Estimation de paramètres structuraux des arbres dans une savane à partir de mesures LiDAR terrestre et d'imagerie à très haute résolution spatiale

This thesis takes its place in a context where information on the biophysical state of forest ecosystems at spatial scales only remote sensing can retrieve is in demand more than ever. In order to provide reliable information using validated approaches, the remote sensing research community recognises the need for new and innovative methods, especially in heterogeneous environments like savannas. The recent emergence of terrestrial LiDAR scanners (TLS) and the increase in the computational capability of computers which allow running ray tracing model simulations with a high level of realism hold great potential to improve our understanding of the processes influencing the radiance measured by satellite sensors. This thesis makes use of these two cutting edge technologies for estimating the spatial distribution of tree leaf area, a key element of modeling radiative transfer processes. The first part of the thesis concerns the development of methods for estimating tridimensional leaf area distribution in a savanna environment from TLS measurements. The methods presented address certain issues related to TLs measures affecting the application of classical theories (the probability of light transmission and the contact frequency) to the estimation of leaf area through indirect means. These issues pertain to the cross-section of laser pulses emitted by a TLS and the occlusion effects caused by the interception of laser pulses by material inside the crown. The developed methods also exploit additional information provided by the active nature of the TLS sensor that is not available to passive sensors like hemispherical photography, i.e. the intensity of a pulse return offers the possibility to distinguish between energy interception by wood and foliage. A simplified approach of this method is presented to promote its use by other research groups. This approach consists of a series of parameterisations and represents a significant gain in terms of the required resources to produce the leaf area, estimates. The second part of the thesis explores the combination of the tree representations generated in the first part with a ray tracing model to simulate the interactions of light with tree crowns. This approach is highly innovative and our study showed its potential to improve our understanding of the factors influencing the radiative environment in a savanna. The methods presented offer a solution to map leaf area at the individual tree scale over large areas from very high spatial resolution imagery

Le cadre écologique forestier du Québec: réalisation et applications dans un secteur de l'Abitibi

L'objectif des travaux de cartographie écologique entrepris par le Service de l'inventaire forestier du Ministère de l'Énergie et des Roussources du Québec (MER) est la délimitation de superficies homogènes sur le plan de l'éménagement forestier. L'inventaire écologique sur le terrain et la photo-interprétation sont combinés en une cartographie des régions, des districts et des types écologiques. Les régions écologiques (1:1 250 000) représentent les variations du climat régional. Les districts écologiques (1:250 000) montrent l'agencement du relier, de la géologie et de la géomorphologie et les types écologiques (1:20 000) sont caractérisés par le dépôt de surtface accompagné de sa classe d'épaisseur, le drainage, la classe de pente et le terme final de la série évolutive de végétation. Les renseignements tirés des travaux de classification écologique réalisés en Abitibi ont permis la réalisation du cadre écologique forestier des cantons d'Hébécourt et de Roquemaure selon les normes du MER. Ce cadre écologique comprend, en plus des cartographies de chacun des niveaux de classification, un document interprétatif incluant sères physiographiques et textes descriptifs détaillés du territoire à l'étude. Des possibilités d'application à l'aménagement forestier sont envisagées entre autres par l'utilisation de travaux de recherche appliquée (inventaire de régénération et effet de la préparation de terrain sur la compétition après coup). Dans l'avenir, l'utilisation effective de la méthode proposée dépendra des incitatifs imposés par le pouvoir politique et de la formation des aménagistes. La démarche tirerait avantage d'une intégration à l'inventaire forestier traditionnel. Étant donné que les variables choisies et la précision obtenue peuvent satisfaire la majorité des utilisateurs, son extension à l'ensemble du territoire québécois est jugée souhaitable

Application de la télédétection et des SIG à l'étude du développement de l'aquaculture et des forêts de mangroves cas du district de Giao Thuy, Viêt-nam

L'aquaculture connaît une croissance plus élevée que tout autre secteur de production alimentaire animale. La crevetticulture est un secteur de l'aquaculture qui a un potentiel important pour le développement rural et la réduction de la pauvreté au Viêt-nam. Malheureusement, certains des changements apportés à l'environnement par les exploitations aquacoles ont aussi des impacts négatifs potentiels, entre autres la dégradation des zones marécageuses. Malgré la croissance rapide de l'aquaculture et l'évolution de la connaissance des impacts environnementaux, peu d'études ont traité ces problématiques de manière objective. L'observation spatiale et les systèmes d'information géographique (SIG) ont été appliqués dans la présente étude à l'analyse de l'altération des ressources engendrée par le développement de la crevetticulture et à la planification de son développement futur dans le district de Giao Thuy, province de Nam Dinh, Viêt-nam. Trois images Landsat ont été traitées et classifiées; les changements détectés entre les classifications ont ensuite été rigoureusement vérifiés par un algorithme de validation. Les années d'acquisition des images sélectionnées sont 1986, 1992 et 2001. L'analyse des résultats conduit aux constats suivants : 63 % de la mangrove présente en 1986 a été remplacée par des bassins d'aquaculture; entre 1986 et 1992, 440 ha de mangrove ont été détruits, tandis qu'entre 1992 et 2001 la superficie occupée par celle-ci s'est accrue de 441 ha, la rétablissant à un hectare près à son niveau de 1986; cette reprise forestière entre 1992 et 2001 est attribuable à des projets de reforestation et à une régénération naturelle favorisée par des efforts de conservation dans une proportion approximative de 58 % et 42 % respectivement. Une deuxième partie de l'étude porte sur le processus d'intensification des méthodes de production en cours et la planification requise. Les SIG y sont mis à profit pour produire une carte d'aptitude des sites au développement durable de l'aquaculture dans le district de Giao Thuy.Abstract: Aquaculture is growing more rapidly than all other food producing sectors. Shrimp culture is a sector of aquaculture which has a high potential for poverty alleviation and rural development in Vietnam. Unfortunately, some of the changes induced by the shrimp farm on the environment have potential negative impacts, one of which is wetland deterioration. Despite the rapid growth of aquaculture and the evolution of the consciousness about its environmental hazards, few studies have considered this matter in an objective manner. Spatial observation and geographic information systems (GIS) have been applied in this study to the analysis of resource alteration caused by aquaculture development and its future development planning in the district of Giao Thuy, Nam Dinh province, Vietnam. Three Landsat images were processed and classified; the detected changes between classifications were then rigorously verified by a validation algorithm. The selected images acquisition years are 1986, 1992 and 2001. The analysis of the results leads to the following observations: 63% of mangrove areas existent in 1986 were replaced by shrimp ponds; between 1986 and 1992, 440 ha of mangrove were destroyed, but between 1992 and 2001 the extent of the mangrove increased by 441 ha, restoring it approximately to its 1986 level; this recovery is attributed to reforestation projects and to natural regeneration promoted by conservation efforts in an approximate proportion of 58% and 42% respectively. A second part of the study examines the ongoing intensification of the production methods process as well as the required planning. GIS is used to produce a site suitability map for sustainable development of aquaculture in the Giao Thuy district

Exploring the potential of two-aged white spruce plantations for the production of sawlog volume with simulations using SORTIE-ND

The main objective for even-aged plantation (EAP) management of producing sawlog material has driven practices towards low initial planting densities and lower post thinning densities. For semi-shade tolerant species, the resulting stand density potentially leaves enough growing space for the introduction of a second cohort of trees in the understory, making it a two-aged plantation (TAP). TAPs could have many silvicultural benefits, especially in sensitive areas where intensive treatments associated with EAPs are incompatible with local management objectives. White spruce (Picea glauca) is a good candidate species for modeling TAPs because it is the most widely planted tree species in Canada and has proven tolerance to understory planting. SORTIE-ND, a single-tree spatially explicit growth model was used to explore the yield of variable density and rotation length scenarios when each white spruce cohort is introduced mid rotation, compared to traditional even-aged management. All TAP scenarios tested produced more sawlog volume and more merchantable volume than equivalent densities of EAPs. The lowest density tested, 400 stems ha-1 planted every 35 years, had the highest sawlog yields (3.23 m3 ha-1 yr-1). Considering smaller size products changes the optimum TAP scenario but maintains the advantage over EAPs

Near real-time deforestation detection in Malaysia and Indonesia using change vector analysis with three sensors

