Transcriptional and translational regulation of sex-specific genes in mouse liver

With the advent of high-throughput sequencing technology, modeling molecular mechanisms for gene regulatory networks has expanded to include the epigenome. Using diverse high-throughput DNA sequencing platforms, previous studies have revealed such mechanisms for sex-differential gene regulation in mouse liver. This thesis describes the contribution of transcription factor (TF) HNF6 to these models. Further, the utility of digital genomic footprinting (DGF) using the DNase-I hypersensitive sites sequencing (DNase-Seq) assay or the Assay for Transposase Accessible Chromatin (ATAC-Seq) is demonstrated. Finally, this thesis characterizes the extent of post-translational control of genes active in mouse liver using the ribosome profiling assay (Ribo-Seq), by way of translational efficiency (TE), and uses Ribo-Seq to interrogate open reading frames from previously characterized untranslated regions of protein-coding genes and in a set of liver-expressed long non-coding RNA genes for evidence of translation. First, mouse liver binding sites for HNF6 are integrated for overlap with sex-biased DNase-I hypersensitivity sites, male-biased STAT5, and female-specific CUX2 binding sites. This analysis showed how epigenetic markers, together with HNF6, target specific sets of sex-biased genes, revealing specific mechanisms involving HNF6 that contribute to the sex-specificity of gene expression in mouse liver. Next, the limited utility of the DGF technique to predict TF-DNA interactions was demonstrated using publicly available datasets for 21 TFs using DNase-seq and ATAC-seq datasets and sequencing libraries prepared using chromatin as well as purified DNA. Additionally, a simple model is proposed that benchmarks performance of DNase-seq vs. ATAC-seq for the same set of 21 TFs. Finally, the extent to which liver-expressed genes are regulated by sex-differential TE was investigated using Ribo-Seq. Limited sex-differential TE was found. Further, this assay predicted novel peptides found in previously characterized non-coding open reading frames within untranslated regions of genes that may regulate TE of upstream genes, and in a set of liver-expressed long non-coding RNAs.2021-02-20T00:00:00

The Limitations of Simple Gene Set Enrichment Analysis Assuming Gene Independence

Since its first publication in 2003, the Gene Set Enrichment Analysis (GSEA) method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach, using a one sample t test score to assess enrichment and ignoring gene-gene correlations was proposed by Irizarry et al. 2009 as a serious contender. The argument criticizes GSEA's nonparametric nature and its use of an empirical null distribution as unnecessary and hard to compute. We refute these claims by careful consideration of the assumptions of the simplified method and its results, including a comparison with GSEA's on a large benchmark set of 50 datasets. Our results provide strong empirical evidence that gene-gene correlations cannot be ignored due to the significant variance inflation they produced on the enrichment scores and should be taken into account when estimating gene set enrichment significance. In addition, we discuss the challenges that the complex correlation structure and multi-modality of gene sets pose more generally for gene set enrichment methods.Comment: Submitted to Statistical Methods in Medical Researc

Correlation of Hydronephrosis Index to Society of Fetal Urology Hydronephrosis Scale

Purpose. We seek to correlate conventional hydronephrosis (HN) grade and hydronephrosis index (HI). Methods. We examined 1207 hydronephrotic kidneys by ultrasound. HN was classified by Society of Fetal Urology guidelines. HN was then gauged using HI, a reproducible, standardized, and dimensionless measurement of renal area. We then calculated average HI for each HN grade. Results. Comparing HI to standard SFU HN grade, average HI is 89.3 for grade I; average HI is 83.9 for grade II; average HI is 73.0 for grade III; average HI is 54.6 for SFU grade IV. Conclusions. HI correlates well with SFU HN grade. The HI serves as a quantitative measure of HN. HI can be used to track HN over time. Versus conventional grading, HI may be more sensitive in defining severe (grades III and IV) HN, and in indicating resolving, stable, or worsening HN, thus providing more information for clinical decision-making and HN management

