inhomogeneous" to "homogeneous" 2D spectra is governed by both vibrational relaxation and solvent motion. Therefore, the time dependence of the 2D spectrum directly reflects the total response of the solvent-solute system. IR144, a cyanine dye with a dipole moment change upon electronic excitation, was used to probe inertial solvation in methanol and propylene carbonate. Since the static Stokes' shift of IR144 in each of these solvents is similar, differences in the 2D spectra result from solvation dynamics. Initial results indicate that the larger propylene carbonate responds more slowly than methanol, but appear to be inconsistent with rotational estimates of the inertial response. To disentangle intra-molecular vibrations from solvent motion, the 2D spectra of IR144 will be compared to the time-dependent 2D spectra of the structurally related nonpolar cyanine dye HDITCP.

  3. Internal Photoemission Spectroscopy of 2-D Materials

    Nguyen, Nhan; Li, Mingda; Vishwanath, Suresh; Yan, Rusen; Xiao, Shudong; Xing, Huili; Cheng, Guangjun; Hight Walker, Angela; Zhang, Qin

    Recent research has shown the great benefits of using 2-D materials in the tunnel field-effect transistor (TFET), which is considered a promising candidate for the beyond-CMOS technology. The on-state current of TFET can be enhanced by engineering the band alignment of different 2D-2D or 2D-3D heterostructures. Here we present the internal photoemission spectroscopy (IPE) approach to determine the band alignments of various 2-D materials, in particular SnSe2 and WSe2, which have been proposed for new TFET designs. The metal-oxide-2-D semiconductor test structures are fabricated and characterized by IPE, where the band offsets from the 2-D semiconductor to the oxide conduction band minimum are determined by the threshold of the cube root of IPE yields as a function of photon energy. In particular, we find that SnSe2 has a larger electron affinity than most semiconductors and can be combined with other semiconductors to form near broken-gap heterojunctions with low barrier heights which can produce a higher on-state current. The details of data analysis of IPE and the results from Raman spectroscopy and spectroscopic ellipsometry measurements will also be presented and discussed.

  4. 2D supergravity in p+1 dimensions

    Gustafsson, H.; Lindstrom, U.

    1998-01-01

    We describe new $N$-extended 2D supergravities on a $(p+1)$-dimensional (bosonic) space. The fundamental objects are moving frame densities that equip each $(p+1)$-dimensional point with a 2D ``tangent space''. The theory is presented in a $[p+1, 2]$ superspace. For the special case of $p=1$ we recover the 2D supergravities in an unusual form. The formalism has been developed with applications to the string-parton picture of $D$-branes at strong coupling in mind.

  5. 2D Barcode for DNA Encoding

    Elena Purcaru; Cristian Toma

    2012-01-01

    The paper presents a solution for endcoding/decoding DNA information in 2D barcodes. First part focuses on the existing techniques and symbologies in 2D barcodes field. The 2D barcode PDF417 is presented as starting point. The adaptations and optimizations on PDF417 and on DataMatrix lead to the solution – DNA2DBC – DeoxyriboNucleic Acid Two Dimensional Barcode. The second part shows the DNA2DBC encoding/decoding process step by step. In conclusions are enumerated the most important features ...

  6. Patterns of molecular evolution of an avian neo-sex chromosome.

    Pala, Irene; Hasselquist, Dennis; Bensch, Staffan; Hansson, Bengt

    2012-12-01

    Newer parts of sex chromosomes, neo-sex chromosomes, offer unique possibilities for studying gene degeneration and sequence evolution in response to loss of recombination and population size decrease. We have recently described a neo-sex chromosome system in Sylvioidea passerines that has resulted from a fusion between the first half (10 Mb) of chromosome 4a and the ancestral sex chromosomes. In this study, we report the results of molecular analyses of neo-Z and neo-W gametologs and intronic parts of neo-Z and autosomal genes on the second half of chromosome 4a in three species within different Sylvioidea lineages (Acrocephalidea, Timaliidae, and Alaudidae). In line with hypotheses of neo-sex chromosome evolution, we observe 1) lower genetic diversity of neo-Z genes compared with autosomal genes, 2) moderate synonymous and weak nonsynonymous sequence divergence between neo-Z and neo-W gametologs, and 3) lower GC content on neo-W than neo-Z gametologs. Phylogenetic reconstruction of eight neo-Z and neo-W gametologs suggests that recombination continued after the split of Alaudidae from the rest of the Sylvioidea lineages (i.e., after ~42.2 Ma) and with some exceptions also after the split of Acrocephalidea and Timaliidae (i.e., after ~39.4 Ma). The Sylvioidea neo-sex chromosome shares classical evolutionary features with the ancestral sex chromosomes but, as expected from its more recent origin, shows weaker divergence between gametologs. PMID:22826461

  7. Unraveling a generic growth pattern in structure evolution of thiolate-protected gold nanoclusters

    Xu, Wen Wu; Li, Yadong; Gao, Yi; Zeng, Xiao Cheng

    2016-03-01

    Precise control of the growth of thiolate-protected gold nanoclusters is a prerequisite for their applications in catalysis and bioengineering. Here, we bring to bear a new series of thiolate-protected nanoclusters with a unique growth pattern, i.e., Au20(SR)16, Au28(SR)20, Au36(SR)24, Au44(SR)28, and Au52(SR)32. These nanoclusters can be viewed as resulting from the stepwise addition of a common structural motif [Au8(SR)4]. The highly negative values of the nucleus-independent chemical shift (NICS) in the center of the tetrahedral Au4 units suggest that the overall stabilities of these clusters stem from the local stability of each tetrahedral Au4 unit. Generalization of this growth-pattern rule to large-sized nanoclusters allows us to identify the structures of three new thiolate-protected nanoclusters, namely, Au60(SR)36, Au68(SR)40, and Au76(SR)44. Remarkably, all three large-sized nanoclusters possess relatively large HOMO-LUMO gaps and negative NICS values, suggesting their high chemical stability. Further extension of the growth-pattern rule to the infinitely long nanowire limit results in a one-dimensional (1D) thiolate-protected gold nanowire (RS-AuNW) with a band gap of 0.78 eV. Such a unique growth-pattern rule offers a guide for precise synthesis of a new class of large-sized thiolate-protected gold nanoclusters or even RS-AuNW which, to our knowledge, has not been reported in the literature.Precise control of the growth of thiolate-protected gold nanoclusters is a prerequisite for their applications in catalysis and bioengineering. Here, we bring to bear a new series of thiolate-protected nanoclusters with a unique growth pattern, i.e., Au20(SR)16, Au28(SR)20, Au36(SR)24, Au44(SR)28, and Au52(SR)32. These nanoclusters can be viewed as resulting from the stepwise addition of a common structural motif [Au8(SR)4]. The highly negative values of the nucleus-independent chemical shift (NICS) in the center of the tetrahedral Au4 units suggest that the overall

  8. Design of Spiking Central Pattern Generators for Multiple Locomotion Gaits in Hexapod Robots by Christiansen Grammar Evolution.

    Espinal, Andres; Rostro-Gonzalez, Horacio; Carpio, Martin; Guerra-Hernandez, Erick I; Ornelas-Rodriguez, Manuel; Sotelo-Figueroa, Marco

    2016-01-01

    This paper presents a method to design Spiking Central Pattern Generators (SCPGs) to achieve locomotion at different frequencies on legged robots. It is validated through embedding its designs into a Field-Programmable Gate Array (FPGA) and implemented on a real hexapod robot. The SCPGs are automatically designed by means of a Christiansen Grammar Evolution (CGE)-based methodology. The CGE performs a solution for the configuration (synaptic weights and connections) for each neuron in the SCPG. This is carried out through the indirect representation of candidate solutions that evolve to replicate a specific spike train according to a locomotion pattern (gait) by measuring the similarity between the spike trains and the SPIKE distance to lead the search to a correct configuration. By using this evolutionary approach, several SCPG design specifications can be explicitly added into the SPIKE distance-based fitness function, such as looking for Spiking Neural Networks (SNNs) with minimal connectivity or a Central Pattern Generator (CPG) able to generate different locomotion gaits only by changing the initial input stimuli. The SCPG designs have been successfully implemented on a Spartan 6 FPGA board and a real time validation on a 12 Degrees Of Freedom (DOFs) hexapod robot is presented. PMID:27516737

  9. Design of Spiking Central Pattern Generators for Multiple Locomotion Gaits in Hexapod Robots by Christiansen Grammar Evolution

    Espinal, Andres; Rostro-Gonzalez, Horacio; Carpio, Martin; Guerra-Hernandez, Erick I.; Ornelas-Rodriguez, Manuel; Sotelo-Figueroa, Marco

    2016-01-01

    This paper presents a method to design Spiking Central Pattern Generators (SCPGs) to achieve locomotion at different frequencies on legged robots. It is validated through embedding its designs into a Field-Programmable Gate Array (FPGA) and implemented on a real hexapod robot. The SCPGs are automatically designed by means of a Christiansen Grammar Evolution (CGE)-based methodology. The CGE performs a solution for the configuration (synaptic weights and connections) for each neuron in the SCPG. This is carried out through the indirect representation of candidate solutions that evolve to replicate a specific spike train according to a locomotion pattern (gait) by measuring the similarity between the spike trains and the SPIKE distance to lead the search to a correct configuration. By using this evolutionary approach, several SCPG design specifications can be explicitly added into the SPIKE distance-based fitness function, such as looking for Spiking Neural Networks (SNNs) with minimal connectivity or a Central Pattern Generator (CPG) able to generate different locomotion gaits only by changing the initial input stimuli. The SCPG designs have been successfully implemented on a Spartan 6 FPGA board and a real time validation on a 12 Degrees Of Freedom (DOFs) hexapod robot is presented. PMID:27516737

  10. Structural patterns, evolution, and seismic expression of Montague County, Texas - Implications concerning past discoveries and future exploration

    Font, R.G. (Strategic Petroleum, Inc., Dallas, TX (USA))

    1990-02-01

    North Texas is a mature province that has yielded abundant hydrocarbons. Opportunities still exist for discovering large reserves by applying new technology and developing innovative concepts for frontier type plays. Montague County can be used to illustrate this point. Analysis of seismic and petrologic data reveals a fascinating scenario concerning structural patterns and tectonic evolution. The Proterozoic and early Paleozoic history is related to the development of the Wichita aulacogen. Similar structural architecture is found on the southern side of the Wichita-Amarillo uplift from the Hardeman basin to Montague County. The early history reflects rifting. Subsequent tectonism relates to the Hercynian orogeny, plate convergence, and collision. Fault patterns mapped from seismic and subsurface data may be explained through reorientation of the principal stresses. Of the major patterns mapped, the northwest-trending system is dominant. Normal faults formed during rifting were selectively reactivated as upthrusts during convergence. Past discoveries are almost invariably related to seismic expression. New Carboniferous reserves will be discovered in subtle traps. State-of-the-art seismic and seismic stratigraphy will equate to exploratory success. New play concepts involve the petroleum potential of the deep Ellenburger, similar to the deep pay found in Oklahoma. Recent deep wells drilled in the county affirm the presence of structure and reservoir, but fail to find the indigenous source potential present north of the Red River. Best opportunities for deep Ellenburger discoveries in Texas lie where faulting juxtaposes Carboniferous source rocks to the Cambrian-Ordovician reservoirs.

  11. Origins of anteroposterior patterning and Hox gene regulation during chordate evolution.

    Schilling, T. F.; Knight, R D

    2001-01-01

    All chordates share a basic body plan and many common features of early development. Anteroposterior (AP) regions of the vertebrate neural tube are specified by a combinatorial pattern of Hox gene expression that is conserved in urochordates and cephalochordates. Another primitive feature of Hox gene regulation in all chordates is a sensitivity to retinoic acid during embryogenesis, and recent developmental genetic studies have demonstrated the essential role for retinoid signalling in verteb...

  12. Interface dynamics under nonequilibrium conditions: from a self-propelled droplet to dynamic pattern evolution

    Chen, Yong-Jun

    2012-01-01

    In this article, we describe the instability of a contact line under nonequilibrium conditions mainly based on the results of our recent studies. Two experimental examples are presented: the self-propelled motion of a liquid droplet and spontaneous dynamic pattern formation. For the self-propelled motion of a droplet, we introduce an experiment in which a droplet of aniline sitting on an aqueous layer moves spontaneously at an air-water interface. The spontaneous symmetry breaking of Marangoni-driven spreading causes regular motion. In a circular Petri dish, the droplet exhibits either beeline motion or circular motion. On the other hand, we show the emergence of a dynamic labyrinthine pattern caused by dewetting of a metastable thin film from the air-water interface. The contact line between the organic phase and aqueous phase forms a unique spatio-temporal pattern characterized as a dynamic labyrinthine. Motion of the contact line is controlled by diffusion processes. We propose a theoretical model to inter...

  13. Matrix models of 2d gravity

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date

  14. 2D Saturable Absorbers for Fibre Lasers

    Robert I. Woodward

    2015-11-01

    Full Text Available Two-dimensional (2D nanomaterials are an emergent and promising platform for future photonic and optoelectronic applications. Here, we review recent progress demonstrating the application of 2D nanomaterials as versatile, wideband saturable absorbers for Q-switching and mode-locking fibre lasers. We focus specifically on the family of few-layer transition metal dichalcogenides, including MoS2, MoSe2 and WS2.

  15. Beltrami States in 2D Electron Magnetohydrodynamics

    Shivamoggi, B. K.

    2015-01-01

    In this paper, the Hamiltonian formulations along with the Poisson brackets for two-dimensional (2D) electron magnetohydrodynamics (EMHD) flows are developed. These formulations are used to deduce the Beltrami states for 2D EMHD flows. In the massless electron limit, the EMHD Beltrami states reduce to the force-free states, though there is no force-free Beltrami state in the general EMHD case.

  16. Matrix models and 2-D gravity

    In these lectures, I shall focus on the matrix formulation of 2-d gravity. In the first one, I shall discuss the main results of the continuum formulation of 2-d gravity, starting from the first renormalization group calculations which led to the concept of the conformal anomaly, going through the Polyakov bosonic string and the Liouville action, up to the recent results on the scaling properties of conformal field theories coupled to 2-d gravity. In the second lecture, I shall discuss the discrete formulation of 2-d gravity in term of random lattices, and the mapping onto random matrix models. The occurrence of critical points in the planar limit and the scaling limit at those critical points will be described, as well as the identification of these scaling limits with continuum 2-d gravity coupled to some matter field theory. In the third lecture, the double scaling limit in the one matrix model, and its connection with continuum non perturbative 2-d gravity, will be presented. The connection with the KdV hierarchy and the general form of the string equation will be discuted. In the fourth lecture, I shall discuss the non-perturbative effects present in the non perturbative solutions, in the case of pure gravity. The Schwinger-Dyson equations for pure gravity in the double scaling limit are described and their compatibility with the solutions of the string equation for pure gravity is shown to be somewhat problematic

  17. 2d index and surface operators

    In this paper we compute the superconformal index of 2d (2,2) supersymmetric gauge theories. The 2d superconformal index, a.k.a. flavored elliptic genus, is computed by a unitary matrix integral much like the matrix integral that computes the 4d superconformal index. We compute the 2d index explicitly for a number of examples. In the case of abelian gauge theories we see that the index is invariant under flop transition and under CY-LG correspondence. The index also provides a powerful check of the Seiberg-type duality for non-abelian gauge theories discovered by Hori and Tong. In the later half of the paper, we study half-BPS surface operators in N=2 superconformal gauge theories. They are engineered by coupling the 2d (2,2) supersymmetric gauge theory living on the support of the surface operator to the 4d N=2 theory, so that different realizations of the same surface operator with a given Levi type are related by a 2d analogue of the Seiberg duality. The index of this coupled system is computed by using the tools developed in the first half of the paper. The superconformal index in the presence of surface defect is expected to be invariant under generalized S-duality. We demonstrate that it is indeed the case. In doing so the Seiberg-type duality of the 2d theory plays an important role

  18. 2D molybdenum disulphide (2D-MoS2) modified electrodes explored towards the oxygen reduction reaction

    Rowley-Neale, Samuel J.; Fearn, Jamie M.; Brownson, Dale A. C.; Smith, Graham C.; Ji, Xiaobo; Banks, Craig E.

    2016-08-01

    Two-dimensional molybdenum disulphide nanosheets (2D-MoS2) have proven to be an effective electrocatalyst, with particular attention being focused on their use towards increasing the efficiency of the reactions associated with hydrogen fuel cells. Whilst the majority of research has focused on the Hydrogen Evolution Reaction (HER), herein we explore the use of 2D-MoS2 as a potential electrocatalyst for the much less researched Oxygen Reduction Reaction (ORR). We stray from literature conventions and perform experiments in 0.1 M H2SO4 acidic electrolyte for the first time, evaluating the electrochemical performance of the ORR with 2D-MoS2 electrically wired/immobilised upon several carbon based electrodes (namely; Boron Doped Diamond (BDD), Edge Plane Pyrolytic Graphite (EPPG), Glassy Carbon (GC) and Screen-Printed Electrodes (SPE)) whilst exploring a range of 2D-MoS2 coverages/masses. Consequently, the findings of this study are highly applicable to real world fuel cell applications. We show that significant improvements in ORR activity can be achieved through the careful selection of the underlying/supporting carbon materials that electrically wire the 2D-MoS2 and utilisation of an optimal mass of 2D-MoS2. The ORR onset is observed to be reduced to ca. +0.10 V for EPPG, GC and SPEs at 2D-MoS2 (1524 ng cm-2 modification), which is far closer to Pt at +0.46 V compared to bare/unmodified EPPG, GC and SPE counterparts. This report is the first to demonstrate such beneficial electrochemical responses in acidic conditions using a 2D-MoS2 based electrocatalyst material on a carbon-based substrate (SPEs in this case). Investigation of the beneficial reaction mechanism reveals the ORR to occur via a 4 electron process in specific conditions; elsewhere a 2 electron process is observed. This work offers valuable insights for those wishing to design, fabricate and/or electrochemically test 2D-nanosheet materials towards the ORR.Two-dimensional molybdenum disulphide nanosheets

  19. Evolution of Xylan Substitution Patterns in Gymnosperms and Angiosperms: Implications for Xylan Interaction with Cellulose.

    Busse-Wicher, Marta; Li, An; Silveira, Rodrigo L; Pereira, Caroline S; Tryfona, Theodora; Gomes, Thiago C F; Skaf, Munir S; Dupree, Paul

    2016-08-01

    The interaction between cellulose and xylan is important for the load-bearing secondary cell wall of flowering plants. Based on the precise, evenly spaced pattern of acetyl and glucuronosyl (MeGlcA) xylan substitutions in eudicots, we recently proposed that an unsubstituted face of xylan in a 2-fold helical screw can hydrogen bond to the hydrophilic surfaces of cellulose microfibrils. In gymnosperm cell walls, any role for xylan is unclear, and glucomannan is thought to be the important cellulose-binding polysaccharide. Here, we analyzed xylan from the secondary cell walls of the four gymnosperm lineages (Conifer, Gingko, Cycad, and Gnetophyta). Conifer, Gingko, and Cycad xylan lacks acetylation but is modified by arabinose and MeGlcA. Interestingly, the arabinosyl substitutions are located two xylosyl residues from MeGlcA, which is itself placed precisely on every sixth xylosyl residue. Notably, the Gnetophyta xylan is more akin to early-branching angiosperms and eudicot xylan, lacking arabinose but possessing acetylation on alternate xylosyl residues. All these precise substitution patterns are compatible with gymnosperm xylan binding to hydrophilic surfaces of cellulose. Molecular dynamics simulations support the stable binding of 2-fold screw conifer xylan to the hydrophilic face of cellulose microfibrils. Moreover, the binding of multiple xylan chains to adjacent planes of the cellulose fibril stabilizes the interaction further. Our results show that the type of xylan substitution varies, but an even pattern of xylan substitution is maintained among vascular plants. This suggests that 2-fold screw xylan binds hydrophilic faces of cellulose in eudicots, early-branching angiosperm, and gymnosperm cell walls. PMID:27325663

  20. A concurrent track evolution algorithm for pattern recognition in the HERA-B main tracking system

    A strategy for pattern recognition in the main tracking system of a forward B spectrometer like HERA-B or LHC-B is presented. Intrinsically a local method, it combines the virtues of track following procedures with the necessary ability to optimize between many available paths in a high occupancy environment. A hit-locating procedure suitable for a multiplanar detector geometry has been developed. The performance of the method is tested on HERA-B Monte Carlo events with full detector simulation and a realistic spectrometer geometry. (orig.)

  1. 2-D DOA Estimation Based on 2D-MUSIC%基于2D-MUSIC算法的DOA估计

    康亚芳; 王静; 张清泉; 行小帅

    2014-01-01

    This paper discussed the performance of classical two-dimensional DOA estimation with 2D-MUSIC, based on the mathematical model of planar array and 2D-MUSIC DOA estimation, Taking uniform planar array for example, comput-er simulation experiment was carried for the effect of three kinds of different parameters on 2-D DOA estimation, and the simulation results were analyzed. And also verification test about the corresponding algorithm performance under the differ-ent parameters was discussed.%利用经典的2D-MUSIC算法对二维阵列的DOA估计进行了研究,在平面阵列数学模型以及2D-MUSIC算法的DOA估计模型基础上,以均匀平面阵列为例,对3种不同参数的DOA估计进行了计算机仿真,分析了仿真结果。得出了在不同参数变化趋势下DOA估计的相应变化情况。

  2. 工作团队研究模式的演进%Evolution of Research Patterns of Work Team

    薛继东

    2011-01-01

    从工作团队定义、分类入手,对已有工作团队研究成果进行归纳总结,指出工作团队研究主要经历三种递进模式:IPO、IMO和IMOI,这三种研究模式的演进体现了团队研究复杂、动态、适应和循环的特征,并为未来的团队研究提出建议.%Starting from the definition and types of work teams, the article summarizes three kinds of evolutionary patterns of work team research: IPO, IMO, IMOI. The evolution reflects four characteristics of work team research: complex, dynamic, adaptive and cycling. The article also concludes briefly emerging directions in work team research.

  3. Size Evolution of Ordered SiGe Islands Grown by Surface Thermal Diffusion on Pit-Patterned Si(100 Surface

    Bollani Monica

    2010-01-01

    Full Text Available Abstract The ordered growth of self-assembled SiGe islands by surface thermal diffusion in ultra high vacuum from a lithographically etched Ge stripe on pit-patterned Si(100 surface has been experimentally investigated. The total surface coverage of Ge strongly depends on the distance from the source stripe, as quantitatively verified by Scanning Auger Microscopy. The size distribution of the islands as a function of the Ge coverage has been studied by coupling atomic force microscopy scans with Auger spectro-microscopy data. Our observations are consistent with a physical scenario where island positioning is essentially driven by energetic factors, which predominate with respect to the local kinetics of diffusion, and the growth evolution mainly depends on the local density of Ge atoms.

  4. A parallel splitting wavelet method for 2D conservation laws

    Schmidt, Alex A.; Kozakevicius, Alice J.; Jakobsson, Stefan

    2016-06-01

    The current work presents a parallel formulation using the MPI protocol for an adaptive high order finite difference scheme to solve 2D conservation laws. Adaptivity is achieved at each time iteration by the application of an interpolating wavelet transform in each space dimension. High order approximations for the numerical fluxes are computed by ENO and WENO schemes. Since time evolution is made by a TVD Runge-Kutta space splitting scheme, the problem is naturally suitable for parallelization. Numerical simulations and speedup results are presented for Euler equations in gas dynamics problems.

  5. Phylogenetic Patterns of Codon Evolution in the ACTIN-DEPOLYMERIZING FACTOR/COFILIN (ADF/CFL Gene Family.

    Eileen M Roy-Zokan

    Full Text Available The actin-depolymerizing factor/cofilin (ADF/CFL gene family encodes a diverse group of relatively small proteins. Once known strictly as modulators of actin filament dynamics, recent research has demonstrated that these proteins are involved in a variety of cellular processes, from signal transduction to the cytonuclear trafficking of actin. In both plant and animal lineages, expression patterns of paralogs in the ADF/CFL gene family vary among tissue types and developmental stages. In this study we use computational approaches to investigate the evolutionary forces responsible for the diversification of the ADF/CFL gene family. Estimating the rate of non-synonymous to synonymous mutations (dN/dS across phylogenetic lineages revealed that the majority of ADF/CFL codon positions were under strong purifying selection, with rare episodic events of accelerated protein evolution. In both plants and animals these instances of accelerated evolution were ADF/CFL subclass specific, and all of the sites under selection were located in regions of the protein that could serve in new functional roles. We suggest these sites may have been important in the functional diversification of ADF/CFL proteins.

  6. A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

    Nickerson Cheryl A

    2006-01-01

    Full Text Available Abstract Background Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred. Results We demonstrate this approach by using a "test" genomic island that we have cloned from the Salmonella typhimurium genome (island 4305 and transferred to a range of Gram negative bacterial hosts of differing evolutionary relationships to S. typhimurium. Systematic analysis of the expression of the island genes in the different hosts compared to proper controls allowed identification of genes with genera-specific expression patterns. The data from the analysis can be arranged in a matrix to give an expression "array" of the island genes in the different bacterial backgrounds. A conserved 19-bp DNA site was found upstream of at least two of the differentially-expressed island genes. To our knowledge, this is the first systematic analysis of horizontally-transferred genomic island gene expression in a broad range of Gram negative hosts. We also present evidence in this study that the IS200 element found in island 4305 in S. typhimurium strain LT2 was inserted after the island had already been acquired by the S. typhimurium lineage and that this element is likely not

  7. Asymmetric patterns of reassortment and concerted evolution in Cardamom bushy dwarf virus.

    Savory, F R; Ramakrishnan, U

    2014-06-01

    Nanoviruses are single-stranded DNA (ssDNA) plant viruses which have multipartite genomes consisting of discrete, individually encapsidated components. This multipartite strategy may lead to high rates of reassortment, whereby entire genome components are exchanged among different strains. However, few studies have explored the extent to which reassortment shapes the genetic diversity of nanovirus populations. Here we present an extensive analysis of reassortment among 163 Cardamom bushy dwarf virus (CBDV; Nanoviridae family, Babuvirus genus) isolates collected in Northeast India. We also examined evidence of recombination, which is known to play a role in the evolutionary dynamics of nanovirus populations. By sequencing six discrete genome components for each isolate, we demonstrate that over 40% of the isolates display evidence of at least one reassortment event during their evolutionary histories. Nevertheless, a bias in the frequencies at which different genome components reassort was observed, with the DNA-M and DNA-N components being the most predisposed to reassortment. This may reflect variation in the ability of different genome components to function efficiently in a foreign genomic background. Comparisons of the common regions of different genome components revealed signatures of concerted evolution mediated by frequent inter-component homologous recombination. This process, which has previously been reported in nanoviruses and other multipartite ssDNA viruses, may allow proteins which initiate replication to maintain control over distinct genome components. Notably, DNA-N, one of the genome components most prone to reassortment, also exhibited the most frequent inter-component homologous recombination. This supports the idea that inter-component homologous recombination may promote the efficient replication of novel components which are introduced into a genome via reassortment. PMID:24613431

  8. Contrasting patterns in the evolution of the Rab GTPase family in Archaeplastida

    Romana Petrželková

    2014-12-01

    Full Text Available Rab GTPases are a vast group of proteins serving a role of master regulators in membrane trafficking in eukaryotes. Previous studies delineated some 23 Rab and Rab-like paralogs ancestral for eukaryotes and mapped their current phylogenetic distribution, but the analyses relied on a limited sampling of the eukaryotic diversity. Taking advantage of the recent growth of genome and transcriptome resources for phylogenetically diverse plants and algae, we reanalyzed the evolution of the Rab family in eukaryotes with the primary plastid, collectively constituting the presumably monophyletic supergroup Archaeplastida. Our most important novel findings are as follows: (i the ancestral set of Rabs in Archaeplastida included not only the paralogs Rab1, Rab2, Rab5, Rab6, Rab7, Rab8, Rab11, Rab18, Rab23, Rab24, Rab28, IFT27, and RTW (=Rabl2, as suggested previously, but also Rab14 and Rab34, because Rab14 exists in glaucophytes and Rab34 is present in glaucophytes and some green algae; (ii except in embryophytes, Rab gene duplications have been rare in Archaeplastida. Most notable is the independent emergence of divergent, possibly functionally novel, in-paralogs of Rab1 and Rab11 in several archaeplastidial lineages; (iii recurrent gene losses have been a significant factor shaping Rab gene complements in archaeplastidial species; for example, the Rab21 paralog was lost at least six times independently within Archaeplastida, once in the lineage leading to the “core” eudicots; (iv while the glaucophyte Cyanophora paradoxa has retained the highest number of ancestral Rab paralogs among all archaeplastidial species studied so far, rhodophytes underwent an extreme reduction of the Rab gene set along their stem lineage, resulting in only six paralogs (Rab1, Rab2, Rab6, Rab7, Rab11, and Rab18 present in modern red algae. Especially notable is the absence of Rab5, a virtually universal paralog essential for the endocytic pathway, suggesting that endocytosis

  9. Optical modulators with 2D layered materials

    Sun, Zhipei; Martinez, Amos; Wang, Feng

    2016-04-01

    Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that 2D layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this Review, we cover the state of the art of optical modulators based on 2D materials, including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as 2D heterostructures, plasmonic structures, and silicon and fibre integrated structures. We also take a look at the future perspectives and discuss the potential of yet relatively unexplored mechanisms, such as magneto-optic and acousto-optic modulation.

  10. Automatic Contour Extraction from 2D Image

    Panagiotis GIOANNIS

    2011-03-01

    Full Text Available Aim: To develop a method for automatic contour extraction from a 2D image. Material and Method: The method is divided in two basic parts where the user initially chooses the starting point and the threshold. Finally the method is applied to computed tomography of bone images. Results: An interesting method is developed which can lead to a successful boundary extraction of 2D images. Specifically data extracted from a computed tomography images can be used for 2D bone reconstruction. Conclusions: We believe that such an algorithm or part of it can be applied on several other applications for shape feature extraction in medical image analysis and generally at computer graphics.

  11. 2D microwave imaging reflectometer electronics.

    Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program. PMID:25430247

  12. 2D microwave imaging reflectometer electronics

    Spear, A. G.; Domier, C. W., E-mail: cwdomier@ucdavis.edu; Hu, X.; Muscatello, C. M.; Ren, X.; Luhmann, N. C. [Electrical and Computer Engineering, University of California, Davis, California 95616 (United States); Tobias, B. J. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States)

    2014-11-15

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  13. Long bone histology and growth patterns in ankylosaurs: implications for life history and evolution.

    Martina Stein

    Full Text Available The ankylosaurs are one of the major dinosaur groups and are characterized by unique body armor. Previous studies on other dinosaur taxa have revealed growth patterns, life history and evolutionary mechanisms based on their long bone histology. However, to date nothing is known about long bone histology in the Ankylosauria. This study is the first description of ankylosaurian long bone histology based on several limb elements, which were sampled from different individuals from the Ankylosauridae and Nodosauridae. The histology is compared to that of other dinosaur groups, including other Thyreophora and Sauropodomorpha. Ankylosaur long bone histology is characterized by a fibrolamellar bone architecture. The bone matrix type in ankylosaurs is closest to that of Stegosaurus. A distinctive mixture of woven and parallel-fibered bone together with overall poor vascularization indicates slow growth rates compared to other dinosaurian taxa. Another peculiar characteristic of ankylosaur bone histology is the extensive remodeling in derived North American taxa. In contrast to other taxa, ankylosaurs substitute large amounts of their primary tissue early in ontogeny. This anomaly may be linked to the late ossification of the ankylosaurian body armor. Metabolically driven remodeling processes must have liberated calcium to ossify the protective osteodermal structures in juveniles to subadult stages, which led to further remodeling due to increased mechanical loading. Abundant structural fibers observed in the primary bone and even in remodeled bone may have improved the mechanical properties of the Haversian bone.

