Development and validation of an episodic memory measure in the Mobile Toolbox (MTB): Arranging Pictures.

INTRODUCTION: Arranging Pictures is a new episodic memory test based on the NIH Toolbox (NIHTB) Picture Sequence Memory measure and optimized for self-administration on a personal smartphone within the Mobile Toolbox (MTB). We describe evidence from three distinct validation studies. METHOD: In Study 1, 92 participants self-administered Arranging Pictures on study-provided smartphones in the lab and were administered external measures of similar and dissimilar constructs by trained examiners to assess validity under controlled circumstances. In Study 2, 1,021 participants completed the external measures in the lab and self-administered Arranging Pictures remotely on their personal smartphones to assess validity in real-world contexts. In Study 3, 141 participants self-administered Arranging Pictures remotely twice with a two-week delay on personal iOS smartphones to assess test-retest reliability and practice effects. RESULTS: Internal consistency was good across samples (ρxx = .80 to .85, p < .001). Test-retest reliability was marginal (ICC = .49, p < .001) and there were significant practice effects after a two-week delay (ΔM = 3.21 (95% CI [2.56, 3.88]). As expected, correlations with convergent measures were significant and moderate to large in magnitude (ρ = .44 to .76, p < .001), while correlations with discriminant measures were small (ρ = .23 to .27, p < .05) or nonsignificant. Scores demonstrated significant negative correlations with age (ρ = -.32 to -.21, p < .001). Mean performance was slightly higher in the iOS compared to the Android group (MiOS = 18.80, NiOS = 635; MAndroid = 17.11, NAndroid = 386; t(757.73) = 4.17, p < .001), but device type did not significantly influence the psychometric properties of the measure. Indicators of potential cheating were mixed; average scores were significantly higher in the remote samples (F(2, 850) = 11.415, p < .001), but there were not significantly more perfect scores. CONCLUSION: The MTB Arranging Pictures measure demonstrated evidence of reliability and validity when self-administered on personal device. Future research should examine the potential for cheating in remote settings and the properties of the measure in clinical samples.

A novel estimator for the two-way partial AUC.

BACKGROUND: The two-way partial AUC has been recently proposed as a way to directly quantify partial area under the ROC curve with simultaneous restrictions on the sensitivity and specificity ranges of diagnostic tests or classifiers. The metric, as originally implemented in the tpAUC R package, is estimated using a nonparametric estimator based on a trimmed Mann-Whitney U-statistic, which becomes computationally expensive in large sample sizes. (Its computational complexity is of order [Formula: see text], where [Formula: see text] and [Formula: see text] represent the number of positive and negative cases, respectively). This is problematic since the statistical methodology for comparing estimates generated from alternative diagnostic tests/classifiers relies on bootstrapping resampling and requires repeated computations of the estimator on a large number of bootstrap samples. METHODS: By leveraging the graphical and probabilistic representations of the AUC, partial AUCs, and two-way partial AUC, we derive a novel estimator for the two-way partial AUC, which can be directly computed from the output of any software able to compute AUC and partial AUCs. We implemented our estimator using the computationally efficient pROC R package, which leverages a nonparametric approach using the trapezoidal rule for the computation of AUC and partial AUC scores. (Its computational complexity is of order [Formula: see text], where [Formula: see text].). We compare the empirical bias and computation time of the proposed estimator against the original estimator provided in the tpAUC package in a series of simulation studies and on two real datasets. RESULTS: Our estimator tended to be less biased than the original estimator based on the trimmed Mann-Whitney U-statistic across all experiments (and showed considerably less bias in the experiments based on small sample sizes). But, most importantly, because the computational complexity of the proposed estimator is of order [Formula: see text], rather than [Formula: see text], it is much faster to compute when sample sizes are large. CONCLUSIONS: The proposed estimator provides an improvement for the computation of two-way partial AUC, and allows the comparison of diagnostic tests/machine learning classifiers in large datasets where repeated computations of the original estimator on bootstrap samples become too expensive to compute.

