Journal: Journal of visualized experiments : JoVE

Article Title: Direct-Coupled Electroretinogram (DC-ERG) for Recording the Light-Evoked Electrical Responses of the Mouse Retinal Pigment Epithelium

doi: 10.3791/61491

Figure Lengend Snippet: Table of Materials

Article Snippet: Maintain at RT In-Line Filter Whatman 6722–5001 To protect vacuum pump from aerosols Low Noise Cable for Microelectrode Holders WPI Inc 5372 Suggested for improving the length and placement of the cables and electrode holder assemblies Magnetic Ball Joint WPI Inc 500871 For magnetically positioning the electrode holder assembly on the stage MatLab Mathworks MatLab: For editing the analysis software MatLab Curvefit Toolbox Mathworks Toolbox for MatLab (only required for editing the analysis software) MatLab Compiler Mathworks Toolbox for MatLab (only required for editing and re-releasing the analysis software) MatLab Runtime version 9.5 Mathworks R2018b (9.5) Required to run the analysis software: https://www.mathworks.com/products/compiler/matlab-runtime.html Microelectrode Holders (45 degrees) WPI Inc MEH345–15 For holding the capillaries Needle (25 ga) Covidien 8881250313 For filling the capillary tubes with HBSS Needle (ground) Electrode Rhythmlink 13mm - one elctrode Subdermal needle electrode (ground) for mouse (13mm long, 0.4mm diameter needle, 1.5m leadwire) Regulator/Power Conditioner Furman P-1800 Or equivalent to remove DC-offset from noise introduced through power line Syringe (12 mL) Monoject 1181200777 For filling the capillary tubes with HBSS T-clip Cole-Parmer 06852–20 For electrode holder assembly Vacuum Desiccator Bel-Art 420120000 Clear polycarbonate bottom & cover Pharmacological treatment Lubricant eye gel Alcon 0078–0429-47 Helps lubricate corneal surface and maintain electrical contact with capillary electrodes Phenylephrine Hydrochloride 2.5% Akorn 17478–201-15 Short acting mydriatic eye drops (for pupil dilation) Proparacaine Hydrochloride 0.5% Akorn 17478–263-12 Local anesthetic for ophthalmic instillation Tropicamide 0.5% Akorn 17478–101-12 Short acting mydriatic eye drops (for pupil dilation) Xylazine AnaSed sc-362949Rx Analgesic and muscle relaxant Zetamine (Ketamine HCl) VetOne 501072 Anesthetic for intramuscular injections Open in a separate window list-behavior=simple prefix-word= mark-type=none max-label-size=4 1.1.

Techniques: Convection, Software, Eye Drops

Journal: STAR Protocols

Article Title: Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP

doi: 10.1016/j.xpro.2022.101991

Figure Lengend Snippet:

Article Snippet: Create your own run_matlab directory and install the MATLAB Compiler Runtime (MATLAB version R2018b, MCR version 9.5) therein: {Bash} > run_matlab install -d run_matlab -v R2018b -r 9.5 a.

Techniques: ChIP-sequencing, Software

Journal: Advances in Radiation Oncology

Article Title: An Automatic Deep Learning–Based Workflow for Glioblastoma Survival Prediction Using Preoperative Multimodal MR Images: A Feasibility Study

doi: 10.1016/j.adro.2021.100746

Figure Lengend Snippet: Deep learning (DL)–based feature extraction scheme using VGG19. VGG19 contains 16 convolutional layers, 5 max-pooling layers, and 3 fully connected layers. The average-pooling layers were used for extracting DL-based features. Feature maps and feature vectors after every layer are shown as cuboids and rectangles, respectively. The feature map depth and feature number are shown. A concatenation of fluid-attenuated inversion recovery (FLAIR), T2-weighted (T2w), and contrast-enhanced T1-weighted (CE-T1w) regions of interest (ROIs) was input into the pretrained VGG19 for feature extraction. By average-pooling along the spatial dimensions, 1472 DL-based features were extracted from max-pooling feature maps. Abbreviations: Conv = convolutional layer; ReLU = rectified linear unit.

Article Snippet: We used a pretrained VGG19 that is available in the deep learning toolbox (version 12.0) from MATLAB (version 9.5, R2018b).

Techniques: Extraction

Journal: Data in Brief

Article Title: Data on yields, sugars and glycosidic-linkage analyses of coffee arabinogalactan and galactomannan mixtures and optimization of their microwave assisted extraction from spent coffee grounds

doi: 10.1016/j.dib.2019.103931

Figure Lengend Snippet: Specifications table

Article Snippet: How data was acquired , Microwave assisted extraction of polysaccharides from spent coffee grounds was conducted using a microwave Labstation (MicroSYNTH, Milestone srl.) Sugar contents were determined as alditol acetates by GC (GC-FID, Perkin-Elmer) Glycosidic-linkage analyses were carried out using partially methylated alditol acetates by GC-MS (Agilent Technologies 6890 N Network with a 5973 Mass selective detector) Statistical analyses was done using Matlab 9.5 (R2018b).

Techniques: Extraction, Methylation