Internal transcribed spacer primer evaluation for vascular plant metabarcoding

The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.

Concordance of MRI-guided and systematic prostate biopsy for the detection of prostate cancer (PCa).

277 Background: MRI/US guided biopsy (fusion biopsy) is increasingly utilized over systemic 12-core transrectal ultrasound biopsy (12-core biopsy) for men with MRI-visible prostate lesions. Methods: Patients with MRI visible prostate lesions who underwent fusion and 12-core biopsy from 2016-2020 in the Intermountain Healthcare (IHC) system were consecutively analyzed. This was in the setting of a continuous quality assurance initiative among the reading radiologists. Primary outcome was PCa detection defined by Gleason grade group (GGG) 1 or higher. Clinically significant cancer (CSC) was defined as GGG 2 or higher. Patients were stratified by date biopsy was performed, 2016-2017 and 2018-2020, and lesions were stratified by PI-RADS v2 category. For men with multiple lesions, the highest PI-RADS v2 category lesion was used. Results: A total of 142 men with 254 MRI-detectable lesions underwent both fusion and 12-core biopsies in the IHC system from 2016 to 2020. CSC was detected in 21.6% (55/254) of fusion biopsies. Comparing PI-RAD v2 categories 1-3 to PI-RADS v2 categories 4-5, the PPV for detecting CSC was 9% (15/162) compared to 44% (40/92) respectively. Fusion and 12-core biopsies were concordant for any PCa in 79% of men (112/142) and CSC in 83% (118/142). Fusion biopsy detected any PCa in 22/84 (26%) and CSC in 15/103 (15%) of men in whom 12-core biopsy was negative. 12-core biopsy detected any PCa in 8/70 (11%) and CSC in 9/97 (9%) of men in whom fusion was negative. In total, 15 patients (11%) had a CSC that would have been missed if fusion biopsy was omitted while 9 (6%) had a CSC that would have been missed without 12-core biopsy. Conclusions: Omitting fusion or 12-core biopsy for PI-RADS v2 lesions would have resulted in a missed CSC in 11% or 6% of patients from 2016-20, respectively. The combination of MRI/US-guided fusion biopsy and systematic 12-core biopsy increased detection rate of CSC. These results are in the setting of a continuous, multi-disciplinary quality assurance program and results are not necessarily applicable to other healthcare systems. [Table: see text]

Implementation of competency-based medical education in a Canadian medical oncology training program: Lessons from our first year.

10514 Background: As part of a university wide initiative, CBME was implemented in our MO training program in July 2017. Stages, Entrustable Professional Activity (EPA) assessments and Required Training Experiences established by the Royal College of Physicians and Surgeons of Canada were adopted. MedTech Central, the electronic portfolio developed at our university was used for assessment collection. We share here observations and experiences from our first year of implementation. Methods: Assessment metrics were obtained through MEdTech. Ethics was granted by Queen’s University as part of an ongoing research study on feedback. Lessons learned were compiled from discussions between the Program Director, Residents, Program Administrator, CBME Education Consultant and CBME lead. Results: A total of 195 assessments were completed July 2017-November 2018. 81% were EPA assessments and the remainder multisource feedback, rubrics and field notes. The median number of assessments per faculty was 17 (0-42). 52% of assessments included written “Comments” or “Next steps”. A median of 6 assessments per faculty member included specific or actionable feedback. Lessons learned centered on: 1) Faculty and Resident development and engagement (critical before, during and after implementation); 2) Value of sharing work of CBME (CBME Education Consultant, CBME Lead, Academic Advisors, Competence Committee); 3) Importance of effective communication strategy with stakeholders 4) Importance of collaboration with other training programs at institutional and national levels; 5) Culture change (a slow process); 6) Resident concerns regarding lack of global assessment; 7) Assessment plan challenges (How many observations required?); 8) Burden of CBME (Resident driven assessments or a better balance?) ; 9) Limitations of e-portfolio (How to live track and by whom?); 10) Costs 11) Value of continuous quality assurance and improvement. Conclusions: Our first year of implementation was successful in introducing CBME concepts, work based assessments and e-portfolios. Ongoing work is needed, including increasing the number of assessments and quality of feedback.

