Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

In silico identification and characterization of protein-ligand binding sites

Protein–ligand binding site prediction methods aim to predict, from amino acid sequence, protein–ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein–ligand interactions has become extremely important to help determine a protein’s functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein–ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein–ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein–ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.

The importance of body-mass exponent optimization for evaluation of performance capability in cross-country skiing

Introduction Performance in cross-country skiing is influenced by the skier’s ability to continuously produce propelling forces and force magnitude in relation to the net external forces. A surrogate indicator of the “power supply” in cross-country skiing would be a physiological variable that reflects an important performance-related capability, whereas the body mass itself is an indicator of the “power demand” experienced by the skier. To adequately evaluate an elite skier’s performance capability, it is essential to establish the optimal ratio between the physiological variable and body mass. The overall aim of this doctoral thesis was to investigate the importance of body-mass exponent optimization for the evaluation of performance capability in cross-country skiing. Methods In total, 83 elite cross-country skiers (56 men and 27 women) volunteered to participate in the four studies. The physiological variables of maximal oxygen uptake (V̇O2max) and oxygen uptake corresponding to a blood-lactate concentration of 4 mmol∙l-1 (V̇O2obla) were determined while treadmill roller skiing using the diagonal-stride technique; mean oxygen uptake (V̇O2dp) and upper-body power output (Ẇ) were determined during double-poling tests using a ski-ergometer. Competitive performance data for elite male skiers were collected from two 15-km classical-technique skiing competitions and a 1.25-km sprint prologue; additionally, a 2-km double-poling roller-skiing time trial using the double-poling technique was used as an indicator of upper-body performance capability among elite male and female junior skiers. Power-function modelling was used to explain the race and time-trial speeds based on the physiological variables and body mass. Results The optimal V̇O2max-to-mass ratios to explain 15-km race speed were V̇O2max divided by body mass raised to the 0.48 and 0.53 power, and these models explained 68% and 69% of the variance in mean skiing speed, respectively; moreover, the 95% confidence intervals (CI) for the body-mass exponents did not include either 0 or 1. For the modelling of race speed in the sprint prologue, body mass failed to contribute to the models based on V̇O2max, V̇O2obla, and V̇O2dp. The upper-body power output-to-body mass ratio that optimally explained time-trial speed was Ẇ ∙ m-0.57 and the model explained 63% of the variance in speed. Conclusions The results in this thesis suggest that V̇O2max divided by the square root of body mass should be used as an indicator of performance in 15-km classical-technique races among elite male skiers rather than the absolute or simple ratio-standard scaled expression. To optimally explain an elite male skier’s performance capability in sprint prologues, power-function models based on oxygen-uptake variables expressed absolutely are recommended. Moreover, to evaluate elite junior skiers’ performance capabilities in 2-km double-poling roller-skiing time trials, it is recommended that Ẇ divided by the square root of body mass should be used rather than absolute or simple ratio-standard scaled expression of power output.

Physiological demands of competitive elite cross-country skiing

Introduction Researchers have, for decades, contributed to an increased collective understanding of the physiological demands in cross-country skiing; however, almost all of these studies have used either non-elite subjects and/or performances that emulate cross-country skiing. To establish the physiological demands of cross-country skiing, it is important to relate the investigated physiological variables to the competitive performance of elite skiers. The overall aim of this doctoral thesis was, therefore, to investigate the external validity of physiological test variables to determine the physiological demands in competitive elite cross-country skiing. Methods The subjects in Study I – IV were elite male (I – III) and female (III – IV) cross-country skiers. In all studies, the relationship between test variables (general and ski-specific) and competitive performances (i.e. the results from competitions or the overall ski-ranking points of the International Ski Federation (FIS) for sprint (FISsprint) and distance (FISdist) races) were analysed. Test variables reflecting the subject’s general strength, upper-body and whole-body oxygen uptake, oxygen uptake and work intensity at the lactate threshold, mean upper-body power, lean mass, and maximal double-poling speed were investigated. Results The ability to maintain a high work rate without accumulating lactate is an indicator of distance performance, independent of sex (I, IV). Independent of sex, high oxygen uptake in whole-body and upper-body exercise was important for both sprint (II, IV) and distance (I, IV) performance. The maximal double-poling speed and 60-s double-poling mean power output were indicators of sprint (IV) and distance performance (I), respectively. Lean mass was correlated with distance performance for women (III), whereas correlations were found between lean mass and sprint performance among both male and female skiers (III). Moreover, no correlations between distance performance and test variables were derived from tests of knee-extension peak torque, vertical jumps, or double poling on a ski-ergometer with 20-s and 360-s durations (I), whereas gross efficiency while treadmill roller skiing showed no correlation with either distance or sprint performance in cross-country skiing (IV). Conclusion The results in this thesis show that, depending on discipline and sex, maximal and peak oxygen uptake, work intensity at the lactate threshold, lean mass, double-poling mean power output, and double-poling maximal speed are all externally valid physiological test variables for evaluation of performance capability among elite cross-country skiers; however, to optimally indicate performance capability different test-variable expressions should be used; in general, the absolute expression appears to be a better indicator of competitive sprint performance whereas the influence of body mass should be considered when evaluating competitive distance performance capability of elite cross-country skiers.

