| 1. |
- Field, Dawn, et al.
(author)
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The minimum information about a genome sequence (MIGS) specification.
- 2008
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In: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 26:5, s. 541-7
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Journal article (peer-reviewed)abstract
- With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.
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| 2. |
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| 3. |
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| 4. |
- Allen, P Danny, et al.
(author)
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Detecting reduced bone mineral density from dental radiographs using statistical shape models
- 2007
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In: IEEE transactions on information technology in biomedicine. - : Institute of Electrical and Electronics Engineers (IEEE). - 1089-7771 .- 1558-0032. ; 11:6, s. 601-610
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Journal article (peer-reviewed)abstract
- We describe a novel method of estimating reduced bone mineral density (BMD) from dental panoramic tomograms (DPTs), which show the entire mandible. Careful expert width measurement of the inferior mandibular cortex has been shown to be predictive of BMD in hip and spine osteopenia and osteoporosis. We have implemented a method of automatic measurement of the width by active shape model search, using as training data 132 DPTs of female subjects whose BMD has been established by dual-energy X-ray absorptiometry. We demonstrate that widths measured after fully automatic search are significantly correlated with BMD, and exhibit less variability than manual measurements made by different experts. The correlation is highest towards the lateral region of the mandible, in a position different from that previously employed for manual width measurement. An receiver-operator characterstic (ROC) analysis for identifying osteopenia (T < -1: BMD more than one standard deviation below that of young healthy females) gives an area under curve (AUC) value of 0.64. Using a minimal interaction to initiate active shape model (ASM) search, the measurement can be made at the optimum region of the mandible, resulting in an AUC value of 0.71. Using an independent test set, AUC for detection of osteoporosis (T < -2.5) is 0.81.
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| 5. |
- Allen, Peter M., et al.
(author)
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Aberration control and vision training as an effective means of improving accommodation in individuals with myopia.
- 2009
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In: Investigative Ophthalmology and Visual Science. - : Association for Research in Vision and Ophthalmology (ARVO). - 0146-0404 .- 1552-5783. ; 50:11, s. 5120-5129
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Journal article (peer-reviewed)abstract
- PURPOSE: To test the efficacy of a novel dual treatment for improving accommodative accuracy and dynamics in young persons with myopia.METHODS: Ninety-three young persons with myopia (mean spherical equivalent, -3.0 +/- 1.8 D; age 16.8 +/- 2.1 years; spherical aberration +0.06 +/- 0.04 microm) participated in the study. Custom-designed soft contact lenses were used to alter ocular SA to -0.10 microm to improve accommodative accuracy and reduce any lag of accommodation. A vision training regimen was performed for 18 minutes per day for up to 6 weeks to improve speed of dynamic accommodation. Control groups had contact lenses with no added SA and/or no exercises. To avoid any effects of natural levels of negative aberration on the results of the study, all participants who had negative SA were excluded.RESULTS: The treatment contact lenses produced a significant reduction in lag of accommodation (P < 0.05) at all proximal viewing distances measured. The vision training measurement and treatment resulted in a significant increase in distance facility rate for all groups compared with their own baselines (P < 0.05). Near facility rate improved in the vision training treatment group only compared with its baseline (P < 0.05). Both positive and negative response times for distant viewing were significantly shorter in all groups after training compared with their baseline values (P < 0.05). At near, the positive response times were decreased significantly (P < 0.05) in both groups, whereas the negative response times decreased significantly only in the vision training treatment group.CONCLUSIONS: After 3 months, the dual treatments (altering SA and vision training) used in the study were effective in modifying accommodation. The static accommodative response to targets at proximal distances was increased by the altered SA contact lenses and rates of dynamic accommodation improved with vision training.
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| 6. |
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| 7. |
- Devlin, Hugh, et al.
