In this issue.

A new issue, once again a bouquet of attractive papers. First of all the paper by Droit-Dupré et al. (10.1007/s00428-015-1724-9). The group studied colonic adenocarcinomas, not otherwise specified, by immunohistochemistry for the expression of markers of intestinal epithelial cell differentiation. Hierarchical clustering analysis identified a major cluster of two thirds of the case series, expressing cytokeratin 20, CDX2 and MUC2 and invariably mismatch repair competent, which they called crypt-like. In stage III colon cancer, the crypt-like cluster had a better prognosis. The paper is a relatively simple example of what is happening in cancer classification beyond morphology: multiparameter differentiation and (epi)genomic markers defining new subtypes of cancer with potential clinical significance in clinical decision making.

Assessing the added value of wastewater-based epidemiology to monitor illicit drug use

Wastewater-based epidemiology consists in acquiring relevant information about the lifestyle and health status of the population through the analysis of wastewater samples collected at the influent of a wastewater treatment plant. Whilst being a very young discipline, it has experienced an astonishing development since its firs application in 2005. The possibility to gather community-wide information about drug use has been among the major field of application. The wide resonance of the first results sparked the interest of scientists from various disciplines. Since then, research has broadened in innumerable directions. Although being praised as a revolutionary approach, there was a need to critically assess its added value, with regard to the existing indicators used to monitor illicit drug use. The main, and explicit, objective of this research was to evaluate the added value of wastewater-based epidemiology with regards to two particular, although interconnected, dimensions of illicit drug use. The first is related to trying to understand the added value of the discipline from an epidemiological, or societal, perspective. In other terms, to evaluate if and how it completes our current vision about the extent of illicit drug use at the population level, and if it can guide the planning of future prevention measures and drug policies. The second dimension is the criminal one, with a particular focus on the networks which develop around the large demand in illicit drugs. The goal here was to assess if wastewater-based epidemiology, combined to indicators stemming from the epidemiological dimension, could provide additional clues about the structure of drug distribution networks and the size of their market. This research had also an implicit objective, which focused on initiating the path of wastewater- based epidemiology at the Ecole des Sciences Criminelles of the University of Lausanne. This consisted in gathering the necessary knowledge about the collection, preparation, and analysis of wastewater samples and, most importantly, to understand how to interpret the acquired data and produce useful information. In the first phase of this research, it was possible to determine that ammonium loads, measured directly in the wastewater stream, could be used to monitor the dynamics of the population served by the wastewater treatment plant. Furthermore, it was shown that on the long term, the population did not have a substantial impact on consumption patterns measured through wastewater analysis. Focussing on methadone, for which precise prescription data was available, it was possible to show that reliable consumption estimates could be obtained via wastewater analysis. This allowed to validate the selected sampling strategy, which was then used to monitor the consumption of heroin, through the measurement of morphine. The latter, in combination to prescription and sales data, provided estimates of heroin consumption in line with other indicators. These results, combined to epidemiological data, highlighted the good correspondence between measurements and expectations and, furthermore, suggested that the dark figure of heroin users evading harm-reduction programs, which would thus not be measured by conventional indicators, is likely limited. In the third part, which consisted in a collaborative study aiming at extensively investigating