<p>Positron Emission Tomography, PET, is a noninvasive medical imaging technique to get functional information of the kinetics of radioactive compound injected in the body. The data used in this thesis comes from a total of five H₂¹⁵O PET studies of one patient. This was done in order to study the blood flow in liver metastasis of the patient, before and after treatment.</p><p>A one compartment model was used to do the ROI based analyses. With a least square method in Matlab the unknown parameters in the model, such as the kinetic rate constants, the dispersion and the fraction of blood in the tissue, was extracted. Also a brief analysis of different parts of the metastases, edge and center, was done to see the variations within the metastases. The results show some increase of the blood flow after the treatment, and two of the three studied metastases showed a distinct difference of the activity in the center versus the edge. Given in the thesis are also some basic PET and compartmental modeling theory.</p> / <p>Positronemissionstomografi, PET, är en icke-invasiv medicinsk bildteknik för att få funktionell information om kinetiken av radioaktiva föreningar injicerade i kroppen. Det data som används i denna kandidatuppsats kommer från totalt fem H₂¹⁵O PET-studier av en patient. Detta gjordes för att studera blodflödet i levermetastaser hos patienten före och efter behandling.</p><p>En 1-kompartmentmodell användes för att göra ROI-baserade analyser. Med en minsta kvadrat-metod i Matlab kunde de okända parametrarna i modellen, såsom den kinetiska hastighetskonstanten, spridningen och andelen blod i vävnaden, fås ut. En kort analys gjordes också av olika delar av metastaserna, kanten och mitten, för att se variationerna inuti metastaserna. Resultaten visar en viss ökning av blodflödet efter behandlingen, och två av de tre studerade metastaser visade en tydlig skillnad av aktiviteten i mitten jämfört med kanten. I rapporten ges också grundläggande teori om bland annat PET och kompartmentmodellering.</p>

Positron Emission Tomography, PET, is a noninvasive medical imaging technique to get functional information of the kinetics of radioactive compound injected in the body. The data used in this thesis comes from a total of five H215O PET studies of one patient. This was done in order to study the blood flow in liver metastasis of the patient, before and after treatment. A one compartment model was used to do the ROI based analyses. With a least square method in Matlab the unknown parameters in the model, such as the kinetic rate constants, the dispersion and the fraction of blood in the tissue, was extracted. Also a brief analysis of different parts of the metastases, edge and center, was done to see the variations within the metastases. The results show some increase of the blood flow after the treatment, and two of the three studied metastases showed a distinct difference of the activity in the center versus the edge. Given in the thesis are also some basic PET and compartmental modeling theory. / Positronemissionstomografi, PET, är en icke-invasiv medicinsk bildteknik för att få funktionell information om kinetiken av radioaktiva föreningar injicerade i kroppen. Det data som används i denna kandidatuppsats kommer från totalt fem H215O PET-studier av en patient. Detta gjordes för att studera blodflödet i levermetastaser hos patienten före och efter behandling. En 1-kompartmentmodell användes för att göra ROI-baserade analyser. Med en minsta kvadrat-metod i Matlab kunde de okända parametrarna i modellen, såsom den kinetiska hastighetskonstanten, spridningen och andelen blod i vävnaden, fås ut. En kort analys gjordes också av olika delar av metastaserna, kanten och mitten, för att se variationerna inuti metastaserna. Resultaten visar en viss ökning av blodflödet efter behandlingen, och två av de tre studerade metastaser visade en tydlig skillnad av aktiviteten i mitten jämfört med kanten. I rapporten ges också grundläggande teori om bland annat PET och kompartmentmodellering.

A three-compartment model is extended to estimate the fate and transport of DEHP in a realistic residential environment. The model considered eight environmental media (i.e. air, particulate matter with six size fractions, vinyl flooring, carpet, furniture, dust, wall and ceiling). Particle movement (deposition and resuspension), dust removal (vacuuming), indoor cooking, and adsorption/absorption on indoor surfaces are included. The predicted airborne DEHP concentrations at steady state are within 0.1 [microgram]/m³ to 0.6 [microgram]/m³, which are similar to those measured in field studies. After vinyl flooring (the primary source) is removed, it takes 2 years for the indoor airborne DEHP level to reduce 0.01 [microgram]/m³, and the time increases significantly when carpet present. The results indicate that carpets as well as other interior surfaces may be important phthalate sinks and if the only removal mechanism is ventilation, strongly sorbing phthalate may persist for years. Phthalate amount in dust is strongly influenced by the deposition surface. The concentration of DEHP presents 10 times higher in dust on the source (vinyl flooring) than on the sink (furniture), and it takes more than a year for DEHP to reach equilibrium between bulk air and dust. The domestic activity of cooking is then included in the model and it shows that suspended particle concentration has a substantial impact on gas-phase DEHP level indoors, while the influence of ventilation is only to some extent. Three other SVOCs (DMP, BBP and DiDP) are also investigated and their environmental fates show that chemical’s vapour pressure and octanol/air partition coefficient have substantial influences on sorbing mechanisms and the gas phase and airborne concentrations. / text

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The use of non-Saccharomyces yeasts together with the yeast S. cerevisiae in multistarter wine fermentations has emerged as a useful tool to modulate wine aroma and/or to decrease the concentration of undesirable compounds. However, upon inoculation, these yeast species do not co-exist passively, but interact in various ways. While competition for nutrients and the excretion of killer toxins in an antagonistic relationship are obvious and well established types of interactions, some studies have suggested the existence of other forms of cellular or molecular interactions. One of these includes physical cell-cell contact and to our knowledge, only one previous study has confirmed its existence in wine yeasts. Yeast interactions are also influenced by other factors, such as ethanol concentration, however some studies have highlighted the role that dissolved oxygen plays on the survival of non-Saccharomyces yeasts and their ability to compete for space with S. cerevisiae and little research has focused on this. This study aimed to investigate the occurrence of a physical cell-cell and/or metabolic interaction between S. cerevisiae and L. thermotolerans in mixed culture fermentations of synthetic grape must. For this purpose, fermentations in a Double Compartment Bioreactor (DCB) which separates yeast population through the use of a membrane were compared to mixed fermentations in the absence of the membrane, using the same reactor. Furthermore, the impact of oxygen supply on yeast behaviour was also assessed. Following mixed culture fermentations in a DCB, it was observed that the presence of S. cerevisiae led to a significant decline in viability in L. thermotolerans. This decline was significantly less prominent in mixed cultures where the cells were in indirect contact. Together, the data provided evidence for both cell-cell and metabolic interactions whereby S. cerevisiae had a strong negative influence on the growth of L. thermotolerans. However, it was also observed that L. thermotolerans had some negative impact on the growth of S. cerevisiae, leading to a reduction in biomass (when in indirect contact) and a reduced maximum CFU/mL compared to pure cultures. The data also suggest that direct physical contact may increase the production of glycerol and propanol, but this needs further investigation. By decreasing the frequency at which oxygen pulses were provided, a reduction in biomass and increase in fermentation duration was observed for all fermentations. However, this effect was somewhat