Radio-frequency (RF) fingerprinting is a process that uses the minute inconsistencies among manufactured radio transmitters to identify wireless devices. Coupled with location fingerprinting, which is a machine learning technique to locate devices based on their radio signals, it can uniquely identify and locate both trusted and rogue wireless devices transmitting over the air. This can have wide-ranging applications for the Internet of Things, security, and networking fields. To contribute to this effort, this research first builds a software-defined radio (SDR) testbed to collect an RF dataset over LTE and WiFi channels. The developed testbed consists of both hardware which are receivers with multiple antennas and software which performs signal preprocessing. Several features that can be used for RF device fingerprinting and location fingerprinting, including received signal strength indicator and channel state information, are also extracted from the signals. With the developed dataset, several data-driven machine learning algorithms have been implemented and tested for fingerprinting performance evaluation. Overall, experimental results show promising performance with a radio fingerprinting accuracy above 90\% and device localization within 1.10 meters.

The primary objective of the proposed research is to develop a framework for smart and robust fingerprinting of networked systems. Many fingerprinting techniques have been proposed in the past, however most of these techniques are designed for a specific purpose, such as Operating System (OS) fingerprinting, Access Point (AP) fingerprinting, etc. Such standalone techniques often have limitations which render them dysfunctional in certain scenarios or against certain counter measures. In order to overcome such limitations, we propose a fingerprinting framework that can combine multiple fingerprinting techniques in a smart manner, using a centralized decision making engine. We believe that any given scenario or a counter measure is less likely to circumvent a group of diverse fingerprinting techniques, which serves as the primary motivation behind the aforementioned method of attack. Another major portion of the thesis concentrates on the design and development of a device and device type fingerprinting sub-module (GTID) that has been integrated into the proposed framework. This sub-module used statistical analysis of packet inter arrival times (IATs) to identify the type of device that is generating the traffic. This work also analyzes the performance of the identification technique on a real campus network and propose modifications that use pattern recognition neural networks to improve the overall performance. Additionally, we impart capabilities to the fingerprinting technique to enable the identification of 'Unknown' devices (i.e., devices for which no signature is stored), and also show that it can be extended to perform both device and device type identification.

La connaissance des principales sources diffuses de sédiments permettrait d'améliorer l'utilisation des ressources publiques investies dans les stratégies de gestion des sols. Les méthodes de traçage (fingerprinting) conventionnelles basées sur la composition géochimique sont laborieuses et nécessitent une préparation importante des échantillons. Cette étude visait à rechercher les sources de sédiments dans des bassins versants agricoles du Rio Grande do Sul (sud du Brésil) et d'évaluer l'utilisation des outils spectroscopiques comme technique alternative. La superficie des bassins versants étudiés est comprise entre 0,80 et 2027 km². Les sources de sédiments correspondent aux terres cultivées, aux prairies, aux chemins agricoles et aux berges des cours d'eau. L'échantillonnage des sédiments est basé sur des préleveurs automatiques pour un suivi temporel, des prélèvements de sédiments fins du lit de la rivière, et lors d'événements de pluvieux. La concentration totale des traceurs géochimiques a été mesurée dans les échantillons de sédiments et de sols. Les mesures spectrales ont été faites dans la gamme ultraviolet-visible, proche infrarouge et infrarouge moyen pour le bassin versant d'Arvorezinha. Les deux méthodes, classiques et spectroscopiques, permettent de discriminer et de fournir la contribution des sources de sédiments. L'information spectrale peut être aussi précise que les traceurs géochimiques. En outre, la combinaison de paramètres de couleur dérivés du spectre dans le visible avec traceurs géochimiques était une façon rapide et peu coûteuse pour améliorer la discrimination entre les sources et la précision des prédictions. La contribution des sources de sédiments démontrent que d'autres facteurs que proportion de l'utilisation des terres, comme la distribution de terres agricoles, les forêts et les chemins agricoles dans le paysage, jouent un rôle important dans la production de sédiments. Forêt riparienne semble être un facteur clé de l'érosion des berges des cours d'eau. L'érosion due aux chemins agricoles semble être fortement liée échelle d'observation et dépend du nombre de points ou les routes traversent le réseau hydrographique. Les terres cultivées, même lorsque cultivées sans labour (semis direct), sont encore la principale source de sédiments dans les bassins versants agricoles dans le sud du Brésil. La quantité de sédiment produite par les terres cultivées et par unité de surface qui atteint efficacement le réseau de drainage variait de 0,06 à 3,95 tonnes ha-1 an-1. Ces variations sont partiellement liées au relief et à la pente, mais elles sont essentiellement influencées par l'utilisation des terres et la gestion des sols. La quantité de sédiments provenant des terres cultivées est encore trop élevée pour des zones de faible érosivité et cultivées sans labour du sol, comme le bassin versant de Conceição (1, tonnes ha-1 an-1). Ceci, indique que des efforts supplémentaires sont encore nécessaires pour réduire l'érosion du sol. Par conséquent, il est urgent de mieux planifier l'utilisation et l'occupation des terres dans ces bassins versants, dans la mesure où les systèmes de gestion des sols utilisés par les agriculteurs sont encore inefficaces pour réduire le ruissellement et l'érosion dans les zones cultivées dans le sud du Brésil. / The knowledge of the main diffuse sources of sediment production can enhance efficiency in the use of public resources invested in management strategies that seek to mitigate sediment transfer. Conventional fingerprinting methods based on geochemical composition are timeconsuming and require critical preliminary sample preparation. In this sense, spectroscopic methods can be less labor-intensive, cheap, and viable alternative for this purpose. The present study aimed to evaluate the sediment sources in agricultural catchments from Rio Grande do Sul State, Brazil, and to evaluate the potential use of spectroscopy measurements as a low cost and easy alternative to fingerprinting sediment sources. The total area of the study includes five catchments as Arvorezinha, Júlio de Castilhos 1, Júlio de Castilhos 2, Conceição, and Guaporé with areas of 1.19, 0.80, 1.43, 804.3, and 2,027.2 km², respectively. Sediment sources evaluated were crop fields, grasslands, unpaved roads, and stream channels. Sediment sampling strategy included time-integrated samplers, fine-bed sediments, and storm-event sediments. The total concentrations of several geochemical tracers were estimated in sediment and source samples. Spectral measurements were made for ultraviolet-visible, near-infrared, and mid-infrared ranges only for the Arvorezinha catchment. Source ascriptions obtained by alternative methods based on spectroscopy analysis were in agreement with ascriptions from classical fingerprinting method based on geochemical composition. Spectral information can be as precise as the geochemical tracers. Besides, combining visible-based-colour to geochemical tracers was a rapid and inexpensive way to enhance discrimination between source types and to improve precision of sediment sources apportionment. Findings of sediment source apportionment demonstrate that other factors than proportion of land use, such as distribution of croplands, forests, and unpaved roads in the landscape; play an important role in sediment production. Riparian forests seems to be a key factor for stream channel erosion. Unpaved roads seems to be strongly scale-related and dependent upon the number of points were roads across directly the stream network. The crop fields, even when cultivated with no-tillage, are still the main source of sediment in agricultural catchments in southern Brazil. The amount of sediment yielded from crop fields per unit of area that actually reaches the stream outlet ranged from 0.06 to 3.95 ton ha-1 yr-1. These variations are attributed partly to the relief and slope, but land use and soil management mostly influences them. The amount of sediment originated from crop fields are still too high for low susceptible areas with no-till, as Conceição catchment (1.30 ton ha-1 yr-1), indicating that further efforts are still necessary to further reduce soil erosion. Therefore, there is an urgent need to better plan land use and occupation in these catchments, inasmuch as the soil management systems used by farmers are still inefficient to reduce runoff and erosion in areas with crops in southern Brazil. / O conhecimento das principais fontes difusas de sedimentos pode aumentar a eficiência de utilização dos recursos investidos em estratégias de gestão que visem mitigar a transferência de sedimentos aos cursos d'água. Métodos convencionais baseados na composição geoquímica ainda tem alto custo, são onerosos e demandam preparação preliminar crítica das amostras. Dessa forma, métodos espectroscópicos podem ser uma alternativa menos trabalhosa, mais rápida e viável para esse propósito. Objetivou-se com o presente trabalho avaliar a contribuição das fontes de sedimentos em bacias hidrográficas agrícolas do estado do Rio Grande do Sul, e avaliar o potencial uso da espectroscopia como uma alternativa para traçar a origem dos sedimentos. As áreas de estudo são representativas dos principais impactos da agricultura nos recursos hídricos no estado. A área total das bacias hidrográficas de Arvorezinha, Júlio de Castilhos 1, Júlio de Castilhos 2, Conceição e Guaporé é de 1,19, 0,80, 1,43, 804,3 e 2.031 km², respectivamente. As fontes de sedimento avaliadas foram lavouras, pastagens, estradas e canais da rede de drenagem. A estratégia de amostragem de sedimentos incluiu coleta com amostradores do tipo integrador no tempo, sedimento de fundo e sedimento coletado durante eventos pluviométricos. A concentração de vários traçadores geoquímicos foram estimados nas amostras de sedimento e das fontes. Análises espectroscópicas foram realizadas na região do ultravioleta-visível, infravermelho próximo e infravermelho médio na bacia hidrográfica de Arvorezinha. A contribuição das fontes estimadas pelos métodos espectroscópicos foram similares às obtidas com traçadores geoquímicos. Além disso, a combinação de parâmetros de cor derivados da faixa espectral do visível pode ser uma alternativa rápida e de baixo custo para melhorar a discriminação das fontes e aumentar a precisão das predições. Os resultados demonstram que outros fatores além da proporção do uso do solo são importantes na produção do sedimento, como a distribuição das lavouras, florestas e estradas na paisagem. As florestas ripárias exercem um fator chave na erosão dos canais de drenagem. As estradas parecem ser fortemente dependentes da escala e do número de pontos em que cruzam os canais de drenagem. As lavouras, mesmo cultivadas sob plantio direto, ainda são as principais fontes de sedimentos nas bacias hidrográficas rurais do sul do Brasil. A quantidade de sedimento produzida nas lavouras que atinge a rede fluvial variou de 0.06 a 3.95 ton ha-1 ano-1. Essa variação é devida em parte às condições naturais intrínsecas de relevo e fortemente influenciada pelo uso e manejo do solo. A quantidade de sedimento erodida das lavouras ainda são muito elevadas para áreas de baixa susceptibilidade à erosão manejadas sob plantio direto, como na bacia hidrográfica do Conceição (1.30 ton ha-1 ano-1), indicando que maiores esforços ainda são necessários para reduzir a erosão do solo. Existe uma necessidade urgente de planejar a utilização e ocupação da terra nessas bacias, uma vez que os sistemas de manejo do solo utilizados pelos agricultores ainda são ineficientes para reduzir a erosão nas lavouras no sul do Brasil.

published_or_final_version / abstract / Civil Engineering / Doctoral / Doctor of Philosophy

<p>The aim of this study was to investigate the forensic usefulness of various Y-chromosome short tandem repeat loci among South African sub-populations. Three different sets of Y-chromosome short tandem repeat loci were chosen for investigation.</p>

Roseate spoonbills are colonial nesting birds with breeding grounds extending from the United States Gulf coast to the pampas of Argentina. The U.S. population suffered a severe bottleneck from 1890 to 1920. The population's recovery was slow and partially credited to migrations from Mexican rookeries, but a gene pool reduction would be expected. Five polymorphic Spoonbill autosomal short tandem repeat (STR) loci [three (GAT)n, one (AAAG)n and one (GT)n] and one Z/W-linked microsatellite exhibiting sex-specific dimorphism were isolated and characterized. The Z/W-linked STR locus accurately confirmed the sex of each bird. Allelic profiles for 51 spoonbills obtained from Dallas (Texas), Fort Worth (Texas) and Sedgwick County (Kansas) zoos revealed a non-continuous distribution of allele frequencies, consistent with the effects of a population bottleneck. Allelic frequencies also differed significantly between the isolated zoo populations. Although extra-pair copulations were suspected and difficult to document, zoos commonly used observational studies of mating pairs to determine familial relationships among adults and offspring. STR parentage analysis of recorded family relationships excluded one or both parents in 10/25 cases studied and it was further possible to identify alternative likely parents in each case. Mistaken familial relationships quickly lead to the loss of genetic variability in captive populations. Here, a decreased heterozygosity (HO) in 2nd generation captive-bred birds was observed at 3 out of 4 loci evaluated. Although these results could not be statistically validated because of the small number of individuals available for study (15 wild birds with no offspring vs. eight 2nd generation captive birds), they are considered biologically important, as decreased HO is an indicator of inbreeding and this apparent decrease occurred within two generations of removal from the wild. Collectively, the evidence obtained from this study suggests that captive spoonbill populations are experiencing rapid loss of diversity from an already depleted wild gene pool.

Sediments negatively impact the quality of surface waters and are a significant source of contaminants, such as nutrients and pesticides in agricultural watersheds. Sediment fingerprinting is a relatively recent technique capable of determining the origin of suspended sediment. In this thesis, we investigated the sources of suspended sediments in a predominantly rural watershed in Atlantic Canada. Our first objective was to determine sediment source apportionment estimates by treating the watershed as a single catchment, and making the assumption that conditions affecting source production and transport, from the land to the stream, were uniform across the watershed. For the first objective, suspended sediments were collected at a single target location for sediment apportionment (main outlet) and used to represent sediment dynamics throughout the entire catchment. For the second objective, we examined not only the whole watershed but also sub-watersheds within it, to better understand processes affecting sediment dynamics. / October 2016

FINGERPRINTING - PAST, PRESENT AND FUTURE The objective of this thesis is to present the forensic fingerprinting as a scientific method which, although in comparison with other forensic sciences being one of the oldest, is not out-dated at all, quite to the contrary - it presents an ever-changing and continuously developing field of science. The objective is approached through three distinctive and yet intertwined chapters corresponding with the title of the thesis - past, present and future of the fingerprinting. They are also designed, at least in part, to capture this constant forward motion. Accordingly, the first chapter aims to describe briefly scientific roots of the method, the way it drew in its beginnings from various scientific discoveries, inspired by the rise of Darwinism. Particular emphasis is put on the description of the formulation and empirical confirmation of three physiological laws of fingerprinting that even today serve as its grounds. The second chapter deals with and tries to describe the current state of knowledge and particular methods used in detection, development and preservation of fingerprints, especially latent ones. To do this it seems to be necessary to describe briefly the anatomy and physiology of friction ridge skin, as it enables to fully comprehend the way in...

L’érosion des sols est intense dans les petits bassins versants montagneux en climat tropical. Lorsqu’ils atteignent les rivières, ces sédiments posent divers problèmes à l’aval. L’identification des sources de sédiments et la compréhension de leur dynamique au sein des bassins versants est donc cruciale pour proposer des mesures de lutte efficaces contre ces problèmes. Cette thèse vise à tester et à développer des méthodes de traçage qui consistent à comparer les propriétés physico-chimiques des sols à celles des sédiments transportés dans les rivières pour en définir les sources et pour en contraindre les temps de transfert. Le site d’étude est un bassin de 22,4 km² au Laos équipé d’un emboîtement de stations de suivi et soumis à un régime de mousson. Trois campagnes de prélèvements ont permis de collecter des échantillons de sols de surface, de ravines et de berges ainsi que des eaux de pluies, de ruissellement et de rivières, les matières en suspension (MES) associées et des laisses, au cours de 3 crues de début de mousson en mai 2012 et juin 2013. Les échantillons ont été analysés afin de déterminer leurs activités en radionucléides apportés au sol par les pluies de manière ponctuelle (¹³⁷Cs) ou continue (⁷Be, ²¹ºPb), la teneur et la composition de la matière organique (C organique, N, C/N, δ¹³C et δ¹⁵N), la granulométrie des MES et la composition de l’eau (conductivité électrique, δ¹⁸O). Plusieurs expériences méthodologiques ont permis de tester et valider les hypothèses qui sous-tendent l’utilisation du marquage en ⁷Be et en excès de ²¹ºPb des sédiments (adsorption rapide sur les particules de sol, rapport ⁷Be / ²¹ºPbxs des particules transportées par le ruissellement comparable à celui de la pluie correspondante). Durant la crue de mai 2012, la contribution des sédiments récemment érodés est élevée en début d’événement (25-35%), mais elle est ensuite diluée par la remobilisation de particules déposées sur le lit du cours d’eau ou stockées dans les zones de dépôt. La caractérisation combinée du carbone organique particulaire (COP) et de l’activité en ¹³⁷Cs des particules a mis en évidence la prédominance de l’érosion des sols de surface marqués par leur signature C₃ à l’amont, et l’augmentation de la contribution de l’érosion des berges (marquage C₄) dans la partie aval du bassin. Les valeurs les plus élevées des taux d’exportation de sédiments (43,3 Mg km-2) et de C (0,83 MgC km-2), du coefficient de ruissellement (11,7%) et du pourcentage d’eau de ruissellement dans l’écoulement total (78-100%) ont été observées au niveau de la station drainant en grande partie des versants sous teck. Les teneurs en C mesurées et les flux de COP calculés ici sont beaucoup plus élevés que ceux qui ont été estimés lors de travaux réalisés il y a 10 ans dans le même bassin versant, lorsque la surface couverte de teck y était beaucoup plus faible (2,5% en 2002-2003 contre 32% en 2012). Ainsi, à l’aval, le taux d’exportation spécifique de C lors d’une seule crue en 2012 s’est révélé être 2,6 fois plus important que celui observé au cours de l’année hydrologique 2002-2003 (34 crues érosives). Lors des deux crues de juin 2013, la variabilité spatio-temporelle des retombées de ⁷Be et ²¹ºPb a pu être quantifiée. Ces résultats indiquent qu’il est indispensable de mesurer le signal d’entrée du marquage ⁷Be /²¹ºPb de chaque événement et qu’il est préférable de réaliser un échantillonnage en plusieurs points du bassin plutôt que de le fractionner en un seul point au cours du temps. Durant ces crues, la composition des sédiments a pu être étudiée le long d’un continuum de dix stations emboitées (0,1 ha à 19,8 km²). Les contributions respectives des différentes sources de sédiments, et leur propagation à travers le bassin, ont pu être déterminées à l’aide des mêmes traceurs que lors de la crue de mai 2012. À l’avenir, la combinaison de traceurs proposée dans cette thèse pourrait être appliquée à d’autres évènements ou d’autres sites. / Soil erosion is particularly intense in small mountainous tropical catchments. When supplied to the rivers, eroded sediment leads to numerous problems downstream (transfer of pollutants, increase of water turbidity, dam siltation…). Identifying sediment sources and understanding their dynamics across catchments constitutes a prerequisite to design and implement efficient measures to reduce these problems. This thesis aimed at testing and developing fingerprinting methods, by comparing physico-chemical properties of soils and riverine suspended sediment to define their origin and constrain their transfer across catchments. The study site is a 22.4 km² catchment in northern Laos equipped with nested monitoring stations and submitted to monsoon rainfalls. Three field campaigns were conducted to collect samples of surface soils, gullies, riverbanks, and rainwater, overland flow, river water, suspended matter and deposited sediment during three floods at the beginning of the monsoon in May 2012 and June 2013. Collected samples were analysed to determine fallout radionuclide activities (¹³⁷Cs, ⁷Be and ²¹ºPb), organic matter composition (organic carbon and nitrogen concentrations, C/N ratio, δ¹³C et δ¹⁵N), particle size distribution and water composition (electric conductivity and δ¹⁸O). Several methodological experiments were performed to check assumptions underlying the use of atmospheric 7Be and ²¹ºPb as tracers of sediment (quick adsorption of rainwater radionuclides to soil particles; similarity between /210Pbxs activity ratio measured in overland flow particles and corresponding rainfall signature). During the flood studied in May 2012, the contribution of recently eroded sediment was high at the beginning of the rising stage (25-35%), but was then diluted by sediment remobilization from the riverbed and deposition areas (swamps). The combined determination of particulate organic carbon (POC) and ¹³⁷Cs activity of sediment indicated the dominance of surface soil ( C₃ vegetation labelling) erosion in upstream parts and the increase of riverbank (labelled by C₄ plants) erosion contribution in the downstream part of the catchment. The highest runoff coefficient (11.7%), sediment specific yield (43.3 Mg km-2), total organic carbon specific yield (0.83 MgC km-2) and overland flow contribution (78–100%) were found at the station draining mainly the areas covered with teak plantations. Total organic carbon concentrations and POC specific yields calculated during this thesis are much higher than those obtained during a previous study carried out 10 years earlier in the same catchment, when teak plantations covered a much lower proportion of its area (2.5% in 2002-2003 vs 32% in 2012). At the downstream station, carbon specific yields for the studied flood in 2012 were twice higher than the annual ones observed in 2002-2003 (34 erosive events). During the two floods analysed in June 2013, the spatial and temporal variability of ⁷Be and ²¹ºPb wet deposition was investigated and quantified. The results indicate that the input signal of ⁷Be/²¹ºPb labelling associated with each storm should be determined and that spatially distributed collection of rainfall should be privileged to the sequential time-fractionated sampling at a single location. During these floods, the composition of exported suspended sediment could be studied along a continuum of ten nested stations draining areas between 0.1 ha and 19.8 km². Respective contributions of the different surface and subsurface sources of sediment and their propagation across the catchment, were successfully determined with the same tracers as during the May 2012 event. In future, the panel of parameters used in this thesis could be applied to characterise suspended matter behaviour during floods occurring later in the rainy season, or along a longer continuum of nested monitoring stations.

