Engineering the strain field for the control of quantum confinement: An analytical model for arbitrary shape nanostructures

We describe an analytical method to calculate the strain field and the corresponding band gap modulation induced in a quantum well by a surface stressor of arbitrary shape. In this way, it is possible to engineer the confinement potential of different strained nanostructures based on patterned heterojunctions. Band gap modulations up to 130–140 meV are predicted for suitably designed II–VI/III–V and III–V/III–V heterostructures

Immobilization of the Glycosylphosphatidylinositol-anchored Gas1 protein into the chitin ring and septum is required for proper morphogenesis in yeast

Gas1p is a glucan-elongase that plays a crucial role in yeast morphogenesis. It is predominantly anchored to the plasma membrane through a glycosylphosphatidylinositol but a fraction was also found covalently bound to the cell wall. We have used fusions with the green or red fluorescent proteins (GFP or RFP) to determine its localization. Gas1p was present in microdomains of the plasma membrane, at the mother-bud neck and in the bud scars. By exploiting the instability of RFP-Gas1p we identified mobile and immobile pools of Gas1p. Moreover, in chs3\uf044 cells the chitin ring and the cross-linked Gas1p were missing but this unveiled an additional unexpected localization of Gas1p along the septum line in cells at cytokinesis. Localization of Gas1p was also perturbed in a chs2\uf044 mutant where a remedial septum is produced. Phenotypic analysis of cells expressing a fusion of Gas1p to a trans-membrane domain unmasked new roles of the cell wall-bound Gas1p in the maintenance of the bud neck size and in cell separation. We present evidence that the Crh1p and Crh2p are required for tethering Gas1p to the chitin ring and bud scar. These results reveal a new mechanism of protein immobilization at specific sites of the cell envelop

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

DOLCE: A descriptive ontology for linguistic and cognitive engineering

DOLCE, the first top-level (foundational) ontology to be axiomatized, has remained stable for twenty years and today is broadly used in a variety of domains. DOLCE is inspired by cognitive and linguistic considerations and aims to model a commonsense view of reality, like the one human beings exploit in everyday life in areas as diverse as socio-technical systems, manufacturing, financial transactions and cultural heritage. DOLCE clearly lists the ontological choices it is based upon, relies on philosophical principles, is richly formalized, and is built according to well-established ontological methodologies, e.g. OntoClean. Because of these features, it has inspired most of the existing top-level ontologies and has been used to develop or improve standards and public domain resources (e.g. CIDOC CRM, DBpedia and WordNet). Being a foundational ontology, DOLCE is not directly concerned with domain knowledge. Its purpose is to provide the general categories and relations needed to give a coherent view of reality, to integrate domain knowledge, and to mediate across domains. In these 20 years DOLCE has shown that applied ontologies can be stable and that interoperability across reference and domain ontologies is a reality. This paper briefly introduces the ontology and shows how to use it on a few modeling cases

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,