@misc{CoutoCruzErtanetal.2017,
  author    = {Couto, Rafael C. and Cruz, Vinicius V. and Ertan, Emelie and Eckert, Sebastian and Fondell, Mattis and Dantz, Marcus and Kennedy, Brian and Schmitt, Thorsten and Pietzsch, Annette and Guimar{\~a}es, Freddy F. and {\AA}gren, Hans and Gel'mukhanov, Faris and Odelius, Michael and Kimberg, Victor and F{\"o}hlisch, Alexander},
  title     = {Selective gating to vibrational modes through resonant X-ray scattering},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1124},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43692},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436926},
  pages     = {9},
  year      = {2017},
  abstract  = {The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.},
  language  = {en}
}
@article{EckertNorellMiedemaetal.2017,
  author    = {Eckert, Sebastian and Norell, Jesper and Miedema, Piter S. and Beye, Martin and Fondell, Mattis and Quevedo, Wilson and Kennedy, Brian and Hantschmann, Markus and Pietzsch, Annette and van Kuiken, Benjamin and Ross, Matthew and Minitti, Michael P. and Moeller, Stefan P. and Schlotter, William F. and Khalil, Munira and Odelius, Michael and F{\"o}hlisch, Alexander},
  title     = {Untersuchung unabh{\"a}ngiger N-H- und N-C-Bindungsverformungen auf ultrakurzen Zeitskalen mit resonanter inelastischer R{\"o}ntgenstreuung},
  series = {Angewandte Chemie},
  volume    = {129},
  journal   = {Angewandte Chemie},
  number    = {22},
  issn      = {1521-3757},
  doi       = {10.1002/ange.201700239},
  pages     = {6184 -- 6188},
  year      = {2017},
  abstract  = {Die Femtosekundendynamik nach resonanten Photoanregungen mit optischen und R{\"o}ntgenpulsen erm{\"o}glicht eine selektive Verformung von chemischen N-H- und N-C-Bindungen in 2-Thiopyridon in w{\"a}ssriger L{\"o}sung. Die Untersuchung der orbitalspezifischen elektronischen Struktur und ihrer Dynamik auf ultrakurzen Zeitskalen mit resonanter inelastischer R{\"o}ntgenstreuung an der N1s-Resonanz am Synchrotron und dem Freie-Elektronen-Laser LCLS in Kombination mit quantenchemischen Multikonfigurationsberechnungen erbringen den direkten Nachweis dieser kontrollierten photoinduzierten Molek{\"u}lverformungen und ihrer ultrakurzen Zeitskala.},
  language  = {de}
}
@misc{EckertNorellMiedemaetal.2017,
  author    = {Eckert, Sebastian and Norell, Jesper and Miedema, Piter S. and Beye, Martin and Fondell, Mattis and Quevedo, Wilson and Kennedy, Brian and Hantschmann, Markus and Pietzsch, Annette and van Kuiken, Benjamin E. and Ross, Matthew and Minitti, Michael P. and Moeller, Stefan P. and Schlotter, William F. and Khalil, Munira and Odelius, Michael and F{\"o}hlisch, Alexander},
  title     = {Untersuchung unabh{\"a}ngiger N-H- und N-C-Bindungsverformungen auf ultrakurzen Zeitskalen mit resonanter inelastischer R{\"o}ntgenstreuung},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1121},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43668},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436688},
  pages     = {7},
  year      = {2017},
  abstract  = {Die Femtosekundendynamik nach resonanten Photoanregungen mit optischen und R{\"o}ntgenpulsen erm{\"o}glicht eine selektive Verformung von chemischen N-H- und N-C-Bindungen in 2-Thiopyridon in w{\"a}ssriger L{\"o}sung. Die Untersuchung der orbitalspezifischen elektronischen Struktur und ihrer Dynamik auf ultrakurzen Zeitskalen mit resonanter inelastischer R{\"o}ntgenstreuung an der N1s-Resonanz am Synchrotron und dem Freie-Elektronen-Laser LCLS in Kombination mit quantenchemischen Multikonfigurationsberechnungen erbringen den direkten Nachweis dieser kontrollierten photoinduzierten Molek{\"u}lverformungen und ihrer ultrakurzen Zeitskala.},
  language  = {de}
}
@misc{EckertNorellMiedemaetal.2017,
  author    = {Eckert, Sebastian and Norell, Jesper and Miedema, Piter S. and Beye, Martin and Fondell, Mattis and Quevedo, Wilson and Kennedy, Brian and Hantschmann, Markus and Pietzsch, Annette and van Kuiken, Benjamin E. and Ross, Matthew and Minitti, Michael P. and Moeller, Stefan P. and Schlotter, William F. and Khalil, Munira and Odelius, Michael and F{\"o}hlisch, Alexander},
  title     = {Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1115},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43687},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436873},
  pages     = {7},
  year      = {2017},
  abstract  = {The femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort time-scale.},
  language  = {en}
}
@misc{WurzbacherFuchsAttermeyeretal.2017,
  author    = {Wurzbacher, Christian and Fuchs, Andrea and Attermeyer, Katrin and Frindte, Katharina and Grossart, Hans-Peter and Hupfer, Michael and Casper, Peter and Monaghan, Michael T.},
  title     = {Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1111},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43196},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431965},
  pages     = {18},
  year      = {2017},
  abstract  = {Background Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. Methods We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Results Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. Conclusions By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.},
  language  = {en}
}
@misc{RibeiroMartinsFickelLeetal.2017,
  author    = {Ribeiro Martins, Renata Filipa and Fickel, J{\"o}rns and Le, Minh and Nguyen, Thanh van and Nguyen, Ha M. and Timmins, Robert and Gan, Han Ming and Rovie-Ryan, Jeffrine J. and Lenz, Dorina and F{\"o}rster, Daniel W. and Wilting, Andreas},
  title     = {Phylogeography of red muntjacs reveals three distinct mitochondrial lineages},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {973},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43078},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430780},
  pages     = {14},
  year      = {2017},
  abstract  = {Background The members of the genus Muntiacus are of particular interest to evolutionary biologists due to their extreme chromosomal rearrangements and the ongoing discussions about the number of living species. Red muntjacs have the largest distribution of all muntjacs and were formerly considered as one species. Karyotype differences led to the provisional split between the Southern Red Muntjac (Muntiacus muntjak) and the Northern Red Muntjac (M. vaginalis), but uncertainties remain as, so far, no phylogenetic study has been conducted. Here, we analysed whole mitochondrial genomes of 59 archival and 16 contemporaneous samples to resolve uncertainties about their taxonomy and used red muntjacs as model for understanding the evolutionary history of other species in Southeast Asia. Results We found three distinct matrilineal groups of red muntjacs: Sri Lankan red muntjacs (including the Western Ghats) diverged first from other muntjacs about 1.5 Mya; later northern red muntjacs (including North India and Indochina) and southern red muntjacs (Sundaland) split around 1.12 Mya. The diversification of red muntjacs into these three main lineages was likely promoted by two Pleistocene barriers: one through the Indian subcontinent and one separating the Indochinese and Sundaic red muntjacs. Interestingly, we found a high level of gene flow within the populations of northern and southern red muntjacs, indicating gene flow between populations in Indochina and dispersal of red muntjacs over the exposed Sunda Shelf during the Last Glacial Maximum. Conclusions Our results provide new insights into the evolution of species in South and Southeast Asia as we found clear genetic differentiation in a widespread and generalist species, corresponding to two known biogeographical barriers: The Isthmus of Kra and the central Indian dry zone. In addition, our molecular data support either the delineation of three monotypic species or three subspecies, but more importantly these data highlight the conservation importance of the Sri Lankan/South Indian red muntjac.},
  language  = {en}
}
@misc{SadovnichiiPanasyukAmelyushkinetal.2017,
  author    = {Sadovnichii, V. A. and Panasyuk, M. I. and Amelyushkin, A. M. and Benghin, V. V. and Garipov, G. K. and Kalegaev, V. V. and Klimov, P. A. and Khrenov, B. A. and Petrov, V. L. and Sharakin, S. A. and Shirokov, A. V. and Svertilov, S. I. and Zotov, M. Y. and Yashin, I. V. and Gorbovskoy, E. S. and Lipunov, V. M. and Park, I. H. and Lee, J. and Jeong, S. and Kim, M. B. and Jeong, H. M. and Shprits, Yuri Y. and Angelopoulos, V. and Russell, C. T. and Runov, A. and Turner, D. and Strangeway, R. J. and Caron, R. and Biktemerova, S. and Grinyuk, A. and Lavrova, M. and Tkachev, L. and Tkachenko, A. and Martinez, O. and Salazar, H. and Ponce, E.},
  title     = {"Lomonosov" satellite-space observatory to study extreme phenomena in space},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {959},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42818},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428185},
  pages     = {1705 -- 1738},
  year      = {2017},
  abstract  = {The "Lomonosov" space project is lead by Lomonosov Moscow State University in collaboration with the following key partners: Joint Institute for Nuclear Research, Russia, University of California, Los Angeles (USA), University of Pueblo (Mexico), Sungkyunkwan University (Republic of Korea) and with Russian space industry organi-zations to study some of extreme phenomena in space related to astrophysics, astroparticle physics, space physics, and space biology. The primary goals of this experiment are to study: -Ultra-high energy cosmic rays (UHECR) in the energy range of the Greizen-ZatsepinKuzmin (GZK) cutoff; -Ultraviolet (UV) transient luminous events in the upper atmosphere; -Multi-wavelength study of gamma-ray bursts in visible, UV, gamma, and X-rays; -Energetic trapped and precipitated radiation (electrons and protons) at low-Earth orbit (LEO) in connection with global geomagnetic disturbances; -Multicomponent radiation doses along the orbit of spacecraft under different geomagnetic conditions and testing of space segments of optical observations of space-debris and other space objects; -Instrumental vestibular-sensor conflict of zero-gravity phenomena during space flight. This paper is directed towards the general description of both scientific goals of the project and scientific equipment on board the satellite. The following papers of this issue are devoted to detailed descriptions of scientific instruments.},
  language  = {en}
}
@misc{BeniniSchenkel2017,
  author    = {Benini, Marco and Schenkel, Alexander},
  title     = {Quantum field theories on categories fibered in groupoids},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {895},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43154},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431541},
  pages     = {48},
  year      = {2017},
  abstract  = {We introduce an abstract concept of quantum field theory on categories fibered in groupoids over the category of spacetimes. This provides us with a general and flexible framework to study quantum field theories defined on spacetimes with extra geometric structures such as bundles, connections and spin structures. Using right Kan extensions, we can assign to any such theory an ordinary quantum field theory defined on the category of spacetimes and we shall clarify under which conditions it satisfies the axioms of locally covariant quantum field theory. The same constructions can be performed in a homotopy theoretic framework by using homotopy right Kan extensions, which allows us to obtain first toy-models of homotopical quantum field theories resembling some aspects of gauge theories.},
  language  = {en}
}
@misc{HartungBenaryWolfetal.2017,
  author    = {Hartung, Niklas and Benary, Uwe and Wolf, Jana and Kofahl, Bente},
  title     = {Paracrine and autocrine regulation of gene expression by Wnt-inhibitor Dickkopf in wild-type and mutant hepatocytes},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {886},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43077},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430778},
  pages     = {18},
  year      = {2017},
  abstract  = {Background Cells are able to communicate and coordinate their function within tissues via secreted factors. Aberrant secretion by cancer cells can modulate this intercellular communication, in particular in highly organised tissues such as the liver. Hepatocytes, the major cell type of the liver, secrete Dickkopf (Dkk), which inhibits Wnt/ β-catenin signalling in an autocrine and paracrine manner. Consequently, Dkk modulates the expression of Wnt/ β-catenin target genes. We present a mathematical model that describes the autocrine and paracrine regulation of hepatic gene expression by Dkk under wild-type conditions as well as in the presence of mutant cells. Results Our spatial model describes the competition of Dkk and Wnt at receptor level, intra-cellular Wnt/ β-catenin signalling, and the regulation of target gene expression for 21 individual hepatocytes. Autocrine and paracrine regulation is mediated through a feedback mechanism via Dkk and Dkk diffusion along the porto-central axis. Along this axis an APC concentration gradient is modelled as experimentally detected in liver. Simulations of mutant cells demonstrate that already a single mutant cell increases overall Dkk concentration. The influence of the mutant cell on gene expression of surrounding wild-type hepatocytes is limited in magnitude and restricted to hepatocytes in close proximity. To explore the underlying molecular mechanisms, we perform a comprehensive analysis of the model parameters such as diffusion coefficient, mutation strength and feedback strength. Conclusions Our simulations show that Dkk concentration is elevated in the presence of a mutant cell. However, the impact of these elevated Dkk levels on wild-type hepatocytes is confined in space and magnitude. The combination of inter- and intracellular processes, such as Dkk feedback, diffusion and Wnt/ β-catenin signal transduction, allow wild-type hepatocytes to largely maintain their gene expression.},
  language  = {en}
}
@misc{ReibisSalzwedelBonaventuraetal.2017,
  author    = {Reibis, Rona Katharina and Salzwedel, Annett and Bonaventura, Klaus and V{\"o}ller, Heinz and Wegscheider, Karl},
  title     = {Improvement of left ventricular ejection fraction in revascularized postmyocardial patients},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {882},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43509},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435093},
  pages     = {10},
  year      = {2017},
  abstract  = {BACKGROUND: Reduced left ventricular ejection fraction (LVEF) ≤30\% is the most powerful prognostic indicator for sudden cardiac death (SCD) in patients after myocardial infarction (MI), but there are little data about long-term changes of LVEF after revascularization and the following implantation of a cardioverter defibrillator (ICD). METHODS: We performed a retrospective analysis of 277 patients with reduced LVEF at least 1month after MI and complete revascularization. Patients (median time post-MI 23.4months; 74.3\% after PCI, 25.7\% after CABG were assigned either to group 1 (LVEF<30\%) or group 2 (LVEF 30-40\%). Biplane echocardiography was redone after a mean follow-up of 441±220days. RESULTS: LVEF increased significantly in both two groups (group 1: 26.2±4.8\% to 32.4±8.5\%; p<0.001; group 2: 38.2±2.5\% to 44.4±9.6\%; p<0.001). However, statistical analysis of first and second LVEF measurement by means of a LOWESS regression and with an appropriate correction of the regression towards the mean effect revealed only a moderate increase of the mean LVEF from 35 to 37\% (p<0.001) with a large interindividual variation. CONCLUSIONS: The impact of early revascularization on LVEF appears to be low in the majority of post-MI heart failure patients. Owing to the high variability, a single measurement may not be reliable enough to justify a decision on ICD indication.},
  language  = {en}
}