| 1. |
- Champion, C., et al.
(författare)
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Dose point kernels in liquid water : An intra-comparison between GEANT4-DNA and a variety of Monte Carlo codes
- 2014
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Ingår i: Applied Radiation and Isotopes. - : Elsevier BV. - 0969-8043 .- 1872-9800. ; 83, s. 137-141
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Tidskriftsartikel (refereegranskat)abstract
- Modeling the radio-induced effects in biological medium still requires accurate physics models to describe the interactions induced by all the charged particles present in the irradiated medium in detail. These interactions include inelastic as well as elastic processes. To check the accuracy of the very low energy models recently implemented into the GEANT4 toolkit for modeling the electron slowing-down in liquid water, the simulation of electron dose point kernels remains the preferential test. In this context, we here report normalized radial dose profiles, for mono-energetic point sources, computed in liquid water by using the very low energy GEANT4-DNA physics processes available in the GEANT4 toolkit. In the present study, we report an extensive intra-comparison of profiles obtained by a large selection of existing and well-documented Monte-Carlo codes, namely, EGSnrc, PENELOPE, CPA100, FLUKA and MCNPX.
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| 2. |
- Demissie, Meaza, et al.
(författare)
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Unequal group variances in microarray data analyses
- 2008
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 24:9, s. 1168-1174
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: In searching for differentially expressed (DE) genes in microarray data, we often observe a fraction of the genes to have unequal variability between groups. This is not an issue in large samples, where a valid test exists that uses individual variances separately. The problem arises in the small-sample setting, where the approximately valid Welch test lacks sensitivity, while the more sensitive moderated t-test assumes equal variance. Methods: We introduce a moderated Welch test (MWT) that allows unequal variance between groups. It is based on (i) weighting of pooled and unpooled standard errors and (ii) improved estimation of the gene-level variance that exploits the information from across the genes. Results: When a non-trivial proportion of genes has unequal variability, false discovery rate (FDR) estimates based on the standard t and moderated t-tests are often too optimistic, while the standard Welch test has low sensitivity. The MWT is shown to (i) perform better than the standard t, the standard Welch and the moderated t-tests when the variances are unequal between groups and (ii) perform similarly to the moderated t, and better than the standard t and Welch tests when the group variances are equal. These results mean that MWT is more reliable than other existing tests over wider range of data conditions. Availability: R package to perform MWT is available at http://www.meb.ki.se/similar to yudpaw Contact: yudi.pawitan@ki.se Supplementary information: Supplementary data are available at Bioinformatics online.
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| 3. |
- Francis, Z., et al.
(författare)
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Molecular scale track structure simulations in liquid water using the Geant4-DNA Monte-Carlo processes
- 2011
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Ingår i: Applied Radiation and Isotopes. - : Elsevier BV. - 0969-8043 .- 1872-9800. ; 69:1, s. 220-226
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a study of energy deposits induced by ionising particles in liquid water at the molecular scale Particles track structures were generated using the Geant4-DNA processes of the Geant4 Monte-Carlo toolkit These processes cover electrons (0 025 eV-1 MeV) protons (1 keV-100 MeV) hydrogen atoms (1 keV-100 MeV) and alpha particles (10 keV-40 MeV) including their different charge states Electron ranges and lineal energies for protons were calculated in nanometric and micrometric volumes
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| 4. |
- Mascialino, Barbara, et al.
(författare)
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Meta-analysis of the prevalence of Leber hereditary optic neuropathy mtDNA mutations in Europe
- 2012
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Ingår i: European Journal of Ophthalmology. - : SAGE Publications. - 1120-6721 .- 1724-6016. ; 22:3, s. 461-465
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE. A meta-analysis was conducted to estimate the prevalence of patients with molecularly confirmed Leber hereditary optic neuropathy (LHON) carrying any of the 3 primary mtDNA mutations (m.11778G > A, m.14484T > C, m.3460G > A) which cause this inherited form of blindness. METHODS. A literature search was conducted to identify primary reports with LHON prevalence data reported for Europe. The overall prevalence of LHON with molecularly confirmed diagnosis was evaluated by weighting the prevalence estimates of the individual studies by the inverse of their variance. RESULTS. Based on this meta-analysis of 5 European studies providing appropriate information, the estimated prevalence of LHON disease associated with the combined m.11778G > A, m.14484T > C, m.3460G > A mutations was similar to 1:45,000 (2.23x10(-5); 95% confidence interval [CI] 2.01-2.44x10(-5)). Patients with LHON carrying either the m.11778G > A or the m.3460G > A mutation have a more severe clinical presentation and a much lower chance of spontaneous recovery from vision loss compared to patients with the m.14484T > C mutation. The estimated prevalence for patients with LHON in Europe carrying either of these severe mutations (m.11778G > A or m.3460G > A) was similar to 1:65,000 (1.54x10(-5); 95% CI 1.33-1.74x10(-5)). CONCLUSIONS. Although this meta-analysis summarizes the existing prevalence data for the primary, disease-causing mitochondrial DNA mutations of LHON in Europe, there is still a clear lack of reliable primary epidemiologic data for this devastating ophthalmologic disease.
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| 5. |
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| 6. |
- Savolainen, Johannes, et al.
(författare)
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Structured intervention plan including component-resolved diagnostics helps reducing the burden of food allergy among school-aged children
- 2019
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Ingår i: Pediatric Allergy and Immunology. - : WILEY. - 0905-6157 .- 1399-3038. ; 30:1, s. 99-106
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Tidskriftsartikel (refereegranskat)abstract
- Background Food allergies can substantially burden patients and families by negatively affecting finances, social relationships, and personal perceptions of health. This study was performed under the Finnish Allergy Programme aimed at reducing avoidance diets to foods in schoolchildren by 50%. The main goal of this study was to investigate how many children could be freed from diet restrictions in a Finnish school district through a diagnostic algorithm including component-resolved diagnostics and food challenge. The secondary aim was to provide a crude estimate of the burden of the elimination food diets in the region, and the savings associated with the proposed intervention. Methods A total of 205 children on a food avoidance diet according to the school register because of food allergy were invited into the study. One hundred and fifty-seven children were interviewed, tested for IgE to extracts and allergen components and food challenged in respective order. Results After two years, 12 children still had an avoidance diet and three of them were treated successfully with sOTI; the rest suspended their avoidance diet (n = 134) or dropped out of the study (n = 11). The cost of the elimination diets was estimated in 172 700euro per year at start and 13 200euro per year at the end of the study; total savings were 128 400euro yearly. Conclusions The results demonstrate a 65% reduction of avoidance diets to foods in school-aged children, exceeding the 50% aim of the Finnish Allergy Programme. Therefore, it is possible to actively reduce the number of food allergy diagnoses that remain unmonitored in the society through a tailored diagnostic work-up.
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