Integrated Model Checking of Static Structure and Dynamic Behavior using Temporal Description Logics

This paper presents a new notation for the formal representation of the static structure and dynamic behavior of software, based on description logics and temporal logics. The static structure as described by UML class diagrams is represented formally by description logics while the dynamic behavior is represented by linear temporal logic and state transition systems. We integrate these descriptions of static and dynamic aspects into a single formalism called LTLDL. LTLDL enables a concise and natural yet precise definition of the behavior of software w.r.t. UML class diagrams and state transition diagrams. We demonstrate our approach on the sake warehouse problem. Further, we describe how properties of finite LTLDL models can be analyzed based on bounded model checking and SMT (satisfiability modulo theory) solving. We implemented a restricted SMT solver for finite sets and relations. This SMT solver helped to reduce the model checking runtime significantly as compared to bounded model checking with existing tools

Dokumentverifikation mit Temporaler Beschreibungslogik

The thesis proposes a new formal framework for checking the content of web documents along individual reading paths. It is vital for the readability of web documents that their content is consistent and coherent along the possible browsing paths through the document. Manually ensuring the coherence of content along the possibly huge number of different browsing paths in a web document is time-consuming and error-prone. Existing methods for document validation and verification are not sufficiently expressive and efficient. The innovative core idea of this thesis is to combine the temporal logic CTL and description logic ALC for the representation of consistency criteria. The resulting new temporal description logics ALCCTL can - in contrast to existing specification formalisms - compactly represent coherence criteria on documents. Verification of web documents is modelled as a model checking problem of ALCCTL. The decidability and polynomial complexity of the ALCCTL model checking problem is proven and a sound, complete, and optimal model checking algorithm is presented. Case studies on real and realistic web documents demonstrate the performance and adequacy of the proposed methods. Existing methods such as symbolic model checking or XML-based document validation are outperformed in both expressiveness and speed.Die Dissertation stellt ein neues formales Framework für die automatische Prüfung inhaltlich-struktureller Konsistenzkriterien an Web-Dokumente vor. Viele Informationen werden heute in Form von Web-Dokumenten zugänglich gemacht. Komplexe Dokumente wie Lerndokumente oder technische Dokumentationen müssen dabei vielfältige Qualitätskriterien erfüllen. Der Informationsgehalt des Dokuments muss aktuell, vollständig und in sich stimmig sein. Die Präsentationsstruktur muss unterschiedlichen Zielgruppen mit unterschiedlichen Informationsbedürfnissen genügen. Die Sicherstellung grundlegender Konsistenzeigenschaften von Dokumenten ist angesichts der Vielzahl der Anforderungen und Nutzungskontexte eines elektronischen Dokuments nicht trivial. In dieser Arbeit werden aus der Hard-/Softwareverifikation bekannte Model-Checking-Verfahren mit Methoden zur Repräsentation von Ontologien kombiniert, um sowohl die Struktur des Dokuments als auch inhaltliche Zusammenhänge bei der Prüfung von Konsistenzkriterien berücksichtigen zu können. Als Spezifikationssprache für Konsistenzkriterien wird die neue temporale Beschreibungslogik ALCCTL vorgeschlagen. Grundlegende Eigenschaften wie Entscheidbarkeit, Ausdruckskraft und Komplexität werden untersucht. Die Adäquatheit und Praxistauglichkeit des Ansatzes werden in Fallstudien mit eLearning-Dokumenten evaluiert. Die Ergebnisse übertreffen bekannte Ansätze wie symbolisches Model-Checking oder Methoden zur Validierung von XML-Dokumenten in Performanz, Ausdruckskraft hinsichtlich der prüfbaren Kriterien und Flexibilität hinsichtlich des Dokumenttyps und -formats

Assessing User Experiences with ZORQ: A Gamification Framework for Computer Science Education

ZORQ is a gamification software framework designed to increase student engagement within undergraduate Computer Science (CS) education. ZORQ is an attractive learning method that (1) utilizes numerous gamification elements, (2) provides a collaborative, game-development based learning approach, (3) offers an opportunity for students to explore a complex, real-world software development implementation, and (4) provides students with a high level of engagement with the system and a high level of social engagement in its collaborative customization. The usage of ZORQ was assessed using quantitative, qualitative and sentiment analyses in a Data Structures and Algorithms course over five years. The overwhelmingly positive results show that students were satisfied with their user experience and ZORQ was beneficial to their educational experience. By triangulating results from multiple analyses, this study adds to a deeper understanding of how gamification can improve learning and retention and provides a novel, robust, holistic methodology for evaluating user experiences

Ferric Ion-Specific Sequestering Agents. 7. Synthesis, Iron Exchange Kinetics, and Stability Constants of N-Substituted, Sulfonated Catechoylamide Analogues of Enterobactin.

For treatment of chronic iron overload (as occurs in Cooley's anemia), ferric ion sequestering agents with specific properties are necessary. Two analogues of enterobactin [a microbial chelating agent with the greatest stability constant known for an Fe(III) complex] are reported which exhibit: i) hydrolytic stability; ii) water solubility; iii) N-substitution to block peptidase hydrolysis. The first compound, N,N',N"- trimethyl-N,N',N"-tris(2,3-dihydroxysulfobenzoyl)1,3,5-triaminomethyl- benzene, [Me{sub 3}MECAMS, 6] was prepared from the amide of trimesloyl chloride (1) and MeNH{sub 2}. The resulting amide was reduced to the triamine (3) and converted in three steps to the final product 6 in 6% overall yield. The proton-dependent formation constant (log K*) for the reaction: Fe{sup 3+} + H{sub 3}L{sup 6-} = FeL{sup 6-} + 3H{sup +} is 4.87, which gives an equilibrium concentration of [Fe{sup 3+}] at pH 7.4 of 2 x 10{sup -27} M for 10{sup -5} M L (6) and 10{sup -6} M total Fe{sup 3+}. The estimated formation constant (log {beta}{sub 110}) is 40. At low pH the FeL{sup 6-} complex undergoes a series of three, one-proton reactions which probably gives a tris-salicylate complex formed by the carbonyl and ortho-catechol oxygen of the 2,3~dihydroxybenzoyl units (the same reaction that occurs with ferric enterobactin). After six hours in the presence of 6 mM ascorbate, Me{sub 3}MECAMS (6.0 mM) removed 3.7% of the ferric ion initially sequestered by the iron storage protein, ferritin. The human iron transport protein transferrin goves up iron to Me{sub 3}MECAMS with a pseudo first-order rate constant of 1.9 x 10{sup -3}min{sup -1} (ligand concentration 2 X 10{sup -4} M). This rate is comparable to that of enterobactin and other catechoyl amide sequestering agents. and greatly exceeds that of desferrioxamine B (Desferal{reg-sign}). the current drug of choice in treating iron overload. Two related compounds have been prepared in which the catechol ring is attached to the amide nitrogen through a methylene group, with amide formation with an acetyl group. In N,N',N"-triacetyl-N,N' ,N"-tris(2,3- dihydroxysulfobenzoyl) -N,N',N"-triaminomethylbenzene [NAcMECAMS, 111... and its unsulfonated precursor, the amide linkage of the catechoyl amides such as Me{sub 3}MECAMS (6) has been shifted from an endo position relative to the benzene and catechol rings to an exo position in which the amide carbonyl is not conjugated with the catechol ring and cannot form a stable chelate ring in conjunction with a catechol oxygen. The preparation of 11 and 10 proceeded from the previously described precursor of TRIMCAM, 7. borane reduction to the tri.amine 8, and amide formation with acetyl chloride to 9, followed by deprotection of the catechol oxygens with BBr{sub 3}/CH{sub 2}Cl{sub 2} to give 10. Sulfonation of 10 to NAcMECAMS, 11, is carried out in fuming sulfuric acid. In comparison with Me{sub 3}MECAMS, the protonation of NAcMECAMS (11) proceeds by an initial two-proton step in contrast to the one-proton reactions typical of the catechoyl amides, which can form a salicylate mode of coordination involving the amide carbonyl group. Also as a result of the removal of the carbonyl group from conjugation with the catechol ring, the acidity of NAcMECAMS (11) is less than Me{sub 3}MECAMS (6). While the estimated log {beta{sub 110} is approximately the same as for Me{sub 3}MECAMS (40). the effective formation constant (log K*) and pM.(- log [Fe{sub aq}{sup 3+}] ) values are lower (4.0 and 25.0, respectively)

