| 1. |
- Lu, Yingchang, et al.
(författare)
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Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians
- 2020
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association for Cancer Research. - 1055-9965 .- 1538-7755. ; 29:2, s. 477-486
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Tidskriftsartikel (refereegranskat)abstract
- Background: Risk variants identified so far for colorectal cancer explain only a small proportion of milial risk of this cancer, particularly in Asians.Methods: We performed a genome-wide association study (GWAS) of colorectal cancer in East Asians, cluding 23,572 colorectal cancer cases and 48,700 controls. To identify novel risk loci, we selected 60 omising risk variants for replication using data from 58,131 colorectal cancer cases and 67,347 controls European descent. To identify additional risk variants in known colorectal cancer loci, we performed nditional analyses in East Asians.Results: An indel variant, rs67052019 at 1p13.3, was found to be associated with colorectal cancer risk P = 3.9 x 10(-8) in Asians (OR per allele deletion = 1.13, 95% confidence interval = 1.08-1.18). This sociation was replicated in European descendants using a variant (rs2938616) in complete linkage sequilibrium with rs67052019 (P = 7.7 x 10(-3)). Of the remaining 59 variants, 12 showed an association P < 0.05 in the European-ancestry study, including rs11108175 and rs9634162 at P < 5 x 10(-8) and o variants with an association near the genome-wide significance level (rs60911071, P = 5.8 x 10(-8); 62558833, P = 7.5 x 10(-8)) in the combined analyses of Asian- and European-ancestry data. In addition, ing data from East Asians, we identified 13 new risk variants at 11 loci reported from previous GWAS.Conclusions: In this large GWAS, we identified three novel risk loci and two highly suggestive loci for lorectal cancer risk and provided evidence for potential roles of multiple genes and pathways in the iology of colorectal cancer. In addition, we showed that additional risk variants exist in many colorectal ncer risk loci identified previously.Impact: Our study provides novel data to improve the understanding of the genetic basis for colorectal ncer risk.
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| 2. |
- Song, Kai, 1988-, et al.
(författare)
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Improve the roles of nature reserves in conservation of endangered pheasant in a highly urbanized region
- 2020
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Nature reserves play an extraordinarily important role in conserving animal populations and their habitats. However, landscape change and unreasonable zoning designations often render these protected areas inadequate. Therefore, regular evaluation of the efficacy of protected lands is critical for maintaining and improving management strategies. Using species distribution models and GAP analysis, we assessed the changes in suitable habitat for the Brown Eared-pheasant (Crossoptilon mantchuricum) in two Chinese nature reserves between 1995 and 2013. Our results showed that the habitat suitability of Brown Eared-pheasant has changed dramatically during this period, and fragmentation analyses showed an increase in concentration area and decrease in patch area. In particular, our findings show that the national nature reserves need to adjust their ranges to ensure the conservation of this flagship species. Our study further provides a new viewpoint for evaluating the efficacy of protected lands, particularly in highly urbanized regions where conservation goals must be balanced with changing landscapes.
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| 3. |
- Sun, Sun, et al.
(författare)
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Mapping the obesity problems scale to the SF-6D : results based on the Scandinavian Obesity Surgery Registry (SOReg)
- 2023
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Ingår i: European Journal of Health Economics. - : Springer. - 1618-7598 .- 1618-7601. ; 24:2, s. 279-292
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Obesity Problem Scale (OP) is a widely applied instrument for obesity, however currently calculation of health utility based on OP is not feasible as it is not a preference-based measure. Using data from the Scandinavian Obesity Surgery Registry (SOReg), we sought to develop a mapping algorithm to estimate SF-6D utility from OP. Furthermore, to test whether the mapping algorithm is robust to the effect of surgery.METHOD: The source data SOReg (n = 36 706) contains both OP and SF-36, collected at pre-surgery and at 1, 2 and 5 years post-surgery. The Ordinary Least Square (OLS), beta-regression and Tobit regression were used to predict the SF-6D utility for different time points respectively. Besides the main effect model, different combinations of patient characteristics (age, sex, Body Mass Index, obesity-related comorbidities) were tested. Both internal validation (split-sample validation) and validation with testing the mapping algorithm on a dataset from other time points were carried out. A multi-stage model selection process was used, accessing model consistency, parsimony, goodness-of-fit and predictive accuracy. Models with the best performance were selected as the final mapping algorithms.RESULTS: The final mapping algorithms were based on OP summary score using OLS models, for pre- and post-surgery respectively. Mapping algorithms with different combinations of patients' characteristics were presented, to satisfy the user with a different need.CONCLUSION: This study makes available algorithms enabling crosswalk from the Obesity Problem Scale to the SF-6D utility. Different mapping algorithms are recommended for the mapping of pre- and post-operative data.
