Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.

Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of within-host dynamics. This limits our ability to interpret epidemiological predictions incorporating within-host evolution and to validate computational inference tools.

Efficacy of Dichrostachys Glomerata Supplementation on Overweight and Mildly Obese Adult's Weight, Mood, and Health-Related Quality of Life: A Randomized Double-Blind Placebo-Controlled Trial.

Despite their widespread use, research is needed to evaluate the weight loss and related health/wellness outcomes of herbal plants. Preliminary research found that the fruit of is safe and has potential weight loss effects. This study aimed to examine the effect of a standardized powder of fruit pods (DYG-400) on weight, food cravings, mood, and health-related quality of life of overweight and mildly obese adults.

Magnesium-L-threonate improves sleep quality and daytime functioning in adults with self-reported sleep problems: A randomized controlled trial.

Objective/background: Sleep problems challenge overall wellbeing. Magnesium has been implicated to benefit sleep, although the clinical evidences varied based on the magnesium source used. Magnesium L-threonate (MgT) is a promising intervention due to its brain bioavailability and effects on cognition, memory and mood.

Effectiveness of a grid mattress on adults' sleep quality and health: A quasi-experimental intervention study.

Background And Aims: Despite that 93% of people indicate that a mattress plays a pivotal role in achieving high-quality sleep, there is a scarcity of research investigating the influence of mattresses on sleep quality, pain, and mood in nonclinical poor sleepers. The purpose was to examine the effectiveness of a pressure-releasing medium-firm grid mattress on sleep and health outcomes (e.g.

Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing.

Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.

Genomic analysis of group A isolated during a correctional facility outbreak of MRSA in 2004.

Background: In 2004-2005, an outbreak of impetigo occurred at a correctional facility during a sentinel outbreak of methicillin- resistant (MRSA) in Alberta, Canada. Next-generation sequencing (NGS) was used to characterize the group A (GAS) isolates and evaluate whether genomic biomarkers could distinguish between those recovered alone and those co-isolated with .

Methods: Superficial wound swabs collected from all adults with impetigo during this outbreak were cultured using standard methods.

Evolving strategy for an evolving virus: Development of real-time PCR assays for detecting all SARS-CoV-2 variants of concern.

In order to detect the SARS-CoV-2 variants of concern (VOCs), five real-time reverse transcriptase PCR (rRT-PCR) assays were designed to target the critical discriminatory mutations responsible for the following amino acid changes in the spike protein: two Δ69-70 + N501Y + E gene triplexes (one optimized for Alpha [B.1.1.

Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance.

SARS-CoV-2 variants of concern (VOCs) have emerged as a global threat to the COVID-19 pandemic response. We implemented a combined approach to quickly detect known VOCs while continuously monitoring for evolving mutations of the virus. To rapidly detect VOCs, two real-time reverse transcriptase PCR assays were designed and implemented, targeting the spike gene H69/V70 deletion and the N501Y mutation.

Effect of a Free-Living Ketogenic Diet on Feasibility, Satiety, Body Composition, and Metabolic Health in Women: The Grading Level of Optimal Carbohydrate for Women (GLOW) Study.

Objective: The study's purpose was to examine a free-living, ketogenic diet (WFKD) on feasibility, satiety, body composition, and metabolic health in women.

Methods: Twenty-two women (age (yr.) 42.

Spatial distribution of Escherichia coli ST131 C subclades in a centralized Canadian urban region.

Introduction: Escherichia coli ST131 is the most common multidrug-resistant (MDR) E. coli clone causing bloodstream infections (BSIs) in Calgary. This study describes patient characteristics and spatial distribution of ST131 subclades C1 and C2 causing BSIs in Calgary.

Trends in Population Dynamics of Escherichia coli Sequence Type 131, Calgary, Alberta, Canada, 2006-2016.

Global expansion of antimicrobial drug-resistant Escherichia coli sequence type (ST) 131 is unrivaled among human bacteria. Understanding trends among ST131 clades will help with designing prevention strategies. We screened E.

Effectiveness of NexQuest Natural Frequency Technology on sleep and mood of adults with insomnia symptoms: a randomized, double blind and placebo controlled crossover trial.

Objectives: The study purpose was to conduct a four-week randomized double-blind placebo-controlled crossover trial on adults with insomnia symptoms to examine the effectiveness of Natural Frequency Technology (NFT), found in Philip Stein Sleep Bracelets, on sleep quality, anxiety/stress levels, and mood.

Methods: Adults ( = 44, age = 41.9 years) were randomized to the Placebo Bracelet (PB) or NFT Sleep Bracelet (SB) for two weeks and then the alternative bracelet for two weeks.

Efficacy of Wholetones 2Sleep and classical music on sleep and health behaviors of adults with insomnia symptoms: A single blind, randomized, controlled, crossover pilot trial.

