Novel Analytic Criteria and Effective Plate Designs for Quality Control in Genome-Scale RNAi Screens

One of the most fundamental challenges in genome-wide RNA interference (RNAi) screens is to glean biological significance from mounds of data, which relies on the development and adoption of appropriate analytic methods and designs for quality control (QC) and hit selection. Currently, a Z-factor-based QC criterion is widely used to evaluate data quality. However, this criterion cannot take into account the fact that different positive controls may have different effect sizes and leads to inconsistent QC results in experiments with 2 or more positive controls with different effect sizes. In this study, based on a recently proposed parameter, strictly standardized mean difference (SSMD), novel QC criteria are constructed for evaluating data quality in genome-wide RNAi screens. Two good features of these novel criteria are: (1) SSMD has both clear original and probability meanings for evaluating the differentiation between positive and negative controls and hence the SSMD-based QC criteria have a solid probabilistic and statistical basis, and (2) these QC criteria obtain consistent QC results for multiple positive controls with different effect sizes. In addition, I propose multiple plate designs and the guidelines for using them in genome-wide RNAi screens. Finally, I provide strategies for using the SSMD-based QC criteria and effective plate design together to improve data quality. The novel SSMD-based QC criteria, effective plate designs, and related guidelines and strategies may greatly help to obtain high quality of data in genome-wide RNAi screens. ( Journal of Biomolecular Screening 2008:363-377)

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Integrating Experimental and Analytic Approaches to Improve Data Quality in Genome-wide RNAi Screens

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057108317145 ◽

2008 ◽

Vol 13 (5) ◽

pp. 378-389 ◽

Cited By ~ 26

Author(s):

Xiaohua Douglas Zhang ◽

Amy S. Espeseth ◽

Eric N. Johnson ◽

Jayne Chin ◽

Adam Gates ◽

...

Keyword(s):

Data Quality ◽

High Throughput Screening ◽

Daily Practice ◽

Systematic Errors ◽

Quality Of Data ◽

Improve Data Quality ◽

Research Journal ◽

Genome Wide ◽

Assess Data Quality

RNA interference (RNAi) not only plays an important role in drug discovery but can also be developed directly into drugs. RNAi high-throughput screening (HTS) biotechnology allows us to conduct genome-wide RNAi research. A central challenge in genome-wide RNAi research is to integrate both experimental and computational approaches to obtain high quality RNAi HTS assays. Based on our daily practice in RNAi HTS experiments, we propose the implementation of 3 experimental and analytic processes to improve the quality of data from RNAi HTS biotechnology: (1) select effective biological controls; (2) adopt appropriate plate designs to display and/or adjust for systematic errors of measurement; and (3) use effective analytic metrics to assess data quality. The applications in 5 real RNAi HTS experiments demonstrate the effectiveness of integrating these processes to improve data quality. Due to the effectiveness in improving data quality in RNAi HTS experiments, the methods and guidelines contained in the 3 experimental and analytic processes are likely to have broad utility in genome-wide RNAi research. ( Journal of Biomolecular Screening 2008:378-389)

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Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem bisulfite and oxidative bisulfite Illumina microarrays

Epigenomics ◽

10.2217/epi-2021-0490 ◽

2022 ◽

Author(s):

Ze Zhang ◽

Min Kyung Lee ◽

Laurent Perreard ◽

Karl T Kelsey ◽

Brock C Christensen ◽

...

Keyword(s):

Quality Control ◽

Data Quality ◽

Dna Extraction ◽

Data Preprocessing ◽

Information Loss ◽

Call Rate ◽

Genome Wide ◽

Nucleotide Resolution

Aim: Tandem bisulfite (BS) and oxidative bisulfite (oxBS) conversion on DNA followed by hybridization to Infinium HumanMethylation BeadChips allows nucleotide resolution of 5-hydroxymethylcytosine genome-wide. Here, the authors compared data quality acquired from BS-treated and oxBS-treated samples. Materials & methods: Raw BeadArray data from 417 pairs of samples across 12 independent datasets were included in the study. Probe call rates were compared between paired BS and oxBS treatments controlling for technical variables. Results: oxBS-treated samples had a significantly lower call-rate. Among technical variables, DNA-specific extraction kits performed better with higher call rates after oxBS conversion. Conclusion: The authors emphasize the importance of quality control during oxBS conversion to minimize information loss and recommend using a DNA-specific extraction kit for DNA extraction and an oxBSQC package for data preprocessing.

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Designing Information Product (IP) Maps On the Process of Data Processing and Academic Information

International Journal of New Media Technology ◽

10.31937/ijnmt.v4i1.534 ◽

2017 ◽

Vol 4 (1) ◽

pp. 25-31 ◽

Cited By ~ 1

Author(s):

Diana Effendi

Keyword(s):

Data Quality ◽

Data Management ◽

Information Management ◽

Information Quality ◽

Quality Data ◽

Management Approach ◽

Quality Of Data ◽

Information Product ◽

Academic Activities

Information Product Approach (IP Approach) is an information management approach. It can be used to manage product information and data quality analysis. IP-Map can be used by organizations to facilitate the management of knowledge in collecting, storing, maintaining, and using the data in an organized. The process of data management of academic activities in X University has not yet used the IP approach. X University has not given attention to the management of information quality of its. During this time X University just concern to system applications used to support the automation of data management in the process of academic activities. IP-Map that made in this paper can be used as a basis for analyzing the quality of data and information. By the IP-MAP, X University is expected to know which parts of the process that need improvement in the quality of data and information management. Index term: IP Approach, IP-Map, information quality, data quality. REFERENCES[1] H. Zhu, S. Madnick, Y. Lee, and R. Wang, “Data and Information Quality Research: Its Evolution and Future,” Working Paper, MIT, USA, 2012.[2] Lee, Yang W; at al, Journey To Data Quality, MIT Press: Cambridge, 2006.[3] L. Al-Hakim, Information Quality Management: Theory and Applications. Idea Group Inc (IGI), 2007.[4] “Access : A semiotic information quality framework: development and comparative analysis : Journal ofInformation Technology.” [Online]. Available: http://www.palgravejournals.com/jit/journal/v20/n2/full/2000038a.html. [Accessed: 18-Sep-2015].[5] Effendi, Diana, Pengukuran Dan Perbaikan Kualitas Data Dan Informasi Di Perguruan Tinggi MenggunakanCALDEA Dan EVAMECAL (Studi Kasus X University), Proceeding Seminar Nasional RESASTEK, 2012, pp.TIG.1-TI-G.6.

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Data Assimilation and Ocean Data Quality Control Upgrades in SWAFS

10.21236/ada626595 ◽

2002 ◽

Author(s):

Clark Rowley ◽

James Cummings

Keyword(s):

Quality Control ◽

Data Assimilation ◽

Data Quality ◽

Data Quality Control

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Response Behavior and Quality of Survey Data: Comparing Elderly Respondents in Institutions and Private Households

Sociological Methods & Research ◽

10.1177/0049124121995534 ◽

2021 ◽

pp. 004912412199553

Author(s):

Jan-Lucas Schanze

Keyword(s):

Data Quality ◽

The Elderly ◽

Response Behavior ◽

Quality Of Data ◽

Social Surveys ◽

Private Households ◽

Confounding Variables ◽

Health Related ◽

Survey Interviews

An increasing age of respondents and cognitive impairment are usual suspects for increasing difficulties in survey interviews and a decreasing data quality. This is why survey researchers tend to label residents in retirement and nursing homes as hard-to-interview and exclude them from most social surveys. In this article, I examine to what extent this label is justified and whether quality of data collected among residents in institutions for the elderly really differs from data collected within private households. For this purpose, I analyze the response behavior and quality indicators in three waves of Survey of Health, Ageing and Retirement in Europe. To control for confounding variables, I use propensity score matching to identify respondents in private households who share similar characteristics with institutionalized residents. My results confirm that most indicators of response behavior and data quality are worse in institutions compared to private households. However, when controlling for sociodemographic and health-related variables, differences get very small. These results suggest the importance of health for the data quality irrespective of the housing situation.

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Nanocarriers of Miconazole or Fluconazole: Effects on Three-Species Candida Biofilms and Cytotoxic Effects In Vitro

Journal of Fungi ◽

10.3390/jof7070500 ◽

2021 ◽

Vol 7 (7) ◽

pp. 500

Author(s):

Anne Caroline Morais Caldeirão ◽

Heitor Ceolin Araujo ◽

Laís Salomão Arias ◽

Wilmer Ramírez Carmona ◽

Gustavo Porangaba Miranda ◽

...

Keyword(s):

Fungal Infections ◽

Artificial Saliva ◽

Cytotoxic Effects ◽

Promising Alternative ◽

Colony Forming Units ◽

Mtt Reduction ◽

Diphenyl Tetrazolium Bromide ◽

Negative Controls ◽

Positive Controls

The contribution of different Candida species in oral fungal infections has stimulated the search for more effective therapies. This study assessed the antibiofilm effects of nanocarriers of miconazole (MCZ) or fluconazole (FLZ) on Candida biofilms, and their cytotoxic effects on murine fibroblasts. Three-species biofilms (Candida albicans/Candida glabrata/Candida tropicalis) were formed on 96-well plates, and they were treated with nanocarriers (iron oxide nanoparticles coated with chitosan—“IONPs-CS”) of MCZ or FLZ at 39/78/156 µg/mL; antifungals alone at 156 µg/mL and artificial saliva were tested as positive and negative controls, respectively. Biofilms were analyzed by colony forming units (CFU), biomass, metabolic activity, and structure/viability. The cytotoxicity (L929 cells) of all treatments was determined via 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) reduction assay. Data were submitted to one- or two-way ANOVA, followed by Tukey’s or Fisher LSD’s tests (p < 0.05). IONPs-CS-MCZ at 78 µg/mL promoted similar antibiofilm and cytotoxic effects compared with MCZ at 156 µg/mL. In turn, IONPs-CS-FLZ at 156 µg/mL was overall the most effective FLZ antibiofilm treatment, surpassing the effects of FLZ alone; this nanocarrier was also less cytotoxic compared with FLZ alone. It can be concluded that both nanocarriers are more effective alternatives to fight Candida biofilms compared with their respective positive controls in vitro, being a promising alternative for the treatment of oral fungal infections.

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Automated Data Quality Control in FDOPA brain PET Imaging using Deep Learning

Computer Methods and Programs in Biomedicine ◽

10.1016/j.cmpb.2021.106239 ◽

2021 ◽

pp. 106239

Author(s):

Antonella D. Pontoriero ◽

Giovanna Nordio ◽

Rubaida Easmin ◽

Alessio Giacomel ◽

Barbara Santangelo ◽

...

Keyword(s):

Quality Control ◽

Deep Learning ◽

Data Quality ◽

Pet Imaging ◽

Data Quality Control ◽

Brain Pet

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A Machine Learning Approach for Data Quality Control of Earth Observation Data Management System

IGARSS 2020 - 2020 IEEE International Geoscience and Remote Sensing Symposium ◽

10.1109/igarss39084.2020.9323615 ◽

2020 ◽

Author(s):

Weiguo Han ◽

Matthew Jochum

Keyword(s):

Machine Learning ◽

Quality Control ◽

Data Quality ◽

Earth Observation ◽

Data Management System ◽

Learning Approach ◽

Observation Data ◽

Data Quality Control ◽

Machine Learning Approach ◽

Earth Observation Data

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Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions

Scientific Reports ◽

10.1038/s41598-021-82656-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Chao Gao ◽

Chong Ma ◽

Huqiang Wang ◽

Haolin Zhong ◽

Jiayin Zang ◽

...

Keyword(s):

Biological Significance ◽

Protein Domains ◽

Functional Requirements ◽

Post Translational Modification ◽

Intrinsically Disordered ◽

Genome Wide ◽

Complex Functions ◽

Disorder Degree ◽

Functional Features ◽

And Function

AbstractInterestingly, some protein domains are intrinsically disordered (abbreviated as IDD), and the disorder degree of same domains may differ in different contexts. However, the evolutionary causes and biological significance of these phenomena are unclear. Here, we address these issues by genome-wide analyses of the evolutionary and functional features of IDDs in 1,870 species across the three superkingdoms. As the result, there is a significant positive correlation between the proportion of IDDs and organism complexity with some interesting exceptions. These phenomena may be due to the high disorder of clade-specific domains and the different disorder degrees of the domains shared in different clades. The functions of IDDs are clade-specific and the higher proportion of post-translational modification sites may contribute to their complex functions. Compared with metazoans, fungi have more IDDs with a consecutive disorder region but a low disorder ratio, which reflects their different functional requirements. As for disorder variation, it’s greater for domains among different proteins than those within the same proteins. Some clade-specific ‘no-variation’ or ‘high-variation’ domains are involved in clade-specific functions. In sum, intrinsic domain disorder is related to both the organism complexity and clade-specific functions. These results deepen the understanding of the evolution and function of IDDs.

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