Towards an Ontological Modelling of Preference Relations

Preference relations are intensively studied in Economics, but they are also approached in AI, Knowledge Representation, and Conceptual Modelling, as they provide a key concept in a variety of domains of application. In this paper, we propose an ontological foundation of preference relations to formalise their essential aspects across domains. Firstly, we shall discuss what is the ontological status of the relata of a preference relation. Secondly, we investigate the place of preference relations within a rich taxonomy of relations (e.g. we ask whether they are internal or external, essential or contingent, descriptive or nondescriptive relations). Finally, we provide an ontological modelling of preference relation as a module of a foundational (or upper) ontology (viz. OntoUML). The aim of this paper is to provide a sharable foundational theory of preference relation that foster interoperability across the heterogeneous domains of application of preference relations

Towards a Cognitive Semantics of Type

Types are a crucial concept in conceptual modelling, logic, and knowledge representation as they are an ubiquitous device to un- derstand and formalise the classification of objects. We propose a logical treatment of types based on a cognitively inspired modelling that ac- counts for the amount of information that is actually available to a cer- tain agent in the task of classification. We develop a predicative modal logic whose semantics is based on conceptual spaces that model the ac- tual information that a cognitive agent has about objects, types, and the classification of an object under a certain type. In particular, we ac- count for possible failures in the classification, for the lack of sufficient information, and for some aspects related to vagueness

DNA glycosylases: in DNA repair and beyond

The base excision repair machinery protects DNA in cells from the damaging effects of oxidation, alkylation, and deamination; it is specialized to fix single-base damage in the form of small chemical modifications. Base modifications can be mutagenic and/or cytotoxic, depending on how they interfere with the template function of the DNA during replication and transcription. DNA glycosylases play a key role in the elimination of such DNA lesions; they recognize and excise damaged bases, thereby initiating a repair process that restores the regular DNA structure with high accuracy. All glycosylases share a common mode of action for damage recognition; they flip bases out of the DNA helix into a selective active site pocket, the architecture of which permits a sensitive detection of even minor base irregularities. Within the past few years, it has become clear that nature has exploited this ability to read the chemical structure of DNA bases for purposes other than canonical DNA repair. DNA glycosylases have been brought into context with molecular processes relating to innate and adaptive immunity as well as to the control of DNA methylation and epigenetic stability. Here, we summarize the key structural and mechanistic features of DNA glycosylases with a special focus on the mammalian enzymes, and then review the evidence for the newly emerging biological functions beyond the protection of genome integrity

Physiological analysis of mutants indicates involvement of the Saccharomyces cerevisiae GPI-anchored protein gp115 in morphogenesis and cell separation.

This paper reports a phenotypic characterization of ggp1 mutants. The cloned GGP1 (GAS1) gene, which encodes a major GPI-anchored glycoprotein (gp115) of Saccharomyces cerevisiae of unknown function, was used to direct the inactivation of the chromosomal gene in haploid and diploid strains by gene replacement. The analysis of the null mutants reveals a reduction in the growth rate of 15 to 40%. Cells are round, with more than one bud, and extensively vacuolized. In the stationary phase, mutant cells are very large, arrest with a high percentage of budded cells (about 54 and 70% for haploid and diploid null mutants, respectively, in comparison with about 10 to 13% for control cells), and have reduced viability. The observed phenotype suggests defects in cell separation. Flow cytometric analysis of DNA reveals an increase in the fraction of cells in the G2+M+G1* compartment during exponential growth. Conjugation and sporulation are not affected. The exocellular location of gp115 led us to examine cell wall properties. Cell wall and septum ultrastructure of abnormally budded cells was analyzed by electron microscopy analysis, and no appreciable differences from wild-type cells were found. Microscopic analysis revealed an increase in chitin content and delocalization. In comparison with control cells, ggp1 null mutants are shown to be resistant to Zymolyase during the exponential growth phase. A fivefold overexpression of gp115 does not bring about any effects on cell growth parameters and cell wall properties

Inherited variants of MYH associated with somatic G:C→T:A mutations in colorectal tumors

Inherited defects of base excision repair have not been associated with any human genetic disorder, although mutations of the genes mutM and mutY, which function in Escherichia coli base excision repair, lead to increased transversions of G:C to T:A1, 2, 3, 4. We have studied family N, which is affected with multiple colorectal adenomas and carcinoma but lacks an inherited mutation of the adenomatous polyposis coli gene (APC) that is associated with familial adenomatous polyposis5. Here we show that 11 tumors from 3 affected siblings contain 18 somatic inactivating mutations of APC and that 15 of these mutations are G:CT:A transversions—a significantly greater proportion than is found in sporadic tumors or in tumors associated with familial adenomatous polyposis. Analysis of the human homolog of mutY, MYH6, showed that the siblings were compound heterozygotes for the nonconservative missense variants Tyr165Cys and Gly382Asp. These mutations affect residues that are conserved in mutY of E. coli (Tyr82 and Gly253). Tyrosine 82 is located in the pseudo-helix-hairpin-helix (HhH) motif and is predicted to function in mismatch specificity7. Assays of adenine glycosylase activity of the Tyr82Cys and Gly253Asp mutant proteins with 8-oxoG:A and G:A substrates show that their activity is reduced significantly. Our findings link the inherited variants in MYH to the pattern of somatic APC mutation in family N and implicate defective base excision repair in predisposition to tumors in humans

Multiagent socio-technical systems: An ontological approach

none4Socio- technical systems constitute a challenge for multiagent systems as they are complex scenarios in which human and artificial agents share informa- tion, interact and make decisions. For example, the design of an airport requires to interface information coming from automatic apparatuses as security cameras, conceptual information coming from agents, and normative information which agents’ behavior must comply with. Thus, in order to design systems that are capable of assisting human agents in organizing and managing socio-technical systems, we need fine grained tools to handle several types of information. The aim of this paper is to discuss a general framework to describe socio-technical systems as cases of complex multiagent systems. In particular, we use a founda- tional ontology to address the problems of interoperability and conceptual analy- sis, we discuss how to interface conceptual information with low level informa- tion obtained by computer vision or perception, and we discuss how to integrate information coming from heterogeneous agents.mixedPorello D; Setti F; Ferrario R; Cristani MPorello, D; Setti, F; Ferrario, R; Cristani,

Generazioni disuguali. Le condizioni di vita dei giovani di ieri e di oggi: un confronto

\uc8 percezione diffusa che, per la prima volta dalla seconda guerra mondiale, i giovani subiscano un arretramento nelle condizioni di vita e, ancor pi\uf9, nelle prospettive future. Sulla gravit\ue0 e sulle cause di questa situazione si confrontano opinioni diverse. Il volume fornisce articolate risposte, affrontando \u2013 da prospettive nuove rispetto a quelle fin qui esplorate \u2013 una pluralit\ue0 di aspetti dell\u2019esistenza giovanile (scolarit\ue0, lavoro, reddito, formazione della famiglia, migrazioni interne e verso l\u2019estero, mobilit\ue0 sociale ed economica). Non vengono considerati solo i giovani di oggi, ma anche i giovani di ieri, cos\uec da capire se davvero, e per quali ragioni, quelli stiano peggio di questi. Sono altres\uec valutati gli effetti delle politiche pubbliche e delle scelte di bilancio degli ultimi cinquant\u2019anni sulle condizioni di vita delle nuove generazioni, passate e presenti. Il volume si caratterizza per l\u2019ampiezza degli argomenti e per il rigore delle analisi, frutto di un\u2019organica collaborazione tra economisti, sociologi e statistici nell\u2019ambito del progetto pluriennale di ricerca \uabOsservatorio sulle disuguaglianze sociali (Ods)\ubb

Unusually strong binding of a designed transition-state analog to a base-excision DNA repair protein

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