On the Complexity of Case-Based Planning

We analyze the computational complexity of problems related to case-based planning: planning when a plan for a similar instance is known, and planning from a library of plans. We prove that planning from a single case has the same complexity than generative planning (i.e., planning "from scratch"); using an extended definition of cases, complexity is reduced if the domain stored in the case is similar to the one to search plans for. Planning from a library of cases is shown to have the same complexity. In both cases, the complexity of planning remains, in the worst case, PSPACE-complete

Vector coherent state representations, induced representations, and geometric quantization: I. Scalar coherent state representations

Coherent state theory is shown to reproduce three categories of representations of the spectrum generating algebra for an algebraic model: (i) classical realizations which are the starting point for geometric quantization; (ii) induced unitary representations corresponding to prequantization; and (iii) irreducible unitary representations obtained in geometric quantization by choice of a polarization. These representations establish an intimate relation between coherent state theory and geometric quantization in the context of induced representations.Comment: 29 pages, part 1 of two papers, published versio

Novel Quantitative Real-Time LCR for the Sensitive Detection of SNP Frequencies in Pooled DNA: Method Development, Evaluation and Application

BACKGROUND: Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. METHODS: The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. CONCLUSIONS: The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. SIGNIFICANCE: The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food

Simian Immunodeficiency Virus Infection of Chimpanzees (Pan troglodytes) Shares Features of Both Pathogenic and Non-pathogenic Lentiviral Infections.

The virus-host relationship in simian immunodeficiency virus (SIV) infected chimpanzees is thought to be different from that found in other SIV infected African primates. However, studies of captive SIVcpz infected chimpanzees are limited. Previously, the natural SIVcpz infection of one chimpanzee, and the experimental infection of six chimpanzees was reported, with limited follow-up. Here, we present a long-term study of these seven animals, with a retrospective re-examination of the early stages of infection. The only clinical signs consistent with AIDS or AIDS associated disease was thrombocytopenia in two cases, associated with the development of anti-platelet antibodies. However, compared to uninfected and HIV-1 infected animals, SIVcpz infected animals had significantly lower levels of peripheral blood CD4+ T-cells. Despite this, levels of T-cell activation in chronic infection were not significantly elevated. In addition, while plasma levels of β2 microglobulin, neopterin and soluble TNF-related apoptosis inducing ligand (sTRAIL) were elevated in acute infection, these markers returned to near-normal levels in chronic infection, reminiscent of immune activation patterns in 'natural host' species. Furthermore, plasma soluble CD14 was not elevated in chronic infection. However, examination of the secondary lymphoid environment revealed persistent changes to the lymphoid structure, including follicular hyperplasia in SIVcpz infected animals. In addition, both SIV and HIV-1 infected chimpanzees showed increased levels of deposition of collagen and increased levels of Mx1 expression in the T-cell zones of the lymph node. The outcome of SIVcpz infection of captive chimpanzees therefore shares features of both non-pathogenic and pathogenic lentivirus infections.This work was supported by the Biotechnology and Biological Sciences Research Council and by the Wellcome Trust.This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.ppat.100514

Symmetry breaking in dynamical systems

Symmetry breaking bifurcations and dynamical systems have obtained a lot of attention over the last years. This has several reasons: real world applications give rise to systems with symmetry, steady state solutions and periodic orbits may have interesting patterns, symmetry changes the notion of structural stability and introduces degeneracies into the systems as well as geometric simplifications. Therefore symmetric systems are attractive to those who study specific applications as well as to those who are interested in a the abstract theory of dynamical systems. Dynamical systems fall into two classes, those with continuous time and those with discrete time. In this paper we study only the continuous case, although the discrete case is as interesting as the continuous one. Many global results were obtained for the discrete case. Our emphasis are heteroclinic cycles and some mechanisms to create them. We do not pursue the question of stability. Of course many studies have been made to give conditions which imply the existence and stability of such cycles. In contrast to systems without symmetry heteroclinic cycles can be structurally stable in the symmetric case. Sometimes the various solutions on the cycle get mapped onto each other by group elements. Then this cycle will reduce to a homoclinic orbit if we project the equation onto the orbit space. Therefore techniques to study homoclinic bifurcations become available. In recent years some efforts have been made to understand the behaviour of dynamical systems near points where the symmetry of the system was perturbed by outside influences. This can lead to very complicated dynamical behaviour, as was pointed out by several authors. We will discuss some of the technical difficulties which arise in these problems. Then we will review some recent results on a geometric approach to this problem near steady state bifurcation points