| 1. |
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| 2. |
- 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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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Fang, Xin, et al.
(författare)
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Comparison of Frequentist and Bayesian Generalized Additive Models for Assessing the Association between Daily Exposure to Fine Particles and Respiratory Mortality : A Simulation Study
- 2019
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Ingår i: International Journal of Environmental Research and Public Health. - Basel, Switzerland : MDPI. - 1661-7827 .- 1660-4601. ; 16:5
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To compare the performance of frequentist and Bayesian generalized additive models (GAMs) in terms of accuracy and precision for assessing the association between daily exposure to fine particles and respiratory mortality using simulated data based on a real time-series study.Methods: In our study, we examined the estimates from a fully Bayesian GAM using simulated data based on a genuine time-series study on fine particles with a diameter of 2.5 m or less (PM2.5) and respiratory deaths conducted in Shanghai, China. The simulation was performed by multiplying the observed daily death with a random error. The underlying priors for Bayesian analysis are estimated using the real world time-series data. We also examined the sensitivity of Bayesian GAM to the choice of priors and to true parameter.Results: The frequentist GAM and Bayesian GAM show similar means and variances of the estimates of the parameters of interest. However, the estimates from Bayesian GAM show relatively more fluctuation, which to some extent reflects the uncertainty inherent in Bayesian estimation.Conclusions: Although computationally intensive, Bayesian GAM would be a better solution to avoid potentially over-confident inferences. With the increasing computing power of computers and statistical packages available, fully Bayesian methods for decision making may become more widely applied in the future.
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| 5. |
- Fang, Xin, et al.
(författare)
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Relationship between fine particulate matter, weather condition and daily non-accidental mortality in Shanghai, China : A Bayesian approach
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- There are concerns that the reported association of ambient fine particulate matter (PM2.5) with mortality might be a mixture of PM2.5 and weather conditions. We evaluated the effects of extreme weather conditions and weather types on mortality as well as their interactions with PM2.5 concentrations in a time series study. Daily non-accidental deaths, individual demographic information, daily average PM2.5 concentrations and meteorological data between 2012 and 2014 were obtained from Shanghai, China. Days with extreme weather conditions were identified. Six synoptic weather types (SWTs) were generated. The generalized additive model was set up to link the mortality with PM2.5 and weather conditions. Parameter estimation was based on Bayesian methods using both the Jeffreys' prior and an informative normal prior in a sensitivity analysis. We estimate the percent increase in non-accidental mortality per 10 mu g/m(3) increase in PM2.5 concentration and constructed corresponding 95% credible interval (CrI). In total, 336,379 non-accidental deaths occurred during the study period. Average daily deaths were 307. The results indicated that per 10 mu g/m(3) increase in daily average PM2.5 concentration alone corresponded to 0.26-0.35% increase in daily non-accidental mortality in Shanghai. Statistically significant positive associations between PM2.5 and mortality were found for favorable SWTs when considering the interaction between PM2.5 and SWTs. The greatest effect was found in hot dry SWT (percent increase = 1.28, 95% CrI: 0.72, 1.83), followed by warm humid SWT (percent increase = 0.64, 95% CrI: 0.15, 1.13). The effect of PM2.5 on non-accidental mortality differed under specific extreme weather conditions and SWTs. Environmental policies and actions should take into account the interrelationship between the two hazardous exposures.
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| 6. |
- Wang, Si-Yu, et al.
(författare)
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Kaempferia galanga L. : Progresses in Phytochemistry, Pharmacology, Toxicology and Ethnomedicinal Uses
- 2021
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Ingår i: Frontiers in Pharmacology. - : Frontiers Media S.A.. - 1663-9812. ; 12
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Forskningsöversikt (refereegranskat)abstract
- K. galanga is an aromatic medicinal herb. It is locally to India and distributed in China, Myanmar, Indonesia, Malaysia, and Thailand. K. galanga is a Traditional Chinese Herb Medicine (TCHM), which has been applied to treat cold, dry cough, toothaches, rheumatism, hypertension and so on. In addition, it has been used widely as spices since its highly aromas. The aim of this review is to compile and update the current progresses of ethnomedicinal uses, phytochemistry, pharmacology and toxicology of K. galanga. All the data on K. galanga were based on different classical literary works, multiple electronic databases including SciFinder, Web of Science, PubMed, etc. The results showed that ninety-seven compounds have been identified from rhizome of K. galanga, including terpenoids, phenolics, cyclic dipeptides, flavonoids, diarylheptanoids, fatty acids and esters. Modern pharmacology studies revealed that extracts or secondary metabolites of the herb possessed anti-inflammatory, anti-oxidant, anti-tumorous, anti-bacterial, and anti-angiogenesis effects, which were closely related to its abundant ethnomedicinal uses. In conclusion, although previous research works have provided various information of K. galanga, more in-depth studies are still necessary to systemically evaluate phytochemistry, pharmacological activities, toxicity and quality control of this herb.
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| 7. |
- Xia, Tian, et al.
(författare)
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Sex differences in associations of fine particulate matter with non-accidental deaths : an ecological time-series study
- 2021
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Ingår i: Air quality, atmosphere and health. - : Springer. - 1873-9318 .- 1873-9326. ; 14, s. 863-872
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Tidskriftsartikel (refereegranskat)abstract
- Sex differences in the impact of exposure to air pollution have been reported previously and epidemiological studies indicate that fine particulate matter (PM2.5) effects on nonaccidental death are modified by sex; however, the results are not conclusive. To introduce a new method incorporating the monotone nonlinear relationship between PM2.5 and deaths to reveal the sex difference in the relationship, we illustrated the use of the constrained generalized additive model (CGAM) to investigate the sex difference in the effects of PM2.5 on nonaccidental deaths in Shanghai, China. Information on daily non-accidental deaths, air pollution, meteorological data, and smoking prevalence between 1 January 2012 and 31 December 2014 was obtained in Shanghai. The CGAM was used to assess the association of interaction between sex and daily PM2.5 concentrations with daily nonaccidental deaths, adjusting for weather type and smoking rate. A 2-week lag analysis was conducted as a sensitivity analysis. During the study period, the total number of non-accidental deaths in Shanghai was 336,379, with a daily mean of 163 deaths and 144 deaths for men and women, respectively. The average daily concentration of PM2.5 in Shanghai was 55.0 mu g/m(3) during the same time period. Women showed a lower risk for non-accidental death (risk ratio (RR) = 0.892, 95% confidence interval (CI): 0.802-0.993). Compared with men, the risk for nonaccidental death in relation to increasing PM2.5 concentration was smaller in women (RR = 0.998, 95% CI: 0.996-1.000, per 10 mu g/m(3) increase in PM2.5 concentration. The difference is consistent during the two lag weeks and more obvious when adjusting for the interaction between PM2.5 concentration and smoking prevalence. The effects of PM2.5 on daily nonaccidental death are different between men and women in Shanghai, China, and women tend to have a lower risk. The underlying mechanisms of the sex difference of PM2.5 effects on death need further investigation. The method displayed in the manuscript can be used for other environmental stressors as well.
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| 8. |
- Fang, Shuhong, et al.
(författare)
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Environment occurrence of perfluoroalkyl acids and associated human health risks near a major fluorochemical manufacturing park in southwest of China
- 2020
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Ingår i: Journal of Hazardous Materials. - : Elsevier BV. - 0304-3894 .- 1873-3336. ; 396
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Tidskriftsartikel (refereegranskat)abstract
- Despite China being the largest global manufacturer of perfluoroalkyl acids (PFAAs), few studies have been carried out on the environmental occurrence and associated human health risks of PFAAs emitted from manufacturing sites in China. Here, river water, tap water, soil and leaf samples were collected around a major fluorochemical manufacturing park (FMP) in the southwest of China in 2019. High EPFAA concentrations (sum of 12 PFAAs) of 3817 ng/L, 3254 ng/L, 322 - 476 ng/g dw and 23401-33749 ng/g dw were measured near the FMP in river water, tap water, soil and leaves, respectively, indicating that the FMP is a point source of PFAAs. PFOA was the predominant PFAA in all samples (58.5-98.6 %) indicating the production or use of PFOA at the FMP. PFOA concentrations in most tap water samples (> 300 ng/L in 31 of 38 samples) exceeded the U.S. EPA health advisory. Proportions of branched PFOA isomers in all samples were in 5.9-47.4 %, suggesting the production or use of PFOA manufactured by electrochemical fluorination at the FMP. It is recommended to focus more attention on branched PFOA isomers in the future because otherwise health risks may be underestimated due to their relatively high proportions in China.
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| 9. |
- Han, Jing, et al.
(författare)
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Changing grains for the prevention and treatment of Kashin-Beck disease in children : a Meta-analysis
- 2015
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Ingår i: Biomedical and environmental sciences. - : Chinese Center for Disease Control and Prevention. - 0895-3988 .- 2214-0190. ; 28:4, s. 308-311
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Tidskriftsartikel (refereegranskat)abstract
- To evaluate the efficacy of changing grains on the prevention and treatment of Kashin-Beck Disease (KBD) in children, community-based trials were acquired from seven electronic databases (up to July 2014). As a result, the methodological quality of the six trials that have been included into our analysis was low. The pooled ORs favoring the prevention and treatment effects of changing grains were 0.15 (95% CI: 0.03-0.70) and 2.13 (95% CI: 1.44-3.16) respectively by meta-analysis. Subgroup analysis demonstrated the pooled OR favoring treatment effect of exchanging grains rather than drying grains both compared with endemic grains. The results showed that changing grains had obvious effects on the prevention and treatment of KBD in children. However, the evidences were limited by the potential biases and confounders. Large and well-designed trials are still needed.
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| 10. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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