  14. Fluctuation-induced patterns and rapid evolution in predator-prey ecosystems

    Goldenfeld, Nigel

    2014-03-01

    Predator-prey ecosystems exhibit noisy, persistent cycles that cannot be described by intuitive population-level differential equations such as the Lotka-Volterra equations. Traditionally this paradox has been met by including additional nonlinearities such as predator satiation to force limit cycle behavior. Over the last few years, it has been realized that individual-level descriptions, combined with systematic perturbation techniques can reproduce the key features of such systems in a minimal way, without requiring many additional assumptions or fine tunings. Here I review work in this area that uses these techniques to treat spatial patterns and the phenomenon of rapidly evolving prey sub-populations. In the latter case, I show how stochastic individual-level models reproduce the key features observed in chemostats and in the wild, including anomalous phase shifts between predator and prey species, evolutionary cycles and cryptic cycles. This work shows that stochastic individual-level models naturally describe systems where evolutionary time scales surprisingly match ecosystem time scales.

  15. Morphotectonic analysis, structural evolution/pattern of a contractional ridge: Giouchtas Mt., Central Crete, Greece

    Kokinou Eleni; Skilodimou Hariklia D; Bathrellos George D; Antonarakou Assimina; Kamberis Evangelos

    2015-04-01

    The Giouchtas Mountain is situated south of Heraklion, Central Crete. It is a N–S trending morphological asymmetric ridge with a steep western slope, whilst its eastern slope is characterized by a smoother relief, composed of Mesozoic limestone and Eocene–lower Oligocene flysch of the Gavrovo–Tripolis zone. The present study focusses on the structural pattern and development of Giouchtas Mountain. Morphotectonic analyses in combination with field mapping and tectonic analysis were performed for this purpose. GIS techniques were used for mapping the spatial distribution of the geological features on the topographic relief of the area. Geomorphic indices, used in the present study, are the mountain front sinuosity index (Smf) and the valley floor/width ratio index (Vf). Based on Smf and Vf values, it is implied that this area can be assigned to a tectonic class I, corresponding to higher tectonic activity. However, spatial variations of the tectonic activity along the segmented fronts point to a general trend of increasing activity towards the north and especially, northeast. The model of this possibly active structural feature corresponds to a compressional mechanism followed by an earliest Mid. Miocene to Holocene late-stage deformation related to extensional faulting.

  16. Patterns of evolution of myocyte damage after human heart transplantation detected by indium-111 monoclonal antimyosin

    Ballester-Rodes, M.; Carrio-Gasset, I.; Abadal-Berini, L.; Obrador-Mayol, D.; Berna-Roqueta, L.; Caralps-Riera, J.M.

    1988-09-15

    The indium-111 labeled Fab fragment of antimyosin monoclonal antibody was used to study cardiac rejection and the time course of myocyte damage after transplantation. Fifty-three studies were performed in 21 patients, 17 men and 4 women, aged 19 to 54 years (mean 37 +/- 8), from 7 to 40 months after transplantation. Repeat studies were available in 8, and 10 were studied after the first year of transplantation. A heart-to-lung ratio was used for quantitation of uptake (normal 1.46 +/- 0.04). Differences between absent (1.69 +/- 0.29) and moderate (1.90 +/- 0.36) rejection were significant (p less than 0.03). Antimyosin ratio at 1 to 3 months (1.89 +/- 0.35) differed from that at greater than 12 months (1.65 +/- 0.2) (p less than 0.01). Repeat studies revealed a decrease in antimyosin ratio in 5 patients with uneventful clinical course; 2 had persistent activity after transplantation and suffered heart failure from rejection. After 1 year of transplantation uptake was within normal limits in 7 of 10 patients, and high uptake was associated with vascular rejection in 1. Because they can define evolving patterns of myocardial lesion activity, antimyosin studies could be useful both in patient management and in concentrating resources for those patients who most require them. The heart-to-lung ratio is suggested to monitor sequentially the degree of myocyte damage after transplantation.

  17. Patterns of evolution of myocyte damage after human heart transplantation detected by indium-111 monoclonal antimyosin

    The indium-111 labeled Fab fragment of antimyosin monoclonal antibody was used to study cardiac rejection and the time course of myocyte damage after transplantation. Fifty-three studies were performed in 21 patients, 17 men and 4 women, aged 19 to 54 years (mean 37 +/- 8), from 7 to 40 months after transplantation. Repeat studies were available in 8, and 10 were studied after the first year of transplantation. A heart-to-lung ratio was used for quantitation of uptake (normal 1.46 +/- 0.04). Differences between absent (1.69 +/- 0.29) and moderate (1.90 +/- 0.36) rejection were significant (p less than 0.03). Antimyosin ratio at 1 to 3 months (1.89 +/- 0.35) differed from that at greater than 12 months (1.65 +/- 0.2) (p less than 0.01). Repeat studies revealed a decrease in antimyosin ratio in 5 patients with uneventful clinical course; 2 had persistent activity after transplantation and suffered heart failure from rejection. After 1 year of transplantation uptake was within normal limits in 7 of 10 patients, and high uptake was associated with vascular rejection in 1. Because they can define evolving patterns of myocardial lesion activity, antimyosin studies could be useful both in patient management and in concentrating resources for those patients who most require them. The heart-to-lung ratio is suggested to monitor sequentially the degree of myocyte damage after transplantation

  18. In silico evolution of gene cooption in pattern-forming gene networks.

    Spirov, Alexander V; Sabirov, Marat A; Holloway, David M

    2012-01-01

    Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN), comes under the control of a new regulatory system. Such re-arrangement of pre-existing networks is likely more common for increasing genomic complexity than the creation of new genes. Using evolutionary computations (EC), we investigate how cooption affects the evolvability, outgrowth and robustness of GRNs. We use a data-driven model of insect segmentation, for the fruit fly Drosophila, and evaluate fitness by robustness to maternal variability-a major constraint in biological development. We compare two mechanisms of gene cooption: a simpler one with gene Introduction and Withdrawal operators; and one in which GRN elements can be altered by transposon infection. Starting from a minimal 2-gene network, insufficient for fitting the Drosophila gene expression patterns, we find a general trend of coopting available genes into the GRN, in order to better fit the data. With the transposon mechanism, we find co-evolutionary oscillations between genes and their transposons. These oscillations may offer a new technique in EC for overcoming premature convergence. Finally, we comment on how a differential equations (in contrast to Boolean) approach is necessary for addressing realistic continuous variation in biochemical parameters. PMID:23365523

  19. In Silico Evolution of Gene Cooption in Pattern-Forming Gene Networks

    Alexander V. Spirov

    2012-01-01

    Full Text Available Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN, comes under the control of a new regulatory system. Such re-arrangement of pre-existing networks is likely more common for increasing genomic complexity than the creation of new genes. Using evolutionary computations (EC, we investigate how cooption affects the evolvability, outgrowth and robustness of GRNs. We use a data-driven model of insect segmentation, for the fruit fly Drosophila, and evaluate fitness by robustness to maternal variability—a major constraint in biological development. We compare two mechanisms of gene cooption: a simpler one with gene Introduction and Withdrawal operators; and one in which GRN elements can be altered by transposon infection. Starting from a minimal 2-gene network, insufficient for fitting the Drosophila gene expression patterns, we find a general trend of coopting available genes into the GRN, in order to better fit the data. With the transposon mechanism, we find co-evolutionary oscillations between genes and their transposons. These oscillations may offer a new technique in EC for overcoming premature convergence. Finally, we comment on how a differential equations (in contrast to Boolean approach is necessary for addressing realistic continuous variation in biochemical parameters.

  20. Hunting down magnetic monopoles in 2D topological insulators?

    He, Xugang; Cmpmsd At Bnl Team

    Contrary to the existence of electric charge, magnetic monopole does not exist in nature. It is thus extraordinary to find that magnetic monopoles can be pictured conceptually in topological insulators. For 2D topological insulators, the topological invariant corresponds to the total flux of an effective magnetic field (the Berry curvature) over the reciprocal space. Upon wrapping the 2D reciprocal space into a compact manifold as a torus, the non-zero total flux can be considered to originate from magnetic monopoles with quantized charge. We will first illustrate the intrinsic difficulty via extending a 2D problem to a 3D reciprocal space, and then demonstrate that analytical continuation to the complex momentum space offers a natural solution in which 1) the magnetic monopoles emerge naturally in pairs each forming a string above and below the real axis possessing opposite charge, and 2) the total charge below the real axis gives exactly the topological invariant. In essence, the robustness of the topology is mapped to the robustness of the total charge in the lower complex plan, a mapping intriguing even mathematically. Finally, we will illustrate the evolution across the topological phase transition, providing a natural description of the metallic nature in the phase boundary, and offering a clear explanation why a change of global topology can be induced via a local change in reciprocal space. Work supported by US DOE BES DE-AC02-98CH10886.

  1. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans.

    Shmuel Sattath

    Full Text Available In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot, and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3% that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis

  2. Experimental evolution alters the rate and temporal pattern of population growth in Batrachochytrium dendrobatidis, a lethal fungal pathogen of amphibians

    Voyles, Jamie; Johnson, Leah R.; Briggs, Cheryl J.; Cashins, Scott D.; Ross A. Alford; Berger, Lee; Lee F Skerratt; Speare, Rick; Rosenblum, Erica Bree

    2014-01-01

    Virulence of infectious pathogens can be unstable and evolve rapidly depending on the evolutionary dynamics of the organism. Experimental evolution can be used to characterize pathogen evolution, often with the underlying objective of understanding evolution of virulence. We used experimental evolution techniques (serial transfer experiments) to investigate differential growth and virulence of Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis. We te...

  3. Path integral quantization of 2 D- gravity

    2 D- gravity is investigated using the Hamilton-Jacobi formalism. The equations of motion and the action integral are obtained as total differential equations in many variables. The integrability conditions, lead us to obtain the path integral quantization without any need to introduce any extra un-physical variables. (author)

  4. Port Adriano, 2D-Model tests

    Burcharth, Hans F.; Meinert, Palle; Andersen, Thomas Lykke

    This report present the results of 2D physical model tests (length scale 1:50) carried out in a waveflume at Dept. of Civil Engineering, Aalborg University (AAU). The objective of the tests was: To identify cross section design which restrict the overtopping to acceptable levels and to record the...

  5. Baby universes in 2d quantum gravity

    Ambjorn, J.; S. Jain; G. Thorleifsson

    1993-01-01

    We investigate the fractal structure of $2d$ quantum gravity, both for pure gravity and for gravity coupled to multiple gaussian fields and for gravity coupled to Ising spins. The roughness of the surfaces is described in terms of baby universes and using numerical simulations we measure their distribution which is related to the string susceptibility exponent $\\g_{string}$.

  6. Horns Rev II, 2-D Model Tests

    Andersen, Thomas Lykke; Frigaard, Peter

    This report present the results of 2D physical model tests carried out in the shallow wave flume at Dept. of Civil Engineering, Aalborg University (AAU), on behalf of Energy E2 A/S part of DONG Energy A/S, Denmark. The objective of the tests was: to investigate the combined influence of the pile...

  7. Patterns in root traits of woody species hosting arbuscular and ectomycorrhizas: implications for the evolution of belowground strategies.

    Comas, Louise H; Callahan, Hilary S; Midford, Peter E

    2014-08-01

    Root traits vary enormously among plant species but we have little understanding of how this variation affects their functioning. Of central interest is how root traits are related to plant resource acquisition strategies from soil. We examined root traits of 33 woody species from northeastern US forests that form two of the most common types of mutualisms with fungi, arbuscular mycorrhizas (AM) and ectomycorrhizas (EM). We examined root trait distribution with respect to plant phylogeny, quantifying the phylogenetic signal (K statistic) in fine root morphology and architecture, and used phylogenetically independent contrasts (PICs) to test whether taxa forming different mycorrhizal associations had different root traits. We found a pattern of species forming roots with thinner diameters as species diversified across time. Given moderate phylogenetic signals (K = 0.44-0.68), we used PICs to examine traits variation among taxa forming AM or EM, revealing that hosts of AM were associated with lower branching intensity (r PIC = -0.77) and thicker root diameter (r PIC = -0.41). Because EM evolved relatively more recently and intermittently across plant phylogenies, significant differences in root traits and colonization between plants forming AM and EM imply linkages between the evolution of these biotic interactions and root traits and suggest a history of selection pressures, with trade-offs for supporting different types of associations. Finally, across plant hosts of both EM and AM, species with thinner root diameters and longer specific root length (SRL) had less colonization (r PIC = 0.85, -0.87), suggesting constraints on colonization linked to the evolution of root morphology. PMID:25247056

  8. Evolution of geographical place and niche space: Patterns of diversification in the North American sedge (Cyperaceae) flora.

    Spalink, Daniel; Drew, Bryan T; Pace, Matthew C; Zaborsky, John G; Li, Pan; Cameron, Kenneth M; Givnish, Thomas J; Sytsma, Kenneth J

    2016-02-01

    The role of geography and ecology in speciation are often discussed in the context of phylogenetic niche conservatism (PNC), the propensity of lineages to retain ancestral niche related traits. However, a recent paradigm shift focuses instead on measuring divergence of these traits in conjunction with patterns of speciation. Under this framework, we analyzed the diversification of North America's third most diverse family, Cyperaceae ("sedges"), using a modified Parsimony Analysis of Endemicity approach to identify floristic regions and ordination statistics to quantify species distribution in a continuous manner. Utilizing over 200,000 georeferenced specimens, we characterized the geographical distribution and climatic and edaphic niche space occupied by each species. We constructed a supermatrix phylogeny of the North American sedge flora, aided in part by the sequencing of all sedges of Wisconsin, and employed a multifaceted approach to assess the role of geographical and ecological divergence on lineage diversification. In addition to measuring phylogenetic signal for these traits, we also measured pairwise phylogenetic distance of species within floristic regions, calculated rates of speciation, and tested for correlations of speciation rate to tempo of geographical and ecological evolution. Our analyses consistently show that evolutionarily related species tend to be geographically unrelated. Rates of geographical and ecological diversification are closely linked to tempo of speciation, and exploration of geographical place coincides with divergence in ecological niche space. We highlight the benefits of treating geography in a continuous manner, and stress the importance of employing a diverse suite of analytical approaches in testing hypotheses regarding the evolution of range and niche. PMID:26702956

  9. Positron beam optics for the 2D-ACAR spectrometer at the NEPOMUC beamline

    In the last year a conventional 2D-ACAR spectrometer has been set up and brought to operation at TUM. Once the NEPOMUC beamline is extended to the new experimental hall at the research reactor FRM-II the conventional 2D-ACAR spectrometer will be upgraded with a second sample chamber in order to be integrated to the NEPOMUC beamline facility. This spectrometer will add a complete new quality to 2D-ACAR experiments as it allows to track the evolution of the electronic structure from the surface to the bulk. We present the design features of the positron beam optics and the sample environment.

  10. Positron beam optics for the 2D-ACAR spectrometer at the NEPOMUC beamline

    Ceeh, H.; Weber, J. A.; Hugenschmidt, C.; Leitner, M.; Boni, P.

    2014-04-01

    In the last year a conventional 2D-ACAR spectrometer has been set up and brought to operation at TUM. Once the NEPOMUC beamline is extended to the new experimental hall at the research reactor FRM-II the conventional 2D-ACAR spectrometer will be upgraded with a second sample chamber in order to be integrated to the NEPOMUC beamline facility. This spectrometer will add a complete new quality to 2D-ACAR experiments as it allows to track the evolution of the electronic structure from the surface to the bulk. We present the design features of the positron beam optics and the sample environment.

  11. ORION, Post-processor for Finite Elements Program NIKE2D and DYNA2D

    Description of program or function: ORION is an interactive post- processor for the analysis programs NIKE2D (NESC 9923), DYNA2D (NESC 9910), TOPAZ, TOPAZ2D (NESC9801), GEM2D (NESC9679), and TACO2D. ORION reads the binary plot data files generated by the two- dimensional finite element programs used at LLNL. Contours and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forces along constrained boundaries, and momentum. ORION has the capability to plot color fringes, contour lines, vector plots, principal stress lines, deformed meshes and material outlines, time histories, reaction forces along constraint boundaries, interface pressures along slide lines, and user-supplied labels

  12. Design Application Translates 2-D Graphics to 3-D Surfaces

    2007-01-01

    Fabric Images Inc., specializing in the printing and manufacturing of fabric tension architecture for the retail, museum, and exhibit/tradeshow communities, designed software to translate 2-D graphics for 3-D surfaces prior to print production. Fabric Images' fabric-flattening design process models a 3-D surface based on computer-aided design (CAD) specifications. The surface geometry of the model is used to form a 2-D template, similar to a flattening process developed by NASA's Glenn Research Center. This template or pattern is then applied in the development of a 2-D graphic layout. Benefits of this process include 11.5 percent time savings per project, less material wasted, and the ability to improve upon graphic techniques and offer new design services. Partners include Exhibitgroup/Giltspur (end-user client: TAC Air, a division of Truman Arnold Companies Inc.), Jack Morton Worldwide (end-user client: Nickelodeon), as well as 3D Exhibits Inc., and MG Design Associates Corp.

  13. Investigating embryonic expression patterns and evolution of AHI1 and CEP290 genes, implicated in Joubert syndrome.

    Yu-Zhu Cheng

    Full Text Available Joubert syndrome and related diseases (JSRD are developmental cerebello-oculo-renal syndromes with phenotypes including cerebellar hypoplasia, retinal dystrophy and nephronophthisis (a cystic kidney disease. We have utilised the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR, to perform in-situ hybridisation studies on embryonic tissues, revealing an early onset neuronal, retinal and renal expression pattern for AHI1. An almost identical pattern of expression is seen with CEP290 in human embryonic and fetal tissue. A novel finding is that both AHI1 and CEP290 demonstrate strong expression within the developing choroid plexus, a ciliated structure important for central nervous system development. To test if AHI1 and CEP290 may have co-evolved, we carried out a genomic survey of a large group of organisms across eukaryotic evolution. We found that, in animals, ahi1 and cep290 are almost always found together; however in other organisms either one may be found independent of the other. Finally, we tested in murine epithelial cells if Ahi1 was required for recruitment of Cep290 to the centrosome. We found no obvious differences in Cep290 localisation in the presence or absence of Ahi1, suggesting that, while Ahi1 and Cep290 may function together in the whole organism, they are not interdependent for localisation within a single cell. Taken together these data support a role for AHI1 and CEP290 in multiple organs throughout development and we suggest that this accounts for the wide phenotypic spectrum of AHI1 and CEP290 mutations in man.

  14. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology.

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct "beyond graphene" domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  15. Structural shifts of aldehyde dehydrogenase enzymes were instrumental for the early evolution of retinoid-dependent axial patterning in metazoans.

    Sobreira, Tiago J P; Marlétaz, Ferdinand; Simões-Costa, Marcos; Schechtman, Deborah; Pereira, Alexandre C; Brunet, Frédéric; Sweeney, Sarah; Pani, Ariel; Aronowicz, Jochanan; Lowe, Christopher J; Davidson, Bradley; Laudet, Vincent; Bronner, Marianne; de Oliveira, Paulo S L; Schubert, Michael; Xavier-Neto, José

    2011-01-01

    Aldehyde dehydrogenases (ALDHs) catabolize toxic aldehydes and process the vitamin A-derived retinaldehyde into retinoic acid (RA), a small diffusible molecule and a pivotal chordate morphogen. In this study, we combine phylogenetic, structural, genomic, and developmental gene expression analyses to examine the evolutionary origins of ALDH substrate preference. Structural modeling reveals that processing of small aldehydes, such as acetaldehyde, by ALDH2, versus large aldehydes, including retinaldehyde, by ALDH1A is associated with small versus large substrate entry channels (SECs), respectively. Moreover, we show that metazoan ALDH1s and ALDH2s are members of a single ALDH1/2 clade and that during evolution, eukaryote ALDH1/2s often switched between large and small SECs after gene duplication, transforming constricted channels into wide opened ones and vice versa. Ancestral sequence reconstructions suggest that during the evolutionary emergence of RA signaling, the ancestral, narrow-channeled metazoan ALDH1/2 gave rise to large ALDH1 channels capable of accommodating bulky aldehydes, such as retinaldehyde, supporting the view that retinoid-dependent signaling arose from ancestral cellular detoxification mechanisms. Our analyses also indicate that, on a more restricted evolutionary scale, ALDH1 duplicates from invertebrate chordates (amphioxus and ascidian tunicates) underwent switches to smaller and narrower SECs. When combined with alterations in gene expression, these switches led to neofunctionalization from ALDH1-like roles in embryonic patterning to systemic, ALDH2-like roles, suggesting functional shifts from signaling to detoxification. PMID:21169504

  16. Structural shifts of aldehyde dehydrogenase enzymes were instrumental for the early evolution of retinoid-dependent axial patterning in metazoans

    Sobreira, Tiago J. P.; Marlétaz, Ferdinand; Simões-Costa, Marcos; Schechtman, Deborah; Pereira, Alexandre C.; Brunet, Frédéric; Sweeney, Sarah; Pani, Ariel; Aronowicz, Jochanan; Lowe, Christopher J.; Davidson, Bradley; Laudet, Vincent; Bronner, Marianne; de Oliveira, Paulo S. L.; Schubert, Michael; Xavier-Neto, José

    2011-01-01

    Aldehyde dehydrogenases (ALDHs) catabolize toxic aldehydes and process the vitamin A-derived retinaldehyde into retinoic acid (RA), a small diffusible molecule and a pivotal chordate morphogen. In this study, we combine phylogenetic, structural, genomic, and developmental gene expression analyses to examine the evolutionary origins of ALDH substrate preference. Structural modeling reveals that processing of small aldehydes, such as acetaldehyde, by ALDH2, versus large aldehydes, including retinaldehyde, by ALDH1A is associated with small versus large substrate entry channels (SECs), respectively. Moreover, we show that metazoan ALDH1s and ALDH2s are members of a single ALDH1/2 clade and that during evolution, eukaryote ALDH1/2s often switched between large and small SECs after gene duplication, transforming constricted channels into wide opened ones and vice versa. Ancestral sequence reconstructions suggest that during the evolutionary emergence of RA signaling, the ancestral, narrow-channeled metazoan ALDH1/2 gave rise to large ALDH1 channels capable of accommodating bulky aldehydes, such as retinaldehyde, supporting the view that retinoid-dependent signaling arose from ancestral cellular detoxification mechanisms. Our analyses also indicate that, on a more restricted evolutionary scale, ALDH1 duplicates from invertebrate chordates (amphioxus and ascidian tunicates) underwent switches to smaller and narrower SECs. When combined with alterations in gene expression, these switches led to neofunctionalization from ALDH1-like roles in embryonic patterning to systemic, ALDH2-like roles, suggesting functional shifts from signaling to detoxification. PMID:21169504

  17. Branes in the 2D black hole

    Ribault, Sylvain E-mail: ribault@mth.kcl.ac.uk; Schomerus, Volker

    2004-02-01

    We present a comprehensive analysis of branes in the Euclidean 2D black hole (cigar). In particular, exact boundary states and annulus amplitudes are provided for D0-branes which are localized at the tip of the cigar as well as for two families of extended D1 and D2-branes. Our results are based on closely related studies for the Euclidean AdS3 model and, as predicted by the conjectured duality between the 2D black hole and the sine-Liouville model, they share many features with branes in Liouville theory. New features arise here due to the presence of closed string modes which are localized near the tip of the cigar. The paper concludes with some remarks on possible applications to exact tachyon condensation and matrix models. (author)

  18. Branes in the 2D black hole

    Ribault, S; Ribault, Sylvain; Schomerus, Volker

    2004-01-01

    We present a comprehensive analysis of branes in the Euclidean 2D black hole (cigar). In particular, exact boundary states and annulus amplitudes are provided for D0-branes which are localized at the tip of the cigar as well as for two families of extended D1 and D2-branes. Our results are based on closely related studies for the Euclidean AdS3 model and, as predicted by the conjectured duality between the 2D black hole and the sine-Liouville model, they share many features with branes in Liouville theory. New features arise here due to the presence of closed string modes which are localized near the tip of the cigar. The paper concludes with some remarks on possible applications to exact tachyon condensation and matrix models.

  19. Branes in the 2D black hole

    We present a comprehensive analysis of branes in the Euclidean 2D black hole (cigar). In particular, exact boundary states and annulus amplitudes are provided for D0-branes which are localized at the tip of the cigar as well as for two families of extended D1 and D2-branes. Our results are based on closely related studies for the Euclidean AdS3 model and, as predicted by the conjectured duality between the 2D black hole and the sine-Liouville model, they share many features with branes in Liouville theory. New features arise here due to the presence of closed string modes which are localized near the tip of the cigar. The paper concludes with some remarks on possible applications to exact tachyon condensation and matrix models. (author)

  20. 2-D geometrical analysis of deformation

    Engineering structures such as dams, bridges, high rise buildings, etc. are subject to deformation. Deformation survey is therefore necessary to determine the magnitude and direction of such movements for the purpose of safety assessment. In this study, a strategy for two-step analyses for deformation survey rising the two dimensional (2-D) geodetic method has been developed, consisting of independent least squares estimation (LSE) of each epoch followed by deformation detection. Important aspects on LSE include global and local testing. In deformation detection, the following aspects were implemented; datum definition by the user. determination of stable datum points, geometrical analysis of deformation and graphic presentation. The developed strategy has been implemented in three computer programs, COMPUT, DEFORM and STRANS. Tests carried out with simulated and known data show that the developed strategy and programs are applicable for 2-D geometrical detection of deformation. (Author)

  1. Realistic and efficient 2D crack simulation

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

    Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

  2. 2D materials: Graphene and others

    Bansal, Suneev Anil; Singh, Amrinder Pal; Kumar, Suresh

    2016-05-01

    Present report reviews the recent advancements in new atomically thick 2D materials. Materials covered in this review are Graphene, Silicene, Germanene, Boron Nitride (BN) and Transition metal chalcogenides (TMC). These materials show extraordinary mechanical, electronic and optical properties which make them suitable candidates for future applications. Apart from unique properties, tune-ability of highly desirable properties of these materials is also an important area to be emphasized on.

  3. 2D-Tasks for Cognitive Rehabilitation

    Caballero Hernandez, Ruth; Martinez Moreno, Jose Maria; García Molina, A.; Ferrer Celma, S.; Solana Sánchez, Javier; Sanchez Carrion, R.; Fernandez Casado, E.; Pérez Rodríguez, Rodrigo; Gomez Pulido, A.; Anglès Tafalla, C.; Cáceres Taladriz, César; Ferre Vergada, M.; Roig Rovira, Teresa; Garcia Lopez, P.; Tormos Muñoz, Josep M.

    2011-01-01

    Neuropsychological Rehabilitation is a complex clinic process which tries to restore or compensate cognitive and behavioral disorders in people suffering from a central nervous system injury. Information and Communication Technologies (ICTs) in Biomedical Engineering play an essential role in this field, allowing improvement and expansion of present rehabilitation programs. This paper presents a set of cognitive rehabilitation 2D-Tasks for patients with Acquired Brain Injury (ABI). These t...

  4. Engineering light outcoupling in 2D materials

    Lien, Derhsien

    2015-02-11

    When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells.

  5. Evolution of Cooperation Patterns in Psoriasis Research: Co-Authorship Network Analysis of Papers in Medline (1942–2013)

    González-Alcaide, Gregorio; Park, Jinseo; Huamaní, Charles; Belinchón, Isabel; Ramos, José M.

    2015-01-01

    Background Although researchers have worked in collaboration since the origins of modern science and the publication of the first scientific journals in the eighteenth century, this phenomenon has acquired exceptional importance in the last several decades. Since the mid-twentieth century, new knowledge has been generated from within an ever-growing network of investigators, working cooperatively in research groups across countries and institutions. Cooperation is a crucial determinant of academic success. Objective The aim of the present paper is to analyze the evolution of scientific collaboration at the micro level, with regard to the scientific production generated on psoriasis research. Methods A bibliographic search in the Medline database containing the MeSH terms “psoriasis” or “psoriatic arthritis” was carried out. The search results were limited to articles, reviews and letters. After identifying the co-authorships of documents on psoriasis indexed in the Medline database (1942–2013), various bibliometric indicators were obtained, including the average number of authors per document and degree of multi-authorship over time. In addition, we performed a network analysis to study the evolution of certain features of the co-authorship network as a whole: average degree, size of the largest component, clustering coefficient, density and average distance. We also analyzed the evolution of the giant component to characterize the changing research patterns in the field, and we calculated social network indicators for the nodes, namely betweenness and closeness. Results The main active research clusters in the area were identified, along with their authors of reference. Our analysis of 28,670 documents sheds light on different aspects related to the evolution of scientific collaboration in the field, including the progressive increase in the mean number of co-authors (which stood at 5.17 in the 2004–2013 decade), and the rise in multi-authored papers

  6. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.

    Guyot, Romain; Garavito, Andrea; Gavory, Frédérick; Samain, Sylvie; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2011-01-01

    A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S(1)A, S(1) and S(1)B (called together the S(1) regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S(1) locus (including a putative F-box gene) were proposed, but candidates for S(1)A and S(1)B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S(1) regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S(1)A, S(1) and the majority of the S(1)B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S(1), (2) the multiple duplication and subsequent divergence of the same F-box gene within S(1)A, (3) an interspecific chromosomal inversion in S(1)B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S(1) regions. Hence, the S(1) regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the

  7. Patterns of Sequence Divergence and Evolution of the S1 Orthologous Regions between Asian and African Cultivated Rice Species

    Gavory, Frédérick; Samain, Sylvie; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2011-01-01

    A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S1A, S1 and S1B (called together the S1 regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S1 locus (including a putative F-box gene) were proposed, but candidates for S1A and S1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S1A, S1 and the majority of the S1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S1, (2) the multiple duplication and subsequent divergence of the same F-box gene within S1A, (3) an interspecific chromosomal inversion in S1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S1 regions. Hence, the S1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal inversion might participate to

  8. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.

