scholarly journals CFEA: a cell-free epigenome atlas in human diseases

2019 ◽  
Vol 48 (D1) ◽  
pp. D40-D44 ◽  
Author(s):  
Fulong Yu ◽  
Kai Li ◽  
Shuangquan Li ◽  
Jiaqi Liu ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Quality Control ◽  
Clinical Information ◽  
High Sensitivity ◽  
Human Diseases ◽  
Epigenetic Alterations ◽  
Web Interface ◽  
Standard Data ◽  
Specific Stage ◽  
A Cell ◽  
Query Visualization

Abstract Epigenetic alterations, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and nucleosome positioning (NP), in cell-free DNA (cfDNA) have been widely observed in human diseases, and many available cfDNA-based epigenome-wide profiles exhibit high sensitivity and specificity in disease detection and classification. However, due to the lack of efficient collection, standardized quality control, and analysis procedures, efficiently integrating and reusing these data remain considerable challenges. Here, we introduce CFEA (http://www.bio-data.cn/CFEA), a cell-free epigenome database dedicated to three types of widely adopted epigenetic modifications (5mC, 5hmC and NP) involved in 27 human diseases. We developed bioinformatic pipelines for quality control and standard data processing and an easy-to-use web interface to facilitate the query, visualization and download of these cell-free epigenome data. We also manually curated related biological and clinical information for each profile, allowing users to better browse and compare cfDNA epigenomes at a specific stage (such as early- or metastasis-stage) of cancer development. CFEA provides a comprehensive and timely resource to the scientific community and supports the development of liquid biopsy-based biomarkers for various human diseases.

scholarly journals Epigenetic roles of PIWI proteins and piRNAs in colorectal cancer

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fatemeh Sadoughi ◽  
Seyyed Mehdi Mirhashemi ◽  
Zatollah Asemi
Keyword(s):  
Colorectal Cancer ◽  
Human Diseases ◽  
Regulatory Function ◽  
Epigenetic Alterations ◽  
Gastrointestinal Malignancy ◽  
Abnormal Expression ◽  
Gene Regulatory ◽  
Non Coding Rnas ◽  
Entire World

AbstractSmall non‐coding RNAs (sncRNAs) are a subgroup of non‐coding RNAs, with less than 200 nucleotides length and no potential for coding proteins. PiRNAs, a member of sncRNAs, were first discovered more than a decade ago and have attracted researcher’s attention because of their gene regulatory function both in the nucleus and in the cytoplasm. Recent investigations have found that the abnormal expression of these sncRNAs is involved in many human diseases, including cancers. Colorectal cancer (CRC), as a common gastrointestinal malignancy, is one of the important causes of cancer‐related deaths through the entire world and appears to be a consequence of mutation in the genome and epigenetic alterations. The aim of this review is to realize whether there is a relationship between CRC and piRNAs or not.

scholarly journals Use of β-D-glucan in diagnosis of suspected Pneumocystis jirovecii pneumonia in adults with HIV infection

2021 ◽  
pp. 095646242110222
Author(s):  
Thomas Juniper ◽  
Chris P Eades ◽  
Eliza Gil ◽  
Harriet Fodder ◽  
Killian Quinn ◽  
...  
Keyword(s):  
Predictive Value ◽  
Diagnostic Tests ◽  
Elevated Serum ◽  
Clinical Information ◽  
High Sensitivity ◽  
Pneumocystis Pneumonia ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Alternative Diagnosis ◽  
Positive Threshold ◽  
Sensitivity Specificity

Objectives: An elevated serum (1-3)-β-D-glucan (BDG) concentration has high sensitivity for a diagnosis of Pneumocystis pneumonia (PCP) in people with HIV (PWH). At the current manufacturer-recommended positive threshold of 80 pg/mL (Fungitell), specificity for PCP is variable and other diagnostic tests are required. We evaluated the utility of serum BDG for diagnosis of suspected PCP in PWH at three inner-London hospitals to determine BDG concentrations for diagnosis and exclusion of PCP. Methods: From clinical case records, we abstracted demographic and clinical information and categorised patients as having confirmed or probable PCP, or an alternative diagnosis. We calculated sensitivity, specificity and positive predictive value (PPV) of serum BDG concentrations >400 pg/mL and negative predictive value (NPV) of BDG <80 pg/mL. Results: 76 patients were included; 29 had laboratory-confirmed PCP, 17 had probable PCP and 30 had an alternative diagnosis. Serum BDG >400 pg/mL had a sensitivity of 83%, specificity of 97% and PPV 97% for diagnosis of PCP; BDG <80 pg/mL had 100% NPV for exclusion of PCP. Conclusions: In PWH with suspected PCP, BDG <80 pg/mL excludes a diagnosis of PCP, whereas BDG concentrations >400 pg/mL effectively confirm the diagnosis. Values 80–400 pg/mL should prompt additional diagnostic tests.

Long-term quality control testing on a high-sensitivity cardiac troponin I assay

2019 ◽  
Vol 498 ◽  
pp. 27-29 ◽  
Author(s):  
Peter A. Kavsak ◽  
Kelsey MacEachern ◽  
Eleonora Petryayeva ◽  
Lorna Clark
Keyword(s):  
Quality Control ◽  
Cardiac Troponin ◽  
Troponin I ◽  
High Sensitivity ◽  
Cardiac Troponin I ◽  
Quality Control Testing

scholarly journals Dynamic instability of clathrin assembly provides proofreading control for endocytosis

2019 ◽  
Vol 218 (10) ◽  
pp. 3200-3211 ◽  
Author(s):  
Yan Chen ◽  
Jeffery Yong ◽  
Antonio Martínez-Sánchez ◽  
Yang Yang ◽  
Yumei Wu ◽  
...  
Keyword(s):  
Quality Control ◽  
Single Molecule ◽  
Dynamic Instability ◽  
Single Molecule Imaging ◽  
Coated Pits ◽  
A Cell ◽  
The Cost ◽  
Dynamic Exchange ◽  
Cargo Sorting

Clathrin-mediated endocytosis depends on the formation of functional clathrin-coated pits that recruit cargos and mediate the uptake of those cargos into the cell. However, it remains unclear whether the cargos in the growing clathrin-coated pits are actively monitored by the coat assembly machinery. Using a cell-free reconstitution system, we report that clathrin coat formation and cargo sorting can be uncoupled, indicating that a checkpoint is required for functional cargo incorporation. We demonstrate that the ATPase Hsc70 and a dynamic exchange of clathrin during assembly are required for this checkpoint. In the absence of Hsc70 function, clathrin assembles into pits but fails to enrich cargo. Using single-molecule imaging, we further show that uncoating takes place throughout the lifetime of the growing clathrin-coated pits. Our results suggest that the dynamic exchange of clathrin, at the cost of the reduced overall assembly rates, primarily serves as a proofreading mechanism for quality control of endocytosis.

scholarly journals Deep learning algorithm helps to standardise ATS/ERS spirometric acceptability and usability criteria

2020 ◽  
pp. 2000603 ◽  
Author(s):  
Nilakash Das ◽  
Kenneth Verstraete ◽  
Sanja Stanojevic ◽  
Marko Topalovic ◽  
Jean-Marie Aerts ◽  
...  
Keyword(s):  
Quality Control ◽  
Deep Learning ◽  
Learning Algorithm ◽  
High Sensitivity ◽  
Current Approach ◽  
Deep Learning Algorithm ◽  
Volume Curve ◽  
Flow Volume Curve ◽  
Shapley Values ◽  
Quality Control Criteria

