Acoustic characterisation of the tonic syllable in portuguese

A particular problem for the automatic prediction of prosody in speech synthesis is the realisation of accented syllables since these are affected by many parameters and are perceptually very salient. For the Portuguese language, in Europe, a set of comprehensive quantitative characterisation data and rules is totally lacking. The present paper is intended to be a quantitative contribution to the solution of this problem. In this paper, a preliminary modelling of duration, intensity and variation of F0 in the tonic syllable will be presented. The dependencies of the model with the syllable position in the word and the word position in the phrase are also presented.

Molecular and biological characterisation of orthobunyaviruses

Orthobunyaviruses are the largest genus within the Bunyaviridae family, with over 170 named viruses classified into 18 serogroups (Elliott and Blakqori, 2001; Plyusnin et al., 2012). Orthobunyaviruses are transmitted by arthropods and have a tripartite negative sense RNA genome, which encodes 4 structural proteins and 2 non-structural proteins. The non-structural protein NSs is the primary virulence factor of orthobunyaviruses and potent antagonist of the type I interferon (IFN) response. However, sequencing studies have identified pathogenic viruses that lack the NSs protein (Mohamed et al., 2009; Gauci et al., 2010). The work presented in this thesis describes the molecular and biological characterisation of divergent orthobunyaviruses. Data on plaque morphology, growth kinetics, protein profiles, sensitivity to IFN and activation of the type I IFN system are presented for viruses in the Anopheles A, Anopheles B, Capim, Gamboa, Guama, Minatitlan, Nyando, Tete and Turlock serogroups. These are complemented with complete genome sequencing and phylogenetic analysis. Low activation of IFN by Tete serogroup viruses, which naturally lack an NSs protein, was also further investigated by the development of a reverse genetics system for Batama virus (BMAV). Recombinant viruses with mutations in the virus nucleocapsid protein amino terminus showed higher activation of type I IFN in vitro and data suggests that low levels of IFN are due to lower activation rather than active antagonism. The anti-orthobunyavirus activity of IFN-stimulated genes IFI44, IFITMs and human and ovine BST2 were also studied, revealing that activity varies not only within the orthobunyavirus genus and virus serogroups but also within virus species. Furthermore, there was evidence of active antagonism of the type I IFN response and ISGs by non-NSs viruses. In summary, the results show that pathogenicity in man and antagonism of the type I IFN response in vitro cannot be predicted by the presence, or absence, of an NSs ORF. They also highlight problems in orthobunyavirus classification with discordance between classical antigen based data and phylogenetic analysis.

Identification and characterisation of telomere regulatory and signalling pathways after induction of telomere dysfunction

Telomeres are DNA-protein complexes which cap the ends of eukaryotic linear chromosomes. In normal somatic cells telomeres shorten and become dysfunctional during ageing due to the DNA end replication problem. This leads to activation of signalling pathways that lead to cellular senescence and apoptosis. However, cancer cells typically bypass this barrier to immortalisation in order to proliferate indefinitely. Therefore enhancing our understanding of telomere dysfunction and pathways involved in regulation of the process is essential. However, the pathways involved are highly complex and involve interaction between a wide range of biological processes. Therefore understanding how telomerase dysfunction is regulated is a challenging task and requires a systems biology approach. In this study I have developed a novel methodology for visualisation and analysis of gene lists focusing on the network level rather than individual or small lists of genes. Application of this methodology to an expression data set and a gene methylation data set allowed me to enhance my understanding of the biology underlying a senescence inducing drug and the process of immortalisation respectively. I then used the methodology to compare the effect of genetic background on induction of telomere uncapping. Telomere uncapping was induced in HCT116 WT, p21-/- and p53-/- cells using a viral vector expressing a mutant variant of hTR, the telomerase RNA template. p21-/- cells showed enhanced sensitivity to telomere uncapping. Analysis of a candidate pathway, Mismatch Repair, revealed a role for the process in response to telomere uncapping and that induction of the pathway was p21 dependent. The methodology was then applied to analysis of the telomerase inhibitor GRN163L and synergistic effects of hypoglycaemia with this drug. HCT116 cells were resistant to GRN163L treatment. However, under hypoglycaemic conditions the dose required for ablation of telomerase activity was reduced significantly and telomere shortening was enhanced. Overall this new methodology has allowed our group and collaborators to identify new biology and improve our understanding of processes regulating telomere dysfunction.

Speech and narrative: characterisation techniques in the "Aeneid"

The thesis provides a comprehensive analysis of the characterisation of two of the major figures in the Aeneid, Aeneas and Turnus. Particular attention is paid to their direct speeches, all of which are examined and, where relevant, compared to Homeric models and parallels. To this purpose considerable use is made of the indices in Knauer's Die Aeneis und Homer. A more general comparison is made between the dramatic (direct speech) role of Aeneas and those of Homer's Achilles (Iliad) and Odysseus (Odyssey). An appraisal is made (from the viewpoint of depiction of character) of the relationship between the direct and indirect speeches in the Aeneid. Reasons are given to suggest that it is not mere chance, or for the sake of variety, that certain speeches of Aeneas and Turnus are expressed in oratio obliqua. In addition, the narrative portrayal of Aeneas and Turnus is considered in apposition to that of the speeches. A distinction is drawn between Vergil's direct method of characterisation (direct speeches) and his indirect methods (narrative/oratio obliqua). Inevitably, the analysis involves major consideration of the Roman values which pervade the work. All speeches, thoughts and actions of Aeneas and Turnus are assessed in terms of pietas, impietas, furor, virtus, ratio, clementia, humanitas (etc.). It is shown that individual concepts (such as pietas and impietas) are reflected in Vergil's direct and indirect methods of characterisation. The workings of fate and their relevance to the pietas concept are discussed throughout.

Downstream processing of reverse osmosis brine: Characterisation of potential scaling compounds

Reverse osmosis (RO) brine produced at a full-scale coal seam gas (CSG) water treatment facility was characterized with spectroscopic and other analytical techniques. A number of potential scalants including silica, calcium, magnesium, sulphates and carbonates, all of which were present in dissolved and non-dissolved forms, were characterized. The presence of spherical particles with a size range of 10-1000nm and aggregates of 1-10 microns was confirmed by transmission electron microscopy (TEM). Those particulates contained the following metals in decreasing order: K, Si, Sr, Ca, B, Ba, Mg, P, and S. Characterization showed that nearly one-third of the total silicon in the brine was present in the particulates. Further, analysis of the RO brine suggested supersaturation and precipitation of metal carbonates and sulphates during the RO process should take place and could be responsible for subsequently capturing silica in the solid phase. However, the precipitation of crystalline carbonates and sulphates are complex. X-ray diffraction analysis did not confirm the presence of common calcium carbonates or sulphates but instead showed the presence of a suite of complex minerals, to which amorphous silica and/or silica rich compounds could have adhered. A filtration study showed that majority of the siliceous particles were less than 220nm in size, but could still be potentially captured using a low molecular weight ultrafiltration membrane. © 2015 Elsevier Ltd.

Characterisation of the Lipid Profile of the Portuguese Population

Cardiovascular disease (CVD), particularly coronary heart disease (CHD) and stroke, are the leading cause of morbidity and mortality worldwide. The common forms of CVD have a complex aetiology in which interactions between multiple genetic and environmental factors play an important roles. The incidence rates of these diseases are increasing in developing countries as a result of the modification of lifestyles and increased prevalence of cardiovascular risk factors. Many independent cardiovascular risk factors could be modifiable, in contrast to the genetic risk factors. However, the associated risk of the genetic factors can be prevented if early identified, making genetic studies a priority in cardiovascular genetics research.

Characterisation of the lipid profile of the portuguese population

Cardiovascular disease (CVD), particularly coronary heart disease (CHD) and stroke, are the leading cause of morbidity and mortality worldwide. The common forms of CVD have a complex aetiology in which interactions between multiple genetic and environmental factors play an important role.

Characterisation and quantification of changes in odorants from litter headspace of meat chickens fed diets varying in protein levels and additives

The effect of dietary crude protein (CP) and additives on odor flux from meat chicken litter was investigated using 180 day-old Ross 308 male chicks randomly allocated to five dietary treatments with three replicates of 12 birds each. A 5 × 3 factorial arrangement of treatments was employed. Factors were: diet (low CP, high CP, high CP+antibiotic, high CP+probiotic, high CP+saponin) and age (15, 29, 35 days). The antibiotic used was Zn bacitracin, the probiotic was a blend of three Bacillus subtilis strains and the saponin came from a blend of Yucca and Quillaja. Odorants were collected from litter headspace with a flux hood and measured using selective ion flow tube mass spectrometry (SIFT-MS). Litter moisture, water activity (Aw), and litter headspace odorant concentrations were correlated. The results showed that low CP group produced lower flux of dimethyl amine, trimethyl amine, H2S, NH3, and phenol in litter compared to high CP group (P < 0.05). Similarly, high CP+probiotic group produced lower flux of H2S (P < 0.05) and high CP+saponin group produced lower flux of trimethylamine and phenol in litter compared to high CP group (P < 0.05). The dietary treatments tended (P = 0.065) to have higher flux of methanethiol in high CP group compared to others. There was a diet × age interaction for litter flux of diacetyl, 3-hydroxy-2-butanone (acetoin), 3-methyl-1-butanol, 3-methylbutanal, ethanethiol, propionic acid, and hexane (P < 0.05). Concentrations of diacetyl, acetoin, propionic acid, and hexane in litter were higher from low CP group compared to all other treatments on d 35 (P < 0.05) but not on d 15 and 29. A high litter moisture increased water activity (P < 0.01) and favored the emissions of methyl mercaptan, hydrogen sulfide, dimethyl sulfide, ammonia, trimethyl amine, phenol, indole, and 3-methylindole over others. Thus, the low CP diet, Bacillus subtilis based probiotic and the blend of Yucca/Quillaja saponin were effective in reducing the emissions of some key odorants from meat chicken litter.

Trapping phosphorus (III) into polyoxometalates: synthesis, characterisation and electronic behaviour study

The introduction of electronically-active heteroanions into polyoxometalates (POMs) is one of the emerging topics in this field. The novel clusters have shown unprecedented intramolecular electron-transfer features that can be directly mediated by the incorporated heteroanions. In this thesis, we will focus on the study of phosphite (HPO32-) as new non-traditional heteroanions, discover HPO32- templated nanostructures, investigate their electronic behaviours as well as understand the self-assembly process of HPO32--templated species. The thesis starts with incorporating HPO32- into POM cages. The feasibility of this work was illustrated by the successful trapping of HPO32- into a “Trojan Horse” type {W18O56} nanocage. The reactivity of embedded {HPO3} was fully studied, showing the cluster undergoes a structural rearrangement in solution whereby the {HPO3} moieties dimerise to form a weakly interacting (O3PH···HPO3) moiety. In the crystalline state a temperature-dependent intramolecular redox reaction and structural rearrangement occurs. This rearrangement appears to proceed via an intermediate containing two different templates, a pyramidal {HPO3} and a tetrahedral {PO4} moiety. {HPO3} templated POM cages were then vigorously expanded and led to the isolation of five either fully oxidised or mixed-valence clusters trapped with mono-, di-, or tri- {HPO3}. Interestingly, an intriguing 3D honeycomb-like host-guest structure was also synthesised. The porous framework was self-aggregated by a tri-phopshite anion templated {W21} cluster with a {VO4} templated Wells-Dawson type {W18} acting as a guest species within the hexagonal channels. Based on this work, we further extended the templating anions to two different redox-active heteroanions, and discovered a unique mixed-heteroatom templated system built by pairing redox-active {HPIIIO3} with {TeO3}, {SeO3} or {AsO3}. Two molecular systems were developed, ie. “Trojan Horse” type [W18O56(HPO3)0.8(SeO3)1.2(H2O)2]8- and cross-shaped [H4P4X4W64O224]32-/36-, where X=TeIV, SeIV, AsIII. In the case of {W18(HPO3)0.8(SeO3)1.2}, the compound is found to be a mixture of heteroleptic {W18(HPO3)(SeO3)} and homoleptic {W18(SeO3)2} and {W18(HPO3)2}, identified by single crystal x-ray diffraction, NMR as well as high resolution mass spectrometry. The cluster exhibited similar temperature-dependent electronic features to “Trojan Horse” type {W18(HPO3)2O56}. However, due to the intrinsic reactivity difference between {HPO3} and {SeO3}, the thermal treatment leads to the formation of an unusual species [W18O55(PO4)(SeO3)]5-, in which {HPO3} was fully oxidised to {PO4} within the cage, whereas and lone-pair-containing {SeO3} heteroanions were kept intact inside the shell. This finding is extremely interesting, as it demonstrated that multiple and independent intramolecular electronic performance can be achieved by the coexistence of distinct heteroatoms within a single molecule. On the other hand, the cross-shaped [H4P4X4W64O224]32-/36- were constructed by four {W15(HPO3)(XO3)} building units linked by four {WO6} octahedra. Each building unit traps two different heteroatoms. It is interesting to note that the mixed heteroatom species show self-sorting, with a highly selective positional preference. Smaller ionic sized {HPO3} are self-organised into the uncapped side of {W15} cavity, whereas closed side are occupied by larger heteroatoms, which is surprisingly opposed to steric hindrance. Density functional theory (DFT) calculations are currently underway to have a full understanding of the preference of heteroatom substitutions. This series of clusters is of great interest in terms of achieving single molecule-based heteroatom-dependent multiple levels of electron transfer. It has opened a new way to design and synthesise POMs with higher diversity of electrical states, which may lead to a new type of Q-bits for quantum computing. The third chapter is focused on developing polyoxotungstate building blocks templated by {HPO3}. A series of building blocks, {W15O48(HPO3)2}, {W9O30(HPO3)} {W12O40(HPO3)2} and hexagonal {W6O18(HPO3)} have been obtained. The first four building blocks have been reported with {SeO3} and/or {TeO3} heteroanions. This result demonstrates {HPO3} has a similar reactivity as {SeO3} and {TeO3}, therefore studying the self-assembly of {HPO3}-based building blocks would be helpful to have a general understanding of pyramidal heteroatom-based molecular systems. The hexagonal {W6O18(HPO3)} is observed for the first time in polyoxotungstates, showing some of reactivity difference between {HPO3} and {SeO3} and {TeO3}. Furthermore, inorganic salts and pH values have some directing influence on the formation and transformation of various building blocks, resulting in the discovery of a family of {HPO3}-based clusters with nuclearity ranging from {W29} to {W106}. High resolution mass spectrometry was also carried out to investigate the cluster solution behaviour and also gain information of building block speciation. It is found that some clusters experienced decomposition, which gives rise to potential building blocks accountable for the self-assembly.

Isotope characterisation of deep aquifers in the Gwda catchment, northern Poland

We present the results of isotope measurements (δ 18 O, δ D, δ 13 C DIC and 14 C) and chemical analyses (TDS, TOC, HCO 3– , SO 42– , Cl – , NO 3– , NH 4+ , Ca 2+ , Mg 2+ Na + and K + ) conducted on groundwater samples collected from deep Cenozoic aqui- fers. These aquifers are the basic source of drinking water at numerous localities within the study area in northern Po- land. Most of the δ 18 O determinations are characterised by low variability (i.e., > 70 per cent of δ 18 O are between –9.5‰ and –9.2‰). In most cases tritium activity was not detected or its content slightly exceeded the uncertainty of measure- ment (from ±0.3 T.U. to ± 0.5 T.U.). On average, 14 C activity is twice higher than that under similar conditions and in hydrogeological systems. The δ 13 C DIC values fall within the –13.6‰ to –12.8‰ range. A slight variability is observed when considering all isotope and chemical data within the study area and under these hydrogeological conditions. In general, the results of isotope and chemical analyses seem to be homogeneous, indicating the presence of closely similar groundwaters in the system, irrespective of geological formation. It is likely that there is a significant hydraulic connec- tion between shallow and deep aquifers in the Gwda catchment, which indicates the potential for seepage of pollutants from shallow Pleistocene to deep Miocene aquifers. This can endanger the latter by e.g., high concentrations of NO 3– , SO 42– and Cl – ions from shallow aquifers within the Gwda catchment.

