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Exploring, exploiting and evolving diversity of aquatic ecosystem models: a community perspective
(2015)
Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5-10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.
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 2017. Selected projects have presented their results on April 25th and November 15th 2017 at the Future SOC Lab Day events.
Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540-3310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF). (C) 2018 Elsevier B.V. All rights reserved.
The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end-member mixing analysis (EMMA) to 10 small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end-members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27-28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45-57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60-89% in pasture watersheds of less than 10 ha to 0% in forest and 27-28% in pastures in watersheds greater than 100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.
Objective: Endocannabinoid system (ECS) activation promotes obesity-associated metabolic disease. Increased dietary fat intake increases blood endocannabinoids and alters adipose and skeletal muscle ECS gene expression in human.
Methods: Two weeks isocaloric low- (LFD) and high-fat diets (HFD) in obese (n = 12) and normal- weight (n = 17) subjects in a randomized cross-over study were compared. Blood endocannabinoids were measured in the fasting condition and after food intake using mass spectrometry. Adipose and skeletal muscle gene expression was determined using real-time RT-PCR.
Results: Baseline fasting plasma endocannabinoids were similar with both diets. Anandamide decreased similarly with high- or low-fat test meals in both groups. Baseline arachidonoylglycerol plasma concentrations were similar between groups and diets, and unresponsive to eating. In subcutaneous adipose tissue, DAGL-alpha mRNA was upregulated and fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL) mRNAs were down-regulated in obese subjects, but the diets had no influence. In contrast, the HFD produced pronounced reductions in skeletal muscle CB1-R and MAGL mRNA expression, whereas obesity did not affect muscular gene expression.
Conclusions: Weight-neutral changes in dietary fat intake cannot explain excessive endocannabinoid availability in human obesity. Obesity and dietary fat intake affect ECS gene expression in a tissue-specific manner.
Core Ideas
3D MRI relaxation time maps reflect water mobility in root, rhizosphere, and soil.
3D NCT water content maps of the same plant complement relaxation time maps.
The relaxation time T1 decreases from soil to root, whereas water content increases.
Parameters together indicate modification of rhizosphere pore space by gel phase.
The zone of reduced T1 corresponds to the zone remaining dry after rewetting.
In situ investigations of the rhizosphere require high‐resolution imaging techniques, which allow a look into the optically opaque soil compartment. We present the novel combination of magnetic resonance imaging (MRI) and neutron computed tomography (NCT) to achieve synergistic information such as water mobility in terms of three‐dimensional (3D) relaxation time maps and total water content maps. Besides a stationary MRI scanner for relaxation time mapping, we used a transportable MRI system on site in the NCT facility to capture rhizosphere properties before desiccation and after subsequent rewetting. First, we addressed two questions using water‐filled test capillaries between 0.1 and 5 mm: which root diameters can still be detected by both methods, and to what extent are defined interfaces blurred by these imaging techniques? Going to real root system architecture, we demonstrated the sensitivity of the transportable MRI device by co‐registration with NCT and additional validation using X‐ray computed tomography. Under saturated conditions, we observed for the rhizosphere in situ a zone with shorter T1 relaxation time across a distance of about 1 mm that was not caused by reduced water content, as proven by successive NCT measurements. We conclude that the effective pore size in the pore network had changed, induced by a gel phase. After rewetting, NCT images showed a dry zone persisting while the MRI intensity inside the root increased considerably, indicating water uptake from the surrounding bulk soil through the still hydrophobic rhizosphere. Overall, combining NCT and MRI allows a more detailed analysis of the rhizosphere's functioning.
Here we report on a light triggered remote control of microgel size in the presence of photosensitive surfactant. The hydrophobic tail of the cationic surfactant contains azobenzene group that undergoes a reversible photo-isomerization reaction from a trans-to a cis-state accompanied by a change in the hydrophobicity of the surfactant. We have investigated light assisted behaviour and the complex formation of the microgels with azobenzene containing surfactant over the broad concentrational range starting far below and exceeding several times of the critical micelle concentration (CMC). At small surfactant concentration in solution (far below CMC), the surfactant in the trans-state accommodates within the microgel causing its compaction, while the cis-isomer desorbs out of microgel resulting in its swelling. The process of the microgel size change can be described as swelling on UV irradiation (trans-cis isomerization) and shrinking on irradiation with blue light (cis-trans isomerization). However, at the surfactant concentrations larger than CMC, the opposite behaviour is observed: the microgel swells on blue irradiation and shrinks during exposure to UV light. We explain this behaviour theoretically taking into account isomer dependent micellization of surfactant within the microgels. Published by AIP Publishing.
We report on light sensitive microgel particles that can change their volume reversibly in response to illumination with light of different wavelengths. To make the anionic microgels photosensitive we add surfactants with a positively charged polyamine head group and an azobenzene containing tail. Upon illumination, azobenzene undergoes a reversible photo-isomerization reaction from a trans- to a cis-state accompanied by a change in the hydrophobicity of the surfactant. Depending on the isomerization state, the surfactant molecules are either accommodated within the microgel (trans- state) resulting in its shrinkage or desorbed back into water (cis-isomer) letting the microgel swell. We have studied three surfactants differing in the number of amino groups, so that the number of charges of the surfactant head varies between 1 and 3. We have found experimentally and theoretically that the surfactant concentration needed for microgel compaction increases with decreasing number of charges of the head group. Utilization of polyamine azobenzene containing surfactants for the light triggered remote control of the microgel size opens up a possibility for applications of light responsive microgels as drug carriers in biology and medicine.
Ihre außergewöhnlich hohen Konversionseffizienzen von über 20 % und die einfache Zellherstellung machen Hybridperowskite zu heißen Kandidaten für alternative Solarzellenmaterialien. CH3NH3PbI3 als Archetyp dieser Materialklasse besitzt außergewöhnliche Eigenschaften wie eine sehr effiziente Umwandlung von Solarenergie, wobei besonders Ferroelektrizität als mögliche Erklärung in den Fokus gerückt ist. Diese erfordert allerdings eine nicht-zentrosymmetrische Kristallstruktur als notwendige Voraussetzung. Wir stellen hier eine Erklärung des Symmetriebruchs in diesem Material auf kristallographischem, d. h. fernordnungs-basiertem, Wege vor. Während das Molekülkation CH3NH3+ intrinsisch polar ist, ist es extrem fehlgeordnet und kann deshalb nicht die einzige Erklärung darstellen. Es verzerrt allerdings das umgebende Kristallgitter und ruft dadurch eine Verschiebung der Iod-Atome von den zentrosymmetrischen Positionen hervor.
Excellent conversion efficiencies of over 20% and facile cell production have placed hybrid perovskites at the forefront of novel solar cell materials, with CH3NH3PbI3 being an archetypal compound. The question why CH3NH3PbI3 has such extraordinary characteristics, particularly a very efficient power conversion from absorbed light to electrical power, is hotly debated, with ferroelectricity being a promising candidate. This does, however, require the crystal structure to be non-centrosymmetric and we herein present crystallographic evidence as to how the symmetry breaking occurs on a crystallographic and, therefore, long-range level. Although the molecular cation CH3NH3+ is intrinsically polar, it is heavily disordered and this cannot be the sole reason for the ferroelectricity. We show that it, nonetheless, plays an important role, as it distorts the neighboring iodide positions from their centrosymmetric positions.
Ihre außergewöhnlich hohen Konversionseffizienzen von über 20 % und die einfache Zellherstellung machen Hybridperowskite zu heißen Kandidaten für alternative Solarzellenmaterialien. CH3NH3PbI3 als Archetyp dieser Materialklasse besitzt außergewöhnliche Eigenschaften wie eine sehr effiziente Umwandlung von Solarenergie, wobei besonders Ferroelektrizität als mögliche Erklärung in den Fokus gerückt ist. Diese erfordert allerdings eine nicht-zentrosymmetrische Kristallstruktur als notwendige Voraussetzung. Wir stellen hier eine Erklärung des Symmetriebruchs in diesem Material auf kristallographischem, d. h. fernordnungs-basiertem, Wege vor. Während das Molekülkation CH3NH3+ intrinsisch polar ist, ist es extrem fehlgeordnet und kann deshalb nicht die einzige Erklärung darstellen. Es verzerrt allerdings das umgebende Kristallgitter und ruft dadurch eine Verschiebung der Iod-Atome von den zentrosymmetrischen Positionen hervor.
Excellent conversion efficiencies of over 20% and facile cell production have placed hybrid perovskites at the forefront of novel solar cell materials, with CH3NH3PbI3 being an archetypal compound. The question why CH3NH3PbI3 has such extraordinary characteristics, particularly a very efficient power conversion from absorbed light to electrical power, is hotly debated, with ferroelectricity being a promising candidate. This does, however, require the crystal structure to be non-centrosymmetric and we herein present crystallographic evidence as to how the symmetry breaking occurs on a crystallographic and, therefore, long-range level. Although the molecular cation CH3NH3+ is intrinsically polar, it is heavily disordered and this cannot be the sole reason for the ferroelectricity. We show that it, nonetheless, plays an important role, as it distorts the neighboring iodide positions from their centrosymmetric positions.
Auxology has developed from mere describing child and adolescent growth into a vivid and interdisciplinary research area encompassing human biologists, physicians, social scientists, economists and biostatisticians. The meeting illustrated the diversity in auxology, with the various social, medical, biological and biostatistical aspects in studies on child growth and development.
We report on light sensitive microgel particles that can change their volume reversibly in response to illumination with light of different wavelengths. To make the anionic microgels photosensitive we add surfactants with a positively charged polyamine head group and an azobenzene containing tail. Upon illumination, azobenzene undergoes a reversible photo-isomerization reaction from a trans- to a cis-state accompanied by a change in the hydrophobicity of the surfactant. Depending on the isomerization state, the surfactant molecules are either accommodated within the microgel (trans-state) resulting in its shrinkage or desorbed back into water (cis-isomer) letting the microgel swell. We have studied three surfactants differing in the number of amino groups, so that the number of charges of the surfactant head varies between 1 and 3. We have found experimentally and theoretically that the surfactant concentration needed for microgel compaction increases with decreasing number of charges of the head group. Utilization of polyamine azobenzene containing surfactants for the light triggered remote control of the microgel size opens up a possibility for applications of light responsive microgels as drug carriers in biology and medicine.