scholarly journals Kesesuaian Hasil Pemeriksaan RT PCR, RDT NS1, dan RDT IgM Pasien Penyakit Dengue

2016 ◽  
Vol 2 (2) ◽  
pp. 56
Author(s):  
Paisal Paisal ◽  
Mukhlis Zuardi ◽  
Reni Herman
Keyword(s):  
Mortality Rate ◽  
Rt Pcr ◽  
Laboratory Examination ◽  
Cohen’S Kappa ◽  
Dengue Disease ◽  
Kappa Test ◽  
Cohen's Kappa ◽  
The World ◽  
Aceh Province ◽  
Test Result

<p style="text-align: justify;">The incidence of dengue disease in the world is estimated at 390 million cases per year. In Indonesia, during 2013 there were 35-40 cases per 100.000 population, with a mortality rate of 0.73%. This study aimed to determine the suitability and the percentage of RT-PCR, RDT NS1, and RDT IgM detection examination. Samples were obtained from hospitals in Aceh province during 2012. The research samples reached 100 collected samples, it was only 82 samples that fulfill the analysis criteria. Cohen’s Kappa test result showed there was moderate suitability between RT-PCR and RDT NS1 (K=0,404, p = 0,000), and weak suitability between RT-PCR began RDT IgM (K=0,139, p = 0,046). While the percentage of detection for RT-PCR, RDT NS1, dan RDT IgM were 16%, 10%, and 60%. RDT IgM is the best alternative for laboratory examination in the hospital.

scholarly journals Diagnostic performances and thresholds: the key to harmonization in serological SARS-CoV-2 assays?

2020 ◽  
Author(s):  
Mario Plebani ◽  
Andrea Padoan ◽  
Davide Negrini ◽  
Benedetta Carpinteri ◽  
Laura Sciacovelli
Keyword(s):  
Likelihood Ratio ◽  
Negative Likelihood Ratio ◽  
Rt Pcr ◽  
Likelihood Ratios ◽  
Cohen’S Kappa ◽  
Viral Spread ◽  
Cohen's Kappa ◽  
Polymerase Chain ◽  
Diagnostic Sensitivity And Specificity ◽  
Test Result

Background: The evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific antibody (Ab) assay performances is of the utmost importance in establishing and monitoring virus spread in the community. In this study focusing on IgG antibodies, we compare reliability of three chemiluminescent (CLIA) and two enzyme linked immunosorbent (ELISA) assays. Methods: Sera from a total of 271 subjects, including 64 reverse transcription-polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 patients were tested for specific Ab using Maglumi (Snibe), Liaison (Diasorin), iFlash (Yhlo), Euroimmun (Medizinische Labordiagnostika AG) and Wantai (Wantai Biological Pharmacy) assays. Diagnostic sensitivity and specificity, positive and negative likelihood ratios were evaluated using manufacturers' and optimized thresholds. Results: Optimized thresholds (Maglumi 2 kAU/L, Liaison 6.2 kAU/L and iFlash 15.0 kAU/L) allowed us to achieve a negative likelihood ratio and an accuracy of: 0.06 and 93.5% for Maglumi; 0.03 and 93.1% for Liaison; 0.03 and 91% for iFlash. Diagnostic sensitivities and specificities were above 93.8% and 85.9%, respectively for all CLIA assays. Overall agreement was 90.3% (Cohen's kappa = 0.805 and SE = 0.041) for CLIA, and 98.4% (Cohen's kappa = 0.962 and SE = 0.126) for ELISA. Conclusions: The results obtained indicate that, for CLIA assays, it might be possible to define thresholds that improve the negative likelihood ratio. Thus, a negative test result enables the identification of subjects at risk of being infected, who should then be closely monitored over time with a view to preventing further viral spread. Redefined thresholds, in addition, improved the overall inter-assay agreement, paving the way to a better harmonization of serologic tests.

scholarly journals Imunocompetent Mice Model for Dengue Virus Infection

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Denise Gonçalves ◽  
Rafael de Queiroz Prado ◽  
Eric Almeida Xavier ◽  
Natália Cristina de Oliveira ◽  
Paulo Marcos da Matta Guedes ◽  
...  
Keyword(s):  
Animal Model ◽  
Virus Infection ◽  
Dengue Virus ◽  
Viral Disease ◽  
Mice Model ◽  
Rt Pcr ◽  
Dengue Virus Infection ◽  
Dengue Disease ◽  
The Family ◽  
The World