RationaleWhile ATS/ERS quality control criteria for spirometry include several quantitative limits, it also requires manual visual inspection. The current approach is time consuming and leads to high inter-technician variability. We propose a deep learning approach called convolutional neural network (CNN), to standardise spirometric manoeuvre acceptability and usability.Methods and methodsIn 36 873 curves from the national health and nutritional examination survey (NHANES) USA 2011–12, technicians labelled 54% of curves as meeting ATS/ERS 2005 acceptability criteria with satisfactory start and end of test but identified 93% of curves with a usable FEV1. We processed raw data into images of maximal expiratory flow-volume curve (MEFVC), calculated ATS/ERS quantifiable criteria, and developed CNNs to determine manoeuvre acceptability and usability on 90% of the curves. The models were tested on the remaining 10% of curves. We calculated Shapley values to interpret the models.ResultsIn the test set (N=3738), CNN showed an accuracy of 87% for acceptability and 92% for usability, with the latter demonstrating a high sensitivity (92%) and specificity (96%). They were significantly superior (p<0.0001) to ATS/ERS quantifiable rule-based models. Shapley interpretation revealed MEFVC<1 s (MEFVC pattern within first second of exhalation) and plateau in volume-time were most important in determining acceptability, while MEFVC<1 s entirely determined usability.ConclusionThe CNNs identified relevant attributes in spirometric curves to standardise ATS/ERS manoeuvre acceptability and usability recommendations, and further provides individual manoeuvre feedback. Our algorithm combines the visual experience of skilled technicians and ATS/ERS quantitative rules in automating the critical phase of spirometry quality control.

scholarly journals Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline

2014 ◽  
Vol 13s3 ◽  
pp. CIN.S14022 ◽  
Author(s):  
Karl W. Kroll ◽  
Nima E. Mokaram ◽  
Alexander R. Pelletier ◽  
David E. Frankhouser ◽  
Maximillian S. Westphal ◽  
...  
Keyword(s):  
Quality Control ◽  
Ease Of Use ◽  
Rna Seq ◽  
Web Interface ◽  
For Profit ◽  
Not For Profit ◽  
Large Numbers ◽  
Sample Data ◽  
Meta Analyses ◽  
User Friendly

QuaCRS ( Quality Control for RNA- Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies. It comprises two main sections. First is the QC Pack wrapper, which executes three QC tools: FastQC, RNA-SeQC, and selected functions from RSeQC. Combining these three tools into one wrapper provides increased ease of use and provides a much more complete view of sample data quality than any individual tool. Second is the QC database, which displays the resulting metrics in a user-friendly web interface. It was designed to allow users with less computational experience to easily generate and view QC information for their data, to investigate individual samples and aggregate reports of sample groups, and to sort and search samples based on quality. The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future. The source code for not-for-profit use and a fully functional sample user interface with mock data are available at http://bioserv.mps.ohio-state.edu/QuaCRS/ .

scholarly journals Effects of undetected data quality issues on climatological analyses

2017 ◽  
Author(s):  
Stefan Hunziker ◽  
Stefan Brönnimann ◽  
Juan Marcos Calle ◽  
Isabel Moreno ◽  
Marcos Andrade ◽  
...  
Keyword(s):  
Quality Control ◽  
Data Quality ◽  
Control Method ◽  
Correlation Coefficients ◽  
Maximum Temperature ◽  
Generation Process ◽  
Data Generation ◽  
Data Quality Control ◽  
Standard Data ◽  
Quality Issues

Abstract. Systematic data quality issues may occur at various stages of the data generation process. They may affect large fractions of observational datasets and remain largely undetected with standard data quality control. This study investigates the effects of such undetected data quality issues on the results of climatological analyses. For this purpose, we quality controlled daily observations of manned weather stations from the Central Andean area with a standard and an enhanced approach. The climate variables analysed are minimum and maximum temperature, and precipitation. About 40 % of the observations are inappropriate for the calculation of monthly temperature means and precipitation sums due to data quality issues. These quality problems undetected with the standard quality control method strongly affect climatological analyses, since they reduce the correlation coefficients of station pairs, deteriorate the performance of data homogenization methods, increase the spread of individual station trends, and significantly bias regional temperature trends. Our findings indicate that undetected data quality issues are included in important and frequently used observational datasets, and hence may affect a high number of climatological studies. It is of utmost importance to apply comprehensive and adequate data quality control approaches on manned weather station records in order to avoid biased results and large uncertainties.

