Adaptive MCMC methods with applications in environmental and geophysical models

This work presents new, efficient Markov chain Monte Carlo (MCMC) simulation methods for statistical analysis in various modelling applications. When using MCMC methods, the model is simulated repeatedly to explore the probability distribution describing the uncertainties in model parameters and predictions. In adaptive MCMC methods based on the Metropolis-Hastings algorithm, the proposal distribution needed by the algorithm learns from the target distribution as the simulation proceeds. Adaptive MCMC methods have been subject of intensive research lately, as they open a way for essentially easier use of the methodology. The lack of user-friendly computer programs has been a main obstacle for wider acceptance of the methods. This work provides two new adaptive MCMC methods: DRAM and AARJ. The DRAM method has been built especially to work in high dimensional and non-linear problems. The AARJ method is an extension to DRAM for model selection problems, where the mathematical formulation of the model is uncertain and we want simultaneously to fit several different models to the same observations. The methods were developed while keeping in mind the needs of modelling applications typical in environmental sciences. The development work has been pursued while working with several application projects. The applications presented in this work are: a winter time oxygen concentration model for Lake Tuusulanjärvi and adaptive control of the aerator; a nutrition model for Lake Pyhäjärvi and lake management planning; validation of the algorithms of the GOMOS ozone remote sensing instrument on board the Envisat satellite of European Space Agency and the study of the effects of aerosol model selection on the GOMOS algorithm.

Macroalgal Defenses Against Herbivory: Causes and Consequences of Intraspecific Variation

In marine benthic communities, herbivores consume a considerable proportion of primary producer biomass and, thus, generate selection for the evolution of resistance traits. According to the theory of plant defenses, resistance traits are costly to produce and, consequently, inducible resistance traits are adaptive in conditions of variable herbivory, while in conditions of constant/strong herbivory constitutive resistance traits are selected for. The evolution of resistance plasticity may be constrained by the costs of resistance or lack of genetic variation in resistance. Furthermore, resource allocation to induced resistance may be affected by higher trophic levels preying on herbivores. I studied the resistance to herbivory of a foundation species, the brown alga Fucus vesiculosus. By using factorial field experiments, I explored the effects of herbivores and fish predators on growth and resistance of the alga in two seasons. I explored genetic variation in and allocation costs of resistance traits as well as their chemical basis and their effects on herbivore performance. Using a field experiment I tested if induced resistance spreads via water-borne cues from one individual to another in relevant ecological conditions. I found that in the northern Baltic Sea F. vesiculosus communities, strength of three trophic interactions strongly vary among seasons. The highly synchronized summer reproduction of herbivores promoted their escape from the top-down control of fish predators in autumn. This resulted into large grazing losses in algal stands. In spring, herbivore densities were low and regulated by fish, which, thus,enhanced algal growth. The resistance of algae to herbivory increased with an increase in constitutive phlorotannin content. Furthermore, individuals adopted induced resistance when grazed and when exposed to water-borne cues originating from grazing of conspecific algae both in the laboratory and in field conditions. Induced resistance was adopted to a lesser extent in the presence of fish predators. The results in this thesis indicate that inducible resistance in F. vesiculosus is an adaptation to varying herbivory in the northern Baltic Sea. The costs of resistance and strong seasonality of herbivory have likely contributed to the evolution of this defense strategy. My findings also show that fish predators have positive cascading effects on F. vesiculosus which arise via reduced herbivory but possibly also through reduced resource allocation to resistance. I further found evidence that the spread of resistance via water-borne cues also occurs in ecologically realistic conditions in natural marine sublittoral. Thus, water-borne induction may enable macroalgae to cope with the strong grazing pressure characteristic of marine benthic communities. The results presented here show that seasonality can have pronounced effects on the biotic interactions in marine benthic communities and thereafter influence the evolution of resistance traits in primary producers.

Physiological reactivity and the perception of emotional stimuli as they relate to social adaptive functioning after traumatic brain injury / y Melonie Jane Hopkins.

Traumatic brain injury (TBI) often affects social adaptive functioning and these changes in social adaptability are usually associated with general damage to the frontal cortex. Recent evidence suggests that certain neurons within the orbitofrontal cortex appear to be specialized for the processing of faces and facial expressions. The orbitofrontal cortex also appears to be involved in self-initiated somatic activation to emotionally-charged stimuli. According to Somatic Marker Theory (Damasio, 1994), the reduced physiological activation fails to provide an individual with appropriate somatic cues to personally-relevant stimuli and this, in turn, may result in maladaptive behaviour. Given the susceptibility of the orbitofrontal cortex in TBI, it was hypothesized that impaired perception and reactivity to socially-relevant information might be responsible for some of the social difficulties encountered after TBL Fifteen persons who sustained a moderate to severe brain injury were compared to age and education matched Control participants. In the first study, both groups were presented with photographs of models displaying the major emotions and either asked to identify the emotions or simply view the faces passively. In a second study, participants were asked to select cards from decks that varied in terms of how much money could be won or lost. Those decks with higher losses were considered to be high-risk decks. Electrodermal activity was measured concurrently in both situations. Relative to Controls, TBI participants were found to have difficulty identifying expressions of surprise, sadness, anger, and fear. TBI persons were also found to be under-reactive, as measured by electrodermal activity, while passively viewing slides of negative expressions. No group difference,in reactivity to high-risk card decks was observed. The ability to identify emotions in the face and electrodermal reactivity to faces and to high-risk decks in the card game were examined in relationship to social monitoring and empathy as described by family members or friends on the Brock Adaptive Functioning Questionnaire (BAFQ). Difficulties identifying negative expressions (i.e., sadness, anger, fear, and disgust) predicted problems in monitoring social situations. As well, a modest relationship was observed between hypo-arousal to negative faces and problems with social monitoring. Finally, hypo-arousal in the anticipation of risk during the card game related to problems in empathy. In summary, these data are consistent with the view that alterations in the ability to perceive emotional expressions in the face and the disruption in arousal to personally-relevant information may be accounting for some of the difficulties in social adaptation often observed in persons who have sustained a TBI. Furthermore, these data provide modest support for Damasio's Somatic Marker Theory in that physiological reactivity to socially-relevant information has some value in predicting social function. Therefore, the assessment of TBI persons, particularly those with adaptive behavioural problems, should be expanded to determine whether alterations in perception and reactivity to socially-relevant stimuli have occurred. When this is the case, rehabilitative strategies aimed more specifically at these difficulties should be considered.

Carbohydrate refeeding rapidly reverses the adaptive upregulation of human skeletal muscle pyruvate dehydrogenase kinase following a high fat diet

The time course for the reversal of the adaptive increase in pyruvate dehydrogenase kinase (PDK) activity following a 6d high fat diet (HP: 4.2 ± 0.2 % carbohydrate; 75.6 ± 0.4 % fat; 19.5 ± 0.8 % protein) was investigated in human skeletal muscle (vastus lateralis). HF feeding increased PDK activity by 44% (from 0.081 ± 0.025 min"' to 0.247 ± 0.025 mm\p < 0.05). Following carbohydrate re-feeding, (88% carbohydrate; 5% fat; 7% protein), PDK activity had returned to baseline (0.111 ± 0.014 min"') within 3h of re-feeding. The active fraction of pyruvate dehydrognease (PDHa) was depressed following 6d of the HF diet (from 0.89 ± 0.21 mmol/min/kg WW to 0.32 ± 0.05 mmol/min/kg ww,p <0.05) and increased to pre-HF levels by 45 min of post re-feeding (0.74 ±0.19 mmol/min/kg ww) and remained elevated for 3h. Western blotting analysis of the PDK isoforms, PDK4 and PDK2, revealed a 31% increase in PDK4 protein content following the HF diet, with no change in PDK2 protein. This adaptive increase in PDK4 protein content was reversed with carbohydrate re-feeding. It was concluded that the adaptive up-regulation in PDK activity and PDK4 protein content was fiilly reversed by 3h following carbohydrate re-feeding.

The practical application of a meta-analysis of deinstitutionalization : adaptive behaviour outcomes and the piloting of a transitional questionnaire for adults with intellectual disabilities

This investigation examined the effects of de institutionalization on the adaptive behaviour and adjustment of adults with intellectual disabilities (ID). In study 1, a meta-analysis was conducted with 23 studies on deinstitutionalization adaptive behaviour outcomes. Deinstitutionalization was associated with modest improvements in adaptive behaviour however outcomes varied across adaptive behaviour domains and other substantive variables. Clinical and service implications of these results were explicated. Noting the trends from the meta-analysis, study 2 used this information in refining and piloting an Agency Transition Survey used to evaluate community transitions for persons with ID. Information derived from the survey was found to be valuable and adequate for the effective evaluation of transitional success. Potential applications of the survey and meta-analysis results were illustrated.

Deinstitutionalization and its Effects on Social Inclusion, Choice-Making, Adaptive and Maladaptive Behavior for Individuals with Intellectual Disabilities: Case Studies Analysis

In the past three decades institutions for persons with intellectual disabilities (ID) have been downsizing and closing in Ontario, Canada. This trend is reflective of the changes that have occurred in society. As of March 2009 the last institution operated by the Ontario government for persons with ID closed, placing the remaining approximately 1000 persons into the community. The current study was an analysis of part of one study in a four-study research project, called the Facilities Initiative Study, to explore the impact of the closures on the lives of individuals who have been reintegrated into community settings. The goal of the current case study analysis was to describe the impact of changes in social inclusion, choice-making/autonomy, and adaptive/maladaptive functioning of four individuals prior to and following transition to the community. The results suggested that, in most cases, community integration was related to more social inclusion opportunities and autonomy in choice-making, a wider range of adaptive behaviors and fewer maladaptive behaviors. In some cases, the evidence suggested that some of these indices of quality of life were not improving. Overall, the study found that the differences observed were unique to each of the individuals who participated in the case study analysis. Some generalized themes were generated that can be applied to future deinstitutionalization endeavors.

Assessing the adaptive capacity of the Ontario wine industry to climate change: A case study

The global wine industry is experiencing the impacts of climate change. Canada’s major wine sector, the Ontario Wine Industry (OWI) is no exception to this trend. Warmer winter and summer temperatures are affecting wine production. The industry needs to adapt to these challenges, but their capacity for this is unclear. To date, only a limited number of studies exist regarding the adaptive capacity of the wine industry to climate change. Accordingly, this study developed an adaptive capacity assessment framework for the wine industry. The OWI became the case study for the implementation of the assessment framework. Data was obtained by means of a questionnaire sent to grape growers, winemakers and supporting institutions in Ontario. The results indicated the OWI has adaptive capacity capabilities in financial, institutional, political, technological, perceptions, knowledge, diversity and social capital resources areas. Based on the OWI case study, this framework provides an effective means of assessing regional wine industries’ capacity to adapt to climate change.

The role of retinoic acid in long-term memory formation and synaptic plasticity in the mollusc Lymnaea stagnalis

The active metabolite of vitamin A, retinoic acid (RA), is involved in memory formation and hippocampal plasticity in vertebrates. A similar role for retinoid signaling in learning and memory formation has not previously been examined in an invertebrate species. However, the conservation of retinoid signaling between vertebrates and invertebrates is supported by the presence of retinoid signaling machinery in invertebrates. For example, in the mollusc Lymnaea stagnalis the metabolic enzymes and retinoid receptors have been cloned from the CNS. In this study I demonstrated that impairing retinoid signaling in Lymnaea by either inhibiting RALDH activity or using retinoid receptor antagonists, prevented the formation of long-term memory (LTM). However, learning and intermediate-term memory were not affected. An additional finding was that exposure to constant darkness (due to the light-sensitive nature of RA) itself enhanced memory formation. This memory-promoting effect of darkness was sufficient to overcome the inhibitory effects of RALDH inhibition, but not that of a retinoid receptor antagonist, suggesting that environmental light conditions may influence retinoid signaling. Since RA also influences synaptic plasticity underlying hippocampal-dependent memory formation, I also examined whether RA would act in a trophic manner to influence synapse formation and/or synaptic transmission between invertebrate neurons. However, I found no evidence to support an effect of RA on post-tetanic potentiation of a chemical synapse. Retinoic acid did, however, reduce transmission at electrical synapses in a cell-specific manner. Overall, these studies provide the first evidence for a role of RA in the formation of implicit long-term memories in an invertebrate species and suggest that the role of retinoid signaling in memory formation has an ancient origin.

