In search of mechanisms associated with mesenchymal stem cell-based therapies for acute kidney injury

Acute kidney injury (AKI) is classically described as a rapid loss of kidney function. AKI affects more than 15% of all hospital admissions and is associated with elevated mortality rates. Although many advances have occurred, intermittent or continuous renal replacement therapies are still considered the best options for reversing mild and severe AKI syndrome. For this reason, it is essential that innovative and effective therapies, without side effects and complications, be developed to treat AKI and the end-stages of renal disease. Mesenchymal stem cell (MSC) based therapies have numerous advantages in helping to repair inflamed and damaged tissues and are being considered as a new alternative for treating kidney injuries. Numerous experimental models have shown that MSCs can act via differentiation-independent mechanisms to help renal recovery. Essentially, MSCs can secrete a pool of cytokines, growth factors and chemokines, express enzymes, interact via cell-to-cell contacts and release bioagents such as microvesicles to orchestrate renal protection. In this review, we propose seven distinct properties of MSCs which explain how renoprotection may be conferred: 1) anti-inflammatory; 2) pro-angiogenic; 3) stimulation of endogenous progenitor cells; 4) anti-apoptotic; 5) anti-fibrotic; 6) anti-oxidant; and 7) promotion of cellular reprogramming. In this context, these mechanisms, either individually or synergically, could induce renal protection and functional recovery. This review summarises the most important effects and benefits associated with MSC-based therapies in experimental renal disease models and attempts to clarify the mechanisms behind the MSC-related renoprotection. MSCs may prove to be an effective, innovative and affordable treatment for moderate and severe AKI. However, more studies need to be performed to provide a more comprehensive global understanding of MSC-related therapies and to ensure their safety for future clinical applications.

Synthesis and properties of substituted Hg-based superconductors

This thesis is focused on studies of substituted Hg-based superconducting copper oxides ((Hg1-xMx)Ba2Can-1CunO2n+2+δ). These compounds are promising objects of investigation, not only from a fundamental point of view but also because of their high values of superconducting transition temperature (Tc) and irreversibility field (Hirr). The first part of the thesis is devoted to optimization of the synthesis procedure for Hg-based cuprates. The influence of different parameters (T, t, p(Hg), p(O2)) on the synthesis of these compounds in sealed silica tubes was studied. Optimal conditions yielded samples containing up to 95% of HgBa2Ca2Cu3O8+δ (Hg-1223). The formation of solid solutions with the formula (Hg1-xCux)Ba2Ca2Cu3O8+δ (where x <= 0.5) was also established. Another technique was developed, using LiF as a flux, for synthesis of samples containing up to 90% of the HgBa2CaCu2O6+δ (Hg-1212) phase. The second part concerns synthesis and studies of oxyfluorides using Hg-1212 and Hg-1223 as starting materials together with XeF2 as a fluorinating agent. It was found that oxyfluorides of both phases have a parabolic dependence of Tc vs. a parameter as well as enhanced Tc values (ΔT ≈ 3-4 K) in comparison with optimally doped non-fluorinated analogues. The crystal structure of Hg-1223 oxyfluoride was studied by X-ray powder and neutron diffraction methods. It is suggested that chemical modification of the crystal structure leads to a decrease in Cu-O distance without noticeable change in Cu-O-Cu angle (in the (CuO2) layers), which may be the significant factors influencing this Tc increase. Hg-1223 oxyfluoride was also studied under high pressure for first time. It was found that this compound has a record-high Tc value (≈ 166 K) at P ≈ 23 GPa. The last part describes the investigation of substituted Hg-based superconductors in the series (Hg0.9M0.1)Ba2CuO4+δ {(Hg,M)-1201}, where M = Tl, Pb, W, Mo, Nb and V. A comprehensive study of these compounds by various methods (X-ray powder diffraction, EDX, IR-, EXAFS- and XANES -spectroscopy) indicated that the change of charge carrier doping level is a crucial factor determining the irreversibility line. (Hg0.9Mo0.1)Ba2CuO4+δ showed the most improved irreversibility line position among the (Hg,M)-1201 compounds studied in this series.

Impatto di rifaximina sul microbiota intestinale: selezione di bifidobatteri antibiotico resistenti

The ideal approach for the long term treatment of intestinal disorders, such as inflammatory bowel disease (IBD), is represented by a safe and well tolerated therapy able to reduce mucosal inflammation and maintain homeostasis of the intestinal microbiota. A combined therapy with antimicrobial agents, to reduce antigenic load, and immunomodulators, to ameliorate the dysregulated responses, followed by probiotic supplementation has been proposed. Because of the complementary mechanisms of action of antibiotics and probiotics, a combined therapeutic approach would give advantages in terms of enlargement of the antimicrobial spectrum, due to the barrier effect of probiotic bacteria, and limitation of some side effects of traditional chemiotherapy (i.e. indiscriminate decrease of aggressive and protective intestinal bacteria, altered absorption of nutrient elements, allergic and inflammatory reactions). Rifaximin (4-deoxy-4’-methylpyrido[1’,2’-1,2]imidazo[5,4-c]rifamycin SV) is a product of synthesis experiments designed to modify the parent compound, rifamycin, in order to achieve low gastrointestinal absorption while retaining good antibacterial activity. Both experimental and clinical pharmacology clearly show that this compound is a non systemic antibiotic with a broad spectrum of antibacterial action, covering Gram-positive and Gram-negative organisms, both aerobes and anaerobes. Being virtually non absorbed, its bioavailability within the gastrointestinal tract is rather high with intraluminal and faecal drug concentrations that largely exceed the MIC values observed in vitro against a wide range of pathogenic microorganisms. The gastrointestinal tract represents therefore the primary therapeutic target and gastrointestinal infections the main indication. The little value of rifaximin outside the enteric area minimizes both antimicrobial resistance and systemic adverse events. Fermented dairy products enriched with probiotic bacteria have developed into one of the most successful categories of functional foods. Probiotics are defined as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host” (FAO/WHO, 2002), and mainly include Lactobacillus and Bifidobacterium species. Probiotic bacteria exert a direct effect on the intestinal microbiota of the host and contribute to organoleptic, rheological and nutritional properties of food. Administration of pharmaceutical probiotic formula has been associated with therapeutic effects in treatment of diarrhoea, constipation, flatulence, enteropathogens colonization, gastroenteritis, hypercholesterolemia, IBD, such as ulcerative colitis (UC), Crohn’s disease, pouchitis and irritable bowel syndrome. Prerequisites for probiotics are to be effective and safe. The characteristics of an effective probiotic for gastrointestinal tract disorders are tolerance to upper gastrointestinal environment (resistance to digestion by enteric or pancreatic enzymes, gastric acid and bile), adhesion on intestinal surface to lengthen the retention time, ability to prevent the adherence, establishment and/or replication of pathogens, production of antimicrobial substances, degradation of toxic catabolites by bacterial detoxifying enzymatic activities, and modulation of the host immune responses. This study was carried out using a validated three-stage fermentative continuous system and it is aimed to investigate the effect of rifaximin on the colonic microbial flora of a healthy individual, in terms of bacterial composition and production of fermentative metabolic end products. Moreover, this is the first study that investigates in vitro the impact of the simultaneous administration of the antibiotic rifaximin and the probiotic B. lactis BI07 on the intestinal microbiota. Bacterial groups of interest were evaluated using culture-based methods and molecular culture-independent techniques (FISH, PCR-DGGE). Metabolic outputs in terms of SCFA profiles were determined by HPLC analysis. Collected data demonstrated that rifaximin as well as antibiotic and probiotic treatment did not change drastically the intestinal microflora, whereas bacteria belonging to Bifidobacterium and Lactobacillus significantly increase over the course of the treatment, suggesting a spontaneous upsurge of rifaximin resistance. These results are in agreement with a previous study, in which it has been demonstrated that rifaximin administration in patients with UC, affects the host with minor variations of the intestinal microflora, and that the microbiota is restored over a wash-out period. In particular, several Bifidobacterium rifaximin resistant mutants could be isolated during the antibiotic treatment, but they disappeared after the antibiotic suspension. Furthermore, bacteria belonging to Atopobium spp. and E. rectale/Clostridium cluster XIVa increased significantly after rifaximin and probiotic treatment. Atopobium genus and E. rectale/Clostridium cluster XIVa are saccharolytic, butyrate-producing bacteria, and for these characteristics they are widely considered health-promoting microorganisms. The absence of major variations in the intestinal microflora of a healthy individual and the significant increase in probiotic and health-promoting bacteria concentrations support the rationale of the administration of rifaximin as efficacious and non-dysbiosis promoting therapy and suggest the efficacy of an antibiotic/probiotic combined treatment in several gut pathologies, such as IBD. To assess the use of an antibiotic/probiotic combination for clinical management of intestinal disorders, genetic, proteomic and physiologic approaches were employed to elucidate molecular mechanisms determining rifaximin resistance in Bifidobacterium, and the expected interactions occurring in the gut between these bacteria and the drug. The ability of an antimicrobial agent to select resistance is a relevant factor that affects its usefulness and may diminish its useful life. Rifaximin resistance phenotype was easily acquired by all bifidobacteria analyzed [type strains of the most representative intestinal bifidobacterial species (B. infantis, B. breve, B. longum, B. adolescentis and B. bifidum) and three bifidobacteria included in a pharmaceutical probiotic preparation (B. lactis BI07, B. breve BBSF and B. longum BL04)] and persisted for more than 400 bacterial generations in the absence of selective pressure. Exclusion of any reversion phenomenon suggested two hypotheses: (i) stable and immobile genetic elements encode resistance; (ii) the drug moiety does not act as an inducer of the resistance phenotype, but enables selection of resistant mutants. Since point mutations in rpoB have been indicated as representing the principal factor determining rifampicin resistance in E. coli and M. tuberculosis, whether a similar mechanism also occurs in Bifidobacterium was verified. The analysis of a 129 bp rpoB core region of several wild-type and resistant bifidobacteria revealed five different types of miss-sense mutations in codons 513, 516, 522 and 529. Position 529 was a novel mutation site, not previously described, and position 522 appeared interesting for both the double point substitutions and the heterogeneous profile of nucleotide changes. The sequence heterogeneity of codon 522 in Bifidobacterium leads to hypothesize an indirect role of its encoded amino acid in the binding with the rifaximin moiety. These results demonstrated the chromosomal nature of rifaximin resistance in Bifidobacterium, minimizing risk factors for horizontal transmission of resistance elements between intestinal microbial species. Further proteomic and physiologic investigations were carried out using B. lactis BI07, component of a pharmaceutical probiotic preparation, as a model strain. The choice of this strain was determined based on the following elements: (i) B. lactis BI07 is able to survive and persist in the gut; (ii) a proteomic overview of this strain has been recently reported. The involvement of metabolic changes associated with rifaximin resistance was investigated by proteomic analysis performed with two-dimensional electrophoresis and mass spectrometry. Comparative proteomic mapping of BI07-wt and BI07-res revealed that most differences in protein expression patterns were genetically encoded rather than induced by antibiotic exposure. In particular, rifaximin resistance phenotype was characterized by increased expression levels of stress proteins. Overexpression of stress proteins was expected, as they represent a common non specific response by bacteria when stimulated by different shock conditions, including exposure to toxic agents like heavy metals, oxidants, acids, bile salts and antibiotics. Also, positive transcription regulators were found to be overexpressed in BI07-res, suggesting that bacteria could activate compensatory mechanisms to assist the transcription process in the presence of RNA polymerase inhibitors. Other differences in expression profiles were related to proteins involved in central metabolism; these modifications suggest metabolic disadvantages of resistant mutants in comparison with sensitive bifidobacteria in the gut environment, without selective pressure, explaining their disappearance from faeces of patients with UC after interruption of antibiotic treatment. The differences observed between BI07-wt e BI07-res proteomic patterns, as well as the high frequency of silent mutations reported for resistant mutants of Bifidobacterium could be the consequences of an increased mutation rate, mechanism which may lead to persistence of resistant bacteria in the population. However, the in vivo disappearance of resistant mutants in absence of selective pressure, allows excluding the upsurge of compensatory mutations without loss of resistance. Furthermore, the proteomic characterization of the resistant phenotype suggests that rifaximin resistance is associated with a reduced bacterial fitness in B. lactis BI07-res, supporting the hypothesis of a biological cost of antibiotic resistance in Bifidobacterium. The hypothesis of rifaximin inactivation by bacterial enzymatic activities was verified by using liquid chromatography coupled with tandem mass spectrometry. Neither chemical modifications nor degradation derivatives of the rifaximin moiety were detected. The exclusion of a biodegradation pattern for the drug was further supported by the quantitative recovery in BI07-res culture fractions of the total rifaximin amount (100 μg/ml) added to the culture medium. To confirm the main role of the mutation on the β chain of RNA polymerase in rifaximin resistance acquisition, transcription activity of crude enzymatic extracts of BI07-res cells was evaluated. Although the inhibition effects of rifaximin on in vitro transcription were definitely higher for BI07-wt than for BI07-res, a partial resistance of the mutated RNA polymerase at rifaximin concentrations > 10 μg/ml was supposed, on the basis of the calculated differences in inhibition percentages between BI07-wt and BI07-res. By considering the resistance of entire BI07-res cells to rifaximin concentrations > 100 μg/ml, supplementary resistance mechanisms may take place in vivo. A barrier for the rifaximin uptake in BI07-res cells was suggested in this study, on the basis of the major portion of the antibiotic found to be bound to the cellular pellet respect to the portion recovered in the cellular lysate. Related to this finding, a resistance mechanism involving changes of membrane permeability was supposed. A previous study supports this hypothesis, demonstrating the involvement of surface properties and permeability in natural resistance to rifampicin in mycobacteria, isolated from cases of human infection, which possessed a rifampicin-susceptible RNA polymerase. To understand the mechanism of membrane barrier, variations in percentage of saturated and unsaturated FAs and their methylation products in BI07-wt and BI07-res membranes were investigated. While saturated FAs confer rigidity to membrane and resistance to stress agents, such as antibiotics, a high level of lipid unsaturation is associated with high fluidity and susceptibility to stresses. Thus, the higher percentage of saturated FAs during the stationary phase of BI07-res could represent a defence mechanism of mutant cells to prevent the antibiotic uptake. Furthermore, the increase of CFAs such as dihydrosterculic acid during the stationary phase of BI07-res suggests that this CFA could be more suitable than its isomer lactobacillic acid to interact with and prevent the penetration of exogenous molecules including rifaximin. Finally, the impact of rifaximin on immune regulatory functions of the gut was evaluated. It has been suggested a potential anti-inflammatory effect of rifaximin, with reduced secretion of IFN-γ in a rodent model of colitis. Analogously, it has been reported a significant decrease in IL-8, MCP-1, MCP-3 e IL-10 levels in patients affected by pouchitis, treated with a combined therapy of rifaximin and ciprofloxacin. Since rifaximin enables in vivo and in vitro selection of Bifidobacterium resistant mutants with high frequency, the immunomodulation activities of rifaximin associated with a B. lactis resistant mutant were also taken into account. Data obtained from PBMC stimulation experiments suggest the following conclusions: (i) rifaximin does not exert any effect on production of IL-1β, IL-6 and IL-10, whereas it weakly stimulates production of TNF-α; (ii) B. lactis appears as a good inducer of IL-1β, IL-6 and TNF-α; (iii) combination of BI07-res and rifaximin exhibits a lower stimulation effect than BI07-res alone, especially for IL-6. These results confirm the potential anti-inflammatory effect of rifaximin, and are in agreement with several studies that report a transient pro-inflammatory response associated with probiotic administration. The understanding of the molecular factors determining rifaximin resistance in the genus Bifidobacterium assumes an applicative significance at pharmaceutical and medical level, as it represents the scientific basis to justify the simultaneous use of the antibiotic rifaximin and probiotic bifidobacteria in the clinical treatment of intestinal disorders.

RNA Interference and cyclooxygenase-2 (COX-2) regulation in colon cancer cells

Despite new methods and combined strategies, conventional cancer chemotherapy still lacks specificity and induces drug resistance. Gene therapy can offer the potential to obtain the success in the clinical treatment of cancer and this can be achieved by replacing mutated tumour suppressor genes, inhibiting gene transcription, introducing new genes encoding for therapeutic products, or specifically silencing any given target gene. Concerning gene silencing, attention has recently shifted onto the RNA interference (RNAi) phenomenon. Gene silencing mediated by RNAi machinery is based on short RNA molecules, small interfering RNAs (siRNAs) and microRNAs (miRNAs), that are fully o partially homologous to the mRNA of the genes being silenced, respectively. On one hand, synthetic siRNAs appear as an important research tool to understand the function of a gene and the prospect of using siRNAs as potent and specific inhibitors of any target gene provides a new therapeutical approach for many untreatable diseases, particularly cancer. On the other hand, the discovery of the gene regulatory pathways mediated by miRNAs, offered to the research community new important perspectives for the comprehension of the physiological and, above all, the pathological mechanisms underlying the gene regulation. Indeed, changes in miRNAs expression have been identified in several types of neoplasia and it has also been proposed that the overexpression of genes in cancer cells may be due to the disruption of a control network in which relevant miRNA are implicated. For these reasons, I focused my research on a possible link between RNAi and the enzyme cyclooxygenase-2 (COX-2) in the field of colorectal cancer (CRC), since it has been established that the transition adenoma-adenocarcinoma and the progression of CRC depend on aberrant constitutive expression of COX-2 gene. In fact, overexpressed COX-2 is involved in the block of apoptosis, the stimulation of tumor-angiogenesis and promotes cell invasion, tumour growth and metastatization. On the basis of data reported in the literature, the first aim of my research was to develop an innovative and effective tool, based on the RNAi mechanism, able to silence strongly and specifically COX-2 expression in human colorectal cancer cell lines. In this study, I firstly show that an siRNA sequence directed against COX-2 mRNA (siCOX-2), potently downregulated COX-2 gene expression in human umbilical vein endothelial cells (HUVEC) and inhibited PMA-induced angiogenesis in vitro in a specific, non-toxic manner. Moreover, I found that the insertion of a specific cassette carrying anti-COX-2 shRNA sequence (shCOX-2, the precursor of siCOX-2 previously tested) into a viral vector (pSUPER.retro) greatly increased silencing potency in a colon cancer cell line (HT-29) without activating any interferon response. Phenotypically, COX-2 deficient HT-29 cells showed a significant impairment of their in vitro malignant behaviour. Thus, results reported here indicate an easy-to-use, powerful and high selective virus-based method to knockdown COX-2 gene in a stable and long-lasting manner, in colon cancer cells. Furthermore, they open up the possibility of an in vivo application of this anti-COX-2 retroviral vector, as therapeutic agent for human cancers overexpressing COX-2. In order to improve the tumour selectivity, pSUPER.retro vector was modified for the shCOX-2 expression cassette. The aim was to obtain a strong, specific transcription of shCOX-2 followed by COX-2 silencing mediated by siCOX-2 only in cancer cells. For this reason, H1 promoter in basic pSUPER.retro vector [pS(H1)] was substituted with the human Cox-2 promoter [pS(COX2)] and with a promoter containing repeated copies of the TCF binding element (TBE) [pS(TBE)]. These promoters were choosen because they are partculary activated in colon cancer cells. COX-2 was effectively silenced in HT-29 and HCA-7 colon cancer cells by using enhanced pS(COX2) and pS(TBE) vectors. In particular, an higher siCOX-2 production followed by a stronger inhibition of Cox-2 gene were achieved by using pS(TBE) vector, that represents not only the most effective, but also the most specific system to downregulate COX-2 in colon cancer cells. Because of the many limits that a retroviral therapy could have in a possible in vivo treatment of CRC, the next goal was to render the enhanced RNAi-mediate COX-2 silencing more suitable for this kind of application. Xiang and et al. (2006) demonstrated that it is possible to induce RNAi in mammalian cells after infection with engineered E. Coli strains expressing Inv and HlyA genes, which encode for two bacterial factors needed for successful transfer of shRNA in mammalian cells. This system, called “trans-kingdom” RNAi (tkRNAi) could represent an optimal approach for the treatment of colorectal cancer, since E. Coli in normally resident in human intestinal flora and could easily vehicled to the tumor tissue. For this reason, I tested the improved COX-2 silencing mediated by pS(COX2) and pS(TBE) vectors by using tkRNAi system. Results obtained in HT-29 and HCA-7 cell lines were in high agreement with data previously collected after the transfection of pS(COX2) and pS(TBE) vectors in the same cell lines. These findings suggest that tkRNAi system for COX-2 silencing, in particular mediated by pS(TBE) vector, could represent a promising tool for the treatment of colorectal cancer. Flanking the studies addressed to the setting-up of a RNAi-mediated therapeutical strategy, I proposed to get ahead with the comprehension of new molecular basis of human colorectal cancer. In particular, it is known that components of the miRNA/RNAi pathway may be altered during the progressive development of colorectal cancer (CRC), and it has been already demonstrated that some miRNAs work as tumor suppressors or oncomiRs in colon cancer. Thus, my hypothesis was that overexpressed COX-2 protein in colon cancer could be the result of decreased levels of one or more tumor suppressor miRNAs. In this thesis, I clearly show an inverse correlation between COX-2 expression and the human miR- 101(1) levels in colon cancer cell lines, tissues and metastases. I also demonstrate that the in vitro modulating of miR-101(1) expression in colon cancer cell lines leads to significant variations in COX-2 expression, and this phenomenon is based on a direct interaction between miR-101(1) and COX-2 mRNA. Moreover, I started to investigate miR-101(1) regulation in the hypoxic environment since adaptation to hypoxia is critical for tumor cell growth and survival and it is known that COX-2 can be induced directly by hypoxia-inducible factor 1 (HIF-1). Surprisingly, I observed that COX-2 overexpression induced by hypoxia is always coupled to a significant decrease of miR-101(1) levels in colon cancer cell lines, suggesting that miR-101(1) regulation could be involved in the adaption of cancer cells to the hypoxic environment that strongly characterize CRC tissues.

Meta-models, environment and layers: agent-oriented engineering of complex systems

Traditional software engineering approaches and metaphors fall short when applied to areas of growing relevance such as electronic commerce, enterprise resource planning, and mobile computing: such areas, in fact, generally call for open architectures that may evolve dynamically over time so as to accommodate new components and meet new requirements. This is probably one of the main reasons that the agent metaphor and the agent-oriented paradigm are gaining momentum in these areas. This thesis deals with the engineering of complex software systems in terms of the agent paradigm. This paradigm is based on the notions of agent and systems of interacting agents as fundamental abstractions for designing, developing and managing at runtime typically distributed software systems. However, today the engineer often works with technologies that do not support the abstractions used in the design of the systems. For this reason the research on methodologies becomes the basic point in the scientific activity. Currently most agent-oriented methodologies are supported by small teams of academic researchers, and as a result, most of them are in an early stage and still in the first context of mostly \academic" approaches for agent-oriented systems development. Moreover, such methodologies are not well documented and very often defined and presented only by focusing on specific aspects of the methodology. The role played by meta- models becomes fundamental for comparing and evaluating the methodologies. In fact a meta-model specifies the concepts, rules and relationships used to define methodologies. Although it is possible to describe a methodology without an explicit meta-model, formalising the underpinning ideas of the methodology in question is valuable when checking its consistency or planning extensions or modifications. A good meta-model must address all the different aspects of a methodology, i.e. the process to be followed, the work products to be generated and those responsible for making all this happen. In turn, specifying the work products that must be developed implies dening the basic modelling building blocks from which they are built. As a building block, the agent abstraction alone is not enough to fully model all the aspects related to multi-agent systems in a natural way. In particular, different perspectives exist on the role that environment plays within agent systems: however, it is clear at least that all non-agent elements of a multi-agent system are typically considered to be part of the multi-agent system environment. The key role of environment as a first-class abstraction in the engineering of multi-agent system is today generally acknowledged in the multi-agent system community, so environment should be explicitly accounted for in the engineering of multi-agent system, working as a new design dimension for agent-oriented methodologies. At least two main ingredients shape the environment: environment abstractions - entities of the environment encapsulating some functions -, and topology abstractions - entities of environment that represent the (either logical or physical) spatial structure. In addition, the engineering of non-trivial multi-agent systems requires principles and mechanisms for supporting the management of the system representation complexity. These principles lead to the adoption of a multi-layered description, which could be used by designers to provide different levels of abstraction over multi-agent systems. The research in these fields has lead to the formulation of a new version of the SODA methodology where environment abstractions and layering principles are exploited for en- gineering multi-agent systems.

Specification and Verification of Declarative Open Interaction Models - A Logic-based framework

The advent of distributed and heterogeneous systems has laid the foundation for the birth of new architectural paradigms, in which many separated and autonomous entities collaborate and interact to the aim of achieving complex strategic goals, impossible to be accomplished on their own. A non exhaustive list of systems targeted by such paradigms includes Business Process Management, Clinical Guidelines and Careflow Protocols, Service-Oriented and Multi-Agent Systems. It is largely recognized that engineering these systems requires novel modeling techniques. In particular, many authors are claiming that an open, declarative perspective is needed to complement the closed, procedural nature of the state of the art specification languages. For example, the ConDec language has been recently proposed to target the declarative and open specification of Business Processes, overcoming the over-specification and over-constraining issues of classical procedural approaches. On the one hand, the success of such novel modeling languages strongly depends on their usability by non-IT savvy: they must provide an appealing, intuitive graphical front-end. On the other hand, they must be prone to verification, in order to guarantee the trustworthiness and reliability of the developed model, as well as to ensure that the actual executions of the system effectively comply with it. In this dissertation, we claim that Computational Logic is a suitable framework for dealing with the specification, verification, execution, monitoring and analysis of these systems. We propose to adopt an extended version of the ConDec language for specifying interaction models with a declarative, open flavor. We show how all the (extended) ConDec constructs can be automatically translated to the CLIMB Computational Logic-based language, and illustrate how its corresponding reasoning techniques can be successfully exploited to provide support and verification capabilities along the whole life cycle of the targeted systems.

Designing and Programming Organizational Infrastructures for Agents situated in Artifact-based Environments

Actual trends in software development are pushing the need to face a multiplicity of diverse activities and interaction styles characterizing complex and distributed application domains, in such a way that the resulting dynamics exhibits some grade of order, i.e. in terms of evolution of the system and desired equilibrium. Autonomous agents and Multiagent Systems are argued in literature as one of the most immediate approaches for describing such a kind of challenges. Actually, agent research seems to converge towards the definition of renewed abstraction tools aimed at better capturing the new demands of open systems. Besides agents, which are assumed as autonomous entities purposing a series of design objectives, Multiagent Systems account new notions as first-class entities, aimed, above all, at modeling institutional/organizational entities, placed for normative regulation, interaction and teamwork management, as well as environmental entities, placed as resources to further support and regulate agent work. The starting point of this thesis is recognizing that both organizations and environments can be rooted in a unifying perspective. Whereas recent research in agent systems seems to account a set of diverse approaches to specifically face with at least one aspect within the above mentioned, this work aims at proposing a unifying approach where both agents and their organizations can be straightforwardly situated in properly designed working environments. In this line, this work pursues reconciliation of environments with sociality, social interaction with environment based interaction, environmental resources with organizational functionalities with the aim to smoothly integrate the various aspects of complex and situated organizations in a coherent programming approach. Rooted in Agents and Artifacts (A&A) meta-model, which has been recently introduced both in the context of agent oriented software engineering and programming, the thesis promotes the notion of Embodied Organizations, characterized by computational infrastructures attaining a seamless integration between agents, organizations and environmental entities.

Lesion detection and classification in breast cancer: evaluation of approaches based on morphological features, tracer kinetic modelling and semi-quantitative parameters in MR functional imaging (DCE-MRI)

The diagnosis, grading and classification of tumours has benefited considerably from the development of DCE-MRI which is now essential to the adequate clinical management of many tumour types due to its capability in detecting active angiogenesis. Several strategies have been proposed for DCE-MRI evaluation. Visual inspection of contrast agent concentration curves vs time is a very simple yet operator dependent procedure, therefore more objective approaches have been developed in order to facilitate comparison between studies. In so called model free approaches, descriptive or heuristic information extracted from time series raw data have been used for tissue classification. The main issue concerning these schemes is that they have not a direct interpretation in terms of physiological properties of the tissues. On the other hand, model based investigations typically involve compartmental tracer kinetic modelling and pixel-by-pixel estimation of kinetic parameters via non-linear regression applied on region of interests opportunely selected by the physician. This approach has the advantage to provide parameters directly related to the pathophysiological properties of the tissue such as vessel permeability, local regional blood flow, extraction fraction, concentration gradient between plasma and extravascular-extracellular space. Anyway, nonlinear modelling is computational demanding and the accuracy of the estimates can be affected by the signal-to-noise ratio and by the initial solutions. The principal aim of this thesis is investigate the use of semi-quantitative and quantitative parameters for segmentation and classification of breast lesion. The objectives can be subdivided as follow: describe the principal techniques to evaluate time intensity curve in DCE-MRI with focus on kinetic model proposed in literature; to evaluate the influence in parametrization choice for a classic bi-compartmental kinetic models; to evaluate the performance of a method for simultaneous tracer kinetic modelling and pixel classification; to evaluate performance of machine learning techniques training for segmentation and classification of breast lesion.

Alpha, Omega end group functionalization of RAFT polymers based on pentafluorophenyl esters and methane thiosulfonates

While polymers with different functional groups along the backbone have intensively been investigated, there is still a challenge in orthogonal functionalization of the end groups. Such well-defined systems are interesting for the preparation of multiblock (co) polymers or polymer networks, for bio-conjugation or as model systems for examining the end group separation of isolated polymer chains. rnHere, Reversible Addition Fragmentation Chain Transfer (RAFT) polymerization was employed as method to investigate improved techniques for an a, w end group functionalization. RAFT produces polymers terminated in an R group and a dithioester-Z group, where R and Z stem from a suitable chain transfer agent (CTA). rnFor alpha end group functionalization, a CTA with an activated pentafluorophenyl (PFP) ester R group was designed and used for the polymerization of various methacrylate monomers, N-isopropylacrylamide and styrene yielding polymers with a PFP ester as a end group. This allowed the introduction of inert propyl amides, of light responsive diazo compounds, of the dyes NBD, Texas Red, or Oregon Green, of the hormone thyroxin and allowed the formation of multiblocks or peptide conjugates. rnFor w end group functionalization, problems of other techniques were overcome through an aminolysis of the dithioester in the presence of a functional methane thiosulfonate (MTS), yielding functional disulfides. These disulfides were stable under ambient conditions and could be cleaved on demand. Using MTS chemistry, terminal methyl disulfides (enabling self-assembly on planar gold surfaces and ligand substitution on gold and semiconductor nanoparticles), butynyl disulfide end groups (allowing the “clicking” of the polymers onto azide functionalized surfaces and the selective removal through reduction), the bio-target biotin, and the fluorescent dye Texas Red were introduced into polymers. rnThe alpha PFP amidation could be performed under mild conditions, without substantial loss of DTE. This way, a step-wise synthesis produced polymers with two functional end groups in very high yields. rnAs examples, polymers with an anchor group for both gold nanoparticles (AuNP) and CdSe / ZnS semi-conductor nanoparticles (QD) and with a fluorescent dye end group were synthesized. They allowed a NP decoration and enabled an energy transfer from QD to dye or from dye to AuNP. Water-soluble polymers were prepared with two different bio-target end groups, each capable of selectively recognizing and binding a certain protein. The immobilization of protein-polymer-protein layers on planar gold surfaces was monitored by surface plasmon resonance.Introducing two different fluorescent dye end groups enabled an energy transfer between the end groups of isolated polymer chains and created the possibility to monitor the behavior of single polymer chains during a chain collapse. rnThe versatility of the synthetic technique is very promising for applications beyond this work.

Functional polymer based nanoparticles : development of defined complex structures as basis for in-vitro and in-vivo applications

In Rahmen der vorliegenden Arbeit wurde ein neuartiger Zugang zu einer Vielzahl von Polymerstrukturen auf Basis des klinisch zugelassenen Polymers Poly(N-(2-Hydroxypropyl)-methacrylamide) (PHPMA) entwickelt. Der synthetische Zugang beruht zum einen auf der Verwendung von Reaktivesterpolymeren und zum anderen auf der Reversible Addition Fragmentation Chain Transfer (RAFT) Polymerisationsmethode. Diese Form einer kontrollierten radikalischen Polymerisation ermöglichte es, neben der Synthese von besser definierten Homopolymeren auch statistische und Blockcopolymere herzustellen. Die Reaktivesterpolymere können durch einfache Aminolyse in HPMA-basierte Systeme überführt werden. Somit können sie als eine vielversprechende Basis zur Synthese von umfangreichen Polymerbibliotheken angesehen werden. Die hergestellten Polymere kombinieren verschiedene Funktionalitäten bei konstantem Polymerisationsgrad. Dies ermöglicht eine Optimierung auf eine gezielte Anwendung hin ohne den Parameter der Kettenlänge zu verändern.rnIm weiteren war es durch Verwendung der RAFT Polymerisation möglich partiell bioabbaubare Blockcopolymere auf Basis von Polylactiden und HPMA herzustellen, in dem ein Kettentransferreagenz (CTA) an ein wohl definiertes Polylactid Homopolymer gekoppelt wurde. Diese Strukturen wurden in ihrer Zusammensetzung variiert und mit Erkennungsstrukturen (Folaten) und markierenden Elementen (Fluoreszenzfarbstoffe und +-emittierenden Radionukleide) versehen und im weiteren in vitro und in vivo evaluiert.rnAuf Grund dieser Errungenschaften war es möglich den Einfluss der Polymermikrostruktur auf das Aggregationsverhalten hin mittel Lichtstreuung und Fluoreszenzkorrelationsspektroskopie zu untersuchen. Es konnte gezeigt werden, dass erst diese Informationen über die Überstrukturbildung die Kinetik der Zellaufnahme erklären können. Somit wurde die wichtige Rolle von Strukturwirkungsbeziehungen nachgewiesen.rnSomit konnte neben der Synthese, Charakterisierung und ersten biologischen Evaluierungen ein Beitrag zum besseres Verständnis zur Interaktion von polymeren Partikeln mit biologischen Systemen geleistet werden.

Einfluss subviraler Partikel des humanen Cytomegalovirus auf die Induktion der antiviralen Immunantwort

Das humane Cytomegalovirus (HCMV) ist ein opportunistischer Krankheitserreger, der insbesondere bei Patienten mit unreifem oder geschwächtem Immunsystem schwere, teilweise lebensbedrohliche Erkrankungen verursacht. Aufgrund der klinischen Relevanz wird die Entwicklung einer Impfung gegen HCMV mit großem Nachdruck verfolgt. Subvirale Partikel des HCMV, sogenannte Dense Bodies (DB), stellen eine vielversprechende Impfstoff-Grundlage dar. Die innere Struktur der Partikel besteht aus viralen Proteinen, die als dominante Antigene der zellulären Immunantwort gegen HCMV identifiziert wurden. Die äußere Hülle der Partikel entspricht der Virushülle, sie enthält die viralen Oberflächenproteine als Zielantigene der neutralisierenden Antikörper (NTAk)-Antwort in ihrer natürlichen Konformation. Die für ein Totantigen außergewöhnlich hohe Immunogenität der Partikel wurde bereits in Vorarbeiten dokumentiert. Ein Ziel dieser Arbeit war es, den molekularen Hintergrund für die herausragenden, immunogenen Eigenschaften von DB aufzuklären. Im ersten Teil der Arbeit wurde daher die Hypothese geprüft, dass DB geeignet sind, die Ausreifung und Aktivierung von dendritischen Zellen (DC) zu vermitteln und damit deren Fähigkeit zur Antigenpräsentation zu stimulieren. Derart aktivierten DC kommt eine wichtige Rolle beim Priming der T-lymphozytären Immunantwort zu. In der Tat konnte gezeigt werden, dass die Behandlung von unreifen dendritischen Zellen (iDC) mit DB zu verstärkter Expression von solchen Molekülen auf der DC-Oberfläche führt, die mit Ausreifung der Zellen verknüpft sind. Der Nachweis der verstärkten Freisetzung proinflammatorischer Zytokine belegte die Aktivierung der Zellen im Sinne einer entzündlichen Reaktion. Die erfolgreiche Stimulation von CD4 und CD8 T-Lymphozyten durch DB-behandelte DC belegte schließlich die funktionelle Relevanz der Ergebnisse. Zusammengefasst konnten in diesem Abschnitt der Arbeit die molekularen Grundlagen der adjuvanten Wirkung von DB aufgeklärt werden. rnIn einem zweiten Abschnitt wurde die NTAk-Antwort nach DB-Immunisierung näher untersucht. Der humoralen Immunantwort kommt eine entscheidende Bedeutung bei der Prävention der HCMV-Übertragung zu. Hier galt es zu prüfen, welchen Einfluss stammspezifische Unterschiede in der Expression viraler Oberflächenproteine auf die Induktion der NTAk-Antwort nach DB-Immunisierung nehmen. Im Fokus stand dabei die variable Expression des pentameren Proteinkomplexes aus den viralen Proteinen gH/gL/pUL128-UL131A. Dieser Komplex wird nur von kliniknahen HCMV-Stämmen (HCMVKlin) exprimiert und ist für deren breiten Zelltropismus verantwortlich. Der pentamere Komplex fehlte in allen bisherigen Analysen der DB-Immunogenität, die auf der Grundlage von Laborstämmen des HCMV (HCMVLab) durchgeführt worden waren. Ein erster Versuchsansatz zeigte, dass die NTAk-Antwort, die durch DB von HCMVLab (DBLab) induziert wird, auch gegen die Infektion mit HCMVKlin einen gewissen Schutz vermittelt. Dies war ein überraschender Befund, da Antikörpern gegen den pentameren Komplex eine entscheidende Rolle bei der Neutralisation von HCMVKlin zugeschrieben wurde. Die Ergebnisse zeigten jedoch, dass Antikörper gegen andere Zielstrukturen zur Neutralisation von HCMVKlin beitragen. Hieraus resultierte unmittelbar die Frage, inwieweit eine Aufnahme des pentameren Komplexes in einen DB-basierten Impfstoff überhaupt notwendig war. Um dies zu beantworten war es notwendig, DB herzustellen, die den pentameren Komplex enthielten. Hierzu wurde ein HCMVLab durch Mutagenese des 235 kpb Genoms so modifiziert, dass von dem resultierenden Stamm der pentamere Komplex exprimiert wurde. In gereinigten DB dieses Stammes konnten die Komponenten des pentameren Komplexes nachgewiesen werden. Die Seren von Tieren, die mit DB dieses neuen Stammes immunisiert wurden, zeigten in der Tat eine deutlich gesteigerte Kapazität zur Neutralisation von HCMVKlin auf verschiedenen Zielzellen. Diese Ergebnisse unterstreichen schlussendlich, dass die Expression des pentameren Komplexes einen Vorteil bei der Induktion der antiviralen NTAk-Antwort erbringt. Zusammengefasst liefern die Erkenntnisse aus dieser Arbeit einen wichtigen Beitrag zum Verständnis der immunogenen Wirkung von DB. Auf dieser Grundlage war es nunmehr möglich, ein Projekt zur Austestung der DB-Vakzine in einer ersten klinischen Studie zu initiieren.

Saccharide based nanocapsules - From monomer building blocks to improved capsules properties

In dieser Arbeit wurde der vielfältige Nutzen von Kohlenhydraten in Nanokapsel Systemen untersucht. Drei verschiedene Nanokapsel-Typen wurden durch Reaktion an der Grenzfläche von inversen Miniemulsionen hergestellt. Es wurde gezeigt, dass die Kohlenhydrate nach Modifizierung als Monomer an der Kapselbildung teilnehmen können, oder zur Erhöhung der Sensitivität eines verkapselten Kontrastmittels beitragen können. Im Folgenden werden die Ergebnisse der einzelnen Projekte zusammengefasst. Eine neuartige Grenzflächen-Synthese zur Herstellung von Nanokapseln wurde entwickelt und untersucht. Bei der Reaktion handelt es sich um eine Ruthenium katalysierte Olefin-Kreuzmetathese, welche für die Reaktion an der Grenzfläche angepasst wurde. Als wasserlösliches Macromonomer wurde Dextranacrylat synthetisiert. Der Reaktionspartner war ein öl-löslichen Phosphoester (Phenyldi(undec-10-en-1-yl)phosphat). Anhand von NMR-Spektren wurde gezeigt, dass die Kapselbildung auf Olefin Kreuzmetathese beruht. Im Vergleich zu konventionellen Estern haben Phosphorester eine weitere Möglichkeit zur chemischen Funktionalisierung. Dies wurde exemplarisch durch die Verwendung von fluoreszenzmarkierten Phosphoestern gezeigt. Die Markierung wurde verwendet, um die pH-induzierte Abbaubarkeit der Nanokapseln mittels Fluoreszenz-Korrelations-Spektroskopie zu beobachten. Ziel des zweiten Projekts war es, Nanostrukturen zu entwickeln, um Infektionen mit Antibiotika-resistenten Bakterien lokal zu behandeln. Dazu wurden mit Dextranmethacrylat vernetzte Poly(acrylamid) basierte Nanogele synthetisiert und Zinknitrat zugesetzt. Die Synthese der Nanogele wurde erweitert, um durch Vernetzung freier Alkoholgruppen mit Toluoldiisocyanat eine Kapselschale zu erhalten. Die Schalenbildung spiegelte sich in einer geringeren Quellbarkeit der Gel- Schale-Hybride wieder. Die erhaltenen Gel-Schale-Hybride waren in der Lage das Wachstum von zwei Methicillin-resistenten Bakterienstämmen (S. aureus) zu unterdrücken und verzögern. Die synthetisierten Hybridstrukturen könnten in der Beschichtung von Wundauflagen Verwendung finden, um bakterielle Infektionen lokal und direkt nach Ausbruch zu behandeln. Ziel des dritten Projektes war es, die wichtigen Parameter in der Herstellung von Nanokapseln mit hoher Kontrastmittel Sensitivität zu identifizieren. Relaxivität/Signalsensitivität des Kontrastmittels ist von großer Bedeutung für die Bildgebung mittels MRI, dies kann durch die Begrenzung der Mobilität des Kontrastmittels erreicht werden. Aufgrund seiner hohen Komplexstabilität und seiner klinischen Bedeutung wurde das Kontrastmittel Gadobutrol für die Verkapselung verwendet. Das Kontrastmittel wurde in Polyharnstoff-Kapseln eingeschlossen, die durch einen inversen Miniemulsion-Prozess hergestellt wurden. Um die Viskosität im Inneren der Nanokapsel zu erhöhen, wurden zusätzlich Saccharose, Dextran und Polyacrylsäure verkapselt. In Gegenwart von Saccharose konnte die Relaxivität verdoppelt werden. Dies gründet sich vermutlich auf einem Second-sphere Effekt der Saccharose, einer auf Wasserstoffbrückenbindungen beruhende Interaktion von Kontrastmittel und Saccharose.

Synthesis, characterization and crystallization of bionanocomposites based on PLLA, PCL and nanocellulose

In recent years, environmental concerns and the expected shortage in the fossil reserves have increased further development of biomaterials. Among them, poly(lactide) PLA possess some potential properties such as good ability process, excellent tensile strength and stiffness equivalent to some commercial petroleum-based polymers (PP, PS, PET, etc.). This biobased polymer is also biodegradable and biocompatible However, one great disadvantage of commercial PLA is slow crystallization rate, which restricts its use in many fields. Using of nanofillers is viewed as an efficient strategy to overcome this problem. In this thesis, the effect of bionanofillers in neat PLA and in blends of poly (L-lactide)(PLA)/poly(ε-Caprolactone) (PCL) has been investigated. The used nanofillers are: poly(L-lactide-co-ε-caprolactone) and poly(L-lactide-b-ε-caprolactone) grafted on cellulose nanowhiskers and neat cellulose nanowhiskers (CNW). The grafting reaction of poly(L-lactide-co-caprolactone) and poly (L-lactide-b-caprolactone) on the nanocellulose has been performed by the grafting from technique. In this way the polymerization reaction it is directly initiated on the substrate surface. The condition of the reaction were chosen after a temperature and solvent screening. By non-isothermal an isothermal DSC analysis the effect of bionanofillers on PLA and 80/20 PLA/PCL was evaluated. Non-isothermal DSC scans show a nucleating effect of the bionanofillers on PLA. This effect is detectable during PLA crystallization from the glassy state. Cold crystallization temperature is reduced upon the addition of the poly(L-lactide-b-caprolactone) grafted on cellulose nanowhiskers that is most performing bionanofiller in acting as a nucleating agent. On the other hand, DSC isothermal analysis on the overall crystallization rate indicate that cellulose nanowhiskers are best nucleating agents during isothermal crystallization from the melt state. In conclusion, nanofillers have different behavior depending on the processing conditions. However, the efficiency of our nanofillers as nucleating agent was clearly demonstrated in both isothermal as in non-isothermal condition.

Design of a semi-implantable hearing device for direct acoustic cochlear stimulation

A new hearing therapy based on direct acoustic cochlear stimulation was developed for the treatment of severe to profound mixed hearing loss. The device efficacy was validated in an initial clinical trial with four patients. This semi-implantable investigational device consists of an externally worn audio processor, a percutaneous connector, and an implantable microactuator. The actuator is placed in the mastoid bone, right behind the external auditory canal. It generates vibrations that are directly coupled to the inner ear fluids and that, therefore, bypass the external and the middle ear. The system is able to provide an equivalent sound pressure level of 125 dB over the frequency range between 125 and 8000 Hz. The hermetically sealed actuator is designed to provide maximal output power by keeping its dimensions small enough to enable implantation. A network model is used to simulate the dynamic characteristics of the actuator to adjust its transfer function to the characteristics of the middle ear. The geometry of the different actuator components is optimized using finite-element modeling.

A comprehensive understanding of thioTEPA metabolism in the mouse using UPLC-ESI-QTOFMS-based metabolomics

ThioTEPA, an alkylating agent with anti-tumor activity, has been used as an effective anticancer drug since the 1950s. However, a complete understanding of how its alkylating activity relates to clinical efficacy has not been achieved, the total urinary excretion of thioTEPA and its metabolites is not resolved, and the mechanism of formation of the potentially toxic metabolites S-carboxymethylcysteine (SCMC) and thiodiglycolic acid (TDGA) remains unclear. In this study, the metabolism of thioTEPA in a mouse model was comprehensively investigated using ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOFMS) based-metabolomics. The nine metabolites identified in mouse urine suggest that thioTEPA underwent ring-opening, N-dechloroethylation, and conjugation reactions in vivo. SCMC and TDGA, two downstream thioTEPA metabolites, were produced from thioTEPA from two novel metabolites 1,2,3-trichloroTEPA (VII) and dechloroethyltrichloroTEPA (VIII). SCMC and TDGA excretion were increased about 4-fold and 2-fold, respectively, in urine following the thioTEPA treatment. The main mouse metabolites of thioTEPA in vivo were TEPA (II), monochloroTEPA (III) and thioTEPA-mercapturate (IV). In addition, five thioTEPA metabolites were detected in serum and all shared similar disposition. Although thioTEPA has a unique chemical structure which is not maintained in the majority of its metabolites, metabolomic analysis of its biotransformation greatly contributed to the investigation of thioTEPA metabolism in vivo, and provides useful information to understand comprehensively the pharmacological activity and potential toxicity of thioTEPA in the clinic.