| 1. |
- Bergkvist, Charlotte, et al.
(författare)
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Exposure to dioxin-like pollutants via different food commodities in Swedish children and young adults.
- 2008
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Ingår i: Food and Chemical Toxicology. - : Elsevier BV. - 0278-6915 .- 1873-6351. ; 46:11, s. 3360-3367
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Tidskriftsartikel (refereegranskat)abstract
- The dietary intake of polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and biphenyls (PCBs) in terms of toxic equivalents (TEQs) was investigated in Swedish children and young adults. Exposure was estimated from concentration data of six groups of individual food commodities (meat, fish, dairy products, egg, edible fats and other foodstuff) combined with food intake data from a 7-day record book obtained from 670 individuals aged 1-24 years. The results showed that Swedish boys and girls, up to the age of ten, had a median TEQ intake that exceeded the tolerable daily intake (TDI) of 2 pg TEQ/kg body weight. Children exceeding the TDI varied from almost all individuals among the youngest children to about 20% among young men and women. Dairy and fish products were the main sources of exposure for the average child, accounting for 59% of the total TEQ intake. The individuals most highly exposed were, on the other hand, characterized by a high consumption of fish. Since children constitute a vulnerable group, results obtained from the present study show that it is essential to perform age specific dietary intake assessments of pollutants and more carefully consider sensitive and/or highly exposed groups in the population in the risk management processes.
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| 2. |
- Berglund, Ann-Charlotte, et al.
(författare)
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Combining local and grid resources in scientific workflows (for Bioinformatics)
- 2009
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Konferensbidrag (refereegranskat)abstract
- We examine some issues that arise when using both local and Gridresources in scientific workflows. Our previous work addresses and illustratesthe benefits of a light-weight and generic workflow engine that manages andoptimizes Grid resource usage. Extending on this effort, we hereillustrate how a client tool for bioinformatics applications employs the engine tointerface with Grid resources. We also explore how to define data flowsthat transparently integrates local and Grid subworkflows. In addition, the benefits of parameter sweep workflows are examined and a means for describing this type of workflows in an abstract and concise manner is introduced. Finally, the above mechanisms are employed to perform an orthology detection analysis.
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| 3. |
- Berglund, Ann-Charlotte, et al.
(författare)
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InParanoid 6 : eukaryotic ortholog clusters with inparalogs
- 2008
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 36, s. D263-D266
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Tidskriftsartikel (refereegranskat)abstract
- The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted in 2 642 187 pairwise ortholog groups in total. The orthology-based species relations are presented in an orthophylogram. InParanoid clusters contain one or more orthologs from each of the two species. Multiple orthologs in the same species, i.e. inparalogs, result from gene duplications after the species divergence. A new InParanoid website has been developed which is optimized for speed both for users and for updating the system. The XML output format has been improved for efficient processing of the InParanoid ortholog clusters.
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| 4. |
- Berglund-Sonnhammer, Ann-Charlotte, et al.
(författare)
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Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
- 2006
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 63:2, s. 240-250
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Tidskriftsartikel (refereegranskat)abstract
- Gene duplication and gene loss as well as other biological events can result in multiple copies of genes in a given species. Because of these gene duplication and loss dynamics, in addition to variation in sequence evolution and other sources of uncertainty, different gene trees ultimately present different evolutionary histories. All of this together results in gene trees that give different topologies from each other, making consensus species trees ambiguous in places. Other sources of data to generate species trees are also unable to provide completely resolved binary species trees. However, in addition to gene duplication events, speciation events have provided some underlying phylogenetic signal, enabling development of algorithms to characterize these processes. Therefore, a soft parsimony algorithm has been developed that enables the mapping of gene trees onto species trees and modification of uncertain or weakly supported branches based on minimizing the number of gene duplication and loss events implied by the tree. The algorithm also allows for rooting of unrooted trees and for removal of in-paralogues (lineage-specific duplicates and redundant sequences masquerading as such). The algorithm has also been made available for download as a software package, Softparsmap.
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| 5. |
- Clark, Charlotte, et al.
