EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

Simulation tools for the analysis of single electronic systems

Developments in theory and experiment have raised the prospect of an electronic technology based on the discrete nature of electron tunnelling through a potential barrier. This thesis deals with novel design and analysis tools developed to study such systems. Possible devices include those constructed from ultrasmall normal tunnelling junctions. These exhibit charging effects including the Coulomb blockade and correlated electron tunnelling. They allow transistor-like control of the transfer of single carriers, and present the prospect of digital systems operating at the information theoretic limit. As such, they are often referred to as single electronic devices. Single electronic devices exhibit self quantising logic and good structural tolerance. Their speed, immunity to thermal noise, and operating voltage all scale beneficially with junction capacitance. For ultrasmall junctions the possibility of room temperature operation at sub picosecond timescales seems feasible. However, they are sensitive to external charge; whether from trapping-detrapping events, externally gated potentials, or system cross-talk. Quantum effects such as charge macroscopic quantum tunnelling may degrade performance. Finally, any practical system will be complex and spatially extended (amplifying the above problems), and prone to fabrication imperfection. This summarises why new design and analysis tools are required. Simulation tools are developed, concentrating on the basic building blocks of single electronic systems; the tunnelling junction array and gated turnstile device. Three main points are considered: the best method of estimating capacitance values from physical system geometry; the mathematical model which should represent electron tunnelling based on this data; application of this model to the investigation of single electronic systems. (DXN004909)

Integration of Social Concerns in Collaborative Logistics and Transportation Networks

Part 21: Mobility and Logistics

The right hippocampus leads the bilateral integration of gamma-parsed lateralized information

It is unclear whether the two hippocampal lobes convey similar or different activities and how they cooperate. Spatial discrimination of electric fields in anesthetized rats allowed us to compare the pathway-specific field potentials corresponding to the gamma-paced CA3 output (CA1 Schaffer potentials) and CA3 somatic inhibition within and between sides. Bilateral excitatory Schaffer gamma waves are generally larger and lead from the right hemisphere with only moderate covariation of amplitude, and drive CA1 pyramidal units more strongly than unilateral waves. CA3 waves lock to the ipsilateral Schaffer potentials, although bilateral coherence was weak. Notably, Schaffer activity may run laterally, as seen after the disruption of the connecting pathways. Thus, asymmetric operations promote the entrainment of CA3-autonomous gamma oscillators bilaterally, synchronizing lateralized gamma strings to converge optimally on CA1 targets. The findings support the view that interhippocampal connections integrate different aspects of information that flow through the left and right lobes.

Building an Ontology of Product/Service-Systems: Using a Maritime Case Study to Elicit Classifications and Characteristics

Part 4: Transition Towards Product-Service Systems

Real-time load-side control of electric power systems

Two trends are emerging from modern electric power systems: the growth of renewable (e.g., solar and wind) generation, and the integration of information technologies and advanced power electronics. The former introduces large, rapid, and random fluctuations in power supply, demand, frequency, and voltage, which become a major challenge for real-time operation of power systems. The latter creates a tremendous number of controllable intelligent endpoints such as smart buildings and appliances, electric vehicles, energy storage devices, and power electronic devices that can sense, compute, communicate, and actuate. Most of these endpoints are distributed on the load side of power systems, in contrast to traditional control resources such as centralized bulk generators. This thesis focuses on controlling power systems in real time, using these load side resources. Specifically, it studies two problems.

(1) Distributed load-side frequency control: We establish a mathematical framework to design distributed frequency control algorithms for flexible electric loads. In this framework, we formulate a category of optimization problems, called optimal load control (OLC), to incorporate the goals of frequency control, such as balancing power supply and demand, restoring frequency to its nominal value, restoring inter-area power flows, etc., in a way that minimizes total disutility for the loads to participate in frequency control by deviating from their nominal power usage. By exploiting distributed algorithms to solve OLC and analyzing convergence of these algorithms, we design distributed load-side controllers and prove stability of closed-loop power systems governed by these controllers. This general framework is adapted and applied to different types of power systems described by different models, or to achieve different levels of control goals under different operation scenarios. We first consider a dynamically coherent power system which can be equivalently modeled with a single synchronous machine. We then extend our framework to a multi-machine power network, where we consider primary and secondary frequency controls, linear and nonlinear power flow models, and the interactions between generator dynamics and load control.

(2) Two-timescale voltage control: The voltage of a power distribution system must be maintained closely around its nominal value in real time, even in the presence of highly volatile power supply or demand. For this purpose, we jointly control two types of reactive power sources: a capacitor operating at a slow timescale, and a power electronic device, such as a smart inverter or a D-STATCOM, operating at a fast timescale. Their control actions are solved from optimal power flow problems at two timescales. Specifically, the slow-timescale problem is a chance-constrained optimization, which minimizes power loss and regulates the voltage at the current time instant while limiting the probability of future voltage violations due to stochastic changes in power supply or demand. This control framework forms the basis of an optimal sizing problem, which determines the installation capacities of the control devices by minimizing the sum of power loss and capital cost. We develop computationally efficient heuristics to solve the optimal sizing problem and implement real-time control. Numerical experiments show that the proposed sizing and control schemes significantly improve the reliability of voltage control with a moderate increase in cost.

