Cytologic and Molecular Assessment of Isthmus Thyroid Nodules and Carcinomas.

Isthmic thyroid nodules are more likely to be malignant and isthmic differentiated thyroid cancer demonstrates less favorable behavior compared with lobar locations. The goal of this study was to assess molecular differences of thyroid nodules and carcinomas from the isthmus relative to the lobes. The Afirma thyroid nodule database ( = 177,227) was assessed for cytologic and molecular differences between isthmus and lobar nodules in this observational cohort study.

Correlation of idiopathic benign paroxysmal positional vertigo with cerebral small vessel disease.

Background: Benign paroxysmal positional vertigo (BPPV) is the most prevalent form of peripheral vertigo, with vascular lesions being one of its suspected causes. The older adults are particularly vulnerable to BPPV. Cerebral small vessel disease (CSVD), on the other hand, is a clinical condition that results from damage of cerebral small vessels.

Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies.

Despite its wide-ranging benefits, whole-transcriptome or RNA exome profiling is challenging to implement in a clinical diagnostic setting. The Unified Assay is a comprehensive workflow wherein exome-enriched RNA-sequencing (RNA-Seq) assays are performed on clinical samples and analyzed by a series of advanced machine learning-based classifiers. Gene expression signatures and rare and/or novel genomic events, including fusions, mitochondrial variants, and loss of heterozygosity were assessed using RNA-Seq data generated from 120,313 clinical samples across three clinical indications (thyroid cancer, lung cancer, and interstitial lung disease).

Housing market capitalization of environmental risk: evidence from the Tianjin explosion.

Do environmental risks affect housing prices in the vicinity of industrial plants? Prior studies concentrated on the capitalization effect of infrequent natural disasters instead of industry-related environmental risks caused by production accidents in our everyday lives. In this paper, we first use the 2015 Tianjin explosion in China as an exogenous shock, which led to serious casualties and property damage with nationwide concern, to estimate the effects of environmental risk on housing prices far away from the explosion site. Based on the housing transaction units and chemical plant datasets in Beijing with the difference-in-differences hedonic model, the results indicate that first, housing prices near chemical plants decreased significantly after the explosion and lasted for at least 2 years.

Real-World Performance of the Afirma Genomic Sequencing Classifier (GSC)-A Meta-analysis.

Context: The Afirma® GSC aids in risk stratifying indeterminate thyroid nodule cytology (ITN). The 2018 GSC validation study (VS) reported a sensitivity (SN) of 91%, specificity (SP) of 68%, positive predictive value (PPV) of 47%, and negative predictive value (NPV) of 96%. Since then, 13 independent real-world (RW) postvalidation studies have been published.

Statistics or biology: the zero-inflation controversy about scRNA-seq data.

Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as missing data to be corrected. To help address the controversy, here we discuss the sources of biological and non-biological zeros; introduce five mechanisms of adding non-biological zeros in computational benchmarking; evaluate the impacts of non-biological zeros on data analysis; benchmark three input data types: observed counts, imputed counts, and binarized counts; discuss the open questions regarding non-biological zeros; and advocate the importance of transparent analysis.

mbImpute: an accurate and robust imputation method for microbiome data.

A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.