Caring for Stroke Survivors: Ethnic Differences in Informal Caregiver Needs Among Mexican American and Non-Hispanic White Communities.

BACKGROUND: After stroke, Mexican American (MA) individuals have worse 90-day neurological, functional, cognitive, and quality of life outcomes and a higher prevalence of poststroke depression compared with non-Hispanic White (NHW) individuals. MA individuals receive more help through informal, unpaid caregiving than NHW individuals. We examined ethnic differences in needs identified by MA and NHW stroke caregivers. METHODS: Caregivers were identified from the population-based BASIC study (Brain Attack Surveillance in Corpus Christi) in Nueces County, Texas from October 2019 to November 2021. Responses to the Caregiver Needs and Concerns Checklist were collected at 90-day poststroke to assess caregiver needs. Using the cross-sectional sample, prevalence scores and bivariate analyses were used to examine ethnic differences between Caregiver Needs and Concerns Checklist items. Linear regression was used to examine adjusted associations of ethnicity with the total average needs for each domain. Models were adjusted for patient and caregiver age and sex, caregiver education level, and employment status, patient insurance status, prestroke function, cognitive status, language, and functional outcome at 90 days, intensity and duration of caregiving, presence of other caregivers (paid/unpaid), and cohabitation of patient and caregiver. RESULTS: A total of 287 were approached, and 186 stroke caregivers were included with a median age of 54.2 years and 80.1% being women caregivers: 74.3% MA and 25.7% NHW individuals. MA caregivers had significantly lower education (

Association between sleep-disordered breathing and post-stroke fatigue in patients with ischemic stroke.

OBJECTIVES: Post-stroke fatigue (PSF) is common and often disabling. Sleep-disordered breathing (SDB) is highly prevalent among stroke survivors and can cause fatigue. We explored the relationship between SDB and PSF over time. MATERIALS AND METHODS: Ischemic stroke (IS) patients within the BASIC project were offered SDB screening with a well-validated cardiopulmonary sleep apnea test at 0, 3-, 6-, and 12-months post-stroke. The primary exposure was the respiratory event index (REI; sum of apneas plus hypopneas per hour). The primary outcome was PSF, measured by the SF-36 vitality scale. Associations between REI and PSF were evaluated using linear regression including time-by-REI interactions, allowing the effect of REI to vary over time. RESULTS: Of the 411 IS patients who completed at least one outcome interview, 44 % were female, 61 % Mexican American (MA), 26 % non-Hispanic white, with a mean age of 64 (SD 10). Averaged across timepoints, REI was not associated with PSF. In a time-varying model, higher REI was associated with greater PSF at 3-months (ß = 1.75, CI = 0.08, 3.43), but not at 6- or 12-months. Across timepoints, female sex, depressive symptoms, and comorbidity burden were associated with greater PSF, whereas MA ethnicity was associated with less PSF. CONCLUSIONS: Higher REI was associated with modestly greater PSF in the early post-stroke period, but no association was observed at 6 months and beyond. SDB may be a modest modifiable risk factor for early PSF, but its treatment is unlikely to have a substantial impact on long-term PSF. MA ethnicity seems to be protective against PSF.

QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration.

DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype-environment interaction in retina.

Novel metrics of sleep-disordered breathing are associated with outcome after ischemic stroke.

