custom-designed routines in matlab 2018b  (MathWorks Inc)

Journal: eLife

Article Title: Learning to stand with unexpected sensorimotor delays

doi: 10.7554/eLife.65085

Figure Lengend Snippet: Data are presented across transition periods where time zero represents the transition point from baseline (20 ms) to 200 ms delayed balance control, which lasted for 8 s (between grayed out areas) and returned to baseline. Data are presented for a representative participant (left) and the group data (right; n = 7) using only data from transitions that were perceived as unexpected and the button was pressed after the delay was introduced (single participant: 77, group: 489). ( A ) Average (black line) 2 s sliding window of velocity variance over transitions with ±s.e.m. (gray lines). Time-varying variance was calculated using the movvar MATLAB function, which calculated variance over 2 s segments using a sliding window. The velocity variance trace begins to decline prior to the end of the delay period because the sliding window starts estimating variances from data points both during and after the delay. ( B ) Time-frequency plots of EVS-EMG coherence and gain (i.e., vestibular-evoked muscle responses) during the delay transition. For illustrative purposes, and because gain values are not reliable when coherence is below the significance threshold, we set coherence and gain data points where coherence was non-significant (i.e., below 99% confidence limit) to zero (dark blue). ( C ) Mean time-dependent EVS-EMG coherence and gain across the 0.5–25 Hz frequency range. For each participant and group data, an exponential decay function: f x = a * exp ⁡ - x b + c was fit to the average coherence over the 8 s period during which the 200 ms delay was present. For gain, we removed values corresponding to non-significant coherence (see single participant trace) and only fit an exponential function to the group mean gain estimate. The average perceptual detection times for the representative participant (3.2 s) and group data (3.4 s) are indicated by the dashed magenta lines, and at these times, vestibulomuscular coherence had attenuated by 83% and 90%, respectively. Group mean gain attenuated by 73% at the group average perceptual detection time.

Article Snippet: All non-statistical processing and analyses were performed using custom-designed routines in MATLAB (2018b version, MathWorks, Natick, MA, USA) and LabVIEW software (LabVIEW 2013, National Instruments).

Techniques: Control

Journal: Cell Division

Article Title: Mitotic arrest affects clustering of tumor cells

doi: 10.1186/s13008-021-00070-z

Figure Lengend Snippet: Aggregation is compromised in MCF-7 cells incubated with paclitaxel or vinorelbine. a Schematic representation of the experimental set-up. MCF-7 cells incubated or not (untreated) with paclitaxel (100 nM) or vinorelbine (20 nM) for 24 h were seeded in 96-well low-attachment (low-attach.) plates and monitored by video-microscopy for 5 h (clustering assay) (adapted from ). b Representative transmitted light microscopy images of cell aggregation at the indicated time points. Segmentation (red line) was performed using a dedicated MATLAB software. Blue lines correspond to isolated cells. c , d An automated image processing procedure was used to measure the aggregate area during the assay in the presence of paclitaxel ( c ) or vinorelbine ( d ) and the percentage of compaction was calculated from the normalized area variation relative to the initial time point. Data correspond to the mean ± SD of 48 aggregates/condition from 3 independent experiments. **P < 0.01; ****P < 0.0001 (Mann–Whitney non-parametric test)

Article Snippet: To quantify compaction over time, the cluster area was determined at each time point by automated image segmentation (red line) with a custom-designed MATLAB routine.

Techniques: Incubation, Microscopy, Light Microscopy, Software, Isolation, MANN-WHITNEY

Journal: Cell Division

Article Title: Mitotic arrest affects clustering of tumor cells

doi: 10.1186/s13008-021-00070-z

Figure Lengend Snippet: Anchorage-independent aggregation is inhibited in metaphase-blocked MCF-7 breast cancer cells. a Schematic representation of the synchronization procedure. Cells were incubated with nocodazole for 20 h, and MG132 was added to the medium for the last 30 min. Then, the culture medium was replaced by medium containing only MG132 for 1.5 h before mitotic shake-off and initiation of the aggregation assay of cells arrested in mitosis to monitor their clustering. b Control (untreated) and metaphase-synchronized MCF-7 cells were seeded in 96-well low-attachment plates and monitored by video-microscopy for 5 h. Representative transmitted light microscopy images of cell aggregation at the indicated time points. Segmentation (red line) was performed using a dedicated MATLAB software. Green lines correspond to the excluded holes, and blue to isolated cells. c Using the automated image processing data, the aggregate area was measured over time. The graph corresponds to the percentage of compaction calculated from the normalized area variation relative to the initial time point. Data correspond to the mean ± SD of 48 aggregates for each condition from 3 independent experiments. *P < 0.001 (Mann–Whitney non-parametric test)

Article Snippet: To quantify compaction over time, the cluster area was determined at each time point by automated image segmentation (red line) with a custom-designed MATLAB routine.

Techniques: Incubation, Control, Microscopy, Light Microscopy, Software, Isolation, MANN-WHITNEY