Sensoriamento remoto e geoprocessamento aplicado ao estudo temporal do uso da terra e na comparação entre classificação não supervisionada e análise visual

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Systematic interpretation of molecular beacon polymerase chain reaction for identifying rpoB mutations in Mycobacterium tuberculosis isolates with mixed resistant and susceptible bacteria

Detection of multidrug-resistant tuberculosis (MDR-TB), a frequent cause of treatment failure, takes 2 or more weeks to identify by culture. RIF-resistance is a hallmark of MDR-TB, and detection of mutations in the rpoB gene of Mycobacterium tuberculosis using molecular beacon probes with real-time quantitative polymerase chain reaction (qPCR) is a novel approach that takes ≤2 days. However, qPCR identification of resistant isolates, particularly for isolates with mixed RIF-susceptible and RIF-resistant bacteria, is reader dependent and limits its clinical use. The aim of this study was to develop an objective, reader-independent method to define rpoB mutants using beacon qPCR. This would facilitate the transition from a research protocol to the clinical setting, where high-throughput methods with objective interpretation are required. For this, DNAs from 107 M. tuberculosis clinical isolates with known susceptibility to RIF by culture-based methods were obtained from 2 regions where isolates have not previously been subjected to evaluation using molecular beacon qPCR: the Texas–Mexico border and Colombia. Using coded DNA specimens, mutations within an 81-bp hot spot region of rpoB were established by qPCR with 5 beacons spanning this region. Visual and mathematical approaches were used to establish whether the qPCR cycle threshold of the experimental isolate was significantly higher (mutant) compared to a reference wild-type isolate. Visual classification of the beacon qPCR required reader training for strains with a mixture of RIF-susceptible and RIF-resistant bacteria. Only then had the visual interpretation by an experienced reader had 100% sensitivity and 94.6% specificity versus RIF-resistance by culture phenotype and 98.1% sensitivity and 100% specificity versus mutations based on DNA sequence. The mathematical approach was 98% sensitive and 94.5% specific versus culture and 96.2% sensitive and 100% specific versus DNA sequence. Our findings indicate the mathematical approach has advantages over the visual reading, in that it uses a Microsoft Excel template to eliminate reader bias or inexperience, and allows objective interpretation from high-throughput analyses even in the presence of a mixture of RIF-resistant and RIF-susceptible isolates without the need for reader training.^

Criteria for graphic representation in musical scores: Visual elements in musical scores

A interdisciplinaridade entre a música e as artes visuais tem sido explorado por conceituados teóricos e filósofos, embora não exista muito na área da interpretação visual do grafismo de partituras musicais. Este estudo investiga como os grafismos na notação e símbolos musicais afectam o intérprete na sua transformação em som, com referência especial a partituras contemporâneas, que utilizam notação menos convencional para a criação de uma interpretação por sugestão. Outras relações entre o som e o visual são exploradas, incluindo a sinestesia, a temporalidade e a relação entre obra de arte e público. O objectivo desta dissertação é a de constituir um estudo inovativo sobre partituras musicais contemporâneas, simultaneamente do ponto de vista musical e visual. Finalmente, também vai mais longe, incluindo desenhos da própria autora inspirados e motivados pela música. Estes já não cumprem uma função de notação convencional para o músico, embora existe uma constante possibilidade de uma reinterpretação. ABSTRACT; The inter-disciplinarity between music and visual art has been explored by leading theorists and philosophers, though very little exists in the area of the visual interpretation of graphic musical scores. This study looks at how the graphics of musical notation and symbols affect the performer in transforming them into sound, with particular reference to contemporary scores that use non¬conventional notation to create an interpretation through suggestion. Other sound-visual relationships are explored, including synaesthesia, temporality and the interconnection between work of art and audience or public. This dissertation aims to be an innovative study of contemporary musical scores, from a musical as well as visual perspective. Finally, it takes a step further with drawings of my own, directly inspired and motivated by the music. These no longer fulfil a conventionally notational function for the musician, yet the potential for a re-interpretation is ever-present.