Development and Validation of a Vocabulary Measure in the Mobile Toolbox.

OBJECTIVE: We describe the development of a new computer adaptive vocabulary test, Mobile Toolbox (MTB) Word Meaning, and validity evidence from 3 studies. METHOD: Word Meaning was designed to be a multiple-choice synonym test optimized for self-administration on a personal smartphone. The items were first calibrated online in a sample of 7,525 participants to create the computer-adaptive test algorithm for the Word Meaning measure within the MTB app. In Study 1, 92 participants self-administered Word Meaning on study-provided smartphones in the lab and were administered external measures by trained examiners. In Study 2, 1,021 participants completed the external measures in the lab and Word Meaning was self-administered remotely on their personal smartphones. In Study 3, 141 participants self-administered Word Meaning remotely twice with a 2-week delay on personal iPhones. RESULTS: The final bank included 1363 items. Internal consistency was adequate to good across samples (ρxx = 0.78 to 0.81, p < .001). Test-retest reliability was good (ICC = 0.65, p < .001), and the mean theta score was not significantly different upon the second administration. Correlations were moderate to large with measures of similar constructs (ρ = 0.67-0.75, p < .001) and non-significant with measures of dissimilar constructs. Scores demonstrated small to moderate correlations with age (ρ = 0.35 to 0.45, p < .001) and education (ρ = 0.26, p < .001). CONCLUSION: The MTB Word Meaning measure demonstrated evidence of reliability and validity in three samples. Further validation studies in clinical samples are necessary.

The STEPWISE study: study protocol for a smartphone-based exercise solution for people with Parkinson's Disease (randomized controlled trial).

BACKGROUND: Exercise has various health benefits for people with Parkinson's disease (PD). However, implementing exercise into daily life and long-term adherence remain challenging. To increase a sustainable engagement with physical activity of people with PD, interventions that are motivating, accessible, and scalable are needed. We primarily aim to investigate whether a smartphone app (STEPWISE app) can increase physical activity (i.e., step count) in people with PD over one year. Our second aim is to investigate the potential effects of the intervention on physical fitness, and motor- and non-motor function. Our third aim is to explore whether there is a dose-response relationship between volume of physical activity and our secondary endpoints. METHODS: STEPWISE is a double-blind, randomized controlled trial. We aim to include 452 Dutch people with PD who can walk independently (Hoehn & Yahr stages 1-3) and who do not take more than 7,000 steps per day prior to inclusion. Physical activity levels are measured as step counts on the participant's own smartphone and scaled as percentage of each participant's baseline. Participants are randomly assigned to an active control group with an increase of 5-20% (active controls) or any of the three intervention arms with increases of 25-100% (intermediate dose), 50-200% (large dose), or 100-400% (very large dose). The primary endpoint is change in step count as measured by the STEPWISE smartphone app from baseline to 52 weeks. For our primary aim, we will evaluate the between-group difference in average daily step count change from baseline to 52 weeks. For our second aim, measures of physical fitness, and motor- and non-motor function are included. For our third aim, we will associate 52-week changes in step count with 52-week changes in secondary outcomes. DISCUSSION: This trial evaluates the potential of a smartphone-based intervention to increase activity levels in people with PD. We envision that motivational apps will increase adherence to physical activity recommendations and could permit conduct of remote clinical trials of exercise for people with PD or those at risk of PD. TRIAL REGISTRATION: ClinicalTrials.gov; NCT04848077; 19/04/2021. CLINICALTRIALS: gov/ct2/show/NCT04848077.

Developing better digital health measures of Parkinson's disease using free living data and a crowdsourced data analysis challenge.

One of the promising opportunities of digital health is its potential to lead to more holistic understandings of diseases by interacting with the daily life of patients and through the collection of large amounts of real-world data. Validating and benchmarking indicators of disease severity in the home setting is difficult, however, given the large number of confounders present in the real world and the challenges in collecting ground truth data in the home. Here we leverage two datasets collected from patients with Parkinson's disease, which couples continuous wrist-worn accelerometer data with frequent symptom reports in the home setting, to develop digital biomarkers of symptom severity. Using these data, we performed a public benchmarking challenge in which participants were asked to build measures of severity across 3 symptoms (on/off medication, dyskinesia, and tremor). 42 teams participated and performance was improved over baseline models for each subchallenge. Additional ensemble modeling across submissions further improved performance, and the top models validated in a subset of patients whose symptoms were observed and rated by trained clinicians.

A Multifaceted benchmarking of synthetic electronic health record generation models.

Synthetic health data have the potential to mitigate privacy concerns in supporting biomedical research and healthcare applications. Modern approaches for data generation continue to evolve and demonstrate remarkable potential. Yet there is a lack of a systematic assessment framework to benchmark methods as they emerge and determine which methods are most appropriate for which use cases. In this work, we introduce a systematic benchmarking framework to appraise key characteristics with respect to utility and privacy metrics. We apply the framework to evaluate synthetic data generation methods for electronic health records data from two large academic medical centers with respect to several use cases. The results illustrate that there is a utility-privacy tradeoff for sharing synthetic health data and further indicate that no method is unequivocally the best on all criteria in each use case, which makes it evident why synthetic data generation methods need to be assessed in context.

A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.

The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.

Disentangling personalized treatment effects from "time-of-the-day" confounding in mobile health studies.

Ideally, a patient's response to medication can be monitored by measuring changes in performance of some activity. In observational studies, however, any detected association between treatment ("on-medication" vs "off-medication") and the outcome (performance in the activity) might be due to confounders. In particular, causal inferences at the personalized level are especially vulnerable to confounding effects that arise in a cyclic fashion. For quick acting medications, effects can be confounded by circadian rhythms and daily routines. Using the time-of-the-day as a surrogate for these confounders and the performance measurements as captured on a smartphone, we propose a personalized statistical approach to disentangle putative treatment and "time-of-the-day" effects, that leverages conditional independence relations spanned by causal graphical models involving the treatment, time-of-the-day, and outcome variables. Our approach is based on conditional independence tests implemented via standard and temporal linear regression models. Using synthetic data, we investigate when and how residual autocorrelation can affect the standard tests, and how time series modeling (namely, ARIMA and robust regression via HAC covariance matrix estimators) can remedy these issues. In particular, our simulations illustrate that when patients perform their activities in a paired fashion, positive autocorrelation can lead to conservative results for the standard regression approach (i.e., lead to deflated true positive detection), whereas negative autocorrelation can lead to anticonservative behavior (i.e., lead to inflated false positive detection). The adoption of time series methods, on the other hand, leads to well controlled type I error rates. We illustrate the application of our methodology with data from a Parkinson's disease mobile health study.

A Smartphone Application as an Exploratory Endpoint in a Phase 3 Parkinson's Disease Clinical Trial: A Pilot Study.

BACKGROUND: Smartphones can generate objective measures of Parkinson's disease (PD) and supplement traditional in-person rating scales. However, smartphone use in clinical trials has been limited. OBJECTIVE: This study aimed to determine the feasibility of introducing a smartphone research application into a PD clinical trial and to evaluate the resulting measures. METHODS: A smartphone application was introduced part-way into a phase 3 randomized clinical trial of inosine. The application included finger tapping, gait, and cognition tests, and participants were asked to complete an assessment battery at home and in clinic alongside the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS). RESULTS: Of 236 eligible participants in the parent study, 88 (37%) consented to participate, and 59 (27 randomized to inosine and 32 to placebo) completed a baseline smartphone assessment. These 59 participants collectively completed 1,292 batteries of assessments. The proportion of participants who completed at least one smartphone assessment was 61% at 3, 54% at 6, and 35% at 12 months. Finger tapping speed correlated weakly with the part III motor portion (r = -0.16, left hand; r = -0.04, right hand) and total (r = -0.14) MDS-UPDRS. Gait speed correlated better with the same measures (r = -0.25, part III motor; r = -0.34, total). Over 6 months, finger tapping speed, gait speed, and memory scores did not differ between those randomized to active drug or placebo. CONCLUSIONS: Introducing a smartphone application midway into a phase 3 clinical trial was challenging. Measures of bradykinesia and gait speed correlated modestly with traditional outcomes and were consistent with the study's overall findings, which found no benefit of the active drug.

