Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Traitement pharmacologique de la schizophrénie : évaluation comparative de la qualité des recommandations de pratique clinique = Comparative evaluation of clinical practice guidelines for the treatment of schizophrenia

De nombreuses recommandations de pratique clinique (RPC) ont été publiées, en réponse au développement du concept de la médecine fondée sur les preuves et comme solution à la difficulté de synthétiser et trier l'abondante littérature médicale. Pour faire un choix parmi le foisonnement de nouvelles RPC, il est primordial d'évaluer leur qualité. Récemment, le premier instrument d'évaluation standardisée de la qualité des RPC, appelé " AGREE " pour appraisal of guidelines for research and evaluation, a été validé. Nous avons comparé - avec l'aide de la grille " AGREE " - les six principales RPC publiées depuis une dizaine d'années sur le traitement de la schizophrénie : (1) les Recommandations de l'Agence nationale pour le développement de l'évaluation médicale (ANDEM) ; (2) The American Psychiatric Association (APA) practice guideline for the treatment of patients with schizophrenia ; (3) The quick reference guide of APA practice guideline for the treatment of patients with schizophrenia [APA - guide rapide de référence] ; (4) The schizophrenia patient outcomes research team (PORT) treatment recommandations ; (5) The Texas medication algorithm project " T-MAP " ; (6) The expert consensus guideline for the treatment of schizophrenia. Les résultats de notre étude ont ensuite été comparés avec ceux d'une étude similaire publiée en 2005 par Gæbel et al. portant sur 24 RPC abordant le traitement de la schizophrénie, réalisée également avec l'aide de la grille " AGREE " et deux évaluateurs [Br J Psychiatry 187 (2005) 248-255]. De manière générale, les scores des deux études ne sont pas trop éloignés et les deux évaluations globales des RPC convergent : chacune des six RPC est perfectible et présente différemment des points faibles et des points forts. La rigueur d'élaboration des six RPC est dans l'ensemble très moyenne, la prise en compte de l'opinion des utilisateurs potentiels est lacunaire et un effort sur la présentation des recommandations faciliterait leur utilisation clinique. L'applicabilité des recommandations est également peu considérée par les auteurs. Globalement, deux RPC se distinguent et peuvent être fortement recommandées selon les critères de la grille " AGREE " : " l'APA - guide rapide de référence " et le " T-MAP ".

Natural aphrodisiacs: studies of commercially-available herbal recipes, and phytochemical investigation of "Erythroxylum vacciniifolium" Mart. (Erythroxylaceae) from Brazil

