TY - JOUR A1 - Wainwright, John A1 - Parsons, Anthony J. A1 - Mueller, Eva N. A1 - Brazier, Richard E. A1 - Powell, D. Mark T1 - Response to Hairsine's and Sander's 'Comment on "A transport-distance based approach to scaling erosionrates" : parts 1, 2 and 3 by Wainwright et al.' Y1 - 2009 UR - http://www3.interscience.wiley.com/cgi-bin/jhome/2388/ U6 - https://doi.org/10.1002/Esp.1781 SN - 0197-9337 ER - TY - JOUR A1 - Wainwright, John A1 - Parsons, Anthony J. A1 - Mueller, Eva N. A1 - Brazier, Richard E. A1 - Powell, D. Mark T1 - Response to Kinnell's 'Comment on " A transport-distance approach to scaling erosion rates: III. Evaluating scaling characteristics of MAHLERAN"' Y1 - 2009 UR - http://www3.interscience.wiley.com/cgi-bin/jhome/2388/ U6 - https://doi.org/10.1002/Esp.1816 SN - 0197-9337 ER - TY - JOUR A1 - Lilie, Hauke A1 - Baer, Dorit A1 - Kettner, Karina A1 - Weininger, Ulrich A1 - Balbach, Jochen A1 - Naumann, Manfred A1 - Mueller, Eva-Christina A1 - Otto, Albrecht A1 - Gast, Klaus A1 - Golbik, Ralph A1 - Kriegel, Thomas T1 - Yeast hexokinase isoenzyme ScHxk2 stability of a two-domain protein with discontinuous domains JF - Protein engineering design & selection N2 - The hexokinase isoenzyme 2 of Saccharomyces cerevisiae (ScHxk2) represents an archetype of a two-domain protein with the active site located in a cleft between the two domains. Binding of the substrate glucose results in a rigid body movement of the two domains leading to a cleft closure of the active site. Both domains of this enzyme are composed of discontinuous peptide sequences. This structural feature is reflected in the stability and folding of the ScHxk2 protein. Structural transitions induced by urea treatment resulted in the population of a thermodynamically stable folding intermediate, which, however, does not correspond to a molecule with one domain folded and the other unfolded. As demonstrated by different spectroscopic techniques, both domains are structurally affected by the partial denaturation. The intermediate possesses only 40% of the native secondary structural content and a substantial increase in the Stokes radius as judged by circular dichroism and dynamic light scattering analyses. One-dimensional H-1 NMR data prove that all tryptophan residues are in a non-native environment in the intermediate, indicating substantial changes in the tertiary structure. Still, the intermediate possesses quite a high stability for a transition intermediate of about Delta G = -22 kJ mol(-1). KW - dynamic light scattering KW - NMR KW - ScHxk2 KW - stability KW - transition intermediate Y1 - 2011 U6 - https://doi.org/10.1093/protein/gzq098 SN - 1741-0126 VL - 24 IS - 1-2 SP - 79 EP - 87 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Grimm, Volker A1 - Berger, Uta A1 - Bastiansen, Finn A1 - Eliassen, Sigrunn A1 - Ginot, Vincent A1 - Giske, Jarl A1 - Goss-Custard, John A1 - Grand, Tamara A1 - Heinz, Simone K. A1 - Huse, Geir A1 - Huth, Andreas A1 - Jepsen, Jane U. A1 - Jorgensen, Christian A1 - Mooij, Wolf M. A1 - Mueller, Birgit A1 - Piou, Cyril A1 - Railsback, Steven Floyd A1 - Robbins, Andrew M. A1 - Robbins, Martha M. A1 - Rossmanith, Eva A1 - Rueger, Nadja A1 - Strand, Espen A1 - Souissi, Sami A1 - Stillman, Richard A. A1 - Vabo, Rune A1 - Visser, Ute A1 - DeAngelis, Donald L. T1 - A standard protocol for describing individual-based and agent-based models JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers. (c) 2006 Elsevier B.V. All rights reserved. KW - individual-based model KW - agent-based model KW - model description KW - scientific communication KW - standardization Y1 - 2006 U6 - https://doi.org/10.1016/j.ecolmodel.2006.04.023 SN - 0304-3800 VL - 198 SP - 115 EP - 126 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bronstert, Axel A1 - de Araujo, Josè Carlos A1 - Batalla Villanueva, Ramon J. A1 - Costa, Alexandre Cunha A1 - Delgado, José Miguel Martins A1 - Francke, Till A1 - Förster, Saskia A1 - Güntner, Andreas A1 - Lopez-Tarazon, José Andrés A1 - Mamede, George Leite A1 - Medeiros, Pedro Henrique Augusto A1 - Mueller, Eva A1 - Vericat, Damia T1 - Process-based modelling of erosion, sediment transport and reservoir siltation in mesoscale semi-arid catchments JF - Journal of soils and sediments : protection, risk assessment and remediation N2 - To support scientifically sound water management in dryland environments a modelling system has been developed for the quantitative assessment of water and sediment fluxes in catchments, transport in the river system, and retention in reservoirs. The spatial scale of interest is the mesoscale because this is the scale most relevant for management of water and land resources. This modelling system comprises process-oriented hydrological components tailored for dryland characteristics coupled with components comprising hillslope erosion, sediment transport and reservoir deposition processes. The spatial discretization is hierarchically designed according to a multi-scale concept to account for particular relevant process scales. The non-linear and partly intermittent run-off generation and sediment dynamics are dealt with by accounting for connectivity phenomena at the intersections of landscape compartments. The modelling system has been developed by means of data from nested research catchments in NE-Spain and in NE-Brazil. In the semi-arid NE of Brazil sediment retention along the topography is the main process for sediment retention at all scales, i.e. the sediment delivery is transport limited. This kind of deposition retains roughly 50 to 60 % of eroded sediment, maintaining a similar deposition proportion in all spatial scales investigated. On the other hand, the sediment retained in reservoirs is clearly related to the scale, increasing with catchment area. With increasing area, there are more reservoirs, increasing the possibility of deposition. Furthermore, the area increase also promotes an increase in flow volume, favouring the construction of larger reservoirs, which generally overflow less frequently and retain higher sediment fractions. The second example comprises a highly dynamic Mediterranean catchment in NE-Spain with nested sub-catchments and reveals the full dynamics of hydrological, erosion and deposition features. The run-off modelling performed well with only some overestimation during low-flow periods due to the neglect of water losses along the river. The simulated peaks in sediment flux are reproduced well, while low-flow sediment transport is less well captured, due to the disregard of sediment remobilization in the riverbed during low flow. This combined observation and modelling study deepened the understanding of hydro-sedimentological systems characterized by flashy run-off generation and by erosion and sediment transport pulses through the different landscape compartments. The connectivity between the different landscape compartments plays a very relevant role, regarding both the total mass of water and sediment transport and the transport time through the catchment. KW - Connectivity KW - Deposition KW - Erosion KW - Modelling KW - Sediment transfer KW - Semi-arid Y1 - 2014 U6 - https://doi.org/10.1007/s11368-014-0994-1 SN - 1439-0108 SN - 1614-7480 VL - 14 IS - 12 SP - 2001 EP - 2018 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Garbusow, Maria A1 - Schad, Daniel A1 - Sebold, Miriam A1 - Friedel, Eva A1 - Bernhardt, Nadine A1 - Koch, Stefan P. A1 - Steinacher, Bruno A1 - Kathmann, Norbert A1 - Geurts, Dirk E. M. A1 - Sommer, Christian A1 - Mueller, Dirk K. A1 - Nebe, Stephan A1 - Paul, Soeren A1 - Wittchen, Hans-Ulrich A1 - Zimmermann, Ulrich S. A1 - Walter, Henrik A1 - Smolka, Michael N. A1 - Sterzer, Philipp A1 - Rapp, Michael A. A1 - Huys, Quentin J. M. A1 - Schlagenhauf, Florian A1 - Heinz, Andreas T1 - Pavlovian-to-instrumental transfer effects in the nucleus accumbens relate to relapse in alcohol dependence JF - Addiction biology N2 - In detoxified alcohol-dependent patients, alcohol-related stimuli can promote relapse. However, to date, the mechanisms by which contextual stimuli promote relapse have not been elucidated in detail. One hypothesis is that such contextual stimuli directly stimulate the motivation to drink via associated brain regions like the ventral striatum and thus promote alcohol seeking, intake and relapse. Pavlovian-to-Instrumental-Transfer (PIT) may be one of those behavioral phenomena contributing to relapse, capturing how Pavlovian conditioned (contextual) cues determine instrumental behavior (e.g. alcohol seeking and intake). We used a PIT paradigm during functional magnetic resonance imaging to examine the effects of classically conditioned Pavlovian stimuli on instrumental choices in n=31 detoxified patients diagnosed with alcohol dependence and n=24 healthy controls matched for age and gender. Patients were followed up over a period of 3 months. We observed that (1) there was a significant behavioral PIT effect for all participants, which was significantly more pronounced in alcohol-dependent patients; (2) PIT was significantly associated with blood oxygen level-dependent (BOLD) signals in the nucleus accumbens (NAcc) in subsequent relapsers only; and (3) PIT-related NAcc activation was associated with, and predictive of, critical outcomes (amount of alcohol intake and relapse during a 3 months follow-up period) in alcohol-dependent patients. These observations show for the first time that PIT-related BOLD signals, as a measure of the influence of Pavlovian cues on instrumental behavior, predict alcohol intake and relapse in alcohol dependence. KW - human Pavlovian-to-instrumental transfer KW - nucleus accumbens KW - relapse in alcohol use disorder Y1 - 2016 U6 - https://doi.org/10.1111/adb.12243 SN - 1355-6215 SN - 1369-1600 VL - 21 SP - 719 EP - 731 PB - Wiley-Blackwell CY - Hoboken ER -