Studies on the repair and conformation of DNA containing O6-alkylguanine and O4-alkylthymine

The carcinogenic N-nitroso compounds alkylate DNA. Among the different products of alkylation, O6-alkylguanine and O4-alkylthymine have attracted most of the attention since they are highly mutagenic and a correlation exists between their formation and persistence, and oncogenesis in animal model systems. Both DNA adducts in E. coli and at least O6-alkylguanine in mammalian cells are repaired by enzymes, the so-called O6-alkylguanine-DNA-alkyltransferases. Based on the HPLC separation of short, self-complementary oligonucleotides containing O6-methylguanine, O6-ethylguanine, or O4-methylthymine from the respective parent non-alkylated oligomers, the rate constants for their repair by the E. coli ada and ogt and the human alkyltransferases were determined. Although all alkyltransferases were able to repair O6-methylguanine, O6-ethylguanine and O4-methylthymine, the relative efficiencies were found to differ significantly. Using an immunoprecipitation assay, the rates of repair of an O6-methylguanine residue in various positions in 15 base-pair DNA duplexes were measured. The sequence of the oligomers was that of the rat H-ras sequence around codon 12 and the rates of repair were found to vary up to 25-fold depending on the sequence flanking the methylguanine. An O6-methylguanine in the second position of the GGA codon 12 was the least well repaired. The combination of this slow repair and sequence selectivity in alkylation appears to be the explanation of the selective mutation of this position observed in rat mammary tumours. The avidity constants between antibody and O6-methylguanine were also dependent on the sequence flanking the adduct, with the most rapidly repaired being those most easily bound to the antibody. It is suggested that the rate of repair is a reflection of the conformation of the oligomers containing O6-methylguanine. An unusual feature of DNA which is often associated with protein-DNA interactions is DNA curvature. A characteristic of curved DNA is that it has less electrophoretic mobility than normal DNA. In order to assess if alkylated adducts in DNA induce DNA curvature or flexibility, DNA duplexes containing O4-alkylthymine or O6-methylguanine were synthesized and self-ligated to form multimers with the alkylated bases out of phase (16 base-pairs apart) or in phase (21 base-pairs apart) with the helical repeat of DNA. All the sequences containing O4-alklylthymine migrated more slowly than expected in a non-denaturing polyacrylamide gel. In general the effect was seen when the alkylated base was out of phase or in phase with the helical repeat suggesting that the altered base-pair confers flexibility which is largely isotropic, i.e has no preferred direction, rather than anisotropic flexibility or bending. The effect of O4-methylthymine in the mobility of the oligonucleotides was much greater than that of O6-methylguanine and the effect of O4-ethylthymine slightly greater than that of O4-methylthymine. DNA duplexes containing O4-alkylT:A base-pairs were more retarded, and had lower thermal point (Tm) than DNA duplexes containing O4-alkylT:G base-pairs

AN ATTEMPT TO DEFINE CONTEXT AWARENESS IN MOBILE E-HEALTH ENVIRONMENTS

Nurses, doctors, physiotherapists, psychologists and other professionals or specialists come together to provide care to home residing patients, making continuous assessment, diagnosis and treatment possible beyond the walls of hospitals. Such teams of professionals are focused on each individual patient, and are virtual, i.e. they make decisions without being together physically, dynamically, i.e. professionals come and go as needed, and collaborate, as they combine their knowledge to provide effective care. Our system, coined DITIS, is a web based system that enables the effective management and collaboration of virtual healthcare teams and accessing medical information in a secure manner from a variety of mobile devices from anytime and anyplace, adapting the information according to various parameters like, user role, access right, device capabilities and wireless medium. This paper introduces the DITIS system, and identifies the needs and challenges of co-ordinated teams of multidisciplinary healthcare professionals (HCPs) functioning in a context awareness environment under the wireless environment. Pilo

Using BIP to reinforce correctness of resource-constrained IoT applications

International audienceIoT applications have either a sense-only or a sense-compute-actuate goal and they implement a capability to process and respond to multiple (external) events while performing computations. Existing IoT operating systems provide a versatile execution environment that adheres to the limitations of the interconnected resource-constrained devices. To reduce the development effort, applications are often built on top of RESTful web services, which can be shared and reused. However, the asynchronous communication between remote nodes is prone to event scheduling delays, which cannot be predicted and taken into account while programming the application. Moreover, to avoid long delays in message processing and communication due to packet collisions, the data transmission frequencies between the system's nodes have to carefully chosen. In general, even when appropriate debugging tools and simulators are available, it is still a hard challenge to guarantee the required functional and non-functional properties at the application and system levels. To this end, we focus on IoT applications for the Contiki OS and we introduce a model-based rigorous analysis approach using the BIP component framework. At the application level, we verify qualitative properties regarding service responsiveness, whereas at the system level we can validate qualitative and quantitative properties using statistical model checking. We present results for an application scenario running on a distributed system infrastructure with nodes executing the Contiki OS

The geographical dimension of income and consumption inequality

This paper aims at examining interpersonal income and consumption inequality within the Attica Metropolitan Region, which includes Athens, the largest metropolis of Greece. It also aims to make comparisons between Attica and the rest of the country. The analysis is based on income and consumption microdata from Greek Household Budget Surveys (HBS) over the period 2008-2019, encapsulating the period from the commencement of the economic crisis until the year before the outset of the COVID-19 pandemic. Results indicate that income inequalities are systematically higher than consumption inequalities. From a spatial comparative perspective, the results show that the Attica Metropolitan Region exhibits a higher degree of income and consumption inequality relative to the rest of the country. Furthermore, the economic crisis increased income inequality in Athens and in the rest of the country, while consumption expenditure inequality increased in the Athens metropolitan area only. Finally, the distance between socio-economic groups, which stands as a measure of the degree of social polarization, increased during the economic crisis. However, this does not hold true for consumption inequality. Overall, the analysis demonstrates the sensitivity of inequality outcomes to the selection of the welfare indicator (income or consumption), as well as a number of noticeable differences in inequality outcomes between the Metropolitan region of Attica and the rest of the country. The paper unveils facets of inequality which necessitate the implementation of more people and place-targeted policies aimed at more inclusive and balanced welfare conditions in metropolitan regions and across the country

Correct-by-Construction Web Service Architecture

Abstract—Service-Oriented Computing aims to facilitate devel-opment of large-scale applications out of loosely coupled services. The service architecture sets the framework for achieving cohe-rence and interoperability despite service autonomy and the hete-rogeneity in data representation and protocols. Service-Oriented Architectures are based on standardized service contracts, in order to infuse characteristic properties (stateless interactions, atomicity etc). However, contracts cannot ensure correctness of services if essential operational details are overlooked, as is usually the case. We introduce a modeling framework for the specification of Web Service architectures, in terms of formal operational semantics. Our approach aims to enable rigorous design of Web Services, based on the Behaviour Interaction Priorities (BIP) component framework and the principles of correctness-by-construction. We provide executable BIP models for SOAP-based and RESTful Web Services and for a service ar-chitecture with session replication. The architectures are treated as reusable design artifacts that may be composed, such that their characteristic properties are preserved