Objectives: To conduct a randomized single-blind placebo-controlled crossover trial on adults with insomnia symptoms to examine the efficacy of Wholetones 2Sleep Music (WM) and Classical Music (CM) on sleep quality, anxiety/stress, fatigue, productivity, and mood.

Methods: Following baseline assessments, 38 adults (M age = 46.6 years) were randomized to either WM or CM conditions for 10 days and then the alternative music for 10 days after a 4 day "wash-out".

A Comprehensive Account of Escherichia coli Sequence Type 131 in Wastewater Reveals an Abundance of Fluoroquinolone-Resistant Clade A Strains.

In the ten years since its discovery, the clone sequence type 131 (ST131) has become a major international health threat, with the multidrug-resistant and extended-spectrum β-lactamase (ESBL)-producing clade C emerging as the globally dominant form. ST131 has previously been isolated from wastewater; however, most of these studies selectively screened for ESBL-producing organisms, thereby missing the majority of remaining ST131 clades. In this study, we used a high-throughput PCR-based screening strategy to comprehensively examine wastewater for the presence of ST131 over a 1-year period.

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.

We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157. We also report draft assemblies, with standardized metadata, for 360 STEC strains isolated from watersheds, animals, farms, food, and human infections.

Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring.

Vaginitis is often diagnosed by microscopy and limited to testing for bacterial vaginosis (BV), vulvovaginal candidiasis, and trichomoniasis. Approximately 10% of vaginal swabs are negative but designated "altered flora" by BV Nugent score, leaving clinicians unsure how to treat patients. Accurate and comprehensive vaginitis diagnostics are needed to direct treatment and reduce risks of recurrent or more severe infections.

JAK2-tree: a simple CBC-based decision rule to guide appropriate JAK2 V617F mutation testing.

Aims: The JAK2 V617F mutation is highly recurrent in many of the myeloproliferative neoplasms, a molecular variant that can be easily detected using sensitive and minimally invasive techniques. Given the ease of JAK2 V617F testing, this test may be improperly requested for the purposes of patient 'screening' and to optimise laboratory resource utilisation, it behooves clinicians and laboratorians to perform JAK2 V617F testing only when most appropriate.

Methods: To assist with the screening of patients being considered for JAK2 V617F testing, we developed a clinical decision rule, "JAK2-tree", which can be easily applied to basic CBC parameters (haemoglobin, platelet and white blood cell counts).

A Primer on Infectious Disease Bacterial Genomics.

The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time.

Reporting on the prevalence of antiretroviral drug resistance in a regional HIV population over 20 years: a word of caution.

Background: Failure to achieve complete viral suppression with antiretroviral drugs (ARV) may lead to uncontrolled HIV replication, ARV resistance and negative outcomes. Monitoring and reporting of HIV resistance trends is important but problematic. We examined prevalent resistance rates in an HIV population over 20 years and document how rates may appear to vary greatly based solely on which parameters are utilized.

Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131.

OXA-48-like enzymes have emerged as important extended-spectrum β-lactamases/carbapenemases in Escherichia coli sequence type 131 (ST131). We report the structures of the first fully sequenced bla plasmid and of two other bla plasmids in this lineage. bla was located on a 71-kb IncN plasmid with other resistance genes.

Molecular Evolution of a Klebsiella pneumoniae ST278 Isolate Harboring blaNDM-7 and Involved in Nosocomial Transmission.

During 2013, ST278 Klebsiella pneumoniae with blaNDM-7 was isolated from the urine (KpN01) and rectum (KpN02) of a patient in Calgary, Canada. The same strain (KpN04) was subsequently isolated from another patient in the same unit. Interestingly, a carbapenem-susceptible K.

First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131.

The blaIMP-14 carbapenem resistance gene has largely previously been observed in Pseudomonas aeruginosa and Acinetobacter spp. As part of global surveillance and sequencing of carbapenem-resistant Escherichia coli, we identified a sequence type 131 strain harboring blaIMP-14 within a class 1 integron, itself nested within an ∼54-kb multidrug resistance region on an epidemic IncA/C2 plasmid. The emergence of blaIMP-14 in this context in the ST131 lineage is of potential clinical concern.

Maintaining the continuity of HIV-care records for patients transferring care between centers: challenges, workloads, needs and risks.

With improved life expectancy, the medical records of HIV-infected patients are likely to be transferred repeatedly between HIV caregivers. The challenges, and risk for introducing medical error from incomplete record transfers are poorly understood. We measured number of requests for record transfer, the workload incurred, and explore, using genotypic antiretroviral resistance testing results (GART), the potential risk of incomplete records.

Whole-genome phylogenomic heterogeneity of Neisseria gonorrhoeae isolates with decreased cephalosporin susceptibility collected in Canada between 1989 and 2013.

A large-scale, whole-genome comparison of Canadian Neisseria gonorrhoeae isolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades.