An Analysis of Some Relations Among Domain Ontologies

* This paper was made according to the program of fundamental scientific research of the Presidium of the Russian Academy of Sciences «Mathematical simulation and intellectual systems», the project "Theoretical foundation of the intellectual systems based on ontologies for intellectual support of scientific researches".

Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.

MOTIVATION: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species. RESULTS: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee. AVAILABILITY: download section of the Bgee website http://bgee.unil.ch/

Predictions of the MCMI-III personality disorders from NEO-PI-R domains and facets: Comparison between American and Spanish samples

Este estudio ex post facto analiza las relaciones entre las dimensiones y facetas del NEO-PI-R y los 14 trastornos de personalidad del MCMI-III en una muestra no clínica española (N = 674). Se exploran las diferencias y similitudes con los resul- tados de Dyce y O’Connor en una muestra americana con los mismos instrumentos. Como se esperaba, los análisis factoriales de facetas reteniendo cinco factores mostraron un modelo de relaciones muy similar entre ambas muestras, con un coeficiente de la congruencia total de 0,92, y coeficientes de congruencia de factor aceptables, salvo para el factor Apertura (0,68). En consonancia con las predicciones de Widiger y Widiger et al. los porcentajes de correlaciones significativas estaban alrededor de 60% en ambas muestras, y la mayoría coincidían. El análisis de regresión múltiple con dimensiones también reveló un gran parecido entre los resultados americanos y españoles, Neuroticismo fue el predictor más relacionado con los trastornos de personalidad. Se encontraron diferencias en las regresiones por facetas, aunque la varianza explicada fue prácticamente la misma que en las dimensiones. Se discute la validez transcultural y el valor predictivo del NEO-PI-R sobre los trastornos de personalidad del MCMI-III, junto con las ventajas relativas de las facetas sobre las dimensiones.

Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings

The study of continuously varying, quantitative traits is important in evolutionary biology, agriculture, and medicine. Variation in such traits is attributable to many, possibly interacting, genes whose expression may be sensitive to the environment, which makes their dissection into underlying causative factors difficult. An important population parameter for quantitative traits is heritability, the proportion of total variance that is due to genetic factors. Response to artificial and natural selection and the degree of resemblance between relatives are all a function of this parameter. Following the classic paper by R. A. Fisher in 1918, the estimation of additive and dominance genetic variance and heritability in populations is based upon the expected proportion of genes shared between different types of relatives, and explicit, often controversial and untestable models of genetic and non-genetic causes of family resemblance. With genome-wide coverage of genetic markers it is now possible to estimate such parameters solely within families using the actual degree of identity-by-descent sharing between relatives. Using genome scans on 4,401 quasi-independent sib pairs of which 3,375 pairs had phenotypes, we estimated the heritability of height from empirical genome-wide identity-by-descent sharing, which varied from 0.374 to 0.617 (mean 0.498, standard deviation 0.036). The variance in identity-by-descent sharing per chromosome and per genome was consistent with theory. The maximum likelihood estimate of the heritability for height was 0.80 with no evidence for non-genetic causes of sib resemblance, consistent with results from independent twin and family studies but using an entirely separate source of information. Our application shows that it is feasible to estimate genetic variance solely from within- family segregation and provides an independent validation of previously untestable assumptions. Given sufficient data, our new paradigm will allow the estimation of genetic variation for disease susceptibility and quantitative traits that is free from confounding with non-genetic factors and will allow partitioning of genetic variation into additive and non-additive components.

Genetics of colouration in birds.

Establishing the links between phenotype and genotype is of great importance for resolving key questions about the evolution, maintenance and adaptive function of phenotypic variation. Bird colouration is one of the most studied systems to investigate the role of natural and sexual selection in the evolution of phenotypic diversity. Given the recent advances in molecular tools that allow discovering genetic polymorphisms and measuring gene and protein expression levels, it is timely to review the literature on the genetics of bird colouration. The present study shows that melanin-based colour phenotypes are often associated with mutations at melanogenic genes. Differences in melanin-based colouration are caused by switches of eumelanin to pheomelanin production or by changes in feather keratin structure, melanoblast migration and differentiation, as well as melanosome structure. Similar associations with other types of colourations are difficult to establish, because our knowledge about the molecular genetics of carotenoid-based and structural colouration is quasi inexistent. This discrepancy stems from the fact that only melanin-based colouration shows pronounced heritability estimates, i.e. the resemblance between related individuals is usually mainly explained by genetic factors. In contrast, the expression of carotenoid-based colouration is phenotypically plastic with a high sensitivity to variation in environmental conditions. It therefore appears that melanin-based colour traits are prime systems to understand the genetic basis of phenotypic variation. In this context, birds have a great potential to bring us to new frontiers where many exciting discoveries will be made on the genetics of phenotypic traits, such as colouration. In this context, a major goal of our review is to suggest a number of exciting future avenues.

