Algorithms for Verification of Analog and Mixed-Signal Integrated Circuits

Over the past few decades, the tremendous growth in the complexity of analog and mixed-signal (AMS) systems has posed great challenges to AMS verification, resulting in a rapidly growing verification gap. Existing formal methods provide appealing completeness and reliability, yet they suffer from their limited efficiency and scalability. Data oriented machine learning based methods offer efficient and scalable solutions but do not guarantee completeness or full coverage. Additionally, the trend towards shorter time to market for AMS chips urges the development of efficient verification algorithms to accelerate with the joint design and testing phases. This dissertation envisions a hierarchical and hybrid AMS verification framework by consolidating assorted algorithms to embrace efficiency, scalability and completeness in a statistical sense. Leveraging diverse advantages from various verification techniques, this dissertation develops algorithms in different categories. In the context of formal methods, this dissertation proposes a generic and comprehensive model abstraction paradigm to model AMS content with a unifying analog representation. Moreover, an algorithm is proposed to parallelize reachability analysis by decomposing AMS systems into subsystems with lower complexity, and dividing the circuit's reachable state space exploration, which is formulated as a satisfiability problem, into subproblems with a reduced number of constraints. The proposed modeling method and the hierarchical parallelization enhance the efficiency and scalability of reachability analysis for AMS verification. On the subject of learning based method, the dissertation proposes to convert the verification problem into a binary classification problem solved using support vector machine (SVM) based learning algorithms. To reduce the need of simulations for training sample collection, an active learning strategy based on probabilistic version space reduction is proposed to perform adaptive sampling. An expansion of the active learning strategy for the purpose of conservative prediction is leveraged to minimize the occurrence of false negatives. Moreover, another learning based method is proposed to characterize AMS systems with a sparse Bayesian learning regression model. An implicit feature weighting mechanism based on the kernel method is embedded in the Bayesian learning model for concurrent quantification of influence of circuit parameters on the targeted specification, which can be efficiently solved in an iterative method similar to the expectation maximization (EM) algorithm. Besides, the achieved sparse parameter weighting offers favorable assistance to design analysis and test optimization

Whole Blood Gene Expression and Atrial Fibrillation: The Framingham Heart Study

Background: Atrial fibrillation (AF) involves substantial electrophysiological, structural and contractile remodeling. We hypothesize that characterizing gene expression might uncover important pathways related to AF. Methods and Results: We performed genome-wide whole blood transcriptomic profiling (Affymetrix Human Exon 1.0 ST Array) of 2446 participants (mean age 66±9 years, 55% women) from the Offspring cohort of Framingham Heart Study. The study included 177 participants with prevalent AF, 143 with incident AF during up to 7 years follow up, and 2126 participants with no AF. We identified seven genes statistically significantly up-regulated with prevalent AF. The most significant gene, PBX1 (P = 2.8×10−7), plays an important role in cardiovascular development. We integrated differential gene expression with gene-gene interaction information to identify several signaling pathways possibly involved in AF-related transcriptional regulation. We did not detect any statistically significant transcriptomic associations with incident AF. Conclusion: We examined associations of gene expression with AF in a large community-based cohort. Our study revealed several genes and signaling pathways that are potentially involved in AF-related transcriptional regulation

Common Genetic Variation at the IL1RL1 Locus Regulates IL-33/ST2 Signaling

The suppression of tumorigenicity 2/IL-33 (ST2/IL-33) pathway has been implicated in several immune and inflammatory diseases. ST2 is produced as 2 isoforms. The membrane-bound isoform (ST2L) induces an immune response when bound to its ligand, IL-33. The other isoform is a soluble protein (sST2) that is thought to be a decoy receptor for IL-33 signaling. Elevated sST2 levels in serum are associated with an increased risk for cardiovascular disease. We investigated the determinants of sST2 plasma concentrations in 2,991 Framingham Offspring Cohort participants. While clinical and environmental factors explained some variation in sST2 levels, much of the variation in sST2 production was driven by genetic factors. In a genome-wide association study (GWAS), multiple SNPs within IL1RL1 (the gene encoding ST2) demonstrated associations with sST2 concentrations. Five missense variants of IL1RL1 correlated with higher sST2 levels in the GWAS and mapped to the intracellular domain of ST2, which is absent in sST2. In a cell culture model, IL1RL1 missense variants increased sST2 expression by inducing IL-33 expression and enhancing IL-33 responsiveness (via ST2L). Our data suggest that genetic variation in IL1RL1 can result in increased levels of sST2 and alter immune and inflammatory signaling through the ST2/IL-33 pathway.Stem Cell and Regenerative Biolog

