In this dissertation, new digital image processing methods for hyperdimensional imagery are developed and experimentally tested on remotely sensed Earth observations and medical imagery. The high dimensionality of the imagery is either inherent due to the type of measurements forming the image, as with imagery obtained with hyperspectral sensors, or the result of preprocessing and feature extraction, as with synthetic aperture radar imagery and digital mammography. In the first study, two omni-directional adaptations of gray level co-occurrence matrix analysis are developed and experimentally evaluated. The adaptations are based on a previously developed rubber band straightening transform that has been used for analysis of segmented masses in digital mammograms. The new methods are beneficial because they can be applied to imagery where the region of interest is either poorly segmented or not segmented. The methods are based on the concept of extracting circular windows s around each pixel in the image which are radially resampled to derive rectangular images. The images derived from the resampling are then suitable for standard GLCM techniques. The methods were applied to both remotely sensed synthetic aperture radar imagery, for the purpose of automated detection of landslides on earthen levees, and to digital mammograms, for the purpose of automated classification of masses as either benign or malignant. Experimental results show the newly developed methods to be valuable for texture feature extraction and classification of un-segmented objects. In the second study, a new technique of using spatial information in spectral band grouping for remotely sensed hyperspectral imagery is developed and experimentally tested. The technique involves clustering the spectral bands based on similarity of spatial features extracted from each band. The newly developed technique is evaluated in automated classification systems that utilize a single classifier and systems that utilize multiple classifiers combined with decision fusion. The systems are experimentally tested on remotely sensed imagery for agricultural applications. The spatial-spectral band grouping approach is compared to uniform band windowing and spectral only band grouping. The results show that the spatial-spectral band grouping method significantly outperforms both of the comparison methods, particularly when using multiple classifiers with decision fusion.

Disease is not a unique or singular phenomenon. The medical literature contains multiple reports discussing disease interactions and co-occurrence which remains an important issue. Despite this, there has been no systematic investigation of disease co-occurrence in paleopathology. This thesis will begin to fill the gap by producing a detailed analysis of the pathological indicators for scurvy, rickets, and their co-occurrence, focussing on features of co-occurrence and their identification. The Collégiale Saint-Amé collection from 16th to 18th century Douai, France includes 48 individuals ranging from fetal to five years of age. Previous research indicated a large number of potential cases of scurvy and rickets in the juveniles (Devriendt et al. 2010). The current study identified 12 cases of possible co-occurrence based on macroscopic, radiographic, and microscopic techniques; biocultural and historical data supported disease presence. Macroscopic results indicate that lesions associated with scurvy are identifiable and the vascular system is not known to be directly affected by rickets. Rickets features are present but changes are subtle and reduced in prevalence. Radiographs demonstrate features of both diseases but the presence or absence of the line of Fraenkel, a scurvy feature, was useful in identifying the likely dominant disease process. Diagenetic change significantly impacted microscopic investigations but the technique provided some supporting evidence for the presence of rickets. The results clearly demonstrate that cases of co-occurrence of scurvy and rickets are present and identifiable in the archaeological record. Important factors for recognition include the sequence in which conditions develop and duration of illness. Presently only cases with moderately or better developed features of both scurvy and rickets can be identified. Use of multiple techniques was critical to observe subtle changes and build a case for disease presence. Further research on co-occurrence of any diseases is encouraged to create a fuller understanding of past disease. / Thesis / Master of Arts (MA)

No description available.