Rice blast disease is caused by the ascomycete fungus Magnaporthe oryzae and is of economic importance worldwide, due to its wide geographical distribution and the severe yield losses it causes on cultivated rice. Understanding the population structure of M. oryzae is key to sustainable management of blast disease. In this study, a total of 290 M. oryzae isolates were collected from rice growing regions in Kenya including Central Kenya (Mwea irrigation scheme), Western Kenya (Ahero and Maugo irrigation schemes in Ahero and Homa-Bay respectively) and Coastal Kenya (Kwale). Initially, I undertook genotyping of a subset of Kenyan isolates by DNA sequence analysis of the internal transcribed spacer regions (ITS 1 and ITS 2) of the rRNA-encoding gene unit and by DNA fingerprinting using the Pot2 repetitive DNA element. Phylogenetic analyses based on ITS sequences clustered together isolates from Western and Coastal Kenya which were distinct from Central Kenya isolates. Cluster analysis based on 80% DNA fingerprint similarity, identified five clonal lineages designated KL1, KL2, KL3, KL4 and KL5 with most isolates belonging to lineages KL2, KL3, KL4. The clustering of isolates was region specific with Western and Coastal isolates closely related to each other and distinct from Central Kenya isolates. Distribution of mating type gene loci (MAT1.1 and MAT1.2) was determined using mating type gene specific primers. My results indicate that MAT1.1 is the predominant mating type and is distributed in all the rice growing regions of Kenya. MAT1.2 isolates were identified only in Coastal Kenya. I further undertook high throughput next-generation DNA sequencing of the genomes of 27 M. oryzae isolates from sub-Saharan Africa (SSA), including Kenya, Uganda, Tanzania, Benin, Togo, Nigeria and Burkina Faso and compared them to other sequenced strains from China, India, USA, Philippines, Thailand, Korea, Japan, France and French Guiana. Single nucleotide polymorphisms (SNPs) indicated that majority of East African isolates of M. oryzae clustered separately from West African isolates. African isolates clustered with isolates from India and China, indicating that rice blast in SSA may have originated from Asia. Pathotype analysis of Kenyan isolates was undertaken using a set of monogenic differential rice varieties, collectively harbouring 24 disease resistance genes. Rice blast resistance gene Pi-z5 conferred resistance to all the isolates tested. Other resistance genes that conferred resistance to majority of isolates tested include Pi-9, Pi-12(t), Pi-ta, Pi-ta2 and Pi-z. These resistance genes are suitable candidates for introgressing into commercially grown varieties in Kenya in combinations. I also investigated the population of M. oryzae isolates to identify cognate avirulence gene loci, including novel genes not yet reported. Finally, I evaluated rice varieties grown in Kenya for resistance to indigenous rice blast isolates under laboratory conditions. Rice variety Basmati 370 was susceptible to rice blast with varieties IR2793-80-1, BW 196, NERICA 1, NERICA 4, NERICA 10, and NERICA 11 showing some disease resistance. Varieties ITA 310 and Duorado Precoce were moderately tolerant to rice blast. This information is being used to develop a durable blast resistance strategy in sub-Saharan Africa.