Developing relational navigation to effectively understand software

Effective comprehension of complex software systems requires understanding of both the individual documents that represent software and the complex relationships that exist within and between documents. Relationships of all kinds play a vital role in a software engineer's comprehension of, and navigation within and between, software documents. User-determined relationships have the additional role of enabling the engineer to create and maintain relational documentation that cannot be generated by tools or derived from other relationships. We argue that for a software development environment to effectively support the understanding of complex software systems, relational navigation must be supported at both the document-focused (intra-document) and relation-focused (inter-document) levels. The need for a relation-focused approach is highlighted by an evaluation of an existing document-focused relational interface. We conclude with the requirements for a relation-focused approach to relational navigation. These requirements focus on the user's perspective when interacting with a collection of related documents. We define the requirements for a software development environment that effectively supports the understanding of the software documents and relationships that define a complex software system.

Structure and dynamics of ASC2, a pyrin domain-only protein that regulates inflammatory signaling

Pyrin domain (PYD)-containing proteins are key components of pathways that regulate inflammation, apoptosis, and cytokine processing. Their importance is further evidenced by the consequences of mutations in these proteins that give rise to autoimmune and hyperinflammatory syndromes. PYDs, like other members of the death domain ( DD) superfamily, are postulated to mediate homotypic interactions that assemble and regulate the activity of signaling complexes. However, PYDs are presently the least well characterized of all four DD subfamilies. Here we report the three-dimensional structure and dynamic properties of ASC2, a PYD-only protein that functions as a modulator of multidomain PYD-containing proteins involved in NF-KB and caspase-1 activation. ASC2 adopts a six-helix bundle structure with a prominent loop, comprising 13 amino acid residues, between helices two and three. This loop represents a divergent feature of PYDs from other domains with the DD fold. Detailed analysis of backbone N-15 NMR relaxation data using both the Lipari-Szabo model-free and reduced spectral density function formalisms revealed no evidence of contiguous stretches of polypeptide chain with dramatically increased internal motion, except at the extreme N and C termini. Some mobility in the fast, picosecond to nanosecond timescale, was seen in helix 3 and the preceding alpha 2-alpha 3 loop, in stark contrast to the complete disorder seen in the corresponding region of the NALP1 PYD. Our results suggest that extensive conformational flexibility in helix 3 and the alpha 2-alpha 3 loop is not a general feature of pyrin domains. Further, a transition from complete disorder to order of the alpha 2-alpha 3 loop upon binding, as suggested for NALP1, is unlikely to be a common attribute of pyrin domain interactions.

Excitation spectra of the spin-1/2 triangular-lattice Heisenberg antiferromagnet

We use series expansion methods to calculate the dispersion relation of the one-magnon excitations for the spin-(1)/(2) triangular-lattice nearest-neighbor Heisenberg antiferromagnet above a three-sublattice ordered ground state. Several striking features are observed compared to the classical (large-S) spin-wave spectra. Whereas, at low energies the dispersion is only weakly renormalized by quantum fluctuations, significant anomalies are observed at high energies. In particular, we find rotonlike minima at special wave vectors and strong downward renormalization in large parts of the Brillouin zone, leading to very flat or dispersionless modes. We present detailed comparison of our calculated excitation energies in the Brillouin zone with the spin-wave dispersion to order 1/S calculated recently by Starykh, Chubukov, and Abanov [Phys. Rev. B74, 180403(R) (2006)]. We find many common features but also some quantitative and qualitative differences. We show that at temperatures as low as 0.1J the thermally excited rotons make a significant contribution to the entropy. Consequently, unlike for the square lattice model, a nonlinear sigma model description of the finite-temperature properties is only applicable at temperatures < 0.1J. Finally, we review recent NMR measurements on the organic compound kappa-(BEDT-TTF)(2)Cu-2(CN)(3). We argue that these are inconsistent with long-range order and a description of the low-energy excitations in terms of interacting magnons, and that therefore a Heisenberg model with only nearest-neighbor exchange does not offer an adequate description of this material.

Existence of multiple solutions for finite difference approximations to second-order boundary value problems

Error condition detected We consider discrete two-point boundary value problems of the form D-2 y(k+1) = f (kh, y(k), D y(k)), for k = 1,...,n - 1, (0,0) = G((y(0),y(n));(Dy-1,Dy-n)), where Dy-k = (y(k) - Yk-I)/h and h = 1/n. This arises as a finite difference approximation to y" = f(x,y,y'), x is an element of [0,1], (0,0) = G((y(0),y(1));(y'(0),y'(1))). We assume that f and G = (g(0), g(1)) are continuous and fully nonlinear, that there exist pairs of strict lower and strict upper solutions for the continuous problem, and that f and G satisfy additional assumptions that are known to yield a priori bounds on, and to guarantee the existence of solutions of the continuous problem. Under these assumptions we show that there are at least three distinct solutions of the discrete approximation which approximate solutions to the continuous problem as the grid size, h, goes to 0. (C) 2003 Elsevier Science Ltd. All rights reserved.

Applying a disciplined approach to the development of a context-aware communication application

Pervasive computing applications must be engineered to provide unprecedented levels of flexibility in order to reconfigure and adapt in response to changes in computing resources and user requirements. To meet these challenges, appropriate software engineering abstractions and infrastructure are required as a platform on which to build adaptive applications. In this paper, we demonstrate the use of a disciplined, model-based approach to engineer a context-aware Session Initiation Protocol (SIP) based communication application. This disciplined approach builds on our previously developed conceptual models and infrastructural components, which enable the description, acquisition, management and exploitation of arbitrary types of context and user preference information to enable adaptation to context changes

Atomic Latin squares of order eleven

A Latin square is pan-Hamiltonian if the permutation which defines row i relative to row j consists of a single cycle for every i j. A Latin square is atomic if all of its conjugates are pan-Hamiltonian. We give a complete enumeration of atomic squares for order 11, the smallest order for which there are examples distinct from the cyclic group. We find that there are seven main classes, including the three that were previously known. A perfect 1-factorization of a graph is a decomposition of that graph into matchings such that the union of any two matchings is a Hamiltonian cycle. Each pan-Hamiltonian Latin square of order n describes a perfect 1-factorization of Kn,n, and vice versa. Perfect 1-factorizations of Kn,n can be constructed from a perfect 1-factorization of Kn+1. Six of the seven main classes of atomic squares of order 11 can be obtained in this way. For each atomic square of order 11, we find the largest set of Mutually Orthogonal Latin Squares (MOLS) involving that square. We discuss algorithms for counting orthogonal mates, and discover the number of orthogonal mates possessed by the cyclic squares of orders up to 11 and by Parker's famous turn-square. We find that the number of atomic orthogonal mates possessed by a Latin square is not a main class invariant. We also define a new sort of Latin square, called a pairing square, which is mapped to its transpose by an involution acting on the symbols. We show that pairing squares are often orthogonal mates for symmetric Latin squares. Finally, we discover connections between our atomic squares and Franklin's diagonally cyclic self-orthogonal squares, and we correct a theorem of Longyear which uses tactical representations to identify self-orthogonal Latin squares in the same main class as a given Latin square.

Existence of Multiple Solutions for Second Order Boundary Value Problems

We give conditions on f involving pairs of lower and upper solutions which lead to the existence of at least three solutions of the two point boundary value problem y" + f(x, y, y') = 0, x epsilon [0, 1], y(0) = 0 = y(1). In the special case f(x, y, y') = f(y) greater than or equal to 0 we give growth conditions on f and apply our general result to show the existence of three positive solutions. We give an example showing this latter result is sharp. Our results extend those of Avery and of Lakshmikantham et al.