The crystal structure of an N-terminal two-domain fragment of vascular cell adhesion molecule 1 (VCAM-1): a cyclic peptide based on the domain 1 C-D loop can inhibit VCAM-1-alpha 4 integrin interaction.

Vascular cell adhesion molecule 1 (VCAM-1) represents a structurally and functionally distinct class of immunoglobulin superfamily molecules that bind leukocyte integrins and are involved in inflammatory and immune functions. X-ray crystallography defines the three-dimensional structure of the N-terminal two-domain fragment that participates in ligand binding. Residues in domain 1 important for ligand binding reside in the C-D loop, which projects markedly from one face of the molecule near the contact between domains 1 and 2. A cyclic peptide that mimics this loop inhibits binding of alpha 4 beta 1 integrin-bearing cells to VCAM-1. These data demonstrate how crystallographic structural information can be used to design a small molecule inhibitor of biological function.

New multivalent calixarene-based ligands for protein recognition and inhibition

One of the challenges that concerns chemistry is the design of molecules able to modulate protein-protein and protein-ligand interactions, since these are involved in many physiological and pathological processes. The interactions occurring between proteins and their natural counterparts can take place through reciprocal recognition of rather large surface areas, through recognition of single contact points and single residues, through inclusion of the substrates in specific, more or less deep binding sites. In many cases, the design of synthetic molecules able to interfere with the processes involving proteins can benefit from the possibility of exploiting the multivalent effect. Multivalency, widely spread in Nature, consists in the simultaneous formation between two entities (cell-cell, cell-protein, protein-protein) of multiple equivalent ligand-recognition site complexes. In this way the whole interaction results particularly strong and specific. Calixarenes furnish a very interesting scaffold for the preparation of multivalent ligands and in the last years calixarene-based ligands demonstrated their remarkable capability to recognize and inhibit or restore the activity of different proteins, with a high efficiency and selectivity in several recognition phenomena. The relevance and versatility of these ligands is due to the different exposition geometries of the binding units that can be explored exploiting the conformational properties of these macrocycles, the wide variety of functionalities that can be linked to their structure at different distances from the aromatic units and to their intrinsic multivalent nature. With the aim of creating new multivalent systems for protein targeting, the work reported in this thesis regards the synthesis and properties of glycocalix[n]arenes and guanidino calix[4]arenes for different purposes. Firstly, a new bolaamphiphile glycocalix[4]arene in 1,3-alternate geometry, bearing cellobiose, was synthesized for the preparation of targeted drug delivery systems based on liposomes. The formed stable mixed liposomes obtained by mixing the macrocycle with DOPC were shown to be able of exploiting the sugar units emerging from the lipid bilayer to agglutinate Concanavalin A, a lectin specific for glucose. Moreover, always thanks to the presence of the glycocalixarene in the layer, the same liposomes demonstrated through preliminary experiments to be uptaken by cancer cells overexpressing glucose receptors on their exterior surface more efficiently respect to simple DOPC liposomes lacking glucose units in their structure. Then a small library of glycocalix[n]arenes having different valency and geometry was prepared, for the creation of potentially active immunostimulants against Streptococcus pneumoniae, particularly the 19F serotype, one of the most virulent. These synthesized glycocalixarenes bearing β-N-acetylmannosamine as antigenic unit were compared with the natural polysaccharide on the binding to the specific anti-19F human polyclonal antibody, to verify their inhibition potency. Among all, the glycocalixarene based on the conformationally mobile calix[4]arene resulted the more efficient ligand, probably due its major possibility to explore the antibody surface and dispose the antigenic units in a proper arrangement for the interaction process. These results pointed out the importance of how the different multivalent presentation in space of the glycosyl units can influence the recognition phenomena. At last, NMR studies, using particularly 1H-15N HSQC experiments, were performed on selected glycocalix[6]arenes and guanidino calix[4]arenes blocked in the cone geometry, in order to better understand protein-ligand interactions. The glycosylated compounds were studied with Ralstonia solanacearum lectin, in order to better understand the nature of the carbohydrate‐lectin interactions in solution. The series of cationic calixarene was employed with three different acidic proteins: GB1, Fld and alpha synuclein. Particularly GB1 and Fld were observed to interact with all five cationic calix[4]arenes but showing different behaviours and affinities.

Logic-Based Outer Approximation for the Design of Discrete-Continuous Dynamic Systems with Implicit Discontinuities

We address the optimization of discrete-continuous dynamic optimization problems using a disjunctive multistage modeling framework, with implicit discontinuities, which increases the problem complexity since the number of continuous phases and discrete events is not known a-priori. After setting a fixed alternative sequence of modes, we convert the infinite-dimensional continuous mixed-logic dynamic (MLDO) problem into a finite dimensional discretized GDP problem by orthogonal collocation on finite elements. We use the Logic-based Outer Approximation algorithm to fully exploit the structure of the GDP representation of the problem. This modelling framework is illustrated with an optimization problem with implicit discontinuities (diver problem).

Interplay Between Structure, Stoichiometry, and Electron Transfer Dynamics in SILAR-based Quantum Dot-Sensitized Oxides

We quantify the rate and efficiency of picosecond electron transfer (ET) from PbS nanocrystals, grown by successive ionic layer adsorption and reaction (SILAR), into a mesoporous SnO2 support. Successive SILAR deposition steps allow for stoichiometry- and size-variation of the QDs, characterized using transmission electron microscopy. Whereas for sulfur-rich (p-type) QD surfaces substantial electron trapping at the QD surface occurs, for lead-rich (n-type) QD surfaces, the QD trapping channel is suppressed and the ET efficiency is boosted. The ET efficiency increase achieved by lead-rich QD surfaces is found to be QD-size dependent, increasing linearly with QD surface area. On the other hand, ET rates are found to be independent of both QD size and surface stoichiometry, suggesting that the donor–acceptor energetics (constituting the driving force for ET) are fixed due to Fermi level pinning at the QD/oxide interface. Implications of our results for QD-sensitized solar cell design are discussed.

Design and synthesis of constrained azacyclic pyrrolidine analogues of FTY720 as anticancer agents & metal coordination-controlled and bifunctional catalysis toward tertiary β-Ketols

Cette thèse se compose en deux parties: Première Partie: La conception et la synthèse d’analogues pyrrolidiniques, utilisés comme agents anticancéreux, dérivés du FTY720. FTY720 est actuellement commercialisé comme médicament (GilenyaTM) pour le traitement de la sclérose en plaques rémittente-récurrente. Il agit comme immunosuppresseur en raison de son effet sur les récepteurs de la sphingosine-1-phosphate. A fortes doses, FTY720 présente un effet antinéoplasique. Cependant, à de telles doses, un des effets secondaires observé est la bradycardie dû à l’activation des récepteurs S1P1 et S1P3. Ceci limite son potentiel d’utilisation lors de chimiothérapie. Nos précédentes études ont montré que des analogues pyrrolidiniques dérivés du FTY720 présentaient une activité anticancéreuse mais aucune sur les récepteurs S1P1 et S1P3. Nous avons soumis l’idée qu’une étude relation structure-activité (SARs) pourrait nous conduire à la découverte de nouveaux agents anti tumoraux. Ainsi, deux séries de composés pyrrolidiniques (O-arylmethyl substitué et C-arylmethyl substitué) ont pu être envisagés et synthétisés (Chapitre 1). Ces analogues ont montré d’excellentes activités cytotoxiques contre diverses cellules cancéreuses humaines (prostate, colon, sein, pancréas et leucémie), plus particulièrement les analogues actifs qui ne peuvent pas être phosphorylés par SphK, présentent un plus grand potentiel pour le traitement du cancer sans effet secondaire comme la bradycardie. Les études mécanistiques suggèrent que ces analogues de déclencheurs de régulation négative sur les transporteurs de nutriments induisent une crise bioénergétique en affamant les cellules cancéreuses. Afin d’approfondir nos connaissances sur les récepteurs cibles, nous avons conçu et synthétisé des sondes diazirine basées sur le marquage d’affinité aux photons (méthode PAL: Photo-Affinity Labeling) (Chapitre 2). En s’appuyant sur la méthode PAL, il est possible de récolter des informations sur les récepteurs cibles à travers l’analyse LC/MS/MS de la protéine. Ces tests sont en cours et les résultats sont prometteurs. Deuxième partie: Coordination métallique et catalyse di fonctionnelle de dérivés β-hydroxy cétones tertiaires. Les réactions de Barbier et de Grignard sont des méthodes classiques pour former des liaisons carbone-carbone, et généralement utilisées pour la préparation d’alcools secondaires et tertiaires. En vue d’améliorer la réaction de Grignard avec le 1-iodobutane dans les conditions « one-pot » de Barbier, nous avons obtenu comme produit majoritaire la β-hydroxy cétone provenant de l’auto aldolisation de la 5-hexen-2-one, plutôt que le produit attendu d’addition de l’alcool (Chapitre 3). La formation inattendue de la β-hydroxy cétone a également été observée en utilisant d’autres dérivés méthyl cétone. Étonnement dans la réaction intramoléculaire d’une tricétone, connue pour former la cétone Hajos-Parrish, le produit majoritaire est rarement la β-hydroxy cétone présentant la fonction alcool en position axiale. Intrigué par ces résultats et après l’étude systématique des conditions de réaction, nous avons développé deux nouvelles méthodes à travers la synthèse sélective et catalytique de β-hydroxy cétones spécifiques par cyclisation intramoléculaire avec des rendements élevés (Chapitre 4). La réaction peut être catalysée soit par une base adaptée et du bromure de lithium comme additif en passant par un état de transition coordonné au lithium, ou bien soit à l’aide d’un catalyseur TBD di fonctionnel, via un état de transition médiée par une coordination bidenté au TBD. Les mécanismes proposés ont été corroborés par calcul DFT. Ces réactions catalytiques ont également été appliquées à d’autres substrats comme les tricétones et les dicétones. Bien que les efforts préliminaires afin d’obtenir une enantioselectivité se sont révélés sans succès, la synthèse et la recherche de nouveaux catalyseurs chiraux sont en cours.

