FLOWViZ: Framework for Phylogenetic Processing

The increasing risk of epidemics and a fast-growing world population has contributed to a great investment in phylogenetic analysis, in order to track numerous diseases and conceive effective medication and treatments. Phylogenetic analysis requires large quantities of information to be analyzed and processed for knowledge extraction, using suitable techniques and, nowadays, specific software and algorithms, to deliver results as efficiently and fast as possible. These algorithms and techniques are already provided by several free and available frameworks and tools. Usually, the process of phylogenetic analysis consists of several processing steps, which define a pipeline. Some phylogenetic frameworks have available more than one processing step, such as inferring phylogenetic trees, data integration, and visualization, but due to the continuous growth in involved data amounts, each step may last several hours or days. Scientific workflow systems may use high performance computing facilities, if available, for processing large volumes of data, concurrently. But most of these scientific workflow systems cannot be easily installed and configured, are available as centralized services, and, usually, it is not easy to integrate tools and processing steps available in phylogenetic frameworks. This paper summarizes the thesis document of the FLOWViZ framework, which main goal is to provide a software integration framework between a phylogenetic framework and a scientific workflow system. This framework makes it possible to build a customized integration with much fewer lines of code, while providing existing phylogenetic frameworks with workflow building and execution, to manage the processing of great amounts of data. The project was supported by funds, for a student grant of FCT - NGPHYLO PTDC/CCI-BIO/29676/2017 and an IPL project - IPL/2021/DIVA

The use of acute responses of endocrine and immune biomarkers to highlight overreaching

A Thesis submitted to the University of Bedfordshire, in fulfilment of the requirements for the degree of Doctor of PhilosophyThe action of overtraining may lead to the different states of overreaching or the overtraining syndrome (OTS). Chronic maladaptation in endocrine and immune mechanisms, and performance decrements occur with the incidence of these states. Circulating cortisol and testosterone have been proposed as endocrine markers of overreaching/OTS. Salivary measurements of these hormones have been used as a non-invasive surrogate for circulating levels. Chapter 4 (study 1) on this Thesis examined the influence of consuming water 10 min, 5 min and 1 min before providing a saliva sample in diluting saliva and consequently providing invalid salivary cortisol and testosterone concentration levels. No trial effect was found. However, exercise-induced salivary cortisol and testosterone significantly elevated in response to the 10 min and 5 min trials only, with lower absolute-changes observed in the 1 min trial. No differences were found in the resting samples. It was suggested that consuming water up to 5 min before providing a saliva sample does not appear to influence the hormone concentrations at rest and during exercise. However, the recommended guidelines for saliva collection have been followed in the subsequent studies. Chapter 5 (study 2) examined the reproducibility of salivary cortisol and testosterone responses to a 30-min cycle named as the 55/80. This test has been proposed as a suitable indicator of hormonal alterations associated with overreaching/OTS. Reproducibility of salivary cortisol and testosterone to the 55/80 was confirmed by determining intra-individual coefficients of variation (CVi). However, the 55/80 is a cycle test and therefore, may not be appropriate for runners. Chapter 6 (study 3) focused on designing a 30-min, running bout (i.e. the RPEtreadmill) to reproduce the effects of the 55/80. The RPEtreadmill is a self-paced test and therefore, will not require aVO2maxtest to determine exercise intensities. An acute elevation of plasma and salivary testosterone, but not cortisol was observed in response to the RPEtreadmill. These responses have been shown to be reproducible. The data from Chapter 6 suggest that the RPEtreadmill may be a suitable tool to indicate hormonal alterations associated with overreaching/OTS. This led to the design of study 4 (Chapter 7). Plasma and salivary cortisol and testosterone responses were examined before and after a 12-day intensified-training period. Immunity markers (specifically salivary immunoglobulin A (SIgA), leucocyte subset proliferation and phagocytic activity) were examined before and after training. Plasma and salivary cortisol were unaffected by acute exercise and training. However, testosterone elevated to the RPEtreadmill Pre-Training, and these responses were reduced Post-Training. Total leucocytes and mucosal immunity were unaffected by exercise and training. However, increased upper respiratory tract infection symptoms were found Post-Training. Baseline phagocytic function was 47% lower Post-Training. This Thesis suggests that testosterone may be a more reliable exercise-stress marker. Moreover, the RPEtreadmill may be a suitable tool to highlight alterations in testosterone when in an overreached state in an attempt to avoid the incidence of OTS, and that this tool may be practically applied in the field of exercise science. Additionally, this Thesis shows that a 12-day intensified-training period induced a marked decrease in phagocytic responses, and therefore using the RPEtreadmill to highlight overreaching may be important to also prevent further impairments in immunity status