    Romain Guyot

    Full Text Available A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S(1A, S(1 and S(1B (called together the S(1 regions interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S(1 locus (including a putative F-box gene were proposed, but candidates for S(1A and S(1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S(1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S(1A, S(1 and the majority of the S(1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1 a local invasion of transposable elements around a putative F-box gene within S(1, (2 the multiple duplication and subsequent divergence of the same F-box gene within S(1A, (3 an interspecific chromosomal inversion in S(1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S(1 regions. Hence, the S(1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal

  9. HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of apobec

    Korber, Bette [Los Alamos National Laboratory; Bhattacharya, Tanmoy [Los Alamos National Laboratory; Giorgi, Elena [Los Alamos National Laboratory; Gaschen, B [Los Alamos National Laboratory; Daniels, M [Los Alamos National Laboratory

    2009-01-01

    The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, represent adaptation for rapid growth in a newly infected host, or reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV -I env coding sequences in 81 very early B SUbtype infections previously shown to have resulted from transmission or expansion of single viruses (n=78) or two closely related viruses (n=3). In these cases the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 envand identified a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either (i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or (ii) in a nucleotide context indicative of APOBEC mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was both embedded in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp4l. We also examined the distribution, extent, and sequence context of insertions and deletions and provide evidence that the length

  10. Human NKG2D-ligands: cell biology strategies to ensure immune recognition

    Lola eFernández-Messina

    2012-09-01

    Full Text Available Immune recognition mediated by the activating receptor NKG2D plays an important role for the elimination of stressed cells, including tumours and virus-infected cells. On the other hand, the ligands for NKG2D can also be shed into the sera of cancer patients where they weaken the immune response by downmodulating the receptor on effector cells, mainly NK and T cells. Although both families of NKG2D-ligands, MICA/B and ULBPs, are related to MHC molecules and their expression is increased after stress, many differences are observed in terms of their biochemical properties and cell trafficking. In this paper, we summarise the variety of NKG2D-ligands and propose that selection pressure has driven evolution of diversity in their trafficking and shedding, but not receptor binding affinity. However, it is also possible to identify functional properties common to individual ULBP molecules and MICA/B alleles, but not generally conserved within the MIC or ULBP families. These characteristics likely represent examples of convergent evolution for efficient immune recognition, but are also attractive targets for pathogen immune evasion strategies. Categorization of NKG2D-ligands according to their biological features, rather than their genetic family, may help to achieve a better understanding of NKG2D-ligand association with disease.

  11. Interparticle attraction in 2D complex plasmas

    Kompaneets, Roman; Ivlev, Alexei V

    2015-01-01

    Complex (dusty) plasmas allow experimental studies of various physical processes occurring in classical liquids and solids by directly observing individual microparticles. A major problem is that the interaction between microparticles is generally not molecular-like. In this Letter, we propose how to achieve a molecular-like interaction potential in laboratory 2D complex plasmas. We argue that this principal aim can be achieved by using relatively small microparticles and properly adjusting discharge parameters. If experimentally confirmed, this will make it possible to employ complex plasmas as a model system with an interaction potential resembling that of conventional liquids.

  12. 2D vector-cyclic deformable templates

    Schultz, Nette; Conradsen, Knut

    1998-01-01

    In this paper the theory of deformable templates is a vector cycle in 2D is described. The deformable template model originated in (Grenander, 1983) and was further investigated in (Grenander et al., 1991). A template vector distribution is induced by parameter distribution from transformation...... matrices applied to the vector cycle. An approximation in the parameter distribution is introduced. The main advantage by using the deformable template model is the ability to simulate a wide range of objects trained by e.g. their biological variations, and thereby improve restoration, segmentation and...

  13. Limit theorems for 2D invasion percolation

    Damron, Michael

    2010-01-01

    We prove limit theorems and variance estimates for quantities related to ponds and outlets for 2D invasion percolation. We first exhibit several properties of a sequence (O(n)) of outlet variables, the n-th of which gives the number of outlets in the box centered at the origin of side length 2^n. The most important of these properties describe the sequence's renewal structure and exponentially fast mixing behavior. We use these to prove a central limit theorem and strong law of large numbers for (O(n)). We then show consequences of these limit theorems for the pond radii and outlet weights.

  14. Instant HTMl5 2D platformer

    Temple, Aidan

    2013-01-01

    Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. The step-by-step approach taken by this book will show you how to develop a 2D HTML5 platformer-based game that you will be able to publish to multiple devices.This book is great for anyone who has an interest in HTML5 games development, and who already has a basic to intermediate grasp on both the HTML markup and JavaScript programming languages. Therefore, due to this requirement, the book will not discuss the inner workings of either of these languages but will instead attempt to

  15. Interparticle Attraction in 2D Complex Plasmas

    Kompaneets, Roman; Morfill, Gregor E.; Ivlev, Alexei V.

    2016-03-01

    Complex (dusty) plasmas allow experimental studies of various physical processes occurring in classical liquids and solids by directly observing individual microparticles. A major problem is that the interaction between microparticles is generally not molecularlike. In this Letter, we propose how to achieve a molecularlike interaction potential in laboratory 2D complex plasmas. We argue that this principal aim can be achieved by using relatively small microparticles and properly adjusting discharge parameters. If experimentally confirmed, this will make it possible to employ complex plasmas as a model system with an interaction potential resembling that of conventional liquids.

  16. Periodically sheared 2D Yukawa systems

    We present non-equilibrium molecular dynamics simulation studies on the dynamic (complex) shear viscosity of a 2D Yukawa system. We have identified a non-monotonic frequency dependence of the viscosity at high frequencies and shear rates, an energy absorption maximum (local resonance) at the Einstein frequency of the system at medium shear rates, an enhanced collective wave activity, when the excitation is near the plateau frequency of the longitudinal wave dispersion, and the emergence of significant configurational anisotropy at small frequencies and high shear rates

  17. Phase Engineering of 2D Tin Sulfides.

    Mutlu, Z; Wu, RJ; Wickramaratne, D.; Shahrezaei, S; Liu, C; Temiz, S; Patalano, A; M Ozkan; Lake, RK; Mkhoyan, KA; Ozkan, CS

    2016-01-01

    Tin sulfides can exist in a variety of phases and polytypes due to the different oxidation states of Sn. A subset of these phases and polytypes take the form of layered 2D structures that give rise to a wide host of electronic and optical properties. Hence, achieving control over the phase, polytype, and thickness of tin sulfides is necessary to utilize this wide range of properties exhibited by the compound. This study reports on phase-selective growth of both hexagonal tin (IV) sulfide SnS2...

  18. The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate

    Wang, Xuzhen; Wang, Jun; He, Shunping;

    2007-01-01

    noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial...... genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon...

  19. Photocurrent spectroscopy of 2D materials

    Cobden, David

    Confocal photocurrent measurements provide a powerful means of studying many aspects of the optoelectronic and electrical properties of a 2D device or material. At a diffraction-limited point they can provide a detailed absorption spectrum, and they can probe local symmetry, ultrafast relaxation rates and processes, electron-electron interaction strengths, and transport coefficients. We illustrate this with several examples, once being the photo-Nernst effect. In gapless 2D materials, such as graphene, in a perpendicular magnetic field a photocurrent antisymmetric in the field is generated near to the free edges, with opposite sign at opposite edges. Its origin is the transverse thermoelectric current associated with the laser-induced electron temperature gradient. This effect provides an unambiguous demonstration of the Shockley-Ramo nature of long-range photocurrent generation in gapless materials. It also provides a means of investigating quasiparticle properties. For example, in the case of graphene on hBN, it can be used to probe the Lifshitz transition that occurs due to the minibands formed by the Moire superlattice. We also observe and discuss photocurrent generated in other semimetallic (WTe2) and semiconducting (WSe2) monolayers. Work supported by DoE BES and NSF EFRI grants.

  20. Comments on Thermalization in 2D CFT

    de Boer, Jan

    2016-01-01

    We revisit certain aspects of thermalization in 2D CFT. In particular, we consider similarities and differences between the time dependence of correlation functions in various states in rational and non-rational CFTs. We also consider the distinction between global and local thermalization and explain how states obtained by acting with a diffeomorphism on the ground state can appear locally thermal, and we review why the time-dependent expectation value of the energy-momentum tensor is generally a poor diagnostic of global thermalization. Since all 2D CFTs have an infinite set of commuting conserved charges, generic initial states might be expected to give rise to a generalized Gibbs ensemble rather than a pure thermal ensemble at late times. We construct the holographic dual of the generalized Gibbs ensemble and show that, to leading order, it is still described by a BTZ black hole. The extra conserved charges, while rendering $c < 1$ theories essentially integrable, therefore seem to have little effect o...

  1. DEPTH-AVERAGED 2-D CALCULATION OF FLOW AND SEDIMENT TRANSPORT IN CURVED CHANNELS

    Weiming WU; Sam S. Y. WANG

    2004-01-01

    The helical flow significantly affects the flow, sediment transport and morphological evolution in curved channels. A semi-empirical formula is proposed to determine the cross-stream distribution of the helical flow intensity in the developed regions of a channel bend. It is then used to evaluate the dispersion terms in the depth-averaged 2-D momentum equations and suspended-load transport equation as well as the bed-load transport angle, thus enhancing the depth-averaged 2-D model to account for the effect of helical flow. The tests in several experimental and field cases show that the enhanced depth-averaged 2-D model can much more reasonably predict the shifting of main flow from inner bank to outer bank, the erosion along outer bank and deposition along inner bank than the depth-averaged 2-D model without considering this effect.

  2. Initial Images of the Synthetic Aperture Radiometer 2D-STAR

    Initial results obtained using a new synthetic aperture radiometer, 2D-STAR, a dual polarized, L-band radiometer that employs aperture synthesis in two dimensions are presented and analyzed. This airborne instrument is the natural evolution of a previous design that employed employs aperture synthes...

  3. 2D Time-lapse Seismic Tomography Using An Active Time Constraint (ATC) Approach

    We propose a 2D seismic time-lapse inversion approach to image the evolution of seismic velocities over time and space. The forward modeling is based on solving the eikonal equation using a second-order fast marching method. The wave-paths are represented by Fresnel volumes rathe...

  4. 2-D or not 2-D, that is the question: A Northern California test

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is

  5. Epigenetic regulation of developmental expression of Cyp2d genes in mouse liver

    Ye Li

    2012-04-01

    Full Text Available CYP2D6 expression in liver is age-dependent. Because epigenetic mechanisms, such as DNA methylation and histone modifications, modulate age-related gene expression during development, and are highly conserved among species, the current study examined the epigenetic regulation of age-related expression of the Cyp2d genes in mouse liver. DNA methylation (DNAme, histone 3 lysine 4 dimethylation (H3K4me2, and histone 3 lysine 27 trimethylation (H3K27me3 was established by ChIP-on-chip tiling microarrays from mouse livers at prenatal, neonatal, and adult stages. Levels of DNAme, H3K4me2, and H3K27me3 were analyzed in a genomic region containing the Cyp2d clustering genes and their surrounding genes. Gradually increased expression levels of the Cyp2d9, Cyp2d10, Cyp2d22, and Cyp2d26 genes from prenatal, through neonatal, to adult are associated with gradually increased levels of H3K4me2 in the nucleosomes associated with these genes. Gene expression patterns during liver development in several Cyp2d surrounding genes, such as Srebf2, Sept3, Ndufa6, Tcf2, Nfam1, and Cyb5r3, could be also explained by changes of DNA methylation, H3K4me2, or H3K27me3 in those genes. In conclusion, the current study demonstrates that the changes of DNA methylation and histone modifications are associated with age-related expression patterns of the Cyp2d genes and their surrounding genes in liver cells during development.

  6. 2D Gridded Surface Data Value-Added Product

    Tang, Q [Lawrence Livermore National Laboratory; Xie, S [Lawrence Livermore National Laboratory

    2015-08-30

    This report describes the Atmospheric Radiation Measurement (ARM) Best Estimate (ARMBE) 2-dimensional (2D) gridded surface data (ARMBE2DGRID) value-added product. Spatial variability is critically important to many scientific studies, especially those that involve processes of great spatial variations at high temporal frequency (e.g., precipitation, clouds, radiation, etc.). High-density ARM sites deployed at the Southern Great Plains (SGP) allow us to observe the spatial patterns of variables of scientific interests. The upcoming megasite at SGP with its enhanced spatial density will facilitate the studies at even finer scales. Currently, however, data are reported only at individual site locations at different time resolutions for different datastreams. It is difficult for users to locate all the data they need and requires extra effort to synchronize the data. To address these problems, the ARMBE2DGRID value-added product merges key surface measurements at the ARM SGP sites and interpolates the data to a regular 2D grid to facilitate the data application.

  7. Locality constraints and 2D quasicrystals

    The plausible assumption that long-range interactions between atoms are negligible in a quasicrystal leaks to the study of tilings that obey constraints on the local configurations of tiles. The theory of such constraints (called matching rules) for 2D quasicrystal tilings is reviewed here. Different types of matching rules are defined and examples of tilings obeying them are given where known. The role of tile decoration is discussed and is shown to be significant in at least two cases (octagonal and dodecagonal duals of periodic 4-grids and 6-grids). A new result is introduced: a constructive procedure is described for generating weak matching rules for tilings with N-fold symmetry, for any N that is either a prime number or twice a prime number. The physics associated with weak matching rules, results on local growth rules, and the case of icosahedral symmetry are all briefly discussed. (author). 29 refs, 4 figs

  8. Numerical Evaluation of 2D Ground States

    Kolkovska, Natalia

    2016-02-01

    A ground state is defined as the positive radial solution of the multidimensional nonlinear problem \\varepsilon propto k_ bot 1 - ξ with the function f being either f(u) =a|u|p-1u or f(u) =a|u|pu+b|u|2pu. The numerical evaluation of ground states is based on the shooting method applied to an equivalent dynamical system. A combination of fourth order Runge-Kutta method and Hermite extrapolation formula is applied to solving the resulting initial value problem. The efficiency of this procedure is demonstrated in the 1D case, where the maximal difference between the exact and numerical solution is ≈ 10-11 for a discretization step 0:00025. As a major application, we evaluate numerically the critical energy constant. This constant is defined as a functional of the ground state and is used in the study of the 2D Boussinesq equations.

  9. 2-D Model Test of Dolosse Breakwater

    Burcharth, Hans F.; Liu, Zhou

    1994-01-01

    The rational design diagram for Dolos armour should incorporate both the hydraulic stability and the structural integrity. The previous tests performed by Aalborg University (AU) made available such design diagram for the trunk of Dolos breakwater without superstructures (Burcharth et al. 1992). To...... extend the design diagram to cover Dolos breakwaters with superstructure, 2-D model tests of Dolos breakwater with wave wall is included in the project Rubble Mound Breakwater Failure Modes sponsored by the Directorate General XII of the Commission of the European Communities under Contract MAS-CT92......-0042. Furthermore, Task IA will give the design diagram for Tetrapod breakwaters without a superstructure. The more complete research results on Dolosse can certainly give some insight into the behaviour of Tetrapods armour layer of the breakwaters with superstructure. The main part of the experiment was on the...

  10. Graphene suspensions for 2D printing

    Soots, R. A.; Yakimchuk, E. A.; Nebogatikova, N. A.; Kotin, I. A.; Antonova, I. V.

    2016-04-01

    It is shown that, by processing a graphite suspension in ethanol or water by ultrasound and centrifuging, it is possible to obtain particles with thicknesses within 1-6 nm and, in the most interesting cases, 1-1.5 nm. Analogous treatment of a graphite suspension in organic solvent yields eventually thicker particles (up to 6-10 nm thick) even upon long-term treatment. Using the proposed ink based on graphene and aqueous ethanol with ethylcellulose and terpineol additives for 2D printing, thin (~5 nm thick) films with sheet resistance upon annealing ~30 MΩ/□ were obtained. With the ink based on aqueous graphene suspension, the sheet resistance was ~5-12 kΩ/□ for 6- to 15-nm-thick layers with a carrier mobility of ~30-50 cm2/(V s).

  11. Area preserving diffeomorphisms and 2-d gravity

    La, H S

    1995-01-01

    Area preserving diffeomorphisms of a 2-d compact Riemannian manifold with or without boundary are studied. We find two classes of decompositions of a Riemannian metric, namely, h- and g-decomposition, that help to formulate a gravitational theory which is area preserving diffeomorphism (SDiffM-) invariant but not necessarily diffeomorphism invariant. The general covariance of equations of motion of such a theory can be achieved by incorporating proper Weyl rescaling. The h-decomposition makes the conformal factor of a metric SDiffM-invariant and the rest of the metric invariant under conformal diffeomorphisms, whilst the g-decomposition makes the conformal factor a SDiffM scalar and the rest a SDiffM tensor. Using these, we reformulate Liouville gravity in SDiffM invariant way. In this context we also further clarify the dual formulation of Liouville gravity introduced by the author before, in which the affine spin connection is dual to the Liouville field.

  12. Metrology for graphene and 2D materials

    Pollard, Andrew J.

    2016-09-01

    The application of graphene, a one atom-thick honeycomb lattice of carbon atoms with superlative properties, such as electrical conductivity, thermal conductivity and strength, has already shown that it can be used to benefit metrology itself as a new quantum standard for resistance. However, there are many application areas where graphene and other 2D materials, such as molybdenum disulphide (MoS2) and hexagonal boron nitride (h-BN), may be disruptive, areas such as flexible electronics, nanocomposites, sensing and energy storage. Applying metrology to the area of graphene is now critical to enable the new, emerging global graphene commercial world and bridge the gap between academia and industry. Measurement capabilities and expertise in a wide range of scientific areas are required to address this challenge. The combined and complementary approach of varied characterisation methods for structural, chemical, electrical and other properties, will allow the real-world issues of commercialising graphene and other 2D materials to be addressed. Here, examples of metrology challenges that have been overcome through a multi-technique or new approach are discussed. Firstly, the structural characterisation of defects in both graphene and MoS2 via Raman spectroscopy is described, and how nanoscale mapping of vacancy defects in graphene is also possible using tip-enhanced Raman spectroscopy (TERS). Furthermore, the chemical characterisation and removal of polymer residue on chemical vapour deposition (CVD) grown graphene via secondary ion mass spectrometry (SIMS) is detailed, as well as the chemical characterisation of iron films used to grow large domain single-layer h-BN through CVD growth, revealing how contamination of the substrate itself plays a role in the resulting h-BN layer. In addition, the role of international standardisation in this area is described, outlining the current work ongoing in both the International Organization of Standardization (ISO) and the

  13. Effects of burning on the development of 2D turbulence

    Hicks, Elizabeth; Rosner, Robert

    2010-12-01

    We present the results of two-dimensional (2D) direct numerical simulations of a Boussinesq fluid in the presence of gravity. Our simulations compare the evolution of a burning interface between a denser fuel and less dense ashes to the evolution of a non-burning interface. Initially, a dense, cool fluid is placed over a light, hot fluid and the interface between the two fluids is perturbed. Because of the presence of gravity, the system is Rayleigh-Taylor unstable, and the two fluids mix. We compare this Rayleigh-Taylor mixing problem to that in the same setup but with premixed combustion occurring at the interface between the two fluids. In both cases, the boundary conditions are periodic in the horizontal direction. As the force of gravity is increased, the flow behind the flame transitions from an ordered, laminar state to a chaotic, turbulent state. Our simulations explore the effect of burning on the development of the turbulent state, especially the effect of burning on the energy and enstrophy cascades, the mixing of the temperature fields and the shape of the flame front.

  14. Effects of burning on the development of 2D turbulence

    We present the results of two-dimensional (2D) direct numerical simulations of a Boussinesq fluid in the presence of gravity. Our simulations compare the evolution of a burning interface between a denser fuel and less dense ashes to the evolution of a non-burning interface. Initially, a dense, cool fluid is placed over a light, hot fluid and the interface between the two fluids is perturbed. Because of the presence of gravity, the system is Rayleigh-Taylor unstable, and the two fluids mix. We compare this Rayleigh-Taylor mixing problem to that in the same setup but with premixed combustion occurring at the interface between the two fluids. In both cases, the boundary conditions are periodic in the horizontal direction. As the force of gravity is increased, the flow behind the flame transitions from an ordered, laminar state to a chaotic, turbulent state. Our simulations explore the effect of burning on the development of the turbulent state, especially the effect of burning on the energy and enstrophy cascades, the mixing of the temperature fields and the shape of the flame front.

  15. Advecting Procedural Textures for 2D Flow Animation

    Kao, David; Pang, Alex; Moran, Pat (Technical Monitor)

    2001-01-01

    This paper proposes the use of specially generated 3D procedural textures for visualizing steady state 2D flow fields. We use the flow field to advect and animate the texture over time. However, using standard texture advection techniques and arbitrary textures will introduce some undesirable effects such as: (a) expanding texture from a critical source point, (b) streaking pattern from the boundary of the flowfield, (c) crowding of advected textures near an attracting spiral or sink, and (d) absent or lack of textures in some regions of the flow. This paper proposes a number of strategies to solve these problems. We demonstrate how the technique works using both synthetic data and computational fluid dynamics data.

  16. 2-D soft x-ray arrays in the EAST

    Chen, Kaiyun; Xu, Liqing; Hu, Liqun; Duan, Yanmin; Li, Xueqin; Yuan, Yi; Mao, Songtao; Sheng, Xiuli; Zhao, Jinlong

    2016-06-01

    A high spatial and temporal resolution soft x-ray (SXR) imaging diagnostic has been installed in EAST for the study of magnetohydrodynamics activities and core high-Z impurity transport. Up to 122 lines of sight view the poloidal plasma from three directions (two up-down symmetrical horizontal arrays and one vertical array), which renders the diagnostic able to provide detailed tomographic reconstructions under various conditions. Fourier-Bessel method based on flux coordinates was employed for 2-D SXR tomographic reconstruction. Examples of several events measured by SXR diagnostic in EAST are shown, namely the crash patterns of sawtooth, periodical burst of edge localized modes, and the transport of high-Z intrinsic impurities.

  17. Quantification of In Vivo 2D Vector Flow Ultrasound

    Pedersen, Mads Møller

    2012-01-01

    by the vector technique. With the conventional technique, the manual setting of the angle is operator dependent. With the calculated vector angle, this operator is relieved from the angle setting and the measurement is angle corrected by the identical method every time. With study II the carotid bifurcation...... including the carotid bulb and the common carotid artery were scanned on 8 healthy volunteers. The flow patterns of the two structures were outlined and presented to each of 5 experienced radiologists. The complexity of the identical areas were calculated by the vector concentration and compared....... Now, the method has been implemented into a commercial ultrasound scanner made for hospital use. In real-time, the technique measures movements in all directions as 2D vector fields, including movements perpendicular to the ultrasound beam. This is not available with conventional ultrasound scanners...

  18. Seepage Analysis of Upper Gotvand Dam Concerning Gypsum Karstification (2D and 3D Approaches)

    Sadrekarimi, Jamshid; Kiyani, Majid; Fakhri, Behnam;

    2011-01-01

    model locates the phreatic surface somewhat higher than the 2D model. This means that the 2D model estimates lower pore water pressure pattern in comparison with the 3D model. These may be attributed to the fact that with 2D model the lateral components of vectors of seepage velocity are ignored. In the......Upper Gotvand Dam is constructed on the Karun River at the south west of Iran. In this paper, 2D and 3D models of the dam together with the foundation and abutments were established, and several seepage analyses were carried out. Then, the gypsum veins that are scattered throughout the foundation...... ground were included in the models, and the seepage pattern, considering the dissolution law of gypsum, was analyzed. It was disclosed that the discharge fluxes obtained from 2D and 3D analyses are not similar, and the discharge flux in 3D model is about four times that of the 2D model. Also, the 3D...

  19. Local 2D-2D tunneling in high mobility electron systems

    Pelliccione, Matthew; Sciambi, Adam; Bartel, John; Goldhaber-Gordon, David; Pfeiffer, Loren; West, Ken; Lilly, Michael; Bank, Seth; Gossard, Arthur

    2012-02-01

    Many scanning probe techniques have been utilized in recent years to measure local properties of high mobility two-dimensional (2D) electron systems in GaAs. However, most techniques lack the ability to tunnel into the buried 2D system and measure local spectroscopic information. We report scanning gate measurements on a bilayer GaAs/AlGaAs heterostructure that allows for a local modulation of tunneling between two 2D electron layers. We call this technique Virtual Scanning Tunneling Microscopy (VSTM) [1,2] as the influence of the scanning gate is analogous to an STM tip, except at a GaAs/AlGaAs interface instead of a surface. We will discuss the spectroscopic capabilities of the technique, and show preliminary results of measurements on a high mobility 2D electron system.[1] A. Sciambi, M. Pelliccione et al., Appl. Phys. Lett. 97, 132103 (2010).[2] A. Sciambi, M. Pelliccione et al., Phys. Rev. B 84, 085301 (2011).

  20. 2D Seismic Reflection Data across Central Illinois

    Smith, Valerie; Leetaru, Hannes

    2014-09-30

    In a continuing collaboration with the Midwest Geologic Sequestration Consortium (MGSC) on the Evaluation of the Carbon Sequestration Potential of the Cambro-Ordovician Strata of the Illinois and Michigan Basins project, Schlumberger Carbon Services and WesternGeco acquired two-dimensional (2D) seismic data in the Illinois Basin. This work included the design, acquisition and processing of approximately 125 miles of (2D) seismic reflection surveys running west to east in the central Illinois Basin. Schlumberger Carbon Services and WesternGeco oversaw the management of the field operations (including a pre-shoot planning, mobilization, acquisition and de-mobilization of the field personnel and equipment), procurement of the necessary permits to conduct the survey, post-shoot closure, processing of the raw data, and provided expert consultation as needed in the interpretation of the delivered product. Three 2D seismic lines were acquired across central Illinois during November and December 2010 and January 2011. Traversing the Illinois Basin, this 2D seismic survey was designed to image the stratigraphy of the Cambro-Ordovician sections and also to discern the basement topography. Prior to this survey, there were no regionally extensive 2D seismic data spanning this section of the Illinois Basin. Between the NW side of Morgan County and northwestern border of Douglas County, these seismic lines ran through very rural portions of the state. Starting in Morgan County, Line 101 was the longest at 93 miles in length and ended NE of Decatur, Illinois. Line 501 ran W-E from the Illinois Basin – Decatur Project (IBDP) site to northwestern Douglas County and was 25 miles in length. Line 601 was the shortest and ran N-S past the IBDP site and connected lines 101 and 501. All three lines are correlated to well logs at the IBDP site. Originally processed in 2011, the 2D seismic profiles exhibited a degradation of signal quality below ~400 millisecond (ms) which made

  1. A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

    Nickerson Cheryl A; Wilson James W

    2006-01-01

    Abstract Background Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level usi...

  2. Face recognition method based on 2D-PCA and 2D-LDA%基于2D-PCA和2D-LDA的人脸识别方法

    温福喜; 刘宏伟

    2007-01-01

    提出了基于2D-PCA、2D-LDA两种特征采用融合分类器的人脸识别方法.首先提取人脸图像的2D-PCA和2D-LDA特征,对不同特征在决策层对分类器进行融合.在ORL人脸库上的试验结果表明,分类器决策层融合方法在识别性能上优于2D-PCA和2D-LDA,更具有鲁棒性.

  3. 2D DIGITAL SIMPLIFIED FLOW VALVE

    Ruan Jian; Li Sheng; Pei Xiang; Burton R; Ukrainetz P; Bitner D

    2004-01-01

    The 2D digital simplified flow valve is composed of a pilot-operated valve designed with both rotary and linear motions of a single spool,and a stepper motor under continual control.How the structural parameters affect the static and dynamic characteristics of the valve is first clarified and a criterion for stability is presented.Experiments are designed to test the performance of the valve.It is necessary to establish a balance between the static and dynamic characteristics in deciding the structural parameters.Nevertheless,it is possible to maintain the dynamic response at a fairly high level,while keeping the leakage of the pilot stage at an acceptable level.One of the features of the digital valve is stage control.In stage control the nonlinearities,such as electromagnetic saturation and hysteresis,are greatly reduced.To a large extent the dynamic response of the valve is decided by the executing cycle of the control algorithm.

  4. Competing coexisting phases in 2D water

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-05-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules.

  5. 2D manifold-independent spinfoam theory

    A number of background-independent quantization procedures have recently been employed in 4D nonperturbative quantum gravity. We investigate and illustrate these techniques and their relation in the context of a simple 2D topological theory. We discuss canonical quantization, loop or spin network states, path integral quantization over a discretization of the manifold, spin foam formulation and the fully background-independent definition of the theory using an auxiliary field theory on a group manifold. While several of these techniques have already been applied to this theory by Witten, the last one is novel: it allows us to give a precise meaning to the sum over topologies, and to compute background-independent and, in fact, 'manifold-independent' transition amplitudes. These transition amplitudes play the role of Wightman functions of the theory. They are physical observable quantities, and the canonical structure of the theory can be reconstructed from them via a C* algebraic GNS construction. We expect an analogous structure to be relevant in 4D quantum gravity

  6. Ion Transport in 2-D Graphene Nanochannels

    Xie, Quan; Foo, Elbert; Duan, Chuanhua

    2015-11-01

    Graphene membranes have recently attracted wide attention due to its great potential in water desalination and selective molecular sieving. Further developments of these membranes, including enhancing their mass transport rate and/or molecular selectivity, rely on the understanding of fundamental transport mechanisms through graphene membranes, which has not been studied experimentally before due to fabrication and measurement difficulties. Herein we report the fabrication of the basic constituent of graphene membranes, i.e. 2-D single graphene nanochannels (GNCs) and the study of ion transport in these channels. A modified bonding technique was developed to form GNCs with well-defined geometry and uniform channel height. Ion transport in such GNCs was studied using DC conductance measurement. Our preliminary results showed that the ion transport in GNCs is still governed by surface charge at low concentrations (10-6M to 10-4M). However, GNCs exhibits much higher ionic conductances than silica nanochannels with the same geometries in the surface-charge-governed regime. This conductance enhancement can be attributed to the pre-accumulation of charges on graphene surfaces. The work is supported by the Faculty Startup Fund (Boston University, USA).

  7. Phase Engineering of 2D Tin Sulfides.

    Mutlu, Zafer; Wu, Ryan J; Wickramaratne, Darshana; Shahrezaei, Sina; Liu, Chueh; Temiz, Selcuk; Patalano, Andrew; Ozkan, Mihrimah; Lake, Roger K; Mkhoyan, K A; Ozkan, Cengiz S

    2016-06-01

    Tin sulfides can exist in a variety of phases and polytypes due to the different oxidation states of Sn. A subset of these phases and polytypes take the form of layered 2D structures that give rise to a wide host of electronic and optical properties. Hence, achieving control over the phase, polytype, and thickness of tin sulfides is necessary to utilize this wide range of properties exhibited by the compound. This study reports on phase-selective growth of both hexagonal tin (IV) sulfide SnS2 and orthorhombic tin (II) sulfide SnS crystals with diameters of over tens of microns on SiO2 substrates through atmospheric pressure vapor-phase method in a conventional horizontal quartz tube furnace with SnO2 and S powders as the source materials. Detailed characterization of each phase of tin sulfide crystals is performed using various microscopy and spectroscopy methods, and the results are corroborated by ab initio density functional theory calculations. PMID:27099950

  8. Competing coexisting phases in 2D water.

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-01-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules. PMID:27185018

  9. Resolution Independent 2D Cartoon Video Conversion

    MSF. Fayaza

    2016-03-01

    Full Text Available This paper describes a novel system for vectorizing 2D raster cartoon. The output videos are the resolution independent, smaller in file size. As a first step, input video is segment to scene thereafter all processes are done for each scene separately. Every scene contains foreground and background objects so in each and every scene foreground background classification is performed. Background details can occlude by foreground objects but when foreground objects move its previous position such occluded details exposed in one of the next frame so using that frame can fill the occluded area and can generate static background. Classified foreground objects are identified and the motion of the foreground objects tracked for this simple user assistance is required from those motion details of foreground object’s animation generated. Static background and foreground objects segmented using K-means clustering and each and every cluster’s vectorized using potrace. Using vectored background and foreground object animation path vector video regenerated.