(author)
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Automated osteoporosis risk assessment by dentists : a new pathway to diagnosis
- 2007
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In: Bone. - : Elsevier BV. - 8756-3282 .- 1873-2763. ; 40:4, s. 835-842
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Journal article (peer-reviewed)abstract
- General dental practitioners use a vast amount of panoramic radiography in their routine clinical work, but valuable information about patients' osteoporotic status is not collected. There are many reasons for this, but one of the prime reasons must be the disruption involved in clinical routine with lengthy manual radiographic assessment. We have developed computer software, based on active shape modeling that will automatically detect the mandibular cortex on panoramic radiographs, and then measure its width. Automatic or semi-automatic measurement of the cortical width will indicate the osteoporotic risk of the patient. The aim of our work was to assess the computer search technique's ability to measure the mandibular cortical width and to assess its potential for detection of osteoporosis of the hip, spine and femoral neck. Mandibular cortical width was measured using the manually initialized (semi-automatic) method and, when assessed for diagnosing osteoporosis at one of the three measurement sites, gave an area under the ROC curve (A(z))=0.816 (95% CI=0.784 to 0.845) and for the automatically initialized searches, A(z)=0.759 (95% CI=0.724 to 0.791). The difference between areas=0.057 (95% Confidence interval=0.025 to 0.089), p<0.0001. For diagnosing osteoporosis at the femoral neck, mandibular cortical width derived from the manually initialized fit gave an area under the ROC curve (A(z))=0.835 (95% CI=0.805 to 0.863) and for the automatically initialized searches A(z)=0.805 (95% CI=0.773 to 0.835). The difference in A(z) values between active shape modeling search methods=0.030 (95% CI=-0.010 to 0.070), and this was not significant, p=0.138. We concluded that measurement of mandibular cortical width using active shape modeling is capable of diagnosing skeletal osteoporosis with good diagnostic ability and repeatability. PMID: 17188590 [PubMed - indexed for MEDLINE]
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| 8. |
- Devlin, Hugh, et al.
(author)
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The role of the dental surgeon in detecting osteoporosis : the OSTEODENT study
- 2008
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In: British Dental Journal. - : Springer Science and Business Media LLC. - 0007-0610 .- 1476-5373. ; 204:10
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Journal article (pop. science, debate, etc.)abstract
- OBJECTIVE: To determine if thinning (<3 mm width) of the lower cortical border of the mandible on dental panoramic radiographs, as well as other clinical risk factors, may provide a useful diagnostic test for osteoporosis in young postmenopausal women. DESIGN: Six hundred and fifty-two subjects (age range 45-70 years) were involved in this multi-centre, cross-sectional study. SETTING: Patients were recruited from centres in Leuven (Belgium), Athens (Greece), Manchester (UK), and Malmo (Sweden). SUBJECTS AND METHODS: The subject's age, body weight, whether the patient took hormone replacement therapy or had a history of low trauma fracture were used to form a clinical osteoporosis risk assessment (the OSteoporosis Index of RISk or OSIRIS index). Each patient also received a dental panoramic radiographic examination. RESULTS: One hundred and forty subjects had osteoporosis involving at least one of the measurement sites (lumbar spine, femoral neck or total hip). Those with osteoporosis tended to have a low OSIRIS score and a thinned cortical mandibular border. The area under the ROC curve for using both cortical width and OSIRIS to predict osteoporosis was 0.90 (95% CI = 0.87 to 0.92). There was a significant improvement in the diagnostic ability of the combined OSIRIS and cortical width test over both tests applied separately (p <0.001). The cost effectiveness of the cortical width and OSIRIS model was improved by using a high specificity threshold rather than high sensitivity. However, this analysis ignores the costs associated with missed cases of osteoporosis. CONCLUSION: Dentists have a role to play in the detection and referral of patients at high risk of osteoporosis.
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| 9. |
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| 10. |
- Johansson, Mattias, et al.
(author)
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Circulating concentrations of folate and vitamin B12 in relation to prostate cancer risk : results from the European prospective investigation into cancer and nutrition study
- 2008
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In: Cancer Epidemiol Biomarkers Prev. - 1055-9965. ; 17:2, s. 279-285
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Journal article (peer-reviewed)abstract
- Background: Determinants of one-carbon metabolism, such as folate and vitamin B12, have been implicated in cancer development. Previous studies have not provided conclusive evidence for the importance of circulating concentrations of folate and vitamin B12 in prostate cancer etiology. The aim of the present study was to investigate the relationship between prostate cancer risk and circulating concentrations of folate and vitamin B12 in a large prospective cohort. Methods: We analyzed circulating concentrations of folate and vitamin B12 in 869 cases and 1,174 controls, individually matched on center, age, and date of recruitment, nested within the European Prospective Investigation into Cancer and Nutrition cohort. Relative risks (RR) for prostate cancer were estimated using conditional logistic regression models. Results: Overall, no significant associations were observed for circulating concentrations of folate (Ptrend = 0.62) or vitamin B12 (Ptrend = 0.21) with prostate cancer risk. RRs for a doubling in folate and vitamin B12 concentrations were 1.03 [95% confidence interval (95% CI), 0.92-1.16] and 1.12 (95% CI, 0.94-1.35), respectively. In the subgroup of cases diagnosed with advanced stage prostate cancer, elevated concentrations of vitamin B12 were associated with increased risk (RR for a doubling in concentration, 1.69; 95% CI, 1.05-2.72, Ptrend = 0.03). No other subgroup analyses resulted in a statistically significant association. Conclusion: This study does not provide strong support for an association between prostate cancer risk and circulating concentrations of folate or vitamin B12. Elevated concentrations of vitamin B12 may be associated with an increased risk for advanced stage prostate cancer, but this association requires examination in other large prospective studies. (Cancer Epidemiol Biomarkers Prev 2007;17(2):279–85)
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| 11. |
- Nicopoulou-Karayianni, Kety, et al.
