Reproducible Single-Cell Genomic Research in Pulmonary and Critical Care Medicine.
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ABSTRACT:
SUBMITTER: Eickelberg O
PROVIDER: S-EPMC7706163 | biostudies-literature | 2020 Dec
REPOSITORIES: biostudies-literature
Publications
Reproducible Single-Cell Genomic Research in Pulmonary and Critical Care Medicine.
Eickelberg Oliver O Misharin Alexander V AV Sime Patricia J PJ
American journal of respiratory and critical care medicine 20201201 11
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Project description:Background: Little is known about historical and recent application trends for pulmonary critical care medicine (PCCM) or pulmonary medicine (PM) fellowship programs. Describing trends in and characteristics of PCCM and PM applications, applicants, and fellowship programs can help program directors and medical educators understand trainees' interest in and application patterns for these fellowship programs. Objective: The objective of this study was to use National Residency Match Program data to assess recent trends in PCCM and PM fellowship applications and compare characteristics of applicants and fellowship programs. Methods: In 2019, we used National Residency Match Program data to evaluate applicant ranking and matching in PCCM and PM fellowship programs and to compare applicant and fellowship program characteristics. Results: From 2008 through 2019, the majority of applicants (59.1%) matched into PCCM were graduates of U.S. allopathic or osteopathic medical schools, whereas 87% of PM fellows were non-U.S. graduates. PCCM was the preferred specialty for 90.8% of matched applicants versus only 31.6% of matched PM applicants (P < 0.001). The match rate for PCCM applicants was 67.2% versus 23.8% for PM applicants (P < 0.001). Of PCCM applicants, 36.6% matched into their top choice versus 10.8% of PM applicants (P < 0.001). There are far fewer PM fellowship positions (n = 23) and programs (n = 12) than PCCM positions (n = 450) and programs (n = 131). The mean fill rates from the 2004 through 2016 appointment years are 94.1% in PCCM and 97.4% in PM (P = 0.009). Conclusion: PCCM is a prevailing specialty choice over PM among residency graduates, with matched applicants more likely to list PCCM than PM as their preferred specialty. Further exploration into applicants' interest in critical care compared with PM may prove beneficial in guiding applicants to programs that will best meet their career goals.
| S-EPMC8043272 | biostudies-literature
Project description:GDF-15 (growth differentiation factor 15) acts both as a stress-induced cytokine with diverse actions at different body sites and as a cell-autonomous regulator linked to cellular senescence and apoptosis. For multiple reasons, this divergent transforming growth factor-β molecular superfamily member should be better known to pulmonary researchers and clinicians. In ambulatory individuals, GDF-15 concentrations in peripheral blood are an established predictive biomarker of all-cause mortality and of adverse cardiovascular events. Concentrations upon admission of critically ill patients (without or with sepsis) correlate with organ dysfunction and independently predict short- and long-term mortality risk. GDF-15 is a major downstream mediator of p53 activation, but it can also be induced independently of p53, notably by nonsteroidal antiinflammatory agents. GDF-15 blood concentrations are markedly elevated in adults and children with pulmonary hypertension. Concentrations are also increased in chronic obstructive pulmonary disease, in which they contribute to mucus hypersecretion, airway epithelial cell senescence, and impaired antiviral defenses, which together with murine data support a role for GDF-15 in chronic obstructive pulmonary disease pathogenesis and progression. This review summarizes biological and clinical data on GDF-15 relevant to pulmonary and critical care medicine. We highlight the recent discovery of a central nervous system receptor for GDF-15, GFRAL (glial cell line-derived neurotrophic factor family receptor-α-like), an important advance with potential for novel treatments for obesity and cachexia. We also describe limitations and controversies in the existing literature, and we delineate research questions that must be addressed to determine whether GDF-15 can be therapeutically manipulated in other clinical settings.
