Substructure Discovery Using Minimum Description Length and Background Knowledge

The ability to identify interesting and repetitive substructures is an essential component to discovering knowledge in structural data. We describe a new version of our SUBDUE substructure discovery system based on the minimum description length principle. The SUBDUE system discovers substructures that compress the original data and represent structural concepts in the data. By replacing previously-discovered substructures in the data, multiple passes of SUBDUE produce a hierarchical description of the structural regularities in the data. SUBDUE uses a computationally-bounded inexact graph match that identifies similar, but not identical, instances of a substructure and finds an approximate measure of closeness of two substructures when under computational constraints. In addition to the minimum description length principle, other background knowledge can be used by SUBDUE to guide the search towards more appropriate substructures. Experiments in a variety of domains demonstrate SUBDUE's ability to find substructures capable of compressing the original data and to discover structural concepts important to the domain. Description of Online Appendix: This is a compressed tar file containing the SUBDUE discovery system, written in C. The program accepts as input databases represented in graph form, and will output discovered substructures with their corresponding value.Comment: See http://www.jair.org/ for an online appendix and other files accompanying this articl

Cold Atom Ballistics By Coherent Control

We use the technique of Stimulated Raman adiabatic passage (STIRAP) to affect transport of ultracold atoms between two optical lattices in relative motion. We show, using Floquet analysis and degenerate perturbation theory, that the dynamics of atoms in a particular time-dependent optical lattice system can be reduced to the 3-level STIRAP model, allowing for a simple description of their coherent acceleration.Center for Complex Quantum System

A retrospective study of the prevalence of the canine degenerative myelopathy associated superoxide dismutase 1 mutation (SOD1: c. 118G> A) in a referral population of German Shepherd dogs from the UK

BACKGROUND: Canine degenerative myelopathy (CDM) is an adult onset, progressive neurodegenerative disease of the spinal cord. The disease was originally described in the German Shepherd dog (GSD), but it is now known to occur in many other dog breeds. A previous study has identified a mutation in the superoxide dismutase 1 gene (SOD1:c.118G > A) that is associated with susceptibility to CDM. In the present study, restriction fragment length polymorphism (RFLP) analysis was used to genotype GSD for SOD1:c.118G > A in order to estimate the prevalence of the mutation in a referral population of GSD in the UK. RESULTS: This study demonstrated that the RFLP assay, based on use of PCR and subsequent digestion with the Eco571 enzyme, provided a simple genotyping test for the SOD1:c.118G > A mutation. In a young GSD population (i.e. dogs less than 6 years of age, before clinical signs of the disease usually become apparent), 8 of 50 dogs were found to be homozygous and a further 19 were heterozygous for the mutation. In dogs over 8 years of age, 21 of 50 dogs admitted to a tertiary referral hospital with pelvic limb ataxia as a major clinical sign were homozygous for the mutation, compared to none of 50 dogs of similar age, but where no neurological disease was reported on referral. CONCLUSIONS: This data suggests that genotyping for the SOD1:c.118G > A mutation is clinically applicable and that the mutation has a high degree of penetrance. Genotyping might also be useful for screening the GSD population to avoid mating of two carriers, but since the allele frequency is relatively high in the UK population of GSD, care should be taken to avoid reduction in genetic diversity within the breed

Development of a germanium-68 radionuclide production technology by irradiation of enriched isotope zinc-66 in the R7M

In the present study, we performed the evaluation and experimental determination of 68Ge production using alpha particle beams in the R7M cyclotron of the Tomsk Polytechnic University

Searching for "monogenic diabetes" in dogs using a candidate gene approach

BACKGROUND: Canine diabetes is a common endocrine disorder with an estimated breed-related prevalence ranging from 0.005% to 1.5% in pet dogs. Increased prevalence in some breeds suggests that diabetes in dogs is influenced by genetic factors and similarities between canine and human diabetes phenotypes suggest that the same genes might be associated with disease susceptibility in both species. Between 1-5% of human diabetes cases result from mutations in a single gene, including maturity onset diabetes of the adult (MODY) and neonatal diabetes mellitus (NDM). It is not clear whether monogenic forms of diabetes exist within some dog breeds. Identification of forms of canine monogenic diabetes could help to resolve the heterogeneity of the condition and lead to development of breed-specific genetic tests for diabetes susceptibility. RESULTS: Seventeen dog breeds were screened for single nucleotide polymorphisms (SNPs) in eighteen genes that have been associated with human MODY/NDM. Six SNP associations were found from five genes, with one gene (ZFP57) being associated in two different breeds. CONCLUSIONS: Some of the genes that have been associated with susceptibility to MODY and NDM in humans appear to also be associated with canine diabetes, although the limited number of associations identified in this study indicates canine diabetes is a heterogeneous condition and is most likely to be a polygenic trait in most dog breeds. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2052-6687-1-8) contains supplementary material, which is available to authorized users

Cooperation, Proximity, and Social Innovation: Three Ingredients for Industrial Medium-Sized Towns’ Renewal?