The Imprint of Gravitational Waves on the Cosmic Microwave Background

Long-wavelength gravitational waves can induce significant temperature anisotropy in the cosmic microwave background. Distinguishing this from anisotropy induced by energy density fluctuations is critical for testing inflationary cosmology and theories of large-scale structure formation. We describe full radiative transport calculations of the two contributions and show that they differ dramatically at angular scales below a few degrees. We show how anisotropy experiments probing large- and small-angular scales can combine to distinguish the imprint due to gravitational waves.Comment: 11 pages, Penn Preprint-UPR-

Repurposing NGO data for better research outcomes: A scoping review of the use and secondary analysis of NGO data in health policy and systems research

Background Non-government organisations (NGOs) collect and generate vast amounts of potentially rich data, most of which are not used for research purposes. Secondary analysis of NGO data (their use and analysis in a study for which they were not originally collected) presents an important but largely unrealised opportunity to provide new research insights in critical areas including the evaluation of health policy and programmes. Methods A scoping review of the published literature was performed to identify the extent to which secondary analysis of NGO data has been used in health policy and systems research (HPSR). A tiered analytic approach provided a comprehensive overview and descriptive analyses of the studies which: 1) used data produced or collected by or about NGOs; 2) performed secondary analysis of the NGO data (beyond use of an NGO report as a supporting reference); 3) used NGO-collected clinical data. Results Of the 156 studies which performed secondary analysis of NGO-produced or collected data, 64% (n=100) used NGO-produced reports (e.g. to critique NGO activities and as a contextual reference) and 8% (n=13) analysed NGO-collected clinical data.. Of the studies, 55% investigated service delivery research topics, with 48% undertaken in developing countries and 17% in both developing and developed. NGO-collected clinical data enabled HPSR within marginalised groups (e.g. migrants, people in conflict-affected areas), with some limitations such as inconsistencies and missing data. Conclusion We found evidence that NGO-collected and produced data are most commonly perceived as a source of supporting evidence for HPSR and not as primary source data. However, these data can facilitate research in under-researched marginalised groups and in contexts that are hard to reach by academics, such as conflict-affected areas. NGO–academic collaboration could help address issues of NGO data quality to facilitate their more widespread use in research. Their use could enable relevant and timely research in the areas of health policy, programme evaluation and advocacy to improve health and reduce health inequalities, especially in marginalised groups and developing countries

Gravity's rainbow

Could COBE DMR be detecting the imprint from a spectrum of gravitational waves generated during inflation? The conventional inflationary prediction had been that the cosmic microwave anisotropy is dominated by energy density fluctuations generated during inflation and that the gravitational waves contribute negligibly. In this paper, we report on recent work (in collaboration with R. Davis, H. Hodges, and M. Turner) that has shown that the conventional wisdom may be wrong; specifically, gravitational waves may dominate the anisotropy in inflationary models where the spectrum of perturbations deviates significantly from scale invariance (e.g., extended and power-law inflation models and extreme versions of chaotic inflation). If gravitational waves do dominate at the large-angular scales measured by COBE DMR, the expectation and interpretation of anisotropies on small-angular scales is profoundly altered. Invited Paper for Proceedings of the Journees Relativistes, Amsterdam, May 14-16, 1992Comment: 15 pages, UPR-0543

Simple moment-based inferences of generalized concordance correlation

We proposed two simple moment-based procedures, one with (GCCC1) and one without (GCCC2) normality assumptions, to generalize the inference of concordance correlation coefficient for the evaluation of agreement among multiple observers for measurements on a continuous scale. A modified Fisher's Z -transformation was adapted to further improve the inference. We compared the proposed methods with U -statistic-based inference approach. Simulation analysis showed desirable statistical properties of the simplified approach GCCC1, in terms of coverage probabilities and coverage balance, especially for small samples. GCCC2, which is distribution-free, behaved comparably with the U -statistic-based procedure, but had a more intuitive and explicit variance estimator. The utility of these approaches were illustrated using two clinical data examples.