| 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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| 11. |
- Holmberg, Carl Jacob, et al.
(författare)
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The efficacy of immune checkpoint blockade for melanoma in-transit with or without nodal metastases - A multicenter cohort study
- 2022
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Ingår i: EUROPEAN JOURNAL OF CANCER. - : Elsevier BV. - 0959-8049 .- 1879-0852. ; 40:16
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Guidelines addressing melanoma in-transit metastasis (ITM) recommend immune checkpoint inhibitors (ICI) as a first-line treatment option, despite the fact that there are no efficacy data available from prospective trials for exclusively ITM disease. The study aims to analyze the outcome of patients with ITM treated with ICI based on data from a large cohort of patients treated at international referral clinics. Methods: A multicenter retrospective cohort study of patients treated between January 2015 and December 2020 from Australia, Europe, and the USA, evaluating treatment with ICI for ITM with or without nodal involvement (AJCC8 N1c, N2c, and N3c) and without distant disease (M0). Treatment was with PD-1 inhibitor (nivolumab or pembrolizumab) and/or CTLA-4 inhibitor (ipilimumab). The response was evaluated according to the RECIST criteria modified for cutaneous lesions. Results: A total of 287 patients from 21 institutions in eight countries were included. Immunotherapy was first-line treatment in 64 (22%) patients. PD-1 or CTLA-4 inhibitor monotherapy was given in 233 (81%) and 23 (8%) patients, respectively, while 31 (11%) received both in combination. The overall response rate was 56%, complete response (CR) rate was 36%, and progressive disease (PD) rate was 32%. Median PFS was ten months (95% CI 7.4-12.6 months) with a one-, two-, and five-year PFS rate of 48%, 33%, and 18%, respectively. Median MSS was not reached, and the one-, two-, and five-year MSS rates were 95%, 83%, and 71%, respectively. Conclusion: Systemic immunotherapy is an effective treatment for melanoma ITM. Future studies should evaluate the role of systemic immunotherapy in the context of multimodality therapy, including locoregional treatments such as surgery, intralesional therapy, and regional therapies.
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| 12. |
- Hu, Zhipeng, et al.
(författare)
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Wideband High-Reflection Chiral Dielectric Metasurface
- 2021
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Ingår i: Progress In Electromagnetics Research. - : EMW PUBLISHING. - 1070-4698 .- 1559-8985. ; 172, s. 51-60
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Tidskriftsartikel (refereegranskat)abstract
- Compared to natural materials, artificial subwavelength structures can enhance chiroptical effects in a stronger way, and the requirement of low material loss and wideband operation is desired in many situations. Here, we propose an all-dielectric chiral metasurface as a periodic array of centrosymmetric staggered silicon cuboid pairs to achieve strong circular dichroism in a wide band. As a demonstration, the designed chiral metasurface may strongly reflect the chosen circularly polarized light with the spin preserved in the operating wavelength range of 1.51 ti 1.60 mu m while highly transmit (with an efficiency greater than 95%) the opposite circularly polarized light with the spin flipped. Then, two application cases are given for the designed chiral metasurface. A flat chiral meta-lens is constructed to produce wideband focusing in the transmission/reflection side while the disturbing from the opposite circular polarization is well blocked by high reflection/transmission. A chiral Fabry-Perot cavity is also constructed, which has an extremely high quality factor (2.1E4). The proposed method provides an efficient way to produce strong chiroptical effects and has a promising potential for various applications such as signal processing, sensing, radiation and detection.
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| 13. |
- Li, Xinxuan, et al.
(författare)
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Genetically predicted high IGF-1 levels showed protective effects on COVID-19 susceptibility and hospitalization : a Mendelian randomisation study with data from 60 studies across 25 countries
- 2022
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Epidemiological studies observed gender differences in COVID-19 outcomes, however, whether sex hormone plays a causal in COVID-19 risk remains unclear. This study aimed to examine associations of sex hormone, sex hormones-binding globulin (SHBG), insulin-like growth factor-1 (IGF-1), and COVID-19 risk. Methods: Two-sample Mendelian randomization (TSMR) study was performed to explore the causal associations between testosterone, estrogen, SHBG, IGF-1, and the risk of COVID-19 (susceptibility, hospitalization, and severity) using genome-wide association study (GWAS) summary level data from the COVID-19 Host Genetics Initiative (N=1,348,701). Random-effects inverse variance weighted (IVW) MR approach was used as the primary MR method and the weighted median, MR-Egger, and MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO) test were conducted as sensitivity analyses. Results: Higher genetically predicted IGF-1 levels have nominally significant association with reduced risk of COVID-19 susceptibility and hospitalization. For one standard deviation increase in genetically predicted IGF-1 levels, the odds ratio was 0.77 (95% confidence interval [CI], 0.61-0.97, p=0.027) for COVID-19 susceptibility, 0.62 (95% CI: 0.25-0.51, p=0.018) for COVID-19 hospitalization, and 0.85 (95% CI: 0.52-1.38, p=0.513) for COVID-19 severity. There was no evidence that testosterone, estrogen, and SHBG are associated with the risk of COVID-19 susceptibility, hospitalization, and severity in either overall or sex-stratified TSMR analysis. Conclusions: Our study indicated that genetically predicted high IGF-1 levels were associated with decrease the risk of COVID-19 susceptibility and hospitalization, but these associations did not survive the Bonferroni correction of multiple testing. Further studies are needed to validate the findings and explore whether IGF-1 could be a potential intervention target to reduce COVID-19 risk.
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| 14. |
- Luo, Yifei, et al.
(författare)
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Technology Roadmap for Flexible Sensors
- 2023
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Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
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Forskningsöversikt (refereegranskat)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 15. |
- Ning, Zhongrui, et al.
(författare)
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Wetter trend in source region of Yangtze River by runoff simulating based on Grid-RCCC-WBM
- 2024
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Ingår i: Journal of Hydrology. - 0022-1694. ; 631
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Tidskriftsartikel (refereegranskat)abstract
- Exploring the future hydroclimatic conditions of source region of Yangtze River (SRYaR), an alpine affected by climate change significantly, is essential for basin water resources management and development ss global climate change intensifies and the process of climate warming and humidification in Northwest China. This study proposed a practical framework for assessing water resource response to the context of climate changes in alpine catchments from the respective of both runoff and hydroclimatic conditions. Utilizing Grid-RCCC-WBM driven by corrected climatic forcing from the global climate models, this study estimate the prospective overall warmer and wetter pattern in the source region of Yangtze River. The key results indicated that: (1) Under all future scenarios, both temperature and precipitation within the catchment exhibit a significant upward trend. Projections from multi-model ensembles (MME) suggest that during the mid-term period (2041–2060, MT), temperatures are expected to rise by [0.74 °C, 3.08 °C] compared to the baseline period (1995–2014), with precipitation changes ranging from [4.8%, 21.4%]. (2) Future runoff within the catchment exhibits a consistent increase, with a linear trend rate of 1.1 mm/decade. runoff changes in MT compared to the baseline period vary from [−5.1%, 33.7%]. Runoff decreases in the northern part of the catchment, while notable increases occur in the southeastern and western regions. (3) In the future, the ratio of catchment evaporation capacity to precipitation decreases in comparison to the baseline period with an augmentation in soil moisture, enhancing its capacity for water retention and reducing the conversion of precipitation to evaporation, resulting a wetting trend of the catchment. (4) The future snowpack in the catchment continues to decrease, with a significant reduction in both the proportion of snowfall relative to total precipitation and the proportion of snowmelt runoff relative to total runoff, the risk of water resources crisis in the watershed is escalating.
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| 16. |
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| 17. |
- Sun, Jinghao, et al.
(författare)
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Capacity Augmentation Function for Real-Time Parallel Tasks With Constrained Deadlines Under GEDF Scheduling
- 2020
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Ingår i: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0070 .- 1937-4151. ; 39:12, s. 4537-4548
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Tidskriftsartikel (refereegranskat)abstract
- Capacity augmentation bound (CAB) is a widely used quantitative metric in theoretical analysis for directed acyclic graph (DAG) parallel real-time tasks, which reveals the key factors the schedulability of DAG tasks heavily depending on: the normalized utilization (the ratio of the total utilization to the core numbers) and the tensity (the maximum ratio of task's longest path length to task's deadline). However, CAB requires both factors of a schedulable task system to be capped by the same threshold. A task system with a normalized utilization slightly larger than that threshold but very small tensity, or very smaller normalized utilization but slightly larger than that threshold has good chance to be scheduled are both denied by CAB. To this end, we propose a new concept called capacity augmentation function (CAF) to better characterize the schedulability of parallel real-time tasks, which provides a more loose and different threshold for both factors. In particular, we derive a CAF-based linear-time schedulability test for real-time constrained-deadline DAG tasks under global EDF, which entirely dominates the state-of-the-art CAB-based test for constrained-deadline settings. Finally, we conduct experiments to compare the acceptance ratio of our CAF-based test with the existing schedulability tests also having linear-time complexity. The results show that CAF-based test significantly outperforms the existing linear-time schedulability test under different parameter settings.
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| 18. |
- Sun, Jinghao, et al.
(författare)
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On Computing Exact WCRT for DAG Tasks
- 2020
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Ingår i: 57th ACM/IEEE Design Automation Conference, DAC 2020, San Francisco, CA, USA, July 20-24, 2020. - : IEEE. - 9781728110851 ; , s. 1-6
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Konferensbidrag (refereegranskat)abstract
- Most current real-time parallel applications can be modeled as a directed acyclic graph (DAG) task. Existing worst-case response time (WCRT) bounds (e.g., Graham's bound) derived for DAGs may be very pessimistic. No one precisely knows the gap between the WCRT bound and the actual WCRT. In this paper, we aim to derive the exact WCRT of a DAG task under the list scheduling upon multi-core platforms. We encode the WCRT analysis problem into a satisfaction modular theoretical (SNIT) formulation based on insights into the list scheduling algorithm, and prove that our SMT program can solve the WCRT precisely, providing an accurate baseline to measure the tightness of the existing WCRT bounds. Experiments show that our method significantly improves the tightness of the WCRT bound, and is practically quite efficient, e.g., it can analyze DAGs with more than 40 vertices in a few seconds.
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| 19. |
- Sun, Jinghao, et al.
(författare)
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On the Volume Calculation for Conditional DAG Tasks : Hardness and Algorithms
- 2020
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Ingår i: PROCEEDINGS OF THE 2020 DESIGN, AUTOMATION & TEST IN EUROPE CONFERENCE & EXHIBITION (DATE 2020). - NEW YORK, USA. - 9783981926347 ; , s. 204-209
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Konferensbidrag (refereegranskat)abstract
- The hardness of analyzing conditional directed acyclic graph (DAG) tasks remains unknown so far. For example, previous researches asserted that the conditional DAG's volume can be solved in polynomial time. However, these researches all assume well-nested structures that are recursively composed by single-source-single-sink parallel and conditional components. For conditional DAGs in general that do not comply with this assumption, the hardness and algorithms of volume computation are still open. In this paper, we construct counterexamples to show that previous work cannot provide a safe upper bound of the conditional DAG's volume in general. Moreover, we prove that the volume computation problem for conditional DAGs is strongly NP-hard. Finally, we propose an exact algorithm for computing the conditional DAG's volume. Experiments show that our method can significantly improve the accuracy of the conditional DAG's volume estimation.
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| 20. |
- Sun, Jinghao, et al.
(författare)
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Real-Time Scheduling and Analysis of OpenMP DAG Tasks Supporting Nested Parallelism
- 2020
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Ingår i: IEEE Transactions on Computers. - : IEEE COMPUTER SOC. - 0018-9340 .- 1557-9956. ; 69:9, s. 1335-1348
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Tidskriftsartikel (refereegranskat)abstract
- OpenMP is a promising framework to develop parallel real-time software on multi-cores. Although similar to the DAG task model, OpenMP task systems are significantly more difficult to analyze due to constraints posed by OpenMP specifications. One of the most interesting features in OpenMP is the support for nested parallelism, enjoying benefits in enhancing performance transparency of parallel libraries and promoting reuse of black-box code. Previous researches on DAG task scheduling mainly restrict to only one level of parallelism. The problem whether OpenMP tasks with multiple levels of parallelism are suitable to real-time systems remains open. In this paper, we study the real-time scheduling and analysis of OpenMP task systems supporting nested parallelism. First, we show that under existing scheduling algorithms in OpenMP implementations, nested parallelism indeed may lead to extremely bad timing behaviors where the parallel workload is sequentially executed completely. To solve this problem, we propose a new scheduling algorithm and develop two sound response time bounds by considering the trade-off between simplicity and analysis precision. Experiments demonstrate the efficiency of our methods.
