| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Qi, Xiaoying, et al.
(author)
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High Throughput, Absolute Determination of the Content of a Selected Protein at Tissue Levels Using Quantitative Dot Blot Analysis (QDB)
- 2018
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In: Journal of Visualized Experiments. - : MyJove Corporation. - 1940-087X. ; :138
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Journal article (peer-reviewed)abstract
- Lacking a convenient, quantitative, high throughput immunoblot method for absolute determination of the content of a specific protein at cellular and tissue level significantly hampers the progress in proteomic research. Results derived from currently available immunoblot techniques are also relative, preventing any efforts to combine independent studies with a large-scale analysis of protein samples. In this study, we demonstrate the process of quantitative dot blot analysis (QDB) to achieve absolute quantification in a high throughput format. Using a commercially available protein standard, we are able to determine the absolute content of capping actin protein, gelsolin-like (CAPG) in protein samples prepared from three different mouse tissues (kidney, spleen, and prostate) together with a detailed explanation of the experimental details. We propose the QDB analysis as a convenient, quantitative, high throughput immunoblot method of absolute quantification of individual proteins at the cellular and tissue level. This method will substantially aid biomarker validation and pathway verification in various areas of biological and biomedical research.
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| 3. |
- Zheng, Fenglian, et al.
(author)
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Structural and functional hippocampal alterations in Multiple sclerosis and neuromyelitis optica spectrum disorder
- 2022
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In: Multiple Sclerosis Journal. - : SAGE Publications. - 1352-4585 .- 1477-0970. ; 28:5, s. 707-717
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Journal article (peer-reviewed)abstract
- Background: Hippocampal involvement may differ between multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD). Objective: To investigate the morphometric, diffusion and functional alterations in hippocampus in MS and NMOSD and the clinical significance. Methods: A total of 752 participants including 236 MS, 236 NMOSD and 280 healthy controls (HC) were included in this retrospective multi-center study. The hippocampus and subfield volumes, fractional anisotropy (FA) and mean diffusivity (MD), amplitude of low frequency fluctuation (ALFF) and degree centrality (DC) were analyzed, and their associations with clinical variables were investigated. Results: The hippocampus showed significantly lower volume, FA and greater MD in MS compared to NMOSD and HC (p < 0.05), while no abnormal ALFF or DC was identified in any group. Hippocampal subfields were affected in both diseases, though subiculum, presubiculum and fimbria showed significantly lower volume only in MS (p < 0.05). Significant correlations between diffusion alterations, several subfield volumes and clinical variables were observed in both diseases, especially in MS (R = -0.444 to 0.498, p < 0.05). FA and MD showed fair discriminative power between MS and HC, NMOSD and HC (AUC > 0.7). Conclusions: Hippocampal atrophy and diffusion abnormalities were identified in MS and NMOSD, partly explaining how clinical disability and cognitive impairment are differentially affected.
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| 4. |
- Jin, Ying, et al.
(author)
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"Soap bubble" sign as an imaging marker for posterior fossa ependymoma Group B
- 2023
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In: Neuroradiology. - : Springer. - 0028-3940 .- 1432-1920. ; 65, s. 1707-1714
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Journal article (peer-reviewed)abstract
- Purpose: To investigate the predictive value of the "soap bubble" sign on molecular subtypes (Group A [PFA] and Group B [PFB]) of posterior fossa ependymomas (PF-EPNs).Methods: MRI scans of 227 PF-EPNs (internal retrospective discovery set) were evaluated by two independent neuroradiologists to assess the "soap bubble" sign, which was defined as clusters of cysts of various sizes that look like "soap bubbles" on T2-weighted images. Two independent cohorts (external validation set [n = 31] and prospective validation set [n = 27]) were collected to validate the "soap bubble" sign.Results: Across three datasets, the "soap bubble" sign was observed in 21 PFB cases (7.4% [21/285] of PF-EPNs and 12.9% [21/163] of PFB); none in PFA. Analysis of the internal retrospective discovery set demonstrated substantial interrater agreement (1st Rating: kappa = 0.71 [0.53-0.90], 2nd Rating: kappa = 0.83 [0.68-0.98]) and intrarater agreement (Rater 1: kappa = 0.73 [0.55-0.91], Rater 2: kappa = 0.74 [0.55-0.92]) for the "soap bubble" sign; all 13 cases positive for the "soap bubble" sign were PFB (p = 0.002; positive predictive value [PPV] = 100%, negative predictive value [NPV] = 44%, sensitivity = 10%, specificity = 100%). The findings from the external validation set and the prospective validation set were similar, all cases positive for the "soap bubble" sign were PFB (p < 0.001; PPV = 100%).Conclusion: The "soap bubble" sign represents a highly specific imaging marker for the PFB molecular subtype of PF-EPNs.
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| 5. |
- Li, Furong, et al.
(author)
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Relative pollen productivity estimates for major plant taxa of cultural landscapes in central eastern China
- 2017
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In: Vegetation History and Archaeobotany. - : Springer. - 0939-6314 .- 1617-6278. ; 26:6, s. 587-605
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Journal article (peer-reviewed)abstract
- In this study we estimate relative pollen productivity (RPP) for plant taxa characteristic of human-induced vegetation in ancient cultural landscapes of the low mountain ranges of Shandong province in eastern temperate China. RPP estimates are required to achieve pollen-based reconstructions of Holocene plant cover using modelling approaches based on Prentice's and Sugita's theoretical background and models (REVEALS and LOVE). Pollen counts in moss samples and vegetation data from 36 sites were used in the Extended R-Value (ERV) model to estimate the relevant source area of pollen (RSAP) of moss polsters and RPP of major plant taxa. The best results were obtained with the ERV sub-model 3 and Prentice's taxon-specific method (using a Gaussian Plume dispersal model) to distance weight vegetation data. RSAP was estimated to 145 m using the maximum likelihood method. RPP was obtained for 18 taxa of which two taxa had unreliable RPP (Amaranthaceae/Chenopodiaceae and Vitex negundo). RPPs for Castanea, Cupressaceae, Robinia/Sophora, Aster/Anthemis-type, Cannabis/Humulus, Caryophyllaceae, Brassicaceae and Galium-type are the first ones for China. Trees, except Robinia/Sophora (RPP = 0.78 +/- 0.03) have larger RPPs than herbs other than Artemisia (RPP = 24.7 +/- 0.36). The RPPs for Quercus, Pinus and Artemisia are comparable with other RPPs obtained in China, the RPPs for Pinus, Quercus, Ulmus, Cyperaceae and Galium-type with the mean RPPs obtained in Europe, and RPP for Cupressaceae with that for Juniperus in Europe. The values for Aster/Anthemis-type, Caryophyllaceae, Asteraceae SF Cichorioideae and Juglans differ from the few RPPs available in China and/or Europe.
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| 6. |
- Li, Yunyun, et al.
(author)
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Understanding Enhanced Microbial MeHg Production in Mining-Contaminated Paddy Soils under Sulfate Amendment : Changes in Hg Mobility or Microbial Methylators?
- 2019
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In: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 53:4, s. 1844-1852
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Journal article (peer-reviewed)abstract
- Elevated methylmercury (MeHg) production in mining-contaminated paddy soils, despite the high fraction of refractory HgS(s), has been frequently reported, while the underlying mechanisms are not fully understood. Here, we hypothesized that sulfate input, via fertilization, rainfall, and irrigation, is critical in mobilizing refractory HgS(s) and thus enhancing Hg methylation in mining-contaminated paddy soils. To test this hypothesis, the effects of sulfate amendment on Hg methylation and MeHg bioaccumulation in mining-contaminated soil-rice systems were examined. The results indicated 28-61% higher net MeHg production in soils under sulfate amendment (50-1000 mg kg-1), which in turn increased grain MeHg levels by 22-55%. The enhancement of Hg methylation by Hg mobilization in sulfate-amended soils was supported by two observations: (1) the increased Hg(aq) release from HgS(s), the dominant Hg species in the paddy soils, in the presence of sulfide produced following sulfate reduction and (2) the decreases of refractory HgS(s) in soils under sulfate amendment. By contrast, changes in the abundances/activities of potential microbial Hg methylators in different Hg-contaminated soils were not significant following sulfate amendment. Our results highlight the importance to consider enhanced Hg mobility and thus methylation in soils under sulfate amendment.
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| 7. |
- Liu, Yunyun, et al.
(author)
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Association of depression with incident sarcopenia and modified effect from healthy lifestyle : The first longitudinal evidence from the CHARLS
- 2024
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In: Journal of Affective Disorders. - 0165-0327. ; 344, s. 373-379
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Journal article (peer-reviewed)abstract
- Background: The prospective association of depression with incident sarcopenia remains unknown, as does whether such an association is modified by a healthy lifestyle. Thus, the goal of this study was to determine whether depression is independently related to the risk of developing sarcopenia and to detect the effect of a healthy lifestyle on its modification. Methods: The prospective study included 9486 participants from the China Health and Retirement Longitudinal Study who were followed from 2011 to 2015. We calculated a lifestyle score based on body mass index, drinking, smoking, social activities, and sleeping time. Cox proportional hazards regression models with hazard ratios (HRs) and 95 % confidence intervals were used to estimate the effect of depression on the risk of sarcopenia and the modification effect of lifestyle (CIs). Results: During a mean of 3.53 years of follow-up, 1373 individuals developed sarcopenia. After adjusting for confounding factors, depression was significantly associated with a higher risk of incident sarcopenia (HR = 1.34; 95 % CI: 1.19, 1.50). In addition, we observed that individuals adhering to a healthy lifestyle had an 18 % lower risk of sarcopenia onset, compared with individuals with an unhealthy lifestyle. Limitations: We couldn't completely rule out potential residual bias due to its observational design. Second, ascertainment of the history of diseases in CHARLS was based on self-reported information, which may introduce recall bias or misclassification. Conclusions: Depression was associated with a higher risk of sarcopenia in Chinese adults, and such a risk may be alleviated by adhering to a healthy lifestyle.
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| 8. |
- Qin, Xingna, et al.
(author)
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Does having vulnerable friends help vulnerable youth? The co-evolution of friendships, victimization, and depressive symptoms in Chinese adolescents social networks
- 2023
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In: Child Development. - : WILEY. - 0009-3920 .- 1467-8624. ; 94:6, s. 1419-1780
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Journal article (peer-reviewed)abstract
- This study examined whether having vulnerable friends helps or hurts victimized and depressed (i.e., vulnerable) adolescents and whether this depends on classroom supportive norms. Students (n = 1461, 46.7% girls, 93.4% Han nationality) were surveyed four times from seventh and eighth grade (M-age = 13 years) in 2015 and 2016 in Central China. Longitudinal social network analyses indicated that having vulnerable friends can both hurt and help vulnerable adolescents. Depressed adolescents with depressed friends increased in victimization over time. Victimized adolescents with victimized friends increased in victimization but decreased in depressive symptoms. These processes were most likely in classrooms with high supportive norms. Having friends and a supportive classroom may hurt vulnerable adolescents social position but help victims emotional development.
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| 9. |
- Qin, Xingna, et al.
(author)
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Parents on the Sidelines: The Role of Parental Directing in Chinese Adolescents' Friendship Dynamics Related to Academic Achievement, Aggression, and Prosocial Behavior
- 2024
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In: Journal of Early Adolescence. - : SAGE PUBLICATIONS INC. - 0272-4316 .- 1552-5449.
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Journal article (peer-reviewed)abstract
- Adolescents' peer interactions strongly influence their school behavior, raising the question of whether parents can still direct adolescents' friendship choices or whether they are mostly on the sidelines. Chinese cultural values emphasize the importance of having "good" friends, raising questions about adolescents' adherence to parental direction of friendships. This study examined friendship dynamics among seventh and eighth graders in central China (n = 1,454, 46.7% girls), focusing on achievement, aggression, and prosocial behavior. Social network analysis revealed that Chinese students tended to select friends who were more similar to them in achievement, aggression, and prosocial behavior. Interestingly, they avoided aggressive peers but were attracted to high-achieving and prosocial peers. Despite parental emphasis on friendship quality, the study found no parental direction in adolescent friendship selection. These findings underscore the central role of peer characteristics in friendship dynamics, while highlighting the limited impact of parental directing on Chinese adolescents' friendship selection.
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