3-amino-1,2,4-triazole inhibits macrophage NO synthase.

Murine macrophages activated by interferon-gamma and lipopolysaccharide become leishmanicidal through a process involving L-arginine-derived nitrogen oxidation products. Both nitrite secretion and parasite killing by activated macrophages were inhibited by 3-amino-1,2,4-triazole as well as the related compound, 3-amino-1,2,4-triazine. Moreover, NO synthase activity in cytosolic extracts of activated cells was inhibited by both compounds. 4-amino-1,2,4-triazole, an isomer of 3-amino-1,2,4-triazole, was without effect. Our results suggest that besides its known inhibitory effect on catalases and peroxidases, 3-amino-1,2,4-triazole is an inhibitor of NO synthase. The resemblance between the tautomeric form of 3-amino-1,2,4-triazole and the guanidino group of L-arginine, the natural substrate for NO synthase, might be responsible for the observed inhibition.

Bgee: integrating and comparing heterogeneous transcriptome data among species

Gene expression patterns are a key feature in understanding gene function, notably in development. Comparing gene expression patterns between animals is a major step in the study of gene function as well as of animal evolution. It also provides a link between genes and phenotypes. Thus we have developed Bgee, a database designed to compare expression patterns between animals, by implementing ontologies describing anatomies and developmental stages of species, and then designing homology relationships between anatomies and comparison criteria between developmental stages. To define homology relationships between anatomical features we have developed the software Homolonto, which uses a modified ontology alignment approach to propose homology relationships between ontologies. Bgee then uses these aligned ontologies, onto which heterogeneous expression data types are mapped. These already include microarrays and ESTs.

La teneur du standard de fiabilité des moyens électroniques de signature

Les institutions juridiques ont été bâties autour des réalités connues depuis des millénaires, que nous appelons de nos jours des phénomènes du monde réel. Ces phénomènes retrouvent présentement un nouveau théâtre – le cyberespace, et les règles du droit font face au défi de s’approprier ce nouvel environnement. Entre autres, les technologies du cyberespace ont mis au monde divers moyens qui nous permettent de nous identifier et de manifester notre attitude envers les actes juridiques – des finalités qui ont été assurées de longue date par la signature manuscrite. Bien que ces nouveaux moyens aient mérité un nom similaire à leur contrepartie traditionnelle – l’appellation de signature électronique, ils restent des phénomènes dont la proximité avec la signature manuscrite est discutable. Force est de constater que le seul point commun entre les moyens classiques et électroniques de signer réside dans les fonctions qu’ils remplissent. C’est en se basant sur ces fonctions communes que le droit a adopté une attitude identique envers les moyens d’authentification traditionnels et électroniques et a accueilli ces derniers sous l’emprise de ses institutions. Cependant, ceci ne signifie pas que ces institutions se soient avérées appropriées et qu’elles ne demandent aucun ajustement. Un des buts de notre étude sera de mettre en relief les moyens d’adaptation qu’offre le droit pour réconcilier ces deux environnements. Ainsi, pour ajuster l’institution de la signature aux phénomènes électroniques, le droit s’est tourné vers le standard de fiabilité de la signature électronique. Le standard de fiabilité est un complément de l’institution juridique de signature qui ne se rapporte qu’à la signature électronique et dont cette étude démontrera les applications. Les composantes du standard de fiabilité qui occuperont un deuxième volet de notre étude représentent un ensemble de règles techniques liées à la signature électronique. Ainsi, comme le standard de fiabilité puise sa substance dans les propriétés de l’architecture du cyberespace, l’attitude du droit envers la signature électronique s’avère tributaire de la morphologie du cyberespace. Étant donné que les possibilités qui nous sont offertes par la technologie continue à déterminer la réglementation juridique, il est légitime de conclure que l’examen des tendances dans l’évolution du cyberespace nous fournira un point de vue prospectif sur l’évolution des règles du droit.

