@inproceedings{BorowskiGlowinskiFristeretal.2018, author = {Borowski, Andreas and Glowinski, Ingrid and Frister, Jonas and H{\"o}ttecke, Dietmar and Buth, Katrin and Koenen, Jenna and Masanek, Nicole and Reichwein, Wilko and Scholten, Nina and Sprenger, Sandra and Stender, Peter and W{\"o}hlke, Carina and Komorek, Michael and Freckmann, Janine and Hofmann, Josefine and Niesel, Verena and Richter, Chris and Mehlmann, Nelli and Bikner-Ahsbahs, Angelika and Unverricht, Katja and Schanze, Sascha and Bittorf, Robert Marten and Meier, Monique and Grospietsch, Finja and Mayer, J{\"u}rgen and Gimbel, Katharina and Ziepprecht, Kathrin and Hofmann, Judith and Kramer, Charlotte and M{\"u}ller, Britta-Kornelia and Rohde, Andreas and Z{\"u}hlsdorf, Felix and Winkler, Iris and Laging, Ralf and Peter, Carina and Schween, Michael and H{\"a}rle, Gerhard and Busse, Beatrix and Mahner, Sebastian and K{\"o}stler, Verena and Kufner, Sabrina and M{\"a}gdefrau, Jutta and M{\"u}ller, Christian and Beck, Christina and Kriehuber, Eva and Boch, Florian and Engl, Anna-Teresa and Helzel, Andreas and Pickert, Tina and Reiter, Christian and Blasini, Bettina and Nerdel, Claudia and Lewalter, Doris and Schiffhauer, Silke and Richter-Gebert, J{\"u}rgen and Bannert, Maria and Maahs, Mirjam and Reißner, Maria and Ungar, Patrizia and von Wachter, Jana-Kristin and Hellmann, Katharina and Zaki, Katja and Pohlenz, Philipp}, title = {Koh{\"a}renz in der universit{\"a}ren Lehrerbildung}, editor = {Glowinski, Ingrid and Borowski, Andreas and Gillen, Julia and Schanze, Sascha and von Meien, Joachim}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-438-8}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414267}, year = {2018}, abstract = {One area that is supported by the project "Qualit{\"a}tsoffensive Lehrerbildung" (funded by BMBF) is the improvement of collaboration and coordination between studies in the discipline, studies in pedagogical content knowledge, and studies in pedagogical knowledge during teacher education at university. Aiming a better coordination among these three parts of teacher education at university, many of the supported projects have designed and realized university-specific approaches. This conference proceedings volume comprises contributions by 15 of these projects. Seven of those were introduced and discussed in workshops on the occasion of two cross-regional project-conferences in Hannover and Potsdam. Overall, the contributions give a theoretically funded as well as a practice-oriented overview of current approaches and concepts to achieve a better connection between study units concerning studies in content knowledge, pedagogical content knowledge and pedagogical knowledge in teacher education. The volume presents university projects, which take effect on different levels (at the level of curriculum and content, at a collegiate level, at the level of structural conditions of universities). The different approaches are described in a way that they can provide a basis for transfer to other subjects or further universities. The contributions are aimed at teacher educators as well as other actors working in the field of teaching- and quality development at universities. All of them can take transferable ideas and impulses from the described concepts and formats.}, language = {de} } @misc{KrahThulinFaiersteinetal.2019, author = {Krah, Markus and Thulin, Mirjam and Faierstein, Morris M. and Drori, Danielle and Coors, Maria and Schramm, Netta and Driver, Cory and Holzman, Gitit and Zuckermann, Ghil'ad and Fishbane, Eitan P. and Gruenbaum, Caroline and Schirrmeister, Sebastian and Ferrari, Francesco and Stemberger, G{\"u}nter and Schm{\"o}lz-H{\"a}berlein, Michaela and M{\"u}ller, Judith and Schulz, Michael Karl and Meyer, Thomas and Artwińska, Anna and Walter, Simon}, title = {PaRDeS : Zeitschrift der Vereinigung f{\"u}r J{\"u}dische Studien = Transformative Translations in Jewish History and Culture}, number = {25}, editor = {Krah, Markus and Thulin, Mirjam and Pick, Bianca}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-468-5}, issn = {1614-6492}, doi = {10.25932/publishup-43262}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432621}, pages = {198}, year = {2019}, abstract = {PaRDeS, die Zeitschrift der Vereinigung f{\"u}r J{\"u}dische Studien e. V., erforscht die fruchtbare kulturelle Vielfalt des Judentums sowie ihre Ber{\"u}hrungspunkte zur nichtj{\"u}dischen Umwelt in unterschiedlichen Bereichen. Daneben dient die Zeitschrift als Forum zur Positionierung der F{\"a}cher J{\"u}dische Studien und ­Judaistik innerhalb des wissenschaftlichen Diskurses sowie zur Diskussion ihrer historischen und gesellschaftlichen Verantwortung.}, language = {en} } @misc{AskinEmmerichFritscheGoppeletal.2012, author = {Askin, Elif and Emmerich-Fritsche, Angelika and Goppel, Anna and Hemmerling, Mario and Kapaun, Nina and Lohmann, Georg and M{\"u}ller, Sebastian and Niederberger, Andreas and Pabel, Katharina and Putzer, Max and Roth-Isigkeit, David and Seidler, Christoph and Tiedemann, Paul and Vasel, J. Justus and Weiß, Norman}, title = {MenschenRechtsMagazin : Informationen | Meinungen | Analysen}, volume = {17}, number = {2}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {1434-2820}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-62122}, year = {2012}, abstract = {Aus dem Inhalt: - Themenschwerpunkt: Menschenrechte und Staatsb{\"u}rgerschaft - Gibt es Menschenrechte ohne B{\"u}rgerschaft? - Menschenw{\"u}rde und Staatsb{\"u}rgerschaft - Die General Comments des Menschenrechtsausschusses der Vereinten Nationen - ein Beitrag zur Rechtsentwicklung im V{\"o}lkerrecht - Politische Selbstbestimmung als Menschenrecht und im V{\"o}lkerrecht - Libyen und der von außen unterst{\"u}tzte Systemwechsel}, language = {de} } @article{PipekStevensVeithetal.2010, author = {Pipek, Volkmar and Stevens, Gunnar and Veith, Michael and M{\"u}ller, Claudia and Draxler, Sebastian}, title = {Jede Software ist "Social"}, series = {Analyse Sozialer Netzwerke und Social Software}, journal = {Analyse Sozialer Netzwerke und Social Software}, publisher = {GITO}, address = {Berlin}, isbn = {978-3-940019-26-4}, pages = {199 -- 233}, year = {2010}, language = {de} } @article{MullerRatschSonnenburgetal.2005, author = {Muller, K. R. and Ratsch, G. and Sonnenburg, S. and Mika, Sebastian and Grimm, M. and Heinrich, N.