Information Exchange and Fusion in Dynamic and Heterogeneous Distributed Environments

Context awareness, dynamic reconfiguration at runtime and heterogeneity are key characteristics of future distributed systems, particularly in ubiquitous and mobile computing scenarios. The main contributions of this dissertation are theoretical as well as architectural concepts facilitating information exchange and fusion in heterogeneous and dynamic distributed environments. Our main focus is on bridging the heterogeneity issues and, at the same time, considering uncertain, imprecise and unreliable sensor information in information fusion and reasoning approaches. A domain ontology is used to establish a common vocabulary for the exchanged information. We thereby explicitly support different representations for the same kind of information and provide Inter-Representation Operations that convert between them. Special account is taken of the conversion of associated meta-data that express uncertainty and impreciseness. The Unscented Transformation, for example, is applied to propagate Gaussian normal distributions across highly non-linear Inter-Representation Operations. Uncertain sensor information is fused using the Dempster-Shafer Theory of Evidence as it allows explicit modelling of partial and complete ignorance. We also show how to incorporate the Dempster-Shafer Theory of Evidence into probabilistic reasoning schemes such as Hidden Markov Models in order to be able to consider the uncertainty of sensor information when deriving high-level information from low-level data. For all these concepts we provide architectural support as a guideline for developers of innovative information exchange and fusion infrastructures that are particularly targeted at heterogeneous dynamic environments. Two case studies serve as proof of concept. The first case study focuses on heterogeneous autonomous robots that have to spontaneously form a cooperative team in order to achieve a common goal. The second case study is concerned with an approach for user activity recognition which serves as baseline for a context-aware adaptive application. Both case studies demonstrate the viability and strengths of the proposed solution and emphasize that the Dempster-Shafer Theory of Evidence should be preferred to pure probability theory in applications involving non-linear Inter-Representation Operations.

Studies of cap-independent mRNA translation in Drosophila melanogaster

Control of protein synthesis is a key step in the regulation of gene expression during apoptosis and the heat shock response. Under such conditions, cap-dependent translation is impaired and Internal Ribosome Entry Site (IRES)-dependent translation plays a major role in mammalian cells. Although the role of IRES-dependent translation during apoptosis has been mainly studied in mammals, its role in the translation of Drosophila apoptotic genes has not been yet studied. The observation that the Drosophila mutant embryos for the cap-binding protein, the eukaryotic initiation factor eIF4E, exhibits increased apoptosis in correlation with up-regulated proapoptotic gene reaper (rpr) transcription constitutes the first evidence for the existence of a cap-independent mechanism for the translation of Drosophila proapoptotic genes. The mechanism of translation of rpr and other proapoptotic genes was investigated in this work. We found that the 5 UTR of rpr mRNA drives translation in an IRES-dependent manner. It promotes the translation of reporter RNAs in vitro either in the absence of cap, in the presence of cap competitors, or in extracts derived from heat shocked and eIF4E mutant embryos and in vivo in cells transfected with reporters bearing a non functional cap structure, indicating that cap recognition is not required in rpr mRNA for translation. We also show that rpr mRNA 5 UTR exhibits a high degree of similarity with that of Drosophila heat shock protein 70 mRNA (hsp70), an antagonist of apoptosis, and that both are able to conduct IRES-mediated translation. The proapoptotic genes head involution defective (hid) and grim, but not sickle, also display IRES activity. Studies of mRNA association to polysomes in embryos indicate that both rpr, hsp70, hid and grim endogenous mRNAs are recruited to polysomes in embryos in which apoptosis or thermal stress was induced. We conclude that hsp70 and, on the other hand, rpr, hid and grim which are antagonizing factors during apoptosis, use a similar mechanism for protein synthesis. The outcome for the cell would thus depend on which protein is translated under a given stress condition. Factors involved in the differential translation driven by these IRES could play an important role. For this purpose, we undertook the identification of the ribonucleoprotein (RNP) complexes assembled onto the 5 UTR of rpr mRNA. We established a tobramycin-affinity-selection protocol that allows the purification of specific RNP that can be further analyzed by mass spectrometry. Several RNA binding proteins were identified as part of the rpr 5 UTR RNP complex, some of which have been related to IRES activity. The involvement of one of them, the La antigen, in the translation of rpr mRNA, was established by RNA-crosslinking experiments using recombinant protein and rpr 5 UTR and by the analysis of the translation efficiency of reporter mRNAs in Drosophila cells after knock down of the endogenous La by RNAi experiments. Several uncharacterized proteins were also identified, suggesting that they might play a role during translation, during the assembly of the translational machinery or in the priming of the mRNA before ribosome recognition. Our data provide evidence for the involvement of La antigen in the translation of rpr mRNA and set a protocol for purification of tagged-RNA-protein complexes from cytoplasmic extracts. To further understand the mechanisms of translation initiation in Drosophila, we analyzed the role of eIF4B on cap-dependent and cap-independent translation. We showed that eIF4B is mostly involved in cap-, but not IRES-dependent translation as it happens in mammals.

