Elementary Patterns Research Articles

Analysis of Metabolic Subnetworks by Flux Cone Projection

BackgroundAnalysis of elementary modes (EMs) is proven to be a powerful constraint-based method in the study of metabolic networks. However, enumeration of EMs is a hard computational task. Additionally, due to their large number, EMs cannot be simply used as an input for subsequent analysis. One possibility is to limit the analysis to a subset of interesting reactions. However, analysing an isolated subnetwork can result in finding incorrect EMs which are not part of any steady-state flux distribution of the original network. The ideal set to describe the reaction activity in a subnetwork would be the set of all EMs projected to the reactions of interest. Recently, the concept of "elementary flux patterns" (EFPs) has been proposed. Each EFP is a subset of the support (i.e., non-zero elements) of at least one EM.ResultsWe introduce the concept of ProCEMs (Projected Cone Elementary Modes). The ProCEM set can be computed by projecting the flux cone onto a lower-dimensional subspace and enumerating the extreme rays of the projected cone. In contrast to EFPs, ProCEMs are not merely a set of reactions, but projected EMs. We additionally prove that the set of EFPs is included in the set of ProCEM supports. Finally, ProCEMs and EFPs are compared for studying substructures of biological networks.ConclusionsWe introduce the concept of ProCEMs and recommend its use for the analysis of substructures of metabolic networks for which the set of EMs cannot be computed.

Normal forms for elementary patterns

AbstractA notation for an ordinal using patterns of resemblance is based on choosing an isominimal set of ordinals containing the given ordinal. There are many choices for this set meaning that notations are far from unique. We establish that among all such isominimal sets there is one which is smallest under inclusion thus providing an appropriate notion of normal form notation in this context. In addition, we calculate the elements of this isominimal set using standard notations based on collapsing functions. This provides a capstone to the results in [2, 6, 8, 9, 7], using further refinement of ordinal arithmetic developed in [8] which then both allows for a simple characterization of normal forms for patterns of order one and will play a key role in the arithmetical analysis of pure patterns of order two, [5].

Development and mechanical characterization of porous titanium bone substitutes

Commercially Pure Porous Titanium (CPPTi) can be used for surgical implants to avoid the stress shielding effect due to the mismatch between the mechanical properties of titanium and bone. Most researchers in this area deal with randomly distributed pores or simple architectures in titanium alloys. The control of porosity, pore size and distribution is necessary to obtain implants with mechanical properties close to those of bone and to ensure their osseointegration. The aim of the present work was therefore to develop and characterize such a specific porous structure. First of all, the properties of titanium made by Selective Laser Melting (SLM) were characterized through experimental testing on bulk specimens. An elementary pattern of the porous structure was then designed to mimic the orthotropic properties of the human bone following several mechanical and geometrical criteria. Finite Element Analysis (FEA) was used to optimize the pattern. A porosity of 53% and pore sizes in the range of 860 to 1500 μm were finally adopted. Tensile tests on porous samples were then carried out to validate the properties obtained numerically and identify the failure modes of the samples. Finally, FE elastoplastic analyses were performed on the porous samples in order to propose a failure criterion for the design of porous substitutes.

Elementary visual hallucinations and their relationships to neural pattern-forming mechanisms.

An extraordinary variety of experimental (e.g., flicker, magnetic fields) and clinical (epilepsy, migraine) conditions give rise to a surprisingly common set of elementary hallucinations, including spots, geometric patterns, and jagged lines, some of which also have color, depth, motion, and texture. Many of these simple hallucinations fall into a small number of perceptual geometries-the Klüver forms-that (via a nonlinear mapping from retina to cortex) correspond to even simpler sets of oriented stripes of cortical activity (and their superpositions). Other simple hallucinations (phosphenes and fortification auras) are linked to the Klüver forms and to pattern-forming cortical mechanisms by their spatial and temporal scales. The Klüver cortical activity patterns are examples of self-organized pattern formation that arise from nonlinear dynamic interactions between excitatory and inhibitory cortical neurons; with reasonable modifications, this model accounts for a wide range of hallucinated patterns. The Klüver cortical activity patterns are a subset of autonomous spatiotemporal cortical patterns, some of which have been studied with functional imaging techniques. Understanding the interaction of these intrinsic patterns with stimulus-driven cortical activity is an important problem in neuroscience. In line with this, hallucinatory pattern formation interacts with physical stimuli, and many conditions that induce hallucinations show interesting interactions with one another. Both types of interactions are predictable from neural and psychophysical principles such as localized processing, excitatory-inhibitory neural circuits, lateral inhibition, simultaneous and sequential contrast, saccadic suppression, and perceptual opponency. Elementary hallucinations arise from familiar mechanisms stimulated in unusual ways.