Does land use and landscape contribute to self-harm? A sustainability cities framework

Self-harm has become one of the leading causes of mortality in developed countries. The overall rate for suicide in Canada is 11.3 per 100,000 according to Statistics Canada in 2015. Between 2000 and 2007 the lowest rates of suicide in Canada were in Ontario, one of the most urbanized regions in Canada. However, the interaction between land use, landscape and self-harm has not been significantly studied for urban cores. It is thus of relevance to understand the impacts of land-use and landscape on suicidal behavior. This paper takes a spatial analytical approach to assess the occurrence of self-harm along one of the densest urban cores in the country: Toronto. Individual self-harm data was gathered by the National Ambulatory Care System (NACRS) and geocoded into census tract divisions. Toronto’s urban landscape is quantified at spatial level through the calculation of its land use at di erent levels: (i) land use type, (ii) sprawl metrics relating to (a) dispersion and (b) sprawl/mix incidence; (iii) fragmentation metrics of (a) urban fragmentation and (b) density and (iv) demographics of (a) income and (b) age. A stepwise regression is built to understand the most influential factors leading to self-harm from this selection generating an explanatory model.This research was supported by the Canadian Institutes of Health Research Strategic Team Grant in Applied Injury Research # TIR-103946 and the Ontario Neurotrauma Foundation grantinfo:eu-repo/semantics/publishedVersio

On the numerical convergence properties of the calculation of the flow around the KVLCC2 tanker in unstructured grids

This paper addresses the estimation of numerical errors in the calculation of the flow around the KVLCC2 tanker at model scale Reynolds number in unstructured grids. The flow solution is based on the Reynolds-Averaged Navier-Stokes equations supplemented by the k − ω SST two-equation eddy-viscosity model using the so-called double-body approach, i.e. free surface effects are neglected. Grid refinement studies are performed for sets of grids gener- ated with the open source code SnappyHexMesh and with the HEXPRESSTM grid generator. Definition of grid refinement ratio in unstructured grids and its consequences for the estima- tion of numerical errors is discussed. Friction and pressure resistance coefficients and mean velocity components at the propeller plane are compared with reference solutions obtained in nearly-orthogonal multi-block structured grids with the same flow solver ReFRESCO

Fitness profiles of elite Portuguese rugby union players

The aim of this study was to describe the fitness profiles of senior elite Portuguese rugby players. Forty-six senior Portuguese rugby players, classified as backs (n=22; age 26.2±2.8) and forwards (n=24; age 26.7±2.9) were assessed during physical testing sessions carried out for the Portuguese National rugby team. The body composition, maximum strength and anaerobic capacity of players are hypothesized to be important physical characteristics as successful performance in rugby is predicated on the ability to undertake skilled behaviours both quickly and whilst withstanding large forces when in contact situations. No absolute differences were found between the backs and forwards for the speed performance variables although positional differences were found across all speeds when assessed relative to body mass since the forwards were significantly heavier. Coaches and the management team can use this information for monitoring progressive improvements in the physiological capacities of rugby players. These physical characteristics of elite rugby players provide normative profiles for specific positions and should form the basis of developmental programmes for adolescents

Coaches perceived importance of tactical items in basketball players' long term development

