Search

The modeling of the dynamics of interaction between ERK and STAT signaling pathways in the cell needs to establish the biochemical diagram of the corresponding proteins interactions as well as the corresponding reaction-diffusion scheme. Starting from the verbal description available in the literature of the cross talk between the two pathways, a simple diagram of interaction between ERK and STAT5a proteins is chosen to write corresponding kinetic equations. The dynamics of interaction is modeled in a form of two-dimensional nonlinear dynamical system for ERK--and STAT5a--protein concentrations. Then the spatial modeling of the interaction is accomplished by introducing an appropriate diffusion-reaction scheme. The obtained system of partial differential equations is analyzed and it is argued that the possibility of Turing bifurcation is presented by loss of stability of the homogeneous steady state and forms dissipative structures in the ERK and STAT interaction process. In these terms, a possible scaffolding effect in the protein interaction is related to the process of stabilization and destabilization of the dissipative structures (pattern formation) inherent to the model of ERK and STAT cross talk.

Abell, Felin and Foss argue that “macro-explanations” in strategic management, explanations in which organizational routines figure prominently and in which both the explanandum and explanans are at the macro-level, are necessarily incomplete. They take a diagram (which has the form of a trapezoid) from Coleman, Foundations of Social Theory, The Belknap Press of Harvard University Press, Cambridge (Mass.)/London, (1990) to task to show that causal chains connecting two macro-phenomena always involve “macro-to-micro” and “micro-to-macro” links, links that macro-explanations allegedly fail to recognize. Their plea for micro-foundations in strategic management is meant to shed light on these “missing links”. The paper argues that while there are good reasons for providing micro-foundations, Abell, Felin and Foss’s causal incompleteness argument is not one of them. Their argument does not sufficiently distinguish between causal and constitutive relations. Once these relations are carefully distinguished, it follows that Coleman’s diagram has to be squared. This in turn allows us to see that macro-explanations need not be incomplete.

This article thoroughly reviews the state-of-the-art methods for setting ALARP upper border as a straight line in logarithmic graph, which is the common practice in the risk assessments of nuclear, chemical plants and maritime facilities. It also reviews methods for setting ALARP upper border based on economic importance of a considered ship type. As a result, inconsistency related to ALARP upper border has been identified and new methods to resolve such inconsistency are developed. Here, firstly a method for approximating FN diagrams of existing major ship types is proposed and it is applied to ship types which consist of ships above 100 gross tonnage. After that the approximated FN diagrams were checked by goodness-of-fit test by 5 % significance level, and it was validated that those approximated FN diagrams well express corresponding FN diagrams made from IHSF casualty and ship databases. This method can extrapolate FN diagrams made from those databases to the area of severer accidents with more fatalities, which have not been occurred yet, rationally. Secondly, problems that accompany with an existing method for setting ALARP upper border are discussed and methods for resolving the problems using the approximated FN diagrams are proposed. The methods can set ALARP upper border keeping consistency of ALARP upper border between individual risk and FN diagram. Lastly, the new method for safety analysis of ships using approximated FN diagrams of major ship types is introduced. The method is used in order to find ships’ groups which should be considered preferentially. The method for approximating FN diagrams and the method for setting ALARP upper border proposed here is so general that they can be applied to risk analysis of the fields which have a lot of accident records like maritime field, such as aviation or automotive fields.

This short note classifies the interactions between different objects in the solar system and their environments with the solar wind or magnetospheric plasma. The classification is performed using a simple but physically justified M-B diagram, where M is the total mass of the neutral gas around the object and B is the magnetic field (either intrinsic or external) at the object. The solar system objects form groups within the diagram that correspond to the following general classes: magnetospheres, mini-magnetospheres, induced magnetospheres, cometary and Moon-like interactions. The Martian magnetic anomalies are unique objects. We also identify a class termed as combined magnetospheres, which does not contain any objects that meet the present conditions.