(author)
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Tooth loss and osteoporosis : the OSTEODENT Study
- 2009
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In: Journal of Clinical Periodontology. - 0303-6979 .- 1600-051X. ; 36:3, s. 190-197
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Journal article (peer-reviewed)abstract
- AIM: To determine the cross-sectional association of the osteoporotic status of patients with the number of their teeth, with and without taking into account age and/or smoking. MATERIAL & METHODS: At four centres, the study recruited 665 females aged 45-70 years and the number of teeth was counted for 651 subjects. Bone density was measured at the total hip, femoral neck and lumbar spine. RESULTS: The mean number of teeth in the osteoporotic subjects was 3.3 fewer than normal subjects and 2.1 fewer if those with no teeth were excluded. The association between osteoporosis and having 0, three clusters were identified corresponding to different degrees of tooth loss. The overall effect of osteoporosis was as follows: -1.8 teeth before and after adjusting for smoking, -1.2 teeth after adjusting for age, and -1.1 teeth after adjusting for both age and smoking. CONCLUSIONS: We have established a significant association between osteoporosis and tooth loss after adjusting the effect for age and smoking.
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| 12. |
- Nieters, Alexandra, et al.
(author)
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Smoking and lymphoma risk in the european prospective investigation into cancer and nutrition
- 2008
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In: American Journal of Epidemiology. - : Oxford University Press (OUP). - 0002-9262 .- 1476-6256. ; 167:9, s. 1081-1089
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Journal article (peer-reviewed)abstract
- Lymphomas are one of the few cancers that have been increasing in incidence over the past decades. So far, only a few established risk factors have been identified, including immunosuppression and viral infections. Recent evidence suggests etiologic heterogeneity of different lymphoma subtypes. Smoking may affect risk differently, depending on the lymphoma entity. The European Prospective Investigation into Cancer and Nutrition was used to study the role of smoking in the etiology of lymphomas and individual subtypes within a prospective study. Information on baseline and lifetime tobacco smoking by 478,590 participants was collected between 1992 and 2000. Cox proportional hazards regression was used to calculate multivariate-adjusted hazard ratios and 95% confidence intervals. During 3,567,410 person-years of follow-up, 1,371 lymphoma cases (1,304 non-Hodgkin's lymphomas and 67 Hodgkin's lymphomas) were identified. Relative risk for smokers at recruitment was more than twofold higher for Hodgkin's lymphoma (hazard ratio = 2.14, 95% confidence interval: 1.18, 3.87) but was not elevated for non-Hodgkin's lymphoma (hazard ratio = 1.06, 95% confidence interval: 0.94, 1.19) and individual B-cell non-Hodgkin's lymphoma subtypes. In this prospective study, smoking appeared to increase Hodgkin's lymphoma risk consistently in both genders, whereas B-cell non-Hodgkin's lymphoma risk was not associated. Future analysis should involve viral biomarkers and genetic susceptibility markers to elucidate potential mechanisms of smoking-induced carcinogenesis, particularly for Hodgkin's lymphoma.
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| 13. |
- Poole, Jill A., et al.
(author)
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Repetitive organic dust exposure in vitro impairs macrophage differentiation and function
- 2008
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In: Journal of Allergy and Clinical Immunology. - : Elsevier BV. - 1097-6825 .- 0091-6749. ; 122:2, s. 375-382
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Journal article (peer-reviewed)abstract
- Organic dust exposure in the agricultural industry results in significant airway disease and lung function decrease. Mononuclear phagocytes are key cells that mediate the inflammatory and innate immune response after dust exposure. Objective: We sought to investigate the effect of organic dust extract (ODE) from modern swine operations on monocyte-derived macrophage (MDM) phenotype and function. Methods: Peripheral blood monocytes were obtained by means of elutriation methodology (> 99% CD14(+)) and differentiated into macrophages in the presence of GM-CSF (1 week) with and without ODE (0.1 %). At 1 week, cells were analyzed by means of flow cytometry for cell-surface marker expression (HLA-DR, CD80, CD86, Toll-like receptor 2, Toll-like receptor 4, mCD14, and CD16), phagocytosis (IgG-opsonized zymosan particles), and intracellular killing of Streptococcus pneumoniae. At 1 week, MDMs were rechallenged with high-dose ODE (1%), LPS, and peptidoglycan (PGN), and cytokine levels TNF-alpha, IL-6, IL-10, and CXCL8/IL-8) were measured. Comparisons were made to MDMs conditioned with heat-inactivated dust, endotoxin-depleted dust, LPS, and PGN to elucidate ODE-associated factors. Results: Expression of HLA-DR, CD80, and CD86; phagocytosis; and intracellular bacterial killing were significantly decreased with ODE-challenged versus control MDMs. Responses were retained after marked depletion of endotoxin. PGN, LPS, and PGN plus LPS significantly reduced MDM surface marker expression and, except for LPS alone, also reduced phagocytosis. ODE-challenged MDMs had significantly diminished cytokine responses (TNF-alpha, IL-6, and IL-10) after repeat challenge with high-dose ODE. Cross-tolerant cytokine responses were also observed. Conclusion: Repetitive organic dust exposure significantly decreases markers of antigen presentation and host defense function in MDMs. Bacterial cell components appear to be driving these impaired responses.
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| 15. |
- Schael, S, et al.
(author)
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Precision electroweak measurements on the Z resonance
- 2006
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In: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454
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Research review (peer-reviewed)abstract
- We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
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| 16. |
- Suzuki, Reiko, et al.
(author)
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A prospective analysis of the association between dietary fiber intake and prostate cancer risk in EPIC
- 2009
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In: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 124:1, s. 245-249
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Journal article (peer-reviewed)abstract
- Few studies have examined the association between dietary fiber intake and prostate cancer risk. We evaluated the association between dietary fiber intake and the risk of prostate cancer among 142,590 men in the European Prospective Investigation into Cancer and Nutrition (EPIC). Consumption of dietary fiber (total, cereal, fruit and vegetable fiber) seas estimated by validated dietary questionnaires and calibrated using 24-hr dietary recalls. Incidence rate ratios were estimated using Cox regression and adjusted for potential confounding factors. During all average of 8.7 years follow-up, prostate cancer was diagnosed in 2,747 men. Overall, there was no association between dietary fiber intake (total, cereal, fruit or vegetable fiber) and prostate cancer risk, although calibrated intakes of total fiber and fruit fiber were associated with nonstatistically significant reductions in risk. There was no association between fiber derived from cereals or vegetables and risk and no evidence for heterogeneity in any of the risk estimates by stage or grade of disease. Our results suggest that dietary fiber intake is not associated with prostate cancer risk. (C) 2008 Wiley-Liss, Inc.
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| 17. |
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| 18. |
- Travis, Ruth C, et al.
(author)
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Serum vitamin D and risk of prostate cancer in a case-control analysis nested within the European Prospective Investigation into Cancer and Nutrition (EPIC).
- 2009
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In: American Journal of Epidemiology. - : Oxford University Press (OUP). - 0002-9262 .- 1476-6256. ; 169:10, s. 1223-1232
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Journal article (peer-reviewed)abstract
- Results from the majority of studies show little association between circulating concentrations of vitamin D and prostate cancer risk, a finding that has not been demonstrated in a wider European population, however. The authors examined whether vitamin D concentrations were associated with prostate cancer risk in a case-control study nested within the European Prospective Investigation into Cancer and Nutrition (1994-2000). Serum concentrations of 25-hydroxyvitamin D were measured in 652 prostate cancer cases matched to 752 controls from 7 European countries after a median follow-up time of 4.1 years. Conditional logistic regression models were used to calculate odds ratios for prostate cancer risk in relation to serum 25-hydroxyvitamin D after standardizing for month of blood collection and adjusting for covariates. No significant association was found between 25-hydroxyvitamin D and risk of prostate cancer (highest vs. lowest quintile: odds ratio = 1.28, 95% confidence interval: 0.88, 1.88; P for trend = 0.188). Subgroup analyses showed no significant heterogeneity by cancer stage or grade, age at diagnosis, body mass index, time from blood collection to diagnosis, or calcium intake. In summary, the results of this large nested case-control study provide no evidence in support of a protective effect of circulating concentrations of vitamin D on the risk of prostate cancer.
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