geographical differences in drug use, wastewater analysis was shown to be a useful complement to existing indicators. In particular for stigmatised drugs, such as cocaine and heroin, it allowed to decipher the complex picture derived from surveys and crime statistics. Globally, it provided relevant information to better understand the drug market, both from an epidemiological and repressive perspective. The fourth part focused on cannabis and on the potential of combining wastewater and survey data to overcome some of their respective limitations. Using a hierarchical inference model, it was possible to refine current estimates of cannabis prevalence in the metropolitan area of Lausanne. Wastewater results suggested that the actual prevalence is substantially higher compared to existing figures, thus supporting the common belief that surveys tend to underestimate cannabis use. Whilst being affected by several biases, the information collected through surveys allowed to overcome some of the limitations linked to the analysis of cannabis markers in wastewater (i.e., stability and limited excretion data). These findings highlighted the importance and utility of combining wastewater-based epidemiology to existing indicators about drug use. Similarly, the fifth part of the research was centred on assessing the potential uses of wastewater-based epidemiology from a law enforcement perspective. Through three concrete examples, it was shown that results from wastewater analysis can be used to produce highly relevant intelligence, allowing drug enforcement to assess the structure and operations of drug distribution networks and, ultimately, guide their decisions at the tactical and/or operational level. Finally, the potential to implement wastewater-based epidemiology to monitor the use of harmful, prohibited and counterfeit pharmaceuticals was illustrated through the analysis of sibutramine, and its urinary metabolite, in wastewater samples. The results of this research have highlighted that wastewater-based epidemiology is a useful and powerful approach with numerous scopes. Faced with the complexity of measuring a hidden phenomenon like illicit drug use, it is a major addition to the panoply of existing indicators. -- L'épidémiologie basée sur l'analyse des eaux usées (ou, selon sa définition anglaise, « wastewater-based epidemiology ») consiste en l'acquisition d'informations portant sur le mode de vie et l'état de santé d'une population via l'analyse d'échantillons d'eaux usées récoltés à l'entrée des stations d'épuration. Bien qu'il s'agisse d'une discipline récente, elle a vécu des développements importants depuis sa première mise en oeuvre en 2005, notamment dans le domaine de l'analyse des résidus de stupéfiants. Suite aux retombées médiatiques des premiers résultats de ces analyses de métabolites dans les eaux usées, de nombreux scientifiques provenant de différentes disciplines ont rejoint les rangs de cette nouvelle discipline en développant plusieurs axes de recherche distincts. Bien que reconnu pour son coté objectif et révolutionnaire, il était nécessaire d'évaluer sa valeur ajoutée en regard des indicateurs couramment utilisés pour mesurer la consommation de stupéfiants. En se focalisant sur deux dimensions spécifiques de la consommation de stupéfiants, l'objectif principal de cette recherche était focalisé sur l'évaluation de la valeur ajoutée de l'épidémiologie basée sur l'analyse des eaux usées. La première dimension abordée était celle épidémiologique ou sociétale. En d'autres termes, il s'agissait de comprendre si et comment l'analyse des eaux usées permettait de compléter la vision actuelle sur la problématique, ainsi que déterminer son utilité dans la planification des mesures préventives et des politiques en matière de stupéfiants actuelles et futures. La seconde dimension abordée était celle criminelle, en particulier, l'étude des réseaux qui se développent autour du trafic de produits stupéfiants. L'objectif était de déterminer si cette nouvelle approche combinée aux indicateurs conventionnels, fournissait de nouveaux indices quant à la structure et l'organisation des réseaux de distribution ainsi que sur les dimensions du marché. Cette recherche avait aussi un objectif implicite, développer et d'évaluer la mise en place de l'épidémiologie basée