Combining iCn3D and NextStrain to create a novel undergraduate research experience around SARS-CoV-2 variants and commercial antibodies.

Undergraduate research experiences are increasingly important in biology education with efforts underway to provide more projects by embedded them in a course. The shift to online learning at the beginning of the pandemic presented a challenge. How could biology instructors provide research experiences to students who were unable to attend in-person labs? During the 2021 ISMB (Intelligent Systems for Molecular Biology) iCn3D Hackathon-Collaborative Tools for Protein Analysis-we learned about new capabilities in iCn3D for analyzing the interactions between amino acids in the paratopes of antibodies with amino acids in the epitopes of antigens and predicting the effects of mutations on binding.

The MedSafer Study-Electronic Decision Support for Deprescribing in Hospitalized Older Adults: A Cluster Randomized Clinical Trial.

Importance: Scalable deprescribing interventions may reduce polypharmacy and the use of potentially inappropriate medications (PIMs); however, few studies have been large enough to evaluate the impact that deprescribing may have on adverse drug events (ADEs).

Objective: To evaluate the effect of an electronic deprescribing decision support tool on ADEs after hospital discharge among older adults with polypharmacy.

Design, Setting, And Participants: This was a cluster randomized clinical trial of older (≥65 years) hospitalized patients with an expected survival of more than 3 months who were admitted to 1 of 11 acute care hospitals in Canada from August 22, 2017, to January 13, 2020.

COVID-SAFER: Deprescribing Guidance for Hydroxychloroquine Drug Interactions in Older Adults.

Background/objectives: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes high morbidity and mortality in older adults with chronic illnesses. Several trials are currently underway evaluating the antimalarial drug hydroxychloroquine as a potential treatment for acute infection. However, polypharmacy predisposes patients to increased risk of drug-drug interactions with hydroxychloroquine and may render many in this population ineligible to participate in trials.

Chronic Obstructive Pulmonary Disease: A Palliative Medicine Review of the Disease, Its Therapies, and Drug Interactions.

Despite significant advances in treatment, chronic obstructive pulmonary disease (COPD) remains a chronic and progressive disease that frequently leads to premature mortality. COPD is associated with a constellation of significant symptoms, including dyspnea, cough, wheezing, pain, fatigue, anxiety, depression, and insomnia, and is associated with increased morbidity. Palliative care is appropriate to support these patients.

Idiopathic Pulmonary Fibrosis: A Review of Disease, Pharmacological, and Nonpharmacological Strategies With a Focus on Symptoms, Function, and Health-Related Quality of Life.

Despite several advances in treatment, idiopathic pulmonary fibrosis (IPF) remains a progressive, symptomatic, and terminal disease in patients not suitable for lung transplantation. With disease progression, IPF often leads to a constellation of symptoms, including dyspnea, cough, anxiety, and depression. Palliative care is appropriate to support these patients.

Pulmonary Arterial Hypertension: A Palliative Medicine Review of the Disease, Its Therapies, and Drug Interactions.

Pulmonary arterial hypertension (PAH) is often a progressive and ultimately fatal disease. It is characterized by an elevated mean pulmonary arterial pressure because of disease of the small pulmonary arterioles. PAH leads to a constellation of symptoms, including dyspnea, fatigue, syncope, chest discomfort, and peripheral edema.

The MedSafer Study: A Controlled Trial of an Electronic Decision Support Tool for Deprescribing in Acute Care.

Objectives: Polypharmacy is common, costly, and harmful for hospitalized older adults. Scalable strategies to reduce the burden of potentially inappropriate medications (PIMs) are needed. We sought to leverage medication reconciliation in hospitalized older adults by pairing with MedSafer, an electronic decision support tool for deprescribing.

A pilot study of a Medication Rationalization (MERA) intervention.

Background: Many seriously ill and frail inpatients receive potentially inappropriate or harmful medications and do not receive medications for symptoms of advanced illness. We developed and piloted an interprofessional Medication Rationalization (MERA) approach to deprescribing inappropriate medications and prescribing appropriate comfort medications.

Methods: We conducted a single-centre pilot study of inpatients at risk of 6-month mortality from advanced age or morbidity.

Comparative safety and tolerability of endothelin receptor antagonists in pulmonary arterial hypertension.

Pulmonary arterial hypertension (PAH) is a condition that leads to progressive right heart failure and death unless recognized and treated early. Endothelin, a potent endogenous vasoconstrictor, has been identified as an important mediator of PAH. Endothelin receptor antagonists (ERAs) have been associated with an improvement in exercise capacity and time to clinical worsening in patients with Group 1 PAH, and three different ERAs are currently approved for use in this population: bosentan, ambrisentan, and macitentan.

Characterizing multi-omic data in systems biology.

In today's biology, studies have shifted to analyzing systems over discrete biochemical reactions and pathways. These studies depend on combining the results from scores of experimental methods that analyze DNA; mRNA; noncoding RNAs, DNA, RNA, and protein interactions; and the nucleotide modifications that form the epigenome into global datasets that represent a diverse array of "omics" data (transcriptional, epigenetic, proteomic, metabolomic). The methods used to collect these data consist of high-throughput data generation platforms that include high-content screening, imaging, flow cytometry, mass spectrometry, and nucleic acid sequencing.

Bioinformatics education in high school: implications for promoting science, technology, engineering, and mathematics careers.

We investigated the effects of our Bio-ITEST teacher professional development model and bioinformatics curricula on cognitive traits (awareness, engagement, self-efficacy, and relevance) in high school teachers and students that are known to accompany a developing interest in science, technology, engineering, and mathematics (STEM) careers. The program included best practices in adult education and diverse resources to empower teachers to integrate STEM career information into their classrooms. The introductory unit, Using Bioinformatics: Genetic Testing, uses bioinformatics to teach basic concepts in genetics and molecular biology, and the advanced unit, Using Bioinformatics: Genetic Research, utilizes bioinformatics to study evolution and support student research with DNA barcoding.

Analyzing gene expression data from microarray and next-generation dna sequencing transcriptome profiling assays using GeneSifter analysis edition.

Transcription profiling with microarrays has become a standard procedure for comparing the levels of gene expression between pairs of samples, or multiple samples following different experimental treatments. New technologies, collectively known as next-generation DNA sequencing methods, are also starting to be used for transcriptome analysis. These technologies, with their low background, large capacity for data collection, and dynamic range, provide a powerful and complementary tool to the assays that formerly relied on microarrays.

Exploring DNA structure with Cn3D.

Researchers in the field of bioinformatics have developed a number of analytical programs and databases that are increasingly important for advancing biological research. Because bioinformatics programs are used to analyze, visualize, and/or compare biological data, it is likely that the use of these programs will have a positive impact on biology education. Over the past years, we have been working to help biology instructors introduce bioinformatics activities into their curricula by providing them with instructional materials that use bioinformatics programs and databases as educational tools.

A sequence variation scan of the coagulation factor VIII (FVIII) structural gene and associations with plasma FVIII activity levels.

Plasma factor VIII coagulant activity (FVIII:C) level is a highly heritable quantitative trait that is strongly correlated with thrombosis risk. Polymorphisms within only 1 gene, the ABO blood-group locus, have been unequivocally demonstrated to contribute to the broad population variability observed for this trait. Because less than 2.