Sports and mediatization : a case of women´s ski-jumping

Ski jumping was the only sport included in the Winter Olympics, where women were not allowed to take part until the first week of April 2011, when IOC decided to let them in to the Olympic family, a major victory for women´s ski-jumping. Since 2004 the Norwegian media had women ski jumping as one important topic in their media coverage. The third of March 2010 the new Holmenkollen ski-jumping hill was inaugurated. It had been rebuilt for the World Championships 2011. The first jump on the hill was surrounded by an intense debate. Annette Sagen was decided to be the first jumper on the hill after a poll on the social media channel Facebook that gave Annette Sagen over 40 000 votes.  However Tuesday the second of March Björn Einar Romören, a world cup jumper, did the first jump during a training session. This act started a significant chain of events. The biggest Norwegian web – magazines Verldens Gang and Aftenposten made this the head story and they invited the readers to interaction. Within 24 hours 11 000 comments were written, most of them in favor of Sagen and against Romören´s behavior. The Norwegian Ski Association excluded Romören from two World Cup competitions. What did happen during these days in the media?  I want to present the activities, which went on in two web-magazines, and analyze the articles written on the topic. Main issues are to show what an impact a social media network had on the sport in this specific case and how different actors appeared in the media and discuss if Romörens exclusion was a result of the mediatization.

Espirito de catimbo: a moral magico-religiosa da jurema

This participative research interested in the social praxis attempts to understand the moral principles that set the magic rituals and the places of worship of three jurema centers of the potiguar region of Canguaretama. Among other inner particularly aspects of each focused catimbó-jurema center, it is being discussed the collective standards involved in the reliance and fellowship values assumed in the private magical gatherings by the juremeiras leaders and their partners, in contrast to the prestige seeking and the individualism that influence both the symbolic competitions and the witchcraft works that link these agents to the broader catimbozeiro universe of this region. Finally, the moral practices which make part of the juremeiro left-right dualism are investigated based on the understanding that the referred native pantheonic-ritual dichotomy does not necessarily express two moralities substantially adversed in terms of benefits or harms, but a series of moral actions subject to the specular logic of the tit-for tat. Thus, this research seeks to prove that this moral structure of symbolic reciprocity, as well as the witchcraft centrality in the catimbozeiro world, finds a certain causal link in a world view which guiding principle is the ontological evil of the catholic cosmology

A prática docente de Myriam Coeli na década de 1960

The present work has as objective to reconstitute the biographical profile and pedagogical practices of the teacher Myriam Coeli de Araújo Dantas da Silveira, in the Professionalizing scholl of the Federal Net of the Rio Grande do Norte, in the 60 s years. The choice of the period is justified by being this the time of important changes in the Education, as an example we have the implementation of the Law of Lines of direction and Bases of the National Education, the 4.024/1961. This teacher contributed for the formation of the potiguar s society scholar, acting in the press, the journalism and the teaching, activity that I analyzed in this study. How the pedagogical practices of her had happened in the 60 s years? This question guided the research and, in the search to answer it I used as source the Public Archive of the Rio grande do Norte, the Historical and Geographic Institute of the Rio grande do Norte, the periodicals of the time, photographs, sketch books of Myriam Coeli and interviews with familiar, former-pupils and contemporaries of this master. I verified that her performance always was based in the educational changes lived deeply for her, carrying through a series of activities in the school as: elaboration of the annual program of Portuguese Language, organization of literary competitions and an practice based on the effective norms without leaving to unite respect and the understanding for the pupils. Of this form, the analysis is not summarized only to the practices of a teacher, but the configuration, in part, of the Rio Grande do Norte educational history in a determined period, the 60 s years