| S-EPMC6543753 | biostudies-literature
Project description:ObjectivesDelay or failure to consistently adopt evidence-based or consensus-based best practices into routine clinical care is common, including for patients in the PICU. PICU patients can fail to receive potentially beneficial diagnostic or therapeutic interventions, worsening the burden of illness and injury during critical illness. Implementation science (IS) has emerged to systematically address this problem, but its use of in the PICU has been limited to date. We therefore present a conceptual and methodologic overview of IS for the pediatric intensivist.DesignThe members of Excellence in Pediatric Implementation Science (ECLIPSE; part of the Pediatric Acute Lung Injury and Sepsis Investigators Network) represent multi-institutional expertise in the use of IS in the PICU. This narrative review reflects the collective knowledge and perspective of the ECLIPSE group about why IS can benefit PICU patients, how to distinguish IS from quality improvement (QI), and how to evaluate an IS article.ResultsIS requires a shift in one's thinking, away from questions and outcomes that define traditional clinical or translational research, including QI. Instead, in the IS rather than the QI literature, the terminology, definitions, and language differs by specifically focusing on relative importance of generalizable knowledge, as well as aspects of study design, scale, and timeframe over which the investigations occur.ConclusionsResearch in pediatric critical care practice must acknowledge the limitations and potential for patient harm that may result from a failure to implement evidence-based or professionals' consensus-based practices. IS represents an innovative, pragmatic, and increasingly popular approach that our field must readily embrace in order to improve our ability to care for critically ill children.
| S-EPMC10624111 | biostudies-literature
Project description:Introduction The mastery of mechanical ventilation (MV) management is challenging, as it requires the integration of physiological and technological knowledge with critical thinking. Our aim was to create a standardized curriculum with assessment tools based on evidence-based practices to identify the skill deficit and improve knowledge in MV management. Methods For 3 years, 3 hours of standardized curriculum for each first-year pulmonary critical care medicine (PCCM) and critical care medicine (CCM) fellows was integrated into the orientation (chronologically): (1) a baseline knowledge pretest; (2) a 1-hour one-on-one case-based simulation session with debriefing. A 34-item competency checklist was used to assess critically thinking and skills and guide the debriefing; (3) a 1-hour group didactic on respiratory mechanics and physiology; (4) a 45-minute hands-on session in small groups of one to three fellows for basic knobology, waveforms, and various modes of mechanical ventilators; (5) a 15-minute group bedside teaching of vented patients covering topics such as techniques to alleviate dyssynchrony and advanced ventilator modes; (6) a one-on-one simulation reassessment session; (7) a knowledge posttest. Fellows' performances at baseline, 1-month posttest, and end-of-first year post-test were compared. Results Fellows ( n = 24) demonstrated significant improvement at 1-month posttest in knowledge (54.2% ± 11.0 vs. 76.6 ± 11.7%, p < 0.001) and MV competency (40.7 ± 11.0% vs. 69.7 ± 9.3%, p < 0.001), compared with pretest. These improvements were retained at the end-of-year reassessments (knowledge 75.1 ± 14.5% and MV competency 85.5 ± 8.7%; p < 0.001). Conclusion Standardized simulation-based MV curriculum may improve the medical knowledge competency, and confidence of first-year PCCM and CCM fellows toward MV management before encountering actual ventilated patients.
| S-EPMC10550363 | biostudies-literature
Project description:Patient-centered outcomes research (PCOR) represents a paradigm shift in research methods aimed to create the body of evidence that supports clinical practice and informs health care decisions. PCOR integrates patients and other key stakeholders including family members, policy makers, clinicians, and patient advocates and advocacy groups as research partners throughout all stages of the research process. The importance of PCOR has received increased recognition, yet there is little evidence available to help guide researchers interested in the design and conduct of PCOR. In May 2014, we convened a workshop to identify key issues related to designing, conducting, and disseminating findings from PCOR studies. Workshop participants included a diverse group of patients, patient advocates, clinicians (physicians, nurses, psychologists, and advanced practice providers), researchers, administrators, and funders within and beyond the pulmonary, critical care, and sleep medicine communities. Participants identified important issues and considerations to address when undertaking PCOR. In this report, we summarize the results of this workshop to inform members of the pulmonary, sleep, and critical care community interested in participating in PCOR. Key findings include the following: 1) requirements for research to be considered PCOR; 2) the potential significant impact of PCOR on patients, clinicians, and researchers; 3) guiding principles and practical strategies to form successful patient-centered research partnerships, conduct PCOR, and disseminate study results to a broad audience of stakeholders; 4) benefits and challenges of PCOR for researchers; and 5) resources available within the American Thoracic Society to help with the conduct of PCOR.
