Article Figures & Data
Figures
Visual Abstract
- Figure 1.
Stages of the development of the method. (1) Pipeline of algorithm evaluation and template selection and (2) iterative feature enhancement process.
- Figure 2.
Network and CB detection pipeline. A, Steps of the novel method. The detected spikes are pooled into a histogram, and the ISIN threshold is defined for initial NB detection. B, The first five steps are visualized with single-compartment raster segments of various lengths. The green and red vertical lines represent the start and end times, respectively, of the captured local NBs. The blue arrows in STEPS 3 and 4 indicate limitations of the simple “minimum participating channels” criterion. C, The last step (STEP 6) is shown as a combined raster of three MEMO compartments. The purple polygons at the top depict time intervals with detected circuitry-level bursts involving all three compartments; the orange polygons indicate intermediate circuitry-level bursts with two-compartment synchronicity; and the yellow polygons indicate local NBs in a single compartment. The length of the polygons corresponds to the duration of the corresponding phenomenon.
- Figure 3.
Cumulative circuitry-level burst duration. The scatter plots depict scores for the derived metric among 5,000 simulations for 11 MEMOs labeled with their MEMO platform identification codes. The simulations included compartmental NB shuffling for each plate for two conditions: baseline and KA exposure. The real observed condition scores are indicated with red triangles. The bold line on each scatter plot represents the mean value for the scores of 5,000 simulations together with the single entity calculated from the observed data.
- Figure 4.
Pairwise comparisons. A, Six of the eight NB output parameters from the proximal C compartment and B, Three of the eight CB output parameters that showed significant (p < 0.05) KA-induced alterations prior to Bonferroni’s adjustment of the significance level. Wilcoxon matched-pairs signed-rank test. The color codes for the corresponding MEMO labels are shown on the side. The bar charts with whiskers present means and standard deviations. n = 11 for each pairwise comparison. The p values are presented on top of each plot. The NB/CB parameters with alterations that remained significant (p < 0.00625) after Bonferroni’s correction for the families of eight hypotheses are marked with asterisk *. The full lists of pairwise comparisons for the NB and CB parameters are available in Extended Data Figures 4-1–4-4.
- Figure 5.
Binned heatmap of baseline-normalized percentage changes in eight parameters in three compartments and at the circuitry level among 11 MEMOs. The last 5fmin bin of the baseline recording was used to calculate the percentage change in the subsequent six 5fmin bins recorded after KA exposure. The upper and lower limits of percentage change were set to 50% for visualization purposes.
- Figure 6.
Functional connectivity analysis results before and after KA exposure. In the upper half of the figure, the average intracompartmental and intercompartmental average connectivity values are plotted for both experimental conditions for all 11 MEMOs. The exposed proximal C compartment is highlighted in purple. The first scheme embeds the compartment labels. The lower half of the figure shows the heatmap of percentage changes in the connectivity values after KA exposure. The upper and lower limits of percentage change were set to 50% for visualization purposes. Extended Data Figure 6-1 shows pairwise comparisons of average intra- and intercompartmental CorSE values before and after KA exposure among 11 MEMOs. Extended Data Figure 6-2 presents pairwise comparisons of average intra- and intercompartmental CorSE values within each MEMO.
Tables
Approach i ii iii iv v vi Detailed description and usage information Yes Yes Yes Yes Yes Yes Parametrization and adaptivity Internal adaptivity is due to the nature of the algorithm The ISI distribution reflects the data specifics The ISIN distribution reflects the data specifics Automatic adaptive firing rate threshold is present. A likely good fit to the data may be achieved with parameter tuning Four main parameters are available to adjust the detection Code obtained from the author Yes Yes Yes Yes No No Code description Yes Yes Yes Yes No No Verdict for acquired data Some tendency to break NBs into shorter components Good performance but NB borders appeared to be widened; NB merging due to tonic spiking in, e.g., one channel Sufficient adaptivity for the test data; NB borders assigned relatively well The method detected some short NBs in addition to evident synchronous patterns Not available Not available Visualizations and a quantitative comparison of the NB detection results for approaches i–iv with available codes are shown in Extended Data Table 1-1.
N2698 N2699 N2704 N2705a,b N2708a,b N2711a,b N2712b N2713 N2714a,b N2715b N2716 NB A 158 189 126 179 70 121 68 85 113 76 74 NB B 85 64 189 179 70 121 130 161 113 76 74 NB C 152 128 63 179 70 121 68 168 113 159 84 ICB AB 10 0 64 0 0 0 0 2 0 0 13 ICB BC 0 0 0 0 0 0 0 82 0 0 0 ICB AC 76 64 0 0 0 0 0 0 0 0 0 ICB total 86 64 64 0 0 0 0 84 0 0 13 CB 76 64 63 179 70 121 68 85 113 76 61 The top row shows the MEMO platform identification code. The table lists the numbers of detected synchronous activity patterns among 11 MEMOs at baseline. ICB labels are created from the two letters of the corresponding involved compartment labels. The ICBs that were associated with the CBs were not considered and hence were not included in the table. ICB refers to intermediate circuitry burst, and CB refers to circuitry burst. The a symbol indicates the cases of full synchrony in the network, and the b symbol indicates the cases without intermediate circuitry synchronization. Table 2-1 presents the numbers of the different synchronous patterns after KA exposure.
Table 1-1
The figure demonstrates an example of the detection results of the 4 selected algorithms (I, ii, iii and iv) with available codes. A, The default parameters of the methods were used where present. The raster segments visualize the same segment of baseline data from the C compartment of a MEMO. The green and red vertical lines represent the start and end timings, respectively, of the captured local NBs for each method. Very short NB instances detected within the presented segment were not depicted in the raster plots due to the selected temporal resolution, and the number of such NBs is indicated above each raster plot. B, The histogram shows the distributions of NBs’ durations detected by each of the methods when applied to the MEMO data at baseline condition. Download Table 1-1, TIF file.
Pseudocode
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Table 2-1
The top row shows the MEMO platform identification code. The table lists the numbers of detected synchronous activity patterns among 11 MEMOs after KA exposure. ICB labels are created from the two letters of the corresponding involved compartment labels. The ICBs that were associated with the CBs were not considered and hence were not included in the table. ICB refers to intermediate circuitry burst, and CB refers to circuitry burst. Download Table 2-1, DOCX file.
Figure 4-1
Pairwise comparisons of NB parameters before and after KA treatment in the distal A compartment. The color codes for the corresponding MEMO codes are shown on the side. The bar charts with whiskers present means and standard deviations. n = 11 for each pairwise comparison. p values are presented on top of each plot. The Wilcoxon matched-pairs signed-rank test was used. Download Figure 4-1, TIF file.
Figure 4-2
Pairwise comparisons of NB parameters before and after KA treatment in the distal B compartment. The color codes for the corresponding MEMO codes are shown on the side. The bar charts with whiskers present means and standard deviations. n = 11 for each pairwise comparison. p values are presented on top of each plot. The Wilcoxon matched-pairs signed-rank test was used. Download Figure 4-2, TIF file.
Figure 4-3
Pairwise comparisons of NB parameters before and after KA treatment in the proximal C compartment. The color codes for the corresponding MEMO codes are shown on the side. The bar charts with whiskers present means and standard deviations. n = 11 for each pairwise comparison. p values are presented on top of each plot. The Wilcoxon matched-pairs signed-rank test was used. Download Figure 4-3, TIF file.
Figure 4-4
Pairwise comparisons of CB parameters before and after KA treatment at the circuit level. The color codes for the corresponding MEMO codes are shown on the side. The bar charts with whiskers present means and standard deviations. n = 11 for each pairwise comparison. p values are presented on top of each plot. The Wilcoxon matched-pairs signed-rank test was used. Download Figure 4-4, TIF file.
Figure 6-1
Pairwise comparisons of average intra- and intercompartmental CorSE values before and after KA treatment among MEMOs. The color codes for the corresponding MEMO codes are shown on the side. The bar charts with whiskers present means and standard deviations. n = 11 for each pairwise comparison. p values are presented on top of each plot. The Wilcoxon matched-pairs signed-rank test was used. Download Figure 6-1, TIF file.
Figure 6-2
Pairwise comparisons of average intra- and intercompartmental CorSE values within each MEMO. Symbolic codes for corresponding connectivity are shown on the side. Download Figure 6-2, TIF file.
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