| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Fazey, Ioan, et al.
(author)
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Transforming knowledge systems for life on Earth : Visions of future systems and how to get there
- 2020
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In: Energy Research & Social Science. - : Elsevier. - 2214-6296 .- 2214-6326. ; 70
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Journal article (peer-reviewed)abstract
- Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
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| 3. |
- Feiler, Ute, et al.
(author)
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Inter-laboratory trial of a standardized sediment contact test with the aquatic plant Myriophyllum aquaticum (ISO 16191)
- 2014
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In: Environmental Toxicology and Chemistry. - : Wiley. - 0730-7268 .- 1552-8618. ; 33:3, s. 662-670
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Journal article (peer-reviewed)abstract
- A whole-sediment toxicity test with Myriophyllum aquaticum has been developed by the German Federal Institute of Hydrology and standardized within the International Organization for Standardization (ISO; ISO 16191). An international ring-test was performed to evaluate the precision of the test method. Four sediments (artificial, natural) were tested. Test duration was 10 d, and test endpoint was inhibition of growth rate (r) based on fresh weight data. Eighteen of 21 laboratories met the validity criterion of r >= 0.09 d(-1) in the control. Results from 4 tests that did not conform to test-performance criteria were excluded from statistical evaluation. The inter-laboratory variability of growth rates (20.6%-25.0%) and inhibition (26.6%-39.9%) was comparable with the variability of other standardized bioassays. The mean test-internal variability of the controls was low (7% [control], 9.7% [solvent control]), yielding a high discriminatory power of the given test design (median minimum detectable differences [MDD] 13% to 15%). To ensure these MDDs, an additional validity criterion of CV <= 15% of the growth rate in the controls was recommended. As a positive control, 90 mg 3,5-dichlorophenol/kg sediment dry mass was tested. The range of the expected growth inhibition was proposed to be 35 +/- 15%. The ring test results demonstrated the reliability of the ISO 16191 toxicity test and its suitability as a tool to assess the toxicity of sediment and dredged material. Environ Toxicol Chem 2014;33:662-670. (c) 2013 SETAC
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| 4. |
- Koeck, Kathleen, et al.
(author)
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Risk Factors for Development of Cholestatic Drug-Induced Liver Injury : Inhibition of Hepatic Basolateral Bile Acid Transporters Multidrug Resistance-Associated Proteins 3 and 4
- 2014
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In: Drug Metabolism And Disposition. - : American Society for Pharmacology & Experimental Therapeutics (ASPET). - 0090-9556 .- 1521-009X. ; 42:4, s. 665-674
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Journal article (peer-reviewed)abstract
- Impaired hepatic bile acid export may contribute to development of cholestatic drug-induced liver injury (DILI). The multidrug resistance-associated proteins (MRP) 3 and 4 are postulated to be compensatory hepatic basolateral bile acid efflux transporters when biliary excretion by the bile salt export pump (BSEP) is impaired. BSEP inhibition is a risk factor for cholestatic DILI. This study aimed to characterize the relationship between MRP3, MRP4, and BSEP inhibition and cholestatic potential of drugs. The inhibitory effect of 88 drugs (100 mu M) on MRP3- and MRP4-mediated substrate transport was measured in membrane vesicles. Drugs selected for investigation included 50 BSEP non-inhibitors (24 non-cholestatic; 26 cholestatic) and 38 BSEP inhibitors (16 non-cholestatic; 22 cholestatic). MRP4 inhibition was associated with an increased risk of cholestatic potential among BSEP non-inhibitors. In this group, for each 1% increase in MRP4 inhibition, the odds of the drug being cholestatic increased by 3.1%. Using an inhibition cutoff of 21%, which predicted a 50% chance of cholestasis, 62% of cholestatic drugs inhibited MRP4 (P < 0.05); in contrast, only 17% of non-cholestatic drugs were MRP4 inhibitors. Among BSEP inhibitors, MRP4 inhibition did not provide additional predictive value of cholestatic potential; almost all BSEP inhibitors were also MRP4 inhibitors. Inclusion of pharmacokinetic predictor variables (e. g., maximal unbound concentration in plasma) in addition to percent MRP4 inhibition in logistic regression models did not improve cholestasis prediction. Association of cholestasis with percent MRP3 inhibition was not statistically significant, regardless of BSEP-inhibition status. Inhibition of MRP4, in addition to BSEP, may be a risk factor for the development of cholestatic DILI.
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| 5. |
- Nikpay, Majid, et al.
(author)
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A comprehensive 1000 Genomes-based genome-wide association meta-analysis of coronary artery disease
- 2015
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:10, s. 1121-1121
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Journal article (peer-reviewed)abstract
- Existing knowledge of genetic variants affecting risk of coronary artery disease (CAD) is largely based on genome-wide association study (GWAS) analysis of common SNPs. Leveraging phased haplotypes from the 1000 Genomes Project, we report a GWAS meta-analysis of similar to 185,000 CAD cases and controls, interrogating 6.7 million common (minor allele frequency (MAF) > 0.05) and 2.7 million low-frequency (0.005 < MAF < 0.05) variants. In addition to confirming most known CAD-associated loci, we identified ten new loci (eight additive and two recessive) that contain candidate causal genes newly implicating biological processes in vessel walls. We observed intralocus allelic heterogeneity but little evidence of low-frequency variants with larger effects and no evidence of synthetic association. Our analysis provides a comprehensive survey of the fine genetic architecture of CAD, showing that genetic susceptibility to this common disease is largely determined by common SNPs of small effect size.
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| 6. |
- Rothfels, Carl J., et al.
(author)
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The evolutionary history of ferns inferred from 25 low-copy nuclear genes
- 2015
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In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 102:7, s. 1089-1107
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Journal article (peer-reviewed)abstract
- PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35 877 bp), along with rigorous alignment, orthology inference and model selection. KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to similar to 200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data. CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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| 7. |
- Sarmiento, Luis, et al.
(author)
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Comparing net zero pathways across the Atlantic A model inter-comparison exercise between the Energy Modeling Forum 37 and the European Climate and Energy Modeling Forum
- 2024
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In: Energy and Climate Change. - : Elsevier BV. - 2666-2787. ; 5
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Journal article (peer-reviewed)abstract
- Europe and North America account for 32 % of current carbon emissions. Due to distinct legacy systems, energy infrastructure, socioeconomic development, and energy resource endowment, both regions have different policy and technological pathways to reach net zero by the mid-century. Against this background, our paper examines the results from the net zero emission scenarios for Europe and North America that emerged from the collaboration of the European and American Energy Modeling Forums. In our analysis, we perform an inter-comparison of various integrated assessments and bottom-up energy system models. A clear qualitative consensus emerges on five main points. First, Europe and the United States reach net zero targets with electrification, demand-side reductions, and carbon capture and sequestration technologies. Second, the use of carbon capture and sequestration is more predominant in the United States due to a steeper decarbonization schedule. Third, the buildings sector is the easiest to electrify in both regions. Fourth, the industrial sector is the hardest to electrify in the United States and transportation in Europe. Fifth, in both regions, the transition in the energy mix is driven by the substitution of coal and natural gas with solar and wind, but to a different extent.
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| 8. |
- Stewart, Kathleen, et al.
(author)
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Spatiotemporal patterns of drug use disorder in Sweden assessed using population-based registries
- 2023
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In: BMC Public Health. - : Springer Science and Business Media LLC. - 1471-2458. ; 23:1
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Journal article (peer-reviewed)abstract
- Background: Drug Use Disorder (DUD) is a major contributor to world-wide morbidity and mortality. The extensive national registers in Sweden provide the basis for a study of spatial and temporal patterns of DUD onset and recurrence in Sweden from 2001–2015. Methods: To identify patterns of DUD over space, time and gender for Swedish individuals aged 15–35, space–time clustering using SaTScan was applied. We used yearly information on residential locations in Demographic Statistical Areas (DeSO) for all of Sweden. The clustering analysis used a Poisson probability model and a null hypothesis that the expected number of cases in each DeSO was proportional to the population size of DeSOs. As SaTScan results can be unstable, steps were taken to determine stable clusters and to refine and optimize cluster size. Results for each gender-register combination were compared to the results of spatial clustering using Gi* statistics. The space–time scanning model was also run with an adjustment for neighborhood socioeconomic status to determine DUD prevalence as it relates to education, income, unemployment and receipt of social welfare. Results: DUD prevalence increased over time. Males yielded more significant clusters than females for both criminal and medical registers. Female DUD prevalence rates increased over time, especially after 2012. Higher correlations in DUD rates existed across the two registers than across gender. Male clusters were present from 2004 onwards while female–criminal clusters appeared after 2007, and female–medical clusters not until 2010. By 2013, clusters existed for all gender–register combinations. Male–criminal clusters were concentrated in Stockholm, Göteborg and Malmö as were male and female-medical clusters. Neighborhood SES was more highly related to the distribution of criminal than medical DUD clusters. A persistent gap in core clusters was identified in Stockholm in an area with notably high SES. Conclusions: Persistent hotspots of DUD in Sweden were confirmed as well as new and emerging hotspots, especially in Stockholm, Göteborg and Malmö. Higher correlations existed in DUD rates across registers than across gender. The findings are useful for monitoring the current drug problem and for identifying drivers underlying patterns of spread and important causal pathways to DUD.
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| 9. |
- Sumaila, U. Rashid, et al.
(author)
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WTO must ban harmful fisheries subsidies
- 2021
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6567, s. 544-544
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Journal article (other academic/artistic)
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| 10. |
- Taylor, Carolyn, et al.
(author)
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Estimating the Risks of Breast Cancer Radiotherapy : Evidence From Modern Radiation Doses to the Lungs and Heart and From Previous Randomized Trials
- 2017
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In: Journal of clinical oncology : official journal of the American Society of Clinical Oncology. - 0732-183X .- 1527-7755. ; 35:15, s. 1641-1649
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Journal article (peer-reviewed)abstract
- Purpose Radiotherapy reduces the absolute risk of breast cancer mortality by a few percentage points in suitable women but can cause a second cancer or heart disease decades later. We estimated the absolute long-term risks of modern breast cancer radiotherapy. Methods First, a systematic literature review was performed of lung and heart doses in breast cancer regimens published during 2010 to 2015. Second, individual patient data meta-analyses of 40,781 women randomly assigned to breast cancer radiotherapy versus no radiotherapy in 75 trials yielded rate ratios (RRs) for second primary cancers and cause-specific mortality and excess RRs (ERRs) per Gy for incident lung cancer and cardiac mortality. Smoking status was unavailable. Third, the lung or heart ERRs per Gy in the trials and the 2010 to 2015 doses were combined and applied to current smoker and nonsmoker lung cancer and cardiac mortality rates in population-based data. Results Average doses from 647 regimens published during 2010 to 2015 were 5.7 Gy for whole lung and 4.4 Gy for whole heart. The median year of irradiation was 2010 (interquartile range [IQR], 2008 to 2011). Meta-analyses yielded lung cancer incidence ≥ 10 years after radiotherapy RR of 2.10 (95% CI, 1.48 to 2.98; P < .001) on the basis of 134 cancers, indicating 0.11 (95% CI, 0.05 to 0.20) ERR per Gy whole-lung dose. For cardiac mortality, RR was 1.30 (95% CI, 1.15 to 1.46; P < .001) on the basis of 1,253 cardiac deaths. Detailed analyses indicated 0.04 (95% CI, 0.02 to 0.06) ERR per Gy whole-heart dose. Estimated absolute risks from modern radiotherapy were as follows: lung cancer, approximately 4% for long-term continuing smokers and 0.3% for nonsmokers; and cardiac mortality, approximately 1% for smokers and 0.3% for nonsmokers. Conclusion For long-term smokers, the absolute risks of modern radiotherapy may outweigh the benefits, yet for most nonsmokers (and ex-smokers), the benefits of radiotherapy far outweigh the risks. Hence, smoking can determine the net effect of radiotherapy on mortality, but smoking cessation substantially reduces radiotherapy risk.
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