@article{BirnickBlaesiusFriedrichetal.2020,
  author    = {Birnick, Johann and Bl{\"a}sius, Thomas and Friedrich, Tobias and Naumann, Felix and Papenbrock, Thorsten and Schirneck, Friedrich Martin},
  title     = {Hitting set enumeration with partial information for unique column combination discovery},
  series = {Proceedings of the VLDB Endowment},
  volume    = {13},
  journal   = {Proceedings of the VLDB Endowment},
  number    = {11},
  publisher = {Association for Computing Machinery},
  address   = {[New York, NY]},
  issn      = {2150-8097},
  doi       = {10.14778/3407790.3407824},
  pages     = {2270 -- 2283},
  year      = {2020},
  abstract  = {Unique column combinations (UCCs) are a fundamental concept in relational databases. They identify entities in the data and support various data management activities. Still, UCCs are usually not explicitly defined and need to be discovered. State-of-the-art data profiling algorithms are able to efficiently discover UCCs in moderately sized datasets, but they tend to fail on large and, in particular, on wide datasets due to run time and memory limitations. <br /> In this paper, we introduce HPIValid, a novel UCC discovery algorithm that implements a faster and more resource-saving search strategy. HPIValid models the metadata discovery as a hitting set enumeration problem in hypergraphs. In this way, it combines efficient discovery techniques from data profiling research with the most recent theoretical insights into enumeration algorithms. Our evaluation shows that HPIValid is not only orders of magnitude faster than related work, it also has a much smaller memory footprint.},
  language  = {en}
}
@article{BlaesiusFriedrichSchirneck2021,
  author    = {Blaesius, Thomas and Friedrich, Tobias and Schirneck, Friedrich Martin},
  title     = {The complexity of dependency detection and discovery in relational databases},
  series = {Theoretical computer science},
  volume    = {900},
  journal   = {Theoretical computer science},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3975},
  doi       = {10.1016/j.tcs.2021.11.020},
  pages     = {79 -- 96},
  year      = {2021},
  abstract  = {Multi-column dependencies in relational databases come associated with two different computational tasks. The detection problem is to decide whether a dependency of a certain type and size holds in a given database, the discovery problem asks to enumerate all valid dependencies of that type. We settle the complexity of both of these problems for unique column combinations (UCCs), functional dependencies (FDs), and inclusion dependencies (INDs). We show that the detection of UCCs and FDs is W[2]-complete when parameterized by the solution size. The discovery of inclusion-wise minimal UCCs is proven to be equivalent under parsimonious reductions to the transversal hypergraph problem of enumerating the minimal hitting sets of a hypergraph. The discovery of FDs is equivalent to the simultaneous enumeration of the hitting sets of multiple input hypergraphs. We further identify the detection of INDs as one of the first natural W[3]-complete problems. The discovery of maximal INDs is shown to be equivalent to enumerating the maximal satisfying assignments of antimonotone, 3-normalized Boolean formulas.},
  language  = {en}
}
@article{BlaesiusFriedrichLischeidetal.2022,
  author    = {Bl{\"a}sius, Thomas and Friedrich, Tobias and Lischeid, Julius and Meeks, Kitty and Schirneck, Friedrich Martin},
  title     = {Efficiently enumerating hitting sets of hypergraphs arising in data profiling},
  series = {Journal of computer and system sciences : JCSS},
  volume    = {124},
  journal   = {Journal of computer and system sciences : JCSS},
  publisher = {Elsevier},
  address   = {San Diego},
  issn      = {0022-0000},
  doi       = {10.1016/j.jcss.2021.10.002},
  pages     = {192 -- 213},
  year      = {2022},
  abstract  = {The transversal hypergraph problem asks to enumerate the minimal hitting sets of a hypergraph. If the solutions have bounded size, Eiter and Gottlob [SICOMP'95] gave an algorithm running in output-polynomial time, but whose space requirement also scales with the output. We improve this to polynomial delay and space. Central to our approach is the extension problem, deciding for a set X of vertices whether it is contained in any minimal hitting set. We show that this is one of the first natural problems to be W[3]-complete. We give an algorithm for the extension problem running in time O(m(vertical bar X vertical bar+1) n) and prove a SETH-lower bound showing that this is close to optimal. We apply our enumeration method to the discovery problem of minimal unique column combinations from data profiling. Our empirical evaluation suggests that the algorithm outperforms its worst-case guarantees on hypergraphs stemming from real-world databases.},
  language  = {en}
}
@misc{BlaesiusEubeFeldtkelleretal.2018,
  author    = {Blaesius, Thomas and Eube, Jan and Feldtkeller, Thomas and Friedrich, Tobias and Krejca, Martin Stefan and Lagodzinski, Gregor J. A. and Rothenberger, Ralf and Severin, Julius and Sommer, Fabian and Trautmann, Justin},
  title     = {Memory-restricted Routing With Tiled Map Data},
  series = {2018 IEEE International Conference on Systems, Man, and Cybernetics (SMC)},
  journal   = {2018 IEEE International Conference on Systems, Man, and Cybernetics (SMC)},
  publisher = {IEEE},
  address   = {New York},
  isbn      = {978-1-5386-6650-0},
  issn      = {1062-922X},
  doi       = {10.1109/SMC.2018.00567},
  pages     = {3347 -- 3354},
  year      = {2018},
  abstract  = {Modern routing algorithms reduce query time by depending heavily on preprocessed data. The recently developed Navigation Data Standard (NDS) enforces a separation between algorithms and map data, rendering preprocessing inapplicable. Furthermore, map data is partitioned into tiles with respect to their geographic coordinates. With the limited memory found in portable devices, the number of tiles loaded becomes the major factor for run time. We study routing under these restrictions and present new algorithms as well as empirical evaluations. Our results show that, on average, the most efficient algorithm presented uses more than 20 times fewer tile loads than a normal A*.},
  language  = {en}
}
@misc{GuentherMangelsdorfMitzneretal.2012,
  author    = {G{\"u}nther, Oliver and Mangelsdorf, Birgit and Mitzner, Rolf and Loschelder, Wolfgang and Peter, Andreas and Eckert, Barbara and Mikelskis, Helmut and Klein, Alfred and Kirsch, B{\"a}rbel and Edelstein, Wolfgang and Thomas, Gr{\"u}newald and Thomas, P{\"o}sl and Wagner, Dieter and Winskowski, Friedrich and Schad, Martina and Frey, Anne and Bickenbach, Wulf and Madani, Roya and Olaka, Lydia},
  title     = {Portal alumni},
  series = {Das Ehemaligen-Magazin der Universit{\"a}t Potsdam},
  journal   = {Das Ehemaligen-Magazin der Universit{\"a}t Potsdam},
  number    = {9},
  organization    = {Stabsstelle Studierendenmarketing/Alumniprogramm Im Auftrag der Pr{\"a}sidentin der Universit{\"a}t Potsdam},
  issn      = {1613-2343},
  doi       = {10.25932/publishup-44494},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-444943},
  pages     = {60},
  year      = {2012},
  abstract  = {Das zur{\"u}ckliegende Jahr stand an der Universit{\"a}t Potsdam auch im Zeichen des zwanzigj{\"a}hrigen Jubil{\"a}ums der Hochschule. Am 15. Juli 1991, wurde sie gegr{\"u}ndet und w{\"a}hrend einer Festwoche feierten Professorinnen und Professoren, Mitarbeiterinnen, Mitarbeiter und Studierende dieses Jubil{\"a}um geb{\"u}hrend. Seit der Gr{\"u}ndung der gr{\"o}ßten brandenburgischen Hochschule sind wissenschaftliches Renommee, Ansehen und Attraktivit{\"a}t stetig gewachsen. Gerade in den letzten Jahren hat sie ihr Profil gesch{\"a}rft. Vor allem die Kognitions-, die Geo- und Biowissenschaften sind hier zu nennen. Aber auch die Lehrerbildung besitzt einen hohen Stellenwert. International anerkannte Forschungsbereiche, Wissenschaftspreise, eine erfolgreiche Drittmittelbilanz und nicht zuletzt die bauliche Entwicklung an allen drei Standorten sind sichtbare Indikatoren f{\"u}r die erfolgreiche Entwicklung, die die Universit{\"a}t Potsdam in den letzten zwei Jahrzehnten durchlaufen hat. Die drei ehemaligen Pr{\"a}sidenten sowie verschiedene andere Protagonisten werfen in dieser Ausgabe der Portal Alumni einen Blick auf unterschiedliche Aspekte der zur{\"u}ckliegenden Entwicklung der Universit{\"a}t. Vom Erfolg der Universit{\"a}t zeugt auch die wachsende Zahl der Absolventinnen und Absolventen, die die Universit{\"a}t verlassen. Portal Alumni stellt in der vorliegenden Ausgabe deshalb Absolventen und deren universit{\"a}re und berufliche Lebenswege genauer vor und l{\"a}sst damit zugleich kaleidoskopartig 20 Jahre Studium an der Universit{\"a}t Potsdam Revue passieren.},
  language  = {de}
}
@article{VorburgerNedielkovBrosigetal.2016,
  author    = {Vorburger, Thomas and Nedielkov, Ruslan and Brosig, Alexander and Bok, Eva and Schunke, Emina and Steffen, Wojtek and Mayer, Sonja and Goetz, Friedrich and M{\"o}ller, Heiko Michael and Steuber, Julia},
  title     = {Role of the Na+-translocating NADH:quinone oxidoreductase in voltage generation and Na+ extrusion in Vibrio cholerae},
  series = {Biochimica et biophysica acta : Bioenergetics},
  volume    = {1857},
  journal   = {Biochimica et biophysica acta : Bioenergetics},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0005-2728},
  doi       = {10.1016/j.bbabio.2015.12.010},
  pages     = {473 -- 482},
  year      = {2016},
  abstract  = {For Vibrio cholerae, the coordinated import and export of Na+ is crucial for adaptation to habitats with different osmolarities. We investigated the Na+-extruding branch of the sodium cycle in this human pathogen by in vivo Na-23-NMR spectroscopy. The Na+ extrusion activity of cells was monitored after adding glucose which stimulated respiration via the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR). In a V. cholerae deletion mutant devoid of the Na+-NQR encoding genes (nqrA-F), rates of respiratory Na+ extrusion were decreased by a factor of four, but the cytoplasmic Na+ concentration was essentially unchanged. Furthermore, the mutant was impaired in formation of transmembrane voltage (Delta psi, inside negative) and did not grow under hypoosmotic conditions at pH 8.2 or above. This growth defect could be complemented by transformation with the plasmid encoded nqr operon. In an alkaline environment, Na+/H+ antiporters acidify the cytoplasm at the expense of the transmembrane voltage. It is proposed that, at alkaline pH and limiting Na+ concentrations, the Na+-NQR is crucial for generation of a transmembrane voltage to drive the import of H+ by electrogenic Na+/H+ antiporters. Our study provides the basis to understand the role of the Na+-NQR in pathogenicity of V. cholerae and other pathogens relying on this primary Na+ pump for respiration. (C) 2015 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@article{FriedrichKrejcaRothenbergeretal.2019,
