The Human Touch:Using a Webcam to Autonomously Monitor Compliance During Visual Field Assessments

Purpose: To explore the feasibility of using various easy-to-obtain biomarkers to monitor non-compliance (measurement error) during visual field assessments. Methods: Forty-two healthy adults (42 eyes) and seven glaucoma patients (14 eyes) underwent two same-day visual field assessments. An ordinary webcam was used to compute seven potential biomarkers of task compliance, based primarily on eye gaze, head pose, and facial expression. We quantified the association between each biomarker and measurement error, as defined by (1) test-retest differences in overall test scores (mean sensitivity), and (2) failures to respond to visible stimuli on individual trials (stimuli -3 dB or more brighter than threshold). Results: In healthy eyes, three of the seven biomarkers were significantly associated with overall (test-retest) measurement error (P = 0.003-0.007), and at least two others exhibited possible trends (P = 0.052-0.060). The weighted linear sum of all seven biomarkers was associated with overall measurement error, in both healthy eyes (r = 0.51, P <0.001) and patients (r = 0.65, P <0.001). Five biomarkers were each associated with failures to respond to visible stimuli on individual trials (all P <0.001). Conclusions: Inexpensive, autonomous measures of task compliance are associated with measurement error in visual field assessments, in terms of both the overall reliability of a test and failures to respond on particular trials ("lapses"). This could be helpful for identifying low-quality assessments and for improving assessment techniques (e.g., by discounting suspect responses or by automatically triggering comfort breaks or encouragement). Translational Relevance: This study explores a potential way of improving the reliability of visual field assessments, a crucial but notoriously unreliable clinical measure

The Human Touch: Using a Webcam to Autonomously Monitor Compliance During Visual Field Assessments

Purpose: To explore the feasibility of using various easy-to-obtain biomarkers to monitor non-compliance (measurement error) during visual field assessments.Methods: Forty-two healthy adults (42 eyes) and seven glaucoma patients (14 eyes) underwent two same-day visual field assessments. An ordinary webcam was used to compute seven potential biomarkers of task compliance, based primarily on eye gaze, head pose, and facial expression. We quantified the association between each biomarker and measurement error, as defined by (1) test-retest differences in overall test scores (mean sensitivity), and (2) failures to respond to visible stimuli on individual trials (stimuli -3 dB or more brighter than threshold).Results: In healthy eyes, three of the seven biomarkers were significantly associated with overall (test-retest) measurement error (P = 0.003-0.007), and at least two others exhibited possible trends (P = 0.052-0.060). The weighted linear sum of all seven biomarkers was associated with overall measurement error, in both healthy eyes (r = 0.51, P < 0.001) and patients (r = 0.65, P < 0.001). Five biomarkers were each associated with failures to respond to visible stimuli on individual trials (all P < 0.001).Conclusions: Inexpensive, autonomous measures of task compliance are associated with measurement error in visual field assessments, in terms of both the overall reliability of a test and failures to respond on particular trials ("lapses"). This could be helpful for identifying low-quality assessments and for improving assessment techniques (e.g., by discounting suspect responses or by automatically triggering comfort breaks or encouragement).Translational Relevance: This study explores a potential way of improving the reliability of visual field assessments, a crucial but notoriously unreliable clinical measure

Occupational exposure to gases/fumes and mineral dust affect DNA methylation levels of genes regulating expression

Many workers are daily exposed to occupational agents like gases/fumes, mineral dust or biological dust, which could induce adverse health effects. Epigenetic mechanisms, such as DNA methylation, have been suggested to play a role. We therefore aimed to identify differentially methylated regions (DMRs) upon occupational exposures in never-smokers and investigated if these DMRs associated with gene expression levels. To determine the effects of occupational exposures independent of smoking, 903 never-smokers of the LifeLines cohort study were included. We performed three genome-wide methylation analyses (Illumina 450 K), one per occupational exposure being gases/fumes, mineral dust and biological dust, using robust linear regression adjusted for appropriate confounders. DMRs were identified using comb-p in Python. Results were validated in the Rotterdam Study (233 never-smokers) and methylation-expression associations were assessed using Biobank-based Integrative Omics Study data (n = 2802). Of the total 21 significant DMRs, 14 DMRs were associated with gases/fumes and 7 with mineral dust. Three of these DMRs were associated with both exposures (RPLP1 and LINC02169 (2x)) and 11 DMRs were located within transcript start sites of gene expression regulating genes. We replicated two DMRs with gases/fumes (VTRNA2-1 and GNAS) and one with mineral dust (CCDC144NL). In addition, nine gases/fumes DMRs and six mineral dust DMRs significantly associated with gene expression levels. Our data suggest that occupational exposures may induce differential methylation of gene expression regulating genes and thereby may induce adverse health effects. Given the millions of workers that are exposed daily to occupational exposures, further studies on this epigenetic mechanism and health outcomes are warranted

Tomato: a crop species amenable to improvement by cellular and molecular methods

Tomato is a crop plant with a relatively small DNA content per haploid genome and a well developed genetics. Plant regeneration from explants and protoplasts is feasable which led to the development of efficient transformation procedures. In view of the current data, the isolation of useful mutants at the cellular level probably will be of limited value in the genetic improvement of tomato. Protoplast fusion may lead to novel combinations of organelle and nuclear DNA (cybrids), whereas this technique also provides a means of introducing genetic information from alien species into tomato. Important developments have come from molecular approaches. Following the construction of an RFLP map, these RFLP markers can be used in tomato to tag quantitative traits bred in from related species. Both RFLP's and transposons are in the process of being used to clone desired genes for which no gene products are known. Cloned genes can be introduced and potentially improve specific properties of tomato especially those controlled by single genes. Recent results suggest that, in principle, phenotypic mutants can be created for cloned and characterized genes and will prove their value in further improving the cultivated tomato.

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

Background: Epigenetic change is a hallmark of ageing but its link to ageing mechanisms in humans remains poorly understood. While DNA methylation at many CpG sites closely tracks chronological age, DNA methylation changes relevant to biological age are expected to gradually dissociate from chronological age, mirroring the increased heterogeneity in health status at older ages. Results: Here, we report on the large-scale identification of 6366 age-related variably methylated positions (aVMPs) identified in 3295 whole blood DNA methylation profiles, 2044 of which have a matching RNA-seq gene expression profile. aVMPs are enriched at polycomb repressed regions and, accordingly, methylation at those positions is associated with the expression of genes encoding components of polycomb repressive complex 2 (PRC2) in trans. Further analysis revealed trans-associations for 1816 aVMPs with an additional 854 genes. These trans-associated aVMPs are characterized by either an age-related

Blood lipids influence DNA methylation in circulating cells

Background: Cells can be primed by external stimuli to obtain a long-term epigenetic memory. We hypothesize that long-term exposure to elevated blood lipids can prime circulating immune cells through changes in DNA methylation, a process that may contribute to the development of atherosclerosis. To interrogate the causal relationship between triglyceride, low-density lipoprotein (LDL) cholesterol, and high-density lipoprotein (HDL) cholesterol levels and genome-wide DNA methylation while excluding confounding and pleiotropy, we perform a stepwise Mendelian randomization analysis in whole blood of 3296 individuals. Results: This analysis shows that differential methylation is the consequence of inter-individual variation in blood lipid levels and not vice versa. Specifically, we observe an effect of triglycerides on DNA methylation at three CpGs, of LDL cholesterol at one CpG, and of HDL cholesterol at two CpGs using multivariable Mendelian randomization. Using RNA-seq data available for a large subset of individuals (N = 2044), DNA methylation of these six CpGs is associated with the expression of CPT1A and SREBF1 (for triglycerides), DHCR24 (for LDL cholesterol) and

Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution

We show that epigenome- and transcriptome-wide association studies (EWAS and TWAS) are prone to significant inflation and bias of test statistics, an unrecognized phenomenon introducing spurious findings if left unaddressed. Neither GWAS-based methodology nor state-of-the-art confounder adjustment methods completely remove bias and inflation. We propose a Bayesian method to control bias and inflation in EWAS and TWAS based on estimation of the empirical null distribution. Using simulations and real data, we demonstrate that our method maximizes power while properly controlling the false positive rate. We illustrate the utility of our method in large-scale EWAS and TWAS meta-analyses of age and smoking