DNA microarray technology makes it possible to analyze the expression levels of many thousands of genes simultaneously. One of the goals of microarray data analysis is to understand the multiple biological roles of genes and their interactions in complex biological processes. Genes with similar expression patterns are likely to share similar functions or biological processes. Therefore, analysis of changes in gene expression of a certain biological processes over time is of particular interest. Unsupervised clustering methods provide an efficient way of finding overall patterns and tendencies by clustering microarray gene expression data. The genes in the same cluster are regulated in a similar manner based on the assumption above. But traditional unsupervised clustering methods usually end up with clusters of genes with similar expression patterns but without interpretations describing the clusters in terms of gene functions or processes involved. In this project, some statistical techniques are applied to analyze the data set from microarray experiments of sporulation in yeast. These techniques include LOWESS data normalization, which is intended to remove the systematic variations from the data; a partitional clustering method, K-means, is used with initial centroids obtained from hierarchical clustering method of DIANA; the "gap statistic" technique is implemented to estimate the "optimal" number of clusters in the data set; and finally multiple hypothesis testing is used to determine whether biologically related genes are statistically over-represented in the gene clusters using the web query tool FatiGO. These methods are combined with graphical representation of cluster profile shape and colour maps of up and down regulation via heat maps. Application of these methods to a yeast sporulation time-course data set [Chu 𝘦𝘵 𝘢𝘭. 1998] demonstrates the utility of cluster analysis to such data sets and provides an automated method for including biological information about gene function and characteristics. / Thesis / Master of Science (MSc)

Explicit and implicit processes play a role in visuomotor adaptation. (Bond & Taylor, 2015; Werner et al, 2015). The purpose of the current experiment was to investigate the potential contributions of explicit and implicit processes to visuomotor adaptation when awareness was manipulated directly and indirectly. To manipulate the degree of awareness directly, participants were assigned to a Strategy or No-Strategy group, in which they were made aware or remained unaware of the distortion respectively. They were then further subdivided into groups to train with a large (60°), medium (40°) or small (20°) visuomotor distortion, such that participants could become aware of the distortion indirectly with increasing sizes. All participants performed a reaching task to three targets with a cursor that was rotated clockwise relative to their hand by the assigned degrees, and then completed a series of no-cursor reaches without visual feedback to establish the contribution of explicit and implicit processes to visuomotor adaptation. Within the no-cursor reaching trials, the contribution of explicit and implicit processes to visuomotor adaptation were determined by having subjects reach (i) with any strategies they had gained during training (explicit + implicit processes), and (ii) as they did before training with the cursor rotation (implicit processes). Our results showed that the contribution of implicit processes to visuomotor adaptation was greater in the No-Strategy group compared to the Strategy group. Moreover, implicit processes took time to develop, and decayed following a 5-minute break. In contrast, the contribution of explicit processes was greatest in the Strategy group, and increased with rotation size in the No-Strategy group. Explicit contributions also remained consistent over Blocks, as well as when re-tested following a 5-minute break. Thus, the results of the current experiment indicate that there are notable differences in explicit and implicit contributions to visuomotor distortions depending on if, and how participants become aware of the perturbation. The results also highlight the importance of instructions when evaluating reaching performance in aftereffect trials, as they can modulate reaching errors observed.

When subjects are presented with distorted visual feedback of their hand during a goal-directed movement (i.e. subjects view a cursor representing their hand that is rotated from their hand’s actual position while reaching in a virtual reality environment), they typically adapt their movements so that the cursor is brought to the target, thus reducing reaching errors. In addition to motor adaptation, it has recently been shown that reaching with distorted visual feedback of the hand results in sensory changes, such that proprioceptive estimates of hand position are shifted in the direction of the visual feedback (Cressman and Henriques 2009). The current study looked to establish how quickly these sensory changes arise while training to reach with distorted visual feedback of the hand. Additionally, by comparing sensory to motor changes across time, we looked to determine the relationship between their underlying processes. Subjects trained to reach to a single visual target while seeing a cursor that was aligned with their actual hand position (50 trials: aligned reach training), or rotated 30° clockwise (CW) relative to their actual hand position (150 trials: rotated reach training). Reach errors and proprioceptive estimates of felt hand position were assessed following the aligned reach training trials and at 7 different times during the rotated reach training trials by having subjects reach to the target without visual feedback, and provide estimates of the position of their hand relative to a visual reference marker respectively. Results revealed a slow change in proprioceptive estimates over the course of reach training with the rotated cursor relative to estimates after the aligned reach training, and in fact, significant sensory changes were not observed until after 70 trials. In contrast, reach adaptation showed a much steeper increase and significant adaptation after a limited number of reach training trials with a rotated cursor. These different time courses suggest that proprioceptive recalibration and reach adaptation arise due to separate neural processes.

