| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Miao, Yuyang, et al.
(författare)
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Bidirectional Association between Major Depressive Disorder and Gastroesophageal Reflux Disease : Mendelian Randomization Study
- 2022
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 13:11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Observational research has found a bidirectional relationship between major depressive disorder and gastroesophageal reflux disease; however, the causal association of this relationship is undetermined. Aims: A bidirectional Mendelian randomization study was performed to explore the causal relationships between major depressive disorder and gastroesophageal reflux disease. Methods: For the instrumental variables of major depressive disorder and gastroesophageal reflux disease, 31 and 24 single-nucleotide polymorphisms without linkage disequilibrium (r(2) <= 0.001) were selected from relevant genome-wide association studies, respectively, at the genome-wide significance level (p <= 5 x 10(-8)). We sorted summary-level genetic data for major depressive disorder, gastroesophageal reflux disease, gastroesophageal reflux disease without esophagitis, and reflux esophagitis from meta-analysis study of genome-wide association studies involving 173,005 individuals (59,851 cases and 113,154 non-cases), 385,276 individuals (80,265 cases and 305,011 non-cases), 463,010 individuals (4360 cases and 458,650 non-cases), and 383,916 individuals (12,567 cases and 371,349 non-cases), respectively. Results: Genetic liability to major depressive disorder was positively associated with gastroesophageal reflux disease and its subtypes. Per one-unit increase in log-transformed odds ratio of major depressive disorder, the odds ratio was 1.31 (95% confidence interval [CI], 1.19-1.43; p = 1.64 x 10(-8)) for gastroesophageal reflux disease, 1.51 (95% CI, 1.15-1.98; p = 0.003) for gastroesophageal reflux disease without esophagitis, and 1.21 (95% CI, 1.05-1.40; p = 0.010) for reflux esophagitis. Reverse-direction analysis suggested that genetic liability to gastroesophageal reflux disease was causally related to increasing risk of major depressive disorder. Per one-unit increase in log-transformed odds ratio of gastroesophageal reflux disease, the odds ratio of major depressive disorder was 1.28 (95% confidence interval, 1.11-1.47; p = 1.0 x 10(-3)). Conclusions: This Mendelian randomization study suggests a bidirectional causal relationship between major depressive disorder and gastroesophageal reflux disease.
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| 3. |
- Wei, Lai, et al.
(författare)
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Multiscale identification of urban functional polycentricity for planning implications : An integrated approach using geo-big transport data and complex network modeling
- 2020
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Ingår i: Habitat International. - : Elsevier BV. - 0197-3975. ; 97
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Tidskriftsartikel (refereegranskat)abstract
- Polycentrism has gradually become a newly emergent dimension of global urbanization. Many countries worldwide have tailored plans suited to functional polycentricity, in light of the prevalent “ghost cities” or “empty towns” as lessons from the morphologically polycentric development practices. However, the subject of defining and measuring functional polycentricity is still in an initial development phase, both in theory and in methodology. This paper first establishes a general theoretical framework for understanding functional polycentricity from the lens of interactive human mobility among spatial units. Then, a new approach is proposed to identify and measure urban functional polycentricity from a multiscale perspective and further applied to the case of Shanghai, China. More specifically, the pick-up and drop-off points from taxi GPS data are used to examine the linkages among different urban units across various scales (e.g., census tract, 3000-m grid, 5000-m grid, and community). Complex network modeling, together with the sensitivity analysis, is further employed to identify the centers according to the spatial importance of each unit. The results show that (1) the approach proposed can effectively identify functional centers within urban setting; (2) an obvious polycentric structure exists in Shanghai and is sensitive to scale effects; (3) the estimates are more accurate and precise with the shrink of analysis unit size from community level to census tract level; and (4) under the same spatial scale, the grid-based analysis produces a more elaborated polycentric pattern compared with the traditional administration-based analysis. Finally, scale-dependent differences between morphological and functional polycentricity are distinguished for providing implications for urban planning. Our study is believed to renew the knowledge of polycentricity conceptualization.
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| 4. |
- Yuan, Shuai, et al.
(författare)
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Therapeutic role of interleukin-1 receptor antagonist in pancreatic diseases : mendelian randomization study
- 2023
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Ingår i: Frontiers in Immunology. - : Frontiers Media S.A.. - 1664-3224. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: The interleukin-1 pathway has been linked to pancreatic diseases. We applied the Mendelian randomization approach to explore whether higher interleukin-1 receptor antagonist (IL-1RA) levels reduce the risk of acute and chronic pancreatitis and pancreatic cancer.Methods: Genetic variants associated with blood IL-1RA levels at the genome-wide significance level and located 5MB downstream or upstream of the IL1RN gene were extracted from a genome-wide meta-analysis of 21,758 participants. After pruning, genetic variants without linkage disequilibrium were used as genetic instrument for IL-1RA. Summary-level data on acute and chronic pancreatitis and pancreatic cancer were obtained from the UK Biobank and FinnGen studies. The associations were meta-analyzed for one outcome from two sources.Results: Genetically predicted higher levels of IL-1RA were associated with a lower risk of acute and chronic pancreatitis and pancreatic cancer. In the meta-analysis of UK Biobank and FinnGen, the combined odds ratio was 0.87 (95% confidence interval [CI] 0.77-0.97, P=0.003) for acute pancreatitis, 0.73 (95% CI 0.65-0.82, P=2.93x10-8) for chronic pancreatitis, and 0.86 (95% CI 0.77-0.96, P=0.009) for pancreatic cancer per one standard deviation increment in genetically predicted levels of IL-1RA.Conclusion: This study suggests a protective role of IL-1RA in three major pancreatic diseases, which hints the therapeutic potentials of IL-1RA in pancreatic diseases.
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