Over several decades, medium-sized industrial towns have suffered from a combination of economic and political processes: Deindustrialization, metropolization, and withdrawal of public services. After two decades in which they have been somewhat neglected (in favor of metropolises), there have recently been State and European public policies aimed at them. Medium-sized cities are not homogeneous and present several trajectories. Based on quantitative approach in France, we highlight the very diverse socio-economic dynamics of French medium-sized industrial towns. Thus, far from widespread decline or shrinking dynamics, some of these cities are experiencing an economic rebound. This is the case of Romans-sur-Isère, a medium-sized town located in the south-east of France. Focusing our qualitative analyze on this city, we try to understand this type of process. In this medium-sized town, former capital of the shoe industry, local stakeholders, private, and public try to support a productive renewal. The results of our case study highlight the role that cooperation, spatial and organizational proximity, and social innovation could play in the renewal of productive economy in medium-sized industrial towns. Even if the economic situation remains difficult for many medium-sized cities in France as in Europe, we argue that they could have a productive future making and ultimately take advantages of their “medium-sized” attributes. Over several decades, medium-sized industrial towns have suffered from a combination of economic and political processes: Deindustrialization, metropolization, and withdrawal of public services. After two decades in which they have been somewhat neglected (in favor of metropolises), there have recently been State and European public policies aimed at them. Medium-sized cities are not homogeneous and present several trajectories. Based on quantitative approach in France, we highlight the very diverse socio-economic dynamics of French medium-sized industrial towns. Thus, far from widespread decline or shrinking dynamics, some of these cities are experiencing an economic rebound. This is the case of Romans-sur-Isère, a medium-sized town located in the south-east of France. Focusing our qualitative analyze on this city, we try to understand this type of process. In this medium-sized town, former capital of the shoe industry, local stakeholders, private, and public try to support a productive renewal. The results of our case study highlight the role that cooperation, spatial and organizational proximity, and social innovation could play in the renewal of productive economy in medium-sized industrial towns. Even if the economic situation remains difficult for many medium-sized cities in France as in Europe, we argue that they could have a productive future making and ultimately take advantages of their “medium-sized” attributes. &nbsp

Experimental approaches for 100 TeV gamma-ray astronomy

The high energy end of gamma-ray source spectra might provide important clues regarding the nature of the processes involved in gamma-ray emission. Several galactic sources with hard emission spectra extending up to more than 30TeV have already been reported. Measurements around 100TeV and above should be an important goal for the next generation of high energy gamma-ray astronomy experiments. Here we present several techniques providing the required exposure (100 km^2.h). We focus our study on three Imaging Atmospheric Cherenkov Technique (IACT) based approaches: low elevation observations, large field of view telescopes, and large telescope arrays. We comment on the advantages and disadvantages of each approach and report simulation based estimates of their energy ranges and sensitivities.Comment: 3 pages 1 figure. Proceedings of TeV particle astrophysics 2, Madison, August 2006. http://www.icecube.wisc.edu/TeV/presentations/colin_poster.pd

TLR5 Risk-Associated Haplotype for Canine Inflammatory Bowel Disease Confers Hyper-Responsiveness to Flagellin

Single nucleotide polymorphisms (SNP) in the TLR5 gene have been associated with human inflammatory bowel disease (IBD) and animal models of this disease. We recently demonstrated a significant association between three non-synonymous SNPs in the canine TLR5 gene and IBD in German shepherd dogs (GSDs). However, so far, no direct link between these SNPs and a disturbance in TLR5 function was shown. In the present study, we determined the functional significance of the canine TLR5 SNPs by transfecting the identified risk-protective and risk-associated haplotype into human embryonic kidney cells (HEK) and assessed nuclear factor-kappa B (NF-κB) activation and CXCL8 production after stimulation. In addition, a whole blood assay for TLR5 activation was developed using blood derived from carrier dogs of either haplotype. There was a significant increase in NF-kB activity when cells transfected with the risk-associated TLR5 haplotype were stimulated with flagellin compared to the cells expressing the risk-protective TLR5 haplotype. This difference in NFkB activation correlated with CXCL8 expression in the supernatant measured by ELISA. Furthermore, whole blood taken from carrier dogs of the risk-associated TLR5 haplotype produced significantly more TNF after stimulation with flagellin compared to that taken from carriers of the risk-protective haplotype. Thus, we show for the first time a direct functional impact of the canine IBD risk-associated TLR5 haplotype, which results in hyper-responsiveness to flagellin compared to the IBD risk-protective TLR5 haplotype. Our data potentially suggest that similarly to human IBD and experimental models, TLR5 may also play a role in canine IBD. Blocking the hyper-responsive receptor found in susceptible dogs with IBD may alleviate the inappropriate inflammation seen in this disease