Consolidation Carnival: A Case-Based Approach to Reviewing Musculoskeletal Anatomy in an Undergraduate Medical Curriculum.

Introduction: Recent changes in undergraduate medical curricula have resulted in time constraints that are particularly challenging, especially when students must learn large blocks of musculoskeletal anatomy content. Consequently, students have resorted to rote memorization to cope, which counteracts our established collaborative self-directed learning model. Methods: For a 6-week musculoskeletal anatomy course, two structured case-based review sessions are described, each following the completion of two five-hour lab sessions, two on the upper extremities and two on the lower extremities. These largely self-directed review sessions consisted of 6 students rotating through 7 to 8 stations every 10 minutes where clinical cases with follow-up questions were projected on large screens. The students were expected to work collaboratively to solve the cases utilizing the prosected specimens provided and discuss the accompanying answers at the end of each case. Results: Ninety-four per cent of the students who participated in this study agreed that the case-based review sessions provided a helpful overview of musculoskeletal anatomy content. Student performance on the open-ended, case-based musculoskeletal examination questions showed no significant difference in performance on shoulder, hand, hip, thigh, and leg questions. There was, however, a statistically significant decrease in the students' scores on a forearm question in 2021 compared to 2019. Conclusion: This paper describes our integrated, collaborative musculoskeletal course, including case-based review sessions, which was positively received by students as having value in reviewing the musculoskeletal content though it was not found to improve examination performance.

Integration of physiology in a curriculum on human structure: a snapshot of the cardiovascular block.

With the gradual shift from discipline-based to competency-based medical education, the integrated curriculum has become a popular model for connecting basic science and clinical content in undergraduate medical education. Despite its popularity, there are concerns that important physiological concepts are not adequately addressed. We describe the spiral integration of physiology content in the 5-week Cardiovascular block of our Homeostasis course at the Zucker School of Medicine. We also describe our approach to incorporating physiology into an integrated, constructed response, short-answer assessment format. Our approach to spiral integration consists of rotating lab stations that highlight the distinction between normal and abnormal states, linked with appropriate clinical interventions. Physiology is at the core of integration in any curriculum and the basis of all applied fields of medicine, hence our approach is that teaching structural relationships would not be valuable without consideration of its functions, which can then be utilized in discussion of clinical presentations, imaging, and relevant pathologies. Likewise, our integrated assessments require the students to compose their answers to the questions from scratch, which creates a shift in mode of students' preparation from rote memorizations to more cognitive processing that enhances critical thinking.

N 6-methyladenosine enhances post-transcriptional gene regulation by microRNAs.

MOTIVATION: N 6-methyladenosine (m6A) is the most prevalent modification in eukaryotic messenger RNAs. MicroRNAs (miRNAs) are abundant post-transcriptional regulators of gene expression. Correlation between m6A and miRNA-targeting sites has been reported to suggest possible involvement of m6A in miRNA-mediated gene regulation. However, it is unknown what the regulatory effects might be. In this study, we performed comprehensive analyses of high-throughput data on m6A and miRNA target binding and regulation. RESULTS: We found that the level of miRNA-mediated target suppression is significantly enhanced when m6A is present on target mRNAs. The evolutionary conservation for miRNA-binding sites with m6A modification is significantly higher than that for miRNA-binding sites without modification. These findings suggest functional significance of m6A modification in post-transcriptional gene regulation by miRNAs. We also found that methylated targets have more stable structure than non-methylated targets, as indicated by significantly higher GC content. Furthermore, miRNA-binding sites that can be potentially methylated are significantly less accessible without methylation than those that do not possess potential methylation sites. Since either RNA-binding proteins or m6A modification by itself can destabilize RNA structure, we propose a model in which m6A alters local target secondary structure to increase accessibility for efficient binding by Argonaute proteins, leading to enhanced miRNA-mediated regulation. AVAILABILITY AND IMPLEMENTATION: N/A.

Gel Rounds: Integrating Bedside Ultrasound Training for Third-Year Medical Students Into the Internal Medicine Clerkship.

Despite formal ultrasound training becoming prevalent in preclinical medical student education, significant barriers remain to the continuation of this training during clinical years. We sought to develop a program for third-year medical students to continue ultrasound training after an already robust preclinical ultrasound curriculum and evaluate their scanning confidence after participation. We developed a program to facilitate bedside ultrasound scanning of patients being cared for by third-year students. Students identified appropriate patients to be scanned, obtained consent for scanning, and determined which scans were most appropriate given the patient's clinical problems. Trained facilitators met with students at the bedside in 1-hour sessions called Gel Rounds to observe and direct the students' scans of their patients. Fifty-one students were surveyed after completing Gel Rounds. Students were significantly more likely to feel comfortable with independently acquiring and interpreting images after Gel Rounds than before completing the activity. Approximately 67% of students felt that ultrasound had utility in assisting bedside clinical reasoning, and this proportion did not change significantly after completing Gel Rounds. Gel Rounds was a positive continuation of the ultrasound curriculum into the third-year clerkship environment. A minority of students reported prior ultrasound exposure in their third year, reflecting difficulty with developing a longitudinal curriculum. The activity helped students to independently acquire and interpret images in patients. Because Gel Rounds can be performed at the discretion of students and faculty, it fits naturally in a variety of existing longitudinal curricula.

Sfold Tools for MicroRNA Target Prediction.

Computational prediction of miRNA binding sites on target mRNAs facilitates experimental investigation of miRNA functions. In this chapter, we describe STarMir and STarMirDB, two application modules of the Sfold RNA package. STarMir is a Web server for performing miRNA binding site predictions for mRNA and target sequences submitted by users. STarMirDB is a database of precomputed transcriptome-scale predictions. Both STarMir and STarMirDB provide comprehensive sequence, thermodynamic, and target structure features, a logistic probability as a measure of confidence for each predicted site, and a publication-quality diagram of the predicted miRNA-target hybrid. In addition, STarMir now offers a new quantitative score to address combined regulatory effects of multiple seed and seedless sites. This score provides a quantitative measure of the overall regulatory effects of both seed and seedless sites on the target. STarMir and STarMirDB are freely available to all through the Sfold Web application server at http://sfold.wadsworth.org .

Trusting early learners with critical professional activities through emergency medical technician certification.

BACKGROUND: Two dominant themes face medical education: developing integrated curricula and improving the undergraduate medical education (UME) to graduate medical education (GME) transition. An innovative solution to both of these challenges at the Zucker School of Medicine has been the application of the cognitive apprenticeship framework in requiring emergency medical technician (EMT) certification during the first course in medical school as the core on which to build an integrated curriculum and provide entrustable clinical skills. METHODS: Beginning with the Class of 2011, student feedback about the short-term impact of the experience was collected annually. In addition, perceptions of near graduates and alumni were surveyed in 2017 to explore the long-term impact of the experience. Theme analysis was conducted via inductive coding. RESULTS: Both first-year and more experienced learners report the value of the EMT curriculum as an integrated component of the first course of medical school. Reported positive long-term impacts included the first-hand observation of social determinants of health and interprofessionalism. Negative comments by early learners focused on course logistics, whereas older learners recalled the variability of clinical experiences during ambulance runs. CONCLUSIONS: The integration of the EMT curriculum as a core component of the first course serves multiple purposes: 1) it provides the foundation of a spiral learning approach; 2) it contextualizes the basic sciences within clinical practice; 3) it provides opportunities for students to engage in authentic clinical activities under the guidance of mentors; 4) it introduces students to the interdisciplinary nature of medicine; and 5) it serves as the first entrustable professional activity (EPA) for our students.

Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation.

Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36 ± 3 nt is optimal for pri-miRNA processing. We identify two bulge-depleted regions on the miRNA stem, located ∼16-21 nt and ∼28-32 nt from the base of the stem, that are less tolerant of unpaired bases. We further show that the CNNC primary sequence motif selectively enhances the processing of optimal-length hairpins. We predict that a small but significant fraction of human single-nucleotide polymorphisms (SNPs) alter pri-miRNA processing, and confirm several predictions experimentally including a disease-causing mutation. Our study enhances the rules governing mammalian pri-miRNA processing and suggests a diverse impact of human genetic variation on miRNA biogenesis.

Hunger Games: Interactive Ultrasound Imaging for Learning Gastrointestinal Physiology.

Ultrasound is playing an increasingly important role in medical student education. Although most uses of ultrasound have focused on learning purely anatomic relationships or augmentation of the physical examination, there is little documentation of the value of ultrasound as a learning tool regarding physiology alone or in association with anatomy. We devised an interactive learning session for first-year medical students using ultrasound to combine both anatomic and physiologic principles as an integration of gastrointestinal and vascular function. The incorporation of our activity, The Hunger Games, provides the foundation for a powerful integration tool for medical student education.

STarMir Tools for Prediction of microRNA Binding Sites.

MicroRNAs (miRNAs) are a class of endogenous short noncoding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs), which results in translational repression and/or mRNA degradation. As regulatory molecules, miRNAs are involved in many mammalian biological processes and also in the manifestation of certain human diseases. As miRNAs play central role in the regulation of gene expression, understanding miRNA-binding patterns is essential to gain an insight of miRNA mediated gene regulation and also holds promise for therapeutic applications. Computational prediction of miRNA binding sites on target mRNAs facilitates experimental investigation of miRNA functions. This chapter provides protocols for using the STarMir web server for improved predictions of miRNA binding sites on a target mRNA. As an application module of the Sfold RNA package, the current version of STarMir is an implementation of logistic prediction models developed with high-throughput miRNA binding data from cross-linking immunoprecipitation (CLIP) studies. The models incorporated comprehensive thermodynamic, structural, and sequence features, and were found to make improved predictions of both seed and seedless sites, in comparison to the established algorithms (Liu et al., Nucleic Acids Res 41:e138, 2013). Their broad applicability was indicated by their good performance in cross-species validation. STarMir is freely available at http://sfold.wadsworth.org/starmir.html .

STarMirDB: A database of microRNA binding sites.

microRNAs (miRNAs) are an abundant class of small endogenous non-coding RNAs (ncRNAs) of ∼22 nucleotides (nts) in length. These small regulatory molecules are involved in diverse developmental, physiological and pathological processes. miRNAs target mRNAs (mRNAs) for translational repression and/or mRNA degradation. Predictions of miRNA binding sites facilitate experimental validation of miRNA targets. Models developed with data from CLIP studies have been used for predictions of miRNA binding sites in the whole transcriptomes of human, mouse and worm. The prediction results have been assembled into STarMirDB, a new database of miRNA binding sites available at http://sfold.wadsworth.org/starmirDB.php . STarMirDB can be searched by miRNAs or mRNAs separately or in combination. The search results are categorized into seed and seedless sites in 3' UTR, CDS and 5' UTR. For each predicted site, STarMirDB provides a comprehensive list of sequence, thermodynamic and target structural features that are known to influence miRNA: target interaction. A high resolution PDF diagram of the conformation of the miRNA:target hybrid is also available for visualization and publication. The results of a database search are available through both an interactive viewer and downloadable text files.

Identification of bacterial sRNA regulatory targets using ribosome profiling.

Bacteria express large numbers of non-coding, regulatory RNAs known as 'small RNAs' (sRNAs). sRNAs typically regulate expression of multiple target messenger RNAs (mRNAs) through base-pairing interactions. sRNA:mRNA base-pairing often results in altered mRNA stability and/or altered translation initiation. Computational identification of sRNA targets is challenging due to the requirement for only short regions of base-pairing that can accommodate mismatches. Experimental approaches have been applied to identify sRNA targets on a genomic scale, but these focus only on those targets regulated at the level of mRNA stability. Here, we utilize ribosome profiling (Ribo-seq) to experimentally identify regulatory targets of the Escherichia coli sRNA RyhB. We not only validate a majority of known RyhB targets using the Ribo-seq approach, but also discover many novel ones. We further confirm regulation of a selection of known and novel targets using targeted reporter assays. By mutating nucleotides in the mRNA of a newly discovered target, we demonstrate direct regulation of this target by RyhB. Moreover, we show that Ribo-seq distinguishes between mRNAs regulated at the level of RNA stability and those regulated at the level of translation. Thus, Ribo-seq represents a powerful approach for genome-scale identification of sRNA targets.

Effects of genetic variations on microRNA: target interactions.

Genetic variations within microRNA (miRNA) binding sites can affect miRNA-mediated gene regulation, which may lead to phenotypes and diseases. We perform a transcriptome-scale analysis of genetic variants and miRNA:target interactions identified by CLASH. This analysis reveals that rare variants tend to reside in CDSs, whereas common variants tend to reside in the 3' UTRs. miRNA binding sites are more likely to reside within those targets in the transcriptome with lower variant densities, especially target regions in which nucleotides have low mutation frequencies. Furthermore, an overwhelming majority of genetic variants within or near miRNA binding sites can alter not only the potential of miRNA:target hybridization but also the structural accessibility of the binding sites and flanking regions. These suggest an interpretation for certain associations between genetic variants and diseases, i.e. modulation of miRNA-mediated gene regulation by common or rare variants within or near miRNA binding sites, likely through target structure alterations. Our data will be valuable for discovering new associations among miRNAs, genetic variations and human diseases.

Medical students as EMTs: skill building, confidence and professional formation.

OBJECTIVE: The first course of the medical curriculum at the Hofstra North Shore-LIJ School of Medicine, From the Person to the Professional: Challenges, Privileges and Responsibilities, provides an innovative early clinical immersion. The course content specific to the Emergency Medical Technician (EMT) curriculum was developed using the New York State Emergency Medical Technician curriculum. Students gain early legitimate clinical experience and practice clinical skills as team members in the pre-hospital environment. We hypothesized this novel curriculum would increase students' confidence in their ability to perform patient care skills and enhance students' comfort with team-building skills early in their training. METHODS: Quantitative and qualitative data were collected from first-year medical students (n=97) through a survey developed to assess students' confidence in patient care and team-building skills. The survey was completed prior to medical school, during the final week of the course, and at the end of their first year. A paired-samples t-test was conducted to compare self-ratings on 12 patient care and 12 team-building skills before and after the course, and a theme analysis was conducted to examine open-ended responses. RESULTS: Following the course, student confidence in patient care skills showed a significant increase from baseline (p<0.05) for all identified skills. Student confidence in team-building skills showed a significant increase (p<0.05) in 4 of the 12 identified skills. By the end of the first year, 84% of the first-year students reported the EMT curriculum had 'some impact' to 'great impact' on their patient care skills, while 72% reported the EMT curriculum had 'some impact' to 'great impact' on their team-building skills. CONCLUSIONS: The incorporation of EMT training early in a medical school curriculum provides students with meaningful clinical experiences that increase their self-reported level of confidence in the performance of patient care skills early in their medical education.

STarMir: a web server for prediction of microRNA binding sites.

STarMir web server predicts microRNA (miRNA) binding sites on a target ribonucleic acid (RNA). STarMir is an implementation of logistic prediction models developed with miRNA binding data from crosslinking immunoprecipitation (CLIP) studies (Liu,C., Mallick, B., Long, D., Rennie, W.A., Wolenc, A., Carmack, C.S. and Ding, Y. (2013). CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res., 41(14), e138). In both intra-dataset and inter-dataset validations, the models showed major improvements over established algorithms in predictions of both seed and seedless sites. General applicability of the models was indicated by good performance in cross-species validations. The input data for STarMir is processed by the web server to perform prediction of miRNA binding sites, compute comprehensive sequence, thermodynamic and target structure features and a logistic probability as a measure of confidence for each predicted site. For each of seed and seedless sites and for all three regions of a mRNA (3' UTR, CDS and 5' UTR), STarMir output includes the computed binding site features, the logistic probability and a publication-quality diagram of the predicted miRNA:target hybrid. The prediction results are available through both an interactive viewer and downloadable text files. As an application module of the Sfold RNA package (http://sfold.wadsworth.org), STarMir is freely available to all at http://sfold.wadsworth.org/starmir.html.

MicroRNA binding sites in C. elegans 3' UTRs.

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression. Since the discovery of lin-4, the founding member of the miRNA family, over 360 miRNAs have been identified for Caenorhabditis elegans (C. elegans). Prediction and validation of targets are essential for elucidation of regulatory functions of these miRNAs. For C. elegans, crosslinking immunoprecipitation (CLIP) has been successfully performed for the identification of target mRNA sequences bound by Argonaute protein ALG-1. In addition, reliable annotation of the 3' untranslated regions (3' UTRs) as well as developmental stage-specific expression profiles for both miRNAs and 3' UTR isoforms are available. By utilizing these data, we developed statistical models and bioinformatics tools for both transcriptome-scale and developmental stage-specific predictions of miRNA binding sites in C. elegans 3' UTRs. In performance evaluation via cross validation on the ALG-1 CLIP data, the models were found to offer major improvements over established algorithms for predicting both seed sites and seedless sites. In particular, our top-ranked predictions have a substantially higher true positive rate, suggesting a much higher likelihood of positive experimental validation. A gene ontology analysis of stage-specific predictions suggests that miRNAs are involved in dynamic regulation of biological functions during C. elegans development. In particular, miRNAs preferentially target genes related to development, cell cycle, trafficking, and cell signaling processes. A database for both transcriptome-scale and stage-specific predictions and software for implementing the prediction models are available through the Sfold web server at http://sfold.wadsworth.org.

CLIP-based prediction of mammalian microRNA binding sites.

Prediction and validation of microRNA (miRNA) targets are essential for understanding functions of miRNAs in gene regulation. Crosslinking immunoprecipitation (CLIP) allows direct identification of a huge number of Argonaute-bound target sequences that contain miRNA binding sites. By analysing data from CLIP studies, we identified a comprehensive list of sequence, thermodynamic and target structure features that are essential for target binding by miRNAs in the 3' untranslated region (3' UTR), coding sequence (CDS) region and 5' untranslated region (5' UTR) of target messenger RNA (mRNA). The total energy of miRNA:target hybridization, a measure of target structural accessibility, is the only essential feature common for both seed and seedless sites in all three target regions. Furthermore, evolutionary conservation is an important discriminating feature for both seed and seedless sites. These features enabled us to develop novel statistical models for the predictions of both seed sites and broad classes of seedless sites. Through both intra-dataset validation and inter-dataset validation, our approach showed major improvements over established algorithms for predicting seed sites and a class of seedless sites. Furthermore, we observed good performance from cross-species validation, suggesting that our prediction framework can be valuable for broad application to other mammalian species and beyond. Transcriptome-wide binding site predictions enabled by our approach will greatly complement the available CLIP data, which only cover small fractions of transcriptomes and known miRNAs due to non-detectable levels of expression. Software and database tools based on the prediction models have been developed and are available through Sfold web server at http://sfold.wadsworth.org.

The Bin3 RNA methyltransferase targets 7SK RNA to control transcription and translation.

Bicoid-interacting protein 3 (Bin3) is a conserved RNA methyltransferase found in eukaryotes ranging from fission yeast to humans. It was originally discovered as a Bicoid (Bcd)-interacting protein in Drosophila, where it is required for anterior-posterior and dorso-ventral axis determination in the early embryo. The mammalian ortholog of Bin3 (BCDIN3), also known as methyl phosphate capping enzyme (MePCE), plays a key role in repressing transcription. In transcription, MePCE binds the non-coding 7SK RNA, which forms a scaffold for an RNA-protein complex that inhibits positive-acting transcription elongation factor b, an RNA polymerase II elongation factor. MePCE uses S-adenosyl methionine to transfer a methyl group onto the γ-phosphate of the 5' guanosine of 7SK RNA generating an unusual cap structure that protects 7SK RNA from degradation. Bin3/MePCE also has a role in translation regulation. Initial studies in Drosophila indicate that Bin3 targets 7SK RNA and stabilizes a distinct RNA-protein complex that assembles on the 3'-untranslated region of caudal mRNAs to prevent translation initiation. Much remains to be learned about Bin3/MeCPE function, including how it recognizes 7SK RNA, what other RNA substrates it might target, and how widespread a role it plays in gene regulation and embryonic development.

Residents' quality of life during an orthopedic trauma rotation: a multicentre prospective observational study.

OBJECTIVE: Fewer orthopedic surgery trainees are choosing careers in trauma. The impact of stressors on health-related quality of life has not been evaluated among orthopedic surgical residents. The current study aimed to determine predictors of unsatisfactory resident quality of life during trauma rotations. METHOD: This was a prospective observational study in which we chose orthopedic trauma rotations within 2 training programs at 3 level 1 trauma centres. A sample of 15 orthopedic surgery residents participated in the study. The main outcome measure was the 36-Item Short-Form Health Survey taken at baseline, 2 and 6 months into the rotation. Residents ranked level of stress for 15 work-related and 13 individual problems on 5-point Likert scales. RESULTS: The residents ranged from training years 1 through 5, and their mean age was 31 (standard deviation [SD] 2.8) years. Fear of error decreased at 6 months, compared with baseline (p = 0.007). Lack of time for family decreased as a problem at 2 and 6 months, compared with baseline (p = 0.025). Baseline Physical Component Summary scores were above population norms (p = 0.007). At 2 months, scores for the concept role limitations (physical) decreased significantly (p = 0.019), compared with the baseline. Mean Physical Component Summary scores declined from 57.59 (SD 3.51) at baseline to 53.68 (SD 6.50) at 2 months (p = 0.015) and 53.94 (SD 3.52) at 6 months (p = 0.008). At 2 months, mean general health scores significantly decreased, compared with baseline (p = 0.022). Social functioning scores at 6 months were decreased from population norms (p = 0.02). More resident social time was spent with medical people exclusively at 6 months, compared with baseline (p < 0.02). CONCLUSION: Trauma rotations affect residents' emotional well-being. Training programs should equip residents with coping strategies to improve quality of life during trauma rotations.

Tissue plasminogen activator for acute ischemic stroke: a New York city emergency medicine perspective.

Nationally, only 2-3% of patients with acute ischemic stroke (AIS) currently receive tissue plasminogen activator (TPA). To better understand the reasons, we investigated the practice patterns, level of familiarity and acceptance of TPA for AIS among emergency physicians in New York City (NYC). Fifty-seven 911-receiving hospital emergency department directors were surveyed regarding TPA use. Of those responding, 37% had never used TPA to treat AIS. Lack of neurological support was reported by 33%. Departments with formal protocols were more likely to use TPA for AIS. In conclusion, there is considerable variation in the practice, knowledge, and attitudes regarding the use of TPA for AIS in NYC emergency departments. Improved educational efforts and institutional support may be necessary to ensure the appropriate use of TPA by emergency physicians.

A review of clinically relevant human anatomy in emergency medicine.

The objectives of this project were to establish a practical model for the review of clinical anatomy relevant to the assessment and care of the ill and injured patient, and to design practice models for invasive procedures using human cadaver, porcine cadaver, and plastic model material. A practical course based on the human gross anatomy of the face, neck, thorax, airway, arm, and leg was designed. Regional anesthesia techniques, arthrocentesis, saphenous vein cutdown, central venous and arterial cannulation, surgical airway, thoracostomy tube placement and thoracotomy were integrated into the appropriate practice stations. A syllabus was developed. A clinically relevant, online anatomy atlas demonstrating all of the above was developed. In conclusion, an anatomy review course combining clinically relevant, human, gross anatomy and procedure practice stations was established.