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| 21. |
- Sun, Jinghao, et al.
(författare)
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Schedulability Analysis for Timed Automata With Tasks
- 2021
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Ingår i: ACM Transactions on Embedded Computing Systems. - : Association for Computing Machinery (ACM). - 1539-9087 .- 1558-3465. ; 20:5s
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Tidskriftsartikel (refereegranskat)abstract
- Research on modeling and analysis of real-time computing systems has been done in two areas, model checking and real-time scheduling theory. In model checking, an expressive modeling formalism such as timed automata (TA) is used to model complex systems, but the analysis is typically very expensive due to state-space explosion. In real-time scheduling theory, the analysis techniques are highly efficient, but the models are often restrictive. In this paper, we aim to exploit the possibility of applying efficient analysis techniques rooted in real-time scheduling theory to analysis of real-time task systems modeled by timed automata with tasks (TAT). More specifically, we develop efficient techniques to analyze the feasibility of TAT-based task models (i.e., whether all tasks can meet their deadlines on single-processor) using demand bound functions (DBF), a widely used workload abstraction in real-time scheduling theory. Our proposed analysis method has a pseudo-polynomial time complexity if the number of clocks used to model each task is bounded by a constant, which is much lower than the exponential complexity of the traditional model-checking based analysis approach (also assuming the number of clocks is bounded by a constant). We apply dynamic programming techniques to implement the DBF-based analysis framework, and propose state space pruning techniques to accelerate the analysis process. Experimental results show that our DBF-based method can analyze a TAT system with 50 tasks within a few minutes, which significantly outperforms the state-of-the-art TAT-based schedulability analysis tool TIMES.
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| 22. |
- Sun, Xiaohong, et al.
(författare)
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In-situ electrochemical synthesis of heteroatoms-doped reduced graphene oxide toward nonradical degradation of tetracycline
- 2023
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Ingår i: Chemical Engineering Journal. - 1385-8947. ; 471
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Tidskriftsartikel (refereegranskat)abstract
- Nonradical-based advanced oxidation processes (AOPs) catalyzed by defective carbonaceous materials have exhibited great superiorities in trace antibiotics removal from natural water matrices. However, the complicated, extensive and highly-energy consumed synthesis methods are seriously hindering its development and application. Herein an in-situ electrochemical synthesis technology was developed and N/B/F-codoped RGO was assembled on the Ti foam effectively by using ionic liquid (IL) as the heteroatoms parents. Other benefits of the IL including anti-RGO agglomeration, suppressing hydrolysis side reaction and reducing internal resistance were also demonstrated. Based on the diverse substrates exploration and comprehensive characterizations, adsorption and desolvation of the water molecules around IL-GO was found the two critical procedures for GO reduction and heteroatoms-doping. Hydrophilicity and porosity are the two essential properties for substrate selection. The solvent substitute experiments indicated electrochemical reduction of GO is a proton-mediated electron transfer reaction and the protons come from the solvent. Remarkable heteroatoms content was obtained from −1.0 V ∼ -1.2 V within 30 min under normal temperature and pressure. The degradation performance of N/B/F-codoped RGO was examined in an electrochemical system without any chemical additive. 93.0 % of trace tetracycline (5 mg L-1) was removed at −0.6 V within 60 min and the corresponding TOC removal efficiency was 40 %. Electron transfer efficiency can be even improved in the natural water matrices. The degradation mechanism investigation suggested that N/B/F-codoped RGO is able to simultaneously catalyze two nonradical pathways including electron transfer and singlet-dominated AOP. This work provides a highly effective, green and low-cost nonradical-based AOP technology for controlling antibiotics pollution in the environmental water matrices.