Investigation of the faecal microbiota associated with canine chronic diarrhoea.

Diarrhoea is a common problem in dogs and can result in disturbance of the normal intestinal microbiota. However, little is known about the gastrointestinal microbiota of dogs with chronic diarrhoea and controlled canine studies of dietary management are scarce. The aims of this study were to investigate the predominant faecal microbiota of chronic diarrhoea dogs and to examine the effect(s) of a fibre blend on the canine faecal microbiota. A 3-week fibre supplementation feeding study was performed in nine chronic diarrhoea and eight control dogs. Atopobium cluster, Lactobacillus-Enterococcus group and Clostridium cluster XIV were the predominant bacterial groups in all dogs. Chronic diarrhoea dogs had significantly higher Bacteroides counts at baseline and significantly lower Atopobium cluster counts following fibre supplementation compared with control dogs. Atopobium cluster levels increased significantly in control dogs, while counts of sulphate-reducing bacteria decreased significantly and Clostridium clusters I and II counts increased significantly in chronic diarrhoea dogs during fibre supplementation. Microbial profiles (detected by denaturing gradient gel electrophoresis) demonstrated interindividual variation, with greater similarity seen between the chronic diarrhoea and control dogs' profiles after fibre supplementation compared with baseline. In conclusion, fibre supplementation induced changes in the canine faecal microbiota, with greater resemblance between the microbiota of chronic diarrhoea and control dogs after this dietary modulation.

Redesign av Vagabonds guideboksserieThe travelguides of Vagabond - Redesign

Todays travel trends go towards independence and self planning. If you need advice or help when performing your trip, there are several different series of guidebooks on the market and one of these series comes from the travel magazine Vagabond. This degree project concerns the redesigning of the travelguides of Vagabond, or to be precise: their cityguide over Istanbul. The purpose of the new design is to assure the resemblance between the guidebook and the magazine, as wanted by the Art Director of Vagabond Angelica Zander.Prior to the redesigning process preliminary studies that make up the fundamental ideas were made. Three other big titles of guidebooks on the market were analyzed, and in addition a great deal of focus – considering the final purpose – was put on the concept of magazine design. Some color psychology has also been studied to make out what a difference color makes in printed media and what power color can contribute with, when delivering the message. Finally redesign as a concept has been investigated to clarify why the way of expression should be renewed from time to time.The result is presented as spread examples from the cityguide over Istanbul. The new design is applied on the existing content and the result is supposed to appear as a miniature magazine.

