Announcement—guidance document for acquiring reliable data in ecological restoration projects

The Laurentian Great Lakes are undergoing intensive ecological restoration in Canada and the United States. In the United States, an interagency committee was formed to facilitate implementation of quality practices for federally funded restoration projects in the Great Lakes basin. The Committee's responsibilities include developing a guidance document that will provide a common approach to the application of quality assurance and quality control (QA/QC) practices for restoration projects. The document will serve as a “how‐to” guide for ensuring data quality during each aspect of ecological restoration projects. In addition, the document will provide suggestions on linking QA/QC data with the routine project data and hints on creating detailed supporting documentation. Finally, the document will advocate integrating all components of the project, including QA/QC applications, into an overarching decision‐support framework. The guidance document is expected to be released by the U.S. EPA Great Lakes National Program Office in 2017.     

Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies

Background

Quality assurance (QA) and quality control (QC) are two quality management processes that are integral to the success of metabolomics including their application for the acquisition of high quality data in any high-throughput analytical chemistry laboratory. QA defines all the planned and systematic activities implemented before samples are collected, to provide confidence that a subsequent analytical process will fulfil predetermined requirements for quality. QC can be defined as the operational techniques and activities used to measure and report these quality requirements after data acquisition.

Aim of review

This tutorial review will guide the reader through the use of system suitability and QC samples, why these samples should be applied and how the quality of data can be reported.

Key scientific concepts of review

System suitability samples are applied to assess the operation and lack of contamination of the analytical platform prior to sample analysis. Isotopically-labelled internal standards are applied to assess system stability for each sample analysed. Pooled QC samples are applied to condition the analytical platform, perform intra-study reproducibility measurements (QC) and to correct mathematically for systematic errors. Standard reference materials and long-term reference QC samples are applied for inter-study and inter-laboratory assessment of data.

     

Quality assurance and quality control processes: summary of a metabolomics community questionnaire

Introduction

The Metabolomics Society Data Quality Task Group (DQTG) developed a questionnaire regarding quality assurance (QA) and quality control (QC) to provide baseline information about current QA and QC practices applied in the international metabolomics community.

Objectives

The DQTG has a long-term goal of promoting robust QA and QC in the metabolomics community through increased awareness via communication, outreach and education, and through the promotion of best working practices. An assessment of current QA and QC practices will serve as a foundation for future activities and development of appropriate guidelines.

Method

QA was defined as the set of procedures that are performed in advance of analysis of samples and that are used to improve data quality. QC was defined as the set of activities that a laboratory does during or immediately after analysis that are applied to demonstrate the quality of project data. A questionnaire was developed that included 70 questions covering demographic information, QA approaches and QC approaches and allowed all respondents to answer a subset or all of the questions.

Result

The DQTG questionnaire received 97 individual responses from 84 institutions in all fields of metabolomics covering NMR, LC-MS, GC-MS, and other analytical technologies.

Conclusion

There was a vast range of responses concerning the use of QA and QC approaches that indicated the limited availability of suitable training, lack of Standard Operating Procedures (SOPs) to review and make decisions on quality, and limited use of standard reference materials (SRMs) as QC materials. The DQTG QA/QC questionnaire has for the first time demonstrated that QA and QC usage is not uniform across metabolomics laboratories. Here we present recommendations on how to address the issues concerning QA and QC measurements and reporting in metabolomics.

     

Pollen monitoring: minimum requirements and reproducibility of analysis

Training, quality assurance (QA) and quality control (QC) play an important role in building competence in monitoring and research in aerobiology. The main goals of this paper were to: (a) formulate an updated Minimum Requirements Report for pollen monitoring; (b) carry out a pilot QC exercise of staff involved in pollen counting from various national networks in order to examine between analysts reproducibility and develop a methodology that can be used in future QC exercises. A questionnaire survey was sent to coordinators of participating pollen monitoring networks. In addition, a total of 45 technicians from 15 European countries participated in the pilot QC exercise. All technicians were instructed to analyse two slides containing the following pollen types: (a) Poaceae and Betula pollen grains in the north of Europe; (b) Poaceae and Olea pollen grains in the south of Europe. Minimum Recommendations were produced based on the results of the questionnaire survey, published literature, and the outcomes of a workshop. In the QC exercise, it was noticed that technicians who followed the Minimum Recommendations and examined at least 10 % of the slide tended to have better indicators of precision and accuracy than those technicians who did not follow the Minimum Recommendations. The proposed Minimum Recommendations will help to improve the quality of scientific work, particularly for those who are considering the setting up of new monitoring sites. The results of the pilot QC exercise will help to develop a methodology that can be used again in the future, thereby ensuring data quality.     

High-throughput selected reaction monitoring liquid chromatography-mass spectrometry determination of methylphenidate and its major metabolite,ritalinic acid,in rat plasma employing monolithic columns

This work presents a high-throughput selected reaction monitoring (SRM) LC-MS method for the determination of methylphenidate (MPH), a central nervous stimulant, and its de-esterified metabolite, ritalinic acid (RA) in rat plasma samples. A separation of these two compounds was achieved in 15 s by employing a 3.5-ml/min flow-rate, a porous monolithic column and a TurboIonSpray source compatible with relatively high flow-rates. In addition, a relatively fast autosampler and a new data acquisition system resulted in a time lag of less than 17 s between consecutive injections. Overall, 768 protein-precipitated rat plasma samples (eight 96-well plates) containing both MPH and RA were analyzed within 3 h and 45 min. The partial method validation described in this report included an assessment of linearity, intra and inter-assay precision and accuracy, and method robustness. Deuterated internal standards for the target compounds, d(3)-MPH and d(5)-RA, were employed. The calibration curves ranged from 0.1 to 50 ng/ml for MPH and from 0.5 to 50 ng/ml for RA. The limit of quantification (LOQ) for MPH and RA was 0.1 and 0.5 ng/ml, respectively. For both analytes, the intra- and inter-assay precision (relative standard deviation, % C.V.) and accuracy (relative error) did not exceed 15% for the quality control samples (QCs) QC1, QC2 or QC3 (0.3, 1.5 and 40 ng/ml for MPH and 0.15, 15 and 40 ng/ml for RA) for either analyte and did not exceed 20% at the lower limit of quantitation (LOQ) level. No carry-over from the autosampler was detected. The retention times remained constant throughout the experiment. Baseline resolution of MPH and RA was consistently observed throughout the plates analyzed. The described method demonstrates the feasibility for employing monolithic HPLC columns to effect rapid bioanalytical SRM LC-MS analysis of representative biological samples.     

A review of dose calculation approaches with cone beam CT in photon and proton therapy

Background and purposeThe use of cone beam computed tomography (CBCT) for performing dose calculations in radiation therapy has been widely investigated as it could provide a quantitative analysis of the dosimetric impact of changes in patients during the treatment. The aim of this review was to classify different techniques adopted to perform CBCT dose calculation and to report their dosimetric accuracy with respect to the metrics used.Methods and materialsA literature search was carried out in PubMed and ScienceDirect databases, based upon the following keywords: “cone beam computed tomography”, “CBCT”, “cone beam CT”, “dose calculation”, “accuracy”. Sixty-nine peer-reviewed relevant articles were included in this review: thirty-one patient studies, fifteen phantom studies and twenty-three patient & phantom studies. Most studies were found to have focused on head and neck, lung and prostate cancers.ResultsThe techniques adopted to perform CBCT dose calculation have been grouped in six categories labelled as (1) pCT calibration, (2) CBCT calibration, (3) HU override, (4) Deformable image registration, (5) Dose deformation, and (6) Combined techniques. Differences between CBCT dose and reference dose were reported both for target volumes and OARs.ConclusionsA comparison among the available techniques for CBCT dose calculations is challenging as many variables are involved. Therefore, a set of reporting standards is recommended to enable meaningful comparisons among different studies. The accuracy of the results was strongly dependent on the image quality, regardless of the methods used, highlighting the need for dose validation and quality assurance standards.     

A 3-year experience of quality control and quality assurance in the multisite delivery of a lymphocyte-based cellular therapy for renal cell carcinoma

Autolymphocyte therapy (ALT) is outpatient-based adoptive immunotherapy using ex vivo-activated memory T-cells. To support the safe and reproducible delivery of ALT at three cell processing facilities (Boston, MA; Atlanta, GA; Orange, CA) we created a comprehensive quality assurance/quality control program compliant with recent FDA guidance relevant to activated lymphocytes and somatic cell therapies. Each facility performed extensive QC testing to ensure sterility, viability, and proper cell yield. Additonally, several QC tests were performed at Cellocr's centralized reference laboratory to monitor cell potency and identity of the ex vivo-processed lymphocytes. We report here the successful implementation of this QA/QC program for ALT which has resulted in the safe preparation and delivery of cell infusion products amounting to over 3600 treatments at seven clinical sites nationwide. We believe this program will serve as a model for other cellular therapies.     

pseudoQC: A Regression‐Based Simulation Software for Correction and Normalization of Complex Metabolomics and Proteomics Datasets

Various types of unwanted and uncontrollable signal variations in MS‐based metabolomics and proteomics datasets severely disturb the accuracies of metabolite and protein profiling. Therefore, pooled quality control (QC) samples are often employed in quality management processes, which are indispensable to the success of metabolomics and proteomics experiments, especially in high‐throughput cases and long‐term projects. However, data consistency and QC sample stability are still difficult to guarantee because of the experimental operation complexity and differences between experimenters. To make things worse, numerous proteomics projects do not take QC samples into consideration at the beginning of experimental design. Herein, a powerful and interactive web‐based software, named pseudoQC, is presented to simulate QC sample data for actual metabolomics and proteomics datasets using four different machine learning‐based regression methods. The simulated data are used for correction and normalization of the two published datasets, and the obtained results suggest that nonlinear regression methods perform better than linear ones. Additionally, the above software is available as a web‐based graphical user interface and can be utilized by scientists without a bioinformatics background. pseudoQC is open‐source software and freely available at https://www.omicsolution.org/wukong/pseudoQC/ .     

Quantitative analysis of Variolin analog (PM01218) in mouse and rat plasma by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry

PM01218 is a novel marine-derived alkaloid and has shown potent growth inhibitory activity against several human cancer cell lines. A rapid and sensitive high performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) method was developed and validated to quantify PM01218 in mouse and rat plasma. The lower limit of quantitation (LLOQ) was 0.05 ng/mL. The calibration curve was linear from 0.05 to 100 ng/mL (R(2)>0.999). The assay was specifically based on the multiple reaction monitoring (MRM) transitions at m/z 278.4-->184.2, no endogenous material interfaced with the analysis of PM01218 and its internal standard from blank mouse and rat plasma. The mean intra- and inter-day assay accuracy remained below 15 and 8%, respectively, for all calibration standards and QC samples. The intra- and inter-day assay precision was less than 12.8 and 8.5% for all QC levels, respectively. The utility of the assay was demonstrated by pharmacokinetics studies of i.v. (bolus) PM01218 on SD rats.     

High-throughput sample preparation procedures for the quantitation of a new bone integrin alpha(nu)beta(3) antagonist in human plasma and urine using liquid chromatography-tandem mass spectrometry

High throughput LC-MS/MS assays to quantitate a new alpha(nu)beta(3) bone integrin antagonist (I) in human plasma and urine have been developed using instruments programmed to automate sample preparation procedures. Packard liquid handling system-MultiPROBE II EX was programmed for preparing calibration standards in control plasma and urine, acidifying all standards, quality control (QC), and clinical samples with necessary dilutions, and adding the internal standard to the acidified samples. TOMTEC Quadra 96 was programmed to perform the solid phase extraction (SPE) process on a 3M 96-well mixed phase cation standard density (MPC-SD) plate to isolate the analytes from the sample matrix. The extract collected from both types of matrices was directly injected into reversed-phase LC-MS/MS system with a Turbo Ion Spray (TIS) interface in the positive ionization mode. The plasma and urine assays have the calibration range of 0.5-1500 and 2-6000 ng/mL, respectively. Validation of the automated and the manual plasma assays showed that application of MultiPROBE II to sample preparation gave comparable accuracy and precision. Overall, the automated approaches with minimum manual intervention enhanced the throughput of sample preparation.     

Standardization of a broth microdilution susceptibility testing method to determine minimum inhibitory concentrations of aquatic bacteria

A multiple laboratory study was conducted in accordance with the standards established by the Clinical and Laboratory Standards Institute (CLSI), formerly the National Committee for Clinical Laboratory Standards (NCCLS), for the development of quality control (QC) ranges using dilution antimicrobial susceptibility testing methods for bacterial isolates from aquatic animal species. QC ranges were established for Escherichia coli ATCC 25922 and Aeromonas salmonicida subsp. salmonicida ATCC 33658 when testing at 22, 28 and 35 degrees C (E. coli only) for 10 different antimicrobial agents (ampicillin, enrofloxacin, erythromycin, florfenicol, flumequine, gentamicin, ormetoprim/sulfadimethoxine, oxolinic acid, oxytetracycline and trimethoprim/sulfamethoxazole). Minimum inhibitory concentration (MIC) QC ranges were determined using dry- and frozen-form 96-well plates and cation-adjusted Mueller-Hinton broth. These QC ranges were accepted by the CLSI/NCCLS Subcommittee on Veterinary Antimicrobial Susceptibility Testing in January 2004. This broth microdilution testing method represents the first standardized method for determining MICs of bacterial isolates whose preferred growth temperatures are below 35 degrees C. Methods and QC ranges defined in this study will enable aquatic animal disease researchers to reliably compare quantitative susceptibility testing data between laboratories, and will be used to ensure both precision and inter-laboratory harmonization.     

A repeated measures approach to pooled and calibrated biomarker data

Participant-level meta-analysis across multiple studies increases the sample size for pooled analyses, thereby improving precision in effect estimates and enabling subgroup analyses. For analyses involving biomarker measurements as an exposure of interest, investigators must first calibrate the data to address measurement variability arising from usage of different laboratories and/or assays. In practice, the calibration process involves reassaying a random subset of biospecimens from each study at a central laboratory and fitting models that relate the study-specific “local” and central laboratory measurements. Previous work in this area treats the calibration process from the perspective of measurement error techniques and imputes the estimated central laboratory value among individuals with only a local laboratory measurement. In this work, we propose a repeated measures method to calibrate biomarker measurements pooled from multiple studies with study-specific calibration subsets. We account for correlation between measurements made on the same person and between measurements made at the same laboratory. We demonstrate that the repeated measures approach provides valid inference, and compare it to existing calibration approaches grounded in measurement error techniques in an example describing the association between circulating vitamin D and stroke.     

Simultaneous quantitation of 7-methyl- and O6-methylguanine adducts in DNA by liquid chromatography-positive electrospray tandem mass spectrometry

A methodology has been developed and validated for the simultaneous quantitation of O6-methyl- and 7-methylguanine in DNA isolated from in vitro exposure to the model alkylating agents: N-methyl-N-nitrosourea (MNU) and methyl methane sulfonate (MMS). After exposure, DNA was isolated and directly hydrolyzed under acid conditions to hydrolytes containing DNA bases (modified and unmodified). The hydrolytes were used for direct O6- and 7-methylguanine quantitation using a rapid and selective liquid chromatography-electrospray tandem mass spectrometry (LC/ESI-MS/MS). The lower limits of quantitation for O6-methyl- and 7-methylguanine were 75.8 and 151.5 fmol, respectively. Linearity of the calibration curve was greater than 0.999 from 75.8 to 151,600.0 fmol for O6-methylguanine and 0.999 from 151.5 to 303,200.0 fmol for 7-methylguanine. The intra-day assay precision relative standard deviation (R.S.D.) values for O6-methylguanine for quality control (QC) samples were < or =9.2% with accuracy values ranging from 90.8 to 118%, and for 7-methylguanine the R.S.D. values for QC samples were < or =11%, with accuracy values ranging from 92.9 to 119%. The inter-day assay precision (R.S.D.) values for O6-methylguanine QC samples were < or =7.9% with accuracy values ranging from 94.5 to 116%, and for 7-methylguanine QC samples were < or =7.1% with accuracy values ranging from 95.2 to 110.2%. This method was used for simultaneous determination of the levels of 7-methyl- and O6-methylguanine in DNA acidic hydrolytes present in a series of incubations from salmon testis DNA treated with either MNU or MMS.     

DoRGaN: Development of Quality Assurance and Quality Control Systems for High Dose Rate Brachytherapy Based on GaN Dosimetry Probes

Background

Safe High Dose Rate Brachytherapy (HDR-BT) requires quality assurance/quality control (QA/QC) according to IPEM and ESTRO recommendations. Recent advances in real-time dosimetry and related developments of QA, QC and in vivo dosimetry (IVD) systems have offered new possibilities for effective independent treatment verification, and thus for improving the patient safety.

A candidate vegetation index of biological integrity based on species dominance and habitat fidelity

Indices of biological integrity of wetlands based on vascular plants (VIBIs) have been developed in many areas of the USA and are used in some states to make critical management decisions. An underlying concept of all VIBIs is that they respond negatively to disturbance. The Ohio VIBI (OVIBI) is calculated from 10 metrics, which are different for each wetland vegetation class. We present a candidate vegetation index of biotic integrity based on floristic quality (VIBI-FQ) that requires only two metrics to calculate an overall score regardless of vegetation class. These metrics focus equally on the critical ecosystem elements of diversity and dominance as related to a species’ degree of fidelity to habitat requirements. The indices were highly correlated but varied among vegetation classes. Both indices responded negatively with a published index of wetland disturbance in 261 Ohio wetlands. Unlike VIBI-FQ, however, errors in classifying wetland vegetation may lead to errors in calculating OVIBI scores. This is especially critical when assessing the ecological condition of rapidly developing ecosystems typically associated with wetland restoration and creation projects. Compared to OVIBI, the VIBI-FQ requires less field work, is much simpler to calculate and interpret, and can potentially be applied to all habitat types. This candidate index, which has been “standardized” across habitats, would make it easier to prioritize funding because it would score the “best” and “worst” of all habitats appropriately and allow for objective comparison across different vegetation classes.     

Global metabolic profiling analysis on human urine by UPLC-TOFMS: issues and method validation in nutritional metabolomics

Optimisation and method validation was assessed here for metabolic profiling analysis of urine samples using UPLC-TOFMS. A longer run time of 31 min revealed greater reproducibility, and the higher number of variables was identified as compared to shortened run times (10 and 26 min). We have also implemented two QC urine samples enabling the assessment of the quality and reproducibility of the data generated during the whole analytical workflow (retention time drift, mass precision and fluctuation of the ion responses over time). Based on the QC data, suitable standards for ensuring consistent analytical results for metabolomics applications using the UPLC-MS techniques are recommended.     

Assemblage diversity,cell density and within-slide variability: Implications for quality assurance/quality control and uncertainty assessment in diatom-based monitoring

This study was undertaken to evaluate the variability associated with the microscope analysis step in the application of the Eastern Canadian Diatom Index (IDEC: Indice Diatomées de l’Est du Canada), with the general objective of developing a suitable quality assurance/quality control (QA/QC) program for this biological index. For this purpose, we estimated within-slide variability (replicability) and inter-analysts variability (reproducibility), as a function of diatom assemblage diversity and slide cell density. Overall, our results show that variability associated with diatom assemblage characterization is low, which ensures that IDEC scores reflect environmental changes rather than variability at the microscope analysis step. The main recommendations ensuing from this study are (for the IDEC in particular but also for diatom-based monitoring in general):

• (1)An error term of ±2 IDEC units corresponding to the within-slide variability (replicability) should accompany all reported IDEC scores.
• (2)A deviation of ±3 points from the audit's IDEC scores should be considered as an acceptable difference. Considering the above-mentioned estimated error term of ±2 associated with all IDEC scores, an overall deviation of 7 would still be satisfactory.
• (3)Samples showing low diversity (Hill's N2 ≤5) should automatically be submitted for QA/QC.
• (4)A Bray–Curtis (analyst vs audit) similarity of ≥60% should also be included as a QA/QC criterion, and should increase to ≥70% for poorly diversified assemblages (Hill's N2 ≤5).
• (5)A diatom valve density of ≤15 per field of view should be targeted in order to reduce variability at the enumeration step.

The results of this study illustrate how a relatively simple and straightforward approach to QA/QC can greatly strengthen the reliability of ecological inferences from an index based on a group of organisms with a high taxonomical diversity. It also highlights the importance of regular communication between analysts in order to maintain a high degree of concordance within taxonomical identification.     

Determination of urinary zinc,chromium, and copper in steel production workers

The aim of our investigation was to determine the concentrations of Cu, Zn, and Cr in urine samples under routine clinical laboratory conditions. To asses the reliability of these methods, critical factors such as detection limit(s), calibration range(s), cost, accuracy, and precision were studied. Our method was employed for the quantitative determination of zinc, chromium, and copper in urine samples from steel production and quality control (QC) workers and healthy unexposed controls. After pretreatment with acids, the samples were digested via a microwave oven. Zinc was determined by flame absorption spectrophotometry (FAAS), whereas chromium and copper were determined by a graphite-furnace atomic absorption spectrophotometry (GFAAS). Our results indicate that urinary zinc, chromium, and copper levels of the exposed workers are significantly higher than those of the controls. The possibility that these metals are involved in the etiology of diseases is discussed and recommendations are made to improve workplace ventilation and industrial hygiene practices.     

High-precision quality assurance of robotic couches with six degrees of freedom

A robotic couch capable of six degrees of freedom (6-DoF) of motion was introduced for state-of-the-art radiation therapy. Patient treatment requires precise quality assurance (QA) of 6-DoF. Unfortunately, conventional methods do not provide the requisite accuracy and precision. Therefore, we developed a high-precision automated QA system using a visual tracking system (VTS). The VTS comprises four motion-sensing cameras, a cube with infrared reflective markers. To acquire data in treatment room coordinates, a transformation matrix from VTS coordinates to treatment room coordinates was determined.The mean error and standard deviation of linear and rotational motions, as well as couch sagging were analyzed from continuously acquired images in the moving couch. The accuracy of VTS was 0.024 mm deviation for the sinusoidal motion, and the accuracy of the transformation matrix was 0.02 mm. In a cross-comparison, the difference between Laser Tracker (FARO) measurements was 0.14 ± 0.12 mm for translation and 0.032 ± 0.026° on average for yaw rotation. The new system provides QA of yaw, pitch and roll motion as well as sagging of the couch and sub-millimeter/degree accuracy together with precision.