Quality control of protein reagents for the improvement of research data reproducibility.
Ontology highlight
ABSTRACT:
SUBMITTER: de Marco A
PROVIDER: S-EPMC8121922 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Murine Cytomegalovirus pSM3fr
| PRJEB64494 | ENA
Project description:BackgroundSuccessful implementation of pay-for-quality (P4Q) programs mostly depends upon a valid, timely, and reliable data about quality measures generated by providers, and interpreted by payers. The aim of this study was to establish a data reporting method for P4Q program through an action research.MethodsQualitative method was used to align theory with action through a three-cycle action research. The study was conducted in September 15, 2015 to March 15, 2017, in East-Azerbaijan, Iran. The purposeful sampling was used to select participants. The participants included healthcare providers, staff in district health centers (DHC), experts, and managers in the provincial primary health center (PPHC). Data was collected by interviews, focus group discussions, and expert panels. Content analysis was used to synthesize the data. In each step, decisions about data reporting methods were made through a consensus of expert panel members.ResultsThe most important dimensions of data reporting method were data entry and accuracy, data reporting, data analysis and interpretations, the flexibility of method, and training. By establishment of an online data reporting system for the P4Q program, a major improvement was observed in the documentation of performance data, the satisfaction of health care providers and staff (e.g. either in DHCs or PPHC), improvement of the P4Q program and acceptance of the P4Q program by providers. Following the present study, the online system was expanded in Iran's public health system for data collection and estimating the amount of incentive payments in P4Q program. Moreover, more improvements were achieved by linking the system to EMRs and also, providing automated feedback to providers about their own performance.ConclusionsA web-based computerized system with the capability of linking medical record and also its ability to provide feedback to healthcare providers was identified as an appropriate method of data reporting in the P4Q program from the viewpoints of participants in this study.
| S-EPMC6128004 | biostudies-literature
Project description:Tests for immunoglobulin reactivity with specific antigens are some of the oldest and most used assays in immunology. With efforts to understand B cell development, B cell dysregulation in autoimmunity, and to generate B cell vaccines for infectious agents, investigators have found the need to understand the ontogeny and regulation of epitope-specific B cell responses. The synchrony between surface and secreted antibodies for individual B cells has led to the development of reagents and techniques to identify antigen-specific B cells via reagent interactions with the B cell receptor complex. B cell antigen-specific reagents have been reported for model systems of haptens, for whole proteins, and for identification of double stranded (ds) DNA antibody-producing B cells using peptide mimics. Here we provide an overview of reported techniques for the detection of antigen-specific B cell responses via secreted antibody or by the surface B cell receptor and briefly discuss our recent work developing a panel of reagents to probe the B cell response to HIV-1 envelope. We also present an analysis of strengths and weaknesses of various methods for flow cytometric analysis of antigen-specific B cells.
| S-EPMC3105373 | biostudies-literature
Project description:BackgroundHi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study.ResultsUsing real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector, and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established measures, such as the ratio of intra- to interchromosomal interactions, and novel ones, such as QuASAR-QC, to identify low-quality experiments.ConclusionsIn this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http://github.com/kundajelab/3DChromatin_ReplicateQC to facilitate adoption in the community.
| S-EPMC6423771 | biostudies-literature
Project description:BackgroundGiven the growing interest in using microRNAs (miRNAs) as biomarkers of early disease, establishment of robust protocols and platforms for miRNA quantification in biological fluids is critical.ObjectiveThe goal of this multi-center pilot study was to evaluate the reproducibility of NanoString nCounter™ technology when analyzing the abundance of miRNAs in plasma and cystic fluid from patients with pancreatic lesions.MethodsUsing sample triplicates analyzed across three study sites, we assessed potential sources of variability (RNA isolation, sample processing/ligation, hybridization, and lot-to-lot variability) that may contribute to suboptimal reproducibility of miRNA abundance when using nCounter™, and evaluated expression of positive and negative controls, housekeeping genes, spike-in genes, and miRNAs.ResultsPositive controls showed a high correlation across samples from each site (median correlation coefficient, r> 0.9). Most negative control probes had expression levels below background. Housekeeping and spike-in genes each showed a similar distribution of expression and comparable pairwise correlation coefficients of replicate samples across sites. A total of 804 miRNAs showed a similar distribution of pairwise correlation coefficients between replicate samples (p= 0.93). After normalization and selecting miRNAs with expression levels above zero in 80% of samples, 55 miRNAs were identified; heatmap and principal component analysis revealed similar expression patterns and clustering in replicate samples.ConclusionsFindings from this pilot investigation suggest the nCounter platform can yield reproducible results across study sites. This study underscores the importance of implementing quality control procedures when designing multi-center evaluations of miRNA abundance.
| S-EPMC9428925 | biostudies-literature
Project description:There is broad interest to improve the reproducibility of published research. We developed a survey tool to assess the availability of digital research artifacts published alongside peer-reviewed journal articles (e.g. data, models, code, directions for use) and reproducibility of article results. We used the tool to assess 360 of the 1,989 articles published by six hydrology and water resources journals in 2017. Like studies from other fields, we reproduced results for only a small fraction of articles (1.6% of tested articles) using their available artifacts. We estimated, with 95% confidence, that results might be reproduced for only 0.6% to 6.8% of all 1,989 articles. Unlike prior studies, the survey tool identified key bottlenecks to making work more reproducible. Bottlenecks include: only some digital artifacts available (44% of articles), no directions (89%), or all artifacts available but results not reproducible (5%). The tool (or extensions) can help authors, journals, funders, and institutions to self-assess manuscripts, provide feedback to improve reproducibility, and recognize and reward reproducible articles as examples for others.
| S-EPMC6390703 | biostudies-literature
Project description:BackgroundThe availability of high fidelity electronic health record (EHR) data is a hallmark of the learning health care system. Washington State's Surgical Care Outcomes and Assessment Program (SCOAP) is a network of hospitals participating in quality improvement (QI) registries wherein data are manually abstracted from EHRs. To create the Comparative Effectiveness Research and Translation Network (CERTAIN), we semi-automated SCOAP data abstraction using a centralized federated data model, created a central data repository (CDR), and assessed whether these data could be used as real world evidence for QI and research.ObjectivesDescribe the validation processes and complexities involved and lessons learned.MethodsInvestigators installed a commercial CDR to retrieve and store data from disparate EHRs. Manual and automated abstraction systems were conducted in parallel (10/2012-7/2013) and validated in three phases using the EHR as the gold standard: 1) ingestion, 2) standardization, and 3) concordance of automated versus manually abstracted cases. Information retrieval statistics were calculated.ResultsFour unaffiliated health systems provided data. Between 6 and 15 percent of data elements were abstracted: 51 to 86 percent from structured data; the remainder using natural language processing (NLP). In phase 1, data ingestion from 12 out of 20 feeds reached 95 percent accuracy. In phase 2, 55 percent of structured data elements performed with 96 to 100 percent accuracy; NLP with 89 to 91 percent accuracy. In phase 3, concordance ranged from 69 to 89 percent. Information retrieval statistics were consistently above 90 percent.ConclusionsSemi-automated data abstraction may be useful, although raw data collected as a byproduct of health care delivery is not immediately available for use as real world evidence. New approaches to gathering and analyzing extant data are required.
| S-EPMC5983060 | biostudies-literature
Project description:The notion of data transparency is gaining a strong awareness among the scientific community. The availability of raw data is actually regarded as a fundamental way to advance science by promoting both integrity and reproducibility of research outcomes. Particularly, in the field of natural product and chemical research, NMR spectroscopy is a fundamental tool for structural elucidation and quantification (qNMR). As such, the accessibility of original NMR data, i.e., Free Induction Decays (FIDs), fosters transparency in chemical research and optimizes both peer review and reproducibility of reports by offering the fundamental tools to perform efficient structural verification. Although original NMR data are known to contain a wealth of information, they are rarely accessible along with published data. This viewpoint discusses the relevance of the availability of original NMR data as part of good research practices not only to promote structural correctness, but also to enhance traceability and reproducibility of both chemical and biological results.
| S-EPMC5001890 | biostudies-literature
Project description:BACKGROUND:The shift toward value-based care in the United States emphasizes the role of quality measures in payment models. Many diseases, such as prostate cancer, have a proliferation of quality measures, resulting in resource burden and physician burnout. This study aimed to identify and summarize proposed prostate cancer quality measures and describe their frequency and use in peer-reviewed literature. METHODS:The PubMed database was used to identify quality measures relevant to prostate cancer care, and included articles in English through April 2018. A gray literature search for other documents was also conducted. After the selection process of the pertinent articles, measure characteristics were abstracted, and uses were summarized for the 10 most frequently utilized measures in the literature. RESULTS:A total of 26 articles were identified for review. Of the 71 proposed prostate cancer quality measures, only 47 were used, and less than 10% of these were endorsed by the National Quality Forum. Process measures were most frequently reported (84.5%). Only 6 outcome measures (8.5%) were proposed-none of which were among the most frequently utilized. CONCLUSION:Although a high number of proposed prostate cancer quality measures are reported in the literature, few were assessed, and the majority of these were non-endorsed process measures. Process measures were most commonly assessed; outcome measures were rarely evaluated. In a step to close the quality chasm, a "top 5" core set of quality measures for prostate cancer care, including structure, process, and outcomes measures, is suggested. Future studies should consider this comprehensive set of quality measures.
| S-EPMC6494082 | biostudies-literature
Project description:The yeast Hsp104 protein disaggregase is often used as a reporter for misfolded or damaged protein aggregates and protein quality control and ageing research. Observing Hsp104 fusions with fluorescent proteins is a popular approach to follow post stress protein aggregation, inclusion formation and disaggregation. While concerns that bigger protein tags, such as genetically encoded fluorescent tags, may affect protein behaviour and function have been around for quite some time, experimental evidence of how exactly the physiology of the protein of interest is altered within fluorescent protein fusions remains limited. To address this issue, we performed a comparative assessment of endogenously expressed Hsp104 fluorescent fusions function and behaviour. We provide experimental evidence that molecular behaviour may not only be altered by introducing a fluorescent protein tag but also varies depending on such a tag within the fusion. Although our findings are especially applicable to protein quality control and ageing research in yeast, similar effects may play a role in other eukaryotic systems.
| S-EPMC8211707 | biostudies-literature