Post-hatch heat warms adult beaks: irreversible physiological plasticity in Japanese quail

Across taxa, the early rearing environment contributes to adult morphological and physiological variation. For example, in birds, environmental temperature plays a key role in shaping bill size and clinal trends across latitudinal/thermal gradients. Such patterns support the role of the bill as a thermal window and in thermal balance. It remains unknown whether bill size and thermal function are reversibly plastic. We raised Japanese quail in warm (308C) or cold (158C) environments and then at a common intermediate temperature. We predicted that birds raised in cold temperatures would develop smaller bills than warm-reared individuals, and that regulation of blood flow to the bill in response to changing temperatures would parallel the bill’s role in thermal balance. Cold-reared birds developed shorter bills, although bill size exhibited ‘catch-up’ growth once adults were placed at a common temperature. Despite having lived in a common thermal environment as adults, individuals that were initially reared in the warmth had higher bill surface temperatures than coldreared individuals, particularly under cold conditions. This suggests that blood vessel density and/or the control over blood flow in the bill retained a memory of early thermal ontogeny. We conclude that post-hatch temperature reversibly affects adult bill morphology but irreversibly influences the thermal physiological role of bills and may play an underappreciated role in avian energetics

Fit For Action: A Comparative Case Study of the Implementation of an Adaptive Fitness and Conditioning Program for Moderate Functioning Teens and Transition Age Youth with ASD

The purpose of my research was to develop and refine pedagogic approaches, and establish fitness baselines to adapt fitness and conditioning programs for Moderate-functioning ASD individuals. I conducted a seven-week study with two teens and two trainers. The trainers implemented individualized fitness and conditioning programs that I developed. I conducted pre and post fitness baselines for each teen, a pre and post study interview with the trainers, and recorded semi-structured observations during each session. I used multi-level, within-case and across case analyses, working inductively and deductively. My findings indicated that fundamental movement concepts can be used to establish fitness baselines and develop individualized fitness programs. I tracked and evaluated progressions and improvements using conventional measurements applied to unconventional movements. This process contributed to understanding and making relevant modifications to activities as effective pedagogic strategies for my trainers. Further research should investigate fitness and conditioning programs with lower functioning ASD individuals.

Codage de l’information visuelle par la plasticité et la synchronisation des réponses neuronales dans le cortex visuel primaire du chat

Les systèmes sensoriels encodent l’information sur notre environnement sous la forme d’impulsions électriques qui se propagent dans des réseaux de neurones. Élucider le code neuronal – les principes par lesquels l’information est représentée dans l’activité des neurones – est une question fondamentale des neurosciences. Cette thèse constituée de 3 études (E) s’intéresse à deux types de codes, la synchronisation et l’adaptation, dans les neurones du cortex visuel primaire (V1) du chat. Au niveau de V1, les neurones sont sélectifs pour des propriétés comme l’orientation des contours, la direction et la vitesse du mouvement. Chaque neurone ayant une combinaison de propriétés pour laquelle sa réponse est maximale, l’information se retrouve distribuée dans différents neurones situés dans diverses colonnes et aires corticales. Un mécanisme potentiel pour relier l’activité de neurones répondant à des items eux-mêmes reliés (e.g. deux contours appartenant au même objet) est la synchronisation de leur activité. Cependant, le type de relations potentiellement encodées par la synchronisation n’est pas entièrement clair (E1). Une autre stratégie de codage consiste en des changements transitoires des propriétés de réponse des neurones en fonction de l’environnement (adaptation). Cette plasticité est présente chez le chat adulte, les neurones de V1 changeant d’orientation préférée après exposition à une orientation non préférée. Cependant, on ignore si des neurones spatialement proches exhibent une plasticité comparable (E2). Finalement, nous avons étudié la dynamique de la relation entre synchronisation et plasticité des propriétés de réponse (E3). Résultats principaux — (E1) Nous avons montré que deux stimuli en mouvement soit convergent soit divergent élicitent plus de synchronisation entre les neurones de V1 que deux stimuli avec la même direction. La fréquence de décharge n’était en revanche pas différente en fonction du type de stimulus. Dans ce cas, la synchronisation semble coder pour la relation de cocircularité dont le mouvement convergent (centripète) et divergent (centrifuge) sont deux cas particuliers, et ainsi pourrait jouer un rôle dans l’intégration des contours. Cela indique que la synchronisation code pour une information qui n’est pas présente dans la fréquence de décharge des neurones. (E2) Après exposition à une orientation non préférée, les neurones changent d’orientation préférée dans la même direction que leurs voisins dans 75% des cas. Plusieurs propriétés de réponse des neurones de V1 dépendent de leur localisation dans la carte fonctionnelle corticale pour l’orientation. Les comportements plus diversifiés des 25% de neurones restants sont le fait de différences fonctionnelles que nous avons observé et qui suggèrent une localisation corticale particulière, les singularités, tandis que la majorité des neurones semblent situés dans les domaines d’iso-orientation. (E3) Après adaptation, les paires de neurones dont les propriétés de réponse deviennent plus similaires montrent une synchronisation accrue. Après récupération, la synchronisation retourne à son niveau initial. Par conséquent, la synchronisation semble refléter de façon dynamique la similarité des propriétés de réponse des neurones. Conclusions — Cette thèse contribue à notre connaissance des capacités d’adaptation de notre système visuel à un environnement changeant. Nous proposons également des données originales liées au rôle potentiel de la synchronisation. En particulier, la synchronisation semble capable de coder des relations entre objets similaires ou dissimilaires, suggérant l’existence d’assemblées neuronales superposées.

