Ontology supported comparison in vague domains

It is problematic to use standard ontology tools when describing vague domains. Standard ontologies are designed to formally define one view of a domain, and although it is possible to define disagreeing statements, it is not advisable, as the resulting inferences could be incorrect. Two different solutions to the above problem in two different vague domains have been developed and are presented. The first domain is the knowledge base of conversational agents (chatbots). An ontological scripting language has been designed to access ontology data from within chatbot code. The solution developed is based on reifications of user statements. It enables a new layer of logics based on the different views of the users, enabling the body of knowledge to grow automatically. The second domain is competencies and competency frameworks. An ontological framework has been developed to model different competencies using the emergent standards. It enables comparison of competencies using a mix of linguistic logics and descriptive logics. The comparison results are non-binary, therefore not simple yes and no answers, highlighting the vague nature of the comparisons. The solution has been developed with small ontologies which can be added to and modified in order for the competency user to build a total picture that fits the user’s purpose. Finally these two approaches are viewed in the light of how they could aid future work in vague domains, further work in both domains is described and also in other domains such as the semantic web. This demonstrates two different approaches to achieve inferences using standard ontology tools in vague domains.

Bernoulli free-boundary problems in strip-like domains and a property of permanent waves on water of finite depth

We study weak solutions for a class of free-boundary problems which includes as a special case the classical problem of travelling gravity waves on water of finite depth. We show that such problems are equivalent to problems in fixed domains and study the regularity of their solutions. We also prove that in very general situations the free boundary is necessarily the graph of a function.

A simple method of calculating eigenvalues and resonances in domains with infinite regular ends

A new approach is presented for the solution of spectral problems on infinite domains with regular ends, which avoids the need to solve boundary-value problems for many trial values of the spectral parameter. We present numerical results both for eigenvalues and for resonances, comparing with results reported by Aslanyan, Parnovski and Vassiliev.

Generalised Dirichelt-to-Neumann map in time dependent domains

We study the heat, linear Schrodinger and linear KdV equations in the domain l(t) < x < ∞, 0 < t < T, with prescribed initial and boundary conditions and with l(t) a given differentiable function. For the first two equations, we show that the unknown Neumann or Dirichlet boundary value can be computed as the solution of a linear Volterra integral equation with an explicit weakly singular kernel. This integral equation can be derived from the formal Fourier integral representation of the solution. For the linear KdV equation we show that the two unknown boundary values can be computed as the solution of a system of linear Volterra integral equations with explicit weakly singular kernels. The derivation in this case makes crucial use of analyticity and certain invariance properties in the complex spectral plane. The above Volterra equations are shown to admit a unique solution.

Mapping of domains on HIV envelope protein mediating association with calnexin and protein-disulfide isomerase.

The cell catalysts calnexin (CNX) and protein-disulfide isomerase (PDI) cooperate in establishing the disulfide bonding of the HIV envelope (Env) glycoprotein. Following HIV binding to lymphocytes, cell-surface PDI also reduces Env to induce the fusogenic conformation. We sought to define the contact points between Env and these catalysts to illustrate their potential as therapeutic targets. In lysates of Env-expressing cells, 15% of the gp160 precursor, but not gp120, coprecipitated with CNX, whereas only 0.25% of gp160 and gp120 coprecipitated with PDI. Under in vitro conditions, which mimic the Env/PDI interaction during virus/cell contact, PDI readily associated with Env. The domains of Env interacting in cellulo with CNX or in vitro with PDI were then determined using anti-Env antibodies whose binding site was occluded by CNX or PDI. Antibodies against domains V1/V2, C2, and the C terminus of V3 did not bind CNX-associated Env, whereas those against C1, V1/V2, and the CD4-binding domain did not react with PDI-associated Env. In addition, a mixture of the latter antibodies interfered with PDI-mediated Env reduction. Thus, Env interacts with intracellular CNX and extracellular PDI via discrete, largely nonoverlapping, regions. The sites of interaction explain the mode of action of compounds that target these two catalysts and may enable the design of further new competitive agents.

Rapid protein domain assignment from amino acid sequence using predicted secondary structure

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed

A survey of primary homology assessment: different botanists perceive and define characters in different ways

Cladistic analyses begin with an assessment of variation for a group of organisms and the subsequent representation of that variation as a data matrix. The step of converting observed organismal variation into a data matrix has been considered subjective, contentious, under-investigated, imprecise, unquantifiable, intuitive, as a black-box, and at the same time as ultimately the most influential phase of any cladistic analysis (Pimentel and Riggins, 1987; Bryant, 1989; Pogue and Mickevich, 1990; de Pinna, 1991; Stevens, 1991; Bateman et al., 1992; Smith, 1994; Pleijel, 1995; Wilkinson, 1995; Patterson and Johnson, 1997). Despite the concerns of these authors, primary homology assessment is often perceived as reproducible. In a recent paper, Hawkins et al. (1997) reiterated two points made by a number of these authors: that different interpretations of characters and coding are possible and that different workers will perceive and define characters in different ways. One reviewer challenged us: did we really think that two people working on the same group would come up with different data sets? The conflicting views regarding the reproducibility of the cladistic character matrix provoke a number of questions. Do the majority of workers consistently follow the same guidelines? Has the theoretical framework informing primary homology assessment been adequately explored? The objective of this study is to classify approaches to primary homology assessment, and to quantify the extent to which different approaches are found in the literature by examining variation in the way characters are defined and coded in a data matrix.

