Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

Dialogic learning and interactive groups: an IMS LD template integrated in runtime systems

Dialogic learning and interactive groups have proved to be a useful methodological approach appliedin educational situations for lifelong adult learners. The principles of this approach stress theimportance of dialogue and equal participation also when designing the training activities. This paperadopts these principles as the basis for a configurable template that can be integrated in runtimesystems. The template is formulated as a meta-UoL which can be interpreted by IMS Learning Designplayers. This template serves as a guide to flexibly select and edit the activities at runtime (on the fly).The meta-UoL has been used successfully by a practitioner so as to create a real-life example, withpositive and encouraging results

Systems medicine and integrated care to combat chronic noncommunicable diseases

We propose an innovative, integrated, cost-effective health system to combat major non-communicable diseases (NCDs), including cardiovascular, chronic respiratory, metabolic, rheumatologic and neurologic disorders and cancers, which together are the predominant health problem of the 21st century. This proposed holistic strategy involves comprehensive patient-centered integrated care and multi-scale, multi-modal and multi-level systems approaches to tackle NCDs as a common group of diseases. Rather than studying each disease individually, it will take into account their intertwined gene-environment, socio-economic interactions and co-morbidities that lead to individual-specific complex phenotypes. It will implement a road map for predictive, preventive, personalized and participatory (P4) medicine based on a robust and extensive knowledge management infrastructure that contains individual patient information. It will be supported by strategic partnerships involving all stakeholders, including general practitioners associated with patient-centered care. This systems medicine strategy, which will take a holistic approach to disease, is designed to allow the results to be used globally, taking into account the needs and specificities of local economies and health systems.

Systems Medicine and Integrated Care to Combat Chronic Noncommunicable Diseases.

We propose an innovative, integrated, cost-effective health system to combat major non-communicable diseases (NCDs), including cardiovascular, chronic respiratory, metabolic, rheumatologic and neurologic disorders and cancers, which together are the predominant health problem of the 21st century. This proposed holistic strategy involves comprehensive patient-centered integrated care and multi-scale, multi-modal and multi-level systems approaches to tackle NCDs as a common group of diseases. Rather than studying each disease individually, it will take into account their intertwined gene-environment, socio-economic interactions and co-morbidities that lead to individual-specific complex phenotypes. It will implement a road map for predictive, preventive, personalized and participatory (P4) medicine based on a robust and extensive knowledge management infrastructure that contains individual patient information. It will be supported by strategic partnerships involving all stakeholders, including general practitioners associated with patient-centered care. This systems medicine strategy, which will take a holistic approach to disease, is designed to allow the results to be used globally, taking into account the needs and specificities of local economies and health systems.

Landscape Systems and Human Land-Use Interactions in Mediterranean Highlands and Littoral Plains during the Late Holocene: Integrated Analysis from the InterAmbAr Project (North-Eastern Catalonia).

The main goal of the InterAmbAr reseach project is to analyze the relationships between landscape systems and human land-use strategies on mountains and littoral plains from a long-term perspective. The study adopts a high resolution analysis of small-scale study areas located in the Mediterranean region of north-eastern Catalonia. The study areas are distributed along an altitudinal transect from the high mountain (above 2000m a.s.l.) to the littoral plain of Empordà (Fig. 1). High resolution interdisciplinary research has been carried out from 2010, based on the integration of palaeoenvironmental and archaeological data. The micro-scale approach is used to understand human-environmental relationships. It allows better understanding of the local-regional nature of environmental changes and the synergies between catchment-based systems, hydro-sedimentary regimes, human mobility, land-uses, human environments, demography, etc.

Preventive health care and payment systems to providers

Prevention has been a main issue of recent policy orientations in health care. This renews the interest on how different organizational designs and the definition of payment schemes to providers may affect the incentives to provide preventive health care. We present, both the normative and the positive analyses of the change from independent providers to integrated services. We show the evaluation of that change to depend on the particular way payment to providers is done. We focus on the externality resulting from referral decisions from primary to acute care providers. This makes our analysis complementary to most works in the literature allowing to address in a more direct way the issue of preventive health care.

