On The Dirichlet Distribution

The Dirichlet distribution is a multivariate generalization of the Beta distribution. It is an important multivariate continuous distribution in probability and statistics. In this report, we review the Dirichlet distribution and study its properties, including statistical and information-theoretic quantities involving this distribution. Also, relationships between the Dirichlet distribution and other distributions are discussed. There are some different ways to think about generating random variables with a Dirichlet distribution. The stick-breaking approach and the Pólya urn method are discussed. In Bayesian statistics, the Dirichlet distribution and the generalized Dirichlet distribution can both be a conjugate prior for the Multinomial distribution. The Dirichlet distribution has many applications in different fields. We focus on the unsupervised learning of a finite mixture model based on the Dirichlet distribution. The Initialization Algorithm and Dirichlet Mixture Estimation Algorithm are both reviewed for estimating the parameters of a Dirichlet mixture. Three experimental results are shown for the estimation of artificial histograms, summarization of image databases and human skin detection.

Targeting the actin cytoskeleton in HER2+ metastatic cancer cells using a macrolide toxin

Breast and ovarian cancers are among the leading causes of cancer related deaths in women worldwide. In a subset of these cancers, dysregulation of the human epidermal growth factor receptor 2 (HER2) leads to overexpression of the receptor on the cell surface. Previous studies have found that these HER2+ cancers show high rates of progression to metastatic disease. Metastasis is driven by cytoskeletal rearrangements that produce filamentous actin (F-actin) based structures that penetrate and degrade extracellular matrix to facilitate tumour invasion. Advancements in targeted therapy have made F-actin an attractive target for the development of new cancer therapies. In this thesis, we tested the actin-depolymerizing macrolide toxin, Mycalolide B (MycB), as a potential warhead for a novel antibody drug conjugate (ADC) to target highly metastatic HER2+ breast and ovarian cancers. We found that MycB treatment of HER2+ breast (SKBR3, MDA-MB-453) and ovarian (SKOV3) cancer cells led to loss of viability (IC50 values ≤ 64 nM). Sub-lethal doses of MycB treatment caused potent suppression of leading edge protrusions, migration and invasion potential of HER2+ cancer cells (IC50 ≤ 32 nM). In contrast, other F-actin based processes such as receptor endocytosis were less sensitive to MycB treatment. MycB treatment skewed the size of endocytic vesicles, which may reflect defects in F-actin based vesicle motility or maturation. Given that HER2+ cancers have been effectively targeted by Trastuzumab and Trastuzumab-based ADCs, we tested the effects of a combination of Trastuzumab and MycB on cell migration and invasion. We found that MycB/ Trastuzumab combination treatments inhibited motility of SKOV3 cells to a greater degree than either treatment alone. Altogether, our results provide proof-of-principle that actin toxins such as MycB can be used as a novel class of warheads for ADCs to target and combat highly metastatic cancers.

Polymer Light-Emitting Electrochemical Cells with Embedded Bipolar Electrodes: Visualizing Bipolar Electrochemistry in Solid State

The work presented in this thesis examines the properties of BPEs of various configurations and under different operating conditions in a large planar LEC system. Detailed analysis of time-lapsed fluorescence images allows us to calculate the doping propagation speed from the BPEs. By introducing a linear array of BPEs or dispersed ITO particles, multiple light-emitting junctions or a bulk homojunction have been demonstrated. In conclusion, it has been observed that both applied bias voltages and sizes of BPEs affected the electrochemical doping from the BPE. If the applied bias voltage was initially not sufficiently high enough, a delay in appearance of doping from the BPE would take place. Experiments of parallel BPEs with different sizes (large, medium, small) demonstrate that the potential difference across the BPEs has played a vital role in doping initiation. Also, the p-doping propagation distance from medium-sized BPE has displayed an exponential growth over the time-span of 70 seconds. Experiments with a linear array of BPEs with the same size demonstrate that the doping propagation speed of each floating BPE was the same regardless of its position between the driving electrodes. Probing experiments under high driving voltages further demonstrated the potential of having a much more efficient light emission from an LEC with multiple BPEs.

"Lancea", Lusitanian Word, and the "Lancienses" Ethnogenesis

Analysis of the word lancea, of Hispanic origin after Varro, and of place names, people´s names and personal names derived from it. It confirms that the spear was the most important weapon in the Bronze Age, belonging to the iuventus and used as heroic and divine symbol. This analysis confirms also the personality of the Lusitanians, a people related to the Celts but with more archaic archaeological, linguistic and cultural characteristics originated in the tradition of the Atlantic Bronze in the II millennium BC. It is also relevant to better know the organisation of Broze and Iron Age societies and the origin of Indo-Europeans peoples in Western Europe and of pre-Roman peoples of Iberia.

Enhancement of the Cytotoxic Effect of Anticancer Agent by Cytochrome c Functionalised Hybrid Nanoparticles in Hepatocellular Cancer Cells

Treatment of hepatocellular cancer with chemotherapeutic agents has limited successin clinical practice and their efficient IC50 concentration would require extremely highdoses of drug administration which could not be tolerated due to systemic side effects.In order to potentiate the efficacy of anticancer agents we explored the potentialof co-treatment with pro-apoptotic Cytochrome c which activates the apoptoticpathway downstream of p53 that is frequently mutated in cancer. To this end weused hybrid iron oxide-gold nanoparticles as a drug delivery system to facilitate theinternalisation of Cytochrome c into cultured HepG2 hepatocellular carcinoma cells.Our results showed that Cytochrome c can be easily conjugated to the gold shell ofthe nanoparticles which are readily taken up by the cells. We used Cytochrome cin concentration (0.2μgmL-1) below the threshold required to induce apoptosis onits own. When the conjugate was administered to cells treated by doxorubicin, itsignificantly reduced its IC50 concentration from 9μgmL-1 to 3.5μgmL-1 as detectedby cell viability assay, and the efficiency of doxorubicin on decreasing viability ofHepG2 cells was significantly enhanced in the lower concentration range between0.01μgmL-1 to 5μgmL-1. The results demonstrate the potential of the application oftherapeutic proteins in activating the apoptotic pathway to complement conventionalchemotherapy to increase its efficacy. The application of hybrid iron oxide-goldnanoparticles can also augment the specificity of drug targeting and could serve as amodel drug delivery system for pro-apoptotic protein targeting and delivery.

Surface plasmon resonance biosensing: Approaches for screening and characterising antibodies for food diagnostics

Research in biosensing approaches as alternative techniques for food diagnostics for the detection of chemical contaminants and foodborne pathogens has increased over the last twenty years. The key component of such tests is the biorecognition element whereby polyclonal or monoclonal antibodies still dominate the market. Traditionally the screening of sera or cell culture media for the selection of polyclonal or monoclonal candidate antibodies respectively has been performed by enzyme immunoassays. For niche toxin compounds, enzyme immunoassays can be expensive and/or prohibitive methodologies for antibody production due to limitations in toxin supply for conjugate production. Automated, self-regenerating, chip-based biosensors proven in food diagnostics may be utilised as rapid screening tools for antibody candidate selection. This work describes the use of both single channel and multi-channel surface plasmon resonance (SPR) biosensors for the selection and characterisation of antibodies, and their evaluation in shellfish tissue as standard techniques for the detection of domoic acid, as a model toxin compound. The key advantages in the use of these biosensor techniques for screening hybridomas in monoclonal antibody production were the real time observation of molecular interaction and rapid turnaround time in analysis compared to enzyme immunoassays. The multichannel prototype instrument was superior with 96 analyses completed in 2h compared to 12h for the single channel and over 24h for the ELISA immunoassay. Antibodies of high sensitivity, IC50's ranging from 4.8 to 6.9ng/mL for monoclonal and 2.3-6.0ng/mL for polyclonal, for the detection of domoic acid in a 1min analysis time were selected. Although there is a progression for biosensor technology towards low cost, multiplexed portable diagnostics for the food industry, there remains a place for laboratory-based SPR instrumentation for antibody development for food diagnostics as shown herein.

