Progressive Meshes in an Operational Rate-Distortion Sense with Application to Terrain Data

This paper presents an efficient simplification method for regular meshes obtained with a binary subdivision scheme. Our mesh connectivity is constrained with a quadtree data structure. We propose a quadtree built especially for this class of meshes having a constant-time traversal property. We introduce a rate-distortion (RD) framework to decimate the mesh and build a progressive representation for the model. We propose to achieve the RD-optimal solutions for our quadtree-restricted setting: to obtain the optimal solutions, we show how to find the vertex in the quadtree yielding the best RD trade-off and then perform optimizations at variable rate, where the rate is given by a cost function (for example the number of triangles). All previous methods are restricted to constant rate optimization only. We compare the optimal approach to its greedy counterpart. We give computationally optimal formulations for all our algorithms on the quadtree. We apply our technique to a large dataset of terrains and give extensive experimental results

Highly analysable, reusable, and realisable architectural designs with XCD

Connector-Centric Design (XcD) is a new approach to specifying software architectures. XcD views complex connectors as highly significant in architectural designs, as it is the complex connectors that non-functional quality properties in systems can emanate from. So, XcD promotes in designs a clean separation of connectors (interaction behaviours) from components (functional behaviours). Designers can then specify connectors in detail explicitly thus easing the analysis of system designs for quality properties. Furthermore, XcD separates control behaviour from connectors as control strategies. Architectural designs in XcD thus become highly modular with re-usable components, connectors, and control strategies (representing design solutions for quality properties). The end result is the eased architectural experimentation with different design solutions by re-using components/connectors and formal analysis of these solutions to find out the optimal ones

Xcd - Modular, Realizable Software Architectures

Connector-Centric Design (Xcd) is centred around a new formal architectural description language, focusing mainly on complex connectors. Inspired by Wright and BIP, Xcd aims to cleanly separate in a modular manner the high-level functional, interaction, and control system behaviours. This can aid in both increasing the understandability of architectural specifications and the reusability of components and connectors themselves. Through the independent specification of control behaviours, Xcd allows designers to experiment more easily with different design decisions early on, without having to modify the functional behaviour specifications (components) or the interaction ones(connectors). At the same time Xcd attempts to ease the architectural specification by following (and extending) a Design-by-Contract approach, which is more familiar to software developers than process algebras like CSP or languages like BIP that are closer to synchronous/hardware specification languages. Xcd extends Design-by-Contract (i) by separating component contracts into functional and interaction sub-contracts, and (ii) by allowing service consumers to specify their own contractual clauses. Xcd connector specifications are completely decentralized, foregoing Wright’s connector glue, to ensure their realizability by construction

Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins

The Lyme disease spirochete, Borrelia burgdorferi, encodes a novel type of DNA-binding protein named EbfC. Orthologs of EbfC are encoded by a wide range of bacterial species, so characterization of the borrelial protein has implications that span the eubacterial kingdom. The present work defines the DNA sequence required for high-affinity binding by EbfC to be the 4 bp broken palindrome GTnAC, where ‘n’ can be any nucleotide. Two high-affinity EbfC-binding sites are located immediately 5′ of B. burgdorferi erp transcriptional promoters, and binding of EbfC was found to alter the conformation of erp promoter DNA. Consensus EbfC-binding sites are abundantly distributed throughout the B. burgdorferi genome, occurring approximately once every 1 kb. These and other features of EbfC suggest that this small protein and its orthologs may represent a distinctive type of bacterial nucleoid-associated protein. EbfC was shown to bind DNA as a homodimer, and site-directed mutagenesis studies indicated that EbfC and its orthologs appear to bind DNA via a novel α-helical ‘tweezer’-like structure

Activation and modulation of antiviral and apoptotic genes in pigs infected with classical swine fever viruses of high, moderate or low virulence

The immune response to CSFV and the strategies of this virus to evade and suppress the pigs’ immune system are still poorly understood. Therefore, we investigated the transcriptional response in the tonsils, median retropharyngeal lymph node (MRLN), and spleen of pigs infected with CSFV strains of similar origin with high, moderate, and low virulence. Using a porcine spleen/intestinal cDNA microarray, expression levels in RNA pools prepared from infected tissue at 3 dpi (three pigs per virus strain) were compared to levels in pools prepared from uninfected homologue tissues (nine pigs). A total of 44 genes were found to be differentially expressed. The genes were functionally clustered in six groups: innate and adaptive immune response, interferon-regulated genes, apoptosis, ubiquitin-mediated proteolysis, oxidative phosphorylation and cytoskeleton. Significant up-regulation of three IFN-γ-induced genes in the MRLNs of pigs infected with the low virulence strain was the only clear qualitative difference in gene expression observed between the strains with high, moderate and low virulence. Real-time PCR analysis of four response genes in all individual samples largely confirmed the microarray data at 3 dpi. Additional PCR analysis of infected tonsil, MRLN, and spleen samples collected at 7 and 10 dpi indicated that the strong induction of expression of the antiviral response genes chemokine CXCL10 and 2′–5′ oligoadenylate synthetase 2, and of the TNF-related apoptosis-inducing ligand (TRAIL) gene at 3 dpi, decreased to lower levels at 7 and 10 dpi. For the highly and moderately virulent strains, this decrease in antiviral and apoptotic gene expression coincided with higher levels of virus in these immune tissues

Global gene expression profiling of myeloid immune cell subsets in response to in vitro challenge with porcine circovirus 2b

Compelling evidence suggests that the early interaction between porcine circovirus 2 (PCV-2) and the innate immune system is the key event in the pathogenesis of Post-Weaning Multisystemic Wasting Syndrome (PMWS). Furthermore, PCV2 has been detected in bone-marrow samples, potentially enabling an easy spread and reservoir for the virus. To assess the gene-expression differences induced by an in-vitro PCV2b infection in different three different myeloid innate immune cell subsets generated from the same animal, we used the Agilent Porcine Gene Expression Microarray (V2). Alveolar macrophages (AMØs), monocyte-derived dendritic cells (MoDCs) and bone-marrow cells (BMCs) were generated from each animal, and challenged with a UK-isolate of a PCV2 genotype b-strain at a MOI of 0.5. Remarkably, analysis showed a highly distinct and cell-type dependent response to PCV2b challenge. Overall, MoDCs showed the most marked response to PCV2b challenge in vitro and revealed a key role for TNF in the interaction with PCV2b, whereas only few genes were affected in BMCs and AMØs. These observations were further supported by an enrichment of genes in the downstream NF-κB Signalling pathway as well as an up regulation of genes with pro-apoptotic functions post-challenge. PCV2b challenge increases the expression of a large number of immune-related and pro-apoptotic genes mainly in MoDC, which possibly explain the increased inflammation, granulomatous inflammation and lymphocyte depletion seen in PMWS-affected pigs