Thèses sur le sujet « C05X »

The key components of the scaffold in pharmaceutical chemistry are ring systems, of different sizes, and are the fundamental factors of most of the drugs on the market today. Nowadays, the importance of cyclic structures is well understood by medicinal chemists, since they play a significant role in molecular properties such as the electronic distribution, three dimensionality, and molecule rigidity. They are often key factors in whole molecule properties such as lipophilicity or polarity and can determine molecular reactivity, metabolic stability, and toxicity. Cyclic structures have always fascinated organic and medicinal chemists, and many organic molecules form cycles with appealing biological properties. Research in cyclic chemistry continued to advance in synthetic methods development, conformational studies and investigation of their role for controlling biological functions. This work, carried out in the Prof. Marcantoni’s research group at the University of Camerino (Camerino, Italy) with the collaboration of Dompé S.p.A. (L’Aquila, Italy) from December 2015 to December 2018 and in the Prof. Poli’s research group from January 2018 to July 2018 at the University Pierre and Marie Curie (Paris, France), had the objective to investigate new synthetic methodologies for the functionalization of cyclic compounds, as well as the formation of cyclic structures from acyclic precursor, for advanced biological purposes. The first chapter focuses on the functionalization of the primary face of a β-cyclodextrin, in order to obtain a synthetic human receptor model, used for studying the possible interactions of this compound with a new class of biologically active compounds in development at Dompé S.p.A. The second chapter, carried out in the Poli’s research group, describes the selective C-3 functionalization trials of 2-furaldehyde and its derivatives by Directed ortho Metalation (DoM) chemistry in presence of organolithium compounds and focuses on the study of degradation products. The reaction of an alkyllithium compound with an aromatic structure bearing a Direct Metalation Group (DMG) normally leads to an ortho-metalated intermediate. Good DMGs are strong complexing or chelating groups that have the effect of increasing the kinetic acidity of protons in the ortho position. The third chapter focuses on the in-depth study of the mechanistic aspect on the formation of 5acylaminothiazoles starting from α-chloroglycinates, obtained by a new synthetic methodology developed in the Marcantoni’s research group. Finally, the fourth chapter focuses on the study of the role of Cerium trichloride in the formation of cyclic compounds via Nazarov cyclization.

The present thesis is the result of three years’ collaboration between the University of Camerino and ELANTAS Europe Srl. The strong collaboration between university and companies allows to students like others and me to do research with an industrial approach, facing with the problematics of working life. The work was carried out among the laboratory of Organic Chemistry of Prof. Enrico Marcantoni at the University of Camerino (Camerino, Italy), the R&D laboratory of ELANTAS Europe in Ascoli Piceno (Italy) and the R&D laboratory of ELANTAS PDG INC in Saint Louis (Missouri, USA). The thesis concern the environmental impact of some industrial polymeric materials. Polymeric materials are very important in modern society: they have considerable advantages over products of other origins with lower costs with the same performance. Nevertheless, they allow some applications that some years ago would have been unthinkable (microencapsulation, shape memory materials, and many others). At the same time, environmental impact is a crucial topic strictly linked to polymeric materials (as all others materials), and to the period we are living. The production of such materials is constantly growing, exceeding the production of many others materials, and it is becoming increasingly important to find ways to produce them more efficiently and to recover waste products. The consequences of a production without limitation and control could be catastrophic for the whole world and humankind too. During my PhD, I worked on three industrial products in order to reduce their environmental impact, keeping their physical properties unchanged. After a first general introduction on polymeric materials, their uses, and their production, the second chapter concern about improving a recovery process for waste PMMA. The study allowed identifying undesirable by-products formed during the thermal depolymerization of PMMA and removing them in the consequent re-polymerization by an innovative dissolution/re-precipitation method. The third and fourth chapters deal with two coatings for wires electrical insulation, one based on polyurethanes (PU) and the other on polyesterimides (PEI). With the PU-based one, the target was to reduce the amount of loss material during the application stage and to increase the speed of application in order to reduce the energy consumption of the process. Whereas with the PEI-based enamel the purpose was to synthesized a solvent-free product using a twin-screw extruder and using recycled PET as alternative raw material to form the polyester part. The extruder technology is less energy consuming compare to the batches ones and allows working without solvents, since it can work with high viscosity materials. Moreover, the extruded product, with an additional system, can be potentially applied onto the wire with a higher thickness compare to the respective solventbased product, allowing a greater flow of current along the wire, thus improving the performance of the finished products (i.e. reducing the charging time of electrical motors).

For centuries, African natives have been facing various infectious tropical illnesses, among which African trypanosomiases are some of the most frequent relevant parasitic diseases. African trypanosomiases, commonly called sleeping sickness in humans (HAT; Human African Trypanosomiasis) and Nagana in domestic livestock, affect a huge number of people living in poverty in 36 sub-Saharan countries, resulting in a key socioeconomic impact. After a century of outbreaks, due to political instability and lack of funding, around 70 million people and 50 million cattle are still at risk of exposure in Africa. Trypanosomiasis is transmitted by the bite of insects from the Glossina spp (Glossinidae) and is fatal in humans, if untreated. While taking a blood meal, infected Glossina flies can spread extracellular protozoans from the species Trypanosoma brucei. There are three morphologically indistinguishable subspecies of T. brucei. The subspecies T. b. gambiense is responsible for a chronic form of the human disease, while T. b. rhodesiense causes an acute form, which more rapidly leads to death. Both subspecies are infective to humans, whereas T. b. brucei is only infective to animals. During the early stage of the disease or hemolymphatic phase, the parasite is restricted to the blood and lymph and after months or years it invades the central nervous system resulting in various neurological symptoms including sleeping disturbance. As for other neglected tropical diseases, the chemotherapeutical arsenal against HAT is based on limited, expensive and often toxic medicines that are administered parentally in a context of poverty and lack of qualified personnell in healthcare centers. The few drugs that are available are pentamidine and suramin for the early stage disease and eflornithine (also in combination with nifurtimox) and melarsoprol for the late stage when the parasite infects the brain. Overall, the situation described above highlights the critical nature of this phenomena and the urgent need to explore new sources of potentially effective and safe compounds for therapy. In this scenario the naturally-occurring products may play a crucial role as source of bioactive drug candidates. With this vision in mind, in Chapter 2 I performed a complete phytochemical analysis on both polar and volatile compounds of T. diversifolia collected from a geographically isolated population living in Dschang, Cameroon and I assessed their biological activities (antitrypanosomal and amtimicrobial activities). The main secondary metabolites occurring in the T. diversifolia methanolic extract were isolated by column chromatography and structurally elucidated by MS and NMR techniques. Tagitinins C emerged as the most active compound against T. brucei (TC221) with an IC50 value  of  0.0042  μg/mL.  This  activity  was  4.5  times  better  than  that of the reference drug suramin. Then I analysed the chemical composition and the antimicrobial effects of the essential oil (EO) hydrodistilled from inflorescences of T. diversifolia. Results showed that T. diversifolia EO was mostly active against Staphylococcus aureus and selectively inhibited in vitro the NAD biosynthetic enzyme NadD from S. aureus (IC50 of ∼60 g/mL). Besides its extensive utilizations in the traditional medicine, the plant is believed to have a great potential in agriculture. For this reason, I decided to evaluate the T. diversifolia polar extracts against the two-spotted spider mite Tetranychus urticae (Tetranychidae), which is one of the most economically important arthropod pests worldwide. The ethyl acetate extract resulted as the most active oviposition inhibitor, with an ED50 value of 44.3 µg.cm-3 and an ED90 of 121.5 µg.cm-3. In Chapter 3, I investigated a lipophilic extract of Onosma visianii roots containing 12% of shikonin derivatives. The phytochemical investigation of the lipophilic extract resulted in the isolation of 12 naphtoquinone derivatives which were evaluated against Trypanosoma brucei. Isobutylshikonin and isovalerylshikonin emerged as the most active naphtoquinone derivatives, showing an IC50 of 3.3 and 2.7 g/mL, respectively. Furthermore, isovalerylshikonin provided an inhibition of Glossina palpalis acetylcholinesterase (gpAChE) (IC50 =  7.1  μg/mL),  stronger  than   isobutyrylshikonin (IC50 =  91.3  μg/mL),  with  a  significant  tse-tse fly versus human selectivity (SI = 7.2). In Chapter 4, I oriented my attention to the Apiaceae family, which is a class of aromatic plants rich of EOs. Four out of nine Apiaceae EOs resulted active against T. brucei showing an IC50 in the range 2.7-10.7 g/mL. Terpinolene, one the major isolated component of these oils, was particularly active with an IC50 value of 0.035 g/mL (0.26 µM) and a selectivity index (SI) of 180. As part of the extended family of naturally-occurring products, sesquiterpenes hold promising inhibitory effects against the bloodstream forms of T. brucei. For this reason, in Chapter 5, I decided to explore the potential of Smyrnium olusatrum EOs obtained and its main oxygenated sesquiterpenes,  namely  germacrone,  isofuranodiene,  and  β-acetoxyfuranoeudesm-4(15)-ene, as potential inhibitors of T. brucei. The EOs obtained efficiently inhibited the growth of parasite with IC50 ranging from 1.9 to 4.0 g/mL. Among the isolated main EOs components, isofuranodiene exhibited a significant and selective inhibitory activity against T. brucei (IC50 = 0.6 g/mL, SI = 30). In Chapter 6, I finally selected six medicinal and aromatic plants traditionally used in Cameroon to treat several disorders, including infections and parasitic diseases. Then I evaluated the activity of their EOs against T. brucei TC221 and their selectivity against Balb/3T3 cells, used as counter-screen for cytotoxicity. The most relevant outcomes showed that the EOs from A. indica, A. daniellii and E. giganteus were the most active ones, with IC50 values of 15.21, 7.65 and 10.50 g/mL, respectively. Overall, the results of my PhD thesis provided new insights into the potential of naturallyoccurring compounds as valuable sources for the development of innovative trypanocidal drugs or botanical insecticides.

Adenosine (Ado) is an endogenous nucleoside ubiquitous in mammals promoting protection and cells repair during metabolic stress conditions. Through interaction with the four Ado receptor subtypes (ARs), AR ligands have shown potential therapeutic interest for many disorders. In this work both new A2AAR agonists and A3AR antagonists were designed, synthesized and tested in vitro. Although  Ado  5’-N-ethylcarboxamide derivatives like VT 7 and GCS21680 display a good affinity and selectivity for A2AAR, the development of new agonists for this receptor subtype is still a big challenge in nucleoside chemistry. In this current decade, some papers have reported  that  a  tetrazolyl  residue  in  4’-position of Ado derivatives led to compounds endowed with good A2AAR affinity. Hence, in this work, compounds bearing the Nethyltetrazoyl  moiety  in  4’- position of the Ado ribose portion together with different arylalkylthio and arylalkylamino chains in C2-position were designed and synthesized. The new compounds were prepared using a convergent approach. To this purpose, 2,6- dichloropurine was coupled with the suitable modified sugar to afford a nucleoside which was further modified by introducing an amino group at the C6- and the suitable side chain at the C2- position. The modified sugar used in the coupling reaction was synthesized starting from the commercially available D-ribose in seven steps. The binding assay and functional study performed with the new compounds at all AR subtypes transfected on Chinese hamster ovary (CHO) cells revealed that the 2-phenylethylthio derivative was the compound endowed with the better affinity for the A2AAR/A3AR subtypes (17: Ki hA2AR = 5.8 nM; Ki hA3R = 1.2 nM). It is worthwhile to note that the presence of the ethyltetrazolyl substituent in the sugar moiety favors the interaction with the receptor respect to the ethylcarboxamido group. As expected, the new derivatives show a dual behavior at ARs, resulting A2AAR agonists and A3AR antagonists (17: IC50 at hA3AR of 8.4 nM). Furthermore, the wound healing potential of the news nucleosides was evaluated respect to VT 7, CGS21680 and epidermal growth factor (EGF, used as positive control). The compounds, 17, 19, 20, 21 and 22 showed all better wound healing potential respect to VT 7, CGS21680 and EGF. Therefore such compounds are good candidates for further investigation in in vivo model of wound healing. New A3AR antagonists were also prepared based on the observations that, the substitution of the 8-bromine atom of 8-bromo-9-ethyladenine (Ki hA2AAR = 52 nM, Ki hA3AR = 2,800 nM) with phenylacetylene shifts the preference of the resulting compound (Ki hA3AAR = 86 nM, hA2AAR= 600 nM) from A2AAR to A3AR. Hence, from these facts, three series of compounds were prepared. The first one was 8-phenylethynyladenine derivatives substituted at N-9 position with different alkyl/arylalkyl chains. The second one combines substitution on the phenyl ring of 8- phenylethynyladenine with either N-9 cyclopentyl or N9 phenethyl since they resulted being the best N-9 substituents of the first series. The third series combines a fixed para-methoxy- phenylacetylene in C-8 with either N-9 cyclopentyl or N-9 phenethyl, 2-chloro, and with different N6 substituents. The 8-arylethynyladenine derivatives substituted at 9 position with different alkyl/arylalkyl chains, and the corresponding compounds further substituted at the 2 and N6 position, were synthesized starting from commercially available adenine or 2,6- dichlorpurine in three/five steps, respectively. The results of the in vitro test reported that: N-9 cyclopentyl improved affinity while N-9 phenylethyl improved selectivity, the chlorine atom is well tolerated especially when combined with C-8 para-methoxy-phenylacetylene, the N6 substitution gave compounds with maintained selectivity in the same range of the non- substituted derivatives but with a slight decrease of the affinity. Most of the new compounds are endowed with high affinity and different degree of selectivity for the A3AR subtype. In particular, the tetrasubstituted adenine derivative 38 (Ki A3R = 8.4 nM; Ki A1R and Ki A2AR >30,000 nM) resulting the most active and selective ligand and it represents a very good ligand to study the A3AR subtype and its function.

This thesis is focused on the preparation of organic-inorganic hybrid systems with targeted properties. In particular, thesis presents the synthesis, characterization and application of two types of functional coating, which are hydrophobic / self-cleaning and anticorrosion coatings. Chapter 1 is dedicated to general introduction and the state of art of advanced functional coating. The chapter includes a brief description of the current functional market size and possible applications of functional coatings. Chapter 2 provides a general introduction of superhydrophobic coatings, their possible applications on the glass surface and methods to produce them. In the chapter 3, sol-gel methods has been describe in detail. The sol gel process by employed alkoxysilanes was used in this work to fabricate the functional coatings. Chapters 4, 5 and 6 describes the experimental works of this thesis. In the chapter 4, the solgel process and dip-coating technique were employed for the preparation of hydrophobic self-cleaning hybrid materials. The process has been optimized to obtain transparent and highly hydrophobic sol-gel coatings by using different alkoxysilane. These hybrid sol-gel coatings are a good alternative to provide anti-stick and easy-to-clean properties to glass substrates being quite easy to scale up. In the chapter 5, a method for the preparation of transparent superhydrophobic silica coatings on glass substrates via aerosol‐assisted chemical vapour deposition (AACVD) is described. A multi-layer process to produce dual scale silica nanoparticles films, by using different functional alkoxysilanes was investigated. In this study, a novel strategy to achieve highly transparent superhydrophobic glass surfaces using AACVD of alkoxysilanes, to produce surfaces with excellent durability is described. This shows great potential to obtain silica superhydrophobic films for large–scale applications Finally, in the chapter 6, a preliminary study about the protective barrier coating to protect the integrity of the silver from deleterious chemical degradation in a mirror structure is investigated. Sol-gel hybrid coating has been deposited on mirror to avoid corrosion degradation process of silver layer. Salt spray test was performed on mirror coated with hybrid coating and the results showed a no signs of corrosion on the mirror. The results indicate excellent barrier protection performance of the coating.

The behaviour of individual cells must be carefully coordinated across a tissue to achieve correct function. In particular, proliferation and differentiation decisions must be precisely regulated throughout development, tissue maintenance, and repair. A better understanding of how these processes are controlled would have implications for human health; cancer is, after all, dysregulated proliferation, while regenerative medicine relies on being able to influence cell decisions accurately. To investigate such fundamental biological processes, it is common practice to use an experimentally tractable model organism. Here, we focus on the germ line of the nematode worm C. elegans, which provides opportunities to study organogenesis, tissue maintenance, and ageing effects. Despite the advantages of this organism as a biological model, certain questions about germ cell behaviour and coordination remain challenging to address in the lab. There is therefore a need for computational models of the germ line to complement experimental approaches. In this thesis, we develop a new in silico model of the C. elegans germ line. Novel aspects include working in three dimensions, covering the late larval period, and integrating a logical model of germ cell behaviour into a wider cell mechanics simulation. Our model produces a reasonable fit to wild-type germline behaviour, and provides the first cell tracking and labelling predictions for the larval period. It also suggests two new biological hypotheses: 1) that “stretching” growth plays a significant role in gonadogenesis, and 2) that a feedback mechanism acts on the germ cell cycle to prevent overproliferation. Having introduced the full model, we address some technical questions arising from our work, namely: what is the effect of applying a more physically realistic force law?; and can simulation performance be improved by changing the numerical scheme? Finally, we use in silico modelling to compare a number of hypothesised germ line maintenance mechanisms. There, our results support a model with functionally equivalent germ cells undergoing at most infrequent, transient cell cycle arrests.

In order for computers to interact with and understand the visual world, they must be equipped with reasoning systems that include high–level quantities such as objects, actions, and scenes. This thesis is concerned with extracting such representations of the world from visual input. The first part of this thesis describes an approach to scene understanding in which texture characteristics of the visual world are used to infer scene categories. We show that in the context of a moving camera, it is common to observe images containing very few individually salient image regions, yet overall texture structure often allows our system to derive powerful contextual cues about the environment. Our approach builds on ideas from texture recognition, and we show that our algorithm out–performs the well–known Gist descriptor on several classification tasks. In the second part of this thesis we we are interested in scene understanding in the context of multiple calibrated views of a scene, as might be obtained from a Structure–from–Motion or Simultaneous Localization and Mapping (SLAM) system. Though such systems are capable of localizing the camera robustly and efficiently, the maps produced are typically sparse point-clouds that are difficult to interpret and of little use for higher–level reasoning tasks such as scene understanding or human-machine interaction. In this thesis we begin to address this deficiency, presenting progress towards modeling scenes using semantically meaningful primitives such as floor, wall, and ceiling planes. To this end we adopt the indoor Manhattan representation, which was recently proposed for single–view reconstruction. This thesis presents the first in–depth description and analysis of this model in the literature. We describe a probabilistic model relating photometric features, stereo photo–consistencies, and 3D point clouds to Manhattan scene structure in a Bayesian framework. We then present a fast dynamic programming algorithm that solves exact MAP inference in this model in time linear in image size. We show detailed comparisons with the state–of–the art in both the single– and multiple–view contexts. Finally, we present a framework for learning within the indoor Manhattan hypothesis class. Our system is capable of extrapolating from labelled training examples to predict scene structure for unseen images. We cast learning as a structured prediction problem and show how to optimize with respect to two realistic loss functions. We present experiments in which we learn to recover scene structure from both single and multiple views — from the perspective of our learning algorithm these problems differ only by a change of feature space. This work constitutes one of the most complicated output spaces (in terms of internal constraints) yet considered within a structure prediction framework.

Diffusion MRI provides a unique opportunity to study the brain tissue architecture at a microscopic level. More specifically, it allows to infer biophysical properties of the axons in the white matter in-vivo. Microstructural parameters are widely used in multi-subject studies to track pathological processes, follow normal development and aging, or investigate behaviour. This thesis aims to identify and potentially address the limitations and pitfalls in voxelwise comparison of diffusion MRI parameters across subjects. To allow for accurate matching of brain structures across subjects, non-linear transformation that spatially aligns the data is required. We demonstrate that using advanced registration methods, we can outperform the standard registration-projection approach both in terms of sensitivity and specificity. The coarse resolution of the data typically causes partial volume effects that bias the diffusion parameters and potentially mislead the interpretation of a group study outcome. We provide evidence that these effects can be addressed by constraining the diffusion model parameter space, which leads to marginally lower sensitivity, but allows an accurate interpretation of the results. Additionally, we suggest that additional information inferred with a data driven approach might mitigate the loss in sensitivity. Finally, we design an original tract-specific modelling framework that enables to estimate microstructural parameters unbiased by the presence of foreign fibre populations or tissues. We demonstrate the sensitivity of our method in a study relating microstructure and behaviour.

This thesis documents patterns in plant species distribution across tropical Africa. Geographic patterns in the distribution of globally rare plants within Upper Guinea are emphasised, and correlates with these patterns are investigated. This thesis argues that globally rare species can and should be emphasised in conservation strategy. Approximately 3.7 million global occurrence records of 28,803 tropical mainland African vascular plant species are compiled into a database framework. The database is used to propose an updated biogeographic framework for tropical Africa, which is sympathetic to previous chorological frameworks but maximises regional endemism within quantitatively defined boundaries. A definition of Upper Guinea as the forests of West Africa between Sierra Leone and Ghana is recovered. The concentration of globally rare species in the tropical African flora (bioquality as measured by the GHI) is calculated and mapped at one degree square and half degree square resolution, revealing high bioquality of the horn of Africa. Bioquality is calculated by categorising the global area of occupancy of all tropical African taxa into a Star rating, with the result that a bioquality score can now be calculated at a local scale anywhere in tropical Africa to inform conservation strategy. At the local scale, variation in bioquality is modelled in two areas of high global endemism within Upper Guinea: the Nimba Mountains and SW Ghana. Disturbance is the only significant variable retained in both models, and shows a strong negative relationship with bioquality. Bioquality scores in forest reserves of SW Ghana are shown to have been stable over 20 years, although our perception of the global rarity and identity of species within the area has altered substantially. This finding supports the GHI as a metric of conservation priority in the face of partial information. At half degree square resolution, 55% of tropical African cells are estimated to have less than 2.5% of their likely species richness documented. A regression tree model is used to interpolate bioquality scores for cells lacking species distribution data, making use of a range of modern climatic, paleo climatic, geographic and biogeographic variables, found to be predictive of bioquality scores. Areas showing the most stable climates over the past 21,000 years are shown to have the highest modern-day bioquality across tropical Africa. Areas with relatively stable climates during periods of past climate change have been hypothesised to show high modern endemism as the result of increased speciation in isolated refugia, and/or a lower rate of extinction within the refugia. Two dated phylogenies are estimated for African magnoliids and Rubiaceae species, which show that most of Upper Guinea's globally rare species are young, vicariant species, although at least one species is likely to be a paleo-endemic, supporting both hypotheses. Areas with historically stable climates showing present day climatic or topological isolation explain areas of high global endemism in tropical Africa, although the introduction of a high disturbance regime can remove this pattern. A conservation strategy which promotes the protection of globally rare species in tropical Africa is feasible, given what we now know of the African flora, and is wise, at least given the success of the Ghanaian programme over 20 years.

Baseline data on a species' distribution and abundance are essential for developing practical conservation management plans. Such data are difficult to obtain for many low density cryptic carnivores. The Scottish wildcat, Felis silvestris silvestris, is no exception with <400 individuals thought to remain. Its conservation has been further complicated by extensive hybridisation and introgression with the domestic cat (F.s.catus). Hybridisation has also resulted in difficulties in discriminating between wildcats, wildcat x domestic hybrids (hybrids) and tabby coloured feral domestic cats. This has inhibited survey efforts, leading to a lack of general ecological information. Using the most recent identification tools available, extensive surveys using various methods including camera trapping were carried out across Northern Scotland in order to examine the current status of the Scottish wildcat. Current distribution indicates a more restricted range than recent studies. Wildcats are at risk of hybridisation from feral domestic cats and in particular, hybrids, throughout their current probable range. The distribution of hybrids overlaps with both feral domestic cats and wildcats, pointing to a significant threat from hybrids acting as a bridge between wildcats and feral cats. Mean density estimates of 3.5 (SD=0.7) wildcats/100 km² were comparable with those from other studies in Scotland using different survey methods. Total population size estimates ranged between 115-314 individuals depending on local densities and home range size. Population viability analysis (PVA) indicated the current population is not viable unless management actions are undertaken in the near future (Mean time to extinction = 48.2 years (SD = 9.39), probability of extinction=1, SE = 0), and that reducing mortality rates and/or supplementing populations from captive bred cats are likely to be necessary to achieve viability. Based on these data, the Scottish wildcat may be more endangered than many other species classified as Endangered and the current status of the Scottish wildcat should be reviewed.

Cord-forming fungi form extensive networks that continuously adapt to maintain an efficient transport system, and we can photograph their growth, digitize the network structure, and measure the movement of radio-tracers. Mycelial networks are more accessible than the transport networks of other multicellular organisms, but there are many open questions concerning the coordination of growth and transport within fungal networks. As osmotically driven water uptake is often distal from the growing margin, and aqueous fluids are effectively incompressible, we propose that growth induces mass flows across the mycelium, towards the growing regions. We imaged the temporal evolution of networks formed by Phanerochaete velutina, and at each stage calculated the unique set of currents that account for the observed changes in cord volume, while minimizing the work required to overcome viscous drag. Predicted speeds were in reasonable agreement with experimental data, and cords that were predicted to carry large currents were significantly more likely to increase in size than cords with small currents. We have also developed an efficient method for calculating the exact quantity of resource in each part of an arbitrary network, where the resource is lost or delivered out of the network at a given rate, while being subject to advection and diffusion. This method enabled us to model the spatial distribution of resource that emerges as a fungal network grows over time, and we found good empirical agreement between our model and experimental data gathered using radio-labelled tracers. Our results suggest that in well insulated fungal networks, growth-induced mass flow is sufficient to account for long distance transport. We conclude that active transport mechanisms may only be required at the very end of the transport pathway, near the growing tips. We also developed a simple model of glucose delivery through vascular networks, which indicates that increasing the number of blood vessels in a region can actually decrease the total rate of glucose delivery.

Fossil tracks represent the only direct record of behaviour and locomotion of extinct animals. A computer model using finite element analysis (FEA) has been developed to simulate vertebrate track formation in cohesive substrates. This model has been designed for, and successfully run on, high performance computing (HPC) resources. A number of individual studies were carried out using the computer model to simulate both abstract indenters and virtual dinosaur autopodia. In addition to the simulation studies, two fossil tracks were described, including the first report of bird tracks at the Mammoth Site of Hot Springs, South Dakota (USA) and a re-description of a 'dinosaur tail drag' as the trace of a crocodilian. Using the computer model, it has been shown that in a wet, soft mud the indentation of a non-webbed virtual tridactyl foot created a resultant track with features analogous to 'webbing' between digits. This 'webbing' was a function of sediment deformation and subsequent failure in 3D, specific to rheology. Apparent webbing impressions were clearly developed only within a limited range of sediment conditions and pedal geometry. Indenter (pedal) geometry and morphology affect track depth independently of substrate and loading parameters. More complex morphologies interact with the cohesive substrate creating a lower effective load than that applied. In non-cohesive substrates such as sand, this effect is reversed, and it is the more compact morphologies that indent to a lesser degree. Virtual sauropod tracks were modelled, based on published soft tissue reconstructions of autopodia anatomy, and published mass/centre of mass estimates. It was shown that foot morphology and differential loading between fore- and hind- limbs leads to a range of substrates in which only the manus or pes are able to generate tracks. This offers a new mechanism for the formation of manus-only sauropod trackways, previously interpreted as having been made by swimming dinosaurs. A series of tracks were simulated using input data (loads, pedal morphologies) from four different dinosaurs (Brachiosaurus, Tyrannosaurus, Struthiomimus, and Edmontosaurus). The cohesive substrates used displayed a 'Goldilocks' effect, allowing the formation for tracks only for a very limited range of loads for any given foot. In addition, there was a strong bias toward larger animals, both in homogeneous and theoretically heterogeneous substrates. These findings imply that interpretations from track assemblages must consider that only a small proportion of the total fauna present may be recorded as a track assemblage due to substrate properties. The use of FEA to simulate dinosaur track formation has been shown to be successful, and offers a number of advantages over physical modelling including; consistency between experiments, specific control over input variables, rapid undertaking of repeatable experiments, and the ability to view subsurface deformation non-destructively. It is hoped that this work will lead to an increased interest in modelling tracks, and offer a quantitative method for studying fossil tracks.