Characterization of DnmA, the Dnmt2 homolog in Dictyostelium discoideum

Eukaryotic DNA m5C methyltransferases (MTases) play a major role in many epigenetic regulatory processes like genomic imprinting, X-chromosome inactivation, silencing of transposons and gene expression. Members of the two DNA m5C MTase families, Dnmt1 and Dnmt3, are relatively well studied and many details of their biological functions, biochemical properties as well as interaction partners are known. In contrast, the biological functions of the highly conserved Dnmt2 family, which appear to have non-canonical dual substrate specificity, remain enigmatic despite the efforts of many researchers. The genome of the social amoeba Dictyostelium encodes Dnmt2-homolog, the DnmA, as the only DNA m5C MTase which allowed us to study Dnmt2 function in this organism without interference by the other enzymes. The dnmA gene can be easily disrupted but the knock-out clones did not show obvious phenotypes under normal lab conditions, suggesting that the function of DnmA is not vital for the organism. It appears that the dnmA gene has a low expression profile during vegetative growth and is only 5-fold upregulated during development. Fluorescence microscopy indicated that DnmA-GFP fusions were distributed between both the nucleus and cytoplasm with some enrichment in nuclei. Interestingly, the experiments showed specific dynamics of DnmA-GFP distribution during the cell cycle. The proteins colocalized with DNA in the interphase and were mainly removed from nuclei during mitosis. DnmA functions as an active DNA m5C MTase in vivo and is responsible for weak but detectable DNA methylation of several regions in the Dictyostelium genome. Nevertheless, gel retardation assays showed only slightly higher affinity of the enzyme to dsDNA compared to ssDNA and no specificity towards various sequence contexts, although weak but detectable specificity towards AT-rich sequences was observed. This could be due to intrinsic curvature of such sequences. Furthermore, DnmA did not show denaturant-resistant covalent complexes with dsDNA in vitro, although it could form covalent adducts with ssDNA. Low binding and methyltransfer activity in vitro suggest the necessity of additional factor in DnmA function. Nevertheless, no candidates could be identified in affinity purification experiments with different tagged DnmA fusions. In this respect, it should be noted that tagged DnmA fusion preparations from Dictyostelium showed somewhat higher activity in both covalent adduct formation and methylation assays than DnmA expressed in E.coli. Thus, the presence of co-purified factors cannot be excluded. The low efficiency of complex formation by the recombinant enzyme and the failure to define interacting proteins that could be required for DNA methylation in vivo, brought up the assumption that post-translational modifications could influence target recognition and enzymatic activity. Indeed, sites of phosphorylation, methylation and acetylation were identified within the target recognition domain (TRD) of DnmA by mass spectrometry. For phosphorylation, the combination of MS data and bioinformatic analysis revealed that some of the sites could well be targets for specific kinases in vivo. Preliminary 3D modeling of DnmA protein based on homology with hDNMT2 allowed us to show that several identified phosphorylation sites located on the surface of the molecule, where they would be available for kinases. The presence of modifications almost solely within the TRD domain of DnmA could potentially modulate the mode of its interaction with the target nucleic acids. DnmA was able to form denaturant-resistant covalent intermediates with several Dictyostelium tRNAs, using as a target C38 in the anticodon loop. The formation of complexes not always correlated with the data from methylation assays, and seemed to be dependent on both sequence and structure of the tRNA substrate. The pattern, previously suggested by the Helm group for optimal methyltransferase activity of hDNMT2, appeared to contribute significantly in the formation of covalent adducts but was not the only feature of the substrate required for DnmA and hDNMT2 functions. Both enzymes required Mg2+ to form covalent complexes, which indicated that the specific structure of the target tRNA was indispensable. The dynamics of covalent adduct accumulation was different for DnmA and different tRNAs. Interestingly, the profiles of covalent adduct accumulation for different tRNAs were somewhat similar for DnmA and hDNMT2 enzymes. According to the proposed catalytic mechanism for DNA m5C MTases, the observed denaturant-resistant complexes corresponded to covalent enamine intermediates. The apparent discrepancies in the data from covalent complex formation and methylation assays may be interpreted by the possibility of alternative pathways of the catalytic mechanism, leading not to methylation but to exchange or demethylation reactions. The reversibility of enamine intermediate formation should also be considered. Curiously, native gel retardation assays showed no or little difference in binding affinities of DnmA to different RNA substrates and thus the absence of specificity in the initial enzyme binding. The meaning of the tRNA methylation as well as identification of novel RNA substrates in vivo should be the aim of further experiments.

Understanding Recreational Services of Urban Riverfront Space for Planning Purposes

In the process of urbanization, natural and semi-natural landscapes are increasingly cherished as open space and recreational resource. Urban rivers are part of this kind of resource and thus play an important role in managing urban resilience and health. Employing the example of Tianjin, this doctoral dissertation research aims at learning to understand how to plan and design for the interface zones between urban water courses and for the land areas adjacent to such water courses. This research also aims at learning how to link waterfront space with other urban space in order to make a recreational space system for the benefit of people. Five questions of this dissertation are: 1) what is the role of rivers in spatial and open space planning? 2) What are the human needs regarding outdoor open space? 3) How do river and water front spatial structures affect people's recreational activities? 4) How to define the recreational service of urban river and waterfront open space? 5) How might answering these question change planning and design of urban open space? Quantitative and qualitative empirical approaches were combined in this study for which literature review and theoretical explorations provide the basis. Empirical investigations were conducted in the city of Tianjin. The quantitative approach includes conducting 267 quantitative interviews, and the qualitative approach includes carrying out field observations and mappings. GIS served to support analysis and visualization of empirical information that was generated through this study. By responding to the five research questions, findings and lessons include the following: 1) In the course of time rivers have gained importance in all levels and scales of spatial planning and decision making. Regarding the development of ecological networks, mainly at national scale, rivers are considered significant linear elements. Regarding regional and comprehensive development, river basins and watersheds are often considered as the structural link for strategic ecological, economic, social and recreational planning. For purposes of urban planning, particularly regarding recreational services in cities, the distribution of urban open spaces often follows the structure of river systems. 2) For the purpose of classifying human recreational needs that relate to outdoor open space Maslow's hierarchy of human needs serves as theoretical basis. The classes include geographical, safety, physiological, social and aesthetic need. These classes serve as references while analyzing river and waterfront open space and other kinds of open space. 3) Regarding the question how river and waterfront spatial structures might affect people's recreational activities, eight different landscape units were identified and compared in the case study area. Considering the thermal conditions of Tianjin, one of these landscape units was identified as affording the optimal spatial arrangement which mostly meets recreational needs. The size and the shape of open space, and the plants present in an open space have been observed as being most relevant regarding recreational activities. 4) Regarding the recreational service of urban river and waterfront open space the results of this research suggest that the recreational service is felt less intensively as the distances between water 183 front and open space user’s places of residence are increasing. As a method for estimating this ‘Service Distance Effect’ the following formula may be used: Y = a*ebx. In this equation Y means the ‘Service Distance’ between homes and open space, and X means the percentage of the people who live within this service distance. Coefficient "a" represents the distance of the residential area nearest to the water front. The coefficient "b" is a comprehensive capability index that refers to the size of the available and suitable recreational area. 5) Answers found to the questions above have implications for the planning and design of urban open space. The results from the quantitative study of recreational services of waterfront open space were applied to the assessment of river-based open space systems. It is recommended that such assessments might be done employing the network analysis function available with any GIS. In addition, several practical planning and designing suggestions are made that would help remedy any insufficient base for satisfying recreational needs. The understanding of recreational need is considered helpful for the proposing planning and designing ideas and for the changing of urban landscapes. In the course of time Tianjin's urban water system has shrunk considerably. At the same time rivers and water courses have shaped Tianjin's urban structure in noticeable ways. In the process of urbanization water has become increasingly important to the citizens and their everyday recreations. Much needs to be changed in order to improve recreational opportunities and to better provide for a livable city, most importantly when considering the increasing number of old people. Suggestions made that are based on results of this study, might be implemented in Tianjin. They are 1) to promote the quality of the waterfront open space and to make all linear waterfront area accessible recreational spaces. Then, 2), it is advisable to advocate the concept of green streets and to combine green streets with river open space in order to form an everyday recreational network. And 3) any sound urban everyday recreational service made cannot rely on only urban rivers; the whole urban structure needs to be improved, including adding small open space and optimize the form of urban communities, finally producing a multi-functional urban recreational network.

