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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Annelieke S. Wentzel; Joëlle J. E. Janssen; Joëlle J. E. Janssen; Vincent C. J. de Boer; +3 Authors

    Macrophages play important roles in conditions ranging from host immune defense to tissue regeneration and polarize their functional phenotype accordingly. Next to differences in the use of L-arginine and the production of different cytokines, inflammatory M1 macrophages and anti-inflammatory M2 macrophages are also metabolically distinct. In mammals, M1 macrophages show metabolic reprogramming toward glycolysis, while M2 macrophages rely on oxidative phosphorylation to generate energy. The presence of polarized functional immune phenotypes conserved from mammals to fish led us to hypothesize that a similar metabolic reprogramming in polarized macrophages exists in carp. We studied mitochondrial function of M1 and M2 carp macrophages under basal and stressed conditions to determine oxidative capacity by real-time measurements of oxygen consumption and glycolytic capacity by measuring lactate-based acidification. In M1 macrophages, we found increased nitric oxide production and irg1 expression in addition to altered oxidative phosphorylation and glycolysis. In M2 macrophages, we found increased arginase activity, and both oxidative phosphorylation and glycolysis were similar to control macrophages. These results indicate that M1 and M2 carp macrophages show distinct metabolic signatures and indicate that metabolic reprogramming may occur in carp M1 macrophages. This immunometabolic reprogramming likely supports the inflammatory phenotype of polarized macrophages in teleost fish such as carp, similar to what has been shown in mammals.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Other literature type . Article . 2020
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    Frontiers in Immunology
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    Frontiers in Immunology
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    Frontiers in Immunology
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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      Other literature type . Article . 2020
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      Frontiers in Immunology
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    Authors: Xia, H. (author); Bakker, M.C.M. (author);

    In the C2CA project, an online sensor system is required to measure and control the quality and homogeneity of demolition concrete continuously. Laser-induced breakdown spectroscopy is a candidate to fulfil the objective in several tasks. Investigated is the ability of LIBS as an online semi-quantitative composition analysis technique. The maximum laser repetition rate of 100 Hz and each measurement by single laser shot within 5 ms enable the online application in real time. The wavelength range between 273 nm and 326 nm is chosen for differentiations between mineral alloys and CaO powder. Principal component analysis is applied to differentiate between slag concrete, cement and calcium oxide samples, as based on the Ca II photon counts at 315.76 nm, 317.916 nm, 393.189 nm and 396.608 nm. The effects of different sample preparation procedures on the laser shot-to-shot repeatability are also characterized. The encouraging results indicate the eligibility of LIBS for online quality inspection of concrete products. Structural Engineering Civil Engineering and Geosciences

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    Authors: Jantsje M. van Loon-Steensma; Christopher Goldsworthy;

    AbstractIn this paper, we introduce and test a framework to qualitatively assess the environmental impact of climate adaptation innovations with the ambition to facilitate the implementation of these adaptations. The framework was designed to enable continuous environmentally conscious benchmarking based on three environmental performance indicators: sustainable design, environmental impact and ecological impact. It was pilot tested by uninvolved experts and key-persons for two large-scale nature-based flood adaptation innovations in the Netherlands and discussed with environmental assessment professionals. Our findings indicate how the inclusion of our framework helps to identify important knowledge gaps regarding environmental co-benefits and trade-offs, and can be beneficial to both those developing the innovation and the local authorities charged with assessing the suitability of innovations. We conclude by noting how the incorporation of environmental impact assessment from the design stage of adaptations could supplement existing environmental assessment regulations pre-empting concerns rather than reacting to them.

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    NARCIS; Research@WUR
    Article . 2022
    License: CC BY
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    AMBIO
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    Other literature type . Article . 2022 . 2021 . Peer-reviewed
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      Article . 2022
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      AMBIO
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      Other literature type . Article . 2022 . 2021 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Bexton, Steve; Wiersma, Lidewij C.; Getu, Sarah; van Run, Peter R.; +8 Authors

    A fox circovirus was identified in serum samples from foxes with unexplained neurologic signs by using viral metagenomics. Fox circovirus nucleic acid was localized in histological lesions of the cerebrum by in situ hybridization. Viruses from the family Circoviridae may have neurologic tropism more commonly than previously anticipated.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Emerging Infectious Diseases
    Other literature type . Article . 2015 . Peer-reviewed
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      Emerging Infectious Diseases
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    Authors: Fallaize, R.; Macready, A.L.; Butler, L.T.; Ellis, J.A.; +9 Authors

    Personalised nutrition (PN) has the potential to reduce disease risk and optimise health and performance. Although previous research has shown good acceptance of the concept of PN in the UK, preferences regarding the delivery of a PN service (e.g. online v. face-to-face) are not fully understood. It is anticipated that the presence of a free at point of delivery healthcare system, the National Health Service (NHS), in the UK may have an impact on end-user preferences for deliverances. To determine this, supplementary analysis of qualitative data obtained from focus group discussions on PN service delivery, collected as part of the Food4Me project in the UK and Ireland, was undertaken. Irish data provided comparative analysis of a healthcare system that is not provided free of charge at the point of delivery to the entire population. Analyses were conducted using the ‘framework approach’ described by Rabiee (Focus-group interview and data analysis. Proc Nutr Soc 63, 655-660). There was a preference for services to be led by the government and delivered face-to-face, which was perceived to increase trust and transparency, and add value. Both countries associated paying for nutritional advice with increased commitment and motivation to follow guidelines. Contrary to Ireland, however, and despite the perceived benefit of paying, UK discussants still expected PN services to be delivered free of charge by the NHS. Consideration of this unique challenge of free healthcare that is embedded in the NHS culture will be crucial when introducing PN to the UK.

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    NARCIS; Research@WUR
    Article . 2015
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    Bradford Scholars
    Article . 2015
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    Research@WUR; British Journal Of Nutrition
    Other literature type . Article . 2015 . Peer-reviewed
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    British Journal Of Nutrition
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      NARCIS; Research@WUR
      Article . 2015
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      Research@WUR; British Journal Of Nutrition
      Other literature type . Article . 2015 . Peer-reviewed
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      British Journal Of Nutrition
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    Authors: Kruppa, Jochen; Jo, Wendy K; van der Vries, Erhard; Ludlow, Martin; +6 Authors

    Discovery of novel viruses in host samples is a multidisciplinary process which relies increasingly on next-generation sequencing (NGS) followed by computational analysis. A crucial step in this analysis is to separate host sequence reads from the sequence reads of the virus to be discovered. This becomes especially difficult if no reference genome of the host is available. Furthermore, if the total number of viral reads in a sample is low, de novo assembly of a virus which is a requirement for most existing pipelines is hard to realize. We present a new modular, computational pipeline for discovery of novel viruses in host samples. While existing pipelines rely on the availability of the hosts reference genome for filtering sequence reads, our new pipeline can also cope with cases for which no reference genome is available. As a further novelty of our method a decoy module is used to assess false classification rates in the discovery process. Additionally, viruses with a low read coverage can be identified and visually reviewed. We validate our pipeline on simulated data as well as two experimental samples with known virus content. For the experimental samples, we were able to reproduce the laboratory findings. Our newly developed pipeline is applicable for virus detection in a wide range of host species. The three modules we present can either be incorporated individually in other pipelines or be used as a stand-alone pipeline. We are the first to present a decoy approach within a virus detection pipeline that can be used to assess error rates so that the quality of the final result can be judged. We provide an implementation of our modules via Github. However, the principle of the modules can easily be re-implemented by other researchers.

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    Infection, Genetics and Evolution
    Other literature type . Article . 2018 . Peer-reviewed
    License: Elsevier TDM
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      Infection, Genetics and Evolution
      Other literature type . Article . 2018 . Peer-reviewed
      License: Elsevier TDM
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    In e-health intervention studies, there are concerns about the reliability of internet-based, self-reported (SR) data and about the potential for identity fraud. This study introduced and tested a novel procedure for assessing the validity of internet-based, SR identity and validated anthropometric and demographic data via measurements performed face-to-face in a validation study (VS). Participants (n = 140) from seven European countries, participating in the Food4Me intervention study which aimed to test the efficacy of personalised nutrition approaches delivered via the internet, were invited to take part in the VS. Participants visited a research centre in each country within 2 weeks of providing SR data via the internet. Participants received detailed instructions on how to perform each measurement. Individual’s identity was checked visually and by repeated collection and analysis of buccal cell DNA for 33 genetic variants. Validation of identity using genomic information showed perfect concordance between SR and VS. Similar results were found for demographic data (age and sex verification). We observed strong intra-class correlation coefficients between SR and VS for anthropometric data (height 0.990, weight 0.994 and BMI 0.983). However, internet-based SR weight was under-reported (Δ −0.70 kg [−3.6 to 2.1], p < 0.0001) and, therefore, BMI was lower for SR data (Δ −0.29 kg m−2 [−1.5 to 1.0], p < 0.0001). BMI classification was correct in 93 % of cases. We demonstrate the utility of genotype information for detection of possible identity fraud in e-health studies and confirm the reliability of internet-based, SR anthropometric and demographic data collected in the Food4Me study. Trial registration: NCT01530139 (http://clinicaltrials.gov/show/NCT01530139© 2015, European Union.

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      Article . 2015
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    Authors: Saskia M. Willers; Marcel F. Jonker; Lisette Klok; Menno Keuken; +5 Authors

    BackgroundElevated temperature and air pollution have been associated with increased mortality. Exposure to heat and air pollution, as well as the density of vulnerable groups varies within cities. The objective was to investigate the extent of neighbourhood differences in mortality risk due to heat and air pollution in a city with a temperate maritime climate.MethodsA case-crossover design was used to study associations between heat, air pollution and mortality. Different thermal indicators and air pollutants (PM10, NO2, O3) were reconstructed at high spatial resolution to improve exposure classification. Daily exposures were linked to individual mortality cases over a 15 year period.ResultsSignificant interaction between maximum air temperature (Tamax) and PM10 was observed. During “summer smog” days (Tamax > 25 °C and PM10 > 50 μg/m3), the mortality risk at lag 2 was 7% higher compared to the reference (Tamax 15 °C and PM10 15 μg/m3). Persons above age 85 living alone were at highest risk.ConclusionWe found significant synergistic effects of high temperatures and air pollution on mortality. Single living elderly were the most vulnerable group. Due to spatial differences in temperature and air pollution, mortality risks varied substantially between neighbourhoods, with a difference up to 7%.

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    Environment International
    Article . 2016
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    Article . 2016
    Data sources: NARCIS
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Article . 2016
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    Authors: Bellassen, Valentin; Drut, Marion; Antonioli, Federico; Brečić, Ružica; +17 Authors

    Abstract The carbon and land footprint of 26 certified food products – geographical indications and organic products and their conventional references are assessed. This assessment goes beyond existing literature by (1) designing a calculation method fit for the comparison between certified food and conventional production, (2) using the same calculation method and parameters for 52 products – 26 Food Quality Schemes and their reference products – to allow for a meaningful comparison, (3) transparently documenting this calculation method and opening access to the detailed results and the underlying data, and (4) providing the first assessment of the carbon and land footprint of geographical indications. The method used is Life Cycle Assessment, largely relying on the Cool Farm Tool for the impact assessment. The most common indicator of climate impact, the carbon footprint expressed per ton of product, is not significantly different between certified foods and their reference products. The only exception to this pattern are vegetal organic products, whose carbon footprint is 16% lower. This is because the decrease in greenhouse gas emissions from the absence of mineral fertilizers is never fully offset by the associated lower yield. The climate impact of certified food per hectare is however 26% than their reference and their land footprint is logically 24% higher. Technical specifications directly or indirectly inducing a lower use of mineral fertilizers are a key driver of this pattern. So is yield, which depends both on terroir and farming practices. Overall, this assessment reinforces the quality policy of the European Union: promoting certified food is not inconsistent with mitigating climate change.

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    Authors: Gianluca Campanella; Marc J. Gunter; Silvia Polidoro; Vittorio Krogh; +31 Authors

    BackgroundObesity is an established risk factor for several common chronic diseases such as breast and colorectal cancer, metabolic and cardiovascular diseases; however, the biological basis for these relationships is not fully understood. To explore the association of obesity with these conditions, we investigated peripheral blood leucocyte (PBL) DNA methylation markers for adiposity and their contribution to risk of incident breast and colorectal cancer and myocardial infarction.MethodsDNA methylation profiles (Illumina Infinium® HumanMethylation450 BeadChip) from 1941 individuals from four population-based European cohorts were analysed in relation to body mass index, waist circumference, waist-hip and waist-height ratio within a meta-analytical framework. In a subset of these individuals, data on genome-wide gene expression level, biomarkers of glucose and lipid metabolism were also available. Validation of methylation markers associated with all adiposity measures was performed in 358 individuals. Finally, we investigated the association of obesity-related methylation marks with breast, colorectal cancer and myocardial infarction within relevant subsets of the discovery population.ResultsWe identified 40 CpG loci with methylation levels associated with at least one adiposity measure. Of these, one CpG locus (cg06500161) in ABCG1 was associated with all four adiposity measures (P = 9.07×10−8 to 3.27×10−18) and lower transcriptional activity of the full-length isoform of ABCG1 (P = 6.00×10−7), higher triglyceride levels (P = 5.37×10−9) and higher triglycerides-to-HDL cholesterol ratio (P = 1.03×10−10). Of the 40 informative and obesity-related CpG loci, two (in IL2RB and FGF18) were significantly associated with colorectal cancer (inversely, P < 1.6×10−3) and one intergenic locus on chromosome 1 was inversely associated with myocardial infarction (P < 1.25×10−3), independently of obesity and established risk factors.ConclusionOur results suggest that epigenetic changes, in particular altered DNA methylation patterns, may be an intermediate biomarker at the intersection of obesity and obesity-related diseases, and could offer clues as to underlying biological mechanisms.

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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    NARCIS
    Article . 2018
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Article . 2018
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Annelieke S. Wentzel; Joëlle J. E. Janssen; Joëlle J. E. Janssen; Vincent C. J. de Boer; +3 Authors

    Macrophages play important roles in conditions ranging from host immune defense to tissue regeneration and polarize their functional phenotype accordingly. Next to differences in the use of L-arginine and the production of different cytokines, inflammatory M1 macrophages and anti-inflammatory M2 macrophages are also metabolically distinct. In mammals, M1 macrophages show metabolic reprogramming toward glycolysis, while M2 macrophages rely on oxidative phosphorylation to generate energy. The presence of polarized functional immune phenotypes conserved from mammals to fish led us to hypothesize that a similar metabolic reprogramming in polarized macrophages exists in carp. We studied mitochondrial function of M1 and M2 carp macrophages under basal and stressed conditions to determine oxidative capacity by real-time measurements of oxygen consumption and glycolytic capacity by measuring lactate-based acidification. In M1 macrophages, we found increased nitric oxide production and irg1 expression in addition to altered oxidative phosphorylation and glycolysis. In M2 macrophages, we found increased arginase activity, and both oxidative phosphorylation and glycolysis were similar to control macrophages. These results indicate that M1 and M2 carp macrophages show distinct metabolic signatures and indicate that metabolic reprogramming may occur in carp M1 macrophages. This immunometabolic reprogramming likely supports the inflammatory phenotype of polarized macrophages in teleost fish such as carp, similar to what has been shown in mammals.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    NARCIS; Research@WUR
    Other literature type . Article . 2020
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    Frontiers in Immunology
    Article . 2020
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    Frontiers in Immunology
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    Frontiers in Immunology
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      Other literature type . Article . 2020
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      Frontiers in Immunology
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      Frontiers in Immunology
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    Authors: Xia, H. (author); Bakker, M.C.M. (author);