sur l'analyse des eaux usées. En particulier, il s'agissait d'acquérir les connaissances nécessaires quant à la manière de collecter, traiter et analyser des échantillons d'eaux usées, mais surtout, de comprendre comment interpréter les données afin d'en extraire les informations les plus pertinentes. Dans la première phase de cette recherche, il y pu être mis en évidence que les charges en ammonium, mesurées directement dans les eaux usées permettait de suivre la dynamique des mouvements de la population contributrice aux eaux usées de la station d'épuration de la zone étudiée. De plus, il a pu être démontré que, sur le long terme, les mouvements de la population n'avaient pas d'influence substantielle sur le pattern de consommation mesuré dans les eaux usées. En se focalisant sur la méthadone, une substance pour laquelle des données précises sur le nombre de prescriptions étaient disponibles, il a pu être démontré que des estimations exactes sur la consommation pouvaient être tirées de l'analyse des eaux usées. Ceci a permis de valider la stratégie d'échantillonnage adoptée, qui, par le bais de la morphine, a ensuite été utilisée pour suivre la consommation d'héroïne. Combinée aux données de vente et de prescription, l'analyse de la morphine a permis d'obtenir des estimations sur la consommation d'héroïne en accord avec des indicateurs conventionnels. Ces résultats, combinés aux données épidémiologiques ont permis de montrer une bonne adéquation entre les projections des deux approches et ainsi démontrer que le chiffre noir des consommateurs qui échappent aux mesures de réduction de risque, et qui ne seraient donc pas mesurés par ces indicateurs, est vraisemblablement limité. La troisième partie du travail a été réalisée dans le cadre d'une étude collaborative qui avait pour but d'investiguer la valeur ajoutée de l'analyse des eaux usées à mettre en évidence des différences géographiques dans la consommation de stupéfiants. En particulier pour des substances stigmatisées, telles la cocaïne et l'héroïne, l'approche a permis d'objectiver et de préciser la vision obtenue avec les indicateurs traditionnels du type sondages ou les statistiques policières. Globalement, l'analyse des eaux usées s'est montrée être un outil très utile pour mieux comprendre le marché des stupéfiants, à la fois sous l'angle épidémiologique et répressif. La quatrième partie du travail était focalisée sur la problématique du cannabis ainsi que sur le potentiel de combiner l'analyse des eaux usées aux données de sondage afin de surmonter, en partie, leurs limitations. En utilisant un modèle d'inférence hiérarchique, il a été possible d'affiner les actuelles estimations sur la prévalence de l'utilisation de cannabis dans la zone métropolitaine de la ville de Lausanne. Les résultats ont démontré que celle-ci est plus haute que ce que l'on s'attendait, confirmant ainsi l'hypothèse que les sondages ont tendance à sous-estimer la consommation de cannabis. Bien que biaisés, les données récoltées par les sondages ont permis de surmonter certaines des limitations liées à l'analyse des marqueurs du cannabis dans les eaux usées (i.e., stabilité et manque de données sur l'excrétion). Ces résultats mettent en évidence l'importance et l'utilité de combiner les résultats de l'analyse des eaux usées aux indicateurs existants. De la même façon, la cinquième partie du travail était centrée sur l'apport de l'analyse des eaux usées du point de vue de la police. Au travers de trois exemples, l'utilisation de l'indicateur pour produire du renseignement concernant la structure et les activités des réseaux de distribution de stupéfiants, ainsi que pour guider les choix stratégiques et opérationnels de la police, a été mise en évidence. Dans la dernière partie, la possibilité d'utiliser cette approche pour suivre la consommation de produits pharmaceutiques dangereux, interdits ou contrefaits, a été démontrée par l'analyse dans les eaux usées de la sibutramine et ses métabolites. Les résultats de cette recherche ont mis en évidence que l'épidémiologie par l'analyse des eaux usées est une approche pertinente et puissante, ayant de nombreux domaines d'application. Face à la complexité de mesurer un phénomène caché comme la consommation de stupéfiants, la valeur ajoutée de cette approche a ainsi pu être démontrée.