Spatial patterns of malaria in a land reform colonization project, Juruena municipality, Mato Grosso, Brazil

Background: In Brazil, 99% of malaria cases are concentrated in the Amazon, and malaria's spatial distribution is commonly associated with socio-environmental conditions on a fine landscape scale. In this study, the spatial patterns of malaria and its determinants in a rural settlement of the Brazilian agricultural reform programme called ""Vale do Amanhecer"" in the northern Mato Grosso state were analysed. Methods: In a fine-scaled, exploratory ecological study, geocoded notification forms corresponding to malaria cases from 2005 were compared with spectral indices, such as the Normalized Difference Vegetation Index (NDVI) and the third component of the Tasseled Cap Transformation (TC_3) and thematic layers, derived from the visual interpretation of multispectral TM-Landsat 5 imagery and the application of GIS distance operators. Results: Of a total of 336 malaria cases, 102 (30.36%) were caused by Plasmodium falciparum and 174 (51.79%) by Plasmodium vivax. Of all the cases, 37.6% (133 cases) were from residents of a unique road. In total, 276 cases were reported for the southern part of the settlement, where the population density is higher, with notification rates higher than 10 cases per household. The local landscape mostly consists of open areas (38.79 km(2)). Training forest occupied 27.34 km(2) and midsize vegetation 7.01 km(2). Most domiciles with more than five notified malaria cases were located near areas with high NDVI values. Most domiciles (41.78%) and malaria cases (44.94%) were concentrated in areas with intermediate values of the TC_3, a spectral index representing surface and vegetation humidity. Conclusions: Environmental factors and their alteration are associated with the occurrence and spatial distribution of malaria cases in rural settlements.

Quantification of Regional Left and Right Ventricular Deformation Indices in Healthy Neonates by Using Strain Rate and Strain Imaging

Background: Color Doppler myocardial imaging (CDMI) allows the calculation of local longitudinal or radial strain rate (SR) and strain (epsilon). The aims of this study were to determine the feasibility and reproducibility of longitudinal and radial SR and epsilon in neonates during the first hours of life and to establish reference values. Methods: Data were obtained from 55 healthy neonates (29 male; mean age, 20 +/- 14 hours; mean birth weight, 3,174 +/- 374 g). Apical and parasternal views quantified regional longitudinal and radial SR and epsilon in differing ventricular wall segments. Values at peak systole, early diastole, and late diastole were calculated from the extracted curves. CDMI data acquired at 300 +/- 50 frames/s were analyzed offline. Three consecutive cardiac cycles were measured during normal respiration. The timing of specific systolic or diastolic regional events was determined. Multiple comparisons between walls and segments were made. Results: Left ventricular (LV) longitudinal deformation showed basal differences compared with apical segments within one specific wall. Right ventricular (RV) longitudinal deformation was not homogeneous, with significant differences between basal and apical segments. Longitudinal 3 values were higher in the RV free basal and middle wall segments compared with the left ventricle. In the RV free wall apical segment, longitudinal SR and 3 were maximal. LV systolic SR and epsilon values were higher radially compared with longitudinally (radial peak systolic SR midportion, 2.9 +/- 0.6 s(-1); radial peak systolic epsilon 53.8 +/- 19%; longitudinal peak systolic SR midportion, -1.8 +/- 0.5 s(-1); longitudinal peak systolic epsilon, -24.8 +/- 3%; P < .01). Longitudinal systolic epsilon and SR interobserver variability values were 1.2% and 0.7%, respectively. Conclusion: Ultrasound-based SR and 3 imaging is a practical and reproducible clinical technique in neonates, allowing the calculation of regional longitudinal and radial deformation in RV and LV segments. These regional SR and epsilon indices represent new, noninvasive parameters that can quantify normal neonate regional cardiac function. Independent from visual interpretation, they can be used as reference values for diagnosis in ill neonates. (J Am Soc Echocardiogr 2009;22:369-375.)

Land use/ land cover change and its impact on soil erosion process in Begnas Tal Rupa Tal watershed using geospatial tools, Kaski district, Nepal

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Identification and characterization of deforestation hot spots in Venezuela using MODIS satellite images

Land cover changes over time as a result of human activity. Nowadays deforestation may be considered one of the main environmental problems. The objective of this study was to identify and characterize changes to forest cover in Venezuela between 2005-2010. Two maps of deforestation hot spots were generated on the basis of MODIS data, one using digital techniques and the other by means of direct visual interpretation by experts. These maps were validated against Landsat ETM+ images. The accuracy of the map obtained digitally was estimated by means of a confusion matrix. The overall accuracy of the maps obtained digitally was 92.5%. Expert opinions regarding the hot spots permitted the causes of deforestation to be identified. The main processes of deforestation were concentrated to the north of the Orinoco River, where 8.63% of the country's forests are located. In this region, some places registered an average annual forest change rate of between 0.72% and 2.95%, above the forest change rate for the country as a whole (0.61%). The main causes of deforestation for the period evaluated were agricultural and livestock activities (47.9%), particularly family subsistence farming and extensive farming which were carried out in 94% of the identified areas.

Differentiation of focal liver lesions: usefulness of parametric imaging with contrast-enhanced US.

Purpose: To evaluate whether parametric imaging with contrast material-enhanced ultrasonography (US) is superior to visual assessment for the differential diagnosis of focal liver lesions (FLLs). Materials and Methods: This study had institutional review board approval, and verbal patient informed consent was obtained. Between August 2005 and October 2008, 146 FLLs in 145 patients (63 women, 82 men; mean age, 62.5 years; age range, 22-89 years) were imaged with real-time low-mechanical-index contrast-enhanced US after a bolus injection of 2.4 mL of a second-generation contrast agent. Clips showing contrast agent uptake kinetics (including arterial, portal, and late phases) were recorded and subsequently analyzed off-line with dedicated image processing software. Analysis of the dynamic vascular patterns (DVPs) of lesions with respect to adjacent parenchyma allowed mapping DVP signatures on a single parametric image. Cine loops of contrast-enhanced US and results from parametric imaging of DVP were assessed separately by three independent off-site readers who classified each lesion as benign, malignant, or indeterminate. Sensitivity, specificity, accuracy, and positive and negative predictive values were calculated for both techniques. Interobserver agreement (κ statistics) was determined. Results: Sensitivities for visual interpretation of cine loops for the three readers were 85.0%, 77.9%, and 87.6%, which improved significantly to 96.5%, 97.3%, and 96.5% for parametric imaging, respectively (P < .05, McNemar test), while retaining high specificity (90.9% for all three readers). Accuracy scores of parametric imaging were higher than those of conventional contrast-enhanced US for all three readers (P < .001, McNemar test). Interobserver agreement increased with DVP parametric imaging compared with conventional contrast-enhanced US (change of κ from 0.54 to 0.99). Conclusion: Parametric imaging of DVP improves diagnostic performance of contrast-enhanced US in the differentiation between malignant and benign FLLs; it also provides excellent interobserver agreement.

Land use/cover classification in the Brazilian Amazon using satellite images

Land use/cover classification is one of the most important applications in remote sensing. However, mapping accurate land use/cover spatial distribution is a challenge, particularly in moist tropical regions, due to the complex biophysical environment and limitations of remote sensing data per se. This paper reviews experiments related to land use/cover classification in the Brazilian Amazon for a decade. Through comprehensive analysis of the classification results, it is concluded that spatial information inherent in remote sensing data plays an essential role in improving land use/cover classification. Incorporation of suitable textural images into multispectral bands and use of segmentation‑based method are valuable ways to improve land use/cover classification, especially for high spatial resolution images. Data fusion of multi‑resolution images within optical sensor data is vital for visual interpretation, but may not improve classification performance. In contrast, integration of optical and radar data did improve classification performance when the proper data fusion method was used. Among the classification algorithms available, the maximum likelihood classifier is still an important method for providing reasonably good accuracy, but nonparametric algorithms, such as classification tree analysis, have the potential to provide better results. However, they often require more time to achieve parametric optimization. Proper use of hierarchical‑based methods is fundamental for developing accurate land use/cover classification, mainly from historical remotely sensed data.

Constituintes químicos de Ottonia corcovadensis Miq. da floresta Amazônica: atribuição dos deslocamentos químicos dos átomos de hidrogênio e carbono

In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae) were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-pentamethoxyflavone (1), 3',4',5,7-tetramethoxyflavone (2) and 5-hydroxy-3',4',5',7-tetramethoxyflavone (3) and cafeic acid (4). Two amides (5 and 6) were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D) and mass spectra. Extensive NMR analysis was also used to complete ¹H and 13C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra.