  author    = {Friedrich, Tobias and Krejca, Martin Stefan and Rothenberger, Ralf and Arndt, Tobias and Hafner, Danijar and Kellermeier, Thomas and Krogmann, Simon and Razmjou, Armin},
  title     = {Routing for on-street parking search using probabilistic data},
  series = {AI communications : AICOM ; the European journal on artificial intelligence},
  volume    = {32},
  journal   = {AI communications : AICOM ; the European journal on artificial intelligence},
  number    = {2},
  publisher = {IOS Press},
  address   = {Amsterdam},
  issn      = {0921-7126},
  doi       = {10.3233/AIC-180574},
  pages     = {113 -- 124},
  year      = {2019},
  abstract  = {A significant percentage of urban traffic is caused by the search for parking spots. One possible approach to improve this situation is to guide drivers along routes which are likely to have free parking spots. The task of finding such a route can be modeled as a probabilistic graph problem which is NP-complete. Thus, we propose heuristic approaches for solving this problem and evaluate them experimentally. For this, we use probabilities of finding a parking spot, which are based on publicly available empirical data from TomTom International B.V. Additionally, we propose a heuristic that relies exclusively on conventional road attributes. Our experiments show that this algorithm comes close to the baseline by a factor of 1.3 in our cost measure. Last, we complement our experiments with results from a field study, comparing the success rates of our algorithms against real human drivers.},
  language  = {en}
}
@article{PrasseRistowKlemmetal.2001,
  author    = {Prasse, R{\"u}diger and Ristow, Michael and Klemm, Gunther and Machatzi, Bernd and Raus, Thomas and Scholz, Hildemar and Stohr, Gerrit and Sukopp, Herbert and Zimmermann, Friedrich},
  title     = {Liste der wildwachsenden Gef{\"a}ßpflanzen des Landes Berlin : mit Roter Liste},
  publisher = {Kulturbuch-Verl.},
  address   = {Berlin},
  isbn      = {3-88961-137-0},
  pages     = {85 S.},
  year      = {2001},
  language  = {de}
}
@article{CastellanosFriedrichPetrovicetal.2020,
  author    = {Castellanos, Reynel Urrea and Friedrich, Thomas and Petrovic, Nevena and Altmann, Simone and Brzezinka, Krzysztof and Gorka, Michal and Graf, Alexander and B{\"a}urle, Isabel},
  title     = {FORGETTER2 protein phosphatase and phospholipase D modulate heat stress memory in Arabidopsis},
  series = {The plant journal},
  volume    = {104},
  journal   = {The plant journal},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.14927},
  pages     = {7 -- 17},
  year      = {2020},
  abstract  = {Plants can mitigate environmental stress conditions through acclimation. In the case of fluctuating stress conditions such as high temperatures, maintaining a stress memory enables a more efficient response upon recurring stress. In a genetic screen forArabidopsis thalianamutants impaired in the memory of heat stress (HS) we have isolated theFORGETTER2(FGT2) gene, which encodes a type 2C protein phosphatase (PP2C) of the D-clade.Fgt2mutants acquire thermotolerance normally; however, they are defective in the memory of HS. FGT2 interacts with phospholipase D alpha 2 (PLD alpha 2), which is involved in the metabolism of membrane phospholipids and is also required for HS memory. In summary, we have uncovered a previously unknown component of HS memory and identified the FGT2 protein phosphatase and PLD alpha 2 as crucial players, suggesting that phosphatidic acid-dependent signaling or membrane composition dynamics underlie HS memory.},
  language  = {en}
}
@article{KabelitzBrzezinkaFriedrichetal.2016,
  author    = {Kabelitz, Tina and Brzezinka, Krzysztof and Friedrich, Thomas and Gorka, Michal and Graf, Alexander and Kappel, Christian and B{\"a}urle, Isabel},
  title     = {A JUMONJI Protein with E3 Ligase and Histone H3 Binding Activities Affects Transposon Silencing in Arabidopsis},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {171},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.15.01688},
  pages     = {344 -- 358},
  year      = {2016},