Predators play a critical role in regulating the structure and function of ecosystems by exhibiting top-down forces on lower trophic levels. Despite their important contributions in maintaining ecosystem health, lethal predator control remains a global wildlife management strategy to reduce predation on livestock, culturally and/or economically important species, and species at risk, as well as to reduce conflict with humans. Predator control has received criticism due in part to a paucity of rigorous research on the community-level impacts of this practice, beyond the target prey species. Specifically, there is a lack of understanding of the behavioural consequences of predator control on the wider ecological community. In this thesis, I used a multi-year camera trap dataset to evaluate how government-mandated grey wolf (Canis lupus) population reduction to conserve boreal woodland caribou (Rangifer tarandus caribou) could impact the resource selection of the carnivore community in northeast Alberta, Canada. In my second chapter, I investigated whether perceived persecution risk due to predator control may alter wolf habitat selection. I found that wolves switched from positively associating with roads before predator control to avoiding anthropogenic linear features and selecting for block features after predator control. These results suggest that lethal control may prompt wolves to prioritize local prey acquisition near block features over movement on linear features. In my third chapter, I examined whether coyote, lynx, and black bear exhibited shifts in co-occurrence with habitat features, competitors, and prey consistent with a release from top-down suppression in response to predator control. I found that predator control triggered unexpected behavioural changes among coyote and lynx consistent with a release from top-down suppression, but not among black bears. Non-apex predator response to predator control may depend on the strength of competition between the apex and non-apex predator, emphasizing the need to consider bottom-up processes when trying to understand the indirect effects of predator control. This research demonstrates that predator control can have trickle-down effects within the larger ecological community, specifically affecting how species utilize resources. As predator control continues to be a recommended wildlife management strategy, it is imperative to continue investigating its unintended consequences throughout the ecological community. / Graduate

As technology advances in all areas of society and industry, the technology used to produce one of life's essentials - food - is also improving. The majority of agriculture production in developed countries has gone from family farms to industrial operations. With the advent of large-scale farming, the automation of basic farming operations has increasingly made practical and economic sense. Broccoli, which is still harvested by hand, is one of the most expensive crops to produce. Investing in sensing technology that can provide detailed information about the location, maturity and viability of broccoli heads has the potential to produce great commercial benefits. This technology is also a prerequisite for developing an autonomous harvester that could select and harvest mature heads of broccoli. This thesis details the work done to develop a computer vision algorithm that has the ability to locate the broccoli head within an image of an entire broccoli plant and to distinguish between mature and immature broccoli heads. Locating the head involves the use of a Hough transform to find the leaf stems and, once the stems are found, the location and extent of the broccoli head can be ascertained with the use of contrast texture analysis at the intersection of the stems. A co-occurrence matrix is then produced of the head and statistical texture analysis is performed to determine the maturity of the broccoli head. The conceptual design of a selective autonomous broccoli harvester, as well as suggestions for further research, is also presented. / Master of Science

The carnivores of Madagascar are likely the least studied of the world's carnivores, thus little is known about threats to their persistence. I provide the first long-term assessment of Madagascar's rainforest carnivore community, including: 1) how multiple forms of habitat degradation (i.e., fragmentation, exotic carnivores, human encroachment, and hunting) affect native and exotic carnivore occupancy; 2) how native and exotic carnivore temporal activity overlap and how body size and niche explain these patterns; 3) how native and exotic carnivores spatially co-occur across the landscape and which variables explain these relationships; and 4) how native and exotic carnivores and humans co-occur with lemurs across Madagascar's largest protected landscape: the Masoala-Makira landscape. From 2008 to 2013 I photographically sampled carnivores and conducted line-transect surveys of lemurs at seven study sites with varying degrees of degradation and human encroachment, including repeat surveys of two sites. As degradation increased, exotic carnivores showed increases in activity and occupancy while endemic carnivore, small mammal, and lemur occupancy and/or activity decreased. Wild/feral cats (Felis sp.) and dogs (Canis familiaris) had higher occupancy (0.37 ± SE 0.08 and 0.61 ± SE 0.07, respectively) than half of the endemic carnivore species across the landscape. Additionally, exotic carnivores had both direct and indirect negative effects on native carnivore occupancy. For example, spotted fanaloka (Fossa fossana) occupancy (0.70 ± SE 0.07) was negatively impacted by both wild/feral cat (beta = -2.65) and Indian civets (beta = -1.20). My results revealed intense pressure from hunting (ex. n = 31 fosa Cryptoprocta ferox consumed per year from 2005-2011 across four villages), including evidence that hunters target intact forest where native carnivore and lemur occupancy and/or activity are highest. I found evidence of high temporal overlap between native and exotic carnivores (ex. temporal overlap between brown-tail vontsira Salanoia concolor and dogs is 0.88), including fosa (Cryptoprocta ferox) avoiding dogs and humans across all seasons. However, I found no evidence of body size or correlates of ecological niche explaining temporal overlap among carnivores. Estimates of spatial co-occurrence among native and exotic carnivores in rainforest habitat revealed strong evidence that native and exotic carnivores occur together less often than expected and that exotic carnivores may be replacing native carnivores in forests close to human settlements. For example, falanouc show a strong increase in occupancy when dogs are absent (0.69 ± SE 0.11) compared to when they are present (0.23 ± SE 0.05). Finally, the two-species interaction occupancy models for carnivores and lemurs, revealed a higher number of interactions among species across contiguous forest where carnivore and lemur occupancy were highest. These various anthropogenic pressures and their effects on carnivore and lemur populations, particularly increases in exotic carnivores and hunting, have wide-ranging, global implications and demand effective management plans to target the influx of exotic carnivores and unsustainable hunting affecting carnivore and primate populations across Madagascar and worldwide. / Ph. D.

