| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)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. |
- Axfors, Cathrine, et al.
(författare)
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Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19 from an international collaborative meta-analysis of randomized trials
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Substantial COVID-19 research investment has been allocated to randomized clinical trials (RCTs) on hydroxychloroquine/chloroquine, which currently face recruitment challenges or early discontinuation. We aim to estimate the effects of hydroxychloroquine and chloroquine on survival in COVID-19 from all currently available RCT evidence, published and unpublished. We present a rapid meta-analysis of ongoing, completed, or discontinued RCTs on hydroxychloroquine or chloroquine treatment for any COVID-19 patients (protocol: https://osf.io/QESV4/). We systematically identified unpublished RCTs (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform, Cochrane COVID-registry up to June 11, 2020), and published RCTs (PubMed, medRxiv and bioRxiv up to October 16, 2020). All-cause mortality has been extracted (publications/preprints) or requested from investigators and combined in random-effects meta-analyses, calculating odds ratios (ORs) with 95% confidence intervals (CIs), separately for hydroxychloroquine and chloroquine. Prespecified subgroup analyses include patient setting, diagnostic confirmation, control type, and publication status. Sixty-three trials were potentially eligible. We included 14 unpublished trials (1308 patients) and 14 publications/preprints (9011 patients). Results for hydroxychloroquine are dominated by RECOVERY and WHO SOLIDARITY, two highly pragmatic trials, which employed relatively high doses and included 4716 and 1853 patients, respectively (67% of the total sample size). The combined OR on all-cause mortality for hydroxychloroquine is 1.11 (95% CI: 1.02, 1.20; I-2=0%; 26 trials; 10,012 patients) and for chloroquine 1.77 (95%CI: 0.15, 21.13, I-2=0%; 4 trials; 307 patients). We identified no subgroup effects. We found that treatment with hydroxychloroquine is associated with increased mortality in COVID-19 patients, and there is no benefit of chloroquine. Findings have unclear generalizability to outpatients, children, pregnant women, and people with comorbidities. Hydroxychloroquine and chloroquine have been investigated as a potential treatment for Covid-19 in several clinical trials. Here the authors report a meta-analysis of published and unpublished trials, and show that treatment with hydroxychloroquine for patients with Covid-19 was associated with increased mortality, and there was no benefit from chloroquine.
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| 3. |
- Chen, Kai, et al.
(författare)
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Ambient carbon monoxide and daily mortality: a global time-series study in 337 cities
- 2021
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Ingår i: The Lancet Planetary Health. - 2542-5196. ; 5:4, s. e191-e199
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Tidskriftsartikel (refereegranskat)abstract
- Background: Epidemiological evidence on short-term association between ambient carbon monoxide (CO) and mortality is inconclusive and limited to single cities, regions, or countries. Generalisation of results from previous studies is hindered by potential publication bias and different modelling approaches. We therefore assessed the association between short-term exposure to ambient CO and daily mortality in a multicity, multicountry setting. Methods: We collected daily data on air pollution, meteorology, and total mortality from 337 cities in 18 countries or regions, covering various periods from 1979 to 2016. All included cities had at least 2 years of both CO and mortality data. We estimated city-specific associations using confounder-adjusted generalised additive models with a quasi-Poisson distribution, and then pooled the estimates, accounting for their statistical uncertainty, using a random-effects multilevel meta-analytical model. We also assessed the overall shape of the exposure–response curve and evaluated the possibility of a threshold below which health is not affected. Findings: Overall, a 1 mg/m3 increase in the average CO concentration of the previous day was associated with a 0·91% (95% CI 0·32–1·50) increase in daily total mortality. The pooled exposure–response curve showed a continuously elevated mortality risk with increasing CO concentrations, suggesting no threshold. The exposure–response curve was steeper at daily CO levels lower than 1 mg/m3, indicating greater risk of mortality per increment in CO exposure, and persisted at daily concentrations as low as 0·6 mg/m3 or less. The association remained similar after adjustment for ozone but was attenuated after adjustment for particulate matter or sulphur dioxide, or even reduced to null after adjustment for nitrogen dioxide. Interpretation: This international study is by far the largest epidemiological investigation on short-term CO-related mortality. We found significant associations between ambient CO and daily mortality, even at levels well below current air quality guidelines. Further studies are warranted to disentangle its independent effect from other traffic-related pollutants. Funding: EU Horizon 2020, UK Medical Research Council, and Natural Environment Research Council.
