Anna Plantinga
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View article: Multivariate Predictors of Lyman Continuum Escape. II. Predicting Lyman Continuum Escape Fractions for High-redshift Galaxies*
Multivariate Predictors of Lyman Continuum Escape. II. Predicting Lyman Continuum Escape Fractions for High-redshift Galaxies* Open
JWST is uncovering the properties of ever-increasing numbers of galaxies at z > 6, during the epoch of reionization. Connecting these observed populations to the process of reionization requires understanding how efficiently they produce L…
View article: Comparing Insulin Against Glucagon-Like Peptide-1 Receptor Agonists, Dipeptidyl Peptidase-4 Inhibitors, and Sodium-Glucose Cotransporter 2 Inhibitors on 5-Year Incident Heart Failure Risk for Patients With Type 2 Diabetes Mellitus: Real-World Evidence Study Using Insurance Claims
Comparing Insulin Against Glucagon-Like Peptide-1 Receptor Agonists, Dipeptidyl Peptidase-4 Inhibitors, and Sodium-Glucose Cotransporter 2 Inhibitors on 5-Year Incident Heart Failure Risk for Patients With Type 2 Diabetes Mellitus: Real-World Evidence Study Using Insurance Claims Open
Background Type 2 diabetes mellitus (T2DM) is a common health issue, with heart failure (HF) being a common and lethal long-term complication. Although insulin is widely used for the treatment of T2DM, evidence regarding the efficacy of in…
View article: Multivariate Predictors of Lyman Continuum Escape. I. A Survival Analysis of the Low-redshift Lyman Continuum Survey*
Multivariate Predictors of Lyman Continuum Escape. I. A Survival Analysis of the Low-redshift Lyman Continuum Survey* Open
To understand how galaxies reionized the Universe, we must determine how the escape fraction of Lyman continuum (LyC) photons ( f esc ) depends on galaxy properties. Using the z ∼ 0.3 Low-redshift Lyman Continuum Survey (LzLCS), we develop…
View article: Multivariate Predictors of LyC Escape II: Predicting LyC Escape Fractions for High-Redshift Galaxies
Multivariate Predictors of LyC Escape II: Predicting LyC Escape Fractions for High-Redshift Galaxies Open
JWST is uncovering the properties of ever increasing numbers of galaxies at z>6, during the epoch of reionization. Connecting these observed populations to the process of reionization requires understanding how efficiently they produce Lym…
View article: Multivariate Predictors of LyC Escape I: A Survival Analysis of the Low-redshift Lyman Continuum Survey
Multivariate Predictors of LyC Escape I: A Survival Analysis of the Low-redshift Lyman Continuum Survey Open
To understand how galaxies reionized the universe, we must determine how the escape fraction of Lyman Continuum (LyC) photons (fesc) depends on galaxy properties. Using the z~0.3 Low-redshift Lyman Continuum Survey (LzLCS), we develop and …
View article: Improving and Evaluating Machine Learning Methods for Forensic Shoeprint Matching
Improving and Evaluating Machine Learning Methods for Forensic Shoeprint Matching Open
We propose a machine learning pipeline for forensic shoeprint pattern matching that improves on the accuracy and generalisability of existing methods. We extract 2D coordinates from shoeprint scans using edge detection and align the two sh…
View article: U.S. Mental Health Dashboard
U.S. Mental Health Dashboard Open
In this paper, we present the U.S. Mental Health Dashboard, an R Shiny web application that facilitates exploratory data analysis of U.S. mental health data collected through national surveys. Mental health affects almost every aspect of p…
View article: Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity
Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity Open
View article: Exploration of associations among dietary tryptophan, microbiome composition and function, and symptom severity in irritable bowel syndrome
Exploration of associations among dietary tryptophan, microbiome composition and function, and symptom severity in irritable bowel syndrome Open
Background Imbalance of the tryptophan (TRP) pathway may influence symptoms among patients with irritable bowel syndrome (IBS). This study explored relationships among different components that contribute to TRP metabolism (dietary intake,…
View article: Accommodating multiple potential normalizations in microbiome associations studies
Accommodating multiple potential normalizations in microbiome associations studies Open
Background Microbial communities are known to be closely related to many diseases, such as obesity and HIV, and it is of interest to identify differentially abundant microbial species between two or more environments. Since the abundances …
View article: Impact of Data and Study Characteristics on Microbiome Volatility Estimates
Impact of Data and Study Characteristics on Microbiome Volatility Estimates Open
The human microbiome is a dynamic community of bacteria, viruses, fungi, and other microorganisms. Both the composition of the microbiome (the microbes that are present and their relative abundances) and the temporal variability of the mic…
View article: Exploring the Role of Vitamin D and the Gut Microbiome: A Cross-Sectional Study of Individuals with Irritable Bowel Syndrome and Healthy Controls
Exploring the Role of Vitamin D and the Gut Microbiome: A Cross-Sectional Study of Individuals with Irritable Bowel Syndrome and Healthy Controls Open
Irritable bowel syndrome (IBS) is a common disorder of gut-brain interaction with multifaceted pathophysiology. Prior studies have demonstrated higher rates of vitamin D deficiency in individuals with IBS compared to healthy controls (HC),…
View article: Additional file 2 of Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity
Additional file 2 of Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity Open
Additional file 2. An XLSX file that includes supplemental long tables (Table S3-S5).
