Label-aware distance mitigates temporal and spatial variability for clustering and visualization of single-cell gene expression data.

Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. The batch effect, i.

Transcriptional and phenotypic heterogeneity underpinning venetoclax resistance in AML.

The venetoclax BCL2 inhibitor in combination with hypomethylating agents represents a cornerstone of induction therapy for older AML patients, unfit for intensive chemotherapy. Like other targeted therapies, venetoclax-based therapies suffer from innate and acquired resistance. While several mechanisms of resistance have been identified, the heterogeneity of resistance mechanism across patient populations is poorly understood.

Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data.

Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. The batch effect, i.

Selective parenchymal clamping in open partial nephrectomy: Early experience with a low cost, reusable novel parenchymal clamp.

Objectives: The objective of this study is to present our initial experience with a novel parenchymal clamp (NPC) developed to allow partial nephrectomies (PN) to be performed without whole kidney ischaemia. We compare patients who underwent PN with the NPC with those undergoing standard PNs.

Methods: The NPC applies pressure only to the portion of the parenchyma containing the small renal mass (≤3.

Metastatic renal cell carcinoma presenting as jaundice with biliary and gastric outlet obstruction. A case report.

Renal cell carcinoma (RCC) can be an aggressive malignancy that has a propensity to spread to atypical locations, most commonly to lung, bone, lymph node. RCC presenting as obstructive jaundice with gastric outlet obstruction has rarely been cited in literature. This study presents a case of advanced RCC in a patient with obstructive jaundice and associated gastric outlet obstruction from a large right renal RCC with malignant retrocaval lymphadenopathy invading the duodenum and distal common bile duct.

Ab initio spillover compensation in mass cytometry data.

Signal intensity measured in a mass cytometry (CyTOF) channel can often be affected by the neighboring channels due to technological limitations. Such signal artifacts are known as spillover effects and can substantially limit the accuracy of cell population clustering. Current approaches reduce these effects by using additional beads for normalization purposes known as single-stained controls.

Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data.

Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. Batch effect, i.

Integrated transcriptomic-genomic tool Texomer profiles cancer tissues.

Profiling of both the genome and the transcriptome promises a comprehensive, functional readout of a tissue sample, yet analytical approaches are required to translate the increased data dimensionality, heterogeneity and complexity into patient benefits. We developed a statistical approach called Texomer ( https://github.com/KChen-lab/Texomer ) that performs allele-specific, tumor-deconvoluted transcriptome-exome integration of autologous bulk whole-exome and transcriptome sequencing data.

FBXW7 regulates a mitochondrial transcription program by modulating MITF.

FBXW7 is well characterized as a tumor suppressor in many human cancers including melanoma; however, the mechanisms of tumor-suppressive function have not been fully elucidated. We leveraged two distinct RNA sequencing datasets: human melanoma cell lines (n = 10) with control versus silenced FBXW7 and a cohort of human melanoma tumor samples (n = 51) to define the transcriptomic fingerprint regulated by FBXW7. Here, we report that loss of FBXW7 enhances a mitochondrial gene transcriptional program that is dependent on MITF in human melanoma and confers poor patient outcomes.

Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation.

Background: Melanoma is a heterogeneous malignancy. We set out to identify the molecular underpinnings of high-risk melanomas, those that are likely to progress rapidly, metastasize, and result in poor outcomes.

Methods: We examined transcriptome changes from benign states to early-, intermediate-, and late-stage tumors using a set of 78 treatment-naive melanocytic tumors consisting of primary melanomas of the skin and benign melanocytic lesions.

Case-control study of factors that trigger inflammatory bowel disease flares.

Aim: To explore the association between inflammatory bowel diseases (IBD) flares and potential triggers.

Methods: Patients evaluated for an acute flare of IBD by a gastroenterologist at the Dallas VA Medical Center were invited to participate, as were a control group of patients with IBD in remission. Patients were systematically queried about nonsteroidal anti-inflammatory drug use, antibiotic use, stressful life events, cigarette smoking, medication adherence, infections, and travel in the preceding 3 mo.

The prophylactic placement of hemoclips to prevent delayed post-polypectomy bleeding: an unnecessary practice? A case control study.

Background: With the recent, widespread availability of endoscopic hemoclips, it has become common clinical practice to apply hemoclips to some non-bleeding polypectomy sites "prophylactically" to prevent delayed post-polypectomy bleeding (PPB). Few published data support this practice, however.

Aim: The aim of this study was to compare rates of delayed PPB in matched patients who had polypectomies performed with and without the prophylactic placement of hemoclips.

Helicobacter gastritis induces changes in the oxyntic mucosa indistinguishable from the effects of proton pump inhibitors.

A causal relationship between oxyntic glands dilatation with protruding parietal cells, referred to as proton pump inhibitor (PPI) effects, and PPI use has been suspected but not established. We designed this study to evaluate the association between these changes and the use of PPIs and histamine2-receptor blockers (H2-blockers). We obtained five Sydney System-compliant biopsy specimens from patients recruited into a therapeutic trial for H.

Clinical implications of histologic abnormalities in colonic biopsy specimens from patients with ulcerative colitis in clinical remission.

Background: For patients with ulcerative colitis (UC) who have colonoscopy while their disease is in clinical remission, the clinical implications of finding histologic abnormalities of colitis are not clear.

Methods: We reviewed the medical records of patients with UC who had elective colonoscopy at our VA Medical Center while their UC was in clinical remission and who had at least 6 months of follow-up data available. The Mayo endoscopic subscore was used to assess endoscopic disease activity.

Low rate of postpolypectomy bleeding among patients who continue thienopyridine therapy during colonoscopy.

Background & Aims: It is not clear whether the cardiovascular risk of discontinuing treatment with antiplatelet agents, specifically the thienopyridines, before elective colonoscopy outweighs the risks of postpolypectomy bleeding (PPB). We studied the rate of PPB in patients who continue thienopyridine therapy during colonoscopy.

Methods: We performed a prospective study of 516 patients not taking warfarin who received polypectomies during elective colonoscopies; 219 were receiving thienopyridines, and 297 were not (controls).

Prone positioning of obese patients for colonoscopy results in shortened cecal intubation times: a randomized trial.

Background: Obesity is a risk factor for colorectal cancer, and colonoscopy can be technically challenging in obese patients. It has been proposed (with little supporting data) that prone positioning of obese patients might facilitate a difficult colonoscopy.

Aim: The aim of this study was to determine if starting colonoscopy in the prone position for obese patients decreases cecal intubation times.