Joint Analysis of Multiple Algorithms and Performance Measures

There has been an increasing interest in the development of new methods using Pareto optimality to deal with multi-objective criteria (for example, accuracy and time complexity). Once one has developed an approach to a problem of interest, the problem is then how to compare it with the state of art. In machine learning, algorithms are typically evaluated by comparing their performance on different data sets by means of statistical tests. Standard tests used for this purpose are able to consider jointly neither performance measures nor multiple competitors at once. The aim of this paper is to resolve these issues by developing statistical procedures that are able to account for multiple competing measures at the same time and to compare multiple algorithms altogether. In particular, we develop two tests: a frequentist procedure based on the generalized likelihood-ratio test and a Bayesian procedure based on a multinomial-Dirichlet conjugate model. We further extend them by discovering conditional independences among measures to reduce the number of parameters of such models, as usually the number of studied cases is very reduced in such comparisons. Data from a comparison among general purpose classifiers is used to show a practical application of our tests.

Stimuli-Responsive Microneedle Arrays For On-Demand Drug Delivery

Pulsatile, or “on-demand”, delivery systems have the capability to deliver a therapeutic molecule at the right time/site of action and in the right amount (1). Pulsatile delivery systems present multiple benefits over conventional dosage forms and provide higher patient compliance. The combination of stimuli-responsive materials with the drug delivery capabilities of hydrogel-forming MN arrays (2) opens an interesting area of research. In the present work we describe, a stimuli-responsive hydrogel-forming microneedle (MN) array that enable delivery of a clinically-relevant model drug (ibuprofen) upon application of UV radiation (Figure 1A). MN arrays were prepared using a micromolding technique using a polymer prepared from 2-hydroxyethyl methacrylate (HEMA) and ethylene glycol dimethacrylate (EGDMA) (Figure 1B). The arrays were loaded with up to 5% (w/w) ibuprofen included in a light-responsible conjugate (3,5-dimethoxybenzoin conjugate) (2). The presence of the conjugate inside the MN arrays was confirmed by Raman spectroscopy measurements. MN arrays were tested in vitro showing that they were able to deliver up to three doses of 50 mg of ibuprofen after application of an optical trigger (wavelength of 365 nm) over a long period of time (up to 160 hours) (Figure 1C and 1D). The work presented here is a probe of concept and a modified version of the system should be used as UV radiation is shown to be the major etiologic agent in the development of skin cancers. Consequently, for future applications of this technology an alternative design should be developed. Based on the previous research dealing with hydrogel forming MN arrays a suitable strategy will be to use hydrogel-forming MN arrays containing a backing layer made with the material described in this work as the drug reservoir (2). Finally, a porous layer of a material that blocks UV radiation should be included between the MN array and the drug reservoir. Therefore radiation can be applied to the system without reaching the skin surface. Therefore after modification, the system described here interesting properties as “on-demand” release system for prolonged periods of time. This technology has potential for use in “on-demand” delivery of a wide range of drugs in a variety of applications relevant to enhanced patient care.

Phosphate Deficiency Induces the Jasmonate Pathway and Enhances Resistance to Insect Herbivory.

During their life cycle, plants are typically confronted by simultaneous biotic and abiotic stresses. Low inorganic phosphate (Pi) is one of the most common nutrient deficiencies limiting plant growth in natural and agricultural ecosystems, while insect herbivory accounts for major losses in plant productivity and impacts ecological and evolutionary changes in plant populations. Here, we report that plants experiencing Pi deficiency induce the jasmonic acid (JA) pathway and enhance their defense against insect herbivory. Pi-deficient Arabidopsis (Arabidopsis thaliana) showed enhanced synthesis of JA and the bioactive conjugate JA-isoleucine, as well as activation of the JA signaling pathway, in both shoots and roots of wild-type plants and in shoots of the Pi-deficient mutant pho1 The kinetics of the induction of the JA signaling pathway by Pi deficiency was influenced by PHOSPHATE STARVATION RESPONSE1, the main transcription factor regulating the expression of Pi starvation-induced genes. Phenotypes of the pho1 mutant typically associated with Pi deficiency, such as high shoot anthocyanin levels and poor shoot growth, were significantly attenuated by blocking the JA biosynthesis or signaling pathway. Wounded pho1 leaves hyperaccumulated JA/JA-isoleucine in comparison with the wild type. The pho1 mutant also showed an increased resistance against the generalist herbivore Spodoptera littoralis that was attenuated in JA biosynthesis and signaling mutants. Pi deficiency also triggered increased resistance to S. littoralis in wild-type Arabidopsis as well as tomato (Solanum lycopersicum) and Nicotiana benthamiana, revealing that the link between Pi deficiency and enhanced herbivory resistance is conserved in a diversity of plants, including crops.