De tout temps, hommes et femmes ont cherché par tous les moyens à développer, préserver ou recouvrer leurs propres capacités sexuelles mais également à stimuler le désir du partenaire. L?utilisation d?aphrodisiaques naturels a été l?un des recours les plus répandus. De nos jours, la commercialisation de nouvelles "love drugs" de synthèse, e.g. Viagra®, Cialis®, Levitra®, a remis au goût du jour les aphrodisiaques classiques et à relancer la recherche sur des molécules nouvelles. La pratique croissante de l?automédication, le matraquage publicitaire sur les aphrodisiaques naturels, la prolifération sur le marché de compléments alimentaires non contrôlés et l?absence de véritable législation accroissent les risques qui pèsent sur la santé publique. Dans le but d?évaluer les risques potentiels sur le consommateur de produits aphrodisiaques commercialisés, le développement et la validation d?une méthode rapide d?analyse qualitative et quantitative de la yohimbine dans ces préparations du marché sont exposés dans la première partie de ce travail. La yohimbine est un antagoniste ?2-adrénocepteur du système nerveux central et périphérique, elle est employée depuis plus d?un siècle dans le traitement des dysfonctionnements érectiles. Cette méthode analytique utilise la chromatographie liquide couplée à l?ultraviolet et à la spectrométrie de masse (LC-UV-MS) et au total, vingt préparations aphrodisiaques ont été étudiées. La dose journalière de yohimbine mesurée s?est révélée très variable selon les produits puisqu?elle varie de 1.32 à 23.16 mg. La seconde partie de ce travail concerne l?étude phytochimique et pharmacologique d?Erythroxylum vacciniifolium Mart. (Erythroxylaceae), une plante, appelée localement catuaba, utilisée dans la médecine traditionnelle brésilienne comme tonique et aphrodisiaque. Dans un premier temps, l?extrait alcaloïdique a été analysé par chromatographie liquide haute performance (HPLC) couplée soit à un détecteur UV à barrette d?iode (LC-UV-DAD), soit à un spectromètre de masse (LC-MS), ou soit à un spectromètre de résonance magnétique nucléaire (LC-RMN). L?interprétation de ces données spectrales enregistrées en ligne a permis d?obtenir des informations structurales et d?identifier partiellement près de 24 alcaloïdes appartenant à la classe des tropanes et potentiellement originaux. Par des méthodes classiques de chromatographie liquide sur l?extrait alcaloïdique de la plante, dix sept tropanes nouveaux ont ensuite été isolés dont les catuabines et leurs dérivés, et les vaccinines. Tous ces composés sont des tropane-diols ou triols estérifiés par au moins un groupe acide 1-méthyl-1H-pyrrole-2-carboxylique. Un de ces composés a été identifié comme un tropane N-oxyde. Toutes les structures ont été déterminées par spectrométrie de masse haute résolution et spectroscopie RMN multi-dimensionnelle. Parmi les nombreux tests biologiques réalisés sur ces tropanes, seuls les tests de cytotoxicité se sont révélés faiblement positifs pour certains de ces composés.<br/><br/>Throughout the ages, men and women have incessantly pursued every means to increase, preserve or recapture their sexual capacity, or to stimulate the sexual desire of selected individuals. One of the most recurrent methods has been the use of natural aphrodisiacs. Nowadays, the commercialization of new synthetic "love drugs", e.g. Viagra®, Cialis® and Levitra®, has fascinated the public interest and has led to a reassessment of classical aphrodisiacs and to the search for new ones. The practice of self-medication by an increasing number of patients, the incessant aggressive advertising of these herbal aphrodisiacs, the invasion of the medicinal market with uncontrolled dietary supplements and the absence of real directives amplifies the potential health hazards to the community. In order to evaluate the possible risks of commercialized aphrodisiac products on consumer health, the development and validation of a rapid qualitative and quantitative method for the analysis of yohimbine in these products, is reported in the first part of the present work. Yohimbine, a pharmacologically well-characterized ?2-adrenoceptor antagonist with activity in the central and peripheral nervous system, has been used for over a century in the treatment of erectile dysfunction. The analytical method is based on liquid chromatography coupled with ultraviolet and mass spectrometry (LC-UV-MS) and in total, 20 commercially-available aphrodisiac preparations were analyzed. The amount of yohimbine measured and expressed as the maximal dose per day suggested on product labels ranged from 1.32 to 23.16 mg. The second part of this work involved the phytochemical and pharmacological investigation of Erythroxylum vacciniifolium Mart. (Erythroxylaceae), a plant used in Brazilian traditional medicine as an aphrodisiac and tonic, and locally known as catuaba. With the aim of obtaining preliminary structure information on-line, the alkaloid extract was analyzed by high performance liquid chromatography (HPLC) coupled to diode array UV detection (LC-UVDAD), to mass spectrometry (LC-MS) and to nuclear magnetic resonance spectroscopy (LCNMR). Interpretation of on-line spectroscopic data led to structure elucidation and partial identification of 24 potentially original alkaloids bearing the same tropane skeleton. Seventeen new tropane alkaloids were then isolated from the alkaloid extract of the plant, including catuabines D to I, their derivatives and vaccinines A and B. All compounds were elucidated as tropane-diol or -triol alkaloids esterified by at least one 1-methyl-1H-pyrrole-2-carboxylic acid. One of the isolated compounds was identified as a tropane alkaloid N-oxide. Their structures were determined by high resolution mass spectrometry and multi-dimensional NMR spectroscopy. Among the numerous bioassays undertaken, only the cytotoxicity tests exhibited a weak positive activity of certain compounds.

Comparative efficacy of chelators to remove renal cadmium burden in isolated perfused rat kidneys

Trois agents chélateurs (l?acide diéthylène triamine penta-acétique, DTPA; l?acide méso-2,3- dimercaptosucchique, DMSA; l?acide 2,3-dimercapto- 1 -propanesulfonique, DMPS) ont été comparés quant à leur efficacité à mobiliser du cadmium (Cd) accumulé dans le tissu rénal. Des reins prélevés chez des rats exposés durant 3 j au Cd (acétate de Cd , 0.75 mg/kg.j, i.p) ont été isolés et perfusés in vitro, à l?aide d?un système de reperfusion utilisant une solution de Krebs-Henseleit, pH 7.4, contenant 8 acides aminés et 6% d?albumine. Les concentrations de Cd dans le perfusat et l?urine ont été mesurées par spectrométrie d?absorption atomique. Six périodes de clearance, après une période d?équilibration de 20 min, ont ?été obtenues. Le DMSA et le DMPS ont mobilisé le Cd à partir du tissu rénal, comme l?ont montré les augmentations dose-dépendantes des concentrations de Cd dans l?urine et le perfusat. L?accumulation de Cd était nettement plus élevée dans le perfusat que dans l?urine, indiquant que l?effet des chélateurs se marquait surtout au niveau tubulaire basolatéral. Le DTPA n?induisait qu?une faible mobilisation de Cd dans l?urine et le perfusat, et son efficacité était clairement inférieure à celle des autres chélateurs. Comme prévu, la quantité de Cd présente dans le tissu rénal après perfùsion par le DMSA ou le DMPS diminuait en fonction de l?efficacité des chélateurs, jusqu?à des valeurs inférieures de 46% au taux rénal de Cd avant perfusion. Le DMPS apparaissait induire une excretion urinaire de Cd plus importante que celle induite par le DMSA, une caractéristique qui pourrait être liée à une sécrétion tubulaire du chélateur, qui a été décrite antérieurement. Un intervalle de temps prolongé (1 -2 semaines) entre le moment de l?administration du Cd et la perfusion du rein avec le DMPS induisait une augmentation de l?excrétion urinaire de Cd. Tous les chélateurs se sont montrés néphrotoxiques à concentrations élevées.

Comparative study of the mandarin hybrid fruit characteristics: Nova, Murcott and Ortanique in Capão Bonito SP, Brazil

The Murcott tangor represent 20% of the tangerines trees in São Paulo State being the second more grown. Their fruits have good acceptance in the market cause of the good characteristics presented as: size, attractive internal and external color, transport resistance, high juice rate and industry potential. It is necessary to study the behavior of others varieties, in order to amplify the diversity of tangerine industry, which show suitable characteristics to the fresh fruit market and that make possible different harvest season. Many tangerine varieties, selected from the Citrus Germplasm Bank of the do Centro Avançado de Pesquisa Tecnológica do Agronegócio de Citros "Sylvio Moreira"/IAC, belong to trials carried out in 15 places in São Paulo State. The Capão Bonito area, south-west of the state, is one of this places where the Nova tangelo, the Ortanique and the Murcott tangors are showing quite good results about their fruit qualities. This paper had as an objective to compare the fruit characteristics of the Nova tangelo, the Murcott and the Ortanique tangors grafted on two rootstocks: Rangpur lime and Cleopatra mandarin. Accordingly to the gotten results, is possible to conclude that Nova and Ortanique had shown weight, width, fruit shape and juice percent, similar to the Murcott. In compliance with the harvest season, the Nova present suitable conditions to fresh fruit market in May and June. By the other hand the Murcott fruits can be harvested in July to August and the Ortanique in August to September. For this reason, is possible extend the harvest season of this mandarin-like, from two to five month, occurring inclusive in a period out of the crop at the north hemisphere.

Validation Studies of Thermal-hydraulic Code for Safety Analysis of Nuclear Power Plants

This thesis gives an overview of the validation process for thermal hydraulic system codes and it presents in more detail the assessment and validation of the French code CATHARE for VVER calculations. Three assessment cases are presented: loop seal clearing, core reflooding and flow in a horizontal steam generator. The experience gained during these assessment and validation calculations has been used to analyze the behavior of the horizontal steam generator and the natural circulation in the geometry of the Loviisa nuclear power plant. The cases presented are not exhaustive, but they give a good overview of the work performed by the personnel of Lappeenranta University of Technology (LUT). Large part of the work has been performed in co-operation with the CATHARE-team in Grenoble, France. The design of a Russian type pressurized water reactor, VVER, differs from that of a Western-type PWR. Most of thermal-hydraulic system codes are validated only for the Western-type PWRs. Thus, the codes should be assessed and validated also for VVER design in order to establish any weaknesses in the models. This information is needed before codes can be used for the safety analysis. Theresults of the assessment and validation calculations presented here show that the CATHARE code can be used also for the thermal-hydraulic safety studies for VVER type plants. However, some areas have been indicated which need to be reassessed after further experimental data become available. These areas are mostly connected to the horizontal stem generators, like condensation and phase separation in primary side tubes. The work presented in this thesis covers a large numberof the phenomena included in the CSNI code validation matrices for small and intermediate leaks and for transients. Also some of the phenomena included in the matrix for large break LOCAs are covered. The matrices for code validation for VVER applications should be used when future experimental programs are planned for code validation.

