General, PDB-based collective variables for protein folding

New, automated forms of data-analysis are required in order to understand the high-dimensional trajectories that are obtained from molecular dynamics simulations on proteins. Dimensionality reduction algorithms are particularly appealing in this regard as they allow one to construct unbiased, low-dimensional representations of the trajectory using only the information encoded in the trajectory. The downside of this approach is that different sets of coordinates are required for each different chemical systems under study precisely because the coordinates are constructed using information from the trajectory. In this paper we show how one can resolve this problem by using the sketch-map algorithm that we recently proposed to construct a low-dimensional representation of the structures contained in the protein data bank (PDB). We show that the resulting coordinates are as useful for analysing trajectory data as coordinates constructed using landmark configurations taken from the trajectory and that these coordinates can thus be used for understanding protein folding across a range of systems.

Finite domination and Novikov rings. Laurent polynomial rings in several variables

We present a homological characterisation of those chain complexes of modules over a Laurent polynomial ring in several indeterminates which are finitely dominated over the ground ring (that is, are a retract up to homotopy of a bounded complex of finitely generated free modules). The main tools, which we develop in the paper, are a non-standard totalisation construction for multi-complexes based on truncated products, and a high-dimensional mapping torus construction employing a theory of cubical diagrams that commute up to specified coherent homotopies.

Learning Bayesian Networks with Thousands of Variables

We present a method for learning Bayesian networks from data sets containing thousands of variables without the need for structure constraints. Our approach is made of two parts. The first is a novel algorithm that effectively explores the space of possible parent sets of a node. It guides the exploration towards the most promising parent sets on the basis of an approximated score function that is computed in constant time. The second part is an improvement of an existing ordering-based algorithm for structure optimization. The new algorithm provably achieves a higher score compared to its original formulation. Our novel approach consistently outperforms the state of the art on very large data sets.

Latent vs. Observed Variables: Analysis of Irrigation Water Efficiency Using SEM and SUR

In this paper we compare conceptualising single factor technical and allocative efficiency as indicators of a single latent variable, or as separate observed variables. In the former case, the impacts on both efficiency types are analysed by means of structural equation modeling (SEM), in the latter by seemingly unrelated regression (SUR). We compare estimation results of the two approaches based on a dataset on single factor irrigation water use efficiency obtained from a survey of 360 farmers in the Guanzhong Plain, China. The main methodological findings are that SEM allows identification of the most important dimension of irrigation water efficiency (technical efficiency) via comparison of their factor scores and reliability. Moreover, it reduces multicollinearity and attenuation bias. It thus is preferable to SUR. The SEM estimates show that perception of water scarcity is the most important positive determinant of both types of efficiency, followed by irrigation infrastructure, income and water price. Furthermore, there is a strong negative reverse effect from efficiency on perception.

Educação de infância como tempo fundador: repensar a formação de educadores para uma acção educativa integrada