External Quality Assessment (EQA) for Molecular Diagnostics of Zika Virus: Experiences from an International EQA Programme, 2016–2018

Quality Control for Molecular Diagnostics (QCMD), an international provider for External Quality Assessment (EQA) programmes, has introduced a programme for molecular diagnostics of Zika virus (ZIKV) in 2016, which has been continuously offered to interested laboratories since that time. The EQA schemes provided from 2016 to 2018 revealed that 86.7% (92/106), 82.4% (89/108), and 88.2% (90/102) of the participating laboratories reported correct results for all samples, respectively in 2016, 2017, and 2018. The review of results indicated a need for improvement concerning analytical sensitivity and specificity of the test methods. Comparison with the outcomes of other EQA initiatives briefly summarized here show that continuous quality assurance is important to improve laboratory performance and to increase preparedness with reliable diagnostic assays for effective patient management, infection and outbreak control.

A Practical Approach to Continuous Quality Control of Pipeline System Records

In recent years there has been an industry wide initiative to verify operating pressures by reviewing source records and ensuring they are traceable, verifiable, and complete. A methodology was presented in a recent paper (A Practical Approach to Pipeline System Materials Verification by Lutz and Bubenik) to systematically review and organize records into an auditable framework (i.e. a GIS compatible listing or database). Once operators have completed their systematic records review, they are advised to maximize their investment by performing appropriate on-going records maintenance. An effective records maintenance program will include the following elements to ensure effective management-of-change and continuous quality assurance and quality control. 1. Source documents will be made available to the company engineers and technicians that use the verified information to make everyday integrity and operational decisions (i.e. use a GIS interface to link verified information to the source documents). 2. A controlled process for management-of-change that effectively integrates new construction and replacement records into the existing database. 3. Continuously verify and cross-check pipeline system material properties with… a. …destructive material testing of any pipe that is removed or replaced. b. …in-the-ditch NDE methodologies, such as UT wall-thickness measurements and hardness to yield strength testing. c. …global survey data such as GIS and in-line inspection. 4. A controlled process to resolve records failures that includes the following steps: a. Identify and isolate the data point(s) that are the cause of the records failure. b. Establish a boundary around the potential extents of the records failure. c. Systematically investigate within the established boundary and verify the data discrepancies until the records failure is resolved to a reasonable certainty. By implementing a records maintenance program with these elements, operators will ensure that their records database will be maintained and that the information being relied upon for daily integrity and operational decisions is reliable. Operators will decrease the likelihood of issues resulting from records failures and will ensure their records organization will with stand the scrutiny of future audits and records investigations.

Detecting Changing Balance of Plant Indicators Using Ultrasonic Flowmeters

LEFM (Leading Edge Flow Meter) Ultrasonic Flowmeters have been installed in feedwater pipes in over 68 Pressurized Water Reactor (PWR) and Boiling Water Reactor (BWR) nuclear plants worldwide since the late 1970s. The 8-path, crossed-plane configuration commonly installed in feedwater pipes has been demonstrated through extensive calibrations at nationally certified calibration laboratories to provide feedwater mass flow accuracy better than ±0.3%, regardless of upstream hydraulic conditions. The increased accuracy has been accepted by nuclear regulators in several countries as the basis for an increase in licensed thermal power of nuclear power plants. LEFM technology provides the ability to methodically check all key contributors to flow measurement uncertainty, thereby providing continuous quality assurance of flow data provided by the system and assuring plant operators that the meters remain within their design basis. This paper will describe how LEFM chordal ultrasonic flowmeter operation and data quality can be verified, thereby providing the basis for troubleshooting changing balance of plant indicators. The paper will discuss a methodology for estimating changes in moisture content of the steam produced by steam generators at a PWR and will present a recent case study showing how detailed analysis of on-line feedwater flow data has been used to reconcile readings of other plant instrumentation to identify changes in steam moisture of ±0.1%.