  10. Coalescence of Anderson-localized modes at an exceptional point in 2D random media

    Bachelard, Nicolas; Arlandis, Julien; Touzani, Rachid; Sebbah, Patrick

    2014-01-01

    In non-hermitian systems, the particular position at which two eigenstates coalesce under a variation of a parameter in the complex plane is called an exceptional point. A non-perturbative theory is proposed which describes the evolution of modes in 2D open dielectric systems when permittivity distribution is modified. We successfully test this theory in a 2D disordered system to predict the position in the parameter space of the exceptional point between two Anderson-localized states. We observe that the accuracy of the prediction depends on the number of localized states accounted for. Such an exceptional point is experimentally accessible in practically relevant disordered photonic systems

  11. 2D to 3D transition of polymeric carbon nitride nanosheets

    The transition from a prevalent turbostratic arrangement with low planar interactions (2D) to an array of polymeric carbon nitride nanosheets with stronger interplanar interactions (3D), occurring for samples treated above 650 °C, was detected by terahertz-time domain spectroscopy (THz-TDS). The simulated 3D material made of stacks of shifted quasi planar sheets composed of zigzagged polymer ribbons, delivered a XRD simulated pattern in relatively good agreement with the experimental one. The 2D to 3D transition was also supported by the simulation of THz-TDS spectra obtained from quantum chemistry calculations, in which the same broad bands around 2 THz and 1.5 THz were found for 2D and 3D arrays, respectively. This transition was also in accordance with the tightening of the interplanar distance probably due to an interplanar π bond contribution, as evidenced also by a broad absorption around 2.6 eV in the UV–vis spectrum, which appeared in the sample treated at 650 °C, and increased in the sample treated at 700 °C. The band gap was calculated for 1D and 2D cases. The value of 3.374 eV for the 2D case is, within the model accuracy and precision, in a relative good agreement with the value of 3.055 eV obtained from the experimental results. - Graphical abstract: 2D lattice mode vibrations and structural changes correlated with the so called “2D to 3D transition”. - Highlights: • A 2D to 3D transition has been detected for polymeric carbon nitride. • THz-TDS allowed us to discover and detect the 2D to 3D transition of polymeric carbon nitride. • We propose a structure for polymeric carbon nitride confirming it with THz-TDS

  12. 2D to 3D transition of polymeric carbon nitride nanosheets

    Chamorro-Posada, Pedro [Dpto. de Teoría de la Señal y Comunicaciones e IT, Universidad de Valladolid, ETSI Telecomunicación, Paseo Belén 15, 47011 Valladolid (Spain); Vázquez-Cabo, José [Dpto. de Teoría de la Señal y Comunicaciones, Universidad de Vigo, ETSI Telecomunicación, Lagoas Marcosende s/n, Vigo (Spain); Sánchez-Arévalo, Francisco M. [Instituto de Investigaciones en Materiales (IIM), Universidad Nacional Autónoma de México, Apdo. Postal 70–360, Cd. Universitaria, México D.F. 04510 (Mexico); Martín-Ramos, Pablo [Dpto. de Teoría de la Señal y Comunicaciones e IT, Universidad de Valladolid, ETSI Telecomunicación, Paseo Belén 15, 47011 Valladolid (Spain); Laboratorio de Materiales Avanzados (Advanced Materials Laboratory) ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia (Spain); Martín-Gil, Jesús; Navas-Gracia, Luis M. [Laboratorio de Materiales Avanzados (Advanced Materials Laboratory) ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia (Spain); Dante, Roberto C., E-mail: rcdante@yahoo.com [Laboratorio de Materiales Avanzados (Advanced Materials Laboratory) ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia (Spain)

    2014-11-15

    The transition from a prevalent turbostratic arrangement with low planar interactions (2D) to an array of polymeric carbon nitride nanosheets with stronger interplanar interactions (3D), occurring for samples treated above 650 °C, was detected by terahertz-time domain spectroscopy (THz-TDS). The simulated 3D material made of stacks of shifted quasi planar sheets composed of zigzagged polymer ribbons, delivered a XRD simulated pattern in relatively good agreement with the experimental one. The 2D to 3D transition was also supported by the simulation of THz-TDS spectra obtained from quantum chemistry calculations, in which the same broad bands around 2 THz and 1.5 THz were found for 2D and 3D arrays, respectively. This transition was also in accordance with the tightening of the interplanar distance probably due to an interplanar π bond contribution, as evidenced also by a broad absorption around 2.6 eV in the UV–vis spectrum, which appeared in the sample treated at 650 °C, and increased in the sample treated at 700 °C. The band gap was calculated for 1D and 2D cases. The value of 3.374 eV for the 2D case is, within the model accuracy and precision, in a relative good agreement with the value of 3.055 eV obtained from the experimental results. - Graphical abstract: 2D lattice mode vibrations and structural changes correlated with the so called “2D to 3D transition”. - Highlights: • A 2D to 3D transition has been detected for polymeric carbon nitride. • THz-TDS allowed us to discover and detect the 2D to 3D transition of polymeric carbon nitride. • We propose a structure for polymeric carbon nitride confirming it with THz-TDS.

  13. Identification of novel CYP2D7-2D6 hybrids: non-functional and functional variants

    Andrea Gaedigk

    2010-10-01

    Full Text Available Polymorphic expression of CYP2D6 contributes to the wide range of activity observed for this clinically important drug metabolizing enzyme. In this report we describe novel CYP2D7/2D6 hybrid genes encoding non-functional and functional CYP2D6 protein and a CYP2D7 variant that mimics a CYP2D7/2D6 hybrid gene. Five kb long PCR products encompassing the novel genes were entirely sequenced. A quantitative assay probing in different gene regions was employed to determine CYP2D6 and 2D7 copy number variations and the relative position of the hybrid genes within the locus was assessed by long-range PCR. In addition to the previously known CYP2D6*13 and *66 hybrids, we describe three novel non-functional CYP2D7-2D6 hybrids with gene switching in exon 2 (CYP2D6*79, intron 2 (CYP2D6*80 and intron 5 (CYP2D6*67. A CYP2D7-specific T-ins in exon 1 causes a detrimental frame shift. One subject revealed a CYP2D7 conversion in the 5’-flanking region of a CYP2D6*35 allele, was otherwise unaffected (designated CYP2D6*35B. Finally, three DNAs revealed a CYP2D7 gene with a CYP2D6-like region downstream of exon 9 (designated CYP2D7[REP6]. Quantitative copy number determination, sequence analyses and long-range PCR mapping were in agreement and excluded the presence of additional gene units. Undetected hybrid genes may cause over-estimation of CYP2D6 activity (CYP2D6*1/*1 vs *1/hybrid, etc, but may also cause results that may interfere with the genotype determination. Detection of hybrid events, ‘single’ and tandem, will contribute to more accurate phenotype prediction from genotype data.

  14. Climate and evolution: implications of some extinction patterns in African and European Machairodontine Cats of the Plio-Pleistocene

    Antón, M.

    1998-12-01

    Full Text Available Estudios recientes sobre las correlaciones entre cambios climáticos globales y la evolución de la biota del Plio-Pleistoceno Africano han revelado aparentes discrepancias entre las fechas y la significación de eventos registrados en distintas fuentes. Las diferencias mas notables se refieren a un importante cambio en la proporción de isótopos de oxígeno marinas hace 2,5 millones de años, y a la posibilidad de una transición biótica relacionada causalmente con dicho cambio. Cambios en la vegetación detectados a través de los valores de isótopos estables en los paleosuelos sugieren que el principal cambio hacia una vegetación mas abierta ocurrió mas tarde, hace ∼1,7 millones de años. Nosotros estudiamos el problema refiriendonos en particular a los eventos de hace 1,7 millones de años, y a la extinción en Africa de los félidos con dientes de sable que se produce poco después, puesto que las extinciones de taxones euritópicos como estos probablemente señala cambios significativos en las condiciones ambientales. Nosotros comparamos el patrón de dichas extinciones con los de taxones semejantes 0 idénticos, en Eurasia y América, y sugerimos que en cada caso hay claros indicios de importantes cambios ambientales. Es probable que los cambios en la vegetación de Africa registrados hace ∼1,7 millones de años representen una respuesta en el medio terrestre alas cambios climáticos globales reflejados en el registro marino hace ∼1,9 millones de años.Recent discussions of correlations between global climatic change and evolution of the African Plio-Pleistocene biota have revealed apparent discrepancies between the timing and significance of events recorded in different data sets. The most notable differences have occurred in relation to a major shift in the ratio of marine oxygen isotopes by 2.5 myr and claims for a causally related transition in the biota. Vegetational changes recorded in palaeosol stable isotope

  15. Finite state models of constrained 2d data

    Justesen, Jørn

    2004-01-01

    This paper considers a class of discrete finite alphabet 2D fields that can be characterized using tools front finite state machines and Markov chains. These fields have several properties that greatly simplify the analysis of 2D coding methods.......This paper considers a class of discrete finite alphabet 2D fields that can be characterized using tools front finite state machines and Markov chains. These fields have several properties that greatly simplify the analysis of 2D coding methods....

  16. Ultrasonic 2D matrix PVDF transducer

    Ptchelintsev, A.; Maev, R. Gr.

    2000-05-01

    During the past decade a substantial amount of work has been done in the area of ultrasonic imaging technology using 2D arrays. The main problems arising for the two-dimensional matrix transducers at megahertz frequencies are small size and huge count of the elements, high electrical impedance, low sensitivity, bad SNR and slower data acquisition rate. The major technological difficulty remains the high density of the interconnect. To solve these problems numerous approaches have been suggested. In the present work, a 24×24 elements (24 transmit+24 receive) matrix and a switching board were developed. The transducer consists of two 52 μm PVDF layers each representing a linear array of 24 elements placed one on the top of the other. Electrodes in these two layers are perpendicular and form the grid of 0.5×0.5 mm pitch. The layers are bonded together with the ground electrode being monolithic and located between the layers. The matrix is backed from the rear surface with an epoxy composition. During the emission, a linear element from the emitting layer generates a longitudinal wave pulse propagating inside the test object. Reflected pulses are picked-up by the receiving layer. During one transmit-receive cycle one transmit element and one receive element are selected by corresponding multiplexers. These crossed elements emulate a small element formed by their intersection. The present design presents the following advantages: minimizes number of active channels and density of the interconnect; reduces the electrical impedance of the element improving electrical matching; enables the transmit-receive mode; due to the efficient backing provides bandwidth and good time resolution; and, significantly reduces the electronics complexity. The matrix can not be used for the beam steering and focusing. Owing to this impossibility of focusing, the penetration depth is limited as well by the diffraction phenomena.

  17. Polynomial solution of 2D Kalman-Bucy filtering problem

    Sebek, M.

    1992-01-01

    The 2D version of the Kalman-Bucy filtering problem is formulated and then solved via 2D polynomial methods. The optimal filter is restricted to be a linear causal system. The design procedure is shown to consist of one 2D spectral factorization equation only. In fact, it works for n-D signals (n>2)

  18. Polynomial solution of 2D Kalman-Bucy filtering problem

    Sebek, M.

    1992-01-01

    The 2D version of the Kalman-Bucy filtering problem is formulated and then solved via 2D polynomial methods. The optimal filter is restricted to be a linear causal system. The design procedure is shown to consist of one 2D spectral factorization equation only. In fact, it works for n-D signals (n>2) as well.

  19. Sparse Non-negative Matrix Factor 2-D Deconvolution for Automatic Transcription of Polyphonic Music

    Schmidt, Mikkel N.; Mørup, Morten

    2006-01-01

    We present a novel method for automatic transcription of polyphonic music based on a recently published algorithm for non-negative matrix factor 2-D deconvolution. The method works by simultaneously estimating a time-frequency model for an instrument and a pattern corresponding to the notes which...... are played based on a log-frequency spectrogram of the music....

  20. Power loss analysis of n-PASHA cells validated by 2D simulations

    Janssen, G.J.M.; Gutjahr, A.; Burgers, A.R.; Saynova, D.S.; Cesar, I.; Romijn, I.G.

    2013-10-15

    To reach >21% efficiency for the n-Pasha (passivated all sides H-pattern) cell of ECN, reliable power-loss analyses are essential. A power-loss analysis is presented that is based on experimental data but validated and completed by 2D simulations. The analysis is used to identify the key factors that will contribute most to achieving >21% efficiency.

  1. A Bioactive Carbon Nanotube-Based Ink for Printing 2D and 3D Flexible Electronics.

    Shin, Su Ryon; Farzad, Raziyeh; Tamayol, Ali; Manoharan, Vijayan; Mostafalu, Pooria; Zhang, Yu Shrike; Akbari, Mohsen; Jung, Sung Mi; Kim, Duckjin; Comotto, Mattia; Annabi, Nasim; Al-Hazmi, Faten Ebrahim; Dokmeci, Mehmet R; Khademhosseini, Ali

    2016-05-01

    The development of electrically conductive carbon nanotube-based inks is reported. Using these inks, 2D and 3D structures are printed on various flexible substrates such as paper, hydrogels, and elastomers. The printed patterns have mechanical and electrical properties that make them beneficial for various biological applications. PMID:26915715

  2. A COMPREHENSIVE ANALYSIS OF FERMI GAMMA-RAY BURST DATA. II. Ep EVOLUTION PATTERNS AND IMPLICATIONS FOR THE OBSERVED SPECTRUM-LUMINOSITY RELATIONS

    We present a time-resolved spectral analysis of 51 long and 11 short bright gamma-ray bursts (GRBs) observed with the Fermi/Gamma-Ray Burst Monitor, paying special attention to Ep evolution within each burst. Among eight single-pulse long GRBs, five show an evolution from hard to soft, while three show intensity tracking. The multi-pulse long GRBs have more complicated patterns. Statistically, the hard-to-soft evolution pulses tend to be more asymmetric than the intensity-tracking ones, with a steeper rising wing than the falling wing. Short GRBs have Ep tracking intensity exclusively with the 16 ms time-resolution analysis. We performed a simulation analysis and suggest that for at least some bursts, the late intensity-tracking pulses could be a consequence of overlapping hard-to-soft pulses. However, the fact that the intensity-tracking pattern exists in the first pulse of the multi-pulse long GRBs and some single-pulse GRBs, suggests that intensity tracking is an independent component, which may operate in some late pulses as well. For the GRBs with measured redshifts, we present a time-resolved Ep – Lγ,iso correlation analysis and show that the scatter of the correlation is comparable to that of the global Amati/Yonetoku relation. We discuss the predictions of various radiation models regarding Ep evolution, as well as the possibility of a precessing jet in GRBs. The data pose a great challenge to each of these models, and hold the key to unveiling the physics behind GRB prompt emission.

  3. FEM-2D, 2-D MultiGroup Diffusion in X-Y Geometry

    1 - Nature of physical problem solved: FEM-2D solves the two-dimensional diffusion equation in x-y geometry. This is done by the finite elements method. 2 - Method of solution: FEM-2D uses triangular elements with first and second order Lagrange approximations. The systems equations are formulated in multigroup form and solved by Cholesky procedure which operates only on nonzero elements. Various acceleration techniques are available for the outer iteration. Fluxes along various lines and rates in arbitrary zones may be output. 3 - Restrictions on the complexity of the problem: The code uses variable dimensioning. Thus, the problem size is restricted by the largest array which usually is the systems matrix. Fluxes of all groups are kept in memory. This might become another restrictive data set for a large number of groups. The validity of the results is restricted by the approximations used. FEM-2D requires a finite element net which allows the approximation of fluxes by at most parabolas. The node distribution should be more dense in areas of heavy flux changes (near absorbers or the reflector)

  4. DNTM/R2D, 2-D Transport in X-Y Geometry

    1 - Description of program or function: DNTM/R2D solves the neutron transport equation in two-dimensional X-Y geometry by the discrete nodal transport method. Source and eigenvalue problems can be solved. As compared to the two-dimensional nodal transport code DNTM/2D, the following new improved features are included: - Anisotropic scattering is considered. The order of anisotropic scattering is from P0 to P3. - The cross section input format is the same as for ANISN. Multi- group cross section libraries such as DLC-37 and DLC-BUGLE-80 can be used. 2 - Method of solution: DNTM/R2D uses the discrete nodal transport method. Anisotropic scattering is treated using Legendre expansion. Order of interior flux approximation is 2. Plane leakage approximation of surface flux is used. 3 - Restrictions on the complexity of the problem: Maximum number of: anisotropic scattering order = 3; material composition = 20; energy groups = 2; angular quadrature = 8; zones = 30. When coarse-mesh re-balancing is used, the maximum number of coarse meshes is 12 in each direction. If the computer permits some arrays can be enlarged to reduce the above restrictions

  5. Streamflow recession patterns can help unravel the role of climate and humans in landscape co-evolution

    Bogaart, Patrick W.; van der Velde, Ype; Lyon, Steve W.; Dekker, Stefan C.

    2016-04-01

    Traditionally, long-term predictions of river discharges and their extremes include constant relationships between landscape properties and model parameters. However, due to the co-evolution of many landscape properties more sophisticated methods are necessary to quantify future landscape-hydrological model relationships. As a first step towards such an approach we use the Brutsaert and Nieber (1977) analysis method to characterize streamflow recession behaviour of ≈ 200 Swedish catchments within the context of global change and landscape co-evolution. Results suggest that the Brutsaert-Nieber parameters are strongly linked to the climate, soil, land use, and their interdependencies. Many catchments show a trend towards more non-linear behaviour, meaning not only faster initial recession but also slower recession towards base flow. This trend has been found to be independent from climate change. Instead, we suggest that land cover change, both natural (restoration of natural soil profiles in forested areas) and anthropogenic (reforestation and optimized water management), is probably responsible. Both change types are characterised by system adaptation and change, towards more optimal ecohydrological conditions, suggesting landscape co-evolution is at play. Given the observed magnitudes of recession changes during the past 50 years, predictions of future river discharge critically need to include the effects of landscape co-evolution. The interconnections between the controls of land cover and climate on river recession behaviour, as we have quantified in this paper, provide first-order handles to do so.

  6. Estimating rates and patterns of morphological evolution from phylogenies: lessons in limb lability from Australian Lerista lizards

    Wiens John J

    2009-02-01

    Full Text Available Abstract Squamates (lizards and snakes offer an exciting model system for research on the evolution of body form. A new phylogenetic study in BMC Evolutionary Biology of Australian lizards shows remarkable evolutionary lability in digit numbers among closely related species, but also highlights important challenges in this area.

  7. Stability Test for 2-D Continuous-Discrete Systems

    2002-01-01

    Models of 2-D continuous-discrete systems are introduced, which can be used to describe some complex systems. Different from classical 2-D continuous systems or 2-D discrete systems, the asymptotic stability of the continuous-discrete systems is determined by Hurwitz-Schur stability (hybrid one) of 2-D characteristic polynomials of the systems. An algebraic algorithm with simpler test procedure for Hurwitz-Schur stability test of 2-D polynomials is developed. An example to illustrate the applications of the test approach is provided.

  8. Correlated Electron Phenomena in 2D Materials

    Lambert, Joseph G.

    In this thesis, I present experimental results on coherent electron phenomena in layered two-dimensional materials: single layer graphene and van der Waals coupled 2D TiSe2. Graphene is a two-dimensional single-atom thick sheet of carbon atoms first derived from bulk graphite by the mechanical exfoliation technique in 2004. Low-energy charge carriers in graphene behave like massless Dirac fermions, and their density can be easily tuned between electron-rich and hole-rich quasiparticles with electrostatic gating techniques. The sharp interfaces between regions of different carrier densities form barriers with selective transmission, making them behave as partially reflecting mirrors. When two of these interfaces are set at a separation distance within the phase coherence length of the carriers, they form an electronic version of a Fabry-Perot cavity. I present measurements and analysis of multiple Fabry-Perot modes in graphene with parallel electrodes spaced a few hundred nanometers apart. Transition metal dichalcogenide (TMD) TiSe2 is part of the family of materials that coined the term "materials beyond graphene". It contains van der Waals coupled trilayer stacks of Se-Ti-Se. Many TMD materials exhibit a host of interesting correlated electronic phases. In particular, TiSe2 exhibits chiral charge density waves (CDW) below TCDW ˜ 200 K. Upon doping with copper, the CDW state gets suppressed with Cu concentration, and CuxTiSe2 becomes superconducting with critical temperature of T c = 4.15 K. There is still much debate over the mechanisms governing the coexistence of the two correlated electronic phases---CDW and superconductivity. I will present some of the first conductance spectroscopy measurements of proximity coupled superconductor-CDW systems. Measurements reveal a proximity-induced critical current at the Nb-TiSe2 interfaces, suggesting pair correlations in the pure TiSe2. The results indicate that superconducting order is present concurrently with CDW in

  9. Shared human-chimpanzee pattern of perinatal femoral shaft morphology and its implications for the evolution of hominin locomotor adaptations.

    Naoki Morimoto

    Full Text Available BACKGROUND: Acquisition of bipedality is a hallmark of human evolution. How bipedality evolved from great ape-like locomotor behaviors, however, is still highly debated. This is mainly because it is difficult to infer locomotor function, and even more so locomotor kinematics, from fossil hominin long bones. Structure-function relationships are complex, as long bone morphology reflects phyletic history, developmental programs, and loading history during an individual's lifetime. Here we discriminate between these factors by investigating the morphology of long bones in fetal and neonate great apes and humans, before the onset of locomotion. METHODOLOGY/PRINCIPAL FINDINGS: Comparative morphometric analysis of the femoral diaphysis indicates that its morphology reflects phyletic relationships between hominoid taxa to a greater extent than taxon-specific locomotor adaptations. Diaphyseal morphology in humans and chimpanzees exhibits several shared-derived features, despite substantial differences in locomotor adaptations. Orangutan and gorilla morphologies are largely similar, and likely represent the primitive hominoid state. CONCLUSIONS/SIGNIFICANCE: These findings are compatible with two possible evolutionary scenarios. Diaphyseal morphology may reflect retained adaptive traits of ancestral taxa, hence human-chimpanzee shared-derived features may be indicative of the locomotor behavior of our last common ancestor. Alternatively, diaphyseal morphology might reflect evolution by genetic drift (neutral evolution rather than selection, and might thus be more informative about phyletic relationships between taxa than about locomotor adaptations. Both scenarios are consistent with the hypothesis that knuckle-walking in chimpanzees and gorillas resulted from convergent evolution, and that the evolution of human bipedality is unrelated to extant great ape locomotor specializations.

  10. Statistical mechanics of 2D turbulence with a prior vorticity distribution

    Chavanis, Pierre-Henri

    2009-01-01

    We adapt the formalism of the statistical theory of 2D turbulence in the case where the Casimir constraints are replaced by the specification of a prior vorticity distribution. A phenomenological relaxation equation is obtained for the evolution of the coarse-grained vorticity. This equation monotonically increases a generalized entropic functional (determined by the prior) while conserving circulation and energy. It can be used as a thermodynamical parametrization of forced 2D turbulence, or as a numerical algorithm to construct (i) arbitrary statistical equilibrium states in the sense of Ellis-Haven-Turkington (ii) particular statistical equilibrium states in the sense of Miller-Robert-Sommeria (iii) arbitrary stationary solutions of the 2D Euler equation that are formally nonlinearly dynamically stable according to the Ellis-Haven-Turkington stability criterion refining the Arnold theorems.

  11. CYP2D7 sequence variation interferes with TaqMan CYP2D6*15 and *35 genotyping

    Amanda K Riffel

    2016-01-01

    Full Text Available TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35 which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696 SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe

  12. 2D and 3D Chromosome Painting in Malaria Mosquitoes

    George, Phillip; Sharma, Atashi; Sharakhov, Igor V

    2014-01-01

    Fluorescent in situ hybridization (FISH) of whole arm chromosome probes is a robust technique for mapping genomic regions of interest, detecting chromosomal rearrangements, and studying three-dimensional (3D) organization of chromosomes in the cell nucleus. The advent of laser capture microdissection (LCM) and whole genome amplification (WGA) allows obtaining large quantities of DNA from single cells. The increased sensitivity of WGA kits prompted us to develop chromosome paints and to use them for exploring chromosome organization and evolution in non-model organisms. Here, we present a simple method for isolating and amplifying the euchromatic segments of single polytene chromosome arms from ovarian nurse cells of the African malaria mosquito Anopheles gambiae. This procedure provides an efficient platform for obtaining chromosome paints, while reducing the overall risk of introducing foreign DNA to the sample. The use of WGA allows for several rounds of re-amplification, resulting in high quantities of DNA that can be utilized for multiple experiments, including 2D and 3D FISH. We demonstrated that the developed chromosome paints can be successfully used to establish the correspondence between euchromatic portions of polytene and mitotic chromosome arms in An. gambiae. Overall, the union of LCM and single-chromosome WGA provides an efficient tool for creating significant amounts of target DNA for future cytogenetic and genomic studies. PMID:24429496

  13. Latent heat induced rotation limited aggregation in 2D ice nanocrystals

    Bampoulis, Pantelis; Siekman, Martin H.; Kooij, E. Stefan; Lohse, Detlef; Zandvliet, Harold J. W.; Poelsema, Bene

    2015-07-01

    The basic science responsible for the fascinating shapes of ice crystals and snowflakes is still not understood. Insufficient knowledge of the interaction potentials and the lack of relevant experimental access to the growth process are to blame for this failure. Here, we study the growth of fractal nanostructures in a two-dimensional (2D) system, intercalated between mica and graphene. Based on our scanning tunneling spectroscopy data, we provide compelling evidence that these fractals are 2D ice. They grow while they are in material contact with the atmosphere at 20 °C and without significant thermal contact to the ambient. The growth is studied in situ, in real time and space at the nanoscale. We find that the growing 2D ice nanocrystals assume a fractal shape, which is conventionally attributed to Diffusion Limited Aggregation (DLA). However, DLA requires a low mass density mother phase, in contrast to the actual currently present high mass density mother phase. Latent heat effects and consequent transport of heat and molecules are found to be key ingredients for understanding the evolution of the snow (ice) flakes. We conclude that not the local availability of water molecules (DLA), but rather them having the locally required orientation is the key factor for incorporation into the 2D ice nanocrystal. In combination with the transport of latent heat, we attribute the evolution of fractal 2D ice nanocrystals to local temperature dependent rotation limited aggregation. The ice growth occurs under extreme supersaturation, i.e., the conditions closely resemble the natural ones for the growth of complex 2D snow (ice) flakes and we consider our findings crucial for solving the "perennial" snow (ice) flake enigma.

  14. Program package for 2D burnup calculation

    The program package for 2 dimension burnup calculation was developed for TRIGA Mark III reactor. The package consists of 3 modules: PRESIX, SIXTUS-2, and BURN; 1 library, and 2 input files. PRESIX module prepared cross sections for diffusion calculation. SIXTUS-2 module, a two dimensional diffusion code in hexagonal geometry, calculates keff, neutron fluxes and power distributions. BURN module performs the burnup of fuel elements and stored the result in the ELEM.DAT file. PRESIX.LIB is two group cross section library for major reactor core components prepared using WIMS-D4 code. PRES.INP, the first input file, reads information on reactor power and core loading pattern. ELEM.DAT, the second input file, is prepared for specific TRIGA reactor and dependent on operation history. To verify the reactor model and computational methods, the calculated excess reactivities were compared to the measurement. The results are in good agreement. (author)

  15. Microstructural properties and dislocation evolution on a GaN grown on patterned sapphire substrate: A transmission electron microscopy study

    Kim, Y. H.; Ruh, H.; Noh, Y. K.; Kim, M. D.; Oh, J. E.

    2010-03-01

    The microstructural properties of a GaN layer grown on a patterned sapphire substrate (PSS) were studied in detail using transmission electron microscope techniques to determine dislocation and growth behaviors. Regular and uniform recrystallized GaN islands were observed on the protruding pattern. On a flat sapphire surface, the crystallographic orientation relationship of ⟨1¯21¯0⟩GaN on FS//⟨11¯00⟩sapphire and {11¯01}GaN on FS//{12¯13}sapphire existed between the GaN and the substrate. On the other hand, the orientation relationship of ⟨1¯21¯0⟩GaN layer//⟨1¯21¯0⟩GaN island on IS//⟨11¯00⟩sapphire and {11¯01}GaN layer//{0002}GaN island on IS//{12¯13}sapphire was confirmed among the GaN layer, the recrystallized GaN islands on an inclined sapphire surface and the PSS. The flat surface among the protruding patterns began to fill rapidly with GaN. Then, the GaN gradually overgrew the protruding pattern and coalesced near the summit as the growth time increased. The generation of threading dislocations was observed in the vicinity of the coalescence points near the top of the protruding patterns.

  16. Interpreting digit ratio (2D:4D)-behavior correlations: 2D:4D sex difference, stability, and behavioral correlates and their replicability in young children.

    Wong, Wang I; Hines, Melissa

    2016-02-01

    The popularity of using the ratio of the second to the fourth digit (2D:4D) to study influences of early androgen exposure on human behavior relies, in part, on a report that the ratio is sex-dimorphic and stable from age 2 years (Manning etal., 1998). However, subsequent research has rarely replicated this finding. Moreover, although 2D:4D has been correlated with many behaviors, these correlations are often inconsistent. Young children's 2D:4D-behavior correlations may be more consistent than those of older individuals, because young children have experienced fewer postnatal influences. To evaluate the usefulness of 2D:4D as a biomarker of prenatal androgen exposure in studies of 2D:4D-behavior correlations, we assessed its sex difference, temporal stability, and behavioral correlates over a 6- to 8-month period in 126, 2- to 3-year-old children, providing a rare same-sample replicability test. We found a moderate sex difference on both hands and high temporal stability. However, between-sex overlap and within-sex variability were also large. Only 3 of 24 correlations with sex-typed behaviors-scores on the Preschool Activities Inventory (PSAI), preference for a boy-typical toy, preference for a girl-typical toy, were significant and in the predicted direction, all of which involved the PSAI, partially confirming findings from another study. Correlation coefficients were larger for behaviors that showed larger sex differences. But, as in older samples, the overall pattern showed inconsistency across time, sex, and hand. Therefore, although sex-dimorphic and stable, 2D:4D-behavior correlations are no more consistent for young children than for older samples. Theoretical and methodological implications are discussed. PMID:26542674

  17. Pattern of Nucleotide Substitutions in Growth Hormone-Prolactin Gene Family: A Paradigm for Evolution by Gene Duplication

    Ohta, T.

    1993-01-01

    The growth hormone-prolactin gene family in mammals is an interesting example of evolution by gene duplication. Divergence among members of duplicated gene families and among species was examined by using reported gene sequences of growth hormone, prolactin and their receptors. Sequence divergence among species was found to show a general tendency in which a generation-time effect is pronounced for synonymous substitutions but not so for nonsynonymous substitutions. Divergence among duplicate...

  18. Genome structure drives patterns of gene family evolution in ciliates, a case study using Chilodonella uncinata (Protista, Ciliophora, Phyllopharyngea).

