DOI: 10.5281/zenodo.17886744
title: Data (The glymphatic system clears amyloid beta and tau from brain to plasma in humans)

description: The source data for Figure 3 can be found here.

To access all other study data, please complete the Data User Agreement by filling out the form provided in the link below

https://tinyurl.com/appliedcognition-dua

Once completed, kindly send it to research@appliedcognition.com along with your Zenodo ID for processing.
description: Column Naming Conventions

The summary files contain multiple variations of device-derived metrics. Column names follow specific patterns with suffixes indicating aggregation method, sleep stage filter, and time period.Example: "delta rel (norm mean N2,N3)_p1-p2" means:- delta: the frequency band- rel: relative power (vs. abs for absolute)- (norm mean N2,N3): normalized mean, using only N2/N3 sleep stages- _p1-p2: overnight period

EEG Power Bands

Each band has both absolute (abs) and relative (rel) power variants:

- abs: Absolute power - raw spectral power in the frequency band

- rel: Relative power - power normalized to total power across all bands

 

Frequency bands:





slow: 0.5-1 Hz




delta: 1-4 Hz




total_delta: 0.5-4 Hz




theta: 4-8 Hz




alpha: 8-12 Hz




sigma: 12-15 Hz (spindle)




beta: 15-30 Hz




gamma: 30-50 Hz



 





spectral exponent: 1/f slope of the power spectrum



Sleep Stage Filters

Metrics can be computed using all epochs or filtered by sleep stage:





(N2,N3): N2 and N3 epochs only




(REM): REM sleep epochs only




(no suffix): All sleep epochs (N1, N2, N3, REM, Wake)



Time Periods (Device)





_p1-p2: Overnight period (from evening p1 to morning p2)




_p2-p3: Morning period (from morning p2 to late morning p3)



Time Periods (MRI/Blood)





_p1: Evening baseline (before sleep)




_p2: Morning (after sleep)




_p3: Late morning



Pre/Post Contrast (MRI)





(Pre): Precontrast acquisition




(Post): Postcontrast acquisition



Aggregation Methods





(norm mean): Normalized mean - values normalized to the average of first three epochs of the period, then averaged




(norm sum): Normalized sum - values normalized to the average of the first three epochs of the period, then summed




(avg): Average - average of values across the period




(sum): Sum - sum of values across the period



samples_morning.csv

These files contain device data at the block level. A block is approximately 300sec long of device recording that multiplexes EEG recordings with EIS recordings. Data in samples_night_keep_waso.csv file include the “wake after sleep onset” blocks.

 

Device metrics (EEG power bands, HRV) are also included. See 'Column Naming Conventions' section for details on these metrics and their sleep stage filter variations ((N2,N3), (REM)).





Study: Study identifier (Benchmarking / Replication)




ID: Unique identifier created from study identifier + participant identifier + sleep period (morning/night)




PID: Participant identifier




visit: Visit number (visit 1 or visit 2)




intervention: Random assignment to sleep/wake




Sleep: Set to true for sleep intervention




block_number: Block number




timestamp: Block start timestamp




block hypnogram: Hypnogram label assigned to the block the majority of label of the EEG epochs in that block. Hypnogram labels mapping: 0: Wake, 1: N1, 2: N2, 3: N3, 4: REM




dR: Change in resistance from previous block to current block




dDelta: Change in delta power from previous block to current block




dTheta: Change in theta power from previous block to current block




dAlpha: Change in alpha power from previous block to current block




dBeta: Change in beta power from previous block to current block




dGamma: Change in gamma power from previous block to current block




dHR: Change in heart rate from previous block to current block




dLFHFratio: Change in the HRV ratio of LF and HF from previous block to current block




dz_ref: Change in electrode impedance of sense electrode (right side) from previous block to current block




dz_eeg: Change in electrode impedance of sense electrode (left side) from previous block to current block




dz_bias_drvp: Change in electrode impedance of drive electrode (left side) from previous block to current block




dz_drvn: Change in electrode impedance of reference electrode (right side) from previous block to current block




dHypno: Change in hypnogram label from previous block to current block (eg. 2->3)




Resistance: Parenchymal resistance




Resistance_Norm_Factor: Parenchymal resistance starting normalization




Resistance_End_Avg: Parenchymal resistance ending value




sleep_start_ts: Sleep onset timestamp




sleep_end_ts: Sleep end timestamp




sleep_start_block: Sleep onset block number




sleep_end_block: Sleep end block number



samples_night.csv / samples_night_keep_waso.csv

These files contain device data at the block level. A block is approximately 300sec long of device recording that multiplexes EEG recordings with EIS recordings. Data in samples_night_keep_waso.csv file include the “wake after sleep onset” blocks.

