Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes.

Circulating FABP4 Is a prognostic biomarker in patients with acute coronary syndrome but not in asymptomatic individuals.

OBJECTIVE: Blood-borne biomarkers reflecting atherosclerotic plaque burden have great potential to improve clinical management of atherosclerotic coronary artery disease and acute coronary syndrome (ACS). APPROACH AND RESULTS: Using data integration from gene expression profiling of coronary thrombi versus peripheral blood mononuclear cells and proteomic analysis of atherosclerotic plaque-derived secretomes versus healthy tissue secretomes, we identified fatty acid-binding protein 4 (FABP4) as a biomarker candidate for coronary artery disease. Its diagnostic and prognostic performance was validated in 3 different clinical settings: (1) in a cross-sectional cohort of patients with stable coronary artery disease, ACS, and healthy individuals (n=820), (2) in a nested case-control cohort of patients with ACS with 30-day follow-up (n=200), and (3) in a population-based nested case-control cohort of asymptomatic individuals with 5-year follow-up (n=414). Circulating FABP4 was marginally higher in patients with ST-segment-elevation myocardial infarction (24.9 ng/mL) compared with controls (23.4 ng/mL; P=0.01). However, elevated FABP4 was associated with adverse secondary cerebrovascular or cardiovascular events during 30-day follow-up after index ACS, independent of age, sex, renal function, and body mass index (odds ratio, 1.7; 95% confidence interval, 1.1-2.5; P=0.02). Circulating FABP4 predicted adverse events with similar prognostic performance as the GRACE in-hospital risk score or N-terminal pro-brain natriuretic peptide. Finally, no significant difference between baseline FABP4 was found in asymptomatic individuals with or without coronary events during 5-year follow-up. CONCLUSIONS: Circulating FABP4 may prove useful as a prognostic biomarker in risk stratification of patients with ACS.

Virtualització de servidors i escriptoris

Aquest treball explica com una pime passa d'un entorn de servidors majoritàriament físic a un entorn virtual aprofitant la necessitat d'actualitzar la infraestructura. La plataforma de virtualització utilitzada serà VMware tant per a servidors com per a escriptoris.

Presence of Leishmania RNA Virus 1 in Leishmania guyanensis Increases the Risk of First-Line Treatment Failure and Symptomatic Relapse.

Treatment failure and symptomatic relapse are major concerns in American tegumentary leishmaniasis (TL). Such complications are seen frequently in Leishmania guyanensis infections, in which patients respond variously to first-line antileishmanials and are more prone to develop chronic cutaneous leishmaniasis. The factors underlying this pathology, however, are unknown. Recently, we reported that a double-stranded RNA virus, Leishmania RNA virus 1 (LRV1), nested within L. guyanensis parasites is able to exacerbate experimental murine leishmaniasis by inducing a hyperinflammatory response. This report investigates the prevalence of LRV1 in human L. guyanensis infection and its effect on treatment efficacy, as well as its correlation to symptomatic relapses after the completion of first-line treatment. In our cohort of 75 patients with a diagnosis of primary localized American TL, the prevalence of LRV1-positive L. guyanensis infection was elevated to 58%. All patients infected with LRV1-negative L. guyanensis were cured after 1 dose (22 of 31 [71%]) or 2 doses (31 of 31 [100%]) of pentamidine. In contrast, 12 of 44 LRV1-positive patients (27%) presented with persistent infection and symptomatic relapse that required extended therapy and the use of second-line drugs. Finally, LRV1 presence was associated with a significant increase in levels of intra-lesional inflammatory markers. In conclusion, LRV1 status in L. guyanensis infection is significantly predictive (P = .0009) of first-line treatment failure and symptomatic relapse and has the potential to guide therapeutic choices in American TL.

Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (~800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.

Phase diagram and complex patterns in the modeling of the bromate-oxalic acid-Ce-acetone oscillating reaction

Simulations have been carried out on the bromate - oxalic acid - Ce(IV) - acetone oscillating reaction, under flow conditions, using Field and Boyd's model (J. Phys. Chem. 1985, 89, 3707). Many different complex dynamic behaviors were found, including simple periodic oscillations, complex periodic oscillations, quasiperiodicity and chaos. Some of these complex oscillations can be understood as belonging to a Farey sequence. The many different behaviors were systematized in a phase diagram which shows that some regions of complex patterns were nested with one inside the other. The existence of almost all known dynamic behavior for this system allows the suggestion that it can be used as a model for some very complex phenomena that occur in biological systems.