Application of the Equivalent Static Analysis method to the design of a steel frame structure with added viscous dampers

All the structures designed by engineers are vulnerable to natural disasters including floods and earthquakes. The energy released during strong ground motions should be dissipated by structural elements. Before 1990’s, this energy was expected to be dissipated through the beams and columns which at the same time were a part of gravity-load-resisting system. However, the main disadvantage of this idea was that gravity-resisting-frame was not repairable. Hence, during 1990’s, the idea of designing passive energy dissipation systems, including dampers, emerged. At the beginning, main problem was lack of guidelines for passive energy dissipation systems. Although till 2000 many guidelines and procedures where published, yet most of them were based on complicated analysis which was not so convenient for engineers and practitioners. In order to solve this problem recently some alternative design methods are proposed including 1. Lopez Garcia (2001) simple procedure for optimal damper configuration in MDOF structures 2. Christopoulos and Filiatrault (2006) trial and error procedure 3. Silvestri et al. (2010) Five-Step Method. 4. Palermo et al. (2015) Direct Five-Step Method. 5. Palermo et al. (2016) Simplified Equivalent Static Analysis (ESA). In this study, effectiveness and differences between last three alternative methods have been evaluated.

Design and synthesis of constrained azacyclic pyrrolidine analogues of FTY720 as anticancer agents & metal coordination-controlled and bifunctional catalysis toward tertiary β-Ketols

