| 1. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 2. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 3. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 4. |
- Jacobs, Kevin B, et al.
(författare)
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Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
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Ingår i: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
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Tidskriftsartikel (refereegranskat)abstract
- In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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| 5. |
- Machiela, Mitchell J, et al.
(författare)
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Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
- 2016
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
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| 6. |
- Murawski, Christopher D., et al.
(författare)
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Terminology for osteochondral lesions of the ankle: proceedings of the International Consensus Meeting on Cartilage Repair of the Ankle
- 2022
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Ingår i: JOURNAL OF ISAKOS JOINT DISORDERS & ORTHOPAEDIC SPORTS MEDICINE. - : Elsevier BV. - 2059-7754 .- 2059-7762. ; 7:2, s. 62-66
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Tidskriftsartikel (refereegranskat)abstract
- Background: The evidence supporting best practice guidelines in the field of cartilage repair of the ankle is based on both low quality and low levels of evidence. Therefore, an international consensus group of experts was convened to collaboratively advance toward consensus opinions based on the best available evidence on key topics within cartilage repair of the ankle. The purpose of this article is to report the consensus statements on "terminology for osteochondral lesions of the ankle" developed at the 2019 International Consensus Meeting on Cartilage Repair of the Ankle. Methods: Forty-three international experts in cartilage repair of the ankle representing 20 countries were convened and participated in a process based on the Delphi method of achieving consensus. Questions and statements were drafted within four working groups focusing on specific topics within cartilage repair of the ankle, after which a comprehensive literature review was performed, and the available evidence for each state-ment was graded. Discussion and debate occurred in cases where statements were not agreed on in unanimous fashion within the working groups. A final vote was then held, and the strength of consensus was characterised as follows: consensus, 51%-74%; strong consensus, 75%-99%; unanimous, 100%. Results: A total of 11 statements on terminology and classification reached consensus during the 2019 Interna-tional Consensus Meeting on Cartilage Repair of the Ankle. Definitions are provided for osseous, chondral and osteochondral lesions, as well as bone marrow stimulation and injury chronicity, among others. An osteochondral lesion of the talus can be abbreviated as OLT. Conclusions: This international consensus derived from leaders in the field will assist clinicians with the appro-priate terminology for osteochondral lesions of the ankle.
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| 7. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 8. |
- Ulmert, David, et al.
(författare)
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A novel automated platform for quantifying the extent of skeletal tumour involvement in prostate cancer patients using the bone scan index
- 2012
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Ingår i: European Urology. - : Elsevier BV. - 0302-2838 .- 1873-7560. ; 62:1, s. 78-84
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is little consensus on a standard approach to analysing bone scan images. The Bone Scan Index (BSI) is predictive of survival in patients with progressive prostate cancer (PCa), but the popularity of this metric is hampered by the tedium of the manual calculation. Objective: Develop a fully automated method of quantifying the BSI and determining the clinical value of automated BSI measurements beyond conventional clinical and pathologic features. Design, setting, and participants: We conditioned a computer-assisted diagnosis system identifying metastatic lesions on a bone scan to automatically compute BSI measurements. A training group of 795 bone scans was used in the conditioning process. Independent validation of the method used bone scans obtained ≤3 mo from diagnosis of 384 PCa cases in two large population-based cohorts. An experienced analyser (blinded to case identity, prior BSI, and outcome) scored the BSI measurements twice. We measured prediction of outcome using pretreatment Gleason score, clinical stage, and prostate-specific antigen with models that also incorporated either manual or automated BSI measurements. Measurements: The agreement between methods was evaluated using Pearson's correlation coefficient. Discrimination between prognostic models was assessed using the concordance index (C-index). Results and limitations: Manual and automated BSI measurements were strongly correlated (ρ = 0.80), correlated more closely (ρ = 0.93) when excluding cases with BSI scores ≥10 (1.8%), and were independently associated with PCa death (p < 0.0001 for each) when added to the prediction model. Predictive accuracy of the base model (C-index: 0.768; 95% confidence interval [CI], 0.702-0.837) increased to 0.794 (95% CI, 0.727-0.860) by adding manual BSI scoring, and increased to 0.825 (95% CI, 0.754-0.881) by adding automated BSI scoring to the base model. Conclusions: Automated BSI scoring, with its 100% reproducibility, reduces turnaround time, eliminates operator-dependent subjectivity, and provides important clinical information comparable to that of manual BSI scoring. © 2012 European Association of Urology.
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| 9. |
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| 10. |
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| 11. |
- Olsson, Richard T., et al.
(författare)
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Controlled synthesis of near-stoichiometric cobalt ferrite nanoparticles
- 2005
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Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 17:20, s. 5109-5118
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Tidskriftsartikel (refereegranskat)abstract
- Large batches of more than 18 g of cobalt ferrite nanoparticles (CoxFe3-xO4, x being close to 1) have been prepared by the chemie douce approach using aqueous solutions of metal salts at 90 degrees C mixed with solutions of hydroxide ions under air atmosphere. By suitable choice of the metal ion to hydroxide ion ratio, it was possible to prepare nanoparticles with the stoichiometric composition (CoFe2O4). The composition and the density of the nanoparticles could be controlled by varying the metal ion to hydroxide ion molar ratio in the reactor. Adjusting the initial concentration ratios of the reactants prior to the mixing allowed the variation of the average size of the nanoparticles. The repeatability of the average particle diameter of the synthesis was typically 5 nm and average particle sizes could be controlled between 50 and 80 nm determined by nitrogen adsorption measurements (consistent with the number size average 35-60 mn obtained by transmission electron microscopy studies). Aging of the suspensions resulted in a narrowing of the initial broad unimodal distribution. The narrowing of the size distribution was associated with the phase transformation of delta-FeOOH platelets to spinel phase. The spinel nanoparticles had different morphologies: cubic, spherical, and occasionally irregular. Nanoparticles with the stoichiometric composition were a mixture of cubical and spherical shapes. Nanoparticles with less than the stoichiometric cobalt content had an irregular morphology, whereas nanoparticles with greater than the stoichiometric concentration of cobalt were predominantly spherical.
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| 12. |
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| 13. |
- Qadeer, Muhammad Ifran, et al.
(författare)
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High temperature magnetic properties of Sm-Co and Sm-Co/polyamide-12 materials : effects of temperature, particle size, and silanization
- 2013
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Ingår i: Journal of Materials Science. - : Springer Science and Business Media LLC. - 0022-2461 .- 1573-4803. ; 48:23, s. 8163-8170
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Tidskriftsartikel (refereegranskat)abstract
- There is an increasing demand for polymer-bonded magnets (PBM) in high temperature applications. While most research deals with high temperature properties of NdFeB-PBM, only a few studies consider Sm-Co PBM. Therefore, this study, on the thermal and magnetic properties of Sm-Co alloy powders and blends of these with polyamide-12 (PA12), was undertaken. Since the Sm-Co powders were the product of ball milling, they contained a variety of shapes and sizes. Studies on size fractions of these showed that the thermal stability and magnetic properties were improved as the particle size increased. It was suggested that higher residual strains and smaller crystallite sizes in the small particles were responsible for a decrease in the thermal stability and magnetic properties. In addition, energy dispersive X-ray spectroscopy revealed that the oxygen content increased with decreasing particle size (larger specific surface area) and higher oxygen content was possibly also responsible for a decrease in the magnetic properties. It was shown that, in general, the surface modification by silanization, using (3-aminopropyl)trimethoxsilane, increased the saturation magnetization and remanence of both the particles and the Sm-Co/PA12 composite. The silanization also improved the thermal stability of the particles.
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| 14. |
- Qadeer, Muhammad Ifran, et al.
