dir fluorescent dye d12731  (Thermo Fisher)

Journal: ACS Omega

Article Title: Ultrasound-Responsive Micelle-Encapsulated Mesenchymal Stem Cell-Derived EVs for the Treatment of Lower Limb Microcirculation Disease

doi: 10.1021/acsomega.3c08133

Figure Lengend Snippet: EVs release from DMAEMA- b -THPMA micelles. (A) Fluorescence image of EVs-loaded micelles. (B) Fluorescence image of EVs released after ultrasound. (C) Release profiles of EVs from micelles under different ultrasound conditions ( n = 3). (D) (db/db) mice received a tail intravenous injection of DiR-stained EVs or EVs-loaded micelles. In vivo imaging techniques were used for the visualization of the spatial distribution of EVs labeled with fluorescent markers within an organism. In the EVs group, fluorescently labeled EVs exhibited a predominant distribution within the thoracic cavity and kidney region. In the EVs+micelle group, the distribution of fluorescently labeled EVs was predominantly observed in the lower extremities following ultrasound treatment.

Article Snippet: The extracted EVs were stained with a DiR fluorescent dye kit (Thermo Fisher, D12731).

Techniques: Fluorescence, Injection, Staining, In Vivo Imaging, Labeling

Journal: BMC Biology

Article Title: Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans

doi: 10.1186/s12915-020-0745-2

Figure Lengend Snippet: Outline of the neuron ID dataset. a The expression pattern of cell-specific promoter tax-4p (modified from WormAtlas) and an example image of the strain JN3006 in which the landmark fluorescent protein was expressed by tax-4p . The maximum intensity projection of the right side of a representative animal is shown. b The list of the cell-specific promoters and the number of animals used in the neuron ID dataset. c The number of the detected and the identified nuclei in each animal. d The names of identified cells and the number of animals (“counts”) in which the cells were identified. The names and the positions of all identified cells in each animal were summarized in Figshare Dataset S1 and Additional file : Table S1

Article Snippet: Day 1 adult animals were stained by the fluorescent dye DiR (D12731, Thermo Fisher Scientific) with the standard method [ ].

Techniques: Expressing, Modification

Journal: BMC Biology

Article Title: Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans

doi: 10.1186/s12915-020-0745-2

Figure Lengend Snippet: Optimal combination of the cell-specific promoters increases the number of identified cells in an animal. a Number of positive cells and stability of expression of cell-specific promoters. A cell was counted as positive for a promoter if the cell expresses the landmark fluorescent protein in at least one animal. The positive ratio is a ratio of positive (expressing) cells over the total number of the cells (= number of tested animals). Stability of expression was calculated as an average of the positive ratio over the cells in which at least one cell is positive for the promoter. b Number of positive cells and sparseness of the expression pattern (see the “ ” section) of the cell-specific promoters. Note that, for visibility, only the several labels are shown in a and b . Fully labeled panels are shown in Additional file : Figure S8. c Visualization of the optimal combination of the cell-specific promoters. The cells in the right half of the body are shown. d A part of c is zoomed for comparison with e . e An example fluorescent image of JN3039 strain and annotated cell names. See Additional file : Figure S9 for enlarged image. f The number of the detected and the identified nuclei in each animal. g The names of identified cells and the identification ratio, which is a ratio of identified cells over the total number of the cells. The solid lines are guide for visualization

Article Snippet: Day 1 adult animals were stained by the fluorescent dye DiR (D12731, Thermo Fisher Scientific) with the standard method [ ].

Techniques: Expressing, Labeling, Comparison

Journal: BMC Biology

Article Title: Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans

doi: 10.1186/s12915-020-0745-2

Figure Lengend Snippet: An automatic annotation method and evaluation. a The outline of the atlas generation method. b The outline of the automatic annotation method. The schemes of bipartite graph matching and majority voting are shown. c Error rates of the automatic annotation method for the animals in the neuron ID dataset. The names of the cells were estimated based on their positions. The error rate was calculated as 1 – ( N correct )/( N annotated ) for each animal, where N annotated is the number of human-annotated cells (ground truth) and N correct is the number of cells whose annotation by the algorithm was correct. Cells un-annotated by human were not included in the calculation of error rate. The rank R indicates that it is considered correct if the correct annotation appeared in the top R estimations by the algorithm. The error rates were evaluated by cross-validation, and mean ± standard deviation over well-annotated six animals is shown. d Error rates of the automatic annotation method for the strain JN3039 that expresses the fluorescent landmarks. The names of the cells were estimated based on their positions with or without the expression of landmark promoters. Mean ± standard deviation over 15 animals is shown. e The automatic annotation method was integrated in the graphical user interface roiedit3d that enables feedback between automatic and manual annotations. f The effect of manual correction on the error rate of automatic annotation. A wrong annotation of a cell in rank 1 estimation for JN3039 (see Fig. 4d) was corrected, and the automatic annotation method was performed by using the correction information. This step was repeated sequentially

Article Snippet: Day 1 adult animals were stained by the fluorescent dye DiR (D12731, Thermo Fisher Scientific) with the standard method [ ].

Techniques: Biomarker Discovery, Standard Deviation, Expressing