VICTOR: Validation and inspection of cell type annotation through optimal regression.

Single-cell RNA sequencing provides unprecedent opportunities to explore the heterogeneity and dynamics inherent in cellular biology. An essential step in the data analysis involves the automatic annotation of cells. Despite development of numerous tools for automated cell annotation, assessing the reliability of predicted annotations remains challenging, particularly for rare and unknown cell types.

Multi-epitope vaccine design of African swine fever virus considering T cell and B cell immunogenicity.

T and B cell activation are equally important in triggering and orchestrating adaptive host responses to design multi-epitope African swine fever virus (ASFV) vaccines. However, few design methods have considered the trade-off between T and B cell immunogenicity when identifying promising ASFV epitopes. This work proposed a novel Pareto front-based ASFV screening method PFAS to identify promising epitopes for designing multi-epitope vaccines utilizing five ASFV Georgia 2007/1 sequences.

The microtubule-dynamin binding inhibitor peptide PHDP5 rescues spatial learning and memory deficits in Alzheimer's disease model mice.

Dynamin is a microtubule (MT) binding protein playing a key role in vesicle endocytosis. In a brain slice model, tau loaded in presynaptic terminals assembles MTs, thereby impairing vesicle endocytosis via depletion of cytosolic dynamin. The peptide PHDP5, derived from the pleckstrin homology domain of dynamin 1, inhibits dynamin-MT interaction and rescues endocytosis and synaptic transmission impaired by tau when co-loaded in presynaptic terminals.

Mitochondrial Glutathione in Cellular Redox Homeostasis and Disease Manifestation.

Mitochondria are critical for providing energy to maintain cell viability. Oxidative phosphorylation involves the transfer of electrons from energy substrates to oxygen to produce adenosine triphosphate. Mitochondria also regulate cell proliferation, metastasis, and deterioration.

scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data.

Motivation: Single-cell RNA-seq normalization is an essential step to correct unwanted biases caused by sequencing depth, capture efficiency, dropout, and other technical factors. Existing normalization methods primarily reduce biases arising from sequencing depth by modeling count-depth relationship and/or assuming a specific distribution for read counts. However, these methods may lead to over or under-correction due to presence of technical biases beyond sequencing depth and the restrictive assumption on models and distributions.

Possible Pathogenesis and Prevention of Long COVID: SARS-CoV-2-Induced Mitochondrial Disorder.

Patients who have recovered from coronavirus disease 2019 (COVID-19) infection may experience chronic fatigue when exercising, despite no obvious heart or lung abnormalities. The present lack of effective treatments makes managing long COVID a major challenge. One of the underlying mechanisms of long COVID may be mitochondrial dysfunction.

Using Transfer Learning of Convolutional Neural Network on Neck Radiographs to Identify Acute Epiglottitis.

Acute epiglottitis (AE) is a life-threatening condition and needs to be recognized timely. Diagnosis of AE with a lateral neck radiograph yields poor reliability and sensitivity. Convolutional neural networks (CNN) are powerful tools to assist the analysis of medical images.

SiO Fibers of Two Lengths and Their Effect on Cellular Responses of Macrophage-like Cells.

The immunoreactivity or/and stress response can be induced by nanomaterials' different properties, such as size, shape, etc. These effects are, however, not yet fully understood. This study aimed to clarify the effects of SiO nanofibers (SiONFs) on the cellular responses of THP-1-derived macrophage-like cells.

A Computational Pitting Corrosion Model of Magnesium Alloys.

Controlling the corrosion rate of implants to maintain mechanical properties during tissue healing is significant in developing magnesium alloy implants. In addition to surface treatment and material properties, the study of geometric alteration and mechanical strength are also vital for implant development. In this study, we developed a three-dimensional model for semi-autonomous computational pitting corrosion.

Neurovascular Dysregulation and Acute Exercise Intolerance in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Randomized, Placebo-Controlled Trial of Pyridostigmine.

