I examined impacts of thinning on bird population densities and habitat use in Appalachian mixed-hardwood forests during 1984 and 1985 at three thinned and three unthinned stands in the Jefferson National Forest, southwestern Virginia. Densities of shrubs, saplings, trees, and snags, canopy and ground cover, and foliage volume were the structural variables most influenced by thinning. Populations of shrub/understory birds were higher in thinned stands than unthinned stands. Canopy-dwelling species showed variable population responses to thinning. Habitat use similarities were used to group 13 bird species into three categories: (1) shrub/conifer species included the tufted titmouse, blue-gray gnatcatcher, wood thrush, ovenbird, and hooded warbler, (2) generalist species included the eastern wood-pewee, red-eyed vireo, black-and-white warbler, and scarlet tanager, and (3) mature/deciduous species included the white-breasted nuthatch, solitary vireo, blackburnian warbler, and worm-eating warbler. Shrub, snag, and conifer density and ground cover were the four habitat variables most important in separating used from unused sites. Foraging behavior and resource use of seven bird species were examined in two thinned and two unthinned stands. No differences in foraging methods or niche breadth were found between the stands for all species. Differences in foraging and tree heights were due to tree height differences between the stands. For most species, foraging resource use was equal to availability. Short, small diameter trees were rarely used. Oaks were used most often, and red maple and conifers were rarely used for foraging. The opportunistic nature of avian foraging behavior and the vegetative differences between thinned and unthinned stands led to the foraging differences noted. / Master of Science

A trait based approach was used to assess impacts of overstory density and thinning on understory vegetation components related to wildlife habitat. The relationship between overstory basal area and understory vegetation for species grouped by traits, such as production of flowers, fleshy-fruit and palatable leaves, was characterized in thinned and unthinned stands at seven Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) forests in western Oregon six years following harvests. The ranges of overstory densities within thinned and unthinned stands represent gradients of resource availability and thinning disturbance. Lower overstory densities and thinnings were associated with improved ecosystem functions, specifically the provision of wildlife habitat, as evident by higher cover of flowering and fleshy-fruit and palatable leaf producing species. Greater cover of drought, fire and heat tolerant species in low density stands and after thinnings suggested that these ecosystem functions are more likely to be maintained under climate change conditions, indicating higher resilience. The response of specific functions and response types reflect the traits characteristic for each species group and the impact of these traits on sensitivity to resource availability and disturbances. Thus, the correlation between grouping criteria and the main gradients created by management activities can provide an indication of the expected vegetation response, and therefore the impact of management practices on resilience. / Graduation date: 2012

Paleoclimatic archives, such as lake sediments, extend our understanding of terrestrial and aquatic ecosystem dynamics in relation to climate variability beyond the period covered by instrumental data. In this context, annually laminated (i.e. varved) lake sediments are particularly valuable, as they offer high temporal resolution and undisturbed sediment. However, in order to extract reliable climate information from lake sediments, a careful calibration with the processes controlling the sediment formation is essential. This thesis combines limnological and paleolimnological data from a varved, boreal lake in northern Sweden (Nylandssjön, Nordingrå) collected over different time scales. The main aim of the thesis is to gain a more refined insight into which processes are reflected in the sedimentary diatom assemblage. More specifically, sequential sediment trap records were coupled with physical, chemical and biological lake monitoring and environmental data for comparison and validation with the varved sediment record. The main result of the thesis is that timing, succession and inter-annual variability of key limnological and environmental processes (e.g. ice-cover duration, lake over-turn or catchment run-off) are of major importance for the sedimentary diatom assemblage formation. Continuous monitoring of physico-chemical parameters over three consecutive years identified varying winter air temperature as a major factor influencing in-lake processes and hence the diatom record. Timing of lake over-turn and catchment run-off seemed to be the driver for monospecific diatom blooms, which are reflected in the annual sediment signal. The integrated annual diatom signal in the sediment was dominated by spring or autumn blooms, resulting either from a Cyclotella glomerata dominated spring bloom after relatively warm winter conditions, or a Asterionella formosa dominated autumn bloom after relatively cold winter conditions. The analysis of the diatom stratigraphy in the varved sediment over several decades corroborated the importance of climatic variables (late winter air temperature and NAO), even though the variables with the most predictive power for variance in the diatom data were associated with sediment composition (C, N and sedimentation rate) and pollution (Pb and Cu). Overall, the analysis of the drivers of inter-annual and decadal diatom assemblage fluctuations emphasizes the importance of winter air temperature, indicating that weather extremes may be disproportionately represented in annual sediment records in contrast to nutrient concentrations or sedimentation rate.