  abstract  = {Transposable elements (TEs) make up a large proportion of eukaryotic genomes. As their mobilization creates genetic variation that threatens genome integrity, TEs are epigenetically silenced through several pathways, and this may spread to neighboring sequences. JUMONJI (JMJ) proteins can function as antisilencing factors and prevent silencing of genes next to TEs. Whether TE silencing is counterbalanced by the activity of antisilencing factors is still unclear. Here, we characterize JMJ24 as a regulator of TE silencing. We show that loss of JMJ24 results in increased silencing of the DNA transposon AtMu1c, while overexpression of JMJ24 reduces silencing. JMJ24 has a JumonjiC (JmjC) domain and two RING domains. JMJ24 autoubiquitinates in vitro, demonstrating E3 ligase activity of the RING domain(s). JMJ24-JmjC binds the N-terminal tail of histone H3, and full-length JMJ24 binds histone H3 in vivo. JMJ24 activity is anticorrelated with histone H3 Lys 9 dimethylation (H3K9me2) levels at AtMu1c. Double mutant analyses with epigenetic silencing mutants suggest that JMJ24 antagonizes histone H3K9me2 and requires H3K9 methyltransferases for its activity on AtMu1c. Genome-wide transcriptome analysis indicates that JMJ24 affects silencing at additional TEs. Our results suggest that the JmjC domain of JMJ24 has lost demethylase activity but has been retained as a binding domain for histone H3. This is in line with phylogenetic analyses indicating that JMJ24 (with the mutated JmjC domain) is widely conserved in angiosperms. Taken together, this study assigns a role in TE silencing to a conserved JmjC-domain protein with E3 ligase activity, but no demethylase activity.},
  language  = {en}
}
@article{DebatinThomasKellingetal.2010,
  author    = {Debatin, Franziska and Thomas, Arne and Kelling, Alexandra and Hedin, Niklas and Bacsik, Zoltan and Senkovska, Irena and Kaskel, Stefan and Junginger, Matthias and M{\"u}ller, Holger and Schilde, Uwe and J{\"a}ger, Christian and Friedrich, Alwin and Holdt, Hans-J{\"u}rgen},
  title     = {In situ synthesis of an imidazolate-4-amide-5-imidate ligand and formation of a microporous zinc-organic framework with H2-and CO2-storage ability},
  issn      = {1433-7851},
  doi       = {10.1002/anie.200906188},
  year      = {2010},
  abstract  = {Narrow channels with polar walls are the structural and functional features responsible for the high capacity of a zinc-organic framework based on an imidazolate-amide-imidate ligand for the uptake of H2 and CO2 (see structure: orange Zn, blue N, red O, dark gray C, light gray H). The rigid and stable chelating ligand was synthesized in situ by partial hydrolysis of a dicyanoimidazole compound.},
  language  = {en}
}
@article{MeierStumpeFischeretal.1998,
  author    = {Meier, Johann Georg and Stumpe, Joachim and Fischer, Birgit and Thieme, Cathrin and Fischer, Thomas M. and Kremer, Friedrich and {\"O}ge, Tanja and Zentel, Rudolf},
  title     = {Optical suppression of Ferroelectricity in polysiloxane copolymers with chiral an potochromic side groups},
  year      = {1998},
  language  = {en}
}
@misc{ChaykovskaHeunischvonEinemetal.2016,
  author    = {Chaykovska, Lyubov and Heunisch, Fabian and von Einem, Gina and Alter, Markus L. and Hocher, Carl-Friedrich and Tsuprykov, Oleg and Dschietzig, Thomas and Kretschmer, Axel and Hocher, Berthold},
  title     = {Urinary vitamin D binding protein and KIM-1 are potent new biomarkers of major adverse renal events in patients undergoing coronary angiography},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {558},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41192},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-411928},
  pages     = {11},
  year      = {2016},
  abstract  = {Background Vitamin-D-binding protein (VDBP) is a low molecular weight protein that is filtered through the glomerulus as a 25-(OH) vitamin D 3/VDBP complex. In the normal kidney VDBP is reabsorbed and catabolized by proximal tubule epithelial cells reducing the urinary excretion to trace amounts. Acute tubular injury is expected to result in urinary VDBP loss. The purpose of our study was to explore the potential role of urinary VDBP as a biomarker of an acute renal damage. Method We included 314 patients with diabetes mellitus or mild renal impairment undergoing coronary angiography and collected blood and urine before and 24 hours after the CM application. Patients were followed for 90 days for the composite endpoint major adverse renal events (MARE: need for dialysis, doubling of serum creatinine after 90 days, unplanned emergency rehospitalization or death). Results Increased urine VDBP concentration 24 hours after contrast media exposure was predictive for dialysis need (no dialysis: 113.06 +/- 299.61ng/ml, n = 303; need for dialysis: 613.07 +/- 700.45 ng/ml, n = 11, Mean +/- SD, p < 0.001), death (no death during follow-up: 121.41 +/- 324.45 ng/ml, n = 306; death during follow-up: 522.01 +/- 521.86 ng/ml, n = 8; Mean +/- SD, p < 0.003) and MARE (no MARE: 112.08 +/- 302.00ng/ml, n = 298; MARE: 506.16 +/- 624.61 ng/ml, n = 16, Mean +/- SD, p < 0.001) during the follow-up of 90 days after contrast media exposure. Correction of urine VDBP concentrations for creatinine excretion confirmed its predictive value and was consistent with increased levels of urinary Kidney Injury Molecule1 (KIM-1) and baseline plasma creatinine in patients with above mentioned complications. The impact of urinary VDBP and KIM-1 on MARE was independent of known CIN risk factors such as anemia, preexisting renal failure, preexisting heart failure, and diabetes. Conclusions Urinary VDBP is a promising novel biomarker of major contrast induced nephropathy-associated events 90 days after contrast media exposure.},
  language  = {en}
}
@article{ChaykovskaHeunischvonEinemetal.2016,