Remote smartphone monitoring of Parkinson's disease and individual response to therapy.

Remote health assessments that gather real-world data (RWD) outside clinic settings require a clear understanding of appropriate methods for data collection, quality assessment, analysis and interpretation. Here we examine the performance and limitations of smartphones in collecting RWD in the remote mPower observational study of Parkinson's disease (PD). Within the first 6 months of study commencement, 960 participants had enrolled and performed at least five self-administered active PD symptom assessments (speeded tapping, gait/balance, phonation or memory). Task performance, especially speeded tapping, was predictive of self-reported PD status (area under the receiver operating characteristic curve (AUC) = 0.8) and correlated with in-clinic evaluation of disease severity (r = 0.71; P < 1.8 × 10-6) when compared with motor Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS). Although remote assessment requires careful consideration for accurate interpretation of RWD, our results support the use of smartphones and wearables in objective and personalized disease assessments.

Smartphone-Based VO2max Measurement With Heart Snapshot in Clinical and Real-world Settings With a Diverse Population: Validation Study.

BACKGROUND: Maximal oxygen consumption (VO2max) is one of the most predictive biometrics for cardiovascular health and overall mortality. However, VO2max is rarely measured in large-scale research studies or routine clinical care because of the high cost, participant burden, and requirement for specialized equipment and staff. OBJECTIVE: To overcome the limitations of clinical VO2max measurement, we aim to develop a digital VO2max estimation protocol that can be self-administered remotely using only the sensors within a smartphone. We also aim to validate this measure within a broadly representative population across a spectrum of smartphone devices. METHODS: Two smartphone-based VO2max estimation protocols were developed: a 12-minute run test (12-MRT) based on distance measured by GPS and a 3-minute step test (3-MST) based on heart rate recovery measured by a camera. In a 101-person cohort, balanced across age deciles and sex, participants completed a gold standard treadmill-based VO2max measurement, two silver standard clinical protocols, and the smartphone-based 12-MRT and 3-MST protocols in the clinic and at home. In a separate 120-participant cohort, the video-based heart rate measurement underlying the 3-MST was measured for accuracy in individuals across the spectrum skin tones while using 8 different smartphones ranging in cost from US $99 to US $999. RESULTS: When compared with gold standard VO2max testing, Lin concordance was pc=0.66 for 12-MRT and pc=0.61 for 3-MST. However, in remote settings, the 12-MRT was significantly less concordant with the gold standard (pc=0.25) compared with the 3-MST (pc=0.61), although both had high test-retest reliability (12-MRT intraclass correlation coefficient=0.88; 3-MST intraclass correlation coefficient=0.86). On the basis of the finding that 3-MST concordance was generalizable to remote settings whereas 12-MRT was not, the video-based heart rate measure within the 3-MST was selected for further investigation. Heart rate measurements in any of the combinations of the six Fitzpatrick skin tones and 8 smartphones resulted in a concordance of pc≥0.81. Performance did not correlate with device cost, with all phones selling under US $200 performing better than pc>0.92. CONCLUSIONS: These findings demonstrate the importance of validating mobile health measures in the real world across a diverse cohort and spectrum of hardware. The 3-MST protocol, termed as heart snapshot, measured VO2max with similar accuracy to supervised in-clinic tests such as the Tecumseh (pc=0.94) protocol, while also generalizing to remote and unsupervised measurements. Heart snapshot measurements demonstrated fidelity across demographic variation in age and sex, across diverse skin pigmentation, and between various iOS and Android phone configurations. This software is freely available for all validation data and analysis code.

Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge.

Consumer wearables and sensors are a rich source of data about patients' daily disease and symptom burden, particularly in the case of movement disorders like Parkinson's disease (PD). However, interpreting these complex data into so-called digital biomarkers requires complicated analytical approaches, and validating these biomarkers requires sufficient data and unbiased evaluation methods. Here we describe the use of crowdsourcing to specifically evaluate and benchmark features derived from accelerometer and gyroscope data in two different datasets to predict the presence of PD and severity of three PD symptoms: tremor, dyskinesia, and bradykinesia. Forty teams from around the world submitted features, and achieved drastically improved predictive performance for PD status (best AUROC = 0.87), as well as tremor- (best AUPR = 0.75), dyskinesia- (best AUPR = 0.48) and bradykinesia-severity (best AUPR = 0.95).

Accelerometer data collected with a minimum set of wearable sensors from subjects with Parkinson's disease.

Parkinson's disease (PD) is a neurodegenerative disorder associated with motor and non-motor symptoms. Current treatments primarily focus on managing motor symptom severity such as tremor, bradykinesia, and rigidity. However, as the disease progresses, treatment side-effects can emerge such as on/off periods and dyskinesia. The objective of the Levodopa Response Study was to identify whether wearable sensor data can be used to objectively quantify symptom severity in individuals with PD exhibiting motor fluctuations. Thirty-one subjects with PD were recruited from 2 sites to participate in a 4-day study. Data was collected using 2 wrist-worn accelerometers and a waist-worn smartphone. During Days 1 and 4, a portion of the data was collected in the laboratory while subjects performed a battery of motor tasks as clinicians rated symptom severity. The remaining of the recordings were performed in the home and community settings. To our knowledge, this is the first dataset collected using wearable accelerometers with specific focus on individuals with PD experiencing motor fluctuations that is made available via an open data repository.

Limb and trunk accelerometer data collected with wearable sensors from subjects with Parkinson's disease.

Parkinson's disease (PD) is a neurodegenerative disorder characterized by motor and non-motor symptoms. Dyskinesia and motor fluctuations are complications of PD medications. An objective measure of on/off time with/without dyskinesia has been sought for some time because it would facilitate the titration of medications. The objective of the dataset herein presented is to assess if wearable sensor data can be used to generate accurate estimates of limb-specific symptom severity. Nineteen subjects with PD experiencing motor fluctuations were asked to wear a total of five wearable sensors on both forearms and shanks, as well as on the lower back. Accelerometer data was collected for four days, including two laboratory visits lasting 3 to 4 hours each while the remainder of the time was spent at home and in the community. During the laboratory visits, subjects performed a battery of motor tasks while clinicians rated limb-specific symptom severity. At home, subjects were instructed to use a smartphone app that guided the periodic performance of a set of motor tasks.

Design of a virtual longitudinal observational study in Parkinson's disease (AT-HOME PD).

OBJECTIVE: The expanding power and accessibility of personal technology provide an opportunity to reduce burdens and costs of traditional clinical site-centric therapeutic trials in Parkinson's disease and generate novel insights. The value of this approach has never been more evident than during the current COVID-19 pandemic. We sought to (1) establish and implement the infrastructure for longitudinal, virtual follow-up of clinical trial participants, (2) compare changes in smartphone-based assessments, online patient-reported outcomes, and remote expert assessments, and (3) explore novel digital markers of Parkinson's disease disability and progression. METHODS: Participants from two recently completed phase III clinical trials of inosine and isradipine enrolled in Assessing Tele-Health Outcomes in Multiyear Extensions of Parkinson's Disease trials (AT-HOME PD), a two-year virtual cohort study. After providing electronic informed consent, individuals complete annual video visits with a movement disorder specialist, smartphone-based assessments of motor function and socialization, and patient-reported outcomes online. RESULTS: From the two clinical trials, 226 individuals from 42 states in the United States and Canada enrolled. Of these, 181 (80%) have successfully downloaded the study's smartphone application and 161 (71%) have completed patient-reported outcomes on the online platform. INTERPRETATION: It is feasible to conduct a large-scale, international virtual observational study following the completion of participation in brick-and-mortar clinical trials in Parkinson's disease. This study, which brings research to participants, will compare established clinical endpoints with novel digital biomarkers and thereby inform the longitudinal follow-up of clinical trial participants and design of future clinical trials.

