Outlier detection with partial information:Application to emergency mapping

This paper, addresses the problem of novelty detection in the case that the observed data is a mixture of a known 'background' process contaminated with an unknown other process, which generates the outliers, or novel observations. The framework we describe here is quite general, employing univariate classification with incomplete information, based on knowledge of the distribution (the 'probability density function', 'pdf') of the data generated by the 'background' process. The relative proportion of this 'background' component (the 'prior' 'background' 'probability), the 'pdf' and the 'prior' probabilities of all other components are all assumed unknown. The main contribution is a new classification scheme that identifies the maximum proportion of observed data following the known 'background' distribution. The method exploits the Kolmogorov-Smirnov test to estimate the proportions, and afterwards data are Bayes optimally separated. Results, demonstrated with synthetic data, show that this approach can produce more reliable results than a standard novelty detection scheme. The classification algorithm is then applied to the problem of identifying outliers in the SIC2004 data set, in order to detect the radioactive release simulated in the 'oker' data set. We propose this method as a reliable means of novelty detection in the emergency situation which can also be used to identify outliers prior to the application of a more general automatic mapping algorithm. © Springer-Verlag 2007.

Overlap between neurodegenerative disorders

Neurodegenerative disorders are characterized by the formation of distinct pathological changes in the brain, including extracellular protein deposits, cellular inclusions, and changes in cell morphology. Since the earliest published descriptions of these disorders, diagnosis has been based on clinicopathological features, namely, the coexistence of a specific clinical profile together with the presence or absence of particular types of lesion. In addition, the molecular profile of lesions has become an increasingly important feature both in the diagnosis of existing disorders and in the description of new disease entities. Recent studies, however, have reported considerable overlap between the clinicopathological features of many disorders leading to difficulties in the diagnosis of individual cases and to calls for a new classification of neurodegenerative disease. This article discusses: (i) the nature and degree of the overlap between different neurodegenerative disorders and includes a discussion of Alzheimer's disease, dementia with Lewy bodies, the fronto-temporal dementias, and prion disease; (ii) the factors that contribute to disease overlap, including historical factors, the presence of disease heterogeneity, age-related changes, the problem of apolipoprotein genotype, and the co-occurrence of common diseases; and (iii) whether the current nosological status of disorders should be reconsidered.

A longitudinal study of the diffusion of the ISO/IEC information resource dictionary system standard (IRDS.)

The IRDS standard is an international standard produced by the International Organisation for Standardisation (ISO). In this work the process for producing standards in formal standards organisations, for example the ISO, and in more informal bodies, for example the Object Management Group (OMG), is examined. This thesis examines previous models and classifications of standards. The previous models and classifications are then combined to produce a new classification. The IRDS standard is then placed in a class in the new model as a reference anticipatory standard. Anticipatory standards are standards which are developed ahead of the technology in order to attempt to guide the market. The diffusion of the IRDS is traced over a period of eleven years. The economic conditions which affect the diffusion of standards are examined, particularly the economic conditions which prevail in compatibility markets such as the IT and ICT markets. Additionally the consequences of the introduction of gateway or converter devices into a market where a standard has not yet been established is examined. The IRDS standard did not have an installed base and this hindered its diffusion. The thesis concludes that the IRDS standard was overtaken by new developments such as object oriented technologies and middleware. This was partly because of the slow development process of developing standards in traditional organisations which operate on a consensus basis and partly because the IRDS standard did not have an installed base. Also the rise and proliferation of middleware products resulted in exchange mechanisms becoming dominant rather than repository solutions. The research method used in this work is a longitudinal study of the development and diffusion of the ISO/EEC IRDS standard. The research is regarded as a single case study and follows the interpretative epistemological point of view.

Services for activities in group editing 'sage'

The project described in this thesis investigates the needs of a group of people working cooperatively in an OSI environment, and recommends tools and services to meet these needs. The project looks specifically at Services for Activities in Group Editing, and is identified as the `SAGE' project. The project uses case studies to identify user requirements and to determine common functionalities for a variety of group editing activities. A prototype is implemented in an X.400 environment to help refine user requirements, as a source of new ideas and to test the proposed functionalities. The conceptual modelling follows current CCITT proposals, but a new classification of group activities is proposed: Informative, Objective and Supportive application groups. It is proposed that each of these application groups have their own Service Agent. Use of this classification allows the possibility of developing three sets of tools which will cover a wide range of group activities, rather than developing tools for individual activities. Group editing is considered to be in the Supportive application group. A set of additional services and tools to support group editing are proposed in the context of the CCITT draft on group communication, X.gc. The proposed services and tools are mapped onto the X.400 series of recommendations, with the Abstract Service Definition of the operational objects defined, along with their associated component files, by extending the X.420 protocol functionality. It is proposed that each of the Informative, Objective and Supportive application groups should be implemented as a modified X.420 inter-personal messaging system.

The West Midlands road transport industry

The object of this project was to identify those elements of management practice which characterised firms in the West Midlands Road Transport Industry. The object being to establish the contents of what might be termed a management policy portfolio for growth. The First Phase was the review of those factors which were generally accepted as having an influence on the success rate of transport firms in order to ascertain if they explained observed patterns. Secondly, if this were not the case, to instigate a field work study to isolate those policies which were associated with growth organizations. Investigation of the vehicle movements for the entire West Midlands Fleet over a complete licence cycle suggested that conventional explanations could not fully account for the observed patterns. To carry out the second phase of the study a sample of growth firms were visited in order to measure their attitudes on a range of factors hypothesised to affect growth. Field data were analysed to establish management activities over a wide range of areas and the results further investigated through a Principal Components and Cluster Analysis programme. The outcome of the study indicates that some past attitudes on the skills and attitudes of transport managers may have to be re-examined. As a result, the project produced a new classification of road transport firms based not on the conventional categories of long and short haul, or the types of traffics carried, but on the marketing policies and management skills employed within the organization.

La mesure alternative d’hostilité dans les relations de rivalité interacteur.

Le présent travail explore le phénomène de la rivalité interétatique1 et les mesures de son intensité. Chacune des définitions existantes de la rivalité fait la lumière sur l’une de ses caractéristiques. La rivalité durable met l’accent sur la compétition militarisée, la rivalité stratégique accorde une importance particulière à la perception de l’ennemi, tandis que la rivalité interétatique est axée sur les questions autour desquelles la compétition se déroule. Ces visions différentes du phénomène de la rivalité laissent leur empreinte sur son opérationnalisation et sur le choix des paramètres visant à le capter. Nous réunissons ces trois interprétations dans une seule définition de rivalité interacteur, en proposant une nouvelle classification des actions hostiles, ainsi que la mesure alternative d’hostilité fondée sur la fréquence de ces dernières. Les quatre études de cas suivantes nous ont permis d’atteindre ces objectifs : les relations de rivalité entre l’Afghanistan et le Pakistan, entre l’Arménie et l’Azerbaïdjan, entre le Bélize et le Guatemala, ainsi qu’entre la Somalie et l’Éthiopie.

Evolution of the diatoms: major steps in their evolution and a review of the supporting molecular and morphological evidence.

Over the years, many reviews of different aspects of diatom biology, ecology and evolution have appeared. Since 1993 many molecular trees have been produced to infer diatom phylogeny. In 2004, Medlin & Kaczmarska revised the systematics of the diatoms based on more than 20 years of consistent recovery of two major clades of diatoms that did not correspond to a traditional concept of centrics and pennates and established three classes of diatoms: Clade 1 = Coscinodiscophyceae (radial centrics) and Clade 2 = Mediophyceae (polar centrics + radial Thalassiosirales) and Bacillariophyceae (pennates). However, under certain analytical conditions, an alternative view of diatom evolution, a grades of clades, has been recovered that suggests a gradual evolution from centric to pennate symmetry. These two schemes of diatom evolution are evaluated in terms of whether or not the criteria advocated by Medlin & Kaczmarska that should be met to recover monophyletic classes have been used. The monophyly of the three diatom classes can only be achieved if (1) a secondary structure of the small subunit (SSU) rRNA gene was used to construct the alignment and not an alignment based on primary structure and (2) multiple outgroups were used. These requirements have not been met in each study of diatom evolution; hence, the grade of clades, which is useful in reconstructing the sequence of evolution, is not useful for accepting the new classification of the diatoms. Evidence for how these two factors affect the recovery of the three monophyletic classes is reviewed here. The three classes have been defined by clear morphological differences primarily based on gametangia and auxospore ontogeny and envelope structure, the presence or absence of a structure (tube process or sternum) associated with the annulus and the location of the cribrum in those genera with loculate areolae. New evidence supporting the three clades is reviewed. Other features of the cell are examined to determine whether they can also be used to support the monophyly of the three classes.

Evolution of the diatoms: major steps in their evolution and a review of the supporting molecular and morphological evidence.

Over the years, many reviews of different aspects of diatom biology, ecology and evolution have appeared. Since 1993 many molecular trees have been produced to infer diatom phylogeny. In 2004, Medlin & Kaczmarska revised the systematics of the diatoms based on more than 20 years of consistent recovery of two major clades of diatoms that did not correspond to a traditional concept of centrics and pennates and established three classes of diatoms: Clade 1 = Coscinodiscophyceae (radial centrics) and Clade 2 = Mediophyceae (polar centrics + radial Thalassiosirales) and Bacillariophyceae (pennates). However, under certain analytical conditions, an alternative view of diatom evolution, a grades of clades, has been recovered that suggests a gradual evolution from centric to pennate symmetry. These two schemes of diatom evolution are evaluated in terms of whether or not the criteria advocated by Medlin & Kaczmarska that should be met to recover monophyletic classes have been used. The monophyly of the three diatom classes can only be achieved if (1) a secondary structure of the small subunit (SSU) rRNA gene was used to construct the alignment and not an alignment based on primary structure and (2) multiple outgroups were used. These requirements have not been met in each study of diatom evolution; hence, the grade of clades, which is useful in reconstructing the sequence of evolution, is not useful for accepting the new classification of the diatoms. Evidence for how these two factors affect the recovery of the three monophyletic classes is reviewed here. The three classes have been defined by clear morphological differences primarily based on gametangia and auxospore ontogeny and envelope structure, the presence or absence of a structure (tube process or sternum) associated with the annulus and the location of the cribrum in those genera with loculate areolae. New evidence supporting the three clades is reviewed. Other features of the cell are examined to determine whether they can also be used to support the monophyly of the three classes.

IFRS 9 ‘Financial instruments’: Anticipated effects of the standard change at Kesko Group

IFRS 9 Financial instruments presents the classification and measurement, the impairment and the hedge accounting requirements for accounting of financial instruments. The standard was set by the International Accounting Standards Board to replace IAS 39 Financial instruments: Recognition and Measurement on 1 January 2018. Hence, the long-criticized and complexly experienced requirements for accounting of financial instruments will undergo the most significant reform. This thesis addresses anticipated effects of IFRS 9, focusing on the challenges the new classification and measurement requirements bring forth in the case organization Kesko. This thesis was conducted as an action research, in which, a case study method was applied. The thesis was conducted with a twofold manner, which involved general analysis of IFRS 9 and further covered distinct ambitions related to the case organization. For the general part, empirical data was gathered by interviewing two IFRS experts from KPMG and PwC, while the interviews within the case organization constituted for the case study. Further, the literature on the IFRS 9 was such scant that the theoretical examination was merged with the IFRS experts’ quotations that also strived to contribute to the overall objective of reinforcing the body of research related to the subject. This thesis indicates that IFRS 9 will most fundamentally reform the impairment and the hedge accounting requirements of financial instruments. Regard to impairment, the changes are anticipated to increase the amount of loan-loss provisions, whereas the relaxed hedge accounting requirements are expected to encourage more companies to commence the application of hedge accounting. The thesis provides empirical support on that the term business model for managing financial assets, introduced in IFRS 9, is ably hard to comprehend and remains ambiguous. It goes on to argue that the most prominent issue in defining the business model for managing financial assets is the limits set in IFRS 9 for selling financial assets. In consideration of Kesko, this thesis finds that the key effects of IFRS 9 are anticipated to be the reshaping of the organization’s treasury policy and further examination of the possibility to apply hedge accounting for foreign exchange derivatives. What is more, the thesis presumes that complying the requirements of IFRS 9 Kesko will apply the hold to collect and sell model for managing financial assets in future.

Bacterial collagenases: a review

Bacterial collagenases are metalloproteinases involved in the degradation of the extracellular matrices of animal cells, due to their ability to digest native collagen. These enzymes are important virulence factors in a variety of pathogenic bacteria. Nonetheless, there is a lack of scientific consensus for a proper and well-defined classification of these enzymes and a vast controversy regarding the correct identification of collagenases. Clostridial collagenases were the first ones to be identified and characterized and are the reference enzymes for comparison of newly discovered collagenolytic enzymes. In this review we present the most recent data regarding bacterial collagenases and overview the functional and structural diversity of bacterial collagenases. An overall picture of the molecular diversity and distribution of these proteins in nature will also be given. Particular aspects of the different proteolytic activities will be contextualized within relevant areas of application, mainly biotechnological processes and therapeutic uses. At last, we will present a new classification guide for bacterial collagenases that will allow the correct and straightforward classification of these enzymes.

