A cophenetic correlation coefficient for Tocher's method

The objective of this work was to propose a way of using the Tocher's method of clustering to obtain a matrix similar to the cophenetic one obtained for hierarchical methods, which would allow the calculation of a cophenetic correlation. To illustrate the obtention of the proposed cophenetic matrix, we used two dissimilarity matrices - one obtained with the generalized squared Mahalanobis distance and the other with the Euclidean distance - between 17 garlic cultivars, based on six morphological characters. Basically, the proposal for obtaining the cophenetic matrix was to use the average distances within and between clusters, after performing the clustering. A function in R language was proposed to compute the cophenetic matrix for Tocher's method. The empirical distribution of this correlation coefficient was briefly studied. For both dissimilarity measures, the values of cophenetic correlation obtained for the Tocher's method were higher than those obtained with the hierarchical methods (Ward's algorithm and average linkage - UPGMA). Comparisons between the clustering made with the agglomerative hierarchical methods and with the Tocher's method can be performed using a criterion in common: the correlation between matrices of original and cophenetic distances.

Gestión de confianza en redes ad hoc

El despliegue de un esquema de confianza es fundamental para poder desarrollar servicios de seguridad que permitan administrar y operar una red. Sin embargo, las soluciones empleadas en las redes tradicionales no se adaptan a un entorno ad hoc debido a la naturaleza dinámica y sin infraestructura de estas redes. En el presente trabajo se propone un esquema de confianza práctico y eficiente basado en una infraestructura de clave pública distribuida, umbral y jerárquica, que no requiere sincronización temporal entre todos los nodos de la red. La autorización de usuarios en el sistema se hace a través de certificados de corta duración que eliminan la necesidad de mantener la publicación y diseminación de unas listas de revocación. Por otro lado, una entidad externa de confianza permite alargar la reputación de un usuario de la red más allá de la existencia de la propia red.

Comparison of molecular signatures from multiple skin diseases identifies mechanisms of immunopathogenesis.

The ability to obtain gene expression profiles from human disease specimens provides an opportunity to identify relevant gene pathways, but is limited by the absence of data sets spanning a broad range of conditions. Here, we analyzed publicly available microarray data from 16 diverse skin conditions in order to gain insight into disease pathogenesis. Unsupervised hierarchical clustering separated samples by disease as well as common cellular and molecular pathways. Disease-specific signatures were leveraged to build a multi-disease classifier, which predicted the diagnosis of publicly and prospectively collected expression profiles with 93% accuracy. In one sample, the molecular classifier differed from the initial clinical diagnosis and correctly predicted the eventual diagnosis as the clinical presentation evolved. Finally, integration of IFN-regulated gene programs with the skin database revealed a significant inverse correlation between IFN-β and IFN-γ programs across all conditions. Our study provides an integrative approach to the study of gene signatures from multiple skin conditions, elucidating mechanisms of disease pathogenesis. In addition, these studies provide a framework for developing tools for personalized medicine toward the precise prediction, prevention, and treatment of disease on an individual level.

Classification and fingerprinting of different berries based on biochemical profiling and antioxidant capacity

The objective of this work was to evaluate the biochemical composition of six berry types belonging to Fragaria, Rubus, Vaccinium and Ribes genus. Fruit samples were collected in triplicate (50 fruit each) from 18 different species or cultivars of the mentioned genera, during three years (2008 to 2010). Content of individual sugars, organic acids, flavonols, and phenolic acids were determined by high performance liquid chromatography (HPLC) analysis, while total phenolics (TPC) and total antioxidant capacity (TAC), by using spectrophotometry. Principal component analysis (PCA) and hierarchical cluster analysis (CA) were performed to evaluate the differences in fruit biochemical profile. The highest contents of bioactive components were found in Ribes nigrum and in Fragaria vesca, Rubus plicatus, and Vaccinium myrtillus. PCA and CA were able to partially discriminate between berries on the basis of their biochemical composition. Individual and total sugars, myricetin, ellagic acid, TPC and TAC showed the highest impact on biochemical composition of the berry fruits. CA separated blackberry, raspberry, and blueberry as isolate groups, while classification of strawberry, black and red currant in a specific group has not occurred. There is a large variability both between and within the different types of berries. Metabolite fingerprinting of the evaluated berries showed unique biochemical profiles and specific combination of bioactive compound contents.