Workplace Social Capital and Employee Health

Työyhteisön sosiaalinen pääoma ja työntekijöiden terveys Monien tutkimusten mukaan sosiaalinen pääoma vaikuttaa terveyteen. Vaikka työssä käyvä väestönosa on merkittävän osan valveillaoloajastaan työyhteisössä, siellä kertyvää sosiaalista pääomaa on toistaiseksi tutkittu vähän. Tässä tutkimuksessa selvitettiin työyhteisön sosiaalisen pääoman ja kuntatyöntekijöiden terveyden välistä yhteyttä pitkittäisasetelmassa hyödyntäen Kuntasektorin henkilöstön seurantatutkimuksen aineistoa vuosilta 2000–2005. Yhteensä 48592 kuntatyöntekijää vastasi kyselyyn vuosina 2000–02 (vastausprosentti 68 %). Heistä 35914 (77 %) osallistui myös seurantatutkimukseen vuosina 2004–05. Tutkimuksessa kehitettiin kyselyyn perustuva työyhteisön sosiaalisen pääoman mittausmenetelmä. Työntekijän omaan arvioon perustuvan sosiaalisen pääoman lisäksi mitattiin työyhteisön sosiaalista pääomaa käyttämällä samassa työyhteisössä työskentelevien muiden työntekijöiden keskimääräistä arviota sosiaalisesta pääomasta. Terveyttä mitattiin kysymyksellä koetusta terveydestä. Masennusta arvioitiin sekä kysymällä lääkärin toteamasta masennuksesta että masennuslääkeostoilla Kelan lääkerekistereistä. Analyyseihin otettiin mukaan vain ne kuntatyöntekijät, jotka olivat lähtötilanteissa terveitä eli kokivat terveytensä hyväksi tai heillä ei ollut aiempaa diagnosoitua tai lääkehoitoa vaatinutta masennusta. Tulosten analysointiin käytettiin monitasomallinnusta. Tulokset vakioitiin sosiodemografisten tekijöiden ja terveyskäyttäytymisen suhteen. Neljän vuoden seurannassa sekä jatkuvasti vähäinen että vähenevä yksilön sosiaalinen pääoma työssä lisäsi riskiä koetun terveyden heikkenemiseen niillä kuntatyöntekijöillä, jotka eivät vaihtaneet työpaikkaa seurannan aikana ja jotka seurannan alussa kokivat terveytensä hyväksi. Tulos ei selittynyt sosiodemografisilla tekijöillä tai terveyskäyttäytymisen eroilla. Tuloksen merkittävyyttä tuki havainto, että myös työtoverien arvioon perustuva sosiaalinen pääoma ennusti oman terveyden huononemista seuranta-aikana. Niillä työntekijöillä, jotka työskentelivät sellaisissa työyhteisöissä, joissa koko seurannan ajan oli vähiten sosiaalista pääomaa, oli lähes 1.3 -kertainen riski terveyden heikentymiseen. Vähäinen omaan arvioon perustuva sosiaalinen pääoma työssä ennusti myös masennuksen ilmaantuvuutta lähtötilanteessa ei-masentuneilla lähes neljän vuoden seurannassa. Matalaan sosiaaliseen pääomaan liittyi 20–50 % suurempi todennäköisyys sairastua masennukseen seurannan aikana niin itseraportoidun lääkärin totea-man masennuksen kuin masennuslääkeostojen perusteella. Tätä tulosta ei kuitenkaan pystytty toistamaan käyttämällä oman arvion sijasta työtoverien arviota työyhteisön sosiaalisesta pääomasta. Tutkimusta sosiaalisen pääoman vaikutusta masennuksen ilmaantumiseen jatkettiin selvittämällä miten sosiaalisen pääoman eri ulottuvuudet vaikuttivat masennuksen ilmaantumiseen. Tulosten mukaan sosiaalisen pääoman vertikaalinen komponentti (työntekijöiden ja esimiesten välinen luottamus, vastavuoroisuus ja jaetut arvot ja normit, jotka edesauttavat yhteistyötä) sekä horisontaalinen komponentti (työntekijöiden välisissä suhteissa yhteistyöstä, luottamuksesta ja vastavuoroisuudesta syntyvä sosiaalinen pääoma) vaikuttivat itsenäisesti masennusriskiin. Tutkimuksen perusteella korkea työyhteisön sosiaalinen pääoma saattaa vaikuttaa edullisesti työntekijöiden terveyteen. Jos näin on, olisi tärkeää edistää työyhteisöjen sosiaalista pääomaa ja kannustaa sellaiseen toimintaan, joka lisää suvaitsevaisuutta, luottamusta ja vastavuoroisuutta sekä työntekijöiden kesken että työntekijöiden ja esimiesten välillä.

On the structure of cooperative and competitive solutions for a generalized assignment game

We study cooperative and competitive solutions for a many- to-many generalization of Shapley and Shubik (1972)'s assignment game. We consider the Core, three other notions of group stability and two al- ternative definitions of competitive equilibrium. We show that (i) each group stable set is closely related with the Core of certain games defined using a proper notion of blocking and (ii) each group stable set contains the set of payoff vectors associated to the two definitions of competitive equilibrium. We also show that all six solutions maintain a strictly nested structure. Moreover, each solution can be identified with a set of ma- trices of (discriminated) prices which indicate how gains from trade are distributed among buyers and sellers. In all cases such matrices arise as solutions of a system of linear inequalities. Hence, all six solutions have the same properties from a structural and computational point of view.

Virtualització de servidors. Avantatges. Implantació en una PIME real

En la societat d’avui dia, les empreses depenen en gran part dels seus recursos informàtics. La seva capacitat de supervivència i innovació en el mercat actual, on la competitivitat és cada dia més forta, passa per una infraestructura informàtica que els permeti, no només desplegar i implantar ordinadors i servidors de manera ràpida i eficient sinó que també les protegeixi contra parades del sistema informàtic, problemes amb servidors, caigudes o desastres físics de hardware. Per evitar aquests problemes informàtics susceptibles de poder parar el funcionament d’una empresa es va començar a treballar en el camp de la virtualització informàtica amb l’objectiu de poder trobar solucions a aquests problemes a la vegada que s’aprofitaven els recursos de hardware existents d’una manera més òptim a i eficient, reduint així també el cost de la infraestructura informàtica. L’objectiu principal d’aquest treball és veure en primer pla la conversió d’una empresa real amb una infraestructura informàtica del tipus un servidor físic -una funció cap a una infraestructura virtual del tipus un servidor físic -varis servidors virtual -vàries funcions. Analitzarem l’estat actual de l’empresa, servidors i funcions, adquirirem el hardware necessari i farem la conversió de tots els seus servidors cap a una nova infraestructura virtual. Faig especial atenció a les explicacions de perquè utilitzo una opció i no un altre i també procuro sempre donar vàries opcions. Igualment remarco en quadres verds observacions a tenir en compte complementàries al que estic explicant en aquell moment, i en quadres vermells temes en els que s’ha de posar especial atenció en el moment en que es fan. Finalment, un cop feta la conversió, veurem els molts avantatges que ens ha reportat aquesta tecnologia a nivell de fiabilitat, estabilitat, capacitat de tolerància a errades, capacitat de ràpid desplegament de noves màquines, capacitat de recuperació del sistema i aprofitament de recursos físics

Supermatrix-hankkeen vahvuudet, heikkoudet, mahdollisuudet ja uhat

Supermatrix on Finnet-liitto ry:n jäsenyritysten hanke, joka tuo nopeiden valokuituyhteyksien avulla erilaisia sähköisiä palveluita kuluttajien koteihin ja yritysten toimipisteisiin. Näitä palveluita ovat mm. virtualisoidut henkilö-kohtaiset tietokoneet, tiedon tallennuspalvelut ja multimediasisältö, kuten teräväpiirtotelevisio. Tässä diplomityössä arvioidaan Supermatrixin palveluiden toteutumis-mahdollisuuksia sekä teknologian, että markkinoiden kannalta. Työn tarkoituksena oli myös laskea virtualisoitujen tietokoneiden avulla tuotetun työpöytäpalvelun tuotantokustannus. Kustannuslaskentaa varten testattiin useiden valmistajien teknologioita, ja parhaimmista vaihtoehdoista laskettiin tuotantokustannukset. Tulevia Supermatrix-operaattoreita varten kehitettiin työkalu, jolla työpöytäpalvelun vaatimien investointien kannattavuus saadaan nopeasti selville. Tuotantohintojen laskelmat osoittavat, että työpöytäpalvelua on taloudelli-sesti mahdollista tuottaa luomaan lisäarvoa nopeille laajakaistayhteyksille. Yrityksissä työpöytien virtualisointi on jo tämän päivän teknologiaa, mutta kuluttaja-asiakkaiden innostuminen palvelusta vaatii uuden markkinan luomisen. Uhkana on, että kuluttajien ostokäyttäytymisen muuttaminen ei onnistu, koska Supermatrix ei tuota fyysisen tuotteen ostamisen tarjoamaa mielihyvää.

Candidatus Phytoplasma brasiliense associado ao superbrotamento do hibisco (Hibiscus rosa-sinensis L.) no Estado de São Paulo

Plantas de hibisco com superbrotamento e definhamento seguido de morte têm sido observadas nos municípios de São Paulo, Campinas e Piracicaba. Como os sintomas são sugestivos daqueles induzidos por fitoplasmas, o presente trabalho buscou identificar o possível fitoplasma associado com a doença. Assim, 14 plantas sintomáticas de hibisco foram coletadas em Piracicaba (SP) e submetidas ao PCR duplo com os primers P1/Tint-R16F2n/R2 e ao exame em microscópio eletrônico de transmissão. A identificação foi realizada por análise de RFLP com as enzimas de restrição BfaI, DraI, HaeIII, HhaI, HpaII, MboI, MseI, RsaI e TaqI. Testes de transmissão foram conduzidos com enxertia de ramos e uso de Cuscuta subinclusa. Os resultados de nested-PCR revelaram a presença consistente de fitoplasmas em todas as plantas sintomáticas e foram confirmados pela observação de corpúsculos pleomórficos no floema, através da microscopia eletrônica. A análise de RFLP mostrou que o fitoplasma encontrado em hibisco pertence ao grupo 16SrXV, o mesmo grupo do Candidatus Phytoplasma brasiliense. O fitoplasma foi transmitido de planta doente para sadia, tanto pela enxertia como pela C. subinclusa, demonstrando ser o agente do superbrotamento do hibisco.

Motivational Influences on Transfer: Dimensions and Boundary Conditions

The focus of this dissertation is the motivational influences on transfer in higher education and professional training contexts. To estimate these motivational influences, the dissertation includes seven individual studies that are structured in two parts. Part I, Dimensions, aims at identifying the dimensionality of motivation to transfer and its structural relations with training-related antecedents and outcomes. Part II, Boundary Conditions, aims at testing the predictive validity of motivation theories used in contemporary training research under different study conditions. Data in this dissertation was gathered from multi-item questionnaires, which were analyzed differently in Part I and Part II. Studies in Part I employed exploratory and confirmatory factor analysis, structural equation modeling, partial least squares (PLS) path modeling, and mediation analysis. Studies in Part II used artifact distribution meta-analysis, (nested) subgroup analysis, and weighted least squares (WLS) multiple regression. Results demonstrate that motivation to transfer can be conceptualized as a three-dimensional construct, including autonomous motivation to transfer, controlled motivation to transfer, and intention to transfer, given a theoretical framework informed by expectancy theory, self-determination theory, and the theory of planned behavior. Results also demonstrate that a range of boundary conditions moderates motivational influences on transfer. To test the predictive validity of expectancy theory, social cognitive theory, and the theory of goal orientations under different study settings, a total of 17 boundary conditions were meta-analyzed, including age; assessment criterion; assessment source; attendance policy; collaboration among trainees; computer support; instruction; instrument used to measure motivation; level of education; publication type; social training context; SS/SMC bias; study setting; survey modality; type of knowledge being trained; use of a control group; and work context. Together, the findings cumulated in this thesis support the basic premise that motivation is centrally important for transfer, but that motivational influences need to be understood from a more differentiated perspective than commonly found in the literature, in order to account for several dimensions and boundary conditions. The results of this dissertation across the seven individual studies are reflected in terms of their implications for theory development and their significance for training evaluation and the design of training environments. Limitations and directions to take in future research are discussed.

