boxplot function in r studio  (RStudio)

Journal: Nature Communications

Article Title: Cerebellar stimulation prevents Levodopa-induced dyskinesia in mice and normalizes activity in a motor network

doi: 10.1038/s41467-022-30844-0

Figure Lengend Snippet: a Experimental timeline. Dyskinetic mice (LID, magenta): 6 weeks of levodopa treatment. Preventive mice (LID_PREV, blue): 6 weeks of levodopa treatment + 4 weeks of cerebellar stimulation. Corrective mice (LID_CORR, green): 6 weeks of levodopa treatment + 2 weeks of cerebellar stimulation. AIMs corresponds to the evaluation of Abnormal Involuntary Movements (LID). b Sagittal schematic of a mouse brain showing cerebello-thalamo-cortical and -striatal pathways, ChR2-YFP in Purkinje cells (PC + ChR2, green), and injection site of 6-OHDA or saline. M1: Primary motor cortex, ST: striatum, VAL: Ventroanterior-ventrolateral complex of the thalamus, PF: Parafascicular nucleus of the thalamus, SNc: Substantia nigra pars compacta , CN: cerebellar nuclei, CrusII: Crus2 of the ansiform lobule. c Upper panel : Coronal section from a mouse unilaterally-lesioned with 6-OHDA stained with anti-tyrosine hydroxylase (TH). Scale bar: 0.5 mm. Bottom panel : Boxplot showing the average loss of striatal TH-positive fibers (%) between the lesioned and the intact striatum in SHAM (gray, N = 17), LID (magenta, N = 13), LID_CORR (green, N = 10), and LID_PREV (blue, N = 17). d Examples of orolingual (top), axial (middle), and limb (bottom) levodopa-induced dyskinesia in dyskinetic mice. e Boxplot showing the sum of oral LID scores across the 6 weeks of levodopa treatment (6 mg/kg) (light gray bar) for SHAM ( N = 18), LID ( N = 19); LID_CORR ( N = 17); LID_PREV ( N = 24). f Boxplot showing the sum of axial LID across the 6 weeks of levodopa treatment (6 mg/kg) (light gray bar) for SHAM ( N = 12), LID ( N = 8), LID_CORR ( N = 14), LID_PREV ( N = 6). g Boxplot showing the sum of limb LID scores across the 6 weeks of levodopa treatment (6 mg/kg) (light gray bar) for SHAM (N = 14), LID ( N = 9), LID_CORR ( N = 15), LID_PREV ( N = 9). Boxplots represents the lower and the upper quartiles as well as the median of LID score. Each boxplot corresponds to 1 week. Vertical lines represent the median ± the standard deviation. Isolated points represent outliers of the distribution. Stripped blue lines: weeks of theta-burst PC stimulation. Kruskal-Wallis test with pairwise two-sided Wilcoxon test and Benjamini & Hochberg correction. *** p < 0.001; ** p < 0.01; * p < 0.05; * compared to SHAM; # to LID. Source data are provided as a Source Data file. See also Table .

Article Snippet: Unless otherwise stated, data are presented as boxplots (from boxplot function in R Studio software 4.1.2).

Techniques: Injection, Saline, Staining, Standard Deviation, Isolation

Journal: Nature Communications

Article Title: Cerebellar stimulation prevents Levodopa-induced dyskinesia in mice and normalizes activity in a motor network