}, title = {Classifying 'drug-likeness' with kernel-based learning methods}, issn = {1549-9596}, year = {2005}, abstract = {In this article we report about a successful application of modern machine learning technology, namely Support Vector Machines, to the problem of assessing the 'drug-likeness' of a chemical from a given set of descriptors of the Substance. We were able to drastically improve the recent result by Byvatov et al. (2003) on this task and achieved an error rate of about 7\% on unseen compounds using Support Vector Machines. We see a very high potential of such machine learning techniques for a variety of computational chemistry problems that occur in the drug discovery and drug design process}, language = {en} } @book{ScherbaumMzhavanadzeArometal.2020, author = {Scherbaum, Frank and Mzhavanadze, Nana and Arom, Simha and Rosenzweig, Sebastian and M{\"u}ller, Meinard}, title = {Tonal Organization of the Erkomaishvili Dataset: Pitches, Scales, Melodies and Harmonies}, series = {Computational Analysis Of Traditional Georgian Vocal Music}, journal = {Computational Analysis Of Traditional Georgian Vocal Music}, number = {1}, editor = {Scherbaum, Frank}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {2702-2641}, doi = {10.25932/publishup-47614}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476141}, publisher = {Universit{\"a}t Potsdam}, pages = {64}, year = {2020}, abstract = {In this study we examine the tonal organization of a series of recordings of liturgical chants, sung in 1966 by the Georgian master singer Artem Erkomaishvili. This dataset is the oldest corpus of Georgian chants from which the time synchronous F0-trajectories for all three voices have been reliably determined (M{\"u}ller et al. 2017). It is therefore of outstanding importance for the understanding of the tuning principles of traditional Georgian vocal music. The aim of the present study is to use various computational methods to analyze what these recordings can contribute to the ongoing scientific dispute about traditional Georgian tuning systems. Starting point for the present analysis is the re-release of the original audio data together with estimated fundamental frequency (F0) trajectories for each of the three voices, beat annotations, and digital scores (Rosenzweig et al. 2020). We present synoptic models for the pitch and the harmonic interval distributions, which are the first of such models for which the complete Erkomaishvili dataset was used. We show that these distributions can be very compactly be expressed as Gaussian mixture models, anchored on discrete sets of pitch or interval values for the pitch and interval distributions, respectively. As part of our study we demonstrate that these pitch values, which we refer to as scale pitches, and which are determined as the mean values of the Gaussian mixture elements, define the scale degrees of the melodic sound scales which build the skeleton of Artem Erkomaishvili's intonation. The observation of consistent pitch bending of notes in melodic phrases, which appear in identical form in a group of chants, as well as the observation of harmonically driven intonation adjustments, which are clearly documented for all pure harmonic intervals, demonstrate that Artem Erkomaishvili intentionally deviates from the scale pitch skeleton quite freely. As a central result of our study, we proof that this melodic freedom is always constrained by the attracting influence of the scale pitches. Deviations of the F0-values of individual note events from the scale pitches at one instance of time are compensated for in the subsequent melodic steps. This suggests a deviation-compensation mechanism at the core of Artem Erkomaishvili's melody generation, which clearly honors the scales but still allows for a large degree of melodic flexibility. This model, which summarizes all partial aspects of our analysis, is consistent with the melodic scale models derived from the observed pitch distributions, as well as with the melodic and harmonic interval distributions. In addition to the tangible results of our work, we believe that our work has general implications for the determination of tuning models from audio data, in particular for non-tempered music.}, language = {en} } @article{FabianKunzMuelleretal.2013, author = {Fabian, Benjamin and Kunz, Steffen and M{\"u}ller, Sebastian and G{\"u}nther, Oliver}, title = {Secure federation of semantic information services}, series = {Decision support systems : DSS ; the international journal}, volume = {55}, journal = {Decision support systems : DSS ; the international journal}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-9236}, doi = {10.1016/j.dss.2012.05.049}, pages = {385 -- 398}, year = {2013}, abstract = {fundamental challenge for product-lifecycle management in collaborative value networks is to utilize the vast amount of product information available from heterogeneous sources in order to improve business analytics, decision support, and processes. This becomes even more challenging if those sources are distributed across multiple organizations. Federations of semantic information services, combining service-orientation and semantic technologies, provide a promising solution for this problem. However, without proper measures to establish information security, companies will be reluctant to join an information federation, which could lead to serious adoption barriers. Following the design science paradigm, this paper presents general objectives and a process for designing a secure federation of semantic information services. Furthermore, new as well as established security measures are discussed. Here, our contributions include an access-control enforcement system for semantic information services and a process for modeling access-control policies across organizations. In addition, a comprehensive security architecture is presented. An implementation of the architecture in the context of an application scenario and several performance experiments demonstrate the practical viability of our approach.}, language = {en} } @article{MuellerZechHesse2021, author = {M{\"u}ller, Sebastian and Zech, Alraune and Hesse, Falk}, title = {ogs5py: APython-APIfor theOpenGeoSys5 Scientific Modeling Package}, series = {Groundwater : journal of the Association of Ground-Water Scientists and Engineers, a division of the National Ground Water Association}, volume = {59}, journal = {Groundwater : journal of the Association of Ground-Water Scientists and Engineers, a division of the National Ground Water Association}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0017-467X}, doi = {10.1111/gwat.13017}, pages = {117 -- 122}, year = {2021}, abstract = {High-performance numerical codes are an indispensable tool for hydrogeologists when modeling subsurface flow and transport systems. But as they are written in compiled languages, like C/C++ or Fortran, established software packages are rarely user-friendly, limiting a wider adoption of such tools. OpenGeoSys (OGS), an open-source, finite-element solver for thermo-hydro-mechanical-chemical processes in porous and fractured media, is no exception. Graphical user interfaces may increase usability, but do so at a dramatic reduction of flexibility and are difficult or impossible to integrate into a larger workflow. Python offers an optimal trade-off between these goals by providing a highly flexible, yet comparatively user-friendly environment for software applications. Hence, we introduceogs5py, a Python-API for the OpenGeoSys 5 scientific modeling package. It provides a fully Python-based representation of an OGS project, a large array of convenience functions for users to interact with OGS and connects OGS to the scientific and computational environment of Python.}, language = {en} } @article{WalterRueckertVossetal.2009, author = {Walter, Juliane K. and R{\"u}ckert, Christine and Voss, Martin and M{\"u}ller, Sebastian L. and Piontek, Joerg and Gast, Klaus and Blasig, Ingolf E.