Somnath Datta
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View article: Conditional-Marginal Nonparametric Estimation for Stage Waiting Times from Multi-Stage Models under Dependent Right Censoring
Conditional-Marginal Nonparametric Estimation for Stage Waiting Times from Multi-Stage Models under Dependent Right Censoring Open
We investigate two population-level quantities (corresponding to complete data) related to uncensored stage waiting times in a progressive multi-stage model, conditional on a prior stage visit. We show how to estimate these quantities cons…
View article: Can the Unit Size Predict Outcomes? Testing for Informativeness in Three‐Level Designs
Can the Unit Size Predict Outcomes? Testing for Informativeness in Three‐Level Designs Open
Multilevel data are frequently encountered in biomedical research, and several statistical methods have been developed to analyze such data. Informativeness of the number of units on certain levels often manifests itself in multilevel data…
View article: First Measurement: Proactive Immune Cell Sparing in Radiation Therapy
First Measurement: Proactive Immune Cell Sparing in Radiation Therapy Open
Purpose Radiation Therapy (RT) can modulate the immune system and generate anti-tumor T cells. However, this anti-tumor-activity is countered by radiation-induced immunosuppression (RIIS). Clinical advantages of proactively sparing RT dose…
View article: Analyzing zero-inflated clustered longitudinal ordinal outcomes using GEE-type models with an application to dental fluorosis studies
Analyzing zero-inflated clustered longitudinal ordinal outcomes using GEE-type models with an application to dental fluorosis studies Open
Motivated by the Iowa Fluoride Study (IFS), which tracked fluoride intake and dental outcomes from childhood to young adulthood (ages 9, 13, 17, and 23), we analyze dental fluorosis - a condition caused by excessive fluoride exposure durin…
View article: Syntaxin11 Deficiency Inhibits CRAC Channel Priming to Suppress Cytotoxicity and Gene Expression in FHLH4 Patient T Lymphocytes
Syntaxin11 Deficiency Inhibits CRAC Channel Priming to Suppress Cytotoxicity and Gene Expression in FHLH4 Patient T Lymphocytes Open
Mutations in Syntaxin11, a Q-SNARE, result in a fatal immune disorder known as familial hemophagocytic lymphohistiosis 4 (FHLH4) in human patients. A key diagnostic feature of FHLH4 is defective T and natural killer cell cytotoxicity. Here…
View article: Modeling Zero-Inflated Correlated Dental Data through Gaussian Copulas and Approximate Bayesian Computation
Modeling Zero-Inflated Correlated Dental Data through Gaussian Copulas and Approximate Bayesian Computation Open
We develop a new longitudinal count data regression model that accounts for zero-inflation and spatio-temporal correlation across responses. This project is motivated by an analysis of Iowa Fluoride Study (IFS) data, a longitudinal cohort …
View article: Selection of single cell clustering methodologies through rank aggregation of multiple performance measures
Selection of single cell clustering methodologies through rank aggregation of multiple performance measures Open
As single-cell gene expression data analysis continues to grow, the need for reliable clustering methods has become increasingly important. The prevalence of heuristic means for method choice could lead to inaccurate reports if comprehensi…
View article: Nonparametric estimation of a future entry time distribution given the knowledge of a past state occupation in a progressive multistate model with current status data
Nonparametric estimation of a future entry time distribution given the knowledge of a past state occupation in a progressive multistate model with current status data Open
Case-I interval-censored (current status) data from multistate systems are often encountered in cancer and other epidemiological studies. In this article, we focus on the problem of estimating state entry distribution and occupation probab…
View article: SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data
SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data Open
Summary The SOHPIE R package implements a novel functionality for “multivariable” differential co-abundance network (DN, hereafter) analyses of microbiome data. It incorporates a regression approach that adjusts for additional covariates f…
View article: Replication Data for: "Bilateral Subdiaphragmatic Vagal Nerve Stimulation Using a Novel Waveform Decreases Body Weight, Food Consumption, Adiposity, and Activity in Obesity-Prone Rats"
Replication Data for: "Bilateral Subdiaphragmatic Vagal Nerve Stimulation Using a Novel Waveform Decreases Body Weight, Food Consumption, Adiposity, and Activity in Obesity-Prone Rats" Open
Data were obtained during a longitudinal study in obesity prone rats maintained on either a high fat or a standard diet. The treatment group received vagal nerve stimulation with a novel stimulus waveform. Three control groups are also inc…
View article: Bilateral Subdiaphragmatic Vagal Nerve Stimulation Using a Novel Waveform Decreases Body Weight, Food Consumption, Adiposity, and Activity in Obesity-Prone Rats
Bilateral Subdiaphragmatic Vagal Nerve Stimulation Using a Novel Waveform Decreases Body Weight, Food Consumption, Adiposity, and Activity in Obesity-Prone Rats Open
Introduction Obesity affects millions of Americans. The vagal nerves convey the degree of stomach fullness to the brain via afferent visceral fibers. Studies have found that vagal nerve stimulation (VNS) promotes reduced food intake, cause…
View article: Identification of shared biological features in four different lung cell lines infected with SARS-CoV-2 virus through RNA-seq analysis
Identification of shared biological features in four different lung cell lines infected with SARS-CoV-2 virus through RNA-seq analysis Open
The COVID-19 pandemic caused by SARS-CoV-2 has resulted in millions of confirmed cases and deaths worldwide. Understanding the biological mechanisms of SARS-CoV-2 infection is crucial for the development of effective therapies. This study …
View article: Executive function improvement in response to meta-cognitive training in chronic mTBI / PTSD
Executive function improvement in response to meta-cognitive training in chronic mTBI / PTSD Open
Objective We tested Goal Management Training (GMT), which has been recommended as an executive training protocol that may improve the deficits in the complex tasks inherent in life role participation experienced by those with chronic mild …
View article: Pseudo-value regression of clustered multistate current status data with informative cluster sizes
Pseudo-value regression of clustered multistate current status data with informative cluster sizes Open
Multistate current status data presents a more severe form of censoring due to the single observation of study participants transitioning through a sequence of well-defined disease states at random inspection times. Moreover, these data ma…
View article: Adjusting for informative cluster size in pseudo‐value‐based regression approaches with clustered time to event data
Adjusting for informative cluster size in pseudo‐value‐based regression approaches with clustered time to event data Open
Informative cluster size (ICS) arises in situations with clustered data where a latent relationship exists between the number of participants in a cluster and the outcome measures. Although this phenomenon has been sporadically reported in…
View article: Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values.
Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values. Open
A recent breakthrough in differential network (DN) analysis of microbiome data has been realized with the advent of next-generation sequencing technologies. The DN analysis disentangles the microbial co-abundance among taxa by comparing th…
View article: Analyzing dental fluorosis data using a novel Bayesian model for clustered longitudinal ordinal outcomes with an inflated category
Analyzing dental fluorosis data using a novel Bayesian model for clustered longitudinal ordinal outcomes with an inflated category Open
We propose a Bayesian hurdle mixed‐effects model to analyze longitudinal ordinal data under a complex multilevel structure. This research was motivated by the dataset gathered from the Iowa Fluoride Study (IFS) in order to establish the re…
View article: A Pseudo-Value Regression Approach for Differential Network Analysis of Co-Expression Data
A Pseudo-Value Regression Approach for Differential Network Analysis of Co-Expression Data Open
The differential network (DN) analysis identifies changes in measures of association among genes under two or more experimental conditions. In this article, we introduce a Pseudo-value Regression Approach for Network Analysis (PRANA). This…
View article: Pseudo-value regression of clustered multistate current status data with informative cluster sizes
Pseudo-value regression of clustered multistate current status data with informative cluster sizes Open
Multistate current status (CS) data presents a more severe form of censoring due to the single observation of study participants transitioning through a sequence of well-defined disease states at random inspection times. Moreover, these da…
View article: Adjusting for informative cluster size in pseudo-value based regression approaches with clustered time to event data
Adjusting for informative cluster size in pseudo-value based regression approaches with clustered time to event data Open
Informative cluster size (ICS) arises in situations with clustered data where a latent relationship exists between the number of participants in a cluster and the outcome measures. Although this phenomenon has been sporadically reported in…
View article: htestClust: A Package for Marginal Inference of Clustered Data Under Informative Cluster Size
htestClust: A Package for Marginal Inference of Clustered Data Under Informative Cluster Size Open
When observations are collected in/organized into observational units, within which observations may be dependent, those observational units are often referred to as \"clustered\" and the data as \"clustered data\". Examples of clustered d…
View article: Selection of the Optimal Personalized Treatment from Multiple Treatments with Right-censored Multivariate Outcome Measures
Selection of the Optimal Personalized Treatment from Multiple Treatments with Right-censored Multivariate Outcome Measures Open
We propose a novel personalized concept for the optimal treatment selection for a situation where the response is a multivariate vector, that could contain right-censored variables such as survival time. The proposed method can be applied …
View article: A Bayesian Nonparametric Approach for Identifying Differentially Abundant Taxa in Multigroup Microbiome Data with Covariates
A Bayesian Nonparametric Approach for Identifying Differentially Abundant Taxa in Multigroup Microbiome Data with Covariates Open
Scientific studies in the last two decades have established the central role of the microbiome in disease and health. Differential abundance analysis seeks to identify microbial taxa associated with sample groups defined by a factor such a…
View article: A novel probabilistic generator for large-scale gene association networks
A novel probabilistic generator for large-scale gene association networks Open
Motivation Gene expression data provide an opportunity for reverse-engineering gene-gene associations using network inference methods. However, it is difficult to assess the performance of these methods because the true underlying network …
View article: Frailty modeling under a selective sampling protocol: an application to type 1 diabetes related autoantibodies
Frailty modeling under a selective sampling protocol: an application to type 1 diabetes related autoantibodies Open
In studies following selective sampling protocols for secondary outcomes, conventional analyses regarding their appearance could provide misguided information. In the large type 1 diabetes prevention and prediction (DIPP) cohort study moni…
View article: The Analysis of Gene Expression Data Incorporating Tumor Purity Information
The Analysis of Gene Expression Data Incorporating Tumor Purity Information Open
The tumor microenvironment is composed of tumor cells, stroma cells, immune cells, blood vessels, and other associated non-cancerous cells. Gene expression measurements on tumor samples are an average over cells in the microenvironment. Ho…