Analysis of RNA-seq data from the interaction of Coffea spp. - Colletotrichum kahawae

Tese de mestrado em Bioinformática e Biologia Computacional (Bioinformática), apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2014

Perturbation of Cytokinin and Ethylene-signalling Pathways Explain the Strong Rooting Phenotype Exhibited by Arabidopsis Expressing the Schizosaccharomyces Pombe mitotic inducer, cdc25.

Background Entry into mitosis is regulated by cyclin dependent kinases that in turn are phosphoregulated. In most eukaryotes, phosphoregulation is through WEE1 kinase and CDC25 phosphatase. In higher plants a homologous CDC25 gene is unconfirmed and hence the mitotic inducer Schizosaccharomyces pombe (Sp) cdc25 has been used as a tool in transgenic plants to probe cell cycle function. Expression of Spcdc25 in tobacco BY-2 cells accelerates entry into mitosis and depletes cytokinins; in whole plants it stimulates lateral root production. Here we show, for the first time, that alterations to cytokinin and ethylene signaling explain the rooting phenotype elicited by Spcdc25 expression in Arabidopsis. Results Expressing Spcdc25 in Arabidopsis results in increased formation of lateral and adventitious roots, a reduction of primary root width and more isodiametric cells in the root apical meristem (RAM) compared with wild type. Furthermore it stimulates root morphogenesis from hypocotyls when cultured on two way grids of increasing auxin and cytokinin concentrations. Microarray analysis of seedling roots expressing Spcdc25 reveals that expression of 167 genes is changed by > 2-fold. As well as genes related to stress responses and defence, these include 19 genes related to transcriptional regulation and signaling. Amongst these was the up-regulation of genes associated with ethylene synthesis and signaling. Seedlings expressing Spcdc25 produced 2-fold more ethylene than WT and exhibited a significant reduction in hypocotyl length both in darkness or when exposed to 10 ppm ethylene. Furthermore in Spcdc25 expressing plants, the cytokinin receptor AHK3 was down-regulated, and endogenous levels of iPA were reduced whereas endogeous IAA concentrations in the roots increased. Conclusions We suggest that the reduction in root width and change to a more isodiametric cell phenotype in the RAM in Spcdc25 expressing plants is a response to ethylene over-production. The increased rooting phenotype in Spcdc25 expressing plants is due to an increase in the ratio of endogenous auxin to cytokinin that is known to stimulate an increased rate of lateral root production. Overall, our data reveal important cross talk between cell division and plant growth regulators leading to developmental changes.

A evolução do défice tarifário em Portugal

Segundo as previsões da Entidade Reguladora dos Serviços Energéticos (ERSE), o défice tarifário deverá atingir em finais do 2013 um valor acumulado de 3,7 mil milhões de Euros. Na comunicação social, o défice tarifário (DT) é considerado como mais uma “renda” a alguns grupos de interesse. Na realidade o DT é justificado por uma acumulação sucessiva de diversos tipos de sobrecustos do sistema elétrico que não foi considerada nas tarifas e preços da eletricidade nos anos anteriores aos respetivos consumidores elétricos. O trabalho aqui apresentado corresponde a uma primeira tentativa de analisar as razões políticas e económicofinanceiras para a existência do défice tarifário. Nesse sentido serão abordadas: as origens e justificações dos diferentes sobrecustos (CAE’s, CMEC’s, Garantia de Potência, Produção em Regime geral (PRE), convergência tarifária com as regiões autónomas dos Açores (RAA) e da Madeira (RAM), entre outros); a análise dos diferentes tipos de mecanismos; os parâmetros no cálculo dos sobrecustos bem como as possíveis soluções e medidas já implementadas para reduzir os efeitos do défice tarifário nas tarifas nos consumidores.

