Preliminary Overview over Requirements Regarding Tools and Methods Derived from LUDA Cases

LUDA is a research project of Key Action 4 "City of Tomorrow & Cultural Heritage" of the programme "Energy, Environment and Sustainable Development" within the Fifth Framework Programme of the European Commission

Data analysis tools and methods for DNA microarray and high-throughput sequencing data

The recent rapid development of biotechnological approaches has enabled the production of large whole genome level biological data sets. In order to handle thesedata sets, reliable and efficient automated tools and methods for data processingand result interpretation are required. Bioinformatics, as the field of studying andprocessing biological data, tries to answer this need by combining methods and approaches across computer science, statistics, mathematics and engineering to studyand process biological data. The need is also increasing for tools that can be used by the biological researchers themselves who may not have a strong statistical or computational background, which requires creating tools and pipelines with intuitive user interfaces, robust analysis workflows and strong emphasis on result reportingand visualization. Within this thesis, several data analysis tools and methods have been developed for analyzing high-throughput biological data sets. These approaches, coveringseveral aspects of high-throughput data analysis, are specifically aimed for gene expression and genotyping data although in principle they are suitable for analyzing other data types as well. Coherent handling of the data across the various data analysis steps is highly important in order to ensure robust and reliable results. Thus,robust data analysis workflows are also described, putting the developed tools andmethods into a wider context. The choice of the correct analysis method may also depend on the properties of the specific data setandthereforeguidelinesforchoosing an optimal method are given. The data analysis tools, methods and workflows developed within this thesis have been applied to several research studies, of which two representative examplesare included in the thesis. The first study focuses on spermatogenesis in murinetestis and the second one examines cell lineage specification in mouse embryonicstem cells.

Tools and methods for the quality assurance of force platforms in human movement analysis

The human movement analysis (HMA) aims to measure the abilities of a subject to stand or to walk. In the field of HMA, tests are daily performed in research laboratories, hospitals and clinics, aiming to diagnose a disease, distinguish between disease entities, monitor the progress of a treatment and predict the outcome of an intervention [Brand and Crowninshield, 1981; Brand, 1987; Baker, 2006]. To achieve these purposes, clinicians and researchers use measurement devices, like force platforms, stereophotogrammetric systems, accelerometers, baropodometric insoles, etc. This thesis focus on the force platform (FP) and in particular on the quality assessment of the FP data. The principal objective of our work was the design and the experimental validation of a portable system for the in situ calibration of FPs. The thesis is structured as follows: Chapter 1. Description of the physical principles used for the functioning of a FP: how these principles are used to create force transducers, such as strain gauges and piezoelectrics transducers. Then, description of the two category of FPs, three- and six-component, the signals acquisition (hardware structure), and the signals calibration. Finally, a brief description of the use of FPs in HMA, for balance or gait analysis. Chapter 2. Description of the inverse dynamics, the most common method used in the field of HMA. This method uses the signals measured by a FP to estimate kinetic quantities, such as joint forces and moments. The measures of these variables can not be taken directly, unless very invasive techniques; consequently these variables can only be estimated using indirect techniques, as the inverse dynamics. Finally, a brief description of the sources of error, present in the gait analysis. Chapter 3. State of the art in the FP calibration. The selected literature is divided in sections, each section describes: systems for the periodic control of the FP accuracy; systems for the error reduction in the FP signals; systems and procedures for the construction of a FP. In particular is detailed described a calibration system designed by our group, based on the theoretical method proposed by ?. This system was the “starting point” for the new system presented in this thesis. Chapter 4. Description of the new system, divided in its parts: 1) the algorithm; 2) the device; and 3) the calibration procedure, for the correct performing of the calibration process. The algorithm characteristics were optimized by a simulation approach, the results are here presented. In addiction, the different versions of the device are described. Chapter 5. Experimental validation of the new system, achieved by testing it on 4 commercial FPs. The effectiveness of the calibration was verified by measuring, before and after calibration, the accuracy of the FPs in measuring the center of pressure of an applied force. The new system can estimate local and global calibration matrices; by local and global calibration matrices, the non–linearity of the FPs was quantified and locally compensated. Further, a non–linear calibration is proposed. This calibration compensates the non– linear effect in the FP functioning, due to the bending of its upper plate. The experimental results are presented. Chapter 6. Influence of the FP calibration on the estimation of kinetic quantities, with the inverse dynamics approach. Chapter 7. The conclusions of this thesis are presented: need of a calibration of FPs and consequential enhancement in the kinetic data quality. Appendix: Calibration of the LC used in the presented system. Different calibration set–up of a 3D force transducer are presented, and is proposed the optimal set–up, with particular attention to the compensation of non–linearities. The optimal set–up is verified by experimental results.