Comparative genomics of yeast species: new insights into their biology

The genomes of two hemiascomycetous yeasts (Saccharomyces cerevisiae and Candida albicans) and one archiascomycete (Schizosaccharomyces pombe) have been completely sequenced and the genes have been annotated. In addition, the genomes of 13 more Hemiascomycetes have been partially sequenced. The amount of data thus obtained provides information on the evolutionary relationships between yeast species. In addition, the differential genetic characteristics of the microorganisms explain a number of distinctive biological traits. Gene order conservation is observed between phylogenetically close species and is lost in distantly related species, probably due to rearrangements of short regions of DNA. However, gene function is much more conserved along evolution. Compared to S. cerevisiae and S. pombe, C. albicans has a larger number of specific genes, i.e., genes not found in other organisms, a fact that can account for the biological characteristics of this pathogenic dimorphic yeast which is able to colonize a large variety of environments.

A comparative study of ballpoint ink ageing parameters using GC/MS.

For more than a decade scientists tried to develop methods capable of dating ink by monitoring the loss of phenoxyethanol (PE) over time. While many methods were proposed in the literature, few were really used to solve practical cases and they still raise much concern within the scientific community. In fact, due to the complexity of ink drying processes it is particularly difficult to find a reliable ageing parameter to reproducibly follow ink ageing. Moreover, systematic experiments are required in order to evaluate how different factors actually influence the results over time. Therefore, this work aimed at evaluating the capacity of four different ageing parameters to reliably follow ink ageing over time: (1) the quantity of solvent PE in an ink line, (2) the relative peak area (RPA) normalising the PE results using stable volatile compounds present in the ink formulation, (3) the solvent loss ratio (R%) calculated from PE results obtained by the analyses of naturally and artificially aged samples, (4) a modified solvent loss ratio version (R%*) calculated from RPA results. After the determination of the limits of reliable measurements of the analytical method, the repeatability of the different ageing parameters was evaluated over time, as well as the influence of ink composition, writing pressure and storage conditions on the results. Surprisingly, our results showed that R% was not the most reliable parameter, as it showed the highest standard deviation. Discussion of the results in an ink dating perspective suggests that other proposed parameters, such as RPA values, may be more adequate to follow ink ageing over time.

Comblike poly(a-alkyl g glutamate)s: computer simulation studies of an intermediate thermal phase.

Monte Carlo (MC) simulations have been used to study the structure of an intermediate thermal phase of poly(R-octadecyl ç,D-glutamate). This is a comblike poly(ç-peptide) able to adopt a biphasic structure that has been described as a layered arrangement of backbone helical rods immersed in a paraffinic pool of polymethylene side chains. Simulations were performed at two different temperatures (348 and 363 K), both of them above the melting point of the paraffinic phase, using the configurational bias MC algorithm. Results indicate that layers are constituted by a side-by-side packing of 17/5 helices. The organization of the interlayer paraffinic region is described in atomistic terms by examining the torsional angles and the end-to-end distances for the octadecyl side chains. Comparison with previously reported comblike poly(â-peptide)s revealed significant differences in the organization of the alkyl side chains.

A comparative study of silver amalgam and compomer as retrograde filling materials in periapical surgery

Objective: A comparative study is made of the histological effects of silver amalgam versus compomer (Dyract®) 90 days after placement as retrograde filling materials in experimental animals. Method: Six Beagle dogs were used, with total pulpectomy and orthograde material filling followed by periapical surgery of the 6 upper and 6 lower incisors (for a total of 72 teeth). Thirty-six teeth corresponded to the right side and were filled with the control material (silver amalgam), while the 36 teeth on the left side were filled with the compomer study material (Dyract®). After three months the animals were sacrificed and the histological study was carried out, with evaluation of bone formation, inflammation, and the tissue in contact with the filler material. The results obtained were subjected to a descriptive and comparative statistical analysis (chi-square test). Results: The samples retrogradely filled with compomer showed significantly greater percentage inflammation (76.19% versus 26.66% in the control group). On the other hand, a large proportion of samples with root cement growth were found in the compomer group. Filler material expulsion was also significantly more common when compomer was used. Conclusions: the comparative study of the histological findings showed greater inflammation but also greater root cement growth in the compomer group versus the controls