One of the topics of sport sciences that have not been adequately investigated is the importance that specialists dedicate to tactical skills in long-term players development. The purpose of this study was to evaluate the importance that basketball coaches give to the development of these abilities in both sexes. Data were collected using a questionnaire. Items tapped six areas tactic related to: small sided games, offensive superiority games, defensive superiority games, formal game, offense and defense. The sample was divided according to team's sex and stage of long-term development: initiation, orientation, specialization, or high-performance. No significant differences were found in small sided games and formal game. Significant differences in assigned importance between coaches of boys to offensive superiority and defensive superiority games were found, supporting that these items should be the subject of more intense development primarily until 14 years of age. Significant differences in assigned importance between coaches of girls to defense were found. Coaches reinforced the importance of developing team offensive aspects, primarily at highperformance stage. Finally, significant differences in assigned importance between coaches of both sexes to defensive tactical work were found. Results confirmed that defensive tactical work should be the subject of more intense development between 11 and 14 years old but mostly after 19 years of age, reinforcing the importance of tactical work in later stages of development, i.e., high-level performance

Continuous flow Aza-Michael reaction for preparing the fast-acting synthetic opioid drug Remifentanil

Remifentanil is a modern fentanyl analogue with ultrashort-action granted by an esterase-labile methyl propanoate chain. Here, we present the development of a continuous flow methodology for the key N-alkylation step of remifentanil preparation in a biphasic, “slug-flow” regime. We screened parameters under microwave-assisted reactions, translated conditions to flow settings, and obtained remifentanil under 15-min residence time in a 1-mL microreactor, with a space-time yield of 89 mg/mL·h and 94% yield

A ocupação do espaço de Viseu na época romana

The bimillenarian occupation of the land where Viseu is now, is this article’s subject. The author starts by giving a brief notion of space occupation theories in archaeology, referring the main characteristics of the occupation of the Civitas location in Viseu in the roman era. The conclusions on display are drawn from observation of around three hundred inventoried roman sites to this day. What was the place of Viseu when the Romans arrived here? What were the main alterations they introduced? How did they delimit the urban space and organized the interior of the new city? Are questions that are answered.A ocupação bimilenar do espaço que onde hoje assenta Viseu é o tema deste artigo. O autor começa por dar uma breve noção das teorias da ocupação do espaço em arqueologia, referindo-se às características principais da ocupação do espaço na Civitas de Viseu na época romana. As conclusões expostas são retiradas da observação de cerca de trezentas estações romanas inventariadas até ao momento. O que era o sítio de Viseu quando os Romanos aqui chegaram? Quais as principais alterações que eles introduziram? Como delimitaram o espaço urbano e organizaram o espaço interior na nova cidade? São questões a que se procura dar resposta. &nbsp

Análisis cinemático de los saques de lateral en el Torneo de Rugby del Seis Naciones

