Evaluation of the SpotChecks contrast sensitivity test in healthy adults.

PURPOSE: SpotChecks is a new contrast sensitivity (CS) test designed for self-monitoring of vision. This study assessed the test-retest repeatability of take-home SpotChecks, in-office SpotChecks and near Pelli-Robson charts in healthy adults. METHODS: One eye of 61 healthy adults with near visual acuity (VA) of 6/9 or better (age range 22-84, mean 49 [18] years) was tested during two office visits (mean 10 [8] days apart). Each visit included high-contrast VA, then 12 randomly ordered CS tests (6 different SpotChecks and 6 different Pelli-Robson) under the same lighting (luminance 110 cd/m2), all at near in the same eye with habitual correction. The same eye was self-tested with take-home SpotChecks once a day on 6 days between the office visits. SpotChecks was scored by the logCS at the highest line with ≥2 errors. Pelli-Robson was scored by [0.05 × number of letters read correctly - 0.15]. Repeatability of logCS was defined as 1.96 2 $$ \sqrt{2} $$ Sw, Sw representing within-subject standard deviation. Comparison for repeatability was performed with Bootstrap hypothesis test. RESULTS: SpotChecks and Pelli-Robson showed similar intra-session or inter-visit repeatability (p = 0.14-0.81). Inter-day repeatability for take-home SpotChecks was 0.18 logCS, the same as that from the first measurements of two office visits with SpotChecks or Pelli-Robson. Inter-visit repeatability improved to 0.15 by using the average of two repeated measurements for SpotChecks (p = 0.02) or three repeated measurements for Pelli-Robson (p = 0.04). Age showed a small effect on logCS (-0.015/decade, p = 0.02) for both SpotChecks and Pelli-Robson. Mean logCS was 0.05 lower in those ≥50 years (SpotChecks 1.84 [0.10] and Pelli-Robson 1.77 [0.10]) compared with those <50 years of age (SpotChecks 1.89 [0.07] and Pelli-Robson 1.83 [0.07]). CONCLUSIONS: SpotChecks showed good repeatability with take-home and in-office testing in healthy adults, making it a promising tool for monitoring disease progression at home.

Bayesian graph selection consistency under model misspecification.

Gaussian graphical models are a popular tool to learn the dependence structure in the form of a graph among variables of interest. Bayesian methods have gained in popularity in the last two decades due to their ability to simultaneously learn the covariance and the graph. There is a wide variety of model-based methods to learn the underlying graph assuming various forms of the graphical structure. Although for scalability of the Markov chain Monte Carlo algorithms, decomposability is commonly imposed on the graph space, its possible implication on the posterior distribution of the graph is not clear. An open problem in Bayesian decomposable structure learning is whether the posterior distribution is able to select a meaningful decomposable graph that is "close" to the true non-decomposable graph, when the dimension of the variables increases with the sample size. In this article, we explore specific conditions on the true precision matrix and the graph, which results in an affirmative answer to this question with a commonly used hyper-inverse Wishart prior on the covariance matrix and a suitable complexity prior on the graph space. In absence of structural sparsity assumptions, our strong selection consistency holds in a high-dimensional setting where p = O(nα ) for α < 1/3. We show when the true graph is non-decomposable, the posterior distribution concentrates on a set of graphs that are minimal triangulations of the true graph.

Dietary Intakes of Amino Acids and Other Nutrients by Adult Humans.

Measuring usual dietary intake in freely living humans is difficult to accomplish. As a part of our recent study, a food frequency questionnaire was completed by healthy adult men and women at days 0 and 90 of the study. Data from the food questionnaire were analyzed with a nutrient analysis program ( www.Harvardsffq.date ). Healthy men and women consumed protein as 19-20% and 17-19% of their total energy intakes, respectively, with animal protein representing about 75 and 70% of their total protein intakes, respectively. The intake of each nutritionally essential amino acid (EAA) by the persons exceeded that recommended for healthy adults with a minimal physical activity. In all individuals, the dietary intake of leucine was the highest, followed by lysine, valine, and isoleucine in descending order, and the ingestion of amino acids that are synthesizable de novo in animal cells (AASAs) was about 20% greater than that of total EAAs. The intake of each AASA met those recommended for healthy adults with a minimal physical activity. Intakes of some AASAs (alanine, arginine, aspartate, glutamate, and glycine) from a typical diet providing 90-110 g food protein/day does not meet the requirements of adults with an intensive physical activity. Within the male or female group, there were not significant differences in the dietary intakes of all amino acids between days 0 and 90 of the study, and this was also true for nearly all other essential nutrients. Our findings will help to improve amino acid nutrition and health in both the general population and exercising individuals.

Multiple Omics Data Integration to Identify Long Noncoding RNA Responsible for Breast Cancer-Related Mortality.

Long non-coding RNAs (lncRNAs) are a large and diverse class of transcribed RNAs, which have been shown to play a significant role in developing cancer. In this study, we apply integrative modeling framework to integrate the DNA copy number variation (CNV), lncRNA expression, and downstream target protein expression to predict patient survival in breast cancer. We develop a 3-stage model combining a mechanical model (lncRNA regressed on CNV and target proteins regressed on lncRNA) and a clinical model (survival regressed on estimated effects from the mechanical models). Using lncRNAs (such as HOTAIR and MALAT1) along with their CNV, target protein expressions, and survival outcomes from The Cancer Genome Atlas (TCGA) database, we show that predicted mean square error and integrated Brier score (IBS) are both lower for the proposed 3-step integrated model than that of 2-step model. Therefore, the integrative model has better predictive ability than the 2-step model not considering target protein information.