Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra.

Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.

Treatment of pediatric antimuscarinic delirium with oral rivastigmine.

Antimuscarinic drug toxicity is a common pediatric emergency, which produces central and peripheral symptoms. Treatment of agitation and hyperactive antimuscarinic delirium, with first-line agents like cholinesterase inhibitors or benzodiazepines, is imperative to prevent severe toxicity. Intravenous physostigmine salicylate is a cholinesterase inhibitor that is commonly used to treat central antimuscarinic delirium. Its chemical structure facilitates crossing of the blood-brain barrier. Overlapping nationwide physostigmine and benzodiazepine shortages have prompted consideration of therapeutic alternatives. Rivastigmine is a long-acting cholinesterase inhibitor with a similar chemical structure to physostigmine. It represents a potential therapeutic option for antimuscarinic delirium. Rivastigmine offers potential benefits over physostigmine including a longer duration of action, slower rate of central nervous system penetration, more favorable side effect profile, and availability in multiple formulations. A paucity of literature exists describing the use of rivastigmine for central antimuscarinic delirium. We describe the effective use of oral rivastigmine in a child with central antimuscarinic delirium.

A First-Class Simulation: In-Situ In-Flight Medical Emergencies Curriculum for Emergency Medicine Residents Aboard a Commercial Airliner.

INTRODUCTION: In-flight medical emergencies occur in an estimated one out of 604 flights. Responding in this environment poses a unique set of challenges unfamiliar to most emergency medicine (EM) providers, including physical space and resource limitations. We developed a novel high-fidelity in-situ training curriculum focused on frequent or high-risk in-flight medical scenarios while replicating this austere environment. METHODS: Our residency program coordinated with our local airport's chief of security and an airline-specific station manager to arrange the use of a grounded Boeing 737 commercial airliner during late evening/early morning hours. Eight stations reviewing in-flight medical emergency topics were reviewed, five of which were simulation scenarios. We created medical and first-aid kits that reflect equipment used by commercial airlines. Residents' self-assessed competency and medical knowledge were assessed both initially and post-curriculum using a standardized questionnaire. RESULTS: Forty residents attended the educational event as learners. Self-assessed competency and medical knowledge increased after curriculum participation. All tested aspects of self-assessed competency had a statistically significant increase from a mean of 15.04 to 29.20 out of a maximum score of forty. The mean medical knowledge score increased from 4.65 to 6.93 out of 10 maximum points. CONCLUSION: A five-hour in-situ curriculum for reviewing in-flight medical emergencies increased self-assessed competency and medical knowledge for EM and EM-internal medicine residents. The curriculum was overwhelmingly well-received by learners.

Functional expression of diverse post-translational peptide-modifying enzymes in Escherichia coli under uniform expression and purification conditions.

RiPPs (ribosomally-synthesized and post-translationally modified peptides) are a class of pharmaceutically-relevant natural products expressed as precursor peptides before being enzymatically processed into their final functional forms. Bioinformatic methods have illuminated hundreds of thousands of RiPP enzymes in sequence databases and the number of characterized chemical modifications is growing rapidly; however, it remains difficult to functionally express them in a heterologous host. One challenge is peptide stability, which we addressed by designing a RiPP stabilization tag (RST) based on a small ubiquitin-like modifier (SUMO) domain that can be fused to the N- or C-terminus of the precursor peptide and proteolytically removed after modification. This is demonstrated to stabilize expression of eight RiPPs representative of diverse phyla. Further, using Escherichia coli for heterologous expression, we identify a common set of media and growth conditions where 24 modifying enzymes, representative of diverse chemistries, are functional. The high success rate and broad applicability of this system facilitates: (i) RiPP discovery through high-throughput "mining" and (ii) artificial combination of enzymes from different pathways to create a desired peptide.

From the ground up: Creating and leading fellowship programs in emergency medicine.

Background: A methodical and evidence-based approach to the creation and implementation of fellowship programs is not well described in the graduate medical education literature. The Society for Academic Emergency Medicine (SAEM) convened an expert panel to promote standardization and excellence in fellowship training. The purpose of the expert panel was to develop a fellowship guide to give prospective fellowship directors the necessary skills to successfully implement and maintain a fellowship program. Methods: Under direction of the SAEM Board of Directors, SAEM Education Committee, and SAEM Fellowship Approval Committee, a panel of content experts convened to develop a fellowship guide using an evidence-based approach and best practices content method. The resource guide was iteratively reviewed by all panel members. Results: Utilizing Kern's six-step model as a conceptual framework, the fellowship guide summarizes the construction, implementation, evaluation, and dissemination of a novel fellowship curriculum to meet the needs of trainees, educators, and sponsoring institutions. Other key areas addressed include Accreditation Council for Graduate Medical Education and nonaccredited fellowships, programmatic assessment, finances, and recruitment. Conclusions: The fellowship guide summarizes the conceptual framework, best practices, and strategies to create and implement a new fellowship program.

Characterizing chemical signaling between engineered "microbial sentinels" in porous microplates.

Living materials combine a material scaffold, that is often porous, with engineered cells that perform sensing, computing, and biosynthetic tasks. Designing such systems is difficult because little is known regarding signaling transport parameters in the material. Here, the development of a porous microplate is presented. Hydrogel barriers between wells have a porosity of 60% and a tortuosity factor of 1.6, allowing molecular diffusion between wells. The permeability of dyes, antibiotics, inducers, and quorum signals between wells were characterized. A "sentinel" strain was constructed by introducing orthogonal sensors into the genome of Escherichia coli MG1655 for IPTG, anhydrotetracycline, L-arabinose, and four quorum signals. The strain's response to inducer diffusion through the wells was quantified up to 14 mm, and quorum and antibacterial signaling were measured over 16 h. Signaling distance is dictated by hydrogel adsorption, quantified using a linear finite element model that yields adsorption coefficients from 0 to 0.1 mol m-3 . Parameters derived herein will aid the design of living materials for pathogen remediation, computation, and self-organizing biofilms.

Selection for constrained peptides that bind to a single target protein.

Peptide secondary metabolites are common in nature and have diverse pharmacologically-relevant functions, from antibiotics to cross-kingdom signaling. Here, we present a method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a single target-of-interest. Constrained peptide scaffolds were produced using modified enzymes gleaned from microbial RiPP (ribosomally synthesized and post-translationally modified peptide) pathways and diversified to build large libraries. The binding of a RiPP to a protein target leads to the intein-catalyzed release of an RNA polymerase σ factor, which drives the expression of selectable markers. As a proof-of-concept, a selection was performed for binding to the SARS-CoV-2 Spike receptor binding domain. A 1625 Da constrained peptide (AMK-1057) was found that binds with similar affinity (990 ± 5 nM) as an ACE2-derived peptide. This demonstrates a generalizable method to identify constrained peptides that adhere to a single protein target, as a step towards "molecular glues" for therapeutics and diagnostics.

Flipping the Classroom in Graduate Medical Education: A Systematic Review.

BACKGROUND: Flipped classroom (FC) instruction has become increasingly common in graduate medical education (GME). OBJECTIVE: The purpose of this study was to profile the use of FC in the GME setting and assess the current status of research quality. METHODS: We conducted a systematic literature search of major health and social science databases from July 2017 to July 2018. Articles were screened to ensure they described use of the FC method in an Accreditation Council for Graduate Medical Education-accredited residency program and included research outcomes. Resulting articles were analyzed, described, and evaluated for research quality using the Kirkpatrick framework and the Medical Education Research Study Quality Instrument (MERSQI). RESULTS: Twenty-two articles were identified, all of which were recently published. Five were only indirectly related to FC methods. Most studies reported Kirkpatrick-level outcomes. Studies involving resident learner opinions were generally positive. Pre-posttest studies resulted in large positive improvements in knowledge or skills attainment. Control group study results ranged from large positive (1.56) to negative effects (-0.51). Average MERSQI scores of 12.1 (range, 8.5-15.5) were comparable to GME research norms. CONCLUSIONS: Varying methods for implementing and studying the FC in GME has led to variable results. While residents expressed a positive attitude toward FC learning, shortcomings were reported. Approximately half of the studies comparing the flipped to the traditional classroom reported better achievement under the FC design. As indicated by the MERSQI score, studies captured by this review, on average, were as rigorous as typical research on residency education.

Performance Standards of Comprehensive Airway Management for Emergency Medicine Residents.