    Gao, Feng; Song, Weibo; Katz, Laura A

    2014-08-01

    In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that (1) alternative processing is extensive among gene families; and (2) such gene families are likely to be C. uncinata specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family-a protein kinase domain containing protein (PKc)-from two C. uncinata strains. Analysis of the PKc sequences reveals that (1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and (2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes. PMID:24749903

  19. Combining the switched-beam and beam-steering capabilities in a 2-D phased array antenna system

    Tsai, Yi-Che; Chen, Yin-Bing; Hwang, Ruey-Bing

    2016-01-01

    This paper presents the development, fabrication, and measurement of a novel beam-forming system consisting of 16 subarray antennas, each containing four aperture-coupled patch antennas, and the application of this system in smart wireless communication systems. The beam patterns of each of the subarray antennas can be switched toward one of nine zones over a half space by adjusting the specific phase delay angles among the four antenna elements. Furthermore, when all subarrays are pointed at the same zone, slightly continuous beam steering in around 1° increments can be achieved by dynamically altering the progressive phase delay angle among the subarrays. Phase angle calibration was implemented by coupling each transmitter output and down converter into the in-phase/quadrature baseband to calculate the correction factor to the weight. In addition, to validate the proposed concepts and the fabricated 2-D phased array antenna system, this study measured the far-field radiation patterns of the aperture-coupled patch array integrated with feeding networks and a phase-calibration system to carefully verify its spatially switched-beam and beam-steering characteristics at a center frequency of 2.4 GHz which can cover the industrial, scientific, and medical band and some long-term evolution applications. In addition, measured results were compared with calculated results, and agreement between them was observed.

  20. Functional characterization of a first avian cytochrome P450 of the CYP2D subfamily (CYP2D49.

    Hua Cai

    Full Text Available The CYP2D family members are instrumental in the metabolism of 20-25% of commonly prescribed drugs. Although many CYP2D isoforms have been well characterized in other animal models, research concerning the chicken CYP2Ds is limited. In this study, a cDNA encoding a novel CYP2D enzyme (CYP2D49 was cloned from the chicken liver for the first time. The CYP2D49 cDNA contained an open reading frame of 502 amino acids that shared 52%-57% identities with other CYP2Ds. The gene structure and neighboring genes of CYP2D49 are conserved and similar to those of human CYP2D6. Additionally, similar to human CYP2D6, CYP2D49 is un-inducible in the liver and expressed predominantly in the liver, kidney and small intestine, with detectable levels in several other tissues. Metabolic assays of the CYP2D49 protein heterologously expressed in E. coli and Hela cells indicated that CYP2D49 metabolized the human CYP2D6 substrate, bufuralol, but not debrisoquine. Moreover, quinidine, a potent inhibitor of human CYP2D6, only inhibited the bufuralol 1'-hydroxylation activity of CYP2D49 to a negligible degree. All these results indicated that CYP2D49 had functional characteristics similar to those of human CYP2D6 but measurably differed in the debrisoquine 4'-hydroxylation and quinidine inhibitory profile. Further structure-function investigations that employed site-directed mutagenesis and circular dichroism spectroscopy identified the importance of Val-126, Glu-222, Asp-306, Phe-486 and Phe-488 in keeping the enzymatic activity of CYP2D49 toward bufuralol as well as the importance of Asp-306, Phe-486 and Phe-488 in maintaining the conformation of CYP2D49 protein. The current study is only the first step in characterizing the metabolic mechanism of CYP2D49; further studies are still required.

  1. MAZE, Input Generator for Program DYNA2D and NIKE2D

    Description of program or function: MAZE is an interactive input generator for two-dimensional finite element codes. MAZE has three phases. In the first phase, lines and parts are defined. The first phase is terminated by the 'ASSM' or 'PASSM' command which merges all parts. In the second phase, boundary conditions may be specified, slide-lines may be defined, parts may be merged to eliminate nodes along common interfaces, boundary nodes may be moved for graded zoning, the mesh may be smoothed, and load curves may be defined. The second phase is terminated by the 'WBCD' command which causes MAZE to write the output file as soon as the 'T' terminate command is typed. In the third phase, material properties may be defined. Commands that apply to the first phase may not be used in the second or third; likewise, commands that apply in the second may not be used in the first and third, or commands that apply in the third in the first and second. Nine commands - TV, Z, GSET, PLOTS, GRID, NOGRID, FRAME, NOFRAME, and RJET are available in all phases. Comments may be added anywhere in the input stream by prefacing the comment with 'C'. Any DYNA2D or NIKE2D material and equation-of- state model may be defined via the MAT and EOS commands respectively. Maze may be terminated after phase two; it is not necessary to define the materials

  2. Wavelet characterization of 2D turbulence and intermittency in magnetized electron plasmas

    Romé, M.; Chen, S.; Maero, G.

    2016-06-01

    A study of the free relaxation of turbulence in a two-dimensional (2D) flow is presented, with a focus on the role of the initial vorticity conditions. Exploiting a well-known analogy with 2D inviscid incompressible fluids, the system investigated here is a magnetized pure electron plasma. The dynamics of this system are simulated by means of a 2D particle-in-cell code, starting from different spiral density (vorticity) distributions. A wavelet multiresolution analysis is adopted, which allows the coherent and incoherent parts of the flow to be separated. Comparison of the turbulent evolution in the different cases is based on the investigation of the time evolution of statistical properties, including the probability distribution functions and structure functions of the vorticity increments. It is also based on an analysis of the enstrophy evolution and its spectrum for the two components. In particular, while the statistical features assess the degree of flow intermittency, spectral analysis allows us not only to estimate the time required to reach a state of fully developed turbulence, but also estimate its dependence on the thickness of the initial spiral density distribution, accurately tracking the dynamics of both the coherent structures and the turbulent background. The results are compared with those relevant to annular initial vorticity distributions (Chen et al 2015 J. Plasma Phys. 81 495810511).

  3. Project Paleonao: How know the pattern of the rains. Spanish and Portuguese researchers reconstruct the climatic evolution of the North

    NAO, the effect of the North Atlantic oscillation, is the difference of air pressure between Iceland and the Azores, and that which governs climate variation every twelve months. To study and understand this phenomenon, which determines the arrival or not of the rains and influence on marine and terrestrial ecosystems are It launched the Paleonao Project. Based on historical weather records, its researchers use sensors natural lakes to collect data. is the case of the Penalara glacial lagoon, whose sediments they allow to know the evolution of the climate since thousands of years and to observe long-term trends of what will eventually passing in terms of precipitation and temperature changes. (Author)

  4. Surface Approximation Using the 2D FFENN Architecture

    Panagopoulos S

    2004-01-01

    Full Text Available A new two-dimensional feed-forward functionally expanded neural network (2D FFENN used to produce surface models in two dimensions is presented. New nonlinear multilevel surface basis functions are proposed for the network's functional expansion. A network optimization technique based on an iterative function selection strategy is also described. Comparative simulation results for surface mappings generated by the 2D FFENN, multilevel 2D FFENN, multilayered perceptron (MLP, and radial basis function (RBF architectures are presented.

  5. Maximizing entropy of image models for 2-D constrained coding

    Forchhammer, Søren; Danieli, Matteo; Burini, Nino; Zamarin, Marco; Ukhanova, Ann

    2010-01-01

    This paper considers estimating and maximizing the entropy of two-dimensional (2-D) fields with application to 2-D constrained coding. We consider Markov random fields (MRF), which have a non-causal description, and the special case of Pickard random fields (PRF). The PRF are 2-D causal finite context models, which define stationary probability distributions on finite rectangles and thus allow for calculation of the entropy. We consider two binary constraints and revisit the hard square const...

  6. Topological phase transition in 2D porous media flows

    Waisbord, Nicolas; Stoop, Norbert; Kantsler, Vasily; Guasto, Jeffrey S.; Dunkel, Jorn; Guasto Team; Dunkel Team; Kantsler Team

    2015-11-01

    Since the establishment of Darcy's law, analysis of porous-media flows has focused primarily on linking macroscopic transport properties, such as mean flow rate and dispersion, to the pore statistics of the material matrix. Despite intense efforts to understand the fluid velocity statistics from the porous-media structure, a qualitative and quantitative connection remains elusive. Here, we combine precisely controlled experiments with theory to quantify how geometric disorder in the matrix affects the flow statistics and transport in a quasi-2D microfluidic channel. Experimentally measured velocity fields for a range of different microstructure configurations are found to be in excellent agreement with large-scale numerical simulations. By successively increasing the matrix disorder, we study the transition from periodic flow structures to transport networks consisting of extended high-velocity channels. Morse-Smale complex analysis of the flow patterns reveals a topological phase transition that is linked to a qualitative change in the physical transport properties. This work demonstrates that topological flow analysis provides a mathematically well-defined, broadly applicable framework for understanding and quantifying fluid transport in complex geometries.

  7. Iterative 2D deconvolution of portal imaging radiographs

    Portal imaging has become an integral part of modern radiotherapy techniques such as IMRT and IGRT. It serves to verify the accuracy of day-to-day patient positioning, a prerequisite for treatment success. However, image blurring attributable to different physical and geometrical effects, analysed in this work, impairs the image quality of the portal images, and anatomical structures cannot always be clearly outlined. A 2D iterative deconvolution method was developed to reduce this image blurring. The affiliated data basis was generated by the separate measurement of the components contributing to image blurring. Secondary electron transport and pixel size within the EPID, as well as geometrical penumbra due to the finite photon source size were found to be the major contributors, whereas photon scattering in the patient is less important. The underlying line-spread kernels of these components were shown to be Lorentz functions. This implies that each of these convolution kernels and also their combination can be characterized by a single characteristic, the width parameter λ of the Lorentz function. The overall resulting λ values were 0.5 mm for 6 MV and 0.65 mm for 15 MV. Portal images were deconvolved using the point-spread function derived from the Lorentz function together with the experimentally determined λ values. The improvement of the portal images was quantified in terms of the modulation transfer function of a bar pattern. The resulting clinical images show a clear enhancement of sharpness and contrast. (orig.)

  8. Soccer players awarded one or more red cards exhibit lower 2D:4D ratios.

    Mailhos, Alvaro; Buunk, Abraham P; Del Arca, Denise; Tutte, Verónica

    2016-09-01

    Anatomical, cognitive and behavioral sex differences are widely recognized in many species. It has been proposed that some of these differences might result from the organizing effects of prenatal sex steroids. In humans, males usually exhibit higher levels of physical aggression and prowess. In this study, we analyze the relationship between second-to-fourth digit (2D:4D) ratios-a proxy for prenatal androgen levels-and foul play and sporting performance in a sample of junior soccer players from a professional Uruguayan soccer club. Our results show that the most aggressive players (i.e., those awarded one or more red cards) have a more masculine finger pattern (lower 2D:4D ratio), while no relationship could be found between sporting performance and 2D:4D ratios. The results are discussed in the context of previous findings. Aggr. Behav. 42:417-426, 2016. © 2015 Wiley Periodicals, Inc. PMID:26699684

  9. Maximizing entropy of image models for 2-D constrained coding

    Forchhammer, Søren; Danieli, Matteo; Burini, Nino;

    2010-01-01

    This paper considers estimating and maximizing the entropy of two-dimensional (2-D) fields with application to 2-D constrained coding. We consider Markov random fields (MRF), which have a non-causal description, and the special case of Pickard random fields (PRF). The PRF are 2-D causal finite...... of the Markov random field defined by the 2-D constraint is estimated to be (upper bounded by) 0.8570 bits/symbol using the iterative technique of Belief Propagation on 2 £ 2 finite lattices. Based on combinatorial bounding techniques the maximum entropy for the constraint was determined to be 0.848....

  10. Common Patterns in the Evolution between the Luminous Neutron Star Low-Mass X-ray Binary Subclasses

    Fridriksson, Joel K; Remillard, Ronald A

    2015-01-01

    The X-ray transient XTE J1701-462 was the first source seen to evolve through all known subclasses of low-magnetic-field neutron star low-mass X-ray binaries (NS-LMXBs), as a result of large changes in its mass accretion rate. To investigate to what extent similar evolution is seen in other NS-LMXBs we have performed a detailed study of the color-color and hardness-intensity diagrams (CDs and HIDs) of Cyg X-2, Cir X-1, and GX 13+1 -- three luminous X-ray binaries, containing weakly magnetized neutron stars, known to exhibit strong secular changes in their CD/HID tracks. Using the full set of Rossi X-ray Timing Explorer Proportional Counter Array data collected for the sources over the 16-year duration of the mission, we show that Cyg X-2 and Cir X-1 display CD/HID evolution with close similarities to XTE J1701-462. Although GX 13+1 shows behavior that is in some ways unique, it also exhibits similarities to XTE J1701-462, and we conclude that its overall CD/HID properties strongly indicate that it should be c...

  11. Evolution of seismic signals and slip patterns along subduction zones: insights from a friction lab scale experiment

    Voisin, Christophe; Larose, Eric; Renard, François

    2008-01-01

    Continuous GPS and broadband seismic monitoring have revealed a variety of disparate slip patterns especially in shallow dipping subduction zones, among which regular earthquakes, slow slip events and silent quakes1,2. Slow slip events are sometimes accompanied by Non Volcanic Tremors (NVT), which origin remains unclear3, either related to fluid migration or to friction. The present understanding of the whole menagerie of slip patterns is based upon numerical simulations imposing ad hoc values of the rate and state parameters a and b4-6 derived from the temperature dependence of a and b of a wet granite gouge7. Here we investigate the influence of the cumulative slip on the frictional and acoustic patterns of a lab scale subduction zone. Shallow loud earthquakes (stick-slip events), medium depth slow, deeper silent quakes (smooth sliding oscillations) and deepest steady-state creep (continuous sliding) are reproduced by the ageing of contact interface with cumulative displacement8. The Acoustic Emission evolv...

  12. Klassifikation von Standardebenen in der 2D-Echokardiographie mittels 2D-3D-Bildregistrierung

    Bergmeir, Christoph; Subramanian, Navneeth

    Zum Zweck der Entwicklung eines Systems, das einen unerfahrenen Anwender von Ultraschall (US) zur Aufnahme relevanter anatomischer Strukturen leitet, untersuchen wir die Machbarkeit von 2D-US zu 3D-CT Registrierung. Wir verwenden US-Aufnahmen von Standardebenen des Herzens, welche zu einem 3D-CT-Modell registriert werden. Unser Algorithmus unterzieht sowohl die US-Bilder als auch den CT-Datensatz Vorverarbeitungsschritten, welche die Daten durch Segmentierung auf wesentliche Informationen in Form von Labein für Muskel und Blut reduzieren. Anschließend werden diese Label zur Registrierung mittels der Match-Cardinality-Metrik genutzt. Durch mehrmaliges Registrieren mit verschiedenen Initialisierungen ermitteln wir die im US-Bild sichtbare Standardebene. Wir evaluierten die Methode auf sieben US-Bildern von Standardebenen. Fünf davon wurden korrekt zugeordnet.

  13. A post-processing framework for localized 2D MR spectroscopy in vivo

    We propose a post-processing framework for localized two-dimensional (2D) magnetic resonance spectroscopy (MRS) in vivo. Our framework consists of corrections on eddy current and subject motion along with the framework used in conventional analytical 2D nuclear magnetic resonance (NMR) spectroscopy. In the eddy current correction, the phases of the free induction decays (FIDs) of the metabolite 1H are corrected along the t2 direction by the phase of the FID of water 1H. The corrected FIDs are Fourier transformed along the t2 direction, and interferograms of F(t1, ω2) are calculated. In the motion correction, the zero-order phase of the N-acetyl aspartate (NAA) singlet peak for each t1 axis is corrected after correction of frequency drift. We applied this framework in phantom and human brain measurements in a 4.7 T whole-body MR system. Two-dimensional data were collected by the localized 2D constant-time correlation spectroscopy (CT-COSY) sequence. We used a phantom containing a brain metabolite mixture of NAA, creatine (Cr), glutamate (Glu), glutamine (Gln) and γ-amino butyric acid (GABA). We demonstrated the eddy current correction procedure in the phantom experiments and the subject motion correction in human measurements. Though asymmetric patterns of the singlets of NAA and Cr were shown around the peak along the F2 direction in the reconstructed phantom spectra without eddy current correction, symmetric patterns arose after the correction. The t1 noise caused by those singlets was found in the human brain spectra without motion correction. The t1 noise was sufficiently suppressed by the motion correction. Our proposed post-processing framework for localized 2D MRS can improve the quality of in vivo 2D spectra and may allow improved quantitation and robustness of in vivo 2D spectroscopy. (author)

  14. 2D Four-Channel Perfect Reconstruction Filter Bank Realized with the 2D Lattice Filter Structure

    Sezen S

    2006-01-01

    Full Text Available A novel orthogonal 2D lattice structure is incorporated into the design of a nonseparable 2D four-channel perfect reconstruction filter bank. The proposed filter bank is obtained by using the polyphase decomposition technique which requires the design of an orthogonal 2D lattice filter. Due to constraint of perfect reconstruction, each stage of this lattice filter bank is simply parameterized by two coefficients. The perfect reconstruction property is satisfied regardless of the actual values of these parameters and of the number of the lattice stages. It is also shown that a separable 2D four-channel perfect reconstruction lattice filter bank can be constructed from the 1D lattice filter and that this is a special case of the proposed 2D lattice filter bank under certain conditions. The perfect reconstruction property of the proposed 2D lattice filter approach is verified by computer simulations.

  15. Understanding the interaction between energetic ions and freestanding graphene towards practical 2D perforation

    Buchheim, Jakob; Wyss, Roman M.; Shorubalko, Ivan; Park, Hyung Gyu

    2016-04-01

    We report experimentally and theoretically the behavior of freestanding graphene subjected to bombardment of energetic ions, investigating the capability of large-scale patterning of freestanding graphene with nanometer sized features by focused ion beam technology. A precise control over the He+ and Ga+ irradiation offered by focused ion beam techniques enables investigating the interaction of the energetic particles and graphene suspended with no support and allows determining sputter yields of the 2D lattice. We found a strong dependency of the 2D sputter yield on the species and kinetic energy of the incident ion beams. Freestanding graphene shows material semi-transparency to He+ at high energies (10-30 keV) allowing the passage of >97% He+ particles without creating destructive lattice vacancy. Large Ga+ ions (5-30 keV), in contrast, collide far more often with the graphene lattice to impart a significantly higher sputter yield of ~50%. Binary collision theory applied to monolayer and few-layer graphene can successfully elucidate this collision mechanism, in great agreement with experiments. Raman spectroscopy analysis corroborates the passage of a large fraction of He+ ions across graphene without much damaging the lattice whereas several colliding ions create single vacancy defects. Physical understanding of the interaction between energetic particles and suspended graphene can practically lead to reproducible and efficient pattern generation of unprecedentedly small features on 2D materials by design, manifested by our perforation of sub-5 nm pore arrays. This capability of nanometer-scale precision patterning of freestanding 2D lattices shows the practical applicability of focused ion beam technology to 2D material processing for device fabrication and integration.We report experimentally and theoretically the behavior of freestanding graphene subjected to bombardment of energetic ions, investigating the capability of large-scale patterning of

  16. PiCode: A New Picture-Embedding 2D Barcode.

    Chen, Changsheng; Huang, Wenjian; Zhou, Baojian; Liu, Chenchen; Mow, Wai Ho

    2016-08-01

    Nowadays, 2D barcodes have been widely used as an interface to connect potential customers and advertisement contents. However, the appearance of a conventional 2D barcode pattern is often too obtrusive for integrating into an aesthetically designed advertisement. Besides, no human readable information is provided before the barcode is successfully decoded. This paper proposes a new picture-embedding 2D barcode, called PiCode, which mitigates these two limitations by equipping a scannable 2D barcode with a picturesque appearance. PiCode is designed with careful considerations on both the perceptual quality of the embedded image and the decoding robustness of the encoded message. Comparisons with the existing beautified 2D barcodes show that PiCode achieves one of the best perceptual qualities for the embedded image, and maintains a better tradeoff between image quality and decoding robustness in various application conditions. PiCode has been implemented in the MATLAB on a PC and some key building blocks have also been ported to Android and iOS platforms. Its practicality for real-world applications has been successfully demonstrated. PMID:27249833

  17. Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution.

    Fučíková, Karolina; Lewis, Paul O; Lewis, Louise A

    2016-05-01

    Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny - yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution. PMID:26903036

  18. An Incompressible 2D Didactic Model with Singularity and Explicit Solutions of the 2D Boussinesq Equations

    Chae, Dongho; Constantin, Peter; Wu, Jiahong

    2014-09-01

    We give an example of a well posed, finite energy, 2D incompressible active scalar equation with the same scaling as the surface quasi-geostrophic equation and prove that it can produce finite time singularities. In spite of its simplicity, this seems to be the first such example. Further, we construct explicit solutions of the 2D Boussinesq equations whose gradients grow exponentially in time for all time. In addition, we introduce a variant of the 2D Boussinesq equations which is perhaps a more faithful companion of the 3D axisymmetric Euler equations than the usual 2D Boussinesq equations.

  19. Importance of Overpressure in 2D Gas Hydrate Modeling

    Hauschildt, J.; Unnithan, V.

    2005-12-01

    Numerical models for sub-seafloor gas hydrate formation [1],[2],[3] which describe the driving fluid transport processes only in the vertical direction, restrict the computationally expensive problem to one dimension. This assumption is only valid in regions where permeable sediments induce no overpressure and where there is little lateral variation of physical properties and boundary conditions. Local accumulations of gas hydrates or authigenic carbonates can significantly reduce the porosity and permeability. In combination with topographic and structural features, subtle but important deviations from the 1D model are considered to occur. This poster shows results obtained from a 2D finite difference model developed for describing the evolution of the gas hydrate zone in structurally complex areas. The discretisation of the terms governing the thermodynamic and transport processes is implemented explicitely in time for the advection and diffusion processes, but implicitely for phase transitions. Although the time scales for transport and phase transitions can differ by several orders of magnitude, this scheme allows for an efficient computation for model runs both over the system's equilibration period in the order of 107 yr or to resolve the effects of sea-level changes within 103 yr. A sensitivity analysis confines the parameter space relevant for hydrate formation influenced by lateral fluid flow, and results for the predicted deviations from a multi-1D model for high gas hydrate fractions and fluid flow rates are presented. References [1] M.K. Davie and B.A. Buffett. Sources of methane for marine gas hydrate: inferences from a comparison of observations and numerical models. Earth and Planetary Science Letters, 206:51-63, 2003. [2] W. Xu and C. Ruppell. Predicting the occurrence, distribution, and evolution of methane hydrate in porous marine sediments. Journal of Geohphysical Research, (B3):5081-5095, 1999. [3] J.B. Klauda and S.I. Sandler. Predictions of

  20. Understanding the interaction between energetic ions and freestanding graphene towards practical 2D perforation.

    Buchheim, Jakob; Wyss, Roman M; Shorubalko, Ivan; Park, Hyung Gyu

    2016-04-14

    We report experimentally and theoretically the behavior of freestanding graphene subjected to bombardment of energetic ions, investigating the capability of large-scale patterning of freestanding graphene with nanometer sized features by focused ion beam technology. A precise control over the He(+) and Ga(+) irradiation offered by focused ion beam techniques enables investigating the interaction of the energetic particles and graphene suspended with no support and allows determining sputter yields of the 2D lattice. We found a strong dependency of the 2D sputter yield on the species and kinetic energy of the incident ion beams. Freestanding graphene shows material semi-transparency to He(+) at high energies (10-30 keV) allowing the passage of >97% He(+) particles without creating destructive lattice vacancy. Large Ga(+) ions (5-30 keV), in contrast, collide far more often with the graphene lattice to impart a significantly higher sputter yield of ∼50%. Binary collision theory applied to monolayer and few-layer graphene can successfully elucidate this collision mechanism, in great agreement with experiments. Raman spectroscopy analysis corroborates the passage of a large fraction of He(+) ions across graphene without much damaging the lattice whereas several colliding ions create single vacancy defects. Physical understanding of the interaction between energetic particles and suspended graphene can practically lead to reproducible and efficient pattern generation of unprecedentedly small features on 2D materials by design, manifested by our perforation of sub-5 nm pore arrays. This capability of nanometer-scale precision patterning of freestanding 2D lattices shows the practical applicability of focused ion beam technology to 2D material processing for device fabrication and integration. PMID:27043304

  1. Fabrication of 2D polymer nanochannels by sidewall lithography and hot embossing

    A novel method for fabricating two-dimensional (2D) polymer nanochannels by combining the sidewall lithography technique with the hot embossing approach is presented in this paper. A layer of nano-thick Au film was first sputtered on the surface of the micro-sized photoresist mesas. Then, arrays of one-dimensional (1D) Au nano-sidewalls were formed by anisotropic sputter etching. By taking the 1D Au nano-sidewalls as a mask, the 2D silicon nano-mold was obtained by deep reactive ion etching. The patterns of the 2D nano-mold were replicated directly into a 1 mm thick polyethylene terephthalate substrate by using the hot embossing technique. Polymer nanochannel arrays with dimensions of about 100 nm in width, 100 nm in depth and 4 mm in length fabricated uniformly over a large area were obtained. The resolution of nano-mold patterns fabricated in our work is not limited by ultraviolet optical lithography but by the thickness of the Au film deposited onto the photoresist mesas. The proposed method provides a low-cost way to produce high-quality and high-throughput 2D polymer nanochannels. (paper)

  2. Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants.

    Huang, Zhinan; Duan, Weike; Song, Xiaoming; Tang, Jun; Wu, Peng; Zhang, Bei; Hou, Xilin

    2016-02-01

    Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion, and expression patterns of Aux/IAAs and ARFs in Brassica rapa and their evolution in eight other plant species, including algae, bryophytes, lycophytes, and angiosperms. All 33 of the ARFs, including 1 ARF-like (AL) (a type of ARF-like protein) and 53 Aux/IAAs, were identified in the B. rapa genome. The genes mainly diverged approximately 13 Ma. After the split, no Aux/IAA was completely lost, and they were more preferentially retained than ARFs. In land plants, compared with ARFs, which increased in stability, Aux/IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants adapt to complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of Aux/IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both Aux/IAAs and ARFs. PMID:26721260

  3. Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants

    Huang, Zhinan; Duan, Weike; Song, Xiaoming; Tang, Jun; Wu, Peng; Zhang, Bei; Hou, Xilin

    2016-01-01

    Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion, and expression patterns of Aux/IAAs and ARFs in Brassica rapa and their evolution in eight other plant species, including algae, bryophytes, lycophytes, and angiosperms. All 33 of the ARFs, including 1 ARF-like (AL) (a type of ARF-like protein) and 53 Aux/IAAs, were identified in the B. rapa genome. The genes mainly diverged approximately 13 Ma. After the split, no Aux/IAA was completely lost, and they were more preferentially retained than ARFs. In land plants, compared with ARFs, which increased in stability, Aux/IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants adapt to complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of Aux/IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both Aux/IAAs and ARFs. PMID:26721260

  4. Symmetries and solvable models for evaporating 2D black holes

    Cruz Muñoz, José Luis; Navarro-Salas, José; Navarro Navarro, Miguel; Talavera, C. F.

    1997-01-01

    We study the evaporation process of a 2D black hole in thermal equilibrium when the ingoing radiation is suddenly switched off. We also introduce global symmetries of generic 2D dilaton gravity models which generalize the extra symmetry of the CGHS model. © Elsevier Science B.V

  5. Cascading Constrained 2-D Arrays using Periodic Merging Arrays

    Forchhammer, Søren; Laursen, Torben Vaarby

    2003-01-01

    We consider a method for designing 2-D constrained codes by cascading finite width arrays using predefined finite width periodic merging arrays. This provides a constructive lower bound on the capacity of the 2-D constrained code. Examples include symmetric RLL and density constrained codes....... Numerical results for the capacities are presented....

  6. 2D gravity, random surfaces and all that

    I review the recent progress in 2d gravity and discuss the new numerical simulations for 2d gravity and for random surfaces in d>2. The random surface theories of interest in d>2 have extrinsic curvature terms, and for a finite value of the extrinsic curvature coupling there seems to be a second order phase transition where the string tension scales. (orig.)

  7. Van der Waals stacked 2D layered materials for optoelectronics

    Zhang, Wenjing; Wang, Qixing; Chen, Yu; Wang, Zhuo; Wee, Andrew T. S.

    2016-06-01

    The band gaps of many atomically thin 2D layered materials such as graphene, black phosphorus, monolayer semiconducting transition metal dichalcogenides and hBN range from 0 to 6 eV. These isolated atomic planes can be reassembled into hybrid heterostructures made layer by layer in a precisely chosen sequence. Thus, the electronic properties of 2D materials can be engineered by van der Waals stacking, and the interlayer coupling can be tuned, which opens up avenues for creating new material systems with rich functionalities and novel physical properties. Early studies suggest that van der Waals stacked 2D materials work exceptionally well, dramatically enriching the optoelectronics applications of 2D materials. Here we review recent progress in van der Waals stacked 2D materials, and discuss their potential applications in optoelectronics.

  8. Phylogeography, Interaction Patterns and the Evolution of Host Choice in Drosophila-Parasitoid Systems in Ryukyu Archipelago and Taiwan.

    Biljana Novković

    Full Text Available Island biotas provide a great opportunity to study not only the phylogeographic patterns of a group of species, but also to explore the differentiation in their coevolutionary interactions. Drosophila and their parasitoids are exemplary systems for studying complex interaction patterns. However, there is a lack of studies combining interaction-based and molecular marker-based methods. We applied an integrated approach combining phylogeography, interaction, and host-choice behavior studies, with the aim to understand how coevolutionary interactions evolve in Drosophila-parasitoid island populations. The study focused on the three most abundant Drosophila species in Ryukyu archipelago and Taiwan: D. albomicans, D. bipectinata, and D. takahashii, and the Drosophila-parasitoid Leptopilina ryukyuensis. We determined mitochondrial COI haplotypes for samples representing five island populations of Drosophila and four island populations of L. ryukyuensis. We additionally sequenced parts of the autosomal Gpdh for Drosophila samples, and the ITS2 for parasitoid samples. Phylogenetic and coalescent analyses were used to test for demographic events and to place them in a temporal framework. Geographical differences in Drosophila-parasitoid interactions were studied in host-acceptance, host-suitability, and host-choice experiments. All four species showed species-specific phylogeographic patterns. A general trend of the haplotype diversity increasing towards the south was observed. D. albomicans showed very high COI haplotype diversity, and had the most phylogeographically structured populations, with differentiation into the northern and the southern population-group, divided by the Kerama gap. Differentiation in host suitability was observed only between highly structured populations of D. albomicans, possibly facilitated by restricted gene flow. Differentiation in host-acceptance in D. takahashii, and host-acceptance and host-choice in L. ryukyuensis was

  9. Phylogeography, Interaction Patterns and the Evolution of Host Choice in Drosophila-Parasitoid Systems in Ryukyu Archipelago and Taiwan.

