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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. 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.

  12. 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

  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. 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.

  10. 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.

  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. 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...

  14. 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...

  15. 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...

  16. 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

  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. 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

  19. 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.

  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

    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.

  9. 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.

  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

    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

    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.

  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. 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

  4. 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.

  5. 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

  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

    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)

  10. 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.

  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. 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

  20. 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.

  1. 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.

  2. 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 ...

  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. 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.

  5. 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

  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. 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

  9. 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.

  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. 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

  12. 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.

  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. 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

  17. 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

  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. [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

  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. 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...

  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. 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...

  18. 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

  19. 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.

  20. 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.

  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. 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

  4. 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

  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. 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 ...

  10. 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

  11. 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.

  12. 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

  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. 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...

  17. 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...

  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

    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.

  3. 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.

  4. 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_...

  5. 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...

  6. 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.

  7. 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.

  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. 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)

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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...

  15. 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.

  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. 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.

  3. 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.

  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. 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.

  10. 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

  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. 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.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.)

  20. 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

  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. 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.

  5. 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.

  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. 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

  8. 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

  9. 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.

  10. 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