A comparative study of ballpoint ink ageing parameters using GC/MS

For more than a decade scientists tried to develop methods capable of dating ink by monitoring the loss of phenoxyethanol (PE) over time. While many methods were proposed in the literature, few were really used to solve practical cases and they still raise much concern within the scientific community. In fact, due to the complexity of ink drying processes it is particularly difficult to find a reliable ageing parameter to reproducibly follow ink ageing. Moreover, systematic experiments are required in order to evaluate how different factors actually influence the results over time. Therefore, this work aimed at evaluating the capacity of four different ageing parameters to reliably follow ink ageing over time: (1) the quantity of solvent PE in an ink line, (2) the relative peak area (RPA) normalising the PE results using stable volatile compounds present in the ink formulation, (3) the solvent loss ratio (R%) calculated from PE results obtained by the analyses of naturally and artificially aged samples, (4) a modified solvent loss ratio version (R%*) calculated from RPA results. After the determination of the limits of reliable measurements of the analytical method, the repeatability of the different ageing parameters was evaluated over time, as well as the influence of ink composition, writing pressure and storage conditions on the results. Surprisingly, our results showed that R% was not the most reliable parameter, as it showed the highest standard deviation. Discussion of the results in an ink dating perspective suggests that other proposed parameters, such as RPA values, may be more adequate to follow ink ageing over time.

An Evaluation of the Paper Profile - a comparative assessment of the applicability of an emerging environmental communication tool in pulp and paper industry

Diplomityön tavoitteena oli arvioida uutta sellu-, paperi- ja kartonkiteollisuuden Paper Profile -ympäristötuoteselostetta. Paper Profilen tarkoituksena on tarjota paperiteollisuuden asiakkaille ja muille kiinnostuneilla sidosryhmille yhtenäistä ympäristöinformaatiota koskien paperituotteiden koostumusta ja tuotteiden tärkeimpiä ympäristöparametrejä. Työn tärkein tavoite oli arvioida kriittisesti Paper Profilea ja verrata konseptia ISO:n, Kansainvälisen stardardisoimisliiton tuoteselosteeseen sekä löytää konseptien yhtäläisyydet ja erot. Tärkein tehtävä oli tunnistaa ne avaintekijät, joiden avulla Paper Profile -tuoteselostetta voitaisiin pitää yhtenevänä ISO/TR 14025 teknisen raportin kanssa. Lisäksi Paper Profile -tuoteselosteen mahdolliset kehittämistarpeet arvioitiin ISO-tuoteselosteen näkökulmasta. Työn toinen tavoite oli kerätä ja analysoida uuteen tuoteselosteeseen liittyvä asiakaspalaute ja verrata sitä Stora Enson tehtaiden ympäristöpäälliköiden antamiin Paper Profilea koskeviin kommentteihin. Työn tuloksena huomattiin, että Paper Profile -konsepti sellaisenaan ei ole kovin informatiivinen vaan tuoteseloste jättää monia ympäristökysymyksiä avoimeksi. Siitä huolimatta Paper Profile tarjoaa riittävän taustan eri paperituotteiden ympäristökuormitusten keskinäiselle vertailuille. Konseptin viestinnällinen näkökulma paranisi huomattavasti, jos tuoteselosteeseen lisättäisiin kolmannen osapuolen verifiointi. Lisäksi referenssiarvot kertoisivat asiakkaille paremmin esitettyjen parametrien taustoista. Stora Enson tehtaiden ympäristöpäälliköiden, samoin kuin asiakkaidenkin mielestä Paper Profile on yleisesti ottaen potentiaalinen ympäristöviestinnän työkalu, mutta silti konseptiin ehdotettiin joitakin pieniä muutoksia. Avoinna olevat metsäsertifiointikysymykset ja niiden puutteellinen tiedottaminen tuoteselosteessa puhututtivat sekä tehtaiden henkilöstöä että yritysasiakkaita.