Cadastral maps of irrigated areas by center pivots in the State of Minas Gerais, using CBERS-2B/CCD satellite imaging

Medium-resolution satellite images have been widely used for the identification and quantification of irrigated areas by center pivot. These areas, which present predominantly circular forms, can be easily identified by visual analyses of these images. In addition to identifying and quantifying areas irrigated by center pivot, other information that is associated to these areas is fundamental for producing cadastral maps. The goal of this work was to generate cadastral mapping of areas irrigated by center pivots in the State of Minas Gerais, Brazil, with the purpose of supplying information on irrigated agriculture. Using the satellite CBERS2B/CCD, images were used to identify and quantify irrigated areas and then associate these areas with a database containing information about: irrigated area, perimeter, municipality, path row, basin in which the pivot is located, and the date of image acquisition.3,781 center pivots systems were identified. The smallest area irrigated was 4.6 hectares and the largest one was 192.6 hectares. The total estimated value of irrigated area was 254,875 hectares. The largest number of center pivots appeared in the municipalities of Unaí and Paracatu, with 495 and 459 systems, respectively. Cadastral mapping is a very useful tool to assist and enhance information on irrigated agriculture in the State of Minas Gerais.

Environmental adaptation of the source of the subbasin of Rico Stream, Monte Alto - SP, Brazil

The aim of this study was to define the photographic patterns that represent the use and occupation of the landcover of the "spring" of the Rico Stream subbasin, located at Monte Alto, state of São Paulo (SP), Brazil, for environmental adaptation regarding the Brazilian Forest Law. The mapping was performed using remote sensing techniques and visual interpretation of the World View image, followed by the digitalization of the net of drainage and vegetation (natural and agricultural) at the AutoCad software with documents and field work. The study area has 2141.53 ha and the results demonstrated that the main crop is sugarcane with 546.34 ha, followed by 251.22 ha of pastures, 191.71 ha of perennial crops, 57.31 ha of Eucalyptus and 49.52 ha of onion, confirming the advance of sugarcane culture in the region. The region has 375.04 ha of areas of permanent preservation (APPs), and of this area it was found that only 72.17 ha (19.24%) has arboreal vegetation or natural forest, and 302.87 ha of these areas need to be enriched and reforested with native vegetation from the region, according to the current legislation. The data of the area enable future proposals of models for environmental adaptation to the microbasin according to the current environmental legislation.

Caractérisation des occupations du sol en milieu urbain par imagerie radar

Cette étude vise à tester la pertinence des images RSO - de moyenne et de haute résolution - à la caractérisation des types d’occupation du sol en milieu urbain. Elle s’est basée sur des approches texturales à partir des statistiques de deuxième ordre. Plus spécifiquement, on recherche les paramètres de texture les plus pertinents pour discriminer les objets urbains. Il a été utilisé à cet égard des images Radarsat-1 en mode fin en polarisation HH et Radarsat-2 en mode fin en double et quadruple polarisation et en mode ultrafin en polarisation HH. Les occupations du sol recherchées étaient le bâti dense, le bâti de densité moyenne, le bâti de densité faible, le bâti industriel et institutionnel, la végétation de faible densité, la végétation dense et l’eau. Les neuf paramètres de textures analysés ont été regroupés, en familles selon leur définition mathématique. Les paramètres de ressemblance/dissemblance regroupent l’Homogénéité, le Contraste, la Similarité et la Dissimilarité. Les paramètres de désordre sont l’Entropie et le Deuxième Moment Angulaire. L’Écart-Type et la Corrélation sont des paramètres de dispersion et la Moyenne est une famille à part. Il ressort des expériences que certaines combinaisons de paramètres de texture provenant de familles différentes utilisés dans les classifications donnent de très bons résultants alors que d’autres associations de paramètres de texture de définition mathématiques proches génèrent de moins bons résultats. Par ailleurs on constate que si l’utilisation de plusieurs paramètres de texture améliore les classifications, la performance de celle-ci plafonne à partir de trois paramètres. Malgré la bonne performance de cette approche basée sur la complémentarité des paramètres de texture, des erreurs systématiques dues aux effets cardinaux subsistent sur les classifications. Pour pallier à ce problème, il a été développé un modèle de compensation radiométrique basé sur la section efficace radar (SER). Une simulation radar à partir du modèle numérique de surface du milieu a permis d'extraire les zones de rétrodiffusion des bâtis et d'analyser les rétrodiffusions correspondantes. Une règle de compensation des effets cardinaux fondée uniquement sur les réponses des objets en fonction de leur orientation par rapport au plan d'illumination par le faisceau du radar a été mise au point. Des applications de cet algorithme sur des images RADARSAT-1 et RADARSAT-2 en polarisations HH, HV, VH, et VV ont permis de réaliser de considérables gains et d’éliminer l’essentiel des erreurs de classification dues aux effets cardinaux.

