Global parameter identification of stochastic reaction networks from single trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell--cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and efficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems Biology

Synergistic and antagonistic effects of land use and non‐native species on community responses to climate change

Climate change, land‐use change and introductions of non‐native species are key determinants of biodiversity change worldwide. However, the extent to which anthropogenic drivers of environmental change interact to affect biological communities is largely unknown, especially over longer time periods. Here, we show that plant community composition in 996 Swedish landscapes has consistently shifted to reflect the warmer and wetter climate that the region has experienced during the second half of the 20th century. Using community climatic indices, which reflect the average climatic associations of the species within each landscape at each time period, we found that species compositions in 74% of landscapes now have a higher representation of warm‐associated species than they did previously, while 84% of landscapes now host more species associated with higher levels of precipitation. In addition to a warmer and wetter climate, there have also been large shifts in land use across the region, while the fraction of non‐native species has increased in the majority of landscapes. Climatic warming at the landscape level appeared to favour the colonization of warm‐associated species, while also potentially driving losses in cool‐associated species. However, the resulting increases in community thermal means were apparently buffered by landscape simplification (reduction in habitat heterogeneity within landscapes) in the form of increased forest cover. Increases in non‐native species, which generally originate from warmer climates than Sweden, were a strong driver of community‐level warming. In terms of precipitation, both landscape simplification and increases in non‐natives appeared to favour species associated with drier climatic conditions, to some extent counteracting the climate‐driven shift towards wetter communities. Anthropogenic drivers can act both synergistically and antagonistically to determine trajectories of change in biological communities over time. Therefore, it is important to consider multiple drivers of global change when trying to understand, manage and predict biodiversity in the future

Integrating isotopes and documentary evidence : dietary patterns in a late medieval and early modern mining community, Sweden

We would like to thank the Archaeological Research Laboratory, Stockholm University, Sweden and the Tandem Laboratory (Ångström Laboratory), Uppsala University, Sweden, for undertaking the analyses of stable nitrogen and carbon isotopes in both human and animal collagen samples. Also, thanks to Elin Ahlin Sundman for providing the δ13C and δ15N values for animal references from Västerås. This research (Bäckström’s PhD employment at Lund University, Sweden) was supported by the Berit Wallenberg Foundation (BWS 2010.0176) and Jakob and Johan Söderberg’s foundation. The ‘Sala project’ (excavations and analyses) has been funded by Riksens Clenodium, Jernkontoret, Birgit and Gad Rausing’s Foundation, SAU’s Research Foundation, the Royal Physiographic Society of Lund, Berit Wallenbergs Foundation, Åke Wibergs Foundation, Lars Hiertas Memory, Helge Ax:son Johnson’s Foundation and The Royal Swedish Academy of Sciences.Peer reviewedPublisher PD

Regional changes in wind energy potential over Europe using regional climate model ensemble projections

The impact of climate change on wind power generation potentials over Europe is investigated by considering ensemble projections from two regional climate models (RCMs) driven by a global climate model (GCM). Wind energy density and its interannual variability are estimated based on hourly near-surface wind speeds. Additionally, the possible impact of climatic changes on the energy output of a sample 2.5-MW turbine is discussed. GCM-driven RCM simulations capture the behavior and variability of current wind energy indices, even though some differences exist when compared with reanalysis-driven RCM simulations. Toward the end of the twenty-first century, projections show significant changes of energy density on annual average across Europe that are substantially stronger in seasonal terms. The emergence time of these changes varies from region to region and season to season, but some long-term trends are already statistically significant in the middle of the twenty-first century. Over northern and central Europe, the wind energy potential is projected to increase, particularly in winter and autumn. In contrast, energy potential over southern Europe may experience a decrease in all seasons except for the Aegean Sea. Changes for wind energy output follow the same patterns but are of smaller magnitude. The GCM/RCM model chains project a significant intensification of both interannual and intra-annual variability of energy density over parts of western and central Europe, thus imposing new challenges to a reliable pan-European energy supply in future decades

Forest fire danger projections in the Mediterranean using ENSEMBLES regional climate change scenarios

We present future fire danger scenarios for the countries bordering the Mediterranean areas of Europe and north Africa building on a multi-model ensemble of state-of-the-art regional climate projections from the EU-funded project ENSEMBLES. Fire danger is estimated using the Canadian Forest Fire Weather Index (FWI) System and a related set of indices. To overcome some of the limitations of ENSEMBLES data for their application on the FWI System?recently highlighted in a previous study by Herrera et al. (Clim Chang 118:827?840, 2013)?we used an optimal proxy variable combination. A robust assessment of future fire danger projections is undertaken by disentangling the climate change signal from the uncertainty derived from the multi-model ensemble, unveiling a positive signal of fire danger potential over large areas of the Mediterranean. The increase in the fire danger signal is accentuated towards the latest part of the transient period, thus pointing to an elevated fire potential in the region with time. The fire-climate links under present and future conditions are further discussed building upon observed climate data and burned area records along a representative climatic gradient within the study region.The research leading to these results has received funding from the EXTREMBLES project (CGL2010-21869) funded by the Spanish R&D programme and from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement 243888 (FUME Project). The authors acknowledge the RCM data sets from the EU-FP6 project ENSEMBLES (http://ensemblesrt3.dmi.dk) and would also like to thank Erik van Meijgaard from the Royal Netherlands Meteorological Institute (KNMI) for making available ENSEMBLES RACMO2 climate model output verifying at 12:00 UTC. We are also grateful to Jesus Fernandez and three anonymous reviewers for their insightful comments that greatly contributed to the improvement of the original manuscript

Non-heat related impacts of climate change on working populations

Environmental and social changes associated with climate change are likely to have impacts on the well-being, health, and productivity of many working populations across the globe. The ramifications of climate change for working populations are not restricted to increases in heat exposure. Other significant risks to worker health (including physical hazards from extreme weather events, infectious diseases, under-nutrition, and mental stresses) may be amplified by future climate change, and these may have substantial impacts at all scales of economic activity. Some of these risks are difficult to quantify, but pose a substantial threat to the viability and sustainability of some working populations. These impacts may occur in both developed and developing countries, although the latter category is likely to bear the heaviest burden

Highly temporally resolved response to seasonal surface melt of the Zachariae and 79N outlet glaciers in northeast Greenland

The seasonal response to surface melting of the Northeast Greenland Ice Stream outlets, Zachariae and 79N, is investigated using new highly temporally resolved surface velocity maps for 2016 combined with numerical modeling. The seasonal speedup at 79N of 0.15 km/yr is suggested to be driven by a decrease in effective basal pressure induced by surface melting, whereas for Zachariae its 0.11 km/yr seasonal speedup correlates equally well with the breakup of its large ice mélange. We investigate the influence 76 km long floating tongue at 79N, finding it provides little resistance and that most of it could be lost without impacting the dynamics of the area. Furthermore, we show that reducing the slipperiness along the tongue-wall interfaces produces a velocity change spatially inconsistent with the observed seasonal speedup. Finally, we find that subglacial sticky spots such as bedrock bumps play a negligible role in the large-scale response to a seasonally enhanced basal slipperiness of the region

Relation between dietary cadmium intake and biomarkers of cadmium exposure in premenopausal women accounting for body iron stores

<p>Abstract</p> <p>Background</p> <p>Cadmium is a widespread environmental pollutant with adverse effects on kidneys and bone, but with insufficiently elucidated public health consequences such as risk of end-stage renal diseases, fractures and cancer. Urinary cadmium is considered a valid biomarker of lifetime kidney accumulation from overall cadmium exposure and thus used in the assessment of cadmium-induced health effects. We aimed to assess the relationship between dietary cadmium intake assessed by analyses of duplicate food portions and cadmium concentrations in urine and blood, taking the toxicokinetics of cadmium into consideration.</p> <p>Methods</p> <p>In a sample of 57 non-smoking Swedish women aged 20-50 years, we assessed Pearson's correlation coefficients between: 1) Dietary intake of cadmium assessed by analyses of cadmium in duplicate food portions collected during four consecutive days and cadmium concentrations in urine, 2) Partial correlations between the duplicate food portions and urinary and blood cadmium concentrations, respectively, and 3) Model-predicted urinary cadmium concentration predicted from the dietary intake using a one-compartment toxicokinetic model (with individual data on age, weight and gastrointestinal cadmium absorption) and urinary cadmium concentration.</p> <p>Results</p> <p>The mean concentration of cadmium in urine was 0.18 (+/- s.d.0.12) μg/g creatinine and the model-predicted urinary cadmium concentration was 0.19 (+/- s.d.0.15) μg/g creatinine. The partial Pearson correlations between analyzed dietary cadmium intake and urinary cadmium or blood concentrations were r = 0.43 and 0.42, respectively. The correlation between diet and urinary cadmium increased to r = 0.54 when using a one-compartment model with individual gastrointestinal cadmium absorption coefficients based on the women's iron status.</p> <p>Conclusions</p> <p>Our results indicate that measured dietary cadmium intake can reasonably well predict biomarkers of both long-term kidney accumulation (urine) and short-term exposure (blood). The predictions are improved when taking data on the iron status into account.</p