La technique d’empreinte génétique par rep-PCR, qui utilise des séquences d’ADN répétitives, a été utilisée pour mettre en évidence la présence de groupes d’Escherichia coli signatures pour divers poulaillers et d’évaluer leur évolution suite au détassement. L’amorce (GTG)5 a été utilisée pour générer des empreintes d’ADN de 522 isolats provenant de 7 poulaillers échantillonnés deux fois : juste avant et 5 jours après le détassement. Les empreintes d’ADN ont été analysées selon l’algorithme de correspondance de bandes de Jaccard. Les analyses de Jackknife des coefficients de similitude ont révélé qu’entre 73% et 93% des isolats ont pu être correctement regroupés selon leur poulailler d’origine. Un dendrogramme construit à partir des coefficients de similitude de Jaccard a groupé les isolats dans 42 grappes avec près de la moitié dans une seule grappe. Environ 80% des isolats ont été groupés dans les 6 plus grosses grappes. Quatre de ces grappes été constituées majoritairement d’isolats provenant d’un seul site. Ces grappes pourraient être des grappes signatures qui permettraient d’identifier des poulaillers en particulier. La comparaison des nombres de grappes présentes avant et après le détassement a révélé une variabilité de l’impact du détassement sur les populations fécales d’E. coli. Pour certains sites, il y avait peu d’agrégats présents tant avant qu’après le détassement alors que pour d’autres sites c’était le contraire. Quoique plus de recherches soient nécessaires afin de valider les conclusions, nos résultats suggèrent la présence de sous-populations signatures d’E. coli pour certains poulaillers et une réponse variable à l’effet du détassement. / Rep-PCR genomic fingerprinting, which uses repetitive intergenic DNA sequences, was investigated as a mean to identify signature pattern of chicken fecal Escherichia coli populations and evaluate their changes over time. The (GTG)5 primer was used to generate DNA fingerprints from 522 isolates originating from 7 chicken houses just prior to, and five days after, thinning. The DNA fingerprints were analysed by using the Jaccard band-matching algorithm. Jackknife analysis of the resulting similarity coefficients revealed that between 73% and 93% of the isolates could correctly be grouped in their house of origin. A dendrogram constructed by using Jaccard similarity coefficients grouped the isolates in 42 clusters with approximately half of them in the same cluster. Out of the 6 largest clusters, containing 80% of all isolates, 4 consisted mostly of isolates coming from only 1 house. These clusters could represent signature clusters identifying specific houses. A comparison of the number of clusters present before and after thinning for each house revealed a substantial difference in the behaviour of the fecal E. coli. For some houses, there were few clusters represented both before and after thinning, with a high number of new clusters appearing after thinning whereas in other houses, the contrary was observed. Our results suggest the presence of a signature subpopulation in some chicken houses and a variable response of the E. coli population to the effect of thinning.

L'objectif de cette thèse est de fournir une analyse de la transition vers la turbulence d'un fluide rhéofluidifiant (fluide de Carreau) dans une conduite cylindrique. Pour cela, un code pseudo-spectral de type Petrov-Galerkin a été développé. Une analyse linéaire de stabilité de l'écoulement laminaire est effectuée, montrant que cet écoulement est linéairement stable. Ensuite, des perturbations sous la forme des rouleaux longitudinaux contra-rotatifs sont utilisées comme condition initiale. Les termes non linéaires d'inertie et visqueux créent un écoulement secondaire avec des points d'inflexion, linéairement instable vis-à-vis de perturbations 3D. Une analyse linéaire de stabilité de ce nouvel écoulement de base bidimensionnelle est réalisée. La forme des vecteurs propres critiques est analysé. Enfin, une analyse non linéaire de stabilité de rouleaux vis-à-vis des perturbations tridimensionnelles de faible amplitude est effectuée, obtenant un retard pour la transition vers la turbulence des fluides rhéofluidifiants par rapport au cas Newtonien et une tendance à l'asymétrie du profil de vitesse axiale / The main objective of this thesis is to provide a description of the transition to turbulence of a shear thinning fluid in pipe flow. A linear stability analysis of the base flow is done. Results show that the flow is linearly stable and the optimal perturbation is given by a pair of counter rotating vortex. This kind of perturbation is used as an initial condition of a computational code which integrates the governing equations. Inertial and viscous non linear terms generate a secondary base flow with inflection points, which is linearly unstable to 3D perturbations. A secondary instability analysis is done, regarding the shape of unstable eigenvectors. Depending the rheological parameters and the size of the primary perturbation, the unstable mode might be near the wall or the center of the pipe. Finally, a non linear stability analysis of the streaks to 3D perturbations of weak amplitude, obtaining a delay in the transition to turbulence due to shear thinning

O objetivo deste trabalho foi analisar o efeito de quatro intensidades de redução da área basal, representadas pela exploração e desbastes sistemáticos, na composição florística, diversidade, estrutura e dinâmica do extrato arbóreo, durante um período de 22 anos. O experimento se localiza na Floresta Nacional do Tapajós, município de Belterra, Pará, a altura do km 114 da Rodovia Santarém-Cuiabá. O delineamento estatístico utilizado foi Blocos ao Acaso com 4 repetições onde foram testados os seguintes tratamentos: T0: controle, representado pela floresta não explorada; T1: Abate de árvores comerciais com DAP ≥ 45cm, sem nenhuma intervenção posterior; T2: Abate de árvores comerciais DAP ≥ 55cm + desbaste de espécies não comerciais para reduzir a área basal em 20% da original; T3: Abate de árvores comerciais DAP ≥ 55cm + desbaste de espécies não comerciais para reduzir a área basal em 40% da original; T4: Abate de árvores comerciais DAP ≥ 55cm + desbaste de espécies não comerciais para reduzir a área basal em 60% da original. Cada bloco possui uma área de 36ha, sendo 9ha por tratamento. Em cada tratamento foram instaladas ao acaso 12 parcelas permanentes (PP) de 0,25ha, onde foram medidas todas árvores com diâmetro ≥ 5,0cm. A exploração de madeira foi realizada em 1982 e os desbastes foram iniciados em 1993 e concluídos em 1994, com a finalidade de reduzir a área basal do povoamento e, com isso, propiciar a maior penetração de luz, favorecendo o desenvolvimento e estabelecimento das espécies comerciais. As medições das PP na área explorada foram realizadas 1 ano antes da exploração (1981), e após a exploração nos anos de 1983, 1987, 1989, 1995 e 2003. Para a área testemunha foram realizadas 5 medições: 1983, 1987, 1989, 1995 e 2003. Os resultados mostraram que, 21 anos depois da exploração e nove após os desbastes, todos os tratamentos, exceto o testemunha, apresentaram aumento no número de espécies, o que indica o efeito positivo das intervenções. Cinco anos após a exploração, todos os tratamentos apresentaram número de árvores superior ao encontrado antes da intervenção, inclusive considerando somente as espécies de valor comercial. Porém, a área basal e o volume apresentaram recuperação mais lenta, ocorrendo de forma mais efetiva nas primeiras classes de diâmetro (5-45cm). Nas classes acima de 45cm, que foram as mais afetadas pela extração de madeira, a área basal, 21 anos após a exploração, ainda está, em média, 30% abaixo do valor original. As intervenções também alteraram a dinâmica da floresta, elevando as taxas de mortalidade, estimulando o aumento no número de ingressos e a aceleração nas taxas crescimento das árvores remanescentes. O tratamento T3 foi considerado o mais adequado porque induziu ao maior aumento na riqueza florística e favoreceu várias espécies de valor comercial madeireiro que aumentaram sua participação na abundância e área basal no povoamento. Esse tratamento também mostrou a maior taxa de recuperação da área basal comercial (aproximadamente 90%), e as maiores taxas de incremento em AB e volume, no período após a aplicação do desbaste. / The objective of this work was to analyze the effect of four intensities of basal area reduction, represented by systematic logging and liberation thinning, on the floristic composition, diversity, structure and dynamics of arboreal extract, over a period of 22 years. The experiment is located in the Tapajós National Forest, municipality of Belterra, Pará, at km 114 of the Santarém-Cuiabá Highway. The statistical delineation employed was Random Blocks with 4 repetitions, in which the following treatments were tested: T0: control, represented by unlogged forest; T1: Felling of commercial trees with DBH ≥ 45cm, with no posterior intervention; T2: Felling of commercial trees DBH ≥ 55cm + thinning of non-commercial species to reduce the original basal area by 20%; T3: Felling of commercial trees DBH ≥ 55cm + thinning of non-commercial species to reduce the original basal area by 40%; T4: Felling of commercial trees DBH ≥ 55cm + thinning of non-commercial species to reduce the original basal area by 60%. Each block measured 36ha, with 9ha for each treatment. In each treatment 12 0,25ha permanent parcels (PP) were randomly installed, in which all trees with diameter ≥ 5,0cm were measured. Logging was carried out in 1982 and the thinning treatments were begun in 1993 and concluded in 1994, with the purpose of reducing the basal area of the population and, so provide greater light penetration, favoring the development and establishment of commercial species The measurements of PP in the harvested area were carried out 1 year before logging (1981), and after logging in the years 1983, 1987, 1989, 1995 and 2003. For the unlogged area 5 measurements were done: 1983, 1987, 1989, 1995 and 2003. The results showed that, 21 years after logging nine after the thinnings, all of the treatments, except the witness, showed an increase in the number of species, which indicates the positive effect of the interventions. Five years after logging, all the treatments showed a greater number of trees than what was found before the intervention, including a count only of species with commercial value. However, the basal area and volume showed a lower recovery, occurring most effectively in the first diameter classes (5-45cm). In the classes above 45cm, which were the ones most affected by timber harvesting, the basal area, 21 years after logging, is still on average 30% below the original value. The interventions also alter forest dynamics, increasing mortality rates, stimulating an increase in the number of ingresses and acceleration in growth of remaining trees. Treatment T3 was considered the most adequate one, because it induced a greater increase in floristic diversity and favored several species with commercially valuable timber, which increased their participation in terms of abundance and basal area in the population. This treatment also showed the highest recovery rate for the commercial basal area (approximately 90%), and the greatest increments in AB and volume, in the period after application of the thinnings.

A neuroimaging feature extraction model is designed to extract region-based image features whose values are predicted by base learners trained on raw neuroimaging morphological variables. The main objectives are to identify Alzheimer’s disease (AD) in its earliest manifestations, and be able to predict and gauge progression of the disease through the stages of mild cognitive impairment (EMCI), late MCI (LMCI) and AD. The model was evaluated on the ADNI database and showed 75.26% accuracy for the challenging EMCI diagnosis based on the 10-fold cross-validation. Our approach also performed well for the other binary classifications: EMCI vs. LMCI (72.3%), EMCI vs. AD (95%), LMCI vs. AD (84.3%), CN vs. LMCI (77.5%), and CN vs. AD (96.5%). By applying the model to the Genome-wide Association Study, along with the sparse Partial Least Squares regression method, we successfully detected risk genes such as the APOE, TOMM40, RVRL2 and APOC1 along with the new finding of rs917100. Moreover, the research aimed to investigate the relationship of different biomarkers; especially the imaging biomarkers to better understand the precise biologic changes that characterize Alzheimer’s disease. The unique and independent contribution of APOE4 allele status (E4+\E4-), amyloid (Aβ) load status (Amy+\Amy-) and combined APOE4 and Aβ status on regional cortical thickness (CTh) and cognition were evaluated via a series of two-way ANCOVAs with post-hoc Tukey HSD tests. Results showed that decreased CTh is independently associated with Amy+ status in many brain regions, but with E4+ status in very restricted number of brain regions. Among CN and EMCI participants, E4+ status is associated with increased CTh, in medial and inferior temporal regions. Diverging association patterns of global and regional Aβ load with cortical volume were found in the entorhinal, temporal pole and parahippocampal regions, which were positively associated with regional Aβ load, but with a negative correlation for global Aβ load in MCI stages. In addition, strong positive correlations were shown between baseline regional CTh and the difference of CTh in each region between the CN and AD, even after adjusting for the regional Aβ and APOE genotype (E4+: r = 0.521 and E4-: r = 0.694).

Graduation date: 2006 / Canopy gap formation is a major factor contributing to maintenance of overstory species diversity and stand structure in forests and may be integral to development of understory shrub and herb layers as well. Acknowledgement of gap formation as a fundamental feature of natural forests has led to consideration of gaps as an option in forest management regimes. This study examined understory vegetation communities across canopy gaps created as a part of the Density Management Study (DMS), which investigates the effectiveness of a thinning regime in promoting late-successional habitat development in young Douglas-fir forests of western Oregon. Patterns in understory vegetation community composition in and around 0.1 and 0.4ha gaps created as a part of the DMS treatment were investigated. The primary goal of this research was to investigate the potential role of canopy gap creation in fostering heterogeneity in understory vegetation communities, and to examine the extent of gap influence on the surrounding thinned forest matrix. Tree species distributions have been shown to partition across gaps in tropical forest systems through differential responses of species to gradients in resource availability, a pattern known as gap partitioning. In temperate forests, understory vegetation communities are much more diverse than the overstories, and display a greater array of habitat requirements. Therefore, understory communities may be more likely than overstories to exhibit gap partitioning in these forests. Patterns in understory community composition across gaps suggest that gap partitioning has occurred. The strength of this partitioning effect appears to differ between gap sizes, as smaller gaps showed a less powerful effect. Abundance of ruderal species was strongly related to gap partitioning in larger gaps, while smaller gaps were dominated by competitor species. Partitioning may be related to an interactive relationship between harvest-related ground disturbance and resource gradients. Therefore, considerations of gap partitioning processes should take into account intensity and spatial distribution of ground disturbance in relation to resource gradients. In addition, conditions necessary for the expression of gap partitioning in understory vegetation communities may be rare in natural gaps in this region. The influence of gaps on understory vegetation communities in the surrounding forest appears to be relatively small. This small influence extent may help explain the lack of a stand level response to gap formation in these stands. Larger gaps exhibit a slight influence on the understory plant community in the surrounding forest to the north of the gap. In small gaps, there seemed to be an influence of the surrounding forest on gap interiors, resulting in an area of influence smaller than the physical gap area. This relationship may indicate that the area of gap influence on understory vegetation may not scale linearly with physical gap size. Species diversity was higher in gap interiors than in surrounding thinned forests. However this effect was partially due to the presence of exotic species, which showed an affinity for gap interiors. Late successional associated species were negatively related to gap interiors, but only in the larger gap size. Gap creation appears to be promoting small scale species diversity in these stands, but creation of large gaps may also promote the establishment of exotic species and may have a negative effect on late successional associated species. However, any and all of these effects may be transient, as understory communities will be strongly affected by overstory re-establishment, and related changes in resource availability. In general, gap formation may influence small-scale stand heterogeneity as evidenced by understory plant communities, but this effect may rely strongly on the nature of gap formation and intensity of disturbance related to this formation.