Mastocitose na infância : estudo anátomo-patológico e imuno-histoquímico

Introdução A mastocitose abrange um grupo heterogêneo de condições crônicas caracterizado pela proliferação excessiva de mastócitos nos tecidos. Os sinais e sintomas clínicos são decorrentes da distribuição anatômica dos mastócitos e do efeito funcional dos mediadores produzidos e liberados por estas células. Na infância, a doença é considerada uma condição benigna na maioria dos casos, cujo comprometimento característico é o cutâneo. As mais freqüentes manifestações na pele são os mastocitomas e a urticária pigmentosa. Lesões cutâneas bolhosas podem manifestar-se e acompanhar todas as formas de mastocitose e quando esta apresentação é a predominante, é denominada de mastocitose bolhosa. O diagnóstico de mastocitose é suspeitado clinicamente e confirmado pela histologia. A demonstração do aumento do número de mastócitos nas lesões cutâneas características se constitui no principal critério diagnóstico. Contudo, este método tem dificuldades técnicas que impedem a adequada reprodutibilidade dos achados, dificultando a elucidação de casos duvidosos e retardando seu tratamento. Considerando as propriedades imunológicas e a importância clínica dos mastócitos reveste-se de maior importância compreender o papel destas células nas doenças, sendo indispensável identificá-las e enumerá-las com acurácia nos tecidos. Objetivos Quantificar o número de mastócitos marcados com anticorpo monoclonal antitriptase, através de técnica imuno-histoquímica e análise de imagem, em biópsias cutâneas de crianças, com diagnóstico clínico de mastocitose. Descrever os achados histológicos; quantificar o número de mastócitos marcados com o anticorpo antitriptase entre as diferentes expressões clínicas da mastocitose cutânea; comparar o número de mastócitos entre os casos de mastocitose cutânea e mastocitose associada à sintomas sistêmicos e correlacionar as contagens de mastócitos entre os dois diferentes métodos (coloração por Giemsa com contagem manual e marcação com anticorpo antitriptase e análise digital). Material e Método Foram incluídas no estudo biópsias cutâneas de crianças de 0 a 14 anos, com diagnóstico clínico e histológico de mastocitose. Os casos foram classificados de acordo com a apresentação clínica cutânea em mastocitoma, urticária pigmentosa ou mastocitose bolhosa e assinalada a presença de sintomas sistêmicos associados. Os fragmentos de pele fixados em formalina e emblocados em parafina foram cortados e utilizados para diagnóstico histopatológico convencional, corados com hematoxilina-eosina e Giemsa, e para análise imuno-histoquímica com estreptavidina peroxidase marcados com anticorpo antitriptase. A densidade de mastócitos (número de células por área) foi realizada por um único observador na técnica histológica e através de um sistema de análise de imagem de vídeo no método imuno-histoquímico. Resultados Foram avaliados 33 casos de mastocitose, sendo 21 do sexo masculino. Dez casos (30,3%) apresentavam mastocitoma, 21 (63,6%) urticária pigmentosa e 2 (6,1%) mastocitose bolhosa. Todos os casos da amostra foram classificados como tendo mastocitose incipiente e em 6 (18,8%) pacientes pôde ser identificada a associação com sintomas sistêmicos. Prurido foi o sintoma mais freqüente, sendo relatado em 21 casos. Em 21 dos 33 casos foi identificada a infiltração de mastócitos na derme havendo predominância pela região perivascular (p=0,001, teste exato de Fisher). Não houve diferenças significativas entre a presença de infiltrado mastocitário e as várias formas cutâneas de mastocitose ou a mastocitose sistêmica. A presença de eosinófilos foi identificada em 15 casos (45,5%) e em 10 casos associadamente ao infiltrado perivascular de mastócitos. A densidade de mastócitos na técnica histológica, incluindo-se todos os casos, foi 50,00 células/mm2. Não houve diferença significativa das contagens entre os pacientes com mastocitoma e aqueles com urticária pigmentosa, assim como entre os pacientes com e sem sintomas sistêmicos associados aos cutâneos. A densidade de mastócitos encontrada com a técnica imuno-histoquímica e contagem por análise de imagem foi 158,85 células/mm2. Não houve diferença significativa das contagens entre os pacientes com mastocitoma e aqueles com urticária pigmentosa, assim como entre aqueles com e sem sintomas sistêmicos. Comparando-se a contagem dos mastócitos por área (densidade) entre a histologia e a imuno-histoquímica houve uma diferença significativa (p=0,0001 teste não-paramétrico de Wilcoxon). A média da diferença entre as contagens foi 199,98 células/mm2 (±365,31 DP). Também não houve semelhança, entre os dois métodos, nos grupos mastocitoma e urticária pigmentosa (p=0,005 e p=0,01, respectivamente, teste não-paramétrico de Wilcoxon). Puderam ser identificados 518% a mais de mastócitos com a técnica imunohistoquímica quando comparada com a histológica. Conclusões O presente estudo permite concluir que: 1) a localização preferencial da infiltração de mastócitos é dérmica e perivascular, não sendo possível identificar diferenças histológicas entre casos de urticária pigmentosa e mastocitoma; 2) o número de mastócitos marcados com o anticorpo monoclonal antitriptase e contados com análise digital de imagem, em biópsia de pele de crianças com diagnóstico clínico de mastocitose, foi 159 células por milímetro quadrado; 3) a densidade de mastócitos, foi semelhante entre os casos de urticária pigmentosa e mastocitoma e entre os casos com e sem sintomas sistêmicos associados nas duas diferentes técnicas empregadas; 4) o número de mastócitos por milímetro quadrado com a técnica imuno-histoquímica e a contagem através de análise de imagem foi significativamente maior quando comparada com a coloração através de Giemsa e a contagem manual, com uma diferença média entre os dois métodos de 200 células por milímetro quadrado; 5) a densidade de mastócitos com a técnica imunohistoquímica foi significativamente maior tanto nos casos com urticária pigmentosa quanto nos com mastocitoma, quando comparada com a técnica empregada rotineiramente e 6) com a técnica imuno-histoquímica e a contagem através de análise de imagem foi possível identificar 518% a mais de mastócitos quando comparada com a técnica histológica.

