Achilleas Achilleos

Context modelling and a context-aware framework for pervasive service creation: A model-driven approach

Pervasive service creation entails a complex process that involves a diversity of development aspects. Context-awareness is an important facet of pervasive service creation, which deals with the acquisition, rendering, representation and utilisation of context information. In this paper we tackle context-awareness at the application level dealing with the representation and utilisation of context by services. We propose a model-driven approach that facilitates the creation of a context modelling framework and simplifies the design and implementation of pervasive services. To conclude, we demonstrate the benefits of our model-driven approach via the creation of a pervasive museum service and its evaluation using selected software metrics.

Cell-Free DNA Analysis of Targeted Genomic Regions in Maternal Plasma for Non-Invasive Prenatal Testing of Trisomy 21, Trisomy 18, Trisomy 13, and Fetal Sex

BACKGROUND There is great need for the development of highly accurate cost effective technologies that could facilitate the widespread adoption of noninvasive prenatal testing (NIPT). METHODS We developed an assay based on the targeted analysis of cell-free DNA for the detection of fetal aneuploidies of chromosomes 21, 18, and 13. This method enabled the capture and analysis of selected genomic regions of interest. An advanced fetal fraction estimation and aneuploidy determination algorithm was also developed. This assay allowed for accurate counting and assessment of chromosomal regions of interest. The analytical performance of the assay was evaluated in a blind study of 631 samples derived from pregnancies of at least 10 weeks of gestation that had also undergone invasive testing. RESULTS Our blind study exhibited 100% diagnostic sensitivity and specificity and correctly classified 52/52 (95% CI, 93.2%-100%) cases of trisomy 21, 16/16 (95% CI, 79.4%-100%) cases of trisomy 18, 5/5 (95% CI, 47.8%-100%) cases of trisomy 13, and 538/538 (95% CI, 99.3%-100%) normal cases. The test also correctly identified fetal sex in all cases (95% CI, 99.4%-100%). One sample failed prespecified assay quality control criteria, and 19 samples were nonreportable because of low fetal fraction. CONCLUSIONS The extent to which free fetal DNA testing can be applied as a universal screening tool for trisomy 21, 18, and 13 depends mainly on assay accuracy and cost. Cell-free DNA analysis of targeted genomic regions in maternal plasma enables accurate and cost-effective noninvasive fetal aneuploidy detection, which is critical for widespread adoption of NIPT.

Pervasive Service Creation using a Model Driven Petri Net Based Approach

Service creation is a complex process that involves service analysis design, implementation and testing. Traditionally, the service is validated at the late stage of testing. This increases development costs since any necessary amendments would require an iterative improving cycle on service design and implementation; until the desired result is eventually reached. This paper proposes a service creation methodology and tooling with a twofold contribution: (i) based on its design, a service is validated early on and prior to implementation, (ii) the service code is automatically generated out of the validated service designs. To achieve this, our approach integrates model-driven architecture (MDA) with Petri Nets (PN). MDA is used to define the (i) Information, (ii) Service Oriented Petri Net (SOPN) and (iii) User Interface modelling languages, which support the service design and implementation phases. Petri Nets facilitate the service validation phase through the use of the SOPN language. By merging the two techniques we obtain a systematic and cost-effective approach for the creation of pervasive services. Concluding the methodology is applied in practice for the creation of a Flight Itinerary booking service.

Developing win-win solutions for virtual placements in informatics: the VALS case

The placements and internships are one of the main paths to get professional background and some skills for students, especially in areas like informatics and computer sciences. The European-funded VALS project tries to promote the virtual placements and establish a new initiative in virtual placements called Semester of Code. This initiative binds higher education institutions, students, companies, foundations and Open Source projects in order to create virtual placements and solve needs that they have in relation with those placements. This paper introduces some projects about virtual placements that other institutions and companies perform, also the paper describes the needs, opinions and considerations about the virtual placements for each stakeholder involved in the placements, to finally explain the design decisions and actions behind the Semester of Code, and how they are intended to get better virtual placements and successful results.

A Model Driven Approach to Generate Service Creation Environments

The creation of services is a complex activity that involves several tasks. Furthermore this complexity is augmented by the fact that supporting service creation environments are technology-specific. Consequently a technology-independent approach and framework are required to generate service creation environments and drive service creation. In this paper we present such an approach and a generic framework for supporting service creation. The approach realizes service creation via the phases of: (i) domain specific language definition, (ii) model definition and validation, (iii) model-to-model transformation and (iv) model-to-code generation. Each phase maps to a corresponding phase in service creation starting from service analysis to service implementation. The applicability of the approach and its accompanying framework is demonstrated via an example scenario that illustrates the automatic generation of a service creation environment for an online survey system.

