Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq.

In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA) poses challenges in accurate read mapping and the interpretation of count matrices. The traditional transcriptome reference, defining the "region of interest" in bulk RNA-seq, restricts its focus to mature mRNA transcripts. This restriction leads to two problems: reads originating outside of the "region of interest" are prone to mismapping within this region, and additionally, such external reads cannot be matched to specific transcript targets.

kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq.

The term 'RNA-seq' refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto, bustools and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples or both.

A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes.

Background: Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxford Nanopore Technologies (ONT) and single molecule real-time (SMRT) sequencing developed by Pacific Bioscience (PacBio). In this study, we systematically compare the performance of CpG methylation detection from long-read sequencing.

kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.

The term "RNA-seq" refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, from single cells, or from single nuclei. The kallisto, bustools, and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples, or both.

Private Landowners' Perspectives on Feral Swine and Regulation-Evidence from Arkansas, Louisiana, and East Texas.

Feral swine (FS) (Sus scrofa) are an invasive species that has spread widely across the southern United States, including the West Gulf region. With their rapidly increasing population, they have caused severe damage to landowners. To better understand private landowners' knowledge and attitudes toward FS, we conducted a mail survey in the West Gulf region including Arkansas, Louisiana, and East Texas in 2021.

Sequence variants affecting the genome-wide rate of germline microsatellite mutations.

Microsatellites are polymorphic tracts of short tandem repeats with one to six base-pair (bp) motifs and are some of the most polymorphic variants in the genome. Using 6084 Icelandic parent-offspring trios we estimate 63.7 (95% CI: 61.

The sequences of 150,119 genomes in the UK Biobank.

Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data. Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank.

Population-scale detection of non-reference sequence variants using colored de Bruijn graphs.

Motivation: With the increasing throughput of sequencing technologies, structural variant (SV) detection has become possible across tens of thousands of genomes. Non-reference sequence (NRS) variants have drawn less attention compared with other types of SVs due to the computational complexity of detecting them. When using short-read data, the detection of NRS variants inevitably involves a de novo assembly which requires high-quality sequence data at high coverage.

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits.

Long-read sequencing (LRS) promises to improve the characterization of structural variants (SVs). We generated LRS data from 3,622 Icelanders and identified a median of 22,636 SVs per individual (a median of 13,353 insertions and 9,474 deletions). We discovered a set of 133,886 reliably genotyped SV alleles and imputed them into 166,281 individuals to explore their effects on diseases and other traits.

BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs.

BlastFrost is a highly efficient method for querying 100,000s of genome assemblies, building on Bifrost, a dynamic data structure for compacted and colored de Bruijn graphs. BlastFrost queries a Bifrost data structure for sequences of interest and extracts local subgraphs, enabling the identification of the presence or absence of individual genes or single nucleotide sequence variants. We show two examples using Salmonella genomes: finding within minutes the presence of genes in the SPI-2 pathogenicity island in a collection of 926 genomes and identifying single nucleotide polymorphisms associated with fluoroquinolone resistance in three genes among 190,209 genomes.

Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly.

A major challenge to long read sequencing data is their high error rate of up to 15%. We present Ratatosk, a method to correct long reads with short read data. We demonstrate on 5 human genome trios that Ratatosk reduces the error rate of long reads 6-fold on average with a median error rate as low as 0.

Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs.

Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in memory. We present a parallel and memory-efficient algorithm enabling the direct construction of the compacted de Bruijn graph without producing the intermediate uncompacted graph.

Evaluation of Acridine Orange Staining for a Semi-Automated Urinalysis Microscopic Examination at the Point-of-Care.

A urinary tract infection (UTI) can be diagnosed via urinalysis, consisting of a dipstick test and manual microscopic examination. Point-of-care (POC) image-based systems have been designed to automate the microscopic examination for low-volume laboratories or low-resource clinics. In this pilot study, acridine orange (AO) was evaluated as a fluorescence-based contrast agent to aid in detecting and enumerating urine sediment specific for diagnosing a UTI.

Expanded feasibility of ferritin testing: stability of ferritin stored as whole blood and validation of plastic tubes.

Background: Ferritin testing is a recommended strategy to mitigate iron depletion in blood donors. A barrier for some testing platforms is a requirement to complete sample management and testing within a temporal window incompatible with the logistics of many blood collectors. The ability to delay separation of plasma/serum from red cells and subsequent testing would enhance the feasibility of ferritin testing on a broader scale.

Dynamic Alignment-Free and Reference-Free Read Compression.

The advent of high throughput sequencing (HTS) technologies raises a major concern about storage and transmission of data produced by these technologies. In particular, large-scale sequencing projects generate an unprecedented volume of genomic sequences ranging from tens to several thousands of genomes per species. These collections contain highly similar and redundant sequences, also known as pangenomes.

A Comprehensive Review of Medical Imaging Equipment Used in Cadaveric Studies.

Medical imaging techniques have led to great advances in clinical anatomy and forensic pathology. New and emerging technologies allow healthcare professionals to view and understand the human body from different perspectives. This gives way to new and improved interventions, treatment plans, and an overall understanding of the human body.

Pan-Genome Storage and Analysis Techniques.

Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the concept has spread to a variety of species, such as plants or viruses. Characterizing a pan-genome provides insights into intra-species evolution, functions, and diversity.

A new teaching model for demonstrating the movement of the extraocular muscles.

The extraocular muscles consist of the superior, inferior, lateral, and medial rectus muscles and the superior and inferior oblique muscles. This study aimed to create a new teaching model for demonstrating the function of the extraocular muscles. A coronal section of the head was prepared and sutures attached to the levator palpebral superioris muscle and six extraocular muscles.

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.

Background: High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high number of sequences sampled from each genome. Such a highly redundant collection of very similar sequences is called a pan-genome.

Protecting West Virginians from secondhand smoke through regulation at the local level.

West Virginia's communities have made substantial progress in protecting citizens from secondhand smoke exposure (SHS) through adoption of local regulations through county boards of health. The EPA and the U.S.

3-D phantom and in vivo cardiac speckle tracking using a matrix array and raw echo data.

Cardiac motion has been tracked using various methods, which vary in their invasiveness and dimensionality. One such noninvasive modality for cardiac motion tracking is ultrasound. Three-dimensional ultrasound motion tracking has been demonstrated using detected data at low volume rates.

Evaluation of endothelial mucin layer thickness after phacoemulsification with next generation ophthalmic irrigating solution.

Purpose: To evaluate human corneal endothelial mucin layer thickness and ultrastructure after phacoemulsification and irrigation-aspiration with either next generation ophthalmic irrigating solution (NGOIS) or BSS PLUS.

Methods: Paired human corneas were mounted in an artificial anterior chamber, exposed to 3 minutes of continuous ultrasound (US) at 80% power using the Alcon SERIES 20000 LEGACY surgical system (n = 9) or to 2 minutes of pulsed US at 50% power, 50% of the time at 20 pps using the Alcon INFINITI Vision System (n = 5), and irrigated with 250 mL of either NGOIS or BSS PLUS. A control group of paired corneas did not undergo phacoemulsification or irrigation-aspiration (n = 5).

Effect of mitomycin C on the corneal endothelium when used for corneal subepithelial haze prophylaxis following photorefractive keratectomy.

Purpose: To evaluate the potential effect of topical mitomycin C (MMC) on the corneal endothelium of myopic patients undergoing photorefractive keratectomy (PRK).

Methods: Sixteen eyes with a planned ablation depth >75 microm underwent PRK followed by 0.02% MMC applied for 12 seconds using a methylcellulose sponge.

Interface fluid syndrome in human eye bank corneas after LASIK: causes and pathogenesis.

Purpose: To evaluate the effects of corneal edema on human donor corneas that had previous LASIK using a laboratory model with histologic and ultrastructural correlations.

Design: Experimental study.

Participants: Thirty human eye bank corneas from 15 donors (mean age +/- standard deviation, 49.

Antibody blockade of junctional adhesion molecule-A in rabbit corneal endothelial tight junctions produces corneal swelling.

Purpose: The ultrastructure of tight junctions in the corneal endothelium has been studied extensively, yet little is known about their molecular composition. Junctional adhesion molecule-A (JAM-A) is a tight junction-associated adhesion protein previously implicated in tight junction assembly and regulation of barrier function. In this study, we sought to investigate the expression and function of JAM-A in the corneal endothelium.