Treatment intensification and risk factor control: toward more clinically relevant quality measures.

BACKGROUND: Intensification of pharmacotherapy in persons with poorly controlled chronic conditions has been proposed as a clinically meaningful process measure of quality. OBJECTIVE: To validate measures of treatment intensification by evaluating their associations with subsequent control in hypertension, hyperlipidemia, and diabetes mellitus across 35 medical facility populations in Kaiser Permanente, Northern California. DESIGN: Hierarchical analyses of associations of improvements in facility-level treatment intensification rates from 2001 to 2003 with patient-level risk factor levels at the end of 2003. PATIENTS: Members (515,072 and 626,130; age >20 years) with hypertension, hyperlipidemia, and/or diabetes mellitus in 2001 and 2003, respectively. MEASUREMENTS: Treatment intensification for each risk factor defined as an increase in number of drug classes prescribed, of dosage for at least 1 drug, or switching to a drug from another class within 3 months of observed poor risk factor control. RESULTS: Facility-level improvements in treatment intensification rates between 2001 and 2003 were strongly associated with greater likelihood of being in control at the end of 2003 (P < or = 0.05 for each risk factor) after adjustment for patient- and facility-level covariates. Compared with facility rankings based solely on control, addition of percentages of poorly controlled patients who received treatment intensification changed 2003 rankings substantially: 14%, 51%, and 29% of the facilities changed ranks by 5 or more positions for hypertension, hyperlipidemia, and diabetes, respectively. CONCLUSIONS: Treatment intensification is tightly linked to improved control. Thus, it deserves consideration as a process measure for motivating quality improvement and possibly for measuring clinical performance.

Effects of colonization asymmetries on metapopulation persistence.

Ocean currents, prevailing winds, and the hierarchical structures of river networks are known to create asymmetries in re-colonization between habitat patches. The impacts of such asymmetries on metapopulation persistence are seldom considered, especially rarely in theoretical studies. Considering three classical models (the island, the stepping stone and the distance-dependent model), we explore how metapopulation persistence is affected by (i) asymmetry in dispersal strength, in which the colonization rate between two patches differs in direction, and (ii) asymmetry in connectivity, in which the overall colonization pattern displays asymmetry (circulating or dendritic networks). Viability can be drastically reduced when directional bias in dispersal strength is higher than 25%. Re-colonization patterns that allow for strong local connectivity provide the highest persistence compared to systems that allow circulation. Finally, asymmetry has relatively weak effects when metapopulations maintain strong general connectivity.

How do plants feel the heat?

In plants, the heat stress response (HSR) is highly conserved and involves multiple pathways, regulatory networks and cellular compartments. At least four putative sensors have recently been proposed to trigger the HSR. They include a plasma membrane channel that initiates an inward calcium flux, a histone sensor in the nucleus, and two unfolded protein sensors in the endoplasmic reticulum and the cytosol. Each of these putative sensors is thought to activate a similar set of HSR genes leading to enhanced thermotolerance, but the relationship between the different pathways and their hierarchical order is unclear. In this review, we explore the possible involvement of different thermosensors in the plant response to warming and heat stress.

The neural basis for writing from dictation in the temporoparietal cortex.

Cortical electrical stimulation mapping was used to study neural substrates of the function of writing in the temporoparietal cortex. We identified the sites involved in oral language (sentence reading and naming) and writing from dictation, in order to spare these areas during removal of brain tumours in 30 patients (23 in the left, and 7 in the right hemisphere). Electrostimulation of the cortex impaired writing ability in 62 restricted cortical areas (.25 cm2). These were found in left temporoparietal lobes and were mostly located along the superior temporal gyrus (Brodmann's areas 22 and 42). Stimulation of right temporoparietal lobes in right-handed patients produced no writing impairments. However there was a high variability of location between individuals. Stimulation resulted in combined symptoms (affecting oral language and writing) in fourteen patients, whereas in eight other patients, stimulation-induced pure agraphia symptoms with no oral language disturbance in twelve of the identified areas. Each detected area affected writing in a different way. We detected the various different stages of the auditory-to-motor pathway of writing from dictation: either through comprehension of the dictated sentences (word deafness areas), lexico-semantic retrieval, or phonologic processing. In group analysis, barycentres of all different types of writing interferences reveal a hierarchical functional organization along the superior temporal gyrus from initial word recognition to lexico-semantic and phonologic processes along the ventral and the dorsal comprehension pathways, supporting the previously described auditory-to-motor process. The left posterior Sylvian region supports different aspects of writing function that are extremely specialized and localized, sometimes being segregated in a way that could account for the occurrence of pure agraphia that has long-been described in cases of damage to this region.