Evaluating the Utility of Smartphone-Based Sensor Assessments in Persons With Multiple Sclerosis in the Real-World Using an App (elevateMS): Observational, Prospective Pilot Digital Health Study.

BACKGROUND: Multiple sclerosis (MS) is a chronic neurodegenerative disease. Current monitoring practices predominantly rely on brief and infrequent assessments, which may not be representative of the real-world patient experience. Smartphone technology provides an opportunity to assess people's daily-lived experience of MS on a frequent, regular basis outside of episodic clinical evaluations. OBJECTIVE: The objectives of this study were to evaluate the feasibility and utility of capturing real-world MS-related health data remotely using a smartphone app, "elevateMS," to investigate the associations between self-reported MS severity and sensor-based active functional tests measurements, and the impact of local weather conditions on disease burden. METHODS: This was a 12-week, observational, digital health study involving 3 cohorts: self-referred participants who reported an MS diagnosis, clinic-referred participants with neurologist-confirmed MS, and participants without MS (controls). Participants downloaded the elevateMS app and completed baseline assessments, including self-reported physical ability (Patient-Determined Disease Steps [PDDS]), as well as longitudinal assessments of quality of life (Quality of Life in Neurological Disorders [Neuro-QoL] Cognitive, Upper Extremity, and Lower Extremity Function) and daily health (MS symptoms, triggers, health, mobility, pain). Participants also completed functional tests (finger-tapping, walk and balance, voice-based Digit Symbol Substitution Test [DSST], and finger-to-nose) as an independent assessment of MS-related cognition and motor activity. Local weather data were collected each time participants completed an active task. Associations between self-reported baseline/longitudinal assessments, functional tests, and weather were evaluated using linear (for cross-sectional data) and mixed-effects (for longitudinal data) regression models. RESULTS: A total of 660 individuals enrolled in the study; 31 withdrew, 495 had MS (n=359 self-referred, n=136 clinic-referred), and 134 were controls. Participation was highest in clinic-referred versus self-referred participants (median retention: 25.5 vs 7.0 days). The top 5 most common MS symptoms, reported at least once by participants with MS, were fatigue (310/495, 62.6%), weakness (222/495, 44.8%), memory/attention issues (209/495, 42.2%), and difficulty walking (205/495, 41.4%), and the most common triggers were high ambient temperature (259/495, 52.3%), stress (250/495, 50.5%), and late bedtime (221/495, 44.6%). Baseline PDDS was significantly associated with functional test performance in participants with MS (mixed model-based estimate of most significant feature across functional tests [ß]: finger-tapping: ß=-43.64, P<.001; DSST: ß=-5.47, P=.005; walk and balance: ß=-.39, P=.001; finger-to-nose: ß=.01, P=.01). Longitudinal Neuro-QoL scores were also significantly associated with functional tests (finger-tapping with Upper Extremity Function: ß=.40, P<.001; walk and balance with Lower Extremity Function: ß=-99.18, P=.02; DSST with Cognitive Function: ß=1.60, P=.03). Finally, local temperature was significantly associated with participants' test performance (finger-tapping: ß=-.14, P<.001; DSST: ß=-.06, P=.009; finger-to-nose: ß=-53.88, P<.001). CONCLUSIONS: The elevateMS study app captured the real-world experience of MS, characterized some MS symptoms, and assessed the impact of environmental factors on symptom severity. Our study provides further evidence that supports smartphone app use to monitor MS with both active assessments and patient-reported measures of disease burden. App-based tracking may provide unique and timely real-world data for clinicians and patients, resulting in improved disease insights and management.