}, title = {The oligomerization of the coiled coil-domain of occluddin is redox sensitive}, issn = {0077-8923}, doi = {10.1111/j.1749-6632.2009.04058.x}, year = {2009}, abstract = {The transmembrane tight junction protein occludin is sensitive to oxidative stress. Occludin oligomerizes; however, its function in the tight junction is unknown. The cytosolic C-terminal tail contains a coiled coil-domain and forms dimers contributing to the oligomerization. The regulation of the oligomerization remains unclear. As the domain area contains sulfhydryl residues, we tested the hypothesis that the dimerization of the coiled coil-domain depends on these residues. We showed that the dimerization is modulated by the thiol concentration in the low-millimolar range, which is relevant both for physiological and pathophysiological conditions. Masking the sulfhydryl residues in the fragment by covalent binding of 4-vinyl pyridine prevented the dimerization but did not affect its helical structure and cylindric shape. The data demonstrate, for the first time, that disulfide bridge formation of murine cystein 408 is involved in the dimerization. This process is redox-sensitive but the secondary structure of the domain is not. It is concluded that the dimerization of occludin may play a regulatory role in the tight junction assembly under physiological and pathological conditions.}, language = {en} } @article{FabianKunzKonnegenetal.2012, author = {Fabian, Benjamin and Kunz, Steffen and Konnegen, Marcel and M{\"u}ller, Sebastian and G{\"u}nther, Oliver}, title = {Access control for semantic data federations in industrial product-lifecycle management}, series = {Computers in industry : an international, application oriented research journal}, volume = {63}, journal = {Computers in industry : an international, application oriented research journal}, number = {9}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0166-3615}, doi = {10.1016/j.compind.2012.08.015}, pages = {930 -- 940}, year = {2012}, abstract = {Information integration across company borders becomes increasingly important for the success of product lifecycle management in industry and complex supply chains. Semantic technologies are about to play a crucial role in this integrative process. However, cross-company data exchange requires mechanisms to enable fine-grained access control definition and enforcement, preventing unauthorized leakage of confidential data across company borders. Currently available semantic repositories are not sufficiently equipped to satisfy this important requirement. This paper presents an infrastructure for controlled sharing of semantic data between cooperating business partners. First, we motivate the need for access control in semantic data federations by a case study in the industrial service sector. Furthermore, we present an architecture for controlling access to semantic repositories that is based on our newly developed SemForce security service. Finally, we show the practical feasibility of this architecture by an implementation and several performance experiments.}, language = {en} } @article{ZienRaetschMikaetal.2000, author = {Zien, Alexander and R{\"a}tsch, Gunnar and Mika, Sebastian and Sch{\"o}lkopf, Bernhard and Lengauer, Thomas and M{\"u}ller, Klaus-Robert}, title = {Engineering support vector machine kernels that recognize translation initiation sites}, issn = {1367-4803}, year = {2000}, language = {en} } @article{RaetschSchoelkopfSmolaetal.2000, author = {R{\"a}tsch, Gunnar and Sch{\"o}lkopf, B. and Smola, Alexander J. and Mika, Sebastian and Onoda, T. and M{\"u}ller, Klaus-Robert}, title = {Robust ensemble learning}, isbn = {0-262-19448-1}, year = {2000}, language = {en} } @book{RaetschSchoelkopfMikaetal.2000, author = {R{\"a}tsch, Gunnar and Sch{\"o}lkopf, B. and Mika, Sebastian and M{\"u}ller, Klaus-Robert}, title = {SVM and boosting : one class}, series = {GMD-Report}, volume = {119}, journal = {GMD-Report}, publisher = {GMD-Forschungszentrum Informationstechnik}, address = {Sankt Augustin}, pages = {36 S.}, year = {2000}, language = {en} } @article{RaetschSchoelkopfSmolaetal.2000, author = {R{\"a}tsch, Gunnar and Sch{\"o}lkopf, B. and Smola, Alexander J. and M{\"u}ller, Klaus-Robert and Mika, Sebastian}, title = {V-Arc : ensemble learning in the preence of outliers}, year = {2000}, language = {en} } @article{MikaRaetschWestonetal.2000, author = {Mika, Sebastian and R{\"a}tsch, Gunnar and Weston, J. and Sch{\"o}lkopf, B. and Smola, Alexander J. and M{\"u}ller, Klaus-Robert}, title = {Invariant feature extraction and classification in kernel spaces}, year = {2000}, language = {en} } @article{RaetschSchoelkopfSmolaetal.2000, author = {R{\"a}tsch, Gunnar and Sch{\"o}lkopf, B. and Smola, Alexander J. and Mika, Sebastian and Onoda, T. and M{\"u}ller, Klaus-Robert}, title = {Robust ensemble learning for data analysis}, year = {2000}, language = {en} } @article{KoeslinFindekleeRiziBeckeretal.2015, author = {K{\"o}slin-Findeklee, Fabian and Rizi, Vajiheh Safavi and Becker, Martin A. and Parra-Londono, Sebastian and Arif, Muhammad and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd and Kunze, Reinhard and Horst, Walter J.}, title = {Transcriptomic analysis of nitrogen starvation- and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus L.)}, series = {Plant science : an international journal of experimental plant biology}, volume = {233}, journal = {Plant science : an international journal of experimental plant biology}, publisher = {Elsevier}, address = {Clare}, issn = {0168-9452}, doi = {10.1016/j.plantsci.2014.11.018}, pages = {174 -- 185}, year = {2015}, abstract = {High nitrogen (N) efficiency, characterized by high grain yield under N limitation, is an important agricultural trait in Brassica napus L. cultivars related to delayed senescence of older leaves during reproductive growth (a syndrome called stay-green). The aim of this study was thus to identify genes whose expression is specifically altered during N starvation-induced leaf senescence and that can be used as markers to distinguish cultivars at early stages of senescence prior to chlorophyll loss. To this end, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analyzed 4 days after the induction of senescence by either N starvation, leaf shading or detaching. In addition to N metabolism genes, N starvation mostly (and specifically) repressed genes related to photosynthesis, photorespiration and cell-wall structure, while genes related to mitochondrial electron transport and flavonoid biosynthesis were predominately up-regulated. A kinetic study over a period of 12 days with four B. napus cultivars differing in their stay-green characteristics confirmed the cultivar-specific regulation of six genes in agreement with their senescence behavior: the senescence regulator ANAC029, the anthocyanin synthesis-related genes ANS and DFR-like1, the ammonium transporter AMT1:4, the ureide transporter UPSS, and SPS1 involved in sucrose biosynthesis. The identified genes represent markers for the detection of cultivar-specific differences in N starvation-induced leaf senescence and can thus be employed as valuable tools in B. napus breeding. (C) 2015 Elsevier Ireland Ltd. All rights reserved.