Applicability of an assessment model for healthcare information systems in a public hospital

Assessment processes are essential to guarantee quality and continuous improvement of software in healthcare, as they measure software attributes in their lifecycle, verify the degree of alignment between the software and its objectives and identify unpredicted events. This article analyses the use of an assessment model based on software metrics for three healthcare information systems from a public hospital that provides secondary and tertiary care in the region of Ribeirão Preto. Compliance with the metrics was investigated using questionnaires in guided interviews of the system analysts responsible for the applications. The outcomes indicate that most of the procedures specified in the model can be adopted to assess the systems that serves the organization, particularly in the attributes of compatibility, reliability, safety, portability and usability.

Integration of process planning and scheduling using mobile-agent based approach in a networked manufacturing environment

Effective and efficient implementation of intelligent and/or recently emerged networked manufacturing systems require an enterprise level integration. The networked manufacturing offers several advantages in the current competitive atmosphere by way to reduce, by shortening manufacturing cycle time and maintaining the production flexibility thereby achieving several feasible process plans. The first step in this direction is to integrate manufacturing functions such as process planning and scheduling for multi-jobs in a network based manufacturing system. It is difficult to determine a proper plan that meets conflicting objectives simultaneously. This paper describes a mobile-agent based negotiation approach to integrate manufacturing functions in a distributed manner; and its fundamental framework and functions are presented. Moreover, ontology has been constructed by using the Protégé software which possesses the flexibility to convert knowledge into Extensible Markup Language (XML) schema of Web Ontology Language (OWL) documents. The generated XML schemas have been used to transfer information throughout the manufacturing network for the intelligent interoperable integration of product data models and manufacturing resources. To validate the feasibility of the proposed approach, an illustrative example along with varied production environments that includes production demand fluctuations is presented and compared the proposed approach performance and its effectiveness with evolutionary algorithm based Hybrid Dynamic-DNA (HD-DNA) algorithm. The results show that the proposed scheme is very effective and reasonably acceptable for integration of manufacturing functions.

Constraint-Informed Information Systems in Space Management Utilization

Declarative techniques such as Constraint Programming can be very effective in modeling and assisting management decisions. We present a method for managing university classrooms which extends the previous design of a Constraint-Informed Information System to generate the timetables while dealing with spatial resource optimization issues. We seek to maximize space utilization along two dimensions: classroom use and occupancy rates. While we want to maximize the room use rate, we still need to satisfy the soft constraints which model students’ and lecturers’ preferences. We present a constraint logic programming-based local search method which relies on an evaluation function that combines room utilization and timetable soft preferences. Based on this, we developed a tool which we applied to the improvement of classroom allocation in a University. Comparing the results to the current timetables obtained without optimizing space utilization, the initial versions of our tool manages to reach a 30% improvement in space utilization, while preserving the quality of the timetable, both for students and lecturers.

10th European Conference on Information Systems Management

The 10th European Conference on Information Systems Management is being held at The University of Evora, Portugal on the 8 /9 September 2016. The Conference Chair is Paulo Silva and the Programme Chairs are Prof. Rui Quaresma and Prof. António Guerreiro. ECISM provides an opportunity for individuals researching and working in the broad field of information systems management, including IT evaluation to come together to exchange ideas and discuss current research in the field. This has developed into a particularly important forum for the present era, where the modern challenges of managing information and evaluating the effectiveness of related technologies are constantly evolving in the world of Big Data and Cloud Computing. We hope that this year’s conference will provide you with plenty of opportunities to share your expertise with colleagues from around the world. The keynote speakers for the Conference are Carlos Zorrinho from the Portuguese Delegation and Isabel Ramos from University of Minho, Portugal. ECISM 2016 received an initial submission of 84 abstracts. After the double blind peer review process 25 aca demic papers, 7 PhD research papers, 3 Masters research paper and 5 work in progress papers have been ac cepted for publication in these Conference Proceedings. These papers represent research from around the world, including Belgium, Brazil, China, Czech Republic, Kazakhstan, Malaysia, New Zealand, Norway, Oman, Poland, Portugal, South Africa, Sweden, The Netherlands, UK and Vietnam.

Advances in integration of photovoltaic power and energy production in practical systems

This thesis presents advances in integration of photovoltaic (PV) power and energy in practical systems, such as existing power plants in buildings or directly integrated in the public electrical grid. It starts by providing an analyze of the current state of PV power and some of its limitations. The work done in this thesis begins by providing a model to compute mutual shading in large PV plants, and after provides a study of the integration of a PV plant in a biogas power plant. The remainder sections focus on the work done for project PVCROPS, which consisted on the construction and operation of two prototypes composed of a PV system and a novel battery connected to a building and to the public electrical grid. These prototypes were then used to test energy management strategies and validate the suitability of the two advanced batteries (a lithium-ion battery and a vanadium redox ow battery) for households (BIPV) and PV plants. This thesis is divided in 7 chapters: Chapter 1 provides an introduction to explain and develop the main research questions studied for this thesis; Chapter 2 presents the development of a ray-tracing model to compute shading in large PV elds (with or without trackers); Chapter 3 shows the simulation of hybridizing a biogas plant with a PV plant, using biogas as energy storage; Chapters 4 and 5 present the construction, programming, and initial operation of both prototypes (Chapter 4), EMS testing oriented to BIPV systems (Chapter 5). Finally, Chapters 6 provides some future lines of investigation that can follow this thesis, and Chapter 7 shows a synopsis of the main conclusions of this work; Resumo: Avanços na integracão de potência fotovoltaica e producão de energia em sistemas práticos Esta tese apresenta avanços na integração de potência e energia fotovoltaica (PV) em sistemas práticos, tais como centrais existentes ou a rede eléctrica pública. Come ça por analisar o estado corrente do fotovoltaico no mundo e aborda algumas das suas limitações. O trabalho feito para esta tese de doutoramento começou pelo desenvolvimento de um modelo para calcular os sombreamentos que ocorrem em grandes campos fotovoltaicos, e depois apresenta um estudo sobre a integração um sistema fotovoltaico em uma central eléctrica a bióg as. As ultimas secções da tese focam-se no trabalho feito para o projecto PVCROPS, que consistiu na construção e operação de dois demonstratores, cada um formado por um sistema fotovoltaico e bateria conectados a um edíficio e a rede eléctrica pública. Estes protótipos foram posteriormente utilizados para testar estratégias de gestão de energia (EMS) e para validar a operação de duas baterias avançadas (bateria de Iões de Li tio e bateria de Fluxo Redox de Van adio) e a sua utiliza ção para habitações e centrais PV. A tese está dividida em 7 capitulos: O capitulo 1 apresenta uma introdução para explicar e desenvolver as principais questões que foram investigadas nesta tese; O capitulo 2 mostra o desenvolvimento de um modelo baseado em traçados de raios para calcular sombreamentos mútuos em grandes centrais PV (com e sem seguidores); O capitulo 3 mostra a simulação da hibridização de uma central electrica a biogas com uma central PV, e utilizando o biógas como armazenamento de energia. Os capitulos 4 e 5 apresentam a construção, programação e operação inicial dos dois demonstradores (Capitúlo 4), o teste de EMS orientadas para sistemas PV em habitações (Capítulo 5). Finalmente, o capítulo 6 sugere algumas futuras linhas de investigação que poderão seguir esta tese, e o Capítulo 7 faz uma sinopse das principais conclusões deste trabalho.

Geographic Information Systems (GIS) in Assessing Dental Health

The present study investigated the distribution profile of dental caries and its association with areas of social deprivation at the individual and contextual level. The cluster sample consisted of 1,002 12-year-old schoolchildren from Piracicaba, SP, Brazil. The DMFT Index was used for dental caries and the Care Index was used to determine access to dental services. On the individual level, variables were associated with a better oral status. On the contextual level, areas were not associated with oral status. However, maps enabled determining that the central districts have better social and oral conditions than the deprived outlying districts.

Decoherence-free evolution of time-dependent superposition states of two-level systems and thermal effects

In this paper we detail some results advanced in a recent letter [Prado et al., Phys. Rev. Lett. 102, 073008 (2009).] showing how to engineer reservoirs for two-level systems at absolute zero by means of a time-dependent master equation leading to a nonstationary superposition equilibrium state. We also present a general recipe showing how to build nonadiabatic coherent evolutions of a fermionic system interacting with a bosonic mode and investigate the influence of thermal reservoirs at finite temperature on the fidelity of the protected superposition state. Our analytical results are supported by numerical analysis of the full Hamiltonian model.

New perspectives on the processing and release of public information

This article discusses issues related to the organization and reception of information in the context of services and public information systems driven by technology. It stems from the assumption that in a ""technologized"" society, the distance between users and information is almost always of cognitive and socio-cultural nature, a product of our effort to design communication. In this context, we favor the approach of the information sign, seeking to answer how a documentary message turns into information, i.e. a structure recognized as socially useful. Observing the structural, cognitive and communicative aspects of the documentary message, based on Documentary Linguistics, Terminology, as well as on Textual Linguistics, the policy of knowledge management and innovation of the Government of the State of Sao Paulo is analyzed, which authorizes the use of Web 2.0, also questioning to what extent this initiative represents innovation in the environment of libraries.

Information from managing information systems as a fundamental element to support decision-making in hospitals

This article deals with the activity of defining information of hospital systems as fundamental for choosing the type of information systems to be used and also the organizational level to be supported. The use of hospital managing information systems improves the user`s decision -making process by allowing control report generation and following up the procedures made in the hospital as well.