Дисертації з теми "Invasion time"

The naturalisation and subsequent spread of non-indigenous plant species (NIPS) is a major problem for most regions of the world. Managing plant invasions requires greater understanding of factors that determine initial naturalisation and distribution of wild NIPS. By the year 2000, 2252 NIPS were recorded as wild (1773 fully naturalised and 479 casual) in New Zealand. From published literature and electronic herbaria records, I recorded year of discovery of wild populations, and regional distribution of these wild NIPS. I also recorded species related attributes hypothesised to affect naturalisation and/or distribution, including global trade, human activities, native range and biological data; and regional attributes hypothesised to affect distribution, including human population densities, land use/cover, and environmental data. I used interval-censored time-to-event analyses to estimate year of naturalisation from discovery records, then analysed the importance of historical, human activity, biogeographical and biological attributes in determining patterns of naturalisation. Typically, NIPS that naturalised earlier were herbaceous, utilitarian species that were also accidentally introduced and/or distributed, with a wide native range that included Eurasia, naturalised elsewhere, with a native congener in New Zealand. In the year 2000, 28% of wild NIPS occupied only one region, 18% occupied two regions, decreasing incrementally to 2.5 % for nine regions, but with 13.5% occupying all ten regions. I used generalised linear models (GLMs) with binomial distribution to determine predictors of whether a wild NIPS occupied ten regions or not, and GLMs with Poisson distribution for wild NIPS occupying 0 – 9 regions. As expected, the dominant effect was that species discovered earlier occupied more regions. Utilitarian wild NIPS that were also accidentally introduced and/or distributed, and wild NIPS with a native congener tended to be more widely distributed, but results for other attributes varied between datasets. Although numbers of wild NIPS recorded in regions of New Zealand were sometimes similar, composition of wild NIPS was often very different. I used nonmetric multidimensional scaling (NMDS) to determine dissimilarity in composition between regions. Then, after reducing correlation between predictor variables using principal components analyses (PCAs), I tested the importance of regional variables in determining the regional composition of wild NIPS using metaMDS. The density of human populations best explained the dissimilarity in composition, but temperature gradients and water availability gradients were also important. In the year 2000 more than 1100 (60%) of the 1773 fully naturalised NIPS in mainland New Zealand had each been recorded in Northland/Auckland and Canterbury, and at the other end of the scale, Southland and Westland each had fewer than 500 (30%). I used GLMs to analyse the importance of people and environment in determining the numbers of wild NIPS in each region. Because I conducted multiple tests on the same dataset I used sequential Bonferroni procedures to adjust the critical P-value. Only human population density was important in explaining the numbers of NIPS in the regions. Overall, humans were the dominant drivers in determining the patterns of naturalisation and spread, although environment helps determine the composition of NIPS in regions. Incorporating human associated factors into studies of wild NIPS helps improve the understanding of the stages in the naturalisation and spread process.

Cette thèse porte sur l'étude de deux modèles stochastiques liés à des problèmes médicaux. Le premier vise à comprendre le processus épidémique généré par des bactériophages coopératifs dans une population de bactéries résistantes aux antibiotiques. Pour cela, nous introduisons un modèle épidémiologique où les infections sont générées par la coopération de parasites dans une population d'hôtes structurée selon un modèle de configuration. Une transition de phase est observée pour la probabilité d'invasion dépendant du degré de connectivité des sommets et du nombre de parasites générés lors d'une infection d'un hôte. Au seuil critique, la probabilité d'invasion est identifiée comme la probabilité de survie d'un processus de Galton-Watson.Dans le but d'obtenir un modèle biologiquement plus pertinent, nous avons analysé un modèle similaire où une structure spatiale est ajoutée à la population d'hôtes en utilisant un "random geometric graph". Nous avons montré qu'une telle structure spatiale facilite la coopération des parasites. Une transition de phase similaire se produit où au seuil critique, des bornes supérieure et inférieure sont obtenues pour la probabilité d'invasion en tant que probabilités de survie de deux processus de branchement avec coopération.La deuxième question médicale concerne la compréhension de l'évolution de la composition génétique d'une tumeur en formation, en utilisant des processus de naissance et de mort multitypes branchants sur un espace de traits fini. Considérant une évolution neutre et délétère, nous fournissons des résultats au premier ordre asymptotique pour toutes les tailles des sous-populations mutantes. En particulier, nous capturons la stochasticité associée aux tailles des sous-populations mutantes lorsqu'une tumeur est observée cliniquement, et surtout nous caractérisons les chemins évolutifs effectifs, fournissant des informations sur le passé, le présent et le futur de l'évolution tumorale.Au-delà de ce cadre restrictif d'évolution neutre et délétère, nous proposons une nouvelle méthode pour comprendre le premier ordre asymptotique du premier trait mutant sélectif
This thesis focuses on the study of two stochastic models related to medical problems. The first one lies on understanding infection spread of cooperating bacteriophages on a structured multi-drug resistant bacterial host population. Motivated by this example, we introduce an epidemiological model where infections are generated by cooperation of parasites in a host population structured on a configuration model. We analysed the invasion probability for which we obtain a phase transition depending on the connectivity degree of the vertices and the offspring number of parasites during an infection of a host. At the critical scaling, the invasion probability is identified as the survival probability of a Galton-Watson process. With the aim to get a biological more relevant model, we analysed a similar model where a spatial structure is added for the host population using a random geometric graph. We have shown that such spatial structure facilitates cooperation of parasites. A similar phase transition occurs where at the same critical scaling the invasion probability is upper and lower bounded by the survival probabilities of two discrete branching processes with cooperation. The second medical question deals with understanding the evolution of the genetic composition of a tumor under carcinogenesis, using multitype birth and death branching process models on a general finite trait space. In the case of neutral and deleterious cancer evolution, we provide first-order asymptotics results on all mutant subpopulation sizes. In particular such results capture the randomness of all cell trait sizes when a tumor is clinically observed, and mostly it allows to characterize the effective evolutionary pathways, providing information on the past, present, and future of tumor evolution.Moving beyond this restrictive neutral and deleterious cancer evolution framework, we provide a new method to understand the first selective mutant trait size

In this study, we have demonstrated that the preproghrelin derived hormones, ghrelin and obestatin, may play a role in ovarian cancer. Ghrelin and obestatin stimulated an increase in cell migration in ovarian cancer cell lines and may play a role in cancer progression. Ovarian cancer is the leading cause of death among gynaecological cancers and is the sixth most common cause of cancer-related deaths in women in developed countries. As ovarian cancer is difficult to diagnose at a low tumour grade, two thirds of ovarian cancers are not diagnosed until the late stages of cancer development resulting in a poor prognosis for the patient. As a result, current treatment methods are limited and not ideal. There is an urgent need for improved diagnostic markers, as well better therapeutic approaches and adjunctive therapies for this disease. Ghrelin has a number of important physiological effects, including roles in appetite regulation and the stimulation of growth hormone release. It is also involved in regulating the immune, cardiovascular and reproductive systems and regulates sleep, memory and anxiety, and energy metabolism. Over the last decade, the ghrelin axis, (which includes the hormones ghrelin and obestatin and their receptors), has been implicated in the pathogenesis of many human diseases and it may t may also play an important role in the development of cancer. Ghrelin is a 28 amino acid peptide hormone that exists in two forms. Acyl ghrelin (usually referred to as ghrelin), has a unique n-octanoic acid post-translational modification (which is catalysed by ghrelin O-acyltransferase, GOAT), and desacyl ghrelin, which is a non-octanoylated form. Octanoylated ghrelin acts through the growth hormone secretagogue receptor type 1a (GHSR1a). GHSR1b, an alternatively spliced isoform of GHSR, is C-terminally truncated and does not bind ghrelin. Ghrelin has been implicated in the pathophysiology of a number of diseases Obestatin is a 23 amino acid, C-terminally amidated peptide which is derived from preproghrelin. Although GPR39 was originally thought to be the obestatin receptor this has been disproven, and its receptor remains unknown. Obestatin may have as diverse range of roles as ghrelin. Obestatin improves memory, inhibits thirst and anxiety, increases pancreatic juice secretion and has cardioprotective effects. Obestatin also has been shown to regulate cell proliferation, differentiation and apoptosis in some cell types. Prior to this study, little was known regarding the functions and mechanisms of action ghrelin and obestatin in ovarian cancer. In this study it was demonstrated that the full length ghrelin, GHSR1b and GOAT mRNA transcripts were expressed in all of the ovarian-derived cell lines examined (SKOV3, OV-MZ-6 and hOSE 17.1), however, these cell lines did not express GHSR1a. Ovarian cancer tissue of varying stages and normal ovarian tissue expressed the coding region for ghrelin, obestatin, and GOAT, but not GHSR1a, or GHSR1b. No correlations between cancer grade and the level of expression of these transcripts were observed. This study demonstrated for the first time that both ghrelin and obestatin increase cell migration in ovarian cancer cell lines. Treatment with ghrelin (for 72 hours) significantly increased cell migration in the SKOV3 and OV-MZ-6 ovarian cancer cell lines. Ghrelin (100 nM) stimulated cell migration in the SKOV3 (2.64 +/- 1.08 fold, p <0.05) and OV-MZ-6 (1.65 +/- 0.31 fold, p <0.05) ovarian cancer cell lines, but not in the representative normal cell line hOSE 17.1. This increase in migration was not accompanied by an increase in cell invasion through Matrigel. In contrast to other cancer types, ghrelin had no effect on proliferation. Ghrelin treatment (10nM) significantly decreased attachment of the SKOV3 ovarian cancer cell line to collagen IV (24.7 +/- 10.0 %, p <0.05), however, there were no changes in attachment to the other extracellular matrix molecules (ECM) tested (fibronectin, vitronectin and collagen I), and there were no changes in attachment to any of the ECM molecules in the OV-MZ-6 or hOSE 17.1 cell lines. It is, therefore, unclear if ghrelin plays a role in cell attachment in ovarian cancer. As ghrelin has previously been demonstrated to signal through the ERK1/2 pathway in cancer, we investigated ERK1/2 signalling in ovarian cancer cell lines. In the SKOV3 ovarian cancer cell line, a reduction in ERK1/2 phosphorylation (0.58 fold +/- 0.23, p <0.05) in response to 100 nM ghrelin treatment was observed, while no significant change in ERK1/2 signalling was seen in the OV-MZ-6 cell line with treatment. This suggests that this pathway is unlikely to be involved in mediating the increased migration seen in the ovarian cancer cell lines with ghrelin treatment. In this study ovarian cancer tissue of varying stages and normal ovarian tissue expressed the coding region for obestatin, however, no correlation between cancer grade and level of obestatin transcript expression was observed. In the ovarian-derived cell lines studied (SKOV3, OV-MZ-6 and hOSE 17.1) it was demonstrated that the full length preproghrelin mRNA transcripts were expressed in all cell lines, suggesting they have the ability to produce mature obestatin. This is the first study to demonstrate that obestatin stimulates cell migration and cell invasion. Obestatin induced a significant increase in migration in the SKOV3 ovarian cancer cell line with 10 nM (2.80 +/- 0.52 fold, p <0.05) and 100 nM treatments (3.12 +/- 0.68 fold, p <0.05) and in the OV-MZ-6 cancer cell line with 10 nM (2.04 +/- 0.10 fold, p <0.01) and 100 nM treatments (2.00 +/- 0.37 fold, p <0.05). Obestatin treatment did no affect cell migration in the hOSE 17.1normal ovarian epithelial cell line. Obestatin treatment (100 nM) also stimulated a significant increase in cell invasion in the OV-MZ-6 ovarian cancer cell line (1.45 fold +/- 0.13, p <0.05) and in the hOSE17.1 normal ovarian cell line cells (1.40 fold +/- 0.04 and 1.55 fold +/- 0.05 respectively, p <0.01) with 10 nM and 100 nM treatments. Obestatin treatment did not stimulate cell invasion in the SKOV3 ovarian cancer cell line. This lack of obestatin-stimulated invasion in the SKOV3 cell line may be a cell line specific result. In this study, obestatin did not stimulate cell proliferation in the ovarian cell lines and it has previously been shown to have no effect on cell proliferation in the BON-1 pancreatic neuroendocrine and GC rat somatotroph tumour cell lines. In contrast, obestatin has been shown to affect cell proliferation in gastric and thyroid cancer cell lines, and in some normal cell lines. Obestatin also had no effect on attachment of any of the cell lines to any of the ECM components tested (fibronectin, vitronectin, collagen I and collagen IV). The mechanism of action of obestatin was investigated further using a two dimensional-difference in gel electrophoresis (2D-DIGE) proteomic approach. After treatment with obestating (0, 10 and 100 nM), SKOV3 ovarian cancer and hOSE 17.1 normal ovarian cell lines were collected and 2D-DIGE analysis and mass spectrometry were performed to identify proteins that were differentially expressed in response to treatment. Twenty-six differentially expressed proteins were identified and analysed using Ingenuity Pathway Analysis (IPA). This linked 16 of these proteins in a network. The analysis suggested that the ERK1/2 MAPK pathway was a major mediator of obestatin action. ERK1/2 has previously been shown to be associated with obestatin-stimulated cell proliferation and with the anti-apoptotic effects of obestatin. Activation of the ERK1/2 signalling pathway by obestatin was, therefore, investigated in the SKOV3 and OV-MZ-6 ovarian cancer cell lines using anti-active antibodies and Western immunoblots. Obestatin treatment significantly decreased ERK1/2 phosphorylation at higher obestatin concentrations in both the SKOV3 (100 nM and 1000 nM) and OV-MZ-6 (1000 nM) cell lines compared to the untreated controls. Currently, very little is known about obestatin signalling in cancer. This thesis has demonstrated for the first time that the ghrelin axis may play a role in ovarian cancer migration. Ghrelin and obestatin increased cell migration in ovarian cancer cell lines, indicating that they may be a useful target for therapies that reduce ovarian cancer progression. Further studies investigating the role of the ghrelin axis using in vivo ovarian cancer metastasis models are warranted.

De nos jours, les traitements mini-invasifs, tels que l'ablation par radiofréquence, sont de plus en plus utilisés car ils permettent d'éliminer localement les tumeurs à partir de l'insertion d'une aiguille. Cependant, le succès de ces procédures dépend de la précision du positionnement de l'aiguille par rapport aux structures anatomiques. Afin de garantir un placement correct, l'imagerie échographique est souvent utilisée car elle a l'avantage d'être temps-réelle, bas coût, et non-invasive. En revanche, celle modalité peut compliquer la visualisation de certaines structures en raison de sa qualité et de son champ de vue limité. En outre, la précision des interventions peut aussi être perturbée par les déplacements de tissus liés aux mouvements physiologiques du patient et à la manipulation d'instruments médicaux. Afin d'aider le chirurgien à mieux cibler certaines structures anatomiques, de nombreuses équipes de recherche ont proposé des travaux permettant d'estimer la position de régions d'intérêts dans l'imagerie échographique. Cette thèse propose plusieurs contributions permettant de suivre en temps réel des structures déformables dans des séquences d'échographie 3D. Une première contribution repose sur l'utilisation conjointe de l'information visuelle dense et d'une méthode de simulation physique. Dans cette thèse, nous avons aussi proposé un nouveau critère de similarité spécifique à l'imagerie échographique basé sur une étape de détection d'ombres. Enfin, la dernière contribution est liée à une stratégie de suivi hybride permettant d'améliorer la qualité des images. A partir de ces contributions, nous proposons une méthode de suivi robuste au bruit de type« speckle », aux ombres et aux changements d'intensité perturbant l'imagerie échographique. Les performances des différentes contributions sont évaluées à partir de données simulées et de données acquises sur maquettes et sur volontaires humains. Ces résultats montrent que notre méthode est robuste à différents artefacts de l'imagerie échographique. En outre, nous démontrons la performance de notre approche par rapport à différentes méthodes de l'état de l'art sur des bases de données publiques fournies par les challenges MICCAI CLUST'14 et CLUST'15. Dans cette thèse, nous proposons également une application permettant de combiner l'imagerie échographique à l'imagerie par résonance magnétique (IRM). Cette méthode permet d'observer des structures anatomiques non-visibles dans l'imagerie échographique durant l'intervention. Elle est basée sur la combinaison d'une méthode de suivi et d'un recalage multi-modal obtenu à partir d'un système de localisation externe. Cette application a été évaluée sur un volontaire sain à partir d'une plateforme liée au centre Hospitalier Universitaire de Rennes
Nowadays, mini-invasive treatments, such as radio-frequency ablation, are increasingly being used because they allow eliminating tumors locally from needle insertion. However, the success of these therapies depends on the accurate positioning of the needle with respect to anatomical structures. To ensure correct placement, ultrasound (US) imaging is often used since this system has the advantage to be real-time, low-cost, and non-invasive. However, during the intervention, US imaging can complicate the visualization of targeted structures due to its poor quality and its limited field of view. Furthermore, the accuracy of these interventions may also be perturbed by both physiological movements and medical tools displacements that introduce motions of anatomical structures. To help the surgeon to better target malignant tissues, many research teams have proposed different method in order to estimate the position of regions of interest in ultrasound imaging. This thesis provides several contributions that allow tracking deformable structures in 3D ultrasound sequences. We first present a method that allows providing robust estimation of target positions by combining an intensity-based approach and mechanical model simulation. In this thesis, we also propose novel ultrasound-specific similarity criterion based on prior step that aims at detecting shadows. The last contribution is related to a hybrid tracking strategy that allows improving quality of ultrasound images. From these contributions, we propose a tracking method that has the advantage to be invariant to speckle noise, shadowing and intensity changes that can occur in US imaging. The performance and limitations of the proposed contributions are evaluated through simulated data, phantom data, and real-data obtained from different volunteers. Simulation and phantom results show that our method is robust to several artefacts of US imaging such as shadows and speckle decorrelation. Furthermore, we demonstrate that our approach outperforms state-of-the-art methods on the 3D public databases provided by MICCAI CLUST'14 and CLUST'15 challenges. In this thesis, we also propose an application that combines ultrasound imaging to Magnetic Resonance lmaging (MRI). This method allows observing anatomical structures that are not visible in US imaging during the intervention. It is based on the combination between US tracking method and multi modal registration obtained from external localization system. This application was evaluated on a volunteer thanks to an MRJ imaging platform locate at the University Hospital of Rennes

Biological invasions are rapidly gaining importance due to the ever-increasing number of introduced species. Alongside the plenitude of empirical data on invasive species there exists an equally broad range of mathematical models that might be of use in understanding biological invasions. This thesis aims to address several issues related to modelling invasive species and provide insight into their dynamics. Part I (Chapter 2) documents a case study of the gypsy moth, Lymantria dispar, invasion in the US. We propose an alternative hypothesis to explain the patchiness of gypsy moth spread entailing the interplay between dispersal, predation or a viral infection and the Allee effect. Using a reaction-diffusion framework we test the two models (prey-predator and susceptible-infected) and predict qualitatively similar patterns as are observed in natural populations. As high density gypsy moth populations cause the most damage, estimating the spread rate would be of help in any suppression strategy. Correspondingly, using a diffusive SI model we are able to obtain estimates of the rate of spread comparable to historical data. Part II (Chapters 3, 4 and 5) is more methodological in nature, and in a single species context we examine the effect of an ubiquitous phenomenon influencing population dynamics time delay. In Chapter 3 we show that contrary to the general opinion, time delays are not always destabilising, using a delay differential equation with discrete time delay. The concept of distributed delay is introduced in Chapter 4 and studied through an integrodifferential model. Both Chapters 3 and 4 focus on temporal dynamics of populations, so we further this consideration to include spatial effects in Chapter 5. Using two different representations of movement, we show that the onset of spatiotemporal chaos in the wake of population fronts is possible in a single species model.

A endometriose é uma doença de origem multifatorial, caracterizada por presença de tecido endometrial fora da cavidade uterina, responsável por sintomas álgicos com grande impacto na qualidade de vida da paciente, além de ser um dos principais fatores de infertilidade. Muitos estudos já foram realizados no intuito de explicar a etiopatogenia da endometriose, assim como muito tem sido estudado para encontrar novas estratégias de tratamento. Várias linhas de medicamentos têm sido estudadas com este intuito, agindo em diferentes pontos da etiopatogênese da doença, uma delas na inibição de metaloproteinases da matriz extracelular, que tem papel no remodelamento do mesotélio do peritônio e angiogênese. O objetivo deste estudo foi avaliar a influência de uma droga (doxiciclina) de baixo custo, com ação conhecida na inibição das metaloproteinases, em endometriose peritoneal induzida em ratas. Para isso, foram usadas 30 ratas adultas Wistar com lesão induzida de endometriose, divididas em três grupos, um grupo controle (C, n=10) sem tratamento, um grupo onde foi administrado doxiciclina em baixa dose (BD, n=10) e um grupo onde foi realizado doxiciclina em alta dose (AD, n=10). Foi realizada avaliação da área das lesões de cada rata e estudo imunohistoquímico para positividade de anticorpo primário de metaloproteinase de matriz 9 (MMP9) e de inibidor de metaloproteinase de matriz 2 (TIMP2). A doxiciclina atuou reduzindo a área das lesões nos grupos BD e AD (p=0,0052) em relação ao grupo C e reduzindo a expressão do TIMP2 no grupo AD (p=0,0009) em relação aos grupos BD e C. Não houve resultado significativo na expressão da MMP9.
Endometriosis is a multifactorial origin disease, characterized by the presence of endometrial tissue outside the uterine cavity, responsible for painful symptoms with important impact on the life quality of the patient, besides being one of the main factors of infertility. Many studies have already been carried out to explain the etiopathogenesis of endometriosis, and much has been studied to find new treatment strategies. Several lines of drugs have been studied for this purpose, acting at different points in the etiopathogenesis of the disease, one of them in the inhibition of extracellular matrix metalloproteinases, which plays a role in the remodeling of the peritoneum mesothelium and angiogenesis. The purpose of this study was to evaluate the influence of a low-cost drug (doxycycline), with known action on the inhibition of metalloproteinases, in induced peritoneal endometriosis in rats. Thirty adult Wistar rats with endometriosis-induced lesions were divided into three groups: one untreated control group (C, n = 10), one group receiving low dose doxycycline (BD, n = 10) and a group where high dose doxycycline (AD, n = 10) was performed. An evaluation of the lesion area of each rat and immunohistochemical study for primary antibody to matrix metalloproteinase 9 (MMP9) and matrix metalloproteinase inhibitor 2 (TIMP2) was performed. Doxycycline worked by reducing the area of lesions in the BD and AD groups (p = 0.0052) in relation to the C group and reducing the expression of TIMP2 in the AD group (p = 0.0009) in relation to the BD and C groups. There was no significant effect on MMP9 expression in the present study.

Wood-boring beetles are a cause of significant economic and environmental cost across the world. A number of species which are not currently found in the United Kingdom are constantly at risk of being accidentally imported due to the volume of global trade in trees and timber. The species which are of particular concern are the Asian Longhorn (Anoplophora glabripennis), Citrus Longhorn (A. chinensis) and Emerald Ash Borer (Agrilus planipennis). The Food and Environment Research Agency's plant health inspectors currently manually inspect high risk material at the point of import. The development of methods which will enable them to increase the probability of detection of infestation in imported material are therefore highly sought after. This thesis describes research into improving acoustic larvae detection and species identification methods, and the development of a real-time system incorporating them. The detection algorithm is based upon fractal dimension analysis and has been shown to outperform previously used short-time energy based detection. This is the first time such a detection method has been applied to the analysis of insect sourced sounds. The species identification method combines a time domain feature extraction technique based upon the relational tree representation of discrete waveforms and classification using artificial neural networks. Classification between two species, A. glabripennis and H. bajulus, can be performed with 92% accuracy using Multilayer Perceptron and 96.5% accuracy using Linear Vector Quantisation networks. Classification between three species can be performed with 88.8% accuracy using LVQ. A real-time hand-held PC based system incorporating these methods has been developed and supplied to FERA for further testing. This system uses a combination of dual piezo-electric based USB connected sensors and custom written software which can be used to analyse live recordings of larvae in real-time or use previously recorded data.

Abstract Bladder cancer when superficial has a good prognosis but it has a high recurrence risk and about 10–15% of the superficial carcinomas will progress into muscle invasive or metastatic type. The most powerful factor for predicting the behavior of bladder carcinoma is the stage of the tumor. Invasion to the lamina propria increases the risk of recurrence and progress to muscle-invasive tumor. Also grade of the tumor and tumor multiplicity associates with high risk for recurrence. New markers are still needed to find those patients who need more and better treatments to avoid the recurrence and progress. The need for new non-invasive markers to diminish the need for frequent cystoscopy in follow-up is also obvious. Gelatinases MMP-2 and MMP-9 are known to associate to tumor invasion and progression. Also their tissue inhibitors TIMP-1 and TIMP-2 take part in these diversified processes and metastasis formation. In the present work the expression and clinical value of gelatinases MMP-2 and MMP-9 and their tissue inhibitors TIMP-1 and TIMP-2 were evaluated in bladder carcinoma. Primary tissue samples of 121 patients were analyzed for expression of MMP-2 and/or MMP-9 using immunohistochemistry. The serum samples of 87 patients who were treated in the Oncology Department of Oulu University Hospital were collected and studied with ELISA. The control group consisted of 44 healthy volunteers. Overexperssion of MMP-2 protein correlated significantly to disease-specific survival and showed an independent prognostic value as a biomarker. High MMP-9 expression instead correlated to favorable overall survival of bladder cancer patients. Circulating proMMP-2, TIMP-2 and MMP-2:TIMP-2 complex levels were lower in cancer patients than in healthy volunteers in control group. High levels of all these three markers correlated with better prognosis in bladder cancer patients.

Streptococcus pneumoniae (S. pneumoniae) és un colonitzador habitual del tracte respiratori superior dels humans. Es tracta d’un patogen comú de l’espècie humana que presenta una elevada taxa de morbiditat i mortalitat arreu del món. El bacteri pot causar otitis mitjana, sinusitis o infeccions de tracte respiratori superior, (per contigüitat) però també pot causar malaltia invasiva, quan habita en un territori habitualment estèril, produint pneumònia, bacterièmia, septicèmies i meningitis, entre d’altres. La malaltia pneumocòccica és un important problema de salut pública i és la principal causa individual de mortalitat infantil en el món. Segons dades de la Organització Mundial de la Salut (OMS), s’estima que a l’any 2000 es van produir 14.5 milions d’episodis greus de malaltia pneumocòccica, que va resultar en 826 000 morts en nens menors de dos anys. Un 61% d’aquestes morts es van produir a l’Àfrica subsahariana i al sud-est asiàtic. Tanmateix, en aquests països i, en especial a les zones rurals, les capacitats de diagnòstic són limitades o inexistents i la identificació de l’agent etiològic es basa en signes i símptomes clínics. És molt important aïllar l’agent etiològic causant de malaltia per tal de poder avaluar el millor tractament possible. No obstant, les tècniques actuals per al diagnòstic de la malaltia presenten una limitada sensibilitat i especificitat. El cultiu microbiològic, com a mètode de diagnòstic clàssic, té una baixa sensibilitat per a detectar el pneumococ. L’objectiu d’aquesta tesi és avaluar el potencial de les tècniques moleculars per al diagnòstic i caracterització de la malaltia pneumocòccica i discernir si l’ús de tècniques moleculars com la reacció en cadena de la polimerasa (PCR) poden suposar un avantatge tant per la rapidesa del mètode com per la detecció del patogen present en una mostra a baixa concentració. L’aplicació d’aquest tipus de tècniques en mostres biològiques impregnades en paper de filtre (dried-spot) i conservades a temperatura ambient poden ser un excel•lent sistema per a la detecció i serotipat de S. pneumoniae en països en vies de desenvolupament on la falta de recursos econòmics esdevé una de les principals limitacions. La capacitat del pneumococ de causar malaltia depèn de la presència d’una càpsula polisacàrida que impedeix la fagocitosi. Tot i que la presència de la càpsula és un requisit perquè produeixi malaltia, no és suficient per conferir virulència, sinó que són necessaris una varietat de factors determinants addicionals, com ara les adhesines, les proteases, les toxines, els sistemes de transport i enzims que modifiquen el medi extracel•lular. Recentment, s’ha descobert un determinant de virulència del pneumococ que és la proteïna rica en repeticions de serina, PsrP (Pneumococcal-serine rich protein). Es tracta d’una adhesina que intervé en l’adhesió del pneumococ a les cèl•lules pulmonars. PsrP és un important factor de virulència capaç de causar malaltia i un potencial candidat a una nova vacuna proteica.
Streptococcus pneumoniae (S. pneumoniae) is a common colonizer of the upper respiratory tract of humans. This is a major human pathogen and leading cause of morbidity and mortality worldwide. The bacteria can cause otitis media, sinusitis or upper respiratory tract infections (contiguity) but can also cause invasive disease, when living in an area usually sterile, causing pneumonia, bacteraemia, sepsis and meningitis, among others. According to the World Health Organization, in 2000, pneumococcal disease was estimated to have caused about 14.5 million severe episodes. There were approximately 826 000 deaths from pneumococcal disease in children under five years and 61% of these deaths occurred in sub-Saharan Africa and Southeast Asia. However, in these countries, especially in rural areas, diagnostic capabilities are limited or nonexistent and agent identification is based on clinical signs and symptoms. It is very important to isolate the etiologic agent of disease in order to assess the best treatment possible. However, present techniques for the diagnosis of the disease have a limited sensitivity and specificity. Microbiological culture, considered the “gold-standard” in microbiological diagnosis has low sensitivity to detect pneumococcus. The aim of this Thesis is to evaluate the potential of molecular techniques for diagnosis and characterization of pneumococcal disease and to discern whether the use of molecular techniques such as PCR, can be an advantage both for the speed of method as for the detection of the pathogen present in a sample in low concentration. The application of these techniques in biological samples impregnated filter paper (dried-spot) and kept at room temperature can be an excellent system for the detection and serotyping of S. pneumoniae in developing countries where lack of financial resources is a major constraint. The ability of the pneumococcus to cause disease depends on the presence of a polysaccharide capsule that prevents phagocytosis. Although the presence of the capsule is a requirement to produce disease, is not sufficient to confer virulence, but need a large number of additional factors such as adhesins, proteases, toxins, transportation systems and enzymes that modify the extracellular medium. One recently identified pneumococcal virulence determinant is the pneumococcal serine-rich repeat protein (PsrP). This is an adhesin involved in adherence of pneumococci to lung cells. PsrP is an important virulence factor capable of causing disease and a potential new vaccine candidate protein.

