Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities

Amplified ribosomal DNA restriction analysis (ARDRA) and restriction fragment length polymorphism were originally used for strain typing and for screening clone libraries to identify phylogenetic clusters within a microbial community. Here we used ARDRA as a model to examine the capacity of restriction-based techniques for clone identification, and the possibility of deriving phylogenetic information from ARDRA-based dendrograms. ARDRA was performed in silico on 48,759 sequences from the Ribosomal Database Project, and it was found that the fragmentation profiles were not necessarily unique for each sequence in the database, resulting in different species sharing fragmentation profiles. Although ARDRA-based clusters separated clones into different genera, these phylogenetic clusters did not overlap with trees constructed according to sequence alignment, calling into question the intra-genus ARDRA-based phylogeny. It is thus suggested that the prediction power of ARDRA clusters in identifying clone phylogeny be regarded with caution

TOIMINNANOHJAUSJÄRJESTELMÄN KÄYTTÖÖNOTON VAIKUTUS

Tässä tutkielmassa tutkitaan kuinka toiminnanohjausjärjestelmän käyttöönotto on vaikuttanut yrityksen tulokseen ja suorituskykyyn suomalaisissa yrityksissä 1999-2015. Tavoitteena on testata empiirisesti aiheuttaako toiminnanohjausjärjestelmän käyttöönotto merkittäviä säästöjä, yrityk-sen toiminnan tehokkuuden parannuksia ja muutoksia yrityksen kannattavuudessa. Toiminnanohjaus- eli ERP-järjestelmät integroivat yrityksen eri toimintoja esimerkiksi logistiikkaa, tuotantoa, kirjanpitoa, varastointia ja laskutusta yhteen järjestelmään ja näin ollen tehostavat yrityksen toimintaa useiden eri järjestelmien käytön sijaan. Onkin tärkeää selvittää kuinka toiminnanohjausjärjestelmien käyttöönotto on vaikuttanut yritysten kannattavuuteen ja voidaanko investointi nähdä tuottavana. Aikaisempien tutkimusten perusteella tulokset ovat ristiriitaisia; tutkimukset osoittavat, että vaikka ERP- järjestelmien käyttöönotto tutkitusti vaikuttaa ei-rahamääräisiin mittareihin, vaikutusta rahamääräisiin mittareihin ei aina pystytä todistamaan. Yritysten kannalta mielenkiintoista onkin ovatko kalliit ERP-järjestelmät, sekä niiden implementointiprosessit todella kannattavia investointeja. Tutkimuksen empiirisessä osiossa selvitettiin toiminnanohjausjärjestelmien käyttöönoton vaiku-tuksia suorituskykyyn suomalaisissa yhtiöissä, jotka ovat implementoineet toiminnanohjausjärjestelmän vuosina 1999-2015. Aineistona on käytetty julkisuudessa ilmoitettuja järjestelmähank-keita sekä tilinpäätöstietoja implementointiprosessin jälkeisiltä sekä edeltäviltä vuosilta. Suorituskyvyn muutosta on seurattu vertailemalla suorituskyvyn ja kannattavuuden muutosta implementoinnin jälkeen. Tutkimus on suoritettu määrällisenä tutkimuksena ja tilastollisina menetelminä on käytetty toistomittausten varianssianalyysiä sekä t-testiä parivertailulle. Tutkimuksessa havaittiin, että näyttäisi siltä, ettei toiminnanohjausjärjestelmien käyttöönotolla ei ole ollut vaikutusta kohdeyhtiöiden rahamääräiseen suorituskykyyn.fi=Opinnäytetyö kokotekstinä PDF-muodossa.|en=Thesis fulltext in PDF format.|sv=Lärdomsprov tillgängligt som fulltext i PDF-format

O papel de um instrumento de apoio à comunicação matemática numa turma do 4.º ano

