Loop Formulas for Description Logic Programs

Description Logic Programs (dl-programs) proposed by Eiter et al. constitute an elegant yet powerful formalism for the integration of answer set programming with description logics, for the Semantic Web. In this paper, we generalize the notions of completion and loop formulas of logic programs to description logic programs and show that the answer sets of a dl-program can be precisely captured by the models of its completion and loop formulas. Furthermore, we propose a new, alternative semantics for dl-programs, called the {\em canonical answer set semantics}, which is defined by the models of completion that satisfy what are called canonical loop formulas. A desirable property of canonical answer sets is that they are free of circular justifications. Some properties of canonical answer sets are also explored.Comment: 29 pages, 1 figures (in pdf), a short version appeared in ICLP'1

Large Alphabets and Incompressibility

We briefly survey some concepts related to empirical entropy -- normal numbers, de Bruijn sequences and Markov processes -- and investigate how well it approximates Kolmogorov complexity. Our results suggest $\ell$th-order empirical entropy stops being a reasonable complexity metric for almost all strings of length $m$ over alphabets of size $n$ about when $n^\ell$ surpasses $m$

Web Service Discovery in a Semantically Extended UDDI Registry: the Case of FUSION

Service-oriented computing is being adopted at an unprecedented rate, making the effectiveness of automated service discovery an increasingly important challenge. UDDI has emerged as a de facto industry standard and fundamental building block within SOA infrastructures. Nevertheless, conventional UDDI registries lack means to provide unambiguous, semantically rich representations of Web service capabilities, and the logic inference power required for facilitating automated service discovery. To overcome this important limitation, a number of approaches have been proposed towards augmenting Web service discovery with semantics. This paper discusses the benefits of semantically extending Web service descriptions and UDDI registries, and presents an overview of the approach put forward in project FUSION, towards semantically-enhanced publication and discovery of services based on SAWSDL

Mining microbial genomes for new natural products and biosynthetic pathways

Analyses of microbial genome sequences have revealed numerous examples of ‘cryptic’ or ‘orphan’ biosynthetic gene clusters, with the potential to direct the production of novel, structurally complex natural products. This article summarizes the various methods that have been developed for discovering the products of cryptic biosynthetic gene clusters in microbes and gives an account of my group's discovery of the products of two such gene clusters in the model actinomycete Streptomyces coelicolor M145. These discoveries hint at new mechanisms, roles and specificities for natural product biosynthetic enzymes. Our efforts to elucidate these are described. The identification of new secondary metabolites of S. coelicolor raises the question: what is their biological function? Progress towards answering this question is also summarized

Strategy for Treating Motor Neuron Diseases Using a Fusion Protein of Botulinum Toxin Binding Domain and Streptavidin for Viral Vector Access: Work in Progress

Although advances in understanding of the pathogenesis of amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) have suggested attractive treatment strategies, delivery of agents to motor neurons embedded within the spinal cord is problematic. We have designed a strategy based on the specificity of botulinum toxin, to direct entry of viral vectors carrying candidate therapeutic genes into motor neurons. We have engineered and expressed fusion proteins consisting of the binding domain of botulinum toxin type A fused to streptavidin (SAv). This fusion protein will direct biotinylated viral vectors carrying therapeutic genes into motor nerve terminals where they can enter the acidified endosomal compartments, be released and undergo retrograde transport, to deliver the genes to motor neurons. Both ends of the fusion proteins are shown to be functionally intact. The binding domain end binds to mammalian nerve terminals at neuromuscular junctions, ganglioside GT1b (a target of botulinum toxin), and a variety of neuronal cells including primary chick embryo motor neurons, N2A neuroblastoma cells, NG108-15 cells, but not to NG CR72 cells, which lack complex gangliosides. The streptavidin end binds to biotin, and to a biotinylated Alexa 488 fluorescent tag. Further studies are in progress to evaluate the delivery of genes to motor neurons in vivo, by the use of biotinylated viral vectors

