@article{BanksNishiyamaHasebeetal.2011, author = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, Cedric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and M{\"u}ller-R{\"o}ber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Mauricio Riano-Pachon, Diego and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and Sorensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, Guenter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W. G. T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loque, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.}, title = {The selaginella genome identifies genetic changes associated with the evolution of vascular plants}, series = {Science}, volume = {332}, journal = {Science}, number = {6032}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.1203810}, pages = {960 -- 963}, year = {2011}, abstract = {Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.}, language = {en} } @article{AartsAndersonAndersonetal.2015, author = {Aarts, Alexander A. and Anderson, Joanna E. and Anderson, Christopher J. and Attridge, Peter R. and Attwood, Angela and Axt, Jordan and Babel, Molly and Bahnik, Stepan and Baranski, Erica and Barnett-Cowan, Michael and Bartmess, Elizabeth and Beer, Jennifer and Bell, Raoul and Bentley, Heather and Beyan, Leah and Binion, Grace and Borsboom, Denny and Bosch, Annick and Bosco, Frank A. and Bowman, Sara D. and Brandt, Mark J. and Braswell, Erin and Brohmer, Hilmar and Brown, Benjamin T. and Brown, Kristina and Bruening, Jovita and Calhoun-Sauls, Ann and Callahan, Shannon P. and Chagnon, Elizabeth and Chandler, Jesse and Chartier, Christopher R. and Cheung, Felix and Christopherson, Cody D. and Cillessen, Linda and Clay, Russ and Cleary, Hayley and Cloud, Mark D. and Cohn, Michael and Cohoon, Johanna and Columbus, Simon and Cordes, Andreas and Costantini, Giulio and Alvarez, Leslie D. Cramblet and Cremata, Ed and Crusius, Jan and DeCoster, Jamie and DeGaetano, Michelle A. and Della Penna, Nicolas and den Bezemer, Bobby and Deserno, Marie K. and Devitt, Olivia and Dewitte, Laura and Dobolyi, David G. and Dodson, Geneva T. and Donnellan, M. Brent and Donohue, Ryan and Dore, Rebecca A. and Dorrough, Angela and Dreber, Anna and Dugas, Michelle and Dunn, Elizabeth W. and Easey, Kayleigh and Eboigbe, Sylvia and Eggleston, Casey and Embley, Jo and Epskamp, Sacha and Errington, Timothy M. and Estel, Vivien and Farach, Frank J. and Feather, Jenelle and Fedor, Anna and Fernandez-Castilla, Belen and Fiedler, Susann and Field, James G. and Fitneva, Stanka A. and Flagan, Taru and Forest, Amanda L. and Forsell, Eskil and Foster, Joshua D. and Frank, Michael C. and Frazier, Rebecca S. and Fuchs, Heather and Gable, Philip and Galak, Jeff and Galliani, Elisa Maria and Gampa, Anup and Garcia, Sara and Gazarian, Douglas and Gilbert, Elizabeth and Giner-Sorolla, Roger and Gl{\"o}ckner, Andreas and G{\"o}llner, Lars and Goh, Jin X. and Goldberg, Rebecca and Goodbourn, Patrick T. and Gordon-McKeon, Shauna and Gorges, Bryan and Gorges, Jessie and Goss, Justin and Graham, Jesse and Grange, James A. and Gray, Jeremy and Hartgerink, Chris and Hartshorne, Joshua and Hasselman, Fred and Hayes, Timothy and Heikensten, Emma and Henninger, Felix and Hodsoll, John and Holubar, Taylor and Hoogendoorn, Gea and Humphries, Denise J. and Hung, Cathy O. -Y. and Immelman, Nathali and Irsik, Vanessa C. and Jahn, Georg and Jaekel, Frank and Jekel, Marc and Johannesson, Magnus and Johnson, Larissa G. and Johnson, David J. and Johnson, Kate M. and Johnston, William J. and Jonas, Kai and Joy-Gaba, Jennifer A. and Kappes, Heather Barry and Kelso, Kim and Kidwell, Mallory C. and Kim, Seung Kyung and Kirkhart, Matthew and Kleinberg, Bennett and Knezevic, Goran and Kolorz, Franziska Maria and Kossakowski, Jolanda J. and Krause, Robert Wilhelm and Krijnen, Job and Kuhlmann, Tim and Kunkels, Yoram K. and Kyc, Megan M. and Lai, Calvin K. and Laique, Aamir and Lakens, Daniel and Lane, Kristin A. and Lassetter, Bethany and Lazarevic, Ljiljana B. and LeBel, Etienne P. and Lee, Key Jung and Lee, Minha and Lemm, Kristi and Levitan, Carmel A. and Lewis, Melissa and Lin, Lin and Lin, Stephanie and Lippold, Matthias and Loureiro, Darren and Luteijn, Ilse and Mackinnon, Sean and Mainard, Heather N. and Marigold, Denise C. and Martin, Daniel P. and Martinez, Tylar and Masicampo, E. J. and Matacotta, Josh and Mathur, Maya and May, Michael and Mechin, Nicole and Mehta, Pranjal and Meixner, Johannes and Melinger, Alissa and Miller, Jeremy K. and Miller, Mallorie and Moore, Katherine and M{\"o}schl, Marcus and Motyl, Matt and M{\"u}ller, Stephanie M. and Munafo, Marcus and Neijenhuijs, Koen I. and Nervi, Taylor and Nicolas, Gandalf and Nilsonne, Gustav and Nosek, Brian A. and Nuijten, Michele B. and Olsson, Catherine and Osborne, Colleen and Ostkamp, Lutz and Pavel, Misha and Penton-Voak, Ian S. and Perna, Olivia and Pernet, Cyril and Perugini, Marco and Pipitone, R. Nathan and Pitts, Michael and Plessow, Franziska and Prenoveau, Jason M. and Rahal, Rima-Maria and Ratliff, Kate A. and Reinhard, David and Renkewitz, Frank and Ricker, Ashley A. and Rigney, Anastasia and Rivers, Andrew M. and Roebke, Mark and Rutchick, Abraham M. and Ryan, Robert S. and Sahin, Onur and Saide, Anondah and Sandstrom, Gillian M. and Santos, David and Saxe, Rebecca and Schlegelmilch, Rene and Schmidt, Kathleen and Scholz, Sabine and Seibel, Larissa and Selterman, Dylan Faulkner and Shaki, Samuel and Simpson, William B. and Sinclair, H. Colleen and Skorinko, Jeanine L. M. and Slowik, Agnieszka and Snyder, Joel S. and Soderberg, Courtney and Sonnleitner, Carina and Spencer, Nick and Spies, Jeffrey R. and Steegen, Sara and Stieger, Stefan and Strohminger, Nina and Sullivan, Gavin B. and Talhelm, Thomas and Tapia, Megan and te Dorsthorst, Anniek and Thomae, Manuela and Thomas, Sarah L. and Tio, Pia and Traets, Frits and Tsang, Steve and Tuerlinckx, Francis and Turchan, Paul and Valasek, Milan and Van Aert, Robbie and van Assen, Marcel and van Bork, Riet and van de Ven, Mathijs and van den Bergh, Don and van der Hulst, Marije and van Dooren, Roel and van Doorn, Johnny and van Renswoude, Daan R. and van Rijn, Hedderik and Vanpaemel, Wolf and Echeverria, Alejandro Vasquez and Vazquez, Melissa and Velez, Natalia and Vermue, Marieke and Verschoor, Mark and Vianello, Michelangelo and Voracek, Martin and Vuu, Gina and Wagenmakers, Eric-Jan and Weerdmeester, Joanneke and Welsh, Ashlee and Westgate, Erin C. and Wissink, Joeri and Wood, Michael and Woods, Andy and Wright, Emily and Wu, Sining and Zeelenberg, Marcel and Zuni, Kellylynn}, title = {Estimating the reproducibility of psychological science}, series = {Science}, volume = {349}, journal = {Science}, number = {6251}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, organization = {Open Sci Collaboration}, issn = {1095-9203}, doi = {10.1126/science.aac4716}, pages = {8}, year = {2015}, abstract = {Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47\% of original effect sizes were in the 95\% confidence interval of the replication effect size; 39\% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68\% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.}, language = {en} } @article{WilkinParrishYangetal.2019, author = {Wilkin, Kyle J. and Parrish, Robert M. and Yang, Jie and Wolf, Thomas J. A. and Nunes, J. Pedro F. and G{\"u}hr, Markus and Li, Renkai and Shen, Xiaozhe and Zheng, Qiang and Wang, Xijie and Martinez, Todd J. and Centurion, Martin}, title = {Diffractive imaging of dissociation and ground-state dynamics in a complex molecule}, series = {Physical review : A, Atomic, molecular, and optical physics}, volume = {100}, journal = {Physical review : A, Atomic, molecular, and optical physics}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {2469-9926}, doi = {10.1103/PhysRevA.100.023402}, pages = {10}, year = {2019}, abstract = {We have investigated the structural dynamics in photoexcited 1,2-diiodotetrafluoroethane molecules (C2F4I2) in the gas phase experimentally using ultrafast electron diffraction and theoretically using FOMO-CASCI excited-state dynamics simulations. The molecules are excited by an ultraviolet femtosecond laser pulse to a state characterized by a transition from the iodine 5p perpendicular to orbital to a mixed 5p parallel to sigma hole and CF2 center dot antibonding orbital, which results in the cleavage of one of the carbon-iodine bonds. We have observed, with sub-Angstrom resolution, the motion of the nuclear wave packet of the dissociating iodine atom followed by coherent vibrations in the electronic ground state of the C2F4I radical. The radical reaches a stable classical (nonbridged) structure in less than 200 fs.}, language = {en} } @article{WolfParrishMyhreetal.2019, author = {Wolf, Thomas J. A. and Parrish, Robert M. and Myhre, Rolf H. and Martinez, Todd J. and Koch, Henrik and G{\"u}hr, Markus}, title = {Observation of Ultrafast Intersystem Crossing in Thymine by Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy}, series = {The journal of physical chemistry : A, Molecules, spectroscopy, kinetics, environment \& general theory}, volume = {123}, journal = {The journal of physical chemistry : A, Molecules, spectroscopy, kinetics, environment \& general theory}, number = {32}, publisher = {American Chemical Society}, address = {Washington}, issn = {1089-5639}, doi = {10.1021/acs.jpca.9b05573}, pages = {6897 -- 6903}, year = {2019}, abstract = {We studied the photoinduced ultrafast relaxation dynamics of the nucleobase thymine using gas-phase time-resolved photoelectron spectroscopy. By employing extreme ultraviolet pulses from high harmonic generation for photoionization, we substantially extend our spectral observation window with respect to previous studies. This enables us to follow relaxation of the excited state population all the way to low-lying electronic states including the ground state. In thymine, we observe relaxation from the optically bright (1)pi pi* state of thymine to a dark (1)n pi* state within 80 +/- 30 fs. The (1)n pi* state relaxes further within 3.5 +/- 0.3 ps to a low-lying electronic state. By comparison with quantum chemical simulations, we can unambiguously assign its spectroscopic signature to the (3)pi pi* state. Hence, our study draws a comprehensive picture of the relaxation mechanism of thymine including ultrafast intersystem crossing to the triplet manifold.}, language = {en} } @phdthesis{Wolf2013, author = {Wolf, Robert}, title = {Die prostitutive Einrichtung und ihre Mitarbeiter im {\"O}ffentlichen Recht - Rechtslage und Perspektiven}, series = {Europ{\"a}ische Hochschulschriften}, volume = {5540}, journal = {Europ{\"a}ische Hochschulschriften}, publisher = {PL Academic Research}, address = {Frankfurt am Main}, isbn = {978-3-631-64541-3}, pages = {227 S.}, year = {2013}, language = {de} } @article{MooijBredervelddeKleinetal.2014, author = {Mooij, Wolf M. and Brederveld, Robert J. and de Klein, Jeroen J. M. and DeAngelis, Don L. and Downing, Andrea S. and Faber, Michiel and Gerla, Daan J. and Hipsey, Matthew R. and Janse, Jan H. and Janssen, Annette B. G. and Jeuken, Michel and Kooi, Bob W. and Lischke, Betty and Petzoldt, Thomas and Postma, Leo and Schep, Sebastiaan A. and Scholten, Huub and Teurlincx, Sven and Thiange, Christophe and Trolle, Dennis and van Dam, Anne A. and van Gerven, Luuk P. A. and van Nes, Egbert H. and Kuiper, Jan J.}, title = {Serving many at once: How a database approach can create unity in dynamical ecosystem modelling}, series = {Environmental modelling \& software with environment data news}, volume = {61}, journal = {Environmental modelling \& software with environment data news}, publisher = {Elsevier}, address = {Oxford}, issn = {1364-8152}, doi = {10.1016/j.envsoft.2014.04.004}, pages = {266 -- 273}, year = {2014}, abstract = {Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).}, language = {en} } @article{vanGervenBredervelddeKleinetal.2015, author = {van Gerven, Luuk P. A. and Brederveld, Robert J. and de Klein, Jeroen J. M. and DeAngelis, Don L. and Downing, Andrea S. and Faber, Michiel and Gerla, Daan J. and Janse, Jan H. and Janssen, Annette B. G. and Jeuken, Michel and Kooi, Bob W. and Kuiper, Jan J. and Lischke, Betty and Liu, Sien and Petzoldt, Thomas and Schep, Sebastiaan A. and Teurlincx, Sven and Thiange, Christophe and Trolle, Dennis and van Nes, Egbert H. and Mooij, Wolf M.}, title = {Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach}, series = {Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology}, volume = {186}, journal = {Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology}, number = {1-2}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {1863-9135}, doi = {10.1127/fal/2015/0631}, pages = {5 -- 20}, year = {2015}, abstract = {Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.}, language = {en} } @book{WeyandChromikWolfetal.2017, author = {Weyand, Christopher and Chromik, Jonas and Wolf, Lennard and K{\"o}tte, Steffen and Haase, Konstantin and Felgentreff, Tim and Lincke, Jens and Hirschfeld, Robert}, title = {Improving hosted continuous integration services}, number = {108}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-377-0}, issn = {1613-5652}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94251}, publisher = {Universit{\"a}t Potsdam}, pages = {viii, 114}, year = {2017}, abstract = {Developing large software projects is a complicated task and can be demanding for developers. Continuous integration is common practice for reducing complexity. By integrating and testing changes often, changesets are kept small and therefore easily comprehensible. Travis CI is a service that offers continuous integration and continuous deployment in the cloud. Software projects are build, tested, and deployed using the Travis CI infrastructure without interrupting the development process. This report describes how Travis CI works, presents how time-driven, periodic building is implemented as well as how CI data visualization can be done, and proposes a way of dealing with dependency problems.}, language = {en} } @misc{GuerreroChuHamannetal.2011, author = {Guerrero, Mart{\´i}n A. and Chu, You-Hua and Hamann, Wolf-Rainer and Oskinova, Lida and Sch{\"o}nberner, Detlef and Todt, Helge Tobias and Steffen, Matthias and Ruiz, Nieves and Gruendl, Robert A. and Blair, William P.}, title = {Ablation and wind mass-loading in the born-again planetary nebula A 30}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {563}, issn = {1866-8372}, doi = {10.25932/publishup-41234}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412341}, pages = {2}, year = {2011}, abstract = {We present XMM-Newton and Chandra observations of the born-again planetary nebula A 30. These X-ray observations reveal a bright unresolved source at the position of the central star whose X-ray luminosity exceeds by far the model expectations for photospheric emission and for shocks within the stellar wind. We suggest that a "born-again hot bubble" may be responsible for this X-ray emission. Diffuse X-ray emission associated with the petal-like features and one of the H-poor knots seen in the optical is also found. The weakened emission of carbon lines in the spectrum of the diffuse emission can be interpreted as the dilution of stellar wind by mass-loading or as the detection of material ejected during a very late thermal pulse.}, language = {en} } @article{HeinzelLorenzBrockhausetal.2014, author = {Heinzel, Stephan and Lorenz, Robert C. and Brockhaus, Wolf-Ruediger and Wuestenberg, Torsten and Kathmann, Norbert and Heinz, Andreas and Rapp, Michael A.}, title = {Working memory load-dependent brain response predicts behavioral training gains in older adults}, series = {The journal of neuroscience}, volume = {34}, journal = {The journal of neuroscience}, number = {4}, publisher = {Society for Neuroscience}, address = {Washington}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.2463-13.2014}, pages = {1224 -- 1233}, year = {2014}, abstract = {In the domain of working memory (WM), a sigmoid-shaped relationship between WM load and brain activation patterns has been demonstrated in younger adults. It has been suggested that age-related alterations of this pattern are associated with changes in neural efficiency and capacity. At the same time, WM training studies have shown that some older adults are able to increase their WM performance through training. In this study, functional magnetic resonance imaging during an n-back WM task at different WM load levels was applied to compare blood oxygen level-dependent (BOLD) responses between younger and older participants and to predict gains in WM performance after a subsequent 12-session WM training procedure in older adults. We show that increased neural efficiency and capacity, as reflected by more "youth-like" brain response patterns in regions of interest of the frontoparietal WM network, were associated with better behavioral training outcome beyond the effects of age, sex, education, gray matter volume, and baseline WM performance. Furthermore, at low difficulty levels, decreases in BOLD response were found after WM training. Results indicate that both neural efficiency (i. e., decreased activation at comparable performance levels) and capacity (i. e., increasing activation with increasing WM load) of a WM-related network predict plasticity of the WM system, whereas WM training may specifically increase neural efficiency in older adults.}, language = {en} }