TY - JOUR A1 - Kinsky-Ehritt, Andrea T1 - The British Music Hall BT - between politics and entertainment JF - Victorian highways, Victorian byways : new approaches to nineteenth century British literature and culture Y1 - 2010 SN - 978-3-89626-939-3 SP - 243 EP - 267 PB - Trafo CY - Berlin ER - TY - JOUR A1 - Havemann, Anna T1 - Victorian Women Artists BT - their Quest for Independence and Professional Artistic Training JF - Victorian highways, Victorian byways : new approaches to nineteenth century British literature and culture Y1 - 2010 SN - 978-3-89626-939-3 SP - 15 EP - 40 PB - Trafo CY - Berlin ER - TY - JOUR A1 - Drexler, Peter T1 - Labour and Gender BT - Ford Madox Brown's Work and Victorian Navvy Stories JF - Victorian highways, Victorian byways : new approaches to nineteenth century British literature and culture Y1 - 2010 SN - 978-3-89626-939-3 SP - 67 EP - 101 PB - Trafo CY - Berlin ER - TY - JOUR A1 - Böhnke, Dietmar A1 - Brusberg-Kiermeier, Stefanie A1 - Drexler, Peter T1 - Introduction JF - Victorian highways, Victorian byways : new approaches to nineteenth century British literature and culture Y1 - 2010 SN - 978-3-89626-939-3 SP - 7 EP - 11 PB - Trafo CY - Berlin ER - TY - BOOK ED - Böhnke, Dietmar ED - Brusberg-Kiermeier, Stefanie ED - Drexler, Peter T1 - Victorian highways, Victorian byways BT - new approaches to nineteenth century British literature and culture T3 - Potsdamer Beiträge zur Kultur- und Sozialgeschichte Y1 - 2010 SN - 978-3-89626-939-3 VL - 8 PB - Trafo CY - Berlin ER - TY - GEN A1 - Riaño-Pachón, Diego Mauricio A1 - Kleessen, Sabrina A1 - Neigenfind, Jost A1 - Durek, Pawel A1 - Weber, Elke A1 - Engelsberger, Wolfgang R. A1 - Walther, Dirk A1 - Selbig, Joachim A1 - Schulze, Waltraud X. A1 - Kersten, Birgit T1 - Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites. Results: From the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented. These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected. Conclusions: We analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1328 KW - Gene Ontology KW - Phosphorylation Site KW - phosphorylated amino acid KW - slim term KW - single nucleotide polymorphism mapping Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431181 SN - 1866-8372 IS - 1328 ER - TY - JOUR A1 - Riaño-Pachón, Diego Mauricio A1 - Kleessen, Sabrina A1 - Neigenfind, Jost A1 - Durek, Pawel A1 - Weber, Elke A1 - Engelsberger, Wolfgang R. A1 - Walther, Dirk A1 - Selbig, Joachim A1 - Schulze, Waltraud X. A1 - Kersten, Birgit T1 - Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana JF - BMC Genomics N2 - Background: Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites. Results: From the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented. These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected. Conclusions: We analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future. KW - Gene Ontology KW - Phosphorylation Site KW - phosphorylated amino acid KW - slim term KW - single nucleotide polymorphism mapping Y1 - 2010 U6 - https://doi.org/10.1186/1471-2164-11-411 SN - 1471-2164 VL - 11 PB - Biomed Central CY - London ER - TY - JOUR ED - Mackert, Jürgen ED - Schmidt, Michael T1 - Editorial JF - Berliner Journal für Soziologie N2 - In der Wissenschaft sollten Geburtstage oder Jubiläen bestenfalls Anlass, nicht aber der eigentliche Grund sein, sich in Form eines Schwerpunktheftes erneut mit dem Werk eines wichtigen Vertreters der Zunft zu befassen. Nur allzu leicht geraten Rückblicke zu einer bloßen Einordnung eines Werkes in den Kontext seiner Zeit und beschränken sich damit auf seine schlichte Historisierung. Das lange Schaffen Robert King Mertons ließe sich ohne Probleme als bedeutender Teil der Geschichte der Soziologie in der zweiten Hälfte des 20. Jahrhunderts beschreiben. Doch Merton selbst hat schon früh betont, dass in der Wissenschaft ein grundlegender Unterschied zwischen erzählter (Wissenschafts-)Geschichte und systematischer Analyse eines klassischen theoretischen Werkes besteht. In diesem Sinne geht es darum, jenem Diktum Alfred N. Whiteheads gerecht zu werden, das Merton selbst seinem Hauptwerk Social Theory and Social Structure vorangestellt hat: „A science that hesitates to forget its founders is lost.“ Damit sollte keineswegs die fortbestehende Bedeutung einer Auseinandersetzung mit den klassischen Texten der Soziologie in Zweifel gezogen werden, aber eben nicht in der Form immer wiederkehrender Exegese, die zum gebetsmühlenhaften Wiederholen bereits bekannten Wissens oder zu dessen Banalisierung führen muss. Vielmehr ging es Merton darum, dass der theoretische Wissensfundus sowie die forschungspraktischen und methodischen Erfahrungen und Kenntnisse der Soziologie im Zentrum der Beschäftigung mit den Klassikern und Gründervätern der Disziplin stehen sollten. Y1 - 2010 U6 - https://doi.org/10.1007/s11609-010-0131-y SN - 0863-1808 SN - 1862-2593 IS - 20 SP - 281 EP - 284 PB - Springer CY - Wiesbaden ER - TY - JOUR A1 - Mooij, Wolf M. A1 - Trolle, Dennis A1 - Jeppesen, Erik A1 - Arhonditsis, George B. A1 - Belolipetsky, Pavel V. A1 - Chitamwebwa, Deonatus B. R. A1 - Degermendzhy, Andrey G. A1 - DeAngelis, Donald L. A1 - Domis, Lisette Nicole de Senerpont A1 - Downing, Andrea S. A1 - Elliott, J. Alex A1 - Fragoso Jr, Carlos Ruberto A1 - Gaedke, Ursula A1 - Genova, Svetlana N. A1 - Gulati, Ramesh D. A1 - Håkanson, Lars A1 - Hamilton, David P. A1 - Hipsey, Matthew R. A1 - ‘t Hoen, Jochem A1 - Hülsmann, Stephan A1 - Los, F. Hans A1 - Makler-Pick, Vardit A1 - Petzoldt, Thomas A1 - Prokopkin, Igor G. A1 - Rinke, Karsten A1 - Schep, Sebastiaan A. A1 - Tominaga, Koji A1 - Van Dam, Anne A. A1 - Van Nes, Egbert H. A1 - Wells, Scott A. A1 - Janse, Jan H. T1 - Challenges and opportunities for integrating lake ecosystem modelling approaches JF - Aquatic ecology N2 - A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models. KW - aquatic KW - food web dynamics KW - plankton KW - nutrients KW - spatial KW - lake KW - freshwater KW - marine KW - community KW - population KW - hydrology KW - eutrophication KW - global change KW - climate warming KW - fisheries KW - biodiversity KW - management KW - mitigation KW - adaptive processes KW - non-linear dynamics KW - analysis KW - bifurcation KW - understanding KW - prediction KW - model limitations KW - model integration Y1 - 2010 U6 - https://doi.org/10.1007/s10452-010-9339-3 SN - 1573-5125 SN - 1386-2588 VL - 44 SP - 633 EP - 667 PB - Springer Science + Business Media B.V. CY - Dordrecht ER - TY - GEN A1 - Mooij, Wolf M. A1 - Trolle, Dennis A1 - Jeppesen, Erik A1 - Arhonditsis, George B. A1 - Belolipetsky, Pavel V. A1 - Chitamwebwa, Deonatus B. R. A1 - Degermendzhy, Andrey G. A1 - DeAngelis, Donald L. A1 - Domis, Lisette Nicole de Senerpont A1 - Downing, Andrea S. A1 - Elliott, J. Alex A1 - Fragoso Jr., Carlos Ruberto A1 - Gaedke, Ursula A1 - Genova, Svetlana N. A1 - Gulati, Ramesh D. A1 - Håkanson, Lars A1 - Hamilton, David P. A1 - Hipsey, Matthew R. A1 - ‘t Hoen, Jochem A1 - Hülsmann, Stephan A1 - Los, F. Hans A1 - Makler-Pick, Vardit A1 - Petzoldt, Thomas A1 - Prokopkin, Igor G. A1 - Rinke, Karsten A1 - Schep, Sebastiaan A. A1 - Tominaga, Koji A1 - Van Dam, Anne A. A1 - Van Nes, Egbert H. A1 - Wells, Scott A. A1 - Janse, Jan H. T1 - Challenges and opportunities for integrating lake ecosystem modelling approaches T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1326 KW - aquatic KW - food web dynamics KW - plankton KW - nutrients KW - spatial KW - lake KW - freshwater KW - marine KW - community KW - population KW - hydrology KW - eutrophication KW - global change KW - climate warming KW - fisheries KW - biodiversity KW - management KW - mitigation KW - adaptive processes KW - non-linear dynamics KW - analysis KW - bifurcation KW - understanding KW - prediction KW - model limitations KW - model integration Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429839 SN - 1866-8372 IS - 1326 ER - TY - JOUR A1 - Mackert, Jürgen T1 - Opportunitätsstrukturen und Lebenschancen T1 - Opportunity structures and life-chances T1 - Structures d’opportunités et chances de vie JF - Berliner Journal für Soziologie N2 - Der Beitrag diskutiert Genese, Bedeutungsgehalt und theoretischen Kontext des Merton’schen Konzepts der Opportunitätsstruktur und des von ihm bei Weber entliehenen Konzepts der Lebenschancen. Die These lautet, dass beide Konzepte konflikttheoretisch interpretiert werden müssen, damit sie ihr volles analytisches und erklärendes Potenzial zur Analyse zentraler sozialer Konflikte entfalten können. Es wird davon ausgegangen, dass beide Konzepte in ihrem Bedeutungsgehalt konvergieren, ein konflikttheoretisch inspiriertes Verständnis aber unterschiedliche theoretische Strategien erfordert. Während die Opportunitätsstrukturen jenseits des Merton’schen Verständnisses reinterpretiert werden müssen, um verstehen zu können, dass das Handeln sozialer Akteure die Optionen anderer beschränken kann, ist für die Lebenschancen ein Zurück zu Max Webers ursprünglicher Idee angezeigt, um der Bedeutung sozialer Schließung als sozialen Mechanismus einer Auseinandersetzung um knappe Güter nachgehen zu können N2 - The article discusses the development, meaning and theoretical context of both Robert Merton’s concept of “opportunity structure” and the concept of “life-chances” that he took up from Max Weber. In order to analyze crucial social conflicts, I argue that both concepts should follow along the lines of conflict theory. While they converge in terms of meaning, we need different theoretical strategies to make their analytical and explanatory power explicit. First, a reinterpretation of the concept of opportunity structure shows that social actors might reduce others’ access to options while realizing their own aims; second, life-chances should be put again in a Weberian perspective for two reasons. On the one hand Weber already conceptualizes them in the context of social struggles, on the other hand he shows that the mechanism of social closure helps to understand how people exclude others from life-chances by monopolizing resources. N2 - Cet article discute la genèse, la signification et le contexte théorique du concept mertonien de structure d’opportunités et du concept wébérien de chances de vie (Lebenschancen) dont il s’inspire. La thèse défendue ici est que ces deux concepts doivent être interprétés à la lumière de la théorie du conflit pour révéler tout leur potentiel analytique et explicatif pour l’analyse de conflits sociaux majeurs. Nous partons de l’idée que ces deux concepts, qui sont la plupart du temps utilisés de manière intuitive, ont une signification convergente et nécessitent une compréhension inspirée par la théorie du conflit mais différentes stratégies théoriques. Tandis qu’il faut réinterpréter les structures d’opportunités au-delà de leur acception mertonienne pour comprendre que l’action des acteurs sociaux peut limiter les options d’autres acteurs, il convient pour le concept de chances de vie de revenir à l’idée originelle de Max Weber pour mettre en évidence la signification de la clôture sociale comme un mécanisme social de lutte pour des biens rares. KW - Opportunitätsstruktur KW - Lebenschancen KW - Sozialstruktur KW - Konflikttheorie KW - Soziale Schließung KW - Opportunity structure KW - Life-chances KW - Social structure KW - Conflict theory KW - Social closure KW - Structure d’opportunités KW - Chances de vie KW - Structure sociale KW - Théorie du conflit KW - Clôture sociale Y1 - 2010 U6 - https://doi.org/https://doi.org/10.1007/s11609-010-0135-7 SN - 1862-2593 SN - 0863-1808 VL - 20 IS - 3 SP - 401 EP - 420 PB - Springer CY - Wiesbaden ER - TY - JOUR A1 - Mackert, Jürgen T1 - Auf den Schultern von Robert Merton? BT - zu Peter Hedströms Analytischer Soziologie JF - die analytische Soziologie in der Diskussion Y1 - 2010 SN - 978-3-531-16914-9 SP - 91 EP - 115 PB - VS, Verl. für Sozialwiss. CY - Wiesbaden ER - TY - JOUR A1 - Mackert, Jürgen T1 - Lebenschancen und die Dynamik sozialer Ungleichheit BT - Grundzüge eines schliessungstheoretischen Erklärungsansatzes JF - Soziale Ungleichheiten Y1 - 2010 SN - 978-3-03-777067-2 SP - 11 EP - 33 PB - Seismo CY - Zürich ER - TY - JOUR A1 - Faber, Eike T1 - The Visigoths as the other T1 - Los visigodos como el otro BT - Barbarians, heretics, martyrs BT - Bárbaros, herejes, mártire JF - Espacio, tiempo y forma : revista de la Facultad de Geografia e Historia / Universidad Nacional de Educación a Distancia. Serie 2, Historia antigua N2 - An analysis of Roman -Visigothic relations in different terms than the usual presupposition of constant military and confessional/Christia n antagonism. Structuralist methodology demonstrates how Roman needs at precise historical moments determ in e how Visigoths were perceived and, therefore, portrayed in our source. N2 - Se pretenden analizar los contactos romano-visigodos fuera de las líneas convencionales que enmarcan estas relaciones en un entramado religiosomilitar. Recurriendo al estructuralismo histórico podemos mostrar cómo las necesidades concretas de Roma determinan la percepción de los visigodos así como su representación en las fuentes. KW - estructuralismo KW - Imperio romano KW - godos KW - cristianismo KW - siglos IV-V d.C KW - Structuralism KW - Roman Empires KW - goths KW - Christianity KW - 4th-5th century AD. Y1 - 2010 U6 - https://doi.org/10.5944/etfii.22.2009.1751 SN - 2340-1370 SN - 1130-1082 IS - 22 SP - 287 EP - 296 PB - Univ. CY - Madrid ER - TY - JOUR A1 - Faber, Eike T1 - Athanarich, Alarich, Athaulf BT - zum Wandel westgotischer Herrschaftskonzeptionen JF - Klio : Beiträge zur Alten Geschichte N2 - In den drei Generationen von Athanarich bis Athaulf unterlag die terwingische/westgotische Konzeption und Ausübung von Herrschaft einem tiefgreifenden Wandlungsprozeß. Athanarich, der letzte „Richter“ der Terwingen regierte in traditioneller Weise, innerhalb der (sakralen) Grenzen seiner Position und ohne seinen Machtanspruch durch römische Ämter oder Titel zu stärken. Alarich etablierte ein Heerkönigtum und trug durch die Erfolge, zu denen er seine Gruppe führte, wesentlich zur Ethnogenese der Westgoten bei. Athaulf, sein Schwiegersohn und Nachfolger, unternahm durch seine Heirat mit Galla Placidia, der Halbschwester des Kaisers Honorius einen neuartigen Versuch, die Westgoten ins weströmische Reich zu integrieren. N2 - Tervingian/Visigothic ideas and practices of rulership underwent rapid change from Athanaric to Athaulf. The last of the so-called Tervinginan judges, Athanaric, ruled in the traditional way, within the (sacred) boundaries of his office and without recourse to Roman offices or titles. Alaric, the epitome of a migration period leader, established kingship and advanced the ethnogenesis of the Visigoths a great deal with the successes he lead his people to. Athaulf, his brother-in-law and successor, ruled as Visigothic king on occupied land in Aquitania. Instead of attempting to rise through Roman military ranks, as Alaric had done, he married the ruling emperor′s half-sister Galla Placidia and tried to establish and integrate himself and his Visigoths in the Western Roman Empire. KW - Westgoten KW - Athanarich KW - Alarich KW - Athaulf KW - Spätantike Y1 - 2010 U6 - https://doi.org/10.1524/klio.2010.0009 SN - 2192-7669 SN - 0075-6334 VL - 92 IS - 1 SP - 157 EP - 169 PB - de Gruyter CY - Berlin ER - TY - JOUR A1 - Faber, Eike T1 - Armut als Ideal BT - der Fundamentalismus der Wohlhabenden JF - Religiöser Fundamentalismus in der römischen Kaiserzeit Y1 - 2010 SN - 978-3-515-10023-6 SN - 978-3-515-09444-3 SP - 179 EP - 196 PB - Steiner CY - Stuttgart ER - TY - GEN A1 - Margaria, Tiziana A1 - Steffen, Bernhard A1 - Kubczak, Christian T1 - Evolution support in heterogeneous service-oriented landscapes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We present an approach that provides automatic or semi-automatic support for evolution and change management in heterogeneous legacy landscapes where (1) legacy heterogeneous, possibly distributed platforms are integrated in a service oriented fashion, (2) the coordination of functionality is provided at the service level, through orchestration, (3) compliance and correctness are provided through policies and business rules, (4) evolution and correctness-by-design are supported by the eXtreme Model Driven Development paradigm (XMDD) offered by the jABC (Margaria and Steffen in Annu. Rev. Commun. 57, 2004)—the model-driven service oriented development platform we use here for integration, design, evolution, and governance. The artifacts are here semantically enriched, so that automatic synthesis plugins can field the vision of Enterprise Physics: knowledge driven business process development for the end user. We demonstrate this vision along a concrete case study that became over the past three years a benchmark for Semantic Web Service discovery and mediation. We enhance the Mediation Scenario of the Semantic Web Service Challenge along the 2 central evolution paradigms that occur in practice: (a) Platform migration: platform substitution of a legacy system by an ERP system and (b) Backend extension: extension of the legacy Customer Relationship Management (CRM) and Order Management System (OMS) backends via an additional ERP layer. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 918 KW - evolving systems KW - semantic web services KW - service mediation KW - web services KW - SOA Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432405 SN - 1866-8372 IS - 918 ER - TY - GEN A1 - Weiße, Andrea Y. A1 - Middleton, Richard H. A1 - Huisinga, Wilhelm T1 - Quantifying uncertainty, variability and likelihood for ordinary differential equation models T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background In many applications, ordinary differential equation (ODE) models are subject to uncertainty or variability in initial conditions and parameters. Both, uncertainty and variability can be quantified in terms of a probability density function on the state and parameter space. Results The partial differential equation that describes the evolution of this probability density function has a form that is particularly amenable to application of the well-known method of characteristics. The value of the density at some point in time is directly accessible by the solution of the original ODE extended by a single extra dimension (for the value of the density). This leads to simple methods for studying uncertainty, variability and likelihood, with significant advantages over more traditional Monte Carlo and related approaches especially when studying regions with low probability. Conclusions While such approaches based on the method of characteristics are common practice in other disciplines, their advantages for the study of biological systems have so far remained unrecognized. Several examples illustrate performance and accuracy of the approach and its limitations. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 894 KW - ordinary differential equation KW - Unscented Kalman Filter KW - global sensitivity analysis KW - Ordinary Differential Equation model KW - joint normal distribution Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431340 SN - 1866-8372 IS - 894 ER - TY - GEN A1 - Breitenstein, Michael A1 - Hölzel, Ralph A1 - Bier, Frank Fabian T1 - Immobilization of different biomolecules by atomic force microscopy T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Background Micrometer resolution placement and immobilization of probe molecules is an important step in the preparation of biochips and a wide range of lab-on-chip systems. Most known methods for such a deposition of several different substances are costly and only suitable for a limited number of probes. In this article we present a flexible procedure for simultaneous spatially controlled immobilization of functional biomolecules by molecular ink lithography. Results For the bottom-up fabrication of surface bound nanostructures a universal method is presented that allows the immobilization of different types of biomolecules with micrometer resolution. A supporting surface is biotinylated and streptavidin molecules are deposited with an AFM (atomic force microscope) tip at distinct positions. Subsequent incubation with a biotinylated molecule species leads to binding