Relatório de Estágio apresentado à Escola Superior de Educação de Lisboa para obtenção de grau de mestre em Ensino do 1.º e 2.º Ciclos do Ensino BásicoA criação de ambientes de sala de aula onde os alunos são agentes efetivos da sua aprendizagem e têm espaço para participar e expor os seus conhecimentos, sabendo que vão ser ouvidos pelo professor e colegas, é, cada vez mais, uma recomendação curricular da atualidade e objeto de estudo. Este relatório dá conta da intervenção realizada numa turma do 4.º ano de escolaridade, com o propósito de promover a aprendizagem, valorizando, sistematicamente, a comunicação. Em simultâneo, explana-se a investigação realizada nesta turma, que envolveu a avaliação do impacto da construção de um instrumento de apoio aos momentos de Comunicação Matemática, no contexto de uma rotina semanal da turma, a Apresentação do Problema da Semana. Com a pretensão de dar resposta às questões (i) quais os contributos de um instrumento de apoio à organização e estruturação dos momentos de comunicação matemática? e (ii) de que forma esse mesmo instrumento contribui para o desenvolvimento de estratégias de resolução de problemas?, investigou-se a evolução da turma quanto à comunicação das resoluções dos problemas e à variedade das estratégias utilizadas, antes e após a construção coletiva do instrumento de apoio. A análise de resultados, feita através da análise das produções dos alunos e das respostas a um questionário que instigou a reflexão sobre o papel do instrumento de apoio ao longo das várias apresentações do problema da semana, permitiu perceber uma crescente variedade de estratégias utilizadas e uma maior preocupação, por parte dos alunos, em organizar e estruturar os momentos de comunicação matemática, bem como em mobilizar um discurso com correção matemática. Este é um estudo que se limita a uma turma, não sendo as suas conclusões generalizáveis, mas que pode contribuir com uma estratégia para melhorar a comunicação matemática dos alunos, de uma forma que os envolve de forma direta e que prevê a sua participação e papel ativo na aprendizagem.ABSTRACT Creating classroom environments where students are effective agents of their learning process and have space to participate and exhibit their skills, knowing that they will be heard by the teacher and classmates, is an increasingly curricular recomendation and object of stdy nowadays. This report gives an account of the intervention carried out on a 4th grade level class, with the purpose of promoting learning, valuing, systematically, the communication. At the same time, explains research performed in this class, which involved the evaluation of the impact of the construction of an instrument in support of Mathematical Communication moments, in the context of a weekly routine of the class, The Presentation of rhe Problem of the Week. With the pretense of responding to questions (i) what are the contributions of an instrument of support to the organization and structuring of moments of mathematical communication? and (ii) how this same instrument contributes to the development of problem solving strategies?, it was investigated the evolution of the class regarding the communication of the resolutions of the problems and the variety of strategies used in problem solving, before and after the collective construction of the instrument. The analysis of results, through the analysis of students’ productions and the replies to a questionnaire that instigated the reflection about the role of the instrument of support along the various presentations of the problem of the week, allowed to realize a growing variety of strategies used and greater concern, on the part of students, to organise and structure the moments of mathematical communication as well as in mobilizing a discourse with mathematical correction. This is a study that is limited to a class, which makes its conclusions not generalizable, but that can contribute with a strategy to improve students’ math communication, in a way that involves them directly and provides their participation and active role in their own learning process.N/

Erica: Prevalences Of Hypertension And Obesity In Brazilian Adolescents

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)To estimate the prevalence of arterial hypertension and obesity and the population attributable fraction of hypertension that is due to obesity in Brazilian adolescents. METHODS: Data from participants in the Brazilian Study of Cardiovascular Risks in Adolescents (ERICA), which was the first national school-based, cross-section study performed in Brazil were evaluated. The sample was divided into 32 geographical strata and clusters from 32 schools and classes, with regional and national representation. Obesity was classified using the body mass index according to age and sex. Arterial hypertension was defined when the average systolic or diastolic blood pressure was greater than or equal to the 95th percentile of the reference curve. Prevalences and 95% confidence intervals (95% CI) of arterial hypertension and obesity, both on a national basis and in the macro-regions of Brazil, were estimated by sex and age group, as were the fractions of hypertension attributable to obesity in the population. RESULTS: We evaluated 73,399 students, 55.4% female, with an average age of 14.7 years (SD = 1.6). The prevalence of hypertension was 9.6% (95% CI 9.0-10.3); with the lowest being in the North, 8.4% (95% CI 7.7-9.2) and Northeast regions, 8.4% (95% CI 7.6-9.2), and the highest being in the South, 12.5% (95% CI 11.0-14.2). The prevalence of obesity was 8.4% (95% CI 7.9-8.9), which was lower in the North region and higher in the South region. The prevalences of arterial hypertension and obesity were higher in males. Obese adolescents presented a higher prevalence of hypertension, 28.4% (95% CI 25.5-31.2), than overweight adolescents, 15.4% (95% CI 17.0-13.8), or eutrophic adolescents, 6.3% (95% CI 5.6-7.0). The fraction of hypertension attributable to obesity was 17.8%. CONCLUSIONS: ERICA was the first nationally representative Brazilian study providing prevalence estimates of hypertension in adolescents. Regional and sex differences were observed. The study indicates that the control of obesity would lower the prevalence of hypertension among Brazilian adolescents by 1/5.501Brazilian Department of Science and Technology at the Secretariat of Science and TechnologyStrategic Inputs of the Ministry of Health (Departamento de Ciencia e Tecnologia da Secretaria de Ciencia e Tecnologia e Insumos Estrategicos do Ministerio da Saude - Decit/SCTIE/MS)Health Fund Sector (Fundo Setorial de Saude - CT-health) at the Ministry of science, Technology and Innovation (Ministerio da Ciencia, Tecnologia e Inovacao - MCTI)FINEP [01090421]CNPq [2010/565037-2]hospital research incentive fund for Clinics in Porto Alegre (fundo de incentivo a Pesquisa do Hospital de Clinicas de Porto Alegre - HCPA) [405,009/FIPE-2012-7]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Erica: Prevalence Of Metabolic Syndrome In Brazilian Adolescents

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)To determine the prevalence of metabolic syndrome and its components in Brazilian adolescents. METHODS: We evaluated 37,504 adolescents who were participants in the Study of Cardiovascular Risks in Adolescents (ERICA), a cross-sectional, school-based, national study. The adolescents, aged from 12 to 17 years, lived in cities with populations greater than 100,000 inhabitants. The sample was stratified and clustered into schools and classes. The criteria set out by the International Diabetes Federation were used to define metabolic syndrome. Prevalences of metabolic syndrome were estimated according to sex, age group, school type and nutritional status. RESULTS: Of the 37,504 adolescents who were evaluated: 50.2% were female; 54.3% were aged from 15 to 17 years, and 73.3% were from public schools. The prevalence of metabolic syndrome was 2.6% (95% CI 2.3-2.9), slightly higher in males and in those aged from 15 to 17 years in most macro-regions. The prevalence was the highest in residents from the South macro-region, in the younger female adolescents and in the older male adolescents. The prevalence was higher in public schools (2.8% [95% CI 2.4-3.2]), when compared with private schools (1.9% [95% CI 1.4-2.4]) and higher in obese adolescents when compared with nonobese ones. The most common combinations of components, referring to 3/4 of combinations, were: enlarged waist circumference (WC), low HDL-cholesterol (HDL-c) and high blood pressure; followed by enlarged WC, low HDL-c and high triglycerides; and enlarged WC, low HDL-c, high triglycerides and blood pressure. Low HDL was the second most frequent component, but the highest prevalence of metabolic syndrome (26.8%) was observed in the presence of high triglycerides. CONCLUSIONS: ERICA is the first Brazilian nation-wide study to present the prevalence of metabolic syndrome and describe the role of its components. Despite the prevalence of Metabolic Syndrome being low, the high prevalences of some components and participation of others in the syndrome composition shows the importance of early diagnosis of this changes, even if not grouped within the metabolic syndrome.501Department of Science and Technology of the Secretariat of Science, Technology and Strategic Inputs of the Ministry of Health (Decit/SCTIE/MS)Health Sectorial Fund (Fundo Setorial de Saude - CT-Saude) of the Ministry of Science, Technology and Innovation (MCTI)FINEP [01090421]CNPq [2010/565037-2]Research Incentive Fund of the Hospital de Clinicas de Porto Alegre - (Fundo de Incentivo a Pesquisa do Hospital de Clinicas de Porto Alegre - FIPE-HCPA) [405.009/2012-7]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery