Microstructure, growth and remodeling of the non-deformed and deformed vertebrae of the Red Porgy (Pagrus pagrus)

Máster Oficial en Cultivos Marinos. VI Máster Internacional en Acuicultura. Trabajo presentado como requisito parcial para la obtención del Título de Máster Oficial en Cultivos Marinos, otorgado por la Universidad de Las Palmas de Gran Canaria (ULPGC), el Instituto Canario de Ciencias Marinas (ICCM), y el Centro Internacional de Altos Estudios Agronómicos Mediterráneos de Zaragoza (CIHEAM)

Ecology of an uncultured heterotrophic flagellate lineage: MAST-4

Programa de oceanografía

Advances in the study of soil-structure interaction effects on the dynamic response of piled structures

[EN]This Ph. D. thesis presents a simple and stable procedure for the estimation of periods and dampings of pile shear buildings taking soil-structure interaction into account. The coupled-system response is obtained by using a substructuring model. A boundary element-finite element coupling formulation is used to compute impedances and kinematic interaction factors of the pile group configurations under investigation. The proposed procedure is applied to perform parametric analyses to determine the influence of the main parameters of soil-structure interaction problems on the dynamic response of the superstructure. The scope of this thesis also encompasses the study of foundations including battered piles.

Design and synthesis of novel non peptidomimtic beta-secretase inhibitors in the treatment of Alzheimer's disease

The aspartic protease BACE1 (β-amyloid precursor protein cleaving enzyme, β-secretase) is recognized as one of the most promising targets in the treatment of Alzheimer's disease (AD). The accumulation of β-amyloid peptide (Aβ) in the brain is a major factor in the pathogenesis of AD. Aβ is formed by initial cleavage of β-amyloid precursor protein (APP) by β-secretase, therefore BACE1 inhibition represents one of the therapeutic approaches to control progression of AD, by preventing the abnormal generation of Aβ. For this reason, in the last decade, many research efforts have focused at the identification of new BACE1 inhibitors as drug candidates. Generally, BACE1 inhibitors are grouped into two families: substrate-based inhibitors, designed as peptidomimetic inhibitors, and non-peptidomimetic ones. The research on non-peptidomimetic small molecules BACE1 inhibitors remains the most interesting approach, since these compounds hold an improved bioavailability after systemic administration, due to a good blood-brain barrier permeability in comparison to peptidomimetic inhibitors. Very recently, our research group discovered a new promising lead compound for the treatment of AD, named lipocrine, a hybrid derivative between lipoic acid and the AChE inhibitor (AChEI) tacrine, characterized by a tetrahydroacridinic moiety. Lipocrine is one of the first compounds able to inhibit the catalytic activity of AChE and AChE-induced amyloid-β aggregation and to protect against reactive oxygen species. Due to this interesting profile, lipocrine was also evaluated for BACE1 inhibitory activity, resulting in a potent lead compound for BACE1 inhibition. Starting from this interesting profile, a series of tetrahydroacridine analogues were synthesised varying the chain length between the two fragments. Moreover, following the approach of combining in a single molecule two different pharmacophores, we designed and synthesised different compounds bearing the moieties of known AChEIs (rivastigmine and caproctamine) coupled with lipoic acid, since it was shown that dithiolane group is an important structural feature of lipocrine for the optimal inhibition of BACE1. All the tetrahydroacridines, rivastigmine and caproctamine-based compounds, were evaluated for BACE1 inhibitory activity in a FRET (fluorescence resonance energy transfer) enzymatic assay (test A). With the aim to enhancing the biological activity of the lead compound, we applied the molecular simplification approach to design and synthesize novel heterocyclic compounds related to lipocrine, in which the tetrahydroacridine moiety was replaced by 4-amino-quinoline or 4-amino-quinazoline rings. All the synthesized compounds were also evaluated in a modified FRET enzymatic assay (test B), changing the fluorescent substrate for enzymatic BACE1 cleavage. This test method guided deep structure-activity relationships for BACE1 inhibition on the most promising quinazoline-based derivatives. By varying the substituent on the 2-position of the quinazoline ring and by replacing the lipoic acid residue in lateral chain with different moieties (i.e. trans-ferulic acid, a known antioxidant molecule), a series of quinazoline derivatives were obtained. In order to confirm inhibitory activity of the most active compounds, they were evaluated with a third FRET assay (test C) which, surprisingly, did not confirm the previous good activity profiles. An evaluation study of kinetic parameters of the three assays revealed that method C is endowed with the best specificity and enzymatic efficiency. Biological evaluation of the modified 2,4-diamino-quinazoline derivatives measured through the method C, allow to obtain a new lead compound bearing the trans-ferulic acid residue coupled to 2,4-diamino-quinazoline core endowed with a good BACE1 inhibitory activity (IC50 = 0.8 mM). We reported on the variability of the results in the three different FRET assays that are known to have some disadvantages in term of interference rates that are strongly dependent on compound properties. The observed results variability could be also ascribed to different enzyme origin, varied substrate and different fluorescent groups. The inhibitors should be tested on a parallel screening in order to have a more reliable data prior to be tested into cellular assay. With this aim, preliminary cellular BACE1 inhibition assay carried out on lipocrine confirmed a good cellular activity profile (EC50 = 3.7 mM) strengthening the idea to find a small molecule non-peptidomimetic compound as BACE1 inhibitor. In conclusion, the present study allowed to identify a new lead compound endowed with BACE1 inhibitory activity in submicromolar range. Further lead optimization to the obtained derivative is needed in order to obtain a more potent and a selective BACE1 inhibitor based on 2,4-diamino-quinazoline scaffold. A side project related to the synthesis of novel enzymatic inhibitors of BACE1 in order to explore the pseudopeptidic transition-state isosteres chemistry was carried out during research stage at Università de Montrèal (Canada) in Hanessian's group. The aim of this work has been the synthesis of the δ-aminocyclohexane carboxylic acid motif with stereochemically defined substitution to incorporating such a constrained core in potential BACE1 inhibitors. This fragment, endowed with reduced peptidic character, is not known in the context of peptidomimetic design. In particular, we envisioned an alternative route based on an organocatalytic asymmetric conjugate addition of nitroalkanes to cyclohexenone in presence of D-proline and trans-2,5-dimethylpiperazine. The enantioenriched obtained 3-(α-nitroalkyl)-cyclohexanones were further functionalized to give the corresponding δ-nitroalkyl cyclohexane carboxylic acids. These intermediates were elaborated to the target structures 3-(α-aminoalkyl)-1-cyclohexane carboxylic acids in a new readily accessible way.

Implementation of a non ground meta interpreter for defeasible logic

Human reasoning is a fascinating and complex cognitive process that can be applied in different research areas such as philosophy, psychology, laws and financial. Unfortunately, developing supporting software (to those different areas) able to cope such as complex reasoning it’s difficult and requires a suitable logic abstract formalism. In this thesis we aim to develop a program, that has the job to evaluate a theory (a set of rules) w.r.t. a Goal, and provide some results such as “The Goal is derivable from the KB5 (of the theory)”. In order to achieve this goal we need to analyse different logics and choose the one that best meets our needs. In logic, usually, we try to determine if a given conclusion is logically implied by a set of assumptions T (theory). However, when we deal with programming logic we need an efficient algorithm in order to find such implications. In this work we use a logic rather similar to human logic. Indeed, human reasoning requires an extension of the first order logic able to reach a conclusion depending on not definitely true6 premises belonging to a incomplete set of knowledge. Thus, we implemented a defeasible logic7 framework able to manipulate defeasible rules. Defeasible logic is a non-monotonic logic designed for efficient defeasible reasoning by Nute (see Chapter 2). Those kind of applications are useful in laws area especially if they offer an implementation of an argumentation framework that provides a formal modelling of game. Roughly speaking, let the theory is the set of laws, a keyclaim is the conclusion that one of the party wants to prove (and the other one wants to defeat) and adding dynamic assertion of rules, namely, facts putted forward by the parties, then, we can play an argumentative challenge between two players and decide if the conclusion is provable or not depending on the different strategies performed by the players. Implementing a game model requires one more meta-interpreter able to evaluate the defeasible logic framework; indeed, according to Göedel theorem (see on page 127), we cannot evaluate the meaning of a language using the tools provided by the language itself, but we need a meta-language able to manipulate the object language8. Thus, rather than a simple meta-interpreter, we propose a Meta-level containing different Meta-evaluators. The former has been explained above, the second one is needed to perform the game model, and the last one will be used to change game execution and tree derivation strategies.

Taxonomy, phylogeny and reproductive ecology of Gentiana lutea L.

This research focuses on taxonomy, phylogeny and reproductive ecology of Gentiana lutea. L.. Taxonomic analysis is a critical step in botanical studies, as it is necessary to recognize taxonomical unit. Herbarium specimens were observed to assess the reliability of several subspecies-diagnostic characters. The analysis of G. lutea genetic variability and the comparison with that of the other species of sect. Gentiana were performed to elucidate phylogenetic relationships among G. lutea subspecies and to propose a phylogenetic hypothesis for the evolution and the colonization dynamics of the section. Appropriate scientific information is critical for the assessment of species conservation status and for effective management plans. I carried out field work on five natural populations and performed laboratory analyses on specific critical aspects, with special regard to G. lutea breeding system and type and efficiency of plant-pollinator system. Bracts length is a reliable character to identify subsp. vardjanii, however it is not exclusive, hence to clearly identify subsp. vardjanii, other traits have to be considered. The phylogenetic hypotheses obtained from nuclear and chloroplast data are not congruent. Nuclear markers show a monophyly of sect. Gentiana, a strongly species identity of G. lutea and clear genetic identity of subsp. vardjanii. The little information emerging from plastid markers indicate a weak signal of hybridization and incomplete sorting of ancestral lineages. G. lutea shows a striking variation in intra-floral dichogamy probably evolved to reduce pollen-stigma interference. Although the species is partially self-compatible, pollen vectors are necessary for a successful reproduction, and moreover it shows a strong inbreeding depression. G. lutea is a generalist species: within its spectrum of visitors is possible to recognize "nectar thieves" and pollinators with sedentary or dynamic behaviour. Pollen limitation is frequent and it could be mainly explained by poor pollen quality.

Numerical investigation of turbulent/non-turbulent interface

The subject of this work is the diffusion of turbulence in a non-turbulent flow. Such phenomenon can be found in almost every practical case of turbulent flow: all types of shear flows (wakes, jet, boundary layers) present some boundary between turbulence and the non-turbulent surround; all transients from a laminar flow to turbulence must account for turbulent diffusion; mixing of flows often involve the injection of a turbulent solution in a non-turbulent fluid. The mechanism of what Phillips defined as “the erosion by turbulence of the underlying non-turbulent flow”, is called entrainment. It is usually considered to operate on two scales with different mechanics. The small scale nibbling, which is the entrainment of fluid by viscous diffusion of turbulence, and the large scale engulfment, which entraps large volume of flow to be “digested” subsequently by viscous diffusion. The exact role of each of them in the overall entrainment rate is still not well understood, as it is the interplay between these two mechanics of diffusion. It is anyway accepted that the entrainment rate scales with large properties of the flow, while is not understood how the large scale inertial behavior can affect an intrinsically viscous phenomenon as diffusion of vorticity. In the present work we will address then the problem of turbulent diffusion through pseudo-spectral DNS simulations of the interface between a volume of decaying turbulence and quiescent flow. Such simulations will give us first hand measures of velocity, vorticity and strains fields at the interface; moreover the framework of unforced decaying turbulence will permit to study both spatial and temporal evolution of such fields. The analysis will evidence that for this kind of flows the overall production of enstrophy , i.e. the square of vorticity omega^2 , is dominated near the interface by the local inertial transport of “fresh vorticity” coming from the turbulent flow. Viscous diffusion instead plays a major role in enstrophy production in the outbound of the interface, where the nibbling process is dominant. The data from our simulation seems to confirm the theory of an inertially stirred viscous phenomenon proposed by others authors before and provides new data about the inertial diffusion of turbulence across the interface.

Risk analysis of tractor rollover in the normal operation in field

Tractor rollover represent a primary cause of death or serious injury in agriculture and despite the mandatory Roll-Over Protective Structures (ROPS), that reduced the number of injuries, tractor accidents are still of great concern. Because of their versatility and wide use many studies on safety are concerned with the stability of tractors, but they often prefer controlled tests or laboratory tests. The evaluation of tractors working in field, instead, is a very complex issue because the rollover could be influenced by the interaction among operator, tractor and environment. Recent studies are oriented towards the evaluation of the actual working conditions developing prototypes for driver assistance and data acquisition. Currently these devices are produced and sold by manufacturers. A warning device was assessed in this study with the aim to evaluate its performance and to collect data on different variables influencing the dynamics of tractors in field by monitoring continuously the working conditions of tractors operating at the experimental farm of the Bologna University. The device consists of accelerometers, gyroscope, GSM/GPRS, GPS for geo-referencing and a transceiver for the automatic recognition of tractor-connected equipment. A microprocessor processes data and provides information, through a dedicated algorithm requiring data on the geometry of the tested tractor, on the level of risk for the operator in terms of probable loss of stability and suggests corrective measures to reduce the potential instability of the tractor.