 

Both files have the same columns. The 'keep_waso' variant includes samples from Wake After Sleep Onset (WASO) periods, while samples_night.csv excludes WASO samples.

 

Device metrics (EEG power bands, HRV) are also included. See 'Column Naming Conventions' section for details on these metrics and their sleep stage filter variations ((N2,N3), (REM)).





Study: Study identifier (Benchmarking / Replication)




ID: Unique identifier created from study identifier + participant identifier + sleep period (morning/night)




PID: Participant identifier




visit: Visit number (visit 1 or visit 2)




intervention: Random assignment to sleep/wake




Sleep: Set to true for sleep intervention




block_number: Block number




timestamp: Block start timestamp




block hypnogram: Hypnogram label assigned to the block using EEG epochs. Hypnogram labels mapping: 0: Wake, 1: N1, 2: N2, 3: N3, 4: REM




dR: Change in resistance from previous block to current block




dDelta: Change in delta power from previous block to current block




dTheta: Change in theta power from previous block to current block




dAlpha: Change in alpha power from previous block to current block




dBeta: Change in beta power from previous block to current block




dGamma: Change in gamma power from previous block to current block




dHR: Change in heart rate from previous block to current block




dLFHFratio: Change in the HRV ratio of LF and HF from previous block to current block




dz_ref: Change in electrode impedance of sense electrode (right side) from previous block to current block




dz_eeg: Change in electrode impedance of sense electrode (left side) from previous block to current block




dz_bias_drvp: Change in electrode impedance of drive electrode (left side) from previous block to current block




dz_drvn: Change in electrode impedance of reference electrode (right side) from previous block to current block




dHypno: Change in hypnogram label from previous block to current block (eg. 2->3)




Resistance: Parenchymal resistance




Resistance_Norm_Factor: Parenchymal resistance starting normalization




Resistance_End_Avg: Parenchymal resistance ending value




sleep_start_ts: Sleep start timestamp




sleep_end_ts: Sleep end timestamp




sleep_start_block: Sleep start block number




sleep_end_block: Sleep end block number



bootstrapping.csv

Results from bootstrap analysis of single index models. Each row represents one bootstrap iteration for a specific model and amyloid status combination. Generated by the R bootstrapping script using linear mixed-effects models with Nelder-Mead optimization.

Identifier Columns





descriptor: Model and amyloid status combination ID (e.g., "sleep_physio exclude_positive", "sleep_hypno only_positive")




b: Bootstrap iteration number (1 to N, where N is the number of bootstrap samples)




convergence: Optimization convergence code from optim(): 0=successful, 1=iteration limit reached, 10=Nelder-Mead simplex degeneracy



Model Predictor Weights

The remaining columns represent single index weights for each predictor in the model. Column names use R-style naming (dots instead of spaces/hyphens). The weight values indicate the relative contribution of each predictor to the composite single index.

Sleep Physio Model Predictors





Resistance_p1.p2: Single index weight for overnight parenchymal resistance change




beta.rel..norm.mean.REM._p1.p2: Single index weight for beta relative power (REM sleep, overnight)




beta.rel..norm.mean._p1.p2: Single index weight for beta relative power (all sleep, overnight)




ipg.ppg.PTT..norm.mean.N2.N3._p1.p2: Single index weight for IPG-PPG pulse transit time (N2,N3 sleep, overnight)




ipg.ppg.PTT..norm.mean._p1.p2: Single index weight for IPG-PPG pulse transit time (all sleep, overnight)




sdnn.HRV..norm.mean.N2.N3._p1.p2: Single index weight for SDNN HRV (N2,N3 sleep, overnight)