St. Petersburg Court Chant and the Tradition of Eastern Slavic Church Singing

The present study examines the repertory of liturgical chant known as St. Petersburg Court Chant which emerged within the Imperial Court of St. Petersburg, Russia, and appeared in print in a number of revisions during the course of the 19th century, eventually to spread throughout the Russian Empire and even abroad. The study seeks answers to questions on the essence and composition of Court Chant, its history and liturgical background, and most importantly, its musical relationship to other repertories of Eastern Slavic chant. The research questions emerge from previous literary accounts of Court Chant (summarized in the Introduction), which have tended to be inaccurate and generally not based on critical research. The study is divided into eight main chapters. Chapter 1 provides a survey of the history of Eastern Slavic chant and the Imperial Court Chapel of St. Petersburg until 1917, with special emphasis on the history of singing traditional chant in polyphony, the status of the Court Chapel as a government authority, and its endeavours in publishing church music. Chapter 2 deals with the liturgical background of Eastern chant, the chant genres, and main repertories of Eastern Slavic chant. Chapter 3 concentrates on chant sources: it introduces the musical notations utilised, after which a typology of chant books is presented. The discussion continues with a survey of the sources of Court Chant and their content, the specimens selected for closer analysis, the comparative materials from other repertories, and ends with a commentary on some chant sources that have been excluded. The comparative sources include a specimen from around the beginning of the 12th century, a few manuscripts from the 17th century, and printed and manuscript chant books from the early 18th to early 20th century, covering the geographical area that delimits to the western Ukraine, Astrakhan, Nizhny Novgorod, and the Solovetsky Monastery. Chapter 4 presents the approach and methods used in the subsequent analytical comparisons. After a survey of the pitch organization of Eastern Slavic chant, the customary harmonization strategy of traditional chant polyphony is examined, according to which a method for meaningful analysis of the harmony is proposed. The method is based on the observation that the harmonic framework of chant polyphony derives from the standard pitch collection of monodic chant known as the Church Gamut, specific pitches of which form eight harmonic regions that behave like the usual tonalities of major and harmonic minor. Because of the considerable quantity of comparative chant forms, computer-assisted statistical methods are applied to the analysis of chant melodies. The primary chant forms and their respective comparative forms have been pre-processed into reduced chant prototypes and divided into redactions. The analyses are carried out by measuring the formal dissimilarities of the primary chant forms of the Court Chant repertory against each comparative form, and also by measuring the reciprocal dissimilarities of all chant versions in a redaction, the results of which are subjected to agglomerative hierarchical clustering in order to find out how the chant forms relate to each other. The dissimilarities are determined by applying a metric dissimilarity function that is based on the Levenshtein Distance. Chapter 5 provides the melodic and harmonic analyses of generic chants (chants used for multiple texts of different lengths), i.e., chants for stichera samoglasny and troparia, Chapter 6 of pseudo-generic chants (chants that are used for multiple texts but with certain restrictions), i.e., chants for heirmoi, prokeimena, and three other hymns, and Chapter 7 of non-generic chants, covering nine chants that in the Court repertory are not shared by multiple texts. The results are summarized and evaluated in Chapter 8. Accordingly, it can be established that, contrary to previous conceptions, melodically, Court Chant is in effect a full part of the wider Eastern Slavic chant tradition. Even if it is somewhat detached from the chant versions of the Synodal square-note chant books and the local tradition of Moscow, it is particularly close to chant forms of East Ukraine and some vernacular repertories from Russia. Respectively, the harmonization strategies of Court Chant do not show significant individuality in comparison with those of the available polyphonic comparative sources, the main difference being the part-writing, which generally conforms to western common practice standard, whereas the deviations from this tend to be more significant in other analysed repertories of polyphonic chant. Thus, insofar as the subsequent prevalence of Court Chant is not based on its forceful dissemination by authorities (as suggested in previous literature but for which little tangible evidence could be found in Chapter 1), in the present author’s interpretation, Court Chant attained its dominance principally because musically it was considered sufficiently traditional, and as a chant body supported by the government, was conveniently available in print in serviceable harmonizations.

Sélection de modèle d'imputation à partir de modèles bayésiens hiérarchiques linéaires multivariés

Les logiciels utilisés sont Splus et R.

Facteurs contextuels influençant l’implantation d’un modèle de hiérarchisation des soins en santé mentale : une étude de cas en milieu montréalais

Cette étude de cas vise à comparer le modèle de soins implanté sur le territoire d’un centre de santé et des services sociaux (CSSS) de la région de Montréal aux modèles de soins en étapes et à examiner l’influence de facteurs contextuels sur l’implantation de ce modèle. Au total, 13 cliniciens et gestionnaires travaillant à l’interface entre la première et la deuxième ligne ont participé à une entrevue semi-structurée. Les résultats montrent que le modèle de soins hiérarchisés implanté se compare en plusieurs points aux modèles de soins en étapes. Cependant, certains éléments de ces derniers sont à intégrer afin d’améliorer l’efficience et la qualité des soins, notamment l’introduction de critères d’évaluation objectifs et la spécification des interventions démontrées efficaces à privilégier. Aussi, plusieurs facteurs influençant l’implantation d’un modèle de soins hiérarchisés sont dégagés. Parmi ceux-ci, la présence de concertation et de lieux d’apprentissage représente un élément clé. Néanmoins, certains éléments sont à considérer pour favoriser sa réussite dont l’uniformisation des critères et des mécanismes de référence, la clarification des rôles du guichet d’accès en santé mentale et l’adhésion des omnipraticiens au modèle de soins hiérarchisés. En somme, l’utilisation des cadres de référence et d’analyse peut guider les gestionnaires sur les enjeux à considérer pour favoriser l’implantation d’un modèle de soins basé sur les données probantes, ce qui, à long terme, devrait améliorer l’efficience des services offerts et leur adéquation avec les besoins populationnels.

Extraction automatique et visualisation des thèmes abordés dans des résumés de mémoires et de thèses en anthropologie au Québec, de 1985 à 2009

S’insérant dans les domaines de la Lecture et de l’Analyse de Textes Assistées par Ordinateur (LATAO), de la Gestion Électronique des Documents (GÉD), de la visualisation de l’information et, en partie, de l’anthropologie, cette recherche exploratoire propose l’expérimentation d’une méthodologie descriptive en fouille de textes afin de cartographier thématiquement un corpus de textes anthropologiques. Plus précisément, nous souhaitons éprouver la méthode de classification hiérarchique ascendante (CHA) pour extraire et analyser les thèmes issus de résumés de mémoires et de thèses octroyés de 1985 à 2009 (1240 résumés), par les départements d’anthropologie de l’Université de Montréal et de l’Université Laval, ainsi que le département d’histoire de l’Université Laval (pour les résumés archéologiques et ethnologiques). En première partie de mémoire, nous présentons notre cadre théorique, c'est-à-dire que nous expliquons ce qu’est la fouille de textes, ses origines, ses applications, les étapes méthodologiques puis, nous complétons avec une revue des principales publications. La deuxième partie est consacrée au cadre méthodologique et ainsi, nous abordons les différentes étapes par lesquelles ce projet fut conduit; la collecte des données, le filtrage linguistique, la classification automatique, pour en nommer que quelques-unes. Finalement, en dernière partie, nous présentons les résultats de notre recherche, en nous attardant plus particulièrement sur deux expérimentations. Nous abordons également la navigation thématique et les approches conceptuelles en thématisation, par exemple, en anthropologie, la dichotomie culture ̸ biologie. Nous terminons avec les limites de ce projet et les pistes d’intérêts pour de futures recherches.

Noninvasive Clinical Assessment of Trunk Deformities Associated With Scoliosis

Besides the spinal deformity, scoliosis modifies notably the general appearance of the trunk resulting in trunk rotation, imbalance, and asymmetries that constitutes patients' major concern. Existing classifications of scoliosis, based on the type of spinal curve as depicted on radiographs, are currently used to guide treatment strategies. Unfortunately, even though a perfect correction of the spinal curve is achieved, some trunk deformities remain, making patients dissatisfied with the treatment received. The purpose of this study is to identify possible shape patterns of trunk surface deformity associated with scoliosis. First, trunk surface is represented by a multivariate functional trunk shape descriptor based on 3-D clinical measurements computed on cross sections of the trunk. Then, the classical formulation of hierarchical clustering is adapted to the case of multivariate functional data and applied to a set of 236 trunk surface 3-D reconstructions. The highest internal validity is obtained when considering 11 clusters that explain up to 65% of the variance in our dataset. Our clustering result shows a concordance with the radiographic classification of spinal curves in 68% of the cases. As opposed to radiographic evaluation, the trunk descriptor is 3-D and its functional nature offers a compact and elegant description of not only the type, but also the severity and extent of the trunk surface deformity along the trunk length. In future work, new management strategies based on the resulting trunk shape patterns could be thought of in order to improve the esthetic outcome after treatment, and thus patients satisfaction.

Social bees and food plant associations in the Nilgiri Biosphere Reserve, India

The diversity of social bees was assessed at 15 sites across five locations of the Nilgiri Biosphere Reserve, Western Ghats, India, from January to December 2007. We also conducted floristic analyses of local vegetation in each site using one-hectare sample plots. All woody species with a dbh (diameter at breast height) : 30 cm were recorded within the plots. A total area of 9.72 ha was assessed for floristic composition. Similarity of floristic composition between sites was determined using the Jaccard's distance measure and a dendrogram constructed based on the hierarchical clustering of floristic dissimilarities between sites. A Bee Importance Index (BII) was developed to give a measure of the bee diversity at each site. This index was a sum of the species richness of bee species in a site and their visitation frequencies to flowers, calculated as mean flower visits hour 1 within 2 focal patches within one hectare plots. The visits of bee species to flowers were also recorded. The Jaccard distance measure indicated that the montane sites were quite dissimilar to the low elevation sites in floristic diversity. The BII was 7-9 for the wet forest sites and ranged from 4-6 for drier forest sites. Seventy three plant species were identified as social bee plants and of them 45% were visited by one species of bee, 37% by two bee species and 18% by more than two bee species, indicating a certain degree of floral specialization among bees.

Space partitioning for scalable K-means

K-Means is a popular clustering algorithm which adopts an iterative refinement procedure to determine data partitions and to compute their associated centres of mass, called centroids. The straightforward implementation of the algorithm is often referred to as `brute force' since it computes a proximity measure from each data point to each centroid at every iteration of the K-Means process. Efficient implementations of the K-Means algorithm have been predominantly based on multi-dimensional binary search trees (KD-Trees). A combination of an efficient data structure and geometrical constraints allow to reduce the number of distance computations required at each iteration. In this work we present a general space partitioning approach for improving the efficiency and the scalability of the K-Means algorithm. We propose to adopt approximate hierarchical clustering methods to generate binary space partitioning trees in contrast to KD-Trees. In the experimental analysis, we have tested the performance of the proposed Binary Space Partitioning K-Means (BSP-KM) when a divisive clustering algorithm is used. We have carried out extensive experimental tests to compare the proposed approach to the one based on KD-Trees (KD-KM) in a wide range of the parameters space. BSP-KM is more scalable than KDKM, while keeping the deterministic nature of the `brute force' algorithm. In particular, the proposed space partitioning approach has shown to overcome the well-known limitation of KD-Trees in high-dimensional spaces and can also be adopted to improve the efficiency of other algorithms in which KD-Trees have been used.

On the use of geometric moments to examine the continuum of sudden stratospheric warmings

The polar winter stratospheric vortex is a coherent structure that undergoes different types of deformation that can be revealed by the geometric invariant moments. Three moments are used—the aspect ratio, the centroid latitude, and the area of the vortex based on stratospheric data from the 40-yr ECMWF Re-Analysis (ERA-40) project—to study sudden stratospheric warmings. Hierarchical clustering combined with data image visualization techniques is used as well. Using the gap statistic, three optimal clusters are obtained based on the three geometric moments considered here. The 850-K potential vorticity field, as well as the vertical profiles of polar temperature and zonal wind, provides evidence that the clusters represent, respectively, the undisturbed (U), displaced (D), and split (S) states of the polar vortex. This systematic method for identifying and characterizing the state of the polar vortex using objective methods is useful as a tool for analyzing observations and as a test for climate models to simulate the observations. The method correctly identifies all previously identified major warmings and also identifies significant minor warmings where the atmosphere is substantially disturbed but does not quite meet the criteria to qualify as a major stratospheric warming.

Use of virulence determinants and seropathotypes to distinguish high- and low-risk Escherichia coli O157 and non-O157 isolates from Europe

The presence of 10 virulence genes was examined using polymerase chain reaction (PCR) in 365 European O157 and non-O157 Escherichia coli isolates associated with verotoxin production. Strain-specific PCR data were analysed using hierarchical clustering. The resulting dendrogram clearly separated O157 from non-O157 strains. The former clustered typical high-risk seropathotype (SPT) A strains from all regions, including Sweden and Spain, which were homogenous by Cramer's V statistic, and strains with less typical O157 features mostly from Hungary. The non-O157 strains divided into a high-risk SPTB harbouring O26, O111 and O103 strains, a group pathogenic to pigs, and a group with few virulence genes other than for verotoxin. The data demonstrate SPT designation and selected PCR separated verotoxigenic E. coli of high and low risk to humans; although more virulence genes or pulsed-field gel electrophoresis will need to be included to separate high-risk strains further for epidemiological tracing.

Network optimization for enhanced resilience of urban heat island measurements

The urban heat island is a well-known phenomenon that impacts a wide variety of city operations. With greater availability of cheap meteorological sensors, it is possible to measure the spatial patterns of urban atmospheric characteristics with greater resolution. To develop robust and resilient networks, recognizing sensors may malfunction, it is important to know when measurement points are providing additional information and also the minimum number of sensors needed to provide spatial information for particular applications. Here we consider the example of temperature data, and the urban heat island, through analysis of a network of sensors in the Tokyo metropolitan area (Extended METROS). The effect of reducing observation points from an existing meteorological measurement network is considered, using random sampling and sampling with clustering. The results indicated the sampling with hierarchical clustering can yield similar temperature patterns with up to a 30% reduction in measurement sites in Tokyo. The methods presented have broader utility in evaluating the robustness and resilience of existing urban temperature networks and in how networks can be enhanced by new mobile and open data sources.