Cette thèse se compose en deux parties: Première Partie: La conception et la synthèse d’analogues pyrrolidiniques, utilisés comme agents anticancéreux, dérivés du FTY720. FTY720 est actuellement commercialisé comme médicament (GilenyaTM) pour le traitement de la sclérose en plaques rémittente-récurrente. Il agit comme immunosuppresseur en raison de son effet sur les récepteurs de la sphingosine-1-phosphate. A fortes doses, FTY720 présente un effet antinéoplasique. Cependant, à de telles doses, un des effets secondaires observé est la bradycardie dû à l’activation des récepteurs S1P1 et S1P3. Ceci limite son potentiel d’utilisation lors de chimiothérapie. Nos précédentes études ont montré que des analogues pyrrolidiniques dérivés du FTY720 présentaient une activité anticancéreuse mais aucune sur les récepteurs S1P1 et S1P3. Nous avons soumis l’idée qu’une étude relation structure-activité (SARs) pourrait nous conduire à la découverte de nouveaux agents anti tumoraux. Ainsi, deux séries de composés pyrrolidiniques (O-arylmethyl substitué et C-arylmethyl substitué) ont pu être envisagés et synthétisés (Chapitre 1). Ces analogues ont montré d’excellentes activités cytotoxiques contre diverses cellules cancéreuses humaines (prostate, colon, sein, pancréas et leucémie), plus particulièrement les analogues actifs qui ne peuvent pas être phosphorylés par SphK, présentent un plus grand potentiel pour le traitement du cancer sans effet secondaire comme la bradycardie. Les études mécanistiques suggèrent que ces analogues de déclencheurs de régulation négative sur les transporteurs de nutriments induisent une crise bioénergétique en affamant les cellules cancéreuses. Afin d’approfondir nos connaissances sur les récepteurs cibles, nous avons conçu et synthétisé des sondes diazirine basées sur le marquage d’affinité aux photons (méthode PAL: Photo-Affinity Labeling) (Chapitre 2). En s’appuyant sur la méthode PAL, il est possible de récolter des informations sur les récepteurs cibles à travers l’analyse LC/MS/MS de la protéine. Ces tests sont en cours et les résultats sont prometteurs. Deuxième partie: Coordination métallique et catalyse di fonctionnelle de dérivés β-hydroxy cétones tertiaires. Les réactions de Barbier et de Grignard sont des méthodes classiques pour former des liaisons carbone-carbone, et généralement utilisées pour la préparation d’alcools secondaires et tertiaires. En vue d’améliorer la réaction de Grignard avec le 1-iodobutane dans les conditions « one-pot » de Barbier, nous avons obtenu comme produit majoritaire la β-hydroxy cétone provenant de l’auto aldolisation de la 5-hexen-2-one, plutôt que le produit attendu d’addition de l’alcool (Chapitre 3). La formation inattendue de la β-hydroxy cétone a également été observée en utilisant d’autres dérivés méthyl cétone. Étonnement dans la réaction intramoléculaire d’une tricétone, connue pour former la cétone Hajos-Parrish, le produit majoritaire est rarement la β-hydroxy cétone présentant la fonction alcool en position axiale. Intrigué par ces résultats et après l’étude systématique des conditions de réaction, nous avons développé deux nouvelles méthodes à travers la synthèse sélective et catalytique de β-hydroxy cétones spécifiques par cyclisation intramoléculaire avec des rendements élevés (Chapitre 4). La réaction peut être catalysée soit par une base adaptée et du bromure de lithium comme additif en passant par un état de transition coordonné au lithium, ou bien soit à l’aide d’un catalyseur TBD di fonctionnel, via un état de transition médiée par une coordination bidenté au TBD. Les mécanismes proposés ont été corroborés par calcul DFT. Ces réactions catalytiques ont également été appliquées à d’autres substrats comme les tricétones et les dicétones. Bien que les efforts préliminaires afin d’obtenir une enantioselectivité se sont révélés sans succès, la synthèse et la recherche de nouveaux catalyseurs chiraux sont en cours.

Hybrid knowledge representation in a blackboard KBS for liquid retaining structure design

This paper highlights the importance of design expertise, for designing liquid retaining structures, including subjective judgments and professional experience. Design of liquid retaining structures has special features different from the others. Being more vulnerable to corrosion problem, they have stringent requirements against serviceability limit state of crack. It is the premise of the study to transferring expert knowledge in a computerized blackboard system. Hybrid knowledge representation schemes, including production rules, object-oriented programming, and procedural methods, are employed to express engineering heuristics and standard design knowledge during the development of the knowledge-based system (KBS) for design of liquid retaining structures. This approach renders it possible to take advantages of the characteristics of each method. The system can provide the user with advice on preliminary design, loading specification, optimized configuration selection and detailed design analysis of liquid retaining structure. It would be beneficial to the field of retaining structure design by focusing on the acquisition and organization of expert knowledge through the development of recent artificial intelligence technology. (C) 2003 Elsevier Ltd. All rights reserved.

Design options for sample-based mortality surveillance

Background Reliable information on causes of death is a fundamental component of health development strategies, yet globally only about one-third of countries have access to such information. For countries currently without adequate mortality reporting systems there are useful models other than resource-intensive population-wide medical certification. Sample-based mortality surveillance is one such approach. This paper provides methods for addressing appropriate sample size considerations in relation to mortality surveillance, with particular reference to situations in which prior information on mortality is lacking. Methods The feasibility of model-based approaches for predicting the expected mortality structure and cause composition is demonstrated for populations in which only limited empirical data is available. An algorithm approach is then provided to derive the minimum person-years of observation needed to generate robust estimates for the rarest cause of interest in three hypothetical populations, each representing different levels of health development. Results Modelled life expectancies at birth and cause of death structures were within expected ranges based on published estimates for countries at comparable levels of health development. Total person-years of observation required in each population could be more than halved by limiting the set of age, sex, and cause groups regarded as 'of interest'. Discussion The methods proposed are consistent with the philosophy of establishing priorities across broad clusters of causes for which the public health response implications are similar. The examples provided illustrate the options available when considering the design of mortality surveillance for population health monitoring purposes.

Towards pattern-based design recovery

A method and a corresponding tool is described which assist design recovery and program understanding by recognising instances of design patterns semi-automatically. The approach taken is specifically designed to overcome the existing scalability problems caused by many design and implementation variants of design pattern instances. Our approach is based on a new recognition algorithm which works incrementally rather than trying to analyse a possibly large software system in one pass without any human intervention. The new algorithm exploits domain and context knowledge given by a reverse engineer and by a special underlying data structure, namely a special form of an annotated abstract syntax graph. A comparative and quantitative evaluation of applying the approach to the Java AWT and JGL libraries is also given.

The application of knowledge based expert systems to mechanical engineering design

Investigation of the different approaches used by Expert Systems researchers to solve problems in the domain of Mechanical Design and Expert Systems was carried out. The techniques used for conventional formal logic programming were compared with those used when applying Expert Systems concepts. A literature survey of design processes was also conducted with a view to adopting a suitable model of the design process. A model, comprising a variation on two established ones, was developed and applied to a problem within what are described as class 3 design tasks. The research explored the application of these concepts to Mechanical Engineering Design problems and their implementation on a microcomputer using an Expert System building tool. It was necessary to explore the use of Expert Systems in this manner so as to bridge the gap between their use as a control structure and for detailed analytical design. The former application is well researched into and this thesis discusses the latter. Some Expert System building tools available to the author at the beginning of his work were evaluated specifically for their suitability for Mechanical Engineering design problems. Microsynics was found to be the most suitable on which to implement a design problem because of its simple but powerful Semantic Net Knowledge Representation structure and the ability to use other types of representation schemes. Two major implementations were carried out. The first involved a design program for a Helical compression spring and the second a gearpair system design. Two concepts were proposed in the thesis for the modelling and implementation of design systems involving many equations. The method proposed enables equation manipulation and analysis using a combination of frames, semantic nets and production rules. The use of semantic nets for purposes other than for psychology and natural language interpretation, is quite new and represents one of the major contributions to knowledge by the author. The development of a purpose built shell program for this type of design problems was recommended as an extension of the research. Microsynics may usefully be used as a platform for this development.

A Proposed Structure of Knowledge-Based Hybrid Intelligent Systems for Sophisticated Environments

The paper deals with a problem of intelligent system’s design for complex environments. There is discussed a possibility to integrate several technologies into one basic structure. One possible structure is proposed in order to form a basis for intelligent system that would be able to operate in complex environments. The basic elements of the proposed structure have found their implemented in software system. This software system is shortly presented in the paper. The most important results of experiments are outlined and discussed at the end of the paper. Some possible directions of further research are sketched.

A generalized multidimensional index structure for multimedia data to support content-based similarity searches in a collaborative search environment

Since multimedia data, such as images and videos, are way more expressive and informative than ordinary text-based data, people find it more attractive to communicate and express with them. Additionally, with the rising popularity of social networking tools such as Facebook and Twitter, multimedia information retrieval can no longer be considered a solitary task. Rather, people constantly collaborate with one another while searching and retrieving information. But the very cause of the popularity of multimedia data, the huge and different types of information a single data object can carry, makes their management a challenging task. Multimedia data is commonly represented as multidimensional feature vectors and carry high-level semantic information. These two characteristics make them very different from traditional alpha-numeric data. Thus, to try to manage them with frameworks and rationales designed for primitive alpha-numeric data, will be inefficient. An index structure is the backbone of any database management system. It has been seen that index structures present in existing relational database management frameworks cannot handle multimedia data effectively. Thus, in this dissertation, a generalized multidimensional index structure is proposed which accommodates the atypical multidimensional representation and the semantic information carried by different multimedia data seamlessly from within one single framework. Additionally, the dissertation investigates the evolving relationships among multimedia data in a collaborative environment and how such information can help to customize the design of the proposed index structure, when it is used to manage multimedia data in a shared environment. Extensive experiments were conducted to present the usability and better performance of the proposed framework over current state-of-art approaches.

Design, fabrication and characterization of resonant waveguide grating based optical biosensors

The absence of rapid, low cost and highly sensitive biodetection platform has hindered the implementation of next generation cheap and early stage clinical or home based point-of-care diagnostics. Label-free optical biosensing with high sensitivity, throughput, compactness, and low cost, plays an important role to resolve these diagnostic challenges and pushes the detection limit down to single molecule. Optical nanostructures, specifically the resonant waveguide grating (RWG) and nano-ribbon cavity based biodetection are promising in this context. The main element of this dissertation is design, fabrication and characterization of RWG sensors for different spectral regions (e.g. visible, near infrared) for use in label-free optical biosensing and also to explore different RWG parameters to maximize sensitivity and increase detection accuracy. Design and fabrication of the waveguide embedded resonant nano-cavity are also studied. Multi-parametric analyses were done using customized optical simulator to understand the operational principle of these sensors and more important the relationship between the physical design parameters and sensor sensitivities. Silicon nitride (SixNy) is a useful waveguide material because of its wide transparency across the whole infrared, visible and part of UV spectrum, and comparatively higher refractive index than glass substrate. SixNy based RWGs on glass substrate are designed and fabricated applying both electron beam lithography and low cost nano-imprint lithography techniques. A Chromium hard mask aided nano-fabrication technique is developed for making very high aspect ratio optical nano-structure on glass substrate. An aspect ratio of 10 for very narrow (~60 nm wide) grating lines is achieved which is the highest presented so far. The fabricated RWG sensors are characterized for both bulk (183.3 nm/RIU) and surface sensitivity (0.21nm/nm-layer), and then used for successful detection of Immunoglobulin-G (IgG) antibodies and antigen (~1μg/ml) both in buffer and serum. Widely used optical biosensors like surface plasmon resonance and optical microcavities are limited in the separation of bulk response from the surface binding events which is crucial for ultralow biosensing application with thermal or other perturbations. A RWG based dual resonance approach is proposed and verified by controlled experiments for separating the response of bulk and surface sensitivity. The dual resonance approach gives sensitivity ratio of 9.4 whereas the competitive polarization based approach can offer only 2.5. The improved performance of the dual resonance approach would help reducing probability of false reading in precise bio-assay experiments where thermal variations are probable like portable diagnostics.

Web-based museum trails on PDAs for university-level design students: Design and evaluation

This paper describes the development and evaluation of web-based museum trails for university-level design students to access on handheld devices in the Victoria and Albert Museum (V&A) in London. The trails offered students a range of ways of exploring the museum environment and collections, some encouraging students to interpret objects and museum spaces in lateral and imaginative ways, others more straightforwardly providing context and extra information. In a three-stage qualitative evaluation programme, student feedback showed that overall the trails enhanced students’ knowledge of, interest in, and closeness to the objects. However, the trails were only partially successful from a technological standpoint due to device and network problems. Broader findings suggest that technology has a key role to play in helping to maintain the museum as a learning space which complements that of universities as well as schools. This research informed my other work in visitor-constructed learning trails in museums, specifically in the theoretical approach to data analysis used, in the research design, and in informing ways to structure visitor experiences in museums. It resulted in a conference presentation, and more broadly informed my subsequent teaching practice.