Wastewater QC workflow in GalaxyTrakr (SSQuAWK) v2

2022 ◽  
Author(s):  
Jasmine Amirzadegan ◽  
tunc.kayikcioglu not provided ◽  
hugh.rand not provided ◽  
Ruth E Timme ◽  
Maria Balkey
Keyword(s):  
Quality Assurance ◽  
Illumina Miseq ◽  
Video Tutorial ◽  
Basic Protocol ◽  
Wastewater Samples ◽  
Set Up ◽  
Quality Assessments ◽  
Sequence Quality

PURPOSE: Step-by-step instructions for checking sequence quality for SARS-CoV-2 wastewater samples using SSQuAWK: SARS - CoV - 2 Sequence Quality Assurance Workflow and Kontraption. The SSQuAWK workflow, implemented in a custom Galaxy instance, will produce quality assessments for raw reads (Illumina MiSeq paired-end fastq files). SCOPE: This protocol covers the following tasks: 1. Set up an account in GalaxyTrakr 2. Create a new history 3. Upload data 4. Execute the SSQuAWK workflow 5. Interpret the results Version history: V1: Basic protocol steps with screenshots V2: Addition of a detailed 12 minute video tutorial

scholarly journals Investigation of Biotransformation Products of p-Methoxymethylamphetamine and Dihydromephedrone in Wastewater by High-Resolution Mass Spectrometry

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 66
Author(s):  
Juliet Kinyua ◽  
Aikaterini K. Psoma ◽  
Nikolaos I. Rousis ◽  
Maria-Christina Nika ◽  
Adrian Covaci ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Wastewater Treatment Plants ◽  
High Resolution Mass Spectrometry ◽  
Transformation Products ◽  
New Psychoactive Substances ◽  
Batch Reactors ◽  
Flight Mass Spectrometry ◽  
Detection And Identification ◽  
Wastewater Samples ◽  
Set Up

There is a paucity of information on biotransformation and stability of new psychoactive substances (NPS) in wastewater. Moreover, the fate of NPS and their transformation products (TPs) in wastewater treatment plants is not well understood. In this study, batch reactors seeded with activated sludge were set up to evaluate biotic, abiotic, and sorption losses of p-methoxymethylamphetamine (PMMA) and dihydromephedrone (DHM) and identify TPs formed during these processes. Detection and identification of all compounds was performed with target and suspect screening approaches using liquid chromatography quadrupole-time-of-flight mass spectrometry. Influent and effluent 24 h composite wastewater samples were collected from Athens from 2014 to 2020. High elimination rates were found for PMMA (80%) and DHM (97%) after a seven-day experiment and degradation appeared to be related to biological activity in the active bioreactor. Ten TPs were identified and the main reactions were O- and N-demethylation, oxidation, and hydroxylation. Some TPs were reported for the first time and some were confirmed by reference standards. Identification of some TPs was enhanced by the use of an in-house retention time prediction model. Mephedrone and some of its previously reported human metabolites were formed from DHM incubation. Retrospective analysis showed that PMMA was the most frequently detected compound.

Operational storm surge forecasting in the Netherlands: developments in the last decade

2005 ◽  
Vol 363 (1831) ◽  
pp. 1441-1453 ◽  
Author(s):  
Martin Verlaan ◽  
Annette Zijderveld ◽  
Hans de Vries ◽  
Jan Kroos
Keyword(s):  
Quality Assurance ◽  
The Netherlands ◽  
Kalman Filtering ◽  
Model Calibration ◽  
Storm Surges ◽  
Operational Environment ◽  
Hydrodynamic Models ◽  
Future Developments ◽  
Set Up ◽  
Storm Surge Forecasting

The accurate forecasting of storm surges is an important issue in the Netherlands. With the emergence of the first numerical hydrodynamic models for surge forecasting at the beginning of the 1980s, new demands and possibilities were raised. This article describes the main phases of the development and the present operational set-up of the Dutch continental shelf model, which is the main hydrodynamic model for storm surges in the Netherlands. It includes a brief discussion of applied data-assimilation techniques, such as Kalman filtering, the model calibration process and some thoughts on quality assurance in an operational environment. After further describing some select recent investigations, the paper concludes with some remarks on future developments in a European context.

scholarly journals Implementation of a quality approach in Human Resources Management within the Moroccan university

2016 ◽  
Vol 6 (7) ◽  
Author(s):  
Rachid ELKACHRADI
Keyword(s):  
Quality Assurance ◽  
Human Resources ◽  
Human Resources Management ◽  
Resources Management ◽  
Higher Education System ◽  
Effectiveness And Efficiency ◽  
Set Up ◽  
Hr Function ◽  
The University ◽  
Quality Approach

The university reform in Morocco introduced principles of quality assurance into the Higher Education System. In this regard, the law 01-00 has set up a device which is mainly articulated around the establishment of a system of accreditation of training and the establishment of a global system of evaluation in the whole system. However, Human Resources Management, the keystone of any change project, is not put at the center of the operationalization of reform projects. In our research, we will look at the factors that impede the operationalization of the principles of quality assurance to improve the effectiveness and efficiency of the HR function. Based on the results obtained within the framework of this exploratory study, we let's propose the key determinants for the implementation of a quality approach in Human Resources Management within Moroccan universities.

scholarly journals Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

Viruses ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 694 ◽  
Author(s):  
Neil T. Parkin ◽  
Santiago Avila-Rios ◽  
David F. Bibby ◽  
Chanson J. Brumme ◽  
Susan H. Eshleman ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Illumina Miseq ◽  
Next Generation ◽  
Sequence Comparisons ◽  
Consensus Sequences ◽  
Drug Resistance Genotyping ◽  
Next Generation Sequencing Ngs ◽  
Sequence Quality ◽  
Average Sequence Identity ◽  
Hiv 1

Next-generation sequencing (NGS) is increasingly used for HIV-1 drug resistance genotyping. NGS methods have the potential for a more sensitive detection of low-abundance variants (LAV) compared to standard Sanger sequencing (SS) methods. A standardized threshold for reporting LAV that generates data comparable to those derived from SS is needed to allow for the comparability of data from laboratories using NGS and SS. Ten HIV-1 specimens were tested in ten laboratories using Illumina MiSeq-based methods. The consensus sequences for each specimen using LAV thresholds of 5%, 10%, 15%, and 20% were compared to each other and to the consensus of the SS sequences (protease 4–99; reverse transcriptase 38–247). The concordance among laboratories’ sequences at different thresholds was evaluated by pairwise sequence comparisons. NGS sequences generated using the 20% threshold were the most similar to the SS consensus (average 99.6% identity, range 96.1–100%), compared to 15% (99.4%, 88.5–100%), 10% (99.2%, 87.4–100%), or 5% (98.5%, 86.4–100%). The average sequence identity between laboratories using thresholds of 20%, 15%, 10%, and 5% was 99.1%, 98.7%, 98.3%, and 97.3%, respectively. Using the 20% threshold, we observed an excellent agreement between NGS and SS, but significant differences at lower thresholds. Understanding how variation in NGS methods influences sequence quality is essential for NGS-based HIV-1 drug resistance genotyping.

An intelligent fixture with a dynamic clamping scheme

2000 ◽  
Vol 214 (3) ◽  
pp. 183-196 ◽  
Author(s):  
A Y C Nee ◽  
A Senthil Kumar ◽  
Z J Tao
Keyword(s):  
Quality Assurance ◽  
Control Strategy ◽  
Sensory Feedback ◽  
Design Procedure ◽  
Integrated Approach ◽  
Fixture Design ◽  
On Line ◽  
Thin Walled ◽  
Set Up ◽  
Dynamic Clamps

Both proper fixture design and optimum fixturing execution are crucial to workpiece quality assurance in manufacturing. This paper deals with an integrated approach to fixturing problems and, in particular, a ‘live’ fixture with sensory feedback and on-line fixturing control strategy to perform an optimal fixturing operation. The framework of an integrated fixture design procedure is first presented. The functions and structure of an intelligent fixture are proposed. The prototype intelligent fixture with dynamic clamps capable of delivering accurate but varying clamping intensity is developed. This novel set-up has been proven to be effective for workpiece quality improvement and productivity enhancement through machining experiments on thin-walled workpieces.

scholarly journals PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens

2017 ◽  
Author(s):  
Philipp N. Spahn ◽  
Tyler Bath ◽  
Ryan J. Weiss ◽  
Jihoon Kim ◽  
Jeffrey D. Esko ◽  
...  
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Sequencing Data ◽  
Bioinformatic Tools ◽  
Link Type ◽  
Screening Experiments ◽  
Independent Analysis ◽  
Wide Range ◽  
Set Up ◽  
Sequence Quality

AbstractBackgroundLarge-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise.ResultsTo make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots.ConclusionsPinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions, documentation and test datasets. The source code is available at https://github.com/LewisLabUCSD/PinAPL-Py

scholarly journals Clinical implementation and initial experience with a 1.5 Tesla MR-linac for MR-guided radiotherapy for gynecologic cancer: An R-IDEAL stage 1/2a first in humans/feasibility study of new technology implementation

2021 ◽  
Author(s):  
David S Lakomy ◽  
Jinzhong Yang ◽  
Sastry Vedam ◽  
Jihong Wang ◽  
Belinda Lee ◽  
...  
Keyword(s):  
Quality Assurance ◽  
Technology Implementation ◽  
New Technology ◽  
Gynecologic Cancer ◽  
Dose Calculations ◽  
Gynecologic Malignancies ◽  
Clinical Implementation ◽  
Set Up ◽  
Stage 1 ◽  
Accumulated Dose

Purpose: Magnetic resonance imaging-guided linear accelerator systems (MR-linacs) can facilitate the daily adaptation of radiotherapy plans. Here, we report our early clinical experience using an MR-linac for adaptive radiotherapy of gynecologic malignancies. Methods and Materials: Treatments were planned with an Elekta Monaco v5.4.01 and delivered by a 1.5 Tesla Elekta Unity MR-linac. The system offers a choice of daily adaptation based on either position (ATP) or shape (ATS) of the tumor and surrounding normal structures. The ATS approach has the option of manually editing the contours of tumors and surrounding normal structures before the plan is adapted. Here we documented the duration of each treatment fraction; set-up variability (assessed by isocenter shifts in each plan) between fractions; and, for quality assurance, calculated the percentage of plans meeting the ;γ-criterion of 3%/3-mm distance to agreement. Deformable accumulated dose calculations were used to compare ATP plans with reference dose plans. Results: Of the 10 patients treated with 90 fractions on the MR-linac, most received boost doses to recurrence in nodes or isolated tumors. Each treatment fraction lasted a median 32 minutes; fractions were shorter with ATP than with ATS (30 min vs 42 min, P<0.0001). The γ-criterion for all fraction plans exceeded >90% (median 99.9%, range 92.4%-100%), i.e., all plans passed quality assurance testing. The average extent of isocenter shift was <0.5 cm in each axis. The accumulated dose to the gross tumor volume was within 10% of the reference plan for all ATP cases. Accumulated doses for lesions in the pelvic periphery were within 1% of the reference plan as opposed to -5.8% to -9.6% for central tumors. Conclusions: The MR-linac is a reliable and clinically feasible tool for treating patients with gynecologic cancer.

scholarly journals Eukaryotic Viruses in Wastewater Samples from the United States

2009 ◽  
Vol 75 (5) ◽  
pp. 1402-1409 ◽  
Author(s):  
Erin M. Symonds ◽  
Dale W. Griffin ◽  
Mya Breitbart
Keyword(s):  
United States ◽  
Water Quality ◽  
The United States ◽  
Fecal Pollution ◽  
Fecal Matter ◽  
Pathogenic Viruses ◽  
Wastewater Samples ◽  
Quality Assessments ◽  
Final Effluent ◽  
Unknown Sequence

ABSTRACT Human fecal matter contains a large number of viruses, and current bacterial indicators used for monitoring water quality do not correlate with the presence of pathogenic viruses. Adenoviruses and enteroviruses have often been used to identify fecal pollution in the environment; however, other viruses shed in fecal matter may more accurately detect fecal pollution. The purpose of this study was to develop a baseline understanding of the types of viruses found in raw sewage. PCR was used to detect adenoviruses, enteroviruses, hepatitis B viruses, herpesviruses, morbilliviruses, noroviruses, papillomaviruses, picobirnaviruses, reoviruses, and rotaviruses in raw sewage collected throughout the United States. Adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples and 25% and 33% of final effluent samples, respectively. Enteroviruses and noroviruses were detected in 75% and 58% of raw sewage samples, respectively, and both viral groups were found in 8% of final effluent samples. This study showed that adenoviruses, enteroviruses, noroviruses, and picobirnaviruses are widespread in raw sewage. Since adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples, they are potential markers of fecal contamination. Additionally, this research uncovered previously unknown sequence diversity in human picobirnaviruses. This baseline understanding of viruses in raw sewage will enable educated decisions to be made regarding the use of different viruses in water quality assessments.

Multicenter trial for the set-up of a MRI quality assurance programme

2004 ◽  
Vol 22 (1) ◽  
pp. 93-101 ◽  
Author(s):  
P. Colombo ◽  
A. Baldassarri ◽  
M. Del Corona ◽  
L. Mascaro ◽  
S. Strocchi
Keyword(s):  
Quality Assurance ◽  
Multicenter Trial ◽  
Quality Assurance Programme ◽  
Set Up
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