Trimethyltin (TMT) produces prominent neuron death in the hippocampus. The time-course of TMT-induced damage was studied using reduced-silver procedures for impregnation of degenerating axons and their terminals, and a modified Timm's stain procedure for visualization of hippocampal transitional metals. Standard cell body stains were also used. Fifty-four, adult, Long-Evans rats were gavaged with 6.0 mg TMT/kg b.wt. and 10 rats were gavaged with distilled water as controls. Five TMT-gavaged rats and one saline-gavaged rat were sacrificed on either postgavage day 1, 3, 6, 9, 14, 19, 30, 45, 70 or 99. Histological examination revealed a band of degenerating terminals in the stratum lucidum, below the hippocampal subfields CA3a,b pyramidal cells, by postgavage day 3. This preceded dentate gyrus granule cell loss supplying the mossy fiber input to the stratum lucidum by several days. Hippocampal pyramidal cell necrosis continued through the examination period while dentate granule cell loss subsided between postgavage days 9 and 14. Fiber and terminal degeneration was more extensive in the dorsal hippocampus than in the ventral hippocampus, although Timm's-stained sections revealed "bleaching" of stainable metal in the mossy fiber pathway of the ventral hippocampus. These data suggest that loss of ventral dentate granule cells might reduce TMT-induced necrosis of pyramidal cells in the ventral (temporal) part of the Ammon's horn, possibly by preventing the spread of seizure activity in this region of the hippocampus. Additionally, although previous studies have reported the toxic effects of TMT to last approximately 60 days, the results of the present study indicate that TMT-induced degeneration continues for more than 3 months. Reduced-silver stains, such as the Fink-Heimer procedure, appear to be more sensitive indicators of enduring neuropathology than more traditional cell stains.

The feasibility of using an integrated rate equation to analyze the kinetics of a second-order, enzyme-catalyzed reaction has been investigated. The inducible arginine decarboxylase from Escherichia coli B. was chosen for this study because it catalyzes an irreversible reaction with stoichiometry A --> P + Q, the simplest second order case. Values for five of the eight possible kinetic constants were determined from 21 time courses. Of the remaining three, the uncompetitive product inhibition constant for CO2 was shown to be between O and 0.06, while the values of the competitive product inhibition for CO2 and the uncompetitive constant for arginine, agmatine and CO2 simultaneously do not appear to be appreciably different from zero. Initial rate analysis of the time courses gave similar results. The results obtained by varying the initial agmatine concentration at a low initial arginine concentration were not consistent with the rest of the data. This appears to be due to a. fundamental difference in the behavior of the enzyme under those conditions rather than to a problem associated with the analysis.

<p> Individuals often display preferences for the morning or evening; this preference is referred to as a chronotype and is supported by distinct diurnal physiological and behavioural fluctuations. Whereas prior work suggests an increase in individuals executive control throughout the day, the current study assesses the diurnal time course of executive control and the tendency to mind wander as a function of chronotype. Results suggest that executive control processes are modulated by time of day, with chronotype match conditions associated with increased executive control, akin to the 'Synchrony Effect' of chronotypes (Hasher et al., 2002). Results suggest that variations in the level of semantic processing in a task influences time of day effects on non-automatic (executive control) functioning. </p> / Thesis / Master of Science (MSc)