Soil microbial communities mediate important ecological processes and play essential roles in biogeochemical cycling. Ecosystem disturbances such as surface mining significantly alter soil microbial communities, which could lead to changes or impairment of ecosystem functions. Reforestation procedures were designed to accelerate the reestablishment of plant community and the recovery of the forest ecosystem after reclamation. However, the microbial recovery during reforestation has not been well studied even though this information is essential for evaluating ecosystem restoration success. In addition, the similar starting conditions of mining sites of different ages facilitate a chronosequence approach for studying decades-long microbial community change, which could help generalize theories about ecosystem succession. In this study, the recovery of microbial communities in a chronosequence of reclaimed mine sites spanning 30 years post reforestation along with unmined reference sites was analyzed using next-generation sequencing to characterize soil-microbial abundance, richness, taxonomic composition, interaction patterns and functional genes. Generally, microbial succession followed a trajectory along the chronosequence age, with communities becoming more similar to reference sites with increasing age. However, two major branches of soil microbiota, bacteria and fungi, showed some contrasting dynamics during ecosystem recovery, which are likely related to the difference in their growth rates, tolerance to environmental change and relationships with plants. For example, bacterial communities displayed more intra-annual variability and more complex co-occurrence networks than did fungi. A transition from copiotrophs to oligotrophs during succession, suggested by taxonomic composition shifts, indicated that the nutrient availability is one important factor driving microbial succession. This theory was also supported by metagenomic analysis of the functional genes. For example, the increased abundance of genes involved in virulence, defense and stress response along ages indicated increased competition between microorganisms, which is likely related to a decrease of available nutrients. Metagenomic analysis also revealed that lower relative abundances of methanotrophs and methane monooxygenase at previously-mined sites compared with unmined sites, which supports previous observations that ecological function of methane sink provided by many forest soils has not recovered after 30 years. Because of the difficulty identifying in situ functional mechanisms that link soil microorganisms with environmental change, modeling can be a valuable tool to infer those relationships of microbial communities. However, the extremely high richness of soil microbial communities can result in extremely complicated models that are difficult to interpret. Furthermore, uncertainty about the coherence of ecological function at high microbial taxonomic levels, grouping operational taxonomic units (OTUs) based on phylogenetic linkages can mask trends and relationships of some important OTUs. To investigate other ways to simplify soil microbiome data for modeling, I used co-occurrence patterns of bacterial OTUs to construct functional groups. The resulting groups performed better at characterizing age-related microbial community dynamics and predicted community structures and environmental factors with lower error. / PHD / Disturbances to ecosystems are known to largely impact important ecological functions such as soil carbon loss, decreased nutrient retention and increased greenhouse gas emission. As a result, surface mining, which totally removes the topsoil and original vegetation, has severe negative influences on forest ecosystem function. Reforestation is performed on reclaimed mined sites to accelerate the return of forest vegetation and ecosystem functions. Although considerable research has shown that the plant community can be well developed after 30 years, little is known on whether ecosystem functions are also recovered during a similar time period. As direct mediators of many ecological processes in the environment, soil microorganisms are important for understanding the restoration progress of ecosystems. They could also provide early indications of restoration progress compared to plants. Historically, most soil microorganisms have been difficult to study because they are highly diverse and the majority cannot be cultured in