Quality control of purified proteins to improve data quality and reproducibility: results from a large-scale survey

2021 ◽  
Author(s):  
Nick Berrow ◽  
Ario de Marco ◽  
Mario Lebendiker ◽  
Maria Garcia-Alai ◽  
Stefan H. Knauer ◽  
...  
Keyword(s):  
Quality Control ◽  
Data Quality ◽  
Large Scale ◽  
Improve Data Quality ◽  
Large Scale Survey

scholarly journals A fully automated approach for quality control of cancer mutations in the era of high-resolution whole genome sequencing

2021 ◽  
Author(s):  
Jacob Househam ◽  
William CH Cross ◽  
Giulio Caravagna
Keyword(s):  
Quality Control ◽  
Data Quality ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Control Method ◽  
Point Mutations ◽  
Basic Research ◽  
Whole Genome ◽  
Colorectal Cancer Patients

AbstractCancer is a global health issue that places enormous demands on healthcare systems. Basic research, the development of targeted treatments, and the utility of DNA sequencing in clinical settings, have been significantly improved with the introduction of whole genome sequencing. However the broad applications of this technology come with complications. To date there has been very little standardisation in how data quality is assessed, leading to inconsistencies in analyses and disparate conclusions. Manual checking and complex consensus calling strategies often do not scale to large sample numbers, which leads to procedural bottlenecks. To address this issue, we present a quality control method that integrates point mutations, copy numbers, and other metrics into a single quantitative score. We demonstrate its power on 1,065 whole-genomes from a large-scale pan-cancer cohort, and on multi-region data of two colorectal cancer patients. We highlight how our approach significantly improves the generation of cancer mutation data, providing visualisations for cross-referencing with other analyses. Our approach is fully automated, designed to work downstream of any bioinformatic pipeline, and can automatise tool parameterization paving the way for fast computational assessment of data quality in the era of whole genome sequencing.

Data Quality

2011 ◽  
pp. 265-286
Author(s):  
Jeretta Horn Nord ◽  
G. Daryl Nord ◽  
Hongjiang Xu ◽  
Elizabeth S. Myrin
Keyword(s):  
Data Quality ◽  
Large Scale ◽  
Critical Success Factors ◽  
Success Factors ◽  
Actual Performance ◽  
Factors Affecting ◽  
Accounting Information Systems ◽  
Critical Success ◽  
Large Scale Survey ◽  
And Performance

This chapter presents results from a large-scale survey of Australian CPA members regarding data quality. The research investigates and reports major stakeholders’ opinions on the importance of critical success factors affecting data quality and the actual performance on each of those factors. The results reveal whether dissimilarly sized organizations differ in the way they measure the importance and performance of critical success factors for data quality in accounting information systems.

scholarly journals Workflow and Metrics for Image Quality Control in Large-Scale High-Content Screens

2011 ◽  
Vol 17 (2) ◽  
pp. 266-274 ◽  
Author(s):  
Mark-Anthony Bray ◽  
Adam N. Fraser ◽  
Thomas P. Hasaka ◽  
Anne E. Carpenter
Keyword(s):  
Quality Control ◽  
Image Analysis ◽  
Image Quality ◽  
Data Quality ◽  
Large Scale ◽  
Visual Inspection ◽  
Quantitative Information ◽  
Automated Image Analysis ◽  
High Content Screening ◽  
Image Quality Control

Automated microscopes have enabled the unprecedented collection of images at a rate that precludes visual inspection. Automated image analysis is required to identify interesting samples and extract quantitative information for high-content screening (HCS). However, researchers are impeded by the lack of metrics and software tools to identify image-based aberrations that pollute data, limiting experiment quality. The authors have developed and validated approaches to identify those image acquisition artifacts that prevent optimal extraction of knowledge from high-content microscopy experiments. They have implemented these as a versatile, open-source toolbox of algorithms and metrics readily usable by biologists to improve data quality in a wide variety of biological experiments.

Quality Control of Data in a Large-Scale Cancer Register Program

1966 ◽  
Vol 05 (02) ◽  
pp. 67-74 ◽  
Author(s):  
W. I. Lourie ◽  
W. Haenszeland
Keyword(s):  
United States ◽  
Quality Control ◽  
Cancer Patients ◽  
Large Scale ◽  
The United States ◽  
Newly Diagnosed ◽  
Related Data ◽  
Cancer Register ◽  
Independent Review ◽  
End Results

Quality control of data collected in the United States by the Cancer End Results Program utilizing punchcards prepared by participating registries in accordance with a Uniform Punchcard Code is discussed. Existing arrangements decentralize responsibility for editing and related data processing to the local registries with centralization of tabulating and statistical services in the End Results Section, National Cancer Institute. The most recent deck of punchcards represented over 600,000 cancer patients; approximately 50,000 newly diagnosed cases are added annually.Mechanical editing and inspection of punchcards and field audits are the principal tools for quality control. Mechanical editing of the punchcards includes testing for blank entries and detection of in-admissable or inconsistent codes. Highly improbable codes are subjected to special scrutiny. Field audits include the drawing of a 1-10 percent random sample of punchcards submitted by a registry; the charts are .then reabstracted and recoded by a NCI staff member and differences between the punchcard and the results of independent review are noted.

scholarly journals Occurrence and Molecular Variability of Kiwifruit Viruses in Actinidia deliciosa ‘Xuxiang’ in the Shaanxi Province of China

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1309-1318 ◽  
Author(s):  
Lei Zhao ◽  
Wen Yang ◽  
Yuanle Zhang ◽  
Zhanmin Wu ◽  
Qiao-Chun Wang ◽  
...  
Keyword(s):  
Large Scale ◽  
Primary Source ◽  
Potato Virus X ◽  
Shaanxi Province ◽  
Multiple Infection ◽  
First Report ◽  
Molecular Variability ◽  
Large Scale Survey ◽  
Actinidia Spp ◽  
Main Producer

