Online learning the consensus of multiple correspondences between sets.

When several subjects solve the assignment problem of two sets, differences on the correspondences computed by these subjects may occur. These differences appear due to several factors. For example, one of the subjects may give more importance to some of the elements’ attributes than another subject. Another factor could be that the assignment problem is computed through a suboptimal algorithm and different non-optimal correspondences can appear. In this paper, we present a consensus methodology to deduct the consensus of several correspondences between two sets. Moreover, we also present an online learning algorithm to deduct some weights that gauge the impact of each initial correspondence on the consensus. In the experimental section, we show the evolution of these parameters together with the evolution of the consensus accuracy. We observe that there is a clear dependence of the learned weights with respect to the quality of the initial correspondences. Moreover, we also observe that in the first iterations of the learning algorithm, the consensus accuracy drastically increases and then stabilises

Multimodal Biometrics Enhancement Recognition System based on Fusion of Fingerprint and PalmPrint: A Review

This article is an overview of a current multimodal biometrics research based on fingerprint and palm-print. It explains the pervious study for each modal separately and its fusion technique with another biometric modal. The basic biometric system consists of four stages: firstly, the sensor which is used for enrolmen

CHARACTERISATION AND MOLECULAR TYPING OF CLINICAL AND ENVIRONMENTAL ISOLATES OF VIBRIO PARAHAEMOLYTICUS

Vibrio parahaemolyticus is a natural inhabitant of coastal waters worldwide and is the leading cause of seafood-borne gastroenteritis. This study reports on the use of several molecular characterisation methods to screen clinical and environmental isolates of V parahaemolyticus to assess whether such techniques can be used to distinguish pathogenic isolates reliably. In a total of 86 isolates mainly of V parahaemolyticus but also including V cholerae, V vulnificus and several other species, serotypes of the more virulent clonal group 03:K6 were identified, but otherwise there appeared no association with serotype and phenotype. The tdh and trh genes encoding haemolysins that are typically associated with virulent isolates were found in a significantly large number of isolates; however, poor concordance between haemolytic activity and the presence of the gene tdh was found. In an effort to establish more accurate relationships amongst clinical and environmental isolates of V parahaemolyticus, four molecular typing systems were employed; namely pulsed-field gel electrophoresis (PFGE), intergenic transcribed spacer (ITS) analysis, tDNA intergenic length polymorphisms (tDNA-ILPs) and randomly amplified polymorphic DNA (RAPD). Typing patterns and clustering analysis using these methods differentiated V parahaemolyticus from other marine species as well as at the subspecies level. PFGE with NotI was shown to be the most discriminative but suffered from not being universally applicable. Both ITS and tDNA-ILP methods were sufficiently discriminatory with discrimination indices (DI) of between 0.568 and 0.724, depending on the primers employed. The discriminatory ability of RAPD was also affected by the primers used (DI= 0.959 - 0.965) but closely matched that of PFGE (DI = 0.976). Additionally, both RAPD methods were able to distinguish putative markers for the pandemic clonal group. Typing systems appeared largely stable in duplicate and triplicate analyses with multiple primer pairs with some obvious variability in the reproduction of faint amplicons. All methods except PFGE were simple to execute but none of the methods could distinguish V parahaemolyticus into obvious lineages based on the clinical or environmental source. With the recent implication of a type Ill secretion system {TTSS) involved in the pathogenicity of V parahaemolyticus, a multiplex PCR system using PCR primers that spanned both TTSSl and TTSS2 regions was developed. Dot-blot analysis confirmed TTSS2 genes in at least 30% of environmental isolates. Nucleotide sequence analysis revealed l00% sequence homology in three loci of TTSS2 putative structural genes. In comparison, a total of 34 single nucleotide polymorphisms (SNP) were identified in three TTSS1 regions. In two of the regions, the SNPs were synonymous, whereas a non-synonymous substitution in the structural gene vcrDI resulted in valine replacement with isoleucine. In addition, nucleotide deletions in TTSS1 with resultant frameshift mutations were identified. The finding that significant numbers of environmental isolates also possess TTSS2 genes is contrary to currently held opinion that TTSS2 is only present in clinical isolates. It is hypothesed that the high incidences of V parahaemolyticus infections may be related to active TTSS2 genes, whereas a high degree of polymorphisms in TTSS1 suggest it may be inactive.The Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratories, Dorset, United Kingdo

Learning the Consensus of Multiple Correspondences between Data Structures

En aquesta tesi presentem un marc de treball per aprendre el consens donades múltiples correspondències. S'assumeix que les diferents parts involucrades han generat aquestes correspondències per separat, i el nostre sistema actua com un mecanisme que calibra diferents característiques i considera diferents paràmetres per aprendre les millors assignacions i així, conformar una correspondència amb la major precisió possible a costa d'un cost computacional raonable. Aquest marc de treball de consens és presentat en una forma gradual, començant pels desenvolupaments més bàsics que utilitzaven exclusivament conceptes ben definits o únicament un parell de correspondències, fins al model final que és capaç de considerar múltiples correspondències, amb la capacitat d'aprendre automàticament alguns paràmetres de ponderació. Cada pas d'aquest marc de treball és avaluat fent servir bases de dades de naturalesa variada per demostrar efectivament que és possible tractar diferents escenaris de matching. Addicionalment, dos avanços suplementaris relacionats amb correspondències es presenten en aquest treball. En primer lloc, una nova mètrica de distància per correspondències s'ha desenvolupat, la qual va derivar en una nova estratègia per a la cerca de mitjanes ponderades. En segon lloc, un marc de treball específicament dissenyat per a generar correspondències al camp del registre d'imatges s'ha modelat, on es considera que una de les imatges és una imatge completa, i l'altra és una mostra petita d'aquesta. La conclusió presenta noves percepcions de com el nostre marc de treball de consens pot ser millorada, i com els dos desenvolupaments paral·lels poden convergir amb el marc de treball de consens.En esta tesis presentamos un marco de trabajo para aprender el consenso dadas múltiples correspondencias. Se asume que las distintas partes involucradas han generado dichas correspondencias por separado, y nuestro sistema actúa como un mecanismo que calibra distintas características y considera diferentes parámetros para aprender las mejores asignaciones y así, conformar una correspondencia con la mayor precisión posible a expensas de un costo computacional razonable. El marco de trabajo de consenso es presentado en una forma gradual, comenzando por los acercamientos más básicos que utilizaban exclusivamente conceptos bien definidos o únicamente un par de correspondencias, hasta el modelo final que es capaz de considerar múltiples correspondencias, con la capacidad de aprender automáticamente algunos parámetros de ponderación. Cada paso de este marco de trabajo es evaluado usando bases de datos de naturaleza variada para demostrar efectivamente que es posible tratar diferentes escenarios de matching. Adicionalmente, dos avances suplementarios relacionados con correspondencias son presentados en este trabajo. En primer lugar, una nueva métrica de distancia para correspondencias ha sido desarrollada, la cual derivó en una nueva estrategia para la búsqueda de medias ponderadas. En segundo lugar, un marco de trabajo específicamente diseñado para generar correspondencias en el campo del registro de imágenes ha sido establecida, donde se considera que una de las imágenes es una imagen completa, y la otra es una muestra pequeña de ésta. La conclusión presenta nuevas percepciones de cómo nuestro marco de trabajo de consenso puede ser mejorada, y cómo los dos desarrollos paralelos pueden converger con éste.In this work, we present a framework to learn the consensus given multiple correspondences. It is assumed that the several parties involved have generated separately these correspondences, and our system acts as a mechanism that gauges several characteristics and considers different parameters to learn the best mappings and thus, conform a correspondence with the highest possible accuracy at the expense of a reasonable computational cost. The consensus framework is presented in a gradual form, starting from the most basic approaches that used exclusively well-known concepts or only two correspondences, until the final model which is able to consider multiple correspondences, with the capability of automatically learning some weighting parameters. Each step of the framework is evaluated using databases of varied nature to effectively demonstrate that it is capable to address different matching scenarios. In addition, two supplementary advances related on correspondences are presented in this work. Firstly, a new distance metric for correspondences has been developed, which lead to a new strategy for the weighted mean correspondence search. Secondly, a framework specifically designed for correspondence generation in the image registration field has been established, where it is considered that one of the images is a full image, and the other one is a small sample of it. The conclusion presents insights of how our consensus framework can be enhanced, and how these two parallel developments can converge with it

Development of a comparative genomic fingerprinting assay for rapid and high resolution genotyping of Arcobacter butzleri