sdnn.HRV..norm.mean._p1.p2: Single index weight for SDNN HRV (all sleep, overnight)




theta.rel..norm.mean.N2.N3._p1.p2: Single index weight for theta relative power (N2,N3 sleep, overnight)




theta.rel..norm.mean.REM._p1.p2: Single index weight for theta relative power (REM sleep, overnight)




theta.rel..norm.mean._p1.p2: Single index weight for theta relative power (all sleep, overnight)




total_delta.rel..norm.mean.N2.N3._p1.p2: Single index weight for total delta relative power (N2,N3 sleep, overnight)




total_delta.rel..norm.mean._p1.p2: Single index weight for total delta relative power (all sleep, overnight)



Sleep Hypno Model Predictors





N1_p1.p2: Single index weight for N1 sleep duration




NREM_p1.p2: Single index weight for NREM sleep duration (N2+N3)




REM_p1.p2: Single index weight for REM sleep duration




WASO_p1.p2: Single index weight for Wake After Sleep Onset duration



summary.csv

This file contains aggregated data for every participant’s visit. This file contains participant information, aggregated device data, MRI data, APOE4 status and screening assessments (MoCa & GDS)Visit and Participant ColumnsGeneral visit information and participant details.

Participant and Visit Columns





Study: Study identifier




pid: Participant identifier




visit: Visit number (v1 or v2)




visit_type: Random assignment to sleep/wake




age: Participant's age




gender: Participant's gender




APOEe4: Boolean flag set to true in the presence of at least one copy of APOEe4




Visit_p1-p2: Visit identifier for the overnight period



Screening Assessment





MoCA: Montreal Cognitive Assessment




GDS: Geriatric Depression Scale



Polysomnography

Columns with time period suffixes (_p1-p2, _p2-p3) follow the conventions described in 'Column Naming Conventions'.





N1: Total time in minutes the participant was in N1 sleep computed using the device EEG




N2: Total time in minutes the participant was in N2 sleep computed using the device EEG




N3: Total time in minutes the participant was in N3 sleep computed using the device EEG




REM: Total time in minutes the participant was in REM sleep computed using the device EEG




WASO: Total time in minutes the participant was in WASO computed using the device EEG




C4 N1: Total time in minutes the participant was in N1 sleep using PSG channel C4




C4 N2: Total time in minutes the participant was in N2 sleep using PSG channel C4




C4 N3: Total time in minutes the participant was in N3 sleep using PSG channel C4




C4 REM: Total time in minutes the participant was in REM sleep using PSG channel C4




C4 WASO: Total time in minutes the participant was in WASO using PSG channel C4




sleep_start_ts: Sleep start timestamp




sleep_end_ts: Sleep end timestamp




sleep_start_block: Sleep start block number




sleep_end_block: Sleep end block number




EEG Sample Time %: Percentage of time that was spent doing EEG sampling. It is fixed per recording.




sleep_start p1-p2 minus blood draw p1 (minutes): Time difference between sleep start and blood draw p1 (minutes)



Other Columns

Device Metrics

The following metrics appear with variations described in 'Column Naming Conventions' (aggregation method, sleep stage filter, time period).

EEG Power Bands

Each band has absolute (abs) and relative (rel) power variants. See 'EEG Power Bands' in Column Naming Conventions for frequency ranges.

Note: These power bands are computed from epoch-level readings, in contrast to the block-level mean from the previous dataset.





slow abs / slow rel: 0.5-1 Hz




delta abs / delta rel: 1-4 Hz




total_delta abs / total_delta rel: 0.5-4 Hz




theta abs / theta rel: 4-8 Hz




alpha abs / alpha rel: 8-12 Hz




sigma abs / sigma rel: 12-15 Hz (spindle)




beta abs / beta rel: 15-30 Hz




gamma abs / gamma rel: 30-50 Hz




spectral exponent: Spectral exponent (1/f slope of the power spectrum)



Heart Rate Variability (HRV)





heart rate: Heart rate in beats per minute




sdnn HRV: Standard deviation of NN intervals




lf HRV: Low frequency power (0.04-0.15 Hz)




hf HRV: High frequency power (0.15-0.4 Hz)




lf_hf_ratio HRV: Ratio of LF to HF power



Pulse Transit Time (PTT)





ppg-ppg PTT: Pulse transit time between two PPG sensors




ipg-ppg PTT: Pulse transit time from IPG to PPG




ipg-ppg ratio PTT: Ratio of IPG-PPG transit times



Parenchymal Resistance





Resistance: Parenchymal resistance



MRI Columns

MRI columns use time period and pre/post contrast suffixes as described in 'Column Naming Conventions'. Some measurements are only available at specific time points (e.g., CBV at p2, Signal Enhancement at p3).