    In the C2CA project, an online sensor system is required to measure and control the quality and homogeneity of demolition concrete continuously. Laser-induced breakdown spectroscopy is a candidate to fulfil the objective in several tasks. Investigated is the ability of LIBS as an online semi-quantitative composition analysis technique. The maximum laser repetition rate of 100 Hz and each measurement by single laser shot within 5 ms enable the online application in real time. The wavelength range between 273 nm and 326 nm is chosen for differentiations between mineral alloys and CaO powder. Principal component analysis is applied to differentiate between slag concrete, cement and calcium oxide samples, as based on the Ca II photon counts at 315.76 nm, 317.916 nm, 393.189 nm and 396.608 nm. The effects of different sample preparation procedures on the laser shot-to-shot repeatability are also characterized. The encouraging results indicate the eligibility of LIBS for online quality inspection of concrete products. Structural Engineering Civil Engineering and Geosciences

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    Authors: Jantsje M. van Loon-Steensma; Christopher Goldsworthy;

    AbstractIn this paper, we introduce and test a framework to qualitatively assess the environmental impact of climate adaptation innovations with the ambition to facilitate the implementation of these adaptations. The framework was designed to enable continuous environmentally conscious benchmarking based on three environmental performance indicators: sustainable design, environmental impact and ecological impact. It was pilot tested by uninvolved experts and key-persons for two large-scale nature-based flood adaptation innovations in the Netherlands and discussed with environmental assessment professionals. Our findings indicate how the inclusion of our framework helps to identify important knowledge gaps regarding environmental co-benefits and trade-offs, and can be beneficial to both those developing the innovation and the local authorities charged with assessing the suitability of innovations. We conclude by noting how the incorporation of environmental impact assessment from the design stage of adaptations could supplement existing environmental assessment regulations pre-empting concerns rather than reacting to them.

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    NARCIS; Research@WUR
    Article . 2022
    License: CC BY
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    AMBIO
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    Other literature type . Article . 2022 . 2021 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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      Article . 2022
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      Other literature type . Article . 2022 . 2021 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Bexton, Steve; Wiersma, Lidewij C.; Getu, Sarah; van Run, Peter R.; +8 Authors

    A fox circovirus was identified in serum samples from foxes with unexplained neurologic signs by using viral metagenomics. Fox circovirus nucleic acid was localized in histological lesions of the cerebrum by in situ hybridization. Viruses from the family Circoviridae may have neurologic tropism more commonly than previously anticipated.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Emerging Infectious Diseases
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      Emerging Infectious Diseases
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    Authors: Fallaize, R.; Macready, A.L.; Butler, L.T.; Ellis, J.A.; +9 Authors

    Personalised nutrition (PN) has the potential to reduce disease risk and optimise health and performance. Although previous research has shown good acceptance of the concept of PN in the UK, preferences regarding the delivery of a PN service (e.g. online v. face-to-face) are not fully understood. It is anticipated that the presence of a free at point of delivery healthcare system, the National Health Service (NHS), in the UK may have an impact on end-user preferences for deliverances. To determine this, supplementary analysis of qualitative data obtained from focus group discussions on PN service delivery, collected as part of the Food4Me project in the UK and Ireland, was undertaken. Irish data provided comparative analysis of a healthcare system that is not provided free of charge at the point of delivery to the entire population. Analyses were conducted using the ‘framework approach’ described by Rabiee (Focus-group interview and data analysis. Proc Nutr Soc 63, 655-660). There was a preference for services to be led by the government and delivered face-to-face, which was perceived to increase trust and transparency, and add value. Both countries associated paying for nutritional advice with increased commitment and motivation to follow guidelines. Contrary to Ireland, however, and despite the perceived benefit of paying, UK discussants still expected PN services to be delivered free of charge by the NHS. Consideration of this unique challenge of free healthcare that is embedded in the NHS culture will be crucial when introducing PN to the UK.