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| 4. |
- Hartley, Philippa, et al.
(författare)
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SKA Science Data Challenge 2: analysis and results
- 2023
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Ingår i: Monthly Notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 523:2, s. 1967-1993
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Tidskriftsartikel (refereegranskat)abstract
- The Square Kilometre Array Observatory (SKAO) will explore the radio sky to new depths in order to conduct transformational science. SKAO data products made available to astronomers will be correspondingly large and complex, requiring the application of advanced analysis techniques to extract key science findings. To this end, SKAO is conducting a series of Science Data Challenges, each designed to familiarize the scientific community with SKAO data and to drive the development of new analysis techniques. We present the results from Science Data Challenge 2 (SDC2), which invited participants to find and characterize 233 245 neutral hydrogen (H i) sources in a simulated data product representing a 2000 h SKA-Mid spectral line observation from redshifts 0.25-0.5. Through the generous support of eight international supercomputing facilities, participants were able to undertake the Challenge using dedicated computational resources. Alongside the main challenge, 'reproducibility awards' were made in recognition of those pipelines which demonstrated Open Science best practice. The Challenge saw over 100 participants develop a range of new and existing techniques, with results that highlight the strengths of multidisciplinary and collaborative effort. The winning strategy - which combined predictions from two independent machine learning techniques to yield a 20 per cent improvement in overall performance - underscores one of the main Challenge outcomes: that of method complementarity. It is likely that the combination of methods in a so-called ensemble approach will be key to exploiting very large astronomical data sets.
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| 5. |
- Masselot, Pierre, et al.
(författare)
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Differential mortality risks associated with PM2.5 components : a multi-country, multi-city study
- 2022
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Ingår i: Epidemiology. - : Wolters Kluwer. - 1044-3983 .- 1531-5487. ; 33:2, s. 167-175
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The association between fine particulate matter (PM2.5) and mortality widely differs between as well as within countries. Differences in PM2.5 composition can play a role in modifying the effect estimates, but there is little evidence about which components have higher impacts on mortality.METHODS: We applied a two-stage analysis on data collected from 210 locations in 16 countries. In the first stage, we estimated location-specific relative risks (RR) for mortality associated with daily total PM2.5 through time series regression analysis. We then pooled these estimates in a meta-regression model that included city-specific logratio-transformed proportions of seven PM2.5 components as well as meta-predictors derived from city-specific socio-economic and environmental indicators.RESULTS: We found associations between RR and several PM2.5 components. Increasing the ammonium (NH4+) proportion from 1% to 22%, while keeping a relative average proportion of other components, increased the RR from 1.0063 (95%CI: 1.0030-1.0097) to 1.0102 (95%CI:1.0070-1.0135). Conversely, an increase in nitrate (NO3-) from 1% to 71% resulted in a reduced RR, from 1.0100 (95%CI: 1.0067-1.0133) to 1.0037 (95%CI: 0.9998- 1.0077). Differences in composition explained a substantial part of the heterogeneity in PM2.5 risk.CONCLUSIONS: These findings contribute to the identification of more hazardous emission sources. Further work is needed to understand the health impacts of PM2.5 components and sources given the overlapping sources and correlations among many components.
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| 6. |
- Botteri, Edoardo, et al.
(författare)
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Lifestyle changes in middle age and risk of cancer : evidence from the European Prospective Investigation into Cancer and Nutrition
- 2024
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Ingår i: European Journal of Epidemiology. - 0393-2990. ; 39:2, s. 147-159
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we aimed to provide novel evidence on the impact of changing lifestyle habits on cancer risk. In the EPIC cohort, 295,865 middle-aged participants returned a lifestyle questionnaire at baseline and during follow-up. At both timepoints, we calculated a healthy lifestyle index (HLI) score based on cigarette smoking, alcohol consumption, body mass index and physical activity. HLI ranged from 0 (most unfavourable) to 16 (most favourable). We estimated the association between HLI change and risk of lifestyle-related cancers—including cancer of the breast, lung, colorectum, stomach, liver, cervix, oesophagus, bladder, and others—using Cox regression models. We reported hazard ratios (HR) with 95% confidence intervals (CI). Median time between the two questionnaires was 5.7 years, median age at follow-up questionnaire was 59 years. After the follow-up questionnaire, we observed 14,933 lifestyle-related cancers over a median follow-up of 7.8 years. Each unit increase in the HLI score was associated with 4% lower risk of lifestyle-related cancers (HR 0.96; 95%CI 0.95–0.97). Among participants in the top HLI third at baseline (HLI > 11), those in the bottom third at follow-up (HLI ≤ 9) had 21% higher risk of lifestyle-related cancers (HR 1.21; 95%CI 1.07–1.37) than those remaining in the top third. Among participants in the bottom HLI third at baseline, those in the top third at follow-up had 25% lower risk of lifestyle-related cancers (HR 0.75; 95%CI 0.65–0.86) than those remaining in the bottom third. These results indicate that lifestyle changes in middle age may have a significant impact on cancer risk.
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| 7. |
- Chen, Gongbo, et al.
(författare)
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Mortality risk attributable to wildfire-related PM2·5 pollution : a global time series study in 749 locations
- 2021
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Ingår i: The Lancet Planetary Health. - : Elsevier. - 2542-5196. ; 5:9, s. e579-e587
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Many regions of the world are now facing more frequent and unprecedentedly large wildfires. However, the association between wildfire-related PM2·5 and mortality has not been well characterised. We aimed to comprehensively assess the association between short-term exposure to wildfire-related PM2·5 and mortality across various regions of the world.METHODS: For this time series study, data on daily counts of deaths for all causes, cardiovascular causes, and respiratory causes were collected from 749 cities in 43 countries and regions during 2000-16. Daily concentrations of wildfire-related PM2·5 were estimated using the three-dimensional chemical transport model GEOS-Chem at a 0·25° × 0·25° resolution. The association between wildfire-related PM2·5 exposure and mortality was examined using a quasi-Poisson time series model in each city considering both the current-day and lag effects, and the effect estimates were then pooled using a random-effects meta-analysis. Based on these pooled effect estimates, the population attributable fraction and relative risk (RR) of annual mortality due to acute wildfire-related PM2·5 exposure was calculated.FINDINGS: 65·6 million all-cause deaths, 15·1 million cardiovascular deaths, and 6·8 million respiratory deaths were included in our analyses. The pooled RRs of mortality associated with each 10 μg/m3 increase in the 3-day moving average (lag 0-2 days) of wildfire-related PM2·5 exposure were 1·019 (95% CI 1·016-1·022) for all-cause mortality, 1·017 (1·012-1·021) for cardiovascular mortality, and 1·019 (1·013-1·025) for respiratory mortality. Overall, 0·62% (95% CI 0·48-0·75) of all-cause deaths, 0·55% (0·43-0·67) of cardiovascular deaths, and 0·64% (0·50-0·78) of respiratory deaths were annually attributable to the acute impacts of wildfire-related PM2·5 exposure during the study period.INTERPRETATION: Short-term exposure to wildfire-related PM2·5 was associated with increased risk of mortality. Urgent action is needed to reduce health risks from the increasing wildfires.
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| 8. |
- Chen, Kai, et al.
(författare)
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Impact of population aging on future temperature-related mortality at different global warming levels
- 2024
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Ingår i: Nature Communications. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Older adults are generally amongst the most vulnerable to heat and cold. While temperature-related health impacts are projected to increase with global warming, the influence of population aging on these trends remains unclear. Here we show that at 1.5 °C, 2 °C, and 3 °C of global warming, heat-related mortality in 800 locations across 50 countries/areas will increase by 0.5%, 1.0%, and 2.5%, respectively; among which 1 in 5 to 1 in 4 heat-related deaths can be attributed to population aging. Despite a projected decrease in cold-related mortality due to progressive warming alone, population aging will mostly counteract this trend, leading to a net increase in cold-related mortality by 0.1%–0.4% at 1.5–3 °C global warming. Our findings indicate that population aging constitutes a crucial driver for future heat- and cold-related deaths, with increasing mortality burden for both heat and cold due to the aging population.
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| 9. |
- Chen, Yuanying
(författare)
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Land-Sea Interactions in the Coastal-Marine System of the Baltic Sea under Hydro-Climatic Variability
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis investigates a few important component processes for understanding and quantifying eutrophication in the Baltic Sea, that include characterization of nutrient loadings from land, water flow in the sea under changing climate conditions and transport of solutes originating from different locations along the coast. Furthermore, this study aims to improve our understanding on how processes from land (the nutrient loading conditions) and the sea (transport dynamics and water quality) couple to determine the fate of nutrients in the sea and the water quality in a selected localized coastal area, the Himmerfjärden Bay.Comprehensive data are compiled as a basis for numerical simulations. An open source tool for oceanographic studies FVCOM is used to simulate flow and transport processes in the Baltic Sea. Hydrodynamic simulations are verified in terms of temperature, salinity and water level for the year 2005. Results show that most of the investigated Swedish watersheds along the coastline are dominated by subsurface legacy sources, the loads of which are positively and linearly correlated with river discharges. Moreover, subsurface legacy sources are less likely to decrease over time compared with the current surface sources. The Baltic Sea has a stable flow structure considering flux directions between basins, while the flux magnitudes between basins are mainly determined by different wind conditions. The spreading patterns in the sea with solute released from different coastal areas are similar when the released amounts are comparable, even though different cases have different source input and water flow conditions. The overall spreading patterns in the sea are generally dominated by the total mass of released solute. Local transport dynamics and patterns around the coast differ greatly for different cases and are determined by the local flow conditions. Different water quality indicators are influenced by different land-based or sea-based measures for water quality improvement. The dry-cold hydro-climatic condition is the most favorable for improving the water quality and elevating the ecological status in the Himmerfjärden Bay.Based on this investigation, varying hydro-climatic factors impose important influence on the different component processes of nutrient loading from land to the sea. For example, the change of river discharges from land in the future would influence the total load into the sea from subsurface legacy sources, and finally influence the general spreading patterns of nutrients in the sea. The change of wind conditions would affect the flow and transport dynamics at local scale and flow fluxes magnitudes between marine basins at the sea scale. Change towards a dry-cold condition would be beneficial for the water quality and lead to improvement of coastal water quality, while the change towards a wet-warm condition will be generally unfavorable for improving the water quality. Clearly more comprehensive studies are needed based on the component processes considered in this thesis, for mapping water quality and eutrophication long-term trends in the Baltic Sea with confidence that is sufficient for effective mitigation measures and policies.
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| 10. |
- Chen, Yuanying, et al.
(författare)
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Nutrient source attribution : Quantitative typology distinction of active and legacy source contributions to waterborne loads
- 2021
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Ingår i: Hydrological Processes. - : Wiley. - 0885-6087 .- 1099-1085. ; 35:7
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Tidskriftsartikel (refereegranskat)abstract
- Distinction between active and legacy sources of nutrients is needed for effective reduction of waterborne nutrient loads and associated eutrophication. This study quantifies main typological differences in nutrient load behaviour versus water discharge for active and legacy sources. This quantitative typology is used for source attribution based on monitoring data for water discharge and concentrations of total nitrogen (TN) and total phosphorous (TP) from 37 catchments draining into the Baltic Sea along the coastline of Sweden over the period 2003-2013. Results indicate dominant legacy source contributions to the monitored loads of TN and TP in most (33 of the total 37) study catchments. Dominant active sources are indicated in 1 catchment for TN, and mixed sources are indicated in 3 catchments for TN, and 4 catchments for TP. The TN and TP concentration contributions are quantified to be overall higher from the legacy than the active sources. Legacy concentrations also correlate well with key indicators of human activity in the catchments, agricultural land share for TN (R-2 = 0.65) and population density for TP (R-2 = 0.56). Legacy-dominated nutrient concentrations also change more slowly than in catchments with dominant active or mixed sources. Various data-based results and indications converge in indicating legacy source contributions as largely dominant, mainly anthropogenic, and with near-zero average change trends in the present study of catchments draining into the Baltic Sea along the coastline of Sweden, as in other parts of the world. These convergent indications emphasize needs to identify and map the different types of sources in each catchment, and differentiate strategies and measures to target each source type for possible achievement of shorter- and longer-term goals of water quality improvement.
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