Malaysia and Indonesia have been affected by deforestation caused in great part by the proliferation of oil palm plantations. To survey this loss of forest, several studies have monitored these southeast Asian nations with satellite remote sensing alert systems. The methods used have shown potential for this approach, but they are limited by imagery with coarse spatial resolution, low revisit times, and cloud cover. The objective of this research is to improve near real-time operational deforestation detection by combining three sensors: Sentinel-1, Sentinel-2 and Landsat-8. We used Change Vector Analysis to detect changes between non-affected forest and images under analysis. The results were validated using 166 plots of undisturbed forest and confirmed deforestation events throughout Sabah Malaysian State, and from 70 points from drone pictures in Sumatra, Indonesia. Sentinel-2 and Landsat-8 yielded sufficient results in terms of accuracy (less than 11% of commission and omission error). Sentinel-1 had lower accuracy (14% of commission error and 28% of omission error), probably resulting from geometric distortions and speckle noise. During the high cloud-cover season optical sensors took about twice the time to detect deforestation compared to Sentinel-1 which was not affected by cloud cover. By combining the three sensors, we detected deforestations about 8 days after forest clearing events. Deforestations were only detectable during approximately the first 100 days, before bare soils were often coved by legume crop. Our results indicate that near real-time deforestation detection can reveal most events, but the number of false detections could be improved using a multiple event detection process

Automatic 3D Mapping for Tree Diameter Measurements in Inventory Operations

Forestry is a major industry in many parts of the world. It relies on forest inventory, which consists of measuring tree attributes. We propose to use 3D mapping, based on the iterative closest point algorithm, to automatically measure tree diameters in forests from mobile robot observations. While previous studies showed the potential for such technology, they lacked a rigorous analysis of diameter estimation methods in challenging forest environments. Here, we validated multiple diameter estimation methods, including two novel ones, in a new varied dataset of four different forest sites, 11 trajectories, totaling 1458 tree observations and 1.4 hectares. We provide recommendations for the deployment of mobile robots in a forestry context. We conclude that our mapping method is usable in the context of automated forest inventory, with our best method yielding a root mean square error of 3.45 cm for our whole dataset, and 2.04 cm in ideal conditions consisting of mature forest with well spaced trees

Selection of summer feeding sites and food resources by female migratory caribou (Rangifer tarandus) determined using camera collars

Migratory caribou (Rangifer tarandus) is a socioeconomically and culturally key species for northern communities in the Arctic, and most of its populations are experiencing a sharp decline. Female migratory caribou depend on the availability of summer habitat resources to meet the needs associated with lactation and the accumulation of fat reserves to survive when resources are less abundant. Because of the large scales at which habitat and resource data are usually available, information on how female migratory caribou select habitat and resources at fine scales in the wild is lacking. To document selection of summer feeding sites, we equipped 60 female caribou with camera collars from 2016 to 2018. We collected a total of 65,150 10-sec videos between June 1 st and September 1 st for three years with contrasted spring phenology. We determined the selection at the feeding site scale (3 rd scale of Johnson) and food item scale (4 th scale of Johnson) using resource selection probability functions. Wetlands were highly selected as feeding sites in June and July while they were avoided in August. Shrublands were mostly selected in July and August. At the resources scale, lichen, birch, willow, and mushrooms were the most strongly selected resources. Our results provide precise and novel information on habitat selection at feeding sites and food resources selected by female caribou in the wild. This information will help understand foraging patterns and habitat selection behavior of female migratory caribou and will contribute to the management and conservation of its declining populations

Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome

<p>Abstract</p> <p>Background</p> <p>Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand <it>Brucella abortus </it>virulence, we consolidated the proteomic data collected and compared it to publically available genomic data.</p> <p>Results</p> <p>The proteomic data was compiled from several independent comparative studies of <it>Brucella abortus </it>that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes.</p> <p>Conclusions</p> <p>An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of <it>Brucella abortus </it>strain 2308.</p

The nomenclature, definition and classification of discordant atrioventricular connections

Congenitally corrected transposition is a complex cardiac lesion that is often associated with ventricular septal defect, obstruction of the outflow tract of the morphologically left ventricle, and abnormalities of the morphologically tricuspid valve.1,2Nomenclature for this lesion has been variable and confusing.1In this review, we define, and hopefully clarify this terminology. The lesion is a combination of discordant union of the atrial chambers with the ventricles, and the ventricles with the arterial trunks.1,2In rare circumstances, discordant atrioventricular connections can be associated with concordant ventriculo-arterial connections. This malformation has been called "isolated ventricular inversion". The term is less than precise, and the descriptive approach using the phrase "discordant atrioventricular connections with concordant ventriculo-arterial connections" is preferred, as discussed below