La mesure alternative d’hostilité dans les relations de rivalité interacteur

Le présent travail explore le phénomène de la rivalité interétatique1 et les mesures de son intensité. Chacune des définitions existantes de la rivalité fait la lumière sur l’une de ses caractéristiques. La rivalité durable met l’accent sur la compétition militarisée, la rivalité stratégique accorde une importance particulière à la perception de l’ennemi, tandis que la rivalité interétatique est axée sur les questions autour desquelles la compétition se déroule. Ces visions différentes du phénomène de la rivalité laissent leur empreinte sur son opérationnalisation et sur le choix des paramètres visant à le capter. Nous réunissons ces trois interprétations dans une seule définition de rivalité interacteur, en proposant une nouvelle classification des actions hostiles, ainsi que la mesure alternative d’hostilité fondée sur la fréquence de ces dernières. Les quatre études de cas suivantes nous ont permis d’atteindre ces objectifs : les relations de rivalité entre l’Afghanistan et le Pakistan, entre l’Arménie et l’Azerbaïdjan, entre le Bélize et le Guatemala, ainsi qu’entre la Somalie et l’Éthiopie.

AnnoTALE: Bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present 'AnnoTALE', a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities. © 2016, Nature Publishing Group. All rights reserved.

Order fulfillment in high variety production environments

Providing high levels of product variety and product customization is challenging for many companies. This paper presents a new classification of production and order fulfillment approaches available to manufacturing companies that offer high variety and/or product customization. Six categories of approaches are identified and described. An important emerging approach - open pipeline planning – is highlighted for high variety manufacturing environments. It allows a customer order to be fulfilled from anywhere in the system, enabling greater responsiveness in Build-to-Forecast systems. The links between the open pipeline approach, decoupling concepts and postponement strategies are discussed and the relevance of the approach to the volume automotive sector is highlighted. Results from a simulation study are presented illustrating the potential benefits when products can be reconfigured in an open pipeline system. The application of open pipeline concepts to different manufacturing domains is discussed and the operating characteristics of most relevance are highlighted. In addition to the automotive, sectors such as machinery and instrumentation, computer servers, telecommunications and electronic equipment may benefit from an open pipeline planning approach. When properly designed these systems can significantly enhance order fulfillment performance.

Insights into the Specificity of Thioredoxin Reductase-Thioredoxin Interactions. A Structural and Functional Investigation of the Yeast Thioredoxin System

The enzymatic activity of thioredoxin reductase enzymes is endowed by at least two redox centers: a flavin and a dithiol/disulfide CXXC motif. The interaction between thioredoxin reductase and thioredoxin is generally species-specific, but the molecular aspects related to this phenomenon remain elusive. Here, we investigated the yeast cytosolic thioredoxin system, which is composed of NADPH, thioredoxin reductase (ScTrxR1), and thioredoxin 1 (ScTrx1) or thioredoxin 2 (ScTrx2). We showed that ScTrxR1 was able to efficiently reduce yeast thioredoxins (mitochondrial and cytosolic) but failed to reduce the human and Escherichia coli thioredoxin counterparts. To gain insights into this specificity, the crystallographic structure of oxidized ScTrxR1 was solved at 2.4 angstrom resolution. The protein topology of the redox centers indicated the necessity of a large structural rearrangement for FAD and thioredoxin reduction using NADPH. Therefore, we modeled a large structural rotation between the two ScTrxR1 domains (based on the previously described crystal structure, PDB code 1F6M). Employing diverse approaches including enzymatic assays, site-directed mutagenesis, amino acid sequence alignment, and structure comparisons, insights were obtained about the features involved in the species-specificity phenomenon, such as complementary electronic parameters between the surfaces of ScTrxR1 and yeast thioredoxin enzymes and loops and residues (such as Ser(72) in ScTrx2). Finally, structural comparisons and amino acid alignments led us to propose a new classification that includes a larger number of enzymes with thioredoxin reductase activity, neglected in the low/high molecular weight classification.

Pattern recognition methods for EMG prosthetic control

In this work we focus on pattern recognition methods related to EMG upper-limb prosthetic control. After giving a detailed review of the most widely used classification methods, we propose a new classification approach. It comes as a result of comparison in the Fourier analysis between able-bodied and trans-radial amputee subjects. We thus suggest a different classification method which considers each surface electrodes contribute separately, together with five time domain features, obtaining an average classification accuracy equals to 75% on a sample of trans-radial amputees. We propose an automatic feature selection procedure as a minimization problem in order to improve the method and its robustness.