This study examines 126 successful, six- or seven-man lineouts of the 2013 Six Nations Tournament. Data were extracted from footage of the competition to calculate kinematic variables along with jumper position. Through cluster analysis, six types of throw were identified according to distance and velocity: short-fast, short-slow, medium short-fast, medium short-slow, medium long and long. Significant differences were detected in all the variables examined depending on the throw category (throw distance P<0.001; Partial eta square η2=0.932, height P=0.032; η2=0.096, flight time P<0.001; η2=0.789, starting angle P<0.001; η2=0.502, initial velocity P<0.001; η2=0.767 and jumper position P<0.001; η2=0.641). In the discriminant analysis, all variables except jumper position were able to correctly classify 100% of the throws. In addition, we differentiated the six participating teams, finding significant differences in throw height (Scotland vs England difference means d=0.32m, Ireland d=0.36m or France d=0.37m), flight time (Italy vs England d=0.34s or Ireland d=0.33s) and angle (Italy vs England d=9.72º or Ireland d=8.49º and Scotland vs England d=8.27º or Ireland d=7.04º). Our findings have implications for training and team analysis (own and rival) and also provide direction for future investigations.El presente estudio ha investigado 126 saques de lateral ganados con seis o siete jugadores en el alineamiento del torneo de las Seis Naciones de 2013 La observación se ha realizado a partir del estudio de los videos, por lo que los datos están extraídos en competición real. Un análisis cluster nos ha permitido establecer seis tipos de lanzamientos en función de la distancia y la velocidad: cortos-rápidos, cortos-lentos, mediocortos-rápidos, mediocortos-lentos, mediolargos y largos. Hemos encontrado diferencias significativas en todas las variables estudiadas en función de los tipos de lanzamiento (distancia del lanzamiento P<0.001; η2=0.932, altura P=0.032; η2=0.096, tiempo de vuelo P<0.001; η2=0.789, ángulo de salida P<0.001; η2=0.502, velocidad inicial P<0.001; η2=0.767 y posición del saltador P<0.001; η2=0.641). El análisis discriminante incluyó todas las variables excepto la posición del saltador, clasificando correctamente el 100% de los casos. Además, hemos diferenciado a los seis equipos participantes encontrando diferencias significativas en altura (entre Escocia con Inglaterra d=0.32m, Irlanda d=0.36m y Francia d=0.37m), tiempo de vuelo (entre Italia con Inglaterra d=0.34s e Irlanda d=0.33s) y ángulo de salida (entre Italia con Inglaterra d=9.72º e Irlanda d=8.49º y de Escocia con Inglaterra d=8.27º e Irlanda d=7.04º). Del presente trabajo se derivan implicaciones para el entrenamiento, el análisis del equipo propio y del rival y para futuras investigaciones en los saques de lateral