Notch signaling in T cells is essential for allergic airway inflammation, but expression of the Notch ligands Jagged 1 and Jagged 2 on dendritic cells is dispensable

__Background:__ Allergic asthma is characterized by a TH2 response induced by dendritic cells (DCs) that present inhaled allergen. Although the mechanisms by which they instruct TH2 differentiation are still poorly understood, expression of the Notch ligand Jagged on DCs has been implicated in this process. __Objective:__ We sought to establish whether Notch signaling induced by DCs is critical for house dust mite (HDM)-driven allergic airway inflammation (AAI) in vivo. __Methods:__ The induction of Notch ligand expression on DC subsets by HDM was quantified by using quantitative real-time PCR. We used an HDM-driven asthma mouse model to compare the capacity of Jagged 1 and Jagged 2 single- and double-deficient DCs to induce AAI. In addition, we studied AAI in mice with a T cell-specific deletion of recombination signal-binding protein for immunoglobulin Jκ region (RBPJκ), a downstream effector of Notch signaling. __Results:__ HDM exposure promoted expression of Jagged 1, but not Jagged 2, on DCs. In agreement with published findings, in vitro-differentiated and HDM-pulsed Jagged 1 and Jagged 2 double-deficient DCs lacked the capacity to induce AAI. However, after in vivo intranasal sensitization and challenge with HDM, DC-specific Jagged 1 or Jagged 2 single- or double-deficient mice had eosinophilic airway inflammation and a TH2 cell activation phenotype that was not different from that in control littermates. In contrast, RBPJκ-def

Subregional localization and characterization of Ly6aGFP-expressing hematopoietic cells in the mouse embryonic head

Hematopoietic cell generation in the midgestation mouse embryo occurs through the natural transdifferentiation of temporally and spatially restricted set of hemogenic endothelial cells. These cells take on hematopoietic fate in the aorta, vitelline and umbilical arteries and appear as hematopoietic cell clusters that emerge from the vascular wall. Gen

Extraction of bodily features for gait recognition and gait attractiveness evaluation

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s11042-012-1319-2. Copyright @ 2012 Springer.Although there has been much previous research on which bodily features are most important in gait analysis, the questions of which features should be extracted from gait, and why these features in particular should be extracted, have not been convincingly answered. The primary goal of the study reported here was to take an analytical approach to answering these questions, in the context of identifying the features that are most important for gait recognition and gait attractiveness evaluation. Using precise 3D gait motion data obtained from motion capture, we analyzed the relative motions from different body segments to a root marker (located on the lower back) of 30 males by the fixed root method, and compared them with the original motions without fixing root. Some particular features were obtained by principal component analysis (PCA). The left lower arm, lower legs and hips were identified as important features for gait recognition. For gait attractiveness evaluation, the lower legs were recognized as important features.Dorothy Hodgkin Postgraduate Award and HEFCE

Bio-inspired mineral growth on porous spherulitic textured poly(L-lactic acid)/bioactive glass composite scaffolds

It has been shown that texture can strongly influence the adhesion, orientation and proliferation of cells onto the surface of biomaterials. Additionally, it is possible to imprint micrometer level textures throughout the scaffolds by melt compounding PLLA/polyethylene oxide (PEO) blend, quenching followed by leaching of PEO in water. The objective of this work is to verify how the texture in 3D porous PLLA/Bioglass®composite scaffolds may influence the precipitation of apatite in vitro. © 2008 WILEY-VCH Verlag GmbH & Co. KGaA.Financial support for this work was provided by FCT, through tire POCTI and FEDER programmes, and projects POCTI/FIS/61621/2004 and PTDC/QUI/69263/2006. S. Ghosh thanks FCT for awarding the PhD grant, SFRH/BD/12657/2003. This work was also partially supported by the European Union funded STREP Project HIPPOCRATES(NMP3-CT-2003-505758)