Conceptualizations of anger have suffered from a lack of research investigating the temporal dynamics of anger episodes. Furthermore, though some studies have provided valuable insights into the time course of anger, no study to date has utilized a standardized laboratory paradigm designed to mimic an interpersonal provocation. The purpose of this study was to characterize the time course of the affective, physiological, and behavioral components of anger in response to a standardized provocation. Our second aim was to assess potential effects of trait anger, trait aggression, trait hostility, and emotion regulation deficits on the time course of the different components of anger. Participants (n = 82) engaged in the Modified Taylor Aggression Paradigm (MTAP), a laboratory measure of anger/aggression in which provocation is manipulated by varying electric shocks selected for the participant by an (unbeknownst to the participant) fictitious opponent. This study utilized a modified version of the classic TAP that simulated an acute interpersonal provocation that one might encounter in the “real world.” Subjective anger, physiological arousal (as evidenced by heart rate [HR], galvanic skin response [GSR], and high-frequency heart rate variability [HF HRV]), and the behavioral expression of anger (aggression) were measured throughout the task before, during and after provocation. Consistent with previous research, results showed that the rise time to peak levels of most outcome variables was significantly faster than the return time from peak back to baseline. Additionally, results showed that the majority of the time course variables were not correlated with one another providing evidence for the idea that different components of anger have independent time courses. Contrary to our hypotheses, trait variables were largely unrelated to time course variables. The current study provides further evidence for the relationship between the rise time and return time in the time course of subjective, physiological and behavioral manifestations of anger using a standardized and ecologically valid provocation task. / Psychology

São escassos os estudos que analisam o contínuo temporal dos estados de ânimo ao longo de um período competitivo esportivo. Embora os estados de ânimo pareçam estáveis ao longo do tempo, diferentes estímulos e contextos presentes modificam a intensidade e a valência desses estados. Além disso, há fenômenos psicológicos como decaimento, em que traços de informação perdem sua ativação devido, principalmente, à passagem do tempo e a expectativa, que é a espera pela ocorrência de um evento em um determinado tempo. O objetivo desse estudo foi examinar as alterações dos estados de ânimo em jovens atletas de futebol, separados por posição e função, que ocorreram num período competitivo, em função do decurso temporal. Assim, processos como decaimento dos estados de ânimo e a influência da expectativa pela ocorrência jogo foram analisados, bem como a influência do contexto nas variações dos estados de ânimo dos atletas. Participaram deste estudo 18 jovens atletas (média de 15,4 anos ± 0,266) de um clube de futebol que estava disputando um campeonato estadual. Para o acesso aos estados de ânimo, foi utilizada a versão reduzida da Lista de Estados de Ânimo Presentes (LEAP), juntamente com um formulário de instruções de preenchimento, aplicada minutos antes de alguns treinamentos e jogos. Foram calculados os valores de presença de cada Fator da LEAP em cada evento para cada participante. Os dados foram coletados em três tipos de Eventos: antes do último treino antecedente ao jogo (Treino-Pré), antes do jogo (Pré-jogo) e antes do primeiro treino subsequente ao jogo (Treino-Pós). Os 18 jogadores foram divididos em dois grupos: Ações Defensivas (AD) e Ações Ofensivas (AO). Foram encontrados padrões de alteração dos estados de ânimo, representados pelos Fatores II (Fadiga), VII (Interesse) e XII (Serenidade) da LEAP, em função do decurso temporal, permitindo a análise dos processos de decaimento desses estados de ânimo e a influência da expectativa nessas alterações. Também foi encontrado que alguns estados de ânimo diferiram seus padrões de alteração de acordo com um intervalo temporal (Fatores IV Limerência/Empatia e; VII Interesse), bem como tiveram valores de presença diferentes na comparação entre esses intervalos. Além disso, os Fatores III (Esperança), V (Fisiológico) e XI (Receptividade) apresentaram padrões de alteração em função do decurso temporal em diferentes intervalos temporais. Variáveis contextuais, como o resultado das partidas e a competição esportiva em si, também foram influentes nessas alterações. Fadiga, esperança, empatia, estados ligados à propriocepção, interesse, receptividade e serenidade foram os estados de ânimo presentes durante todo o estudo. Ressalta-se a importância de incluir a temporalidade como variável influente nos modelos de variação de processos neurobiológicos, sobretudo nas investigações acerca de aspectos subjetivos como os estados de ânimo. / There are few studies analyzing the time course of mood during a competitive sports season. Although moods seem stable over the time course, different stimuli and present contexts change their intensity and valence. Furthermore, there are psychological phenomena like the decay process, in which information traces lose activation with the passage of time and expectancy, which is a waiting for an occurrence of an event in a given time. Therefore, the aim of this study was to exam mood changes in youth soccer players, grouped by position and role, which occurred during a competitive season, in function of time course. Processes like mood decay and the influence of expectation for the game were analyzed, as well as the influence of context in the athletes mood variations. Eighteen young players (15.4 ± 0,266 year-old) from a soccer club, which was playing for a state championship, participated in this study. For the assessment of mood, a short form of Lista de Estados de Ânimo Presentes (LEAP Present Mood List) was used, along with instructions to fill the form, applied few moments before some training sessions and matches. Presence values of each LEAPs Factor were calculated for each participant in each event. The data was collected in three types of events: prior to the last trainning session before the match (Treino-Pré), at a few moments before the match (Pré-jogo) and prior to the first training session after the match. The eighteen players were divided in two groups: Defensive Actions (AD) and Offensive Actions (AO). Results have shown patterns of mood changes, represented by LEAPs Factors II (Fatigue), VII (Interest) and XII (Serenity), in function of time course, allowing the analysis of mood decay process and the influence of the expectation in these changes. Also, some moods showed different patterns in function of a given time interval (Factors IV Limerence/Empathy and VII Interest), as well as different presence values in these time intervals comparison. Moreover, Factors III (Hope), V (Physiologic) and XI (Receptivity) have shown patterns of mood changes in function of time course in different intervals of time. Contextual variables, like the outcome of the matches and the sport competition itself, were influential in these changes. Fatigue, hope, empathy, states related to proprioception, interest, receptivity and serenity were the present moods all along the study. The importance of including temporality as an influential variable in neurobiological models is noteworthy, especially in the investigations about subjective aspects like mood.

