scholarly journals A highly endemic area of Echinococcus multilocula is identified through a comparative re-assessment of prevalence in red fox (Vulpes vulpes), Alto Adige (Italy: 2019-2020)

2021 ◽  
Author(s):  
Federica Obber ◽  
Roberto Celva ◽  
Graziana Da Rold ◽  
Karin Trevisiol ◽  
Silvia Ravagnan ◽  
...  
Keyword(s):  
Sample Size ◽  
Gold Standard ◽  
Endemic Area ◽  
Geographic Scale ◽  
Real Time Quantitative Pcr ◽  
True Prevalence ◽  
Southern Border ◽  
Low Prevalence ◽  
Small Geographic Scale ◽  
Higher Sensitivity

Background: Surveillance of E. multilocularis at the edge of its range is hindered by fragmented distributional patterns and low prevalence and burden in definitive hosts. Thus, tests with adequate levels of sensitivity are especially important for discriminating between infected and non-infected areas. Aim: We reassessed the prevalence of E. multilocularis at the southern border of its distribution in Alto Adige (Italy), to improve surveillance in wildlife and provide more accurate estimates of exposure risk. Methods: We compared results from the diagnostic test currently implemented for surveillance (based on Coproscopy+Multiplex PCR - CMPCR), against a real-time quantitative PCR (qPCR) for 235 fox faeces collected in 2019-2020. The performances of the two tests were estimated using a scraping technique (SFCT) as the gold standard applied to the small intestines of a subsample (n=123) of the same hosts. True prevalence was calculated and sample size required by each faecal test for the detection of the parasite was then estimated. Results: True prevalence of E. multilocularis in foxes (14.3%) was definitely higher than reported in the last decade (never >5% from 2012 to 2018). The qPCR also had a higher sensitivity (83%) compared to CMPCR (21%). Agreement with the gold standard was far higher for qPCR (0.816) than CMPCR (0.298) as well, determining a smaller sample size required to detect the disease. Conclusions: Alto Adige should be considered a highly endemic area. Surveillance at the edges of E. multilocularis distribution should adopt qPCR diagnostics on definitive hosts on a small geographic scale.

scholarly journals Diagnosing SARS-CoV-2 with Antigen Testing, Transcription-Mediated Amplification and Real-Time PCR

2021 ◽  
Vol 10 (11) ◽  
pp. 2404
Author(s):  
Sascha Dierks ◽  
Oliver Bader ◽  
Julian Schwanbeck ◽  
Uwe Groß ◽  
Michael Weig ◽  
...  
Keyword(s):  
Real Time ◽  
Sensitivity And Specificity ◽  
Real Time Pcr ◽  
Gold Standard ◽  
Latent Class ◽  
Antigen Assay ◽  
Low Prevalence ◽  
Antigen Testing ◽  
Positive Results ◽  
Higher Sensitivity

This study was performed as a head-to-head comparison of the performance characteristics of (1) two SARS-CoV-2-specific rapid antigen assays with real-time PCR as gold standard as well as (2) a fully automated high-throughput transcription-mediated amplification (TMA) assay and real-time PCR in a latent class analysis-based test comparison without a gold standard with several hundred samples in a low prevalence “real world” setting. Recorded sensitivity and specificity of the NADAL and the LumiraDx antigen assays and the Hologic Aptima SARS-CoV-2 TMA assay were 0.1429 (0.0194, 0.5835), 0.7644 (0.7016, 0.8174), and 0.7157 (0, 1) as well as 0.4545 (0.2022, 0.7326), 0.9954 (0.9817, 0.9988), and 0.9997 (not estimable), respectively. Agreement kappa between the positive results of the two antigen-based assays was 0.060 (0.002, 0.167) and 0.659 (0.492, 0.825) for TMA and real-time PCR. Samples with low viral load as indicated by cycle threshold (Ct) values > 30 were generally missed by both antigen assays, while 1:10 pooling suggested higher sensitivity of TMA compared to real-time PCR. In conclusion, both sensitivity and specificity speak in favor of the use of the LumiraDx rather than the NADAL antigen assay, while TMA results are comparably as accurate as PCR, when applied in a low prevalence setting.

scholarly journals A20 DIAGNOSTIC ACCURACY OF A LOW COST, WIDELY AVAILABLE TEST STRIP FOR PREDICTING A POSITIVE FECAL CALPROTECTIN TEST