    Novković, Biljana; Kimura, Masahito T

    2015-01-01

    Island biotas provide a great opportunity to study not only the phylogeographic patterns of a group of species, but also to explore the differentiation in their coevolutionary interactions. Drosophila and their parasitoids are exemplary systems for studying complex interaction patterns. However, there is a lack of studies combining interaction-based and molecular marker-based methods. We applied an integrated approach combining phylogeography, interaction, and host-choice behavior studies, with the aim to understand how coevolutionary interactions evolve in Drosophila-parasitoid island populations. The study focused on the three most abundant Drosophila species in Ryukyu archipelago and Taiwan: D. albomicans, D. bipectinata, and D. takahashii, and the Drosophila-parasitoid Leptopilina ryukyuensis. We determined mitochondrial COI haplotypes for samples representing five island populations of Drosophila and four island populations of L. ryukyuensis. We additionally sequenced parts of the autosomal Gpdh for Drosophila samples, and the ITS2 for parasitoid samples. Phylogenetic and coalescent analyses were used to test for demographic events and to place them in a temporal framework. Geographical differences in Drosophila-parasitoid interactions were studied in host-acceptance, host-suitability, and host-choice experiments. All four species showed species-specific phylogeographic patterns. A general trend of the haplotype diversity increasing towards the south was observed. D. albomicans showed very high COI haplotype diversity, and had the most phylogeographically structured populations, with differentiation into the northern and the southern population-group, divided by the Kerama gap. Differentiation in host suitability was observed only between highly structured populations of D. albomicans, possibly facilitated by restricted gene flow. Differentiation in host-acceptance in D. takahashii, and host-acceptance and host-choice in L. ryukyuensis was found, despite there

  10. Sub-wavelength Lithography of Complex 2D and 3D Nanostructures without Dyes

    Chaudhary, Raghvendra P; Ummethala, Govind; Hawal, Suyog R; Saxena, Sumit; Shukla, Shobha

    2016-01-01

    One-photon or two photon absorption by dye molecules in photopolymers enable direct 2D & 3D lithography of micro/nano structures with high spatial resolution and can be used effectively in fabricating artificially structured nanomaterials. However, the major bottleneck in unleashing the potential of this useful technique is the indispensable usage of dyes that are extremely expensive, highly toxic and usually insoluble in commercially available photopolymers. Here we report a simple, inexpensive and one-step technique for direct-writing of micro/nanostructures, with sub-wavelength resolution at extremely high speeds without using any one photon or two photon absorbing dye. We incorporated large amount (20 weight %) of inexpensive photoinitiator into the photopolymer and utilized its two-photon absorbing property for sub-wavelength patterning. Complex 2D and 3D patterns were fabricated with sub-micron resolution, in commercially available liquid photopolymer to show the impact/versatility of this technique...

  11. DYNA-2D, 2-D Hydrodynamic Finite Elements Method Program with Interactive Rezoning

    1 - Description of program or function: DYNA2D is an explicit, two-dimensional, axisymmetric and plane strain finite element program for analyzing the large deformation dynamic and hydrodynamic response of inelastic solids. A contact-impact algorithm permits gaps and sliding with friction along material interfaces. By a specialization of this algorithm, such interfaces can be rigidly tied to admit variable zoning with no need for transition regions. Spatial discretization is achieved by the use of 4-node solid elements, and the equations-of-motion are integrated by the central difference method. The material models implemented are: elastic, orthotropic elastic, kinematic/isotropic elastic-plastic, thermo- elastic-plastic, soil and crushable foam, linear visco-elastic, rubber, isotropic elastic-plastic, and temperature-dependent elastic-plastic. The latter two models determine only the deviatoric stresses. Pressure is determined by one of 9 equations of state. 2 - Restrictions on the complexity of the problem - Maxima of: 60,000 elements (Cray 1), 5,000 elements (CDC7600)

  12. Targeted fluorescence imaging enhanced by 2D materials: a comparison between 2D MoS2 and graphene oxide.

    Xie, Donghao; Ji, Ding-Kun; Zhang, Yue; Cao, Jun; Zheng, Hu; Liu, Lin; Zang, Yi; Li, Jia; Chen, Guo-Rong; James, Tony D; He, Xiao-Peng

    2016-08-01

    Here we demonstrate that 2D MoS2 can enhance the receptor-targeting and imaging ability of a fluorophore-labelled ligand. The 2D MoS2 has an enhanced working concentration range when compared with graphene oxide, resulting in the improved imaging of both cell and tissue samples. PMID:27378648

  13. Gel2DE - A software tool for correlation analysis of 2D gel electrophoresis data

    Øye, Ola Kristoffer; Jørgensen, Katarina Mariann; Hjelle, Sigrun Margrethe; Sulen, André; Ulvang, Dag Magne; Gjertsen, Bjørn Tore

    2013-01-01

    Background: Two-dimensional gel electrophoresis (2DE) is a powerful technique for studying protein isoforms and their modifications. Existing commercial 2D image analysis tools rely on spot detection that limits analysis of complex protein profiles, e.g. spot appearance/disappearance or overlapping spots. Pixel-by-pixel correlation analysis, an analysis technique for identifying relations between protein patterns in gel images and external variables, can overcome such limitations ...

  14. Fabrication of Capacitive Acoustic Resonators Combining 3D Printing and 2D Inkjet Printing Techniques

    Rubaiyet Iftekharul Haque; Erick Ogam; Christophe Loussert; Patrick Benaben; Xavier Boddaert

    2015-01-01

    A capacitive acoustic resonator developed by combining three-dimensional (3D) printing and two-dimensional (2D) printed electronics technique is described. During this work, a patterned bottom structure with rigid backplate and cavity is fabricated directly by a 3D printing method, and then a direct write inkjet printing technique has been employed to print a silver conductive layer. A novel approach has been used to fabricate a diaphragm for the acoustic sensor as well, where the conductive ...

  15. A general route to 2D nanoleaves and nanoplates of polyaniline

    Tao, Yulun; Cheng, Guojun; Zhang, Miao; Hu, Leilei; Yu, Qingbo; Ding, Guoxing

    2015-12-01

    Novel 2D nanoleaves and nanoplates are synthesized by a facile and general method. A set of doping control experiments are carried out to show how PANI self-assemble to nanoleaves and nanoplates. Interestingly, the nanoleaves and nanorods have high crystallinity, according to their XRD patterns. The novel method will be readily scalable to produce polyaniline crystals with different morphologies with high quality and low cost. The polymer semiconductor crystals could be useful for next generation organic electronics such as nanotransistors.

  16. The influence of pressure on the structure of a 2D uranium(VI) carboxyphosphonoate compound

    Spencer, Elinor C. [Dept. of Geosciences, Virginia Tech, Blacksburg, VA 24060 (United States); Ross, Nancy L., E-mail: nross@vt.edu [Dept. of Geosciences, Virginia Tech, Blacksburg, VA 24060 (United States); Surbella, Robert G.; Cahill, Christopher L. [Dept. of Chemistry, The George Washington University, 725 21st Street NW, Washington, DC 20052 (United States)

    2014-10-15

    We report the first quantitative analysis of the structural evolution of a uranyl bearing coordination polymer in response to pressure. The material that is central to this study, (UO{sub 2})(O{sub 3}PCH{sub 2}CO{sub 2}H) (1), is constructed from rigid 2D inorganic layers comprising edge sharing UO{sub 7} pentagonal bipyramids cross-linked by [PO{sub 3}(COOH)]{sup 2−} anions. Strong hydrogen bonding interactions exist between the pendent carboxylic acid groups on adjacent layers. Under pressure, 1 exhibits compressional behaviour primarily in the direction perpendicular to the inorganic layers, which is aided by a reduction in the interlayer distance and shifting of the layers with respect to each other. The bulk modulus for the 2D compound 1 is unexpectedly high [18.1(1) GPa] and is within the range reported for 3D CPs assembled from Zn{sup II} cations and inflexible imidazolate anions, and is at the lower end of the range of moduli observed for aluminosilicate zeolites (19–59 GPa). - Graphical Abstract: The compression mechanism and elastic constants for a 2D Uranium(VI) carboxyphosphonoate compound are reported. - Highlights: • The response to pressure of a uranium carboxyphosphonoate compound has been studied. • High-pressure single-crystal XRD data for this 2D uranium compound were collected. • Elastic constants for this material have been determined. • The compression mechanism for the compound has been elucidated.

  17. Continuous 1.3-million-year record of East African hydroclimate, and implications for patterns of evolution and biodiversity.

    Lyons, Robert P; Scholz, Christopher A; Cohen, Andrew S; King, John W; Brown, Erik T; Ivory, Sarah J; Johnson, Thomas C; Deino, Alan L; Reinthal, Peter N; McGlue, Michael M; Blome, Margaret W

    2015-12-22

    The transport of moisture in the tropics is a critical process for the global energy budget and on geologic timescales, has markedly influenced continental landscapes, migratory pathways, and biological evolution. Here we present a continuous, first-of-its-kind 1.3-My record of continental hydroclimate and lake-level variability derived from drill core data from Lake Malawi, East Africa (9-15° S). Over the Quaternary, we observe dramatic shifts in effective moisture, resulting in large-scale changes in one of the world's largest lakes and most diverse freshwater ecosystems. Results show evidence for 24 lake level drops of more than 200 m during the Late Quaternary, including 15 lowstands when water levels were more than 400 m lower than modern. A dramatic shift is observed at the Mid-Pleistocene Transition (MPT), consistent with far-field climate forcing, which separates vastly different hydroclimate regimes before and after ∼800,000 years ago. Before 800 ka, lake levels were lower, indicating a climate drier than today, and water levels changed frequently. Following the MPT high-amplitude lake level variations dominate the record. From 800 to 100 ka, a deep, often overfilled lake occupied the basin, indicating a wetter climate, but these highstands were interrupted by prolonged intervals of extreme drought. Periods of high lake level are observed during times of high eccentricity. The extreme hydroclimate variability exerted a profound influence on the Lake Malawi endemic cichlid fish species flock; the geographically extensive habitat reconfiguration provided novel ecological opportunities, enabling new populations to differentiate rapidly to distinct species. PMID:26644580

  18. Continuous 1.3-million-year record of East African hydroclimate, and implications for patterns of evolution and biodiversity

    Lyons, Robert P.; Scholz, Christopher A.; Cohen, Andrew S.; King, John W.; Brown, Erik T.; Ivory, Sarah J.; Johnson, Thomas C.; Deino, Alan L.; Reinthal, Peter N.; McGlue, Michael M.; Blome, Margaret W.

    2015-12-01

    The transport of moisture in the tropics is a critical process for the global energy budget and on geologic timescales, has markedly influenced continental landscapes, migratory pathways, and biological evolution. Here we present a continuous, first-of-its-kind 1.3-My record of continental hydroclimate and lake-level variability derived from drill core data from Lake Malawi, East Africa (9-15° S). Over the Quaternary, we observe dramatic shifts in effective moisture, resulting in large-scale changes in one of the world's largest lakes and most diverse freshwater ecosystems. Results show evidence for 24 lake level drops of more than 200 m during the Late Quaternary, including 15 lowstands when water levels were more than 400 m lower than modern. A dramatic shift is observed at the Mid-Pleistocene Transition (MPT), consistent with far-field climate forcing, which separates vastly different hydroclimate regimes before and after ∼800,000 years ago. Before 800 ka, lake levels were lower, indicating a climate drier than today, and water levels changed frequently. Following the MPT high-amplitude lake level variations dominate the record. From 800 to 100 ka, a deep, often overfilled lake occupied the basin, indicating a wetter climate, but these highstands were interrupted by prolonged intervals of extreme drought. Periods of high lake level are observed during times of high eccentricity. The extreme hydroclimate variability exerted a profound influence on the Lake Malawi endemic cichlid fish species flock; the geographically extensive habitat reconfiguration provided novel ecological opportunities, enabling new populations to differentiate rapidly to distinct species.

  19. Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

    Engelen Stefan

    2012-02-01

    Full Text Available Abstract Background Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase. Results Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome. Conclusion DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves with a set of RNA degradation enzymes that does not derive from the degradosome identified in gamma-Proteobacteria. This suggests that at least two independent RNA degradation pathways existed in the progenote community at the end of the RNA genome world.

  20. An amphioxus Gli gene reveals conservation of midline patterning and the evolution of hedgehog signalling diversity in chordates.

    Sebastian M Shimeld

    Full Text Available BACKGROUND: Hedgehog signalling, interpreted in receiving cells by Gli transcription factors, plays a central role in the development of vertebrate and Drosophila embryos. Many aspects of the signalling pathway are conserved between these lineages, however vertebrates have diverged in at least one key aspect: they have evolved multiple Gli genes encoding functionally-distinct proteins, increasing the complexity of the hedgehog-dependent transcriptional response. Amphioxus is one of the closest living relatives of the vertebrates, having split from the vertebrate lineage prior to the widespread gene duplication prominent in early vertebrate evolution. PRINCIPAL FINDINGS: We show that amphioxus has a single Gli gene, which is deployed in tissues adjacent to sources of hedgehog signalling derived from the midline and anterior endoderm. This shows the duplication and divergence of the Gli gene family, and hence the origin of vertebrate Gli functional diversity, was specific to the vertebrate lineage. However we also show that the single amphioxus Gli gene produces two distinct transcripts encoding different proteins. We utilise three tests of Gli function to examine the transcription regulatory capacities of these different proteins, demonstrating one has activating activity similar to Gli2, while the other acts as a weak repressor, similar to Gli3. CONCLUSIONS: These data show that vertebrates and amphioxus have evolved functionally-similar repertoires of Gli proteins using parallel molecular routes; vertebrates via gene duplication and divergence, and amphioxus via alternate splicing of a single gene. Our results demonstrate that similar functional complexity of intercellular signalling can be achieved via different evolutionary pathways.

  1. 2D vs. 3D mammography observer study

    Fernandez, James Reza F.; Hovanessian-Larsen, Linda; Liu, Brent

    2011-03-01

    Breast cancer is the most common type of non-skin cancer in women. 2D mammography is a screening tool to aid in the early detection of breast cancer, but has diagnostic limitations of overlapping tissues, especially in dense breasts. 3D mammography has the potential to improve detection outcomes by increasing specificity, and a new 3D screening tool with a 3D display for mammography aims to improve performance and efficiency as compared to 2D mammography. An observer study using a mammography phantom was performed to compare traditional 2D mammography with this ne 3D mammography technique. In comparing 3D and 2D mammography there was no difference in calcification detection, and mass detection was better in 2D as compared to 3D. There was a significant decrease in reading time for masses, calcifications, and normals in 3D compared to 2D, however, as well as more favorable confidence levels in reading normal cases. Given the limitations of the mammography phantom used, however, a clearer picture in comparing 3D and 2D mammography may be better acquired with the incorporation of human studies in the future.

  2. Patterning of the dorsal-ventral axis in echinoderms: insights into the evolution of the BMP-chordin signaling network.

    François Lapraz

    2009-11-01

    Full Text Available Formation of the dorsal-ventral axis of the sea urchin embryo relies on cell interactions initiated by the TGFbeta Nodal. Intriguingly, although nodal expression is restricted to the ventral side of the embryo, Nodal function is required for specification of both the ventral and the dorsal territories and is able to restore both ventral and dorsal regions in nodal morpholino injected embryos. The molecular basis for the long-range organizing activity of Nodal is not understood. In this paper, we provide evidence that the long-range organizing activity of Nodal is assured by a relay molecule synthesized in the ventral ectoderm, then translocated to the opposite side of the embryo. We identified this relay molecule as BMP2/4 based on the following arguments. First, blocking BMP2/4 function eliminated the long-range organizing activity of an activated Nodal receptor in an axis rescue assay. Second, we demonstrate that BMP2/4 and the corresponding type I receptor Alk3/6 functions are both essential for specification of the dorsal region of the embryo. Third, using anti-phospho-Smad1/5/8 immunostaining, we show that, despite its ventral transcription, the BMP2/4 ligand triggers receptor mediated signaling exclusively on the dorsal side of the embryo, one of the most extreme cases of BMP translocation described so far. We further report that the pattern of pSmad1/5/8 is graded along the dorsal-ventral axis and that two BMP2/4 target genes are expressed in nested patterns centered on the region with highest levels of pSmad1/5/8, strongly suggesting that BMP2/4 is acting as a morphogen. We also describe the very unusual ventral co-expression of chordin and bmp2/4 downstream of Nodal and demonstrate that Chordin is largely responsible for the spatial restriction of BMP2/4 signaling to the dorsal side. Thus, unlike in most organisms, in the sea urchin, a single ventral signaling centre is responsible for induction of ventral and dorsal cell fates. Finally

  3. The NH$_2$D hyperfine structure revealed by astrophysical observations

    Daniel, F.; Coudert, L. H.; Punanova, A.; Harju, J.; Faure, A.; Roueff, E.; Sipilä, O.; Caselli, P.; Güsten, R.; Pon, A.; Pineda, J E

    2016-01-01

    The 1$_{11}$-1$_{01}$ lines of ortho and para--NH$_2$D (o/p-NH$_2$D), respectively at 86 and 110 GHz, are commonly observed to provide constraints on the deuterium fractionation in the interstellar medium. In cold regions, the hyperfine structure due to the nitrogen ($^{14}$N) nucleus is resolved. To date, this splitting is the only one which is taken into account in the NH$_2$D column density estimates. We investigate how the inclusion of the hyperfine splitting caused by the deuterium (D) n...

  4. Materials for Flexible, Stretchable Electronics: Graphene and 2D Materials

    Kim, Sang Jin; Choi, Kyoungjun; Lee, Bora; Kim, Yuna; Hong, Byung Hee

    2015-07-01

    Recently, 2D materials have been intensively studied as emerging materials for future electronics, including flexible electronics, photonics, and electrochemical energy storage devices. Among representative 2D materials (such as graphene, boron nitride, and transition metal dichalcogenides) that exhibit extraordinary properties, graphene stands out in the flexible electronics field due to its combination of high electron mobility, high thermal conductivity, high specific surface area, high optical transparency, excellent mechanical flexibility, and environmental stability. This review covers the synthesis, transfer, and characterization methods of graphene and 2D materials and graphene's application to flexible devices as well as comparison with other competing materials.

  5. Introduction to game physics with Box2D

    Parberry, Ian

    2013-01-01

    Written by a pioneer of game development in academia, Introduction to Game Physics with Box2D covers the theory and practice of 2D game physics in a relaxed and entertaining yet instructional style. It offers a cohesive treatment of the topics and code involved in programming the physics for 2D video games. Focusing on writing elementary game physics code, the first half of the book helps you grasp the challenges of programming game physics from scratch, without libraries or outside help. It examines the mathematical foundation of game physics and illustrates how it is applied in practice thro

  6. Comparison of 2D and 3D gamma analyses

    Pulliam, Kiley B.; Huang, Jessie Y.; Howell, Rebecca M.; Followill, David; Kry, Stephen F., E-mail: sfkry@mdanderson.org [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center and The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030 (United States); Bosca, Ryan [Department of Imaging Physics, The University of Texas MD Anderson Cancer Center and The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030 (United States); O’Daniel, Jennifer [Department of Radiation Oncology, Duke University, Durham, North Carolina 27705 (United States)

    2014-02-15

    Purpose: As clinics begin to use 3D metrics for intensity-modulated radiation therapy (IMRT) quality assurance, it must be noted that these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, in part because of the different search space available. In the present investigation, the authors compared the results of 2D and 3D gamma analysis (where both datasets were generated in the same manner) for clinical treatment plans. Methods: Fifty IMRT plans were selected from the authors’ clinical database, and recalculated using Monte Carlo. Treatment planning system-calculated (“evaluated dose distributions”) and Monte Carlo-recalculated (“reference dose distributions”) dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose-difference (5%, 3%, 2%, and 1%) and distance-to-agreement (5, 3, 2, and 1 mm) acceptance criteria, low-dose thresholds (5%, 10%, and 15% of the prescription dose), and data grid sizes (1.0, 1.5, and 3.0 mm). Each comparison was evaluated to determine the average 2D and 3D gamma, lower 95th percentile gamma value, and percentage of pixels passing gamma. Results: The average gamma, lower 95th percentile gamma value, and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. The average difference in the percentage of passing pixels between the 2D and 3D analyses with no low-dose threshold ranged from 0.9% to 2.1%. Similarly, using a low-dose threshold resulted in a difference between the mean 2D and 3D results, ranging from 0.8% to 1.5%. The authors observed no appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs 3D). Conclusions: The authors found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis. It must

  7. Optimization and practical implementation of ultrafast 2D NMR experiments

    Luiz H. K. Queiroz Júnior

    2013-01-01

    Full Text Available Ultrafast 2D NMR is a powerful methodology that allows recording of a 2D NMR spectrum in a fraction of second. However, due to the numerous non-conventional parameters involved in this methodology its implementation is no trivial task. Here, an optimized experimental protocol is carefully described to ensure efficient implementation of ultrafast NMR. The ultrafast spectra resulting from this implementation are presented based on the example of two widely used 2D NMR experiments, COSY and HSQC, obtained in 0.2 s and 41 s, respectively.

  8. Optimization and practical implementation of ultrafast 2D NMR experiments

    Queiroz Junior, Luiz H. K., E-mail: professorkeng@gmail.com [Universidade Federal de Sao Carlos (UFSC), SP (Brazil). Departamento de Quimica; Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Inst. de Quimica; Ferreira, Antonio G. [Universidade Federal de Sao Carlos (UFSC), SP (Brazil). Departamento de Quimica; Giraudeau, Patrick [Universite de Nantes (France). CNRS, Chimie et Interdisciplinarite: Synthese, Analyse, Modelisation

    2013-09-01

    Ultrafast 2D NMR is a powerful methodology that allows recording of a 2D NMR spectrum in a fraction of second. However, due to the numerous non-conventional parameters involved in this methodology its implementation is no trivial task. Here, an optimized experimental protocol is carefully described to ensure efficient implementation of ultrafast NMR. The ultrafast spectra resulting from this implementation are presented based on the example of two widely used 2D NMR experiments, COSY and HSQC, obtained in 0.2 s and 41 s, respectively. (author)

  9. Kalman Filter for Generalized 2-D Roesser Models

    SHENG Mei; ZOU Yun

    2007-01-01

    The design problem of the state filter for the generalized stochastic 2-D Roesser models, which appears when both the state and measurement are simultaneously subjected to the interference from white noise, is discussed. The wellknown Kalman filter design is extended to the generalized 2-D Roesser models. Based on the method of "scanning line by line", the filtering problem of generalized 2-D Roesser models with mode-energy reconstruction is solved. The formula of the optimal filtering, which minimizes the variance of the estimation error of the state vectors, is derived. The validity of the designed filter is verified by the calculation steps and the examples are introduced.

  10. 2D electron cyclotron emission imaging at ASDEX Upgrade (invited)

    Classen, I. G. J. [Max Planck Institut fuer Plasmaphysik, 85748 Garching (Germany); FOM-Institute for Plasma Physics, Rijnhuizen, 3430 BE Nieuwegein (Netherlands); Boom, J. E.; Vries, P. C. de [FOM-Institute for Plasma Physics, Rijnhuizen, 3430 BE Nieuwegein (Netherlands); Suttrop, W.; Schmid, E.; Garcia-Munoz, M.; Schneider, P. A. [Max Planck Institut fuer Plasmaphysik, 85748 Garching (Germany); Tobias, B.; Domier, C. W.; Luhmann, N. C. Jr. [University of California at Davis, Davis, California 95616 (United States); Donne, A. J. H. [FOM-Institute for Plasma Physics, Rijnhuizen, 3430 BE Nieuwegein (Netherlands); Eindhoven University of Technology, 5600 MB Eindhoven (Netherlands); Jaspers, R. J. E. [Eindhoven University of Technology, 5600 MB Eindhoven (Netherlands); Park, H. K. [POSTECH, Pohang, Gyeongbuk, 790-784 (Korea, Republic of); Munsat, T. [University of Colorado, Boulder, Colorado 80309 (United States)

    2010-10-15

    The newly installed electron cyclotron emission imaging diagnostic on ASDEX Upgrade provides measurements of the 2D electron temperature dynamics with high spatial and temporal resolution. An overview of the technical and experimental properties of the system is presented. These properties are illustrated by the measurements of the edge localized mode and the reversed shear Alfven eigenmode, showing both the advantage of having a two-dimensional (2D) measurement, as well as some of the limitations of electron cyclotron emission measurements. Furthermore, the application of singular value decomposition as a powerful tool for analyzing and filtering 2D data is presented.

  11. Soil evolution dynamics and cultural response: Transformation of habitation patterns in NW Europe (3000-1000 yrs BP)

    Kluiving, Sjoerd; Roymans, Nico; Bekkema, Marijke

    2014-05-01

    Long-term archaeological data gathering in the southern Netherlands delivers an interesting scale model that may be tested on the Pleistocene sand areas of the Northwest European Plain. On a micro-scale level it has become clear that Bronze Age and Iron Age farmers intensively used the landscape, resulting in relatively dense distribution patterns of settlements all over the sand plateaus. However, this agricultural use of the landscape - related to the 'celtic field' system - led to a process of soil degeneration during which initially brown moder podzols gradually transformed into degenerated humus podzols that could no longer be used as farmland. Measured loam values of over 250 soil samples of 5 case studies in the southern Netherlands, are in general agreement with the described model that the plaggen cover is located on soils containing high loam% and that humus podzolsoils of former heath areas have low loam content. Local spatial as well as vertical variations in loam content of sand layers are warning against single parameter research. Other potential causes for the deviation of the model are: a) impact of fluctuating groundwater, b) grain size and transmissivity of the sediments, c) organic matter content, d) land management and e) palaeo-climate change. Also studies from nearby NW European Pleistocene sand areas will be presented that show deviations and similarities with the shifting habitation model in the past due to soil degradation.

  12. ChromEvol: assessing the pattern of chromosome number evolution and the inference of polyploidy along a phylogeny.

    Glick, Lior; Mayrose, Itay

    2014-07-01

    We announce the release of chromEvol version 2.0, a software tool for inferring the pattern of chromosome number change along a phylogeny. The software facilitates the inference of the expected number of polyploidy and dysploidy transitions along each branch of a phylogeny and estimates ancestral chromosome numbers at internal nodes. The new version features a novel extension of the model accounting for general multiplication events, other than doubling of the number of chromosomes. This allows the monoploid number (commonly referred to as x, or the base-number) of a group of interest to be inferred in a statistical framework. In addition, we devise an inference scheme, which allows explicit categorization of each terminal taxon as either diploid or polyploid. The new version also supports intraspecific variation in chromosome number and allows hypothesis testing regarding the root chromosome number. The software, alongside a detailed usage manual, is available at http://www.tau.ac.il/∼itaymay/cp/chromEvol/. PMID:24710517

  13. Evolution of central pattern generators for the control of a five-link planar bipedal walking mechanism

    Baydin, Atilim Gunes

    2008-01-01

    With the aim of producing a stable human-like bipedal gait, a five-link planar walking mechanism was coupled with a central pattern generator (CPG) network, consisting of units based on Matsuoka's half-center oscillator model. As a minimalistic approach to bipedal walking, this type of walking mechanism contains only four actuators (two in the hip joints and two in the knee joints), and is lacking feet and ankles. Firstly, the mechanism was designed and built as a physical simulation programmed from scratch, providing a platform for hand-tuned tests and the creation of a CPG controller by genetic algorithms (GA). The oscillatory characteristics of the CPG network together with its internal connection structure and the feedback pathways from the environment were subject to GA optimization. The approach proved successful and the results were then transferred to a hardware realization of the five-link walking mechanism, to test how well these perform under real-world dynamics. Results suggest that the biological...

  14. Evolution of patterns of regional groundwater flow in southeastern New Mexico: Response to post-Pleistocene changes in climate

    The Waste Isolation Pilot Plant (WIPP) is a potential repository for transuranic wastes generated by defense programs of the US Department of Energy. The repository site is located 42 km east of the city of Carlsbad, New Mexico in a thick, Permian-age deposit of bedded salt. One consideration in evaluating the performance of the repository is that a future society might inadvertently penetrate the repository with one or more drill holes. Given certain circumstances, these holes could provide a pathway for contaminated brine to move upward into relatively permeable strata located above the bedded salt. There is concern that flowing groundwater could then transport radionuclides laterally to the sub-surface portion of the accessible environment, currently defined by the disposal regulations as the region more than 5 kilometers from the radioactive waste. The simulations presented here are part of a numerical modeling study of the possible impact that a change in climate over the next 10,000 years could have on the pattern of groundwater flow and, consequently, on the migration of radionuclides in strata overlying the repository

  15. SALE-2D, 2-D Fluid Flow, Navier Stokes Equation Using Lagrangian or Eulerian Method

    1 - Description of problem or function: SALE2D calculates two- dimensional fluid flows at all speeds, from the incompressible limit to highly supersonic. An implicit treatment of the pressure calculation similar to that in the Implicit Continuous-fluid Eulerian (ICE) technique provides this flow speed flexibility. In addition, the computing mesh may move with the fluid in a typical Lagrangian fashion, be held fixed in an Eulerian manner, or move in some arbitrarily specified way to provide a continuous rezoning capability. This latitude results from use of an Arbitrary Lagrangian-Eulerian (ALE) treatment of the mesh. The partial differential equations solved are the Navier-Stokes equations and the mass and internal energy equations. The fluid pressure is determined from an equation of state and supplemented with an artificial viscous pressure for the computation of shock waves. The computing mesh consists of a two-dimensional network of quadrilateral cells for either cylindrical or Cartesian coordinates, and a variety of user-selectable boundary conditions are provided in the program. 2 - Method of solution: The basic hydrodynamic part of each cycle of SALE is divided into three phases. Phase 1 is a typical explicit Lagrangian calculation in which the velocity field is updated by the effects of all forces. Phase 2 is a Newton-Raphson iteration that provides time-advanced pressures and velocities. It is used for calculations in the low-speed and even completely incompressible regimes. Phase 3 performs all the advective flux calculations. It is required for runs that are Eulerian or contain some other form of mesh rezoning. A powerful feature of SALE is the ease with which different phases can be combined to suit the requirements of individual problems

  16. Holographic method for site-resolved detection of a 2D array of ultracold atoms

    Hoffmann, Daniel Kai; Limmer, Wolfgang; Denschlag, Johannes Hecker

    2016-01-01

    We propose a novel approach to site-resolved detection of a 2D gas of ultracold atoms in an optical lattice. A near resonant laser beam is coherently scattered by the atomic array and its interference pattern is holographically recorded by superimposing it with a reference laser beam on a CCD chip. Fourier transformation of the recorded intensity pattern reconstructs the atomic distribution in the lattice with single-site resolution. The holographic detection method requires only a few hundred scattered photons per atom in order to achieve a high reconstruction fidelity. Therefore, additional cooling during detection might not be necessary even for light atomic elements such as lithium.

  17. Cellular automaton model with dynamical 2D speed-gap relation reproduces empirical and experimental features of traffic flow

    Tian, Junfang; Ma, Shoufeng; Zhu, Chenqiang; Jiang, Rui; Ding, YaoXian

    2015-01-01

    This paper proposes an improved cellular automaton traffic flow model based on the brake light model, which takes into account that the desired time gap of vehicles is remarkably larger than one second. Although the hypothetical steady state of vehicles in the deterministic limit corresponds to a unique relationship between speeds and gaps in the proposed model, the traffic states of vehicles dynamically span a two-dimensional region in the plane of speed versus gap, due to the various randomizations. It is shown that the model is able to well reproduce (i) the free flow, synchronized flow, jam as well as the transitions among the three phases; (ii) the evolution features of disturbances and the spatiotemporal patterns in a car-following platoon; (iii) the empirical time series of traffic speed obtained from NGSIM data. Therefore, we argue that a model can potentially reproduce the empirical and experimental features of traffic flow, provided that the traffic states are able to dynamically span a 2D speed-gap...