Gene Expression Profile of Mesenchymal Stem Cells from Paired Umbilical Cord Units: Cord is Different from Blood

Mesenchymal stem cells (MSC) are multipotent cells which can be obtained from several adult and fetal tissues including human umbilical cord units. We have recently shown that umbilical cord tissue (UC) is richer in MSC than umbilical cord blood (UCB) but their origin and characteristics in blood as compared to the cord remains unknown. Here we compared, for the first time, the exonic protein-coding and intronic noncoding RNA (ncRNA) expression profiles of MSC from match-paired UC and UCB samples, harvested from the same donors, processed simultaneously and under the same culture conditions. The patterns of intronic ncRNA expression in MSC from UC and UCB paired units were highly similar, indicative of their common donor origin. The respective exonic protein-coding transcript expression profiles, however, were significantly different. Hierarchical clustering based on protein-coding expression similarities grouped MSC according to their tissue location rather than original donor. Genes related to systems development, osteogenesis and immune system were expressed at higher levels in UCB, whereas genes related to cell adhesion, morphogenesis, secretion, angiogenesis and neurogenesis were more expressed in UC cells. These molecular differences verified in tissue-specific MSC gene expression may reflect functional activities influenced by distinct niches and should be considered when developing clinical protocols involving MSC from different sources. In addition, these findings reinforce our previous suggestion on the importance of banking the whole umbilical cord unit for research or future therapeutic use.

Semiparametric Bayesian measurement error modeling

This work presents a Bayesian semiparametric approach for dealing with regression models where the covariate is measured with error. Given that (1) the error normality assumption is very restrictive, and (2) assuming a specific elliptical distribution for errors (Student-t for example), may be somewhat presumptuous; there is need for more flexible methods, in terms of assuming only symmetry of errors (admitting unknown kurtosis). In this sense, the main advantage of this extended Bayesian approach is the possibility of considering generalizations of the elliptical family of models by using Dirichlet process priors in dependent and independent situations. Conditional posterior distributions are implemented, allowing the use of Markov Chain Monte Carlo (MCMC), to generate the posterior distributions. An interesting result shown is that the Dirichlet process prior is not updated in the case of the dependent elliptical model. Furthermore, an analysis of a real data set is reported to illustrate the usefulness of our approach, in dealing with outliers. Finally, semiparametric proposed models and parametric normal model are compared, graphically with the posterior distribution density of the coefficients. (C) 2009 Elsevier Inc. All rights reserved.

Análise multivariada na compactação de um latossolo vermelho cultivado com milho

Os solos submetidos aos sistemas de produção sem preparo estão sujeitos à compactação, provocada pelo tráfego de máquinas, tornando necessário o acompanhamento das alterações do ambiente físico, que, quando desfavorável, restringe o crescimento radicular, podendo reduzir a produtividade das culturas. O objetivo do trabalho foi avaliar o efeito de diferentes intensidades de compactação na qualidade física de um Latossolo Vermelho textura média, localizado em Jaboticabal (SP), sob cultivo de milho, usando métodos de estatística multivariada. O delineamento experimental foi inteiramente casualizado, com seis intensidades de compactação e quatro repetições. Foram coletadas amostras indeformadas do solo nas camadas de 0,02-0,05, 0,08-0,11 e 0,15-0,18 m para determinação da densidade do solo (Ds), na camada de 0-0,20 m. As características da cultura avaliadas foram: densidade radicular, diâmetro radicular, matéria seca das raízes, altura das plantas, altura de inserção da primeira espiga, diâmetro do colmo e matéria seca das plantas. As análises de agrupamentos e componentes principais permitiram identificar três grupos de alta, média e baixa produtividade de plantas de milho, segundo variáveis do solo, do sistema radicular e da parte aérea das plantas. A classificação dos acessos em grupos foi feita por três métodos: método de agrupamentos hierárquico, método não-hierárquico k-means e análise de componentes principais. Os componentes principais evidenciaram que elevadas produtividades de milho estão correlacionadas com o bom crescimento da parte aérea das plantas, em condições de menor densidade do solo, proporcionando elevada produção de matéria seca das raízes, contudo, de pequeno diâmetro. A qualidade física do Latossolo Vermelho para o cultivo do milho foi assegurada até à densidade do solo de 1,38 Mg m-3.