Expressing Adaptation Strategies Using Adaptation Patterns

Today, there is a real challenge to enable personalized access to information. Several systems have been proposed to address this challenge including Adaptive Hypermedia Systems (AHSs). However, the specification of adaptation strategies remains a difficult task for creators of such systems. In this paper, we consider the problem of the definition of adaptation strategies at a high level. We present two main contributions: a typology of elementary adaptation patterns for the adaptive navigation; and a process to generate adaptation strategies based on the use and the semiautomatic combination of patterns. We also describe how the generated adaptation strategies can be integrated into existing AHSs. A prototype has been implemented and an experiment in the e-learning domain has been conducted with a group of volunteers. This experiment shows that our pattern-based approach for defining adaptation strategies is more suitable than those based on “traditional” AH languages.

Geriatric Elementary-Type Acetabulum Fractures: Open Reduction and Internal Fixation Techniques

Geriatric acetabulum fractures commonly occur because of low-energy falls. The decision-making and treatment strategies can be difficult independent of the fracture pattern. Elementary fracture patterns in the elderly are more commonly treated with open reduction and internal fixation versus acute total hip arthroplasty. Osteopenia further challenges surgeons' ability to obtain and maintain the reduction of these fractures. We present techniques regarding open reduction and internal fixation of elementary type acetabulum fractures in the elderly/geriatric population.

Defect generation during silicon oxidation: A Kinetic Monte Carlo study

We present a synthetic review of elementary chemical mechanisms source of the oxidation of pure silicon (100) surfaces. These mechanisms are then discussed from their ability to build a mesoscale model of the Kinetic Monte Carlo type dedicated to the process simulation of silicon thermal oxidation. We show that oxidation is driven by two main processes: (i) charge transfer arising from the formation of SiO bonds in contact to pure silicon at the interface, (ii) destructive oxidation in which SiO building blocks rearrange at the interface to form a hexagonal-based oxide network directly in contact to cubic Si layers. Based on these considerations, simulations at the process scale exhibit epitaxial behavior within the interfacial domain. The resulting oxide layers are analyzed in terms of local to more extended defects. We observe two types of defects: (i) “intra-domain defects” which are related to local distortion of the elementary hexagonal oxide pattern Si6O6 (ii) “inter-domain defects”, which are related to global oxide structural transitions from one orientation to another.

Signal synthesis by means of evolutionary algorithms

In this article, we investigate a procedure for generating signals with genetic algorithms. Signals are obtained from elementary patterns characterized by different degrees of freedom. These patterns are repeated and combined in order to reach specific signal shapes. The whole signal parametrization has to be determined by solving a difficult inverse problem of high dimensionality and strong multimodality. This can be carried out using evolutionary algorithms with the aim of finding all pattern configurations in the signal. The different signal synthesis schemes are evaluated, tested and applied to the generation of particular railway driving profiles.

On the Array Performance of Printed, Ultra-Wideband “Eared” Antennas

The performance of an ultra-wideband (UWB) radiator is examined in a 15-element linear-array environment. The numerically predicted array impedance is validated by means of physical measurements. The broadside scanned radiation patterns of the array are measured and proven to be extremely favorable. A zoom-in on the measured elementary radiation patterns is employed for evidencing the effect of embedding the radiator in an array environment. The study is rounded off by a post-processing phase, in which the measured array radiation pattern results are employed for predicting the array's scanning performance.

