Over the last 20 years, Lyme disease has grown to become the most common vector-borne disease affecting Americans. Spread in the eastern U.S. primarily by the bite of Ixodes scapularis, the black-legged tick, the disease affects an estimated 329,000 Americans per year. Originally confined to New England, it has since spread across much of the east coast and has become endemic in Virginia. Since 2010 the state has averaged 1200 cases per year, with 200 annually in the New River Health District (NRHD), the location of our study. Efforts to geographically model Lyme disease primarily focus on landscape and climatic variables. The disease depends highly on the survival of the tick vector, and white-footed mouse, the primary reservoir. Both depend on the existence of forest-herbaceous edge-habitats, as well as warm summer temperatures, mild winter lows, and summer wetness. While many studies have investigated the effect of forest fragmentation on Lyme, none have made use of high-resolution land cover data to do so at the peridomestic level. To fill this knowledge gap, we made use of the Virginia Geographic Information Network’s 1-meter land cover dataset and identified forest-herbaceous edge-habitats for the NRHD. We then calculated the density of these edge-habitats at 100, 200 and 300-meter radii, representing the peridomestic environment. We also calculated the density of <2-hectare forest patches at the same distance thresholds. To avoid confounding from climatic variation, we also calculated mean summer temperatures, total summer rainfall, and number of consecutive days below freezing of the prior winters. Adding to these data, elevation, terrain shape index, slope, and aspect, and including lags on each of our climatic variables, we created environmental niche models of Lyme in the NRHD. We did so using both Boosted Regression Trees (BRT) and Maximum Entropy (MaxEnt) modeling, the two most common niche modeling algorithms in the field today. We found that Lyme is strongly associated with higher density of developed-herbaceous edges within 100-meters from the home. Forest patch density was also significant at both 100-meter and 300-meter levels. This supports the notion that the fine scale peridomestic environment is significant to Lyme outcomes, and must be considered even if one were to account for fragmentation at a wider scale, as well as variations in climate and terrain. / M.S. / Lyme disease is the most common vector-borne disease in the United States today. Infecting about 330,000 Americans per year, the disease continues to spread geographically. Originally found only in New England, the disease is now common in Virginia. The New River Health District, where we did our study, sees over 200 cases per year. Lyme disease is mostly spread by the bite of the black-legged tick. As such we can predict where Lyme cases might be found if we understand the environmental needs of these ticks. The ticks themselves depend on warm summer temperatures, mild winter lows, and summer wetness. But they are also affected by forest fragmentation which drives up the population of white-footed mice, the tick’s primary host. The mice are particularly fond of the interface between forests and open fields. These edge habitats provide food and cover for the mice, and in turn support a large population of ticks. Many existing studies have demonstrated this link, but all have done so across broad scales such as counties or census tracts. To our knowledge, no such studies have investigated forest fragmentation near the home of known Lyme cases. To fill this gap in our knowledge, we made use of high-resolution forest cover data to identify forest-field edge habitats and small isolated forest patches. We then calculated the total density of both within 100, 200 and 300 meters of the homes of known Lyme cases, and compared these to values from non-cases using statistical modeling. We also included winter and summer temperatures, rainfall, elevation, slope, aspect, and terrain shape. We found that a large amount of forest-field edges within 100 meters of a home increases the risk of Lyme disease to residents of that home. The same can be said for isolated forest patches. Even after accounting for all other variables, this effect was still significant. This information can be used by health departments to predict which neighborhoods may be most at risk for Lyme. They can then increase surveillance in those areas, warn local doctors, or send out educational materials.

Die Nutzung von terrestrischen Ökosystemen zur Befriedigung der Grundbedürfnisse der Menschheit hat tiefgreifende Auswirkungen auf das Erdsystem und führte zur Ausprägung von anthropogen dominierten Landsystemen. Diese sind von hoher Komplexität, da sie aus einer Vielzahl von unterschiedlichsten Einflussfaktoren angetriebenen Landnutzungsveränderungen hervorgegangen sind. Aktuelle Forderungen nach einer nachhaltigen zukünftigen Landnutzung erfordern ein fundiertes und integratives Verständnis dieser Komplexität. Das Hauptziel dieser Arbeit ist es, ein besseres Verständnis der raum-zeitlichen Muster und Determinanten des Landsystemwandels, insbesondere der Landnutzungsintensität, in Europa zwischen 1990 und 2010 zu erlangen. Europa ist ein interessantes Studiengebiet, da es jüngst starke Landnutzungsveränderungen erlebte und seine Heterogenität zu einer Vielfalt von Landsystemen und Landsystemveränderungen führte. Das Ziel der Arbeit wurde durch (i) die Kartierung von Intensitätsmustern und deren Veränderungen in Forst- und Agrarsystemen sowie der Ermittlung der dafür einflussreichsten räumlichen Determinanten und (ii) die Kartierung und Charakterisierung archetypischer Muster und Entwicklungsverläufe von Landsystemen untersucht. Die Ergebnisse dieser Arbeit zeigten einen deutlichen Ost-West-Unterschied in Landsystemmustern und -veränderungen in Europa, mit intensiv genutzten und intensivierenden Regionen vor allem in Westeuropa. Dennoch wurde Europa vor allem durch relativ stabile Landsystemmuster gekennzeichnet und (De-)Intensivierungstrends waren nur von untergeordneter Bedeutung. Intensitätsmuster und -veränderungen waren stark an Standortbedingungen gebunden, vor allem an edaphische, klimatische, und länderspezifische Besonderheiten. Diese Arbeit erweitert das Verständnis des Landsystemwandels in Europa und kann zur Entwicklung wissenschaftlicher und politikbezogener Maßnahmen sowie zur Erreichung einer nachhaltigeren Landnutzung in Europa beitragen. / The utilisation of terrestrial ecosystems to satisfy the basic needs of humankind has profound impacts on the Earth System and led to the development of human-dominated land systems. These are substantially complex as they evolved from a multitude of land-change pathways driven by a variety of influential factors. Current calls for a more sustainable future land-use require a sound and integrative understanding of this complexity. The main goal of this thesis is to better understand the spatio-temporal patterns and the determinants of land-system change in Europe between 1990 and 2010, especially with regard to land-use intensity. Europe serves as an interesting study region as it recently experienced a period of marked land-use change, and since its large environmental, political, and socio-economic heterogeneity resulted in a diversity of land systems and land-change pathways. Land-system changes in Europe were examined by (i) mapping patterns and changes in forestry and agricultural intensity and identifying the most influential spatial determinants related to these changes, and (ii) mapping and characterising archetypical patterns and trajectories of land systems considering both land-use extent and intensity indicators. Results revealed a distinct east-west divide in Europe’s land-system patterns and change trajectories, with intensively used and intensifying regions particularly located in Western Europe. However, Europe was mainly characterised by relatively stable land-systems patterns with (de-) intensification trends being only of minor importance. Land-use intensity levels and changes were strongly related to site conditions, especially with regard to soil and climate, as well as to country-specific characteristics. By fostering the understanding of land-system change, this thesis has the potential to contribute to scientific and policy-related actions that address current efforts to guide future land systems in Europe to a more sustainable use.

Le virus de l’influenza aviaire hautement pathogène (IAHP) de type H5N1 apparu en Chine en 1996 constitue une menace pour la santé humaine en raison de sa circulation endémique dans les volailles domestiques et de son potentiel zoonotique. La sévérité de l'infection liée à l'IAHP H5N1 est variable selon les espèces d'oiseaux: certains anatidés sont porteurs sains et asymptomatiques du virus tandis que dans les élevages de poulets, l'IAHP est fortement contagieux et caractérisé par des taux de mortalité supérieurs à 90%. Chez les humains, l'impact de l'IAHP H5N1 reste à ce jour modéré (630 cas humains dont 375 morts, World Health Organization Juin, 2013) en raison de la faible transmission du virus des volailles aux humains et d'humain à humain. Cependant, étant donné les taux de létalité élevés (>50%), un changement des modalités de transmission pourrait mener à un impact beaucoup plus élevé.<p>Depuis son émergence, l'IAHP H5N1 a eu un impact économique important dans de nombreux pays d’Asie du Sud-Est. La Thaïlande, pays qui fait partie des principaux exportateurs mondiaux de viande de volaille, a été sévèrement touchée par les multiples vagues épidémiques entre 2003 et 2005. Ces épisodes ont eu un impact sur les revenus des petits et moyens producteurs, mais également causé des pertes économiques importantes dans le secteur de la production intensive de volailles en raison de l'embargo imposé par les principaux marchés d'exportation. <p>L'objectif de ce travail est d’étudier quantitativement l'association entre la production intensive de la volaille et la distribution spatio-temporelle de l'IAHP H5N1 en Thaïlande. Deux approches ont été développées pour aborder cette étude: le développement d’une part de modèles statistiques visant à identifier les déterminants du risque d'IAHP H5N1, et d'autre part, de modèles mécanistiques visant à simuler des trajectoires épidémiques sur base de la connaissance des mécanismes de transmission de l'IAHP H5N1, de la structure du secteur de la production de volaille et des mesures d'intervention mises en place. <p>A l’aide de facteurs environnementaux et anthropogéniques, nous montrons que: (i) la distribution des canards domestiques en Asie peut être prédite en utilisant des modèles de régression non-linéaire, et (ii) la production de volailles peut être désagrégée entre production extensive et intensive sur base du nombre de volailles par éleveur. Enfin (iii), nous montrons en utilisant des arbres de régression boostés ("Boosted Regression Trees", BRT) que les principaux déterminants de la distribution du risque d'IAHP H5N1 sont les canards élevés en systèmes intensifs, le nombre de cycles de culture de riz et la proportion d'eau présente dans le paysage. Finalement, nous illustrons les potentialités des modèles mécanistiques pour évaluer l'efficacité des mesures d'intervention implémentées, tester des scénarios alternatifs d'intervention et identifier des stratégies optimales de prévention et d'intervention contre de futures épidémies<p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Thesis (PhD)--Stellenbosch University, 2010. / ENGLISH ABSTRACT: Biological invasions are a growing threat to biodiversity, trade and agriculture in South Africa. Though alien reptiles and amphibians (herpetofauna) are not currently a major issue, escalating problems worldwide and increased trade in South Africa suggest a possible increase in future problems. In this thesis I explore practical measures for risk assessment implementable under national legislation. I began by documenting record-keeping and legislative differences between provinces in South Africa. This revealed some serious deficiencies, complicating attempts to compile accurate inventories and discern import trends. International trade data, however, revealed an exponential increase in the number of imports to South Africa over the last 30 years. Characterising the abundance of species in this trade is important as species introduced in large numbers pose a higher establishment risk. In South Africa, I found a tendency for venomous and expensive species to be traded in low numbers, whereas species that are easy to breed and handle, or that are colourful or patterned are traded in higher numbers. Unlike South Africa, California and Florida have had a large number of well-documented herpetofaunal introductions. These introductions were used to verify the role of several key predictors in species establishment. I first evaluated the role of each variable separately. I examined different approaches for bioclimatic modelling, the predictive power of different sources of distribution data, and methods of assigning a climate-match score. I also present the first test of Darwin’s naturalization hypothesis for land vertebrates using two new phylogenies inferred for native and introduced reptiles in California and Florida. I then used boosted regression trees (BRT) to infer the relative contribution of each factor to species establishment success. Results from the BRTs were incorporated into a user-friendly spreadsheet model for use by assessors inexperienced in complex modelling techniques. Introduction effort was found to be the strongest contributor to establishment success. Furthermore, species with short juvenile periods were more likely to establish than species that started breeding later, as were species with more distant relatives in regional biotas. Average climate match and life form were also important. Of the herpetofaunal groups, frogs and lizards were most likely to establish, while snakes and turtles established at much lower rates, though analysis of all recorded herpetofaunal introductions shows slightly different patterns. Predictions made by the BRT model to independent data were relatively poor, though this is unlikely to be unique to this study and can be partially explained by missing data. Though numerous uncertainties remain in this field, many can be lessened by applying case by case rules rather than generalising across all herpetofaunal groups. The purpose for import and potential trade volume of a species will influence the threat it poses. Considering this in conjunction with a species’ environmental tolerances and previous success of species with similar life histories, should provide a reasonable and defendable estimate of establishment risk. Finally, a brief summary of the potential impacts of introduced alien herpetofauna is provided in the thesis. / AFRIKAANSE OPSOMMING: Indringer spesies hou ‘n al groter bedreiging in vir die biodiversiteit, handel en landbou van Suid- Afrika. Alhoewel