Sherpa Romeo green journal. Open access, distributed under the terms of the Creative Commons Attribution (CC-BY) License.Background Molecular typing methods are critical for epidemiological investigations, facilitating disease outbreak detection and source identification. Study of the epidemiology of the emerging human pathogen Arcobacter butzleri is currently hampered by the lack of a subtyping method that is easily deployable in the context of routine epidemiological surveillance. In this study we describe a comparative genomic fingerprinting (CGF) method for high-resolution and high-throughput subtyping of A. butzleri. Comparative analysis of the genome sequences of eleven A. butzleri strains, including eight strains newly sequenced as part of this project, was employed to identify accessory genes suitable for generating unique genetic fingerprints for high-resolution subtyping based on gene presence or absence within a strain. Results A set of eighty-three accessory genes was used to examine the population structure of a dataset comprised of isolates from various sources, including human and non-human animals, sewage, and river water (n=156). A streamlined assay (CGF40) based on a subset of 40 genes was subsequently developed through marker optimization. High levels of profile diversity (121 distinct profiles) were observed among the 156 isolates in the dataset, and a high Simpson’s Index of Diversity (ID) observed (ID > 0.969) indicate that the CGF40 assay possesses high discriminatory power. At the same time, our observation that 115 isolates in this dataset could be assigned to 29 clades with a profile similarity of 90% or greater indicates that the method can be used to identify clades comprised of genetically similar isolates. Conclusions The CGF40 assay described herein combines high resolution and repeatability with high throughput for the rapid characterization of A. butzleri strains. This assay will facilitate the study of the population structure and epidemiology of A. butzleri.Ye

Global expression mapping of mammalian genomes

he aim of genome projects is to decipher all the information contained within the DNA of an organism and to study the way this information is processed in physiological processes. It is believed that more than 95% of the information content of the mammalian genome is represented in the protein coding sequences that make up only approximately 2% of the DNA sequence. Consequently much effort is being invested in the study of coding sequences in the form of cDNA analysis. This thesis is concerned with the development of a new strategy for a highly parallel approach to analyse entire cDNA libraries. The strategy is based upon generating sufficient sequence information to identify uniquely more than 100,000 cDNA clones by hybridisation with short oligonucleotides, typically 7 - 10 mers. Each oligonucleotide is hybridised to all cDNA clones in parallel and under stringent conditions positively identifies a subset (3 - 10%) of clones. Oligonucleotides are designed in such a way that each will positively identify a different subset of clones and statistical simulations estimate that approximately 200 such hybridisation events are required to identify uniquely upto 100,000 cDNA sequences. Such a fingerprint can be generated from many cDNA libraries constructed from different tissue mRNAs and will not only lead to the identification of most sequecnes expressed from the genome but also indicate the level of expression by determining the number of times any given sequence is represented across different cDNA libraries. A human foetal brain cDNA library has been constructed and 100,000 clones arrayed into microtitre plates and on nylon membranes. All the required technological developments have been carried out successfully and are presented. In excess of 200 oligonucleotide hybridisations have been performed on a subset of 32,000 cDNA clones and 1,000 sequenced control clones. A detailed analysis of the data on the control clones is presented and the implications for cDNA fingerprinting discussed

Recognition of the Cladosporium fulvum Ecp2 elicitor in tomato and non-host plants