Veränderungen des Raum-Zeit-Verhaltens im Zuge von Lebensumbrüchen und ihre Anforderungen an die Stadt- und Verkehrsplanung am Beispiel des Eintritts in den Ruhestand

Veränderungen des Raum-Zeit-Verhaltens im Zuge von Lebensumbrüchen und ihre Anforderungen an die Stadt- und Verkehrsplanung am Beispiel des Eintritts in den Ruhestand. In der vorliegenden Dissertation wurde untersucht, ob und in welchem Maße sich das Raum-Zeit-Verhalten im Alltag mit dem Eintritt in den Ruhestand verändert. Bei der Untersuchung handelt es sich um eine mehrjährige Panel-Studie, die in den Regionen Hamburg und Kassel durchgeführt wurde. Mit insgesamt 50 Studienteilnehmern wurden vor und nach ihrem Ausscheiden aus dem Erwerbsleben umfassende Interviews geführt. Hierbei kam die an der Oxford University entwickelte „HATS“-Methode („Household Activity Travel Simulator“) zum Einsatz, die einen tiefen Einblick in die Alltagsstrukturen und das aus ihnen resultierende raum-zeitliche Verhalten ermöglicht. Ein Untersuchungsschwerpunkt lag auf der Verkehrsmittelwahl. Auf Grundlage der Untersuchungsergebnisse wurden Handlungsempfehlungen für die Stadt- und Verkehrsplanung abgeleitet. Es zeigte sich, dass die Studienteilnehmer mit ihrem Eintritt in den Ruhestand grundsätzlich deutlich später im Tagesverlauf als Verkehrsteilnehmer in Erscheinung treten. Darüber hinaus zeichnete sich ein Bedeutungszuwachs des Stadtquartiers bzw. der nahräumlichen Mobilität ab; der Fuß- und Fahrradverkehr gewinnt für die Alltagsmobilität an Bedeutung. Versorgungs- und Dienstleistungsangebote im eigenen Wohnquartier – und somit nutzungsgemischte Stadtquartiere – erweisen sich demnach insbesondere für die Gruppe der Ruheständler als besonders relevant. Trotz der steigenden Bedeutung des Fuß-und Fahrradverkehrs zeigt die Studie, dass dem Pkw in der Alltagsmobilität eine (nach wie vor) dominante Rolle zukommt – eine Entwicklung, die sich aufgrund des Kohorteneffekts eher noch verstärken wird. Im Rahmen der Diskussion geeigneter Handlungsansätze für die Stadt- und Verkehrsplanung zur Stärkung des Umweltverbundes werden – neben Interventionen zur Attraktivitätsminderung des Pkw – insbesondere verschiedene Maßnahmen zu Angebotsverbesserungen im ÖPNV behandelt. Dabei wird u. a. auch die Verhaltensrelevanz von Kostenwahrnehmungen betrachtet. Zusätzlich wird deutlich, dass bei der Etablierung verkehrsplanerischer Maßnahmen auch die zu-nehmende Bedeutung von Wegen, die in Begleitung anderer Haushaltsmitglieder zurückgelegt werden (Stichwort: Haushaltsmobilität), berücksichtigt werden muss. Der Eintritt in den Ruhestand erweist sich grundsätzlich als eine Umbruchsituation im Lebensverlauf, die ein Aufbrechen von (Verkehrs-)Gewohnheiten im Alltag begünstigt und die Betroffenen besonders empfänglich für Informationen zu verschiedenen Verkehrsangeboten bzw. Verhaltens-alternativen werden lässt. Hinsichtlich möglicher Handlungsansätze wird in dieser Studie u. a. thematisiert, wie im Rahmen einer zielgruppenspezifischen Kommunikation im ÖPNV dieses Zeit-fenster genutzt werden kann, um Menschen an der Schwelle zum Eintritt in den Ruhestand als regelmäßige Nutzer von Bus und Bahn (neu) zu gewinnen bzw. zu halten.

Ecosystem services and adaptation for agriculture and food security: analysis of two decades (1991–2011) of financing by the Global Environment Facility

Investing in global environmental and adaptation benefits in the context of agriculture and food security initiatives can play an important role in promoting sustainable intensification. This is a priority for the Global Environment Facility (GEF), created in 1992 with a mandate to serve as financial mechanism of several multilateral environmental agreements. To demonstrate the nature and extent of GEF financing, we conducted an assessment of the entire portfolio over a period of two decades (1991–2011) to identify projects with direct links to agriculture and food security. A cohort of 192 projects and programs were identified and used as a basis for analyzing trends in GEF financing. The projects and programs together accounted for a total GEF financing of US$1,086.8 million, and attracted an additional US$6,343.5 million from other sources. The value-added of GEF financing for ecosystem services and resilience in production systems was demonstrated through a diversity of interventions in the projects and programs that utilized US$810.6 million of the total financing. The interventions fall into the following four main categories in accordance with priorities of the GEF: sustainable land management (US$179.3 million), management of agrobiodiversity (US$113.4 million), sustainable fisheries and water resource management (US$379.8 million), and climate change adaptation (US$138.1 million). By aligning GEF priorities with global aspirations for sustainable intensification of production systems, the study shows that it is possible to help developing countries tackle food insecurity while generating global environmental benefits for a healthy and resilient planet.