Tracking chains of [formula omitted]-elementarity

We apply the ordinal arithmetical tools that were developed in Wilken (2007) [10] and Carlson and Wilken (in press) [4] in order to introduce tracking chains as the crucial means in the arithmetical analysis of (pure) elementary patterns of resemblance of order 2; see Carlson (2001) [2], Carlson (2009) [3], and Carlson and Wilken (in preparation) [5]. Although underlying heuristics for an analysis of Σ 2 -elementarity within the structure R 2 is given in [5], this article is independent of [5] and provides a complete arithmetical analysis of the structure R 2 below the least ordinal α such that any pure pattern of order 2 has a covering below α . α is shown to be the proof-theoretic ordinal of KP ℓ 0 .

Dynamics of topological defects in a two-dimensional magnetic domain stripe pattern

Two-dimensional magnetic films with perpendicular magnetization spontaneously form magnetic domain patterns that evolve or undergo symmetry transformations as a function of temperature. When the system is driven from equilibrium by a rapid change in temperature, topological pattern defects are the elementary pattern excitations that affect this evolution. An elastic continuum model is adapted to describe how a metastable population of topological defects alters the domain density and the magnetic susceptibility of the ``stripe'' magnetic domain pattern. Temporal changes in the susceptibility are interpreted using a dynamical equation describing the defect population. Recent experiments provide a quantitative verification of the model, and illustrate the use of the magnetic susceptibility to follow the population dynamics of topological defects in this system, and its potential role in investigating a pattern melting phase transition.

Petri net based Grid workflow verification and optimization

Graphical workflow modeling tools, such as UML and DAG, can facilitate users to express workflow process logic, but lack of abilities to carry out simulation and correctness checking. In this paper, based on Petri net, we propose a service composition oriented Grid workflow model and its related six elementary workflow patterns: sequence, condition, iteration, concurrency, synchronization, and triggering. In addition, we present our Grid workflow analysis approaches on three aspects: workflow reachability verification, workflow deadlock verification, and workflow optimization. The experimental results show that our workflow verification and optimization mechanisms are feasible and efficient.

The H-microdirectional model: Accounting for a mesoscopic scale

Solving boundary value problems requires implementation of sufficiently robust constitutive models. Most models try to incorporate a great deal of phenomenological ingredients, but this refining often leads to overcomplicated formulations, requiring a large number of parameters to be identified. A powerful alternative can be found with micromechanical models, where the medium is described as a distribution of elementary sets of grains. The complexity is not related to the constitutive description, but to the multiplicity of contacts oriented along all the directions of the physical space. This paper proposes an advanced micromechanical model that introduces an intermediate scale (mesoscopic scale): elementary hexagonal patterns of adjoining particles. This is advantageous with respect to current micromechanical models that generally describe the material through a single distribution of contacts. This new approach makes it possible to take many constitutive properties into account in a very natural way, such as the occurrence of diffuse failure modes. These preliminary results are presented in order to give clear insights into the capability of such multiscale approaches.

Evidence of convective instability in congested traffic flow: A systematic empirical and theoretical investigation

An extended open system such as traffic flow is said to be convectively unstable if perturbations of the stationary state grow but propagate in only one direction, so they eventually leave the system. By means of data analysis, simulations, and analytical calculations, we give evidence that this concept is relevant for instabilities of congested traffic flow. We analyze detector data from several hundred traffic jams and propose estimates for the linear growth rate, the wavelength, the propagation velocity, and the severity of the associated bottleneck that can be evaluated semi-automatically. Scatter plots of these quantities reveal systematic dependencies. On the theoretical side, we derive, for a wide class of microscopic and macroscopic traffic models, analytical criteria for convective and absolute linear instabilities. Based on the relative positions of the stability limits in the fundamental diagram, we divide these models into five stability classes which uniquely determine the set of possible elementary spatiotemporal patterns in open systems with a bottleneck. Only two classes, both dominated by convective instabilities, are compatible with observations. By means of approximate solutions of convectively unstable systems with sustained localized noise, we show that the observed spatiotemporal phenomena can also be described analytically. The parameters of the analytical expressions can be inferred from observations, and also (analytically) derived from the model equations.