Bipartite on-shell diagrams are the latest tool in constructing scattering amplitudes. In this paper we prove that a Britto-Cachazo-Feng-Witten (BCFW)-decomposable on-shell diagram process a rational top-form if and only if the algebraic ideal comprised of the geometrical constraints is shifted linearly during successive BCFW integrations. With a proper geometric interpretation of the constraints in the Grassmannian manifold, the rational top-form integration contours can thus be obtained, and understood, in a straightforward way. All rational top-form integrands of arbitrary higher loops leading singularities can therefore be derived recursively, as long as the corresponding on-shell diagram is BCFW-decomposable., Comment: 13 pages with 12 figures; final version appeared in Eur.Phys.J. C77 (2017) no.2, 80

Background Statisticians investigate new methods in simulations to evaluate their properties for future real data applications. Results are often presented in a number of figures, e.g., Trellis plots. We had conducted a simulation study on six statistical methods for estimating the treatment effect in binary outcome meta-analyses, where selection bias (e.g., publication bias) was suspected because of apparent funnel plot asymmetry. We varied five simulation parameters: true treatment effect, extent of selection, event proportion in control group, heterogeneity parameter, and number of studies in meta-analysis. In combination, this yielded a total number of 768 scenarios. To present all results using Trellis plots, 12 figures were needed. Methods Choosing bias as criterion of interest, we present a ‘nested loop plot’, a diagram type that aims to have all simulation results in one plot. The idea was to bring all scenarios into a lexicographical order and arrange them consecutively on the horizontal axis of a plot, whereas the treatment effect estimate is presented on the vertical axis. Results The plot illustrates how parameters simultaneously influenced the estimate. It can be combined with a Trellis plot in a so-called hybrid plot. Nested loop plots may also be applied to other criteria such as the variance of estimation. Conclusion The nested loop plot, similar to a time series graph, summarizes all information about the results of a simulation study with respect to a chosen criterion in one picture and provides a suitable alternative or an addition to Trellis plots. Electronic supplementary material The online version of this article (doi:10.1186/1471-2288-14-129) contains supplementary material, which is available to authorized users.

The supersymmetric contributions to the muon anomalous magnetic moment $a_\mu$ and to the decay $\mu\to e\gamma$ are given by very similar Feynman diagrams. Previous works reported correlations in specific scenarios, in particular if $a_\mu$ is dominated by a single diagram. In this work we give an extensive survey of the possible correlations. We discuss examples of single-diagram domination with particularly strong correlations, and provide corresponding benchmark parameter points. We show how the correlations are weakened by significant cancellations between diagrams in large parts of the MSSM parameter space. Nevertheless, the order of magnitude of $\text{BR}(\mu \to e \gamma)$ for a fixed flavor-violating parameter can often be predicted. We summarize the behavior by plotting the correlations as well as resulting bounds on the flavor-violating parameters under various assumptions on the MSSM spectrum.

The effective diagram technique based on the Schwinger-Dyson equations is constructed for N $$ \mathcal{N} $$ = 1 SQED with N f flavors, regularized by higher derivatives. Using these effective diagrams, it is possible to derive the exact NSVZ relation between the β -function and the anomalous dimension of the matter superfields exactly in all loops, if the renormalization group functions are defined in terms of the bare coupling constant. In particular, we verify that all integrals which give the β -function defined in terms of the bare coupling constant are integrals of double total derivatives and prove some identities relating Green functions.

We report here on the utilization of signal in-phase-quadrature (I-Q) diagrams in a novel modulation classification (MC) technique. This MC technique is able to classify linear digital single-carrier modulations as well as multi-carrier modulations. The method uses the waveforms’ I-Q diagrams and, by employing a combination of k-center and k-means algorithms, determines the type of modulation. Implementation and refinement of the novel single-carrier modulation classification technique using the I-Q diagrams are discussed in detail. Further, a model for classification of multi-carrier signals is presented, including Gaussianity, cyclostationarity, and autocorrelation tests for further extracting orthogonal frequency division multiplexing signal parameters. Finally, results of this method are presented and compared to other classification methods, and the considerations for implementing the method in hardware are briefly discussed. As a future direction of this research, the performance of the algorithm in fading channels is an interesting topic to pursue.

A numerical study on the response of steel beams to fire and explosion is presented in this paper. First, a unified computing model, which can be used to simulate the behaviour of beams under four loading scenarios that involve fire and explosion or impact, is constructed. The proposed technique allows complete transparency of the influence of the various parameters on the structural behaviour. Second, the effects of load level on critical temperature are analyzed for various static and explosion load ratios. Two cases of explosion and fire loading sequences are compared, it is shown that the critical temperature of the beam subjected to fire followed by an explosion is lower than that of the beam subjected to an explosion followed by fire. The influence of temperature on the p–i diagram is investigated, an iso-damage surface is introduced to distinguish safe and unsafe regions. Third, the limiting temperature criteria are further examined. That is, the first and second limiting temperatures can be determined when the dimensional catenary force is equal to zero or to one, which corresponds to the bending or stretching plastic hinge, respectively.

