SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes.

The incorporation of sequencing technologies in frontline and public health healthcare settings was vital in developing virus surveillance programs during the Coronavirus Disease 2019 (COVID-19) pandemic caused by transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, increased data acquisition poses challenges for both rapid and accurate analyses. To overcome these hurdles, we developed the SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) for quick bulk analyses of Illumina short-read sequencing data.

Diversity, functional classification and genotyping of SHV β-lactamases in .

Interpreting the phenotypes of alleles in genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal alleles or additional plasmid-borne alleles that have extended-spectrum β-lactamase (ESBL) activity and/or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood.

Prevention of radial artery occlusion after transradial angiography and intervention: a best practice implementation project.

Introduction: Among the complications associated with transradial artery access, radial artery occlusion (RAO) is the most frequent and serious, limiting the reuse of the same radial artery for subsequent procedures and as a graft for coronary artery bypass grafting.

Objective: The objective of this project was to implement best practices to reduce the incidence of RAO, thereby enhancing the quality of patient care after transradial coronary angiography or intervention.

Methods: The project was conducted in cardiology department of the Huadong Hospital, Shanghai, China.

The last word: An analysis of power dynamics in clinical notes documenting against-medical-advice discharges.

Against Medical Advice (AMA) discharges pose significant challenges to the healthcare system, straining patient-clinician relationships while contributing to avoidable morbidity and mortality. Furthermore, though these discharges culminate in patients' departure from hospitals, their effects reverberate long after, propagated by clinician notes stored in patients' medical records. These notes capture exceptionally fraught interactions between patients and providers, describing the circumstances surrounding breakdowns in clinical relationships.

Minimal Impact on the Resistome of Children in Botswana After Azithromycin Treatment for Acute Severe Diarrheal Disease.

Background: Macrolide antibiotics, including azithromycin, can reduce under 5 years of age mortality rates and treat various infections in children in sub-Saharan Africa. These exposures, however, can select for antibiotic-resistant bacteria in the gut microbiota.

Methods: Our previous randomized controlled trial (RCT) of a rapid-test-and-treat strategy for severe acute diarrheal disease in children in Botswana included an intervention (3-day azithromycin dose) group and a control group that received supportive treatment.

Improving the quality of medication administration practices in a tertiary Australian hospital: a best practice implementation project.

Introduction: Medication safety is an important health priority that focuses on preventing harm from medication-related events. Unsafe medication administration practices can lead to errors, which can cause avoidable injury (or harm) to patients.

Objectives: This paper reports on an evidence implementation project conducted in a large tertiary hospital in Australia to improve nursing compliance with best practice recommendations for medication administration.

Event-related Potential Measures of Visual Word Processing in Monolingual and Bilingual Children and Adults: A Focus on Word Frequency Effects.

How does language background influence the neural correlates of visual word recognition in children? To address this question, we used an ERP lexical decision task to examine first-language (L1) and second-language (L2) visual word processing in monolingual and bilingual school-aged children and young adults (n = 123). In particular, we focused on the effects of word frequency (an index of lexical accessibility) on RTs and the N400 ERP component. Behaviorally, we found larger L1 versus L2 word frequency effects among bilingual children, driven by faster and more accurate responses to higher-frequency words (no other language or age group differences were observed).

Pelvic floor muscle training for urinary incontinence in older adults: a best practice implementation project.

Objectives: This project aimed to implement best practices for pelvic floor muscle training to manage urinary incontinence among older women in long-term care in Kerala, India.

Introduction: Urinary incontinence is a prevalent and distressing condition that affects a significant proportion of older adults and is characterized by involuntary loss of urine, leading to social embarrassment, decreased quality of life, and increased health care costs. It is more prevalent in women and is associated with dementia, limited mobility, and other comorbidities in long-term care.

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.

Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the CZ ID AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data.

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.

Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data.

Early enteral nutrition support for patients with acute pancreatitis in the inpatient setting: a best practice implementation project.

Introduction: Acute pancreatitis is a major disease that endangers the health and lives of people. Historically, clinical therapy has recommended. that patients with acute pancreatitis remain nil by mouth.

When patients demur: Resisting diagnostic closure in US primary care.

Patients are more engaged in their healthcare than ever before, including in the process of diagnostic sensemaking. But in acute primary care encounters, the interactional flow of the visit is shaped by an orientation toward the physician as the authority over diagnostic reasoning. Once physicians close diagnostic inquiry and transition into counseling, their assessment - and the extent to which it converges with the patient's perspective - comes into full view.

Macrophage AMPK β1 activation by PF-06409577 reduces the inflammatory response, cholesterol synthesis, and atherosclerosis in mice.

Atherosclerotic cardiovascular disease is characterized by both chronic low-grade inflammation and dyslipidemia. The AMP-activated protein kinase (AMPK) inhibits cholesterol synthesis and dampens inflammation but whether pharmacological activation reduces atherosclerosis is equivocal. In the current study, we found that the orally bioavailable and highly selective activator of AMPKβ1 complexes, PF-06409577, reduced atherosclerosis in two mouse models in a myeloid-derived AMPKβ1 dependent manner, suggesting a critical role for macrophages.