Numerical simulation of combined heat transfer phenomena (conduction, convection, and radiation). Application to he optimisation of thermal systems

Thermal systems interchanging heat and mass by conduction, convection, radiation (solar and thermal ) occur in many engineering applications like energy storage by solar collectors, window glazing in buildings, refrigeration of plastic moulds, air handling units etc. Often these thermal systems are composed of various elements for example a building with wall, windows, rooms, etc. It would be of particular interest to have a modular thermal system which is formed by connecting different modules for the elements, flexibility to use and change models for individual elements, add or remove elements without changing the entire code. A numerical approach to handle the heat transfer and fluid flow in such systems helps in saving the full scale experiment time, cost and also aids optimisation of parameters of the system. In subsequent sections are presented a short summary of the work done until now on the orientation of the thesis in the field of numerical methods for heat transfer and fluid flow applications, the work in process and the future work.

A multi-purpose grammar generating a multi-scale integrated analysis of Laos

In this study we propose an application of the MuSIASEM approach which is used to provide an integrated analysis of Laos across different scales. With the term “integrated analysis across scales” we mean the generation of a series of packages of quantitative indicators, characterizing the performance of the socioeconomic activities performed in Laos when considering: (i) different hierarchical levels of organization (farming systems described at the level of household, rural villages, regions of Laos, the whole country level); and (ii) different dimensions of analysis (economic dimension, social dimension, ecological dimension, technical dimension). What is relevant in this application is that the information carried out by these different packages of indicators is integrated in a system of accounting which establishes interlinkages across these indicators. This is a essential feature to study sustainability trade-offs and to build more robust scenarios of possible changes. The multi-scale integrated representation presented in this study is based on secondary data (gathered in a three year EU project – SEAtrans and integrated by other available statistical sources) and it is integrated in GIS, when dealing with the spatial representation of Laos. However, even if we use data referring to Laos, the goal of this study is not that of providing useful information about a practical policy issue of Laos, but rather, to illustrate the possibility of using a multipurpose grammar to produce an integrated set of sustainability indicators at three different levels: (i) local; (ii) meso; (iii) macro level. The technical issue addressed is the simultaneous adoption of two multi-level matrices – one referring to a characterization of human activity over a set of different categories, and another referring to a characterization of land uses over the same set of categories. In this way, it becomes possible to explain the characteristics of Laos (an integrated set of indicators defining the performance of the whole country) in relation to the characteristics of the rural Laos and urban Laos. The characteristics of rural Laos, can be explained using the characteristics of three regions defined within Laos (Northern Laos, Central Laos and Southern Laos), which in turn can be defined (using an analogous package of indicators), starting from the characteristics of three main typologies of farming systems found in the regions.

Explicit methods for Hilbert modular forms

We exhibit algorithms to compute systems of Hecke eigenvalues for spaces of Hilbert modular forms over a totally real field. We provide many explicit examples as well as applications to modularity and Galois representations.

Biophysical requirements of power-supply systems: nuclear energy and fossil energy

The report presents a grammar capable of analyzing the process of production of electricity in modular elements for different power-supply systems, defined using semantic and formal categories. In this way it becomes possible to individuate similarities and differences in the process of production of electricity, and then measure and compare “apples” with “apples” and “oranges” with “oranges”. For instance, when comparing the various unit operations of the process of production of electricity with nuclear energy to the analogous unit operations of the process of production of fossil energy, we see that the various phases of the process are the same. The only difference is related to characteristics of the process associated with the generation of heat which are completely different in the two systems. As a matter of facts, the performance of the production of electricity from nuclear energy can be studied, by comparing the biophysical costs associated with the different unit operations taking place in nuclear and fossil power plants when generating process heat or net electricity. By adopting this approach, it becomes possible to compare the performance of the two power-supply systems by comparing their relative biophysical requirements for the phases that both nuclear energy power plants and fossil energy power plants have in common: (i) mining; (ii) refining/enriching; (iii) generating heat/electricity; (iv) handling the pollution/radioactive wastes. This report presents the evaluation of the biophysical requirements for the two powersupply systems: nuclear energy and fossil energy. In particular, the report focuses on the following requirements: (i) electricity; (ii) fossil-fuels, (iii) labor; and (iv) materials.

