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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- 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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| 5. |
- 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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- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2015 challenge results
- 2015
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Ingår i: Proceedings 2015 IEEE International Conference on Computer Vision Workshops ICCVW 2015. - : IEEE. - 9780769557205 ; , s. 564-586
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Konferensbidrag (refereegranskat)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. |
- Li, Qiang, et al.
(författare)
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Microbial Necromass, Lignin, and Glycoproteins for Determining and Optimizing Blue Carbon Formation
- 2024
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 58, s. 468-479
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Tidskriftsartikel (refereegranskat)abstract
- Coastal wetlands contribute to the mitigation of climate change through the sequestration of “blue carbon”. Microbial necromass, lignin, and glycoproteins (i.e., glomalin-related soil proteins (GRSP)), as important components of soil organic carbon (SOC), are sensitive to environmental change. However, their contributions to blue carbon formation and the underlying factors remain largely unresolved. To address this paucity of knowledge, we investigated their contributions to blue carbon formation along a salinity gradient in coastal marshes. Our results revealed decreasing contributions of microbial necromass and lignin to blue carbon as the salinity increased, while GRSP showed an opposite trend. Using random forest models, we showed that their contributions to SOC were dependent on microbial biomass and resource stoichiometry. In N-limited saline soils, contributions of microbial necromass to SOC decreased due to increased N-acquisition enzyme activity. Decreases in lignin contributions were linked to reduced mineral protection offered by short-range-ordered Fe (FeSRO). Partial least-squares path modeling (PLS-PM) further indicated that GRSP could increase microbial necromass and lignin formation by enhancing mineral protection. Our findings have implications for improving the accumulation of refractory and mineral-bound organic matter in coastal wetlands, considering the current scenario of heightened nutrient discharge and sea-level rise.
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| 8. |
- Shi, Shu Wen, et al.
(författare)
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Influence of local anesthesia on the outcomes of non-surgical periodontal treatment
- 2020
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Ingår i: Chinese Medical Journal. - 0366-6999. ; 133:16, s. 1908-1914
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: There is limited evidence of the effects of local anesthesia (LA) on outcomes of non-surgical periodontal treatment (NSPT), in particular among the Chinese. This retrospective cohort study aimed to evaluate the effects of LA on short-term treatment outcomes of NSPT and to determine under what circumstances LA should be prescribed to improve these outcomes. METHODS: Data from periodontal examinations of 3980 patients were used. The data were from 3-month re-evaluation records of an electronic periodontal charting record system in the Department of Periodontology of Peking University School and Hospital of Stomatology from June 2008 to January 2015. Descriptive analyses included changes in probing depth (PD) and the Mazza bleeding index (BI). Two-level (patient and tooth) logistic regression models and three-level (patient, tooth, and site) linear regression models were constructed to analyze the influence of LA on PD for all teeth/sites and teeth/sites with an initial PD ≥ 5 mm. Decreases in PD and BI at sites under LA using the initial PD were also compared. RESULTS: A significantly higher mean decrease in PD after NSPT was found in the LA group than in the no local anesthesia (NLA) group (0.98 vs. 0.54 mm, t = 24.12, P < 0.001). A significantly higher probability of decreases was found in the LA group in BI (percentages of teeth with BI > 1 and BI > 2) for all teeth (16.7% vs. 13.8%, t = 3.75, P < 0.001; 34.7% vs. 28.1%, t = 6.73, P < 0.001) and PD for teeth with PD ≥ 5 mm (32.3% vs. 17.3%, t = 28.48, P < 0.001). The difference in PD between the LA and NLA groups increased as the initial PD increased. The difference between the two groups was 0.12 to 0.22 mm for sites with a baseline PD < 7 mm; however, it increased to 0.41 to 1.37 mm for sites with a baseline PD ≥ 7 mm. CONCLUSIONS: LA improved the decrease in PD after NSPT. Root debridement at sites with initial PD ≥ 7 mm should be performed under routine LA.
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| 9. |
- Chen, Jie, 1974-, et al.
(författare)
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Revisiting Late Pleistocene Loess–Paleosol Sequences in the Azov Sea Region of Russia : Chronostratigraphy and Paleoenvironmental Record
- 2022
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Ingår i: Frontiers in Earth Science. - : Frontiers Media S.A.. - 2296-6463. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Loess-paleosol sequences are the most intensively studied terrestrial archives used for the reconstruction of Late Pleistocene environmental and climatic changes in the Azov Sea region, southwest Russia. Here we present a refined chronostratigraphy and a multiproxy record of Late Pleistocene environmental dynamics of the most complete and representative loess–paleosol sequences (Beglitsa and Chumbur-Kosa sections) from the Azov Sea region. We propose a new chronostratigraphy following the Chinese and Danubean loess stratigraphic models that refines the subdivision of the Last Interglacial paleosol (S1) complex in two Azov Sea sites, resolve the uncertainty of the stratigraphic position of the weakly developed paleosol (L1SSm) in Beglitsa section, and allow for direct correlation of the Azov Sea sections with those in the Danube Basin and the Chinese Loess Plateau. More importantly, it may serve as a basis for better constraining local and regional chronostratigraphic correlations, and facilitate the interpretation of climatic connections and possible forcing mechanisms responsible for the climatic trends in the region. In addition, a general succession of environmental dynamics is reconstructed from these two vital sections, which is broadly consistent with other loess records in the Dnieper Lowland and Lower Danube Basin, demonstrating similar climatic trends at Glacial–Interglacial time scales. Furthermore, our results have important implications for the chronostratigraphic representativeness of Beglitsa as a key regional loess section and for the reconstruction of the temporal and spatial evolution of Late Pleistocene climate in the Azov Sea region.
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| 10. |
- Dang, D. F., et al.
(författare)
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Manipulating backbone structure with various conjugated spacers to enhance photovoltaic performance of D-A-type two-dimensional copolymerse
- 2014
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Ingår i: Organic Electronics: physics, materials, applications. - : Elsevier BV. - 1566-1199. ; 15:11, s. 2876-2884
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Tidskriftsartikel (refereegranskat)abstract
- A class of low band-gap two-dimensional conjugated polymers of PBDTT-FQ PBDTT-TQ PBDTT-BTQ and PBDTT-TTQ was designed and synthesized, which contains the same di(alkylthiophene)-substituted benzo[1,2-b:4,5-b']dithiophene (BDTT) and 6,7-difluoro-quinoxaline (Q) units, as well as various conjugated spacers of furan, thiophene, bithiophene and thieno[3,2-b]thiophene in the main chain. Significant effect of the varied spacers between the BDTT and Q units on the thermal, optical, electrochemical and photovoltaic properties was investigated and observed for these two-dimensional copolymers in the polymer solar cells. The maximum power conversion efficiency of 5.9% with a short circuit current of 13.7 mA/cm(2) and a fill factor of 0.56 was obtained for the PBDTT-TQ with thiophene spacer in the bulk hetero-junction PSCs using [6,6]-phenyl-C-71-butyric acid methyl ester as acceptor.
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