View article: Batch effects removal for microbiome data via conditional quantile regression
Batch effects removal for microbiome data via conditional quantile regression Open
Batch effects in microbiome data arise from differential processing of specimens and can lead to spurious findings and obscure true signals. Strategies designed for genomic data to mitigate batch effects usually fail to address the zero-in…
View article: A Kernel-based Test of Independence for Cluster-correlated Data.
A Kernel-based Test of Independence for Cluster-correlated Data. Open
The Hilbert-Schmidt Independence Criterion (HSIC) is a powerful kernel-based statistic for assessing the generalized dependence between two multivariate variables. However, independence testing based on the HSIC is not directly possible fo…
View article: Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity
Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity Open
Understanding human genetic influences on the gut microbiota helps elucidate the mechanisms by which genetics affects health outcomes. We propose a novel approach, the covariate-adjusted kernel RV (KRV) framework, to map genetic variants a…
View article: Batch effects removal for microbiome data via conditional quantile regression (ConQuR)
Batch effects removal for microbiome data via conditional quantile regression (ConQuR) Open
Batch effects in microbiome data arise from differential processing of specimens and can lead to spurious findings and obscure true signals. Most existing strategies for mitigating batch effects rely on approaches designed for genomic anal…
View article: Testing microbiome association using integrated quantile regression models
Testing microbiome association using integrated quantile regression models Open
Motivation Most existing microbiome association analyses focus on the association between microbiome and conditional mean of health or disease-related outcomes, and within this vein, vast computational tools and methods have been devised f…
View article: Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)
Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ) Open
Background Identification of bacterial taxa associated with diseases, exposures, and other variables of interest offers a more comprehensive understanding of the role of microbes in many conditions. However, despite considerable research i…
View article: A Comprehensive Self-Management Program With Diet Education Does Not Alter Microbiome Characteristics in Women With Irritable Bowel Syndrome
A Comprehensive Self-Management Program With Diet Education Does Not Alter Microbiome Characteristics in Women With Irritable Bowel Syndrome Open
Background and Purpose: Changes in diet and lifestyle factors are frequently recommended for persons with irritable bowel syndrome (IBS). It is unknown whether these recommendations alter the gut microbiome and/or whether baseline microbio…
View article: MiRKAT: kernel machine regression-based global association tests for the microbiome
MiRKAT: kernel machine regression-based global association tests for the microbiome Open
Summary Distance-based tests of microbiome beta diversity are an integral part of many microbiome analyses. MiRKAT enables distance-based association testing with a wide variety of outcome types, including continuous, binary, censored time…
View article: Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity
Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity Open
Artificial sweeteners have been shown to induce glucose intolerance by altering the gut microbiota; however, little is known about the effect of stevia. Here, we investigate whether stevia supplementation induces glucose intolerance by alt…
View article: Vaginal and Extra-Vaginal Bacterial Colonization and Risk for Incident Bacterial Vaginosis in a Population of Women Who Have Sex With Men
Vaginal and Extra-Vaginal Bacterial Colonization and Risk for Incident Bacterial Vaginosis in a Population of Women Who Have Sex With Men Open
Background Bacterial vaginosis (BV) is a common cause of vaginal discharge and associated with vaginal acquisition of BV-associated bacteria (BVAB). Methods We used quantitative polymerase chain reaction assays to determine whether presenc…
View article: Genetic history of the population of Crete
Genetic history of the population of Crete Open
The medieval history of several populations often suffers from scarcity of contemporary records resulting in contradictory and sometimes biased interpretations by historians. This is the situation with the population of the island of Crete…
View article: pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis
pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis Open
Motivation The human microbiome is notoriously variable across individuals, with a wide range of ‘healthy’ microbiomes. Paired and longitudinal studies of the microbiome have become increasingly popular as a way to reduce unmeasured confou…
View article: Statistical Methods for the Analysis of Microbiome Data
Statistical Methods for the Analysis of Microbiome Data Open
View article: Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplantation
Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplantation Open
The stool microbiota around the time of neutrophil recovery post-HCT is predictive of subsequent development of severe acute GVHD in this study.
View article: Powerful Genetic Association Analysis for Common or Rare Variants with High-Dimensional Structured Traits
Powerful Genetic Association Analysis for Common or Rare Variants with High-Dimensional Structured Traits Open
Genetic association studies often collect a wide range of complex traits, including high-dimensional and structured omics measurements. The complex... Many genetic association studies collect a wide range of complex traits. As these traits…
View article: Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks
Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks Open
View article: MiRKAT-S: a community-level test of association between the microbiota and survival times
MiRKAT-S: a community-level test of association between the microbiota and survival times Open
We present MiRKAT-S, a method that facilitates community-level analysis of the association between the microbiota and survival outcomes and therefore provides a new approach to analysis of microbiome data arising from clinical trials.