In a previous report we have investigates subsumption in the presence of terminological cycles for the description logic EL, which allows conjunctions, existential restrictions, and the top concept, and have shown that the subsumption problem remains polynomial for all three types of semantics usually considered for cyclic definitions in description logics. This result depends on a characterization of subsumption through the existence of certain simulation relations on the graph associated with a terminology. In the present report we will use this characterization to show how the most specific concept and the least common subsumer can be computed in EL with cyclic definitions. In addition, we show that subsumption in EL (with or without cyclic definitions) remains polynomial even if one adds a certain restricted form of global role-value-maps to EL. In particular, this kind of role-value-maps can express transitivity of roles.

We investigate the impact that general concept inclusions and role-value maps have on the complexity and decidability of reasoning in the Description Logic FL₀. On the one hand, we give a more direct proof for ExpTimehardness of subsumption w.r.t. general concept inclusions in FL₀. On the other hand, we determine restrictions on role-value maps that ensure decidability of subsumption, but we also show undecidability for the cases where these restrictions are not satisfied.

Classical regular path queries (RPQs) can be too restrictive for some applications and answering such queries under approximate semantics to relax the query is desirable. While for answering regular path queries over graph databases under approximate semantics algorithms are available, such algorithms are scarce for the ontology-mediated setting. In this paper we extend an approach for answering RPQs over graph databases that uses weighted transducers to approximate paths from the query in two ways. The first extension is to answering approximate conjunctive 2-way regular path queries (C2RPQs) over graph databases and the second is to answering C2RPQs over ELH and DL-LiteR ontologies. We provide results on the computational complexity of the underlying reasoning problems and devise approximate query answering algorithms.

We adapt existing approaches for privacy-preserving publishing of linked data to a setting where the data are given as Description Logic (DL) ABoxes with possibly anonymised (formally: existentially quantified) individuals and the privacy policies are expressed using sets of concepts of the DL EL. We provide a chacterization of compliance of such ABoxes w.r.t. EL policies, and show how optimal compliant anonymisations of ABoxes that are noncompliant can be computed. This work extends previous work on privacypreserving ontology publishing, in which a very restricted form of ABoxes, called instance stores, had been considered, but restricts the attention to compliance. The approach developed here can easily be adapted to the problem of computing optimal repairs of quantified ABoxes. / This is an extended version of an article pulished in: Proceedings of the 19th International Semantic Web Conference (ISWC 2020), Springer LNCS

In recent work, we have shown how to compute compliant anonymizations of quantified ABoxes w.r.t. EL policies. In this setting, quantified ABoxes can be used to publish information about individuals, some of which are anonymized. The policy is given by concepts of the Description Logic (DL) EL, and compliance means that one cannot derive from the ABox that some non-anonymized individual is an instance of a policy concept. If one assumes that a possible attacker could have additional knowledge about some of the involved non-anonymized individuals, then compliance with a policy is not sufficient. One wants to ensure that the quantified ABox is safe in the sense that none of the secret instance information is revealed, even if the attacker has additional compliant knowledge. In the present paper, we show that safety can be decided in polynomial time, and that the unique optimal safe anonymization of a non-safe quantified ABox can be computed in exponential time, provided that the policy consists of a single EL concept. / This is an extended version of an article published in: Proceedings of the 36th ACM/SIGAPP Symposium on Applied Computing (SAC ’21), ACM

Η αποικοδόμηση των πρωτεϊνών είναι μια διαδικασία απαραίτητη για τη διατήρηση της ομοιόστασης του κυττάρου. Ένας από τους κύριους μηχανισμούς αποικοδόμησης των βραχύβιων πρωτεϊνών καθώς και όσων εμφανίζουν λανθασμένη αναδίπλωση, χωρεί μέσω του μονοπατιού ουβικιτίνης- πρωτεασώματος. Η ουβικιτινίωση είναι μια μετα-μεταφραστική διαδικασία, η οποία έγκειται στη σηματοδότηση των υποψήφιων για αποικοδόμηση πρωτεϊνών με ουβικιτίνη και περιλαμβάνει τρεις ενζυμικές ενεργότητες: Ε1 (εκκινητής ουβικιτίνης), Ε2(μεταφορέας ουβικιτίνης) και Ε3 (λιγάση ουβικιτίνης). Η πρωτεΐνη Arkadia (Rnf11) είναι μια Ε3 λιγάση ουβικιτίνης με συνολικό μήκος 994 αμινοξέα. Σε μοριακό επίπεδο, ενισχύει το TGF-β σηματοδοτικό μονοπάτι, διαμεσολαβώντας την εξαρτώμενη από το πρωτεάσωμα αποικοδόμηση των αρνητικών ρυθμιστών του, c-Ski και Sno-N. Η δραστικότητα Ε3 λιγάσης ουβικιτίνης εδράζεται στον C΄-τελικό RING-H2 τομέα, που σχηματίζεται από τα τελευταία 60 περίπου αμινοξέα της ακολουθίας. Η δομή και η σταθερότητα του RING τομέα εξαρτώνται από την πρόσδεση δύο ιόντων Zn μέσω ενός χαρακτηριστικού μοτίβου, που περιλαμβάνει 6 κυστεϊνικά και 2 ιστιδινικά κατάλοιπα. Στην προσπάθεια αποσαφήνισης της σχέσης δομής-δράσης της πρωτεΐνης Arkadia, ένα από τα κατάλοιπα που συναρμόζονται με Zn -συγκεκριμένα η His965- αντικαταστάθηκε από κυστεΐνη μέσω κατευθυνόμενης μεταλλαξιγένεσης. Η μετάλλαξη αυτή, με την οποία, ουσιαστικά, μετατρέψαμε τον RING-H2 σε RING-HC τομέα, μελετήθηκε με χρήση πολυπυρηνικής/πολυδιάστατης φασματοσκοπίας πυρηνικού μαγνητικού συντονισμού (NMR). H NMR δομή του RING-H2 τομέα της Η965C Arkadia επιλύθηκε σε υψηλή διακριτικότητα (tf=0.94±7.53*10-2, RMSD=0.75±0.20 και RMSD=1.45±0.24 για τα άτομα του πολυπεπτιδικού σκελετού και τα βαρέα άτομα αντίστοιχα) και αποκάλυψε μια ββαββ τοπολογία. Παράλληλα, πραγματοποιήθηκε μελέτη κινητικότητας, από την οποία προέκυψε ότι η εν λόγω μετάλλαξη υφίσταται ως μονομερές και διαθέτει έναν συμπαγή πυρήνα, που περικλείεται μεταξύ δύο ευκίνητων άκρων. / Protein degradation is necessary for the maintenance of cell homeostasis. A major mechanism for the degradation of short-lived as well as misfolded proteins involves the ubiquitin-proteasome pathway. Ubiquitination is a post translational modification, which targets the proteins to be degraded through the covalent attachment of a ubiquitin tag and consists of three enzyme activities: Ε1 (ubiquitin activator), E2 (ubiquitin carrier) and E3 (ubiquitin ligase). Arkadia (Rnf11) is a 994 amino acid protein, which acts as an E3 ubiquitin ligase. On a molecular level, Arkadia enhances TGF-β signaling by mediating the proteasome-dependent degradation of its negative regulators, c-Ski and Sno-N. Its E3 ubiquitin ligase activity lies on a C΄-terminal RING-H2 domain, formed by the last 60 residues. The structure as well as stability of the RING finger domain depend strongly on the binding of two zinc ions in a unique ΄΄cross-brace΄΄ arrangement through a defined motif of six cysteines and two histidines. Trying to elucidate the structure-activity relationship in the case of Arkadia, one of the amino acid ligands –specifically His965- was replaced by cysteine through site-directed mutagenesis. This particular mutation, which, in reality, transformed the RING-H2 to a RING-HC domain, was studied with the use of multinuclear/multidimensional nuclear magnetic resonance spectroscopy (NMR). The NMR solution structure of the H965 Arkadia RING-H2 domain was determined in high resolution (tf=0.94±7.53*10-2, RMSD=0.75±0.20 και RMSD=1.45±0.24 for backbone and heavy atoms respectively) and revealed a ββαββ topology. Furthermore, a mobility study was conducted with the following results: the mutated protein is not expected to form dimers and shows a compact core region including the four metal binding motifs flanked by two flexibly disordered termini.

We present the synthesis and structural characterization of novel ruthenium complexes containing C^C* cyclometalated N-heterocyclic carbene ligands, η6-arene (p-cymene) ligands and one bridging chlorine ion. Complexes of the general formula [Ru(p-cymene)(C^C*)Cl] were prepared via a one-pot synthesis using in situ transmetalation from the correspondent silver NHC complexes. These complexes react with sodium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (NaBArF4) to form dinuclear complexes of the general structure [Ru(p-cymene)(C^C*)-μ-Cl-(p-cymene)(C^C*)Ru]+[BArF4]−. Solid-state structures confirm that the pseudo-tetrahedral coordination around the metal center with the η6-ligand aligned perpendicularly to the C^C* ligand and the i-Pr group “atop” is retained in the bimetallic complexes.

Une étude comparative des caractéristiques statiques, dynamiques et structurale a été menée sur 8 membranes échangeuses d'ions (MEIs), 4 neuves (MEIN) et les mêmes usagées (MEIU) après 2 ans de fonctionnement en ED dans l'industrie agroalimentaire. L'objectif essentiel était de mieux connaître les mécanismes de vieillissement in situ. Nous avons donc mesuré pour chacune de ces MEIs la capacité d'échange, la teneur en eau, la perméabilité ionique, la conductivité électrique, le nombre de transport, l'angle de contact, le courant limite, le module d'Young et la résistance à la traction. Aussi, nous avons effectué des analyses d'IRTF, de MEB et d'EDX. Cette étude nous a permis de conclure que (i) la MEC2 est restée presque stable après les 2 ans d'ED, alors que la MEA1 s'est très fortement dégradée. D'une manière générale, les MEAs sont plus sensibles au vieillissement que les MECs, (ii) les sites fonctionnels sulfoniques s'éliminent de la MEC. Nous ne pouvons pas affirmer ce mécanisme dans le cas des MEAs, mais nous soupçonnons un phénomène d'empoisonnement des sites fonctionnels, (iii) les MEAs se colmatent en surfaces avec des ampleurs différentes entre la MEA1 et la MEA2 / A comparative study of static characteristics, dynamic and structural was conducted on 8 ion-exchange membranes (MEIS), 4 new (IEMN) and the same used (IEMU) after two years of ED operation in the food industry. The main objective was to better understand the mechanisms of in situ ageing. We therefore measured for each IEMs exchange capacity, water content, ionic permeability, electrical conductivity, transport number, contact angle, current limit, Young's modulus and tensile strength. Therefore, we performed analysis of FTIR, SEM and EDX. This study concluded that (i) CEM2 remained almost stable after 2 years of ED, while AEM1 has sharply deteriorated. In general, the AEMs are more susceptible to ageing than CEMs, (ii) the sulfonic functional sites are eliminated from the CEMs. We cannot confirm this mechanism in the case of AEMs, but we suspect a poisoning phenomenon of functional sites, (iii) the AEMs fouled in surfaces with different degrees between AEM1 and AEM2

Le travail réalisé porte sur la caractérisation et la valorisation de la Biolignine™ de paille de blé extraite à l'échelle semi-industrielle par le procédé CIMV. La première partie est consacrée à l'étude structurale du produit et à la quantification de ses diverses fonctions hydroxyles et acides carboxyliques. Dans la seconde partie, la Biolignine™ a été utilisée, en tant que substituant du bisphénol-A, dans la synthèse de résine époxy. Les études de DSC et DLTMA ont démontré qu'après post-réticulation, les résines époxy Biolignine™-PEGDGE possèdent des caractéristiques thermomécaniques comparables à celles d'une résine époxy à base de bisphénol-A. Les résultats obtenus permettent désormais d'envisager la synthèse de résines époxy à base de Biolignine™ à plus grande échelle. / This thesis relates the structural characterization and the application of wheat straw BiolignineTM extracted at semi-industrial scale by the CIMV process. The first part is the structural study of the BiolignineTM and the quantification of its hydroxyl groups and carboxylic acids functions. In the second part, the BiolignineTM was used, as a substitute of bisphenol-A, in the synthesis of epoxy resins. DSC and DLTMA studies showed that after post-curing, epoxy resins of BiolignineTM-PEGDGE have thermomechanical properties similar to those of a bisphenol-A based epoxy resin. The results lead to the scope of BiolignineTM based epoxy resins synthesis at larger scale.

Protein phosphorylation is a common post-translational protein modification used in almost all cellular processes. When a phosphate group is added to an amino acid side chain, it may alter the protein conformation and protein-protein interactions due to its size and its negative charge. It may also change the protein function, activity and even localization within the cell. Experimental detection of phosphorylation is still extremely labor demanding and very expensive, even when deploying protein mass spectrometry. For this very reason many bioinformatics scientific groups focus on the prediction of protein phosphorylation sites. Recent analyses of phosphorylation sites studied mainly non-phosphorylated phosphorylation sites and the distribution and representation of amino acids sequentially neighboring them. Since sequentially more distant, but structurally close amino acids can contribute to the recognition of protein substrate by protein kinase, structural environment of phosphorylation sites was studied in this thesis. Furthermore, 3D structures of phosphorylation sites were comprehensively studied for the first time in a phosphorylated state and the results were compared with the results obtained from the analysis of non- phosphorylated sites. Phosphorylation sites were found mostly within...