Bibliographic analysis of persuasive systems: techniques, methods and domains of application

This paper presents findings of our study on peer-reviewed papers published in the International Conference on Persuasive Technology from 2006 to 2010. The study indicated that out of 44 systems reviewed, 23 were reported to be successful, 2 to be unsuccessful and 19 did not specify whether or not it was successful. 56 different techniques were mentioned and it was observed that most designers use ad hoc definitions for techniques or methods used in design. Hence we propose the need for research to establish unambiguous definitions of techniques and methods in the field.

Collagen, convulxin, and thrombin stimulate aggregation-independent tyrosine phosphorylation of CD31 in platelets. Evidence for the involvement of Src family kinases

Platelet endothelial cell adhesion molecule-1 (CD31) is a 130-kDa glycoprotein receptor present on the surface of platelets, neutrophils, monocytes, certain T-lymphocytes, and vascular endothelial cells. CD31 is involved in adhesion and signal transduction and is implicated in the regulation of a number of cellular processes. These include transendothelial migration of leukocytes, integrin regulation, and T-cell function, although its function in platelets remains unclear. In this study, we demonstrate the ability of the platelet agonists collagen, convulxin, and thrombin to induce tyrosine phosphorylation of CD31. Furthermore, we show that this event is independent of platelet aggregation and secretion and is accompanied by an increase in surface expression of CD31. A kinase capable of phosphorylating CD31 was detected in CD31 immunoprecipitates, and its activity was increased following activation of platelets. CD31 tyrosine phosphorylation was reduced or abolished by the Src family kinase inhibitor PP2, suggesting a role for these enzymes. In accordance with this, each of the Src family members expressed in platelets, namely Fyn, Lyn, Src, Yes, and Hck, was shown to co-immunoprecipitate with CD31. The involvement of Src family kinases in this process was confirmed through the study of mouse platelets deficient in Fyn.

Complexity theory and planning: examining 'fractals' for organising policy domains in planning practice

This article examines selected methodological insights that complexity theory might provide for planning. In particular, it focuses on the concept of fractals and, through this concept, how ways of organising policy domains across scales might have particular causal impacts. The aim of this article is therefore twofold: (a) to position complexity theory within social science through a ‘generalised discourse’, thereby orienting it to particular ontological and epistemological biases and (b) to reintroduce a comparatively new concept – fractals – from complexity theory in a way that is consistent with the ontological and epistemological biases argued for, and expand on the contribution that this might make to planning. Complexity theory is theoretically positioned as a neo-systems theory with reasons elaborated. Fractal systems from complexity theory are systems that exhibit self-similarity across scales. This concept (as previously introduced by the author in ‘Fractal spaces in planning and governance’) is further developed in this article to (a) illustrate the ontological and epistemological claims for complexity theory, and to (b) draw attention to ways of organising policy systems across scales to emphasise certain characteristics of the systems – certain distinctions. These distinctions when repeated across scales reinforce associated processes/values/end goals resulting in particular policy outcomes. Finally, empirical insights from two case studies in two different policy domains are presented and compared to illustrate the workings of fractals in planning practice.

A generalized collectively compact operator theory with an application to integral equations on unbounded domains

In this paper a generalization of collectively compact operator theory in Banach spaces is developed. A feature of the new theory is that the operators involved are no longer required to be compact in the norm topology. Instead it is required that the image of a bounded set under the operator family is sequentially compact in a weaker topology. As an application, the theory developed is used to establish solvability results for a class of systems of second kind integral equations on unbounded domains, this class including in particular systems of Wiener-Hopf integral equations with L1 convolutions kernels

On the solvability of a class of second kind integral equations on unbounded domains

We consider integral equations of the form ψ(x) = φ(x) + ∫Ωk(x, y)z(y)ψ(y) dy(in operator form ψ = φ + Kzψ), where Ω is some subset ofRn(n ≥ 1). The functionsk,z, and φ are assumed known, withz ∈ L∞(Ω) and φ ∈ Y, the space of bounded continuous functions on Ω. The function ψ ∈ Yis to be determined. The class of domains Ω and kernelskconsidered includes the case Ω = Rnandk(x, y) = κ(x − y) with κ ∈ L1(Rn), in which case, ifzis the characteristic function of some setG, the integral equation is one of Wiener–Hopf type. The main theorems, proved using arguments derived from collectively compact operator theory, are conditions on a setW ⊂ L∞(Ω) which ensure that ifI − Kzis injective for allz ∈ WthenI − Kzis also surjective and, moreover, the inverse operators (I − Kz)−1onYare bounded uniformly inz. These general theorems are used to recover classical results on Wiener–Hopf integral operators of21and19, and generalisations of these results, and are applied to analyse the Lippmann–Schwinger integral equation.