scholarly journals Nowcast Deep Learning Models For Constraining Zero-Day Pathogen Attacks – Application on Chest Radiographs to Covid-19

2020 ◽  
Author(s):  
Michael D. Kuo ◽  
Wan Hang Keith Chiu ◽  
Varut Vardhanabhuti ◽  
Dymtro Poplavskiy ◽  
Philip LH Yu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Sensitivity And Specificity ◽  
Detection System ◽  
Chest Radiographs ◽  
Sufficient Information ◽  
Operating Characteristics ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Prospective Cohorts ◽  
Polymerase Chain

Abstract Outbreaks due to emergent pathogens like Covid-19 are difficult to contain as the time to gather sufficient information to develop a detection system is outpaced by the speed of transmission. Here we develop a general pneumonia (PNA) CXR Deep Learning (DL) model (MAIL1.0) follow by a second-generation DL model (MAIL2.0) for detection of Covid-19 on chest radiographs (CXR). We validate the models on two prospective cohorts of high-risks patients screened for Covid-19 reverse transcriptase-polymerase chain reaction (RT-PCR). MAIL1.0 has an Area Under the Receiver Operating Characteristics (AUC) of 0.93, sensitivity and specificity of 90.5% and 76.7% in detection of visible pneumonia and MAIL2.0 has an AUC of 0.81, sensitivity and specificity of 84.7% and 71.6%, significantly outperforming radiologists, especially amongst asymptomatic and patients presenting with early symptoms. Nowcast DL models may be an effective tool in helping to constrain the outbreak, particularly in resource-stretched healthcare systems.

Comparative Evaluation of Culture- and BAX Polymerase Chain Reaction–Based Detection Methods for Listeria spp. and Listeria monocytogenes in Environmental and Raw Fish Samples

2001 ◽  
Vol 64 (10) ◽  
pp. 1521-1526 ◽  
Author(s):  
ADAM D. HOFFMAN ◽  
MARTIN WIEDMANN
Keyword(s):  
Polymerase Chain Reaction ◽  
Listeria Monocytogenes ◽  
Sensitivity And Specificity ◽  
Environmental Samples ◽  
Detection System ◽  
Detection Methods ◽  
Chain Reaction ◽  
Enrichment Medium ◽  
Raw Fish ◽  
Polymerase Chain

Two commercial polymerase chain reaction (PCR)-based Listeria detection systems, the BAX for Screening/Listeria monocytogenes and the BAX for Screening/Genus Listeria, and a culture-based detection system, the Biosynth L. monocytogenes Detection System (LMDS), were evaluated for their ability to detect L. monocytogenes and Listeria spp. in raw ingredients and the processing environment. For detection of L. monocytogenes from raw fish, enrichment was performed in Listeria enrichment broth (LEB), followed by plating on both Oxford agar and LMDS L. monocytogenes plating medium (LMPM). Detection of Listeria and L. monocytogenes from environmental samples was performed using LMDS enrichment medium, followed by plating on both Oxford agar and LMPM. A total of 512 environmental samples and 315 raw fish were taken from two smoked fish processing facilities and screened using these molecular and cultural Listeria detection methods. The BAX for Screening/L. monocytogenes was used to screen raw fish and was 84.8% sensitive and 100% specific. The BAX for Screening/Genus Listeria was evaluated on environmental samples and had 94.7% sensitivity and 97.4% specificity. In conjunction with enrichment in LEB, LMPM had a sensitivity and specificity for detection of L. monocytogenes from raw fish of 97.8 and 100%, respectively. Use of LMDS enrichment medium followed by plating on LMPM allowed for sensitivity and specificity rates of 94.8 and 100%, respectively, for detection of L. monocytogenes from environmental samples. We conclude that both the BAX systems and the use of LMPM allow for reliable and rapid detection of Listeria spp. and L. monocytogenes. While the BAX systems provide screening results in about 3 days, the use of LMPM allows for L. monocytogenes isolation in 4 to 5 days.

scholarly journals Dynamic Prediction of SARS-CoV-2 RT-PCR status on Chest Radiographs using Deep Learning Enabled Radiogenomics