(författare)
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Psychological restoration, coping strategies and children’s cognitive performance in the RANCH study
- 2006
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Ingår i: Proceedings of Inter-Noise 2006, Honolulu, Hawaii, USA, 3-6 December, 2006, Paper no in06_090 (Available on CD). ; :Paper no in06_090
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Konferensbidrag (refereegranskat)abstract
- The RANCH study found a linear exposure effect association between chronic aircraft noise exposure at primary school and the impairment of children’s reading comprehension, in the Netherlands, Spain and the United Kingdom. This paper presents multilevel modelling analyses, exploring psychological mechanisms, which may moderate the effect of aircraft noise on children’s cognition. Psychological restoration – the process whereby places which afford tranquility and relaxation are utilized to reduce stress and promote well being – has been shown to reduce the adverse effect of noise on children’s annoyance responses. This paper examines whether having places for psychological restoration at home, moderates the adverse effects of chronic aircraft noise exposure at school on children’s cognition. In addition, the effectiveness of coping strategies in relation to noise exposure at school are examined – are specific coping strategies associated with less impairment of cognition? Multi-level models examining the role of psychological restoration and coping strategies, as part of a broader model of environmental risk and protective factors for children’s cognition are presented. The implication of the findings for interventions for children attending noise exposed schools are discussed.
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| 6. |
- Lilja, Hans, et al.
(författare)
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Long-term prediction of prostate cancer up to 25 years before diagnosis of prostate cancer using prostate kallikreins measured at age 44 to 50 years.
- 2007
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Ingår i: Journal of Clinical Oncology. - 1527-7755. ; 25:4, s. 431-436
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Tidskriftsartikel (refereegranskat)abstract
- Purpose We examined whether prostate-specific antigen (PSA) forms and human kallikrein 2 (hK2) measured at age 44 to 50 years predict long-term risk of incident prostate cancer. Methods From 1974 to 1986, 21,277 men age <= 50 years in Malmo, Sweden, enrolled onto a cardiovascular study (74% participation). The rate of PSA screening in this population is low. According to the Swedish Cancer Registry, 498 were later diagnosed with prostate cancer. We measured hK2, free PSA, and total PSA (tPSA) in archived blood plasma from 462 participants later diagnosed with prostate cancer and from 1,222 matched controls. Conditional logistic regression was used to test for association of prostate cancer with hK2 and PSA forms measured at baseline. Results Median delay between venipuncture and prostate cancer diagnosis was 18 years. hK2 and all PSA forms were strongly associated with prostate cancer (all P < .0005). None of the 90 anthropometric, lifestyle, biochemical, and medical history variables measured at baseline was importantly predictive. A tPSA increase of 1 ng/mL was associated with an increase in odds of cancer of 3.69 (95% CI, 2.99 to 4.56); addition of other PSA forms or hK2 did not add to the predictive value of tPSA. tPSA remained predictive for men diagnosed >= 20 years after venipuncture, and the predictive value remained unchanged in an analysis restricted to palpable disease. Conclusion A single PSA test at age 44 to 50 years predicts subsequent clinically diagnosed prostate cancer. This raises the possibility of risk stratification for prostate cancer screening programs.
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| 7. |
- Lyssenko, Valeriya, et al.
(författare)
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Mechanisms by which common variants in the TCF7L2 gene increase risk of type 2 diabetes.
- 2007
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Ingår i: Journal of Clinical Investigation. - 0021-9738. ; 117:8, s. 2155-2163
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants in the gene encoding for transcription factor-7-like 2 (TCF7L2) have been associated with type 2 diabetes (T2D) and impaired beta cell function, but the mechanisms have remained unknown. We therefore studied prospectively the ability of common variants in TCF7L2 to predict future T2D and explored the mechanisms by which they would do this. Scandinavian subjects followed for up to 22 years were genotyped for 3 SNPs (rs7903146, rs12255372, and rs10885406) in TCF7L2, and a subset of them underwent extensive metabolic studies. Expression of TCF7L2 was related to genotype and metabolic parameters in human islets. The CT/TT genotypes of SNP rs7903146 strongly predicted future T2D in 2 independent cohorts (Swedish and Finnish). The risk T allele was associated with impaired insulin secretion, incretin effects, and enhanced rate of hepatic glucose production. TCF7L2 expression in human islets was increased 5-fold in T2D, particularly in carriers of the TT genotype. Overexpression of TCF7L2 in human islets reduced glucose-stimulated insulin secretion. In conclusion, the increased risk of T2D conferred by variants in TCF7L2 involves the enteroinsular axis, enhanced expression of the gene in islets, and impaired insulin secretion.
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| 8. |
- Mishchenko, Kateryna, 1973-
(författare)
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Numerical Algorithms for Optimization Problems in Genetical Analysis
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The focus of this thesis is on numerical algorithms for efficient solution of QTL analysis problem in genetics.Firstly, we consider QTL mapping problems where a standard least-squares model is used for computing the model fit. We develop optimization methods for the local problems in a hybrid global-local optimization scheme for determining the optimal set of QTL locations. Here, the local problems have constant bound constraints and may be non-convex and/or flat in one or more directions. We propose an enhanced quasi-Newton method and also implement several schemes for constrained optimization. The algorithms are adopted to the QTL optimization problems. We show that it is possible to use the new schemes to solve problems with up to 6 QTLs efficiently and accurately, and that the work is reduced with up to two orders magnitude compared to using only global optimization.Secondly, we study numerical methods for QTL mapping where variance component estimation and a REML model is used. This results in a non-linear optimization problem for computing the model fit in each set of QTL locations. Here, we compare different optimization schemes and adopt them for the specifics of the problem. The results show that our version of the active set method is efficient and robust, which is not the case for methods used earlier. We also study the matrix operations performed inside the optimization loop, and develop more efficient algorithms for the REML computations. We develop a scheme for reducing the number of objective function evaluations, and we accelerate the computations of the derivatives of the log-likelihood by introducing an efficient scheme for computing the inverse of the variance-covariance matrix and other components of the derivatives of the log-likelihood.
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| 9. |
- Newton-Cheh, Christopher, et al.
(författare)
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Genome-wide association study identifies eight loci associated with blood pressure
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:6, s. 666-676
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Tidskriftsartikel (refereegranskat)abstract
- Elevated blood pressure is a common, heritable cause of cardiovascular disease worldwide. To date, identification of common genetic variants influencing blood pressure has proven challenging. We tested 2.5 million genotyped and imputed SNPs for association with systolic and diastolic blood pressure in 34,433 subjects of European ancestry from the Global BPgen consortium and followed up findings with direct genotyping (N <= 71,225 European ancestry, N <= 12,889 Indian Asian ancestry) and in silico comparison (CHARGE consortium, N 29,136). We identified association between systolic or diastolic blood pressure and common variants in eight regions near the CYP17A1 (P = 7 x 10(-24)), CYP1A2 (P = 1 x 10(-23)), FGF5 (P = 1 x 10(-21)), SH2B3 (P = 3 x 10(-18)), MTHFR (P = 2 x 10(-13)), c10orf107 (P = 1 x 10(-9)), ZNF652 (P = 5 x 10(-9)) and PLCD3 (P = 1 x 10(-8)) genes. All variants associated with continuous blood pressure were associated with dichotomous hypertension. These associations between common variants and blood pressure and hypertension offer mechanistic insights into the regulation of blood pressure and may point to novel targets for interventions to prevent cardiovascular disease.
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| 10. |
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| 11. |
- Sennblad, Bengt, et al.