Estudo de competição inter e intraespecífica envolvendo Glycine max (L. ) Merril e Cyperus rotundus (L.), em condições de casa de vegetação

O presente experimento teve por objetivo estudar os efeitos da competição inter e intraespecífica envolvendo Glycine max (L.) Merril e Cyperus rotundus L. sobre as características das plantas e acúmulos de N, P, K, Ca e Mg pelas espécies envolvidas. Para tanto, estipulou-se um tratamento em que se desenvolveram três plantas de Glycine max e outro em que se desenvolveram 3 tubérculos de Cyperus rotundus por vaso. Para estudar os efeitos da competição intraespecífica, em dois outros tratamentos dobraram-se as populações por vaso. No estudo da competição interespecífica permitiu-se o desenvolvimento de três plantas de Glycine max e de três tubérculos de Cyperus rotundus num mesmo vaso. de uma maneira geral, pôde-se observar que principalmente devido às diferenças no hábito de crescimento das duas espécies, a expressão da competição inter e intraespecífica, em cada uma delas, assume aspectos distintos. No caso de Cyperus rotundus, o efeito do dobro da densidade pôde ser compensado, em parte, pela maior produção de manifestações epígeas e de tubérculos, aliados ao maior desenvolvimento dos tubérculos na menor densidade de plantio. No caso da competição interespecífica, os resultados sugerem um efeito decisivo do sombreamento de Leguminosae sobre o comportamento da Cyperaceae. Os padrões de efeitos da competição pelos nutrientes foi determinado também pelas diferenças no recrutamento dos elementos do solo pelas espécies envolvidas.

Alterations in muscular enzymes of horses competing long-distance endurance rides under tropical climate

Estudaram-se as alterações de atividade das enzimas musculares creatino quinase (CK), lactato desidrogenase (LDH) e aspartato aminotransferase (AST) em um grupo de cavalos que utilizados em provas de enduro de 70 e 100km de distância, em cinco competições. Os valores (U/l) basais (antes da largada) foram 245,13±9,84 para CK, 496,61±14,76 para LDH e 328,95±8,65 para AST. Todas as atividades das enzimas decresceram no primeiro momento das provas (~30km). Valores de pico, significativamente diferentes, foram alcançados para CK (413,59±50,75) imediatamente após 70km de distância; 24 horas após para LDH (628,61±33,30); e 48 horas após as provas para AST (389,89±16,96). A monitoração do período de recuperação revelou diferente comportamento entre as concentrações enzimáticas com CK retornando aos valores basais 24 horas pós-provas (279,61 ± 23,05). LDH e AST retornaram aos valores basais, 72 horas pós-provas (505,25±33,78 e 359,35±24,90, respectivamente). Os dados obtidos revelaram diferentes alterações na concentração de enzimas musculares de cavalos de enduro, diretamente relacionadas com a duração do esforço.

S-Educ: Um Simulador de Ambiente de Robótica Educacional em Plataforma Virtual

We propose a robotics simulation platform, named S-Educ, developed specifically for application in educational robotics, which can be used as an alternative or in association with robotics kits in classes involving the use of robotics. In the usually known approach, educational robotics uses robotics kits for classes which generally include interdisciplinary themes. The idea of this work is not to replace these kits, but to use the developed simulator as an alternative, where, for some reason, the traditional kits cannot be used, or even to use the platform in association with these kits. To develop the simulator, initially, we conducted research in the literature on the use of robotic simulators and robotic kits, facing the education sector, from which it was possible to define a set of features considered important for creating such a tool. Then, on the software development phase, the simulator S-Educ was implemented, taking into account the requirements and features defined in the design phase. Finally, to validate the platform, several tests were conducted with teachers, students and lay adults, in which it was used the simulator S-Educ, to evaluate its use in educational robotics classes. The results show that robotic simulator allows a reduction of financial costs, facilitate testing and reduce robot damage inherent to its use, in addition to other advantages. Furthermore, as a contribution to the community, the proposed tool can be used to increase adhesion of Brazilian schools to the methodologies of educational robotics or to robotics competitions

Alterações posturais em atletas brasileiros do sexo masculino que participaram de provas de potência muscular em competições internacionais

