7 research outputs found
Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria
<p>Abstract</p> <p>Background</p> <p>A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers.</p> <p>Methods</p> <p>The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries.</p> <p>Results</p> <p>After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals.</p> <p>Conclusion</p> <p>The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode Initiative. The large scale investigation of Ascomycota mitochondrial introns performed through this tool, allowing to exclude the introns-rich sequences from the barcode candidates exploration, could be the first step towards a mitochondrial barcoding strategy for these organisms, similar to the standard approach employed in metazoans.</p
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One-Year Follow-Up of COVID-19 Impact on Surgical Education: Clinical Training Restored but Surgical Trainee Emotional Well-Being Still at Risk.
BackgroundA previous survey documented the severe disruption of the coronavirus disease 2019 pandemic on surgical education and trainee well-being during the initial surge and systemic lockdowns. Herein, we report the results of a follow-up survey inclusive of the 2020 to 2021 academic year.Study designA survey was distributed to education leaders across all surgical specialties in summer 2021. We compared the proportion of participants reporting severe disruption in key areas with those of the spring 2020 survey. Aggregated differences by year were assessed using chi-square analysis.ResultsIn 2021, severe disruption of education programs was reported by 14% compared with 32% in 2020 (p < 0.0001). Severe reductions in nonemergency surgery were reported by 38% compared with 87% of respondents in 2020. Severe disruption of expected progression of surgical trainee autonomy by rank also significantly decreased to 5% to 8% in 2021 from 15% to 23% in 2020 among respondent programs (p < 0.001). In 2021 clinical remediation was reported for postgraduate year 1 to 2 and postgraduate year 3 to 4, typically through revised rotations (19% and 26%) and additional use of simulation (20% and 19%) maintaining trainee promotion and job placement. In 2021, surgical trainees' physical safety and health were reported as less severely impacted compared with 2020; however, negative effects of isolation (77%), burnout (75%), and the severe impact on emotional well-being (17%) were prevalent.ConclusionsOne year after the initial coronavirus disease 2019 outbreak, clinical training and surgical trainee health were less negatively impacted. Disruption of emotional well-being remained high. Future needs include better objective measures of clinical competence beyond case numbers and the implementation of novel programs to promote surgical trainee health and well-being
Impact of the COVID-19 pandemic on surgical trainee education and well-being spring 2020-winter 2020: A path forward
BackgroundThe time course and longitudinal impact of the COVID -19 pandemic on surgical education(SE) and learner well-being (LWB)is unknown.Material and methodsCheck-in surveys were distributed to Surgery Program Directors and Department Chairs, including general surgery and surgical specialties, in the summer and winter of 2020 and compared to a survey from spring 2020. Statistical associations for items with self-reported ACGME Stage and the survey period were assessed using categorical analysis.ResultsStage 3 institutions were reported in spring (30%), summer (4%) [p < 0.0001] and increased in the winter (18%). Severe disruption (SD) was stage dependent (Stage 3; 45% (83/184) vs. Stages 1 and 2; 26% (206/801)[p < 0.0001]). This lessened in the winter (23%) vs. spring (32%) p = 0.02. LWB severe disruption was similar in spring 27%, summer 22%, winter 25% and was associated with Stage 3.ConclusionsSteps taken during the pandemic reduced SD but did not improve LWB. Systemic efforts are needed to protect learners and combat isolation pervasive in a pandemic
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Impact of the COVID-19 Pandemic on Surgical Training and Learner Well-Being: Report of a Survey of General Surgery and Other Surgical Specialty Educators.
BackgroundThe COVID-19 pandemic disrupted the delivery of surgical services. The purpose of this communication was to report the impact of the pandemic on surgical training and learner well-being and to document adaptations made by surgery departments.Study designA 37-item survey was distributed to educational leaders in general surgery and other surgical specialty training programs. It included both closed- and open-ended questions and the self-reported stages of GME during the COVID-19 pandemic, as defined by the ACGME. Statistical associations for items with stage were assessed using categorical analysis.ResultsThe response rate was 21% (472 of 2,196). US stage distribution (n = 447) was as follows: stage 1, 22%; stage 2, 48%; and stage 3, 30%. Impact on clinical education significantly increased by stage, with severe reductions in nonemergency operations (73% and 86% vs 98%) and emergency operations (8% and 16% vs 34%). Variable effects were reported on minimal expected case numbers across all stages. Reductions were reported in outpatient experience (83%), in-hospital experience (70%), and outside rotations (57%). Increases in ICU rotations were reported with advancing stage (7% and 13% vs 37%). Severity of impact on didactic education increased with stage (14% and 30% vs 46%). Virtual conferences were adopted by 97% across all stages. Severity of impact on learner well-being increased by stage-physical safety (6% and 9% vs 31%), physical health (0% and 7% vs 17%), and emotional health (11% and 24% vs 42%). Regardless of stage, most but not all made adaptations to support trainees' well-being.ConclusionsThe pandemic adversely impacted surgical training and the well-being of learners across all surgical specialties proportional to increasing ACGME stage. There is a need to develop education disaster plans to support technical competency and learner well-being. Careful assessment for program advancement will also be necessary. The experience during this pandemic shows that virtual learning and telemedicine will have a considerable impact on the future of surgical education
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Impact of the COVID-19 Pandemic on Surgical Training and Learner Well-Being: Report of a Survey of General Surgery and Other Surgical Specialty Educators.
BackgroundThe COVID-19 pandemic disrupted the delivery of surgical services. The purpose of this communication was to report the impact of the pandemic on surgical training and learner well-being and to document adaptations made by surgery departments.Study designA 37-item survey was distributed to educational leaders in general surgery and other surgical specialty training programs. It included both closed- and open-ended questions and the self-reported stages of GME during the COVID-19 pandemic, as defined by the ACGME. Statistical associations for items with stage were assessed using categorical analysis.ResultsThe response rate was 21% (472 of 2,196). US stage distribution (n = 447) was as follows: stage 1, 22%; stage 2, 48%; and stage 3, 30%. Impact on clinical education significantly increased by stage, with severe reductions in nonemergency operations (73% and 86% vs 98%) and emergency operations (8% and 16% vs 34%). Variable effects were reported on minimal expected case numbers across all stages. Reductions were reported in outpatient experience (83%), in-hospital experience (70%), and outside rotations (57%). Increases in ICU rotations were reported with advancing stage (7% and 13% vs 37%). Severity of impact on didactic education increased with stage (14% and 30% vs 46%). Virtual conferences were adopted by 97% across all stages. Severity of impact on learner well-being increased by stage-physical safety (6% and 9% vs 31%), physical health (0% and 7% vs 17%), and emotional health (11% and 24% vs 42%). Regardless of stage, most but not all made adaptations to support trainees' well-being.ConclusionsThe pandemic adversely impacted surgical training and the well-being of learners across all surgical specialties proportional to increasing ACGME stage. There is a need to develop education disaster plans to support technical competency and learner well-being. Careful assessment for program advancement will also be necessary. The experience during this pandemic shows that virtual learning and telemedicine will have a considerable impact on the future of surgical education