Educação e formação de adultos: reconhecimento, validação e certificação de competências de adultos sem a escolaridade básica obrigatória na Região Autónoma da Madeira

Tese apresentada para cumprimento dos requisitos necessários à obtenção do grau de Doutor em Ciências da Educação, na Área de Especialidade: Educação, Sociedade e Desenvolvimento

O Turismo e o Recreio Náutico na Região Autónoma da Madeira

Dissertação apresentada para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Gestão do Território

Caracterização da carga da doença arterial periférica dos membros inferiores : contributos para um melhor conhecimento do peso desta doença no internamento hospitalar

RESUMO - A doença arterial periférica (DAP) apresenta uma carga de doença significativa, afetando cerca de 3 a 10% da população em geral e 15 a 20% dos indivíduos com idade superior a 70 anos. A sua prevalência em Portugal foi estimada em cerca de 5,9% no continente; 6,6% na Região Autónoma dos Açores (RAA) e 3,8% na Região Autónoma da Madeira (RAM). Para além da importante carga de doença, quer em termos epidemiológicos, quer económicos, a DAP confere aos seus portadores um risco cardiovascular agravado, sendo que os mesmos apresentam cerca do triplo do risco de mortalidade e de eventos cardiovasculares quando comparados com indivíduos sem DAP. Tratou-se de um estudo observacional, transversal e descritivo tendo como base duas populações de estudo. A primeira é referente aos hospitais do Serviço Nacional de Saúde (SNS) com a valência de cirurgia vascular e a segunda à população portuguesa com episódios de internamento por diagnóstico de DAP dos membros inferiores (MI) nos anos de 2013 e 2014 na totalidade dos hospitais do SNS. Através da análise dos resultados do questionário procedeu-se à descrição de algumas das características dos serviços e unidades de cirurgia vascular de sete hospitais do SNS; através da análise da base de dados dos GDH para os anos de 2013 e 2014 procedeu-se à caracterização do peso do internamento por DAP dos membros inferiores a nível nacional no mesmo período. A DAP tem uma carga significativa e atendendo aos seus fatores de risco e história natural da doença, apresenta uma tendência crescente durante os próximos anos, representando por isso um enorme desafio para os sistemas de saúde. São, no entanto, necessários estudos mais aprofundados sobre o tema que permitam conhecer melhor o peso desta patologia e, de forma global, melhorar o planeamento, tendo por base a caracterização quer do lado da procura (dados epidemiológicos e peso no internamento), quer da oferta (capacidade instalada).

Scaling In-Memory databases on multicores

Current computer systems have evolved from featuring only a single processing unit and limited RAM, in the order of kilobytes or few megabytes, to include several multicore processors, o↵ering in the order of several tens of concurrent execution contexts, and have main memory in the order of several tens to hundreds of gigabytes. This allows to keep all data of many applications in the main memory, leading to the development of inmemory databases. Compared to disk-backed databases, in-memory databases (IMDBs) are expected to provide better performance by incurring in less I/O overhead. In this dissertation, we present a scalability study of two general purpose IMDBs on multicore systems. The results show that current general purpose IMDBs do not scale on multicores, due to contention among threads running concurrent transactions. In this work, we explore di↵erent direction to overcome the scalability issues of IMDBs in multicores, while enforcing strong isolation semantics. First, we present a solution that requires no modification to either database systems or to the applications, called MacroDB. MacroDB replicates the database among several engines, using a master-slave replication scheme, where update transactions execute on the master, while read-only transactions execute on slaves. This reduces contention, allowing MacroDB to o↵er scalable performance under read-only workloads, while updateintensive workloads su↵er from performance loss, when compared to the standalone engine. Second, we delve into the database engine and identify the concurrency control mechanism used by the storage sub-component as a scalability bottleneck. We then propose a new locking scheme that allows the removal of such mechanisms from the storage sub-component. This modification o↵ers performance improvement under all workloads, when compared to the standalone engine, while scalability is limited to read-only workloads. Next we addressed the scalability limitations for update-intensive workloads, and propose the reduction of locking granularity from the table level to the attribute level. This further improved performance for intensive and moderate update workloads, at a slight cost for read-only workloads. Scalability is limited to intensive-read and read-only workloads. Finally, we investigate the impact applications have on the performance of database systems, by studying how operation order inside transactions influences the database performance. We then propose a Read before Write (RbW) interaction pattern, under which transaction perform all read operations before executing write operations. The RbW pattern allowed TPC-C to achieve scalable performance on our modified engine for all workloads. Additionally, the RbW pattern allowed our modified engine to achieve scalable performance on multicores, almost up to the total number of cores, while enforcing strong isolation.