  18. 2D Active Antenna Array Design for FD-MIMO System and Antenna Virtualization Techniques

    Ioannis Tzanidis

    2015-01-01

    Full Text Available Full dimension MIMO (FD-MIMO is one of the key technologies presently studied in the 3GPP for the next generation long-term evolution advanced (LTE-A systems. By incorporating FD-MIMO into LTE/LTE-A systems, it is expected that system throughput will be drastically improved beyond what is possible in conventional LTE systems. This paper presets details on the 2D active antenna array design for FD-MIMO systems supporting 32 antenna elements. The FD-MIMO system allows for dynamic and adaptive precoding to be performed jointly across all antennas thus achieving more directional transmissions in the azimuth and elevation domains simultaneously, to a larger number of users. Finally, we discuss 2D antenna array port virtualization techniques for creating beams with wide coverage, necessary for broadcasting signals to all users within a sector, such as the CRS (Common Reference Signal.

  19. To move or to evolve: contrasting patterns of intercontinental connectivity and climatic niche evolution in "Terebinthaceae" (Anacardiaceae and Burseraceae.

    Andrea eWeeks

    2014-11-01

    Full Text Available Many angiosperm families are distributed pantropically, yet for any given continent little is known about which lineages are ancient residents or recent arrivals. Here we use a comprehensive sampling of the pantropical sister pair Anacardiaceae and Burseraceae to assess the relative importance of continental vicariance, long-distance dispersal and niche-conservatism in generating its distinctive pattern of diversity over time. Each family has approximately the same number of species and identical stem age, yet Anacardiaceae display a broader range of fruit morphologies and dispersal strategies and include species that can withstand freezing temperatures, whereas Burseraceae do not. We found that nuclear and chloroplast data yielded a highly supported phylogenetic reconstruction that supports current taxonomic concepts and time-calibrated biogeographic reconstructions that are broadly congruent with the fossil record. We conclude that the most recent common ancestor of these families was widespread and likely distributed in the Northern Hemisphere during the Cretaceous and that vicariance between Eastern and Western Hemispheres coincided with the initial divergence of the families. The tempo of diversification of the families is strikingly different. Anacardiaceae steadily accumulated lineages starting in the Late Cretaceous–Paleocene while the majority of Burseraceae diversification occurred in the Miocene. Multiple dispersal- and vicariance-based intercontinental colonization events are inferred for both families throughout the past 100 million years. However, Anacardiaceae have shifted climatic niches frequently during this time, while Burseraceae have experienced very few shifts between dry and wet climates and only in the tropics. Thus, we conclude that both Anacardiaceae and Burseraceae move easily but that Anacardiaceae have adapted more often, either due to more varied selective pressures or greater intrinsic lability.

  20. Technical Review of the UNET2D Hydraulic Model

    Perkins, William A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Richmond, Marshall C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-05-18

    The Kansas City District of the US Army Corps of Engineers is engaged in a broad range of river management projects that require knowledge of spatially-varied hydraulic conditions such as velocities and water surface elevations. This information is needed to design new structures, improve existing operations, and assess aquatic habitat. Two-dimensional (2D) depth-averaged numerical hydraulic models are a common tool that can be used to provide velocity and depth information. Kansas City District is currently using a specific 2D model, UNET2D, that has been developed to meet the needs of their river engineering applications. This report documents a tech- nical review of UNET2D.

  1. Illumination Compensation for 2-D Barcode Recognition Basing Morphologic

    Jian-Hua Li

    2013-04-01

    Full Text Available Improvement of image quality has been highly demanded in digital imaging systems. This study presents a novel illumination normalization approach for 2-D barcode recognition under varying lighting conditions. MMs (Morphological transformations are employed to original images using big scale multiple SEs (structuring elements. Then we make use of entropy to fuse images. The performance of proposed methodology is illustrated through the processing of images with different kinds of 2-D barcodes under different backgrounds. The experimental results show that this approach can process different kinds of 2-D barcodes under varying lighting conditions adaptively. Compared with other conventional methods, our proposed approach does a better job in processing 2-D barcode under non-uniform illumination.

  2. Recent developments in 2D layered inorganic nanomaterials for sensing

    Kannan, Padmanathan Karthick; Late, Dattatray J.; Morgan, Hywel; Rout, Chandra Sekhar

    2015-08-01

    Two dimensional layered inorganic nanomaterials (2D-LINs) have recently attracted huge interest because of their unique thickness dependent physical and chemical properties and potential technological applications. The properties of these layered materials can be tuned via both physical and chemical processes. Some 2D layered inorganic nanomaterials like MoS2, WS2 and SnS2 have been recently developed and employed in various applications, including new sensors because of their layer-dependent electrical properties. This article presents a comprehensive overview of recent developments in the application of 2D layered inorganic nanomaterials as sensors. Some of the salient features of 2D materials for different sensing applications are discussed, including gas sensing, electrochemical sensing, SERS and biosensing, SERS sensing and photodetection. The working principles of the sensors are also discussed together with examples.

  3. Chemical vapour deposition: Transition metal carbides go 2D

    Gogotsi, Yury

    2015-11-01

    The unique properties of 2D materials, such as graphene or transition metal dichalcogenides, have been attracting much attention in the past decade. Now, metallically conductive and even superconducting transition metal carbides are entering the game.

  4. 2d quantum gravity and black hole formation

    The quantum integral of generic 2d quantum gravity can be performed exactly. The equivalence of dilaton theories to 2d theories with torsion and the use of a light cone gauge are crucial. Scalar matter can be treated perturbatively. A generalization of the Polyakov action emerges. For scattering of scalars in a flat background already in the tree approximation for the first time the intermediate formation of a black hole is observed in an ab initio quantum gravity computation

  5. Sparse Non-negative Matrix Factor 2-D Deconvolution

    Mørup, Morten; Schmidt, Mikkel N.

    2006-01-01

    We introduce the non-negative matrix factor 2-D deconvolution (NMF2D) model, which decomposes a matrix into a 2-dimensional convolution of two factor matrices. This model is an extension of the non-negative matrix factor deconvolution (NMFD) recently introduced by Smaragdis (2004). We derive and ...... this form of factorization. The developed algorithms have been used for source separation and music transcription....

  6. QSAR Models for P-450 (2D6) Substrate Activity

    Ringsted, Tine; Nikolov, Nikolai Georgiev; Jensen, Gunde Egeskov;

    2009-01-01

    activity relationship (QSAR) modelling systems. They cross validated (leave-groups-out) with concordances of 71%, 81% and 82%, respectively. Discrete organic European Inventory of Existing Commercial Chemical Substances (EINECS) chemicals were screened to predict an approximate percentage of CYP 2D6...... substrates. These chemicals are potentially present in the environment. The biological importance of the CYP 2D6 and the use of the software mentioned above were discussed....

  7. The Branching of Graphs in 2-d Quantum Gravity

    Harris, M. G.

    1996-01-01

    The branching ratio is calculated for three different models of 2d gravity, using dynamical planar phi-cubed graphs. These models are pure gravity, the D=-2 Gaussian model coupled to gravity and the single spin Ising model coupled to gravity. The ratio gives a measure of how branched the graphs dominating the partition function are. Hence it can be used to estimate the location of the branched polymer phase for the multiple Ising model coupled to 2d gravity.

  8. Illumination Compensation for 2-D Barcode Recognition Basing Morphologic

    Jian-Hua Li; Yi-Wen Wang; Yi Chen; Meng Zhang

    2013-01-01

    Improvement of image quality has been highly demanded in digital imaging systems. This study presents a novel illumination normalization approach for 2-D barcode recognition under varying lighting conditions. MMs (Morphological transformations) are employed to original images using big scale multiple SEs (structuring elements). Then we make use of entropy to fuse images. The performance of proposed methodology is illustrated through the processing of images with different kinds of 2-D barcode...

  9. The relation between Euclidean and Lorentzian 2D quantum gravity

    Ambjørn, J.; Correia, J; Kristjansen, C.; Loll, R.

    2006-01-01

    Starting from 2D Euclidean quantum gravity, we show that one recovers 2D Lorentzian quantum gravity by removing all baby universes. Using a peeling procedure to decompose the discrete, triangulated geometries along a one-dimensional path, we explicitly associate with each Euclidean space-time a (generalized) Lorentzian spacetime. This motivates a map between the parameter spaces of the two theories, under which their propagators get identified. In two dimensions, Lorentzian quantum gravity ca...

  10. Developmental evolution of flowering plant pollen tube cell walls: callose synthase (CalS gene expression patterns

    Abercrombie Jason M

    2011-07-01

    and pollen-specific functions in early seed plants and was then recruited to novel expression patterns and functions within pollen tube walls in an ancestor of extant angiosperms.

  11. Evaluation of low-dose limits in 3D-2D rigid registration for surgical guidance

    Uneri, A.; Wang, A. S.; Otake, Y.; Kleinszig, G.; Vogt, S.; Khanna, A. J.; Gallia, G. L.; Gokaslan, Z. L.; Siewerdsen, J. H.

    2014-09-01

    An algorithm for intensity-based 3D-2D registration of CT and C-arm fluoroscopy is evaluated for use in surgical guidance, specifically considering the low-dose limits of the fluoroscopic x-ray projections. The registration method is based on a framework using the covariance matrix adaptation evolution strategy (CMA-ES) to identify the 3D patient pose that maximizes the gradient information similarity metric. Registration performance was evaluated in an anthropomorphic head phantom emulating intracranial neurosurgery, using target registration error (TRE) to characterize accuracy and robustness in terms of 95% confidence upper bound in comparison to that of an infrared surgical tracking system. Three clinical scenarios were considered: (1) single-view image + guidance, wherein a single x-ray projection is used for visualization and 3D-2D guidance; (2) dual-view image + guidance, wherein one projection is acquired for visualization, combined with a second (lower-dose) projection acquired at a different C-arm angle for 3D-2D guidance; and (3) dual-view guidance, wherein both projections are acquired at low dose for the purpose of 3D-2D guidance alone (not visualization). In each case, registration accuracy was evaluated as a function of the entrance surface dose associated with the projection view(s). Results indicate that images acquired at a dose as low as 4 μGy (approximately one-tenth the dose of a typical fluoroscopic frame) were sufficient to provide TRE comparable or superior to that of conventional surgical tracking, allowing 3D-2D guidance at a level of dose that is at most 10% greater than conventional fluoroscopy (scenario #2) and potentially reducing the dose to approximately 20% of the level in a conventional fluoroscopically guided procedure (scenario #3).

  12. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    Osiry, H.; Cano, A.; Lemus-Santana, A.A.; Rodríguez, A. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional (Mexico); Carbonio, R.E. [INFIQC-CONICET, Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba (Argentina); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional (Mexico)

    2015-10-15

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.

  13. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework

  14. Genes encoding the alpha-carboxyltransferase subunit of acetyl-CoA carboxylase from Brassica napus and parental species: cloning, expression patterns, and evolution.

    Li, Zhi-Guo; Yin, Wei-Bo; Guo, Huan; Song, Li-Ying; Chen, Yu-Hong; Guan, Rong-Zhan; Wang, Jing-Qiao; Wang, Richard R-C; Hu, Zan-Min

    2010-05-01

    Heteromeric acetyl coenzyme A carboxylase (ACCase), a rate-limiting enzyme in fatty acid biosynthesis in dicots, is a multi-enzyme complex consisting of biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase (alpha-CT and beta-CT). In the present study, four genes encoding alpha-CT were cloned from Brassica napus, and two were cloned from each of the two parental species, B. rapa and B. oleracea. Comparative and cluster analyses indicated that these genes were divided into two major groups. The major divergence between group-1 and group-2 occurred in the second intron. Group-2 alpha-CT genes represented the ancestral form in the genus Brassica. The divergence of group-1 and group-2 genes occurred in their common ancestor 12.96-17.78 million years ago (MYA), soon after the divergence of Arabidopsis thaliana and Brassica (15-20 MYA). This time of divergence is identical to that reported for the paralogous subgenomes of diploid Brassica species (13-17 MYA). Real-time reverse transcription PCR revealed that the expression patterns of the two groups of genes were similar in different organs, except in leaves. To better understand the regulation and evolution of alpha-CT genes, promoter regions from two sets of orthologous gene copies from B. napus, B. rapa, and B. oleracea were cloned and compared. The function of the promoter of gene Bnalpha-CT-1-1 in group-1 and gene Bnalpha-CT-2-1 in group-2 was examined by assaying beta-glucuronidase activity in transgenic A. thaliana. Our results will be helpful in elucidating the evolution and regulation of ACCase in oilseed rape. PMID:20616867

  15. The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones

    Martins Juliana R

    2010-03-01

    Full Text Available Abstract Background Hexamerins are hemocyanin-derived proteins that have lost the ability to bind copper ions and transport oxygen; instead, they became storage proteins. The current study aimed to broaden our knowledge on the hexamerin genes found in the honey bee genome by exploring their structural characteristics, expression profiles, evolution, and functions in the life cycle of workers, drones and queens. Results The hexamerin genes of the honey bee (hex 70a, hex 70b, hex 70c and hex 110 diverge considerably in structure, so that the overall amino acid identity shared among their deduced protein subunits varies from 30 to 42%. Bioinformatics search for motifs in the respective upstream control regions (UCRs revealed six overrepresented motifs including a potential binding site for Ultraspiracle (Usp, a target of juvenile hormone (JH. The expression of these genes was induced by topical application of JH on worker larvae. The four genes are highly transcribed by the larval fat body, although with significant differences in transcript levels, but only hex 110 and hex 70a are re-induced in the adult fat body in a caste- and sex-specific fashion, workers showing the highest expression. Transcripts for hex 110, hex 70a and hex70b were detected in developing ovaries and testes, and hex 110 was highly transcribed in the ovaries of egg-laying queens. A phylogenetic analysis revealed that HEX 110 is located at the most basal position among the holometabola hexamerins, and like HEX 70a and HEX 70c, it shares potential orthology relationship with hexamerins from other hymenopteran species. Conclusions Striking differences were found in the structure and developmental expression of the four hexamerin genes in the honey bee. The presence of a potential binding site for Usp in the respective 5' UCRs, and the results of experiments on JH level manipulation in vivo support the hypothesis of regulation by JH. Transcript levels and patterns in the fat body

  16. Sparse Non-negative Tensor 2D Deconvolution (SNTF2D) for multi channel time-frequency analysis

    Mørup, Morten; Schmidt, Mikkel N.

    2006-01-01

    We recently introduced two algorithms for sparse non-negative matrix factor 2-D deconvolution (SNMF2D) that are useful for single channel source separation and music transcription. We here extend this approach to the analysis of the log-frequency spectrograms of a multichannel recording. The model...... algorithms are demonstrated to successfully identify the components of both artificially generated as well as real stereo music....

  17. Classification of ξ(s)-Quadratic Stochastic Operators on 2D simplex

    A quadratic stochastic operator (in short QSO) is usually used to present the time evolution of differing species in biology. Some QSO has been studied by Lotka and Volterra. The general problem in the nonlinear operator theory is to study the behavior of operators. This problem was not fully finished even for the quadratic stochastic operators. To study this problem it was investigated several classes of such QSO. In this paper we study ξ(s)-QSO class of operators. We study such kind of operators on 2D simplex. We first classify these ξ(s)-QSO into 20 classes. Further, we investigate the dynamics of one class of such operators.

  18. IGUANA A high-performance 2D and 3D visualisation system

    Alverson, G; Muzaffar, S; Osborne, I; Taylor, L; Tuura, L A

    2004-01-01

    The IGUANA project has developed visualisation tools for multiple high-energy experiments. At the core of IGUANA is a generic, high- performance visualisation system based on OpenInventor and OpenGL. This paper describes the back-end and a feature-rich 3D visualisation system built on it, as well as a new 2D visualisation system that can automatically generate 2D views from 3D data, for example to produce R/Z or X/Y detector displays from existing 3D display with little effort. IGUANA has collaborated with the open-source gl2ps project to create a high-quality vector postscript output that can produce true vector graphics output from any OpenGL 2D or 3D display, complete with surface shading and culling of invisible surfaces. We describe how it works. We also describe how one can measure the memory and performance costs of various OpenInventor constructs and how to test scene graphs. We present good patterns to follow and bad patterns to avoid. We have added more advanced tools such as per-object clipping, sl...

  19. IGUANA: a high-performance 2D and 3D visualisation system

    The IGUANA project has developed visualisation tools for multiple high-energy experiments. At the core of IGUANA is a generic, high-performance visualisation system based on OpenInventor and OpenGL. This paper describes the back-end and a feature-rich 3D visualisation system built on it, as well as a new 2D visualisation system that can automatically generate 2D views from 3D data, for example to produce R/Z or X/Y detector displays from existing 3D display with little effort. IGUANA has collaborated with the open-source gl2ps project to create a high-quality vector postscript output that can produce true vector graphics output from any OpenGL 2D or 3D display, complete with surface shading and culling of invisible surfaces. We describe how it works. We also describe how one can measure the memory and performance costs of various OpenInventor constructs and how to test scene graphs. We present good patterns to follow and bad patterns to avoid. We have added more advanced tools such as per-object clipping, slicing, lighting or animation, as well as multiple linked views with OpenInventor, and describe them in this paper. We give details on how to edit object appearance efficiently and easily, and even dynamically as a function of object properties, with instant visual feedback to the user

  20. IGUANA: a high-performance 2D and 3D visualisation system

    Alverson, G. [Department of Physics, Northeastern University, Boston, MA 02115 (United States); Eulisse, G. [Department of Physics, Northeastern University, Boston, MA 02115 (United States); Muzaffar, S. [Department of Physics, Northeastern University, Boston, MA 02115 (United States); Osborne, I. [Department of Physics, Northeastern University, Boston, MA 02115 (United States); Taylor, L. [Department of Physics, Northeastern University, Boston, MA 02115 (United States)]. E-mail: lucas.taylor@cern.ch; Tuura, L.A. [Department of Physics, Northeastern University, Boston, MA 02115 (United States)

    2004-11-21

    The IGUANA project has developed visualisation tools for multiple high-energy experiments. At the core of IGUANA is a generic, high-performance visualisation system based on OpenInventor and OpenGL. This paper describes the back-end and a feature-rich 3D visualisation system built on it, as well as a new 2D visualisation system that can automatically generate 2D views from 3D data, for example to produce R/Z or X/Y detector displays from existing 3D display with little effort. IGUANA has collaborated with the open-source gl2ps project to create a high-quality vector postscript output that can produce true vector graphics output from any OpenGL 2D or 3D display, complete with surface shading and culling of invisible surfaces. We describe how it works. We also describe how one can measure the memory and performance costs of various OpenInventor constructs and how to test scene graphs. We present good patterns to follow and bad patterns to avoid. We have added more advanced tools such as per-object clipping, slicing, lighting or animation, as well as multiple linked views with OpenInventor, and describe them in this paper. We give details on how to edit object appearance efficiently and easily, and even dynamically as a function of object properties, with instant visual feedback to the user.

  1. IGUANA: a high-performance 2D and 3D visualisation system

    Alverson, G.; Eulisse, G.; Muzaffar, S.; Osborne, I.; Taylor, L.; Tuura, L. A.

    2004-11-01

    The IGUANA project has developed visualisation tools for multiple high-energy experiments. At the core of IGUANA is a generic, high-performance visualisation system based on OpenInventor and OpenGL. This paper describes the back-end and a feature-rich 3D visualisation system built on it, as well as a new 2D visualisation system that can automatically generate 2D views from 3D data, for example to produce R/Z or X/Y detector displays from existing 3D display with little effort. IGUANA has collaborated with the open-source gl2ps project to create a high-quality vector postscript output that can produce true vector graphics output from any OpenGL 2D or 3D display, complete with surface shading and culling of invisible surfaces. We describe how it works. We also describe how one can measure the memory and performance costs of various OpenInventor constructs and how to test scene graphs. We present good patterns to follow and bad patterns to avoid. We have added more advanced tools such as per-object clipping, slicing, lighting or animation, as well as multiple linked views with OpenInventor, and describe them in this paper. We give details on how to edit object appearance efficiently and easily, and even dynamically as a function of object properties, with instant visual feedback to the user.

  2. Geodesic patterns

    Pottmann, Helmut

    2010-07-26

    Geodesic curves in surfaces are not only minimizers of distance, but they are also the curves of zero geodesic (sideways) curvature. It turns out that this property makes patterns of geodesics the basic geometric entity when dealing with the cladding of a freeform surface with wooden panels which do not bend sideways. Likewise a geodesic is the favored shape of timber support elements in freeform architecture, for reasons of manufacturing and statics. Both problem areas are fundamental in freeform architecture, but so far only experimental solutions have been available. This paper provides a systematic treatment and shows how to design geodesic patterns in different ways: The evolution of geodesic curves is good for local studies and simple patterns; the level set formulation can deal with the global layout of multiple patterns of geodesics; finally geodesic vector fields allow us to interactively model geodesic patterns and perform surface segmentation into panelizable parts. © 2010 ACM.

  3. 珠江三角洲城市群旅游空间格局演化%The Tourism Spatial Pattern Evolution of the Pearl River Delta

    陈浩; 陆林; 郑嬗婷

    2011-01-01

    旅游地发展演化的研究可以理清旅游地发展的脉络,寻求旅游地发展的内在规律.文章重点分析了改革开放以来珠江三角洲城市群旅游空间格局的演化过程,选取1980、1987、1999、2008年4个时间断面,选取节点发展和交通连接两项指标加以体现城市群旅游空间发展演化过程,以各城市旅游业发展的业绩反映城市节点的发展演化,以城市群各城市之间的公路交通连接反映城市之间连接的演化.通过构建旅游业发展业绩模型,反映城市旅游节点的发展状况,通过公路交通可达性、公路交通运量的演化反映珠三角区域的城际公路交通连接的演化.认为改革开放以来珠三角城市群区域旅游空间格局发生了巨大变化,最主要体现在从以广州为中心的单极格局转化为以广州、深圳为中心的两级格局,珠三角各城市旅游业均取得了高速发展,城际公路交通连接效率和总体运行能力大大提高.但珠三角区域旅游发展的空间布局存在不平衡性,珠江口东西两岸存在较大差异,随着港澳珠跨海大桥的修建及以广州为中心的城际轨道交通的建成,珠三角城市群旅游空间格局将发生革命性变化,区域空间网络体系将更加完善.%Evolution of tourism can sort out the context of tourism development, and search a certain regularity of tourism development. The article focuses on the evolution of tourism destinations in the Pearl River Delta since the reform and opening up started in the late 1970s. The paper, taking 1980, 1987, 1999 and 2008 as the four time sections, uses two indexes of the node development and traffic connection to examine the urban agglomeration tourism spatial evolution, and the urban tourism development to reflect the evolution of city node, and the road traffic between cities to reflect the evolution of cities connected. The development of urban tourism nodes are reflected by building models of

  4. The role of background selection in shaping patterns of molecular evolution and variation: evidence from variability on the Drosophila X chromosome.

    Charlesworth, Brian

    2012-05-01

    In the putatively ancestral population of Drosophila melanogaster, the ratio of silent DNA sequence diversity for X-linked loci to that for autosomal loci is approximately one, instead of the expected "null" value of 3/4. One possible explanation is that background selection (the hitchhiking effect of deleterious mutations) is more effective on the autosomes than on the X chromosome, because of the lack of crossing over in male Drosophila. The expected effects of background selection on neutral variability at sites in the middle of an X chromosome or an autosomal arm were calculated for different models of chromosome organization and methods of approximation, using current estimates of the deleterious mutation rate and distributions of the fitness effects of deleterious mutations. The robustness of the results to different distributions of fitness effects, dominance coefficients, mutation rates, mapping functions, and chromosome size was investigated. The predicted ratio of X-linked to autosomal variability is relatively insensitive to these variables, except for the mutation rate and map length. Provided that the deleterious mutation rate per genome is sufficiently large, it seems likely that background selection can account for the observed X to autosome ratio of variability in the ancestral population of D. melanogaster. The fact that this ratio is much less than one in D. pseudoobscura is also consistent with the model's predictions, since this species has a high rate of crossing over. The results suggest that background selection may play a major role in shaping patterns of molecular evolution and variation. PMID:22377629

  5. Creating bio-inspired hierarchical 3D-2D photonic stacks via planar lithography on self-assembled inverse opals

    Burgess, Ian B; Loncar, Marko

    2012-01-01

    Structural hierarchy and complex 3D architecture are characteristics of biological photonic designs that are challenging to reproduce in synthetic materials. Top-down lithography allows for designer patterning of arbitrary shapes, but is largely restricted to planar 2D structures. Self-assembly techniques facilitate easy fabrication of 3D photonic crystals, but controllable defect-integration is difficult. In this paper we combine the advantages of top-down and bottom-up fabrication, developing two techniques to deposit 2D-lithographically-patterned planar layers on top of or in between inverse-opal 3D photonic crystals and creating hierarchical structures that resemble the architecture of the bright green wing scales of the butterfly, Parides sesostris. These fabrication procedures, combining advantages of both top-down and bottom-up fabrication, may prove useful in the development of omnidirectional coloration elements and 3D-2D photonic crystal devices.

  6. Creating bio-inspired hierarchical 3D–2D photonic stacks via planar lithography on self-assembled inverse opals

    Structural hierarchy and complex 3D architecture are characteristics of biological photonic designs that are challenging to reproduce in synthetic materials. Top–down lithography allows for designer patterning of arbitrary shapes, but is largely restricted to planar 2D structures. Self-assembly techniques facilitate easy fabrication of 3D photonic crystals, but controllable defect-integration is difficult. In this paper we combine the advantages of top–down and bottom–up fabrication, developing two techniques to deposit 2D-lithographically-patterned planar layers on top of or in between inverse-opal 3D photonic crystals and creating hierarchical structures that resemble the architecture of the bright green wing scales of the butterfly, Parides sesostris. These fabrication procedures, combining advantages of both top–down and bottom–up fabrication, may prove useful in the development of omnidirectional coloration elements and 3D–2D photonic crystal devices. (paper)

  7. The NH$_2$D hyperfine structure revealed by astrophysical observations

    Daniel, F; Punanova, A; Harju, J; Faure, A; Roueff, E; Sipilä, O; Caselli, P; Güsten, R; Pon, A; Pineda, J E

    2016-01-01

    The 1$_{11}$-1$_{01}$ lines of ortho and para--NH$_2$D (o/p-NH$_2$D), respectively at 86 and 110 GHz, are commonly observed to provide constraints on the deuterium fractionation in the interstellar medium. In cold regions, the hyperfine structure due to the nitrogen ($^{14}$N) nucleus is resolved. To date, this splitting is the only one which is taken into account in the NH$_2$D column density estimates. We investigate how the inclusion of the hyperfine splitting caused by the deuterium (D) nucleus affects the analysis of the rotational lines of NH$_2$D. We present 30m IRAM observations of the above mentioned lines, as well as APEX o/p-NH$_2$D observations of the 1$_{01}$-0$_{00}$ lines at 333 GHz. The hyperfine spectra are first analyzed with a line list that only includes the hyperfine splitting due to the $^{14}$N nucleus. We find inconsistencies between the line widths of the 1$_{01}$-0$_{00}$ and 1$_{11}$-1$_{01}$ lines, the latter being larger by a factor of $\\sim$1.6$\\pm0.3$. Such a large difference is...

  8. Failure Mechanism of True 2D Granular Flows

    Nguyen, Cuong T; Fukagawa, R

    2015-01-01

    Most previous experimental investigations of two-dimensional (2D) granular column collapses have been conducted using three-dimensional (3D) granular materials in narrow horizontal channels (i.e., quasi-2D condition). Our recent research on 2D granular column collapses by using 2D granular materials (i.e., aluminum rods) has revealed results that differ markedly from those reported in the literature. We assume a 2D column with an initial height of h0 and initial width of d0, a defined as their ratio (a =h0/d0), a final height of h , and maximum run-out distance of d . The experimental data suggest that for the low a regime (a 0.65), the ratio of a to (d-d0)/d0, h0/h , or d/d0 is expressed by power-law relations. In particular, the following power-function ratios (h0/h=1.42a^2/3 and d/d0=4.30a^0.72) are proposed for every a >0.65. In contrast, the ratio (d-d0)/d0=3.25a^0.96 only holds for 0.651.5. In addition, the influence of ground contact surfaces (hard or soft beds) on the final run-out distance and destru...

  9. Ultrafast 2D NMR: An Emerging Tool in Analytical Spectroscopy

    Giraudeau, Patrick; Frydman, Lucio

    2014-06-01

    Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago, a so-called ultrafast (UF) approach was proposed, capable of delivering arbitrary 2D NMR spectra involving any kind of homo- or heteronuclear correlation, in a single scan. During the intervening years, the performance of this subsecond 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool experiencing an expanded scope of applications. This review summarizes the principles and main developments that have contributed to the success of this approach and focuses on applications that have been recently demonstrated in various areas of analytical chemistry—from the real-time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications.

  10. Is digit ratio (2D:4D) a reliable pointer to speech laterality?

    Hudson, John M; Hodgson, Jessica C

    2016-03-15

    The relative length of the second and fourth digits (2D:4D ratio) is sexually dimorphic and a retrospective biomarker of prenatal hormonal exposure. Low ratios indicate higher prenatal testosterone (pT) and lower estrogen exposure, whereas the reverse pattern is associated with high ratios. Elevated levels of pT exposure have long been thought to modulate hemispheric specialisation; subsequently many studies use the 2D:4D ratio as a proxy index for pT to examine the effects of prenatal hormonal exposure on lateralised cognitive abilities. Here we used Transcranial Doppler ultrasonography and digit ratio to investigate whether pT has an influence on speech laterality. We tested 34 right and 14 left handed adults. Our results indicate that speech representation is unrelated to digit characteristics and therefore purportedly pT. We discuss these findings in relation to androgen theories of lateralisation. PMID:26747206

  11. Elastomeric 2D Grating and Hemispherical Optofluidic Chamber for Multifunctional Fluidic Sensing

    Xu, Zhida

    2014-01-01

    We present an optofluidic sensor based on an elastomeric two-dimensional (2D) grating integrated inside a hemispherical fluid chamber. Laser beam is diffracted before (reflection) and after (transmission) going through the grating and liquid in the dome chamber. The sensing mechanism is investigated and simulated with a finite difference time domain (FDTD) based electromagnetic (EM) method. For experiment, by analyzing the size, power and shape of the 2D diffraction patterns, we can retrieve multiple parameters of the liquid including the refractive index, pressure and opacity with high sensitivity. We demonstrate that glucose concentration can be monitored when mixed in different concentrated phosphate buffered saline (PBS) solution. The free-solution binding of bovine serum albumin (BSA) and anti-BSA IgG is detected with this optical sensor. This low-cost, multifunctional and reliable optofluidic sensor has the potential to be used as monitor of biofluid such as blood in hemodialysis.

  12. A Neural-FEM tool for the 2-D magnetic hysteresis modeling

    Cardelli, E.; Faba, A.; Laudani, A.; Lozito, G. M.; Riganti Fulginei, F.; Salvini, A.

    2016-04-01

    The aim of this work is to present a new tool for the analysis of magnetic field problems considering 2-D magnetic hysteresis. In particular, this tool makes use of the Finite Element Method to solve the magnetic field problem in real device, and fruitfully exploits a neural network (NN) for the modeling of 2-D magnetic hysteresis of materials. The NS has as input the magnetic inductions components B at the k-th simulation step and returns as output the corresponding values of the magnetic field H corresponding to the input pattern. It is trained by vector measurements performed on the magnetic material to be modeled. This input/output scheme is directly implemented in a FEM code employing the magnetic potential vector A formulation. Validations through measurements on a real device have been performed.

