Revised; Originally Published: 2007 / 2 pp.

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Within the last decade antibiotic resistant bacteria have become a major public health concern. A possible major contribution to this problem is thought to be the overuse of antibiotics in food animals. An estimated 70% of antibiotics dispensed yearly throughout the United States are distributed to the livestock industry as growth promoters, prophylactic, and therapeutic treatments, according to the Center for Disease Control and FDA. When food animals are exposed to low doses of antibiotics frequently over a long period of time the bacteria are able to develop resistance to antibiotics. Livestock harbor foodborne pathogens that are generally commensal bacteria in the animals themselves but can cause illness to the people exposed. The problem occurs when treatment becomes difficult, there is some speculation that livestock animals are a main contributor to the increase in antibiotic resistant foodborne pathogens. Salmonella spp. and Staphylococcus aureus are pathogens that can be isolated from livestock and cause serious illness in humans. Objectives of this study include isolating S. aureus and Salmonella from samples collected from food animals, investigating the prevalence of antibiotic resistance in the confirmed S. aureus and Salmonella isolates from animals raised in various areas of Southern New Mexico and Arizona. In this study, samples were collected from various food animals post-harvest at a USDA inspected, non-commercial animal harvest facility in Arizona, and evaluated for the presence of S. aureus and Salmonella. Samples were collected from 129 animals of the following types: Bovine (cow), Caprine (goat), Ovine (sheep), and Porcine (pig). S. aureus and Salmonella were isolated from three different types of samples per animal including hide samples, sub iliac and mesenteric lymph nodes, and nasal swabs. Each sample was cultured separately in enrichment media followed by selective/differential media. Once the pathogen was confirmed via 16s rRNA PCR for S. aureus, invA3 PCR for Salmonella, gel electrophoresis, DNA Sequencing, and other biochemical tests, an antibiotic susceptibility test was performed to check the resistance characteristics of each isolate. The pathogen was exposed to eight different antibiotics- Ampicillin, Cefoxitin, Chloramphenicol, Ciprofloxacin, Erythromycin, Streptomycin, Sulfamethoxazole/Trimethoprim, and Tetracycline; commonly used among animals and humans via the disc diffusion assay. A total of 59 and 60 of 369 samples were confirmed positive for S. aureus and Salmonella, respectively. The animal type that harbored the most Salmonella overall were Bovine/cattle and the sample type that harbored the most Salmonella overall were lymph nodes. The animal type that harbored the most S. aureus overall were porcine/pigs and the sample type that harbored the most S. aureus overall were lymph nodes. 18 out of 129 livestock animals sampled in this study were found to carry both Salmonella and S. aureus and were isolated from: 6-Porcine, 5-Bovine, 5-Caprine, and 2-Ovine. The overall antibiotic resistance prevalence in S. aureus and Salmonella were 22.88% and 32.71%, respectively. Antibiotic resistance patterns were seen in both S. aureus and Salmonella isolated from all different livestock and sample types. Of these S. aureus isolates 43 showed resistance to at least one type of antibiotic, and the most resistance was seen to Ampicillin. 53 Salmonella isolates showed resistance to at least one type of antibiotic, and the most resistance was seen to Erythromycin. The implications of this study indicate that there are antibiotic resistant Staphylococcus aureus and Salmonella found in various food animals and sample types. Most of these Salmonella and S. aureus isolates were resistant to more than one antibiotic. Appropriate control measures are needed to mitigate the problem of antibiotic resistant bacteria among food animals. These control measures could also reduce the spread of resistance from one bacterium to another and possibly lessen the antibiotic resistance problem and infections.

Tick-borne encephalitis risk assessment based on classification of vegetation from remote sensing data Abstract The main aim of this thesis has been to find out how to classify various categories of forest vegetation with a different risk of exposure to the tick-borne encephalitis based on the Landsat imagery. The legend used here is derived from the one used in the projects by Daniel, Kolář, Zeman (1995) and Daniel, Kolář, Beneš (1999) but has been reduced to only five classses with no overlaps in their definitions (I. coniferous stands, II. mixed stands, III. young deciduous stands and stand ecotones with a highly heterogeneous structure, IV. deciduous stands with a homogeneous structure, V. deciduous stands with a heterogeneous structure). The supervised classification with the Maximum Likelihood Classifier has been used on the Landsat imagery from various seasons. Difficulties concerned with the presence of clouds and varying Sun elevation across the imagery had to be adressed in the course of the work. The training sites and the control points have been defined by the field research and interpretation of the relevant orthophotomaps and Landsat imagery in 5-4-3 RGB composite. The mask of the forest has been created on the ZABAGED data basis. The time horizon of 2006 - 2010 has been the primary focus....