During medical school students must learn and retain a large volume of information that is important for success in their future career as physicians. Laboratory studies have given insight into the mechanisms underpinning learning and memory, but few studies have examined the time course of memorial retention in a real world setting. The current study aimed to examine the memorial mechanisms used to retain information over time by using a variation of the Remember/Know/New recognition memory procedure to examine memory retention for anatomical information in first year medical students. Participants were presented with anatomical terms and asked to respond whether they Can Define the term, were Familiar with the term or Don’t Know the term. Participants’ Remember and Know responses are thought to be reflective of different processes, recollection and familiarity, respectively. We were particularly interested in examining differences in memorial retention based on retention interval (immediately at course end and after six months). All participants were enrolled in a Medical Gross Anatomy course. The course was divided into three successive modules, each of which culminated in an examination, module 1: Back and Limbs, module 2: Thorax, Abdomen and Pelvis, and module 3: Head and Neck. Participants completed a computer based memory task at three separate time points: prior to course start (session 1), after course completion (session 2); and six months after course completion (session 3). Students were presented with anatomical terms from each module and asked to respond whether they Can Define, are Familiar with or Don’t Know a term. We predicted that responses would differ depending on when the module of the course was taught and when the testing occurred. Following work on primacy and recency, we predicted that at session 2 students would make the most Can Define responses to information learned most recently. We predicted that the second most Can Define responses would be to information learned the longest period of time from the testing session, and that information learned in the middle would be least well recalled (lowest number of Can Define responses). Furthermore, we predicted that familiarity responses would show the reverse pattern to Can Define responses at session 2.We also predicted that performance would differ by session. We hypothesized that the proportion of Can Define responses would be higher for session 2 relative to session 3, due to the processes of forgetting. Furthermore, we predicted that recollective processes characterized by Can Define responses, would be most common in module 3, the module most recently studied relative to session 2. Lastly, we predicted that the number of Familiar responses would increase across the two sessions. Our results showed that responses varied based on when the information was taught in that participants made more Can Define responses to recently learned module 3 and earliest learned module 1 relative to module 2. Responses also varied by session, as the number of Familiar responses increased overall across session 2 and 3. At session 3, there were no significant differences in the proportion of Can Define or Familiar responses between the different modules of the course. Theoretically, these results suggest that while the order of teaching impacts performance at course end, in the longer-term order of teaching ceases to matter and level of forgetting plateaus across modules. Practically however, a teacher’s aim is to maximize retention. Students might benefit from interleaving of course content instead of separate blocks, so that no one module is taught in the middle and more frequent testing to boost overall retention.

São escassos os estudos que analisam o contínuo temporal dos estados de ânimo ao longo de um período competitivo esportivo. Embora os estados de ânimo pareçam estáveis ao longo do tempo, diferentes estímulos e contextos presentes modificam a intensidade e a valência desses estados. Além disso, há fenômenos psicológicos como decaimento, em que traços de informação perdem sua ativação devido, principalmente, à passagem do tempo e a expectativa, que é a espera pela ocorrência de um evento em um determinado tempo. O objetivo desse estudo foi examinar as alterações dos estados de ânimo em jovens atletas de futebol, separados por posição e função, que ocorreram num período competitivo, em função do decurso temporal. Assim, processos como decaimento dos estados de ânimo e a influência da expectativa pela ocorrência jogo foram analisados, bem como a influência do contexto nas variações dos estados de ânimo dos atletas. Participaram deste estudo 18 jovens atletas (média de 15,4 anos ± 0,266) de um clube de futebol que estava disputando um campeonato estadual. Para o acesso aos estados de ânimo, foi utilizada a versão reduzida da Lista de Estados de Ânimo Presentes (LEAP), juntamente com um formulário de instruções de preenchimento, aplicada minutos antes de alguns treinamentos e jogos. Foram calculados os valores de presença de cada Fator da LEAP em cada evento para cada participante. Os dados foram coletados em três tipos de Eventos: antes do último treino antecedente ao jogo (Treino-Pré), antes do jogo (Pré-jogo) e antes do primeiro treino subsequente ao jogo (Treino-Pós). Os 18 jogadores foram divididos em dois grupos: Ações Defensivas (AD) e Ações Ofensivas (AO). Foram encontrados padrões de alteração dos estados de ânimo, representados pelos Fatores II (Fadiga), VII (Interesse) e XII (Serenidade) da LEAP, em função do decurso temporal, permitindo a análise dos processos de decaimento desses estados de ânimo e a influência da expectativa nessas alterações. Também foi encontrado que alguns estados de ânimo diferiram seus padrões de alteração de acordo com um intervalo temporal (Fatores IV Limerência/Empatia e; VII Interesse), bem como tiveram valores de presença diferentes na comparação entre esses intervalos. Além disso, os Fatores III (Esperança), V (Fisiológico) e XI (Receptividade) apresentaram padrões de alteração em função do decurso temporal em diferentes intervalos temporais. Variáveis contextuais, como o resultado das partidas e a competição esportiva em si, também foram influentes nessas alterações. Fadiga, esperança, empatia, estados ligados à propriocepção, interesse, receptividade e serenidade foram os estados de ânimo presentes durante todo o estudo. Ressalta-se a importância de incluir a temporalidade como variável influente nos modelos de variação de processos neurobiológicos, sobretudo nas investigações acerca de aspectos subjetivos como os estados de ânimo. / There are few studies analyzing the time course of mood during a competitive sports season. Although moods seem stable over the time course, different stimuli and present contexts change their intensity and valence. Furthermore, there are psychological phenomena like the decay process, in which information traces lose activation with the passage of time and expectancy, which is a waiting for an occurrence of an event in a given time. Therefore, the aim of this study was to exam mood changes in youth soccer players, grouped by position and role, which occurred during a competitive season, in function of time course. Processes like mood decay and the influence of expectation for the game were analyzed, as well as the influence of context in the athletes mood variations. Eighteen young players (15.4 ± 0,266 year-old) from a soccer club, which was playing for a state championship, participated in this study. For the assessment of mood, a short form of Lista de Estados de Ânimo Presentes (LEAP Present Mood List) was used, along with instructions to fill the form, applied few moments before some training sessions and matches. Presence values of each LEAPs Factor were calculated for each participant in each event. The data was collected in three types of events: prior to the last trainning session before the match (Treino-Pré), at a few moments before the match (Pré-jogo) and prior to the first training session after the match. The eighteen players were divided in two groups: Defensive Actions (AD) and Offensive Actions (AO). Results have shown patterns of mood changes, represented by LEAPs Factors II (Fatigue), VII (Interest) and XII (Serenity), in function of time course, allowing the analysis of mood decay process and the influence of the expectation in these changes. Also, some moods showed different patterns in function of a given time interval (Factors IV Limerence/Empathy and VII Interest), as well as different presence values in these time intervals comparison. Moreover, Factors III (Hope), V (Physiologic) and XI (Receptivity) have shown patterns of mood changes in function of time course in different intervals of time. Contextual variables, like the outcome of the matches and the sport competition itself, were influential in these changes. Fatigue, hope, empathy, states related to proprioception, interest, receptivity and serenity were the present moods all along the study. The importance of including temporality as an influential variable in neurobiological models is noteworthy, especially in the investigations about subjective aspects like mood.