2021 ◽  
Author(s):  
Wan Hang Keith Chiu ◽  
Dmytro Poplavskiy ◽  
Sailong Zhang ◽  
Philip Leong Ho Yu ◽  
Michael D. Kuo
Keyword(s):  
Polymerase Chain Reaction ◽  
Deep Learning ◽  
Reverse Transcription ◽  
Gold Standard ◽  
Chest Imaging ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Dynamic Prediction ◽  
Specialized Equipment ◽  
Polymerase Chain

Reverse Transcription-Polymerase Chain Reaction (RT-PCR) is the gold standard for diagnosis of SARS-CoV-2 infection, but requires specialized equipment and reagents and suffers from long turnaround times. While valuable, chest imaging currently only detects COVID-19 pneumonia, but if it can predict actual RT-PCR SARS-CoV-2 status is unknown. Radiogenomics may provide an effective and accurate RT-PCR-based surrogate. We describe a deep learning radiogenomics (DLR) model (RadGen) that predicts a patient's RT-PCR SARS-CoV-2 status solely from their frontal chest radiograph (CXR).

Reverse-Transcription Polymerase Chain Reaction Detection of the Enteroviruses

1999 ◽  
Vol 123 (12) ◽  
pp. 1161-1169 ◽  
Author(s):  
JoséR. Romero
Keyword(s):  
Polymerase Chain Reaction ◽  
Sensitivity And Specificity ◽  
Reverse Transcription ◽  
Health Care Cost ◽  
Cost Savings ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Reverse Transcription Pcr ◽  
Polymerase Chain ◽  
Pcr Conditions

Abstract Objective.—This review focuses on commercial and in-house–developed reverse-transcription polymerase chain reaction (RT-PCR) assays used for the detection of enteroviral infections. In addition to providing details on the performance of RT-PCR, its specificity, and sensitivity, the clinical utility of this diagnostic method with specific reference to its impact on hospitalization and cost savings is addressed. Data Sources.—MEDLINE was searched for reports relating to RT-PCR detection of the enteroviruses in adults and children. The search was restricted to studies reported in English language journals. Study Selection.—Reports documenting detailed information regarding the RT-PCR conditions, primers, sensitivity, specificity and, if relevant, clinical impact were selected for analysis. Data Extraction.—Details regarding method of extraction of the enteroviral genome, the primers used, RT-PCR conditions, and sensitivity and specificity of the assay were extracted from the literature. For reports detailing the use of RT-PCR in the clinical management of enteroviral infections in children, the reduction in duration of hospitalization and health care cost savings were recorded. Data Synthesis.—Reverse-transcription PCR can increase the yield of detection of enteroviruses from cerebrospinal fluid by a mean of approximately 20% over tissue culture. Reverse-transcription PCR of cerebrospinal fluid has been shown to exhibit sensitivity and specificity values of 86% to 100% and 92% to 100%, respectively. Reductions of 1 to 3 days of hospitalization per patient are predicted if RT-PCR is used to diagnose enteroviral meningitis in children. Conclusions.—Reverse-transcription PCR detection of enteroviral infections is an extremely rapid, sensitive, and specific diagnostic modality. Both commercial assays and assays developed in-house appear to be equivalent with regard to sensitivity and specificity. Reverse-transcription PCR diagnosis of enteroviral infections in children could reduce the length of hospitalization and result in significant health care cost savings.

Development of PCR Methods for Enteric Virus Detection in Water

1993 ◽  
Vol 27 (3-4) ◽  
pp. 211-218 ◽  
Author(s):  
K. J. Schwab ◽  
R. De Leon ◽  
M. D. Sobsey
Keyword(s):  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Detection System ◽  
Virus Detection ◽  
Enteric Virus ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Sample Concentration ◽  
Spin Column ◽  
Polymerase Chain

This study developed a reverse transcriptase-polymerase chain reaction (RT-PCR) detection system for enteric viruses in sample concentrates obtained by conventional filter adsorption-elution methods. One liter beef extract (BE)-glycine (G) eluant seeded with poliovirus 1 and hepatitis A virus (HAV) was used as a model system and the eluant further processed for RT-PCR compatibility. Sample concentration and purification procedures consisted of polyethylene glycol (PEG) precipitation, Pro-Cipitate (Affinity Technology, New Brunswick, NJ) precipitation, a second PEG precipitation, spin-column chromatography, and ultrafiltration. Sample volumes are reduced from 1 L to 20-40 µL and purified sufficiently for viral detection by RT-PCR. As little as 3 PFU of poliovirus 1 in an initial 1 L eluate were detected by RT-PCR.

scholarly journals Real-time PCR assay for the diagnosis of pleural tuberculosis

2017 ◽  
pp. 47-52
Author(s):  
Martha Alejandra Casallas-Rivera ◽  
Ana María Cardenas Bernal ◽  
Luis Fernando Giraldo-Cadavid ◽  
Enrique Prieto Diago ◽  
Paola Santander
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Reference Method ◽  
Operating Characteristics ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Cross Sectional ◽  
Pleural Tuberculosis ◽  
Hybridization Probes ◽  
Polymerase Chain

Introduction: The diagnosis of pleural tuberculosis requires an invasive and time-consuming reference method. Polymerase chain reaction (PCR) is rapid, but validation in pleural tuberculosis is still weak.Objective: To establish the operating characteristics of real-time polymerase chain reaction (RT-PCR) hybridization probes for the diagnosis of pleural tuberculosis.Method: The validity of the RT-PCR hybridization probes was evaluated compared to a composite reference method by a cross-sectional study at the Hospital Universitario de la Samaritana. 40 adults with lymphocytic pleural effusion were included. Pleural tuberculosis was confirmed (in 9 patients) if the patient had at least one of three tests using the positive reference method: Ziehl-Neelsen or Mycobacterium tuberculosis culture in fluid or pleural tissue, or pleural biopsy with granulomas. Pleural tuberculosis was ruled out (in 31 patients) if all three tests were negative. The operating characteristics of the RT-PCR, using the Mid-P Exact Test, were determined using the OpenEpi 2.3 Software (2009).Results: The RT-PCR hybridization probes showed a sensitivity of 66.7% (95% CI: 33.2%-90.7%) and a specificity of 93.5% (95% CI: 80.3%-98.9%). The PPV was 75.0% (95% CI: 38.8%-95.6%) and a NPV of 90.6% (95% CI: 76.6%-97.6%). Two false positives were found for the test, one with pleural mesothelioma and the other with chronic pleuritis with mesothelial hyperplasia.Conclusions: The RT-PCR hybridization probes had good specificity and acceptable sensitivity, but a negative value cannot rule out pleural tuberculosis.

scholarly journals COMPARISON OF AGAR GEL IMMUNODIFFUSION TEST, IMMUNOHISTOCHEMSITRY AND REVERSE TRANSCRIPTION - POLYMERASE CHAIN REACTION FOR DETECTION OF INFECTIOUS BURSAL DISEASE VIRUS

2013 ◽  
Vol 9 (2) ◽  
pp. 121-125 ◽  
Author(s):  
MT Islam ◽  
MN Islam ◽  
MZI Khan ◽  
MA Islam
Keyword(s):  
Polymerase Chain Reaction ◽  
Disease Virus ◽  
Sensitivity And Specificity ◽  
Infectious Bursal Disease Virus ◽  
Infectious Bursal Disease ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Agar Gel ◽  
Bursal Disease ◽  
Polymerase Chain

The objective of this study was to compare agar gel immunodiffusion test (AGID) and immunohistochemistry (IHC) with reverse transcriptase-polymerase chain reaction (RT-PCR) in terms of sensitivity and specificity for the detection of infectious bursal disease virus (IBDV). Thirty-five bursal samples collected from filed outbreak of IBD were evaluated by all 3 diagnostic tests. Sensitivity and specificity of both AGIDT and IHC with RT-PCR was 94.12% and 100%, respectively. Both AGIDT and IHC showed a 94.29% association with RT-PCR with a k value of 0.482, indicating a moderate degree of agreement. The Cochran’s Q value was 4.00, which is lower than the critical value, indicating that the methods did not differ significantly (p>0.05) from each other in detection of samples as positive or negative. However, RT-PCR had distinct edge over these two tests employed in the study.DOI: http://dx.doi.org/10.3329/bjvm.v9i2.13452

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