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. Additionally, new sequence alignment tools in iCn3D support aligning protein sequences with sequences in structure models. We used these methods to create a new undergraduate research project, that students could perform online as part of a course, by combining the use of new features in iCn3D with analysis tools in NextStrain, and a data set of anti-SARS-CoV-2 antibodies. We present results from an example project to illustrate how students would investigate the likelihood of SARS-CoV-2 variants escaping from commercial antibodies and use chemical interaction data to support their hypotheses. We also demonstrate that online tools (iCn3D, NextStrain, and the NCBI databases) can be used to carry out the necessary steps and that this work satisfies the requirements for course-based undergraduate research. This project reinforces major concepts in undergraduate biology-evolution and the relationship between the sequence of a protein, its three-dimensional structure, and its function.

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. At admission, participants were taking 5 or more medications per day. Data analyses were performed from January 3, 2021, to September 23, 2021. INTERVENTIONS: Personalized reports of deprescribing opportunities generated by MedSafer software to address usual home medications and measures of prognosis and frailty. Deprescribing reports provided to the treating team were compared with usual care (medication reconciliation). MAIN OUTCOMES AND MEASURES: The primary outcome was a reduction of ADEs within the first 30 days postdischarge (including adverse drug withdrawal events) captured through structured telephone surveys and adjudicated blinded to intervention status. Secondary outcomes were the proportion of patients with 1 or more PIMs deprescribed at discharge and the proportion of patients with an adverse drug withdrawal event (ADWE). RESULTS: A total of 5698 participants (median [range] age, 78 [72-85] years; 2858 [50.2%] women; race and ethnicity data were not collected) were enrolled in 3 clusters and were adjudicated for the primary outcome (control, 3204; intervention, 2494). Despite cluster randomization, there were group imbalances, eg, the participants in the intervention arm were older and had more PIMS prescribed at baseline. After hospital discharge, 4989 (87.6%) participants completed an ADE interview. There was no significant difference in ADEs within 30 days of discharge (138 [5.0%] of 2742 control vs 111 [4.9%] of 2247 intervention participants; adjusted risk difference [aRD] -0.8%; 95% CI, -2.9% to 1.3%). Deprescribing increased from 795 (29.8%) of 2667 control to 1249 (55.4%) of 2256 intervention participants [aRD, 22.2%; 95% CI, 16.9% to 27.4%]. There was no difference in ADWEs between groups. Several post hoc sensitivity analyses, including the use of a nonparametric test to address the low cluster number, group imbalances, and potential biases, did not alter study conclusions. CONCLUSIONS AND RELEVANCE: This cluster randomized clinical trial showed that providing deprescribing clinical decision support during acute hospitalization had no demonstrable impact on ADEs, although the intervention was safe and led to improvements in deprescribing. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT03272607.

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. We aimed to quantify the degree of polypharmacy and burden of potentially inappropriate medications (PIMs) that older hospitalized adults are taking that would interact with hydroxychloroquine. METHODS: We reanalyzed data from the cohort of patients 65 years and older enrolled in the MedSafer pilot study. We first identified patients taking medications with potentially harmful drug-drug interactions with hydroxychloroquine that might exclude them from participation in a typical 2019 coronavirus disease (COVID-19) therapeutic trial. Next, we identified medications that were flagged by MedSafer as potentially inappropriate and crafted guidance around medication management if contemplating the use of hydroxychloroquine. RESULTS: The cohort contained a total of 1,001 unique patients with complete data on their home medications at admission. Of these 1,001 patients, 590 (58.9%) were receiving one or more home medications that could potentially interact with hydroxychloroquine, and of these, 255 (43.2%) were flagged as potentially inappropriate by the MedSafer tool. Common classes of PIMs observed were antipsychotics, cardiac medications, and antidiabetic agents. CONCLUSION: The COVID-19 pandemic highlights the importance of medication optimization and deprescribing PIMs in older adults. By acting now to reduce polypharmacy and use of PIMs, we can better prepare this vulnerable population for inclusion in trials and, if substantiated, pharmacologic treatment or prevention of COVID-19. J Am Geriatr Soc 68:1636-1646, 2020.