O estudo Educação de Infância como tempo fundador: Repensar a Formação de Educadores para uma acção educativa integrada inscreve-se no processo de reflexão acerca das finalidades da educação básica e da qualidade da formação e da intervenção dos profissionais de educação de infância. Considerando as condições de instabilidade, crescente insegurança e grande imprevisibilidade que caracterizam as sociedades contemporâneas e, considerando também, os avanços científicos que vêm ocorrendo nas últimas décadas, fundamentando e alertando para a importância decisiva das aprendizagens realizadas na Infância nos processos de desenvolvimento subsequentes, releva-se neste estudo a necessidade de dar continuidade e aprofundar essa reflexão procurando responder, também pela investigação, aos desafios que as mudanças sociais suscitam. Nesta linha e tendo como referente o significado que, em termos de estruturação identitária pessoal e colectiva, é reconhecido à educação de infância, enquanto contexto primeiro de educação básica e complementar da acção educativa da família, o principal objectivo do estudo consiste em aprofundar o conhecimento acerca da natureza e qualidade dos saberes básicos a promover na educação pré-escolar e das competências reconfiguradoras do perfil de desempenho profissional dos educadores de infância para que, em articulação com as famílias das crianças, se tornem facilitadores do seu desenvolvimento, no quadro de uma ampla perspectiva de cidadania e de sucesso para todos. Os eixos investigativos que se cruzam no estudo pressupõem uma dimensão de pesquisa (teórica, documental e empírica) de natureza complexa, na qual, se procura tornar compreensíveis as interacções entre os participantes anteriormente referidos, no sentido de uma possível coerência conceptual e funcional, que regule e sustente a qualidade dos processos de desenvolvimento. Do ponto de vista metodológico, a investigação inscreve-se numa abordagem de natureza qualitativa, de matriz complexa e com características de estudo de caso, centrado nos processos de formação e de intervenção dos educadores de infância em exercício de funções, no distrito de Bragança. No sentido de construir uma visão integrada do objecto de estudo foi desenvolvida uma revisão temática de literatura e de análise documental e, na dimensão empírica do estudo, foram promovidos processos mistos de recolha de dados, com recurso à inquirição por questionário e por entrevista (semi-estruturada). A inquirição por questionário foi feita a 229 educadores de infância e a 1340 pais (ou seus representantes), das crianças que frequentavam a educação pré-escolar e a entrevista a 6 educadoras, que integravam os conselhos executivos dos Agrupamentos de Escolas e, cujas funções de gestão e administração, lhes permitiam ter uma perspectiva mais global das problemáticas em estudo. Os instrumentos de recolha e de análise da informação foram validados de modo a garantir-lhes fiabilidade e credibilidade. Os resultados do estudo podem ser lidos em dois níveis, considerando a sua abrangência e especificidade. Num primeiro plano, numa leitura mais global e transversal às questões em estudo e, num segundo plano, como enfoque mais específico em função de quatro dimensões temáticas decorrentes do quadro de fundamentação teórica e organizadoras do processo de reflexão e de pesquisa. Assim, globalmente, os resultados confirmam a importância que todos os inquiridos reconhecem, quer às aprendizagens ocorridas na Infância, como factor importante no desenvolvimento pessoal e social das crianças ao longo da vida, quer ao papel que, nele, os educadores e respectiva formação (inicial e contínua) devem desempenhar. Com algumas variações, as representações dos educadores de infância e dos pais inquiridos neste estudo, embora diferentes em algumas das questões específicas, apresentam-se maioritariamente coerentes e próximas das perspectivas teóricas mais actuais, que consideram a natureza processual das aprendizagens e a importância que a qualidade dos contextos e das transições, que neles ocorrem, assumem nos processos de desenvolvimento. Ou seja, inscrevem-se na linha das teorias socioconstrutivista e ecológica também subjacentes às orientações curriculares, ao nível nacional e aos quadros teóricos de referência, ao nível internacional. Identificam a aprendizagem da cidadania (ou do aprender a ser em sociedade) como o saber mais estruturante a ser desenvolvido no conjunto da acção educativa e perspectivam-na como processo de responsabilidade partilhada e cooperado. Tratando-se de uma amostra extensa e de um distrito geograficamente marcado pela interioridade, e sem esquecer que os dados se referem a representações expressas ao nível dos discursos, é importante reconhecer os sinais de actualidade das perspectivas e das sugestões apontadas para dar continuidade aos processos de desenvolvimento integrado de todos os participantes no processo educativo. Ainda numa leitura global, as principais diferenças, genericamente observadas entre educadores e pais, evidenciam, da parte destes, uma perspectiva de cidadania mais restrita e, da parte dos educadores, uma visão mais alargada do conceito. Com efeito, são os pais com mais elevada qualificação académica que partilham com os educadores esta perspectiva ampliada e transformadora de cidadania. Numa leitura mais enfocada e mais detalhada, e tal como referido anteriormente, os resultados podem ser lidos no cruzamento de quatro dimensões que interligam as questões de pesquisa: os saberes básicos, as estratégias de intervenção para o seu desenvolvimento; a formação e intervenção dos educadores de infância e a identificação de competências que possam vir a aprofundarem a sua formação. No que se refere aos saberes básicos, e não obstante a ocorrência de variações, quer quanto aos próprios saberes, quer quanto à terminologia usada, são considerados como fundamentais: 1. O aprender a ser na perspectiva do desenvolvimento da identidade; 2. O aprender a exercer a cidadania na linha da aprendizagem e da vivência democrática na relação com o mundo e com o outro; 3. O aprender a aprender como ferramenta indispensável à aprendizagem ao longo da vida; 4. O aprender a desenvolver o pensamento crítico, enquanto possibilidade de criteriosa escolha pessoal entre alternativas possíveis e 5. O aprender a comunicar como condição relacional inalienável nos processos de interacção com os contextos e com as pessoas. A segunda dimensão tem a ver com as estratégias consideradas facilitadoras do desenvolvimento destes saberes e são considerados três níveis da intervenção educativa: a acção dos educadores propriamente dita, a cooperação dos pais no processo de aprendizagem das crianças e a interacção da instituição pré-escolar com os pais/família. A acção dos educadores surge, tendencialmente perspectivada como facilitadora do desenvolvimento dos saberes básicos, embora em relação a algumas práticas essa perspectiva surgisse pouco evidente e distingue-se quanto ao desenvolvimento da acção e relação educativa, manifestando os educadores mais experientes uma opinião mais favorável. No que se refere à cooperação dos pais no processo de aprendizagem das crianças, os resultados indicam que a maioria dos pais manifesta uma opinião favorável a práticas configuradoras de um clima facilitador do desenvolvimento dos saberes básicos enunciados, mas variando os seus pontos de vista. São os pais de habilitações académicas mais elevadas, de idade intermédia e situados em contexto urbano os que apresentam opiniões mais favoráveis. Por fim, e no que diz respeito à interacção com as famílias, os resultados evidenciam uma opinião positiva com os meios de interacção utilizados, mas deixando perceber a necessidade de melhorar o processo de cooperação, manifestando os pais uma opinião menos positiva do que os educadores sobre esse processo. A terceira dimensão diz respeito às representações sobre a formação e intervenção profissional dos educadores, evidenciando os resultados que a maioria dos educadores atribuiu muita relevância aos contributos do curso de formação inicial para o desenvolvimento da maioria das competências necessárias para o seu desempenho profissional. Permitem ainda verificar que os educadores de formação mais recente manifestaram uma opinião mais favorável desses contributos, quanto ao desenvolvimento de conhecimentos em áreas, tais como a matemática, conhecimento do mundo e expressão musical, o que significa um avanço relativamente ao reconhecimento da necessidade de fazer investimento nessas áreas sugeridas em alguns estudos e projectos. Quanto ao desenvolvimento da actividade profissional, os resultados relevam que a maior preocupação dos educadores se centra em torno do seu desempenho profissional e das condições de exercício da actividade profissional. No que se refere ao início de carreira, esta última dimensão assume maior evidência, sendo ainda possível perceber que a entrada na vida profissional tem vindo a ocorrer, nos últimos anos, através da rede privada. A quarta dimensão tem a ver com as competências profissionais a desenvolver pelos futuros educadores, e não obstante algumas diferenças nas opiniões manifestadas pelos três grupos de participantes, surgem relevadas competências que a literatura e os perfis de desempenho profissional docente apontam como devendo ser promovidas e incluídas nos programas de formação de educadores de infância/professores. Estas podem ser vistas, quer numa dimensão geral relativa ao grupo docente, quer numa dimensão mais específica da intervenção em educação de infância, tal como é especificado ao longo do trabalho.