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| 23. |
- Sun, Ya-Nan, et al.
(författare)
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Synergetic contribution of nitrogen and fluorine species in porous carbons as metal-free and bifunctional oxygen electrocatalysts for zinc-air batteries
- 2021
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Ingår i: Applied Catalysis B. - : Elsevier BV. - 0926-3373 .- 1873-3883. ; 297
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Tidskriftsartikel (refereegranskat)abstract
- High-efficient bifunctional catalysts for oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are critical to the practical application of zinc–air batteries. Herein, a comprehensive investigation on the synergetic contribution of nitrogen (N) and fluorine (F) species in porous carbon for ORR/OER catalyses is firstly conducted. The metal-free N, F co-doped porous carbon (NFPC) possesses appealing catalytic activities in zinc–air batteries and is superior to many other catalysts. Combined with the careful exploration of N and F dopants, seventeen optimized carbon cluster structures with all possible co-doping of N and F species are considered for density functional theory calculations. It can be inferred that the F doping with graphitic and pyridinic N triggers active paramagnetic centers. The co-doping of covalent F and graphitic N especially gives the lowest free energy barrier for both ORR/OER, which could account for the notable performance of NFPC catalysts in zinc–air batteries.
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| 24. |
- Tsilidis, Konstantinos K., et al.
(författare)
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Genetically predicted circulating concentrations of micronutrients and risk of colorectal cancer among individuals of European descent : a Mendelian randomization study
- 2021
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Ingår i: American Journal of Clinical Nutrition. - : Oxford University Press. - 0002-9165 .- 1938-3207. ; 113:6, s. 1490-1502
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The literature on associations of circulating concentrations of minerals and vitamins with risk of colorectal cancer is limited and inconsistent. Evidence from randomized controlled trials (RCTs) to support the efficacy of dietary modification or nutrient supplementation for colorectal cancer prevention is also limited.OBJECTIVES: To complement observational and RCT findings, we investigated associations of genetically predicted concentrations of 11 micronutrients (β-carotene, calcium, copper, folate, iron, magnesium, phosphorus, selenium, vitamin B-6, vitamin B-12, and zinc) with colorectal cancer risk using Mendelian randomization (MR). METHODS: Two-sample MR was conducted using 58,221 individuals with colorectal cancer and 67,694 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium, Colorectal Cancer Transdisciplinary Study, and Colon Cancer Family Registry. Inverse variance-weighted MR analyses were performed with sensitivity analyses to assess the impact of potential violations of MR assumptions.RESULTS: Nominally significant associations were noted for genetically predicted iron concentration and higher risk of colon cancer [ORs per SD (ORSD): 1.08; 95% CI: 1.00, 1.17; P value = 0.05] and similarly for proximal colon cancer, and for vitamin B-12 concentration and higher risk of colorectal cancer (ORSD: 1.12; 95% CI: 1.03, 1.21; P value = 0.01) and similarly for colon cancer. A nominally significant association was also noted for genetically predicted selenium concentration and lower risk of colon cancer (ORSD: 0.98; 95% CI: 0.96, 1.00; P value = 0.05) and similarly for distal colon cancer. These associations were robust to sensitivity analyses. Nominally significant inverse associations were observed for zinc and risk of colorectal and distal colon cancers, but sensitivity analyses could not be performed. None of these findings survived correction for multiple testing. Genetically predicted concentrations of β-carotene, calcium, copper, folate, magnesium, phosphorus, and vitamin B-6 were not associated with disease risk.CONCLUSIONS: These results suggest possible causal associations of circulating iron and vitamin B-12 (positively) and selenium (inversely) with risk of colon cancer.
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| 25. |
- Wang, Yangong, et al.
(författare)
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Exome sequencing reveals genetic heterogeneity and clinically actionable findings in children with cerebral palsy
- 2024
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Ingår i: NATURE MEDICINE. - 1078-8956 .- 1546-170X. ; 30, s. 1395-1405
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Tidskriftsartikel (refereegranskat)abstract
- Cerebral palsy (CP) is the most common motor disability in children. To ascertain the role of major genetic variants in the etiology of CP, we conducted exome sequencing on a large-scale cohort with clinical manifestations of CP. The study cohort comprised 505 girls and 1,073 boys. Utilizing the current gold standard in genetic diagnostics, 387 of these 1,578 children (24.5%) received genetic diagnoses. We identified 412 pathogenic and likely pathogenic (P/LP) variants across 219 genes associated with neurodevelopmental disorders, and 59 P/LP copy number variants. The genetic diagnostic rate of children with CP labeled at birth with perinatal asphyxia was higher than the rate in children without asphyxia (P = 0.0033). Also, 33 children with CP manifestations (8.5%, 33 of 387) had findings that were clinically actionable. These results highlight the need for early genetic testing in children with CP, especially those with risk factors like perinatal asphyxia, to enable evidence-based medical decision-making. Using exome sequencing data from one of the largest cohorts of children with cerebral palsy, the genetic diagnostic rates of single-nucleotide and copy number variants were assessed and a sizeable fraction found to be clinically actionable.
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| 26. |
- Wu, Biying, et al.
(författare)
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Megakaryocytes Mediate Hyperglycemia-Induced Tumor Metastasis
- 2021
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Ingår i: Cancer Research. - : AMER ASSOC CANCER RESEARCH. - 0008-5472 .- 1538-7445. ; 81:21, s. 5506-5522
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Tidskriftsartikel (refereegranskat)abstract
- High blood glucose has long been established as a risk factor for tumor metastasis, yet the molecular mechanisms underlying this association have not been elucidated. Here we describe that hyperglycemia promotes tumor metastasis via increased platelet activity. Administration of glucose, but not fructose, reprogrammed the metabolism of megakaryocytes to indirectly prime platelets into a prometastatic phenotype with increased adherence to tumor cells. In megakaryocytes, a glucose metabolism-related gene array identified the mitochondrial molecular chaperone glucose-regulated protein 75 (GRP75) as a trigger for platelet activation and aggregation by stimulating the Ca2+-PKC alpha pathway. Genetic depletion of Glut1 in megakaryocytes blocked MYC-induced GRP75 expression. Pharmacologic blockade of platelet GRP75 compromised tumor-induced platelet activation and reduced metastasis. Moreover, in a pilot clinical study, drinking a 5% glucose solution elevated platelet GRP75 expression and activated platelets in healthy volunteers. Platelets from these volunteers promoted tumor metastasis in a plateletadoptive transfer mouse model. Together, under hyperglycemic conditions, MYC-induced upregulation of GRP75 in megakaryocytes increases platelet activation via the Ca2+-PKC alpha pathway to promote cancer metastasis, providing a potential new therapeutic target for preventing metastasis. Significance: This study provides mechanistic insights into a glucose-megakaryocyte-platelet axis that promotes metastasis and proposes an antimetastatic therapeutic approach by targeting the mitochondrial protein GRP75.
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| 27. |
- Ye, Xiaoling, et al.
(författare)
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High Performance Self-Powered Photodetectors Based on Graphene Nanoribbons/Al2O3/InGaZnO Heterojunctions
- 2024
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Ingår i: IEEE Photonics Journal. - : Institute of Electrical and Electronics Engineers (IEEE). - 1943-0655. ; 16:3
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Tidskriftsartikel (refereegranskat)abstract
- Self-powered photodetectors which operate without external power sources hold immense promise in future photodetection systems. To achieve high-performance self-powered optoelectronic devices, efficient electron-hole pair separation is critical to generate high photocurrents. In this work, we successfully synthesized semiconducting graphene nanoribbons (GNRs) with a direct bandgap of 1.80 eV and employed them to construct a high-performance GNR/Al2O3/IGZO heterostructure photodetector. The built-in electric field in the heterojunctions enables this photodetector to exhibit remarkable performance, showing a responsivity of up to 68 mA/W, a detectivity of 8.34 x 1010 Jones, and rapid response times of 21/20 ms at zero bias. Furthermore, the photodetector features a wide spectral detection range of 405 to 1550 nm. These results highlight the promising potential of GNR/IGZO p-n heterojunction-based self-powered photodetectors in optoelectronic applications.
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| 28. |
- Zhang, Dachuan, et al.
(författare)
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FRCD: A comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis
- 2020
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Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146 .- 1873-7072. ; 318
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Tidskriftsartikel (refereegranskat)abstract
- The presence of natural toxins, pesticide residues, and illegal additives in food products has been associated with a range of potential health hazards. However, no systematic database exists that comprehensively includes and integrates all research information on these compounds, and valuable information remains scattered across numerous databases and extensive literature reports. Thus, using natural language processing technology, we curated 12,018 food risk components from 152,737 literature reports, 12 authoritative databases, and numerous related regulatory documents. Data on molecular structures, physicochemical properties, chemical taxonomy, absorption, distribution, metabolism, excretion, toxicity properties, and physiological targets within the human body were integrated to afford the comprehensive food risk component database (FRCD, http://www.rxnfinder.org/frcd/). We also analyzed the molecular scaffold and chemical diversity, in addition to evaluating the toxicity and biodegradability of the food risk components. The FRCD could be considered a highly promising tool for future food safety studies.
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| 29. |
- Zhang, Rongqi, et al.
(författare)
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Field Synopsis of Environmental and Genetic Risk Factors of Sporadic Early-Onset Colorectal Cancer and Advanced Adenoma
- 2023
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association For Cancer Research (AACR). - 1055-9965 .- 1538-7755. ; 32:8, s. 1048-1060
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Tidskriftsartikel (refereegranskat)abstract
- Background: To systematically appraise and synthesize avail-able epidemiologic evidence on the associations of environmental and genetic factors with the risk of sporadic early-onset colorectal cancer (EOCRC) and early-onset advanced colorectal adenoma (EOCRA).Methods: Multiple databases were comprehensively searched to identify eligible observational studies. Genotype data from UK Biobank were incorporated to examine their associations with EOCRC in a nested case-control design. Meta-analyses of envi-ronmental risk factors were performed, and the strength of evidence was graded based on predefined criteria. Meta-analyses of genetic associations were conducted using the allelic, recessive, and dom-inant models, respectively.Results: A total of 61 studies were included, reporting 120 environmental factors and 62 genetic variants. We found 12 risk factors (current overweight, overweight in adolescence, high waist circumference, smoking, alcohol, sugary beverages intake, seden-tary behavior, red meat intake, family history of colorectal cancer, hypertension, hyperlipidemia, and metabolic syndrome) and three protective factors (vitamin D, folate, and calcium intake) for EOCRC or EOCRA. No significant associations between the exam-ined genetic variants and EOCRC risk were observed.Conclusions: Recent data indicate that the changing patterns of traditional colorectal cancer risk factors may explain the rising incidence of EOCRC. However, research on novel risk factors for EOCRC is limited; therefore, we cannot rule out the possibility of EOCRC having different risk factors than late-onset colorectal cancer (LOCRC).Impact: The potential for the identified risk factors to enhance the identification of at-risk groups for personalized EOCRC screen-ing and prevention and for the prediction of EOCRC risk should be comprehensively addressed by future studies.
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| 30. |
- Zhao, Qian, et al.
(författare)
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A flexible ammonia sensor based on MXene membrane with high sensitivity
- 2024
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Ingår i: Electroanalysis. - : WILEY-V C H VERLAG GMBH. - 1040-0397 .- 1521-4109.
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Tidskriftsartikel (refereegranskat)abstract
- Ammonia (NH3) of high concentration will pose a threat to ecological environment or human health, and exhaled NH3 is significant in disease monitoring and diagnosis. Thus, developing a highly sensitive gas sensor is significant to monitor NH3 concentration in complex environments. However, traditional NH3 sensors either need high working temperature, or face the challenge of poor conductivity/ sensitivity. In this work, NH3 sensors based on self-assembled MXene membrane have been fabricated. As-prepared sensors show a high sensitivity of 2.10 ppm-1 towards extremely low concentrations of NH3 (ppb level) at room temperature, attributed to large surface area and high conductivity. In addition, the sensors also display low detection limit (50 ppb), fast response time (41 s), good recoverability, long-term stability (15 days) and excellent flexibility (1000 bending cycles) towards NH3. The results provide insights into the development of highly sensitive NH3 sensors for industrial or biomedical applications. image
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