  author    = {Chaykovska, Lyubov and Heunisch, Fabian and von Einem, Gina and Alter, Markus L. and Hocher, Carl-Friedrich and Tsuprykov, Oleg and Dschietzig, Thomas and Kretschmer, Axel and Hocher, Berthold},
  title     = {Urinary Vitamin D Binding Protein and KIM-1 Are Potent New Biomarkers of Major Adverse Renal Events in Patients Undergoing Coronary Angiography},
  series = {PLoS one},
  volume    = {11},
  journal   = {PLoS one},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0145723},
  pages     = {11},
  year      = {2016},
  abstract  = {Background Vitamin-D-binding protein (VDBP) is a low molecular weight protein that is filtered through the glomerulus as a 25-(OH) vitamin D 3/VDBP complex. In the normal kidney VDBP is reabsorbed and catabolized by proximal tubule epithelial cells reducing the urinary excretion to trace amounts. Acute tubular injury is expected to result in urinary VDBP loss. The purpose of our study was to explore the potential role of urinary VDBP as a biomarker of an acute renal damage. Method We included 314 patients with diabetes mellitus or mild renal impairment undergoing coronary angiography and collected blood and urine before and 24 hours after the CM application. Patients were followed for 90 days for the composite endpoint major adverse renal events (MARE: need for dialysis, doubling of serum creatinine after 90 days, unplanned emergency rehospitalization or death). Results Increased urine VDBP concentration 24 hours after contrast media exposure was predictive for dialysis need (no dialysis: 113.06 +/- 299.61ng/ml, n = 303; need for dialysis: 613.07 +/- 700.45 ng/ml, n = 11, Mean +/- SD, p < 0.001), death (no death during follow-up: 121.41 +/- 324.45 ng/ml, n = 306; death during follow-up: 522.01 +/- 521.86 ng/ml, n = 8; Mean +/- SD, p < 0.003) and MARE (no MARE: 112.08 +/- 302.00ng/ml, n = 298; MARE: 506.16 +/- 624.61 ng/ml, n = 16, Mean +/- SD, p < 0.001) during the follow-up of 90 days after contrast media exposure. Correction of urine VDBP concentrations for creatinine excretion confirmed its predictive value and was consistent with increased levels of urinary Kidney Injury Molecule1 (KIM-1) and baseline plasma creatinine in patients with above mentioned complications. The impact of urinary VDBP and KIM-1 on MARE was independent of known CIN risk factors such as anemia, preexisting renal failure, preexisting heart failure, and diabetes. Conclusions Urinary VDBP is a promising novel biomarker of major contrast induced nephropathy-associated events 90 days after contrast media exposure.},
  language  = {en}
}
@article{BlaesiusFreibergerFriedrichetal.2022,
  author    = {Bl{\"a}sius, Thomas and Freiberger, Cedric and Friedrich, Tobias and Katzmann, Maximilian and Montenegro-Retana, Felix and Thieffry, Marianne},
  title     = {Efficient Shortest Paths in Scale-Free Networks with Underlying Hyperbolic Geometry},
  series = {ACM Transactions on Algorithms},
  volume    = {18},
  journal   = {ACM Transactions on Algorithms},
  number    = {2},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {1549-6325},
  doi       = {10.1145/3516483},
  pages     = {1 -- 32},
  year      = {2022},
  abstract  = {A standard approach to accelerating shortest path algorithms on networks is the bidirectional search, which explores the graph from the start and the destination, simultaneously. In practice this strategy performs particularly well on scale-free real-world networks. Such networks typically have a heterogeneous degree distribution (e.g., a power-law distribution) and high clustering (i.e., vertices with a common neighbor are likely to be connected themselves). These two properties can be obtained by assuming an underlying hyperbolic geometry. <br /> To explain the observed behavior of the bidirectional search, we analyze its running time on hyperbolic random graphs and prove that it is (O) over tilde (n(2-1/alpha) + n(1/(2 alpha)) + delta(max)) with high probability, where alpha is an element of (1/2, 1) controls the power-law exponent of the degree distribution, and dmax is the maximum degree. This bound is sublinear, improving the obvious worst-case linear bound. Although our analysis depends on the underlying geometry, the algorithm itself is oblivious to it.},
  language  = {en}
}
@article{DebatinBehrensWeberetal.2012,
  author    = {Debatin, Franziska and Behrens, Karsten and Weber, Jens and Baburin, Igor A. and Thomas, Arne and Schmidt, Johannes and Senkovska, Irena and Kaskel, Stefan and Kelling, Alexandra and Hedin, Niklas and Bacsik, Zoltan and Leoni, Stefano and Seifert, Gotthard and J{\"a}ger, Christian and G{\"u}nter, Christina and Schilde, Uwe and Friedrich, Alwin and Holdt, Hans-J{\"u}rgen},
  title     = {An isoreticular family of microporous metal-organic frameworks based on zinc and 2-substituted imidazolate-4-amide-5-imidate Syntheses, structures and properties},
  series = {Chemistry - a European journal},
  volume    = {18},
  journal   = {Chemistry - a European journal},
  number    = {37},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {0947-6539},
  doi       = {10.1002/chem.201200889},
  pages     = {11630 -- 11640},
  year      = {2012},