SaaS and Public Cloud from Custom Application Provider’s Perspective

The main objective of this master’s thesis is to provide a comprehensive view to cloud computing and SaaS, and analyze how well CADM, a unit of Capgemini Finland Ltd., would fit to the cloud-based SaaS business. Another objective for this thesis is to investigate how public clouds would fit for CADM as a delivery model, if they would provide SaaS applications to their customers. This master’s thesis is executed by investigating characteristics of cloud computing and SaaS especially from application provider point of view. This is done by exploring what kinds of researches and analysis there have been done regarding these two phenomena during past few years. Then CADM’s current business model and operations are analyzed from SaaS’s and public cloud’s perspective. This analyzing part is conducted by using SWOT analysis which is widely used analytical tool when observing company’s strategic position and when figuring out possibilities how to improve company’s operations. The conducted analysis and observations reveals that CADM should pursue SaaS business as it could provide remarkable advantages and strengthen their position in current markets. However, pure SaaS model would not be the optimal solution for CADM because they do not have own product which could be transformed to SaaS model, and they lack of Infrastructure Management ability. Also public cloud would not be the most suitable delivery model for them if providing SaaS services. The main observation of this thesis is that CADM should adopt the SaaS model via Capgemini Immediate offering.

Evaluation of roof slope and exposure with different roofing materials in reduced models of animal production facilities in spring and summer

The present study was conducted at the Department of Rural Engineering and the Department of Animal Morphology and Physiology of FCAV/Unesp, Jaboticabal, SP, Brazil. The objective was to verify the influence of roof slope, exposure and roofing material on the internal temperature of reduced models of animal production facilities. For the development of the research, 48 reduced and dissemble models with dimensions 1.00 × 1.00 × 0.50 m were used. The roof was shed-type, and the models faced to the North or South directions, with 24 models for each side of exposure. Ceramic, galvanized-steel and fibro tiles were used to build the roofs. Slopes varied between 20, 30, 40 and 50% for the ceramic tile and 10, 30, 40 and 50% for the other two. Inside the models, temperature readings were performed at every hour, for 12 months. The results were evaluated in a general linear model in a nested 3 × 4 × 2 factorial arrangement, in which the effects of roofing material and exposure were nested on the factor Slope. Means were compared by the Tukey test at 5% of probability. After analyzing the data, we observed that with the increase in the slope and exposure to the South, there was a drop in the internal temperature within the model at the geographic coordinates of Jaboticabal city (SP/Brazil).

Abordagem citogenética e molecular em material de abortos espontâneos

OBJETIVOS: avaliar o desempenho da citogenética e das técnicas de hibridização in situ fluorescente (FISH) e reação em cadeia da polimerase (PCR) no estudo das aneuploidias cromossômicas numéricas e na determinação do sexo fetal em amostras de abortos espontâneos. MÉTODOS: duzentos e dezenove amostras de produtos de abortos espontâneos foram submetidas a estudo citogenético. Deste total, 40 amostras foram também submetidas à técnica de PCR-nested para a determinação do sexo fetal: 32 foram selecionadas devido à falha de crescimento no estudo citogenético e oito foram escolhidas ao acaso. Vinte amostras foram selecionadas para detecção de aneuploidias cromossômicas pela técnica de FISH, utilizando-se sondas para os cromossomos 13, 18, 21, X e Y: 13 casos foram submetidos a FISH devido à falha de crescimento no estudo citogenético e sete foram escolhidos ao acaso. Foi calculada a taxa de sucesso (obtenção de cariótipo) de cada técnica. Para comparação das taxas de sucesso foi utilizado o teste de chi2, sendo considerados significantes resultados com p<0,05. Foi avaliado o índice de acerto entre os resultados das amostras submetidas a mais de um exame, tomando-se como padrão-ouro o resultado do estudo citogenético. RESULTADOS: houve crescimento celular em 84,9% das amostras submetidas a análise citogenética. Em 51,1% dos casos foram encontradas alterações cromossômicas: 65,2% trissomias, 17,9% triploidias, 9,4% tetraploidias, 4,2% monossomia do cromossomo X e 1,1% trissomia dupla, tetrassomia e alteração estrutural. A trissomia mais freqüente foi a do cromossomo 16 (39%). FISH e PCR tiveram taxa de sucesso de 90%, não diferindo significativamente do exame citogenético. Em todos os casos submetidos a mais de um exame os resultados foram concordantes. Nas amostras com falha de crescimento celular no exame citogenético e submetidas a outra técnica, a PCR obteve sucesso em 87,5% e a FISH em 84,6%. CONCLUSÃO: o estudo citogenético de restos ovulares de abortamentos espontâneos teve elevada taxa de sucesso e evidenciou anomalias cromossômicas em mais da metade dos casos. As técnicas de biologia molecular (PCR-nested e FISH) complementaram o estudo citogenético e permitiram a obtenção de resultados seguros na detecção de alterações cromossômicas numéricas e na determinação do sexo fetal.