2021 ◽  
Vol 4 (Supplement_1) ◽  
pp. 210-212
Author(s):  
R Trasolini ◽  
S Wong ◽  
B Salh
Keyword(s):  
Sample Size ◽  
Likelihood Ratio ◽  
Gold Standard ◽  
Low Cost ◽  
Positive Likelihood Ratio ◽  
Negative Likelihood Ratio ◽  
Rapid Test ◽  
Test Strip ◽  
Fecal Calprotectin ◽  
Type I

Abstract Background Fecal calprotectin is a non-invasive test of colonic inflammation used for monitoring inflammatory bowel disease activity and for risk stratifying non-specific colonic symptoms. Calprotectin is a leukocyte specific enzyme. A similar test, leukocyte esterase is used to detect leukocytes in urine and is widely available as a low-cost point-of-care test strip. We hypothesize that an unmodified version of the urine test strip would be highly accurate in predicting a positive fecal calprotectin test in a real world sample of patients. Aims To explore a low cost, rapid alternative to the fecal calprotectin test Methods All inpatient and outpatient stool samples tested for calprotectin by the Vancouver General Hospital laboratory from February 2020 to November 2020 were included prospectively. Samples were simultaneously tested for fecal leukocyte esterase using an unmodified Roche Cobas Chemstrip urinalysis test strip by central lab personnel. An identical aliquot was sent to LifeLabs for calprotectin as per standard protocol. All samples were suspended in buffer using established laboratory protocols prior to testing. Fecal leukocyte esterase results were reported as 0–4+ based on visual interpretation, calprotectin results were reported as mcg/g of stool. REB review and approval was obtained prior to data collection. Sensitivity, Specificity and AUROC were calculated using Microsoft Excel and JROCFIT. Results 26 samples were collected. Using a fecal calprotectin greater than 120 mcg/g as a gold standard an AUROC of 0.89 (SE= .06) was calculated. A leukocyte esterase reading of 2+ or greater had the best test characteristics based on ROC curve analysis. Using this cutoff, 21/26 samples were concordant, giving an accuracy of 80.8%, sensitivity of 90.9% and specificity of 73.3%. Positive likelihood ratio was 8.07 and negative likelihood ratio was 0.29. Assuming an AUROC of 0.8, the sample size N=26 is 90% powered (β=0.9) to predict the true AUROC within 0.1 with a type I error rate of .05 (α<.05). Conclusions This study suggests application of a prepared stool sample to a urinalysis test strip gives a result highly predictive of a positive fecal calprotectin test. Further results are being collected prospectively to improve the robustness of these preliminary data. Secondary outcomes including comparison to endoscopy and biopsy results where available are planned if an adequate sample size can be accrued. Future studies justifying independent clinical use of leukocyte esterase would require a common gold standard comparator such as endoscopy. Fecal calprotectin testing is not universally insured and is not available as a rapid test strip. Use of fecal leukocyte esterase may reduce costs and shorten time to results if proven to be independently reliable. Funding Agencies None

scholarly journals Frequency of HIV in Obstructive Lung Disease Patients

2018 ◽  
Vol 2 (2) ◽  
pp. 18-25
Author(s):  
Waqas Ahmed ◽  
Qudrat Ullah ◽  
Mughees Ahmed ◽  
Asif Hanif
Keyword(s):  
Lung Disease ◽  
Sample Size ◽  
Obstructive Lung Disease ◽  
Low Frequency ◽  
Smooth Muscle Contraction ◽  
Hiv Positive ◽  
Mortality And Morbidity ◽  
Causes Of Mortality ◽  
Low Prevalence ◽  
Very High

AbstractBackground: Obstructive lung disease (OLD) is one of the main causes of mortality and morbidity worldwide. Obstructive lung disease is the narrowing of bronchioles mainly due to excessive smooth muscle contraction. The objective of this study is to evaluate the Frequency of HIV in obstructive lung disease patients.Methodology: Samples were collected randomly, and study was completed in almost six months. 100 samples were taken with an informed consent taken from all the patients. EDTA and Clotted blood was collected for HIV ELISA and HIV screening.Results: In this study, 69% Males and 31%Females, 34% Smokers, 26% patients were Hypertensive, 10% patients were diabetic, 3% patients were diagnosed HIV positive by screening and ELISA.Conclusion: The frequency of HIV in obstructive lung disease patients in this research is not very high as compared to the previous researches, showing high frequency and relationship between HIV and obstructive lung disease patients. The reason behind low frequency is due to low sample size so by increasing the sample size we can get better understanding of frequency of HIV in obstructive lung disease patients. Another reason of insignificant results is low prevalence of HIV in Pakistan as compared to the previous researches in certain countries. 

scholarly journals Biostatistical Analysis: A Primer for Clinical Exercise Physiology, Part 1