(författare)
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primetv : a viewer for reconciled trees
- 2007
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 8, s. 148-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Evolutionary processes, such as gene family evolution or parasite-host cospeciation, can often be viewed as a tree evolving inside another tree. Relating two given trees under such a constraint is known as reconciling them. Adequate software tools for generating illustrations of tree reconciliations are instrumental for presenting and communicating results and ideas regarding these phenomena. Available visualization tools have been limited to illustrations of the most parsimonious reconciliation. However, there exists a plethora of biologically relevant non-parsimonious reconciliations. Illustrations of these general reconciliations may not be achieved without manual editing. Results: We have developed a new reconciliation viewer, primetv. It is a simple and compact visualization program that is the first automatic tool for illustrating general tree reconciliations. It reads reconciled trees in an extended Newick format and outputs them as tree-within-tree illustrations in a range of graphic formats. Output attributes, such as colors and layout, can easily be adjusted by the user. To enhance the construction of input to primetv, two helper programs, readReconciliation and reconcile, accompany primetv. Detailed examples of all programs' usage are provided in the text. For the casual user a web-service provides a simple user interface to all programs. Conclusion: With primetv, the first visualization tool for general reconciliations, illustrations of trees-within-trees are easy to produce. Because it clarifies and accentuates an underlying structure in a reconciled tree, e. g., the impact of a species tree on a gene-family phylogeny, it will enhance scientific presentations as well as pedagogic illustrations in an educational setting. primetv is available at http://prime.sbc.su.se/primetv, both as a standalone command-line tool and as a web service. The software is distributed under the GNU General Public License.
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| 12. |
- Ulmert, David, et al.
(författare)
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Long-term prediction of prostate cancer: Prostate-specific antigen (PSA) velocity is predictive but does not improve the predictive accuracy of a single PSA measurement 15 years or more before cancer diagnosis in a large, representative, unscreened population
- 2008
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Ingår i: Journal of Clinical Oncology. - 1527-7755. ; 26:6, s. 835-841
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Tidskriftsartikel (refereegranskat)abstract
- Purpose We tested whether total prostate-specific antigen velocity (tPSAv) improves accuracy of a model using PSA level to predict long-term risk of prostate cancer diagnosis. Methods During 1974 to 1986 in a preventive medicine study in Sweden, 5,722 men aged <= 50 gave two blood samples about 6 years apart. We measured free (fPSA) and total PSA (tPSA) in archived plasma samples from 4,907 participants. Prostate cancer was subsequently diagnosed in 443 (9%) men. Cox proportional hazards regression was used to evaluate tPSA and tPSAv as predictors of prostate cancer. Predictive accuracy was assessed by the concordance index. Results The median time from second blood draw to cancer diagnosis was 16 years; median follow-up for men without prostate cancer was 21 years. In univariate models, tPSA level at second assessment and tPSAv between first and second assessments were associated with prostate cancer (both P < .001). tPSAv was highly correlated with tPSA level (r = 0.93). Twenty-year probabilities of cancer for men at 50th, 90th, and 95th percentile of tPSA and tPSAv were 10.6%, 17.1%, and 21.2% for tPSA, and 9.1%, 11.8%, and 14.1% for tPSAv, respectively. The concordance index for tPSA level was 0.771. Adding tPSAv, fPSA, % fPSA or velocities of fPSA and % fPSA did not importantly increase accuracy of tPSA to predict prostate cancer. Results were unchanged if the analysis was restricted to patients with advanced cancer at diagnosis. Conclusion Although PSA velocity is significantly increased in men with prostate cancer up to two decades before diagnosis, it does not aid long-term prediction of prostate cancer.
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| 13. |
- Ulmert, David, et al.
(författare)
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Prostate-specific antigen at or before age 50 as a predictor of advanced prostate cancer diagnosed up to 25 years later: A case-control study
- 2008
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Ingår i: BMC Medicine. - : Springer Science and Business Media LLC. - 1741-7015. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Background: Based on a large, representative unscreened cohort from Malmo, Sweden, we have recently reported that a single prostate-specific antigen (PSA) measurement at or before age 50 is a strong predictor of prostate cancer occurring up to 25 years subsequently. We aimed to determine whether this association holds for advanced cancers, defined as clinical stage T3 or higher, or skeletal metastasis at the time of the cancer diagnosis. Methods: In 1974-1986 blood samples were obtained from a cohort of 21,277 men aged up to 50. Through 1999, 498 men were diagnosed with prostate cancer, and of these 161 had locally advanced or metastatic prostate cancers. Three controls, matched for age and date of venipuncture, were selected for each case. Conditional logistic regression was used to test associations between molecular markers and advanced cancer. Results: Median time from venipuncture to diagnosis was 17 years. Levels of all PSA forms and hK2 were associated with case status. Total PSA was a strong and statistically significant predictor of subsequent advanced cancer ( area under the curve 0.791; p < 0.0005). Two-thirds of the advanced cancer cases occurred in men with the top 20% of PSA levels (0.9 ng/ml or higher). Conclusion: A single PSA test taken at or before age 50 is a very strong predictor of advanced prostate cancer diagnosed up to 25 years later. This suggests the possibility of using an early PSA test to risk-stratify patients so that men at highest risk are the focus of the most intensive screening efforts.
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| 14. |
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| 15. |
- Ulmert, David, et al.
(författare)
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Reproducibility and Accuracy of Measurements of Free and Total Prostate-Specific Antigen in Serum vs Plasma after Long-Term Storage at -20 {degrees}C.
- 2006
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Ingår i: Clinical Chemistry. - : Oxford University Press (OUP). - 0009-9147 .- 1530-8561. ; 52:2, s. 235-239
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Tidskriftsartikel (refereegranskat)abstract
- Background: Long-term frozen storage may alter the results of prostate-specific antigen (PSA) measurements, mainly because of degradation of free PSA (fPSA) in vitro. We compared the effects of long-term storage on fPSA, total PSA (tPSA), and complexed PSA (cPSA) in serum vs EDTA-plasma samples. Methods: We measured fPSA and tPSA concentrations in matched pairs of archival serum and EDTA-plasma samples (stored frozen at -20 degrees C for 20 years) from a large population-based cohort in Malmo, Sweden. We also compared concentrations in age-matched men with those in samples not subjected to long-term storage, obtained from participants in a population-based study of prostate cancer screening in Goteborg, Sweden. These contemporary samples were handled according to standardized preanalytical. and analytical protocols aimed at minimizing in vitro degradation. tPSA and fPSA measurements were performed with a commercial assay (Prostatus Dual Assay; Perkin-Elmer Life Sciences). Results: Concentrations of tPSA and fPSA and calculated cPSA (tPSA-fPSA) in archival plasma were not significantly different from those in contemporary serum from age-matched men. In archival serum, however, random variability of fPSA was higher vs plasma than in contemporary samples, whereas systematic error of fPSA analyses was similarly small in archival and contemporary serum and plasma. Conclusions: Concentrations of tPSA and calculated cPSA were highly stable in plasma and serum samples subjected to long-term storage at -20 degrees C. Greater random variability, rather than a systematic decrease, may explain differences in fPSA analyses observed in archival serum. (c) 2006 American Association for Clinical Chemistry.
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| 16. |
- van Kempen, Elise E.M.M., et al.
(författare)
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Children's annoyance reactions to aircraft and road traffic noise
- 2009
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Ingår i: Journal of the Acoustical Society of America. - : Acoustical Society of America. - 0001-4966 .- 1520-8524. ; 125:2, s. 895-904
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Tidskriftsartikel (refereegranskat)abstract
- Since annoyance reactions of children to environmental noise have rarely been investigated, no source specific exposure-response relations are available. The aim of this paper is to investigate children’s reactions to aircraft and road traffic noise and to derive exposure-response relations. To this end, children’s annoyance reactions to aircraft and road traffic noise in both the home and the school setting were investigated using the data gathered in a cross-sectional multicenter study, carried out among 2844 children age 9–11 years attending 89 primary schools around three European airports. An exposure-response relation was demonstrated between exposure to aircraft noise at school LAeq, 7–23 h and severe annoyance in children: after adjustment for confounders, the percentage severely annoyed children was predicted to increase from about 5.1% at 50 dB to about 12.1% at 60 dB. The findings were consistent across the three samples. Aircraft noise at home LAeq,7–23 h demonstrated a similar relation with severe annoyance. Children attending schools with higher road traffic noise LAeq,7–23 h were more annoyed. Although children were less annoyed at levels above 55 dB, the shapes of the exposure-response relations found among children were comparable to those found in their parents.
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