Kiwifruit (Actinidia spp.) is an economically substantial fruit crop with China the main producer. China is the primary source of wild kiwifruit and the largest producer of kiwifruit in terms of both production and planting area, and Shaanxi province is the largest kiwifruit producer in China. Previous studies reported presence of kiwifruit viruses in Actinidia chinensis. In this study, six viruses were identified in kiwifruit ‘Xuxiang’ (A. deliciosa) in Shaanxi, China. The incidence, distribution, and genetic diversity of these viruses were studied. The results showed that Actinidia virus A (AcVA), Actinidia virus B (AcVB), Actinidia chlorotic ringspot-associated virus (AcCRaV), cucumber mosaic virus (CMV), apple stem grooving virus (ASGV), and potato virus X (PVX) were the main viruses infecting Xuxiang kiwifruit in Shaanxi, China. Incidence of the various viruses with both single and multiple infection varied with different kiwifruit-growing counties. For single virus infection, the highest and the lowest numbers of samples infected were about 22 for AcCRaV and 0 for AcVB in Meixian out of 170 samples, 12 for AcVA and 0 for CMV in Zhouzhi out of 120 samples, 10 for AcVA and 0 for AcVB, AcCRaV, ASGV, PVX, and CMV in Yangling out of 70 samples, and 8 for AcCRaV and CMV and 0 for AcVA, AcVB, ASGV, and PVX in Hanzhong out of 80 samples, respectively. Samples which were multiply infected with two or more viruses were also detected. Analysis of the phylogenetic tree of these viruses showed some genetic variability in the AcVA, AcVB, and AcCRaV isolates of Shaanxi kiwifruit. There was no obvious molecular variation in the coat protein genes of ASGV, CMV, and PVX virus isolates from Shaanxi kiwifruit. The present study is the first large-scale survey of kiwifruit viruses in Shaanxi, China. To our knowledge, this is the first report of PVX infecting kiwifruit and the first report of molecular variability of AcVA, AcVB, and AcCRaV. These results provide important data for studying the genetic evolution of AcVA, AcVB, AcCRaV, ASGV, CMV, and PVX.

scholarly journals EEG Data Quality: Determinants and Impact in a Multicenter Study of Children, Adolescents, and Adults with Attention-Deficit/Hyperactivity Disorder (ADHD)

2021 ◽  
Vol 11 (2) ◽  
pp. 214
Author(s):  
Anna Kaiser ◽  
Pascal-M. Aggensteiner ◽  
Martin Holtmann ◽  
Andreas Fallgatter ◽  
Marcel Romanos ◽  
...  
Keyword(s):  
Data Quality ◽  
Large Scale ◽  
Linear Models ◽  
Spectral Power ◽  
Control Group ◽  
Continuous Performance Task ◽  
Related Data ◽  
Eyes Closed ◽  
Eeg Data ◽  
Eyes Open

Electroencephalography (EEG) represents a widely established method for assessing altered and typically developing brain function. However, systematic studies on EEG data quality, its correlates, and consequences are scarce. To address this research gap, the current study focused on the percentage of artifact-free segments after standard EEG pre-processing as a data quality index. We analyzed participant-related and methodological influences, and validity by replicating landmark EEG effects. Further, effects of data quality on spectral power analyses beyond participant-related characteristics were explored. EEG data from a multicenter ADHD-cohort (age range 6 to 45 years), and a non-ADHD school-age control group were analyzed (ntotal = 305). Resting-state data during eyes open, and eyes closed conditions, and task-related data during a cued Continuous Performance Task (CPT) were collected. After pre-processing, general linear models, and stepwise regression models were fitted to the data. We found that EEG data quality was strongly related to demographic characteristics, but not to methodological factors. We were able to replicate maturational, task, and ADHD effects reported in the EEG literature, establishing a link with EEG-landmark effects. Furthermore, we showed that poor data quality significantly increases spectral power beyond effects of maturation and symptom severity. Taken together, the current results indicate that with a careful design and systematic quality control, informative large-scale multicenter trials characterizing neurophysiological mechanisms in neurodevelopmental disorders across the lifespan are feasible. Nevertheless, results are restricted to the limitations reported. Future work will clarify predictive value.

scholarly journals Correcting Citizens’ Misperceptions about non-Western Immigrants: Corrective Information, Interpretations, and Policy Opinions

2020 ◽  
pp. 1-10 ◽  
Author(s):  
Frederik Juhl Jørgensen ◽  
Mathias Osmundsen
Keyword(s):  
Immigration Policy ◽  
Large Scale ◽  
Total Population ◽  
Survey Experiment ◽  
Correct Information ◽  
The Usa ◽  
Large Scale Survey ◽  
Nationally Representative ◽  
Information Change ◽  
Corrective Information

Abstract Can corrective information change citizens’ misperceptions about immigrants and subsequently lead to favorable immigration opinions? While prior studies from the USA document how corrections about the size of minority populations fail to change citizens’ immigration-related opinions, they do not examine how other facts that speak to immigrants’ cultural or economic dependency rates can influence immigration policy opinions. To extend earlier work, we conducted a large-scale survey experiment fielded to a nationally representative sample of Danes. We randomly expose participants to information about non-Western immigrants’ (1) welfare dependency rate, (2) crime rate, and (3) proportion of the total population. We find that participants update their factual beliefs in light of correct information, but reinterpret the information in a highly selective fashion, ultimately failing to change their policy preferences.

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