Interacting software-agents to support a kind of expert supervision systems

Expert supervision systems are software applications specially designed to automate process monitoring. The goal is to reduce the dependency on human operators to assure the correct operation of a process including faulty situations. Construction of this kind of application involves an important task of design and development in order to represent and to manipulate process data and behaviour at different degrees of abstraction for interfacing with data acquisition systems connected to the process. This is an open problem that becomes more complex with the number of variables, parameters and relations to account for the complexity of the process. Multiple specialised modules tuned to solve simpler tasks that operate under a co-ordination provide a solution. A modular architecture based on concepts of software agents, taking advantage of the integration of diverse knowledge-based techniques, is proposed for this purpose. The components (software agents, communication mechanisms and perception/action mechanisms) are based on ICa (Intelligent Control architecture), software middleware supporting the build-up of applications with software agent features

Improved earthquake response via simulation and integrated space- and ground-based technologies: the TREMOR proposal

Earthquakes occurring around the world each year cause thousands ofdeaths, millions of dollars in damage to infrastructure, and incalculablehuman suffering. In recent years, satellite technology has been asignificant boon to response efforts following an earthquake and itsafter-effects by providing mobile communications between response teamsand remote sensing of damaged areas to disaster management organizations.In 2007, an international team of students and professionals assembledduring theInternational Space University’s Summer Session Program in Beijing, Chinato examine how satellite and ground-based technology could be betterintegrated to provide an optimised response in the event of an earthquake.The resulting Technology Resources for Earthquake MOnitoring and Response(TREMOR) proposal describes an integrative prototype response system thatwill implement mobile satellite communication hubs providing telephone anddata links between response teams, onsite telemedicine consultation foremergency first-responders, and satellite navigation systems that willlocate and track emergency vehicles and guide search-and-rescue crews. Aprototype earthquake simulation system is also proposed, integratinghistorical data, earthquake precursor data, and local geomatics andinfrastructure information to predict the damage that could occur in theevent of an earthquake. The backbone of these proposals is a comprehensiveeducation and training program to help individuals, communities andgovernments prepare in advance. The TREMOR team recommends thecoordination of these efforts through a centralised, non-governmentalorganization.

The effects of poor financial information systems on the long term sustainability of local public services. Empirical evidence from the Catalan Municipalities

In this paper we describe the existence of financial illusion in public accountingand we comment on its effects for the future sustainability of local publicservices. We relate these features to the lack of incentives amongst publicmanagers for improving the financial reporting and thus management of publicassets. Financial illusion pays off for politicians and managers since it allowsfor larger public expenditure increases and managerial slack, these beingarguments in their utility functions. This preference is strengthen by the shorttime perspective of politically appointed public managers. Both factors runagainst public accountability. This hypothesis is tested for Spain by using anunique sample. We take data from around forty Catalan local authorities withpopulation above 20,000 for the financial years 1993-98. We build this databasis from the Catalan Auditing Office Reports in a way that it can be linkedto some other local social and economic variables in order to test ourassumptions. The results confirm that there is a statistical relationship between the financialillusion index (FI as constructed in the paper) and higher current expenditure.This reflects on important overruns and increases of the delay in payingsuppliers, as well as on a higher difficulties to face capital finance. Mechanismsfor FI creation have to do among other factors, with delays in paying suppliers(and thereafter higher future financial costs per unit of service), no adequateprovision for bad debts and lack of appropriate capital funding either forreposition or for new equipments. For this, it is crucial to monitor the way inwhich capital transfers are accounted in local public sheet balances. As a result,for most of the Municipalities we analyse, the funds for guaranteeing continuityand sustainability of public services provision are today at risk.Given managerial incentives at present in public institutions, we conclude thatpublic regulation recently enforced for assuring better information systems inlocal public management may not be enough to change the current state of affairs.