Quality balancing for parallel adaptive FEM

We present a dynamic distributed load balancing algorithm for parallel, adaptive finite element simulations using preconditioned conjugate gradient solvers based on domain-decomposition. The load balancer is designed to maintain good partition aspect ratios. It can calculate a balancing flow using different versions of diffusion and a variant of breadth first search. Elements to be migrated are chosen according to a cost function aiming at the optimization of subdomain shapes. We show how to use information from the second step to guide the first. Experimental results using Bramble's preconditioner and comparisons to existing state-ot-the-art load balancers show the benefits of the construction.

Load balancing for parallel adaptive FEM

We present a dynamic distributed load balancing algorithm for parallel, adaptive finite element simulations using preconditioned conjugate gradient solvers based on domain-decomposition. The load balancer is designed to maintain good partition aspect ratios. It calculates a balancing flow using different versions of diffusion and a variant of breadth first search. Elements to be migrated are chosen according to a cost function aiming at the optimization of subdomain shapes. We show how to use information from the second step to guide the first. Experimental results using Bramble's preconditioner and comparisons to existing state-of-the-art balancers show the benefits of the construction.

Deep Crustal Structure of the North-West African Margin from Combined Wide-angle and Reflection Seismic Data (MIRROR Seismic Survey)

The structure of the Moroccan and Nova Scotia conjugate rifted margins is of key importance for understanding the Mesozoic break-up and evolution of the northern central Atlantic Ocean basin. Seven combined multichannel reflection (MCS) and wide-angle seismic (OBS) data profiles were acquired along the Atlantic Moroccan margin between the latitudes of 31.5° and 33° N during the MIRROR seismic survey in 2011, in order to image the transition from continental to oceanic crust, to study the variation in crustal structure and to characterize the crust under the West African Coast Magnetic Anomaly (WACMA). The data were modeled using a forward modeling approach. The final models image crustal thinning from 36 km thickness below the continent to approximately 8 km in the oceanic domain. A 100 km wide zone characterized by rough basement topography and high seismic velocities up to 7.4 km/s in the lower crust is observed westward of the West African Coast Magnetic Anomaly. No basin underlain by continental crust has been imaged in this region, as has been identified north of our study area. Comparison to the conjugate Nova Scotian margin shows a similar continental crustal thickness and layer geometry, and the existence of exhumed and serpentinized upper mantle material on the Canadian side only. The oceanic crustal thickness is lower on the Canadian margin.

Applications of functional nucleic acids in imaging, sensing and drug delivery and investigations of DNAzyme-metal interactions