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| 4. |
- Sun, Sun, et al.
(författare)
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Prediction of quality-adjusted life years (QALYs) after bariatric surgery using regularized linear regression models : results from a Swedish nationwide quality register
- 2023
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Ingår i: Obesity Surgery. - : Springer. - 0960-8923 .- 1708-0428. ; 33:8, s. 2452-2462
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: To investigate whether the quality-adjusted life years (QALYs) of the patients who underwent bariatric surgery could be predicted using their baseline information.MATERIALS AND METHODS: All patients who received bariatric surgery in Sweden between January 1, 2011 and March 31, 2019 were obtained from the Scandinavian Obesity Surgery Registry (SOReg). Baseline information included patients' sociodemographic characteristics, details regarding the procedure, and postsurgical conditions. QALYs were assessed by the SF-6D at follow-up years 1 and 2. The general and regularized linear regression models were used to predict postoperative QALYs.RESULTS: All regression models demonstrated satisfactory and comparable performance in predicting QALYs at follow-up year 1, with R2 and relative root mean squared error (RRMSE) values of about 0.57 and 9.6%, respectively. The performance of the general linear regression model increased with the number of variables; however, the improvement was ignorable when the number of variables was more than 30 and 50 for follow-up years 1 and 2, respectively. Although minor L1 and L2 regularization provided better prediction ability, the improvement was negligible when the number of variables was more than 20. All the models showed poorer performance for predicting QALYs at follow-up year 2.CONCLUSIONS: Patient characteristics before bariatric surgery including health related quality of life, age, sex, BMI, postoperative complications within six weeks, and smoking status, may be adequate in predicting their postoperative QALYs after one year. Understanding these factors can help identify individuals who require more personalized and intensive support before, during, and after surgery.
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| 5. |
- Sun, Sun, et al.
(författare)
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Sequential Multiple Imputation for Real-World Health-Related Quality of Life Missing Data after Bariatric Surgery
- 2022
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Ingår i: International Journal of Environmental Research and Public Health. - : MDPI. - 1661-7827 .- 1660-4601. ; 19:17
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Tidskriftsartikel (refereegranskat)abstract
- One of the main challenges for the successful implementation of health-related quality of life (HRQoL) assessments is missing data. The current study examined the feasibility and validity of a sequential multiple imputation (MI) method to deal with missing values in the longitudinal HRQoL data from the Scandinavian Obesity Surgery Registry. All patients in the SOReg who received bariatric surgery between 1 January 2011 and 31 March 2019 (n = 47,653) were included for the descriptive analysis and missingness pattern exploration. The patients who had completed the short-form 36 (SF-36) at baseline (year 0), and one-, two-, and five-year follow-ups were included (n = 3957) for the missingness pattern simulation and the sequential MI analysis. Eleven items of the SF-36 were selected to create the six domains of SF-6D, and the SF-6D utility index of each patient was calculated accordingly. The multiply-imputed variables in previous year were used as input to impute the missing values in later years. The performance of the sequential MI was evaluated by comparing the actual values with the imputed values of the selected SF-36 items and index at all four time points. At the baseline and year 1, where missing proportions were about 20% and 40%, respectively, there were no statistically significant discrepancies between the distributions of the actual and imputed responses (all p-values > 0.05). In year 2, where the missing proportion was about 60%, distributions of the actual and imputed responses were consistent in 9 of the 11 SF-36 items. However, in year 5, where the missing proportion was about 80%, no consistency was found between the actual and imputed responses in any of the SF-36 items. Relatively high missing proportions in HRQoL data are common in clinical registries, which brings a challenge to analyzing the HRQoL of longitudinal cohorts. The experimental sequential multiple imputation method adopted in the current study might be an ideal strategy for handling missing data (even though the follow-up survey had a missing proportion of 60%), avoiding significant information waste in the multivariate analysis. However, the imputations for data with higher missing proportions warrant more research.
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| 6. |
- Sun, Sun, et al.