Efficiency Comparison of DFT/IDFT Algorithms by Evaluating Diverse Hardware Implementations

In this paper we investigate various algorithms for performing Fast Fourier Transformation (FFT)/Inverse Fast Fourier Transformation (IFFT), and proper techniques for maximizing the FFT/IFFT execution speed, such as pipelining or parallel processing, and use of memory structures with pre-computed values (look up tables -LUT) or other dedicated hardware components (usually multipliers). Furthermore, we discuss the optimal hardware architectures that best apply to various FFT/IFFT algorithms, along with their abilities to exploit parallel processing with minimal data dependences of the FFT/IFFT calculations. An interesting approach that is also considered in this paper is the application of the integrated processing-in-memory Intelligent RAM (IRAM) chip to high speed FFT/IFFT computing. The results of the assessment study emphasize that the execution speed of the FFT/IFFT algorithms is tightly connected to the capabilities of the FFT/IFFT hardware to support the provided parallelism of the given algorithm. Therefore, we suggest that the basic Discrete Fourier Transform (DFT)/Inverse Discrete Fourier Transform (IDFT) can also provide high performances, by utilizing a specialized FFT/IFFT hardware architecture that can exploit the provided parallelism of the DFT/IDF operations. The proposed improvements include simplified multiplications over symbols given in polar coordinate system, using sinе and cosine look up tables, and an approach for performing parallel addition of N input symbols.

Efficiency Comparison of DFT/IDFT Algorithms by Evaluating Diverse Hardware : Implementations,Parallelization Prospectsand Possible Improvements

In this paper we investigate various algorithms for performing Fast Fourier Transformation (FFT)/Inverse Fast Fourier Transformation (IFFT), and proper techniquesfor maximizing the FFT/IFFT execution speed, such as pipelining or parallel processing, and use of memory structures with pre-computed values (look up tables -LUT) or other dedicated hardware components (usually multipliers). Furthermore, we discuss the optimal hardware architectures that best apply to various FFT/IFFT algorithms, along with their abilities to exploit parallel processing with minimal data dependences of the FFT/IFFT calculations. An interesting approach that is also considered in this paper is the application of the integrated processing-in-memory Intelligent RAM (IRAM) chip to high speed FFT/IFFT computing. The results of the assessment study emphasize that the execution speed of the FFT/IFFT algorithms is tightly connected to the capabilities of the FFT/IFFT hardware to support the provided parallelism of the given algorithm. Therefore, we suggest that the basic Discrete Fourier Transform (DFT)/Inverse Discrete Fourier Transform (IDFT) can also provide high performances, by utilizing a specialized FFT/IFFT hardware architecture that can exploit the provided parallelism of the DFT/IDF operations. The proposed improvements include simplified multiplications over symbols given in polar coordinate system, using sinе and cosine look up tables,and an approach for performing parallel addition of N input symbols.

The impact of drug-induced dyskinesias on rapid alternating movements in patients with Parkinson's disease

We investigated the likelihood that hypokinesia/bradykinesia coexist with druginduced dyskinesias (DID) in patients with Parkinson's disease (PD). The influence of dyskinesias on rapid alternating movements (RAM) was investigated in ten dyskinetic patients (DPD). Their motor performance was compared to that of ten age/gendermatched non-dyskinetic patients (NDPD) and ten healthy control subjects. Whole-body magnitude (WBM) and fast pronation-supination at the wrist were recorded using 6- degrees of freedom magnetic motion tracker and forearm rotational sensors, respectively. Subjects were asked to pronate-supinate their dominant hand for 10s. Pre- and postmeasures were taken in a neutral position for 20s. RANGE (measure of hypokinesia), DURATION (measure of bradykinesia). VELOCITY (measure of bradykinesia) and IRREGULARITY (measure of fluctuations in movement amplitude) were used to assess RAM performance. Results showed that DPD patients had greater WBM than NDPD and control groups during rest and RAM performance. There were no differences in performance between NDPD and DPD groups for RANGE, DURATION and VELOCITY, despite significant longer disease duration for the DPD group (DPD = 15.5 ± 6.2 years versus NDPD = 6.6 ± 2.6 years). However, both the NDPD and DPD groups showed lower RANGE, longer DURATION, and reduced VELOCITY compared to controls,, suggesting the presence of bradykinesia and hypokinesia. In the case of IRREGULARITY, DPD patients showed clear fluctuations in movement amplitude compared to the NDPD and control groups. However, the lack of correlation between WBM and IRREGULARITY within the DPD group (Spearman's rank order, Rho - 0.31, p > 0.05), suggests that DID was not the primary cause of the fluctuating movementamplitude observed in that group. In conclusion, these findings suggest that DID may coexists with bradykinesia and hypokinesia, but that they are not inevitably accompanied with worsening motor performance.

Effects of dietary restraint and oral contraceptives on bone strength and bone turnover in young women

ABSTRACT Introduction The purpose of this study was to assess specific osteoporosis-related health behaviours and physiological outcomes including daily calcium intake, physical activity levels, bone strength, as assessed by quantitative ultrasound, and bone turnover among women between the ages of 18 and 25. Respective differences on relevant study variables, based on dietary restraint and oral contraceptive use were also examined. Methods One hundred women (20.6 ± 0.2 years of age) volunteered to participate in the study. Informed written consent was obtained by all subjects prior to participation. The study and all related procedures were approved by the Brock University Research Ethics Board. Body mass, height, relative body fat, as well as chest, waist and hip circumferences were measured using standard procedures. The 10-item restrained eating subscale of the Dutch Eating Behaviour Questionnaire (DEBQ) was used to assess dietary restraint (van Strien et al., 1986). Daily calcium intake was assessed by the Rapid Assessment Method (RAM) (Hertzler & Frary 1994). Weekly physical activity was documented by the 4-item Godin Leisure-Time Exercise Questionnaire (Godin & Shephard 1985). Bone strength was determined from the speed of sound (SOS) as measured by QUS (Sunlight 7000S). SOS measurements (m/s) were taken of the dominant and non-dominant sides of the distal one third of the radius and the mid-shaft of the tibia. Resting blood samples were collected from all subjects between 9am and 12pm, in order to evaluate the impact of lifestyle factors on biochemical markers of bone turnover. Blood was collected during the early follicular phase of the menstrual cycle (approximately days 1-5) for all subjects. Samples were centrifliged and the serum or plasma was aliquoted into separate tubes and stored at -80°C until analysis. The bone formation markers measured were Osteocalcin (OC), bone specific alkaline phosphatase (BAP) and 25-OH vitamin D. The bone resorption markers measured were the carboxy (CTx) and amino (NTx) terminal telopeptides of type-I collagen crosslinks. All markers were assessed by ELISA. Subjects were divided into high (HDR) and low dietary restrainers (LDR) based on the median DEBQ score, and also into users (BC) and non-users (nBC) of oral contraceptives. A series of multiple one way ANOVA's were then conducted to identify differences between each set of groups for all relevant variables. A two-way ANOVA analysis was used to explore significant interactions between dietary restraint and use of oral contraceptives while a univariate follow-up analysis was also performed when appropriate. Pearson Product Moment Correlations were used to determine relationships among study variables. Results HDR had significantly higher BMI, %BF and circumference measures but lower daily calcium intake than LDR. There were no significant differences in physical activity levels between HDR and LDR. No significant differences were found between BC and nBC in body composition, calcium intake and physical activity. HDR had significantly lower tibial SOS scores than LDR in both the dominant and non-dominant sites. The post-hoc analysis showed that within the non-birth control group, the HDR had significantly lower tibial SOS scores of bone strength when compared to the LDR but Aere were no significant differences found between the two dietary restraint groups for those currently on birth control. HDR had significantly lower levels of OC than LDR and the BC group had lower levels of BAP than the nBC group. Consistently, the follow-up analysis revealed that within those not on birth control, subjects who were classified as HDR had significantly (f*<0.05) lower levels of OC when compared with LDR but no significant differences were observed in bone turnover between the two dietary restraint groups for those currently on birth control. Physical activity was not correlated with SOS scores and bone turnover markers possibly due to the low physical activity variability in this group of women. Conclusion This is the first study to examine the effects of dietary restraint on bone strength and turnover among this population of women. The most important finding of this study was that bone strength and turnover are negatively influenced by dietary restraint independent of relative body fat. In general, the results of the present thesis suggest that dietary restraint, oral contraceptive use, as well as low daily calcium intake and low physical activity levels were widespread behaviours among this population of college-aged women. The young women who were using dietary restraint as a strategy to lose weight, and thus were in the HDR group, despite their higher relative body fat and weight, had lower scores of bone strength and lower levels of markers of bone turnover compared to the low dietary restrainers. Additionally, bone turnover seemed to be negatively affected by oral contraceptives, while bone strength, as assessed by QUS, seemed unaffected by their use in this population of young women. Physical activity (weekly energy expenditure), on the other hand, was not associated with either bone strength or bone tiimover possibly due to the low variability of this variable in this population of young Canadian women.