This paper discusses the problem of stability in a milling process for titanium super-alloy Ti6242. The phenomenon of chatter vibration is analysed by the multiscale entropy method and Hurst exponent. Although this problem is often considered based on stability lobe diagrams, theoretical findings do not always agree with experimental results. First, a stability lobe diagram is created based on parameters determined by impact testing. Next, cutting forces are measured in an experiment where the axial cutting depth is gradually increased. Finally, the obtained experimental signals are investigated with respect to stability using the multiscale entropy method and Hurst exponent.

We apply the differential equation technique to the calculation of the one-loop massless diagram with five onshell legs. Using the reduction to $\epsilon$-form, we manage to obtain a simple one-fold integral representation exact in space-time dimensionality. The expansion of the obtained result in $\epsilon$ and the analytical continuation to physical regions are discussed., Comment: 16 pages, 2 figures, v2: minor stylistic corrections, acknowlednments updated

A source-type diagram is a visualization tool used to display earthquake sources, including double-couples, compensated linear vector dipoles, and isotropic deformation. Together with recent observations of non-double-couple events in a variety of tectonic settings, it is important to be able to recognize the source type intuitively from a representative diagram. Since previous works have proposed diagrams created using a range of projections, we review these diagrams in the framework of the moment tensor eigenvalue space. For further applications, we also provide complete formulas for conversion between moment tensor representation and the coordinate system of each diagram style. Using both a global catalog and synthetic data, we discuss differences between types of diagrams and the relative effectiveness of each.

Recently the space of tree level color structures for gluon scattering was determined in arXiv:1403.6837 together with its transformation properties under permutations. Here we generalize the discussion to loops, demonstrating a reduction of an arbitrary color diagram to its vacuum skeleton plus rays. For 1-loop there are no residual relations and we determine the space of color structures both diagrammatically and algebraically in terms of certain sunny diagrams. We present the generating function for the characteristic polynomials and a list of irreducible representations for $3 \le n \le 9$ external legs. Finally we present a new proof for the 1-loop shuffle relations based on the cyclic shuffle and split operations., 12 pages, v2: typo corrected in Table 1

We consider Lorentzian correlators of local operators. In perturbation theory, singularities occur when we can draw a position-space Landau diagram with null lines. In theories with gravity duals, we can also draw Landau diagrams in the bulk. We argue that certain singularities can arise only from bulk diagrams, not from boundary diagrams. As has been previously observed, these singularities are a clear diagnostic of bulk locality. We analyze some properties of these perturbative singularities and discuss their relation to the OPE and the dimensions of double-trace operators. In the exact nonperturbative theory, we expect no singularity at these locations. We prove this statement in 1+1 dimensions by CFT methods., Comment: 60 pages, 12 figures

In understanding upper secondary school students’ interpretations of information in graphical representations of a distance–time graph and an ECG graph, little attention has been paid to the analysis of the condition of the conceptual development related to their utterances. Understanding this better can help improve the teaching of interpretations of information in graphical representations of different situations. This paper integrates results from 2 studies and 3 theoretical perspectives: Tall and Vinner’s theoretical perspectives on learning, Chi’s ontological perspectives on conceptual development and Friel’s theoretical perspectives on interpretation of graphical information. The findings provide evidence to support the conjecture that iconic interpretations could be stimulated and generated as a result of student categorisation of a distance–time graph as an event, when in fact the graph is being used to describe and communicate a process. The outcome further indicates that students found a resemblance between the ECG diagram and the periodic function of f(x) = sin(x).

Background A phylogenetic network is a generalization of phylogenetic trees that allows the representation of conflicting signals or alternative evolutionary histories in a single diagram. There are several methods for constructing these networks. Some of these methods are based on distances among taxa. In practice, the methods which are based on distance perform faster in comparison with other methods. The Neighbor-Net (N-Net) is a distance-based method. The N-Net produces a circular ordering from a distance matrix, then constructs a collection of weighted splits using circular ordering. The SplitsTree which is a program using these weighted splits makes a phylogenetic network. In general, finding an optimal circular ordering is an NP-hard problem. The N-Net is a heuristic algorithm to find the optimal circular ordering which is based on neighbor-joining algorithm. Results In this paper, we present a heuristic algorithm to find an optimal circular ordering based on the Monte-Carlo method, called MC-Net algorithm. In order to show that MC-Net performs better than N-Net, we apply both algorithms on different data sets. Then we draw phylogenetic networks corresponding to outputs of these algorithms using SplitsTree and compare the results. Conclusions We find that the circular ordering produced by the MC-Net is closer to optimal circular ordering than the N-Net. Furthermore, the networks corresponding to outputs of MC-Net made by SplitsTree are simpler than N-Net.