Debugging of Web Applications with Web-TLR

Web-TLR is a Web verification engine that is based on the well-established Rewriting Logic--Maude/LTLR tandem for Web system specification and model-checking. In Web-TLR, Web applications are expressed as rewrite theories that can be formally verified by using the Maude built-in LTLR model-checker. Whenever a property is refuted, a counterexample trace is delivered that reveals an undesired, erroneous navigation sequence. Unfortunately, the analysis (or even the simple inspection) of such counterexamples may be unfeasible because of the size and complexity of the traces under examination. In this paper, we endow Web-TLR with a new Web debugging facility that supports the efficient manipulation of counterexample traces. This facility is based on a backward trace-slicing technique for rewriting logic theories that allows the pieces of information that we are interested to be traced back through inverse rewrite sequences. The slicing process drastically simplifies the computation trace by dropping useless data that do not influence the final result. By using this facility, the Web engineer can focus on the relevant fragments of the failing application, which greatly reduces the manual debugging effort and also decreases the number of iterative verifications.Comment: In Proceedings WWV 2011, arXiv:1108.208

Interactions of the periplasmic binding protein CeuE with Fe(III) n-LICAM(4-) siderophore analogues of varied linker length

Bacteria use siderophores to mediate the transport of essential Fe(III) into the cell. In Campylobacter jejuni the periplasmic binding protein CeuE, an integral part of the Fe(III) transport system, has adapted to bind tetradentate siderophores using a His and a Tyr side chain to complete the Fe(III) coordination. A series of tetradentate siderophore mimics was synthesized in which the length of the linker between the two iron-binding catecholamide units was increased from four carbon atoms (4-LICAM(4-)) to five, six and eight (5-, 6-, 8-LICAM(4-), respectively). Co-crystal structures with CeuE showed that the inter-planar angles between the iron-binding catecholamide units in the 5-, 6- and 8-LICAM(4-) structures are very similar (111°, 110° and 110°) and allow for an optimum fit into the binding pocket of CeuE, the inter-planar angle in the structure of 4-LICAM(4-) is significantly smaller (97°) due to restrictions imposed by the shorter linker. Accordingly, the protein-binding affinity was found to be slightly higher for 5- compared to 4-LICAM(4-) but decreases for 6- and 8-LICAM(4-). The optimum linker length of five matches that present in natural siderophores such as enterobactin and azotochelin. Site-directed mutagenesis was used to investigate the relative importance of the Fe(III)-coordinating residues H227 and Y288

The Pneumococcal Iron Uptake Protein a (PiuA) Specifically Recognizes Tetradentate FeIIIbis- and Mono-Catechol Complexes

Streptococcus pneumoniae (Spn) is an important Gram-positive human pathogen that causes millions of infections worldwide with an increasing occurrence of antibiotic resistance. Fe acquisition is a crucial virulence determinant in Spn; further, Spn relies on exogenous FeIII-siderophore scavenging to meet nutritional Fe needs. Recent studies suggest that the human catecholamine stress hormone, norepinephrine (NE), facilitates Fe acquisition in Spn under conditions of transferrin-mediated Fe starvation. Here we show that the solute binding lipoprotein PiuA from the piu Fe acquisition ABC transporter PiuBCDA, previously described as an Fe-hemin binding protein, binds tetradentate catechol FeIII complexes, including NE and the hydrolysis products of enterobactin. Two protein-derived ligands (H238, Y300) create a coordinately-saturated FeIII complex, which parallel recent studies in the Gram-negative intestinal pathogen Campylobacter jejuni. Our in vitro studies using NMR spectroscopy and 54Fe LC-ICP-MS confirm the FeIII can move from transferrin to apo-PiuA in a NE-dependent manner. Structural analysis of PiuA FeIII-bis-catechol and GaIII-bis-catechol and GaIII-(NE)2 complexes by NMR spectroscopy reveals only localized structural perturbations in PiuA upon ligand binding, largely consistent with recent descriptions of other solute binding proteins of type II ABC transporters. We speculate that tetradentate FeIII complexes formed by mono- and bis-catechol species are important Fe sources in Gram-positive human pathogens, since PiuA functions in the same way as SstD from Staphylococcus aureus