Spatial variability of macroinvertebrate assemblages and the influence of hydrological and environmental variables along the Sigi River, Tanzania-East Africa

The study of investigating the spatial and temporal variability of macroinvertebrate and their relation to hydrology, hydraulic and environmental factors was done along the Sigi River during two sampling periods in the dry (March) and wet (May) periods of 2012. The river was demarcated based on slope ranges and five river zones were identified as mountains streams (MS), upper foothills (UF), lower foothills (LF), rejuvenated foothills (REJ) and mature lower river (MR). Samples of macroinvertebrate were collected from the five river zones and measurements of hydrological (discharge), hydraulics (Depth, velocity and Froude number) and Environmental (pH, Temperature, substrate, conductivity) parameters were done in each zone. In characterizing the macroinvertebrate assemblages along the Sigi River diversity indices (number of taxa, total abundances, Margalef richness index and ShannonWiener index) were calculated and the most representative species for the spatial and temporal variation were identified. Melanoides and Afronurous showed differences in abundance in two samplings periods while Cleopatra, Potamonautes, Ephemerythus, Neoperla, Caenis, Ceratogomphus and Cheumatopsyche showed significant difference among the river zones. Spearman rank correlation and Distance Linear Model (DistLM) used to revealed physical factors governing the macroinvertebrate assemblages distribution. The study demonstrated that the variation of physical factors like discharge, temperature, conductivity and pH have an important role in the spatial distribution of macroinvertebrate assemblages along the river and the life cycle of macroinvertebrate (Afronurus) is important in determining the temporal variability.

