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  • 1
    Publication Date: 2008-03-18
    Description: Common human diseases result from the interplay of many genes and environmental factors. Therefore, a more integrative biology approach is needed to unravel the complexity and causes of such diseases. To elucidate the complexity of common human diseases such as obesity, we have analysed the expression of 23,720 transcripts in large population-based blood and adipose tissue cohorts comprehensively assessed for various phenotypes, including traits related to clinical obesity. In contrast to the blood expression profiles, we observed a marked correlation between gene expression in adipose tissue and obesity-related traits. Genome-wide linkage and association mapping revealed a highly significant genetic component to gene expression traits, including a strong genetic effect of proximal (cis) signals, with 50% of the cis signals overlapping between the two tissues profiled. Here we demonstrate an extensive transcriptional network constructed from the human adipose data that exhibits significant overlap with similar network modules constructed from mouse adipose data. A core network module in humans and mice was identified that is enriched for genes involved in the inflammatory and immune response and has been found to be causally associated to obesity-related traits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Emilsson, Valur -- Thorleifsson, Gudmar -- Zhang, Bin -- Leonardson, Amy S -- Zink, Florian -- Zhu, Jun -- Carlson, Sonia -- Helgason, Agnar -- Walters, G Bragi -- Gunnarsdottir, Steinunn -- Mouy, Magali -- Steinthorsdottir, Valgerdur -- Eiriksdottir, Gudrun H -- Bjornsdottir, Gyda -- Reynisdottir, Inga -- Gudbjartsson, Daniel -- Helgadottir, Anna -- Jonasdottir, Aslaug -- Jonasdottir, Adalbjorg -- Styrkarsdottir, Unnur -- Gretarsdottir, Solveig -- Magnusson, Kristinn P -- Stefansson, Hreinn -- Fossdal, Ragnheidur -- Kristjansson, Kristleifur -- Gislason, Hjortur G -- Stefansson, Tryggvi -- Leifsson, Bjorn G -- Thorsteinsdottir, Unnur -- Lamb, John R -- Gulcher, Jeffrey R -- Reitman, Marc L -- Kong, Augustine -- Schadt, Eric E -- Stefansson, Kari -- England -- Nature. 2008 Mar 27;452(7186):423-8. doi: 10.1038/nature06758. Epub 2008 Mar 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉deCODE genetics, 101 Reykjavik, Iceland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18344981" target="_blank"〉PubMed〈/a〉
    Keywords: Adipose Tissue/metabolism ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; Blood/metabolism ; Body Mass Index ; Cohort Studies ; European Continental Ancestry Group/genetics ; Female ; *Gene Expression Profiling ; Gene Expression Regulation/*genetics ; Genome, Human ; Humans ; Iceland ; Lod Score ; Male ; Mice ; Middle Aged ; Obesity/*genetics ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; Sample Size ; Waist-Hip Ratio
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Nowak et al. argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbot, Patrick -- Abe, Jun -- Alcock, John -- Alizon, Samuel -- Alpedrinha, Joao A C -- Andersson, Malte -- Andre, Jean-Baptiste -- van Baalen, Minus -- Balloux, Francois -- Balshine, Sigal -- Barton, Nick -- Beukeboom, Leo W -- Biernaskie, Jay M -- Bilde, Trine -- Borgia, Gerald -- Breed, Michael -- Brown, Sam -- Bshary, Redouan -- Buckling, Angus -- Burley, Nancy T -- Burton-Chellew, Max N -- Cant, Michael A -- Chapuisat, Michel -- Charnov, Eric L -- Clutton-Brock, Tim -- Cockburn, Andrew -- Cole, Blaine J -- Colegrave, Nick -- Cosmides, Leda -- Couzin, Iain D -- Coyne, Jerry A -- Creel, Scott -- Crespi, Bernard -- Curry, Robert L -- Dall, Sasha R X -- Day, Troy -- Dickinson, Janis L -- Dugatkin, Lee Alan -- El Mouden, Claire -- Emlen, Stephen T -- Evans, Jay -- Ferriere, Regis -- Field, Jeremy -- Foitzik, Susanne -- Foster, Kevin -- Foster, William A -- Fox, Charles W -- Gadau, Juergen -- Gandon, Sylvain -- Gardner, Andy -- Gardner, Michael G -- Getty, Thomas -- Goodisman, Michael A D -- Grafen, Alan -- Grosberg, Rick -- Grozinger, Christina M -- Gouyon, Pierre-Henri -- Gwynne, Darryl -- Harvey, Paul H -- Hatchwell, Ben J -- Heinze, Jurgen -- Helantera, Heikki -- Helms, Ken R -- Hill, Kim -- Jiricny, Natalie -- Johnstone, Rufus A -- Kacelnik, Alex -- Kiers, E Toby -- Kokko, Hanna -- Komdeur, Jan -- Korb, Judith -- Kronauer, Daniel -- Kummerli, Rolf -- Lehmann, Laurent -- Linksvayer, Timothy A -- Lion, Sebastien -- Lyon, Bruce -- Marshall, James A R -- McElreath, Richard -- Michalakis, Yannis -- Michod, Richard E -- Mock, Douglas -- Monnin, Thibaud -- Montgomerie, Robert -- Moore, Allen J -- Mueller, Ulrich G -- Noe, Ronald -- Okasha, Samir -- Pamilo, Pekka -- Parker, Geoff A -- Pedersen, Jes S -- Pen, Ido -- Pfennig, David -- Queller, David C -- Rankin, Daniel J -- Reece, Sarah E -- Reeve, Hudson K -- Reuter, Max -- Roberts, Gilbert -- Robson, Simon K A -- Roze, Denis -- Rousset, Francois -- Rueppell, Olav -- Sachs, Joel L -- Santorelli, Lorenzo -- Schmid-Hempel, Paul -- Schwarz, Michael P -- Scott-Phillips, Tom -- Shellmann-Sherman, Janet -- Sherman, Paul W -- Shuker, David M -- Smith, Jeff -- Spagna, Joseph C -- Strassmann, Beverly -- Suarez, Andrew V -- Sundstrom, Liselotte -- Taborsky, Michael -- Taylor, Peter -- Thompson, Graham -- Tooby, John -- Tsutsui, Neil D -- Tsuji, Kazuki -- Turillazzi, Stefano -- Ubeda, Francisco -- Vargo, Edward L -- Voelkl, Bernard -- Wenseleers, Tom -- West, Stuart A -- West-Eberhard, Mary Jane -- Westneat, David F -- Wiernasz, Diane C -- Wild, Geoff -- Wrangham, Richard -- Young, Andrew J -- Zeh, David W -- Zeh, Jeanne A -- Zink, Andrew -- BB/H022716/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2011 Mar 24;471(7339):E1-4; author reply E9-10. doi: 10.1038/nature09831.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430721" target="_blank"〉PubMed〈/a〉
    Keywords: *Altruism ; Animals ; *Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; *Genetic Fitness ; Genetics, Population ; Heredity ; Humans ; Male ; *Models, Biological ; Phenotype ; Reproducibility of Results ; *Selection, Genetic ; Sex Ratio
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2016-03-10
    Description: The origins of the genus Homo are murky, but by H. erectus, bigger brains and bodies had evolved that, along with larger foraging ranges, would have increased the daily energetic requirements of hominins. Yet H. erectus differs from earlier hominins in having relatively smaller teeth, reduced chewing muscles, weaker maximum bite force capabilities, and a relatively smaller gut. This paradoxical combination of increased energy demands along with decreased masticatory and digestive capacities is hypothesized to have been made possible by adding meat to the diet, by mechanically processing food using stone tools, or by cooking. Cooking, however, was apparently uncommon until 500,000 years ago, and the effects of carnivory and Palaeolithic processing techniques on mastication are unknown. Here we report experiments that tested how Lower Palaeolithic processing technologies affect chewing force production and efficacy in humans consuming meat and underground storage organs (USOs). We find that if meat comprised one-third of the diet, the number of chewing cycles per year would have declined by nearly 2 million (a 13% reduction) and total masticatory force required would have declined by 15%. Furthermore, by simply slicing meat and pounding USOs, hominins would have improved their ability to chew meat into smaller particles by 41%, reduced the number of chews per year by another 5%, and decreased masticatory force requirements by an additional 12%. Although cooking has important benefits, it appears that selection for smaller masticatory features in Homo would have been initially made possible by the combination of using stone tools and eating meat.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zink, Katherine D -- Lieberman, Daniel E -- England -- Nature. 2016 Mar 24;531(7595):500-3. doi: 10.1038/nature16990. Epub 2016 Mar 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26958832" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Animals ; Bite Force ; Carnivory ; Diet/*history ; Female ; Food Handling/*history ; Goats ; History, Ancient ; Hominidae ; Humans ; Male ; Mastication/*physiology ; Meat/*history ; Particle Size ; Plants ; Tool Use Behavior ; Tooth/physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2003-02-20
    Description: The homogeneous freezing of supercooled H2SO4/H2O solution droplets was investigated in the aerosol chamber AIDA (Aerosol Interactions and Dynamics in the Atmosphere) of Forschungszentrum Karlsruhe. 24 freezing experiments were performed at temperatures between 189 and 235 K with aerosol particles in the diameter range 0.05 to 1 µm. Individual experiments started at homogeneous temperatures and ice saturation ratios between 0.9 and 0.95. Cloud cooling rates up to -2.8 K min-1 were simulated dynamically in the chamber by expansion cooling using a mechanical pump. Depending on the cooling rate and starting temperature, freezing threshold relative humidities were exceeded after expansion time periods between about 1 and 10 min. The onset of ice formation was measured with three independent methods showing good agreement among each other. Ice saturation ratios measured at the onset of ice formation increased from about 1.4 at 231 K  to about 1.75 at 189 K. The experimental data set including thermodynamic parameters as well as physical and chemical aerosol analysis provides a good basis for microphysical model applications.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 5
    Publication Date: 2013-11-08
    Description: Simulating pollen concentrations with numerical weather prediction (NWP) systems requires a parameterization for pollen emission. We have developed a parameterization that is adaptable for different plant species. Both biological and physical processes of pollen emission are taken into account by parameterizing emission as a two-step process: (1) the release of the pollen from the flowers, and (2) their entrainment into the atmosphere. Key factors influencing emission are temperature, relative humidity, the turbulent kinetic energy and precipitation. We have simulated the birch pollen season of 2012 using the NWP system COSMO-ART (Consortium for Small-scale Modelling – Aerosols and Reactive Trace Gases), both with a parameterization already present in the model and with our new parameterization EMPOL. The statistical results show that the performance of the model can be enhanced by using EMPOL.
    Print ISSN: 1991-959X
    Electronic ISSN: 1991-9603
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 6
    Publication Date: 2016-03-17
    Description: Heterogeneity of landscape features like terrain, soil, and vegetation properties affects the partitioning of water and energy. However, it remains unclear to what extent an explicit representation of this heterogeneity at the sub-grid scale of distributed hydrological models can improve the hydrological consistency and the robustness of such models. In this study, hydrological process complexity arising from sub-grid topography heterogeneity was incorporated into the distributed mesoscale Hydrologic Model (mHM). Seven study catchments across Europe were used to test whether (1) the incorporation of additional sub-grid variability on the basis of landscape-derived response units improves model internal dynamics, (2) the application of semi-quantitative, expert-knowledge-based model constraints reduces model uncertainty, and whether (3) the combined use of sub-grid response units and model constraints improves the spatial transferability of the model. Unconstrained and constrained versions of both the original mHM and mHMtopo, which allows for topography-based sub-grid heterogeneity, were calibrated for each catchment individually following a multi-objective calibration strategy. In addition, four of the study catchments were simultaneously calibrated and their feasible parameter sets were transferred to the remaining three receiver catchments. In a post-calibration evaluation procedure the probabilities of model and transferability improvement, when accounting for sub-grid variability and/or applying expert-knowledge-based model constraints, were assessed on the basis of a set of hydrological signatures. In terms of the Euclidian distance to the optimal model, used as an overall measure of model performance with respect to the individual signatures, the model improvement achieved by introducing sub-grid heterogeneity to mHM in mHMtopo was on average 13 %. The addition of semi-quantitative constraints to mHM and mHMtopo resulted in improvements of 13 and 19 %, respectively, compared to the base case of the unconstrained mHM. Most significant improvements in signature representations were, in particular, achieved for low flow statistics. The application of prior semi-quantitative constraints further improved the partitioning between runoff and evaporative fluxes. In addition, it was shown that suitable semi-quantitative prior constraints in combination with the transfer-function-based regularization approach of mHM can be beneficial for spatial model transferability as the Euclidian distances for the signatures improved on average by 2 %. The effect of semi-quantitative prior constraints combined with topography-guided sub-grid heterogeneity on transferability showed a more variable picture of improvements and deteriorations, but most improvements were observed for low flow statistics.
    Print ISSN: 1027-5606
    Electronic ISSN: 1607-7938
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 7
    Publication Date: 2015-12-21
    Description: Heterogeneity of landscape features like terrain, soil, and vegetation properties affect the partitioning of water and energy. However, it remains unclear to which extent an explicit representation of this heterogeneity at the sub-grid scale of distributed hydrological models can improve the hydrological consistency and the robustness of such models. In this study, hydrological process complexity arising from sub-grid topography heterogeneity was incorporated in the distributed mesoscale Hydrologic Model (mHM). Seven study catchments across Europe were used to test whether (1) the incorporation of additional sub-grid variability on the basis of landscape-derived response units improves model internal dynamics, (2) the application of semi-quantitative, expert-knowledge based model constraints reduces model uncertainty; and (3) the combined use of sub-grid response units and model constraints improves the spatial transferability of the model. Unconstrained and constrained versions of both, the original mHM and mHMtopo, which allows for topography-based sub-grid heterogeneity, were calibrated for each catchment individually following a multi-objective calibration strategy. In addition, four of the study catchments were simultaneously calibrated and their feasible parameter sets were transferred to the remaining three receiver catchments. In a post-calibration evaluation procedure the probabilities of model and transferability improvement, when accounting for sub-grid variability and/or applying expert-knowledge based model constraints, were assessed on the basis of a set of hydrological signatures. In terms of the Euclidian distance to the optimal model, used as overall measure for model performance with respect to the individual signatures, the model improvement achieved by introducing sub-grid heterogeneity to mHM in mHMtopo was on average 13 %. The addition of semi-quantitative constraints to mHM and mHMtopo resulted in improvements of 13 and 19 % respectively, compared to the base case of the unconstrained mHM. Most significant improvements in signature representations were, in particular, achieved for low flow statistics. The application of prior semi-quantitative constraints further improved the partitioning between runoff and evaporative fluxes. Besides, it was shown that suitable semi-quantitative prior constraints in combination with the transfer function based regularization approach of mHM, can be beneficial for spatial model transferability as the Euclidian distances for the signatures improved on average by 2 %. The effect of semi-quantitative prior constraints combined with topography-guided sub-grid heterogeneity on transferability showed a more variable picture of improvements and deteriorations, but most improvements were observed for low flow statistics.
    Print ISSN: 1812-2108
    Electronic ISSN: 1812-2116
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 8
    Publication Date: 2017-05-19
    Description: Hourly NOx concentrations were simulated for the city of Zurich, Switzerland, at 10 m resolution for the years 2013–2014. The simulations were generated with the nested mesoscale meteorology and microscale dispersion model system GRAMM/GRAL (versions v15.12/v14.8) by applying a catalogue-based approach. This approach was specifically designed to enable long-term city-wide building-resolving simulations with affordable computation costs. It relies on a discrete set of possible weather situations and corresponding steady-state flow and dispersion patterns that are pre-computed and then matched hourly with actual meteorological observations. The modelling system was comprehensively evaluated using eight sites continuously monitoring NOx concentrations and 65 passive samplers measuring NO2 concentrations on a 2-weekly basis all over the city. The system was demonstrated to fulfil the European Commission standards for air pollution modelling at nearly all sites. The average spatial distribution was very well represented, despite a general tendency to overestimating the observed concentrations, possibly due to a crude representation of traffic-induced turbulence. The temporal variability of concentrations explained by varying emissions and weather situations was accurately reproduced on different time scales. The seasonal cycle of concentrations, mostly driven by stronger vertical dispersion in summer than in winter, was very well captured in the two year simulation period. Short-term events, such as episodes of particularly high and low concentrations, were detected in most cases by the system, although some unrealistic pollution peaks were occasionally generated, pointing at some limitations of the steady-state approximation. The different patterns of the diurnal cycle of concentrations observed in the city were generally well captured as well. The evaluation confirmed the adequacy of the catalogue-based approach in the context of city scale air pollution modelling. The ability to reproduce not only the spatial gradients but also the hourly temporal variability over multiple years makes the model system particularly suitable for investigating individualized air pollution exposure in the city.