Os esportes de alto nível determinam padrões corporais que extrapolam barreiras geopolíticas, sociais e culturais. Estas peculiaridades resultam em alterações posturais que estão associadas à eficiência do gesto desportivo, porém, em longo prazo, podem evoluir para processos mórbidos que limitam a prática de atividades físicas regulares. O objetivo da pesquisa foi descrever o perfil postural dos atletas que participam de provas de potência muscular e identificar processos anátomo-cinesiológicos responsáveis pelas principais alterações corporais. A casuística foi composta por 15 atletas do sexo masculino, especializados em provas de potência muscular. O protocolo para coleta de dados foi elaborado com base na proposta de: i) Kendall, para o exame físico e observacional, utilizando simetrógrafo e fio de prumo; ii) Souchard, para a análise postural em cadeia. As informações foram organizadas sob a forma de distribuição de freqüência absoluta e relativa. Os resultados apontaram que: i) o tornozelo em valgo (67%) foi a situação mais comum; ii) a rotação interna da pelve à direita (60%), seguida do lado oposto mais elevado (47%), pode estar relacionada com a corrida em curva que sobrecarrega a estrutura da pelve para a manutenção da velocidade com simultânea mudança de direção em função da força gravitacional; iii) a anteversão de pelve (73%) decorre da retração observada nos músculos flexores do quadril e extensores do joelho; iv) a alteração expressa no item iii contribui para a formação de hiperlordose lombar (73%) e desencadeia mecanismo compensatório de retração da cadeia posterior causando cifose torácica (53%) e cabeça em protrusão (73%). O diagnóstico precoce e a adoção de medidas profiláticas efetivas podem contribuir para o aumento da performance, bem como prevenir a ocorrência de lesões desportivas. Estudos envolvendo intervenção fisioterápica deverão avaliar se há redução dos efeitos crônicos que as alterações posturais decorrentes do treinamento causam ao atleta de alto nível.

Respostas do lactato sanguíneo e da freqüência cardíaca em duas diferentes provas do automobilismo

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Taxonomic diversity, niche width and similarity in the use of plant resources by bees (Hymenoptera: Anthophila) in a cerrado area

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Sexual selection and social hierarchy in fishes.

Sexual selection is a crucial element to understand behavioral evolution. Teleost fish have been considered as good models for research on sexual selection in the last decades due to their variety of sexual behavior. Female fish can choose males based on body and behavioral traits, such as body size, body color, ornaments, territorial quality, nest size and courtship behavior. Choices are based upon several types of sensorial inputs, such as visual, chemical, sonorous and electrical signals. Intrasexual selection also acts on females because they can mate with a dominant individual in male-male competitions. For both approaches, there is an expectation regarding the benefits of sexual selection by means of female choice. However, in several cases females do not choose the dominant male. In this mini-review, we present and discuss both intersexual and intrasexual mechanisms of sexual selection in fish and point out that females do not always choose a male for mating.

Índices fisiológicos associados com a performance aeróbia em corredores de endurance: efeitos da duração da prova

O objetivo deste estudo foi analisar a validade do consumo máximo de oxigênio (VO2max), da velocidade correspondente ao VO2max (vVO2max), do tempo de exaustão na vVO2max (Tlim), da economia de corrida (EC) e do limiar anaeróbio (LAn) para a predição da performance de atletas de endurance. Quatorze corredores de endurance (33,4 ± 4,4 anos; 62,7 ± 4,3kg; 166,1 ± 5,0cm; VO2max = 60,4 ± 5,9ml.kg-1.min-1) realizaram os seguintes testes: a) competição simulada nas distâncias de 1.500 e 5.000m. e; b) testes de laboratório para a determinação do VO2max, vVO2max, EC, LAn e Tlim na intensidades de 100% vVO2max. As velocidades (km/h) da vVO2max (18,7 ± 0,8), LAn (17,3 ± 1,1) v1.500m (19,9 ± 0,8) e v5.000m (17,9 ± 0,9) foram significantemente diferentes. A regressão múltipla stepwise revelou que o LAn foi o único preditor da performance da v5.000m, explicando 50% da variação desta performance. Para a v1.500m, o Tlim e a vVO2max explicaram 88% da variação da performance. Com base em nossos resultados, pode-se concluir que a validade dos índices fisiológicos (VO2max, vVO2max, Tlim, EC e LAn), para a predição da performance aeróbia de atletas de endurance, é dependente da distância da prova (1.500 x 5.000m) analisada.