Thesis (PhD (Botany and Zoology))--University of Stellenbosch, 2009.
ENGLISH ABSTRACT: Although the impacts of biological invasions are widely appreciated, a bias exists in research effort to post‐dispersal processes because of the difficulties of measuring propagule pressure and the detecting of newly established species. Here the Antarctic is used as a model system in which to quantify the initial dispersal of alien species and investigate the factors that contribute to the establishment and range dynamics of alien species once they have arrived in the region. Human movements are known to transport alien species into the Antarctic, some of which have successfully established and had wide ranging consequences in recipient ecosystems. Considering terrestrial flora, this research found that over 700 seeds from 99 taxa, including some species known to be invasive, are transported into the Antarctic each year in association with South African National Antarctic Programme (SANAP) passenger luggage and cargo. The first ever assessment of propagule drop‐off indicated that 30‐50% of these propagules will enter the recipient environment. Further results suggested that the construction of the British Antarctic Survey Halley VI station will facilitate the transport of over 5000 seeds from 34 taxa into the region, making this a significant pathway for introductions. Propagule pressure due to SANAP logistics is also considerable for marine species. Fouling assemblages on the external hull surfaces of the SANAP resupply vessel, the SA Agulhas, form only once the vessel’s anti‐fouling paint has been damaged by travel through sea ice and are characterised by low diversity. Ice scour prevents fouling assemblages from being transported to the Antarctic continent, but assemblages remain largely intact when travelling to sub‐Antarctic Islands. In the sea‐chests of the vessel populations of a known invasive, Mytilus galloprovincialis, were found with some individuals having survived transportation to the Antarctic region on multiple occasions. Once species have overcome initial dispersal barriers, they face further ecological and physiological challenges in order to establish in the recipient region. The parasitoid wasp Aphidius matricariae was first recorded on Marion Island in 2001. Surveys around the island show that adult abundance and the frequency of aphid parasitism are highest adjacent to a common anchor point of the SA Agulhas and decline away from this region. Genetic diversity was low, suggesting that the population was established from a single introduction. This highlights that high propagule pressure is not necessary for successful establishment of introduced invertebrates. Another species that has overcome the dispersal barrier is the terrestrial slug Deroceras panormitanum, which was introduced to Marion Island in the 1970’s and has since spread throughout much of the coastal habitat of the island. For this species range limits are set by intolerance of low temperature and salinity, and abundance structure is characterized by patches and gaps which are associated with this species inability to tolerate dry conditions. To prevent further alien introductions in the region, targeted management of high risk pathways is required. In addition, increased vigilance is needed to detect and manage newly established aliens before their ranges expand.
AFRIKAANSE OPSOMMING: Alhoewel die impak van biologiese indringings in die breë waardeer word, bestaan daar vooroordeel in navorsingspogings ten opsigte van na‐verspreidingsprosesse, weens die moeilikhede om verspreidingseenheid druk te meet en in die opsporing van nuut gevestigde spesies. Hier word die Antarktiese streek as ‘n model sisteem gebruik waarin die aanvanklike verspreiding van uitheemse spesies gekwantifiseer kan word en om die faktore wat bydrae tot die vestiging en grens dinamika van uitheemse spesies te ondersoek, wanneer hulle in ’n streek aangekom het. Menslike bewegings is bekend daarvoor om uitheemse spesies na die Antarktiek te vervoer, sommige waarvan suksesvol gevestig het en omvattende gevolge in die ontvanger ekosisteme gehad het. Aangaande terrestriële flora het hierdie navorsing gevind dat oor die 700 sade van 99 taxa, insluitende sommige spesies wat bekend is om indringend te wees, jaarliks na die Antarktiek vervoer word in assosiasie met die Suid Afrikaanse Nasionale Antarktiese Program (SANAP) se bagasie en vrag. Die eerste waardebepaling van verspreidingseenheid afgooi het aangedui dat 30‐50% van hierdie verspreidingseenhede die ontvanger omgewing sal binnedring. Verdere resultate het voorgestel dat die konstruksie van die Britse Antarktiese Opname Halley VI stasie die vervoer van 5000 sade van 34 taxa sal fasiliteer die streek in, wat dit ’n betekenisvolle weg maak vir indringings. Verspreidingseenheid druk is ook, as gevolg van die SANAP logistiek, aanmerklik vir mariene spesies. Vuilgoed versamelings op die eksterne omhullende oppervlaktes van die SANAP her‐voorsieningsvaartuig, die SA Agulhas, vorm wanneer die vaartuig se anti‐vuilgoed verf beskadig is met reis deur see‐ys en word gekenmerk deur lae diversiteit. Ys skuring voorkom dat vuilgoed versamelings vervoer word na die Antarktiese kontinent, maar versamelings bly grootliks vasgeheg wanneer na sub‐Antarktiese eilande gereis word. Populasies van ’n welbekende indringer, Mytilus galloprovincialis, is gevind in die see‐storingsarea van die vaartuig, met sommige individue wat die vervoering na die Antarktiese streek oorleef het op verskeie geleenthede. Wanneer spesies die aanvanklike verspreidingshindernisse oorkom het, staar hulle verdere ekologies en fisiologiese uitdagings in die gesig ten einde in die ontvanger streek te vestig. Die parasitiese wespe Aphidius matricariae is vir die eerste keer op Marion aangeteken in 2001. Opnames om die eiland toon dat volwasse oorvloed en die frekwensie van plantluis parasitisme die hoogste is aangrensend die algemene ankerpunt van die SA Agulhas en afneem weg van die omgewing af. Genetiese diversiteit was laag, wat voorstel dat die populasie gevestig het van ’n enkele bekendstelling. Dit lig uit dat hoë verspreidingseenheid druk nie nodig is vir die suksesvolle vestiging van bekendgestelde invertebrata nie. ‘n Ander spesie wat die verspreidingshindernisse oorkom het is die landslak Deroceras panormitanum wat in die 1970’s op Marion Eiland bekendgestel is en wat sedertdien versprei het oor meeste van die kushabitat van die eiland. Vir hierdie spesie word grens limiete vasgestel deur onverdraagsaamheid vir lae temperature en saliniteit en die oorvloedstruktuur word gekenmerk deur laslappe en gapings wat geassosieer word met die spesie se onvermoë om droë kondisies te hanteer. Om verdere uitheemse bekendstellings in die streek te voorkom, word geteikende bestuur van hoë risiko weë vereis. Toenemende waaksamheid is bykomend nodig vir die opsporing en bestuur van nuutgevestigde uitheemse spesies voordat hulle grense verbreed.

L’elaborato espone sei diversi metodi contact-less per la rilevazione della frequenza respiratoria. Sono stati menzionati i vari studi che si sono occupati dell’acquisizione, l’elaborazione ed il confronto dei dati ricavati con quelli ottenuti tramite altre metodiche considerate gold standard. Le tecniche trattano: segnali di pressione quali OscP e KorS, fotocamere ToF, un sistema ibrido che utilizza il segnale PPGI e IRTI, un sensore capacitivo, uno a radiofrequenze ed un radar CW. Il confronto, prendendo in considerazione i segnali rilevati tramite cintura di pressione o polisonnigrafo, ha dimostrato una forte correlazione. Si è osservato che queste tecniche possono essere una valida alternativa con diversi vantaggi: analisi di pazienti dormienti, allettati o con ferite cutanee per cui sarebbe impossibile utilizzare le classiche tecniche esistenti che prevedono cinture o elettrodi a contatto con il corpo.

Spinal cord injury (SCI) leads to axonal damage and limits the ability of the brain to communicate with the rest of the body. Several bioengineered approaches have been developed for the recovery of SCI. Among these techniques, degradable guidance tubes have shown promising results. However, design of nerve guide tubes requires several design considerations and has been a significant challenge. To assess the efficacy of a prototypical implanted nerve guide tubes, it is essential to perform continuous monitoring. In this respect, magnetic resonance imaging (MRI) is one of the most reliable imaging techniques as it offers the ability to achieve extraordinary high temporal and spatial resolution in addition to its non-invasive features. In spite of the excellent image quality of non-enhanced MRI various types of contrast agents have been developed to further enhance the contrast and allow improved visualization. The MRI contrast agents principally work by shortening the T1 or T2 relaxation times of protons located nearby. The presented study was intended to evaluate the in vitro degradation of the nerve guide tubes made of poly (lactic-co-glycolic acid) (PLGA). PLGA tubes incorporated with different concentrations of superparamagnetic iron oxide (SPIO) were scanned by MRI 3T on weekly basis during the degradation period. Spin-echo (SE) sequence with various echo times (TEs) ranged from 13.3 to 314.4 msec was applied. T2 mapping was computed using in-house algorithm developed in Matlab. Least square fit was used to find the slope of the decay curve by plotting log intensity on the y-axis and echo time on the x-axis. The average T2 values were calculated. Mass loss and water uptake of the degrading tubes were also measured weekly. Moreover, the micro-structural changes of the tubes were investigated using the scanning electron microscope (SEM). The MRI results showed that the concentration of SPIO affects the signal intensity of the T2 weighted images reducing the T2 relaxation time value. Accordingly, a linear correlation between SPIO concentration and T2 relaxation time was found. At the beginning of degradation, the SPIO nanoparticles were trapped within the polymeric network. Therefore, water penetration was the predominant factor affecting the T2 relaxation times. At week 5, a significant mass loss was observed. From this stage onwards, the trapped SPIO were released from the polymeric network increasing T2 relaxation time dramatically. According to SEM images, the size of the pores in PLGA guide tubes was increased with the degradation. Approaching the end of degradation, shrinkage of the tubes was observed and the degraded nerve guide tubes were shown to be collapsed. Similar shape variation was observed in T2 weighted MR images. In summary, this study provided an approach to non-invasive monitoring of degradation behavior of nerve guide tubes using contrast enhancement. The developed technique is of great importance since it opened an insight to non-invasive monitoring of tissue engineered scaffolds for in vivo studies.

Abstract Traditional clinicopathological factors are not accurate enough to predict the behavior of head and neck squamous cell carcinoma (HNSCC). The most powerful indicator of prognosis is the stage of the disease. New prognostic markers have, however, been searched for in order to better identify patient groups in need of different treatments or follow-up. Gelatinases (MMP-2, -9) are endopeptidases associated with tumor invasion and angiogenesis, and their tissue inhibitors (TIMP-1, -2) are also linked to cancer cell invasion and metastasis formation. In some cancer types they are even prognostic and relate with a more aggressive clinical course of the disease. In the present work the expression and the clinical significance of tumor tissue and circulating immunoreactive proteins for MMP-2, -9, TIMP-1 and -2 were assessed in HNSCC. The study group included 74 patients with HNSCC and 44 healthy controls. The expression of immunoreactive proteins was examined in paraffin-embedded tumor sections by immunohistochemical staining using specific antibodies, and the pretreatment serum levels of those proteins were quantitatively measured by ELISA assay. Immunohistochemical overexpression of MMP-9 in tumor was for the first time found to predict the prognosis for shortened survival in HNSCC, the cause-specific survival rates being 45% and 92% and relapse-free survival being 42% and 79% in MMP-9 positive or negative cases, respectively. Additionally, tissue TIMP-1, MMP-2 and TIMP-2 positivity were all also linked with poorer survival of patients with HNSCC. However, these differences remained less distinct than with MMP-9. The expression of gelatinases and their inhibitors in tumor tissue was also an indicator for later lymph node or hematogenic relapses in HNSCC patients. Circulating MMP-9 and TIMP-1 levels were significantly higher in HNSCC patients than in healthy controls. Further, the cause-specific and relapse-free survival rates were lower among HNSCC patients with high MMP-9 and TIMP-1 serum levels compared to patients with low levels of circulating MMP-9 and TIMP-1. A significant correlation was shown between circulating MMP-9 and MMP-9 immunohistochemical staining in the corresponding tumors. No correlation was found between tissue or circulating levels of gelatinases or their inhibitors and the traditional clinical or histopathological factors, except for the association between tissue and circulating TIMP-1 and the size of the primary tumor. Taken together, these results suggest that tissue expression of gelatinases and their inhibitors as well as pretreatment circulating MMP-9 and TIMP-1 levels could be prognostic in estimation of the clinical course of HNSCC. The results indicate further studies are needed with larger patient materials.

Doctor of Philosophy (PhD)
Early recognition of plant invaders is key to their successful management. Yet knowledge of the ecological impacts of species before they become widespread is poor. This thesis examines the ecology of invasive Pinus radiata, a species which is known to spread from introduced plantings in Australia but is currently a low profile invader. Pinus invasions are considered major ecological problems in New Zealand and South Africa where wildlings are beginning to dominate natural areas and suppress native vegetation. Invasion success elsewhere and the large softwood estate in Australia suggest that pines may begin to dominate native eucalypt forests bordering large commercial plantations. This research focused on three components of impact of P. radiata; extent, abundance and effect per individual. The borders of 29 P. radiata plantations in NSW were surveyed in order to quantify the current level of invasion and to identify factors facilitating pine spread. Of particular interest was the role of propagule pressure, vegetation type and fire in the invasion process. The area of land in NSW currently invaded by P. radiata was estimated at almost 4 500 ha, although this is likely to be an underestimate due to an inability to detect wildlings (self-sown pines) at long distances from the plantation. Twenty six of the 29 plantations produced wild pines, however most of the sites are in the very early stages of invasion. Noticeable wildling populations were recorded at nine sites indicating that P. radiata is capable of establishing within native vegetation. Pine spread was most severe in the world heritage listed Blue Mountains region where pine densities reached up to 2000 per hectare in areas adjacent to the plantation and isolated pines were recorded up to 4 km from the source. The presence of isolated pines within intact native vegetation suggests that disturbance is not required for pine establishment in forested environments. Furthermore, high pine emergence and survival rates in eucalypt woodland and evidence of self reproduction by wildlings suggest that in the absence of adequate control measures pines may become established invaders in the Australian landscape. While low levels of current invasion at many sites hindered the ability to examine the factors facilitating invasion some variables that appear to be driving pine success were identified. At the landscape scale plantation size and residence time were significant predictors of the level of invasion at a site. Areas of native vegetation vi adjacent to plantations less than 40 years experienced very low levels of invasion suggesting a lag period between plantation establishment and invasion. However, pines with diameters up to 60 cm were observed growing adjacent to plantations younger than 40 years implying that the first colonisers are capable of establishing soon after plantation trees become reproductive. Propagule pressure was also found to have a strong influence on invasion success on a smaller scale manifesting in a significant positive relationship between the age of a plantation compartment and the likelihood of invasion. A negative relationship between plantation size and level of invasion was a surprising result and was influenced by just two large sites that happened to be located in areas of high rainfall. All sites receiving more than 1300 mm annual rainfall experienced low levels of invasion suggesting that this is a limiting factor for pine spread in NSW. There were significant differences in the level of invasion between vegetation types implying that some communities are more susceptible to invasion. Patterns of spread confirmed ideas regarding the facilitative effect of disturbance in the invasion process and the resistance of wet sclerophyll forest to invasion in Australia. An absence of wildlings in cleared land and areas of remnant bushland was attributed to high levels of grazing pressure. Wind direction did not appear to influence the distribution of pines close to the plantation, but evidence of long distance wind dispersal of pines was provided by an investigation of pine spread from the air at one site where large pines were found growing 10 km downwind from a mature plantation. Fire was found to have both a positive and negative influence on the invasion process. High intensity wildfires are capable of destroying large pines with diameters exceeding 50 cm. However, fire can stimulate seed release from cones resulting in large post-fire recruitment pulses. Seedling densities of up to 3050 per hectare were recorded almost 3 years after wildfire, suggesting that follow up control prior to recruits reaching coning age, i.e. within 5 years, would be beneficial. Surveys of wildling pines exposed to low intensity hazard reduction burns suggest that the majority of pines greater than 3 m in height and with a diameter of more than 10 cm will survive the fire. Low intensity prescribed fires that are carried out after pines have reached this size will fail to control wildling populations. To examine the influence of P. radiata once it has established in the native community this study focused on two mechanisms of impact, the addition of pine litter and increased shade due to an increase in canopy cover. Collection of pine litterfall vii within an invaded eucalypt woodland over a 2 year period recorded rates of up to 1400 kg/ha/year in the most heavily invaded area with a pine basal area of 11.3m2/ha. More than 70 % of pine litter fell directly below the pine canopy suggesting that the most severe litter effects will be limited to these areas. Glasshouse and field experiments were conducted to examine the influence of this increased litter load on the emergence of P. radiata and two native species. Recruitment of native plant species was impeded by litter levels of 6000 kg/ha, the equivalent of approximately 4 years of pine litterfall. Both P. radiata and the two natives responded similarly to pine and eucalypt litter suggesting the two litter types are influencing the recruitment phase equally. However, where pines are added to the system, increased litterfall rates could potentially result in the doubling of the litter load and hence a greater barrier to seedling establishment. Pine invaded eucalypt woodlands are also subjected to three fold increases in canopy cover. Trends in reduced emergence of native species under a pine canopy suggest that the addition of pines to eucalypt forests is likely to have a negative influence on native recruitment and may result in a shift towards a shade tolerant community. However, reversal of trends in emergence below pine canopy between seasons implies that quantifying invasion impacts requires a consideration of temporal variation. Increased levels of disturbance, forest fragmentation and an increasing pine estate are likely to lead to the infestation of new areas. Furthermore the lag phase associated with pine spread means that even if no new plantations are established the number of invasion events will increase. This study has identified a number of risk factors that can be used to guide plantation establishment and the management of invasion events. Minimising disturbance at plantation borders and increasing the ‘no planting’ zone will help to reduce the impacts of pines. Where possible new plantations should be established upwind of cleared land or at least, wet sclerophyll forest. Frequent monitoring of the borders of plantations yet to source invasions, particularly those greater than 40 years of age, will help identify problem areas before control becomes difficult and costly. Maps of the 29 plantations marked with areas of pine infestation will help prioritise sites for control and provide base level knowledge for future monitoring of pine spread. Stringent legislation that binds plantation managers to control wildlings beyond their boundaries is critical for the effective management of pine invasions. With infinite numbers of invaders and limited funds to dedicate to their control, a method of triaging species for management is critical. This is particularly difficult viii when information is typically biased towards invaders that are already widespread. By focussing on the ecological impacts of invaders it becomes possible to rank species on the basis of the threat they pose to native communities. Ecological research is capable of providing the knowledge to quantify invasion impacts and must remain at the centre of policy decisions.

Early recognition of plant invaders is key to their successful management. Yet knowledge of the ecological impacts of species before they become widespread is poor. This thesis examines the ecology of invasive Pinus radiata, a species which is known to spread from introduced plantings in Australia but is currently a low profile invader. Pinus invasions are considered major ecological problems in New Zealand and South Africa where wildlings are beginning to dominate natural areas and suppress native vegetation. Invasion success elsewhere and the large softwood estate in Australia suggest that pines may begin to dominate native eucalypt forests bordering large commercial plantations. This research focused on three components of impact of P. radiata; extent, abundance and effect per individual. The borders of 29 P. radiata plantations in NSW were surveyed in order to quantify the current level of invasion and to identify factors facilitating pine spread. Of particular interest was the role of propagule pressure, vegetation type and fire in the invasion process. The area of land in NSW currently invaded by P. radiata was estimated at almost 4 500 ha, although this is likely to be an underestimate due to an inability to detect wildlings (self-sown pines) at long distances from the plantation. Twenty six of the 29 plantations produced wild pines, however most of the sites are in the very early stages of invasion. Noticeable wildling populations were recorded at nine sites indicating that P. radiata is capable of establishing within native vegetation. Pine spread was most severe in the world heritage listed Blue Mountains region where pine densities reached up to 2000 per hectare in areas adjacent to the plantation and isolated pines were recorded up to 4 km from the source. The presence of isolated pines within intact native vegetation suggests that disturbance is not required for pine establishment in forested environments. Furthermore, high pine emergence and survival rates in eucalypt woodland and evidence of self reproduction by wildlings suggest that in the absence of adequate control measures pines may become established invaders in the Australian landscape. While low levels of current invasion at many sites hindered the ability to examine the factors facilitating invasion some variables that appear to be driving pine success were identified. At the landscape scale plantation size and residence time were significant predictors of the level of invasion at a site. Areas of native vegetation vi adjacent to plantations less than 40 years experienced very low levels of invasion suggesting a lag period between plantation establishment and invasion. However, pines with diameters up to 60 cm were observed growing adjacent to plantations younger than 40 years implying that the first colonisers are capable of establishing soon after plantation trees become reproductive. Propagule pressure was also found to have a strong influence on invasion success on a smaller scale manifesting in a significant positive relationship between the age of a plantation compartment and the likelihood of invasion. A negative relationship between plantation size and level of invasion was a surprising result and was influenced by just two large sites that happened to be located in areas of high rainfall. All sites receiving more than 1300 mm annual rainfall experienced low levels of invasion suggesting that this is a limiting factor for pine spread in NSW. There were significant differences in the level of invasion between vegetation types implying that some communities are more susceptible to invasion. Patterns of spread confirmed ideas regarding the facilitative effect of disturbance in the invasion process and the resistance of wet sclerophyll forest to invasion in Australia. An absence of wildlings in cleared land and areas of remnant bushland was attributed to high levels of grazing pressure. Wind direction did not appear to influence the distribution of pines close to the plantation, but evidence of long distance wind dispersal of pines was provided by an investigation of pine spread from the air at one site where large pines were found growing 10 km downwind from a mature plantation. Fire was found to have both a positive and negative influence on the invasion process. High intensity wildfires are capable of destroying large pines with diameters exceeding 50 cm. However, fire can stimulate seed release from cones resulting in large post-fire recruitment pulses. Seedling densities of up to 3050 per hectare were recorded almost 3 years after wildfire, suggesting that follow up control prior to recruits reaching coning age, i.e. within 5 years, would be beneficial. Surveys of wildling pines exposed to low intensity hazard reduction burns suggest that the majority of pines greater than 3 m in height and with a diameter of more than 10 cm will survive the fire. Low intensity prescribed fires that are carried out after pines have reached this size will fail to control wildling populations. To examine the influence of P. radiata once it has established in the native community this study focused on two mechanisms of impact, the addition of pine litter and increased shade due to an increase in canopy cover. Collection of pine litterfall vii within an invaded eucalypt woodland over a 2 year period recorded rates of up to 1400 kg/ha/year in the most heavily invaded area with a pine basal area of 11.3m2/ha. More than 70 % of pine litter fell directly below the pine canopy suggesting that the most severe litter effects will be limited to these areas. Glasshouse and field experiments were conducted to examine the influence of this increased litter load on the emergence of P. radiata and two native species. Recruitment of native plant species was impeded by litter levels of 6000 kg/ha, the equivalent of approximately 4 years of pine litterfall. Both P. radiata and the two natives responded similarly to pine and eucalypt litter suggesting the two litter types are influencing the recruitment phase equally. However, where pines are added to the system, increased litterfall rates could potentially result in the doubling of the litter load and hence a greater barrier to seedling establishment. Pine invaded eucalypt woodlands are also subjected to three fold increases in canopy cover. Trends in reduced emergence of native species under a pine canopy suggest that the addition of pines to eucalypt forests is likely to have a negative influence on native recruitment and may result in a shift towards a shade tolerant community. However, reversal of trends in emergence below pine canopy between seasons implies that quantifying invasion impacts requires a consideration of temporal variation. Increased levels of disturbance, forest fragmentation and an increasing pine estate are likely to lead to the infestation of new areas. Furthermore the lag phase associated with pine spread means that even if no new plantations are established the number of invasion events will increase. This study has identified a number of risk factors that can be used to guide plantation establishment and the management of invasion events. Minimising disturbance at plantation borders and increasing the ‘no planting’ zone will help to reduce the impacts of pines. Where possible new plantations should be established upwind of cleared land or at least, wet sclerophyll forest. Frequent monitoring of the borders of plantations yet to source invasions, particularly those greater than 40 years of age, will help identify problem areas before control becomes difficult and costly. Maps of the 29 plantations marked with areas of pine infestation will help prioritise sites for control and provide base level knowledge for future monitoring of pine spread. Stringent legislation that binds plantation managers to control wildlings beyond their boundaries is critical for the effective management of pine invasions. With infinite numbers of invaders and limited funds to dedicate to their control, a method of triaging species for management is critical. This is particularly difficult viii when information is typically biased towards invaders that are already widespread. By focussing on the ecological impacts of invaders it becomes possible to rank species on the basis of the threat they pose to native communities. Ecological research is capable of providing the knowledge to quantify invasion impacts and must remain at the centre of policy decisions.

Background: Consistent with the ‘reactivity hypothesis’, monitoring autonomic responses to exercise might be of value in clinical and high-performance settings. Post-exercise autonomic recovery may be non-invasively assessed using heart rate variability indices of cardiac parasympathetic neural activity (cPNA-HRV) and systolic time intervals reflecting cardiac sympathetic neural activity (cSNA-STI). However, the dose of exercise may confound autonomic recovery, independent of underlying pathology or function. This thesis investigated how these indices respond to variations of the factors constituting an acute exercise dose, i.e. intensity, duration, and modality. Methods: Following a literature review, three studies investigated the effect of exercise dose on post-exercise cPNA-HRV and cSNA-STI. Firstly, participants performed three 8-min bouts of different intensities (below, between, and above the ventilation thresholds). Secondly, two durations (8-min vs. 32-min) of moderate-intensity exercise were performed. Finally, participants performed two 8-min bouts of different modes (arm-cranking vs. leg cycling) of heart rate-matched submaximal exercise. Results: Prior research on cPNA-HRV responses to exercise was methodologically diverse, while cSNA-STI responses had rarely been examined. The recovery profiles of cPNA-HRV and cSNA-STI were slower following progressively higher intensity exercise. Longer duration exercise delayed the recovery of cPNA-HRV, but not cSNA-STI. Arm-cranking elicited a slower recovery of cSNA-STI compared with heart rate-matched leg cycling, while cPNA-HRV recovery was similar between modes. Conclusion: The intensity, duration, and modality of exercise can each independently influence the recovery of cPNA-HRV and cSNA-STI. Thus, the exercise dose needs to be considered when interpreting these indices. Acute post-exercise recovery may be a valuable period during which to concurrently monitor autonomic reactivity using cPNA-HRV and cSNA-STI.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 163-170).
This thesis details non-invasive evaluation of a central arterial blood pressure (ABP) waveform using a low-cost ultrasound scanning system. ABP bears significant clinical value in cardiovascular pathophysiology. Non-invasive evaluation of the full ABP waveform has been long desired by medical communities due to its anticipated opportunities to greatly enhance cardiovascular patient care. In addition, central ABP has been focused on because of its close association with the adverse outcomes of cardiovascular events. This work mainly explores monitoring of carotid arterial pulsation and local pulse wave velocity (PWV) by the designed system to estimate the ABP waveform, conducting simultaneous spectral Doppler and M-mode imaging. The system is characterized in electrical and acoustic domains to preserve adequate signal integrity to faithfully extract a spatial mean flow velocity and an arterial distension waveform. The carotid ABP waveform is estimated from the distension waveform and the local PWV with one-time calibration from an arterial-line (A-line) or a volume clamping method. The proof-of-concept study demonstrated that the carotid ABP waveform estimation is feasible. The pulse pressure estimation compared to a sphygmomanometer and a finger ABP waveform differ by 1.49±11.7 and -4.92±12.9 mmHg, respectively. The designed and characterized motion-tolerant ultrasonography extends tolerable lateral offsets up to ±8 mm while limiting error of the flow and distension waveforms within about 5%. The system is also validated under hemodynamic stress of the Valsalva maneuver and in intensive care settings compared to the A-line. This thesis demonstrates the profound potential for a portable low-cost ultrasound system toward non-invasive evaluation of a central ABP waveform in clinically relevant settings.
by Joohyun Seo.
Ph. D.

Thesis (PhD)--Stellenbosch University, 2002.
Some digitised pages may appear illegible due to the condition of the original hard copy.
ENGLISH ABSTRACT: Membrane fouling is universally accepted as one of the most critical problems limiting the wider application of membranes in liquid separations. The development and utilization of a suitable non-invasive technique for the on-line monitoring of fouling in industrial and laboratory applications may enable the effectiveness of fouling remediation and cleaning strategies to be quantified. The overall objective of this research is to develop ultrasonic time-domain reflectometry (UTDR) and its use as an analytical tool for the real-time study of inorganic-, organic- and protein- fouling of various types of membranes including nylon, polysulfone (PSU) and polyethersulfone (PESU) and modules, including flatsheet and tubular types. Different separation systems including microfiltration (MF) and ultrafiltration (UF), flat-sheet and tubular modules, and suitable ultrasonic probes were used in this study. Results of this study show a good correlation between the UTDR signal response and the development of a fouling layer on a membrane surface. UTDR effectively detected the appearance, growth and movement of a fouling layer echo as fouling proceeded. Cake (fouling)-layer compressibility was observed by UTDR. The structure and compaction of an asymmetric PSU membrane could be detected by UTDR. UTDR was also successfully used for monitoring membrane cleaning and evaluating the cleaning effectiveness o f various cleaning methods. UTDR results corroborated the flux measurements and SEM analyses. The ultrasonic unit is a programmed microprocessor, and can be used to compare reference and test signals to produce a differential signal (a fouling layer echo). A differential signal indicates the state and progress o f a fouling layer on the membrane surface in actual operations. Both amplitude and arrival time of differential signals as a function of operation time provide useful quantitative information, i.e. changes in thickness and density of a fouling layer, on the fouling processes. A predictive modelling program, ultrasonic reflection modelling (URM), was developed to describe the processes of ultrasonic testing related to the deposition of fouling layers on membrane surfaces. The mathematical model could substantiate changes in the densities of the fouling layer as well as the thickness. This is important as deposit resistance to flow is related to both thickness and density (compressibility). The predicted results of cake layer deposition are in good agreement with the actual UTDR measurements obtained in MF and UF. Furthermore, protein fouling was successfully detected in tubular UF by UTDR. Ultrasonic frequency spectra could be used as an additional tool for fouling detection.
AFRIKAANSE OPSOMMING: Membraan-aanvuiling of -verstopping is die grootste struikelblok wat die meer algemene aanwending van membrane vir verskillende watersuiweringsprosesse beinvloed. Die ontwikkeling en gebruik van ‘n geskikte nie-inmengende tegniek vir die in-lyn meting van aanvuiling van membrane in laboratorium-en nywerheidstoepassings mag ‘n geleentheid bied vir die kwantifisering van die verwydering van aanvuiling en skoonmaakstrategiee. Die hoofdoel van hierdie studie was die ontwikkeling van ultrasoniese tydgebiedsweerkaatsing (Eng: ultrasonic time-domain reflectometry, UTDR) en die gebruik daarvan as ‘n analitiese metode vir die studie van anorganiese-, organiese- en bio-besoedeling op verskeie tips membrane, insluitend nylon, polisufoon (PSU) en polietersulfoon (PESU), in beide platvel- en buismodules. Verskeie skeidingsisteme, insluitend mikrofiltrasie (MF) en ultrafiltrasie (UF) is ontwerp en gebruik in hierdie studie. Eksperimentele resultate het goeie ooreenstemming tussen die UTDR seinrespons en die ontwikkeling van ‘n aanvuilingslaag op die membraanoppervlakte bewys. Die ultrasoniese tegniek kon die vorming, groei en beweging van ‘n bevuilingslaagterugkaartsing waarneem namate bevuiling vorder. Aanvuilingslaagsamepersing is deur UTDR waargeneem. Die struktuur en samepersing van ‘n asimmetriese PSU membraan is ook deur UTDR gesien. UTDR is verder suksesvol gebruik om die skoonmaak van membrane te monitor en om die skoonmaakgeskiktheid (cleaning effectiveness) van verskeie skoonmaakmetodes te bepaal. UTDR resultate het permeaatvloeimetings en SEM analyses bevestig. Die ultrasoniese eenheid is ‘n geprogrameerde mikroverwerker, en kan gebruik word om verwysings- en toetsseine te vergelyk, en dan ‘n differensiaalsein te gee (‘n aanvuilingslaagweerklank). ‘n Differensiaalsein dui die toestand en vordering van ‘n aanvuilingslaag op die membraanoppervlakte gedurende gebruik aan. Beide amplitude asook aankomstyd van differensiaalseine as funksies van gebruikstyd verskaf bruikbare kwantatiewe inligting, dws. Veranderings in die dikte en digtheid van ‘n aanvuilingslaag, op die aanvuilingsproses. ‘n Voorspellingsmodelleringprogram - ultrasonieseweerkaatsingsmodellering (Eng: ultrasonic reflection modeling, URM) is ontwikkel om die proses van ultrasoniese toetsing by die deponering van aanvuilingslae op membraanoppervlaktes beter te beskryf. Veranderings in die digtheid en dikte van die aanvuilingslaag teenvloei is verwant aan dikte en digtheid (saampersbaarheid). Die voorspelde resultate van aanvuilingslaagdeponering stem goed ooreen met die werklike UTDR-metings wat in MF en UF gemaak is. Bio-aanvuiling is suksesvol waargeneem deur UTDR in buisvormige UF membrane. Ultrasoniese frekwensiespektra kan dus as ‘n bykomende metode gebruik word vir die waarneming van aanvuiling op skeidingsmembrane.

Earth mean surface temperature has increased by 1 °C since the industrial revolution, and this has already had considerable effects on animal and plant species. Ecological responses to the warming climate – often facilitated via phenotypic plasticity – are ubiquitous. However, even though evolution can occur rapidly there are only few examples of genetic adaptation to climate change. In my thesis, I used a near-natural system to study if and how organisms have adapted to 30 years of warming, and how this has affected competitive species interactions. I investigated Baltic Sea populations of the aquatic snails Galba truncatula and Theodoxus fluviatilis, which had been subjected to cooling water discharge from power plants, resulting in water temperatures 4 to 10 °C higher than in the surrounding sea. G. truncatula had high upper thermal limits and large acclimation potential. This plasticity may have helped the species to survive under the new conditions, allowing evolution through natural selection to take place. I found that the populations of the two thermal origins had diverged in SNP markers associated with warmer temperature, whereas divergence in selectively neutral markers was mainly related to geographical distance. Adaptation occurred from standing genetic variation, emphasizing the importance of genetic diversity and population size in enabling the persistence of populations. Changes in thermal sensitivity of growth and survival were subtle yet significant, and complied with theoretical models of thermal adaptation in ectotherms. At the community level, pre-adaptation to warmer conditions aided the native T. fluviatilis when competing with the alien Potamopyrgus antipodarum. However, interspecific competition limited the snails most in those traits favored under warming, highlighting the challenge of adapting to different selecting forces during global change. The persistence of species and populations under climate change depends on several factors - plasticity allowing for initial survival, evolvability in allowing the genetic changes, and species interactions affecting the new ecological niches. The results of my thesis indicate that persistence under climate change is possible when these factors align, but the relative roles of ecology and plasticity may explain why there are so few observed instances of evolution in response to climate change.

"We Have to Record the Downfall of Tyranny": The London Times Perspective on Napoleon Bonaparte's Invasion of Russia aims to illustrate how The London Times interpreted and reported on Napoleon's 1812 invasion of Russia. This thesis explains how England feared its grip on Europe was slipping away due to a French takeover of the continent. This work details the English struggle in order to provide a broader analysis through a newspaper of how nations indirectly involved in the Napoleonic wars understood the conflict.

Le specie aliene invasive possono influenzare negativamente le componenti biotiche e abiotiche delle aree di introduzione, alterare le comunità ecologiche, favorire la diffusione di patogeni e/o malattie determinando gravi danni alla biodiversità, salute ed economia. Capire le dinamiche alla base del processo di invasione, nei suoi aspetti teorici e pratici, è la chiave per prevenire ulteriori invasioni e per migliorare la gestione delle specie introdotte evitando effetti avversi sull’ambiente e sulla biodiversità locale. La cimice marmorizzata bruna, Halyomorpha halys (Hemiptera, Heteroptera) è una specie aliena invasiva nativa dell’Asia orientale. È stata segnalata per la prima volta, al di fuori del suo areale originario, in Nord America e recentemente in Europa, dove si sta rapidamente diffondendo. Oltre ad essere un infestante urbano nelle aree di introduzione, questa cimice sta causando enormi perdite economiche in agricoltura essendo altamente polifaga e presentando due generazioni all’anno. Gli obiettivi di questo studio di Dottorato erano: i. l’applicazione di metodi molecolari per la determinazione delle strategie di introduzione e dispersione delle popolazioni introdotte, ii. l’individuazione precoce dei propaguli di H. halys, iii. l’identificazione dei potenziali predatori autoctoni. Come prima parte del progetto è stata condotta un’analisi esplorativa della struttura genetica delle popolazioni italiane e Greche mediante il metodo del Restriction site associated DNA sequencing (RADseq), al fine di identificare la variabilità genetica, i pattern di introduzione e dispersione degli individui con l’aplotipo mitocondriale più diffuso, secondo uno studio precedente (Cesari et al. 2018). L’analisi ha evidenziato la presenza di due gruppi principali, il primo include solo individui dall’Emilia-Romagna (IT), mentre il secondo include individui dal Nord Italia, Toscana (IT) e Grecia. Un’analisi più dettagliata ha suggerito un’ulteriore suddivisione del secondo gruppo in tre sottogruppi, due includono individui da differenti aree geografiche mentre, uno include solo individui dal Veneto (IT) ed è il gruppo con la maggiore diversità. Tali risultati suggeriscono che le popolazioni analizzate hanno avuto origine da invasioni multiple e la presenza di due gruppi geograficamente misti, ha evidenziato l’elevata mobilità della specie probabilmente avvantaggiata dalle attività umane. Una seconda parte del progetto si è focalizzata sul testare l’efficacia di un protocollo di Real-Time PCR di tipo qualitativo per determinare il potenziale predatorio di diversi animali insettivori, individuando la presenza di DNA di H. halys in campioni di guano di chirotteri e nel contenuto intestinale di artropodi. L’analisi del guano di pipistrelli italiani campionato in Piemonte, Valle d’Aosta e Toscana, ha portato all’identificazione di due generi di pipistrello (Myotis, Nyctalus) che si nutrono di H. halys, come provato da quattro campioni positivi da aree agricole del Piemonte e due campioni positivi da aree naturali della Toscana. Anche con l’analisi del contenuto intestinale di potenziali artropodi predatori, campionati in due parchi urbani in Emilia-Romagna (IT), sono stati ottenuti ventitré campioni positivi, identificando specie predatrici di H. halys tra insetti e aracnidi. Questi dati confermano come, questo saggio di Real-Time PCR specie-specifico, possa essere applicato per diversi quesiti biologici (es. identificazione precoce, tassi di predazione) e operare su substrati molto differenti. Entrambi i metodi validano l’affidabilità degli approcci molecolari per la risoluzione di varie problematiche negli studi di specie invasive, ponendo le basi per lo sviluppo di protocolli facilmente adattabili ai diversi casi studio.
Invasive Alien Species (IAS) can affect negatively the biotic and abiotic components of the areas of introduction, alter ecological communities, enhance the diffusion of pathogens and/or diseases thus, determining severe impacts on biodiversity, healthcare and economy. Understanding the dynamics underlying the invasion process, either in its theoretical and practical aspects, is the key to prevent further invasion and to improve the management of established species avoiding harmful effects on the environment and non-target organisms. The brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera, Heteroptera) is an invasive alien species native to eastern Asia. Its presence outside the original area of distribution has been recorded for the first time in North America and, more recently, in Europe, where it is spreading rapidly across all countries. Other than being a household pest all over its introduced range, this stink bug is causing great economic losses in orchards/crops due to its highly polyphagous nature and bivoltinism. The purposes of this doctoral study were: i. the implementation of molecular tools to determine the patterns of introduction and dispersal of established populations, ii. early detect the presence of H. halys propagules, iii. and identify native potential predators. As first part of the project, the explorative analysis of the genomic structure of Italian and Greek populations of H. halys was investigated with the Restriction site associated DNA sequencing (RADseq) method in order to identify the genetic variability, the patterns of introduction and dispersal of the individuals with the most widespread mitochondrial haplotype as evidenced in the previous study (Cesari et al. 2018). The analysis evidenced the presence of two main clusters, the first one included only individuals from Emilia-Romagna region (IT) while the second one gathered those from North Italy, Tuscany (IT) and Greece. A deeper analysis hinted a further subdivision of the second cluster in three subclusters, two included individuals from different geographic regions, while one included only specimens from Veneto region (IT) and was characterized by the highest within-cluster differentiation. These results suggest that analysed populations have originated from multiple invasion events and highlight high mobility of the species, as evidenced by the presence of two geographically mixed clusters, likely enhanced by human activities. The other part of the project was focused on testing the efficacy of a qualitative Real-Time PCR protocol to assess the predatory potential of different insectivorous animals by detecting the presence of H. halys DNA in chiropteran guano samples and arthropod gut-content. Guano analysis from Italian bat species collected in the Italian regions of Piedmont, Aosta Valley and Tuscany led to the identification of two genera of bats (Myotis, Nyctalus) feeding on H. halys, with four positive hits found from agricultural sites in Piedmont and two positive hits in Tuscany natural areas. The gut-contents analysis of potential arthropod predators collected in two urban parks in Emilia-Romagna (IT), also scored twenty-three positive results, identifying ten H. halys predator species among insects and arachnids. Present data prove that the species-specific Real-Time PCR assay can address different biological questions (e.g. early detection of pests, predation rates) and operate on very different substrates. Both methods validate the reliability of molecular approaches to address various problematics in invasive species studies, thus setting the stage for the development of adaptable protocols for different case studies.

"This thesis presents a single-slice based fast stereotactic registration and tracking technique along with a corresponding modular system for guiding robotic mechanism or interventional instrument to perform needle-based interventions under live MRI guidance. The system can provide tracking of full 6 degree-of-freedom (DOF) in stereotactic interventional surgery based upon a single, rapidly acquired cross-sectional image. The whole system is constructed with a modular data transmission software framework and mechanical structure so that it supports remote supervision and manipulation between a 3D Matlab tracking user interface (UI) and an existing MRI robot controller by using the OpenIGTLink network communication protocol. It provides better closed-loop control by implementing a feedback output interface to the MRI-guided robot. A new compact fiducial frame design is presented, and the fiducial is wrapped with a passive resonant coil. The coil resonates at the Larmor frequency for 3T MRI to enhance signal strength and enable for rapid imaging. The fiducial can be attached near the distal end of the robot and coaxially with a needle so as to visualize target tissue and track the surgical tool synchronously. The MRI-compatible design of fiducial frame, robust tracking algorithm and modular interface allow this tracking system to be conveniently used on different robots or devices and in different size of MRI bores. Several iterations of the tracking fiducial and passive resonant coils were constructed and evaluated in a Phillips Achieva 3T MRI. To assess accuracy and robustness of the tracking algorithm, 25 groups of images with different poses were successively scanned along specific sequence in and MRI experiment. The translational RMS error along depth is 0.271mm with standard deviation of 0.277mm for totally 100 samples. The overall angular RMS error is less than 0.426 degree with standard deviation of 0.526 degree for totally 150 samples. The passive resonant coils were shown to significantly increase signal intensity in the fiducial relative to the surroundings and provide for rapid imaging with low flip angles. "

L'objectif de cette thèse était d'explorer de nouvelles applications cardiaques pour l'histotripsie et de développer les outils permettant leur mise en place non-invasive. La thérapie ultrasonore cardiaque est en effet encore assez peu développée aujourd’hui, à cause de la difficulté à traiter un organe en mouvement permanent, et très bien protégé derrière la cage thoracique.Nous avons d'abord montré in vivo, sur un modèle ovin, que l’on pouvait sectionner les cordages mitraux de manière non-invasive ainsi que traiter la sténose aortique calcifiée. Engendrer de la cavitation sur les feuillets valvulaires permet effectivement d’agir à distance sur les calcifications, et de globalement assouplir la valve.Simultanément, nous avons développé un dispositif pour la thérapie cardiaque non invasive, fondé sur le concept de cavité à retournement temporel. Ce dispositif permet l'émission d'impulsions ultrasonores de haute intensité dans un très grand volume d’intérêt. L’on peut ainsi déplacer le point de thérapie en 3 dimensions de manière entièrement électronique, et sans déplacer mécaniquement l’appareil. Après optimisation, ce dispositif a permis de créer des lésions mécaniques bien contrôlées dans une région d'intérêt de 2 000 cm3.Pour faire face au défi que représente la cage thoracique, nous avons développé une méthode de focalisation adaptative et l'avons mise en œuvre dans un prototype 2D du dispositif. Avec cette méthode, nous pouvons non seulement construire un front d'onde ultrasonore adaptatif qui se propage de manière préférentielle à travers les espaces intercostaux, mais grâce aux propriétés des cavités à retournement temporel, nous pouvons également augmenter la pression focale obtenue sur la cible de thérapie.Enfin, pour approfondir ce travail sur la focalisation adaptative, et nous avons considéré le cas de l'imagerie transcrânienne. Pour cette application, nous avons choisi d’utiliser la focalisation par retournement temporel dans le bruit de speckle, pour corriger les aberrations induites par le crâne. En simulations numériques, nous avons pu calculer les modulations de phase et d'amplitude induites par les os et améliorer le contraste et la résolution d'une image B-mode
The objective of this thesis was to explore new applications for cardiac histotripsy, and to develop the tools making it possible non-invasively. Cardiac ultrasound therapy indeed still remains limited due to the tremendous challenge of treating a constantly and rapidly moving organ, well protected behind the ribcage.We first showed in vivo, on a large animal model, that histotripsy could be used non-invasively to cut mitral chordae, and to treat calcified aortic stenosis in a beating heart. Cavitation on the valve leaflets can indeed locally and remotely act on the calcifications, and globally soften the valve. Simultaneously, we developed a therapeutic device allowing completely non-invasive cardiac shock-wave therapy based on the time reversal cavity concept. In particular, this device allows the emission of high intensity ultrasound pulses, and provides 3D electronical steering of the therapy focal spot in a large volume. After a thorough optimisation process, this device was capable of creating well controlled mechanical lesions over a 2 000 cm3 region of interest. To tackle the challenge of ultrasound propagation through the rib cage, we developed an adaptive focusing method (DORT method through a time reversal cavity), and implemented it in a 2D prototype of the device. With this method, we not only could build an adaptive ultrasonic wavefront propagating preferentially through the intercostal spaces, but due to time reversal cavities properties, we could also increase the peak pressure obtained on target.Finally, we pushed our work on adaptive focusing further, and considered the case of transcranial imaging. For this application, we chose to use the time reversal of speckle noise technique, to correct the aberrations induced by the skull. In numerical simulations, we were able to derive the phase and amplitude modulations induced by the bones, and could improve the contrast and resolution of a B-mode image

Semi-aquatic mammals have evolved to forage in both aquatic and terrestrial environments, and they generally lack locomotor specialisation for either. Having relatively unspecialised adaptations, some semi-aquatic species are generalist foragers, and their activity and diving patterns provide insight into constraints on their foraging behaviour. The recent miniaturisation and improved accuracy of logging devices allow remote data collection from small (<1kg), shallow-diving species. The development of analytical methods has lagged behind technological advances (and techniques developed for fully aquatic animals do not account for the variability of behaviour typical of semi-aquatic animals and their switching between terrestrial and aquatic environments). I applied and developed novel analytical techniques to identify activities and diving patterns of a semi-aquatic mustelid, the American mink (Neovison vison), fitted with Time-Depth Recorders (TDRs). Using a hidden Markov model (HMM) algorithm allowed me to classify dives into three states to identify clustering, and describe sequential diving patterns by mink. TDRs were used to determine active/inactive periods on the basis of rapid TDR temperature changes, and this method was validated empirically. Having developed this methodology, I applied it to 18 datasets collected from 14 mink in lowland England. Terrestrial activity of mink was positively related to ambient temperature (across both sexes), however aquatic activity, especially diving, appeared to be more influenced by daylight than by temperature. Mink showed intersexual differences, with males being more nocturnal and more active on land, and females more diurnal, and more persistent in diving. There was considerable variability between sexes and individuals. This is the first study to use HMM to classify the dives of a semi-aquatic animal, and the first to use TDR temperature records to identify mammalian activity patterns. These methods will be generally applicable to animals that make rapid transitions between environments and have thus far been difficult to study.

Cryosurgery is the destruction of undesired biological tissues by freezing. Modern cryosurgery is frequently performed as a minimally-invasive procedure, where multiple hypodermic, needle-shaped cryoprobes are inserted into the target area to be treated. The aim of the cryosurgeon is to maximize cryoinjury within a target region, while minimizing damage to healthy surrounding tissues. There is an undisputed need for temperature-field reconstruction during minimally invasive cryosurgery to help the cryosurgeon achieve this aim. The work presented in this thesis is a part of ongoing project at the Biothermal Technology Laboratory (BTTL), to develop hardware and software tools to accomplish real-time temperature field reconstruction. The goal in this project is two-fold: (i) to develop the hardware necessary for miniature, wireless, implantable temperature sensors, and (ii) to develop mathematical techniques for temperature-field reconstruction in real time, which is the focus of the work presented in this thesis. To accomplish this goal, this study proposes a computational approach for real-time temperature-field reconstruction, combining data obtained from various sensing modalities such as medical imaging, cryoprobe-embedded sensors, and miniature, wireless, implantable sensors. In practice, the proposed approach aims at solving the inverse bioheat transfer problem during cryosurgery, where spatially distributed input data is used to reconstruct the temperature field. Three numerical methods have been developed and are evaluated in the scope of this thesis. The first is based on a quasi-steady approximation of the transient temperature field, which has been termed Temperature Field Reconstruction Method (TFRM). The second method is based on analogy between the fields of temperature and electrical potential, and is thus termed Potential Field Analogy Method (PFAM). The third method is essentially a hybrid of TFRM and PFAM, which has shown superior results. Each of these methods has been benchmarked against a full-scale finite elements analysis using the commercial code ANSYS. Benchmarking results display an average mismatch of less than 2 mm in 2D cases and less than 3 mm in 3D cases for the location of the clinically significance isotherms of -22°C and -45°C. In an advanced stage of numerical methods evaluation, they have been validated against experimental data, previously obtained at the BTTL. Those experiments were conducted on a gelatin solution, using proprietary liquid-nitrogen cryoprobes and a cryoheater to simulate urethral warming. The design of the experiment was aimed at creating a 2D heat-transfer problem. Validation results against experimental data suggest an average mismatch of less than 2 mm, for the hybrid of TFRM + PFAM method, which is of the order of uncertainty in estimating the freezing front location based on ultrasound imaging.

The non-invasive and, often, continuous measurement of the hemodynamics of the body, and for the main purposes of this thesis, the brain, is desired because both the instantaneous values and their changes over time constantly adapt to the conditions affecting the body and its environment. They are altered in pathological situations and in response to increased function. It is desirable for these measurements to be continuous, reliable, minimally invasive, and relatively inexpensive. In recent years, optical techniques that, by using diffusing and deep-reaching (up to few centimeters) light at skin-safe levels of intensity, combine the aforementioned characteristics, have increasingly become used in clinical and research settings. However, to date there is, on one side the need to expand the number and scope of translational studies, and, on the other, to address shortcomings like the contamination of signals from unwanted tissue volumes (partial volume effects). A further important goal is to increase the depth of penetration of light without affecting the non-invasive nature of diffuse optics. My PhD was aimed at several aspects of this problem; (i) the development of new, more advanced methods, i.e. the time/pathlength resolved, to improve the differentiation between superficial and deeper tissues layers, (ii) the exploration of new application areas, i.e. to characterize the microvascular status of bones, to study the functional response of the baby brain, and (iii) to improve the quality control of the systems , i.e. by introducing a long shelf-life dynamic phantom. In conceptual order, first I introduce long shelf-life reference standards for diffuse correlation spectroscopy. Secondly, I describe the use of an existing hybrid time domain and diffuse correlation spectroscopy system to monitor the changes that some pathological conditions, in this case osteoporosis and human immunodeficiency virus infection, may have on many aspects of the human bone tissue that are currently not easy to measure (i.e. invasively assessed) by conventional techniques. Thirdly, I describe the development of a novel time domain optical technique that intimately combines, introducing many previously unmet advancements, the two previously cited optical spectroscopy techniques. For the first time I was able to produce a time domain device and protocol that can monitor the blood flow in vivo in the head and muscles of healthy humans. Lastly, I describe a device and method that I have used to monitor changes in blood flow in healthy human infants of three to five months of age, for the first time in this age bracket, as a marker of activation following visual stimulation. Overall, this work pushes the limit of the technology that makes use of diffuse light to minimally invasively, continuously, and reliably monitor endogenous markers of pathological and physiological processes in the human body.
La medición no invasiva y, a menudo, continua de la hemodinámica del cuerpo, y para los propósitos principales de esta tesis, del cerebro, es conveniente porque tanto los valores instantáneos como sus variaciones en el tiempo se adaptan constantemente a las condiciones que afectan el cuerpo humano y su entorno. Estas suelen alterarse en situaciones patológicas o como respuesta a una mayor función. Es deseable que estas mediciones sean continuas, confiables, mínimamente invasivas y relativamente asequibles. En los últimos años, las técnicas ópticas que, mediante el uso de luz difusa para medir los tejidos en profundidad (hasta unos pocos centímetros) mediante niveles de intensidad que son seguros para la piel, combinan las características arriba mencionadas, se han utilizado cada vez más tanto en entornos clínicos como de investigación. Sin embargo, al día de hoy hay, por un lado, la necesidad de ampliar el número y el ámbito de los estudios translacionales y, por el otro, de suplir a las deficiencias como por ejemplo la contaminación de volúmenes de tejido no deseados (efectos de volumen parcial). Otro objetivo importante es aumentar la profundidad de penetración de la luz sin afectar la naturaleza no invasiva de la óptica difusa. Mi doctorado está destinado a mejorar varios aspectos de este problema; (i) el desarrollo de nuevos métodos más avanzados, es decir, el método resuelto en el tiempo/trayectoria de los fotones, para mejorar la diferenciación entre los tejidos superficiales y profundos, (ii) la exploración de nuevas áreas de aplicación, es decir, para caracterizar el estado microvascular de los huesos, para estudiar la respuesta funcional del cerebro en los niños, y (iii) para mejorar el control de calidad de los sistemas, es decir, mediante la introducción de un phantom dinámico de larga vida útil. En orden conceptual, primero voy a introducir estándares de referencia de larga vida útil para la espectroscopia de correlación difusa (DCS). En segundo lugar, voy a describir el uso de un sistema híbrido espectroscopia tiempo-resuelta (TRS) con DCS ya existente para monitorizar los cambios que algunas condiciones patológicas, en este caso la osteoporosis y la infección por el virus de la inmunodeficiencia humana, pueden comportar para muchos aspectos del tejido óseo humano que actualmente no se pueden medir con facilidad (es decir, se van evaluado de forma invasiva) mediante técnicas convencionales. En tercer lugar, voy a describir el desarrollo de una novedosa técnica óptica en el dominio temporal que combina íntimamente, introduciendo muchos avances previamente no cumplidos, TRS y DCS. Por primera vez pude producir un dispositivo y un protocolo tiempo-resueltos para medir el flujo de la sangre en la cabeza y en los músculos de seres humanos sanos. Por último, en esta tesis voy a describir un dispositivo y un método que he usado para monitorear los cambios en el flujo sanguíneo como marcadores de activación del cerebro debida a estímulos visivos en bebés entre tres y cinco meses de edad. En general, este trabajo amplia los limites de la tecnología que hace uso de la luz difusa para monitorizar, de forma mínimamente invasiva, continua y confiable los marcadores endógenos de procesos patológicos y fisiológicos en el cuerpo humano.

The use of registered intra-operative to pre-operative imaging has been proposed for many medical interventions, with the goal of providing more informed guidance to the physician. The registration may be difficult to carry out in real-time.Therefore, it is often necessary to track the motion of the anatomy of interest in order to maintain a registration. In this work, a surface based Extended Kalman Filter (EKF) framework is proposed to track a tissue surface based on temporal correspondences of 3D features extracted from the tissue surface. Specifically, an initial 3D surface feature map is generated based on stereo matched Scale Invariant Feature Transform (SIFT) feature pairs extracted from the targeted surface. For each consecutive frame, the proposed EKF framework is used to provide 2D temporal matching guidance in both stereo channels for each feature in the surface map. The 2D feature matching is carried out based on the Binary Robust Independent Elementary Feature (BRIEF) descriptor. If the temporal match is successful in both stereo channels, the stereo feature pair can be used to reconstruct the feature location in 3D. The newly measured 3D locations drive the EKF update to simultaneously estimate the current camera motion states and the feature locations of the 3D surface map. The framework is validated on ex vivo porcine tissue surface and in vivo prostate surface during a da Vinci radical prostatectomy. The peak and mean fiducial errors are 2.5 mm and 1.6 mm respectively. Compared to other methods, the surface based EKF framework can provide a reliable 2D feature matching guidance for each feature in the 3D surface map. This maintains a chance to relocate a feature that was lost for a significant period of time. Such a surface based framework provides persistent feature tracking over time, which is crucial to drift free surface tracking. With implementation on a Graphic Unit Processor (GPU), real time performance is achieved.

Thesis (M.S. in environmental science)--Washington State University, December 2009.
Title from PDF title page (viewed on Jan. 22, 2010). "School of Earth and Environmental Science." Includes bibliographical references (p. 18-23).

Current methods for measuring energy flow rate in a pipe use a variety of invasive sensors, including temperature sensors, turbine flow meters, and vortex shedding devices. These systems are costly to buy and install. A new approach that uses non-invasive sensors that are easy to install and less expensive has been developed. A thermal interrogation method using heat flux and temperature measurements is used. A transient thermal model, lumped capacitance method LCM, before and during activation of an external heater provides estimates of the fluid heat transfer coefficient h and fluid temperature. The major components of the system are a thin-foil thermocouple, a heat flux sensor (PHFS), and a heater. To minimize the thermal contact resistance R" between the thermocouple thickness and the pipe surface, two thermocouples, welded and parallel, were tested together in the same set-up. Values of heat transfer coefficient h, thermal contact resistance R", time constant �[BULLET], and the water temperature �[BULLET][BULLET], were determined by using a parameter estimation code which depends on the minimum root mean square RMS error between the analytical and experimental sensor temperature values. The time for processing data to get the parameter estimation values is from three to four minutes. The experiments were done over a range of flow rates (1.5 gallon/minute to 14.5 gallon/minute). A correlation between the heat transfer coefficient h and the flow rate Q was done for both the parallel and the welded thermocouples. Overall, the parallel thermocouple is better than the welded thermocouple. The parallel thermocouple gives small average thermal contact resistance average R"=0.00001 (m2.�[BULLET][BULLET]/W), and consistence values of water temperature and heat transfer coefficient h, with good repeatability and sensitivity. Consequently, a non-invasive energy flow rate meter or (BTU) meter can be used to estimate the flow rate and the fluid temperature in real life.
MS

Background: The preventable risk factors for cardiovascular diseases (CVD) and diabetes cluster together and can be tracked from childhood into adulthood. There is evidence that sleep, cardiorespiratory fitness and socioeconomic status (SES) are related to the component risk factors of cardiometabolic syndrome, but this is mainly in adults. Current interventions to prevent cardiometabolic syndrome, also, are not robust enough and multisectoral approaches are still lacking in preventing these preventable risk factors. The aim of this thesis is to evaluate prevalence, identify some of the causes of these risk factors, their social determinants and how they are associated with another in English schoolchildren. Setting: Field·based research including schoolchildren from the East of England, United Kingdom. Methods: Cross~section of English state schoolchildren between lO~16 years participating in the East of England Healthy Hearts study. Height, weight and blood pressure (BP) measured by stadiometer, weighing scales and automated BP monitors using standard procedures respectively. Cardiorespiratory fitness assessed by the 20m shuttle~run test. Demographic data, screen time, sleep & wake time and physical activity (P A) levels were measured using questionnaires. Schoolchildren level of deprivation was measured using English Index of Multiple Deprivation. Metabolic risk profiles were categorised based on weight status and SBP status. Findings: Overall, 36% of schoolchildren were exposed to over 2 hours of daily screen time. Those reportiIlg <2h daily screen time were more likely to be active than 1 • . those reporting 2-4 h (OR 1.51, 95%CI 1.26-1.82) or >4h (OR 2.26, 95%CI 1.91 - 2.67). Prevalence of elevated mean arterial pressure (MPJl) was 14.8% overall but rose to 35.7% in those who were both obese and unfit. When compared with schoolchildren engaging in PA daily with adults in their household, schoolchildren who have reported no PA daily with adults in their household were likely (OR 1.54, 95%CI 1.07-2.20) to have an elevated MR profile. Rural children were more active than those from urban areas, but this was not evident when a trilateral division was used. About 40% of schoolchildren go to bed late at night. Late bedtime was associated with deprivation in schoolchildren. Compared to those with <2hours of daily screen time, the odds ratios for late bedtimes were higher in schoolchildren who spend 2-4 hours on screen time (OR 1.50, 95%CI 1.07- 2.09) and highest in those with> 4 hours of daily screen time (OR 1.97, 95%CI 1.34-2.89). Interpretations: Sedentary behaviour, parental influences, cardiorespiratory fitness, place and location of habitation are associated with the causes of CVD and component factors of cardiometabolic syndrome in schoolchildren. There was a high prevalence of>2h daily screen time in English schoolchildren. PA is lower in children reporting 2-4h versus <2h daily screen time and lower still in those classified'as heavy users (>4h) independent of deprivation, Increasing cardiorespiratory fitness level may have a positive impact on the weight-related elevations of MAP seen in obese and overweight schoolchildren. Joint PA with an adult within household could increase schoolchildren's cardiorespiratory fitness level, PA level and may reduce the risk of metabolic diseases. Rural environments support PA in children but not PA of adole scents, Town and fringe areas with mixed elements of rural and urban land use appear to fac ilitate and sustain PA in both children and adolescents, High screen time 2 , j and deprivation may explain lateness in bedtime in English schoolchildren. Family centred interventions may be important to reduce screen time and improve metabolic profile .

Assumptions Advanced MIS procedures in neonates & infants <5 kg are a very demanding field because of: • very small anatomical structures • limited operative spaces (5-7 cm3) Postulate 3D laparoscopy improves operative time & precision in small spaces Advantages in 3D laparoscopy are mostly described in adults for better depth perception, more precise visualization of anatomical structures, as well as for complex manoeuvres such as suturing. In the pediatric field these data are lacking. In collaboration with Neuromed (Neuromed Spa, Torino) and Storz (Karl Storz, Tuttlingen, Germany) we tested 3D 4mm scopes specific for pediatric laparoscopy with a 3D HD camera, with the possibility to shift from 3D to 2D. In vitro setting – 1 With Visionsense III Stereoscopic Endoscopy System (Neuromed Spa), FDA and CE approved for pediatric surgery, we performed a comparative study between surgical skills achievements in subjects without any surgical experience, using 2D and a 3D laparoscopic equipment. 3 skills were evaluated in 2D and 3D modalities. 20 pediatrics residents without any previous laparoscopic experience were randomly divided in two groups and evaluated doing object transfer and basic surgical manoeuvres in a laparoscopic simulator validated for pediatric surgery. Switching the type of vision from 2D to 3D we evaluated bimanual dexterity, efficiency, tissue handling in both modalities. Time and error rates (missed attempts, dropped objects, and failure to complete the task) were recorded. In vitro setting – 2 Experimental project comparing 2D vs 3D laparoscopic camera in a set-up standardized and validated for Pediatric Surgeons. With Storz TipCam 4mm, we performed a comparative study between surgical skills achievements in experienced pediatric surgeons. Four skills were evaluated in 2D and 3D modalities. 10 pediatric surgeons with more than 50 MIS procedures were randomly divided in two groups and evaluated doing 3 training modules (“threading”, “suturing”, “tension suturing” and “intestinal anastomosis”) in a laparoscopic simulator (iSIM2 – iSurgicals, Chorley, UK). Switching the type of vision from 2D to 3D we evaluated bimanual dexterity, efficiency, tissue handling in both modalities. Time and error rates (missed attempts and failure to complete the task) were recorded. Inconveniences related to the 3D vision were also recorded. Surgical Application Using Visionsense III Stereoscopic Endoscopy System and Storz TipCam 4mm we performed 40 laparoscopic/thoracoscopic procedures in children and neonates hospitalized at the Regina Margherita Children’s Hospital. Operative time and intra- or post-operative complications were recorded.

Les activités anthropiques causent des invasions biologiques qui sont devenues un problème mondial susceptible de causer des dommages écologiques (p. ex., sur la biodiversité et l’habitat), économiques (sur les industries) et sociaux (sur le bien-être humain). La prévention et la détection précoce des nouvelles invasions sont des éléments essentiels pour la gestion des risques et des impacts sur les écosystèmes et les économies. Bien sûr, la prévention est préférable, mais la détection précoce est une étape cruciale pour enrayer la propagation ultérieure des espèces envahissantes, car elle offre la possibilité de les éradiquer avant les phases d’établissement de la population et de propagation. Bien qu’il s’agisse d’une option de gestion efficace en matière de coût et de temps, la détection précoce exige un effort d’échantillonnage considérable pour détecter les populations envahissantes aux tout premiers stades de leur invasion. En utilisant le système benthique marin comme modèle, quatre études interdépendantes ont été menées pour identifier des stratégies d’échantillonnage susceptibles d’améliorer notre capacité à détecter des populations envahissantes rares et à comprendre les patrons et processus écologiques de recrutement benthique à multiples échelles spatiales et temporelles. Plus précisément, ces études expérimentales sur le terrain visaient à (1) évaluer la relation entre l’approvisionnement en larves et la fixation dans une population envahissante isolée, (2) déterminer la durée de l’échantillonnage et de la fréquence à l’aide de plaques de fixation pour la détection d’espèces rares, (3) déterminer l’importance relative aux sources de variations spatiales et temporelles du recrutement benthique, et (4) examiner l’effet de l’échelle spatiale de l’échantillonnage sur la détection des espèces en analysant les patrons de recrutement à de multiples échelles sur quatre ordres de grandeur allant de la dizaine de mètres à la dizaine de kilomètres. Première étude : contrairement à l’hypothèse originale d’une relation étroite entre l’approvisionnement et la fixation initiale, l’approvisionnement en larves était plutôt un facteur déterminant de la fixation aux échelles moyennes. Ces résultats suggèrent que la force de cette relation s’affaiblit avec l’augmentation de l’échelle spatiale des observations de terrain. Néanmoins, un quart de la variation de la fixation à moyenne échelle peut encore être expliqué par l’approvisionnement sur des courtes échelles de temps (une semaine). Par conséquent, cette relation confirme l’utilité des plaques de fixation en tant qu’outil efficace pour la détection précoce aux échelles moyennes dans une marina, car une faible densité de recrutement sur les plaques correspond à une faible abondance de propagules envahissantes dans la colonne d’eau...
Les activités anthropiques causent des invasions biologiques qui sont devenues un problème mondial susceptible de causer des dommages écologiques (p. ex., sur la biodiversité et l’habitat), économiques (sur les industries) et sociaux (sur le bien-être humain). La prévention et la détection précoce des nouvelles invasions sont des éléments essentiels pour la gestion des risques et des impacts sur les écosystèmes et les économies. Bien sûr, la prévention est préférable, mais la détection précoce est une étape cruciale pour enrayer la propagation ultérieure des espèces envahissantes, car elle offre la possibilité de les éradiquer avant les phases d’établissement de la population et de propagation. Bien qu’il s’agisse d’une option de gestion efficace en matière de coût et de temps, la détection précoce exige un effort d’échantillonnage considérable pour détecter les populations envahissantes aux tout premiers stades de leur invasion. En utilisant le système benthique marin comme modèle, quatre études interdépendantes ont été menées pour identifier des stratégies d’échantillonnage susceptibles d’améliorer notre capacité à détecter des populations envahissantes rares et à comprendre les patrons et processus écologiques de recrutement benthique à multiples échelles spatiales et temporelles. Plus précisément, ces études expérimentales sur le terrain visaient à (1) évaluer la relation entre l’approvisionnement en larves et la fixation dans une population envahissante isolée, (2) déterminer la durée de l’échantillonnage et de la fréquence à l’aide de plaques de fixation pour la détection d’espèces rares, (3) déterminer l’importance relative aux sources de variations spatiales et temporelles du recrutement benthique, et (4) examiner l’effet de l’échelle spatiale de l’échantillonnage sur la détection des espèces en analysant les patrons de recrutement à de multiples échelles sur quatre ordres de grandeur allant de la dizaine de mètres à la dizaine de kilomètres. Première étude : contrairement à l’hypothèse originale d’une relation étroite entre l’approvisionnement et la fixation initiale, l’approvisionnement en larves était plutôt un facteur déterminant de la fixation aux échelles moyennes. Ces résultats suggèrent que la force de cette relation s’affaiblit avec l’augmentation de l’échelle spatiale des observations de terrain. Néanmoins, un quart de la variation de la fixation à moyenne échelle peut encore être expliqué par l’approvisionnement sur des courtes échelles de temps (une semaine). Par conséquent, cette relation confirme l’utilité des plaques de fixation en tant qu’outil efficace pour la détection précoce aux échelles moyennes dans une marina, car une faible densité de recrutement sur les plaques correspond à une faible abondance de propagules envahissantes dans la colonne d’eau...
Les activités anthropiques causent des invasions biologiques qui sont devenues un problème mondial susceptible de causer des dommages écologiques (p. ex., sur la biodiversité et l’habitat), économiques (sur les industries) et sociaux (sur le bien-être humain). La prévention et la détection précoce des nouvelles invasions sont des éléments essentiels pour la gestion des risques et des impacts sur les écosystèmes et les économies. Bien sûr, la prévention est préférable, mais la détection précoce est une étape cruciale pour enrayer la propagation ultérieure des espèces envahissantes, car elle offre la possibilité de les éradiquer avant les phases d’établissement de la population et de propagation. Bien qu’il s’agisse d’une option de gestion efficace en matière de coût et de temps, la détection précoce exige un effort d’échantillonnage considérable pour détecter les populations envahissantes aux tout premiers stades de leur invasion. En utilisant le système benthique marin comme modèle, quatre études interdépendantes ont été menées pour identifier des stratégies d’échantillonnage susceptibles d’améliorer notre capacité à détecter des populations envahissantes rares et à comprendre les patrons et processus écologiques de recrutement benthique à multiples échelles spatiales et temporelles. Plus précisément, ces études expérimentales sur le terrain visaient à (1) évaluer la relation entre l’approvisionnement en larves et la fixation dans une population envahissante isolée, (2) déterminer la durée de l’échantillonnage et de la fréquence à l’aide de plaques de fixation pour la détection d’espèces rares, (3) déterminer l’importance relative aux sources de variations spatiales et temporelles du recrutement benthique, et (4) examiner l’effet de l’échelle spatiale de l’échantillonnage sur la détection des espèces en analysant les patrons de recrutement à de multiples échelles sur quatre ordres de grandeur allant de la dizaine de mètres à la dizaine de kilomètres. Première étude : contrairement à l’hypothèse originale d’une relation étroite entre l’approvisionnement et la fixation initiale, l’approvisionnement en larves était plutôt un facteur déterminant de la fixation aux échelles moyennes. Ces résultats suggèrent que la force de cette relation s’affaiblit avec l’augmentation de l’échelle spatiale des observations de terrain. Néanmoins, un quart de la variation de la fixation à moyenne échelle peut encore être expliqué par l’approvisionnement sur des courtes échelles de temps (une semaine). Par conséquent, cette relation confirme l’utilité des plaques de fixation en tant qu’outil efficace pour la détection précoce aux échelles moyennes dans une marina, car une faible densité de recrutement sur les plaques correspond à une faible abondance de propagules envahissantes dans la colonne d’eau. Deuxième étude : des durées d’échantillonnage intermédiaires d’une à deux semaines (l’échelle des traitements allant d’un jour à un mois) étaient la durée optimale de déploiement de la plaque de fixation pour la détection des espèces « rares » (c’est-à-dire, des le début du recrutement). Une analyse au niveau de l’assemblage montre toutefois que l’augmentation de la durée et de la fréquence de l’échantillonnage augmentait logarithmiquement le nombre total d’espèces rares observées. Ces résultats espèce par espèce et au niveau de l’assemblage démontrent que la modification des éléments temporels de l’échantillonnage, tels que la durée et la fréquence, peut affecter considérablement la détection d’espèces. Troisième étude : après avoir évalué plusieurs sources spatiales et temporelles (le site, la région, la saison, et l’année), le moment choisi pour le déploiement des plaques est apparu comme étant la plus grande source de variabilité du recrutement benthique d’espèces rares. En particulier, le moment optimal pour la détection précoce serait en automne (a) lorsque le recrutement saisonnier d’espèces envahissantes établies tend à atteindre un pic et (b) lorsque la détection au niveau du site d’espèces envahissantes rares tend à se produire. Quatrième étude : l’échelle spatiale dominante dans le recrutement d’espèces rares est la plus petite (centaine de mètres). Cette échelle dominante peut être interprétée comme étant la bonne échelle spatiale pour la détection d’espèces rares. Une analyse plus poussée a montré que si l’échantillonnage a été structuré de manière aléatoire, l’échantillonnage à des échelles intermédiaires (millier de mètres) devient l’échelle optimale pour la détection d’espèces rares. Ces résultats élucident les différences de variabilité naturelle de la population benthique entre multiples échelles d’espace et de temps pour des espèces rares et communes. Ces études écologiques font partie d’une boîte à outils de détection précoce nécessaire à la gestion des espèces envahissantes marines en renseignant sur la manière dont l’échantillonnage des espèces rares doit être faite à multiples échelles spatio-temporelles. Des expériences de terrain similaires optimisant la détection d’espèces rares (au-delà de l’utilisation de plaques de fixation pour détecter les organismes benthiques dans les provinces Maritimes canadiennes) devraient être réalisées pour d’autres taxons, régions, t outils d’échantillonnage—en particulier, les envahisseurs à haut risque prévus, les invasions futures, et les outils récemment développés.
Les activités anthropiques causent des invasions biologiques qui sont devenues un problème mondial susceptible de causer des dommages écologiques (p. ex., sur la biodiversité et l’habitat), économiques (sur les industries) et sociaux (sur le bien-être humain). La prévention et la détection précoce des nouvelles invasions sont des éléments essentiels pour la gestion des risques et des impacts sur les écosystèmes et les économies. Bien sûr, la prévention est préférable, mais la détection précoce est une étape cruciale pour enrayer la propagation ultérieure des espèces envahissantes, car elle offre la possibilité de les éradiquer avant les phases d’établissement de la population et de propagation. Bien qu’il s’agisse d’une option de gestion efficace en matière de coût et de temps, la détection précoce exige un effort d’échantillonnage considérable pour détecter les populations envahissantes aux tout premiers stades de leur invasion. En utilisant le système benthique marin comme modèle, quatre études interdépendantes ont été menées pour identifier des stratégies d’échantillonnage susceptibles d’améliorer notre capacité à détecter des populations envahissantes rares et à comprendre les patrons et processus écologiques de recrutement benthique à multiples échelles spatiales et temporelles. Plus précisément, ces études expérimentales sur le terrain visaient à (1) évaluer la relation entre l’approvisionnement en larves et la fixation dans une population envahissante isolée, (2) déterminer la durée de l’échantillonnage et de la fréquence à l’aide de plaques de fixation pour la détection d’espèces rares, (3) déterminer l’importance relative aux sources de variations spatiales et temporelles du recrutement benthique, et (4) examiner l’effet de l’échelle spatiale de l’échantillonnage sur la détection des espèces en analysant les patrons de recrutement à de multiples échelles sur quatre ordres de grandeur allant de la dizaine de mètres à la dizaine de kilomètres. Première étude : contrairement à l’hypothèse originale d’une relation étroite entre l’approvisionnement et la fixation initiale, l’approvisionnement en larves était plutôt un facteur déterminant de la fixation aux échelles moyennes. Ces résultats suggèrent que la force de cette relation s’affaiblit avec l’augmentation de l’échelle spatiale des observations de terrain. Néanmoins, un quart de la variation de la fixation à moyenne échelle peut encore être expliqué par l’approvisionnement sur des courtes échelles de temps (une semaine). Par conséquent, cette relation confirme l’utilité des plaques de fixation en tant qu’outil efficace pour la détection précoce aux échelles moyennes dans une marina, car une faible densité de recrutement sur les plaques correspond à une faible abondance de propagules envahissantes dans la colonne d’eau. Deuxième étude : des durées d’échantillonnage intermédiaires d’une à deux semaines (l’échelle des traitements allant d’un jour à un mois) étaient la durée optimale de déploiement de la plaque de fixation pour la détection des espèces « rares » (c’est-à-dire, des le début du recrutement). Une analyse au niveau de l’assemblage montre toutefois que l’augmentation de la durée et de la fréquence de l’échantillonnage augmentait logarithmiquement le nombre total d’espèces rares observées. Ces résultats espèce par espèce et au niveau de l’assemblage démontrent que la modification des éléments temporels de l’échantillonnage, tels que la durée et la fréquence, peut affecter considérablement la détection d’espèces. Troisième étude : après avoir évalué plusieurs sources spatiales et temporelles (le site, la région, la saison, et l’année), le moment choisi pour le déploiement des plaques est apparu comme étant la plus grande source de variabilité du recrutement benthique d’espèces rares. En particulier, le moment optimal pour la détection précoce serait en automne (a) lorsque le recrutement saisonnier d’espèces envahissantes établies tend à atteindre un pic et (b) lorsque la détection au niveau du site d’espèces envahissantes rares tend à se produire. Quatrième étude : l’échelle spatiale dominante dans le recrutement d’espèces rares est la plus petite (centaine de mètres). Cette échelle dominante peut être interprétée comme étant la bonne échelle spatiale pour la détection d’espèces rares. Une analyse plus poussée a montré que si l’échantillonnage a été structuré de manière aléatoire, l’échantillonnage à des échelles intermédiaires (millier de mètres) devient l’échelle optimale pour la détection d’espèces rares. Ces résultats élucident les différences de variabilité naturelle de la population benthique entre multiples échelles d’espace et de temps pour des espèces rares et communes. Ces études écologiques font partie d’une boîte à outils de détection précoce nécessaire à la gestion des espèces envahissantes marines en renseignant sur la manière dont l’échantillonnage des espèces rares doit être faite à multiples échelles spatio-temporelles. Des expériences de terrain similaires optimisant la détection d’espèces rares (au-delà de l’utilisation de plaques de fixation pour détecter les organismes benthiques dans les provinces Maritimes canadiennes) devraient être réalisées pour d’autres taxons, régions, t outils d’échantillonnage—en particulier, les envahisseurs à haut risque prévus, les invasions futures, et les outils récemment développés.
As a consequence of anthropogenic activities, biological invasions have become a global problem that can cause ecological (e.g., biodiversity and habitat), economic (industries), and social (human wellbeing) harm. Prevention and early detection of new invasions are vital components of managing risks and impacts to ecosystems and economies. Prevention is, of course, preferred but early detection is a critical step that can ultimately stop future spread of invasive species because it provides an opportunity for eradication before population growth and spread. Despite being a cost- and time-effective management option, early detection requires considerably high sampling effort to detect incipient invasive populations at the early stages of their invasion. Using the marine benthic system as a model, four inter-related studies were carried out to identify sampling strategies that could enhance our ability to detect rare invasive populations and to understand ecological patterns and processes of benthic recruitment across multiple scales of space and time. Specifically, these experimental field studies aimed to (1) evaluate the relationship between propagule supply and settlement in a closed invasive population, (2) determine the optimal sampling duration and frequency using settlement plates to detect rare species, (3) ascertain the relative importance of spatial and temporal sources of variation in benthic recruitment, and (4) examine how the spatial scale of sampling affects species detection by analyzing recruitment patterns at multiple scales across four orders of magnitudes ranging from tens of metres to tens of kilometres. First study: Contrary to the expectation of a strong relationship between supply and initial settlement, larval supply was instead a limited determinant of settlement at mesoscales. This finding suggests that the strength of this relationship weakens as the spatial scale increased from previously reported small-scale field observations to mesoscales of the present study. Nonetheless, a quarter of the variation in settlement can still be explained by supply over short timescales (one week). Therefore, this relationship supports the utility of settlement plates as an effective tool for early detection at mesoscales within a marina because low densities of recruitment on plates correspond to low abundances of invasive propagules in the water column...
As a consequence of anthropogenic activities, biological invasions have become a global problem that can cause ecological (e.g., biodiversity and habitat), economic (industries), and social (human wellbeing) harm. Prevention and early detection of new invasions are vital components of managing risks and impacts to ecosystems and economies. Prevention is, of course, preferred but early detection is a critical step that can ultimately stop future spread of invasive species because it provides an opportunity for eradication before population growth and spread. Despite being a cost- and time-effective management option, early detection requires considerably high sampling effort to detect incipient invasive populations at the early stages of their invasion. Using the marine benthic system as a model, four inter-related studies were carried out to identify sampling strategies that could enhance our ability to detect rare invasive populations and to understand ecological patterns and processes of benthic recruitment across multiple scales of space and time. Specifically, these experimental field studies aimed to (1) evaluate the relationship between propagule supply and settlement in a closed invasive population, (2) determine the optimal sampling duration and frequency using settlement plates to detect rare species, (3) ascertain the relative importance of spatial and temporal sources of variation in benthic recruitment, and (4) examine how the spatial scale of sampling affects species detection by analyzing recruitment patterns at multiple scales across four orders of magnitudes ranging from tens of metres to tens of kilometres. First study: Contrary to the expectation of a strong relationship between supply and initial settlement, larval supply was instead a limited determinant of settlement at mesoscales. This finding suggests that the strength of this relationship weakens as the spatial scale increased from previously reported small-scale field observations to mesoscales of the present study. Nonetheless, a quarter of the variation in settlement can still be explained by supply over short timescales (one week). Therefore, this relationship supports the utility of settlement plates as an effective tool for early detection at mesoscales within a marina because low densities of recruitment on plates correspond to low abundances of invasive propagules in the water column...