Microbial ecology of biotechnological processes

The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater contaminated by chlorinated aliphatic hydrocarbons inside an immobilized-biomass packed bed bioreactor (PBR). In this case the analyses revealed homogeneous growth and structure of immobilized communities throughout the PBR and the occurrence of dominant microbial phylotypes of the genera Rhodococcus, Comamonas and Acidovorax, which probably drive the biodegradation process. The same molecular approaches were employed to characterize sludge microbial communities selected and enriched during the treatment of municipal wastewater coupled with the production of polyhydroxyalkanoates (PHA). Known PHA-accumulating microorganisms identified were affiliated with the genera Zooglea, Acidovorax and Hydrogenophaga. Finally, the molecular investigation concerned communities of polycyclic aromatic hydrocarbon (PAH) contaminated soil subjected to rhizoremediation with willow roots or fertilization-based treatments. The metabolic ability to biodegrade naphthalene, as a representative model for PAH, was assessed by means of stable isotope probing in combination with high-throughput sequencing analysis. The phylogenetic diversity of microbial populations able to derive carbon from naphthalene was evaluated as a function of the type of treatment.

Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue

The purpose of the work reported here is to test reliable molecular profiles using routinely processed formalin-fixed paraffin-embedded (FFPE) tissues from participants of the clinical trial BIG 1-98 with a median follow-up of 60 months.

Oral health risks of tobacco use and effects of cessation

The purpose of this paper is to review the epidemiologic evidence for the effects of tobacco use and tobacco use cessation on a variety of oral diseases and conditions. Exposures considered include cigarette and bidi smoking, pipe and cigar smoking, and smokeless tobacco use. Oral diseases and disorders considered include oral cancer and precancer, periodontal disease, caries and tooth loss, gingival recession and other benign mucosal disorders as well as implant failure. Particular attention is given to the impact of tobacco use cessation on oral health outcomes. We conclude that robust epidemiologic evidence exists for adverse oral health effects of tobacco smoking and other types of tobacco use. In addition, there is compelling evidence to support significant benefits of tobacco use cessation with regard to various oral health outcomes. Substantial oral health benefits can be expected from abstention and successful smoking cessation in a variety of populations across all ages.

Students' knowledge of symptoms and risk factors of potential life-threatening medical conditions

In order to assess medical students' knowledge of Basic Life Support (BLS) principles, we defined a minimal knowledge (MK) of three life-threatening medical conditions that should be universally known: cardiac arrest, heart attack and stroke, and compared the results with those of laypersons.

[The effect of stress-relieving interventions on inflammatory bowel disease: quality assessment of 10 therapeutic studies]

Patient comments and empirical studies suggest an influence of stress on inflammatory bowel diseases (IBD). We performed a quality assessment of previous studies on the effect of stress reduction on IBD in order to formulate recommendations for future studies and to evaluate their potential for improvement.

Risk stratification of normotensive patients with acute symptomatic pulmonary embolism

Treatment guidelines recommend strong consideration of thrombolysis in patients with acute symptomatic pulmonary embolism (PE) that present with arterial hypotension or shock because of the high risk of death in this setting. For haemodynamically stable patients with PE, the categorization of risk for subgroups may assist with decision-making regarding PE therapy. Clinical models [e.g. Pulmonary Embolism Severity Index (PESI)] may accurately identify those at low risk of overall death in the first 3 months after the diagnosis of PE, and such patients might benefit from an abbreviated hospital stay or outpatient therapy. Though some evidence suggests that a subset of high-risk normotensive patients with PE may have a reasonable risk to benefit ratio for thrombolytic therapy, single markers of right ventricular dysfunction (e.g. echocardiography, spiral computed tomography, or brain natriuretic peptide testing) and myocardial injury (e.g. cardiac troponin T or I testing) have an insufficient positive predictive value for PE-specific mortality to drive decision-making toward such therapy. Recommendations for outpatient treatment or thrombolytic therapy for patients with PE necessitate further development of prognostic models and conduct of clinical trials that assess various treatment strategies.

Risk factors of mortality in different age groups after thoracic endovascular aortic repair

The aim of this study was to determine risk factors for mortality in different age groups after thoracic endovascular aortic repair (TEVAR).