Polymer microspheres: synthesis, characterisation and post-functionalisation by olefin metathesis

Porous polymer particles are used in an extraordinarily wide range of advanced and everyday applications, from combinatorial chemistry, solid-phase organic synthesis and polymer-supported reagents, to environmental analyses and the purification of drinking water. The installation and exploitation of functional chemical handles on the particles is often a prerequisite for their successful exploitation, irrespective of the application and the porous nature of the particles. New methodology for the chemical modification of macroreticular polymers is the primary focus of the work presented in this thesis. Porous polymer microspheres decorated with a diverse range of functional groups were synthesised by the post-polymerisation chemical modification of beaded polymers via olefin cross metathesis. The polymer microspheres were prepared by the precipitation polymerisation of divinylbenzene in porogenic (pore-forming) solvents; the olefin cross-metathesis (CM) functionalisation reactions exploited the pendent (polymer-bound) vinyl groups that were not consumed by polymerisation. Olefin CM reactions involving the pendent vinyl groups were performed in dichloromethane using second-generation Grubbs catalyst (Grubbs II), and a wide range of coupling partners used. The results obtained indicate that high quality, porous polymer microspheres synthesised by precipitation polymerisation in near-θ solvents can be functionalised by olefin CM under very mild conditions to install a diverse range of chemical functionalities into a common polydivinylbenzene precursor. Gel-type polymer microspheres were prepared by the precipitation copolymerisation reaction of divinylbenzene and allyl methacrylate in neat acetonitrile. The unreacted pendent vinyl groups that were not consumed by polymerisation were subjected to internal and external olefin metathesis-based hypercrosslinking reactions. Internal hypercrosslinking was carried out by using ring-closing metathesis (RCM) reactions in toluene using Grubbs II catalyst. Under these conditions, hypercrosslinked (HXL) polymers with specific surface areas around 500 m2g-1 were synthesised. External hypercrosslinking was attempted by using CM/RCM in the presence of a multivinyl coupling partner in toluene using second-generation Hoveyda-Grubbs catalyst. The results obtained indicate that no HXL polymers were obtained. However, during the development of this methodology, a new type of polymerisation was discovered with tetraallylorthosilicate as monomer.

Geological Characterisation of Depleted Oil and Gas Reservoirs for Carbon Sequestration Potentials in a Field in the Niger Delta, Nigeria

The injectivity, containment and storage capacity of sandstone reservoirs in a field in the Coastal Swamp depobelt of the onshore eastern Niger Delta were evaluated using wireline logs and seismic data to assess their potentials for carbon dioxide storage and geosequestration. The reservoir formation consists of multilayered alternating beds of sandstone and shale cap rocks. Active seismicity and fracturing intensity are low and growth faults provide the reservoir sealing mechanisms. Three reservoirs were delineated at depths between 3319 m and 3539 m which will keep injected CO2 in a supercritical state. The reservoir depth of at least 800 m, porosity and permeability of more than 10 percent and 20 mD, and a caprock thickness of at least 10 m, in addition to geothermal gradients of 13.46 to 33.66 ºC /km are the ideal conditions for the efficacy of storage. Comparison of the derived reservoir and seal properties such as porosity, permeability, thickness and depth with the minimum recommended site selection criteria shows that the reservoirs are potential candidates for carbon geosequestration with a total theoretical storage capacity of 147MM tons.

Polyphasic characterisation of Burkholderia cepacia complex species isolated from children with cystic fibrosis

Cystic fibrosis (CF) patients with Burkholderia cepacia complex (Bcc) pulmonary infections have high morbidity and mortality. The aim of this study was to compare different methods for identification of Bcc species isolated from paediatric CF patients. Oropharyngeal swabs from children with CF were used to obtain isolates of Bcc samples to evaluate six different tests for strain identification. Conventional (CPT) and automatised (APT) phenotypic tests, polymerase chain reaction (PCR)-recA, restriction fragment length polymorphism-recA, recA sequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) were applied. Bacterial isolates were also tested for antimicrobial susceptibility. PCR-recA analysis showed that 36 out of the 54 isolates were Bcc. Kappa index data indicated almost perfect agreement between CPT and APT, CPT and PCR-recA, and APT and PCR-recA to identify Bcc, and MALDI-TOF and recA sequencing to identify Bcc species. The recA sequencing data and the MALDI-TOF data agreed in 97.2% of the isolates. Based on recA sequencing, the most common species identified were Burkholderia cenocepacia IIIA (33.4%), Burkholderia vietnamiensis (30.6%), B. cenocepacia IIIB (27.8%), Burkholderia multivorans (5.5%), and B. cepacia (2.7%). MALDI-TOF proved to be a useful tool for identification of Bcc species obtained from CF patients, although it was not able to identify B. cenocepacia subtypes.