Les progrès en anesthésie et en réanimation ont pour objectifs la réduction de la durée de surveillance et l’amélioration de la qualité de la récupération. Pour le cas particulier de l’assistance respiratoire, la capacité de surveiller et d’optimiser l’adaptation entre le patient et sa machine d’assistance est déterminante pour la qualité et la conduite des soins. Ce travail de thèse concerne dans sa première partie la mise en place et la validation d’un outil instrumental permettant de caractériser un comportement respiratoire par l’étude cycle à cycle du délai d’activation inspiratoire entre les muscles des voies aériennes supérieures et de la cage thoracique. Cet outil doit prendre en compte les contraintes imposées par le milieu clinique, telle qu’une mesure non-invasive des muscles respiratoires. La mesure cycle à cycle et par voie de surface du délai d’activation est un véritable challenge dans un environnement clinique qui est fortement perturbé. La démarche choisie ici est double avec en parallèle : i) la mise en place d’un outil de détection d’événements menée sous supervision ; ii) la définition d’un protocole original sur sujets sains prenant en compte les contraintes cliniques et permettant de valider l’outil et de constituer une base de connaissance pour envisager l’automatisation des procédés dans un travail futur. D’un point de vue psychologique, l’influence de la fréquence respiratoire sur le délai d’activation de l’inspiration n’a pas été étudiée à ce jour. Ce délai a donc été mesuré en condition de normocapnie à différentes fréquences respiratoires imposées par un stimulus sonore. Une étude statistique montre que l’instrument permet de distinguer deux situations psychologiques du protocole expérimental, ce qui en démontre la sensibilité. La deuxième partie de ce travail de thèse s’inscrit dans le cadre d’une optimisation des méthodes de détection de singularité d’intérêt. La solution choisie ici se base sur l’intensité structurelle qui calcule la densité de maxima d’ondelettes à différentes échelles et permet une localisation des singularités d’un signal bruité. Une formulation de cet outil qui utilise la transformée de Berkner est proposée. Celle-ci permet le chaînage des maxima d’ondelettes afin de positionner précisément les landmarks du signal. Le filtrage de l’artefact ECG dans l’EMG diaphragmatique sans signal de référence est proposé comme exemple d’application
Better care in an anesthesia and critical care reduces monitoring duration of monitoring and improves the quality of recovery. For the particular case of respiratory assistance, the capacity to track and optimize patient-ventilator synchrony is essential to quality care. As a first step, this thesis addresses the development and validation of an instrument which characterizes respiratory behavior by studying the time lag between onset of upper airway muscles and rib cage muscles, cycle by respiration. This tool must take into account the constraints imposed by the clinical environment; measuring respiratory muscles by surface electromyographic measure (EMG). Measurement of the onset time lag, cycle by cycle and non-invasively, is a true challenge in a critical care clinical environment. Here the approach is two-fold: i) The development of a tool for events detection. Ii) The definition of an original protocol on healthy subjects. The tool development constitutes a knowledge bases to eventually develop automation of the processes in future work. From a physiological point of view, the influence of respiratory rate on the EMG onset time lag during inspiration has not been studied. Thus, we measured this time lag in normocapnia at various respiratory rates imposed by a sound stimulus. Statistically, the instrumental tool can distinguish two physiological situations in this experimental protocol, which confirms its sensitivity. The second step of this thesis is part of an optimization of events detection methods with singularities of interest. The chosen solution is based on structural intensity which computes the "density" of the locations of the modulus maxima of wavelet representation along various scales in order to identify singularities of an unknown signal. An improvement is proposed by applying Berkner transform which allows maxima linkage to insure accurate localization of landmarks. An application to cancel ECG interference in diaphragmatic EMG without a reference signal is also proposed

During last decade, molecular biology evolution has lead to a deep knowledge of human genome allowing the in-utero diagnosis of a large number of genetic diseases. Now adays performing a prenatal diagnosis of chromosomal abnormalities and of genetic diseases, requires genetic material from the fetus and this is possible only by invasive procedures such as amniocentesis and chorionic villus sampling. The risk of miscarriage of these technics is between 0.5% and 1% and considering these limits, new alternative and non-invasive screening methods, based on ultrasound and/or biochemical parameters of maternal blood, were developed. The disavantages of these methods are the probabilistic aspect of the results. There was an increasing interest in a new approach that could keep to zero the risk of miscarriage, with an extension of fetal genetic materials screening to a large number of women at the beginning of pregnancy, leading a decreased physic and psychological impact. In 1997 it was demonstrated the presence of cell-free fetal DNA (cffDNA) in the maternal blood and this has opened up new possibilities for a non-invasive prenatal diagnosis (NIPD). The cell-free fetal DNA originates from apoptotic trophoblasts on placenta’s surface and comprises around 3-6% of total cell-free DNA in maternal circulation. The cffDNA consists of short DNA fragments (<200bp). Fetal DNA can be detected from 32 days of gestation (though only reliably from 7 weeks) and it’s concentration increases with gestational age (21% per week during the first three months) with a sharp peak during last 8 weeks of pregnancy. The cffDNA is completely removed after delivery. The main problem related to the application of this NIPD is the high maternal background, so researchers have initially focused their attention on the detection of sequences that are absent in the maternal genome, such as DNA sequences from chromosome Y of male fetuses, the determination of fetal RhD genotype in women RhD-negative, and the detection of paternal mutations in maternal plasma. Although, the Real Time qPCR amplification of fetal sequences is the widespread method for cffDNA study, there are still a lot of studies focused on the development different protocols for detection of minimal differences between maternal and fetal DNA. The aim of this PhD thesis is the study and setup of different methods to identify fetal genomic sequences in maternal circulation. The research project was divided in three steps: the first one was focused on the validation of Real-Time qPCR protocol, applied to the detection and quantification of total free DNA and of cffDNA in pregnancies with a male fetus; the second was focused on the develop of a reliable protocol for the identification of fetal genomic sequences useful to recognize cffDNA in pregnancies with a female fetus, by the mini-sequencing technics; finally, the last step was focused on the validation of an analytical protocol to verify the presence/absence of paternal mutations in maternal plasma using nested PCR allele-specific. The results demonstrated here for each technic, show a high sensibility and resolution capacity, together with an easy and rapid handling. Furthermore, the combination of the two technics (Real-Time qPCR and mini-sequencing reaction) was essential in order to exclude the presence of a paternal mutation in the fetal genome in every case where a mutation wasn’t identified. The ability to exclude the presence of the paternal mutation in the fetus by analysis of maternal plasma avoid the utilization of invasive prenatal tests and, at the same time, reassures the couple early in the course of the pregnancy about the recurrence of the disease, thus avoiding significant anxiety.
Negli ultimi anni l'evoluzione della biologia molecolare ha permesso una conoscenza sempre maggiore del genoma umano e consente ormai la diagnosi in utero di un numero crescente di patologie genetiche. Al momento attuale la diagnostica prenatale di anomalie cromosomiche o di malattie genetiche richiede il prelievo di cellule fetali ottenibili con metodiche invasive, l'amniocentesi e la villocentesi. Queste tecniche comportano un rischio di provocare un aborto compreso fra 0.5% e 1%. Di fronte a questi limiti delle metodiche invasive sono stati messi a punto alcuni metodi di screening alternativi non invasivi, basati su parametri ecografici fetali e/o biochimici su sangue materno, che però hanno il limite di fornire risposte solo di tipo probabilistico. L'introduzione di un test realmente alternativo di diagnosi prenatale non invasiva che permetta di eliminare il rischio di aborto legato all’amniocentesi e alla villocentesi è fortemente attesa. Infatti un simile test permetterebbe una estensione dell'analisi del materiale genetico fetale a molte più donne all'inizio della gravidanza e diminuirebbe l'impatto fisico e psicologico di questo tipo di indagine. Nel 1997 uno studio ha dimostrato la presenza di DNA libero fetale (cell-free fetal DNA, cffDNA) nel plasma materno e ha evidenziato la sua potenzialità per una diagnosi prenatale non invasiva (NIPD). Durante i 15 anni successivi, si è sviluppata la ricerca di base sulle caratteristiche del DNA libero fetale e molti ricercatori hanno studiato la biologia e il significato clinico del trasporto di cffDNA nel circolo materno. Il DNA libero fetale origina dall’apoptosi dei trofoblasti costantemente rimpiazzati sulla superficie della placenta e comprende circa il 3-6% del DNA libero totale nella circolazione materna. E’ stato inoltre osservato che è costituito da corti frammenti di DNA (<200bp) piuttosto che interi cromosomi e che la sua concentrazione aumenta gradualmente durante la gravidanza: è rilevabile nella circolazione materna già a 32 giorni circa di gestazione (in quantità affidabile solo dopo le 7 settimane) e aumenta del 21% ogni settimana nel primo trimestre, con un forte picco durante le ultime 8 settimane di gravidanza per poi venire rapidamente rimosso dalla circolazione materna subito dopo il parto. L’utilizzo del DNA fetale libero come mezzo per la diagnosi prenatale non invasiva di malattie genetiche fino ad ora è fortemente limitato dall’elevato background di DNA materno pertanto le prime strategie messe a punto per l’identificazione del DNA libero fetale si sono basate sul rilevamento di sequenze assenti nel genoma materno, come le sequenze Y-specifiche, la determinazione del genotipo RhD fetale in donne RhD-negative e l’identificazione di sequenze fetali con mutazioni ereditate dal padre. L’amplificazione tramite Real Time qPCR di sequenze unicamente fetali nel plasma di donne gravide rappresenta ad oggi il metodo di elezione per lo studio del DNA libero fetale, ma numerosi sforzi sono stati realizzati per la messa a punto di sistemi sempre più sensibili ed universali per rilevare le più piccole differenze tra il DNA fetale libero e quello materno, al fine di consentire un utilizzo su larga scala del cffDNA per la diagnosi prenatale non invasiva. Lo scopo di questa ricerca è stato quindi, la messa a punto di protocolli validi per l’identificazione e l’analisi di sequenze geniche fetali nella circolazione materna. Il progetto è stato quindi suddiviso in tre fasi: la prima fase ha comportato la messa a punto di opportuni protocolli di Real-Time qPCR per il rilevamento e la quantificazione sia del DNA libero totale estratto sia del cffDNA estratto in gravidanze con feto di sesso maschile; la seconda fase del progetto si è occupata di testare e sviluppare un protocollo affidabile per l’identificazione di sequenze geniche fetali utili al riconoscimento di cffDNA nelle gravidanze con feto di sesso femminile, mediante l’utilizzo della tecnica di mini-sequencing; l’ultima fase del progetto si è concentrata infine sulla messa a punto di un protocollo di verifica della presenza/assenza di mutazioni paterne in plasma materno mediante nested PCR allele-specifica. L’analisi dei risultati ha dimostrato, per ogni tecnica sviluppata, elevate sensibilità e capacità di risoluzione accoppiate a velocità e facilità di esecuzione, confermandone quindi l’applicabilità per una diagnosi prenatale non invasiva. Inoltre l’utilizzo in combinazione delle due tecniche (Real-Time qPCR e mini-sequencing) per la conferma della presenza del cffDNA nel campione in analisi, si è rilevata indispensabile per poter escludere che il feto abbia ereditato la mutazione paterna, in tutti i casi in cui non viene identificata la mutazione. L’esclusione della mutazione paterna nel feto attraverso l’analisi su plasma materno permetterebbe quindi di evitare l’utilizzo di procedure invasive per il prelievo di cellule fetali e avere questa informazione alla 9-10 settimana di gravidanza consentirebbe di rassicurare la coppia prima di qualsiasi altro test diagnostico di routine.

Background Waiting times of the fast-track of bladder cancer in Sweden are prolonged compared with set lead times.Aim To investigate if stage and grade of tumor affects waiting times.Method Retrospective single center observational study, Örebro University Hospital, Sweden. All patients who underwent resection of tumor or cystoscopy with biopsy via the fast-track between July 1st 2017 and December 31st 2018 were included, n=119.Result The waiting times of muscle invasive tumors were in general longer than for non-invasive tumors. Referral to TURBT - twelve days (p=0.047), referral to information of diagnosis to patient - seven days (p=0.04) and cystoscopy to TURBT - eleven days (p=0.041.Conclusion MIBC had longer waiting times to most steps of the fast-track. There are conflicting results in previous studies regarding whether extended waiting times result in worse outcomes in those with higher stage and grade of tumors or not. It is known that long waiting times results in higher mortality and psychological stress among the patients why reorganizations at the department should take place.

This research investigated the use of DNA fingerprinting to characterise the bacteria Streptococcus pneumoniae or pneumococcus, and hence gain insight into the development of new vaccines or antibiotics. Different bacterial DNA fingerprinting methods were studied, and a novel method was developed and validated, which characterises different cell coatings that pneumococci produce. This method was used to study the epidemiology of pneumococci in Queensland before and after the introduction of the current pneumococcal vaccine. This study demonstrated that pneumococcal disease is highly prevalent in children under four years, that the bacteria can `switch' its cell coating to evade the vaccine, and that some DNA fingerprinting methods are more discriminatory than others. This has an impact on understanding which strains are more prone to cause invasive disease. Evidence of the excellent research findings have been published in high impact internationally refereed journals.

Background Novel theranostic options for high-risk non-muscle invasive bladder cancer are urgently needed. This requires a thorough evaluation of experimental approaches in animal models best possibly reflecting human disease before entering clinical studies. Although several bladder cancer xenograft models were used in the literature, the establishment of an orthotopic bladder cancer model in mice remains challenging. Methods Luciferase-transduced UM-UC-3LUCK1 bladder cancer cells were instilled transurethrally via 24G permanent venous catheters into athymic NMRI and BALB/c nude mice as well as into SCID-beige mice. Besides the mouse strain, the pretreatment of the bladder wall (trypsin or poly-L-lysine), tumor cell count (0.5 × 106–5.0 × 106) and tumor cell dwell time in the murine bladder (30 min – 2 h) were varied. Tumors were morphologically and functionally visualized using bioluminescence imaging (BLI), magnetic resonance imaging (MRI), and positron emission tomography (PET). Results Immunodeficiency of the mouse strains was the most important factor influencing cancer cell engraftment, whereas modifying cell count and instillation time allowed fine-tuning of the BLI signal start and duration – both representing the possible treatment period for the evaluation of new therapeutics. Best orthotopic tumor growth was achieved by transurethral instillation of 1.0 × 106 UM-UC-3LUCK1 bladder cancer cells into SCID-beige mice for 2 h after bladder pretreatment with poly-L-lysine. A pilot PET experiment using 68Ga-cetuximab as transurethrally administered radiotracer revealed functional expression of epidermal growth factor receptor as representative molecular characteristic of engrafted cancer cells in the bladder. Conclusions With the optimized protocol in SCID-beige mice an applicable and reliable model of high-risk non-muscle invasive bladder cancer for the development of novel theranostic approaches was established.