The evolution of Venus: Present state of knowledge and future exploration

A detailed characterization of the formation and evolution of Venus is a key link to the study of terrestrial planets, and to their divergent evolutions. While Earth and to a lesser extent Mars (thanks to the analysis of SNC meteorites) are extensively studied in a comparative planetology context, the history of the most Earth-like planet of the Solar System, Venus, is still poorly understood. For how long has Venus been in its current extreme climate state? When and how did it diverge from a (possible) early Earth-like state? Has Venus been a potentially habitable planet at some time of its early history? Did a “cool early Venus” stage occur between the end of accretion and the late heavy bombardment, like suspected for Earth? What are the implications of the Venus/Earth comparison for the nature and evolution of habitable terrestrial planets throughout the universe? A major observational missing link in our understanding of Venus' climate evolution is the elementary and isotopic pattern of noble gases and of stable isotopes in Venus' atmosphere, still poorly known. The concentrations of heavy noble gases (Kr, Xe) and their isotopes are mostly unknown, and our knowledge of light noble gases and stable isotopes is incomplete and inaccurate. In this paper, we summarize our present understanding of Venus' early evolution, including the crucial question of knowing if water ever condensed at the surface of the planet. Then, we assess the potential contribution of a precise measurement of noble gases, their isotopes and stable isotopes to improve of our understanding of Venus evolution, and list the main questions that noble gases and isotope measurements would help to answer. Finally, we show how future exploration of Venus could allow to gain a glimpse into the early evolution of Venus through a small in-situ mission based on a single balloon probe, called EVE (European Venus Explorer), proposed in the frame of the ESA Cosmic Vision program.

SPECKLE SUPPRESSION BY INTEGRATED SUM OF FULLY DEVELOPED NEGATIVELY CORRELATED PATTERNS IN COHERENT IMAGING

A coherent imaging system images a frame or an object onto a changing difiuser and projects the resulting pattern which generally contains speckles. Using a spatial light modulator (SLM) as the changing difiuser, the speckles in the pattern are suppressed without the need for any other mechanisms. With M random phasor arrays being displayed in the SLM during the integration time of a detector, a suppression factor (Cf) of speckles, 1= p M, is achievable in the projected pattern, which is the sum of the intensity of M uncorrelated patterns. This paper shows both theoretically and in simulations that the Cf of the sum pattern was considerably reduced when two elementary patterns with fully developed speckles were negatively correlated. With the correlation coe-cients of the elementary patterns found at (i0:3, i0:25), the Cf of the sum of 10negatively-correlated speckle patterns was 48% lower than the Cf of the sum of 10uncorrelated speckle patterns. The negatively correlated patterns can be implemented using spatial light modulators or difiractive optical elements, and are used to suppress speckle noise in digital holography, laser projection display, and holographic display projections with relatively high e-ciency.

Evidence of Convective Instability in Congested Traffic Flow: A Systematic Empirical and Theoretical Investigation

An extended open system such as traffic flow is said to be convectively unstable if perturbations of the stationary state grow but propagate in only one direction, so they eventually leave the system. By means of data analysis, simulations, and analytical calculations, we give evidence that this concept is relevant for instabilities of congested traffic flow. We analyze detector data from several hundred traffic jams and propose estimates for the linear growth rate, the wavelength, the propagation velocity, and the severity of the associated bottleneck that can be evaluated semi-automatically. Scatter plots of these quantities reveal systematic dependencies. On the theoretical side, we derive, for a wide class of microscopic and macroscopic traffic models, analytical criteria for convective and absolute linear instabilities. Based on the relative positions of the stability limits in the fundamental diagram, we divide these models into five stability classes which uniquely determine the set of possible elementary spatiotemporal patterns in open systems with a bottleneck. Only two classes, both dominated by convective instabilities, are compatible with observations. By means of approximate solutions of convectively unstable systems with sustained localized noise, we show that the observed spatiotemporal phenomena can also be described analytically. The parameters of the analytical expressions can be inferred from observations, and also (analytically) derived from the model equations.