Caracterização florística e fitossociológica do componente arbustivo-arbóreo de uma floresta paludosa no Município de Rio Claro (SP), Brasil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Geofungos no Córrego do Sapateiro, Parque Municipal do Ibirapuera, São Paulo, SP, Brasil

No Córrego do Sapateiro, situado no Parque Municipal do Ibirapuera, na cidade de São Paulo, SP, Brasil, amostras de água (50 mL) na profundidade de 10 centímetros foram coletadas em locais antes (local 1) e depois (local 2) da estação de tratamento de flotação, durante os meses da estação chuvosa e quente (janeiro, fevereiro e março) e da estação seca e fria (junho, julho e agosto) de 2008. Além disso, a temperatura, oxigênio dissolvido, condutividade e pH da água foram medidos com um equipamento Horiba U10. Coliformes totais e fecais foram analisados com o kit Aquatest®. A partir de cada amostra de água, alíquotas de 1 mL foram inoculadas em meio batata-dextrose-ágar, totalizando 10 placas de Petri para cada local de coleta. Após incubação por 10 dias a 22 ºC, as colônias fúngicas foram quantificadas, purificadas e identificadas. Os parâmetros abióticos da água não foram limitantes para a presença de geofungos, sendo influenciados pelo tratamento de flotação. Nos dois locais o número de coliformes totais e fecais foi predominantemente superior a 8 NMP dL-1 durante o período estudado. Vinte e sete táxons de fungos foram obtidos, distribuídos em 136 ocorrências. de acordo com o índice de similaridade de Sörensen, a micota dos dois locais coletados foram consideravelmente diferentes, apesar da semelhança entre o número de táxons e ocorrências. Os resultados indicam que o tratamento da água do Córrego do Sapateiro pelo sistema de flotação possivelmente causa modificações na composição taxonômica e na quantidade de UFC de fungos, ao contrário do que ocorreu com os coliformes totais e fecais, cujos resultados apresentaram-se menos conclusivos.

Generalized point interactions in one-dimensional quantum mechanics

There is a four-parameter family of point interactions in one-dimensional quantum mechanics. They represent all possible self-adjoint extensions of the kinetic energy operator. If time-reversal invariance is imposed, the number of parameters is reduced to three. One of these point interactions is the familiar delta function potential but the other generalized ones do not seem to be widely known. We present a pedestrian approach to this subject and comment on a recent controversy in the literature concerning the so-called delta' interaction. We emphasize that there is little resemblance between the delta' interaction and what its name suggests.

Fidelity of molluscan assemblages from the touro passo formation (pleistocene-holocene), southern brazil: taphonomy as a tool for discovering natural baselines for freshwater communities

This study is the first assessment of mollusk fossil assemblages relative to the compositional fidelity of modern mollusk living and death assemblages. It also shows that the sedimentary record can provide information on the original, non-human-impacted, freshwater malacofauna biodiversity, based on Late Pleistocene shells. The fossil mollusk assemblage from the Touro Passo Formation (Pleistocene-Holocene) was compared to living and death assemblages of the Touro Passo River, southern Brazil, revealing little resemblance between fossil and live-dead species composition. Although the living and death assemblages agree closely in richness, species composition, and species relative abundances (both proportional and rank), the fossil assemblage differs significantly from both modern assemblages in most of these measures. The fossil assemblage is dominated by the native endemic corbiculid bivalve Cyanocyclas limosa and the gastropod Heleobia aff. bertoniana. These are absent in the living assemblages, and both living and death assemblages are dominated by the alien Asiatic corbiculid C. fluminea, which is absent in the fossil assemblage. The fossil assemblage also contains, overall, a higher proportional abundance of relatively thick-shelled species, suggesting a genuine bias against the thinner- and smaller-shelled species. Our results suggest that contemporary environmental changes, such as the introduction of some alien freshwater mollusk species, together with post-burial taphonomic processes, are the main factors leading to the poor fidelity of the fossil assemblage studied. Hence, the taxonomic composition of the Late Pleistocene mollusks from the Touro Passo Formation probably would show greater similarity to present-day assemblages wherever the mollusk biodiversity is not disturbed by human activities.