Resistance against the tomato fungal pathogen Cladosporium fulvum is often conferred by Hcr9 genes iliomologues of the ~. fulvum resistance gene Cf-~) that are located in the Milky Way cluster on the short arm of Chromosome 1. These Hcr9 genes mediate recognition of matching fungal avirulence gene products. In contrast, the resistance gene Cf-Ecp2 mediates recognition of the pathogenicity factor Ecp2 and is located in the Orlon (OR) cluster on the short arm of Chromosome 1. The main part of this thesis concentrates on the cloning of the Cf-Ecp2 Orion (OR) cluster and the identification of the functional CfEcp2 resistance gene that mediates HR-mediated resistance upon Ecp2 recognition.In CHAPTER 2, we report the map- and homology-based cloning of the OR Hcr9 cluster. A method was optimised to generate clone-specific fingerprint data that were subsequently used in the efficient establishment of genomic DNA contigs. Three Hcr9s were identified as candidate Cf-Ecp2 genes. By PCR-based cloning using specific OR sequences, orthologous Hcr9 genes were identified from different Lycopersicon species and haplotypes. The OR Hcr9s are very homologous to each other. However, based on a relative low sequence homology to other Hcr9s, the OR Hcr9s are classified as a new subgroup. As a consequence, the origin and the mode of action of this unique class of Hcr9s may differ from the other Hcr9s. To support allele mining, mapping, cloning and mRNA profiling of tomato Hcr9 genes, a resistance gene analogue (RGA) fingerprint method was developed to generate novel Hcr9-specific markers (CHAPTER 3). The presence of both conserved and variable sequence domains in Hcr9s is exploited using a combination of PCR amplification and subsequent digestion. By the development of a fluorescent end-Iabelling method for restriction fragments, referred to as A/T labelling, high-resolution size-separation and detection of the complex RGA fingerprint pattern with a LlCOR automated sequencer became possible. The RGA fingerprint method was validated by the analysis of near-isogenic lines and the analysis of two Orlon (OR) Hcr9 loci harbouring the Cf-Ecp2 resistance gene or the recessive cf-ecp2 allele. We identified several RGA-markers cosegregating with Cf-Ecp2 resistance that corresponded to the th ree Hcr9s that are located at the OR locus. In addition, results indicate that the Hcr9 RGA fingerprint method facilitates the discrimination of highly homologous genes in the analysis of a mapping population. Finally, the Hcr9 RGA fingerprint method was applied to study the Hcr9 gene expression and showed that two out of the three OR Hcr9s were expressed in planta. The various methods to identify the functional Cf-Ecp2 gene are described in CHAPTER 4. Transient expression in Nicotiana species and complementation analysis in tomato were exploited to test candidate Cf-Ecp2 genes for the ability to mediate Ecp2 recognition. Despite applying all commonly used functional assays, we were not able to identify which of the three OR Hcr9 represents the functional Cf-Ecp2 gene. 8ased on these results we have to conclude that recognition of the C. fulvum Ecp2 elicitor is not solely mediated by an OR-Hcr9 and an additional tomato-derived HR-stimulating factor is required for Cf-Ecp2/Ecp2 mediated resistance.In addition to the three independent chapters on the cloning and identification of Cf-Ecp2, two related research topics were investigated. Cladosporium fulvum is a fungal pathogen of tomato that grows exclusively in the intercellular spaces of leaves. In tomato, recognition of elicitors is followed by a hypersensitive response (HR) resulting in resistance. However, HR-associated recognition of Ecp2 has also been observed in Nicotiana paniculata, N. sylvestris, N. tabacum and N. undulata that are non-host plants of C. fulvum (CHAPTER 5). Absence of Ecp2-recognition did not lead to growth of C. fulvum on Nicotiana plants. We show that HR-associated recognition of Ecp2 is mediated by a single dominant gene in N. paniculata. However, based on PCR- and hybridisation analysis this gene is not homologous to known Cf-genes.DNA sequence analysis of the Avr proteins (so-called race-specific elicitors) Avr2, Avr4, Avr4E and Avr9 have revealed that the change from a virulence to virulence is associated with DNA mutations in Avr coding regions. The high frequency of these mutations are most likely the result of high selection pressure caused by the frequent use of matching Cf resistance genes in commercial tomato lines. However, the Cf-Ecp resistance genes have rarely been employed and previous research showed that no variation was found the Ecp elicitors. In CHAPTER 6 the Ecotilling method was used in strains of C. fulvum that have been collected world-wide to compare the sequence variation in Avr and Ecp elicitor encoding genes while the variation in ribosomal internal transcribed spacers (lTS) was used as evolutionary clock. No polymorphisms in lTS sequences were observed. Silent mutations in Avrs occurred more frequently. However, the very fast majority of the mutations in Avr proteins were associated with virulence and indicate a high selection pressure in C. fulvum Avr elicitor genes. In Ecp elicitor genes, however, mutations occurred rarely and were not associated with virulence. These results show a very high mutation rate in elicitor proteins and confirms the lack of selection pressure on the Ecp genes by Cf-Ecp resistance genes.The thesis is concluded with a general discussion on Cf- and Cf-like proteins involved in disease resistance (CHAPTER 7). Current knowledge on the genetics and evolution of Cf genes, Cf protein characteristics, elicitor perception and signaI transduction in the tomato - C. fulvum pathosystem is discussed. In addition, the current knowledge on Cf-like proteins that are involved in other pathosystems is presented. Finally, this chapter describes some future directions in research on the described pathosystems