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. However, historically, palliative care has focused on supporting patients with malignant disease, rather than progressive chronic diseases such as COPD. Therapies for COPD often result in functional and symptomatic improvements, including health-related quality of life (HRQL), and palliative care may further improve symptoms and HRQL. Provision of usual palliative care therapies for this patient population requires understanding the pathogenesis of COPD and common disease-targeted pharmacotherapies, as well as an approach to balancing life-prolonging and HRQL care strategies. This review describes COPD and current targeted therapies and their effects on symptoms, exercise tolerance, HRQL, and survival. It is important to note that medications commonly used for symptom management in palliative care can interact with COPD medications resulting in increased risk of adverse effects, enhanced toxicity, or changes in clearance of medications. To address this, we review pharmacologic interactions with and precautions related to use of COPD therapies in conjunction with commonly used palliative care medications.

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. However, traditional curriculum in palliative care has often focused on supporting patients with malignant disease, and clinicians are not universally trained to manage patients with progressive nonmalignant diseases such as IPF. Current antifibrotic therapies aim to slow disease progression but are not able to reduce symptoms or improve daily function and health-related quality of life (HRQL). Palliative care in this patient group requires an understanding of the clinical characteristics of IPF, comorbidities, common medications used, and nonpharmacological strategies that can be undertaken to improve daily function and HRQL. This review focuses on IPF management strategies and their effects on symptoms, exercise tolerance, HRQL, and survival. Pharmacological interactions and considerations related to commonly used palliative care medications are also reviewed. This review highlights the needs of patients with IPF and caregivers, psychosocial function, patient-reported assessment tools, and topics related to advance care planning.

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. Disease-targeted therapies for PAH produce symptomatic and functional improvement, but long-term survival remains uncommon without lung transplantation. Palliative care is appropriate to support patients with advanced PAH who typically have a high symptom burden. However, palliative care has historically focused on supporting patients with malignant disease, rather than progressive chronic disease such as PAH. Our aim is to provide palliative care clinicians with a background in the classification, pathophysiology, and modern treatment of PAH. This review describes disease-targeted therapies and their effects on symptoms, physical functioning, and health-related quality of life. We also review the unique physiology of PAH and its implication for palliative interventions. Pharmacological interactions with, and precautions related to commonly used palliative care medications, are discussed.

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. DESIGN: This was a nonrandomized controlled before-and-after study. SETTING: The study took place on four internal medicine clinical teaching units. PARTICIPANTS: Subjects were aged 65 years and older, had an expected prognosis of 3 or more months, and were taking five or more usual home medications. INTERVENTION: In the baseline phase, patients received usual care that was medication reconciliation. Patients in the intervention arm also had a "deprescribing opportunity report" generated by MedSafer and provided to their in-hospital treating team. MEASUREMENTS: The primary outcome was ascertained at the time of hospital discharge and was the proportion of patients who had one or more PIMs deprescribed. RESULTS: A total of 1066 patients were enrolled, and deprescribing opportunities were present for 873 (82%; 418 during the control and 455 during the intervention phases, respectively). The proportion of patients with one or more PIMs deprescribed at discharge increased from 46.9% in the control period to 54.7% in the intervention period with an adjusted absolute risk difference of 8.3% (2.9%-13.9%). Not all classes of drugs in the intervention arm were associated with an increase in deprescribing, and new PIM starts were equally common in both arms of the study. CONCLUSION: Using an electronic decision support tool for deprescribing, we increased the proportion of patients with one or more PIMs deprescribed at hospital discharge as compared with usual care. Although this type of intervention may help address medication overload in hospitalized patients, it also underscores the importance of powering future trials for a reduction in adverse drug events. TRIAL REGISTRATION: NCT02918058. J Am Geriatr Soc 67:1843-1850, 2019.

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. The MERA team reviewed the patients' medications and made recommendations on the basis of guidelines. We measured end points for feasibility, acceptability, efficiency and effectiveness. RESULTS: We enrolled 61 of 115 (53%) eligible patients with a mean age of 79.6 years (standard deviation [SD] 11.7 yr). Patients were taking an average of 11.5 (SD 5.2) medications before admission and had an average of 2.1 symptoms with greater than 6/10 severity on the revised Edmonton Symptom Assessment System. The MERA team recommended 263 medication changes, of which 223 (85%) were accepted by both the medical team and the patient. MERA team's recommendations resulted in the discontinuation of 162 medications (mean 3.1 per patient), dose changes for 48 medications (mean 0.9 per patient) and the addition of 13 medications (mean 0.2 per patient). Patients who received the MERA intervention stopped significantly more inappropriate medications than similar non-MERA comparison patients for whom data were collected retrospectively (3.1 v. 0.9 medications per patient, p < 0.01). The MERA approach was highly acceptable to patients and medical team members. INTERPRETATION: The MERA intervention is feasible, acceptable, efficient and possibly effective for changing medication use among seriously ill and frail elderly inpatients. Scalability and effectiveness may be improved through automation and integration with medication reconciliation programs.

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. While all three ERAs are generally well-tolerated, they each have important adverse effects that need to be recognized and monitored. In particular, they may cause anemia, peripheral edema, and mild cardiac, respiratory, neurologic, and gastrointestinal adverse effects to varying degrees. Although bosentan increases a patient's risk of developing liver transaminitis, ambrisentan and macitentan do not appear to confer the same risk of hepatotoxicity at this time. Important drug-drug interactions, particularly involving other drugs metabolized via the cytochrome P450 pathway, are important to recognize when prescribing ERAs. In this review, we provide a brief overview of the current state of knowledge as it relates to the adverse effect profiles, tolerability, and drug-drug interactions of this class of medication as informed by the results of randomized clinical trials, drug surveillance programs, and regulatory agencies.

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. Of these, the next-generation DNA sequencing platforms predominate because they provide an inexpensive and scalable way to quickly interrogate the molecular changes at the genetic, epigenetic, and transcriptional level. Furthermore, existing and developing single-molecule sequencing platforms will likely make direct RNA and protein measurements possible, thus increasing the specificity of current assays and making it possible to better characterize "epi-alterations" that occur in the epigenome and epitranscriptome. These diverse data types present us with the largest challenge: how do we develop software systems and algorithms that can integrate these datasets and begin to support a more democratic model where individuals can capture and track their own medical information through biometric devices and personal genome sequencing? Such systems will need to provide the necessary user interactions to work with the trillions of data points needed to make scientific discoveries. Here, we describe novel approaches in the genesis and processing of such data, models to integrate these data, and the increasing ubiquity of self-reporting and self-measured genomics and health data.

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. Pre-post surveys demonstrated significant growth (n = 24) among teachers in their preparation to teach the curricula and infuse career awareness into their classes, and these gains were sustained through the end of the academic year. Introductory unit students (n = 289) showed significant gains in awareness, relevance, and self-efficacy. While these students did not show significant gains in engagement, advanced unit students (n = 41) showed gains in all four cognitive areas. Lessons learned during Bio-ITEST are explored in the context of recommendations for other programs that wish to increase student interest in STEM careers.

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. In this chapter, we describe two protocols for working with microarray data from pairs of samples and samples treated with multiple conditions, and discuss alternative protocols for carrying out similar analyses with next-generation DNA sequencing data from two different instrument platforms (Illumina GA and Applied Biosystems SOLiD).

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. In this study, we measured the impact of a set of these materials on student learning. The activities in these materials asked students to use the molecular structure visualization program Cn3D to locate, identify, or analyze diverse features in DNA structures. Both the experimental groups of college and high school students showed significant increases in learning relative to control groups. Further, learning gains by the college students were correlated with the number of activities assigned. We conclude that working with Cn3D was important for improving student understanding of DNA structure. This study is one example of how a bioinformatics program for visualization can be used to support student learning.

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 2.5% of the structural FVIII gene (F8) has been examined previously, we resequenced all known functional regions in 222 potentially distinct alleles from 137 unrelated nonhemophilic individuals representing 7 racial groups. Eighteen of the 47 variants identified, including 17 single-nucleotide polymorphisms (SNPs), were previously unknown. As the degree of linkage disequilibrium across F8 was weak overall, we used measured-genotype association analysis to evaluate the influence of each polymorphism on the FVIII:C levels in 398 subjects from 21 pedigrees known as the Genetic Analysis of Idiopathic Thrombophilia project (GAIT). Our results suggested that 92714C>G, a nonsynonymous SNP encoding the B-domain substitution D1241E, was significantly associated with FVIII:C level. After accounting for important covariates, including age and ABO genotype, the association persisted with each C-allele additively increasing the FVIII:C level by 14.3 IU dL(-1) (P = .016). Nevertheless, because the alleles of 56010G>A, a SNP within the 3' splice junction of intron 7, are strongly associated with 92714C>G in GAIT, additional studies are required to determine whether D1241E is itself a functional variant.