CSF Flow





CSF Max_Vel: Absolute maximum velocity of CSF in Aqueduct of Sylvius



Pseudodiffusion (Dstr)





Dstr Frontal GM: Pseudodiffusion coefficient in frontal gray matter in mm2/s




Dstr Frontal WM: Pseudodiffusion coefficient in frontal white matter in mm2/s




Dstr Parietal GM: Pseudodiffusion coefficient in parietal gray matter in mm2/s




Dstr Parietal WM: Pseudodiffusion coefficient in parietal white matter in mm2/s




Dstr Temporal GM: Pseudodiffusion coefficient in temporal gray matter in mm2/s




Dstr Temporal WM: Pseudodiffusion coefficient in temporal white matter in mm2/s




Dstr Occipital GM: Pseudodiffusion coefficient in occipital gray matter in mm2/s




Dstr Occipital WM: Pseudodiffusion coefficient in occipital white matter in mm2/s




Dstr SAS: Pseudodiffusion coefficient in the subarachnoid CSF in mm2/s




f SAS: Fluid fraction of the subarachnoid space corresponding to Dstr SAS




fDstr SAS: Product of f SAS and Dstr SAS



Cerebral Blood Flow (CBF)





Cortical CBF: Cortical cerebral blood flow




Frontal CBF: Gray matter cerebral blood flow in the frontal lobe




Parietal CBF: Gray matter cerebral blood flow in the parietal lobe




Temporal CBF: Gray matter cerebral blood flow in the temporal lobe




Occipital CBF: Gray matter cerebral blood flow in the occipital lobe




ACA-MCA: Cerebral blood flow in the borderzone of anterior cerebral artery and middle cerebral artery




MCA-PCA: Cerebral blood flow in the borderzone of middle cerebral artery and posterior cerebral artery



Exchange Time (Tex)





Cortical Tex: Cortical exchange time as a measure of water transport across the endothelium




Frontal Tex: Exchange time as a measure of water transport across the endothelium in the frontal lobe gray matter




Parietal Tex: Exchange time as a measure of water transport across the endothelium in the parietal lobe gray matter




Temporal Tex: Exchange time as a measure of water transport across the endothelium in the temporal lobe gray matter




Occipital Tex: Exchange time as a measure of water transport across the endothelium in the occipital lobe gray matter




ACA-MCA Tex: Exchange time as a measure of water transport across the endothelium in the anterior cerebral artery-middle cerebral artery borderzone




MCA-PCA Tex: Exchange time as a measure of water transport across the endothelium in the middle cerebral artery-posterior cerebral artery borderzone



Raw Signal Intensity (Pre/Post contrast)

These columns use (Pre) and (Post) suffixes indicating pre- or post-contrast acquisition:





Frontal GM: Raw signal intensity in the frontal gray matter




Frontal WM: Raw signal intensity in the frontal white matter




Parietal GM: Raw signal intensity in the parietal gray matter




Parietal WM: Raw signal intensity in the parietal white matter




Temporal GM: Raw signal intensity in the temporal gray matter




Temporal WM: Raw signal intensity in the temporal white matter




Occipital GM: Raw signal intensity in the occipital gray matter




Occipital WM: Raw signal intensity in the occipital white matter




Hipppocampus: Raw signal intensity in the hippocampus




Vit E: Raw signal intensity in the Vit E capsule




SAS: Raw signal intensity in the SAS




Ventricles: Raw signal intensity in the ventricles




ICA: Raw signal intensity in the internal carotid artery




SS: Raw signal intensity in the sagittal sinus




CSS: Raw signal intensity in the confluence of sinuses



Signal Enhancement (SE)