Development of advanced tools and methods for the assessment and management of risk due to atypical major accident scenarios

Proper hazard identification has become progressively more difficult to achieve, as witnessed by several major accidents that took place in Europe, such as the Ammonium Nitrate explosion at Toulouse (2001) and the vapour cloud explosion at Buncefield (2005), whose accident scenarios were not considered by their site safety case. Furthermore, the rapid renewal in the industrial technology has brought about the need to upgrade hazard identification methodologies. Accident scenarios of emerging technologies, which are not still properly identified, may remain unidentified until they take place for the first time. The consideration of atypical scenarios deviating from normal expectations of unwanted events or worst case reference scenarios is thus extremely challenging. A specific method named Dynamic Procedure for Atypical Scenarios Identification (DyPASI) was developed as a complementary tool to bow-tie identification techniques. The main aim of the methodology is to provide an easier but comprehensive hazard identification of the industrial process analysed, by systematizing information from early signals of risk related to past events, near misses and inherent studies. DyPASI was validated on the two examples of new and emerging technologies: Liquefied Natural Gas regasification and Carbon Capture and Storage. The study broadened the knowledge on the related emerging risks and, at the same time, demonstrated that DyPASI is a valuable tool to obtain a complete and updated overview of potential hazards. Moreover, in order to tackle underlying accident causes of atypical events, three methods for the development of early warning indicators were assessed: the Resilience-based Early Warning Indicator (REWI) method, the Dual Assurance method and the Emerging Risk Key Performance Indicator method. REWI was found to be the most complementary and effective of the three, demonstrating that its synergy with DyPASI would be an adequate strategy to improve hazard identification methodologies towards the capture of atypical accident scenarios.

Addressing undernutrition in external assistance: an integrated approach through sectors and aid modalities. Tools and Methods Series: reference document no° 13, September 2011.

doi:10.2783/51319

A theologian's workshop, tools, and methods.

Mode of access: Internet.

Introduction: digital methods and tools for historical research

As an introduction to a series of articles focused on the exploration of particular tools and/or methods to bring together digital technology and historical research, the aim of this paper is mainly to highlight and discuss in what measure those methodological approaches can contribute to improve analytical and interpretative capabilities available to historians. In a moment when the digital world present us with an ever-increasing variety of tools to perform extraction, analysis and visualization of large amounts of text, we thought it would be relevant to bring the digital closer to the vast historical academic community. More than repeating an idea of digital revolution introduced in the historical research, something recurring in the literature since the 1980s, the aim was to show the validity and usefulness of using digital tools and methods, as another set of highly relevant tools that the historians should consider. For this several case studies were used, combining the exploration of specific themes of historical knowledge and the development or discussion of digital methodologies, in order to highlight some changes and challenges that, in our opinion, are already affecting the historians' work, such as a greater focus given to interdisciplinarity and collaborative work, and a need for the form of communication of historical knowledge to become more interactive.

The new metal worker pattern book; a complete course of instruction in the modern methods of developing and cutting the patterns for sheet metal work, giving the principles underlying practically every problem that is likely to come up in practice and explaining the selection and use of drawing tools and linear and geometrical drawing so clearly that one, who has had no previous knowledge of arithmetic or drawing, may understand these essentials and apply them in using the 253 problems in the development of patterns by the parallel line, conical or flaring, and triangulation systems.

Mode of access: Internet.

The mechanician, a treatise on the construction and manipulation of tools, for the use and instruction of young engineers and scientific amateurs; comprising the arts of blacksmithing and forging; the construction and manufacture of hand tools, and the various methods of using and grinding them; description of hand and machine processes; turning and screw cutting; and the various details of setting out work incidental to the mechanical engineer's and machinist's art.