BACKGROUND: The Emergency Medicine (EM) Milestone Project provides guidance for assessment of resident trainee airway management proficiency (PC10). Although milestones provide a general structure for assessment, they do not define performance standards. The objective of this project was to establish comprehensive airway management performance standards for EM trainees at both novice and mastery levels of proficiency. METHODS: Comprehensive airway management standards were derived using standard-setting procedures. A panel of residency education and airway management experts was convened to determine how trainees would be expected to perform on 51 individual tasks in a standardized airway management simulation encompassing preparation, endotracheal intubation, backup airway use, and ventilation. Experts participated in facilitated exercises in which they were asked to 1) define which items were critical for patient safety, 2) predict the performance of a "novice" learner, and 3) predict the performance of a "mastery" learner nearing independent practice. Experts were given a worksheet to complete and descriptive statistics were calculated using STATA 14. RESULTS: Experts identified 39 of 51 (76%) airway management items as critical for patient safety. Experts also noted that novice trainees do not need to complete all the items deemed to be critical prior to starting practice since they will be supervised by a board-certified EM physician. In contrast, mastery-level trainees would be expected to successfully complete not only the critical tasks, but also nearly all the items in the assessment (49/51, 96%) since they are nearing independent practice. CONCLUSION: In this study, we established EM resident performance standards for comprehensive airway management during a simulation scenario. Future work will focus on validating these performance standards in current resident trainees as they move from simulation to actual patient care.

Evaluation of an Intervention to Improve Quality of Single-best Answer Multiple-choice Questions.

INTRODUCTION: Despite the ubiquity of single-best answer multiple-choice questions (MCQ) in assessments throughout medical education, question writers often receive little to no formal training, potentially decreasing the validity of assessments. While lengthy training opportunities in item writing exist, the availability of brief interventions is limited. METHODS: We developed and performed an initial validation of an item-quality assessment tool and measured the impact of a brief educational intervention on the quality of single-best answer MCQs. RESULTS: The item-quality assessment tool demonstrated moderate internal structure evidence when applied to the 20 practice questions (κ=.671, p<.001) and excellent internal structure when applied to the true dataset (κ=0.904, p<.001). Quality scale scores for pre-intervention questions ranged from 2-6 with a mean ± standard deviation (SD) of 3.79 ± 1.23, while post-intervention scores ranged from 4-6 with a mean ± SD of 5.42 ± 0.69. The post-intervention scores were significantly higher than the pre-intervention scores, x 2(1) =38, p <0.001. CONCLUSION: Our study demonstrated short-term improvement in single-best answer MCQ writing quality after a brief, open-access lecture, as measured by a simple, novel, grading rubric with reasonable validity evidence.

Show Me the Money: Successfully Obtaining Grant Funding in Medical Education.

Obtaining grant funding is a fundamental component to achieving a successful research career. A successful grant application needs to meet specific mechanistic expectations of reviewers and funders. This paper provides an overview of the importance of grant funding within medical education, followed by a stepwise discussion of strategies for creating a successful grant application for medical education-based proposals. The last section includes a list of available medical education research grants.

Asteroids® and Electrocardiograms: Proof of Concept of a Simulation for Task-Switching Training.

INTRODUCTION: Emergency physicians are interrupted during patient care with such tasks as reading electrocardiograms (ECGs). This phenomenon is known as task-switching which may be a teachable skill. Our objective was to evaluate the potential of a video game for simulating the cognitive demands required of task-switching. METHODS: Emergency medicine residents took a pretest on ECG interpretation and then a posttest while attending to a video game, Asteroids®. RESULTS: The 35 residents (63%) who participated, scored worse on the ECG posttest then they did on the pretest (p<.001; effect size=1.14). There were no differences between genders or training level. CONCLUSION: Interpreting ECGs while playing the Asteroids® game significantly lowered ECG interpretation scores. This shows the potential of this activity for training residents in task-switching ability. The next phase of research will test whether ECG reading performance while task-switching improves with practice.

The Effect of a Medical Toxicology Inpatient Service in an Academic Tertiary Care Referral Center.

INTRODUCTION: Morbidity and mortality from poison- and drug-related illness continue to rise in the USA. Medical toxicologists are specifically trained to diagnose and manage these patients. Inpatient medical toxicology services exist but their value-based economic benefits are not well established. METHODS: This was a retrospective study where length of stay (LOS) and payments received between a hospital with an inpatient medical toxicology service (TOX) and a similar hospital in close geographic proximity that does not have an inpatient toxicology service (NONTOX) were compared. Controlling for zip code, demographics and distance patients lived from each hospital, we used a fitted multivariate linear regression model to identify factors associated with changes in LOS and payment. RESULTS: Patients admitted to the TOX center had 0.87 days shorter LOS per encounter and the hospital received an average of $1800 more per patient encounter. CONCLUSION: In this study, the presence of an inpatient medical toxicology service was associated with decreased patient LOS and increased reimbursement for admitted patients. Differences may be attributable to improved direct patient care provided by medical toxicologists, but future prospective studies are needed.

Generation and characterisation of recombinant FMDV antibodies: Applications for advancing diagnostic and laboratory assays.

Foot-and-mouth disease (FMD) affects economically important livestock and is one of the most contagious viral diseases. The most commonly used FMD diagnostic assay is a sandwich ELISA. However, the main disadvantage of this ELISA is that it requires anti-FMD virus (FMDV) serotype-specific antibodies raised in small animals. This problem can be, in part, overcome by using anti-FMDV monoclonal antibodies (MAbs) as detecting reagents. However, the long-term use of MAbs may be problematic and they may need to be replaced. Here we have constructed chimeric antibodies (mouse/rabbit D9) and Fabs (fragment antigen-binding) (mouse/cattle D9) using the Fv (fragment variable) regions of a mouse MAb, D9 (MAb D9), which recognises type O FMDV. The mouse/rabbit D9 chimeric antibody retained the FMDV serotype-specificity of MAb D9 and performed well in a FMDV detection ELISA as well as in routine laboratory assays. Cryo-electron microscopy analysis confirmed engagement with antigenic site 1 and peptide competition studies identified the aspartic acid at residue VP1 147 as a novel component of the D9 epitope. This chimeric expression approach is a simple but effective way to preserve valuable FMDV antibodies, and has the potential for unlimited generation of antibodies and antibody fragments in recombinant systems with the concomitant positive impacts on the 3Rs (Replacement, Reduction and Refinement) principles.

A Randomized Comparison of In-hospital Rescuer Positions for Endotracheal Intubation in a Difficult Airway.

INTRODUCTION: Emergency endotracheal intubation (ETI) is a common and critical procedure performed in both prehospital and in-hospital settings. Studies of prehospital providers have demonstrated that rescuer position influences ETI outcomes. However, studies of in-hospital rescuer position for ETI are limited. While we adhere to strict standards for the administration of ETI, we posited that perhaps requiring in-hospital rescuers to stand for ETI is an obstacle to effectiveness. Our objective was to compare in-hospital emergency medicine (EM) trainees' performance on ETI delivered from both the seated and standing positions. METHODS: EM residents performed ETI on a difficult airway mannequin from both a seated and standing position. They were randomized to the position from which they performed ETI first. All ETIs were recorded and then scored using a modified version of the Airway Management Proficiency Checklist. Residents also rated the laryngeal view and the difficulty of the procedure. We analyzed comparisons between ETI positions with paired t-tests. RESULTS: Forty-two of our 49 residents (85.7%) participated. Fifteen (35.7%) were female, and all three levels of training were represented. The average number of prior ETI experiences among our subjects was 44 (standard deviation=34). All scores related to ETI performance were statistically equivalent across the two positions (performance score, number of attempts, time to intubation success, and ratings of difficulty and laryngeal view). We also observed no differences across levels of training. CONCLUSION: The position of the in-hospital provider, whether seated or standing, had no effect on the provider's ETI performance. Since environmental circumstances sometimes necessitate alternative positioning for effective ETI administration, our findings suggest that there may be value in training residents to perform ETI from both positions.

Adjunct Ketamine Use in the Management of Severe Ethanol Withdrawal.

OBJECTIVES: Ketamine offers a plausible mechanism with favorable kinetics in treatment of severe ethanol withdrawal. The purpose of this study is to determine if a treatment guideline using an adjunctive ketamine infusion improves outcomes in patients suffering from severe ethanol withdrawal. DESIGN: Retrospective observational cohort study. SETTING: Academic tertiary care hospital. PATIENTS: Patients admitted to the ICU and diagnosed with delirium tremens by Diagnostic and Statistical Manual of Mental Disorders V criteria. INTERVENTIONS: Pre and post guideline, all patients were treated in a symptom-triggered fashion with benzodiazepines and/or phenobarbital. Postguideline, standard symptom-triggered dosing continued as preguideline, plus, the patient was initiated on an IV ketamine infusion at 0.15-0.3 mg/kg/hr continuously until delirium resolved. Based upon withdrawal severity and degree of agitation, a ketamine bolus (0.3 mg/kg) was provided prior to continuous infusion in some patients. MEASUREMENTS AND MAIN RESULTS: A total of 63 patients were included (29 preguideline; 34 postguideline). Patients treated with ketamine were less likely to be intubated (odds ratio, 0.14; p < 0.01; 95% CI, 0.04-0.49) and had a decreased ICU stay by 2.83 days (95% CI, -5.58 to -0.089; p = 0.043). For ICU days outcome, correlation coefficients were significant for alcohol level and total benzodiazepine dosing. For hospital days outcome, correlation coefficients were significant for patient age, aspartate aminotransferase, and alanine aminotransferase level. Regression revealed the use of ketamine was associated with a nonsignificant decrease in hospital stay by 3.66 days (95% CI, -8.40 to 1.08; p = 0.13). CONCLUSIONS: Mechanistically, adjunctive therapy with ketamine may attenuate the demonstrated neuroexcitatory contribution of N-methyl-D-aspartate receptor stimulation in severe ethanol withdrawal, reduce the need for excessive gamma-aminobutyric acid agonist mediated-sedation, and limit associated morbidity. A ketamine infusion in patients with delirium tremens was associated with reduced gamma-aminobutyric acid agonist requirements, shorter ICU length of stay, lower likelihood of intubation, and a trend toward a shorter hospitalization.

Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018).

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances. An updated Master Species List incorporating the approved changes was released in March 2018 ( https://talk.ictvonline.org/taxonomy/ ).

Documenting the Growth of Ultrasound Research in Emergency Medicine Through a Bibliometric Analysis of Accepted Academic Conference Abstracts.

OBJECTIVES: Ultrasound (US) has become an indispensable skill for emergency physicians. Growth in the use of US in emergency medicine (EM) has been characterized by practice guidelines, education requirements, and the number of EM US practitioners. Our purpose was to further document the growth of EM US by profiling the breadth, depth, and quality of US-related research presented at EM's most prominent annual research conference: the Society for Academic Emergency Medicine Annual Meeting. METHODS: We reviewed published research abstracts from the annual Society for Academic Emergency Medicine conferences from 1999 to 2015. Abstracts related to US were identified and examined for the number of authors and rigor of the research design. Designs were categorized as experimental, quasiexperimental, and nonexperimental. Abstract submissions were analyzed by the average rate of change over time. RESULTS: From 1999 to 2015, we observed a 10.2% increase in the number of accepted abstracts related to US research. This rate compared to a 3.2% average rate of change for all abstracts in general. The number of unique authors engaged in US research increased at a rate of 26.6%. Of the 602 abstracts identified as US related, only 12% could be considered experimental research. CONCLUSIONS: We observed larger increases in the number of US-related research relative to the total number of abstracts presented at a national conference. The number of investigators engaging in this research has also steadily increased. The research design of these studies was found to be primarily quasiexperimental. To improve the quality of EM's use of point-of-care US, more rigorous research with experimental designs is needed.

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.

Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species ( Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.

Replacing Lectures with Small Groups: The Impact of Flipping the Residency Conference Day.

The flipped classroom, an educational alternative to the traditional lecture, has been widely adopted by educators at all levels of education and across many disciplines. In the flipped classroom, learners prepare in advance of the face-to-face meeting by learning content material on their own. Classroom time is reserved for application of the learned content to solving problems or discussing cases. Over the past year, we replaced most residency program lectures with small-group discussions using the flipped-classroom model, case-based learning, simulation and procedure labs. In the new model, residents prepared for conference by reviewing a patient case and studying suggested learning materials. Conference day was set aside for facilitated small-group discussions about the case. This is a cross-cohort study of emergency medicine residents who experienced the lecture-based curriculum to residents in the new flipped-classroom curriculum using paired comparisons (independent t-tests) on in-training exam scores while controlling for program year level. We also compared results of the evaluation of various program components. We observed no differences between cohorts on in-training examination scores. Small-group methods were rated the same across program years. Two program components in the new curriculum, an updated format of both adult and pediatric case conferences, were rated significantly higher on program quality. In preparation for didactics, residents in the new curriculum report spending more time on average with outside learning materials, including almost twice as much time reviewing textbooks. Residents found the new format of the case conferences to be of higher quality because of the inclusion of rapid-fire case discussions with targeted learning points.