Detection and localization of GLUTs in spermatozoa from different domestic species

Sperm cells need hexoses as a substrate for their function, for both the maintenance of membrane homeostasis and the movement of the tail. These cells have a peculiar metabolism that has not yet been fully understood, but it is clear that they obtain energy from hexoses through glycolisis and/or oxidative phosphorylation. Spermatozoa are in contact with different external environments, beginning from the testicular and epididymal fluid, passing to the seminal plasma and finally to the female genital tract fluids; in addition, with the spread of reproductive biotechnologies, sperm cells are diluted and stored in various media, containing different energetic substrates. To utilize these energetic sources, sperm cells, as other eukaryotic cells, have a well-constructed protein system, that is mainly represented by the GLUT family proteins. These transporters have a membrane-spanning α-helix structure and work as an enzymatic pump that permit a fast gradient dependent passage of sugar molecules through the lipidic bilayer of sperm membrane. Many GLUTs have been studied in man, bull and rat spermatozoa; the presence of some GLUTs has been also demonstrated in boar and dog spermatozoa. The aims of the present study were - to determine the presence of GLUTs 1, 2, 3, 4 and 5 in boar, horse, dog and donkey spermatozoa and to describe their localization; - to study eventual changes in GLUTs location after capacitation and acrosome reaction in boar, stallion and dog spermatozoa; - to determine possible changes in GLUTs localization after capacitation induced by insulin and IGF stimulation in boar spermatozoa; - to evaluate changes in GLUTs localization after flow-cytometric sex sorting in boar sperm cells. GLUTs 1, 2, 3 and 5 presence and localization have been demonstrated in boar, stallion, dog and donkey spermatozoa by western blotting and immunofluorescence analysis; a relocation in GLUTs after capacitation has been observed only in dog sperm cells, while no changes have been observed in the other species examined. As for boar, the stimulation of the capacitation with insulin and IGF didn’t cause any change in GLUTs localization, as well as for the flow cytometric sorting procedure. In conclusion, this study confirms the presence of GLUTs 1, 2 ,3 and 5 in boar, dog, stallion and donkey spermatozoa, while GLUT 4 seems to be absent, as a confirmation of other studies. Only in dog sperm cells capacitating conditions induce a change in GLUTs distribution, even if the physiological role of these changes should be deepened.

Cooperative Wireless Networks for Localization

This thesis adresses the problem of localization, and analyzes its crucial aspects, within the context of cooperative WSNs. The three main issues discussed in the following are: network synchronization, position estimate and tracking. Time synchronization is a fundamental requirement for every network. In this context, a new approach based on the estimation theory is proposed to evaluate the ultimate performance limit in network time synchronization. In particular the lower bound on the variance of the average synchronization error in a fully connected network is derived by taking into account the statistical characterization of the Message Delivering Time (MDT) . Sensor network localization algorithms estimate the locations of sensors with initially unknown location information by using knowledge of the absolute positions of a few sensors and inter-sensor measurements such as distance and bearing measurements. Concerning this issue, i.e. the position estimate problem, two main contributions are given. The first is a new Semidefinite Programming (SDP) framework to analyze and solve the problem of flip-ambiguity that afflicts range-based network localization algorithms with incomplete ranging information. The occurrence of flip-ambiguous nodes and errors due to flip ambiguity is studied, then with this information a new SDP formulation of the localization problem is built. Finally a flip-ambiguity-robust network localization algorithm is derived and its performance is studied by Monte-Carlo simulations. The second contribution in the field of position estimate is about multihop networks. A multihop network is a network with a low degree of connectivity, in which couples of given any nodes, in order to communicate, they have to rely on one or more intermediate nodes (hops). Two new distance-based source localization algorithms, highly robust to distance overestimates, typically present in multihop networks, are presented and studied. The last point of this thesis discuss a new low-complexity tracking algorithm, inspired by the Fano’s sequential decoding algorithm for the position tracking of a user in a WLAN-based indoor localization system.

Semantic coordination tuple centres for eHealth Systems

In questa tesi partendo dai limiti sintattici dello scambio di Electronic Patient Records (EHRs), si arriva alla creazione di un framework che supporti lo scambio di informazioni semantiche. Il framework creato si chiama Semantic TuCSoN ed è una estensione di TuCSoN (Tuple Centres Spread over the Network). Semantic TuCSoN viene modellato per il contesto eHealth definendo gli agenti e le politiche di coordinamento atte allo scambio di EHR. Questo framework vine infine testa per verificarne le performance allo scopo di valutare un suo ulteriore utilizzo.

Semantic coordination through programmable Tuple spaces

Two of the main features of today complex software systems like pervasive computing systems and Internet-based applications are distribution and openness. Distribution revolves around three orthogonal dimensions: (i) distribution of control|systems are characterised by several independent computational entities and devices, each representing an autonomous and proactive locus of control; (ii) spatial distribution|entities and devices are physically distributed and connected in a global (such as the Internet) or local network; and (iii) temporal distribution|interacting system components come and go over time, and are not required to be available for interaction at the same time. Openness deals with the heterogeneity and dynamism of system components: complex computational systems are open to the integration of diverse components, heterogeneous in terms of architecture and technology, and are dynamic since they allow components to be updated, added, or removed while the system is running. The engineering of open and distributed computational systems mandates for the adoption of a software infrastructure whose underlying model and technology could provide the required level of uncoupling among system components. This is the main motivation behind current research trends in the area of coordination middleware to exploit tuple-based coordination models in the engineering of complex software systems, since they intrinsically provide coordinated components with communication uncoupling and further details in the references therein. An additional daunting challenge for tuple-based models comes from knowledge-intensive application scenarios, namely, scenarios where most of the activities are based on knowledge in some form|and where knowledge becomes the prominent means by which systems get coordinated. Handling knowledge in tuple-based systems induces problems in terms of syntax - e.g., two tuples containing the same data may not match due to differences in the tuple structure - and (mostly) of semantics|e.g., two tuples representing the same information may not match based on a dierent syntax adopted. Till now, the problem has been faced by exploiting tuple-based coordination within a middleware for knowledge intensive environments: e.g., experiments with tuple-based coordination within a Semantic Web middleware (surveys analogous approaches). However, they appear to be designed to tackle the design of coordination for specic application contexts like Semantic Web and Semantic Web Services, and they result in a rather involved extension of the tuple space model. The main goal of this thesis was to conceive a more general approach to semantic coordination. In particular, it was developed the model and technology of semantic tuple centres. It is adopted the tuple centre model as main coordination abstraction to manage system interactions. A tuple centre can be seen as a programmable tuple space, i.e. an extension of a Linda tuple space, where the behaviour of the tuple space can be programmed so as to react to interaction events. By encapsulating coordination laws within coordination media, tuple centres promote coordination uncoupling among coordinated components. Then, the tuple centre model was semantically enriched: a main design choice in this work was to try not to completely redesign the existing syntactic tuple space model, but rather provide a smooth extension that { although supporting semantic reasoning { keep the simplicity of tuple and tuple matching as easier as possible. By encapsulating the semantic representation of the domain of discourse within coordination media, semantic tuple centres promote semantic uncoupling among coordinated components. The main contributions of the thesis are: (i) the design of the semantic tuple centre model; (ii) the implementation and evaluation of the model based on an existent coordination infrastructure; (iii) a view of the application scenarios in which semantic tuple centres seem to be suitable as coordination media.

Supporting semantic web technologies in the pervasive service ecosystems middleware

Semantic Web technologies are strategic in order to fulfill the openness requirement of Self-Aware Pervasive Service Ecosystems. In fact they provide agents with the ability to cope with distributed data, using RDF to represent information, ontologies to describe relations between concepts from any domain (e.g. equivalence, specialization/extension, and so on) and reasoners to extract implicit knowledge. The aim of this thesis is to study these technologies and design an extension of a pervasive service ecosystems middleware capable of exploiting semantic power, and deepening performance implications.

Semantic Enrichment of Scientific Documents with Semantic Lenses – Developing methodologies, tools and prototypes for their concrete use

Con questa dissertazione di tesi miro ad illustrare i risultati della mia ricerca nel campo del Semantic Publishing, consistenti nello sviluppo di un insieme di metodologie, strumenti e prototipi, uniti allo studio di un caso d‟uso concreto, finalizzati all‟applicazione ed alla focalizzazione di Lenti Semantiche (Semantic Lenses).

Conversione per il Semantic Web di dati Turistico-Culturali: il progetto QRPlaces - Semantic Events

Il progetto QRPlaces - Semantic Events, oggetto di questo lavoro, focalizza l’attenzione sull’analisi, la progettazione e l’implementazione di un sistema che sia in grado di modellare i dati, relativi a diversi eventi facenti parte del patrimonio turistico - culturale della Regione Emilia Romagna 1, rendendo evidenti i vantaggi associati ad una rappresentazione formale incentrata sulla Semantica. I dati turistico - culturali sono intesi in questo ambito sia come una rappresentazione di “qualcosa che accade in un certo punto ad un certo momento” (come ad esempio un concerto, una sagra, una raccolta fondi, una rappresentazione teatrale e quant’altro) sia come tradizioni e costumi che costituiscono il patrimonio turistico-culturale e a cui si fa spesso riferimento con il nome di “Cultural Heritage”. Essi hanno la caratteristica intrinseca di richiedere una conoscenza completa di diverse informa- zioni correlata, come informazioni di geo localizzazione relative al luogo fisico che ospita l’evento, dati biografici riferiti all’autore o al soggetto che è presente nell’evento piuttosto che riferirsi ad informazioni che descrivono nel dettaglio tutti gli oggetti, come teatri, cinema, compagnie teatrali che caratterizzano l’evento stesso. Una corretta rappresentazione della conoscenza ad essi legata richiede, pertanto, una modellazione in cui i dati possano essere interconnessi, rivelando un valore informativo che altrimenti resterebbe nascosto. Il lavoro svolto ha avuto lo scopo di realizzare un dataset rispondente alle caratteristiche tipiche del Semantic Web grazie al quale è stato possibile potenziare il circuito di comunicazione e informazione turistica QRPlaces 2. Nello specifico, attraverso la conversione ontologica di dati di vario genere relativi ad eventi dislocati nel territorio, e sfruttando i principi e le tecnologie del Linked Data, si è cercato di ottenere un modello informativo quanto più possibile correlato e arricchito da dati esterni. L’obiettivo finale è stato quello di ottenere una sorgente informativa di dati interconnessi non solo tra loro ma anche con quelli presenti in sorgenti esterne, dando vita ad un percorso di collegamenti in grado di evidenziare una ricchezza informativa utilizzabile per la creazione di valore aggiunto che altrimenti non sarebbe possibile ottenere. Questo aspetto è stato realizzato attraverso un’in- terfaccia di MashUp che utilizza come sorgente il dataset creato e tutti i collegamenti con la rete del Linked Data, in grado di reperire informazioni aggiuntive multi dominio.

Semantic Publishing: issues, solutions and new trends in scholarly publishing within the Semantic Web era

This work is concerned with the increasing relationships between two distinct multidisciplinary research fields, Semantic Web technologies and scholarly publishing, that in this context converge into one precise research topic: Semantic Publishing. In the spirit of the original aim of Semantic Publishing, i.e. the improvement of scientific communication by means of semantic technologies, this thesis proposes theories, formalisms and applications for opening up semantic publishing to an effective interaction between scholarly documents (e.g., journal articles) and their related semantic and formal descriptions. In fact, the main aim of this work is to increase the users' comprehension of documents and to allow document enrichment, discovery and linkage to document-related resources and contexts, such as other articles and raw scientific data. In order to achieve these goals, this thesis investigates and proposes solutions for three of the main issues that semantic publishing promises to address, namely: the need of tools for linking document text to a formal representation of its meaning, the lack of complete metadata schemas for describing documents according to the publishing vocabulary, and absence of effective user interfaces for easily acting on semantic publishing models and theories.

Semantic Service Architectures for Smart Environments

Many industries and academic institutions share the vision that an appropriate use of information originated from the environment may add value to services in multiple domains and may help humans in dealing with the growing information overload which often seems to jeopardize our life. It is also clear that information sharing and mutual understanding between software agents may impact complex processes where many actors (humans and machines) are involved, leading to relevant socioeconomic benefits. Starting from these two input, architectural and technological solutions to enable “environment-related cooperative digital services” are here explored. The proposed analysis starts from the consideration that our environment is physical space and here diversity is a major value. On the other side diversity is detrimental to common technological solutions, and it is an obstacle to mutual understanding. An appropriate environment abstraction and a shared information model are needed to provide the required levels of interoperability in our heterogeneous habitat. This thesis reviews several approaches to support environment related applications and intends to demonstrate that smart-space-based, ontology-driven, information-sharing platforms may become a flexible and powerful solution to support interoperable services in virtually any domain and even in cross-domain scenarios. It also shows that semantic technologies can be fruitfully applied not only to represent application domain knowledge. For example semantic modeling of Human-Computer Interaction may support interaction interoperability and transformation of interaction primitives into actions, and the thesis shows how smart-space-based platforms driven by an interaction ontology may enable natural ad flexible ways of accessing resources and services, e.g, with gestures. An ontology for computational flow execution has also been built to represent abstract computation, with the goal of exploring new ways of scheduling computation flows with smart-space-based semantic platforms.

Semantic under-determinacy, Content and Context

The aim of the thesis is to investigate the topic of semantic under-determinacy, i.e. the failure of the semantic content of certain expressions to determine a truth-evaluable utterance content. In the first part of the thesis, I engage with the problem of setting apart semantic under-determinacy as opposed to other phenomena such as ambiguity, vagueness, indexicality. As I will argue, the feature that distinguishes semantic under-determinacy from these phenomena is its being explainable solely in terms of under-articulation. In the second part of the thesis, I discuss the topic of how communication is possible, despite the semantic under-determinacy of language. I discuss a number of answers that have been offered: (i) the Radical Contextualist explanation which emphasises the role of pragmatic processes in utterance comprehension; (ii) the Indexicalist explanation in terms of hidden syntactic positions; (iii) the Relativist account, which regards sentences as true or false relative to extra coordinates in the circumstances of evaluation (besides possible worlds). In the final chapter, I propose an account of the comprehension of utterances of semantically under-determined sentences in terms of conceptual constraints, i.e. ways of organising information which regulate thought and discourse on certain matters. Conceptual constraints help the hearer to work out the truth-conditions of an utterance of a semantically under-determined sentence. Their role is clearly semantic, in that they contribute to “what is said” (rather than to “what is implied”); however, they do not respond to any syntactic constraint. The view I propose therefore differs, on the one hand, from Radical Contextualism, because it stresses the role of semantic-governed processes as opposed to pragmatics-governed processes; on the other hand, it differs from Indexicalism in its not endorsing any commitment as to hidden syntactic positions; and it differs from Relativism in that it maintains a monadic notion if truth.

On the path of Exploratory Search Users - A Semantic Web tool

L’Exploratory Search, paradigma di ricerca basato sulle attività di scoperta e d’apprendimento, è stato per diverso tempo ignorato dai motori di ricerca tradizionali. Invece, è spesso dalle ricerche esplorative che nascono le idee più innovative. Le recenti tecnologie del Semantic Web forniscono le soluzioni che permettono d’implementare dei motori di ricerca capaci di accompagnare gli utenti impegnati in tale tipo di ricerca. Aemoo, motore di ricerca sul quale s’appoggia questa tesi ne è un esempio efficace. A partire da quest’ultimo e sempre con l’aiuto delle tecnologie del Web of Data, questo lavoro si propone di fornire una metodologia che permette di prendere in considerazione la singolarità del profilo di ciascun utente al fine di guidarlo nella sua ricerca esplorativa in modo personalizzato. Il criterio di personalizzazione che abbiamo scelto è comportamentale, ovvero basato sulle decisioni che l’utente prende ad ogni tappa che ritma il processo di ricerca. Implementando un prototipo, abbiamo potuto testare la validità di quest’approccio permettendo quindi all’utente di non essere più solo nel lungo e tortuoso cammino che porta alla conoscenza.

Linked Data e bibliometriche: un indice di multidisciplinarieta nel Semantic Publishing

Nel presente lavoro si introduce un nuovo indice per la valutazione dei prodotti della ricerca: l'indice di multidisciplinarieta`. Questa nuova metrica puo` essere un interessante parametro di valutazione: il panorama degli studi multidisciplinari e` vasto ed eterogeneo, ed all'interno di questo sono richieste necessarie competenze trasversali. Le attuali metriche adottate nella valutazione di un accademico, di un journal, o di una conferenza non tengono conto di queste situazioni intermedie, e limitano la loro valutazione dell'impatto al semplice conteggio delle citazioni ricevute. Il risultato di tale valutazione consiste in un valore dell'impatto della ricerca senza una connotazione della direzione e della rilevanza di questa nel contesto delle altre discipline. L'indice di multidisciplinarieta` proposto si integrerebbe allora all'interno dell'attuale panorama delle metriche di valutazione della ricerca, offrendo -accanto ad una quantificazione dell'impatto- una quantificazione della varieta` dei contesti disciplinari nei quali si inserisce.

A Semantic-based Framework for Digital Survey of Architectural Heritage

The research aims at developing a framework for semantic-based digital survey of architectural heritage. Rooted in knowledge-based modeling which extracts mathematical constraints of geometry from architectural treatises, as-built information of architecture obtained from image-based modeling is integrated with the ideal model in BIM platform. The knowledge-based modeling transforms the geometry and parametric relation of architectural components from 2D printings to 3D digital models, and create large amount variations based on shape grammar in real time thanks to parametric modeling. It also provides prior knowledge for semantically segmenting unorganized survey data. The emergence of SfM (Structure from Motion) provides access to reconstruct large complex architectural scenes with high flexibility, low cost and full automation, but low reliability of metric accuracy. We solve this problem by combing photogrammetric approaches which consists of camera configuration, image enhancement, and bundle adjustment, etc. Experiments show the accuracy of image-based modeling following our workflow is comparable to that from range-based modeling. We also demonstrate positive results of our optimized approach in digital reconstruction of portico where low-texture-vault and dramatical transition of illumination bring huge difficulties in the workflow without optimization. Once the as-built model is obtained, it is integrated with the ideal model in BIM platform which allows multiple data enrichment. In spite of its promising prospect in AEC industry, BIM is developed with limited consideration of reverse-engineering from survey data. Besides representing the architectural heritage in parallel ways (ideal model and as-built model) and comparing their difference, we concern how to create as-built model in BIM software which is still an open area to be addressed. The research is supposed to be fundamental for research of architectural history, documentation and conservation of architectural heritage, and renovation of existing buildings.

Cellular localization and mechanism of amyloid precursor protein (APP) homodimer formation in an oxidizing environment

The amyloid precursor protein (APP) is a type I transmembrane glycoprotein, which resembles a cell surface receptor, comprising a large ectodomain, a single spanning transmembrane part and a short C-terminal, cytoplasmic domain. It belongs to a conserved gene family, with over 17 members, including also the two mammalian APP homologues proteins APLP1 and APLP2 („amyloid precursor like proteins“). APP is encoded by 19 exons, of which exons 7, 8, and 15 can be alternatively spliced to produce three major protein isoforms APP770, APP751 and APP695, reflecting the number of amino acids. The neuronal APP695 is the only isoform that lacks a Kunitz Protease Inhibitor (KPI) domain in its extracellular portion whereas the two larger, peripheral APP isoforms, contain the 57-amino-acid KPI insert. rnRecently, research effort has suggested that APP metabolism and function is thought to be influenced by homodimerization and that the oligomerization state of APP could also play a role in the pathology of Alzheimer's disease (AD), by regulating its processing and amyloid beta production. Several independent studies have shown that APP can form homodimers within the cell, driven by motifs present in the extracellular domain, as well as in the juxtamembrane (JM) and transmembrane (TM) regions of the molecule, whereby the exact molecular mechanism and the origin of dimer formation remains elusive. Therefore, we focused in our study on the actual subcellular origin of APP homodimerization within the cell, an underlying mechanism, and a possible impact on dimerization properties of its homologue APLP1. Furthermore, we analyzed homodimerization of various APP isoforms, in particular APP695, APP751 and APP770, which differ in the presence of a Kunitz-type protease inhibitor domain (KPI) in the extracellular region. In order to assess the cellular origin of dimerization under different cellular conditions, we established a mammalian cell culture model-system in CHO-K1 (chinese hamster ovary) cells, stably overexpressing human APP, harboring dilysine based organelle sorting motifs at the very C-terminus [KKAA-Endoplasmic Reticulum (ER); KKFF-Golgi]. In this study we show that APP exists as disulfide-bound, SDS-stable dimers, when it was retained in the ER, unlike when it progressed further to the cis-Golgi, due to the KKFF ER exit determinant. These stable APP complexes were isolated from cells, and analyzed by SDS–polyacrylamide gel electrophoresis under non-reducing conditions, whereas strong denaturing and reducing conditions completely converted those dimers to monomers. Our findings suggested that APP homodimer formation starts early in the secretory pathway and that the unique oxidizing environment of the ER likely promotes intermolecular disulfide bond formation between APP molecules. We particularly visualized APP dimerization employing a variety of biochemical experiments and investigated the origin of its generation by using a Bimolecular Fluorescence Complementation (BiFC) approach with split GFP-APP chimeras. Moreover, using N-terminal deletion constructs, we demonstrate that intermolecular disulfide linkage between cysteine residues, exclusively located in the extracellular E1 domain, represents another mechanism of how an APP sub-fraction can dimerize within the cell. Additionally, mutational studies revealed that cysteines at positions 98 and 105, embedded in the conserved loop region within the E1 domain, are critical for interchain disulfide bond formation. Using a pharmacological treatment approach, we show that once generated in the oxidative environment of the ER, APP dimers remain stably associated during transport, reaching the plasma membrane. In addition, we demonstrate that APP isoforms, encompassing the KPI domain, exhibit a strongly reduced ability to form cis-directed dimers in the ER, whereas trans-directed cell aggregation of Drosophila Schneider (S2)-cells was isoform independent, mediating cell-cell contacts. Thus, suggesting that steric properties of KPI-APP might be the cause for weaker cis-interaction in the ER, compared to APP695. Finally, we provide evidence that APP/APLP1 heterointeractions are likewise initiated in the ER, suggesting a similar mechanism for heterodimerization. Therefore, dynamic alterations of APP between monomeric, homodimeric, and possibly heterodimeric status could at least partially explain some of the variety in the physiological functions of APP.rn