The AD Knowledge Portal: A Repository for Multi-Omic Data on Alzheimer's Disease and Aging.

The AD Knowledge Portal (adknowledgeportal.org) is a public data repository that shares data and other resources generated by multiple collaborative research programs focused on aging, dementia, and Alzheimer's disease (AD). In this article, we highlight how to use the Portal to discover and download genomic variant and transcriptomic data from the same individuals. First, we show how to use the web interface to browse and search for data of interest using relevant file annotations. We demonstrate how to learn more about the context surrounding the data, including diagnostic criteria and methodological details about sample preparation and data analysis. We present two primary ways to download data-using a web interface, and using a programmatic method that provides access using the command line. Finally, we show how to merge separate sources of metadata into a comprehensive file that contains factors and covariates necessary in downstream analyses. © 2020 The Authors. Basic Protocol 1: Find and download files associated with a selected study Basic Protocol 2: Download files in bulk using the command line client Basic Protocol 3: Working with file annotations and metadata.

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.

The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer's Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million significant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 significant eQTL for >10,000 genes). We find substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the Genotype-Tissue Expression (GTEx) Project eQTL. Additionally, we observed differences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a resource for use by the research community. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975).

Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.

We present a consensus atlas of the human brain transcriptome in Alzheimer's disease (AD), based on meta-analysis of differential gene expression in 2,114 postmortem samples. We discover 30 brain coexpression modules from seven regions as the major source of AD transcriptional perturbations. We next examine overlap with 251 brain differentially expressed gene sets from mouse models of AD and other neurodegenerative disorders. Human-mouse overlaps highlight responses to amyloid versus tau pathology and reveal age- and sex-dependent expression signatures for disease progression. Human coexpression modules enriched for neuronal and/or microglial genes broadly overlap with mouse models of AD, Huntington's disease, amyotrophic lateral sclerosis, and aging. Other human coexpression modules, including those implicated in proteostasis, are not activated in AD models but rather following other, unexpected genetic manipulations. Our results comprise a cross-species resource, highlighting transcriptional networks altered by human brain pathophysiology and identifying correspondences with mouse models for AD preclinical studies.

Effects of mood and aging on keystroke dynamics metadata and their diurnal patterns in a large open-science sample: A BiAffect iOS study.

OBJECTIVE: Ubiquitous technologies can be leveraged to construct ecologically relevant metrics that complement traditional psychological assessments. This study aims to determine the feasibility of smartphone-derived real-world keyboard metadata to serve as digital biomarkers of mood. MATERIALS AND METHODS: BiAffect, a real-world observation study based on a freely available iPhone app, allowed the unobtrusive collection of typing metadata through a custom virtual keyboard that replaces the default keyboard. User demographics and self-reports for depression severity (Patient Health Questionnaire-8) were also collected. Using >14 million keypresses from 250 users who reported demographic information and a subset of 147 users who additionally completed at least 1 Patient Health Questionnaire, we employed hierarchical growth curve mixed-effects models to capture the effects of mood, demographics, and time of day on keyboard metadata. RESULTS: We analyzed 86 541 typing sessions associated with a total of 543 Patient Health Questionnaires. Results showed that more severe depression relates to more variable typing speed (P < .001), shorter session duration (P < .001), and lower accuracy (P < .05). Additionally, typing speed and variability exhibit a diurnal pattern, being fastest and least variable at midday. Older users exhibit slower and more variable typing, as well as more pronounced slowing in the evening. The effects of aging and time of day did not impact the relationship of mood to typing variables and were recapitulated in the 250-user group. CONCLUSIONS: Keystroke dynamics, unobtrusively collected in the real world, are significantly associated with mood despite diurnal patterns and effects of age, and thus could serve as a foundation for constructing digital biomarkers.