Dengue fever is a noncontagious infectious disease caused by dengue virus (DENV). DENV belongs to the familyFlaviviridae, genusFlavivirus, and is classified into four antigenically distinct serotypes: DENV-1, DENV-2, DENV-3, and DENV-4. The number of nations and people affected has increased steadily and today is considered the most widely spread arbovirus (arthropod-borne viral disease) in the world. The absence of an appropriate animal model for studying the disease has hindered the understanding of dengue pathogenesis. In our study, we have found that immunocompetent C57BL/6 mice infected intraperitoneally with DENV-1 presented some signs of dengue disease such as thrombocytopenia, spleen hemorrhage, liver damage, and increase in production of IFNγand TNFαcytokines. Moreover, the animals became viremic and the virus was detected in several organs by real-time RT-PCR. Thus, this animal model could be used to study mechanism of dengue virus infection, to test antiviral drugs, as well as to evaluate candidate vaccines.

scholarly journals Flow Cytometry in Detecting Resistant E. Coli Strains

2017 ◽  
Vol 5 (5) ◽  
pp. 592-594
Author(s):  
Lyudmila Akhmaltdinova ◽  
Alyona Lavrinenko ◽  
Ilya Belyayev
Keyword(s):  
Flow Cytometry ◽  
Fluorescent Dyes ◽  
Antibiotic Sensitivity ◽  
Relative Accuracy ◽  
Diagnostic Methods ◽  
Cohen’S Kappa ◽  
E Coli ◽  
Kappa Test ◽  
Cohen's Kappa ◽  
Relative Specificity

Antibacterial drugs are the most consumed group of drugs in the modern hospitals. Standard methods of antibiotic sensitivity are labour and time-consuming, taking up to 24 hours after the pure culture is isolated (the analysis typically lasts up to 72 hours). Working out express diagnostic methods is of importance, and studies are made in various directions. Flow cytometry in detecting resistant E.coli strains was used. Flow cytometry fluorescent dyes were used to stain viable and dead cells. For method validation, relative accuracy, relative susceptibility, relative specificity and Cohen’s kappa test were determined compared to the delusion test. Cytometry method showed acceptable results on the model of E.coli. Relative accuracy comprised 88.8%, sensitivity - 85.7%, specificity was 88.8%, Cohen’s kappa test showed value 0.524, which is a medium agreement between the measurements by different methods.

scholarly journals Evaluation of the similarity between drought indices by correlation analysis and Cohen's Kappa test in a Mediterranean area

2021 ◽  
Author(s):  
L. Vergni ◽  
F. Todisco ◽  
B. Di Lena
Keyword(s):  
Correlation Analysis ◽  
Pearson Correlation ◽  
Central Italy ◽  
Meteorological Drought ◽  
Drought Indices ◽  
Drought Severity ◽  
Cohen’S Kappa ◽  
Kappa Test ◽  
Cohen's Kappa ◽  
Standardised Precipitation Index

AbstractIn the literature, numerous papers report comparative analyses of drought indices. In these types of studies, the similarity between drought indices is usually evaluated using the Pearson correlation coefficient, r, calculated between corresponding severity time series. However, it is well known that the correlation does not describe the strength of agreement between two variables. Two drought indices can exhibit a high degree of correlation but can, at the same time, disagree substantially, for example, if one index is consistently higher than the other. From an operational point of view, two indices can be considered in agreement when they indicate the same severity category for a given period (e.g. moderate drought). In this work, we compared six meteorological drought indices based on both correlation analysis and Cohen's Kappa test. This test is typically used in medical or social sciences to obtain a quantitative assessment of the degree of agreement between different methods or analysts. The indices considered are five timescale-dependent indices, i.e. the Percent of Normal Index, the Deciles Index, the Percentile Index, the Rainfall Anomaly Index, and the Standardised Precipitation Index, computed at the 1-, 3-, and 6-month timescales, and the Effective Drought Index, a relatively new index, which has a self-defined timescale. The indices were calculated for 15 stations in the Abruzzo region (central Italy) during 1951–2018. We found that the strength of agreement depends on both the criteria of drought severity classification and the different indices' calculation method. The Cohen's Kappa test indicates a prevailing moderate or fair agreement among the indices considered, despite the generally very high correlation between the corresponding severity times series. The results demonstrate that the Cohen's Kappa test is more effective than the correlation analysis in discriminating the actual strength of agreement/disagreement between drought indices.

scholarly journals Lung Ultrasound Is More Sensitive for Hospitalized Consolidated Pneumonia Diagnosis Compared to CXR in Children

Children ◽  
2021 ◽  
Vol 8 (8) ◽  
pp. 659
Author(s):  
Ioana Mihaiela Ciuca ◽  
Mihaela Dediu ◽  
Monica Steluta Marc ◽  
Mirabela Lukic ◽  
Delia Ioana Horhat ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Lung Ultrasound ◽  
Clinical Suspicion ◽  
Cohen’S Kappa ◽  
Perfect Agreement ◽  
Kappa Test ◽  
Cohen's Kappa ◽  
Child Pneumonia ◽  
Chest X Ray ◽  
Pneumonia Diagnosis

Background: Pneumonia is the leading cause of death among children; thus, a correct early diagnosis would be ideal. The imagistic diagnosis still uses chest X-ray (CXR), but lung ultrasound (LUS) proves to be reliable for pneumonia diagnosis. The aim of our study was to evaluate the sensitivity and specificity of LUS compared to CXR in consolidated pneumonia. Methods: Children with clinical suspicion of bacterial pneumonia were screened by LUS for pneumonia, followed by CXR. The agreement relation between LUS and CXR regarding the detection of consolidation was evaluated by Cohen’s kappa test. Results: A total of 128 patients with clinical suspicion of pneumonia were evaluated; 74 of them were confirmed by imagery and biological inflammatory markers. The highest frequency of pneumonia was in the 0–3 years age group (37.83%). Statistical estimation of the agreement between LUS and CXR in detection of the consolidation found an almost perfect agreement, with a Cohen’s kappa coefficient of K = 0.89 ± 0.04 SD, p = 0.000. Sensitivity of LUS was superior to CXR in detection of consolidations. Conclusion: Lung ultrasound is a reliable method for the detection of pneumonia consolidation in hospitalized children, with sensitivity and specificity superior to CXR. LUS should be used for rapid and safe evaluation of child pneumonia.

scholarly journals Validation of Snort-spit Saliva in Detecting COVID-19 Using RT-PCR and Rapid Antigen Detection Test

2021 ◽  
Vol 55 (2) ◽  
Author(s):  
RYNER JOSE CARRILLO ◽  
Abigail D. Sarmiento ◽  
Mark Anthony C. Ang ◽  
Michelle H. Diwa ◽  
Cecille C. Dungog ◽  
...  
Keyword(s):  
Likelihood Ratio ◽  
Predictive Value ◽  
Positive Likelihood Ratio ◽  
Negative Likelihood Ratio ◽  
Lateral Flow ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Cohen’S Kappa ◽  
Cohen's Kappa ◽  
Antigen Testing

Objective. To determine the diagnostic accuracy of self-collected snorted and spit saliva in detecting COVID-19 using RT-PCR (ssRT-PCR) and lateral flow antigen test (ssLFA) versus nasopharyngeal swab RT-PCR (npRT-PCR). Methods. One hundred ninety-seven symptomatic subjects for COVID-19 testing in a tertiary hospital underwent snort-spit saliva self-collection for RT-PCR and antigen testing and nasopharyngeal swab for RT-PCR as reference. Positivity rates, agreement, sensitivity, specificity, and likelihood ratios were estimated. Results. Estimated prevalence of COVID-19 using npRT-PCR was 9% (exact 95% CI of 5.5% - 14.1%). A higher positivity rate of 13% in the ssRT-PCR assay suggested possible higher viral RNA in the snort-spit samples. There was 92.9% agreement between ssRT-PCR and npRT-PCR (exact 95% CI of 88.4% to 96.1%; Cohen’s Kappa of 0.6435). If npRT-PCR will be assumed as reference standard, the estimated Sensitivity was 83.3% (exact 95% CI of 60.8% to 94.2%), Specificity 93.9% (exact 95% CI of 89.3% to 96.5%), Positive predictive value of 57.7% (exact 95% CI of 38.9% to 74.5%), Negative predictive value of 98.2% (exact 95% CI of 95% to 99.4%), positive likelihood ratio of 3.65 (95% CI of 7.37 to 24.9), negative likelihood ratio of 0.178 (95% CI of 0.063 to 0.499). There was 84.84% agreement (95% exact CI of 79.1% to 89.5%; Cohen’s Kappa of 0.2356) between ssLFAvs npRT-PCR, sensitivity of 38.9% (exact 95% CI of 20.3% to 61.4%), specificity of 89.4% (exact 95% CI of 84.1% to 93.1%), PPV of 26.9% (95% CI of 13.7% to 46.1%), NPV of 93.6% (exact 95% CI of 88.8% to 96.4%), LR+ of 3.67 (95% CI of 1.79 - 7.51), LR – of 0.68 (95% CI of 0.47 - 0.99). Conclusion. Our data showed that snort-spit saliva RT-PCR testing had acceptable diagnostic performance characteristics and can potentially be used as an alternative to the standard nasopharyngeal/oropharyngeal swab RT-PCR test for COVID-19 in certain situations. However, our data also showed that snort-spit saliva antigen testing using lateral flow assay did not offer acceptable performance.