Biologically derived epicardial patch induces macrophage mediated pathophysiologic repair in chronically infarcted swine hearts.

There are nearly 65 million people with chronic heart failure (CHF) globally, with no treatment directed at the pathologic cause of the disease, the loss of functioning cardiomyocytes. We have an allogeneic cardiac patch comprised of cardiomyocytes and human fibroblasts on a bioresorbable matrix. This patch increases blood flow to the damaged heart and improves left ventricular (LV) function in an immune competent rat model of ischemic CHF.

Facilitation in evidence implementation - experiences, challenges, and determinants of perceived effectiveness: a qualitative systematic review.

Introduction: Facilitation is a key element of evidence implementation. Although quantitative systematic reviews have been undertaken to examine its components and effectiveness, no attempt has been made to synthesize qualitative evidence examining the experiences of facilitators on how facilitation is operationalized, the challenges associated with it, and the factors that can influence its perceived effectiveness.

Methods: A systematic review of qualitative studies was conducted using the JBI methodology.

A standardized nomenclature for resistance-modifying agents in the Comprehensive Antibiotic Resistance Database.

While increasing rates of antimicrobial resistance undermine our current arsenal of antibiotics, resistance-modifying agents (RMAs) hold promise to extend the lifetime of these important molecules. We here provide a standardized nomenclature for RMAs within the Comprehensive Antibiotic Resistance Database in aid of RMA discovery, data curation, and genome mining.

Providing a scaffold for considering theoretical frameworks in evidence implementation projects: the JBI approach to evidence implementation.

There are many theories, models, and frameworks that have been proposed in the field of implementation science. Despite this, many evidence implementation or practice improvement projects do not consider these theories, models, or frameworks in their improvement efforts. The JBI approach is one example of an implementation theory, model, or framework.

Taxonomy and effectiveness of clinician agenda-setting questions in routine ambulatory encounters: A mixed method study.

Objectives: Despite decades of communication training, studies repeatedly demonstrate that clinicians fail to elicit patients' agendas. Our goal was to provide clinicians with actionable guidance about the effectiveness of agenda-soliciting questions.

Methods: We coded clinician agenda-soliciting questions and patient responses in audio-recorded ambulatory encounters at an urban academic hospital.

Optimizing educational methods for the low FODMAP diet in disorders of gut-brain interaction: A feasibility randomized controlled trial.

Background: A diet low in fermentable oligo-saccharides, di-saccharides, mono-saccharides and polyols (low FODMAP diet) is complex and clinical effectiveness is achieved with dietitian-led education, although dietitian availability in clinical practice varies. This study aimed to assess the feasibility of undertaking a trial to investigate the clinical and cost-effectiveness of different education delivery methods of the low FODMAP diet in patients with disorders of gut-brain interaction (DGBI).

Methods: In this feasibility randomized controlled trial, patients with DGBI requiring the low FODMAP diet were randomized to receive one of the following education delivery methods: booklet, app, or dietitian.

Reading to Dogs at Home: A Pilot Study.

In summer 2021, during the coronavirus pandemic, 8 parent-child dyads were recruited to participate in a pilot project to investigate the potential benefit of an at-home adaptation of an Animal-Assisted Intervention (AAI) for literacy. After completing a demographic survey and the Perceived Stress Scale-10 (Cohen et al., 1983), children's reading level was established using the Fry method and past report card information.

Sensitivity to Neutralizing Antibodies and Resistance to Type I Interferons in SARS-CoV-2 R.1 Lineage Variants, Canada.

Isolating and characterizing emerging SARS-CoV-2 variants is key to understanding virus pathogenesis. In this study, we isolated samples of the SARS-CoV-2 R.1 lineage, categorized as a variant under monitoring by the World Health Organization, and evaluated their sensitivity to neutralizing antibodies and type I interferons.

SARS-CoV-2 Outbreak Investigation Using Contact Tracing and Whole-Genome Sequencing in an Ontario Tertiary Care Hospital.

Genomic epidemiology can facilitate an understanding of evolutionary history and transmission dynamics of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak. We used next-generation sequencing techniques to study SARS-CoV-2 genomes isolated from patients and health care workers (HCWs) across five wards of a Canadian hospital with an ongoing SARS-CoV-2 outbreak. Using traditional contact tracing methods, we show transmission events between patients and HCWs, which were also supported by the SARS-CoV-2 lineage assignments.

CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database.

Scientific literature is published at a rate that makes manual data extraction a highly time-consuming task. The Comprehensive Antibiotic Resistance Database (CARD) utilizes literature to curate information on antimicrobial resistance genes and to enable time-efficient triage of publications we have developed a classification algorithm for identifying publications describing first reports of new resistance genes. Trained on publications contained in the CARD, CARD*Shark downloads, processes and identifies publications recently added to PubMed that should be reviewed by biocurators.