Sperm utilization patterns in Gryllus integer (orthoptera: gryllidae

Sperm competition is the competition for fertilizations between ejaculates, within a female, following multiple mating. There are four sperm utilization or precedence patterns: first male precedence, where the first male to mate fertilizes most of the eggs laid by a female; last male precedence, where the last male to mate fertilizes most of the eggs laid by a female; "all-or-none" pattern, where sperm from either male fertilizes all the eggs laid by a female but which male's sperm that is used is random; or sperm mixing, where sperm from each male is used equally in fertilizing eggs laid by a female. Intermediate utilization patterns are also possible. Sperm competition occurs in a wide variety of insect species as well as other animals. This study was undertaken to study sperm competition in the field cricket, Gryllus integer. Four experiments were conducted: a radiation and sterilization experiment, a diapause experiment, and 2 competition experiments. It was found that 7,000 rad of gamma radiation sterilized adult ~ integer males. There was no diapause in the laboratory in ~ integer eggs. In the first competition experiment, three groups of females were used: females mated with a normal male, then with a second normal male (NN group); females mated with a normal male, and then with a sterile male (NR group); and females mated with a sterile male, and then with a normal male (RN group). The results obtained from this experiment showed that the mean proportion of eggs hatched was significantly different between 3 groups of females, with the proportion hatched much greater in the NN group than in either the NR or RN groups. The pattern for the proportion of eggs hatched following a double mating most closely resembled a pattern expected if sperm mixing is occurring. Results obtained in the replicate competition experiment showed that the mean proportion of eggs hatched for the females in the NR group was significantly lower than the proportion hatched in the other two groups. This also supports a model of sperm mixing as a precedence pattern. Values calculated following Boorman and Parker (1976), for the proportion of eggs fertilized by the second male to mate following a double mating, were 0.57 in competition experiment 1 and 0.62 in the replicate. These values indicate that sperm mixing occurs in~ integer.

Estudio de la ultraestructura seminal y de los parámetros seminológicos, en pacientes infértiles con PCR positivo para Ureaplasma urealyticum

Tesis (Maestría en Ciencias con Especialidad en Morfología) UANL

Biografia del Señor D. Joaquín Velásquez de León

UANL