Bayesian classification of forest ecological type from satellite data

The main objective of this study was todo a statistical analysis of ecological type from optical satellite data, using Tipping's sparse Bayesian algorithm. This thesis uses "the Relevence Vector Machine" algorithm in ecological classification betweenforestland and wetland. Further this bi-classification technique was used to do classification of many other different species of trees and produces hierarchical classification of entire subclasses given as a target class. Also, we carried out an attempt to use airborne image of same forest area. Combining it with image analysis, using different image processing operation, we tried to extract good features and later used them to perform classification of forestland and wetland.

Humour and translation, an interdiscipline

This paper calls for greater attention from researchers into the nature of humor translation as an interdisciplinary area that should be of interest to translation and humor studies. It includes a brief review of the complexity of translation and the problems posed by traditional approaches. The paper introduces a number of parameters that may be of assistance in developing joke typologies for translators or translation scholars. A model is presented for structuring joke-types according to binary branching. An attempt is then made to combine the model with ideas and concepts put forward in Attardo (2002). The result is a binary branch tree for the 6 Knowledge Resources and the hierarchical structure that Attardo claims they have. One important conclusion is that sameness, or similarity, may have little to do with funniness, and, if this is so, it is going to create a dilemma for translators wishing to achieve equivalent effect.

Kuvausmenetelmänvalinta ja käyttöönotto ohjelmistotuoteorganisaatiossa

Useiden pitkän kehityskaaren ohjelmistojen ylläpitäminen ja kehittäminen on vaikeaa, sillä niiden dokumentaatio on vajaata tai vanhentunutta. Tässä diplomityössä etsitään ratkaisua tällaisen ohjelmiston ja sen taustalla olevan järjestelmän kuvaukseen. Tavoitteina on tukea nykyisen ohjelmiston ylläpitoa ja uuden työvoiman perehdyttämistä. Tavoitteena on myös pohjustaa uuden korvaavan ohjelmiston suunnittelua kuvaamalla nykyiseen järjestelmään sitoutunutta sovellusalueosaamista. Työssä kehitetään kuvausmenetelmä järjestelmän kuvaamiseen hierarkkisesti laitteistotason yleiskuvauksesta ohjelmiston luokkarakenteeseen sekä toiminnallisuuteen asti. Laite- ja luokkarakennekuvaukset ovat rakenteellisia kuvauksia, joiden tehtävänä on selittää järjestelmän ja sen osien kokoonpano. Toiminnallisuudesta kertovat kuvaukset on toteutettu käyttötapauskuvauksina. Työssä keskityttiin erityisesti kohdejärjestelmän keskeisen ohjelmiston ja tietokannan kuvaamiseen. Ohjelmistosta valittiin tärkeimmät ja eniten sovellusalueen tietotaitoa sisältävät osat, joista työssä luotiin esimerkkikuvaukset. Kuvauksia on kehitettyä menetelmää hyödyntäen helppo laajentaa tarpeiden mukaan paitsi ohjelmiston muihin osiin, myös laitteiston ja järjestelmän kuvaamiseen kokonaisuudessaan syvemmin.

Cluster-based active learning for compact image classification

In this paper, we consider active sampling to label pixels grouped with hierarchical clustering. The objective of the method is to match the data relationships discovered by the clustering algorithm with the user's desired class semantics. The first is represented as a complete tree to be pruned and the second is iteratively provided by the user. The active learning algorithm proposed searches the pruning of the tree that best matches the labels of the sampled points. By choosing the part of the tree to sample from according to current pruning's uncertainty, sampling is focused on most uncertain clusters. This way, large clusters for which the class membership is already fixed are no longer queried and sampling is focused on division of clusters showing mixed labels. The model is tested on a VHR image in a multiclass classification setting. The method clearly outperforms random sampling in a transductive setting, but cannot generalize to unseen data, since it aims at optimizing the classification of a given cluster structure.