Background: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by intractable fatigue, postexertional malaise, and orthostatic intolerance, but its pathophysiology is poorly understood. Pharmacologic cholinergic stimulation was used to test the hypothesis that neurovascular dysregulation underlies exercise intolerance in ME/CFS.

Research Question: Does neurovascular dysregulation contribute to exercise intolerance in ME/CFS, and can its treatment improve exercise capacity?

Study Design And Methods: Forty-five subjects with ME/CFS were enrolled in a single-center, randomized, double-blind, placebo-controlled trial.

Safety and Efficacy of Cone-Beam Computed Tomography-Guided Lung Tumor Localization with a Near-Infrared Marker: A Retrospective Study of 175 Patients.

Preoperative localization holds promise for overcoming the limitations of video-assisted thoracoscopic surgery (VATS) in the treatment of impalpable lung nodules. The purpose of this study was to assess the safety and efficacy of cone-beam computed tomography (CBCT)-guided localization using near-infrared (NIR) marking. Between 2017 and 2021, patients presenting with a solitary pulmonary nodule (SPN) who had undergone CBCT-guided lesion localization with indocyanine green (ICG) in a hybrid operating room were included.

Recommendations and guidelines for the treatment of infections due to multidrug resistant organisms.

Antimicrobial drug resistance is one of the major threats to global health. It has made common infections increasingly difficult or impossible to treat, and leads to higher medical costs, prolonged hospital stays and increased mortality. Infection rates due to multidrug-resistant organisms (MDRO) are increasing globally.

Risk of infection in neonates born in accidental out-of-hospital deliveries.

Accidental out-of-hospital deliveries (OHDs) are known to have a higher incidence of maternal and neonatal complications. However, neonatal infection related to OHDs has not been studied. The aim of this study was to determine the infection risk of OHDs.

Establishment of a Nanopatterned Renal Disease Model by Mimicking the Physical and Chemical Cues of a Diseased Mesangial Cell Microenvironment.

Modulation of mesangial cell (MC) response by disease models offers therapeutic strategies for the treatment of several glomerular diseases. However, traditional cell culture models lack the nanostructured extracellular matrix (ECM), which has unique physical and chemical properties, so they poorly reflect the complexities of the native microenvironment. Therefore, a cell disease model with ECM nanostructures is required to better mimic the diseased nanoenvironment.

Development and Evaluation of DNA Vaccine Against Salmonid Alphavirus.

Despite vaccination, pancreas disease (PD) caused by salmonid alphavirus (SAV) has been the economically most important virus disease in salmon farming in Ireland, Scotland, and Norway. A vaccine based on DNA plasmid has been authorized to be used in Norwegian aquaculture since 2018. DNA vaccination of plasmids expressed subcellular viral proteins have been shown its particular protective effect against SAV3 that surface expression of the E2 protein with the whole viral protein construct, yielding a more effective vaccine.

A Comprehensive Examination of Severely Ill ME/CFS Patients.

One in four myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) patients are estimated to be severely affected by the disease, and these house-bound or bedbound patients are currently understudied. Here, we report a comprehensive examination of the symptoms and clinical laboratory tests of a cohort of severely ill patients and healthy controls. The greatly reduced quality of life of the patients was negatively correlated with clinical depression.

Environmental Cadmium Exposure and Dental Indices in Orthodontic Patients.

Background: Previous studies have shown that environmental cadmium exposure could disrupt salivary gland function and is associated with dental caries and reduced bone density. Therefore, this cross-sectional study attempted to determine whether tooth decay with tooth loss following cadmium exposure is associated with some dental or skeletal traits such as malocclusions, sagittal skeletal pattern, and tooth decay.

Methods: Between August 2019 and June 2020, 60 orthodontic patients with no history of previous orthodontics, functional appliances, or surgical treatment were examined.

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.

Background: Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.

Background: Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S.

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples.