A Roadmap for Selecting and Utilizing Optimal Features in scRNA Sequencing Data Analysis for Stem Cell Research: A Comprehensive Review.

Stem cells and the cells they produce are unique because they vary from one cell to another. Traditional methods of studying cells often overlook these differences. However, the development of new technologies for studying individual cells has greatly changed biological research in recent years. Among these innovations, single-cell RNA sequencing (scRNA-seq) stands out. This technique allows scientists to examine the activity of genes in each cell, across thousands or even millions of cells. This makes it possible to understand the diversity of cells, identify new types of cells, and see how cells differ across different tissues, individuals, species, times, and conditions. This paper discusses the importance of scRNA-seq and the computational tools and software that are essential for analyzing the vast amounts of data generated by scRNA-seq studies. Our goal is to provide practical advice for bioinformaticians and biologists who are using scRNA-seq to study stem cells. We offer an overview of the scRNA-seq field, including the tools available, how they can be used, and how to present the results of these studies effectively. Our findings include a detailed overview and classification of tools used in scRNA-seq analysis, based on a review of 2,733 scientific publications. This review is complemented by information from the scRNA-tools database, which lists over 1,400 tools for analyzing scRNA-seq data. This database is an invaluable resource for researchers, offering a wide range of options for analyzing their scRNA-seq data.

Protocol for generating embedding-free brain organoids enriched with oligodendrocytes.

In response to the scarcity of advanced in vitro models dedicated to human CNS white matter research, we present a protocol to generate neuroectoderm-derived embedding-free human brain organoids enriched with oligodendrocytes. We describe steps for neuroectoderm differentiation, development of neural spheroids, and their transferal to Matrigel. We then detail procedures for the development, maturation, and application of oligodendrocyte-enriched brain organoids. The presence of myelin-producing cells makes these organoids useful for studying human white matter diseases, such as leukodystrophy.

Are SPECT MPI measures of dyssynchrony dyssynchronous?

BACKGROUND: Assessment of left ventricular mechanical dyssynchrony (LVMD) from gated SPECT myocardial perfusion imaging (MPI) aims to aid selection of patients for cardiac resynchronization therapy (CRT), using either the standard deviation of left ventricular phase (PSD) ≥ 43° or phase histogram bandwidth (HBW) of > 38° and > 30.6° in males and females, respectively. We observed dyssynchrony parameters might be affected by test type and alignment. METHODS: We reviewed 242 patients who underwent gated SPECT MPI with use of the Emory Cardiac Toolbox comparing PSD and HBW at rest and stress for Pearson correlation, and substitutability with Bland-Altman analysis. RESULTS: There is statistically significant difference in the mean PSD and HBW during rest vs stress (33.4 ± 17.4° vs 20.7 ± 13.5° and 97.7 ± 59.6° vs 59.4 ± 45.4°, respectively, P < 0.001). Proper valve plane alignment rendered smaller values (i.e., less dyssynchrony) in both phase SD and HBW (16.8 ± 13.5) vs (22.2 ± 14.7) (P = 0.011), and (47.0 ± 38.2) vs (60.7 ± 48.0) (P = 0.023), respectively. CONCLUSION: Proper alignment and test type, particularly low-dose rest vs high-dose stress, should be considered when assessing LVMD using SPECT MPI.

Henry Ford HEART Score Randomized Trial: Rapid Discharge of Patients Evaluated for Possible Myocardial Infarction.

BACKGROUND: Hospital evaluation of patients with chest pain is common and costly. The HEART score risk stratification tool that merges troponin testing into a clinical risk model for evaluation emergency department patients with possible acute myocardial infarction (AMI) has been shown to effectively identify a substantial low-risk subset of patients possibly safe for early discharge without stress testing, a strategy that could have tremendous healthcare savings implications. METHOD AND RESULTS: A total of 105 patients evaluated for AMI in the emergency departments of 2 teaching hospitals in the Henry Ford Health System (Detroit and West Bloomfield, MI), between February 2014 and May 2015, with a modified HEART score ≤3 (which includes cardiac troponin I <0.04 ng/mL at 0 and 3 hours) were randomized to immediate discharge (n=53) versus management in an observation unit with stress testing (n=52). The primary end points were 30-day total charges and length of stay. Secondary end points were all-cause death, nonfatal AMI, rehospitalization for evaluation of possible AMI, and coronary revascularization at 30 days. Patients randomized to early discharge, compared with those who were admitted for observation and cardiac testing, spent less time in the hospital (median 6.3 hours versus 25.9 hours; P<0.001) with an associated reduction in median total charges of care ($2953 versus $9616; P<0.001). There were no deaths, AMIs, or coronary revascularizations in either group. One patient in each group was lost to follow-up. CONCLUSIONS: Among patients evaluated for possible AMI in the emergency department with a modified HEART score ≤3, early discharge without stress testing as compared with transfer to an observation unit for stress testing was associated with significant reductions in length of stay and total charges, a finding that has tremendous potential national healthcare expenditure implications. CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov. Unique identifier: NCT03058120.