Rethinking study and management of agricultural systems for policy design

There is a concern that agriculture will no longer be able to meet, on a global scale, the growing demand for food. Facing such a challenge requires new patterns of thinking in the context of complexity and sustainability sciences. This paper, focused on the social dimension of the study and management of agricultural systems, suggests that rethinking the study of agricultural systems entails analyzing them as complex socio-ecological systems, as well as considering the differing thinking patterns of diverse stakeholders. The intersubjective nature of knowledge, as studied by different philosophical schools, needs to be better integrated into the study and management of agricultural systems than it is done so far, forcing us to accept that there are no simplistic solutions, and to seek a better understanding of the social dimension of agriculture. Different agriculture related problems require different policy and institutional approaches. Finally, the intersubjective nature of knowledge asks for the visualization of different framings and the power relations taking place in the decision-making process. Rethinking management of agricultural systems implies that policy making should be shaped by different principles: learning, flexibility, adaptation, scale-matching, participation, diversity enhancement and precaution hold the promise to significantly improve current standard management procedures.

Generic utilities in chronic obstructive pulmonary disease patients stratified according to different staging systems.

Background To determine generic utilities for Spanish chronic obstructive pulmonary disease (COPD) patients stratified by different classifications: GOLD 2007, GOLD 2013, GesEPOC 2012 and BODEx index. Methods Multicentre, observational, cross-sectional study. Patients were aged ≥40 years, with spirometrically confirmed COPD. Utility values were derived from EQ-5D-3 L. Means, standard deviations (SD), medians and interquartile ranges (IQR) were computed based on the different classifications. Differences in median utilities between groups were assessed by non-parametric tests. Results 346 patients were included, of which 85.5% were male with a mean age of 67.9 (SD = 9.7) years and a mean duration of COPD of 7.6 (SD = 5.8) years; 80.3% were ex-smokers and the mean smoking history was 54.2 (SD = 33.2) pack-years. Median utilities (IQR) by GOLD 2007 were 0.87 (0.22) for moderate; 0.80 (0.26) for severe and 0.67 (0.42) for very-severe patients (p < 0.001 for all comparisons). Median utilities by GOLD 2013 were group A: 1.0 (0.09); group B: 0.87 (0.13); group C: 1.0 (0.16); group D: 0.74 (0.29); comparisons were statistically significant (p < 0.001) except A vs C. Median utilities by GesEPOC phenotypes were 0.84 (0.33) for non exacerbator; 0.80 (0.26) for COPD-asthma overlap; 0.71 (0.62) for exacerbator with emphysema; 0.72 (0.57) for exacerbator with chronic bronchitis (p < 0.001). Comparisons between patients with or without exacerbations and between patients with COPD-asthma overlap and exacerbator with chronic bronchitis were statistically-significant (p < 0.001). Median utilities by BODEx index were: group 02: 0.89 (0.20); group 34: 0.80 (0.27); group 56: 0.67 (0.29); group 79: 0.41 (0.31). All comparisons were significant (p < 0.001) except between groups 34 and 56. Conclusion Irrespective of the classification used utilities were associated to disease severity. Some clinical phenotypes were associated with worse utilities, probably related to a higher frequency of exacerbations. GOLD 2007 guidelines and BODEx index better discriminated patients with a worse health status than GOLD 2013 guidelines, while GOLD 2013 guidelines were better able to identify a smaller group of patients with the best health.