  abstract  = {We report on a new series of isoreticular frameworks based on zinc and 2-substituted imidazolate-4-amide-5-imidate (IFP-14, IFP=imidazolate framework Potsdam) that form one-dimensional, microporous hexagonal channels. Varying R in the 2-substitued linker (R=Me (IFP-1), Cl (IFP-2), Br (IFP-3), Et (IFP-4)) allowed the channel diameter (4.01.7 angstrom), the polarisability and functionality of the channel walls to be tuned. Frameworks IFP-2, IFP-3 and IFP-4 are isostructural to previously reported IFP-1. The structures of IFP-2 and IFP-3 were solved by X-ray crystallographic analyses. The structure of IFP-4 was determined by a combination of PXRD and structure modelling and was confirmed by IR spectroscopy and 1H MAS and 13C CP-MAS NMR spectroscopy. All IFPs showed high thermal stability (345400?degrees C); IFP-1 and IFP-4 were stable in boiling water for 7 d. A detailed porosity analysis was performed on the basis of adsorption measurements by using various gases. The potential of the materials to undergo specific interactions with CO2 was investigated by measuring the isosteric heats of adsorption. The capacity to adsorb CH4 (at 298 K), CO2 (at 298 K) and H2 (at 77 K) at high pressure were also investigated. In situ IR spectroscopy showed that CO2 is physisorbed on IFP-14 under dry conditions and that both CO2 and H2O are physisorbed on IFP-1 under moist conditions.},
  language  = {en}
}
@article{FriedrichOberkoflerTrindadeetal.2021,
  author    = {Friedrich, Thomas and Oberkofler, Vicky and Trindade, In{\^e}s and Altmann, Simone and Brzezinka, Krzysztof and L{\"a}mke, J{\"o}rn S. and Gorka, Michal and Kappel, Christian and Sokolowska, Ewelina and Skirycz, Aleksandra and Graf, Alexander and B{\"a}urle, Isabel},
  title     = {Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis},
  series = {Nature Communications},
  volume    = {12},
  journal   = {Nature Communications},
  number    = {1},
  publisher = {Nature Publishing Group UK},
  address   = {[London]},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-021-23786-6},
  pages     = {15},
  year      = {2021},
  abstract  = {Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory. Moderate heat stress primes plants to acquire tolerance to subsequent, more severe heat stress. Here the authors show that the HSFA3 transcription factor forms a heteromeric complex with HSFA2 to sustain activated transcription of genes required for acquired thermotolerance by promoting H3K4 hyper-methylation.},
  language  = {en}
}
@book{BeckSchoepsGerberetal.2003,
  author    = {Beck, Lorenz Friedrich and Schoeps, Julius H. and Gerber, Thomas and Zabel, Marco},
  title     = {Der Soldatenk{\"o}nig : Friedrich Wilhelm I. in seiner Zeit},
  series = {Brandenburgische Historische Schriften},
  volume    = {12},
  journal   = {Brandenburgische Historische Schriften},
  publisher = {Verl. f{\"u}r Berlin-Brandenburg},
  address   = {Potsdam},
  isbn      = {3-935035-43-8},
  pages     = {345 S.},
  year      = {2003},
  language  = {de}
}
@misc{VossMeyerSchwonbecketal.2005,
  author    = {Voss, Henning and Meyer, Jeannette and Schwonbeck, Susanne and Fritsche, Immo and Hartmann, Bernhard and Wegwarth, Odette and Friedrich, Anke and Buchheister-Knappe, Stefanie and Marwan, Norbert and Bandau, Anja and Bullinger, Hans-J{\"o}rg and Weith, Thomas},
  title     = {Portal alumni},
  series = {Das Ehemaligen-Magazin der Universit{\"a}t Potsdam},
  volume    = {2005},
  journal   = {Das Ehemaligen-Magazin der Universit{\"a}t Potsdam},
  number    = {3},
  organization    = {Stabsstelle Studierendenmarketing/Alumniprogramm Im Auftrag der Pr{\"a}sidentin der Universit{\"a}t Potsdam},
  doi       = {10.25932/publishup-48160},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-481608},
  pages     = {58},
  year      = {2005},
  abstract  = {Liebe Leserin, lieber Leser, erforschen, was die Welt im Innersten zusammenh{\"a}lt- das ist f{\"u}r viele Studierende ein Traum. Doch welche Opfer muss man bringen, um ihn zu verwirklichen? Welche Bemfsperspektive hat der Bemf Forscher heute noch? Auch viele Absolventen der Universit{\"a}t Potsdam m{\"u}ssen sich diese Fragen beantworten. Zu welchen Antworten einige dabei gekommen sind und welche Probleme sie zu bew{\"a}ltigen haben, vom Spaß am Forschen und von Zukunfts{\"a}ngsten berichten sie in der Rubrik "Forscherkarrieren". Gelder f{\"u}r die Forschung fließen in Deutschland zu sp{\"a}rlich, verglichen mit anderen f{\"u}hrenden Industrienationen. So sind die Bedingungen f{\"u}r Forscher hierzulande nicht die besten. Manchen jungen Wissenschaftler zieht es- mitunter notgedrungen- ins Ausland. Wie Deutschland dadurch seine ZukunftsHihigkeit riskiert, thematisiert der Pr{\"a}sident der Fraunhofer-Gesellschaft, Prof. Dr. Hans-J{\"o}rg Bullinger, in der Rubrik "wissenstransfer". Auch die Universit{\"a}t ist kein Garant f{\"u}r eine gesicherte Zukunft in der Forschung. Wer sechs Jahre nach der Promotion den Sprung zur Professur nicht geschafft hat, geht einer ungewissen Zukunft als Privatdozent entgegen. Seit einigen Jahren gibt es neben der Habilitation noch einen zweiten Weg zur Professur- die Juniorprofessur. Auch an der Universit{\"a}t Potsdam gibt es seit 2002 Juniorprofessoren, von denen die ersten jetzt evaluiert wurden. N{\"a}heres dazu finden Sie ebenfalls in der Rubrik "wissenstransfer". Wer noch nach einer Finanzierungsm{\"o}glichkeit f{\"u}r seine Promotion sucht, findet Tipps in der Rubrik "wegweiser". Die Redaktion w{\"u}nscht Ihnen viel Vergn{\"u}gen beim Lesen von Portal alumni und freut sich auf zahlreiche Leserbriefe.},
  language  = {de}
}
@incollection{LueckBalderjahnKammetal.2000,
  author    = {L{\"u}ck, Erika and Balderjahn, Ingo and Kamm, Birgit and Greil, Holle and Wallschl{\"a}ger, Hans-Dieter and Jessel, Beate and B{\"o}ckmann, Christine and Oberh{\"a}nsli, Roland and Soyez, Konrad and Schmeer, Ernst and Blumenstein, Oswald and Berndt, Klaus-Peter and Edeling, Thomas and Friedrich, Sabine and Kaden, Klaus and Scheller, Frieder W. and Petersen, Hans-Georg and Asche, Hartmut and Bronstert, Axel and Giest, Hartmut and Gaedke, Ursula and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Jeltsch, Florian and J{\"a}nkel, Ralph and Gzik, Axel and Bork, Hans-Rudolf and Bork, Hans-Rudolf},
  title     = {Umweltforschung f{\"u}r das Land Brandenburg : Arbeitsgruppen und Professuren},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-3797},
  publisher      = {Universit{\"a}t Potsdam},
  year      = {2000},
  language  = {de}
}
@book{RanaMohapatraSidorovaetal.2022,
  author    = {Rana, Kaushik and Mohapatra, Durga Prasad and Sidorova, Julia and Lundberg, Lars and Sk{\"o}ld, Lars and Lopes Grim, Lu{\´i}s Fernando and Sampaio Gradvohl, Andr{\´e} Leon and Cremerius, Jonas and Siegert, Simon and Weltzien, Anton von and Baldi, Annika and Klessascheck, Finn and Kalancha, Svitlana and Lichtenstein, Tom and Shaabani, Nuhad and Meinel, Christoph and Friedrich, Tobias and Lenzner, Pascal and Schumann, David and Wiese, Ingmar and Sarna, Nicole and Wiese, Lena and Tashkandi, Araek Sami and van der Walt, Est{\´e}e and Eloff, Jan H. P. and Schmidt, Christopher and H{\"u}gle, Johannes and Horschig, Siegfried and Uflacker, Matthias and Najafi, Pejman and Sapegin, Andrey and Cheng, Feng and Stojanovic, Dragan and Stojnev Ilić, Aleksandra and Djordjevic, Igor and Stojanovic, Natalija and Predic, Bratislav and Gonz{\´a}lez-Jim{\´e}nez, Mario and de Lara, Juan and Mischkewitz, Sven and Kainz, Bernhard and van Hoorn, Andr{\´e} and Ferme, Vincenzo and Schulz, Henning and Knigge, Marlene and Hecht, Sonja and Prifti, Loina and Krcmar, Helmut and Fabian, Benjamin and Ermakova, Tatiana and Kelkel, Stefan and Baumann, Annika and Morgenstern, Laura and Plauth, Max and Eberhard, Felix and Wolff, Felix and Polze, Andreas and Cech, Tim and Danz, Noel and Noack, Nele Sina and Pirl, Lukas and Beilharz, Jossekin Jakob and De Oliveira, Roberto C. L. and Soares, F{\´a}bio Mendes and Juiz, Carlos and Bermejo, Belen and M{\"u}hle, Alexander and Gr{\"u}ner, Andreas and Saxena, Vageesh and Gayvoronskaya, Tatiana and Weyand, Christopher and Krause, Mirko and Frank, Markus and Bischoff, Sebastian and Behrens, Freya and R{\"u}ckin, Julius and Ziegler, Adrian and Vogel, Thomas and Tran, Chinh and Moser, Irene and Grunske, Lars and Sz{\´a}rnyas, G{\´a}bor and Marton, J{\´o}zsef and Maginecz, J{\´a}nos and Varr{\´o}, D{\´a}niel and Antal, J{\´a}nos Benjamin},
  title     = {HPI Future SOC Lab - Proceedings 2018},
  number    = {151},
  editor    = {Meinel, Christoph and Polze, Andreas and Beins, Karsten and Strotmann, Rolf and Seibold, Ulrich and R{\"o}dszus, Kurt and M{\"u}ller, J{\"u}rgen},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-547-7},
  issn      = {1613-5652},
  doi       = {10.25932/publishup-56371},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-563712},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {x, 277},
  year      = {2022},
  abstract  = {The "HPI Future SOC Lab" is a cooperation of the Hasso Plattner Institute (HPI) and industry partners. Its mission is to enable and promote exchange and interaction between the research community and the industry partners. The HPI Future SOC Lab provides researchers with free of charge access to a complete infrastructure of state of the art hard and software. This infrastructure includes components, which might be too expensive for an ordinary research environment, such as servers with up to 64 cores and 2 TB main memory. The offerings address researchers particularly from but not limited to the areas of computer science and business information systems. Main areas of research include cloud computing, parallelization, and In-Memory technologies. This technical report presents results of research projects executed in 2018. Selected projects have presented their results on April 17th and November 14th 2017 at the Future SOC Lab Day events.},
  language  = {en}
}
@article{KappelFriedrichOberkofleretal.2023,
  author    = {Kappel, Christian and Friedrich, Thomas and Oberkofler, Vicky and Jiang, Li and Crawford, Tim and Lenhard, Michael and B{\"a}urle, Isabel},
  title     = {Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis},
  series = {Genome biology : biology for the post-genomic era},
  volume    = {24},
  journal   = {Genome biology : biology for the post-genomic era},
  number    = {1},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1474-760X},
  doi       = {10.1186/s13059-023-02970-5},
  pages     = {23},
  year      = {2023},