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    Article . 2015
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    Research@WUR; British Journal Of Nutrition
    Other literature type . Article . 2015 . Peer-reviewed
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    British Journal Of Nutrition
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      Article . 2015
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      Research@WUR; British Journal Of Nutrition
      Other literature type . Article . 2015 . Peer-reviewed
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      British Journal Of Nutrition
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    Authors: Kruppa, Jochen; Jo, Wendy K; van der Vries, Erhard; Ludlow, Martin; +6 Authors

    Discovery of novel viruses in host samples is a multidisciplinary process which relies increasingly on next-generation sequencing (NGS) followed by computational analysis. A crucial step in this analysis is to separate host sequence reads from the sequence reads of the virus to be discovered. This becomes especially difficult if no reference genome of the host is available. Furthermore, if the total number of viral reads in a sample is low, de novo assembly of a virus which is a requirement for most existing pipelines is hard to realize. We present a new modular, computational pipeline for discovery of novel viruses in host samples. While existing pipelines rely on the availability of the hosts reference genome for filtering sequence reads, our new pipeline can also cope with cases for which no reference genome is available. As a further novelty of our method a decoy module is used to assess false classification rates in the discovery process. Additionally, viruses with a low read coverage can be identified and visually reviewed. We validate our pipeline on simulated data as well as two experimental samples with known virus content. For the experimental samples, we were able to reproduce the laboratory findings. Our newly developed pipeline is applicable for virus detection in a wide range of host species. The three modules we present can either be incorporated individually in other pipelines or be used as a stand-alone pipeline. We are the first to present a decoy approach within a virus detection pipeline that can be used to assess error rates so that the quality of the final result can be judged. We provide an implementation of our modules via Github. However, the principle of the modules can easily be re-implemented by other researchers.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Infection, Genetics ...arrow_drop_down
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    Infection, Genetics and Evolution
    Other literature type . Article . 2018 . Peer-reviewed
    License: Elsevier TDM
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      Infection, Genetics and Evolution
      Other literature type . Article . 2018 . Peer-reviewed
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    In e-health intervention studies, there are concerns about the reliability of internet-based, self-reported (SR) data and about the potential for identity fraud. This study introduced and tested a novel procedure for assessing the validity of internet-based, SR identity and validated anthropometric and demographic data via measurements performed face-to-face in a validation study (VS). Participants (n = 140) from seven European countries, participating in the Food4Me intervention study which aimed to test the efficacy of personalised nutrition approaches delivered via the internet, were invited to take part in the VS. Participants visited a research centre in each country within 2 weeks of providing SR data via the internet. Participants received detailed instructions on how to perform each measurement. Individual’s identity was checked visually and by repeated collection and analysis of buccal cell DNA for 33 genetic variants. Validation of identity using genomic information showed perfect concordance between SR and VS. Similar results were found for demographic data (age and sex verification). We observed strong intra-class correlation coefficients between SR and VS for anthropometric data (height 0.990, weight 0.994 and BMI 0.983). However, internet-based SR weight was under-reported (Δ −0.70 kg [−3.6 to 2.1], p < 0.0001) and, therefore, BMI was lower for SR data (Δ −0.29 kg m−2 [−1.5 to 1.0], p < 0.0001). BMI classification was correct in 93 % of cases. We demonstrate the utility of genotype information for detection of possible identity fraud in e-health studies and confirm the reliability of internet-based, SR anthropometric and demographic data collected in the Food4Me study. Trial registration: NCT01530139 (http://clinicaltrials.gov/show/NCT01530139© 2015, European Union.

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    Authors: Saskia M. Willers; Marcel F. Jonker; Lisette Klok; Menno Keuken; +5 Authors

    BackgroundElevated temperature and air pollution have been associated with increased mortality. Exposure to heat and air pollution, as well as the density of vulnerable groups varies within cities. The objective was to investigate the extent of neighbourhood differences in mortality risk due to heat and air pollution in a city with a temperate maritime climate.MethodsA case-crossover design was used to study associations between heat, air pollution and mortality. Different thermal indicators and air pollutants (PM10, NO2, O3) were reconstructed at high spatial resolution to improve exposure classification. Daily exposures were linked to individual mortality cases over a 15 year period.ResultsSignificant interaction between maximum air temperature (Tamax) and PM10 was observed. During “summer smog” days (Tamax > 25 °C and PM10 > 50 μg/m3), the mortality risk at lag 2 was 7% higher compared to the reference (Tamax 15 °C and PM10 15 μg/m3). Persons above age 85 living alone were at highest risk.ConclusionWe found significant synergistic effects of high temperatures and air pollution on mortality. Single living elderly were the most vulnerable group. Due to spatial differences in temperature and air pollution, mortality risks varied substantially between neighbourhoods, with a difference up to 7%.

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    Environment International
    Article . 2016
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Authors: Bellassen, Valentin; Drut, Marion; Antonioli, Federico; Brečić, Ružica; +17 Authors

    Abstract The carbon and land footprint of 26 certified food products – geographical indications and organic products and their conventional references are assessed. This assessment goes beyond existing literature by (1) designing a calculation method fit for the comparison between certified food and conventional production, (2) using the same calculation method and parameters for 52 products – 26 Food Quality Schemes and their reference products – to allow for a meaningful comparison, (3) transparently documenting this calculation method and opening access to the detailed results and the underlying data, and (4) providing the first assessment of the carbon and land footprint of geographical indications. The method used is Life Cycle Assessment, largely relying on the Cool Farm Tool for the impact assessment. The most common indicator of climate impact, the carbon footprint expressed per ton of product, is not significantly different between certified foods and their reference products. The only exception to this pattern are vegetal organic products, whose carbon footprint is 16% lower. This is because the decrease in greenhouse gas emissions from the absence of mineral fertilizers is never fully offset by the associated lower yield. The climate impact of certified food per hectare is however 26% than their reference and their land footprint is logically 24% higher. Technical specifications directly or indirectly inducing a lower use of mineral fertilizers are a key driver of this pattern. So is yield, which depends both on terroir and farming practices. Overall, this assessment reinforces the quality policy of the European Union: promoting certified food is not inconsistent with mitigating climate change.

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    Authors: Gianluca Campanella; Marc J. Gunter; Silvia Polidoro; Vittorio Krogh; +31 Authors

    BackgroundObesity is an established risk factor for several common chronic diseases such as breast and colorectal cancer, metabolic and cardiovascular diseases; however, the biological basis for these relationships is not fully understood. To explore the association of obesity with these conditions, we investigated peripheral blood leucocyte (PBL) DNA methylation markers for adiposity and their contribution to risk of incident breast and colorectal cancer and myocardial infarction.MethodsDNA methylation profiles (Illumina Infinium® HumanMethylation450 BeadChip) from 1941 individuals from four population-based European cohorts were analysed in relation to body mass index, waist circumference, waist-hip and waist-height ratio within a meta-analytical framework. In a subset of these individuals, data on genome-wide gene expression level, biomarkers of glucose and lipid metabolism were also available. Validation of methylation markers associated with all adiposity measures was performed in 358 individuals. Finally, we investigated the association of obesity-related methylation marks with breast, colorectal cancer and myocardial infarction within relevant subsets of the discovery population.ResultsWe identified 40 CpG loci with methylation levels associated with at least one adiposity measure. Of these, one CpG locus (cg06500161) in ABCG1 was associated with all four adiposity measures (P = 9.07×10−8 to 3.27×10−18) and lower transcriptional activity of the full-length isoform of ABCG1 (P = 6.00×10−7), higher triglyceride levels (P = 5.37×10−9) and higher triglycerides-to-HDL cholesterol ratio (P = 1.03×10−10). Of the 40 informative and obesity-related CpG loci, two (in IL2RB and FGF18) were significantly associated with colorectal cancer (inversely, P < 1.6×10−3) and one intergenic locus on chromosome 1 was inversely associated with myocardial infarction (P < 1.25×10−3), independently of obesity and established risk factors.ConclusionOur results suggest that epigenetic changes, in particular altered DNA methylation patterns, may be an intermediate biomarker at the intersection of obesity and obesity-related diseases, and could offer clues as to underlying biological mechanisms.

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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Article . 2018
    Data sources: NARCIS
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    NARCIS
    Article . 2018
    Data sources: NARCIS
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