The use of medicinal nicotine in pregnancy for smoking cessation

Background Smoking during pregnancy is the leading preventable cause of poor birth outcomes for mothers and babies. In 2010, 26% of women smoked during or in the 12 months prior to pregnancy, and 12% smoked throughout pregnancy. 120 trials of nicotine replacement therapy (NRT) have shown that it is effective for smoking cessation in non-pregnant smokers. However, the 9 trials conducted in pregnant smokers, provide no evidence that NRT helps pregnant smokers to stop. In 2012, a large randomised controlled trial (RCT) investigating NRT used in pregnancy for smoking cessation reported that it initially doubled smoking cessation rates, but found no evidence that it enhanced cessation throughout pregnancy. Trial participants reported low adherence to NRT. One possible reason for this is that nicotine metabolism is much faster in pregnancy and so the doses of NRT which have been trialled in pregnancy may not sufficiently treat women’s nicotine withdrawal symptoms. This study not only found that children of mothers in the intervention arm had better developmental outcomes at 2 years of age, but also that a dose-response relationship existed between reported higher NRT use and the latter. Using data from this trial, this thesis aims to further explore factors driving/associated with both higher adherence to NRT in pregnancy and improved birth outcomes, and to raise hypotheses about ways in which NRT may be used effectively to help pregnant smokers attempting to quit. Methods The studies reported in this thesis used data from 1,050 pregnant women recruited to the Smoking, Nicotine and Pregnancy (SNAP) trial. Linear and logistic regressions, mediation analysis, factor analysis and structural equation modelling techniques were employed to answer the following questions: (1) which factors are associated with smoking cessation in pregnancy?; (2) which factors, if any, mediate the negative influence of social disadvantage on cessation in pregnancy?; (3) is greater NRT use is associated with poor birth outcomes?; (4) is adherence to NRT associated with greater odds of cessation?; (5) what are the characteristics associated with the rate of nicotine metabolism and does more rapid metabolism of nicotine reduce a woman’s chances of achieving cessation? Results (1) Within a trial of NRT used for smoking cessation, pregnant women who were more educated (Odds Ratio (OR) at one month post-quit date (one month): 1.82, 95%CI: 1.24-2.67, p=0.002/OR at delivery: 1.89, 95%CI: 1.16-3.07, p=0.010) and less nicotine dependent (OR for baseline cotinine at one month: 0.94, 95%CI: 0.91-0.96, p<0.001/OR for baseline cotinine at delivery: 0.96, 95%CI: 0.92-0.99, p=0.010) / (OR for HSI at one month: 0.50, 95%CI: 0.32-0.76, p=0.001/OR for HSI at delivery: 0.43, 95%CI: 0.23-0.79, P=0.006) were more likely to achieve cessation. (2) There was evidence that the observed relationship between social disadvantage and cessation was mediated by women’s nicotine dependence (17.1% of the effect of social disadvantage on cessation), but not by them living with partners who smoked. (3) In an analysis investigating the relationship between use of NRT in pregnancy and birth outcomes, greater reported use of NRT was not associated with either better or worse birth outcomes, either in a-priori analyses using birth weight (β: -0.46, 95%CI: -3.58 to 2.66, p=0.773) and being born small for gestational age (SGA) (OR: 1.01, 95%CI: 0.99 to 1.03, p=0.184), or in exploratory analyses using all other SNAP trial birth outcomes. (4) In the first ever detailed analysis of the phenomenon of adherence with NRT in pregnancy, women who adhered more completely had lower pre-treatment cotinine concentrations (β: -0.08, 95%CI: -0.15- -0.01, p=0.020), lower heaviness of smoking index (β: -0.27, 95%CI: -0.50- -0.05, p<0.001) and were more likely to have been assigned to active rather than placebo NRT (β: 0.51, 95%CI: 0.29-0.72, p<0.001). Greater adherence with NRT was positively and significantly associated with increased odds of smoking cessation (Adjusted OR at one month: 1.11, 95%CI: 1.08-1.13, p<0.001/Adjusted OR at delivery: 1.06, 95%CI: 1.03-1.09, p<0.001), but there was no treatment allocation (i.e. nicotine or placebo)-adherence interaction with respect to cessation (LRT p=0.151). Analyses could not exclude the possibility that the observed adherence-cessation relationship was caused by women who relapsed to smoking consequently also stopping use of NRT. It also remains unclear whether the adherence-cessation relationship may be due the characteristics of individuals who are more likely to adhere (i.e. women who are prone to following instructions to use NRT, might also be more likely to follow instructions to not smoke). (5) In another novel analysis, pregnant women who metabolised nicotine more quickly had reduced odds of cessation (OR at one month: 0.87, 95%CI: 0.76-0.99, p=0.043/OR at delivery: 0.79, 95%CI: 0.66-0.94, p=0.008); however, there was no evidence that NRT was more effective in slower metabolisers. Conclusions Having higher levels of education and lower levels of nicotine dependence were associated with cessation. Nicotine dependence mediates the negative effect social disadvantage has on achieving smoking cessation in pregnancy. Greater reported use of NRT in pregnancy neither harms the foetus nor protects it from the harms of smoking, with respect to birth weight and SGA, but there is insufficient evidence to draw similar inferences for all birth outcomes. Adherence is associated with better smoking cessation outcomes, and women who exhibit greater adherence have differing characteristics compared to those that adhere less. It was not possible to determine whether or not these better outcomes were a function of women’s characteristics or if they were attributable to the treatment they received. The rate of nicotine metabolism appears to be important in determining whether or not pregnant smokers will manage to successfully stop smoking, but there was no evidence that NRT effectiveness was influenced by nicotine metabolism. Quitting smoking during pregnancy is important for both the mother and the child’s health outcomes. Socially disadvantaged women are less likely to achieve cessation but this thesis provides the first evidence to suggest that these odds may be improved by addressing nicotine dependence; NRT provides an eminently treatable way of doing this. This thesis’s findings suggest that use of NRT is at least as safe as continued smoking with respect to birth outcomes, although probably safer. This thesis also provides the first evidence on the associations between individual pieces of NRT and cessation in pregnancy, as well as the first evidence on nicotine metabolism’s association with cessation in pregnancy. Overall, NRT provides a promising way to increase the odds of cessation for disadvantaged pregnant smokers, however, there is a need for further research and the work in this thesis should provide a spur to investigate the effects that adherence to NRT and an individuals’ metabolism may have on NRT effectiveness in pregnancy