scholarly journals Clinicopathological study of surgery for pulmonary metastases of hepatoblastoma with indocyanine green fluorescent imaging

2021 ◽  
Author(s):  
Misa Yoshida ◽  
Mio Tanaka ◽  
Norihiko Kitagawa ◽  
Masato Shinkai ◽  
Hiroaki Goto ◽  
...  
Keyword(s):  
Indocyanine Green ◽  
Pulmonary Metastases ◽  
False Negative ◽  
Clinical Information ◽  
High Sensitivity ◽  
Fluorescent Imaging ◽  
Metastatic Lesions ◽  
Pulmonary Metastasectomies ◽  
Lung Metastasectomy ◽  
Green Fluorescent

Background: The prognosis of metastatic hepatoblastoma remains poor; to improve it, pulmonary metastasis must be controlled. Indocyanine green (ICG) fluorescent imaging has been used recently for lung metastasectomy. The objective of our study was to clarify the usefulness of ICG imaging for lung metastasectomy of hepatoblastoma using detailed clinicopathological analysis. Procedure: Patients with hepatoblastoma who underwent resection of pulmonary metastases with ICG fluorescent imaging were studied using retrospective analysis of clinical information, a review of their surgical records, and a histological analysis of their metastatic nodules. Results: Sixteen patients were enrolled. In total, 61 ICG-imaging-guided pulmonary metastasectomies were performed, and 350 ICG-positive and 23 ICG-negative specimens were identified. Tumors were confirmed in 250 of the ICG-positive specimens, including eight nonpalpable nodules, on microscopic examination. One hundred ICG-positive specimens and histologically tumor-negative specimens showed histological changes suggesting the regression of a tumor or bloodstream disturbance. The palpable ICG-negative tumors showed more-severe atypia than the ICG-positive tumors. Conclusions: This study demonstrates the high sensitivity of ICG imaging in detecting metastatic lesions of hepatoblastoma. Histological examinations suggested that ICG imaging detects not only tumor cells, but also nontumorous pulmonary tissues affected by bloodstream disturbance. Because a number of false-positive specimens were detected, further optimization of the dose of ICG and the timing of its administration may be required for thorough metastasectomy. Several false-negative specimens were also detected, suggesting the presence of ICG-negative metastatic tumors. Palpation during operation and imaging studies remain essential for detecting metastatic lesions, even in the era of ICG imaging.

scholarly journals A Role for Cell Polarity in Lifespan and Mitochondrial Quality Control in the Budding Yeast Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Emily J. Yang ◽  
Wolfgang M Pernice ◽  
Liza A. Pon
Keyword(s):  
Cell Cycle ◽  
Quality Control ◽  
Cell Division ◽  
Yeast Cell ◽  
Cell Polarity ◽  
Yeast Saccharomyces Cerevisiae ◽  
A Cell ◽  
Mitochondrial Distribution ◽  
Mother Cells ◽  
F Box Protein

SummaryBabies are born young, largely independent of the age of their mothers. Mother-daughter age asymmetry in yeast is achieved, in part, by inheritance of higher-functioning mitochondria by daughter cells and retention of some high-functioning mitochondria in mother cells. The mitochondrial F-box protein, Mfb1p, tethers mitochondria at both poles in a cell cycle-regulated manner: it localizes to and anchors mitochondria to the mother cell tip throughout the cell cycle, and to the bud tip prior to cytokinesis. Here, we report that cell polarity and polarized localization of Mfb1p decline with age in S. cerevisiae. Moreover, deletion of BUD1/RSR1, a Ras protein required for cytoskeletal polarization during asymmetric yeast cell division, results in depolarized Mfb1p localization, defects in mitochondrial distribution and quality control, and reduced replicative lifespan. Our results demonstrate a role for the polarity machinery in lifespan through modulating Mfb1 function in asymmetric inheritance of mitochondria during yeast cell division.

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