reduced in mixed cultures. Here, no impact on fermentation duration was observed and the decrease in biomass was less compared to pure cultures. The impact of these oxygen pulses was also greater on L. thermotolerans. In the latter yeast’s pure culture a slight increase in glycerol was observed when less oxygen was provided and in general there appeared to be no impact on acetic acid production. Furthermore, there was little or no impact on volatile production, however, more repeats might reveal different results and therefore more research is needed to confirm these results. To our knowledge, this is the first study of its kind to confirm a physical cell-cell interaction between the yeast pair S. cerevisiae and L. thermotolerans. / AFRIKAANSE OPSOMMING: Die gebruik van nie-Saccharomyces gis saam met die gis S. cerevisiae in multi-inokuleringskulture het die afgelope paar jaar as n goeie hulpmiddel na vore gekom om wyn aroma te moduleer en/of om die konsentrasie van ongewensde verbindings te verminder. Sodra inokulasie plaasgevind het, het hierdie gis die potensiaal om op verskeie maniere teenoor mekaar te reageer. Kompetisie vir nutriente en die afskeiding van toksiese verbindings in n antagonistiese verhouding is alreeds goed beskryf in die literatuur. Somige studies het, alhoewel, die bestaan van ander vorme van sellulêre of molekulêre interaksies voorgestel. Een van hierdie sluit in n fisiese sell-sell interaksie en so ver as wat ons kennis strek, het nog net een studie van tevore so ‘n interaksie bevestig tussen wyn giste. Gis interaksies word ook beïnvloed deur ander faktore, soos byvoorbeeld etanol konsentrasie. Terwyl sommige studies die rol wat opgelosde suurstof speel in die oorlewing van nie-Saccharomyces gis en hulle vermoë om te kompeteer vir spasie met S. cerevisiae alreeds beklemtoon, het min navorsing al hierop gefokus. Hierdie studie het gestreef om die voorkoms van n fisiese sell-sell en/of metaboliese interaksie tussen S. cerevisie en L. thermotolerans in gemengde kultuur fermentasies van sintetiese druiwe sap te ondersoek. Vir hierdie doeleinde was fermentasies uitgevoer met behulp van ‘n Dubbel Kompartement Bioreaktor (DKB) wat gis populasies skei deur middel van ‘n membraan en hierdie was vergelyk met gemengde kultuur fermentasies sonder die membraan in dieselfde reaktor sisteem. Verder was die impak van suurstof toevoer op gis gedrag ook geassesseer. Na afloop van gemengde kultuur fermentasies in ‘n DKB, was daar waargeneem dat die teenwoordigheid van S. cerevisiae gelei het tot ‘n betekenisvolle afname in lewensvatbaarheid in L. thermotolerans. Hierdie afname was aansienlik minder in gemengde kulture waar die gis in indirekte kontak was. Saam verskaf hierdie data bewyse vir n sell-sell asook metaboliese interaksie waardeur S. cerevisiae ‘n sterk, negatiewe invloed op die groei van L. thermotolerans gehad het. Daar was egter ook waargeneem dat L. thermotolerans tot ‘n mindere mate ‘n negatiewe impak op die groei van S. cerevisiae gehad het en dat dit gelei het tot ‘n verlaging in biomassa (toe die gis in indirekte kontak was) en ‘n verlaagde maksimum CFU/mL in vergelyking met suiwer kulture. Die data dui ook aan dat fisiese kontak kon gelei het tot ‘n verhoging in gliserol en propanol produksie, maar hierdie kort verdere ondersoek. Deur die frekwensie te verminder waardeur suurstof pulse aan die fermentasies verskaf was, was ‘n verlaging in biomassa produksie en ‘n verlenging in fermentasie tydperk waargeneem. Hierdie tendense was waargeneem in almal, behalwe die gemengde kultuur fermentasies. Die effek van suurstof puls verlaging was minder op hierdie fermentasies aangesien daar geen impak op fermentasie tydperk was nie en die verlaging in biomassa minder was. Die impak van hierdie suurstof pulse was ook groter op L. thermotolerans. ‘n Klein toename in gliserol produksie was waargeneem in laasgenoemde gis se suiwer kultuur toe minder suurstof beskikbaar was en oor die algemeen was asynsuur onveranderd. Verder was daar ‘n klein of geen impak op vlugtige verbindings nie, alhoewel, meer herhalings mag verskillende resultate lewer en daarom is meer navorsing nodig om hierde resultate te bevestig. So ver as wat ons kennis strek is hierdie die eerste studie van sy soort om ‘n fisiese sell-sell interaksie tussen die gispaar S. cerevisiae en L. thermotolerans te bevestig.

Les bassins d’infiltration sont de plus en plus utilisés en milieux urbains pour la réduction des eaux de ruissellement et la recharge des nappes phréatiques. Toutefois, leur fonctionnement est souvent affecté par des problèmes de colmatage, physiques, chimiques et/ou biologiques, qui conduisent à une diminution des capacités d’infiltration et à une altération potentielle de la qualité des eaux infiltrées. Aussi, la prévention de ce risque devient-elle un enjeu majeur pour garantir la pérennité des ouvrages d’infiltration et la qualité des eaux infiltrées. Si les mécanismes impliqués dans le colmatage sont décrits assez finement dans le cas des processus purement physiques ou géochimiques, les verrous scientifiques sont encore importants pour comprendre la contribution du compartiment biologique (biofilms, végétation, invertébrés). Ce travail de thèse avait ainsi pour objectif de quantifier l’influence du compartiment biologique sur les processus de colmatage et de décolmatage dans des bassins d’infiltration. Pour cela, il était composé de deux grands volets : (i) le premier visait à évaluer la contribution relative du biofilm et de l’accumulation de particules fines sur les paramètres hydrodynamiques du milieu poreux support d’infiltration, ceci dans 2 bassins aux caractéristiques contrastées, (ii) le second avait pour objectif d’évaluer les potentialités de processus écologiques (bioturbation, broutage, allélopathie) à décolmater les bassins par l’introduction de macro-organismes (invertébrés et macrophytes) en mésocosmes ou par encagements in situ. Les résultats ont mis en évidence le rôle déterminant de la composante phototrophe des biofilms sur la dégradation de perméabilité des supports d’infiltration. Un effet seuil de la biomasse phototrophe a été observé sur le rayon moyen des pores hydrauliquement fonctionnels, avec pour conséquences des effets non-linéaires sur la perméabilité. Face à ce colmatage biologique, les résultats obtenus en mésocosmes ont clairement montré que la présence de macrophytes tels que Vallisneria spiralis L. et Chara globularis L. permettait de réduire la biomasse algale par allélopathie. Par la suite, l'introduction par encagement dans un bassin d'infiltration de l’espèce V. spiralis a démontré sa potentialité à réduire le phénomène de colmatage en affectant la physiologie du biofilm algal. De plus, l'introduction du gastéropode aquatique Viviparus viviparus qui se nourrit directement du biofilm permettait de maintenir et même d’améliorer les capacités d’infiltration du bassin. Ces résultats offrent des perspectives intéressantes pour le développement futur de techniques d’ingénierie écologique dans la gestion et l’amélioration de la durée de vie des ouvrages d’infiltration. / Infiltration basins are increasingly used in urban areas for stormwater management or groundwater recharge. However, their functions are often affected by physical, chemical and / or biological clogging, leading to a decrease in infiltration rate and a potential alteration of infiltrated water quality. The prevention of clogging is therefore becoming a major challenge to ensure the sustainability of infiltration devices and the quality of infiltrated water. Although the mechanisms involved in clogging are accurately described for purely physical and geochemical processes, scientific obstacles still prevent from understanding the contribution of biological compartment (i.e. biofilms, vegetation, invertebrates). The aim of this work was to quantify the influence of biological compartment on clogging/unclogging processes in infiltration basins. It was divided in two objectives: (i) To assess the relative contribution of biofilm and fine particle accumulation on the hydrodynamic parameters of the porous media in two basins with contrasting characteristics. (ii) To assess the potential of ecological processes (bioturbation, grazing, allelopathy) to unclog the basins, by the introduction of macro-organisms (invertebrates and macrophytes) in mesocosms or in situ enclosures. Results highlighted the critical role of the phototrophic component of biofilms on the degradation of infiltration media permeability. A threshold effect of algal biomass was observed on the hydraulically functional pore size, with non-linear consequences on the permeability. Faced with this biological clogging, the results obtained with mesocosm experiments clearly showed that the presence of the macrophytes Vallisneria spiralis L. and Chara globularis L. could reduce algal biomass by allelopathy. The introduction of V. spiralis by enclosure in an infiltration basin then demonstrated its potential to reduce the clogging by affecting algal biofilm physiology. In addition, the introduction of the aquatic gastropod Viviparus viviparus, which feeds directly on the biofilm, allowed to maintain, and even improve, the infiltration capacity of the basin. These outcomes offer interesting perspectives for the future development of ecological engineering techniques, to manage and improve the lifetime of infiltration devices.

This diploma thesis is aimed at verifying the properties of joints of waterproofing membranes generaly used in underground constructions and also deals with the possible addition of a swelling profile as a barrier to permeating water through the defect in the waterproofing system. The most commonly used materials for waterproofing membranes are polymers. The work is focused on verifying the properties of automatic and manual welding joints of polyvinylchloride membrane. In actual practice, there is a pressure test being used for automatic weldings, and for manual weldings there are tests with a tear-off needle and a vacuum bell. In the laboratory, it is also possible to verify the joints using a peeling test and determining the shear strength of the joint using a testing device. In case of damaged waterproofing system and soaking of pressurized water, it is possible to use a swellable strip as a barrier for the water leaking from one injection compartment to another. At the end of the thesis there is a comparison of the waterproofing system without the swelling profile and the system including its application. The swelling profile has shown very good properties with regard to the infiltration of the flowing water into its structure, and so the amount of water that could be applied to the sample with the swelling profile was much higher than in the case of the generaly used waterproofing system.

Various convex analysis of mixtures (CAM) based algorithms have been developed to address real world blind source separation (BSS) problems and proven to have good performances in previous papers. This thesis reported the implementation of a comprehensive software CAM-Java, which contains three different CAM based algorithms, CAM compartment modeling (CAM-CM), CAM non-negative independent component analysis (CAM-nICA), and CAM non-negative well-grounded component analysis (CAM-nWCA). The implementation works include: translation of MATLAB coded algorithms to open-sourced R alternatives. As well as building a user friendly graphic user interface (GUI) to integrate three algorithms together, which is accomplished by adopting Java Swing API. In order to combine R and Java coded modules, an open-sourced project RCaller is used to handle the establishment of low level connection between R and Java environment. In addition, specific R scripts and Java classes are also implemented to accomplish the tasks of passing parameters and input data from Java to R, run R scripts in Java environment, read R results back to Java, display R generated figures, and so on. Furthermore, system stream redirection and multi-threads techniques are used to build a simple R messages displaying window in Java built GUI. The final version of the software runs smoothly and stable, and the CAM-CM results on both simulated and real DCE-MRI data are quite close to the original MATLAB version algorithms. The whole GUI based open-sourced software is easy to use, and can be freely distributed among the communities. Technical details in both R and Java modules implementation are also discussed, which presents some good examples of how to develop software with both complicate and up to date algorithms, as well as decent and user friendly GUI in the scientific or engineering research fields. / Master of Science

The evolution and development of eyespot and non-eyespot colour pattern elements was studied in Vanessa butterflies using a phylogenetic approach. A Bayesian phylogeny of the genus Vanessa was reconstructed from 7750 DNA base pairs from 10 genes. Twenty-four non-eyespot and forty-four eyespot color pattern elements from the Nymphalid ground plan were defined and studied and their evolutionary history was traced on the Vanessa phylogeny. Ancestral character states were predicted and the direction of evolutionary changes was inferred for all characters. Five serially arranged eyespots were predicted for the ancestral Vanessa on all wing surfaces. Homologous eyespot and non-eyespot characters on the surfaces of the forewing were more similar than those on the surfaces of the hindwing. Homologous eyespot characters on the dorsal surfaces of fore and hindwings show more similarities than the ventral surfaces, in contrast to what was found for non-eyespot characters. Independent Contrast analysis was also used to study correlations between eyespot characters. Independent Contrast analysis revealed significant correlations between eyespots 2 and 5 and eyespots 3 and 4 on all wing surfaces. This consistency among highly variable eyespot characters suggested a structural hypothesis: the existence of a Far-Posterior (F-P) compartment boundary and organizer could be responsible for the observed correlations. This hypothesis was tested in several ways. First, examination of wing patterns across species from all families of butterflies revealed correspondence between wing cells 1 and 4 and between cells 2 and 3. Second, evaluation of spontaneous mitotic clones in butterflies and moths reveals a peak abundance of clonal boundaries along the vein dividing wing cells 2 and 3. Finally, experimentally generated FLP/FRT mitotic wing clones produced in Drosophila, reveal a clonal boundary posterior to the L5 wing vein, which is homologous to the vein dividing wing cells 3 and 4 in butterflies. Collectively, this suggests the existence of an additional compartment boundary associated with an organizer in wing cell 3 responsible for patterning the posterior portion of insect wings. A model is proposed that predicts that the wing developmental compartment boundaries produce unique combinations of gene expression for each wing sector, permitting eyespot individuation. / February 2016

Diese Arbeit präsentiert 9 Entwurfsmuster in einer Darstellung durch das Compartment Role Object Model(CROM). Dabei wird dessen graphische Notation für rollenbasierte Modelle mit verschiedenen Möglichkeiten zur Darstellung von Bedingungen des Entwurfsmusters benutzt. Über eine Evaluationsoll ermittelt werden, ob das CROM dazu geeignet ist, die Bedingungen von Entwurfsmustern verständlich und schnell erfassbar darzustellen. Dabei soll die graphische Dokumentation dieser helfen. Das kann positive E ekte auf die Entwicklung von Software haben, wie bessere Codequalität, verkürzte Entwicklungszeiten und die Vereinfachung der Kommunikation zwischen Entwicklern.

Diese Arbeit beschäftigt sich sowohl mit der experimentell motivierten Fragestellung nach der Kontrolle der Einzelzellaktivität kortikaler Neurone sowie mit der theoretischen Beschreibung der neuronalen Dynamik und ihrer Transfereigenschaften anhand einfacher Neuronenmodelle. Hierfür werden in-vivo Daten, die mit Hilfe der juxtazellulären Stimulation mit weißem bandpass limitiertem Gaußschem Rauschen erhoben wurden, verwendet. Mit Parameterfits einfacher Neuronenmodelle werden die experimentell ermittelten Pulszugstatistiken sowie die präzisen Zeitpunkte der einzelnen Aktionspotentiale quantitativ reproduziert. Diese Untersuchungen zeigen, dass mit dynamischen Rauschstimuli in juxtazellulärer Stimulation verlässlich und reproduzierbar Pulszüge in einzelnen kortikalen Neuronen hervorgerufen werden können. Weiterhin offenbart die Analyse der Daten die Eigenschaft der untersuchten Neurone frequenzunabhängig, bishin zu Vielfachen der Feuerrate des Neurons, Information über Signalkomponenten zu transferieren. Diese Eigenschaft steht im Widerspruch zum Verhalten der einfachsten (und populärsten) integrate-and-fire Modelle, die die Zelle ohne Auflösung ihrer räumlichen Struktur näherungsweise beschreiben. Die Erweiterung solcher Ein-Kompartiment Modelle auf ein Zwei-Kompartiment Modell und die damit eingeführte Unterscheidung zwischen Soma und Dendrit ermöglicht es, für einzelne Neuronen sämtliche experimentell erhobenen Statistiken, einschließlich des Hochfrequenz- Transfers, quantitativ zu reproduzieren. Zusätzlich zu den obigen Untersuchungen wird eine Methode vorgestellt, um, anhand von Input-Output Statistiken konkreter Neurone, Gaußsche Stimuli zu berechnen, die in der jeweiligen Zelle einen vorgeschriebenen Pulszug hervorrufen. In Experimenten und Simulationen wird gezeigt, dass diese vorgeschriebenen Pulszüge mit einer Verlässlichkeit erzeugt werden können, die in etwa der intrinsischen Verlässlichkeit des untersuchten Neurons entspricht. / This work elaborates on the question to which extent experimental control about the activity of single cortical neurons can be achieved and deals with the theoretical description of the neuronal dynamics. To this end, in-vivo data that have been recorded from juxtacellular experiments in cortical neurons are used. By means of parameter optimization, simple neuron models are fitted in order to quantitatively reproduce the measured spike train statistics and specific action potential timings. The analysis reveals that dynamic noise-stimuli can be used in juxtacellular stimulation to reliably generate reproducible spike trains in single cortical neurons. The analysis also reveals that the cells show a marked broadband coding of information, up to frequencies that are multiples of the firing rate of the respective neuron. This is in contrast to what is known for the simplest (and most popular) integrate-and-fire models, for which the cellular dynamics are described by a single space-independent variable. The extension of these one-compartment models to two-compartment models introduces a spatially distinction between soma and dendrite and we could show that for particular neurons it is sufficient to quantitatively reproduce all experimentally measured spike-train and input-output statistics, including the highfrequency information-transfer. Therefore, the effect of the spatial structure can be an important (structural) mechanism that can have influence on the neuronal dynamics. Additionally to the above considerations, by means of input-output statistics of particular neurons, we propose a method to compute Gaussian stimuli that are supposed to evoke prescribed spike trains in the respective neuron. Using experiments and simulations, we show that the prescribed spike trains can be evoked with a reliability that is comparable to the intrinsic reliability of the neuron under investigation.