doi: 10.1038/s41467-022-30844-0

Figure Lengend Snippet: a Left : Experimental timeline. Right : Schematic of electrode implantation in the interposed nucleus (IN), ChR2-YFP expression in Purkinje cells (PC + ChR2, green) and injection site of 6-OHDA or saline. ST: Striatum; SNc: substantia nigra pars compacta ; M1: Primary motor cortex; PF: Parafascicular nucleus of the thalamus. b Left : Coronal section from L7-ChR2-YFP mouse. Red lines: electrode’s trajectory. Dotted white lines: IN, dentate (DN), and fastigial (FN) nuclei. Scale bar: 0.5 mm. Crus2: Crus2 of the ansiform lobule. Right : PC expressing YFP. Scale bar: 20 µm. c Top : Theta-burst protocol. Middle : Raster plot of a cerebellar nuclei (CN) neuron for each stimulation. Dotted line: Basal firing rate (FR) before the onset of stimulation. Blue box: Time of optogenetic stimulation. Bottom : Summary of CN firing profiles ( n = 27; N = 3) exhibiting a strong inhibition (>90%) during PC stimulation. The firing rate of each unit was normalized to its baseline. Shaded lines: mean ± the standard deviation (std). d Examples of raw traces recorded in IN in LID ( top ) and SHAM ( bottom ) and their associated spike shape. e Firing rate (Hz) across 9 weeks in IN. Boxplots show the median (horizontal bars) over 4 categories of weeks. First boxplot: 2 nd and 3 rd weeks; second boxplot: 4th and 5th weeks when levodopa begins; third boxplot: 6th and 7th weeks; last boxplot: 8th and 9th weeks when stimulation stopped. f Coefficient of variation 2 (cv2.isi) across 9 weeks in IN. Same order of boxplot as panel e . Gray = SHAM ( N = 5); Magenta = LID ( N = 3); Blue = LID_PREV ( N = 4). Light gray lines: 6 weeks of levodopa treatment (3 boxplots; 6 mg/kg). Stripped blue lines: weeks of theta-burst stimulation. Boxplot represents the lower and the upper quartiles as well as the median rate (horizontal bars). Vertical lines represent the median ± std. Isolated points represent outliers of the distribution. Welch Anova with two-sided Games Howell post-hoc test and one-way Anova’s with two-sided Tukey post-hoc test based on Levene test. *** p < 0.001; ** p < 0.01; * p < 0.05; ns: p > 0.5. Source data are provided as a Source Data file. See also Tables – .

Article Snippet: Unless otherwise stated, data are presented as boxplots (from boxplot function in R Studio software 4.1.2).

Techniques: Expressing, Injection, Saline, Inhibition, Standard Deviation, Isolation

Journal: Nature Communications

Article Title: Cerebellar stimulation prevents Levodopa-induced dyskinesia in mice and normalizes activity in a motor network

doi: 10.1038/s41467-022-30844-0

Figure Lengend Snippet: a Top : Experimental timeline. Bottom : Schematic of electrode implantation in the primary motor cortex (M1) and the parafascicular nucleus of the thalamus (PF), ChR2-YFP expression in the Purkinje cells (PC + ChR2, green), and injection site of 6-OHDA or saline. ST: Striatum; SNc: substantia nigra pars compacta ; CN: cerebellar nuclei: VAL: Ventroanterior-ventrolateral complex of the thalamus. b Top: Coronal section from L7-ChR2-YFP mouse showing the electrode’s trajectory (dotted yellow line) and the lesion site (red circle) in layer 5 of oM1. Scale bar: 0.5 mm. Bottom: Coronal section from L7-ChR2-YFP mouse showing the electrode’s trajectory (dotted yellow line) and the lesion site (red circle) in PF. Scale bar: 0.5 mm. c Firing rate (Hz) across 9 weeks in M1. Boxplots show the median rate (horizontal bars), over 4 categories of weeks. First boxplot: 2nd and 3rd week of the protocol, second boxplot: 4th and 5th weeks when levodopa begins, third boxplot: 6th and 7th weeks, last boxplot: 8th of the protocol when stimulation stopped. Gray = SHAM ( N = 5); Magenta = LID ( N = 4); Blue = LID_PREV ( N = 8). Light gray lines: 6 weeks of levodopa treatment (3 boxplots; 6 mg/kg). Stripped blue lines: weeks of theta-burst stimulation. d Firing rate (Hz) across 9 weeks in PF. Same order of boxplot as panel c Gray = SHAM ( N = 5); Magenta = LID ( N = 4); Blue = LID_PREV ( N = 8). Light gray lines: 6 weeks of levodopa treatment (3 boxplots; 6 mg/kg). Stripped blue lines: weeks of theta-burst stimulation. Boxplot represents the lower and the upper quartiles as well as the median of the firing rate (horizontal bars). Vertical lines represent the median ± std. Isolated points represent outliers of the distribution. One-way Anova with two-sided Tukey HSD post-hoc test. *** p < 0.001; ** p < 0.01; * p < 0.05; ns: p > 0.5. Source data are provided as a Source Data file. See also Tables and .

Article Snippet: Unless otherwise stated, data are presented as boxplots (from boxplot function in R Studio software 4.1.2).