Mode of access: Internet.

Tools and techniques to study ligand-receptor interactions and receptor activation by TNF superfamily members.

Ligands and receptors of the TNF superfamily are therapeutically relevant targets in a wide range of human diseases. This chapter describes assays based on ELISA, immunoprecipitation, FACS, and reporter cell lines to monitor interactions of tagged receptors and ligands in both soluble and membrane-bound forms using unified detection techniques. A reporter cell assay that is sensitive to ligand oligomerization can identify ligands with high probability of being active on endogenous receptors. Several assays are also suitable to measure the activity of agonist or antagonist antibodies, or to detect interactions with proteoglycans. Finally, self-interaction of membrane-bound receptors can be evidenced using a FRET-based assay. This panel of methods provides a large degree of flexibility to address questions related to the specificity, activation, or inhibition of TNF-TNF receptor interactions in independent assay systems, but does not substitute for further tests in physiologically relevant conditions.

Strategic Development of Electricity Distribution Networks – Concept and Methods

Strategic development of distribution networks plays a key role in the asset management in electricity distribution companies. Owing to the capital-intensive nature of the field and longspan operations of companies, the significance of a strategy is emphasised. A well-devised strategy combines awareness of challenges posed by the operating environment and the future targets of the distribution company. Economic regulation, ageing infrastructure, scarcity of resources and tightening supply requirements with challenges created by the climate change put a pressure on the strategy work. On the other hand, technology development related to network automation and underground cabling assists in answering these challenges. This dissertation aims at developing process knowledge and establishing a methodological framework by which key issues related to network development can be addressed. Moreover, the work develops tools by which the effects of changes in the operating environment on the distribution business can be analysed in the strategy work. To this end, the work discusses certain characteristics of the distribution business and describes the strategy process at a principle level. Further, the work defines the subtasks in the strategy process and presents the key elements in the strategy work and long-term network planning. The work delineates the factors having either a direct or indirect effect on strategic planning and development needs in the networks; in particular, outage costs constitute an important part of the economic regulation of the distribution business, reliability being thus a key driver in network planning. The dissertation describes the methodology and tools applied to cost and reliability analyses in the strategy work. The work focuses on determination of the techno-economic feasibility of different network development technologies; these feasibility surveys are linked to the economic regulation model of the distribution business, in particular from the viewpoint of reliability of electricity supply and allowed return. The work introduces the asset management system developed for research purposes and to support the strategy work, the calculation elements of the system and initial data used in the network analysis. The key elements of this asset management system are utilised in the dissertation. Finally, the study addresses the stages of strategic decision-making and compilation of investment strategies. Further, the work illustrates implementation of strategic planning in an actual distribution company environment.

Press forming of paperboard – advancement of converting tools and process control

Press forming is nowadays one of the most common industrial methods in use for producing deeper trays from paperboard. Demands for material properties like recyclability and sustainability have increased also in the packaging industry, but there are still limitations related to the formability of paperboard. A majority of recent studies have focused on material development, but the potential of the package manufacturing process can also be improved by the development of tooling and process control. In this study, advanced converting tools (die cutting tools and the press forming mould) are created for production scale paperboard tray manufacturing. Also monitoring methods that enable the production of paperboard trays with enhanced quality, and can be utilized in process control are developed. The principles for tray blank preparation, including creasing pattern and die cutting tool design are introduced. The mould heating arrangement and determination of mould clearance are investigated to improve the quality of the press formed trays. The effect of the spring back of the tray walls on the tray dimensions can be managed by adjusting the heat-related process parameters and estimating it at the mould design stage. This enables production speed optimization as the process parameters can be adjusted more freely. Real-time monitoring of pressing force by using multiple force sensors embedded in the mould structure can be utilized in the evaluation of material characteristics on a modified production machinery. Comprehensive process control can be achieved with a combination of measurement of the outer dimensions of the trays and pressing force monitoring. The control method enables detection of defects and tracking changes in the material properties. The optimized converting tools provide a basis for effective operation of the control system.