Plasticity of neuroanatomical relationships between cholinergic and dopaminergic axon varicosities and pyramidal cells in the rat medial prefrontal cortex

Les systèmes cholinergique et dopaminergique jouent un rôle prépondérant dans les fonctions cognitives. Ce rôle est exercé principalement grâce à leur action modulatrice de l’activité des neurones pyramidaux du cortex préfrontal. L’interaction pharmacologique entre ces systèmes est bien documentée mais les études de leurs interactions neuroanatomiques sont rares, étant donné qu’ils sont impliqués dans une transmission diffuse plutôt que synaptique. Ce travail de thèse visait à développer une expertise pour analyser ce type de transmission diffuse en microscopie confocale. Nous avons étudié les relations de microproximité entre ces différents systèmes dans le cortex préfrontal médian (mPFC) de rats et souris. En particulier, la densité des varicosités axonales en passant a été quantifiée dans les segments des fibres cholinergiques et dopaminergiques à une distance mutuelle de moins de 3 µm ou à moins de 3 µm des somas de cellules pyramidales. Cette microproximité était considérée comme une zone d’interaction probable entre les éléments neuronaux. La quantification était effectuée après triple-marquage par immunofluorescence et acquisition des images de 1 µm par microscopie confocale. Afin d’étudier la plasticité de ces relations de microproximité, cette analyse a été effectuée dans des conditions témoins, après une activation du mPFC et dans un modèle de schizophrénie par déplétion des neurones cholinergiques du noyau accumbens. Les résultats démontrent que 1. Les fibres cholinergiques interagissent avec des fibres dopaminergiques et ce sur les mêmes neurones pyramidaux de la couche V du mPFC. Ce résultat suggère différents apports des systèmes cholinergique et dopaminergique dans l’intégration effectuée par une même cellule pyramidale. 2. La densité des varicosités en passant cholinergiques et dopaminergiques sur des segments de fibre en microproximité réciproque est plus élevée comparé aux segments plus distants les uns des autres. Ce résultat suggère un enrichissement du nombre de varicosités axonales dans les zones d’interaction. 3. La densité des varicosités en passant sur des segments de fibre cholinergique en microproximité de cellules pyramidales, immunoúactives pour c-Fos après une stimulation visuelle et une stimulation électrique des noyaux cholinergiques projetant au mPFC est plus élevée que la densité des varicosités de segments en microproximité de cellules pyramidales non-activées. Ce résultat suggère un enrichissement des varicosités axonales dépendant de l’activité neuronale locale au niveau de la zone d'interaction avec d'autres éléments neuronaux. 4. La densité des varicosités en passant des fibres dopaminergiques a été significativement diminuée dans le mPFC de rats ayant subi une déplétion cholinergique dans le noyau accumbens, comparée aux témoins. Ces résultats supportent des interrelations entre la plasticité structurelle des varicosités dopaminergiques et le fonctionnement cortical. L’ensemble des donneès démontre une plasticité de la densité locale des varicosités axonales en fonction de l’activité neuronale locale. Cet enrichissement activité-dépendant contribue vraisemblablement au maintien d’une interaction neurochimique entre deux éléments neuronaux.

The effects of Motivation-Adaptive Skills-Trauma Resolution (MASTR) : Eye Movement Desensitization and Reprocessing (EMDR) on traumatized adolescents with conduct problems

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Molecules and mechanisms of glial and synaptic plasticity

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.