Signal enhancement at timepoint p3 compared to baseline timepoint p1. Signal intensities normalized by signal intensity of Vit. E:





SE Frontal GM: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the frontal lobe gray matter




SE Frontal WM: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the frontal lobe white matter




SE Parietal GM: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the parietal lobe gray matter




SE Parietal WM: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the parietal lobe white matter




SE Temporal GM: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the temporal lobe gray matter




SE Temporal WM: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the temporal lobe white matter




SE Occipital GM: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the occipital lobe gray matter




SE Occipital WM: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the occipital lobe white matter




SE SAS: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the SAS




SE Ventricles: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the lateral ventricles




SE ICA: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the ICA




SE SS: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the SS




SE CSS: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the confluence of sinuses




SE Hippocampus: Signal enhancement at timepoint p3 compared to baseline timepoint p1 in the hippocampus



Blood Biomarkers

Blood biomarker measurements are taken at time points p1, p2, and p3. Column names have suffixes _p1, _p2, or _p3 indicating the time point.





Abeta40_Plasma_IPMS: Plasma Amyloid-beta 40 (IPMS assay)




Abeta42_Plasma_IPMS: Plasma Amyloid-beta 42 (IPMS assay)




Abeta4240_Plasma_IPMS: Plasma Amyloid-beta 42/40 ratio (IPMS assay)




pTau181 (pg/mL): Phosphorylated Tau 181 concentration




pTau217 (pg/mL): Phosphorylated Tau 217 concentration




Non-pTau181 (pg/mL): Non-phosphorylated Tau 181 concentration




Non-pTau217 (pg/mL): Non-phosphorylated Tau 217 concentration




pTau181/non-pTau181: Ratio of pTau181 to non-pTau181




pTau217/non-pTau217: Ratio of pTau217 to non-pTau217




APS: Amyloid Probability Score




Proteotype: Proteotype classification




blood_draw_time: Time of blood draw




Comments_ptau: Comments related to pTau measurements




Comments: Comments/notes




blood draw p2 minus sleep_stop p1-p2 (minutes): Time difference between blood draw p2 and sleep stop (minutes)



summary_transposed_by_biomarker.csv

This file contains the same data as summary.csv but transposed by blood biomarker for easier analysis.

Transposition

The data is pivoted from wide to long on biomarkers for multivariate analysis, with values period 1, period 2 and period 3 values extracted into bio_p1, bio_p2, bio_p3 columns:





Abeta40_Plasma_IPMS -> Biomarker = 'Ab40'




Abeta42_Plasma_IPMS -> Biomarker = 'Ab42'




Non-pTau217 (pg/mL) -> Biomarker = 'nTau217'




pTau217 (pg/mL) -> Biomarker = 'pTau217'




Non-pTau181 (pg/mL) -> Biomarker = 'nTau181'




pTau181 (pg/mL) -> Biomarker = 'pTau181'



Added Columns





Biomarker: Identifier for which biomarker the row represents




bio_p1: Biomarker value at time point p1




bio_p2: Biomarker value at time point p2




bio_p3: Biomarker value at time point p3



summary_transposed_by_cbv.csv

This file contains the same data as summary.csv but is pivoted from wide to long on CBV region of interest (ROI) for multivariate analysis.

Transposition

The data is duplicated for each of the following CBV regions, with values extracted into cbv_p2 column:





CBV Frontal GM wrt Sagittal Sinus -> ROI = 'Frontal GM'




CBV Frontal WM wrt Sagittal Sinus -> ROI = 'Frontal WM'




CBV Parietal GM wrt Sagittal Sinus -> ROI = 'Parietal GM'




CBV Parietal WM wrt Sagittal Sinus -> ROI = 'Parietal WM'




CBV Occipital GM wrt Sagittal Sinus -> ROI = 'Occipital GM'




CBV Occipital WM wrt Sagittal Sinus -> ROI = 'Occipital WM'




CBV Temporal GM wrt Sagittal Sinus -> ROI = 'Temporal GM'




CBV Temporal WM wrt Sagittal Sinus -> ROI = 'Temporal WM'



Added Columns





ROI: Region of interest identifier




cbv_p2: CBV value at period p2 for the specified ROI