Las investigaciones traslacionales tienen el objetivo de poner a disposición de investigaciones las evidencias obtenidas en investigaciones básicas para ensayos clínicos. Para facilitar la investigación traslacional es necesario relacionar dicha información mediante la integración de repositorios de información biológica y médica. Debido a la complejidad, cantidad, diversidad y rápida evolución de la información biológica, es imposible gestionar los repositorios biológicos de manera manual ya que supondría una gran inversión en tiempo y en esfuerzo. Por lo tanto, cada vez más es necesario dotar de nuevas herramientas de gestión que faciliten esta tarea y pueda ser realizada de manera autónoma. Esta tesis presenta un entorno para la gestión e integración semántica utilizado las tecnologías de la Web semántica, las cuales son utilizadas para representar, almacenar, explotar y guiar el proceso de integración de la información y conocimiento. Como resultado principal se integraron repositorios de genes y proteínas ortólogas con enfermedades genéticas. / Translational research aims to connect basic biomedical researches with clinical research in order to reach new conclusions based on biomedical evidences. To facilitate the translational research, biological and biomedical information must be related. So, we need to integrate biological and biomedical repositories. Life sciences is a knowledge based discipline, in the data and knowledge is represented through vast amounts of complex and changing information stored in disparate resources and in machine-unfriendly formats. Therefore, the availability of computational methods for organizing, accessing and retrieving information in a systematic way has become crucial for the progress of research in life sciences. In this thesis, we present a framework for the semantic management and integration using semantic web technologies. This framework assists life scientists in the exploration of orthologs/genetic diseases research paths by providing a precise, explicit meaning for information units and intertwining such information.

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Objective of this project was the study of basic interaction and migration processes of actinides in the environment in presence of humic acids (HA). To obtain more basic knowledge on these interaction processes synthetic HA with specific functional properties as well as 14C-labeled HA were synthesized and applied in comparison to the natural HA Aldrich. One focus of the work was on the synthesis of HA with distinct redox functionalities. The obtained synthetic products that are characterized by significantly higher Fe(III) redox capacities than Aldrich HA were applied to study the redox properties of HA and the redox stability of U(VI) humate complexes. It was confirmed that phenolic OH groups play an important role for the redox properties of HA. However, the results indicate that there are also other processes than the single oxidation of phenolic OH groups and/or other functional groups contributing to the redox behavior of HA. A first direct-spectroscopic proof for the reduction of U(VI) by synthetic HA with distinct redox functionality was obtained. The complexation behavior of synthetic and natural HA with actinides (Th, Np, Pu) was studied. Structural parameters of Pu(III), Th(IV), Np(IV) and Np(V) humates were determined by X-ray absorption spectroscopy (XAS). The results show that carboxylate groups dominate the interaction between HA and actinide ions. These are predominant monodentately bound. The influence of phenolic OH groups on the Np(V) complexation by HA was studied with modified HA (blocked phenolic OH groups). The blocking of phenolic OH groups induces a decrease of the number of maximal available complexing sites of HA, whereas complex stability constant and Np(V) near-neighbor surrounding are not affected. The effects of HA on the sorption and migration behavior of actinides was studied in batch and column experiments. Th(IV) sorption onto quartz and Np(V) sorption onto granite and its mineral constituents are affected by the pH value and the presence of HA. HA exhibits a significant influence on the transport of U(IV) and U(VI) in a laboratory quartz sand system. In order to provide the basis for a more reliable modeling of the actinide transport, the metal ion complexation with HA has to be integrated into existing geochemical speciation codes. Within this project the metal ion charge neutralization model was embedded into the geochemical modeling code EQ3/6. In addition to that, a digital data base was developed which covers HA complexation data basing on the charge neutralization model.

Reactive transport modelling has wide applications in geosciences. In the field of hydrogeology, it has been utilised to simulate the biogeochemical processes that disperse and degrade contaminants in the aquifer. For geotechnical applications, such as geological CO2 sequestration, the reaction of CO2 with the ambient saline aquifer determines the final success of storage. In a radioactive waste repository, scientists rely on reactive transport models to predict the mobilisation of hazardous radionuclides within space and time. In this work, the multi-component mass transport code OpenGeoSys, was coupled with two geochemical solvers, the Gibbs Energy Minimization Selektor (GEM) and the Biogeochemical Reaction Network Simulator (BRNS). Both coupled codes were verified against analytical solutions and simulation results from other numerical models. Moreover, the coupling interface was developed for parallel simulation. Test runs showed that the speed-up of reaction part had a very good linearity with number of nodes in the mesh. However, for three dimensional problems with complex geochemical reactions, the model performance was dominated by solving transport equations of mobile chemical components. OpenGeoSys-BRNS was applied to a two dimensional groundwater remediation problem. Its calculated concentration profiles fitted very well with analytical solutions and numerical results from TBC. The model revealed that natural attenuation of groundwater contaminants is mainly controlled by the mixing of carbon source and electron donor. OpenGeoSys-GEM was employed to investigate the retardation mechanism of radionuclides in the near field of a nuclear waste repository. Radium profiles in an idealised bentonite column was modelled with varying clay/water ratios. When clay content is limited, Ba-Sr-Ra sulfate solid solutions have a very strong retardation effect on the aqueous radium. Nevertheless, when clay mineral is abundant, cation exchange sites also attract Sr and Ba, thus dominates the transport of Ra.

The migration behavior of actinides and other radioactive contaminants in the environment is controlled by prominent molecular phenomena such as hydrolysis and complexation reactions in aqueous solutions as well as the diffusion and sorption onto minerals present along groundwater flow paths. These reactions significantly influence the mobility and bioavailability of the metal ions in the environment, in particular at liquid-solid interfaces. Hence, for the assessment of migration processes the knowledge of the mechanisms occurring at interfaces is crucial. The required structural information can be obtained using various spectroscopic techniques. In the present study, the speciation of uranium(VI) and neptunium(V) at environmentally relevant mineral – water interfaces of oxides of titania, alumina, silica, zinc, and alumosilicates has been investigated by the application of attenuated total reflection Fourier-transform infrared (ATR FT-IR) spectroscopy. Moreover, the distribution of the hydrolysis products in micromolar aqueous solutions of U(VI) and Np(V/VI) at ambient atmosphere has been characterized for the first time, by a combination of ATR FT-IR spectroscopy, near infrared (NIR) absorption spectroscopy, and speciation modeling applying updated thermodynamic databases. From the infrared spectra, a significant change of the U(VI) speciation is derived upon lowering the U(VI) concentration from the milli- to the micromolar range, strongly suggesting the dominance of monomeric U(VI) hydrolysis products in the micromolar solutions. In contradiction to the predicted speciation, monomeric hydroxo species are already present at pH ≥ 2.5 and become dominant at pH 3. At higher pH levels (> 6), a complex speciation is evidenced including carbonate containing complexes. For the first time, spectroscopic results of Np(VI) hydrolysis reactions are provided in the submillimolar concentration range and at pH values up to 5.3, and they are comparatively discussed with U(VI). For both actinides, the formation of similar species is suggested at pH ≤ 4, whereas at higher pH, the infrared spectra evidence structurally different species. At pH 5, the formation of a carbonate-containing dimeric complex, that is (NpO2)2CO3(OH)3−, is strongly suggested, whereas carbonate complexation occurs only under more alkaline conditions in the U(VI) system. The results from the experiments of the sorption processes clearly demonstrate the formation of stable U(VI) surface complexes at all investigated mineral phases. This includes several metal oxides, namely TiO2, Al2O3, and SiO2, serving as model systems for the elucidation of more complex mineral systems, and several alumosilicates, such as kaolinite, muscovite and biotite. From a multiplicity of in situ experiments, the impact of sorbent characteristics and variations in the aqueous U(VI) system on the sorption processes was considered. A preferential formation of an inner-sphere complex is derived from the spectra of the TiO2 and SiO2 phases. In addition, since the in situ FT-IR experiments provide an online monitoring of the absorption changes of the sorption processes, the course of the formation of the U(VI) surface complexes can be observed spectroscopically. It is shown that after prolonged sorption time on TiO2, resulting in a highly covered surface, outer-sphere complexation predominates the sorption processes. The prevailing crystallographic modification, namely anatase and rutile, does not significantly contribute to the spectra, whereas surface specific parameters, e.g. surface area or porosity are important. A significant different surface complexation is observed for Al2O3. The formation of inner-spheric species is assumed at low U(VI) surface coverage which is fostered at low pH, high ionic strength and short contact times. At proceeded sorption the surface complexation changes. From the spectra, an outer-spheric coordination followed by surface precipitation or polymerization is deduced. Moreover, in contrast to TiO2, the appearance of ternary U(VI) carbonate complexes on the γ-Al2O3 surface is suggested. The first results of the surface reactions on more complex, naturally occurring minerals (kaolinite, muscovite and biotite) show the formation of U(VI) inner-sphere sorption complexes. These findings are supported by the spectral information of the metal oxide surfaces. In this work, first spectroscopic results from sorption of aqueous Np(V) on solid mineral phases are provided. It is shown that stable inner-sphere surface species of NpO2+ are formed on TiO2. Outer-sphere complexation is found to play a minor role due to the pH independence of the sorption species throughout the pH range 4 – 7.6. The comparative spectroscopic experiments of Np(V) sorption onto TiO2, SiO2, and ZnO indicate structurally similar bidentate surface complexes. The multiplicity of IR spectroscopic experiments carried out within this study yields a profound collection of spectroscopic data which will be used as references for future investigations of more complex sorption systems in aqueous solution. Furthermore, from a methodological point of view, this study comprehensively extends the application of ATR FT-IR spectroscopic experiments to a wide range in the field of radioecology. The results obtained in this work contribute to a better understanding of the geochemical interactions of actinides, in particular U(VI) and Np(V/VI), in the environment. Consequently, more reliable predictions of actinides migration which are essential for the safety assessment of nuclear waste repositories can be performed. / Das Migrationsverhalten von Aktiniden und anderen radioaktiven Schadstoffen in der Umwelt wird von wichtigen molekularen Prozessen entlang der Grundwasserfließwege reguliert. Dazu gehören sowohl die Hydrolyse und Komplexierung in wässrigen Lösungen als auch Diffusion und Sorption der Schwermetalle an Mineralen. Diese Reaktionen beeinflussen entscheidend die Mobilität und Bioverfügbarkeit der Metallionen in der Umwelt, insbesondere an den fest-flüssig Grenzflächen. Genaue Kenntnisse über die an diesen Grenzflächen stattfindenden Mechanismen sind somit entscheidend, um Migrationsprozesse verlässlich abschätzen zu können. Die benötigten strukturellen Informationen können mit verschiedenen spektroskopischen Techniken ermittelt werden. Das Ziel der vorliegenden Arbeit war die Untersuchung der Speziation von Uran(VI) und Neptunium(V) an umweltrelevanten Grenzflächen von Oxiden des Titans, Aluminiums, Siliziums und Zinks und von Alumosilikaten mittels ATR FT-IR Spektroskopie. Des Weiteren wurde die Verteilung aquatischer Spezies in mikromolaren Lösungen des U(VI) und Np(V/VI) unter Normalbedingungen charakterisiert. Diese erstmalige Untersuchung wurde mit einer Kombination aus Speziationsmodellierung unter Anwendung aktueller thermodynamischer Daten und ATR FT-IR und NIR Absorptionsspektroskopie realisiert. Die Infrarotspektren zeigen eine deutliche Änderung der Speziesverteilung im Konzentrationsverlauf vom millimolaren zum mikromolaren Bereich. Dies verweist auf die Bildung monomerer U(VI) Hydrolyseprodukte. Im Gegensatz zu berechneten Speziationen werden diese monomeren Komplexe schon bei pH ≥ 2,5 gebildet und dominieren die Speziation bei pH 3. Bei höheren pH-Werten (> 6) konnte eine komplexe Speziesverteilung mit Anteilen von Karbonatkomplexen nachgewiesen werden. Erstmals konnten im Rahmen dieser Arbeit spektroskopische Befunde der Hydrolysereaktionen des Np(VI) im submillimolaren Konzentrationsbereich bis pH 5,3 erhalten werden. Diese wurden im Vergleich mit der U(VI) Speziation diskutiert. Obwohl im sauren Bereich (pH ≤ 4) die Bildung ähnlicher Komplexe nachgewiesen wurde, zeigen die bei höheren pH-Werten erhaltenen Spektren eine unterschiedliche Speziesverteilung. Im Gegensatz zum U(VI) bildet das Np(VI) schon bei pH 5 karbonathaltige aquatische Spezies wie (NpO2)2CO3(OH)3−. Die Ergebnisse der Sorptionsexperimente von U(VI) zeigen die Bildung stabiler Oberflächenkomplexe an allen untersuchten Mineralphasen. Dies umfasst mehrere als Modellsystem dienende Metalloxide wie TiO2, Al2O3 und SiO2, als auch komplexere Alumosilikate wie Kaolinit, Muskovit und Biotit. Für eine detaillierte Charakterisierung der Oberflächenkomplexe wurde eine Vielzahl von in situ Sorptionsexperimenten durchgeführt, die den Einfluss unterschiedlicher Parameter der mineralischen Phase als auch des wässrigen U(VI) Systems berücksichtigen. Die bevorzugte Bildung von innersphärischen Komplexen an TiO2 und SiO2 wird aus den spektroskopischen Daten abgeleitet. Da die in situ FT-IR Spektroskopie eine kontinuierliche Registrierung der Absorptionsänderungen während der ablaufenden Sorptionsprozesse erlaubt, kann somit der Verlauf dieser Prozesse quasi in Echtzeit spektroskopisch verfolgt werden. Es konnte gezeigt werden, dass mit fortschreitender Sorptionsdauer, d.h. bei hohen Beladungsdichten, die Bildung einer weiteren außersphärischen Spezies die Sorption dominert. Die vorliegende kristallographische Modifikation, Anatas und Rutil, ist nicht maßgeblich für das Auftreten unterschiedlicher Sorptionsprozesse verantwortlich, obwohl Parameter wie die spezifische Oberfläche und die Porosität für den Sorptionsprozess von Bedeutung sind. Deutlich verschiedene Oberflächenreaktionen werden für Al2O3 beobachtet. Aus den Spektren kann die Ausbildung einer innersphärischen Spezies bei sehr niedrigen U(VI) Beladungen, niedrigen pH-Werten, hohen Ionenstärken und kurzen Kontaktzeiten abgeleitet werden. Bei fortschreitender Sorption ändert sich die Art der Oberflächenkomplexe. Zunächst bilden sich außersphärische Spezies, während im weiteren Verlauf die Spektren auf eine beginnende Oberflächenausfällung bzw. Polymerisation hinweisen. Weiterhin wird das Auftreten von ternären U(VI) Karbonatkomplexen an γ-Al2O3 aus den spektroskopischen Daten abgeleitet. Die ersten Ergebnisse der Sorptionsexperimente an komplexeren, natürlich auftretenden Mineralphasen (Kaolinit, Muskovit und Biotit) zeigen eine bevorzugte Ausbildung von innersphärischen U(VI) Komplexen. Diese Resultate werden durch die spektralen Befunde der Experimente der Metalloxide gestützt. Erstmalig werden in dieser Arbeit spektroskopische Ergebnisse der Sorptionsprozesse von wässrigen Np(V) an verschiedenen Mineralphasen präsentiert. Wie U(VI) bildet Np(V) stabile innersphärische Oberflächenkomplexe an TiO2. Die Speziesverteilung an der TiO2 Oberfläche ist im pH Bereich 4 – 7,6 konstant. Daher ist zu erwarten, dass eine außersphärische Komplexierung hier nur eine untergeordnete Rolle spielt. Der Vergleich von Spektren der Np(V) Sorptionskomplexe an TiO2, SiO2 und ZnO weist auf die Bildung strukturell ähnlicher bidentater Komplexe hin. Die Vielzahl der hier vorgestellten infrarotspektroskopischen Experimente bietet eine fundierte Sammlung spektroskopischer Daten, die für zukünftige Untersuchungen komplexer aquatischer und mineralischer Systeme unerlässlich ist. Gleichzeitig wurde der Anwendungsbereich der ATR FT-IR Technik auf dem Gebiet der Radioökologie umfassend erweitert. Die im Rahmen dieser Arbeit gewonnenen Ergebnisse tragen zu einem besseren Verständnis der geochemischen Wechselwirkungen von Aktiniden, im Speziellen von U(VI) und Np(V) in der Umwelt bei. Damit unterstützen sie den Aufklärungsprozess der Migration von radioaktiven Kontaminationen und dienen als Grundlage für zuverlässige Prognosen für die Sicherheitsbewertung von Endlagern für nukleare Abfälle.

The purpose of this project was to create a requirement repository using a methodology, which is being developed in the department of Information Systems of Kaunas University of Technology. The implementation would raise the methodology to the higher level enabling its use in practice. Using the implementation one could either prove or disprove the main idea behind the methodology - the simplification of the stakeholder-analyst dialogue during the IS requirements specification. For that, the experiment was conducted. The purpose of the experiment was to specify requirements for the real-world IS using implemented requirement repository, and compare the results to other similar software.

For the first time microbial tDNA could be isolated from 50 g unperturbed Mont Terri Opalinus Clay. Based on the analysis of the tDNA the bacterial diversity of the unperturbed clay is dominated by representatives of Firmicutes, Betaproteobacteria, and Bacteriodetes. Firmicutes also dominate after treatment of the clay with R2A medium. Bacteria isolated from Mont Terri Opalinus Clay on R2A medium were related to Sporomusa spp., Paenibacillus spp., and Clostridium spp.. All further investigations are concentrated on the unique isolates Sporomusa sp. MT-2 and Paenibacillus sp. MT-2. Cells of the type Sporomusa sp. MT-2 and Paenibacillus sp. MT-2 were comprehensively analyzed in terms of growing, morphology, functional groups of the cell envelope, and cell membrane structure. Strong actinide(An)/lanthanide(Ln)-interactions with the Opalinus Clay isolates and the Äspö-strain Pseudomonas fluorescens (CCUG 32456) could be determined within a broad pH range (2-8). The metals bind as a function of pH on protonated phosphoryl, carboxyl and deprotonated phosphoryl sites of the respective cell membrane. The thermodynamic surface complexation constants of bacterial An/Ln-species were determined and can be used in modeling programs. Depending on the used An different interaction mechanisms were found (U(VI): biosorption, partly biomineralisation; Cm(III): biosorption, indications for embedded Cm(III); Pu: biosorption, bioreduction and indications for embedded Pu). Different strategies of coping with U(VI) were observed comparing P. fluorescens planktonic cells and biofilms under the chosen experimental conditions. An enhanced capability of the biofilm to form meta-autunite in comparison to the planktonic cells was proven. Conclusively, the P. fluorescens biofilm is more efficient in U(VI) detoxification. In conclusion, Mont Terri Opalinus Clay contains bacterial communities, that may influence the speciation and hence the migration behavior of selected An/Ln under environmental conditions.

Kauno kolegijoje yra patvirtinta ir vykdoma nauja e. mokymosi plėtros programa 2009-2013m. Pagal ją Kauno kolegija orientuojasi į atvirą e. mokymąsi, todėl atviras elektroninių išteklių kūrimas, panaudojimas bei talpinimas yra vienas iš pagrindinių šios programos tikslų. Taigi šiame darbe pateikiama: informacija apie atvirus elektroninius išteklius, jų nauda tiek studentui, tiek dėstytojui, tiek institucijai, atvirų elektroninių išteklių kūrimo ir panaudojimo proceso Kauno kolegijoje analizė, atvirų elektroninių išteklių talpinimo programinių įrankių integravimo projektas, sumodeliuotas UML kalba, vartotojo instrukcija. Parengus šį darbą paaiškėjo, kad minėtų programinių įrankių integravimas yra reikalingas ir kad tai tikrai skatintų vartotojus kurti, talpinti bei naudoti atvirus elektroninius išteklius, taip pat buvo surengti mokymai maždaug šimtui vartotojų, ir buvo parengta dalis dokumentų, reglamentuojančių atvirų elektroninių išteklių talpinimo veiklas bei institucinė licencinė sutartis, skirta autorių teisėms apsaugoti. / Kauno kolegija (Kaunas University of Applied Sciences) has adopted and implemented e-Learning Development Program for 2009-2013. One of the key components of the program is orientation to the open e-Learning, so the main tasks are the promotion of the development and use of open educational resources and storage of such resources. Thus, the aim of this work is to promote the development and use of open educational resources by preparing the integration project of Open Journal system, Open Conference System and DSpace systems, by organizing the training courses for users, also by preparing the documents regulating the activities of the hosting of open educational resources. In this document are presented: the information about open educational resources, their advantage for all – student, lecturer and institution, the analysis of the situation of the development and use of open educational resources in Kauno kolegija (Kaunas University of Applied Science), the project of integration of Open Journal System, Open Conference System and DSpace systems, modeled using UML language, and also a short user manual. After the completion of this work revealed that such integration project of the above-mentioned systems was necessary and it would really promote users to develop, load and use open educational resources, also there were organized training courses for about one hundred users, alike there were prepared a part of the documents regulating the activities of hosting open... [to full text]

在臺灣如國史館、國史館臺灣文獻館、中央研究院臺灣史研究所檔案館等機構收藏了非常多珍貴的歷史檔案。這些機構不一定名為檔案館，但典藏許多有價值的檔案，具檔案館之實，因此皆屬於「檔案典藏機構」，且有相當的重要性。 為讓文獻傳遞正確真實的資訊、方便使用者查閱、使用，需提供適當的典藏環境與合適的保存、維護措施。正如檔案館的徵集、編排需制定政策、規範、流程作為行政指引，檔案館藏的保存維護也需要館藏維護政策（Preservation Policy）輔助實行。 本研究透過文獻探討、內容分析了解國內外重要檔案典藏機構的館藏維護政策，提出建議的館藏維護政策綱要，再訪談國內檔案典藏機構人員目前保存維護措施執行的困難、對館藏維護政策功能、是否需要制定等問題的看法。 研究結果顯示臺灣目前尚無機構訂有此政策，相關規範散布於細項法規，但受訪者普遍認可館藏維護政策的正面效益與功能，以及現在機構存在例如專業人力不足、相關規範面向偏狹等問題。 本研究建議機構由自我評估著手，了解機構需求，嘗試制定長期保存維護計畫，再逐漸往制定政策的目標邁進，並對內、外推廣保存維護概念，提升人員對此議題的重視與瞭解。 / There are many institutions in Taiwan like Academia Historica, Taiwan Historica, National Palace Museum, and they reposit many valuable historical archives. Though their name may not called “the Archive”, but they actually have lots of precious archives. Therefore, they all belong to “Archives Repository” and quite important. For the correction of information in archives, and the convenience of search and use, archives repositories have to provide applicable storage environment, preservation and conservation measures for archives. As the acquisition and arrangement of the Archive need to establish policy, standard or procedures as administrative guides, the preservation measures for the historical archives also need a “Preservation Policy” to assist with it. By document analysis and content analysis, this study attempted to comprehend the preservation policies’ content of archives repositories in Taiwan and overseas and then adressed an advised preservation policy schema. Lastly, interviewed with employees in archives repositories discussing the difficulties of implementing preservation measures, the effects and demand of preservation policy, and so forth. The search result shows that there are no archives repositories having this kind of policy in Taiwan. The related directions disperse in diverse legislations and standards. But interviewees generally approved the positive benefits of preservation policy. And they also acknowledged management problems existing in organization such as insufficient professional manpower and related legislations. Based on the findings, this study proposes some suggestions that advices these institutions start from self-survey to assessing preservation needs. In addition, archives repositories can promote the significance of preservation issue, as to raise the conscious about it. Keywords: Preservation Policy, Archives Repository, Policy, Preservation, Conservation

Non-functional requirements such as Security and Dependability (S&D) become more and more important as well as more and more difficult to achieve, particularly in embedded systems development. Such systems come with a large number of common characteristics, including real-time and temperature constraints, security and dependability as well as efficiency requirements. In particular, the development of Resource Constrained Embedded Systems (RCES) has to address constraints regarding memory, computational processing power and/or energy consumption. In this work, we propose a modeling environment which associates model-driven paradigm and a model-based repository, to support the design and the packaging of S&D patterns, resource models and their property models. The approach is based on a set of modeling languages coupled with a model-repository, search and instantiation engines towards specific development environments. These modeling languages allow to specify patterns, resources and a set of property models. These property models will allow to govern the use of patterns and their analysis for reuse. In addition, we propose a specification and generation process of repositories. As part of the assistance for the development of S&D applications, we have implemented a suite of tool-chain based on the Eclipse platform to support the different activities around the repository, including the analysis activities. The proposed solutions were evaluated in the TERESA project through a case study from the railway domain.