}, language = {en} } @article{ProostVanBelVaneechoutteetal.2015, author = {Proost, Sebastian and Van Bel, Michiel and Vaneechoutte, Dries and Van de Peer, Yves and Inze, Dirk and M{\"u}ller-R{\"o}ber, Bernd and Vandepoele, Klaas}, title = {PLAZA 3.0: an access point for plant comparative genomics}, series = {Nucleic acids research}, volume = {43}, journal = {Nucleic acids research}, number = {D1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gku986}, pages = {D974 -- D981}, year = {2015}, abstract = {Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.}, language = {en} } @article{OmidbakhshfardProostFujikuraetal.2015, author = {Omidbakhshfard, Mohammad Amin and Proost, Sebastian and Fujikura, Ushio and M{\"u}ller-R{\"o}ber, Bernd}, title = {Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology}, series = {Molecular plant}, volume = {8}, journal = {Molecular plant}, number = {7}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1016/j.molp.2015.01.013}, pages = {998 -- 1010}, year = {2015}, abstract = {Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level.}, language = {en} } @article{ReadKegelKluteetal.2013, author = {Read, Betsy A. and Kegel, Jessica and Klute, Mary J. and Kuo, Alan and Lefebvre, Stephane C. and Maumus, Florian and Mayer, Christoph and Miller, John and Monier, Adam and Salamov, Asaf and Young, Jeremy and Aguilar, Maria and Claverie, Jean-Michel and Frickenhaus, Stephan and Gonzalez, Karina and Herman, Emily K. and Lin, Yao-Cheng and Napier, Johnathan and Ogata, Hiroyuki and Sarno, Analissa F. and Shmutz, Jeremy and Schroeder, Declan and de Vargas, Colomban and Verret, Frederic and von Dassow, Peter and Valentin, Klaus and Van de Peer, Yves and Wheeler, Glen and Dacks, Joel B. and Delwiche, Charles F. and Dyhrman, Sonya T. and Gl{\"o}ckner, Gernot and John, Uwe and Richards, Thomas and Worden, Alexandra Z. and Zhang, Xiaoyu and Grigoriev, Igor V. and Allen, Andrew E. and Bidle, Kay and Borodovsky, M. and Bowler, C. and Brownlee, Colin and Cock, J. Mark and Elias, Marek and Gladyshev, Vadim N. and Groth, Marco and Guda, Chittibabu and Hadaegh, Ahmad and Iglesias-Rodriguez, Maria Debora and Jenkins, J. and Jones, Bethan M. and Lawson, Tracy and Leese, Florian and Lindquist, Erika and Lobanov, Alexei and Lomsadze, Alexandre and Malik, Shehre-Banoo and Marsh, Mary E. and Mackinder, Luke and Mock, Thomas and M{\"u}ller-R{\"o}ber, Bernd and Pagarete, Antonio and Parker, Micaela and Probert, Ian and Quesneville, Hadi and Raines, Christine and Rensing, Stefan A. and Riano-Pachon, Diego Mauricio and Richier, Sophie and Rokitta, Sebastian and Shiraiwa, Yoshihiro and Soanes, Darren M. and van der Giezen, Mark and Wahlund, Thomas M. and Williams, Bryony and Wilson, Willie and Wolfe, Gordon and Wurch, Louie L.}, title = {Pan genome of the phytoplankton Emiliania underpins its global distribution}, series = {Nature : the international weekly journal of science}, volume = {499}, journal = {Nature : the international weekly journal of science}, number = {7457}, publisher = {Nature Publ. Group}, address = {London}, organization = {Emiliania Huxleyi Annotation}, issn = {0028-0836}, doi = {10.1038/nature12221}, pages = {209 -- 213}, year = {2013}, abstract = {Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.}, language = {en} } @article{DiluisoWalkManychetal.2021, author = {Diluiso, Francesca and Walk, Paula and Manych, Niccolo and Cerutti, Nicola and Chipiga, Vladislav and Workman, Annabelle and Ayas, Ceren and Cui, Ryna Yiyun and Cui, Diyang and Song, Kaihui and Banisch, Lucy A. and Moretti, Nikolaj and Callaghan, Max W. and Clarke, Leon and Creutzig, Felix and Hilaire, Jerome and Jotzo, Frank and Kalkuhl, Matthias and Lamb, William F. and L{\"o}schel, Andreas and M{\"u}ller-Hansen, Finn and Nemet, Gregory F. and Oei, Pao-Yu and Sovacool, Benjamin K. and Steckel, Jan Christoph and Thomas, Sebastian and Wiseman, John and Minx, Jan C.}, title = {Coal transitions - part 1}, series = {Environmental research letters}, volume = {16}, journal = {Environmental research letters}, number = {11}, publisher = {Institute of Physics Publishing (IOP)}, address = {Bristol}, issn = {1748-9326}, doi = {10.1088/1748-9326/ac1b58}, pages = {40}, year = {2021}, abstract = {A rapid coal phase-out is needed to meet the goals of the Paris Agreement, but is hindered by serious challenges ranging from vested interests to the risks of social disruption. To understand how to organize a global coal phase-out, it is crucial to go beyond cost-effective climate mitigation scenarios and learn from the experience of previous coal transitions. Despite the relevance of the topic, evidence remains fragmented throughout different research fields, and not easily accessible. To address this gap, this paper provides a systematic map and comprehensive review of the literature on historical coal transitions. We use computer-assisted systematic mapping and review methods to chart and evaluate the available evidence on historical declines in coal production and consumption. We extracted a dataset of 278 case studies from 194 publications, covering coal transitions in 44 countries and ranging from the end of the 19th century until 2021. We find a relatively recent and rapidly expanding body of literature reflecting the growing importance of an early coal phase-out in scientific and political debates. Previous evidence has primarily focused on the United Kingdom, the United States, and Germany, while other countries that experienced large coal declines, like those in Eastern Europe, are strongly underrepresented. An increasing number of studies, mostly published in the last 5 years, has been focusing on China. Most of the countries successfully reducing coal dependency have undergone both demand-side and supply-side transitions. This supports the use of policy approaches targeting both demand and supply to achieve a complete coal phase-out. From a political economy perspective, our dataset highlights that most transitions are driven by rising production costs for coal, falling prices for alternative energies, or local environmental concerns, especially regarding air pollution. The main challenges for coal-dependent regions are structural change transformations, in particular for industry and labor. Rising unemployment is the most largely documented outcome in the sample. Policymakers at multiple levels are instrumental in facilitating coal transitions. They rely mainly on regulatory instruments to foster the transitions and compensation schemes or investment plans to deal with their transformative processes. Even though many models suggest that coal phase-outs are among the low-hanging fruits on the way to climate neutrality and meeting the international climate goals, our case studies analysis highlights the intricate political economy at work that needs to be addressed through well-designed and just policies.}, language = {en} } @misc{ZechSteinHabereretal.2003, author = {Zech, Christina and Stein, Monika and Haberer, Anke and B{\"o}hne, Alexander and M{\"u}ller-R{\"o}ber, Bernd and Heinig, Angela and Raehse, Sebastian}, title = {Portal = Existenzgr{\"u}ndung: Ein Sprung ins kalte Wasser}, volume = {2003}, organization = {Universit{\"a}t Potsdam, Referat f{\"u}r Presse- und {\"O}ffentlichkeitsarbeit}, issn = {1618-6893}, doi = {10.25932/publishup-50153}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-501536}, pages = {44}, year = {2003}, abstract = {Aus dem Inhalt: Existenzgr{\"u}ndung: Ein Sprung ins kalte Wasser -Bernd Walz {\"u}ber Wettbewerbsf{\"a}higkeit und Nachwuchsf{\"o}rderung -Gertrud Lehnert {\"u}ber Mode bei Marcel Proust -Juniorprofessor Jens Eisert {\"u}ber Quanteninformation}, language = {de} } @article{KirchheckerTroegerMuellerBakeetal.2015, author = {Kirchhecker, Sarah and Tr{\"o}ger-M{\"u}ller, Steffen and Bake, Sebastian and Antonietti, Markus and Taubert, Andreas and Esposito, Davido}, title = {Renewable pyridinium ionic liquids from the continuous hydrothermal decarboxylation of furfural-amino acid derived pyridinium zwitterions}, series = {Green chemistry}, volume = {8}, journal = {Green chemistry}, number = {17}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9262}, doi = {10.1039/c5gc00913h}, pages = {4151 -- 4156}, year = {2015}, abstract = {Fully renewable pyridinium ionic liquids were synthesised via the hydrothermal decarboxylation of pyridinium zwitterions derived from furfural and amino acids in flow. The functionality of the resulting ionic liquid (IL) can be tuned by choice of different amino acids as well as different natural carboxylic acids as the counterions. A representative member of this new class of ionic liquids was successfully used for the synthesis of ionogels and as a solvent for the Heck coupling.}, language = {en} } @article{KirchheckerTroegerMuellerBakeetal.2015, author = {Kirchhecker, Sarah and Tr{\"o}ger-M{\"u}ller, Steffen and Bake, Sebastian and Antonietti, Markus and Taubert, Andreas and Esposito, Davide}, title = {Renewable pyridinium ionic liquids from the continuous hydrothermal decarboxylation of furfural-amino acid derived pyridinium zwitterions}, series = {Green chemistry : an international journal and green chemistry resource}, volume = {17}, journal = {Green chemistry : an international journal and green chemistry resource}, number = {8}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9262}, doi = {10.1039/c5gc00913h}, pages = {4151 -- 4156}, year = {2015}, abstract = {Fully renewable pyridinium ionic liquids were synthesised via the hydrothermal decarboxylation of pyridinium zwitterions derived from furfural and amino acids in flow. The functionality of the resulting ionic liquid (IL) can be tuned by choice of different amino acids as well as different natural carboxylic acids as the counter-ions. A representative member of this new class of ionic liquids was successfully used for the synthesis of ionogels and as a solvent for the Heck coupling.}, language = {en} } @misc{KirchheckerTroegerMuellerBakeetal.2015, author = {Kirchhecker, Sarah and Tr{\"o}ger-M{\"u}ller, Steffen and Bake, Sebastian and Antonietti, Markus and Taubert, Andreas and Esposito, Davido}, title = {Renewable pyridinium ionic liquids from the continuous hydrothermal decarboxylation of furfural-amino acid derived pyridinium zwitterions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-81390}, year = {2015}, abstract = {Fully renewable pyridinium ionic liquids were synthesised via the hydrothermal decarboxylation of pyridinium zwitterions derived from furfural and amino acids in flow. The functionality of the resulting ionic liquid (IL) can be tuned by choice of different amino acids as well as different natural carboxylic acids as the counterions. A representative member of this new class of ionic liquids was successfully used for the synthesis of ionogels and as a solvent for the Heck coupling.}, language = {en} } @article{MuellerSchuelerZechetal.2022, author = {M{\"u}ller, Sebastian and Sch{\"u}ler, Lennart and Zech, Alraune and Heße, Falk}, title = {GSTools v1.3: a toolbox for geostatistical modelling in Python}, series = {Geoscientific model development : an interactive open access journal of the European Geosciences Union}, volume = {15}, journal = {Geoscientific model development : an interactive open access journal of the European Geosciences Union}, number = {7}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1991-959X}, doi = {10.5194/gmd-15-3161-2022}, pages = {3161 -- 3182}, year = {2022}, abstract = {Geostatistics as a subfield of statistics accounts for the spatial correlations encountered in many applications of, for example, earth sciences. Valuable information can be extracted from these correlations, also helping to address the often encountered burden of data scarcity. Despite the value of additional data, the use of geostatistics still falls short of its potential. This problem is often connected to the lack of user-friendly software hampering the use and application of geostatistics. We therefore present GSTools, a Python-based software suite for solving a wide range of geostatistical problems. We chose Python due to its unique balance between usability, flexibility, and efficiency and due to its adoption in the scientific community. GSTools provides methods for generating random fields; it can perform kriging, variogram estimation and much more. We demonstrate its abilities by virtue of a series of example applications detailing their use.}, language = {en} } @misc{ThiekenBesselKienzleretal.2016, author = {Thieken, Annegret and Bessel, Tina and Kienzler, Sarah and Kreibich, Heidi and M{\"u}ller, Meike and Pisi, Sebastian and Schr{\"o}ter, Kai}, title = {The flood of June 2013 in Germany}, series = {National Hazards Earth System Science}, journal = {National Hazards Earth System Science}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-97207}, pages = {21}, year = {2016}, abstract = {In June 2013, widespread flooding and consequent damage and losses occurred in Central Europe, especially in Germany. This paper explores what data are available to investigate the adverse impacts of the event, what kind of information can be retrieved from these data and how well data and information fulfil requirements that were recently proposed for disaster reporting on the European and international levels. In accordance with the European Floods Directive (2007/60/EC), impacts on human health, economic activities (and assets), cultural heritage and the environment are described on the national and sub-national scale. Information from governmental reports is complemented by communications on traffic disruptions and surveys of flood-affected residents and companies. Overall, the impacts of the flood event in 2013 were manifold. The study reveals that flood-affected residents suffered from a large range of impacts, among which mental health and supply problems were perceived more seriously than financial losses. The most frequent damage type among affected companies was business interruption. This demonstrates that the current scientific focus on direct (financial) damage is insufficient to describe the overall impacts and severity of flood events. The case further demonstrates that procedures and standards for impact data collection in Germany are widely missing. Present impact data in Germany are fragmentary, heterogeneous, incomplete and difficult to access. In order to fulfil, for example, the monitoring and reporting requirements of the Sendai Framework for Disaster Risk Reduction 2015-2030 that was adopted in March 2015 in Sendai, Japan, more efforts on impact data collection are needed.