only at these positions. After washing streptavidin is deposited a second time with the same AFM tip and then a second biotinylated molecule species is coupled by incubation. This procedure can be repeated several times. Here we show how to immobilize different types of biomolecules in an arbitrary arrangement whereas most common methods can deposit only one type of molecules. The presented method works on transparent as well as on opaque substrates. The spatial resolution is better than 400 nm and is limited only by the AFM's positional accuracy after repeated z-cycles since all steps are performed in situ without moving the supporting surface. The principle is demonstrated by hybridization to different immobilized DNA oligomers and was validated by fluorescence microscopy. Conclusions The immobilization of different types of biomolecules in high-density microarrays is a challenging task for biotechnology. The method presented here not only allows for the deposition of DNA at submicrometer resolution but also for proteins and other molecules of biological relevance that can be coupled to biotin. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 872 KW - Atomic Force Microscope KW - Immobilization KW - Cross Contamination KW - Roth GmbH KW - Microcontact Printing Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435075 SN - 1866-8372 IS - 872 ER - TY - GEN A1 - Repsilber, Dirk A1 - Kern, Sabine A1 - Telaar, Anna A1 - Walzl, Gerhard A1 - Black, Gillian F. A1 - Selbig, Joachim A1 - Parida, Shreemanta K. A1 - Kaufmann, Stefan H. E. A1 - Jacobsen, Marc T1 - Biomarker discovery in heterogeneous tissue samples BT - taking the in-silico deconfounding approach T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: For heterogeneous tissues, such as blood, measurements of gene expression are confounded by relative proportions of cell types involved. Conclusions have to rely on estimation of gene expression signals for homogeneous cell populations, e.g. by applying micro-dissection, fluorescence activated cell sorting, or in-silico deconfounding. We studied feasibility and validity of a non-negative matrix decomposition algorithm using experimental gene expression data for blood and sorted cells from the same donor samples. Our objective was to optimize the algorithm regarding detection of differentially expressed genes and to enable its use for classification in the difficult scenario of reversely regulated genes. This would be of importance for the identification of candidate biomarkers in heterogeneous tissues. Results: Experimental data and simulation studies involving noise parameters estimated from these data revealed that for valid detection of differential gene expression, quantile normalization and use of non-log data are optimal. We demonstrate the feasibility of predicting proportions of constituting cell types from gene expression data of single samples, as a prerequisite for a deconfounding-based classification approach. Classification cross-validation errors with and without using deconfounding results are reported as well as sample-size dependencies. Implementation of the algorithm, simulation and analysis scripts are available. Conclusions: The deconfounding algorithm without decorrelation using quantile normalization on non-log data is proposed for biomarkers that are difficult to detect, and for cases where confounding by varying proportions of cell types is the suspected reason. In this case, a deconfounding ranking approach can be used as a powerful alternative to, or complement of, other statistical learning approaches to define candidate biomarkers for molecular diagnosis and prediction in biomedicine, in realistically noisy conditions and with moderate sample sizes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 854 KW - differential gene expression KW - quantile normalization KW - heterogeneous tissue KW - gene expression matrix KW - homogeneous cell population KW - selection KW - microdissection Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429343 SN - 1866-8372 IS - 854 ER -