  abstract  = {Background Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. Results HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. Conclusions Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior.},
  language  = {en}
}
@misc{FriedrichFaivreBaeurleetal.2018,
  author    = {Friedrich, Thomas and Faivre, Lea and B{\"a}urle, Isabel and Schubert, Daniel},
  title     = {Chromatin-based mechanisms of temperature memory in plants},
  series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology},
  volume    = {42},
  journal   = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology},
  number    = {3},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0140-7791},
  doi       = {10.1111/pce.13373},
  pages     = {762 -- 770},
  year      = {2018},
  abstract  = {For successful growth and development, plants constantly have to gauge their environment. Plants are capable to monitor their current environmental conditions, and they are also able to integrate environmental conditions over time and store the information induced by the cues. In a developmental context, such an environmental memory is used to align developmental transitions with favourable environmental conditions. One temperature-related example of this is the transition to flowering after experiencing winter conditions, that is, vernalization. In the context of adaptation to stress, such an environmental memory is used to improve stress adaptation even when the stress cues are intermittent. A somatic stress memory has now been described for various stresses, including extreme temperatures, drought, and pathogen infection. At the molecular level, such a memory of the environment is often mediated by epigenetic and chromatin modifications. Histone modifications in particular play an important role. In this review, we will discuss and compare different types of temperature memory and the histone modifications, as well as the reader, writer, and eraser proteins involved.},
  language  = {en}
}
@book{KubanRottaNolteetal.2023,
  author    = {Kuban, Robert and Rotta, Randolf and Nolte, J{\"o}rg and Chromik, Jonas and Beilharz, Jossekin Jakob and Pirl, Lukas and Friedrich, Tobias and Lenzner, Pascal and Weyand, Christopher and Juiz, Carlos and Bermejo, Belen and Sauer, Joao and Coelh, Leandro dos Santos and Najafi, Pejman and P{\"u}nter, Wenzel and Cheng, Feng and Meinel, Christoph and Sidorova, Julia and Lundberg, Lars and Vogel, Thomas and Tran, Chinh and Moser, Irene and Grunske, Lars and Elsaid, Mohamed Esameldin Mohamed and Abbas, Hazem M. and Rula, Anisa and Sejdiu, Gezim and Maurino, Andrea and Schmidt, Christopher and H{\"u}gle, Johannes and Uflacker, Matthias and Nozza, Debora and Messina, Enza and Hoorn, Andr{\´e} van and Frank, Markus and Schulz, Henning and Alhosseini Almodarresi Yasin, Seyed Ali and Nowicki, Marek and Muite, Benson K. and Boysan, Mehmet Can and Bianchi, Federico and Cremaschi, Marco and Moussa, Rim and Abdel-Karim, Benjamin M. and Pfeuffer, Nicolas and Hinz, Oliver and Plauth, Max and Polze, Andreas and Huo, Da and Melo, Gerard de and Mendes Soares, F{\´a}bio and Oliveira, Roberto C{\´e}lio Lim{\~a}o de and Benson, Lawrence and Paul, Fabian and Werling, Christian and Windheuser, Fabian and Stojanovic, Dragan and Djordjevic, Igor and Stojanovic, Natalija and Stojnev Ilic, Aleksandra and Weidmann, Vera and Lowitzki, Leon and Wagner, Markus and Ifa, Abdessatar Ben and Arlos, Patrik and Megia, Ana and Vendrell, Joan and Pfitzner, Bjarne and Redondo, Alberto and R{\´i}os Insua, David and Albert, Justin Amadeus and Zhou, Lin and Arnrich, Bert and Szab{\´o}, Ildik{\´o} and Fodor, Szabina and Ternai, Katalin and Bhowmik, Rajarshi and Campero Durand, Gabriel and Shevchenko, Pavlo and Malysheva, Milena and Prymak, Ivan and Saake, Gunter},
  title     = {HPI Future SOC Lab - Proceedings 2019},
  number    = {158},
  editor    = {Meinel, Christoph and Polze, Andreas and Beins, Karsten and Strotmann, Rolf and Seibold, Ulrich and R{\"o}dszus, Kurt and M{\"u}ller, J{\"u}rgen},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-564-4},
  issn      = {1613-5652},
  doi       = {10.25932/publishup-59791},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-597915},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {xi, 301},
  year      = {2023},
  abstract  = {The "HPI Future SOC Lab" is a cooperation of the Hasso Plattner Institute (HPI) and industry partners. Its mission is to enable and promote exchange and interaction between the research community and the industry partners. The HPI Future SOC Lab provides researchers with free of charge access to a complete infrastructure of state of the art hard and software. This infrastructure includes components, which might be too expensive for an ordinary research environment, such as servers with up to 64 cores and 2 TB main memory. The offerings address researchers particularly from but not limited to the areas of computer science and business information systems. Main areas of research include cloud computing, parallelization, and In-Memory technologies. This technical report presents results of research projects executed in 2019. Selected projects have presented their results on April 9th and November 12th 2019 at the Future SOC Lab Day events.},
  language  = {en}
}