An open source domain-specific tools framework to support model driven development of OSS

Telecommunications companies undergo massive transformations which reflect onto exacting requirements for controlling the costs of new Operation Support Systems (OSS) development and integration. This calls for the adoption of new approaches, which improve agility and reusability. Model Drive Development (MDD), as specified by OMG, can drastically tackle these issues and has, therefore, attracted the interest of the telecommunications industry. Equally important is the Open Source paradigm. For MDD to gain wide industrial adoption, tools should be available to facilitate the OSS development process. In this paper, we specify requirements MDD tools should meet for effective application of the approach. An extensive survey is then carried out to evaluate existing meta-modelling frameworks over the identified tools requirements. Eventually, we present the Integrated Eclipse Model driven Environment (IEME), which comprises a unified environment of bundled Eclipse-based MDD facilities that also supports the automatic generation of domain-specific tools.

A model-driven framework for developing web service oriented applications

The advancements made in terms of the capabilities of mobile devices have shifted the interest of service engineering towards frameworks that are able to deliver applications rapidly and efficiently. The development of services that can be fully functional in mobile environments and operable on a variety of devices is an important and complex task for the research community. In this work, we propose a Model-Driven Web Service oriented framework that combines Model-Driven Engineering (MDE) with Web Services to automate the development of platform-specific web-based applications. The importance of this work is revealed through a case study that involves modelling and generation of a representative Web Service oriented mobile application.

Targeted capture enrichment assay for non-invasive prenatal testing of large and small size sub-chromosomal deletions and duplications

Noninvasive prenatal testing (NIPT) using whole genome and targeted sequencing has become increasingly accepted for clinical detection of Trisomy 21 and sex chromosome aneuploidies. Few studies have shown that sub-chromosomal deletions or duplications associated with genetic syndromes can also be detected in the fetus noninvasively. There are still limitations on these methodologies such as the detection of variants of unknown clinical significance, high number of false positives, and difficulties to detect small aberrations. We utilized a recently developed targeted sequencing approach for the development of a NIPT assay, for large and small size deletions/duplications, which overcomes these existing limitations. Artificial pregnancies with microdeletion/microduplication syndromes were created by spiking DNA from affected samples into cell free DNA (cfDNA) from non-pregnant samples. Unaffected spiked samples and normal pregnancies were used as controls. Target Capture Sequences (TACS) for seven syndromes were designed and utilized for targeted capture enrichment followed by sequencing. Data was analyzed using a statistical pipeline to identify deletions or duplications on targeted regions. Following the assay development a proof of concept study using 33 normal pregnancies, 21 artificial affected and 17 artificial unaffected pregnancies was carried out to test the sensitivity and specificity of the assay. All 21 abnormal spiked-in samples were correctly classified as subchromosomal aneuploidies while the 33 normal pregnancies or 17 normal spiked-in samples resulted in a false positive result. We have developed an NIPT assay for the detection of sub-chromosomal deletions and duplications using the targeted capture enrichment technology. This assay demonstrates high accuracy, high read depth of the genomic region of interest, and can identify deletions/duplications as small as 0.5 Mb. NIPT of fetal microdeletion/microduplication syndromes can be of enormous benefit in the management of pregnancies at risk both for prospective parents and health care providers.

Model-Based Tumor Growth Dynamics and Therapy Response in a Mouse Model of De Novo Carcinogenesis

Tumorigenesis is a complex, multistep process that depends on numerous alterations within the cell and contribution from the surrounding stroma. The ability to model macroscopic tumor evolution with high fidelity may contribute to better predictive tools for designing tumor therapy in the clinic. However, attempts to model tumor growth have mainly been developed and validated using data from xenograft mouse models, which fail to capture important aspects of tumorigenesis including tumor-initiating events and interactions with the immune system. In the present study, we investigate tumor growth and therapy dynamics in a mouse model of de novo carcinogenesis that closely recapitulates tumor initiation, progression and maintenance in vivo. We show that the rate of tumor growth and the effects of therapy are highly variable and mouse specific using a Gompertz model to describe tumor growth and a two-compartment pharmacokinetic/ pharmacodynamic model to describe the effects of therapy in mice treated with 5-FU. We show that inter-mouse growth variability is considerably larger than intra-mouse variability and that there is a correlation between tumor growth and drug kill rates. Our results show that in vivo tumor growth and regression in a double transgenic mouse model are highly variable both within and between subjects and that mathematical models can be used to capture the overall characteristics of this variability. In order for these models to become useful tools in the design of optimal therapy strategies and ultimately in clinical practice, a subject-specific modelling strategy is necessary, rather than approaches that are based on the average behavior of a given subject population which could provide erroneous results.

Virtual Placements Management Process Supported by Technology: Proposal and First Results of the Semester of Code

This paper explains the Virtual Alliances for Learning Society European Project technological approach to support a virtual placements management process. Also, this paper shows the first results of the practical part of the project, the Semester of Code, explaining the detected problems, the issues, the challenges, and some actions to improve the development of these kinds of virtual placements programs. In order to allow the readers to better comprehend the approach and its results, this paper also describes three of the main virtual placements programs around the world, regarding both their organization and technological approach.