The limited specificity, sensitivity and multiplex capacity of detection techniques currently available for important seed-borne pathogens of tomato is a significant risk for the global tomato trade and production industry. These pathogens can be associated with seed at low concentrations but, due to their highly virulent nature, these low levels can be sufficient to infect germinating seedlings and spread to neighbouring plants and fields, potentially causing epidemics and economic losses. In this study, detection techniques currently available for phytodiagnostics were evaluated for the capacity to accurately detect and identify five agronomically important seed-borne pathogens of tomato: Pepino mosaic virus (PepMV), Tomato mosaic virus (ToMV), Clavibacter michiganensis subsp. michiganensis (Cmm), Xanthomonas campestris pv. vesicatoria and Pseudomonas syringae pv. tomato. A prototype diagnostic microarray was also designed in an attempt to develop a tool that could simultaneously detect these five seed-borne pathogens from a single sample. Viral detection based on serological techniques was rapid, accurate and reliable but only detected a single pathogen per assay and required supplementary bioassays to indicate the viability of detected viral pathogens. Selective media plating for bacterial detection demonstrated unreliable recovery of targeted bacteria from infected seed and leaf samples and required supplementary tests to validate the identity of presumptive positives. Assays were lengthy, laborious and sometimes too ambiguous for accurate diagnosis of bacterial pathogens. Nucleic acid-based technologies demonstrated improved sensitivity and specificity for detection of targets from pure culture, leaf and seed extracts, compared to conventional and serological methods, yet also required supplementary bioassays or media assays to validate the viability of detected pathogens. Amplification efficiency however, was affected by the presence of PCR inhibitors and despite positive detection, variable banding intensity in electrophoretic analysis of amplified products necessitated the use of reference cultures to validate diagnosis. The developed microarray incorporated 152 pathogen-specific and control probes to facilitate diagnosis and taxonomic classification of detected pathogens. The array was challenged with pure culture extracts of the five target pathogens, selected related and non-target, unrelated pathogens of tomato. Positive detection of each of the pathogens was demonstrated but the production of hybridisation signals was highly variable and extremely sensitive to minor technical differences. Each of the five pathogens were successfully detected in combination proving that different classes of seed-borne pathogens could be detected from a single sample using the developed microarray. This prototype microarray has good potential for phytodiagnostic screening of the five targeted pathogens, and further validation, optimisation and extension for testing tomato seed samples may facilitate incorporation of this array into standard diagnostic protocols.

Railway induced ground-borne vibration is among the most common and widespread sources of perceptible environmental vibration, adversely impacting on human activity and the operation of sensitive equipment. The rising demand for building new railway lines or upgrading existing lines in order to meet increasing traffic flows has furthered the need for adequate vibration assessment tools during scheme planning and design. In recent years many studies of rail and ground dynamics have produced many vibration prediction techniques which have given rise to a variety of procedures for estimating rail-induced vibration on adjacent buildings. Each method shows potential for application at different levels of complexity and at different stages of a scheme. However, for the majority of the procedures significant challenges arise in obtaining the required input data, which can compromise their routine use in Environmental Impact Assessment (EIA). Moreover, as the majority of prediction procedures do not provide levels of uncertainty (i.e. expected spread of data), little is available on their effectiveness. Additionally, some procedures are restricted in that they require specific modelling approaches or proprietary software. Therefore, from an industrial point of view there is a need for a robust and flexible rail-induced vibration EIA procedure that can be routinely used with a degree of confidence. Based on an existing framework for assessing rail-induced vibration offered by the USA department of transportation (FTA) this project investigates, revises and establishes an empirical procedure capable of predicting rail-induced vibration in nearby buildings that can be routinely applied by the sponsoring company. Special attention is given to the degree of variability inherent to rail-induced vibration prediction, bringing forward the degrees of uncertainty, at all levels (i.e. measuring, analysis and scenario characterisation) that may impact on the procedure performance. The research shows a diminishing confidence when predicting rail-induced absolute vibration levels. It was found that ground-to-transducer coupling method, which is a critical step for acquiring data for characterising the ground, can impact on the results by as much as 10 dB. The ground decay rate, when derived through transfer functions, also showed to vary significantly in accordance to the assessment approach. Here it is shown the extent to which track conditions, which are difficult to account for, can affect predictions; variability in vibration levels of up to 10 dB, at some frequency bands, was found to occur simply due to track issues. The thesis offers general curves that represent modern UK buildings; however, a 15 dB variation should be expected. For urban areas, where the ground structure is significantly heterogeneous, the thesis proposes an empirical modelling technique capable of shortening the FTA procedure, whilst maintain the uncertainty levels within limits. Based on the finding and acknowledging the inherent degree of variability mentioned above, this study proposes a resilient empirical vibration analysis model, where its flexibility is established by balancing the significance of each modelling component with the uncertainty levels likely to arise due to randomness in the system.

Le travail présenté dans ce manuscrit est consacré à la restitution et à l’interprétation des profils verticaux derapports de mélange du chlorure d’hydrogène (HCl) et du formaldéhyde (H2CO) mesurés par l’instrumentsous ballon SPIRALE (SPectroscopie InfraRouge par Absorption de Lasers Embarqués), au cours de deuxvols effectués en région intertropicale depuis Teresina (Brésil, 5.1°S-42.9°S), le 22 Juin 2005 et le 9 Juin2008. Les problématiques scientifiques liées à l’étude de ces composés, les caractéristiques de la hautetroposphère et de la basse stratosphère intertropicale et enfin celles du spectromètre SPIRALE sontdécrites. L’étude de faisabilité de la mesure de H2CO a permis de définir la position et l’intensité de la raied’absorption la plus adéquate pour la mesure stratosphérique de ce composé (à 2912.1 et 1701.5 cm-1). Lesprofils verticaux de rapports de mélange de H2CO obtenus au cours de ces vols de SPIRALE sont présentéset comparés. Les mesures de HCl sont les premières à avoir été réalisées in situ dans la basse et moyennestratosphère intertropicale. Dans la couche de transition intertropicale, celles-ci sont utilisées en lien avecdes mesures récentes de composés à très courte durée de vie (VSLS), afin d’estimer la contribution deceux-ci au bilan du chlore stratosphérique. Dans la moyenne stratosphère, les signatures visibles sur lesprofils verticaux de HCl et sur ceux d’ozone acquis simultanément sont étudiées en lien avec l’oscillationquasi-biennale. En outre, le bon accord entre SPIRALE et l’instrument MLS du satellite Aura a permis deconforter la fiabilité de celui-ci pour la mesure de HCl. / The work presented in this manuscript is devoted to the retrieval and the interpretation of the mixing ratiovertical profiles of hydrogen chloride (HCl) and formaldehyde (H2CO), derived from the measurementsperformed by the SPIRALE balloon-borne instrument (SPectroscopie InfraRouge par Absorption de LasersEmbarqués) over Teresina (Brazil, 5.1°S-42.9°S), on 22 June 2005 and 9 June 2008. The scientificquestions associated with the study of these compounds, the characteristics of the tropical uppertroposphere and lower stratosphere and those of the SPIRALE spectrometer are described. The feasibilitystudy of the H2CO measurement has allowed to define the position and the intensity of the most suitableabsorption line for the stratospheric measurement of this compound (at 2912.1 and 1701.5 cm-1). The mixingratio vertical profiles of H2CO obtained during the SPIRALE flights are presented and compared. The HClmeasurements presented are the first to be made in situ in the lower and mid-stratosphere. In the tropicaltransition layer, they have been combined with recent very short-lived species (VSLS) ones in order toestimate the contribution of these compounds to the chlorine budget of the stratosphere. In the midstratosphere,the signatures present on the vertical profiles of HCl and ozone acquired simultaneously arestudied in connection with the quasi-biennal oscillation.

Nous nous intéressons dans ce travail à la dynamique des opérateurs de Schrödinger unidimensionnels, discrets, associés à un potentiel sturmien quasi-périodique. Le résultat principal de cette thèse est une borne supérieure pour les exposants de transport qui mesurent la vitesse de propagation du système. Cette borne, valide pour presque tous les potentiels sturmiens, est sous balistique pour une force de couplage suffisante. La validité de la borne est couplée à une condition diophantienne liée au nombre irrationnel qui définit le potentiel. Cette condition est vraie presque sûrement. Nous exhibons par ailleurs un exemple d’irrationnel pour lequel une borne supérieure sous balistique est impossible indépendamment de la force de couplage. Nous faisons l’étude de la dimension fractale du spectre de l’opérateur qui minore sous certaines conditions les exposants de transport. Nous obtenons une nouvelle borne inférieure pour la dimension de boîte du spectre grâce aux propriétés connues sur la forme du pseudo spectre. Les restrictions pour obtenir une borne dynamique à partir de notre résultat sont d’avoir une condition initiale cyclique standard et que le potentiel soit associé à un irrationnel à densité bornée. Enfin dans la dernière partie de ce travail, nous démontrons que le spectre de l’opérateur associé au nombre d’argent ß = [2, 2, . . . ] possède une structure hyperbolique. L’expression du pseudo spectre peut être vu comme un système dynamique. Nous conjuguons ledit système à une dynamique symbolique abstraite selon la méthode dite des partitions de Markov. Le système se comporte comme un fer à cheval de Smale. Nous dérivons de l’hyperbolicité des propriétés pour les dimensions fractales du spectre. Dimensions dont l’attrait dynamique a été rappelé dans la partie précédente. Nous déduisons notamment l’égalité des dimensions de Hausdorff et de boîte pour cet opérateur. / In this thesis, we study the dynamics of discrete, one-dimensional, sturmian Schrödinger operators. The main result is a dynamical bound from above for transport exponents that valuate speed of the wavepacket spreading. This bound is true for almost every sturmian potential and is sub-ballistic for a coupling constant big enough. This bound is valid with respect to a diophantine condition on the irrational number that define the potential. This condition is true for almost every irrational numbers. We show an example of irrational number with ballistic motion at any coupling constant. We study the fractal dimension of the spectrum of these operators which can bound from below, under more restrictive assumptions, transport exponents.We get a new bound from below for the box dimension of the spectrum. Assumptions needed to use this bound on dynamical purpose are the initial condition to be cyclic and the potential associated to a bounded means irrational number. In the last part of the thesis, we show that the spectrum of the operator associated to the so-called silver mean ß = [2, 2, . . . ] has a hyperbolic structure. The spectrum can be express as the non wandering set of a dynamical system. Using Markov partition method, we conjugate its dynamics to a symbolic one. The dynamical system behave like a Smale horseshoe. We derive from hyperbolicity spectral information, especially on fractal dimension. For example, we get that Hausdorff and box dimensions coincide for this operator.

Babesiosis is a disease caused by parasites of Babesia species that is spread through ticks. Babesiosis can affect humans and many other mammals all over the world. In the United States, babesiosis is mainly caused by Babesia microti with additional species of Babesia infecting dogs. Dogs have long been known to be a good indicator species for human tick-borne infection due to the shared spaces they have with humans and their tendency to explore and pick up diseases in the environment. This study used a group of hunting dogs to determine the presence of Babesia infection. The goal was to determine a predictive model for human infection. Infection was defined as having a positive antibody test or molecular test for Babesia species in blood samples. Blood samples were taken at two time points, tested, and compared. Statistical methods were used to analyze the results of the tests and compare them with variables such as region, gender, age, and other diseases the dogs were exposed to. Of 214 dogs, 56 had Babesia infections, with a prevalence rate of 26.2%. At the first time point the model showed age and infection with Anaplasma platys as being significant. At the 2nd time point, 29 dogs were lost to follow up, leaving a total of 185 dogs sampled with 63 testing positive for Babesia spp. The rate for the 2nd time point was 34.1%. No variables were found to be significant in the model for the 2nd time point. Despite differences in Babesia that infect humans and dogs, the hunting dog cohort reflects a model that validates the environmental exposures, coinfections, and demographic variables that affect transmission of the pathogen. Furthermore, findings of this study cast doubt on the ability of Ixodes scapularis to act as capable vector for canine-infecting Babesia species.