Early Prediction of Alzheimers Disease Leveraging Symptom Occurrences from Longitudinal Electronic Health Records of US Military Veterans

Early prediction of Alzheimer's disease (AD) is crucial for timely intervention and treatment. This study aims to use machine learning approaches to analyze longitudinal electronic health records (EHRs) of patients with AD and identify signs and symptoms that can predict AD onset earlier. We used a case-control design with longitudinal EHRs from the U.S. Department of Veterans Affairs Veterans Health Administration (VHA) from 2004 to 2021. Cases were VHA patients with AD diagnosed after 1/1/2016 based on ICD-10-CM codes, matched 1:9 with controls by age, sex and clinical utilization with replacement. We used a panel of AD-related keywords and their occurrences over time in a patient's longitudinal EHRs as predictors for AD prediction with four machine learning models. We performed subgroup analyses by age, sex, and race/ethnicity, and validated the model in a hold-out and "unseen" VHA stations group. Model discrimination, calibration, and other relevant metrics were reported for predictions up to ten years before ICD-based diagnosis. The study population included 16,701 cases and 39,097 matched controls. The average number of AD-related keywords (e.g., "concentration", "speaking") per year increased rapidly for cases as diagnosis approached, from around 10 to over 40, while remaining flat at 10 for controls. The best model achieved high discriminative accuracy (ROCAUC 0.997) for predictions using data from at least ten years before ICD-based diagnoses. The model was well-calibrated (Hosmer-Lemeshow goodness-of-fit p-value = 0.99) and consistent across subgroups of age, sex and race/ethnicity, except for patients younger than 65 (ROCAUC 0.746). Machine learning models using AD-related keywords identified from EHR notes can predict future AD diagnoses, suggesting its potential use for identifying AD risk using EHR notes, offering an affordable way for early screening on large population.Comment: 24 page

Gene-gene Interaction Analyses for Atrial Fibrillation

Atrial fibrillation (AF) is a heritable disease that affects more than thirty million individuals worldwide. Extensive efforts have been devoted to the study of genetic determinants of AF. The objective of our study is to examine the effect of gene-gene interaction on AF susceptibility. We performed a large-scale association analysis of gene-gene interactions with AF in 8,173 AF cases, and 65,237 AF-free referents collected from 15 studies for discovery. We examined putative interactions between genome-wide SNPs and 17 known AF-related SNPs. The top interactions were then tested for association in a

Genetic correlations and genome-wide associations of cortical structure in general population samples of 22,824 adults

Cortical thickness, surface area and volumes vary with age and cognitive function, and in neurological and psychiatric diseases. Here we report heritability, genetic correlations and genome-wide associations of these cortical measures across the whole cortex, and in 34 anatomically predefined regions. Our discovery sample comprises 22,824 individuals from 20 cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank. We identify genetic heterogeneity between cortical measures and brain regions, and 160 genome-wide significant associations pointing to wnt/β-catenin, TGF-β and sonic hedgehog pathways. There is enrichment for genes involved in anthropometric traits, hindbrain development, vascular and neurodegenerative disease and psychiatric conditions. These data are a rich resource for studies of the biological mechanisms behind cortical development and aging

Cross-sectional relations of whole-blood miRNA expression levels and hand grip strength in a community sample

MicroRNAs (miRNAs) regulate gene expression with emerging data suggesting miRNAs play a role in skeletal muscle biology. We sought to examine the association of miRNAs with grip strength in a community-based sample. Framingham Heart Study Offspring and Generation 3 participants (n = 5668 54% women, mean age 55 years, range 24, 90 years) underwent grip strength measurement and miRNA profiling using whole blood from fasting morning samples. Linear mixed-effects regression modeling of grip strength (kg) versus continuous miRNA \u27Cq\u27 values and versus binary miRNA expression was performed. We conducted an integrative miRNA-mRNA coexpression analysis and examined the enrichment of biologic pathways for the top miRNAs associated with grip strength. Grip strength was lower in women than in men and declined with age with a mean 44.7 (10.0) kg in men and 26.5 (6.3) kg in women. Among 299 miRNAs interrogated for association with grip strength, 93 (31%) had FDR q value \u3c 0.05, 54 (18%) had an FDR q value \u3c 0.01, and 15 (5%) had FDR q value \u3c 0.001. For almost all miRNA-grip strength associations, increasing miRNA concentration is associated with increasing grip strength. miR-20a-5p (FDR q 1.8 x 10-6 ) had the most significant association and several among the top 15 miRNAs had links to skeletal muscle including miR-126-3p, miR-30a-5p, and miR-30d-5p. The top associated biologic pathways included metabolism, chemokine signaling, and ubiquitin-mediated proteolysis. Our comprehensive assessment in a community-based sample of miRNAs in blood associated with grip strength provides a framework to further our understanding of the biology of muscle strength

Association between deep neural network-derived electrocardiographic-age and incident stroke

BackgroundStroke continues to be a leading cause of death and disability worldwide despite improvements in prevention and treatment. Traditional stroke risk calculators are biased and imprecise. Novel stroke predictors need to be identified. Recently, deep neural networks (DNNs) have been used to determine age from ECGs, otherwise known as the electrocardiographic-age (ECG-age), which predicts clinical outcomes. However, the relationship between ECG-age and stroke has not been well studied. We hypothesized that ECG-age is associated with incident stroke.MethodsIn this study, UK Biobank participants with available ECGs (from 2014 or later). ECG-age was estimated using a deep neural network (DNN) applied to raw ECG waveforms. We calculated the Δage (ECG-age minus chronological age) and classified individuals as having normal, accelerated, or decelerated aging if Δage was within, higher, or lower than the mean absolute error of the model, respectively. Multivariable Cox proportional hazards regression models adjusted for age, sex, and clinical factors were used to assess the association between Δage and incident stroke.ResultsThe study population included 67,757 UK Biobank participants (mean age 65 ± 8 years; 48.3% male). Every 10-year increase in Δage was associated with a 22% increase in incident stroke [HR, 1.22 (95% CI, 1.00–1.49)] in the multivariable-adjusted model. Accelerated aging was associated with a 42% increase in incident stroke [HR, 1.42 (95% CI, 1.12–1.80)] compared to normal aging. In addition, Δage was associated with prevalent stroke [OR, 1.28 (95% CI, 1.11–1.49)].ConclusionsDNN-estimated ECG-age was associated with incident and prevalent stroke in the UK Biobank. Further investigation is required to determine if ECG-age can be used as a reliable biomarker of stroke risk

A whole-blood transcriptome meta-analysis identifies gene expression signatures of cigarette smoking

Cigarette smoking is a leading modifiable cause of death worldwide. We hypothesized that cigarette smoking induces extensive transcriptomic changes that lead to target-organ damage and smoking-related diseases. We performed a metaanalysis of transcriptome-wide gene expression using whole blood-derived RNA from 10,233 participants of European ancestry in six cohorts (including 1421 current and 3955 former smokers) to identify associations between smoking and altered gene expression levels. At a false discovery rate (FDR) < 0.1, we identified 1270 differentially expressed genes in current vs. never smokers, and 39 genes in former vs. never smokers. Expression levels of 12 genes remained elevated up to 30 years after smoking cessation, suggesting that the molecular consequence of smoking may persist for decades. Gene ontology analysis revealed enrichment of smoking-related genes for activation of platelets and lymphocytes, immune response, and apoptosis. Many of the top smoking-related differentially expressed genes, including LRRN3 and GPR15, have DNA methylation loci in promoter regions that were recently reported to be hypomethylated among smokers. By linking differential gene expression with smoking-related disease phenotypes, we demonstrated that stroke and pulmonary function show enrichment for smoking-related gene expression signatures. Mediation analysis revealed the expression of several genes (e.g. ALAS2) to be putative mediators of the associations between smoking and inflammatory biomarkers (IL6 and C-re