(författare)
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Improved oxidation resistance of SmCo magnetic alloy powders by silanization
- 2013
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Ingår i: Progress in organic coatings. - : Elsevier BV. - 0300-9440 .- 1873-331X. ; 76:1, s. 94-100
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Forskningsöversikt (refereegranskat)abstract
- The thermal stability of Sm2Co17 powders coated with four different silanes was studied between 25 degrees C and 500 degrees C and isothermally at 400 degrees C. Thermogravimetry data indicated that the silane-based coatings provided improved oxidation resistance. The microstructural analysis of uncoated powders oxidized for 10 h at 400 degrees C revealed the formation of a featureless ca. 10 mu m thick shell, surrounding the unreacted core. The development of this shell was attributed to the inward diffusion of oxygen, decomposition of intermetallic phases and redistribution of alloying elements. The EDS elemental maps revealed that the shell was rich in O, Fe and Co, and depleted in Sm, Zr and Cu. In the presence of the silane-based coatings the thickness of the shell was reduced by more than 80% (to less than 2 mu m) and the redistribution of alloying elements was insignificant. Based on the thermogravimetric analysis at or above ca. 400 degrees C and the nnicrostructural analysis it was possible to assess the relative effectivity of the different silanes in preventing the oxidation of the SmCo powder. Methyltrimethoxysilane (MTMS), which also formed the thinnest coating, was the best silane. (3-Glycidyloxypropyl)trimethoxysilane, forming a thicker coating, was less effective than MTMS, but superior to the two amine-functionalized silanes ((3-aminopropyl)triethoxysilane and (3-aminopropyl)trimethoxysilane).
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| 15. |
- Qadeer, Muhammad I., et al.
(författare)
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Rheological and dynamic mechanical properties of polymer-bonded magnets based on Sm2Co17 and polyamide-12
- 2014
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Ingår i: Journal of Materials Science. - : Springer Science and Business Media LLC. - 0022-2461 .- 1573-4803. ; 49:21, s. 7529-7538
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Tidskriftsartikel (refereegranskat)abstract
- The rheological and dynamic mechanical properties of polymer-based composites of Sm2Co17 and polyamide-12 with different particle loadings, sizes, and surface treatments are reported. Sm2Co17 particles were surface-treated with three different silanes: 3-glycidoxy(propyl)trimethoxysilane, 3-amino(propyl)trimethoxysilane (APTMS), and methyltrimethoxysilane (MTMS). It was shown, for the composites with untreated particles, that the viscosity and storage modulus increased with increasing filler content (0-60 vol%) and decreasing filler particle size. In addition, the glass transition temperature increased significantly and the damping decreased with increasing filler content. Of the silanes, the MTMS, which yielded only a thin surface layer, had in general the least effect on the rheological properties of the composite. The composite containing the APTMS-coated filler showed the highest storage modulus. The results give new insights on how to prepare polymer-bonded magnets with optimal process conditions (rheology) and dynamic mechanical properties, by varying the amount of particles, their size, and surface treatment.
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| 16. |
- Qadeer, Muhammad Ifran, et al.
(författare)
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The Effect of Silanisation on Microstructural Stability and Magnetic Properties of the Intermetallic Sm2(Co, Fe, Cu, Zr)17
- 2011
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Ingår i: Materials Research Society Symposium Proceedings. - : Springer Science and Business Media LLC. - 0272-9172 .- 1946-4274. ; 1295, s. 443-448
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Tidskriftsartikel (refereegranskat)abstract
- The effects of silanising using the coupling agent γ-glycidoxpropyltrimethoxysilane on microstructural stability and magnetic properties of Sm-Co powder particles have been investigated. The silanisation provides structural stability by improving the oxidation resistance at 400oC for 10 hours. The untreated particles undergo microchemical changes by redistribution of alloying elements which mainly accumulate in parallel black and grey streaks in the interior of the particles. The silanised particles after heat treatment show coercivity of 836 Oe and the untreated particles show a much lower coercivity of 376 Oe. The difference in magnetic properties of uncoated particles is caused by diffusion of oxygen and microstructural instability.
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| 17. |
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