| S-EPMC6850728 | biostudies-literature
Project description:Single-cell RNA-sequencing data have significantly advanced the characterization of cell-type diversity and composition. However, cell-type definitions vary across data and analysis pipelines, raising concerns about cell-type validity and generalizability. With MetaNeighbor, we proposed an efficient and robust quantification of cell-type replicability that preserves dataset independence and is highly scalable compared to dataset integration. In this protocol, we show how MetaNeighbor can be used to characterize cell-type replicability by following a simple three-step procedure: gene filtering, neighbor voting and visualization. We show how these steps can be tailored to quantify cell-type replicability, determine gene sets that contribute to cell-type identity and pretrain a model on a reference taxonomy to rapidly assess newly generated data. The protocol is based on an open-source R package available from Bioconductor and GitHub, requires basic familiarity with Rstudio or the R command line and can typically be run in <5 min for millions of cells.
| S-EPMC8826496 | biostudies-literature
Project description:BackgroundEndotracheal intubation in the intensive care unit (ICU) is a high-risk procedure. Competence in endotracheal intubation is a requirement for Pulmonary and Critical Care Medicine (PCCM) training programs, but fellow experience as the primary operator in intubating ICU patients has not been described on a large scale.ObjectiveWe hypothesized that significant variation surrounding endotracheal intubation practices in medical ICUs exists in United States (US) PCCM training programs.MethodsWe administered a survey to a convenience sample of US PCCM fellows to elicit typical intubation practices in the medical ICU.Results89 discrete US PCCM and Internal Medicine CCM training programs (77% response rate) were represented. At 43% of programs, the PCCM fellow was "always or almost always" designated the primary operator for intubation of a medical ICU patient, whereas at 21% of programs, the PCCM fellow was "rarely or never" the primary operator responsible for intubating in the ICU. Factors influencing this variation included time of day, hospital policies, attending skill or preference, ICU census and acuity, and patient factors. There was an association between location of the training program, but not program size, and whether the PCCM fellow was the primary operator.ConclusionThere is significant variation in whether PCCM fellows are the primary operators to intubate medical ICU patients during training. Further work should explore how this variation affects fellow career development and competence in intubation.
| S-EPMC7959255 | biostudies-literature
Project description:Purpose: Competency assessment standards for Critical Care Ultrasonography (CCUS) for Graduate Medical Education (GME) trainees in pulmonary/critical care medicine (PCCM) fellowship programs are lacking. We sought to answer the following research questions: How are PCCM fellows and teaching faculty assessed for CCUS competency? Which CCUS teaching methods are perceived as most effective by program directors (PDs) and fellows. Methods: Cross-sectional, nationwide, electronic survey of PCCM PDs and fellows in accredited GME training programs. Results: PDs and fellows both reported the highest rates of fellow competence to use CCUS for invasive procedural guidance, but lower rates for assessment of deep vein thrombosis and abdominal organs. 54% and 90% of PDs reported never assessing fellows or teaching faculty for CCUS competency, respectively. PDs and fellows perceived hands-on workshops and directly supervised CCUS exams as more effective learning methods than unsupervised CCUS archival with subsequent review and self-directed learning. Conclusions: There is substantial variation in CCUS competency assessment among PCCM fellows and teaching faculty nationwide. The majority of training programs do not formally assess fellows or teaching faculty for CCUS competence. Guidelines are needed to formulate standardized competency assessment tools for PCCM fellowship programs.
| S-EPMC10721306 | biostudies-literature
Project description: Not available
| S-EPMC8357065 | biostudies-literature
Project description:BackgroundRemediation of struggling learners in pulmonary and critical care fellowship programs is a challenge, even for experienced medical educators.ObjectiveThis evidence-based narrative review provides a framework program leaders may use to address fellows having difficulty achieving competency during fellowship training.MethodsThe relevant evidence for approaches on the basis of each learner's needs is reviewed and interpreted in the context of fellowship training in pulmonary medicine and critical care. Issues addressed include bias in fellow assessments and remediation, the impacts of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the specific challenges of pulmonary and critical care fellowship programs, a brief review of relevant legal issues, guidance on building and leveraging program resources, and a discussion of learner outcomes.ResultsThis results in a concise, evidence-based toolkit for program leaders based around four pillars: early identification, fellow assessment, collaborative intervention, and reassessment. Important concepts also include the need for documentation, clear and written communication, and fellow-directed approaches to the creation of achievable goals.ConclusionEvidence-based remediation helps struggling learners in pulmonary and critical care fellowship to improve their ability to meet Accreditation Council for Graduate Medical Education (ACGME) milestones.
| S-EPMC9590524 | biostudies-literature