Background: Radiotherapy is used in the treatment of over 50% of cancer patients and bar surgery, is the most effective cancer intervention. However, in the clinic secondary malignancies have been observed following radiotherapy and in vitro increased cell migration and invasion have been seen following radiation. The Src/FAK signalling pathway is known to play an important role in the metastatic phenotype through its involvement in cell adhesion, migration and invasion and we have previously demonstrated that radiotherapy can activate this pathway along with the phosphoinositide 3-kinase (PI3K) pathway, also associated with tumour metastases and an aggressive phenotype. Using pharmacological inhibitors, we have investigated combination approaches to evaluate whether Src and PI3K targeting is beneficial in a radiotherapy context, especially focusing on metastatic phenotype. We wished to relate pathway activation to cellular phenotype and increase understanding of the metastatic cascade, the processes involved and the signalling pathways taking the lead. Method: Using thyroid carcinoma cell lines FTC133 and 8505c the effects of Src inhibition using AZD0530, FAK inhibition using FAKi and PI3K inhibition using GDC-0941 were studied. The effects of radiotherapy alone, and in combination with the above inhibitors, were also studied. In vitro MTT, apoptosis and clonogenic assays were used to assess cell proliferation and cell survival and scratch assays, cell adhesion and cell spreading assays were used to assess the effects of the drugs on metastatic characteristics. In vivo tumour growth, survival and ex vivo clonogenics were used to measure the effects of AZD0530 and GDC-0941. Western blotting, immunofluorescence and immunohistochemistry was used to observe the effects on pathway activation and protein localisation. Results: Src and FAK inhibition reduced metastatic characteristics of thyroid carcinoma cell lines in vitro such as cell spreading and migration. FAK inhibition showed a greater effect on cell survival by MTT, clonogenic and apoptosis. In the thyroid carcinoma cell lines radiotherapy enhanced the metastatic phenotype. This was seen by enhanced activation of the Src and PI3K pathways, increased migration and invasion in vitro and enhanced tumour metastasis in vivo. By combining Src inhibition with radiation a reduction in metastatic characteristics was observed and by combining PI3K inhibition with radiotherapy radiosensitivity could be improved. With the triple combination of Src and PI3K inhibition with radiotherapy a significant reduction in cell survival was demonstrated in vitro compared to radiation alone and either inhibitor combined with radiation, with a corresponding significant reduction in tumour growth being observed in vivo. With the combination of Src and PI3K inhibition significant reductions in metastatic characteristics were also observed both in vitro and in vivo seen by a reduction in cell migration and tumour metastasis. Finally combined inhibition of the Src and PI3K pathway reduced the radiation enhanced activation of several pathways in vivo including Src and PI3K.Conclusions: Together these results suggest that the Src and PI3K pathways play a role in radiation enhanced metastatic characteristics in thyroid carcinoma and through combined inhibition of the pathway the negative effects of radiation, enhanced migration and invasion, can be inhibited and the cells can be made more radiosensitive. Full characterisation of the pathways involved in radiation induced motility and radioresistance will provide further rationale for combination therapies and provide potential for application of these therapies in the clinic.

The purpose of this study was to utilise lignin as a partial substitute for phenol in PF resins. To achieve this, initially brown rot lignin was produced by a bioconversion technique. During the course of the study, it became clear that the production of brown rot lignin had a limited success. Since brown rot lignin could not be obtained in sufficient quantity and purity by a bioconversion method, other alternative lignin production methods, as well as commercially available lignin, were chosen; namely production of lignin from black liquor and Alcell® (organosolv) lignin. Before performing production of resin formulations, the lignin sources were characterised in terms of reactivity and physical properties of lignins. Both lignins had a similar reactivity, but organosolv lignin was found to be more pure, with a low ash content. Since isolation of lignin from black liquor in laboratory conditions is more complex and requires more time, it was decided to use organosolv lignin for subsequent production of lignin-based reSIns. The lignin was introduced to the resin in two different ways. The first method was the replacing of a certain percentage of phenol with lignin (as supplied) directly into resins. In the second method, lignin was modified prior to resin manufacture by phenolation. Different degrees of phenol substitution (from 5% to 60%) were tried for the production of lignin-based resins. Bond qualities of lignin-phenol-formaldehyde (LPF) , phenolated-ligninformaldehyde, commercial phenol-formaldehyde (PF _com) and laboratory made phenol-formaldehyde (PF _made) resins were assessed by using an Automatic Bonding Evaluation System (ABES), prior to production of particleboards, in order to eliminate some of the poor quality resins. The effect of press temperature and time on bond strength appeared to be highly significant, as the lignin substitution levels increased. Up to 30% phenol substitution was achieved without sacrificing bond strength. The bond strength values of phenolated-lignin-formaldehyde resins were similar to commercial phenol-formaldehyde and laboratory made phenolformaldehyde resins, but better than the LPF resins. It was apparent that resins containing a high level of lignin substitution gave the poorest bond strength values. From these results, some of the resins were eliminated, prior to particleboard production. In order to evaluate the quality of lignin-based resins, particleboards were produced and mechanical and physical tests performed. Effect of press platen temperature (140°C, 160°C, 180°C) and press cycle time (5 min, 8 min, IS min) on the mechanical properties of particleboard, produced by using lignin-based resins, were investigated. It was found that particleboards bonded with up to 30% lignin content resins gave similar mechanical and physical properties to commercial phenolformaldehyde resin, as long as a sufficient heating regime and time were applied.

Duchenne muscular dystrophy (DMD) is the most common inherited muscle disease in men and currently there is no effective treatment for this debilitating and lethal disorder. Although the absence of dystrophin is identified as the main cause of DMD, multiple secondary changes have been found to result from the dystrophin deficiency both in muscle and in non-muscle tissues. Among these abnormalities, our laboratory and others have demonstrated a dramatic increase in the expression of the P2RX7 receptor in cells and tissues from DMD patients and the mdx mouse model of DMD. The aim of this study was to determine the effects of P2RX7 ablation on biological functions in mdx muscle in situ and to identify suitable diagnostic and prognostic biomarkers for use in studies on the pharmacological inhibition of P2RX7. RNA transcription was profiled in muscle from wild-type and mdx mice, and also from double knock-out mdx/P2rx7^-/- mice which lack both functional Dmd and P2rx7 genes, and the effects of P2RX7 antagonists were assessed on pathological markers at the acute disease stage of disease in mdx mice, which resembles the human pathology. RNA sequencing was performed using the Illumina HiSeq 2000 platform to characterise the differential gene expression in tibialis anterior (TA) muscles from four week old wild type, mdx and mdx/P2rx7^-/- mice. The biological functions and molecules that are most affected in mdx and corrected in mdx/P2rx7^-/- tissues are those of the immune response, including the innate immune response, cytokine regulatory genes and the NF-кB pathway followed by fibrosis, telomerase regulatory genes, atherosclerosis signalling and the LXR/RXR activation pathway. Moreover, activation of the cell cycle, mitochondrial dysfunction, apoptosis and the adherens junction genes were found to be altered in mdx compared to wild type but not normalised in mdx/P2rx7^-/- muscles. This analysis also demonstrated that the mdx mutation disrupts the non-sense-mediated RNA decay and splicing mechanisms, which leads to an increase in out-of-frame transcripts that may have unexpected cellular impact. One of these altered transcripts, Bmp7, was significantly down-regulated in the mdx myoblasts, myofibres and in TA muscles and restored to the normal level in mdx/P2rx7^-/- muscle. Different analyses were used to map this alteration to the 5'exons of Bmp7 but the identification of this abnormal transcript was not successful. Four P2RX7 antagonists (oxidised ATP, A438079, AFC-5128 and azidothymidine (AZT)) were administered to male mdx mice and their effects on the pathology were analysed using different methods and biomarkers. All of the antagonists inhibited P2RX7 receptor-mediated responses in mdx mice without any detectable side effects. A438079 and AZT were found as the most effective in attenuating the wide range of the pathological features. The reduction in dystrophic features as results of ablation and antagonism the P2RX7 confirms the involvement of this purinoreceptor in the DMD pathology and making it an attractive target for a pharmacological treatment of this lethal disease. Additionally, as AZT is already in clinical use for other diseases, also in children, this drug could be relatively easily re-purposed and trialled for the treatment of DMD.

The aim of this study is to investigate the behaviour and application of an evolutionary algorithm (EA) based on a particular approach of cooperative co-evolution algorithm (CCEA), the Parisian Approach. It evolves and keeps an entire population as an optimal solution to the problem instead of keeping only the best individual in classical EAs. The CCEA we selected is called the “Fly algorithm”. It is named after flies, because the individuals are extremely primitive and correspond to three-dimensional (3-D) points. This algorithm has been relatively overlooked despite showing promising results in real-time robotic and image reconstruction in tomography. Our focus in this study is on two types of applications: medical imaging and digital art. i) In the medical application, we aim to improve quantitative results in 3-D reconstructed volumes in positron emission tomography (PET).We investigate the use of density fields, based on Metaballs and on Gaussian functions respectively, to obtain a realistic output. We also investigate how to exploit individuals’ fitness to modulate their individual footprint in the final reconstructed volume. An individual’s fitness can be seen as a level of confidence in its 3-D position. The resulting volumes are compared with previous work in terms of normalised-cross correlation. In our test cases, data fidelity increases by more than 10% when density fields are used instead of using a naive approach. Our method also provides reconstructions comparable to those obtained using well-established techniques used in medicine (e.g., filtered back-projection (FBP) and ordered subset expectation-maximization (OSEM)). Our algorithm relies heavily on the mutation operator. We propose 4 different fully adaptive mutation operators: basic mutation, adaptive mutation variance, dual mutation and directed mutation. Their impact on the algorithm efficiency is analysed and validated on PET reconstruction. ii) In the digital art application, we present the first application of the Fly algorithm in digital art. This branch of digital art is called “evolutionary art”. The motivation is to evaluate the algorithm with a much more complex structure of flies. They are still defined as simplistic primitives (3-D points) but with colours, sizes and rotations. Different visual effects were investigated, such as mosaic-like images and spray paint rendering. An online survey (including 41 participates) was conducted to validate our approach. Participants compared our results with similar ones generated with open-source software (GIMP). Again, our method shows promising results. In conclusion, our investigations confirm that the Fly algorithm works well with a complex search space. We demonstrate a fast and accurate solution to optimise a set of parameters in both applications. The Fly algorithm can improve reconstructed image quality compared to FBP and OSEM in medical application and to GIMP in digital art application.

Asthma is a common chronic inflammatory condition which affects over 300 million people worldwide. Thickening of the subepithelial layer is a key feature of asthmatic airways and the extent of thickening has been correlated with severity of asthma and increased exacerbations. Recent epidemiological studies have shown a link between fungal sensitisation primarily with Aspergillus fumigatus (A. fumigatus) and exacerbations of asthma leading to increased morbidity and mortality. The airway epithelium acts as an initial defence barrier to inhaled allergens such as A. fumigatus and emerging evidence suggests that as well as orchestrating an allergic immune response, it initiates aspects of airway wall remodelling including subepithelial thickening. However, induction of a profibrogenic response by the airway epithelium following exposure to inhaled fungi associated with severe asthma has not been well documented. The epithelial expression and production of the profibrotic growth factors, TGF-β1, TGF-β2, IL-6, endothelin-1 and periostin, selected as implicated in the aetiology of asthma and their profibrotic activity, were investigated in response to both A. fumigatus spores and culture filtrate in vitro. Furthermore, in vivo chronic inhalation models using either live spores or culture filtrate from two different strains of A. fumigatus (AF293 and CEA10) were used to determine the ability of the fungi to induce murine airway wall remodelling. In vitro, spores from both strains were able to induce the expression and production of IL-6 and endothelin-1 from human bronchial epithelial cells but none of the other profibrotic growth factors. In vivo, despite spores from both strains inducing expression and production of IL-6 and endothelin-1, only CEA10 spores caused significant subepithelial collagen deposition however, both strains induced α-SMA, a myofibroblast and smooth muscle marker around the airways. As a secreted factor was suspected of driving airway wall remodelling, subsequent studies used culture filtrate produced by the two strains, AF293, a low and CEA10, a high protease producer in basal medium. Only AF293 culture filtrate induced IL-6 and endothelin-1 from human bronchial epithelial cells in vitro. However, in vivo, culture filtrate from both strains was able to induce IL-6 and endothelin-1 expression, with AF293 causing a more profound subepithelial collagen deposition and significantly increased α-SMA abundance. It was hypothesised that epithelial-derived endothelin-1 drives airway wall remodelling and hence Endothelin receptor A was inhibited in the in vivo culture filtrate inhalation model. A significant reduction in subepithelial collagen deposition and α-SMA localisation around the airways was demonstrated in mice receiving an Endothelin receptor A antagonist compared with culture filtrate alone. This thesis indicates that A. fumigatus exposure can drive features of airway wall remodelling such as subepithelial fibrosis possibly through the epithelial production of profibrotic growth factor, endothelin-1.

In 1290, members of the de Viane family donated a six-volume set of large, deluxe liturgical manuscripts to the Cistercian nuns of Beaupré in Grimminge, East Flanders. The three extant volumes and a later supplement are now known as the Beaupré Antiphoner (Baltimore, Walters Art Museum, W. 759-762). The nuns used, extensively revised, and supplemented the antiphoner for the next five hundred years until the abbey was suppressed in 1796 during the French Revolution. The manuscript offers a bottom-up perspective on the history of Cistercian chant in a women’s community. It also fills lacunae in the documentary sources related to reform and change in the history of the abbey. Revisions made in the late fifteenth century under the Observant movement suggest a revival of interest in St. Bernard and the “Bernardine” recension of Cistercian chant. Further alterations in the early modern period demonstrate that the nuns did not abandon their medieval chant tradition and adopt post-Tridentine versions until the late eighteenth century, approximately two hundred years after the publication of the Roman breviary of Pope Pius V (1568). The nuns viewed their carefully considered revisions as a necessary condition of continuity, not as a threat to it.

Music conservatories are central institutions to the field of classical music. In them, aspiring professional hone their craft, renowned musicians pass on their expertise to upcoming generations, and notions of exactly who and what is considered “musical” are forged and disseminated. However, the apparently self-evident place of conservatories in modern cultures of classical music obscures their historical novelty—it is only since the latter nineteenth century that these institutions have become a pervasive force in classical music pedagogy and culture. This dissertation explores this revolution of institutionalized training in classical music by analyzing the history of German music conservatories over a roughly ninety-year period, from the founding of the Leipzig conservatory in 1843 to the Nazi takeover of power in 1933. Combining archival research, extant musicological scholarship, and theoretical and methodological approaches developed in a variety of social scientific and humanities disciplines, each chapter traces and historicizes a key development in modern music-pedagogical thought and practice: 1) the crystallization of a set of pedagogies designed to produce competency in the performance of canonical musical works; 2) the development of music education as a discipline; 3) the emergence of ear training; 4) the rise of Émile Jaques-Dalcroze’s method of rhythmic gymnastics. Throughout, I show that conservatories not only served to reproduce specific musical practices (such as the faithful performing of musical works, or Werktreue), but that they also functioned as incubators for new ways of thinking about human musicality and the pedagogies that would produce it. In particular, the latter chapters outline central features of what I call the “psychotechnical turn” in music education in the decades surrounding 1900, arguing that this resulted from growing connections between conservatory pedagogy and the psychological sciences.