scholarly journals Nasal-Swab Testing Misses Patients with Low SARS-CoV-2 Viral Loads

2020 ◽  
Author(s):  
Cody Callahan ◽  
Rose A. Lee ◽  
Ghee Rye Lee ◽  
Kate Zulauf ◽  
James E. Kirby ◽  
...  
Keyword(s):  
Large Scale ◽  
Nasal Swab ◽  
Limit Of Detection ◽  
Contact Tracing ◽  
Healthcare Personnel ◽  
Rt Pcr ◽  
Cohen’S Kappa ◽  
Viral Loads ◽  
Cohen's Kappa ◽  
High Concordance

AbstractThe urgent need for large-scale diagnostic testing for SARS-CoV-2 has prompted pursuit of sample-collection methods of sufficient sensitivity to replace sampling of the nasopharynx (NP). Among these alternatives is collection of nasal-swab samples, which can be performed by the patient, avoiding the need for healthcare personnel and personal protective equipment.Previous studies have reached opposing conclusions regarding whether nasal sampling is concordant or discordant with NP. To resolve this disagreement, we compared nasal and NP specimens collected by healthcare workers in a cohort consisting of individuals clinically suspected of COVID-19 and outpatients known to be SARS-CoV-2 RT-PCR positive undergoing follow-up. We investigated three different transport conditions, including traditional viral transport media (VTM) and dry swabs, for each of two different nasal-swab collection protocols on a total of 308 study participants, and compared categorical results and Ct values to those from standard NP swabs collected at the same time from the same patients. All testing was performed by RT-PCR on the Abbott SARS-CoV-2 RealTime EUA (limit of detection [LoD], 100 copies viral genomic RNA/mL transport medium). We found high concordance (Cohen’s kappa >0.8) only for patients with viral loads above 1,000 copies/mL. Those with viral loads below 1,000 copies/mL, the majority in our cohort, exhibited low concordance (Cohen’s kappa = 0.49); most of these would have been missed by nasal testing alone. Previous reports of high concordance may have resulted from use of assays with higher LoD (≥1,000 copies/mL). These findings counsel caution in use of nasal testing in healthcare settings and contact-tracing efforts, as opposed to screening of asymptomatic, low-prevalence, low-risk populations. Nasal testing is an adjunct, not a replacement, for NP.

scholarly journals Lateral throat form classification using a customized gauge and Neil’s method – a comparative study

2018 ◽  
Vol 8 (4) ◽  
pp. 54-57
Author(s):  
Sabina Poudel ◽  
Minu Dhungana ◽  
Rajani Karki ◽  
Prabhat Shrestha
Keyword(s):  
Geriatric Patients ◽  
Observer Variation ◽  
Observer Agreement ◽  
Cohen’S Kappa ◽  
Kappa Test ◽  
Cohen's Kappa ◽  
Kappa Value ◽  
Edentulous Patients ◽  
Observer Accuracy ◽  
Good Agreement