  13. Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

    Pramod Kumar Singh

    2016-01-01

    Full Text Available Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE across a broad range 3.0–10.0 immobilized pH gradient (IPG strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana.

  14. Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry.

    Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna; Sharma, Bechan; Bhagyawant, Sameer S

    2016-01-01

    Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0-10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana. PMID:27144024

  15. Regional Distribution and Its Pattern Evolution of the Winter Olympics Gold Medals%冬奥会金牌区域归属与格局演变

    刘志华

    2014-01-01

    Through the quantitative statistics and regional distribution of the 22 games' gold medals of Winter Olympics from 1924 to 2014,the paper analyzes the dynamic change and pattern evolution of various regional gold medals. It draws a conclusion that the competitive pattern shows the strong is always strong,the polarization is serious with the legible boundary between strong area and weak area,a weak one is difficult to upgrade into strong area for a long time. European and American powers represented by Russia,Germany,Norway and USA have long-term regional monopoly with balanced development. The common countries obviously show selective advantage with unbalanced development, and the weak countries have well development trend by giving priority to choose the breakthrough according to respective national conditions.The fierce competition in the strong area and the rise of some weak ones result in a dispersed trend of gold medals distribution,the difference of competitive strength in various areas is diminishing in the shift. It should be to achieve the harmonious development of winter and summer Olympics in China by project planning based on the regional characteristics according to the evolution rule of competitive pattern.%通过对1924~2014年举办过的22届冬季奥运会金牌数及区域归属进行分类统计,分析各区域金牌的动态变化及竞技格局的演变。得出结论:竞技格局呈现出强者恒强的态势,强势区域与弱势区域界限清晰,两级分化严重,长时间内会继续维持,弱势区域很难升级到强势区域。以俄罗斯、德国、挪威、美国为代表的欧美强势国形成长期性区域垄断,项目发展相对均衡;较强国家项目发展不均衡,存在明显的选择性优势;弱势国家根据各自的国情,有重点地选择性突破,形成了良好的发展态势。强势区域的激烈竞争,弱势区域的突破崛起,导致金牌分布趋于分散,各区域的竞

  16. 2D materials for photon conversion and nanophotonics

    Tahersima, Mohammad H.; Sorger, Volker J.

    2015-09-01

    The field of two-dimensional (2D) materials has the potential to enable unique applications across a wide range of the electromagnetic spectrum. While 2D-layered materials hold promise for next-generation photon-conversion intrinsic limitations and challenges exist that shall be overcome. Here we discuss the intrinsic limitations as well as application opportunities of this new class of materials, and is sponsored by the NSF program Designing Materials to Revolutionize and Engineer our Future (DMREF) program, which links to the President's Materials Genome Initiative. We present general material-related details for photon conversion, and show that taking advantage of the mechanical flexibility of 2D materials by rolling MoS2/graphene/hexagonal boron nitride stack to a spiral solar cell allows for solar absorption up to 90%.

  17. Graphene based 2D-materials for supercapacitors

    Palaniselvam, Thangavelu; Baek, Jong-Beom

    2015-09-01

    Ever-increasing energy demands and the depletion of fossil fuels are compelling humanity toward the development of suitable electrochemical energy conversion and storage devices to attain a more sustainable society with adequate renewable energy and zero environmental pollution. In this regard, supercapacitors are being contemplated as potential energy storage devices to afford cleaner, environmentally friendly energy. Recently, a great deal of attention has been paid to two-dimensional (2D) nanomaterials, including 2D graphene and its inorganic analogues (transition metal double layer hydroxides, chalcogenides, etc), as potential electrodes for the development of supercapacitors with high electrochemical performance. This review provides an overview of the recent progress in using these graphene-based 2D materials as potential electrodes for supercapacitors. In addition, future research trends including notable challenges and opportunities are also discussed.

  18. Design and Realization of Dynamic Obstacle on URWPSSim2D

    Xiao Chen

    2013-07-01

    Full Text Available Simulation system is charged with the strategy validation and dual team meets, and as the 2-dimensional simulation platform for underwater robotic fish game, URWPGSim2D is the assigned platform for Chinese underwater robot contest and Robot cup underwater program. By now on URWPGSim2D, there is only static obstacles,thus short of changeableness. In order to improve the changeableness and innovation of robotic fish contest, to extend the space for the programming of contest strategy, and to increase the interest, this paper study the design of dynamic obstacles on URWPGSim2D, and design and implement two kinds of dynamic obstacles, which are the evadible dynamic obstacle and the forcing dribbling obstacle.  

  19. CYP2D6 genotype determination in the Danish population

    Brøsen, K; Nielsen, P N; Brusgaard, K;

    1994-01-01

    CYP2D6 genotyping was carried out by XbaI restriction fragment length polymorphism analysis and polymerase chain reaction in 168 healthy Danish volunteers, 77 extensive metabolizers (EM) and 91 poor metabolizers (PM) of sparteine. All EM were genotyped correctly as heterozygous or homozygous for.......11-9.10). The median difference was 0.09 (95% confidence interval: 0.02-0.16). CYP2D6 phenotyping is a promising tool in tailoring the individual dose of tricyclic antidepressants, some neuroleplics and some antiarrhythmics. However if the genotype test could be improved with regard to both sensitivity in PM...... and the ability to predict CYP2D6 activity in EM then it would be of even greater clinical value in therapeutic drug monitoring. Udgivelsesdato: 1994-null...

  20. Statistical mechanics on a 2D-random surface

    Various geometrical models first defined in the Euclidean plane or on a regular lattice have been briefly reviewed, including self-avoiding walks, random walk intersections, percolation and Ising clusters. These systems embody infinite sets of field operators defined in a natural way from the (fractal) geometry of these fluctuating critical systems. Their scaling behavior can be linked to that of associated conformal field theories. These systems can also all be redefined on a random lattice or surface, instead of on a regular 2D lattice. They are then coupled to ''quantum gravity'', and live on the ''world-sheet''. The fact that all their new exponents on a random surface can then be related to those in the usual 2D-plane, although now well known in string theory, is worth publicizing in this Physics in 2D conference. We illustrate it by some exact solutions in the case of polymers and branched polymers (animals) on a random fluid surface. (author)

  1. Effective viscosity of 2D suspensions - Confinement effects

    Peyla, Philippe; Priem, Stephane; Vincent, Doyeux; Farutin, Alexander; Ismail, Mourad

    2014-11-01

    We study the rheology of a sheared 2D suspension of non-Brownian disks in presence of walls. Although, it is of course possible today with modern computers and powerful algorithms to perform direct numerical simulations that fully account for multiparticle 3D interactions, the analysis of the simple case of a 2D suspension, provides valuable insights and helps to understand 3D results. For instance, we examine the role of particle-wall and particle-particle interactions in determining the rheology of confined sheared suspensions. In addition we evaluate the intrinsic viscosity as well as the contribution of hydrodynamic interactions to the dissipation as a function of a wide range of confinements. Thanks to the direct visualisation of the whole 2D Stokes flow, we are able to give a clear interpretation about the rheology of semi-dilute confined suspensions.

  2. S-duality and 2d Topological QFT

    Gadde, Abhijit; Rastelli, Leonardo; Razamat, Shlomo S

    2009-01-01

    We study the superconformal index for the class of N=2 4d superconformal field theories recently introduced by Gaiotto. These theories are defined by compactifying the (2,0) 6d theory on a Riemann surface with punctures. We interpret the index of the 4d theory associated to an n-punctured Riemann surface as the n-point correlation function of a 2d topological QFT living on the surface. Invariance of the index under generalized S-duality transformations (the mapping class group of the Riemann surface) translates into associativity of the operator algebra of the 2d TQFT. In the A_1 case, for which the 4d SCFTs have a Lagrangian realization, the structure constants and metric of the 2d TQFT can be calculated explicitly in terms of elliptic gamma functions. Associativity then holds thanks to a remarkable symmetry of an elliptic hypergeometric beta integral, proved very recently by van de Bult.

  3. 2D bifurcations and Newtonian properties of memristive Chua's circuits

    Marszalek, W.; Podhaisky, H.

    2016-01-01

    Two interesting properties of Chua's circuits are presented. First, two-parameter bifurcation diagrams of Chua's oscillatory circuits with memristors are presented. To obtain various 2D bifurcation images a substantial numerical effort, possibly with parallel computations, is needed. The numerical algorithm is described first and its numerical code for 2D bifurcation image creation is available for free downloading. Several color 2D images and the corresponding 1D greyscale bifurcation diagrams are included. Secondly, Chua's circuits are linked to Newton's law φ ''= F(t,φ,φ')/m with φ=\\text{flux} , constant m > 0, and the force term F(t,φ,φ') containing memory terms. Finally, the jounce scalar equations for Chua's circuits are also discussed.

  4. Development of ultra-fast 2D ion Doppler tomography using image intensified CMOS fast camera

    Tanabe, Hiroshi; Kuwahata, Akihiro; Yamanaka, Haruki; Inomoto, Michiaki; Ono, Yasushi; TS-group Team

    2015-11-01

    The world fastest novel time-resolved 2D ion Doppler tomography diagnostics has been developed using fast camera with high-speed gated image intensifier (frame rate: 200kfps. phosphor decay time: ~ 1 μ s). Time evolution of line-integrated spectra are diffracted from a f=1m, F/8.3 and g=2400L/mm Czerny-Turner polychromator, whose output is intensified and recorded to a high-speed camera with spectral resolution of ~0.005nm/pixel. The system can accommodate up to 36 (9 ×4) spatial points recorded at 5 μs time resolution, tomographic reconstruction is applied for the line-integrated spectra, time-resolved (5 μs/frame) local 2D ion temperature measurement has been achieved without any assumption of shot repeatability. Ion heating during intermittent reconnection event which tends to happen during high guide field merging tokamak was measured around diffusion region in UTST. The measured 2D profile shows ion heating inside the acceleration channel of reconnection outflow jet, stagnation point and downstream region where reconnected field forms thick closed flux surface as in MAST. Achieved maximum ion temperature increases as a function of Brec2 and shows good fit with MAST experiment, demonstrating promising CS-less startup scenario for spherical tokamak. This work is supported by JSPS KAKENHI Grant Number 15H05750 and 15K20921.

  5. Discrete tomographic reconstruction of 2D polycrystal orientation maps from X-ray diffraction projections using Gibbs priors

    Rodek, L.; Knudsen, E.; Poulsen, H.F.;

    2005-01-01

    The determination of crystalline structures is a demanding and fundamental task of crystallography. This paper offers a new approach for rendering a 2D grain map of a polycrystal based on an orientation map reconstructed from X-ray diffraction patterns. The orientation map is produced by a Bayesi...... orientations is defined by means of quaternions....

  6. CH2D+, the Search for the Holy Grail

    Roueff, Evelyne; Gerin, Maryvonne; Lis, Dariusz C.; Wootten, Alwyn; Marcelino, Nuria; Cernicharo, Jose; Tercero, Belen

    2013-10-01

    CH2D+, the singly deuterated counterpart of CH3+, offers an alternative way to mediate formation of deuterated species at temperatures of several tens of Kelvin, as compared to the release of deuterated species from grains. We report a longstanding observational search for this molecular ion, whose rotational spectroscopy is not yet completely secure. We summarize the main spectroscopic properties of this molecule and discuss the chemical network leading to the formation of CH2D+, with explicit account of the ortho/para forms of H2, H3+, and CH3+. Astrochemical models support the presence of this molecular ion in moderately warm environments at a marginal level.

  7. CH2D+, the Search for the Holy Grail

    Roueff, E; Lis, D C; Wootten, A; Marcelino, N; cernicharo, J; Tercero, B

    2013-01-01

    CH2D+, the singly deuterated counterpart of CH3+, offers an alternative way to mediate formation of deuterated species at temperatures of several tens of K, as compared to the release of deuterated species from grains. We report a longstanding observational search for this molecular ion, whose rotational spectroscopy is not yet completely secure. We summarize the main spectroscopic properties of this molecule and discuss the chemical network leading to the formation of CH2D+, with explicit account of the ortho/para forms of H2, H3+ and CH3+. Astrochemical models support the presence of this molecular ion in moderately warm environments at a marginal level.

  8. Design of the LRP airfoil series using 2D CFD

    This paper describes the design and wind tunnel testing of a high-Reynolds number, high lift airfoil series designed for wind turbines. The airfoils were designed using direct gradient- based numerical multi-point optimization based on a Bezier parameterization of the shape, coupled to the 2D Navier-Stokes flow solver EllipSys2D. The resulting airfoils, the LRP2-30 and LRP2-36, achieve both higher operational lift coefficients and higher lift to drag ratios compared to the equivalent FFA-W3 airfoils

  9. Isotropic 2D quadrangle meshing with size and orientation control

    Pellenard, Bertrand

    2011-12-01

    We propose an approach for automatically generating isotropic 2D quadrangle meshes from arbitrary domains with a fine control over sizing and orientation of the elements. At the heart of our algorithm is an optimization procedure that, from a coarse initial tiling of the 2D domain, enforces each of the desirable mesh quality criteria (size, shape, orientation, degree, regularity) one at a time, in an order designed not to undo previous enhancements. Our experiments demonstrate how well our resulting quadrangle meshes conform to a wide range of input sizing and orientation fields.

  10. EEG simulation by 2D interconnected chaotic oscillators

    Research highlights: → ANN of 2D interconnected chaotic oscillators is explored for EEG simulation. → An inverse problem solution (PRCGA) is proposed. → Good matching between the simulated and experimental EEG signals has been achieved. - Abstract: An artificial neuronal network composed by 2D interconnected chaotic oscillators is explored for brain waves (EEG) simulation. For the inverse problem solution a parallel real-coded genetic algorithm (PRCGA) is proposed. In order to conduct thorough comparison between the simulated and target signal characteristics, a spectrum analysis of the signals is undertaken. A good matching between the theoretical and experimental EEG signals has been achieved. Numerical results of calculations are presented and discussed.

  11. Design of the LRP airfoil series using 2D CFD

    Zahle, Frederik; Bak, Christian; Sørensen, Niels N.;

    2014-01-01

    This paper describes the design and wind tunnel testing of a high-Reynolds number, high lift airfoil series designed for wind turbines. The airfoils were designed using direct gradient- based numerical multi-point optimization based on a Bezier parameterization of the shape, coupled to the 2D...... Navier-Stokes flow solver EllipSys2D. The resulting airfoils, the LRP2-30 and LRP2-36, achieve both higher operational lift coefficients and higher lift to drag ratios compared to the equivalent FFA-W3 airfoils....

  12. Quantum process tomography by 2D fluorescence spectroscopy

    Pachón, Leonardo A. [Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138 (United States); Marcus, Andrew H. [Department of Chemistry and Biochemistry, Oregon Center for Optics, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 (United States); Aspuru-Guzik, Alán [Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138 (United States)

    2015-06-07

    Reconstruction of the dynamics (quantum process tomography) of the single-exciton manifold in energy transfer systems is proposed here on the basis of two-dimensional fluorescence spectroscopy (2D-FS) with phase-modulation. The quantum-process-tomography protocol introduced here benefits from, e.g., the sensitivity enhancement ascribed to 2D-FS. Although the isotropically averaged spectroscopic signals depend on the quantum yield parameter Γ of the doubly excited-exciton manifold, it is shown that the reconstruction of the dynamics is insensitive to this parameter. Applications to foundational and applied problems, as well as further extensions, are discussed.

  13. Synthesis of 2D materials in arc plasmas

    In this article we review recent efforts focused on synthesis of two-dimensional (2D) materials in an arc-plasma based process with particular focus on graphene. We present state-of-the-art experimental data on various attempts to employ the arc plasma technique for the graphene synthesis and consider growth mechanisms including precipitation, surface-catalyzed processes and a substrate-independent approach. The potential of arc synthesis for the growth of other types of 2D materials and future prospects are discussed. (review article)

  14. Nomenclature for human CYP2D6 alleles.

    Daly, A K; Brockmöller, J; Broly, F; Eichelbaum, M; Evans, W E; Gonzalez, F J; Huang, J D; Idle, J R; Ingelman-Sundberg, M; Ishizaki, T; Jacqz-Aigrain, E; Meyer, U A; Nebert, D W; Steen, V M; Wolf, C R; Zanger, U M

    1996-06-01

    To standardize CYP2D6 allele nomenclature, and to conform with international human gene nomenclature guidelines, an alternative to the current arbitrary system is described. Based on recommendations for human genome nomenclature, we propose that alleles be designated by CYP2D6 followed by an asterisk and a combination of roman letters and arabic numerals distinct for each allele with the number specifying the key mutation and, where appropriate, a letter specifying additional mutations. Criteria for classification as a separate allele and protein nomenclature are also presented. PMID:8807658

  15. Quantum process tomography by 2D fluorescence spectroscopy

    Reconstruction of the dynamics (quantum process tomography) of the single-exciton manifold in energy transfer systems is proposed here on the basis of two-dimensional fluorescence spectroscopy (2D-FS) with phase-modulation. The quantum-process-tomography protocol introduced here benefits from, e.g., the sensitivity enhancement ascribed to 2D-FS. Although the isotropically averaged spectroscopic signals depend on the quantum yield parameter Γ of the doubly excited-exciton manifold, it is shown that the reconstruction of the dynamics is insensitive to this parameter. Applications to foundational and applied problems, as well as further extensions, are discussed

  16. SKIMO: corto de animación 2D

    VALERO BALLESTER, AIDA AMPARO

    2015-01-01

    El siguiente Trabajo Final de Grado llamado “Skimo” consiste en un teaser de animación 2D enfocado a ser finalizado el próximo año durante la realización del Diploma en Animación de personajes 2D del Máster de animación. Realizado en solitario como reto personal durante el curso presente, siendo la primera vez que trabajaba la animación. Para este proyecto he realizado toda la preproducción (layout, animática, storyboard, diseño de personajes, fondos, etc), animación en pape...

  17. Self-dual strings and 2D SYM

    Hosomichi, Kazuo; Lee, Sungjay

    2015-01-01

    We study the system of M2-branes suspended between parallel M5-branes using ABJM model with a natural half-BPS boundary condition. For small separation between M5-branes, the worldvolume theory is shown to reduce to a 2D super Yang-Mills theory with some similarity to q-deformed Yang-Mills theory. The gauge coupling is related to the position of the branes in an interesting manner. The theory is considerably different from the 2D theory proposed for multiple "M-strings". We make a detailed comparison of elliptic genus of the two descriptions and find only a partial agreement.

  18. Self-dual Strings and 2D SYM

    Hosomichi, Kazuo

    2014-01-01

    We study the system of M2-branes suspended between parallel M5-branes using ABJM model with a natural half-BPS boundary condition. For small separation between M5-branes, the worldvolume theory is shown to reduce to a 2D N=(4,4) super Yang-Mills theory with some similarity to q-deformed Yang-Mills theory. The gauge coupling is related to the position of the branes in an interesting manner. The theory is considerably different from the 2D theory proposed for multiple "M-strings". We make a detailed comparison of elliptic genus of the two descriptions and find only a partial agreement.

  19. A novel improved method for analysis of 2D diffusion relaxation data—2D PARAFAC-Laplace decomposition

    Tønning, Erik; Polders, Daniel; Callaghan, Paul T.; Engelsen, Søren B.

    2007-09-01

    This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T2- D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T2- D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T2- D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D = 3 × 10 -12 m 2 s -1 and T2 = 180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D = 10 -9 m 2 s -1, T2 = 10 ms and D = 3 × 10 -13 m 2 s -1, T2 = 13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it

  20. Inferring nonneutral evolution from contrasting patterns of polymorphisms and divergences in different protein coding regions of enterovirus 71 circulating in Taiwan during 1998-2003

    Chen Guang-Wu

    2010-09-01

    Full Text Available Abstract Background Enterovirus (EV 71 is one of the common causative agents for hand, foot, and, mouth disease (HFMD. In recent years, the virus caused several outbreaks with high numbers of deaths and severe neurological complications. Despite the importance of these epidemics, several aspects of the evolutionary and epidemiological dynamics, including viral nucleotide variations within and between different outbreaks, rates of change in immune-related structural regions vs. non-structural regions, and forces driving the evolution of EV71, are still not clear. Results We sequenced four genomic segments, i.e., the 5' untranslated region (UTR, VP1, 2A, and 3C, of 395 EV71 viral strains collected from 1998 to 2003 in Taiwan. The phylogenies derived from different genomic segments revealed different relationships, indicating frequent sequence recombinations as previously noted. In addition to simple recombinations, exchanges of the P1 domain between different species/genotypes of human enterovirus species (HEV-A were repeatedly observed. Contrasting patterns of polymorphisms and divergences were found between structural (VP1 and non-structural segments (2A and 3C, i.e., the former was less polymorphic within an outbreak but more divergent between different HEV-A species than the latter two. Our computer simulation demonstrated a significant excess of amino acid replacements in the VP1 region implying its possible role in adaptive evolution. Between different epidemic seasons, we observed high viral diversity in the epidemic peaks followed by severe reductions in diversity. Viruses sampled in successive epidemic seasons were not sister to each other, indicating that the annual outbreaks of EV71 were due to genetically distinct lineages. Conclusions Based on observations of accelerated amino acid changes and frequent exchanges of the P1 domain, we propose that positive selection and subsequent frequent domain shuffling are two important mechanisms

  1. Modeling and 2-D discrete simulation of dislocation dynamics for plastic deformation of metal

    Liu, Juan; Cui, Zhenshan; Ou, Hengan; Ruan, Liqun

    2013-05-01

    Two methods are employed in this paper to investigate the dislocation evolution during plastic deformation of metal. One method is dislocation dynamic simulation of two-dimensional discrete dislocation dynamics (2D-DDD), and the other is dislocation dynamics modeling by means of nonlinear analysis. As screw dislocation is prone to disappear by cross-slip, only edge dislocation is taken into account in simulation. First, an approach of 2D-DDD is used to graphically simulate and exhibit the collective motion of a large number of discrete dislocations. In the beginning, initial grains are generated in the simulation cells according to the mechanism of grain growth and the initial dislocation is randomly distributed in grains and relaxed under the internal stress. During the simulation process, the externally imposed stress, the long range stress contribution of all dislocations and the short range stress caused by the grain boundaries are calculated. Under the action of these forces, dislocations begin to glide, climb, multiply, annihilate and react with each other. Besides, thermal activation process is included. Through the simulation, the distribution of dislocation and the stress-strain curves can be obtained. On the other hand, based on the classic dislocation theory, the variation of the dislocation density with time is described by nonlinear differential equations. Finite difference method (FDM) is used to solve the built differential equations. The dislocation evolution at a constant strain rate is taken as an example to verify the rationality of the model.

  2. CYP2D6基因与药物代谢%CYP2D6 gene and drug metabolism

    施安国

    2003-01-01

    细胞色素P-450(CYP)中的CYP2D6酶在抗抑郁药、安定药及某些抗心律失常药的代谢中起重要作用,CYP2D6基因位于22号常染色体上为隐性遗传,CYP2D6基因呈多态性约有70余种等位基因变异型,也存在特异人群差别,因而导致所编码的酶活性不同,这些数据有助于理解药物代谢的个体差异、有助于预测药物之间的相互作用.

  3. Influence of Isotope Effects on Product Polarizations of N(2D)+D2,N(2D)+H2 and N(2D)+HD Reactive Systems

    NIE Shan-shan; CHU Tian-shu

    2012-01-01

    To figure out the influence of isotope effect on product polarizations of the N(2D)+D2 reactive system and its isotope variants,quasi-classical trajectory(QCT) calculation was performed on Ho's potential energy surfacc(PES) of 2A" state.Product polarizations such as product distributions ofP(θr),P(φr) and P(θr,φr),as well as the generalized polarization-dependent differential cross sections(PDDCSs) were discussed and compared in detail among the four product channels of the title reactions.Both the intermolecular and intramolecular isotope effects were proved to be influential on product polarizations.

  4. 2D NMR barcoding and differential analysis of complex mixtures for chemical identification: the Actaea triterpenes.

    Qiu, Feng; McAlpine, James B; Lankin, David C; Burton, Ian; Karakach, Tobias; Chen, Shao-Nong; Pauli, Guido F

    2014-04-15

    The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ-δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652

  5. Creation of a scalar potential in 2D dilaton gravity

    Behrndt, K.

    1994-01-01

    We investigate quantum corrections of the 2-d dilaton gravity near the singularity. Our motivation comes from a s-wave reduced cosmological solution which is classically singular in the scalar fields (dilaton and moduli). As result we find, that the singularity disappears and a dilaton/moduli potential is created.

  6. ELLIPT2D: A Flexible Finite Element Code Written Python

    The use of the Python scripting language for scientific applications and in particular to solve partial differential equations is explored. It is shown that Python's rich data structure and object-oriented features can be exploited to write programs that are not only significantly more concise than their counter parts written in Fortran, C or C++, but are also numerically efficient. To illustrate this, a two-dimensional finite element code (ELLIPT2D) has been written. ELLIPT2D provides a flexible and easy-to-use framework for solving a large class of second-order elliptic problems. The program allows for structured or unstructured meshes. All functions defining the elliptic operator are user supplied and so are the boundary conditions, which can be of Dirichlet, Neumann or Robbins type. ELLIPT2D makes extensive use of dictionaries (hash tables) as a way to represent sparse matrices.Other key features of the Python language that have been widely used include: operator over loading, error handling, array slicing, and the Tkinter module for building graphical use interfaces. As an example of the utility of ELLIPT2D, a nonlinear solution of the Grad-Shafranov equation is computed using a Newton iterative scheme. A second application focuses on a solution of the toroidal Laplace equation coupled to a magnetohydrodynamic stability code, a problem arising in the context of magnetic fusion research

  7. Wilson loop in 2d noncommutative gauge theories

    Valtancoli, Paolo

    2009-01-01

    We reconsider the perturbative expansion of the Wilson loop in 2d noncommutative gauge theories, using an improved integration method. For the class of maximally crossed diagrams in the $\\theta \\to \\infty$ limit we find an intriguing formula, easily generalizable to all orders in perturbation theory.

  8. 2D fluid simulations of interchange turbulence with ion dynamics

    Nielsen, Anders Henry; Madsen, Jens; Xu, G. S.;

    2013-01-01

    In this paper we present a first principle global two-dimensional fluid model. The HESEL (Hot Edge SOL Electrostatic) model is a 2D numerical fluid code, based on interchange dynamics and includes besides electron also the ion pressure dynamic. In the limit of cold ions the model almost reduces to...

  9. The 2dF Galaxy Redshift Survey: Preliminary Results

    Maddox, S.

    1997-01-01

    Spectroscopic observations for a new survey of 250 000 galaxy redshifts are underway, using the 2dF instrument at the AAT. The input galaxy catalogue and commissioning data are described. The first result from the preliminary data is a new estimate of the galaxy luminosity function at =0.1.

  10. H on He: sticking and 2d-superfluidity

    The sticking coefficient, which governs the sticking time τs, is discussed for high surface-coverage conditions. We point out that τs must remain large compared to a characteristic vortex diffusion time, if the system is to display 2d-superfluidity

  11. Lattice simulation of 2d Gross-Neveu-type models

    Full text: We discuss a Monte Carlo simulation of 2d Gross-Neveu-type models on the lattice. The four-Fermi interaction is written as a Gaussian integral with an auxiliary field and the fermion determinant is included by reweighting. We present results for bulk quantities and correlators and compare them to a simulation using a fermion-loop representation. (author)

  12. The toroidal Hausdorff dimension of 2d Euclidean quantum gravity

    Ambjorn, Jan; Budd, Timothy George

    2013-01-01

    The lengths of shortest non-contractible loops are studied numerically in 2d Euclidean quantum gravity on a torus coupled to conformal field theories with central charge less than one. We find that the distribution of these geodesic lengths displays a scaling in agreement with a Hausdorff dimension...

  13. Resolution deconvolution method applied to 2D-ACAR measurements

    An inexpensive way to achieve high resolution 2D-ACAR measurements is to utilize resolution deconvolution techniques. We developed a resolution deconvolution method which avoids noise amplification and is applicable to the 3D reconstruction method using Fourier-Bessel transforms. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  14. Validation of minor species of the MIPAS2D database

    Enzo Papandrea; Stefano Casadio; Enrico Arnone; Massimo Carlotti; Elisa Castelli; Marta De Laurentis; Bianca Maria Dinelli

    2014-01-01

    The MIPAS2D [Dinelli et al., 2010] database has been developed applying the tomographic analysis technique GMTR [Carlotti et al., 2001] to measurements acquired in the nominal observation mode of the complete MIPAS (Michelson Interferometer for Passive Atmosphere Sounding) [Fischer et al., 2008] mission. […

  15. Validation of minor species of the MIPAS2D database

    Enzo Papandrea

    2014-01-01

    Full Text Available The MIPAS2D [Dinelli et al., 2010] database has been developed applying the tomographic analysis technique GMTR [Carlotti et al., 2001] to measurements acquired in the nominal observation mode of the complete MIPAS (Michelson Interferometer for Passive Atmosphere Sounding [Fischer et al., 2008] mission. […

  16. High resolution 2D image upconversion of incoherent light

    Dam, Jeppe Seidelin; Pedersen, Christian; Tidemand-Lichtenberg, Peter

    2011-01-01

    An optimized method for continuous wave 2-dimensional (2-D) upconversion of incoherent or thermal light is demonstrated and quantified. Using standard resolution targets a resolution of 200×1000 pixels is obtained. The suggested method is viewed in scope of modern CCD cameras operating in the near...

  17. On the phase diagram of 2d Lorentzian Quantum Gravity

    Ambjørn, Jan; Anagnostopoulos, K. N.; Loll, R.

    The phase diagram of 2d Lorentzian quantum gravity (LQG) coupled to conformal matter is studied. A phase transition is observed at c = c crit ( {1}/{2} < c crit < 4) which can be thought of as the analogue of the c = 1 barrier of Euclidean quantum gravity (EQG). The non-trivial properties of the quantum geometry are discussed.

  18. 2D kinematics of simulated disc merger remnants

    Jesseit, Roland; Naab, Thorsten; Peletier, Reynier F.; Burkert, Andreas

    2007-01-01

    We present a 2D kinematic analysis for a sample of simulated binary disc merger remnants with mass ratios 1:1 and 3:1. For the progenitor discs we used pure stellar models as well as models with 10 per cent of their mass in gas. A multitude of phenomena also observed in real galaxies are found in th

  19. On the sensitivity of the 2D electromagnetic invisibility cloak

    A computational study of the sensitivity of the two dimensional (2D) electromagnetic invisibility cloaks is performed with the finite element method. A circular metallic object is covered with the cloak and the effects of absorption, gain and disorder are examined. Also the effect of covering the cloak with a thin dielectric layer is studied.

  20. On the sensitivity of the 2D electromagnetic invisibility cloak

    Kaproulias, S. [Department of Physics, University of Patras, 26504 Patras (Greece); Sigalas, M.M., E-mail: sigalas@upatras.gr [Department of Materials Science, University of Patras, 26504 Patras (Greece)

    2012-10-15

    A computational study of the sensitivity of the two dimensional (2D) electromagnetic invisibility cloaks is performed with the finite element method. A circular metallic object is covered with the cloak and the effects of absorption, gain and disorder are examined. Also the effect of covering the cloak with a thin dielectric layer is studied.