A massively parallel reporter assay library to screen short synthetic promoters in mammalian cells.

Cellular responses to stimuli underpin discoveries in drug development, synthetic biology, and general life sciences. We introduce a library comprising 6144 synthetic promoters, each shorter than 250 bp, designed as transcriptional readouts of cellular stimulus responses in massively parallel reporter assay format. This library facilitates precise detection and amplification of transcriptional activity from our promoters, enabling the systematic development of tunable reporters with dynamic ranges of 50-100 fold.

Sleep and aberrant eating behaviors in metabolic/bariatric presurgical candidates.

Background: Metabolic/bariatric surgery (MBS) is the most effective treatment for obesity, yet many factors influence successful individual weight loss. Among those are a variety of health behaviors that are assessed in the process of presurgical psychological evaluations, including eating pathology and sleep disturbance (both of which are relatively common among surgical candidates).

Objectives: This study aims to examine the relationship between sleep, binge eating, and night eating behaviors among individuals seeking MBS.

Uncertainty in Breast Cancer Risk Prediction: A Conformal Prediction Study of Race Stratification.

The use of Artificial Intelligence (AI) in medicine has attracted a great deal of attention in the medical literature, but less is known about how to assess the uncertainty of individual predictions in clinical applications. This paper demonstrates the use of Conformal Prediction (CP) to provide insight on racial stratification of uncertainty quantification for breast cancer risk prediction. The results presented here show that CP methods provide important information about the diminished quality of predictions for individuals of minority racial backgrounds.

Discovery and Validation of Context-Dependent Synthetic Mammalian Promoters.

Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery.

The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK).

Purpose: In Mendelian disease diagnosis, variant analysis is a repetitive, error-prone, and time consuming process. To address this, we have developed the Mendelian Analysis Toolkit (MATK), a configurable, automated variant ranking program.

Methods: MATK aggregates variant information from multiple annotation sources and uses expert-designed rules with parameterized weights to produce a ranked list of potentially causal solutions.