uitheemse reptiele en amfibieërs (herpetofauna) tans nie ‘n groot bedreiging in Suid-Afrika is nie, dui groeiende probleme wêreldwyd asook 'n toename in plaaslike handel op moontlike toekomstige probleme. In hierdie tesis, ondersoek ek praktiese metodes vir risikobepaling wat onder nasionale wetgewing toegepas kan word. Ek begin deur die verskille in stoor van rekords en wetgewing tussen provinsies te dokumenteer. Hierdie proses het ernstige tekortkominge uitgewys, wat pogings om akkurate inventarisse saam te stel en invoertendense te bepaal, bemoeilik. Internasionale handelsdata het egter getoon dat daar ‘n eksponensiële toename in die hoeveelheid invoere na Suid-Afrika oor die laaste 30 jaar was. Die hoeveelheid spesies in hierdie handel is belangrik omdat spesies wat in groot hoeveelhede ingevoer word, ‘n hoër vestigingsrisiko het. In Suid-Afrika is ‘n tendens gevind vir handel in giftige en duur spesies teen lae hoeveelhede, terwyl spesies wat maklik teel, maklik hanteer kan word en kleurvol is of mooi patrone het, in groter hoeveelhede mee handel gedryf word. Kalifornië and Florida, in teenstelling met Suid-Afrika, het ‘n hoë aantal goed-gedokumenteerde gevalle van herpetofauna wat in die natuur vrygestel is. Hierdie introduksies was gebruik om die rol van verskeie belangrike faktore in die vestiging van populasies te bepaal. Eerstens het ek die rol van elke faktor apart ondersoek. Ek het verskillende benaderinge vir bioklimatiese model-bou ondersoek, die akuraatheid van verskillende bronne van distribusiedata getoets en drie metodes om ‘n “climate match score” te bereken, voorgestel. Ek bied ook die eerste toets van Darwin se naturalisasie-hipotese vir landwerveldiere aan, deur gebruik te maak van twee nuwe filogenieë wat ek gebou het vir inheemse en ingevoerde reptiele in Kalifornië en Florida. Ek het verder gebruik gemaak van “boosted regression trees” (BRT) om die relatiewe bydrae van elke faktor tot die vestigings-potensiaal van spesies te bepaal. Resultate van hierdie BRTs was ingekorporeerd in ‘n gebruikersvriendelike ontledingstaat wat deur bestuurders, onervare in komplekse modelboutegnieke, gebruik kan word. Invoer-hoeveelheid was die faktor wat die sterktste bygedra het tot suksesvolle vestiging. Verder is spesies met kort jeugperiodes en dié met verlangse familie in streeks-biotas, meer geskik om suksesvol te vestig. Gemiddelde klimaatooreenstemming en lewensvorm was ook belangrik. Paddas en akkedisse was die mees waarskynlikste van die herpetofauna groepe om populasies te vestig, terwyl slange en skilpaaie teen laer tempo’s populasies gevestig het, alhoewel analise van alle gedokumenteerde gevalle van herpetofauna-invoerings wêreldwyd effens verskillende tendense toon. Voorspellings wat deur die BRT-model vir onafhangklike data gemaak is was redelik swak, alhoewel hierdie resultaat onwaarskynlik nie uniek aan die studie is nie, en word gedeeltelik verduidelik deur die gebrek aan data. Alhoewel talle onsekerhede steeds bestaan, kan dié verminder word deur geval-tot-geval reëls toe te pas eerder as om vir herpetofauna as ‘n groep te veralgemeen. Die doel van invoer en potensiële handel-volumes van ‘n spesie, sal die bedreiging wat die spesie toon, bepaal. Hierdie faktore moet saam met omgewingstoleransie en voorafgaande sukses van spesies met soortgelyke lewenswyses oorweeg word, om ‘n aanvaarbare en verdedigbare beraming van vestigingsrisiko te gee. Laastens, word ‘n kort opsomming van die effekte wat uitheemse herpetofauna mag hê, verskaf.

Agriculture is becoming more dependent on computerized solutions to make thefarmer’s job easier. The big step that many companies are working towards is fullyautonomous vehicles that work the fields. To that end, the equipment fitted to saidvehicles must also adapt and become autonomous. Making this equipment autonomoustakes many incremental steps, one of which is developing an accurate and reliable tanklevel measurement system. In this thesis, a system for tank level measurement in a seedplanting machine is evaluated. Traditional systems use load cells to measure the weightof the tank however, these types of systems are expensive to build and cumbersome torepair. They also add a lot of weight to the equipment which increases the fuel consump-tion of the tractor. Thus, this thesis investigates the use of radar sensors together witha number of Machine Learning algorithms. Fourteen radar sensors are fitted to a tankat different positions, data is collected, and a preprocessing method is developed. Then,the data is used to test the following Machine Learning algorithms: Bagged RegressionTrees (BG), Random Forest Regression (RF), Boosted Regression Trees (BRT), LinearRegression (LR), Linear Support Vector Machine (L-SVM), Multi-Layer Perceptron Re-gressor (MLPR). The model with the best 5-fold crossvalidation scores was Random For-est, closely followed by Boosted Regression Trees. A robustness test, using 5 previouslyunseen scenarios, revealed that the Boosted Regression Trees model was the most robust.The radar position analysis showed that 6 sensors together with the MLPR model gavethe best RMSE scores.In conclusion, the models performed well on this type of system which shows thatthey might be a competitive alternative to load cell based systems.