Introduction: Lateral throat form (LTF) is the critical area which has to be recorded properly for obtaining proper retention and stability in complete denture especially in geriatric patients with resorbed ridges. Popular method used for determining LTF is Neil’s method which depends on the forces applied by the floor of mouth when the tongues protrude out. Since the perception of the forces differs among different operators, there are high chances of error in the classification. So, customized instrument was fabricated to prevent this inter-observer variation. The aim of the study was to compare the inter-observer accuracy between Neil’s method of classifi­cation and classification done by customized gauze. Methods and methodology: Total 30 edentulous patients were taken. Two observers measured the LTF depth by customized tool and also by Neil’s method. Cohen’s kappa test was used to evaluate the agreement between two operators in two different classifications. Result: The agreement between the two observers was evaluated by means of Cohen’s kappa value. There was good agreement between observers in proposed classification done by customized tool with kappa value 0.658 and fair inter-observer agreement with kappa value 0.0492. Conclusion: The method of measuring the depth of LTF with fabricated instrument was more accurate and reliable than Neil’s method.

scholarly journals Developing geriatric face makeup enrichment book for students of Skin Beauty program in vocational high school

2020 ◽  
Vol 10 (2) ◽  
Author(s):  
Pramesti Adika Ratri ◽  
Siti Hamidah
Keyword(s):  
High School ◽  
Kappa Coefficient ◽  
Vocational High School ◽  
Cohen’S Kappa ◽  
Ability Test ◽  
Gain Score ◽  
Kappa Test ◽  
Cohen's Kappa ◽  
Cohen’S Kappa Coefficient

This research aims to: (1) produce a Geriatric Makeup Enrichment book as a teaching material of geriatric makeup for students of Purworejo 3 Vocational High School majoring in Beauty that is feasible and effective . This research is research and development applying the four-D. The product feasibility tests were carried out by two material experts and two media experts by validated the enrichment book through a questionnaire using a Likert scale was analyzed using conversion scores into four quantitative categories then tested the agreement between experts through the Cohen's Kappa test and its effectiveness was tested with a one-group case study technique and analyzed with gain scores. The subjects of this research trial were students of class XI Beauty in Purworejo 3 Vocational High School The data collection instruments used are observation guidelines, interview guidelines, experts’ validation questionnaire, teachers’ response questionnaire, students’ response questionnaire and ability test The research results are as follows. The enrichment book developed met the feasibility criteria according to material experts with a score of 3.59 (excellent) and there was agreement between material expert with a Cohen’s Kappa coefficient of 0.64 (good) Tthen, met the feasibility criteria according to media experts with a score of 3.70 (excellent) and there was an agreement between media with a Cohen’s Kappa coefficient value of 1.00 (excellent). Enrichment book developed was declared effective for use in XI grade students of Purworejo 3 Vocational High School majoring in Beauty and was included in medium category for value understanding with the gain score 0.5 and in a high category in skill value with the gain score 0.71.

scholarly journals Porcine Reproductive and Respiratory Syndrome Surveillance in breeding Herds and Nurseries Using Tongue Tips from Dead Animals

2021 ◽  
Vol 8 (11) ◽  
pp. 259
Author(s):  
Jordi Baliellas ◽  
Elena Novell ◽  
Vicens Enric-Tarancón ◽  
Carles Vilalta ◽  
Lorenzo Fraile
Keyword(s):  
Serum Sample ◽  
Kappa Statistic ◽  
Diagnostic Information ◽  
Respiratory Syndrome Virus ◽  
Rt Pcr ◽  
Cohen’S Kappa ◽  
Cohen's Kappa ◽  
Concordance Test ◽  
Syndrome Surveillance

The detection capacity of Porcine Reproductive and Respiratory Syndrome virus (PRRSV) in tongues from dead animals in breeding herds (stillborns and piglets dying during the lactating period) and nursery farms (naturally dead animals) for PRRSV surveillance was evaluated. The samples were selected if pairs of serum and tongues were available from 2018 to 2020. Serum (pools of five) and exudate from tongues (one bag) were analyzed by PRRSV RT-PCR. The agreement between the serum sample procedure versus tongues exudate was assessed using a concordance test (Kappa statistic) at batch level. A total of 32 submissions, corresponding to 14 farms, had PRRSV diagnostic information for serum and tongues exudate. The overall agreement of batch classification as positive or negative, based on RT-PCR PRRSV results, between serum and tongue exudate of the 32 pairs was 76.9%. Cohen’s Kappa was 0.55. The main discrepancy came from the presence of positive samples in tongues exudate and not in serum, suggesting that tongue exudate to monitor PRRSV seems to be more sensitive than serum. These results suggest that this sample procedure could be also used for PRRSV surveillance and monitoring.

Sign in / Sign up

Export Citation Format

Share Document