lab, making it difficult to understand changes in the total soil microbiota. However, technological advances such as DNA sequencing have made it feasible to study soil microorganisms in detail. In this work, we studied soil microbial communities from reclaimed mined sites ranging from 5 to 30 years post-reforestation. We found that overall the microbial community was recovering from the disturbances of surface mining, but many differences from unmined soils still remain after 30 years, such as the unrecovered function as methane sink. Two major groups of soil microorganisms, bacteria and fungi, showed different characteristics during recovery, which are likely due to differences between the two groups with regard to growth rates, tolerance to environmental change and relationships with plants. Mathematical modeling is a useful tool for simulating changes and impacts on microbial communities under different conditions, given that actual interactions between microorganisms and their environment can be difficult to measure. However, the high complexity of soil microbial communities becomes an obstacle for modeling that needs to be addressed by simplifying data describing soil microbial community. One approach is grouping organisms based on their natural evolutionary relationships, but this can mask the trends of some microorganisms since all organisms in these groups do not always respond the same to environmental change. Here we used a method of grouping microorganisms based on their co-occurrence patterns, which resulted in better predictions of changes in community structure and environmental factors when applied in modeling.

The thesis is focused on detection of local disappearance of the neural layer on retina in fundus-camera images. The first chapter describes the human eye physiology, the glaucoma disease and the analyzed data. The second chapter compares four different approaches that should enable automatic detection of a possible damage to the retinal neural layer. These four approaches have been tested and evaluated; three of them showed an acceptable correlation with the medical expert conclusions – the directional spectral approach, the edge based approach and the difference local brightness. The last approch via local co-occurrence matrices has not turned out to be informative with the respect to the issue concerned. Then a program for the automatic detection of the nerve fibre layer loss areas has been designed, realized and evaluated. This task is solved in the last chapter. A relatively good agreement between the medical expert conclusions and the conclusions detected automatically by this program has been reached.

Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2015-08-06T23:09:27Z No. of bitstreams: 1 DISSERTA??O - JACQUELINE REITER.pdf: 5214026 bytes, checksum: 3385648ff5e69e58d30869f0dba4810c (MD5) / Made available in DSpace on 2015-08-06T23:09:27Z (GMT). No. of bitstreams: 1 DISSERTA??O - JACQUELINE REITER.pdf: 5214026 bytes, checksum: 3385648ff5e69e58d30869f0dba4810c (MD5) Previous issue date: 2013-03-25 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / Objectives: To study the profile of sexual violence suffered by children and adolescents and their co-occurrences and the incidence curves over a decade (2001 to 2010) from the notifications made in instances References to the complaint, the Network for the Prevention, Care and Defense of Feira de Santana / BA / Brazil. Methods: Epidemiological study of case series, based on secondary data, produced from the reports of sexual violence (co-occurrence) suffered by children and adolescents (0-18 years) made the Guardianship Councils I and II and the Fair CREAS Santana / BA. In Linkage analysis was used between banks, to avoid duplication of data that has been organized and processed electronically in Statistical Package for the Sciences (SPSS), version 9.0 for Windows. We calculated measures of absolute and relative frequencies, estimated incidences of sexual violence and co-occurrences by calculating the coefficients Incidence in the period, year by year and finally was drafted incidence curves, year after year. Results: A total of 1418 cases, with 21.7% associated with other forms of violence (co-occurrence); rape and incest were the most frequent (30%), with a female majority (80%), adolescence (12-15 years ) (64%), highlighting 66% of victimized children under 11 years (66%). The attackers were known (37, 9%) and family (37%), 13.1% in the range of 13 to 20 years, 23.6% of the complaints were for "Dial 100." The coefficients of incidences of sexual violence and co-occurrences increased in both sexes, stronger in females at the beginning of the decade (2002 to 135.6 cases) and late (2008 to 209.7 cases). For ages, the coefficients showed the same trend in 2002 (49.8 cases, and 110.1 in childhood, adolescence), in 2008 (79.8 cases, and 161.7 in childhood, adolescence); in 2009 (81.6 cases, and 152.2 in childhood, adolescence). The coefficients of co-occurrences increased from the middle of the decade: psychological, in 2005 (9.1 cases) and 2008 (10.5 cases); neglect in 2008 (9.0 cases) and 2009 (9.5 cases), and physical violence in 2008 (6.5 cases) and 2009 (7.0 cases). Conclusions: The increase of incidence sex with or without co-occurrence perpetrated on children and adolescents in the decade, the city studied, highlights the importance of community action, social control complaints via the "Dial 100" as well as the important role of the Guardianship Councils and other instances of "Network" service, given the identification and reporting of cases of sexual violence and their co-occurrences, as well as referrals. These results suggest positive changes, as the process of awareness and popular participation of instances at the same time that instigates the need to redouble efforts towards institutional strengthening, quality of care, given the cases, as well as the quality of data logging system. / Objetivos: Estudar o perfil da viol?ncia sexual sofrida por crian?as e adolescentes e respectivas coocorr?ncias e as curvas de incid?ncia ao longo de um dec?nio (2001 a 2010) a partir das notifica??es efetuadas nas Inst?ncias de Refer?ncias para den?ncia, na Rede de Preven??o, Atendimento e Defesa de Feira de Santana/BA/Brasil. M?todo: Estudo epidemiol?gico do tipo s?rie de casos, com base em dados secund?rios, produzidos a partir das notifica??es de viol?ncia sexual (coocorr?ncia) sofrida por crian?as e adolescentes (0 a 18 anos) efetuadas nos Conselhos Tutelares I e II e CREAS de Feira de Santana/BA. Na an?lise utilizou-se Linkage entre bancos, para evitar duplicidade de dados que foram organizados e processados eletronicamente no Statistical Package for the Sciences (SPSS), vers?o 9.0 for Windows. Foram calculadas as medidas de frequ?ncias simples e relativas; estimado as incid?ncias da viol?ncia sexual e coocorr?ncias pelo c?lculo dos Coeficientes de Incid?ncia, no per?odo, ano a ano e por fim, foi elaborado curvas de incid?ncia, ano a ano. Resultados: Foram estudados 1418 casos, sendo 21,7% associados com outras formas de viol?ncia (coocorr?ncia); estupro e incesto foram os tipos mais frequentes (30%); com maioria feminina (80%), na adolesc?ncia (12-15 anos) (64%), ressaltando 66% de meninos vitimizados at? 11 anos (66%). Os agressores eram conhecidos (37, 9%) e familiares (37%); 13,1% na faixa de 13 a 20 anos; 23,6% das den?ncias foram pelo ?Disque 100?. Os coeficientes de incid?ncias da viol?ncia sexual e coocorr?ncias aumentaram, em ambos os sexos, mais expressivo no feminino, no in?cio do dec?nio (2002 ? 135,6 casos) e no final (2008 ? 209,7 casos). Para faixa et?ria, os coeficientes mostraram a mesma tend?ncia, em 2002 (49,8 casos, na inf?ncia e 110,1, na adolesc?ncia); em 2008 (79,8 casos, na inf?ncia e 161,7, na adolesc?ncia); em 2009 (81,6 casos, na inf?ncia e 152,2, na adolesc?ncia). Os coeficientes das coocorr?ncias aumentaram a partir da metade do dec?nio: viol?ncia psicol?gica, em 2005 (9,1 casos) e 2008 (10,5 casos); neglig?ncia, em 2008 (9,0 casos) e 2009 (9,5 casos); e viol?ncia f?sica, em 2008 (6,5 casos) e 2009 (7,0 casos). Conclus?es: o aumento dos coeficientes de incid?ncia sexual com ou sem coocorr?ncia perpetrada em crian?as e adolescentes no dec?nio, no munic?pio estudado, destaca a import?ncia da atua??o da comunidade, no controle social das den?ncias por meio do ?Disque 100?, assim como o importante papel dos Conselhos Tutelares e demais inst?ncias da ?Rede? de atendimento, face ? identifica??o e notifica??o dos casos de viol?ncia sexual e suas coocorr?ncias, assim como nos encaminhamentos. Esses resultados sugerem mudan?as positivas, quanto ao processo de sensibiliza??o popular e participa??o das Inst?ncias, ao mesmo tempo em que instiga a necessidade de multiplicar esfor?os, no sentido de fortalecimento institucional, na qualidade do atendimento, diante dos casos, assim como, na qualidade do sistema de registro de dados.

A presente tese avaliou os efeitos de dois distúrbios de larga escala sobre estrutura das assembleias de macrófitas aquáticas em distintos ecossistemas neotropicais: uma grande depleção do nível da água no reservatório de Itaipu (Brasil/Paraguai) e os pulsos de cheia e seca na planície do Alto Rio Paraná. O primeiro capítulo da tese avaliou o impacto imediato e de médio prazo da depleção no nível hidrométrico sobre os padrões de co-ocorrência das espécies e a estrutura espaço-temporal da assembleia de macrófitas aquáticas em cinco braços do reservatório de Itaipu. O segundo e terceiro capítulos analisaram os padrões de diversidade beta e a contribuição relativa dos seus diferentes componentes (substituição de espécies e aninhamento) para a estruturação das assembleias no reservatório de Itaipu e na planície de inundação do Alto Rio Paraná, respectivamente. Diferentemente do esperado, a assembleia de macrófitas do reservatório de Itaipu revelou um padrão de organização das espécies diferente do acaso no ano em que ocorreu a depleção, provavelmente devido à colonização de novas espécies na margem exposta e à morte de muitos indivíduos pertencentes a diversas espécies do grupo das submersas. Imediatamente após o distúrbio, evidenciamos um padrão tipicamente aleatório de distribuição, devido ao reestabelecimento das espécies submersas, concomitantemente à colonização de espécies emergentes que haviam se estabelecido nas margens durante o distúrbio. Tanto no reservatório de Itaipu como na planície de inundação do Alto Rio Paraná, a substituição de espécies (turnover) revelou-se como principal mecanismo responsável pelos padrões de diversidade beta, o que provavelmente está diretamente associado com as diferenças de dinâmica hidrológica e limnológica entre cada ambiente dentro dos ecossistemas analisados (braços do reservatório e lagoas da planície). / The present thesis evaluated two large-scale disturbances upon the structure of aquatic macrophytes assemblages in distinct Neotropical ecosystems: an historic drawdown occurred in the Itaipu reservoir (Brazil/Paraguay) and the flood and drought pulses in the Upper Paraná River floodplain. The first chapter evaluated the immediate and long term impact of the drawdown over the co-occurrence patterns and the spatio-temporal structure of the aquatic macrophytes assemblage in five arms of the Itaipu reservoir. The second and third chapters analyzed the beta diversity patterns and the relative contribution of its different components (species turnover and nestedness) to the assemblage’s structure in the Itaipu reservoir and the Upper Paraná River floodplain, respectively. Contrary to expected, the macrophytes assemblage in the Itaipu reservoir presented a non-random spatial organization pattern of the macrophyte species in the year of the drawdown probably due to the colonization of the exposed area by new species and by the death of many individuals of submersed species. Immediately after the disturbance, we evidenced a random distribution guided by the reestablishment of the submersed species concomitantly with the emergents, which occupied the shore since the disturbance. Both Itaipu reservoir and the Upper Paraná River floodplain, the species turnover revealed to be the main process reflecting high values of beta diversity, which probably is directly linked with the distinct hydrological and limnological dynamic within the environments in each analyzed environment (reservoir arms and floodplains lagoons).