NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration.

Non-negative Matrix Factorization (NME) is an algorithm that can reduce high dimensional datasets of tens of thousands of genes to a handful of metagenes which are biologically easier to interpret. Application of NMF on gene expression data has been limited by its computationally intensive nature, which hinders its use on large datasets such as single-cell RNA sequencing (scRNA-seq) count matrices. We have implemented NMF based clustering to run on high performance GPU compute nodes using Cupy, a GPU backed python library, and the Message Passing Interface (MPI).

NMF Clustering: Accessible NMF-based Clustering Utilizing GPU Acceleration.

Non-negative Matrix Factorization (NMF) is an algorithm that can reduce high dimensional datasets of tens of thousands of genes to a handful of metagenes which are biologically easier to interpret. Application of NMF on gene expression data has been limited by its computationally intensive nature, which hinders its use on large datasets such as single-cell RNA sequencing (scRNA-seq) count matrices. We have implemented NMF based clustering to run on high performance GPU compute nodes using CuPy, a GPU backed python library, and the Message Passing Interface (MPI).

Co-Localization of Gastrointestinal Stromal Tumors (GIST) and Peritoneal Mesothelioma: A Case Series.

Purpose: Gastrointestinal stromal tumor (GIST) is associated with increased risk of additional cancers. In this study, synchronous GIST, and peritoneal mesothelioma (PM) were characterized to evaluate the relationship between these two cancers.

Methods: A retrospective chart review was conducted for patients diagnosed with both GIST and PM between July 2010 and June 2021.

A Novel System to Improve Case Capture for Surgery Morbidity and Mortality Conference.

Introduction: Complications are often under-reported at surgical morbidity and mortality (M&M) conferences due to the sole reliance on voluntary case submission. While most institutions have databases used for targeted initiatives in quality improvement, these are not routinely used for M&M. We aimed to increase case capture for M&M conferences by developing a novel system that augments the existing case submission system with cases representing complications from quality improvement databases and the electronic health record (EHR).

Location of Gastrointestinal Stromal Tumor (GIST) in the Stomach Predicts Tumor Mutation Profile and Drug Sensitivity.

Purpose: Gastrointestinal stromal tumors (GIST) commonly arise in different regions of the stomach and are driven by various mutations (most often in KIT, PDGFRA, and SDHx). We hypothesized that the anatomic location of gastric GIST is associated with unique genomic profiles and distinct driver mutations.

Experimental Design: We compared KIT versus non-KIT status with tumor location within the National Cancer Database (NCDB) for 2,418 patients with primary gastric GIST.

Rising Cost of Thyroid Surgery in Adult Patients.

Background: The aim of this study is to describe the economic trends in adults who underwent elective thyroidectomy.

Methods: We performed a population-based study utilizing the Premier Healthcare Database to examine adult patients who underwent elective thyroidectomy between January 2006 and December 2014. Time was divided into three equal time periods (2006-2008, 2009-2011, and 2012-2014).

TIRADS Interobserver Variability Among Indeterminate Thyroid Nodules: A Single-Institution Study.

Objectives: A high proportion of cytologically indeterminate, Afirma Gene Expression Classifier "suspicious" thyroid nodules are benign. The Thyroid Imaging Reporting and Data System (TIRADS), was proposed by the American College of Radiology in 2017 to help classify thyroid nodules based on ultrasound characteristics in a standardized fashion to guide management. We aim to determine the interobserver variability of TIRADS classification among cytologically indeterminate and Afirma suspicious nodules.

Bilateral chylothorax following reoperative central neck dissection for metastatic papillary thyroid cancer.

Locoregional recurrence of papillary thyroid cancer (PTC) can occur in up to 30% of patients within 10 years after initial treatment. Reoperative surgery can be challenging due to scarring, fibrosis and distorted anatomy and may be associated with increased complications compared with initial operations. Chylothorax is an extremely rare and potentially life-threatening complication that can be associated with neck dissections and thyroid surgery.

A case report on 2 unique presentations of upper extremity deep vein thrombosis.

Rationale: Thoracic outlet syndrome (TOS) is a rare cause of upper extremity deep vein thrombosis (UEDVT). The treatment usually involves catheter directed thrombolysis followed by systemic anticoagulation. Surgical decompression is frequently recommended after anticoagulation for definitive therapy.

Evaluation of Dyspnea Outcomes After Endoscopic Airway Surgery for Laryngotracheal Stenosis.

Importance: Endoscopic airway surgery is a frequently used procedure in the management of laryngotracheal stenosis (LTS); however, no established outcome measures are available to assess treatment response.

Objective: To assess acoustics and aerodynamic measures and voice- and dyspnea-related quality of life (QOL) in adult patients with LTS who undergo endoscopic airway surgery.

Design, Setting, And Participants: This case series compared preoperative measures and postoperative outcomes among adult patients who underwent endoscopic airway surgery for LTS from September 1, 2013, to September 30, 2015, at the tertiary care Johns Hopkins Voice Center.