2018 ◽  
Vol 7 (3) ◽  
pp. 63-69
Author(s):  
Suzanne L. Havstad ◽  
George W. Divine
Keyword(s):  
Sample Size ◽  
Gold Standard ◽  
Exercise Physiology ◽  
Analytical Techniques ◽  
Multiple Comparisons ◽  
Inference Process ◽  
P Values ◽  
Advantages And Disadvantages ◽  
Point Estimates ◽  
Biostatistical Analysis

ABSTRACT In this first of a two-part series on introductory biostatistics, we briefly describe common designs. The advantages and disadvantages of six design types are highlighted. The randomized clinical trial is the gold standard to which other designs are compared. We present the benefits of randomization and discuss the importance of power and sample size. Sample size and power calculations for any design need to be based on meaningful effects of interest. We give examples of how the effect of interest and the sample size interrelate. We also define concepts helpful to the statistical inference process. When drawing conclusions from a completed study, P values, point estimates, and confidence intervals will all assist the researcher. Finally, the issue of multiple comparisons is briefly explored. The second paper in this series will describe basic analytical techniques and discuss some common mistakes in the interpretation of data.

scholarly journals Accurate, scalable and integrative haplotype estimation

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Olivier Delaneau ◽  
Jean-François Zagury ◽  
Matthew R. Robinson ◽  
Jonathan L. Marchini ◽  
Emmanouil T. Dermitzakis
Keyword(s):  
Sample Size ◽  
Open Source ◽  
Gold Standard ◽  
Estimation Methods ◽  
Uk Biobank ◽  
Haplotype Estimation ◽  
High Coverage ◽  
Human Genomes ◽  
The Uk

AbstractThe number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.

Relating land cover to stream properties in southern Chilean watersheds: trade-off between geographic scale, sample size, and explicative power

2006 ◽  
Vol 81 (3) ◽  
pp. 313-329 ◽  
Author(s):  
Jaime G. Cuevas ◽  
Doris Soto ◽  
Iván Arismendi ◽  
Mario Pino ◽  
Antonio Lara ◽  
...  
Keyword(s):  
Land Cover ◽  
Sample Size ◽  
Geographic Scale ◽  
Trade Off

scholarly journals Variation in trophic resources in female South American sea lions at a small geographic scale

2020 ◽  
Author(s):  
M. Florencia Grandi ◽  
Damián G. Vales ◽  
Enrique A. Crespo ◽  
Rocío Loizaga
Keyword(s):  
South American ◽  
Geographic Scale ◽  
Sea Lions ◽  
Trophic Resources ◽  
Small Geographic Scale

scholarly journals ROC Curves in Clinical Chemistry: Uses, Misuses, and Possible Solutions

2004 ◽  
Vol 50 (7) ◽  
pp. 1118-1125 ◽  
Author(s):  
Nancy A Obuchowski ◽  
Michael L Lieber ◽  
Frank H Wians
Keyword(s):  
Phase I ◽  
Sample Size ◽  
Gold Standard ◽  
Diagnostic Tests ◽  
Clinical Laboratory ◽  
Clinical Chemistry ◽  
Roc Curves ◽  
Sample Size Determination ◽  
Phase Iii ◽  
Test Accuracy

Abstract Background: ROC curves have become the standard for describing and comparing the accuracy of diagnostic tests. Not surprisingly, ROC curves are used often by clinical chemists. Our aims were to observe how the accuracy of clinical laboratory diagnostic tests is assessed, compared, and reported in the literature; to identify common problems with the use of ROC curves; and to offer some possible solutions. Methods: We reviewed every original work using ROC curves and published in Clinical Chemistry in 2001 or 2002. For each article we recorded phase of the research, prospective or retrospective design, sample size, presence/absence of confidence intervals (CIs), nature of the statistical analysis, and major analysis problems. Results: Of 58 articles, 31% were phase I (exploratory), 50% were phase II (challenge), and 19% were phase III (advanced) studies. The studies increased in sample size from phase I to III and showed a progression in the use of prospective designs. Most phase I studies were powered to assess diagnostic tests with ROC areas ≥0.70. Thirty-eight percent of studies failed to include CIs for diagnostic test accuracy or the CIs were constructed inappropriately. Thirty-three percent of studies provided insufficient analysis for comparing diagnostic tests. Other problems included dichotomization of the gold standard scale and inappropriate analysis of the equivalence of two diagnostic tests. Conclusion: We identify available software and make some suggestions for sample size determination, testing for equivalence in diagnostic accuracy, and alternatives to a dichotomous classification of a continuous-scale gold standard. More methodologic research is needed in areas specific to clinical chemistry.

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