| 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. |
- 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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| 3. |
- Korinek, Michal, et al.
(författare)
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Anti-allergic Hydroxy Fatty Acids from Typhonium blumei Explored through ChemGPS-NP
- 2017
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Ingår i: Frontiers in Pharmacology. - : FRONTIERS MEDIA SA. - 1663-9812. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Increasing prevalence of allergic diseases with an inadequate variety of treatment drives forward search for new alternative drugs. Fatty acids, abundant in nature, are regarded as important bioactive compounds and powerful nutrients playing an important role in lipid homeostasis and inflammation. Phytochemical study on Typhonium blumei Nicolson and Sivadasan (Araceae), a folk anti-cancer and anti-inflammatory medicine, yielded four oxygenated fatty acids, 12R-hydroxyoctadec-9Z, 13E-dienoic acid methyl ester (1) and 10R-hydroxyoctadec-8E, 12Z-dienoic acid methyl ester (2), 9R-hydroxy-10E-octadecenoic acid methyl ester (3), and 12R *-hydroxy-10E-octadecenoic acid methyl ester (4). Isolated compounds were identified by spectroscopic methods along with GC-MS analysis. Isolated fatty acids together with a series of saturated, unsaturated and oxygenated fatty acids were evaluated for their anti-inflammatory and anti-allergic activities in vitro. Unsaturated (including docosahexaenoic and eicosapentaenoic acids) as well as hydroxylated unsaturated fatty acids exerted strong anti-inflammatory activity in superoxide anion generation (IC50 2.14-3.73 mu M) and elastase release (IC50 1.26-4.57 mu M) assays. On the other hand, in the anti-allergic assays, the unsaturated fatty acids were inactive, while hydroxylated fatty acids showed promising inhibitory activity in A23187-and antigen-induced degranulation assays (e.g., 9S-hydroxy-10E, 12Z-octadecadienoic acid, IC50 92.4 and 49.7 mu M, respectively). According to our results, the presence of a hydroxy group in the long chain did not influence the potent anti-inflammatory activity of free unsaturated acids. Nevertheless, hydroxylation of fatty acids (or their methyl esters) seems to be a key factor for the anti-allergic activity observed in the current study. Moreover, ChemGPS-NP was explored to predict the structure-activity relationship of fatty acids. The anti-allergic fatty acids formed different cluster distant from clinically used drugs. The bioactivity of T. blumei, which is historically utilized in folk medicine, might be related to the content of fatty acids and their metabolites.
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| 4. |
- Chen, Han, et al.
(författare)
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LTBP-2 confers pleiotropic suppression and promotes dormancy in a growth factor permissive microenvironment in nasopharyngeal carcinoma
- 2012
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Ingår i: Cancer Letters. - : Elsevier. - 0304-3835 .- 1872-7980. ; 325:1, s. 89-98
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Tidskriftsartikel (refereegranskat)abstract
- This study identified LTBP-2 as a pleiotropic tumor suppressor in nasopharyngeal carcinoma, which safeguards against critical malignant behaviors of tumor cells. LTBP-2 expression was significantly decreased or lost in up to 100% of NPC cell lines (7/7) and 80% of biopsies (24/30). Promoter hypermethylation was found to be involved in LTBP-2 silencing. Using a tetracycline-regulated inducible expression system, we unveiled functional roles of LTBP-2 in suppressing colony formation, anchorage-independent growth, cell migration, angiogenesis, VEGF secretion, and tumorigenicity. Three-dimensional culture studies suggested the involvement of LTBP-2 in maintenance of tumor cell dormancy in a growth factor favorable microenvironment.
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| 5. |
- Nah, Wan Jun, et al.
(författare)
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Rethinking Long-Tailed Visual Recognition with Dynamic Probability Smoothing and Frequency Weighted Focusing
- 2023
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Ingår i: Proceedings - International Conference on Image Processing, ICIP. - 1522-4880. ; , s. 435-439
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Konferensbidrag (refereegranskat)abstract
- Deep learning models trained on long-tailed (LT) datasets often exhibit bias towards head classes with high frequency. This paper highlights the limitations of existing solutions that combine class- and instance-level re-weighting loss in a naive manner. Specifically, we demonstrate that such solutions result in overfitting the training set, significantly impacting the rare classes. To address this issue, we propose a novel loss function that dynamically reduces the influence of outliers and assigns class-dependent focusing parameters. We also introduce a new long-tailed dataset, ICText-LT, featuring various image qualities and greater realism than artificially sampled datasets. Our method has proven effective, outperforming existing methods through superior quantitative results on CIFAR-LT, Tiny ImageNet-LT, and our new ICText-LT datasets. The source code and new dataset are available at \url{https://github.com/nwjun/FFDS-Loss}
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| 6. |
- Yang, P., et al.
(författare)
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Methane dynamics in an estuarine brackish Cyperus malaccensis marsh: Production and porewater concentration in soils, and net emissions to the atmosphere over five years
- 2019
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Ingår i: Geoderma. - : ELSEVIER SCIENCE BV. - 0016-7061 .- 1872-6259. ; 337, s. 132-142
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Tidskriftsartikel (refereegranskat)abstract
- Wetlands can potentially affect global climate change through their role in modulating the atmospheric concentrations of methane (CH4). Their overall CH4 emissions, however, remain the greatest uncertainty in the global CH4 budget. One reason for this is the paucity of long-term field measurements to characterize the variability of CH4 emissions from different types of wetlands. In this study, we quantified CH4 emissions from a brackish, oligohaline Cyperus malaccensis marsh ecosystem in the Min River Estuary in southeast China over five years. Our results showed substantial temporal variability of CH4 emissions from this brackish marsh, with hourly fluxes ranging from 0.7 +/- 0.6 to 5.1 +/- 3.7 mg m(-2) h(-1) (mean +/- 1 SD) during the study period. The inter-annual variability of CH4 emissions was significantly correlated with changes in soil temperature, precipitation and salinity, which highlighted the importance of long-term observations in understanding wetland CH4 dynamics. Distinct seasonal patterns in soil CH4 production rates and porewater CH4 concentrations also were observed, and were both positively correlated with CH4 emissions. The seasonal variations of CH4 emissions and production were highly correlated with salinity and porewater sulfate levels. The mean annual CH4 efflux from our site over the five-year period was 23.8 +/- 18.1 g CH4 m(-2) yr(-1), indicating that subtropical brackish tidal marsh ecosystems could release a large amount of CH4 into the atmosphere. Our findings further highlight the need to obtain high-frequency and continuous field measurements over the long term at multiple spatial scales to improve our current estimates of wetland CH4 emissions.
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| 7. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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