(författare)
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SF-6D Normative Values Among Patients Undergoing Bariatric Surgery : Results Based on Real-World Evidence from the Scandinavian Obesity Surgery Registry (SOReg)
- 2024
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Ingår i: Obesity Surgery. - : Springer. - 0960-8923 .- 1708-0428. ; 34:2, s. 558-567
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The SF-6D index can be used to calculate quality-adjusted life years in economic evaluations, which is required by reimbursement agencies and national advisory bodies, including the Swedish ones. However, despite that SF-36 has been largely applied among patients undergoing bariatric surgery, almost no study has accessed the short form six-dimensions (SF-6D) after bariatric surgery. AIM: To establish normative values for the SF-6D index among patients undergoing bariatric surgery.MATERIALS AND METHODS: All patients who received bariatric surgery in Sweden between 2011-01-01 and 2019-03-31 were obtained from the Scandinavian Obesity Surgery Registry (SOReg). Information includes patients' sociodemographic characteristics, details regarding the procedure, and postsurgical conditions. The SF-36 is applied at baseline and at follow-up years 1, 2, and 5. The multiple sequential imputation method was applied to handle missingness on SF-6D items. Based on the UK tariff, the SF-6D preference scores were calculated. The normative values for the mean (SD) SF-6D index were reported by timepoint and surgical complications for men and women, respectively. Multivariate analyses were applied to investigate how the SF-6D index is associated with timepoint, controlling for age, sex, BMI, and comorbidities in a stepwise manner.RESULTS: The SF-6D index increased at 1 year relative to baseline and was roughly maintained at the same level at 2 years. The normative value of the SF-6D index can be used in economic evaluations for bariatric surgery.
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| 7. |
- Vu Quynh, Mai, et al.
(författare)
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An EQ-5D-5L value set for Vietnam
- 2020
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Ingår i: Quality of Life Research. - : Springer Netherlands. - 0962-9343 .- 1573-2649. ; 29, s. 1923-1933
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: The objective of this study was to develop an EQ-5D-5L value set based on the health preferences of the general adult population of Vietnam.METHODS: The EQ-VT protocol version 2.1 was applied. Multi-stage stratified cluster sampling was employed to recruit a nationally representative sample. Both composite time trade-off (C-TTO) and discrete choice experiment (DCE) methods were used. Several modelling approaches were considered including hybrid; tobit; panel and heteroscedastic models. First, models using C-TTO or DCE data were tested separately. Then possibility of combining the C-TTO and DCE data was examined. Hybrid models were tested if it was sensible to combine both types of data. The best-performing model was selected based on both the consistency of the results produced and the degree to which models used all the available data.RESULTS: Data from 1200 respondents representing the general Vietnamese adult population were included in the analyses. Only the DCE Logit model and the regular Hybrid model that uses all available data produced consistent results. As the priority was to use all available data if possible, the hybrid model was selected to generate the Vietnamese value set. Mobility had the largest effect on health state values, followed by pain/discomfort, usual activities, anxiety/depression and self-care. The Vietnam values ranged from - 0.5115 to 1.CONCLUSION: This is the first value set for EQ-5D-5L based on social preferences obtained from a nationally representative sample in Vietnam. The value set will likely play a key role in economic evaluations and health technology assessments in Vietnam.
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| 8. |
- Akbari, Parsa, et al.
(författare)
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Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity
- 2021
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 373:6550
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale human exome sequencing can identify rare protein-coding variants with a large impact on complex traits such as body adiposity. We sequenced the exomes of 645,626 individuals from the United Kingdom, the United States, and Mexico and estimated associations of rare coding variants with body mass index (BMI). We identified 16 genes with an exome-wide significant association with BMI, including those encoding five brain-expressed G protein-coupled receptors (CALCR, MC4R, GIPR, GPR151, and GPR75). Protein-truncating variants in GPR75 were observed in ∼4/10,000 sequenced individuals and were associated with 1.8 kilograms per square meter lower BMI and 54% lower odds of obesity in the heterozygous state. Knock out of Gpr75 in mice resulted in resistance to weight gain and improved glycemic control in a high-fat diet model. Inhibition of GPR75 may provide a therapeutic strategy for obesity.
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| 9. |
- Ding, Shaozhen, et al.
(författare)
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novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:W1, s. W477-W487
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Tidskriftsartikel (refereegranskat)abstract
- To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/.
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| 10. |
- Han, Mengying, et al.
(författare)
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ChemHub: a knowledgebase of functional chemicals for synthetic biology studies
- 2021
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:22, s. 4275-4276
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Tidskriftsartikel (refereegranskat)abstract
- The field of synthetic biology lacks a comprehensive knowledgebase for selecting synthetic target molecules according to their functions, economic applications and known biosynthetic pathways. We implemented ChemHub, a knowledgebase containing >90 000 chemicals and their functions, along with related biosynthesis information for these chemicals that was manually extracted from >600 000 published studies by more than 100 people over the past 10 years.
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