Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network

Motivation: Prediction methods for identifying binding peptides could minimize the number of peptides required to be synthesized and assayed, and thereby facilitate the identification of potential T-cell epitopes. We developed a bioinformatic method for the prediction of peptide binding to MHC class II molecules. Results: Experimental binding data and expert knowledge of anchor positions and binding motifs were combined with an evolutionary algorithm (EA) and an artificial neural network (ANN): binding data extraction --> peptide alignment --> ANN training and classification. This method, termed PERUN, was implemented for the prediction of peptides that bind to HLA-DR4(B1*0401). The respective positive predictive values of PERUN predictions of high-, moderate-, low- and zero-affinity binder-a were assessed as 0.8, 0.7, 0.5 and 0.8 by cross-validation, and 1.0, 0.8, 0.3 and 0.7 by experimental binding. This illustrates the synergy between experimentation and computer modeling, and its application to the identification of potential immunotheraaeutic peptides.

Knowledge discovery and data mining in biological databases

The new technologies for Knowledge Discovery from Databases (KDD) and data mining promise to bring new insights into a voluminous growing amount of biological data. KDD technology is complementary to laboratory experimentation and helps speed up biological research. This article contains an introduction to KDD, a review of data mining tools, and their biological applications. We discuss the domain concepts related to biological data and databases, as well as current KDD and data mining developments in biology.

Actor-network theory as a theoretical lens and research strategy for investigating firm internationalisation

Totally generalisable theories of firm internationalisation in the post-industrial era of international business, where national barriers are becoming less significant and technology becoming more influential, appear to be illusory. Stepwise or evolutionary models that predict gradual internationalisation are under challenge from empirical evidence of rapid internationalisation such as the phenomenon of the “born global” firm. Similarly, equilibrium models such as the eclectic paradigm have been criticised for being static and unable to account for process and path dependency. In this paper, the information and knowledge assumptions implied in theories of firm internationalisation are outlined and discussed. From this discussion, we suggest that actor-network theory, with its balance between description and explanation, may be a useful theoretical and empirical tool for investigating the complex and heterogeneous process of firm internationalisation whilst creating opportunities for further theory building.

Research, knowledge and design

The discussion about relations between research and design has a number of strands, and presumably motivations. Putting aside the question whether or not design or “creative endeavour” should be counted as research, for reasons to do with institutional recognition or reward, the question remains how, if at all, is design research? This question is unlikely to have attracted much interest but for matters external to Architecture within the modern university. But Architecture as a discipline now needs to understand research much better than in the past when ‘research’ was whatever went on in building science, history or people/environment studies. In this paper, I begin with some common assumptions about design, considered in relation to research, and suggest how the former can constitute or be a mode of the latter. Central to this consideration is an understanding of research as the production of publicly available knowledge. The method is that of conceptual analysis which is much more fruitful than is usually appreciated. This work is part of a larger project in philosophy of design, in roughly the analytical tradition.

Spectral properties of the tandem Jackson network, seen as a quasi-birth-and-death process

Quasi-birth-and-death (QBD) processes with infinite “phase spaces” can exhibit unusual and interesting behavior. One of the simplest examples of such a process is the two-node tandem Jackson network, with the “phase” giving the state of the first queue and the “level” giving the state of the second queue. In this paper, we undertake an extensive analysis of the properties of this QBD. In particular, we investigate the spectral properties of Neuts’s R-matrix and show that the decay rate of the stationary distribution of the “level” process is not always equal to the convergence norm of R. In fact, we show that we can obtain any decay rate from a certain range by controlling only the transition structure at level zero, which is independent of R. We also consider the sequence of tandem queues that is constructed by restricting the waiting room of the first queue to some finite capacity, and then allowing this capacity to increase to infinity. We show that the decay rates for the finite truncations converge to a value, which is not necessarily the decay rate in the infinite waiting room case. Finally, we show that the probability that the process hits level n before level 0 given that it starts in level 1 decays at a rate which is not necessarily the same as the decay rate for the stationary distribution.

A hybrid planning method for transmission networks in a deregulated environment

The reconstruction of power industries has brought fundamental changes to both power system operation and planning. This paper presents a new planning method using multi-objective optimization (MOOP) technique, as well as human knowledge, to expand the transmission network in open access schemes. The method starts with a candidate pool of feasible expansion plans. Consequent selection of the best candidates is carried out through a MOOP approach, of which multiple objectives are tackled simultaneously, aiming at integrating the market operation and planning as one unified process in context of deregulated system. Human knowledge has been applied in both stages to ensure the selection with practical engineering and management concerns. The expansion plan from MOOP is assessed by reliability criteria before it is finalized. The proposed method has been tested with the IEEE 14-bus system and relevant analyses and discussions have been presented.