Techniques: Expressing, Injection, Saline, Isolation

Journal: Nature Communications

Article Title: Cerebellar stimulation prevents Levodopa-induced dyskinesia in mice and normalizes activity in a motor network

doi: 10.1038/s41467-022-30844-0

Figure Lengend Snippet: a Experimental timeline. b Schematic of mouse coronal sections showing the injection site of the retrograde CAV2-Cre-GFP in the parafascicular nucleus (PF, green) ipsilateral-to-the-lesion ( top, left ) and the injection site of the anterograde Cre-dependent pAAV-hSyn-DIO-hM4Di-mCherry in the three cerebellar nuclei (CN, red) contralateral-to-the-lesion. c Coronal section showing the injection site of retrograde CAV2-Cre-GFP in PF. Red dotted lines: needle’s trajectory. White dotted lines: limits of PF. Scale bar: 100 μm. d Coronal section showing the expression of anterograde hM4Di-mCherry in neurons (red) of CN. FN: fastigial nucleus; INant: interposed nucleus, anterior part; InDL: interposed nucleus, dorsolateral hump; Lat: lateral nucleus. Blue = DAPI; green = GFP and YFP; Red = mCherry. Scale bar: 100 μm. Insert: Postmortem histology showing hM4Di-mCherry-expressing neurons in (i) FN, (ii) IN, and (iii) DN. Scale bars: 20 µm. e Top . Pie chart representing the proportions of neurons in CN expressing hM4Di-mCherry (in magenta) and projecting to PF compared to other types of cells (in blue). Bottom . Boxplots showing the average distribution (in %) of the neurons expressing hM4Di-mCherry over the total number of cells (Ratio) in control animals (non-virally injected animals, in gray) and preventive animals either treated with saline (light blue) or CNO (dark blue). Gray dots represent individual data points present in the distribution f Boxplots showing the average scored of oral LID severity at the point time corresponding to 40 min after levodopa injection, 50 min after CNO injection and after theta-burst stimulations. Averaged score comprises the 4 weeks of cerebellar stimulation in two groups: preventive animals receiving saline (LID_PREV saline, N = 5), dark blue represents preventive animals receiving CNO (LID_PREV CNO, N = 6). Boxplots represent the median score (horizontal bars), the lower and the upper quartiles. Vertical lines represent median ± std. One-way Anova with two-sided Tukey HSD post-hoc test was used for 5e and non-parametric Kruskal-Wallis test with pairwise two-sided Wilcoxon test and a Benjamini & Hochberg correction were used for 5f. *** p < 0.001; ** p < 0.01; * p < 0.05; ns: p > 0.05. Source data are provided as a Source Data file. Schemes were taken from Franklin and Paxinos Brain Atlas, 3rd edition.

Article Snippet: Unless otherwise stated, data are presented as boxplots (from boxplot function in R Studio software 4.1.2).

Techniques: Injection, Expressing, Control, Saline

Journal: Nature Communications

Article Title: Cerebellar stimulation prevents Levodopa-induced dyskinesia in mice and normalizes activity in a motor network

doi: 10.1038/s41467-022-30844-0

Figure Lengend Snippet: a Sagittal schematic showing neurons in the striatum expressing the dyskinetic marker FosB/ΔFosB (green). The cerebello-thalamo-cortical and cerebello-thalamo-striatal pathways are represented in mice expressing ChR2-YFP in Purkinje cells (PC + ChR2, green) as well as the injection site 6-OHDA or saline (gray). ST: Striatum; SNc: substantia nigra pars compacta ; M1: Primary motor cortex, VAL: Ventroanterior-ventrolateral complex of the thalamus, PF: Parafascicular nucleus of the thalamus, CN: cerebellar nuclei, CrusII: Crus2 of the ansiform lobule. Insets: Postmortem histology showing FosB-expressing neurons (i), DAPI (ii), and merged (iii). Scale bars: 20 µm. b Boxplots showing the ratio of cells expressing FosB between the striatum ipsilateral to the lesion and the striatum contralateral to the lesion in percentage (%) in the 4 different conditions (LID, magenta, N = 10; SHAM, gray, N = 10; and LID_PREV, blue, N = 10). Horizontal bars in boxplots represent the median. Magenta inset: Postmortem histology showing FosB-expressing neurons in dyskinetic animals in the striatum ipsilateral to the lesion ( left box ) and in the striatum contralateral to the lesion ( right box ). Scale bars: 20 µm. Blue inset: Postmortem histology showing FosB-expressing neurons in preventive animals in the striatum ipsilateral to the lesion ( left box ) and in the striatum contralateral to the lesion ( right box ). Scale bars: 20 µm. Boxplots represents the lower and the upper quartiles as well as the median. Vertical lines represent the median ± std. Isolated points represent outliers of the distribution. Two-sided student t test. *** p < 0.001; ** p < 0.01; * p < 0.05. *Compared to SHAM; # compared to LID. Source data are provided as a Source Data file. See also Table .

Article Snippet: Unless otherwise stated, data are presented as boxplots (from boxplot function in R Studio software 4.1.2).

Techniques: Expressing, Marker, Injection, Saline, Isolation