Functional nucleic acids (FNA), including nucleic acids catalysts (ribozymes and DNAzymes) and ligands (aptamers), have been discovered in nature or isolated in a laboratory through a process called in vitro selection. They are nucleic acids with functions similar to protein enzymes or antibodies. They have been developed into sensors with high sensitivity and selectivity; it is realized by converting the reaction catalyzed by a DNAzyme/ribozyme or the binding event of an aptamer to a fluorescent, colorimetric or electrochemical signal. While a number of studies have been reported for in vitro sensing using DNAzymes or aptamers, there are few reports on in vivo sensing or imaging. MRI is a non-invasive imaging technique; smart MRI contrast agents were synthesized for molecular imaging purposes. However, their rational design remains a challenge due to the difficulty to predict molecular interactions. Chapter 2 focuses on rational design of smart T1-weighted MRI contrast agents with high specificity based on DNAzymes and aptamers. It was realized by changing the molecular weight of the gadolinium conjugated DNA strand with the analytes, which lead to analyte-specific water proton relaxation responses and contrast changes on an MRI image. The designs are general; the high selectivity of FNA was retained. Most FNA-based fluorescent sensors require covalent labeling of fluorophore/quencher to FNAs, which incurrs extra expenses and could interfere the function of FNAs. Chapter 3 describes a new sensor design avoiding the covalent labeling of fluorophore and quencher. The fluorescence of malachite green (MG) was regulated by the presence of adenosine. Conjugate of aptamers of MG and adenosine and a bridge strand were annealed in a solution containing MG. The MG aptamer did not bind MG because of its hybridization to the bridge strand, resulting in low fluorescence signal of MG. The hybridization was weakened in the presence of adenosine, leading to the binding of MG to its aptamer and a fluorescence increase. The sensor has comparable detection limit (20 micromolar) and specificity to its labeled derivatives. Enzymatic activity of most DNAzymes requires metal cations. The research on the metal-DNAzyme interaction is of interest and challenge to scientists because of the lack of structural information. Chapters 4 presents the research on the characterization of the interaction between a Cu2+-dependent DNAzyme and Cu2+. Electron paramagnetic resonance (EPR) and UV-Vis spectroscopy were used to probe the binding of Cu2+ to the DNAzyme; circular dichroism was used to probe the conformational change of the DNAzyme induced by Cu2+. It was proposed that the conformational change by the Cu2+ binding is important for the activity of the DNAzyme. Chapter 5 reports the dependence of the activity of 8-17 DNAzyme on the presence of both Pb2+ and other metal cations including Zn2+, Cd2+ and Mg2+. It was discovered that presence of those metal cations can be cooperative or inhibitive to 8-17 activity. It is hypothesized that the 8-17 DNAzyme had multiple binding sites for metal cations based on the results. Cisplatin is effective killing tumor cells, but with significant side effects, which can be minimized by its targeted delivery. Chapter 6 focuses on the effort to functionalize liposomes encapsulating cisplatin by an aptamer that selectively bind nucleolin, an overexpressed protein by breast cancer cells. The study proved the selective cytotoxicity to breast cancer cells of the aptamer-functionalized liposome.

Atténuation des changements climatiques en Chine : analyse des cibles et des stratégies de réduction des émissions de GES

La Chine est l’acteur le plus important dans la lutte internationale aux changements climatiques. Depuis 2007, ce pays est le plus grand émetteur de dioxyde de carbone avec près du quart des émissions mondiales et la croissance de sa consommation d’énergie depuis les années 2000 met en grand danger l’ensemble de la planète. L’objectif de cet essai est d’analyser la capacité de la Chine à réduire ses émissions de gaz à effet de serre et de participer à sa juste part à l’effort international d’atténuation des changements climatiques. Pour ce faire, la croissance économique chinoise des dernières décennies et ses impacts environnementaux sont présentés. On remarque que le modèle de croissance qui a permis à la Chine de se hisser au sommet de l’économie mondiale a montré ses limites et que le gouvernement a développé une nouvelle stratégie économique qui se veut plus durable. Ensuite, les cibles et engagements climatiques de la Chine sont analysés selon quatre critères (capacité, adéquation, responsabilité et effort). Les résultats de cette analyse montrent que la capacité du pays à réduire ses émissions est grande, mais que ses cibles ne sont ni suffisantes pour maintenir la hausse de la température à 2 °C, ni assez contraignantes et larges. Puis, l’impact de la nouvelle stratégie économique sur différents indicateurs est évalué. Cette évaluation montre que les facteurs qui ont largement contribué à la hausse des émissions de gaz à effet de serre en Chine – à savoir une croissance économique effrénée, une forte dépendance au charbon et une économie dominée par le secteur industriel – subissent d’importants changements. En effet, ces mutations majeures dans l’économie chinoise laissent croire que la Chine atteindra ses cibles d’intensité énergétique, d’énergie renouvelable et de plafonnement des émissions de dioxyde de carbone plus rapidement que prévu. Il est recommandé de bonifier les engagements climatiques de la Chine en imposant une cible absolue sur les émissions de dioxyde de carbone et en élargissant la portée de ces engagements pour inclure d’autres gaz à effet de serre. Aussi, certaines recommandations sont faites pour assurer le bon fonctionnement d’un éventuel système de plafonnement et d’échange en Chine. Le travail se conclut sur l’effort à venir dans la lutte internationale aux changements climatiques et sur la nécessité d’étudier la réduction des émissions de gaz à effet de serre en Chine après leur plafonnement, prévu d’ici 2025.

Host-guest chemistry of solid coordination frameworks (SCFs) based on Copper(II)-Pyridine Ligands

283 p.