Genotypic classification of patients with Wolfram syndrome: insights into the natural history of the disease and correlation with phenotype

Purpose: Wolfram syndrome is a degenerative, recessive rare disease with an onset in childhood. It is caused by mutations in WFS1 or CISD2 genes. More than 200 different variations in WFS1 have been described in patients with Wolfram syndrome, which complicates the establishment of clear genotype-phenotype correlation. The purpose of this study was to elucidate the role of WFS1 mutations and update the natural history of the disease. Methods: This study analyzed clinical and genetic data of 412 patients with Wolfram syndrome published in the last 15 years. Results: (i) 15% of published patients do not fulfill the current ­inclusion criterion; (ii) genotypic prevalence differences may exist among countries; (iii) diabetes mellitus and optic atrophy might not be the first two clinical features in some patients; (iv) mutations are nonuniformly distributed in WFS1; (v) age at onset of diabetes mellitus, hearing defects, and diabetes insipidus may depend on the patient"s genotypic class; and (vi) disease progression rate might depend on genotypic class. Conclusion: New genotype-phenotype correlations were established, disease progression rate for the general population and for the genotypic classes has been calculated, and new diagnostic criteria have been proposed. The conclusions raised could be important for patient management and counseling as well as for the development of treatments for Wolfram syndrome.

Lossless Compression Methods for Multispectral Images: Development and Comparisons

Main purpose of this thesis is to introduce a new lossless compression algorithm for multispectral images. Proposed algorithm is based on reducing the band ordering problem to the problem of finding a minimum spanning tree in a weighted directed graph, where set of the graph vertices corresponds to multispectral image bands and the arcs’ weights have been computed using a newly invented adaptive linear prediction model. The adaptive prediction model is an extended unification of 2–and 4–neighbour pixel context linear prediction schemes. The algorithm provides individual prediction of each image band using the optimal prediction scheme, defined by the adaptive prediction model and the optimal predicting band suggested by minimum spanning tree. Its efficiency has been compared with respect to the best lossless compression algorithms for multispectral images. Three recently invented algorithms have been considered. Numerical results produced by these algorithms allow concluding that adaptive prediction based algorithm is the best one for lossless compression of multispectral images. Real multispectral data captured from an airplane have been used for the testing.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Text Classification and Indexing in IP Networks

Internet on elektronisen postin perusrakenne ja ollut tärkeä tiedonlähde akateemisille käyttäjille jo pitkään. Siitä on tullut merkittävä tietolähde kaupallisille yrityksille niiden pyrkiessä pitämään yhteyttä asiakkaisiinsa ja seuraamaan kilpailijoitansa. WWW:n kasvu sekä määrällisesti että sen moninaisuus on luonut kasvavan kysynnän kehittyneille tiedonhallintapalveluille. Tällaisia palveluja ovet ryhmittely ja luokittelu, tiedon löytäminen ja suodattaminen sekä lähteiden käytön personointi ja seuranta. Vaikka WWW:stä saatavan tieteellisen ja kaupallisesti arvokkaan tiedon määrä on huomattavasti kasvanut viime vuosina sen etsiminen ja löytyminen on edelleen tavanomaisen Internet hakukoneen varassa. Tietojen hakuun kohdistuvien kasvavien ja muuttuvien tarpeiden tyydyttämisestä on tullut monimutkainen tehtävä Internet hakukoneille. Luokittelu ja indeksointi ovat merkittävä osa luotettavan ja täsmällisen tiedon etsimisessä ja löytämisessä. Tämä diplomityö esittelee luokittelussa ja indeksoinnissa käytettävät yleisimmät menetelmät ja niitä käyttäviä sovelluksia ja projekteja, joissa tiedon hakuun liittyvät ongelmat on pyritty ratkaisemaan.

Multispectral Analysis of Paper Production Phases

Paperitehtaissa paperin väriä arvioidaan L*a*b –arvojen perusteella. Tämä lähestymistapa ei ole tarkka ja johtaa siihen, että saman luokkaan kuuluvat paperit saatetaan havaita eri värisinä. Tässä diplomityössä tarkastellaan värien arviointia multispektraalisen kuvantamisen avulla. Menetelmän ajatuksena on verrata standardoidun heijastuman spektriä kohteena olevan paperirullan heijastuman spektriin mittaustapojen avulla. 12:n kirjallisuuteen perustuvan ja yhden tutkimusryhmämme kehittämän mittaustavan joukosta pyrittiin valitsemaan parhaat mittaustavat tutkimuksien perusteella. Mittaustavan tehokkuus tarkoittaa kykä tunnistaa eroavaisuuksia värisävyn, värikylläisyyden ja valoisuuden perusteella. Mittaustapoja tutkittiin sekä keinotekoisilla kuvilla että aidoilla paperinäytteillä. Tuloksena maksimi-minimi-, aritmeettisen keskiarvon minimi- ja geometrisen keskiarvon minimimenetelmä olivat parhaita mittaustapoja.

ICA as a preprocessing technique for classification

In this paper we propose the use of the independent component analysis (ICA) [1] technique for improving the classification rate of decision trees and multilayer perceptrons [2], [3]. The use of an ICA for the preprocessing stage, makes the structure of both classifiers simpler, and therefore improves the generalization properties. The hypothesis behind the proposed preprocessing is that an ICA analysis will transform the feature space into a space where the components are independent, and aligned to the axes and therefore will be more adapted to the way that a decision tree is constructed. Also the inference of the weights of a multilayer perceptron will be much easier because the gradient search in the weight space will follow independent trajectories. The result is that classifiers are less complex and on some databases the error rate is lower. This idea is also applicable to regression

Feature Selection, Ranking of Each Feature and Classification for the Diagnosis of Community Acquired Legionella Pneumonia

Diagnosis of community acquired legionella pneumonia (CALP) is currently performed by means of laboratory techniques which may delay diagnosis several hours. To determine whether ANN can categorize CALP and non-legionella community-acquired pneumonia (NLCAP) and be standard for use by clinicians, we prospectively studied 203 patients with community-acquired pneumonia (CAP) diagnosed by laboratory tests. Twenty one clinical and analytical variables were recorded to train a neural net with two classes (LCAP or NLCAP class). In this paper we deal with the problem of diagnosis, feature selection, and ranking of the features as a function of their classification importance, and the design of a classifier the criteria of maximizing the ROC (Receiving operating characteristics) area, which gives a good trade-off between true positives and false negatives. In order to guarantee the validity of the statistics; the train-validation-test databases were rotated by the jackknife technique, and a multistarting procedure was done in order to make the system insensitive to local maxima.

A definition and classification of status epilepticus - Report of the ILAE Task Force on Classification of Status Epilepticus.

The Commission on Classification and Terminology and the Commission on Epidemiology of the International League Against Epilepsy (ILAE) have charged a Task Force to revise concepts, definition, and classification of status epilepticus (SE). The proposed new definition of SE is as follows: Status epilepticus is a condition resulting either from the failure of the mechanisms responsible for seizure termination or from the initiation of mechanisms, which lead to abnormally, prolonged seizures (after time point t1 ). It is a condition, which can have long-term consequences (after time point t2 ), including neuronal death, neuronal injury, and alteration of neuronal networks, depending on the type and duration of seizures. This definition is conceptual, with two operational dimensions: the first is the length of the seizure and the time point (t1 ) beyond which the seizure should be regarded as "continuous seizure activity." The second time point (t2 ) is the time of ongoing seizure activity after which there is a risk of long-term consequences. In the case of convulsive (tonic-clonic) SE, both time points (t1 at 5 min and t2 at 30 min) are based on animal experiments and clinical research. This evidence is incomplete, and there is furthermore considerable variation, so these time points should be considered as the best estimates currently available. Data are not yet available for other forms of SE, but as knowledge and understanding increase, time points can be defined for specific forms of SE based on scientific evidence and incorporated into the definition, without changing the underlying concepts. A new diagnostic classification system of SE is proposed, which will provide a framework for clinical diagnosis, investigation, and therapeutic approaches for each patient. There are four axes: (1) semiology; (2) etiology; (3) electroencephalography (EEG) correlates; and (4) age. Axis 1 (semiology) lists different forms of SE divided into those with prominent motor systems, those without prominent motor systems, and currently indeterminate conditions (such as acute confusional states with epileptiform EEG patterns). Axis 2 (etiology) is divided into subcategories of known and unknown causes. Axis 3 (EEG correlates) adopts the latest recommendations by consensus panels to use the following descriptors for the EEG: name of pattern, morphology, location, time-related features, modulation, and effect of intervention. Finally, axis 4 divides age groups into neonatal, infancy, childhood, adolescent and adulthood, and elderly.

Preoperative assessment and classification of benign laryngotracheal stenosis: a consensus paper of the European Laryngological Society.

Adult and pediatric laryngotracheal stenoses (LTS) comprise a wide array of various conditions that require precise preoperative assessment and classification to improve comparison of different therapeutic modalities in a matched series of patients. This consensus paper of the European Laryngological Society proposes a five-step endoscopic airway assessment and a standardized reporting system to better differentiate fresh, incipient from mature, cicatricial LTSs, simple one-level from complex multilevel LTSs and finally "healthy" from "severely morbid" patients. The proposed scoring system, which integrates all of these parameters, may be used to help define different groups of LTS patients, choose the best treatment modality for each individual patient and assess distinct post-treatment outcomes accordingly.

Classification and inventory management of abnormal demand items

The main objective of the study is to form a framework that provides tools to recognise and classify items whose demand is not smooth but varies highly on size and/or frequency. The framework will then be combined with two other classification methods in order to form a three-dimensional classification model. Forecasting and inventory control of these abnormal demand items is difficult. Therefore another object of this study is to find out which statistical forecasting method is most suitable for forecasting of abnormal demand items. The accuracy of different methods is measured by comparing the forecast to the actual demand. Moreover, the study also aims at finding proper alternatives to the inventory control of abnormal demand items. The study is quantitative and the methodology is a case study. The research methods consist of theory, numerical data, current state analysis and testing of the framework in case company. The results of the study show that the framework makes it possible to recognise and classify the abnormal demand items. It is also noticed that the inventory performance of abnormal demand items differs significantly from the performance of smoothly demanded items. This makes the recognition of abnormal demand items very important.

The fossil crown wasp Electrostephanus petiolatus Brues in Baltic Amber (Hymenoptera, Stephanidae): designation of a neotype, revised classification,and a key to amber Stephanidae.

The fossil crown wasp Electrostephanus petiolatus Brues comb. rev.(Stephanidae, Electrostephaninae) is re-described from a single male preserved in middle Eocene Baltic Amber. The holotype was lost or destroyed around the time of World War II and subsequent interpretations of its identity have been based solely on the brief descriptive comments provided by Brues in his original account. The new specimen matches the original description and illustration provided by Brues in every detail and we hereby consider them to be conspecific, selecting the specimen as a neotype for the purpose of stabilizing the nomenclature for this fossil species. This neotype exhibits a free first metasomal tergum and sternum, contrary to the assertion of previous workers who indicated these to be fused. Accordingly, this species does indeed belong to the genus Electrostephanus Brues rather than to Denaeostephanus Engel & Grimaldi (Stephaninae). Electrostephanus petiolatus is transferred to a new subgenus, Electrostephanodes n. subgen. , based on its elongate pseudo- petiole and slender gaster, but may eventually warrant generic status as the phylogenetic placement of these fossil lineages continues to be clarifi ed. A revised key to the Baltic amber crown wasps is provided.

Bayesian Networks for the Age Classification of Living Individuals: a Study on Transition Analysis

Over the past few decades, age estimation of living persons has represented a challenging task for many forensic services worldwide. In general, the process for age estimation includes the observation of the degree of maturity reached by some physical attributes, such as dentition or several ossification centers. The estimated chronological age or the probability that an individual belongs to a meaningful class of ages is then obtained from the observed degree of maturity by means of various statistical methods. Among these methods, those developed in a Bayesian framework offer to users the possibility of coherently dealing with the uncertainty associated with age estimation and of assessing in a transparent and logical way the probability that an examined individual is younger or older than a given age threshold. Recently, a Bayesian network for age estimation has been presented in scientific literature; this kind of probabilistic graphical tool may facilitate the use of the probabilistic approach. Probabilities of interest in the network are assigned by means of transition analysis, a statistical parametric model, which links the chronological age and the degree of maturity by means of specific regression models, such as logit or probit models. Since different regression models can be employed in transition analysis, the aim of this paper is to study the influence of the model in the classification of individuals. The analysis was performed using a dataset related to the ossifications status of the medial clavicular epiphysis and results support that the classification of individuals is not dependent on the choice of the regression model.