}, language = {en} } @misc{ThiekenKienzlerKreibichetal.2016, author = {Thieken, Annegret and Kienzler, Sarah and Kreibich, Heidi and Kuhlicke, Christian and Kunz, Michael and M{\"u}hr, Bernhard and M{\"u}ller, Meike and Otto, Antje and Petrow, Theresia and Pisi, Sebastian and Schr{\"o}ter, Kai}, title = {Review of the flood risk management system in Germany after the major flood in 2013}, issn = {1866-8372}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100600}, pages = {12}, year = {2016}, abstract = {Widespread flooding in June 2013 caused damage costs of €6 to 8 billion in Germany, and awoke many memories of the floods in August 2002, which resulted in total damage of €11.6 billion and hence was the most expensive natural hazard event in Germany up to now. The event of 2002 does, however, also mark a reorientation toward an integrated flood risk management system in Germany. Therefore, the flood of 2013 offered the opportunity to review how the measures that politics, administration, and civil society have implemented since 2002 helped to cope with the flood and what still needs to be done to achieve effective and more integrated flood risk management. The review highlights considerable improvements on many levels, in particular (1) an increased consideration of flood hazards in spatial planning and urban development, (2) comprehensive property-level mitigation and preparedness measures, (3) more effective flood warnings and improved coordination of disaster response, and (4) a more targeted maintenance of flood defense systems. In 2013, this led to more effective flood management and to a reduction of damage. Nevertheless, important aspects remain unclear and need to be clarified. This particularly holds for balanced and coordinated strategies for reducing and overcoming the impacts of flooding in large catchments, cross-border and interdisciplinary cooperation, the role of the general public in the different phases of flood risk management, as well as a transparent risk transfer system. Recurring flood events reveal that flood risk management is a continuous task. Hence, risk drivers, such as climate change, land-use changes, economic developments, or demographic change and the resultant risks must be investigated at regular intervals, and risk reduction strategies and processes must be reassessed as well as adapted and implemented in a dialogue with all stakeholders.}, language = {en} } @article{ThiekenBesselKienzleretal.2016, author = {Thieken, Annegret and Bessel, Tina and Kienzler, Sarah and Kreibich, Heidi and M{\"u}ller, Meike and Pisi, Sebastian and Schr{\"o}ter, Kai}, title = {The flood of June 2013 in Germany}, series = {National Hazards Earth System Science}, journal = {National Hazards Earth System Science}, number = {16}, publisher = {Copernicus Publications}, address = {G{\"o}ttingen}, doi = {10.5194/nhess-16-1519-2016}, pages = {1519 -- 1540}, year = {2016}, abstract = {In June 2013, widespread flooding and consequent damage and losses occurred in Central Europe, especially in Germany. This paper explores what data are available to investigate the adverse impacts of the event, what kind of information can be retrieved from these data and how well data and information fulfil requirements that were recently proposed for disaster reporting on the European and international levels. In accordance with the European Floods Directive (2007/60/EC), impacts on human health, economic activities (and assets), cultural heritage and the environment are described on the national and sub-national scale. Information from governmental reports is complemented by communications on traffic disruptions and surveys of flood-affected residents and companies. Overall, the impacts of the flood event in 2013 were manifold. The study reveals that flood-affected residents suffered from a large range of impacts, among which mental health and supply problems were perceived more seriously than financial losses. The most frequent damage type among affected companies was business interruption. This demonstrates that the current scientific focus on direct (financial) damage is insufficient to describe the overall impacts and severity of flood events. The case further demonstrates that procedures and standards for impact data collection in Germany are widely missing. Present impact data in Germany are fragmentary, heterogeneous, incomplete and difficult to access. In order to fulfil, for example, the monitoring and reporting requirements of the Sendai Framework for Disaster Risk Reduction 2015-2030 that was adopted in March 2015 in Sendai, Japan, more efforts on impact data collection are needed.}, language = {en} } @book{ThiekenBesselCallsenetal.2015, author = {Thieken, Annegret and Bessel, Tina and Callsen, Ines and Falter, Daniela and Hasan, Issa and Kienzler, Sarah and Kox, Thomas and Kreibich, Heidi and Kuhlicke, Christian and Kunz, Michael and Matthias, Max and Meyer, Volker and M{\"u}hr, Bernhard and M{\"u}ller, Meike and Otto, Antje and Pech, Ina and Petrow, Theresia and Pisi, Sebastian and Rother, Karl-Heinz and Schr{\"o}ter, Kai}, title = {Das Hochwasser im Juni 2013}, series = {Schriftenreihe des DKKV ; 53}, journal = {Schriftenreihe des DKKV ; 53}, publisher = {Deutsches Komitee Katastrophenvorsorge}, address = {Bonn}, isbn = {978-3-933181-62-6}, publisher = {Universit{\"a}t Potsdam}, pages = {207}, year = {2015}, language = {de} } @article{MuellerBesselPisietal.2015, author = {M{\"u}ller, Meike and Bessel, Tina and Pisi, Sebastian and Kreibich, Heidi and Thieken, Annegret}, title = {Auswirkungen und Sch{\"a}den}, series = {Das Hochwasser im Juni 2013 : Bew{\"a}hrungsprobe f{\"u}r das Hochwasserrisikomanagement in Deutschland}, journal = {Das Hochwasser im Juni 2013 : Bew{\"a}hrungsprobe f{\"u}r das Hochwasserrisikomanagement in Deutschland}, isbn = {978-3-933181-62-6}, pages = {31 -- 45}, year = {2015}, language = {de} } @article{ThiekenKienzlerKreibichetal.2016, author = {Thieken, Annegret and Kienzler, Sarah and Kreibich, Heidi and Kuhlicke, Christian and Kunz, Michael and M{\"u}hr, Bernhard and M{\"u}ller, Meike and Otto, Antje and Petrow, Theresia and Pisi, Sebastian and Schr{\"o}ter, Kai}, title = {Review of the flood risk management system in Germany after the major flood in 2013}, series = {Ecology and society : E\&S ; a journal of integrative science for resilience and sustainability}, volume = {21}, journal = {Ecology and society : E\&S ; a journal of integrative science for resilience and sustainability}, number = {2}, publisher = {Resilience Alliance}, address = {Wolfville, NS}, issn = {1708-3087}, doi = {10.5751/ES-08547-210251}, pages = {12}, year = {2016}, abstract = {Widespread flooding in June 2013 caused damage costs of €6 to 8 billion in Germany, and awoke many memories of the floods in August 2002, which resulted in total damage of €11.6 billion and hence was the most expensive natural hazard event in Germany up to now. The event of 2002 does, however, also mark a reorientation toward an integrated flood risk management system in Germany. Therefore, the flood of 2013 offered the opportunity to review how the measures that politics, administration, and civil society have implemented since 2002 helped to cope with the flood and what still needs to be done to achieve effective and more integrated flood risk management. The review highlights considerable improvements on many levels, in particular (1) an increased consideration of flood hazards in spatial planning and urban development, (2) comprehensive property-level mitigation and preparedness measures, (3) more effective flood warnings and improved coordination of disaster response, and (4) a more targeted maintenance of flood defense systems. In 2013, this led to more effective flood management and to a reduction of damage. Nevertheless, important aspects remain unclear and need to be clarified. This particularly holds for balanced and coordinated strategies for reducing and overcoming the impacts of flooding in large catchments, cross-border and interdisciplinary cooperation, the role of the general public in the different phases of flood risk management, as well as a transparent risk transfer system. Recurring flood events reveal that flood risk management is a continuous task. Hence, risk drivers, such as climate change, land-use changes, economic developments, or demographic change and the resultant risks must be investigated at regular intervals, and risk reduction strategies and processes must be reassessed as well as adapted and implemented in a dialogue with all stakeholders.}, language = {en} } @article{ThiekenOttoPisietal.2015, author = {Thieken, Annegret and Otto, Antje and Pisi, Sebastian and Petrow, Theresia and Kreibich, Heidi and Kuhlicke, Christian and Schr{\"o}ter, Kai and Kienzler, Sarah and M{\"u}ller, Meike}, title = {Schlussfolgerungen und Empfehlungen}, series = {Das Hochwasser im Juni 2013 : Bew{\"a}hrungsprobe f{\"u}r das Hochwasserrisikomanagement in Deutschland}, journal = {Das Hochwasser im Juni 2013 : Bew{\"a}hrungsprobe f{\"u}r das Hochwasserrisikomanagement in Deutschland}, publisher = {Deutsches Komitee Katastrophenvorsorge}, address = {Bonn}, isbn = {978-3-933181-62-6}, pages = {184 -- 196}, year = {2015}, language = {de} } @article{Mueller2012, author = {M{\"u}ller, Sebastian}, title = {Menschenrechtsmonitoring}, series = {MenschenRechtsMagazin : MRM ; Informationen, Meinungen, Analysen}, volume = {17}, journal = {MenschenRechtsMagazin : MRM ; Informationen, Meinungen, Analysen}, number = {2}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {1434-2820}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-63907}, pages = {211 -- 226}, year = {2012}, abstract = {Inhalt: I. Einleitung II. Was ist Menschenrechtsmonitoring? Eine begriffliche Analyse III. Wie erg{\"a}nzt Menschenrechtsmonitoring bestehende Beschwerdemechanismen zum Schutz der Menschenrechte? IV. Ausblick: Grenzen und Zukunft des Menschenrechtsmonitoring V. Fazit}, language = {de} } @article{KyriakosPhilippAdelsbergeretal.2014, author = {Kyriakos, Konstantinos and Philipp, Martine and Adelsberger, Joseph and Jaksch, Sebastian and Berezkin, Anatoly V. and Lugo, Dersy M. and Richtering, Walter and Grillo, Isabelle and Miasnikova, Anna and Laschewsky, Andr{\´e} and M{\"u}ller-Buschbaum, Peter and Papadakis, Christine M.}, title = {Cononsolvency of water/methanol mixtures for PNIPAM and PS-b-PNIPAM: pathway of aggregate formation investigated using time-resolved SANS}, series = {Macromolecules : a publication of the American Chemical Society}, volume = {47}, journal = {Macromolecules : a publication of the American Chemical Society}, number = {19}, publisher = {American Chemical Society}, address = {Washington}, issn = {0024-9297}, doi = {10.1021/ma501434e}, pages = {6867 -- 6879}, year = {2014}, abstract = {We investigate the cononsolvency effect of poly(N-isopropylacrylamide) (PNIPAM) in mixtures of water and methanol. Two systems are studied: micellar solutions of polystyrene-b-poly(N-isopropylacrylamide) (PS-b-PNIPAM) diblock copolymers and, as a reference, solutions of PNIPAM homopolymers, both at a concentration of 20 mg/mL in DO. Using a stopped-flow instrument, fully deuterated methanol was rapidly added to these solutions at volume fractions between 10 and 20\%. Time-resolved turbidimetry revealed aggregate formation within 10-100 s. The structural changes on mesoscopic length scales were followed by time-resolved small-angle neutron scattering (TR-SANS) with a time resolution of 0.1 s. In both systems, the pathway of the aggregation depends on the content of deuterated methanol; however, it is fundamentally different for homopolymer and diblock copolymer solutions: In the former, very large aggregates (>150 nm) are formed within the dead time of the setup, gradient appears at their surface in the late stages. In contrast, the growth of the aggregates in the latter system features different regimes, and the final aggregate size is 50 nm, thus much smaller than for the homopolymer. For the diblock copolymer, the time dependence of the aggregate radius can be described by two models: In the initial stage, the diffusion-limited coalescence model describes the data well; however, the resulting coalescence time is unreasonably high. In the late stage, a logarithmic coalescence model based on an energy barrier which is proportional to the aggregate radius is successfully applied. and a concentration}, language = {en} } @article{SchweppeThoberMuelleretal.2022, author = {Schweppe, Robert and Thober, Stephan and M{\"u}ller, Sebastian and Kelbling, Matthias and Kumar, Rohini and Attinger, Sabine and Samaniego, Luis}, title = {MPR 1.0: a stand-alone multiscale parameter regionalization tool for improved parameter estimation of land surface models}, series = {Geoscientific model development : an interactive open access journal of the European Geosciences Union}, volume = {15}, journal = {Geoscientific model development : an interactive open access journal of the European Geosciences Union}, number = {2}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1991-959X}, doi = {10.5194/gmd-15-859-2022}, pages = {859 -- 882}, year = {2022}, abstract = {Distributed environmental models such as land surface models (LSMs) require model parameters in each spatial modeling unit (e.g., grid cell), thereby leading to a high-dimensional parameter space. One approach to decrease the dimensionality of the parameter space in these models is to use regularization techniques. One such highly efficient technique is the multiscale parameter regionalization (MPR) framework that translates high-resolution predictor variables (e.g., soil textural properties) into model parameters (e.g., porosity) via transfer functions (TFs) and upscaling operators that are suitable for every modeled process. This framework yields seamless model parameters at multiple scales and locations in an effective manner. However, integration of MPR into existing modeling workflows has been hindered thus far by hard-coded configurations and non-modular software designs. For these reasons, we redesigned MPR as a model-agnostic, stand-alone tool. It is a useful software for creating graphs of NetCDF variables, wherein each node is a variable and the links consist of TFs and/or upscaling operators. In this study, we present and verify our tool against a previous version, which was implemented in the mesoscale hydrologic model (mHM; https://www.ufz.de/mhm, last access: 16 January 2022). By using this tool for the generation of continental-scale soil hydraulic parameters applicable to different models (Noah-MP and HTESSEL), we showcase its general functionality and flexibility. Further, using model parameters estimated by the MPR tool leads to significant changes in long-term estimates of evapotranspiration, as compared to their default parameterizations. For example, a change of up to 25 \% in long-term evapotranspiration flux is observed in Noah-MP and HTESSEL in the Mississippi River basin. We postulate that use of the stand-alone MPR tool will considerably increase the transparency and reproducibility of the parameter estimation process in distributed (environmental) models. It will also allow a rigorous uncertainty estimation related to the errors of the predictors (e.g., soil texture fields), transfer function and its parameters, and remapping (or upscaling) algorithms.}, language = {en} } @article{OmranianKlieMuellerRoeberetal.2013, author = {Omranian, Nooshin and Klie, Sebastian and M{\"u}ller-R{\"o}ber, Bernd and Nikoloski, Zoran}, title = {Network-based segmentation of biological multivariate time series}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0062974}, pages = {10}, year = {2013}, abstract = {Molecular phenotyping technologies (e.g., transcriptomics, proteomics, and metabolomics) offer the possibility to simultaneously obtain multivariate time series (MTS) data from different levels of information processing and metabolic conversions in biological systems. As a result, MTS data capture the dynamics of biochemical processes and components whose couplings may involve different scales and exhibit temporal changes. Therefore, it is important to develop methods for determining the time segments in MTS data, which may correspond to critical biochemical events reflected in the coupling of the system's components. Here we provide a novel network-based formalization of the MTS segmentation problem based on temporal dependencies and the covariance structure of the data. We demonstrate that the problem of partitioning MTS data into k segments to maximize a distance function, operating on polynomially computable network properties, often used in analysis of biological network, can be efficiently solved. To enable biological interpretation, we also propose a breakpoint-penalty (BP-penalty) formulation for determining MTS segmentation which combines a distance function with the number/length of segments. Our empirical analyses of synthetic benchmark data as well as time-resolved transcriptomics data from the metabolic and cell cycles of Saccharomyces cerevisiae demonstrate that the proposed method accurately infers the phases in the temporal compartmentalization of biological processes. In addition, through comparison on the same data sets, we show that the results from the proposed formalization of the MTS segmentation problem match biological knowledge and provide more rigorous statistical support in comparison to the contending state-of-the-art methods.}, language = {en} } @misc{OmranianKleessenTohgeetal.2015, author = {Omranian, Nooshin and Kleessen, Sabrina and Tohge, Takayuki and Klie, Sebastian and Basler, Georg and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Differential metabolic and coexpression networks of plant metabolism}, series = {Trends in plant science}, volume = {20}, journal = {Trends in plant science}, number = {5}, publisher = {Elsevier}, address = {London}, issn = {1360-1385}, doi = {10.1016/j.tplants.2015.02.002}, pages = {266 -- 268}, year = {2015}, abstract = {Recent analyses have demonstrated that plant metabolic networks do not differ in their structural properties and that genes involved in basic metabolic processes show smaller coexpression than genes involved in specialized metabolism. By contrast, our analysis reveals differences in the structure of plant metabolic networks and patterns of coexpression for genes in (non)specialized metabolism. Here we caution that conclusions concerning the organization of plant metabolism based on network-driven analyses strongly depend on the computational approaches used.}, language = {en} } @article{BalazadehSchildhauerAraujoetal.2014, author = {Balazadeh, Salma and Schildhauer, Joerg and Araujo, Wagner L. and Munne-Bosch, Sergi and Fernie, Alisdair R. and Proost, Sebastian and Humbeck, Klaus and M{\"u}ller-R{\"o}ber, Bernd}, title = {Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru119}, pages = {3975 -- 3992}, year = {2014}, abstract = {Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated.}, language = {en} } @article{LaiLuoZwirneretal.2022, author = {Lai, Huagui and Luo, Jincheng and Zwirner, Yannick and Olthof, Selina and Wieczorek, Alexander and Ye, Fangyuan and Jeangros, Quentin and Yin, Xinxing and Akhundova, Fatima and Ma, Tianshu and He, Rui and Kothandaraman, Radha K. and Chin, Xinyu and Gilshtein, Evgeniia and Muller, Andre and Wang, Changlei and Thiesbrummel, Jarla and Siol, Sebastian and Prieto, Jose Marquez and Unold, Thomas and Stolterfoht, Martin and Chen, Cong and Tiwari, Ayodhya N. and Zhao, Dewei and Fu, Fan}, title = {High-performance flexible all-Perovskite tandem solar cells with reduced V-OC-deficit in wide-bandgap subcell}, series = {Advanced energy materials}, volume = {12}, journal = {Advanced energy materials}, number = {45}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1614-6832}, doi = {10.1002/aenm.202202438}, pages = {12}, year = {2022}, abstract = {Among various types of perovskite-based tandem solar cells (TSCs), all-perovskite TSCs are of particular attractiveness for building- and vehicle-integrated photovoltaics, or space energy areas as they can be fabricated on flexible and lightweight substrates with a very high power-to-weight ratio. However, the efficiency of flexible all-perovskite tandems is lagging far behind their rigid counterparts primarily due to the challenges in developing efficient wide-bandgap (WBG) perovskite solar cells on the flexible substrates as well as their low open-circuit voltage (V-OC). Here, it is reported that the use of self-assembled monolayers as hole-selective contact effectively suppresses the interfacial recombination and allows the subsequent uniform growth of a 1.77 eV WBG perovskite with superior optoelectronic quality. In addition, a postdeposition treatment with 2-thiopheneethylammonium chloride is employed to further suppress the bulk and interfacial recombination, boosting the V-OC of the WBG top cell to 1.29 V. Based on this, the first proof-of-concept four-terminal all-perovskite flexible TSC with a power conversion efficiency of 22.6\% is presented. When integrating into two-terminal flexible tandems, 23.8\% flexible all-perovskite TSCs with a superior V-OC of 2.1 V is achieved, which is on par with the V-OC reported on the 28\% all-perovskite tandems grown on the rigid substrate.}, language = {en} }