| 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. |
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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. |
- Kristanl, Matej, et al.
(author)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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In: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 5. |
- Fang, Wenzheng, et al.
(author)
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Dual-Isotope Constraints on Seasonally Resolved Source Fingerprinting of Black Carbon Aerosols in Sites of the Four Emission Hot Spot Regions of China
- 2018
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In: Journal of Geophysical Research - Atmospheres. - 2169-897X .- 2169-8996. ; 123:20, s. 11735-11747
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Journal article (peer-reviewed)abstract
- Despite much recent efforts, the emission sources of black carbon (BC) aerosols. central input to understanding and predicting environmental and climate impact. remain highly uncertain. Here we present observational delta C-13/Delta C-14-based constraints on the sources of BC aerosols over the four seasons in each of the four key hot spot emission regions of China: Beijing-Tianjin-Hebei (BTH-Wuqing; where Wuqing is the sampling location), Yangtze River Delta (YRD-Haining), Pearl River Delta (PRD-Zhongshan), and Sichuan Basin (SC-Deyang). Overall, BC loadings were highest in winter, yet elevated loadings were also observed in other seasons, for example, spring at SC-Deyang and fall at PRD-Zhongshan. Annually, the dominant BC sources were coal (50 +/- 20%) for BTH-Wuqing, liquid fossil for YRD-Haining (46 +/- 8%) and PRD-Zhongshan (48 +/- 18%), whereas liquid fossil (42 +/- 17%) and biomass burning (41 +/- 14%) equally affected SC-Deyang. There is also different but distinct seasonalities in BC sources for the different sites. As an example, for BTH-Wuqing coal burning increased from summer to winter, while summer and spring BTH-Wuqing were more influenced by liquid fossil. In contrast, for YRD-Haining, the relative importance of emission sources was more constant over the year. These quantitative observational constraints on source-seasonality of BC aerosols in receptor sites located in China's four key economic zones highlight that regulatory control on BC aerosol emissions from different fuels should consider both seasonal and regional variations. Our results also suggest that models on estimates of BC-induced climate and air quality should consider variations over both regional and seasonal scales.
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| 6. |
- Kristan, Matej, et al.
(author)
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The Visual Object Tracking VOT2015 challenge results
- 2015
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In: Proceedings 2015 IEEE International Conference on Computer Vision Workshops ICCVW 2015. - : IEEE. - 9780769557205 ; , s. 564-586
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge 2015, VOT2015, aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 62 trackers are presented. The number of tested trackers makes VOT 2015 the largest benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the appendix. Features of the VOT2015 challenge that go beyond its VOT2014 predecessor are: (i) a new VOT2015 dataset twice as large as in VOT2014 with full annotation of targets by rotated bounding boxes and per-frame attribute, (ii) extensions of the VOT2014 evaluation methodology by introduction of a new performance measure. The dataset, the evaluation kit as well as the results are publicly available at the challenge website(1).
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| 7. |
- Kristan, Matej, et al.
(author)
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The Visual Object Tracking VOT2016 Challenge Results
- 2016
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In: COMPUTER VISION - ECCV 2016 WORKSHOPS, PT II. - Cham : SPRINGER INT PUBLISHING AG. - 9783319488813 - 9783319488806 ; , s. 777-823
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2016 aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 70 trackers are presented, with a large number of trackers being published at major computer vision conferences and journals in the recent years. The number of tested state-of-the-art trackers makes the VOT 2016 the largest and most challenging benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the Appendix. The VOT2016 goes beyond its predecessors by (i) introducing a new semi-automatic ground truth bounding box annotation methodology and (ii) extending the evaluation system with the no-reset experiment.
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| 8. |
- Wang, Chunyu, et al.
(author)
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Water use efficiency control for a maize field under mulched drip irrigation
- 2023
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 857
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Journal article (peer-reviewed)abstract
- Agricultural ecosystem water use efficiency (WUE) is an important indicator reflecting carbon-water coupling, but its control mechanisms in managed fields remain unclear. In order to reveal the influencing factors of WUE in the agricultural field under mulched drip irrigation (DM), we carried out the 8-year continuous observations in a maize field from Northwestern China. The structural equation model, relative importance analysis and principal component analysis were used to quantify the regulation effects of environmental and biological factors on WUE at different time scales, in different growth stages and under different hydrothermal conditions. The results showed that annual WUE varied between 2.18 g C Kg−1 H2O and 3.60 g C Kg−1 H2O, with a multi-year mean of 2.91 g C Kg−1 H2O. The total effects of air temperature on the daily WUE in the whole growth period, the vegetative growth stage, the warm and dry years, the cold and wet years, and the warm and wet years were the largest, with values of 0.61, 0.80, 0.70, 0.70 and 0.91 respectively. However, vapor pressure deficit and net radiation had the largest total effect in the cold and dry years (−0.63) and the reproductive growth stage (−0.49), respectively. Leaf biomass played a leading role in regulating the daily and interannual WUE, and the relative importance of leaf biomass to WUE in the vegetative growth stage was up to 75 %. In the warm and wet years, the relative importance of root biomass to WUE was 33 %, slightly higher than that of leaf biomass (31 %). At the same time, we found that Ta has the potential to increase WUE under future climate warming. Our results improve the understanding of carbon-water coupling mechanisms and provide important enlightenment on how crop ecosystems should adapt to future climate change.
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| 9. |
- Wang, Fang, et al.
(author)
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Emerging contaminants: A One Health perspective
- 2024
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In: Innovation. - 2666-6758. ; 5
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Research review (peer-reviewed)abstract
- Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
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| 10. |
- Yu, Kuangyou, et al.
(author)
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Characterizing and sourcing ambient PM2.5 over key emission regions in China III : Carbon isotope based source apportionment of black carbon
- 2018
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In: Atmospheric Environment. - : Elsevier BV. - 1352-2310 .- 1873-2844. ; 177, s. 12-17
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Journal article (peer-reviewed)abstract
- Regional haze over China has severe implications for air quality and regional climate. To effectively combat these effects the high uncertainties regarding the emissions from different sources needs to be reduced. In this paper, which is the third in a series on the sources of PM2.5 in pollution hotspot regions of China, we focus on the sources of black carbon aerosols (BC), using carbon isotope signatures. Four-season samples were collected at two key locations: Beijing-Tianjin-Hebei (BTH, part of Northern China plain), and the Pearl River Delta (PAD). We find that that fossil fuel combustion was the predominant source of BC in both BTH and PRD regions, accounting for 75 +/- 5%. However, the contributions of what fossil fuel components were dominating differed significantly between BTH and PRD, and varied dramatically with seasons. Coal combustion is overall the all-important BC source in BTH, accounting for 46 +/- 12% of the BC in BTH, with the maximum value (62%) found in winter. In contrast for the PAD region, liquid fossil fuel combustion (e.g., oil, diesel, and gasoline) is the dominant source of BC, with an annual mean value of 41 +/- 15% and the maximum value of 55% found in winter. Region- and season-specific source apportionments are recommended to both accurately assess the climate impact of carbonaceous aerosol emissions and to effectively mitigate deteriorating air quality caused by carbonaceous aerosols.
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