    Print ISSN: 1991-9611
    Electronic ISSN: 1991-962X
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 9
    Publication Date: 2017-09-22
    Description: Most of the current large scale hydrological models do not contain a physically-based groundwater flow component. The main difficulties in large-scale groundwater modeling include the efficient representation of unsaturated zone flow, the characterization of dynamic groundwater-surface water interaction and the numerical stability while preserving complex physical processes and high resolution. To address these problems, we propose a highly-scalable coupled hydrologic and groundwater model (mHM#OGS) based on the integration of two open-source modeling codes: the mesoscale hydrologic Model (mHM) and the finite element simulator OpenGeoSys (OGS). mHM#OGS is coupled using a boundary condition-based coupling scheme that dynamically links the surface and subsurface parts. Nested time stepping allows smaller time steps for typically faster surface runoff routing in mHM and larger time steps for slower subsurface flow in OGS. mHM#OGS features the coupling interface which can transfer the groundwater recharge and river baseflow rate between mHM and OpenGeoSys. Verification of the coupled model was conducted using the time-series of observed streamflow and groundwater levels. Moreover, we force the transient model using groundwater recharge in two scenarios: (1) spatially variable recharge based on the mHM simulations, and (2) spatially homogeneous groundwater recharge. The modeling result in first scenario has a slightly higher correlation with groundwater head time-series, which further validates the plausibility of spatial groundwater recharge distribution calculated by mHM in the mesocale. The statistical analysis of model predictions shows a promising prediction ability of the model. The offline coupling method implemented here can reproduce reasonable groundwater head time series while keep a desired level of detail in the subsurface model structure with little surplus in computational cost. Our exemplary calculations show that the coupled model mHM#OGS can be a valuable tool to assess the effects of variability in land surface heterogeneity, meteorological, topographical forces and geological zonation on the groundwater flow dynamics.
    Print ISSN: 1991-9611
    Electronic ISSN: 1991-962X
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 10
    Publication Date: 2017-09-19
    Description: Hourly NOx concentrations were simulated for the city of Zürich, Switzerland, at 10 m resolution for the years 2013–2014. The simulations were generated with the nested mesoscale meteorology and micro-scale dispersion model system GRAMM–GRAL (versions v15.12 and v14.8) by applying a catalogue-based approach. This approach was specifically designed to enable long-term city-wide building-resolving simulations with affordable computation costs. It relies on a discrete set of possible weather situations and corresponding steady-state flow and dispersion patterns that are pre-computed and then matched hourly with actual meteorological observations. The modelling system was comprehensively evaluated using eight sites continuously monitoring NOx concentrations and 65 passive samplers measuring NO2 concentrations on a 2-weekly basis all over the city. The system was demonstrated to fulfil the European Commission standards for air pollution modelling at nearly all sites. The average spatial distribution was very well represented, despite a general tendency to overestimate the observed concentrations, possibly due to a crude representation of traffic-induced turbulence and to underestimated dispersion in the vicinity of buildings. The temporal variability of concentrations explained by varying emissions and weather situations was accurately reproduced on different timescales. The seasonal cycle of concentrations, mostly driven by stronger vertical dispersion in summer than in winter, was very well captured in the 2-year simulation period. Short-term events, such as episodes of particularly high and low concentrations, were detected in most cases by the system, although some unrealistic pollution peaks were occasionally generated, pointing at some limitations of the steady-state approximation. The different patterns of the diurnal cycle of concentrations observed in the city were generally well captured as well. The evaluation confirmed the adequacy of the catalogue-based approach in the context of city-scale air pollution modelling. The ability to reproduce not only the spatial gradients but also the hourly temporal variability over multiple years makes the model system particularly suitable for investigating individualized air pollution exposure in the city.
    Print ISSN: 1991-959X
    Electronic ISSN: 1991-9603
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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