* Correspondence: ryo.sakai@esat.kuleuven.be Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium Full list of author information is available at the end of the article Figure 1 Sakai and Aerts BMC Proceedings 2014, 8(Suppl 2):S10 http://www.biomedcentral.com/1753-6561/8/S2/S10

Background The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences. Although it effectively communicates the amount of information present at every position, this visual representation falls short when the domain task is to compare between two or more sets of aligned sequences. We present a new visual presentation called a Sequence Diversity Diagram and validate our design choices with a case study. Methods Our software was developed using the open-source program called Processing. It loads multiple sequence alignment FASTA files and a configuration file, which can be modified as needed to change the visualization. Results The redesigned figure improves on the visual comparison of two or more sets, and it additionally encodes information on sequential position conservation. In our case study of the adenylate kinase lid domain, the Sequence Diversity Diagram reveals unexpected patterns and new insights, for example the identification of subgroups within the protein subfamily. Our future work will integrate this visual encoding into interactive visualization tools to support higher level data exploration tasks.

Background Visualization of orthogonal (disjoint) or overlapping datasets is a common task in bioinformatics. Few tools exist to automate the generation of extensively-customizable, high-resolution Venn and Euler diagrams in the R statistical environment. To fill this gap we introduce VennDiagram, an R package that enables the automated generation of highly-customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams with up to three sets. Results The VennDiagram package offers the user the ability to customize essentially all aspects of the generated diagrams, including font sizes, label styles and locations, and the overall rotation of the diagram. We have implemented scaled Venn and Euler diagrams, which increase graphical accuracy and visual appeal. Diagrams are generated as high-definition TIFF files, simplifying the process of creating publication-quality figures and easing integration with established analysis pipelines. Conclusions The VennDiagram package allows the creation of high quality Venn and Euler diagrams in the R statistical environment.

Background Microarray experiments generate vast amounts of data. The functional context of differentially expressed genes can be assessed by querying the Gene Ontology (GO) database via GoMiner. Directed acyclic graph representations, which are used to depict GO categories enriched with differentially expressed genes, are difficult to interpret and, depending on the particular analysis, may not be well suited for formulating new hypotheses. Additional graphical methods are therefore needed to augment the GO graphical representation. Results We present an alternative visualization approach, area-proportional Euler diagrams, showing set relationships with semi-quantitative size information in a single diagram to support biological hypothesis formulation. The cardinalities of sets and intersection sets are represented by area-proportional Euler diagrams and their corresponding graphical (circular or polygonal) intersection areas. Optimally proportional representations are obtained using swarm and evolutionary optimization algorithms. Conclusion VennMaster's area-proportional Euler diagrams effectively structure and visualize the results of a GO analysis by indicating to what extent flagged genes are shared by different categories. In addition to reducing the complexity of the output, the visualizations facilitate generation of novel hypotheses from the analysis of seemingly unrelated categories that share differentially expressed genes.

Nous présentons une méthode s'adressant plus particulièrement à des sélectionneurs d'espèces végétales qui veulent modéliser leurs observations dans le cadre des modèles linéaires multivariables à effets aléatoires et fixes. Cette méthode est basée sur une description par un schéma de la généalogie des plantes manipulées dans un protocole de sélection . Nous proposons des règles de construction du schéma et les illustrations sur un exemple. En utilisant une représentation de ce schéma à l'aide d'un graphe orienté, nous donnons une méthode pour construire le modèle statistique pour la valeur génétique des individus et énonçons les règles qui permettent de trouver les variance-covariances entre apparentés., We present a methodology addressed particularly to plant breeders who want to model their data by a linear multivariate mixed model. The first part of this methodology is the description of the genealogy for the plants used in the protocol of selection, by a diagram. We propose the rules for drawing the diagram and give an example. Using an oriented graph related to the diagram we present the second part of the methodology for constructing the statistical model for the individual genetic value and set forth a rule for finding the variance-covariances between related individuals.