OBJECTIVE/BACKGROUND: Standard measures of sleep-disordered breathing (SDB) that rely on count data may not sufficiently capture SDB severity or reflect downstream consequences of SDB. We hypothesized that novel metrics derived from pulse rate, oxygen saturation, and nasal pressure would be associated with stroke outcomes. PATIENTS/METHODS: Shortly after ischemic stroke, participants in a population-based study were offered ApneaLink Plus testing. Signal analysis was used to generate 166 metrics from the nasal pressure cannula and finger probe, categorized as: autonomic (based on pulse rate variability), oximetry-derived, nasal pressure-derived, and mixed oxygen and nasal pressure-derived measures. Three-month outcome assessments included functional and cognitive outcomes and stroke recurrence. Tobit regression and Cox proportional hazards models were used to examine associations between each sleep apnea metric and the three outcomes, unadjusted and adjusted for multiple potential confounders. Models were adjusted for multiple comparisons. RESULTS: Of the 530 participants, the median age was 65 (IQR: 57, 73), 49 % were female, and 64 % were Mexican American. Without covariate adjustment, 23 of 166 variables were associated with functional outcome, 43 were associated with cognitive outcome, and 1 was associated with stroke recurrence. After adjustment, 7 mixed, oximetry, or nasal pressure-based metrics and 1 autonomic metric were associated with functional outcome, but none was associated with cognitive outcome or stroke recurrence. CONCLUSIONS: Many novel metrics of SDB were associated with important stroke outcomes, and 8 novel metrics were associated with functional outcome in adjusted models. This raises hypotheses about pathways by which SDB may negatively impact stroke outcomes.

Mexican Americans agree to participate in longitudinal clinical research more than non-Hispanic whites.

BACKGROUND: The National Institutes of Health has advocated for improved minority participation in clinical research, including clinical trials and observational epidemiologic studies since 1993. An understanding of Mexican Americans (MAs) participation in clinical research is important for tailoring recruitment strategies and enrollment techniques for MAs. However, contemporary data on MA participation in observational clinical stroke studies are rare. We examined differences between Mexican Americans (MAs) and non-Hispanic whites (NHWs) participation in a population-based stroke study. METHODS: We included 3,594 first ever stroke patients (57.7% MAs, 48.7% women, median [IQR] age 68 [58-79]) from the Brain Attack Surveillance in Corpus Christi Project, 2009-2020 in Texas, USA, who were approached and invited to participate in a structured baseline interview. We defined participation as completing a baseline interview by patient or proxy. We used log-binomial models adjusting for prespecified potential confounders to estimate prevalence ratios (PR) of participation comparing MAs with NHWs. We tested interactions of ethnicity with age or sex to examine potential effect modification in the ethnic differences in participation. We also included an interaction between year and ethnicity to examine ethnic-specific temporal trends in participation. RESULTS: Baseline participation was 77.0% in MAs and 64.2% in NHWs (Prevalence Ratio [PR] 1.20; 95% CI, 1.14-1.25). The ethnic difference remained after multivariable adjustment (1.17; 1.12-1.23), with no evidence of significant effect modification by age or sex (Pinteraction by age = 0.68, Pinteraction by sex = 0.83). Participation increased over time for both ethnic groups (Ptrend < 0.0001), but the differences in participation between MAs and NHWs remained significantly different throughout the 11-year time period. CONCLUSION: MAs were persistently more likely to participate in a population-based stroke study in a predominantly MA community despite limited outreach efforts towards MAs during study enrollment. This finding holds hope for future research studies to be inclusive of the MA population.

A pilot genome-wide association study meta-analysis of gastroparesis.

BACKGROUND: Gastroparesis (GP) is characterized by delayed gastric emptying in the absence of mechanical obstruction. OBJECTIVE: Genetic predisposition may play a role; however, investigation at the genome-wide level has not been performed. METHODS: We carried out a genome-wide association study (GWAS) meta-analysis on (i) 478 GP patients from the National Institute of Diabetes and Digestive and Kidney Diseases Gastroparesis Clinical Research Consortium (GpCRC) compared to 9931 population-based controls from the University of Michigan Health and Retirement Study; and (ii) 402 GP cases compared to 48,340 non-gastroparesis controls from the Michigan Genomics Initiative. Associations for 5,811,784 high-quality SNPs were tested on a total of 880 GP patients and 58,271 controls, using logistic mixed models adjusted for age, sex, and principal components. Gene mapping was obtained based on genomic position and expression quantitative trait loci, and a gene-set network enrichment analysis was performed. Genetic associations with clinical data were tested in GpCRC patients. Protein expression of selected candidate genes was determined in full thickness gastric biopsies from GpCRC patients and controls. RESULTS: While no SNP associations were detected at strict significance (p ≤ 5 × 10-8 ), nine independent genomic loci were associated at suggestive significance (p ≤ 1 × 10-5 ), with the strongest signal (rs9273363, odds ratio = 1.4, p = 1 × 10-7 ) mapped to the human leukocyte antigen region. Computational annotation of suggestive risk loci identified 14 protein-coding candidate genes. Gene-set network enrichment analysis revealed pathways potentially involved in immune and motor dysregulation (pFDR ≤ 0.05). The GP risk allele rs6984536A (Peroxidasin-Like; PXDNL) was associated with increased abdominal pain severity scores (Beta = 0.13, p = 0.03). Gastric muscularis expression of PXDNL also positively correlated with abdominal pain in GP patients (r = 0.8, p = 0.02). Dickkopf WNT Signaling Pathway Inhibitor 1 showed decreased expression in diabetic GP patients (p = 0.005 vs. controls). CONCLUSION: We report preliminary GWAS findings for GP, which highlight candidate genes and pathways related to immune and sensory-motor dysregulation. Larger studies are needed to validate and expand these findings in independent datasets.

Black Americans have worse stroke outcome compared with non-Hispanic whites.

INTRODUCTION: We studied racial differences in post-stroke outcomes using a prospective, population-based cohort of stroke survivors as part of the Brain Attack Surveillance in Corpus Christi (BASIC) project. METHODS: Neurologic (NIHSS, range of 0-42, higher scores are worse), functional (ADLs/IADLs, range 1-4, higher scores are worse), and cognitive (3MSE, range 0-100, higher scores are better) outcomes were measured 90 days after stroke. Cox proportional hazards and negative binomial linear regression models were used to examine the associations between race and 90-day all-cause mortality and NIHSS, respectively, whereas linear regression was used for ADLs/IADLs and 3MSE scores. Covariates included demographics, initial NIHSS, comorbidities, prior stroke history, tPA treatment status, pre-stroke disability, and pre-stroke cognition. The mortality model was also adjusted for DNR status. RESULTS: At 90 days post-stroke, Black American individuals (BAs) (n = 122) had a median (IQR) NIHSS of 2 (1,6) compared to NIHSS of 1 (0,3) in non-Hispanic White American individuals (NHWs) (n = 795). BAs had a median (IQR) ADL/IADL score of 2.41 (1.50, 3.39) compared to 2.00 (1.27, 2.95) in NHWs. BAs scored a median of 84 (75, 92) on the 3MSE compared to NHWs' score of 91.5 (83, 96). Death occurred in 23 (8%) of BAs and 268 (15%) of NHWs within 90 days among those who participated in baseline. After adjustment for covariates, functional outcomes at 90 days were worse in BAs compared to NHWs, with 15.8% (95% CI=5.2, 26.4) greater limitations in ADLs/IADLs and 43.9% (95% CI=12.0, 84.9) greater severity of stroke symptoms. Cognition at 90 days was 6.5% (95% CI=2.4, 10.6) lower in BAs compared to NHWs. BAs had a 35.4% lower (95% CI=-9.8, 61.9) hazard rate of mortality than NHWs. CONCLUSIONS: In this prospective, population-based community sample, BAs had worse neurologic, functional and cognitive outcomes at 90 days compared to NHWs. Future research should investigate how social determinants of health including structural racism, neighborhood factors and access to preventive and recovery services influences these racial disparities.

QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration.

DNA methylation (DNAm) provides a crucial epigenetic mark linking genetic variations to environmental influence. We analyzed array-based DNAm profiles of 160 human retinas with co-measured RNA-seq and > 8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 mQTLs and 12,505 eQTLs) and 13,747 eQTMs (DNAm loci affecting gene expression), with over one-third specific to the retina. mQTLs and eQTMs show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration (AMD). Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of AMD pathology by genotype-environment interaction in retina.

Machine Learning-Based Prediction of Mental Well-Being Using Health Behavior Data from University Students.

BACKGROUND: Since the onset of the COVID-19 pandemic in early 2020, the importance of timely and effective assessment of mental well-being has increased dramatically. Machine learning (ML) algorithms and artificial intelligence (AI) techniques can be harnessed for early detection, prognostication and prediction of negative psychological well-being states. METHODS: We used data from a large, multi-site cross-sectional survey consisting of 17 universities in Southeast Asia. This research work models mental well-being and reports on the performance of various machine learning algorithms, including generalized linear models, k-nearest neighbor, naïve Bayes, neural networks, random forest, recursive partitioning, bagging, and boosting. RESULTS: Random Forest and adaptive boosting algorithms achieved the highest accuracy for identifying negative mental well-being traits. The top five most salient features associated with predicting poor mental well-being include the number of sports activities per week, body mass index, grade point average (GPA), sedentary hours, and age. CONCLUSIONS: Based on the reported results, several specific recommendations and suggested future work are discussed. These findings may be useful to provide cost-effective support and modernize mental well-being assessment and monitoring at the individual and university level.

Recurrent stroke arrival time.

BACKGROUND: Stroke patients and family members should receive stroke education including recognition of stroke symptoms and prompt activation of emergency medical services (EMS). The impact of this education is unclear. We aimed to measure the associations between EMS use and timing of hospital arrival and first-ever and recurrent strokes as a proxy for stroke education. METHODS: The study analyzed data from validated strokes identified by the Brain Attack Surveillance in Corpus Christi (BASIC) project between 1/1/2000-1/1/2020. We analyzed 5,617 first-ever strokes, 259 instances of recurrent stroke within 1 year of the first (early recurrence), and 451 recurrent strokes over 1 year from the first (late recurrence). Following imputation, associations of both EMS arrival (available starting late 2011) and early arrival (< 3 hours) with first-ever versus recurrent stroke (early and late) were assessed with logistic models, accounting for the clustering of multiple strokes per participant with generalized estimating equations. Full model covariates included stroke type, initial stroke severity, marital status, race/ethnicity, gender, age, insurance, education, and EMS use (early arrival model only). RESULTS: Compared to first-ever stroke, there were significantly higher unadjusted odds of arrival by EMS for the late recurrence group (late recurrence OR = 1.54, 95% CI = 1.18-1.99; early arrival OR = 1.24, 95% CI = 0.87-1.76). The association for late recurrence remained significant after adjustment (aOR = 1.46, 95% CI = 1.09-1.95). The pre-2010 unadjusted odds of early arrival were non-significant for both early and late recurrence groups (late recurrence OR = 1.05, CI = 0.70-1.56; early recurrence OR = 0.85, CI = 0.54-1.33), while late recurrence was associated with early arrival after 2010 (OR = 1.32, 95% CI = 1.03-1.69). After full adjustment, it was no longer significant (aOR = 1.25, 95% CI = 0.96-1.62). Higher initial stroke severity, married status, and EMS use were associated with higher odds of early arrival, while African Americans (AAs) had lower odds than non-Hispanic Whites (NHWs). However, AAs did have higher odds of EMS use relative to NHWs. Those who were married and living together had borderline significant lower odds of EMS use compared to those who were not. CONCLUSIONS: Our study examines the association of repeat stroke on early arrival and EMS use as a surrogate for adequate stroke education. Recurrence at least one year after the first stroke was associated with higher EMS usage, but there was not enough evidence to establish a relationship with early arrival after accounting for EMS usage and possible confounders. By examining subsets, we can identify groups that would benefit from targeted education. For example, younger, non-AA patients with smaller strokes would benefit from more education on EMS use and African American patients would benefit from education related to faster recognition or urgency of presentation.

Positive airway pressure treatment for sleep-disordered breathing is rare during the first year after stroke: The BASIC project.

OBJECTIVE/BACKGROUND: Sleep-disordered breathing (SDB) is very common after ischemic stroke, and its treatment may have a positive impact on recovery from stroke and on secondary stroke prevention. This study sought to determine the prevalence of positive airway pressure (PAP) use after stroke. PATIENTS/METHODS: Participants in the Brain Attack Surveillance in Corpus Christi (BASIC) project underwent a home sleep apnea test shortly after ischemic stroke. Demographics and co-morbidities were ascertained from the medical record. Self-reported PAP use (present vs absent) was assessed at 3, 6, and 12 months after stroke. Fisher exact tests and t-tests were used to compare PAP users versus non-users. RESULTS: Of 328 participants who were found to have SDB after stroke, only 20 (6.1%) indicated using PAP at any point during the 12-month follow up period. High pre-stroke sleep apnea risk based on Berlin Questionnaire score, neck circumference, and co-morbid atrial fibrillation were associated with any self-reported PAP use; race/ethnicity, insurance status and other demographic variables were not associated with PAP use. CONCLUSIONS: Only a small proportion of individuals with ischemic stroke and SDB received treatment with PAP during the initial year after stroke among participants in this population-based cohort study in Nueces County, Texas. Closing the substantial treatment gap for SDB after stroke might improve sleepiness and neurologic recovery.

Cognitive recovery trajectories 3 months following stroke in Mexican American and non-Hispanic white adults.

OBJECTIVES: We examined whether cognitive trajectories from 0-3 months after stroke differ between Mexican Americans (MAs) and non-Hispanic white (NHW) adults. MATERIALS AND METHODS: The sample included 701 participants with ischemic stroke (62% MA; 38% NHW) from the population-based stroke surveillance study, the Brain Attack Surveillance in Corpus Christi (BASIC) Project, between 2008-2013. The outcome was the modified Mini Mental State Examination (3MSE, range 0-100 lower scores worse). Linear mixed effects models were utilized to examine the association between ethnicity and cognitive trajectories from 0-3 months following stroke, adjusting for confounders. RESULTS: MAs were younger, had lower educational attainment, and fewer had health insurance than NHWs (all p< 0.01). A smaller proportion of MAs were rated by informants as exhibiting pre-stroke cognitive decline than NHW (p < .0.05). After accounting for confounders, MAs demonstrated lower cognitive performance at post-stroke baseline and at 3-months following stroke (-2.00; 95% CI =-3.92, -0.07). Cognitive trajectories from 0-3 months following stroke were indicative of modest cognitive recovery (increase of 0.034/day, 95% CI =0.030-0.036) and did not differ between MAs and NHWs (p = 0.68). CONCLUSION: We found no evidence that cognitive trajectories in the first three months following stroke differed between MAs and NHWs. MAs demonstrated lower cognitive performance shortly after stroke and at three months following stroke compared to NHWs. Further research is needed to identify factors contributing to ethnic disparities in cognitive outcomes after stroke.

Outcomes in the Year After First-Ever Ischemic Stroke in a Bi-Ethnic Population.

OBJECTIVE: To investigate stroke outcomes at 3, 6, and 12 months post-stroke overall and by ethnicity in a population-based, longitudinal study. METHODS: First-ever ischemic strokes (2014-2019, n = 1,332) among Mexican American persons (n = 807) and non-Hispanic white persons (n = 525) were identified from the Brain Attack Surveillance in Corpus Christi Project. Data were collected from patient or proxy interviews (baseline, 3, 6, and 12 months post-stroke) and medical records, including functional (activities of daily living/instrumental activities of daily living score), neurological (National Institutes of Health Stroke Scale), cognitive (Modified Mini-Mental State Examination), and quality of life (QOL) outcomes (12-domain Stroke-specific Quality of Life scale). Outcome trajectories were analyzed using multivariable adjusted linear models, with generalized estimating equations to account for within-subject correlations; interactions between ethnicity and time were included to investigate ethnic differences in outcomes. RESULTS: The median age was 67 years (interquartile range 58,78), 48.5% were women, and 60.6% were Mexican American persons. For all outcomes, significant improvement was seen between 3 and 6 months (p < 0.05 for all), with stability between 6 and 12 months. Mexican American persons had significantly worse outcomes compared with non-Hispanic white persons at all time points (3, 6, and 12 months), with the exception of the National Institutes of Health Stroke Scale, which did not differ by ethnicity at 6 and 12 months, and the average change in outcomes did not vary significantly by ethnicity. INTERPRETATION: Outcomes were at their worst at 3 months post-stroke, and ethnic disparities were already present, suggesting the need for early assessment and strategies to improve outcomes and possibly reduce disparities. ANN NEUROL 2023;93:348-356.

Methods and early recruitment of the Brain Attack Surveillance in Corpus Christi-Post-acute Care (BASIC-PAC) Project.

OBJECTIVES: Compared with non-Hispanic whites (NHWs), Mexican Americans (MAs) have worse stroke outcomes. We report here the methods, background literature, and initial recruitment of the Brain Attack Surveillance in Corpus Christi-Post Acute Care (BASIC-PAC) Project which aims to explore PAC in MAs and NHWs from multiple perspectives: patients, caregivers, and community. MATERIALS AND METHODS: Rigorous active and passive stroke surveillance captures all strokes in Nueces County, Texas. Stroke patients are followed for 90 days to determine their care transitions and factors influencing their rehabilitation setting. Informal caregivers of the stroke patients are identified and interviewed at 90 days to determine aspects of their caregiving and caregiver outcomes. Available community resources are compared with stated needs among stroke patient and caregivers to determine unmet needs. RESULTS: Between October, 2019 and October, 2021, among the 629 stroke patients eligible, 413 were MA, 227 were NHW. Of the 629, all of the six follow-up calls were completed by 355 of the MAs (87%) and 191 of the NHWs (87%). During this same time period, we attempted to approach 621 potential caregivers. Of these, 458 (73.8%) potential caregivers participated in interviews to determine caregiver eligibility, and 373 (81.4%) of these participating potential caregivers met the eligibility criteria. CONCLUSIONS: BASIC-PAC has strong initial recruitment and is poised to provide valuable data on multiple aspects of PAC and how PAC differs by ethnicity and contributes to worse stroke outcomes in MAs. Based on the study findings, interventions can be developed that will improve stroke health equity.

Ten-Year Trends in Sleep-Disordered Breathing After Ischemic Stroke: 2010 to 2019 Data From the BASIC Project.

Background Despite good evidence that the prevalence of sleep-disordered breathing (SDB) is increasing in the general population, no data are available about trends in poststroke SDB. We therefore sought to assess changes in poststroke SDB over a 10-year period (2010-2019). Methods and Results Participants in the BASIC (Brain Attack Surveillance in Corpus Christi) project were offered a home sleep apnea test to assess for SDB after stroke. SDB assessment procedures remained unchanged throughout the study period. Respiratory event index was calculated as the sum of apneas and hypopneas per hour of recording. SDB was defined as respiratory event index ≥10/h for optimal sensitivity and specificity of the home sleep apnea test device compared with in-laboratory polysomnography. Regression models were used to test associations between SDB prevalence and severity and time, with adjustment for multiple potential confounders. Among the 1215 participants who completed objective sleep apnea testing, the prevalence of SDB grew from 61% in the first year of the study to 76% in the last, with 1.1 times higher odds each year (95% CI, 1.07-1.19), after adjustment. A linear association was identified between time and respiratory event index (average annual respiratory event index increase of 0.56/h; 95% CI, 0.20/h-0.91/h), after adjustment. There was no difference in time trends by sex or ethnicity. Conclusions The prevalence and severity of SDB after ischemic stroke has increased over the past 10 years in this population-based cohort. These data highlight the need to determine whether SDB treatment improves stroke outcomes.

Prediction Modeling of Mental Well-Being Using Health Behavior Data of College Students.

Background: Since the onset of the COVID-19 pandemic in early 2020, the importance of timely and effective assessment of mental well-being has increased dramatically. Due to heightened risks for developing mental illness, this trend is likely to continue during the post-pandemic period. Machine learning (ML) algorithms and artificial intelligence (AI) techniques can be harnessed for early detection, prognostication and prediction of negative psychological well-being states. Objective: Studies using machine learning classification of mental well-being are scarce in Asian populations. This investigation aims to develop reliable machine learning classifiers based on health behavior indicators applicable to university students in South-East Asia. Methods: Using data from a large, multi-site cross-sectional survey, this research work models mental well-being and reports on the performance of various machine learning algorithms, such as generalized linear models, k-nearest neighbor, naïve-Bayes, neural networks, random forest, recursive partitioning, bagging, and boosting. Prediction models were evaluated using various metrics such as accuracy, error rate, kappa, sensitivity, specificity, Area Under the recursive operating characteristic Curve (AUC), and Gini Index. Results: Random forest and adaptive boosting algorithms achieved the highest accuracy of identifying negative mental well-being traits. The top five most salient features associated with predicting poor mental well-being include body mass index, number of sports activities per week, grade point average (GPA), sedentary hours, and age. Conclusions: Based on the reported results, several specific recommendations and suggested future work are discussed. These findings may be useful to provide cost-effective support and modernize mental well-being assessment and monitoring at the individual and university level.

A mega-analysis of expression quantitative trait loci in retinal tissue.

Significant association signals from genome-wide association studies (GWAS) point to genomic regions of interest. However, for most loci the causative genetic variant remains undefined. Determining expression quantitative trait loci (eQTL) in a disease relevant tissue is an excellent approach to zoom in on disease- or trait-associated association signals and hitherto on relevant disease mechanisms. To this end, we explored regulation of gene expression in healthy retina (n = 311) and generated the largest cis-eQTL data set available to date. Genotype- and RNA-Seq data underwent rigorous quality control protocols before FastQTL was applied to assess the influence of genetic markers on local (cis) gene expression. Our analysis identified 403,151 significant eQTL variants (eVariants) that regulate 3,007 genes (eGenes) (Q-Value < 0.05). A conditional analysis revealed 744 independent secondary eQTL signals for 598 of the 3,007 eGenes. Interestingly, 99,165 (24.71%) of all unique eVariants regulate the expression of more than one eGene. Filtering the dataset for eVariants regulating three or more eGenes revealed 96 potential regulatory clusters. Of these, 31 harbour 130 genes which are partially regulated by the same genetic signal. To correlate eQTL and association signals, GWAS data from twelve complex eye diseases or traits were included and resulted in identification of 80 eGenes with potential association. Remarkably, expression of 10 genes is regulated by eVariants associated with multiple eye diseases or traits. In conclusion, we generated a unique catalogue of gene expression regulation in healthy retinal tissue and applied this resource to identify potentially pleiotropic effects in highly prevalent human eye diseases. Our study provides an excellent basis to further explore mechanisms of various retinal disease etiologies.

Family-based exome sequencing identifies rare coding variants in age-related macular degeneration.

Genome-wide association studies (GWAS) have identified 52 independent variants at 34 genetic loci that are associated with age-related macular degeneration (AMD), the most common cause of incurable vision loss in the elderly worldwide. However, causal genes at the majority of these loci remain unknown. In this study, we performed whole exome sequencing of 264 individuals from 63 multiplex families with AMD and analyzed the data for rare protein-altering variants in candidate target genes at AMD-associated loci. Rare coding variants were identified in the CFH, PUS7, RXFP2, PHF12 and TACC2 genes in three or more families. In addition, we detected rare coding variants in the C9, SPEF2 and BCAR1 genes, which were previously suggested as likely causative genes at respective AMD susceptibility loci. Identification of rare variants in the CFH and C9 genes in our study validated previous reports of rare variants in complement pathway genes in AMD. We then extended our exome-wide analysis and identified rare protein-altering variants in 13 genes outside the AMD-GWAS loci in three or more families. Two of these genes, SCN10A and KIR2DL4, are of interest because variants in these genes also showed association with AMD in case-control cohorts, albeit not at the level of genome-wide significance. Our study presents the first large-scale, exome-wide analysis of rare variants in AMD. Further independent replications and molecular investigation of candidate target genes, reported here, would assist in gaining novel insights into mechanisms underlying AMD pathogenesis.

Author Correction: Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration.

In the version of this article initially published, in Supplementary Data 5, the logFC, FC, P value and adjusted P value for advanced AMD versus control (DE 4/1) without age correction did not correspond to the correct gene IDs. The errors have been corrected in the HTML version of the article.