Development of a tool for discrete event simulations in forest technology, dependent onspatial components, has successfully been initialized in this thesis project. These simulations may be used to optimize the way the forest is used and to evaluate new machine concepts in forestry. The Python library for discrete event simulation, SimPy, was chosen as the foundationfor the tool. The developed tool can handle spatial objects such as moving machines, trees and boulders. Support for continuous linear movements was also added, which has resulted in a model that partially overlaps continuous and discrete event simulations without any additional computational costs. The result is simulations of a forest with machines operating in it. Two pilot simulations,one of a thinning machine and one of a planting machine, were performed with useful results. The new simulation tool shows promising properties. Limitations and improvements arediscussed, with the conclusion that continued development is recommended. / I det här examensarbetet har ett verktyg för diskret event simuleringar inom skogsteknikutvecklats. Sådana simuleringar kan användas för att optimera arbete inom skogsbruk samtför att utvärdera nya maskintekniska koncept. Programmeringsspråket Pythons bibliotek för diskret event simulering, SimPy, valdessom grund för verktyget. Det utvecklade verktyget kan hantera spatiala objekt såsom träd,stenar och stubbar. Stöd för kontinuerliga rörelser har även utvecklats, vilket resulterat i enmodell som delvis överlappar kontinuerliga simuleringar och diskret event simuleringar.Resultatet är kvalitativa simuleringar av skog och skogsmaskiner. Två lyckade simule-ringsstudier har gjorts för Sveriges Lantbruksuniversitet, en simulering av en gallringsmaskinoch en simulering av en planteringsmaskin. Det nya simuleringsverktyget uppvisar lovande egenskaper, även om det har sina be-gränsningar. Fortsatt utveckling av verktyget rekommenderas starkt.

<p>Verification of users’ identities are normally carried out via PIN-codes or ID- cards. Biometric identification, identification of unique body features, offers an alternative solution to these methods. </p><p>Fingerprint scanning is the most common biometric identification method used today. It uses a simple and quick method of identification and has therefore been favored instead of other biometric identification methods such as retina scan or signature verification. </p><p>In this report biometric security systems have been evaluated based on fingerprint scanners. The evaluation method focuses on copies of real fingers, artificial fingers, as intrusion method but it also mentions currently used algorithms for identification and strengths and weaknesses in hardware solutions used. </p><p>The artificial fingers used in the evaluation were made of gelatin, as it resembles the surface of human skin in ways of moisture, electric resistance and texture. Artificial fingers were based on ten subjects whose real fingers and artificial counterpart were tested on three different fingerprint scanners. All scanners tested accepted artificial fingers as substitutes for real fingers. Results varied between users and scanners but the artificial fingers were accepted between about one forth and half of the times. </p><p>Techniques used in image enhancement, minutiae analysis and pattern matching are analyzed. Normalization, binarization, quality markup and low pass filtering are described within image enhancement. In minutiae analysis connectivity numbers, point identification and skeletonization (thinning algorithms) are analyzed. Within pattern matching, direction field analysis and principal component analysis are described. Finally combinations of both minutiae analysis and pattern matching, hybrid models, are mentioned. </p><p>Based on experiments made and analysis of used techniques a recommendation for future use and development of fingerprint scanners is made.</p>