Changes of traditional farming systems and their effects on land degradation and socio-economic conditions in the Inle Lake region, Myanmar

At many locations in Myanmar, ongoing changes in land use have negative environmental impacts and threaten natural ecosystems at local, regional and national scales. In particular, the watershed area of Inle Lake in eastern Myanmar is strongly affected by the environmental effects of deforestation and soil erosion caused by agricultural intensification and expansion of agricultural land, which are exacerbated by the increasing population pressure and the growing number of tourists. This thesis, therefore, focuses on land use changes in traditional farming systems and their effects on socio-economic and biophysical factors to improve our understanding of sustainable natural resource management of this wetland ecosystem. The main objectives of this research were to: (1) assess the noticeable land transformations in space and time, (2) identify the typical farming systems as well as the divergent livelihood strategies, and finally, (3) estimate soil erosion risk in the different agro-ecological zones surrounding the Inle Lake watershed area. GIS and remote sensing techniques allowed to identify the dynamic land use and land cover changes (LUCC) during the past 40 years based on historical Corona images (1968) and Landsat images (1989, 2000 and 2009). In this study, 12 land cover classes were identified and a supervised classification was used for the Landsat datasets, whereas a visual interpretation approach was conducted for the Corona images. Within the past 40 years, the main landscape transformation processes were deforestation (- 49%), urbanization (+ 203%), agricultural expansion (+ 34%) with a notably increase of floating gardens (+ 390%), land abandonment (+ 167%), and marshlands losses in wetland area (- 83%) and water bodies (- 16%). The main driving forces of LUCC appeared to be high population growth, urbanization and settlements, a lack of sustainable land use and environmental management policies, wide-spread rural poverty, an open market economy and changes in market prices and access. To identify the diverse livelihood strategies in the Inle Lake watershed area and the diversity of income generating activities, household surveys were conducted (total: 301 households) using a stratified random sampling design in three different agro-ecological zones: floating gardens (FG), lowland cultivation (LL) and upland cultivation (UP). A cluster and discriminant analysis revealed that livelihood strategies and socio-economic situations of local communities differed significantly in the different zones. For all three zones, different livelihood strategies were identified which differed mainly in the amount of on-farm and off-farm income, and the level of income diversification. The gross margin for each household from agricultural production in the floating garden, lowland and upland cultivation was US$ 2108, 892 and 619 ha-1 respectively. Among the typical farming systems in these zones, tomato (Lycopersicon esculentum L.) plantation in the floating gardens yielded the highest net benefits, but caused negative environmental impacts given the overuse of inorganic fertilizers and pesticides. The Revised Universal Soil Loss Equation (RUSLE) and spatial analysis within GIS were applied to estimate soil erosion risk in the different agricultural zones and for the main cropping systems of the study region. The results revealed that the average soil losses in year 1989, 2000 and 2009 amounted to 20, 10 and 26 t ha-1, respectively and barren land along the steep slopes had the highest soil erosion risk with 85% of the total soil losses in the study area. Yearly fluctuations were mainly caused by changes in the amount of annual precipitation and the dynamics of LUCC such as deforestation and agriculture extension with inappropriate land use and unsustainable cropping systems. Among the typical cropping systems, upland rainfed rice (Oryza sativa L.) cultivation had the highest rate of soil erosion (20 t ha-1yr-1) followed by sebesten (Cordia dichotoma) and turmeric (Curcuma longa) plantation in the UP zone. This study indicated that the hotspot region of soil erosion risk were upland mountain areas, especially in the western part of the Inle lake. Soil conservation practices are thus urgently needed to control soil erosion and lake sedimentation and to conserve the wetland ecosystem. Most farmers have not yet implemented soil conservation measures to reduce soil erosion impacts such as land degradation, sedimentation and water pollution in Inle Lake, which is partly due to the low economic development and poverty in the region. Key challenges of agriculture in the hilly landscapes can be summarized as follows: fostering the sustainable land use of farming systems for the maintenance of ecosystem services and functions while improving the social and economic well-being of the population, integrated natural resources management policies and increasing the diversification of income opportunities to reduce pressure on forest and natural resources.