PMC

BoxCar and shotgun proteomic analyses of control and UBR5-KD PC3 cells to identify UBR5-regulated proteins. (A) Schematic of proteomic analyses. (B) Representative immunoblots of UBR5 in total lysates derived from control and UBR5-KD PC3 cells. (C) Swarm plot of MS/MS scans acquired by BoxCar or shotgun. (D) Bar plot of total protein groups identified or quantified by BoxCar, shotgun, or library analysis. (E) Bar plot of protein groups quantified by BoxCar or shotgun in each of the 11 samples (after excluding an outlier sample). The p-value was determined by unpaired two-tailed Student’s t-test and data are mean ± SEM. (F) Stacked bar plot of protein groups quantified by BoxCar or shotgun consistently in 7-11 out of the 11 samples. (G) Venn diagram of DEPs identified from the two siUBR5 groups, compared with the siCON group, by BoxCar (left) or shotgun (right) using loose criteria. (H) Venn diagram of DEPs identified from siUBR5#1 (left) or siUBR5#2 (right), compared with the siCON group, by BoxCar or shotgun using loose criteria.

Top row (a-c): responses to boxcar and sinusoidal stimuli assuming tight coupling of CBF, CMRO₂, and CBV_v dynamics. Middle row (d-f): responses assuming fast CMRO₂ dynamics, producing an ‘initial dip’ in BOLD response to a boxcar stimulus. Bottom row (g-i): Responses assuming slow CBV_v dynamics, producing a ‘post-stimulus undershoot’ in BOLD response to a boxcar stimulus. Left column (a,d,g): physiological responses to boxcar stimulus. Middle column (b,e,h): BOLD responses to boxcar stimulus. Right column (c,f,i): relationship between BOLD and CBF responses to continuous stimulation during which contrast is oscillating with period of 44s,22s,11s, or 6.3s. The black dashed line represents the BOLD-CBF relationship predicted by .

Tuning for offer side. A: raster plot and average responses of an example vmPFC neuron to task events, separated by offer side. This neuron showed consistently greater firing when the contralateral offer appeared, regardless of its order. B: plot of proportion of vmPFC neurons that show a significant difference in responses to offer 1 depending on its position (500 ms sliding boxcar). C: raster plot and average responses of an example VS neuron to task events, separated by offer side. This neuron also showed greater firing when the contralateral offer appeared. D: plot of proportion of VS neurons that show a significant difference in responses to offer 1 depending on its position (500-ms sliding boxcar). E: raster plot and average responses of an example OFC neuron to task events, separated by offer side. This neuron also showed greater firing when the contralateral offer appeared. F: plot of proportion of OFC neurons that show a significant difference in responses to offer 1 depending on its position (500-ms sliding boxcar). G: raster plot and average responses of an example dACC neuron to task events, separated by offer side. This neuron also showed greater firing when the contralateral offer appeared. H: plot of proportion of dACC neurons that show a significant difference in responses to offer 1 depending on its position (500-ms sliding boxcar). I: raster plot and average responses of an example sgACC neuron to task events, separated by offer side. This neuron also showed greater firing when the contralateral offer appeared. J: plot of proportion of sgACC neurons that show a significant difference in responses to offer 1 depending on its position (500-ms sliding boxcar).

Tuning for choice side. A: raster plot and average responses of an example vmPFC neuron to task events, separated by leftward and rightward choice trials. This neuron showed significantly greater responses on trials with contralateral saccades than on those with ipsilateral saccades. B: plot of proportion of vmPFC neurons that show a significant difference in responses to the side of the chosen offer (500-ms sliding boxcar). C: raster plot and average responses of an example VS neuron to task events, separated by leftward and rightward choice trials. This neuron showed significantly greater responses on trials with ipsilateral saccades than on those with contralateral saccades. D: plot of proportion of VS neurons that show a significant difference in responses to the side of the chosen offer (500-ms sliding boxcar). E: raster plot and average responses of an example OFC neuron to task events, separated by leftward and rightward choice trials. This neuron showed significantly greater responses on trials with ipsilateral saccades than on those with contralateral saccades. F: plot of proportion of OFC neurons that show a significant difference in responses to the side of the chosen offer (500-ms sliding boxcar). G: raster plot and average responses of an example dACC neuron to task events, separated by leftward and rightward choice trials. This neuron showed significantly greater responses on trials with contralateral saccades than on those with ipsilateral saccades. H: plot of proportion of dACC neurons that show a significant difference in responses to the side of the chosen offer (500-ms sliding boxcar). I: raster plot and average responses of an example sgACC neuron to task events, separated by leftward and rightward choice trials. This neuron showed significantly greater responses on trials with contralateral saccades than those with ipsilateral saccades. J: plot of proportion of sgACC neurons that show a significant difference in responses to the side of the chosen offer (500-ms sliding boxcar).