Temporal distribution of the short-beaked common dolphin (Delphinus delphis) in the south of Madeira Island (Portugal) and relationship with oceanographic variables

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Student’s Engagement in School: Conceptualization and relations with Personal Variables and Academic Performance

This article reviews the literature regarding Student’s Engagement in School (SES), its relationship with personal variables, as well as with academic performance. Although SES’ conceptualization may vary across studies, there is general agreement concerning the multidimensional nature of this construct, encompassing three dimensions – cognitive, affective and behavioural. It is seen as an antecedent of several required outcomes, at academic level, but also as a valorous construct itself, both as mediator and product. More particularly, this concept has been the focus of debate concerning academic success and school dropout. There can also be found a significant number of studies which suggest that personal (self-efficacy, self-concept), as well as contextual (peers, school, family) factors are related with school engagement; additionally, the lack of engagement is linked with low academic performance, behavioural problems and school dropout. Thus, Student’s Engagement in School is perceived as a potentially effective response to the problems affecting schools and their students, and an aspect to be considered in preventing problematic patterns related to scholary contexts.

Influence of environmental variables on the predatory sucess of the iberian wolf in the north of Portugal

Tese de mestrado em Biologia da Conservação, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2016

Patterns of cortisol and DHEA secretion and relationships with attachment style and psychosocial variables in female adolescents: a developmental psychopathology approach

This programme of research used a developmental psychopathology approach to investigate females across the adolescent period. A two-sided story is presented; first, a study of neuroendocrine and psychosocial parameters in a group of healthy female adolescents (N = 63), followed by a parallel study of female adolescents with anorexia nervosa (AN) (N = 8). A biopsychosocial, multi-method measurement approach was taken, which utilised self-report, interview and hypothalamic-pituitary-adrenocortical (HPA) axis measures. Saliva samples for the measurement of cortisol and DHEA were collected using the best-recommended methodology: multiple samples over the day, strict reference to time of awakening, and two consecutive sampling weekdays. The research was adolescent-orientated: specifically, by using creative and ageappropriate strategies to ensure participant adherence to protocol, as well as more generally by adopting various procedures to facilitate engagement with the research process. In the healthy females mean (± SD) age 13.9 (± 2.7) years, cortisol and DHEA secretion exhibited typical adult-like diurnal patterns. Developmental markers of chronological age, menarche status and body mass index (BMI) had differential associations with cortisol and DHEA secretory activity. The pattern of the cortisol awakening response (CAR) was sensitive to whether participants had experienced first menses, but not to chronological age or BMI. Those who were post-menarche generally reached their peak point of cortisol secretion at 45 minutes post-awakening, in contrast to the pre-menarche group who were more evenly spread. Subsequent daytime cortisol levels were also higher in post-menarche females, and this effect was also noted for increasing age and BMI. Both morning and evening DHEA were positively associated with developmental markers. None of the situational or self-report psychosocial variables that were measured modulated any of the key findings regarding cortisol and DHEA secretion. The healthy group of girls were within age-appropriate norms for all the self-report measures used, however just under half of this group were insecurely attached (as assessed by interview). Only attachment style was associated with neuroendocrine parameters. In particular, those with an anxious insecure style exhibited a higher awakening sample (levels were 7.16 nmol/l, 10.40 nmol/l and 7.93 nmol/l for secure, anxious and avoidant groups, respectively) and a flatter CAR (mean increases over the awakening period were 6.38 nmol/l, 2.32 nmol/l and 8.61 nmol/l for secure, anxious and avoidant groups, respectively). The afore-mentioned pattern is similar to that consistently associated with psychological disorder in adults, and so this may be a pre-clinical vulnerability factor for subsequent mental health problems. A group of females with AN, mean (± SD) age 15.1 (± 1.6) years, were recruited from a specialist residential clinic and compared to the above group of healthy control (HC) female adolescents. A general picture of cortisol and DHEA hypersecretion was revealed in those with AN. The mean (± SD) change exhibited in cortisol levels over the 30 minute post-awakening period was 7.05 nmol/l (± 5.99) and 8.33 nmol/l (± 6.41) for HC and AN groups, respectively. The mean (± SD) evening cortisol level for the HC girls was 1.95 nmol/l (± 2.11), in comparison to 6.42 nmol/l (± 11.10) for the AN group. Mean (± SD) morning DHEA concentrations were 1.47 nmol/l (± 0.85) and 2.25 nmol/l (± 0.88) for HC and AN groups, respectively. The HC group’s mean (± SD) concentration of 12 hour DHEA was 0.55 nmol/l (± 0.46) and the AN group’s mean level was 0.89 nmol/l (± 0.90). This adrenal steroid hypersecretion evidenced by the AN group was not associated with BMI or eating disorder symptomatology. Insecure attachment characterised by fearfulness and anger was most apparent; a style which was unparalleled in the healthy group of female adolescents. The causal directions of the AN group findings remain unclear. Examining some of the participants with AN as case studies one year post-discharge from the clinic illustrated that for one participant who was recovered, in terms of returning to ordinary school life and no longer exhibiting clinical levels of eating disorder symptomatology, her CARs were no longer inconsistent over sampling days and her DHEA levels were also now generally comparable to the healthy control group. For another participant who had not recovered from her AN one year later, the profile of her CAR continued to be inconsistent over sampling days and her DHEA concentrations over the diurnal period were significantly higher in comparison to the healthy control group. In its entirety, this work’s unique contribution lies in its consideration of methodological and developmental issues specifically pertaining to adolescents. Findings also contribute to knowledge of AN and understanding of vulnerability factors, and how these may be used to develop interventions dedicated to improving adolescent health.

Predictive Variables Affecting Transfusion Requirements in Orthotopic Liver Transplantation

INTRODUCTION AND AIMS: Adult orthotopic liver transplantation (OLT) is associated with considerable blood product requirements. The aim of this study was to assess the ability of preoperative information to predict intraoperative red blood cell (RBC) transfusion requirements among adult liver recipients. METHODS: Preoperative variables with previously demonstrated relationships to intraoperative RBC transfusion were identified from the literature: sex, age, pathology, prothrombin time (PT), factor V, hemoglobin (Hb), and platelet count (plt). These variables were then retrospectively collected from 758 consecutive adult patients undergoing OLT from 1997 to 2007. Relationships between these variables and intraoperative blood transfusion requirements were examined by both univariate analysis and multiple linear regression analysis. RESULTS: Univariate analysis confirmed significant associations between RBC transfusion and PT, factor V, Hb, Plt, pathology, and age (P values all < .001). However, stepwise backward multivariate analysis excluded variables Plt and factor V from the multiple regression linear model. The variables included in the final predictive model were PT, Hb, age, and pathology. Patients suffering from liver carcinoma required more blood products than those suffering from other pathologies. Yet, the overall predictive power of the final model was limited (R(2) = .308; adjusted R(2) = .30). CONCLUSION: Preoperative variables have limited predictive power for intraoperative RBC transfusion requirements even when significant statistical associations exist, identifying only a small portion of the observed total transfusion variability. Preoperative PT, Hb, age, and liver pathology seem to be the most significant predictive factors but other factors like severity of liver disease, surgical technique, medical experience in liver transplantation, and other noncontrollable human variables may play important roles to determine the final transfusion requirements.

Hopelessness and Related Variables among Cancer Patients in the Southern European Psycho-Oncology Study (SEPOS).

BACKGROUND: Although hopelessness has been studied in cancer, no data are available in non-English-speaking countries. OBJECTIVE: The authors sought to amass data from Southern European countries (Italy, Portugal, Spain, and Switzerland) in order to fill this void. METHOD: A group of 312 cancer patients completed the Mini-MAC Hopelessness subscale, the Hospital Anxiety and Depression Scale (HADS), the Cancer Worry Inventory (CWI), and a six-item Visual Analog scale (VAS) to measure intensity of physical symptoms, general well-being, difficulty in coping with cancer, intensity of social support from close relationships, leisure activity, and support from religious beliefs. RESULTS: Regression analysis indicated that HADS-Depression, VAS Maladaptive Coping and Well-Being, and the CWI explained 42% of the variance. CONCLUSION: Hopelessness in cancer patients seems not exclusively to correspond to depression, but is related to various other psychosocial factors, such as maladaptive coping, as well.

Application of Fuzzy Variables for Systems of Management Decision Support

The following article describes an approach covering the variety of opinions and uncertainties of estimates within the chosen technique of decision support. Mathematical operations used for assessment of options are traced to operations of working with functions that are used for assessment of possible options of decision-making. Approach proposed could be used within any technique of decision support based on elementary mathematical operations. In this article the above-mentioned approach is described under analytical hierarchy process.