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

Simulating river flow to the Baltic Sea from climate simulations over the past millennium

The aim of this study was to reconstruct river flow to the Baltic Sea using data from different periods during the past thousand years. A hydrological model coupled to simulations from climate models was used to estimate river flow. A "millennium" simulation of past climate from the ECHO-G coupled atmosphere-ocean global climate model provided climatological inputs. Results from this global model were downscaled with the RCA3 regional climate model over northern Europe. Temperature and precipitation from the downscaled simulation results were then used in the HBV hydrological model to simulate river flows to the Baltic Sea for the periods 1000-1199 and 1551-1929. These were compared with observations for the period 1921-2002. A general conclusion from this work is that although climate has varied during the past millennium, variability in annual river flow to the Baltic Sea does not appear more pronounced in recent years than during the previous millennium, or vice versa

Cadmium-Induced Effects on Bone in a Population-Based Study of Women

High cadmium exposure is known to cause bone damage, but the association between low-level cadmium exposure and osteoporosis remains to be clarified. Using a population-based women’s health survey in southern Sweden [Women’s Health in the Lund Area (WHILA)] with no known historical cadmium contamination, we investigated cadmium-related effects on bone in 820 women (53–64 years of age). We measured cadmium in blood and urine and lead in blood, an array of markers of bone metabolism, and forearm bone mineral density (BMD). Associations were evaluated in multiple linear regression analysis including information on the possible confounders or effect modifiers: weight, menopausal status, use of hormone replacement therapy, age at menarche, alcohol consumption, smoking history, and physical activity. Median urinary cadmium was 0.52 μg/L adjusted to density (0.67 μg/g creatinine). After multivariate adjustment, BMD, parathyroid hormone, and urinary deoxypyridinoline (U-DPD) were adversely associated with concentrations of urinary cadmium (p < 0.05) in all subjects. These associations persisted in the group of never-smokers, which had the lowest cadmium exposure (mainly dietary). For U-DPD, there was a significant interaction between cadmium and menopause (p = 0.022). Our results suggest negative effects of low-level cadmium exposure on bone, possibly exerted via increased bone resorption, which seemed to be intensified after menopause. Based on the prevalence of osteoporosis and the low level of exposure, the observed effects, although slight, should be considered as early signals of potentially more adverse health effects

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

Doubtful outcome of the validation of the Rome II questionnaire: validation of a symptom based diagnostic tool

<p>Abstract</p> <p>Background</p> <p>Questionnaires are used in research and clinical practice. For gastrointestinal complaints the Rome II questionnaire is internationally known but not validated. The aim of this study was to validate a printed and a computerized version of Rome II, translated into Swedish. Results from various analyses are reported.</p> <p>Methods</p> <p>Volunteers from a population based colonoscopy study were included (n = 1011), together with patients seeking general practice (n = 45) and patients visiting a gastrointestinal specialists' clinic (n = 67). The questionnaire consists of 38 questions concerning gastrointestinal symptoms and complaints. Diagnoses are made after a special code. Our validation included analyses of the translation, feasibility, predictability, reproducibility and reliability. Kappa values and overall agreement were measured. The factor structures were confirmed using a principal component analysis and Cronbach's alpha was used to test the internal consistency.</p> <p>Results and Discussion</p> <p>Translation and back translation showed good agreement. The questionnaire was easy to understand and use. The reproducibility test showed kappa values of 0.60 for GERS, 0.52 for FD, and 0.47 for IBS. Kappa values and overall agreement for the predictability when the diagnoses by the questionnaire were compared to the diagnoses by the clinician were 0.26 and 90% for GERS, 0.18 and 85% for FD, and 0.49 and 86% for IBS. Corresponding figures for the agreement between the printed and the digital version were 0.50 and 92% for GERS, 0.64 and 95% for FD, and 0.76 and 95% for IBS. Cronbach's alpha coefficient for GERS was 0.75 with a span per item of 0.71 to 0.76. For FD the figures were 0.68 and 0.54 to 0.70 and for IBS 0.61 and 0.56 to 0.66. The Rome II questionnaire has never been thoroughly validated before even if diagnoses made by the Rome criteria have been compared to diagnoses made in clinical practice.</p> <p>Conclusion</p> <p>The accuracy of the Swedish version of the Rome II is of doubtful value for clinical practice and research. The results for reproducibility and reliability were acceptable but the outcome of the predictability test was poor with IBS as an exception. The agreement between the digital and the paper questionnaire was good.</p

A cluster randomized trial to assess the impact of clinical pathways for patients with stroke: rationale and design of the Clinical Pathways for Effective and Appropriate Care Study [NCT00673491]

<p>Abstract</p> <p>Background</p> <p>Patients with stroke should have access to a continuum of care from organized stroke units in the acute phase, to appropriate rehabilitation and secondary prevention measures. Moreover to improve the outcomes for acute stroke patients from an organizational perspective, the use of multidisciplinary teams and the delivery of continuous stroke education both to the professionals and to the public, and the implementation of evidence-based stroke care are recommended. Clinical pathways are complex interventions that can be used for this purpose. However in stroke care the use of clinical pathways remains questionable because little prospective controlled data has demonstrated their effectiveness. The purpose of this study is to determine whether clinical pathways could improve the quality of the care provided to the patients affected by stroke in hospital and through the continuum of the care.</p> <p>Methods</p> <p>Two-arm, cluster-randomized trial with hospitals and rehabilitation long-term care facilities as randomization units. 14 units will be randomized either to arm 1 (clinical pathway) or to arm 2 (no intervention, usual care). The sample will include 238 in each group, this gives a power of 80%, at 5% significance level. The primary outcome measure is 30-days mortality. The impact of the clinical pathways along the continuum of care will also be analyzed by comparing the length of hospital stay, the hospital re-admissions rates, the institutionalization rates after hospital discharge, the patients' dependency levels, and complication rates. The quality of the care provided to the patients will be assessed by monitoring the use of diagnostic and therapeutic procedures during hospital stay and rehabilitation, and by the use of key quality indicators at discharge. The implementation of organized care will be also evaluated.</p> <p>Conclusion</p> <p>The management of patients affected by stroke involves the expertise of several professionals, which can result in poor coordination or inefficiencies in patient treatment, and clinical pathways can significantly improve the outcomes of these patients. It is proposed that this study will test a new hypothesis and provide evidence of how clinical pathways can work.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov ID [NCT00673491]</p

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

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

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