Turvallisuustoimintojen käyttö ydinvoimalaitoksilla

Tässä diplomityössä tarkastellaan turvallisuustoiminto-käsitteen määrittelyä ja käyttöä osana ydinvoimalaitosten turvallisuuden varmistamista. Työssä kuvataan paine- ja kiehutusvesilaitosten toiminnan yleispiirteet, sekä Teollisuuden Voima Oy:n (TVO) laitosten Olkiluoto 1 & 2 sekä Olkiluoto 3 tarkempi turvallisuustoiminta turvallisuusjärjestelmien ja -automaation osalta. Työssä esitellään eräs tapa määrittää turvallisuustoimintoja. Malli perustuu hierarkkiseen rakenteeseen, jossa ylimpänä ovat laitostason turvallisuustoiminnot ja alimpana turvallisuustoimintoihin osallistuvien laitteiden ja niiden osien toiminnot. Turvallisuustoimintoja on mahdollista käyttää ydinvoimalaitoksen turvallisuusluokituksen tekemiseen ja perustelemiseen. Turvallisuustoiminto kertoo suoraan luokiteltavan kohteen turvallisuusmerkityksen. Kohteen turvallisuusmerkityksen selvittäminen, eli liittäminen turvallisuustoimintoon, voi olla vaikeaa. Turvallisuustoimintoja on myös mahdollista käyttää laitoksen turvallisuusautomaation riittävän varmistamisen (mm. redundanttisuus, diversiteetti ja erotus) osoittamiseen erityisesti ohjelmoitavan automaation yhteydessä. Turvallisuustoimintoja voidaan hyödyntää laitoksen hätätilanneohjeiden kehittämisessä ja myös laitoksenmuun turvallisuusdokumentaation selkeyttämisessä. Työn tuloksena kehitettiin käyville laitoksille (OL1 & 2) aikaisempaa kattavammat turvallisuustoiminnot. Lisäksi tarkasteltiin rakenteilla olevalle laitokselle (OL3) määriteltyjä turvallisuustoimintoja.

Cigarette, cigar, and pipe smoking and the risk of head and neck cancers: pooled analysis in the International Head and Neck Cancer Epidemiology Consortium.

Cigar and pipe smoking are considered risk factors for head and neck cancers, but the magnitude of effect estimates for these products has been imprecisely estimated. By using pooled data from the International Head and Neck Cancer Epidemiology (INHANCE) Consortium (comprising 13,935 cases and 18,691 controls in 19 studies from 1981 to 2007), we applied hierarchical logistic regression to more precisely estimate odds ratios and 95% confidence intervals for cigarette, cigar, and pipe smoking separately, compared with reference groups of those who had never smoked each single product. Odds ratios for cigar and pipe smoking were stratified by ever cigarette smoking. We also considered effect estimates of smoking a single product exclusively versus never having smoked any product (reference group). Among never cigarette smokers, the odds ratio for ever cigar smoking was 2.54 (95% confidence interval (CI): 1.93, 3.34), and the odds ratio for ever pipe smoking was 2.08 (95% CI: 1.55, 2.81). These odds ratios increased with increasing frequency and duration of smoking (Ptrend ≤ 0.0001). Odds ratios for cigar and pipe smoking were not elevated among ever cigarette smokers. Head and neck cancer risk was elevated for those who reported exclusive cigar smoking (odds ratio = 3.49, 95% CI: 2.58, 4.73) or exclusive pipe smoking (odds ratio = 3.71, 95% CI: 2.59, 5.33). These results suggest that cigar and pipe smoking are independently associated with increased risk of head and neck cancers.

UniPathway: a resource for the exploration and annotation of metabolic pathways.

UniPathway (http://www.unipathway.org) is a fully manually curated resource for the representation and annotation of metabolic pathways. UniPathway provides explicit representations of enzyme-catalyzed and spontaneous chemical reactions, as well as a hierarchical representation of metabolic pathways. This hierarchy uses linear subpathways as the basic building block for the assembly of larger and more complex pathways, including species-specific pathway variants. All of the pathway data in UniPathway has been extensively cross-linked to existing pathway resources such as KEGG and MetaCyc, as well as sequence resources such as the UniProt KnowledgeBase (UniProtKB), for which UniPathway provides a controlled vocabulary for pathway annotation. We introduce here the basic concepts underlying the UniPathway resource, with the aim of allowing users to fully exploit the information provided by UniPathway.