Human Processing of Short Temporal Intervals as Revealed by an ERP Waveform Analysis

To clarify the time course over which the human brain processes information about durations up to ∼300 ms, we reanalyzed the data that were previously reported by Mitsudo et al. (2009) using a multivariate analysis method. Event-related potentials were recorded from 19 scalp electrodes on 11 (nine original and two additional) participants while they judged whether two neighboring empty time intervals – called t1 and t2 and marked by three tone bursts – had equal durations. There was also a control condition in which the participants were presented the same temporal patterns but without a judgment task. In the present reanalysis, we sought to visualize how the temporal patterns were represented in the brain over time. A correlation matrix across channels was calculated for each temporal pattern. Geometric separations between the correlation matrices were calculated, and subjected to multidimensional scaling. We performed such analyses for a moving 100-ms time window after the t1 presentations. In the windows centered at <100 ms after the t2 presentation, the analyses revealed the local maxima of categorical separation between temporal patterns of perceptually equal durations versus perceptually unequal durations, both in the judgment condition and in the control condition. Such categorization of the temporal patterns was prominent only in narrow temporal regions. The analysis indicated that the participants determined whether the two neighboring time intervals were of equal duration mostly within 100 ms after the presentation of the temporal patterns. A very fast brain activity was related to the perception of elementary temporal patterns without explicit judgments. This is consistent with the findings of Mitsudo et al. and it is in line with the processing time hypothesis proposed by Nakajima et al. (2004). The validity of the correlation matrix analyses turned out to be an effective tool to grasp the overall responses of the brain to temporal patterns.

PENGARUH DOSIS DAN CARA PENEMPATAN PUPUK NPK TERHADAP TERTUMBUHAN DAN HASIL JAGUNG HIBRIDA ( Zea mays. L ) INFLUENCE OF DOSAGE AND WAY OF LOCATION OF MANURE OF NPK TO GROWTH AND RESULT MAIZE OF HIBRIDA ( Zea mays. L )

Research is done in countryside of Kedokan Sayang of District Of Tarub Sub Province Tegal, with height of place + 25 m above sea surface at land ground type of alluvial. Research is done from 16 Februari 2008 until 8 June 2008, using factorial method with elementary pattern of RCBD (Randomized Completely Block Design) consist of 2 treatment factor that is : (1) Dose Fertilize NPK (D0 = without manure) (D1 = 150 kg/ha) (D2 = 300 kg / ha) (D3 = 450 kg/ha). (2) Way of location of manure ( C1 = disseminated) (C2 = Disseminated and countersinked) (C3 = make off with). Result of research show = (1) treatment of dose fertilize NPK have very significant at all of parameter that is is : High [of] crop, amount of leaf, heavy all is wet weight overall of crop, heavy run dry weight overall of crop, long cob, amount of seed of per cob, amount of making off with per cob, heavy dry minner per plant, heavy of dry minner of per check and heavy 100 seed. Heavy highest per check minner reached at dose 450 kg/ha that is 6,147 and low without manure that is 2,393 kg (2) treatment of location of manure show very significant at wet heavy parameter of overall of crop, heavy run dry weight overall of crop, and seed amount of per cob. While to amount make off with per cob give significant. weight of minner dry of highest per check reached at way of location of manure by disseminated and countersinked by that is 4,982 kgs, lowest by disseminated that is 4,730 kgs. (3) interaction among dose fertilize NPK by location of manure have very significant at parameter of is amount of leaf, wet heavy of overall of crop, heavy run dry weight overall of crop, long of cob, amount of seed of per cob and heavy 100 seed. While to amount make off with per cob give significant. (4) weight of minner highest drought of per check reached at combination of fertilizer dose NPK 450 kg/ha by the way of fertilisers placement disseminated and countersinked, that is 6,260 kgs ( 11128,819 kg/ha). While low at combination without fertilizer by the way of its(the fertilisers placement disseminated that is 2,120 kgs ( 3768,865 kg/ha).

Simple waves for two-dimensional compressible pseudo-steady Euler system

A simple wave is defined as a flow in a region whose image is a curve in the phase space. It is well known that “the theory of simple waves is fundamental in building up the solutions of flow problems out of elementary flow pattern” see Courant and Friedrichs’s chassical book “Supersonic Flow and Shock Waves”. This paper mainly concerned with the geometric construction of simple waves for the 2D pseudo-steady compressible Euler system. Based on the geometric interpretation, the expansion or compression simple wave flow construction around a pseudo-stream line with a bend part are constructed. It is a building block that appears in the global solution to four contact discontinuities Riemann problems.