Comparative performance of three test methods for determining chipping quality in tubers of potato (Solanum tuberosum L.)

1999 ◽  
Vol 79 (4) ◽  
pp. 625-632 ◽  
Author(s):  
Warren K. Coleman ◽  
G. C. C. Tai
Keyword(s):  
Operating Characteristic ◽  
Unit Cost ◽  
False Negative ◽  
Test Methods ◽  
Curve Analysis ◽  
Cost Ratio ◽  
Data Sets ◽  
Glucose Content ◽  
Chipping Quality ◽  
Colour Chart

The capacity of a colour chart and a reflectance photometer (Agtron) to accurately determine chipping quality of potato tubers was assessed using data sets taken over a 4-yr period for 17–32 cultivars. Both tests gave a high diagnostic accuracy for chipping quality regardless of sampling time from storage or the occurrence of high temperature reconditioning when evaluated by receiver operating characteristic (ROC) curve analysis. Receiver operating characteristic curve analysis showed that both tuber glucose content and chip colour provided good diagnostic performance in correctly separating processing from non-processing tubers over a range of growing and storage conditions. Identification of chipping from non-chipping tuber samples from a 13 °C storage across a range of cultivars and growing conditions occurred with a minimum chipping colour threshold range of 41–47 or a maximum glucose concentration range of 4.3–5.4 mmol L−1 of tuber cell sap. The practical value of a test can depend on such factors as prevalence of chippers in a tuber population as well as the cost of misclassifications, i.e., costs associated with false positive or false negative test results and expressed in relative terms as the unit cost ratio. An examination of Prevalence-Value-Accuracy (PVA) plots for one of the data sets indicated that total misclassification costs could increase rapidly, depending on the prevalence of chipping tubers and the relative amounts of false negative and false positive costs. Maximum costs were consistently associated with a prevalence of 50% chippers and a unit cost ratio of 0.5. In a tuber sample containing a high prevalence of chippers (50–70%) and a low unit cost ratio (<0.2), an acceptable colour threshold determined by PVA-Threshold (PVAT) plots would be approximately 40 to 50 from the Agriculture and Agri-Food Canada colour chart. However, if the colour chart was used for screening tuber samples with a low prevalence (20–40%) of chippers and a unit cost ratio >0.20, a threshold between 60 and 65 would be optimum. The latter range would be conservative and agrees with, and supports, current industry standards, which reside at 60 or better. Since a good diagnostic test should be repeatable and subject to minimal inter-observer variation, the more objective glucose or reflectance photometric tests may be preferable and provide acceptable diagnostic accuracy for processing quality. However, the present study indicates that all three test methods are acceptable for accurately separating chipping from non-chipping tubers regardless of sampling or storage protocols. Key words: Potato, colour chart, reflectance colorimetry, glucose content

scholarly journals Clinical Exome Performance for Reporting Secondary Genetic Findings

2015 ◽  
Vol 61 (1) ◽  
pp. 213-220 ◽  
Author(s):  
Jason Y Park ◽  
Peter Clark ◽  
Eric Londin ◽  
Marialuisa Sponziello ◽  
Larry J Kricka ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
False Negative ◽  
Gc Content ◽  
Test Methods ◽  
Data Sets ◽  
Sequencing Data ◽  
Exome Data ◽  
Sequencing Coverage ◽  
Mutation Database ◽  
Genetics And Genomics

Abstract BACKGROUND Reporting clinically actionable incidental genetic findings in the course of clinical exome testing is recommended by the American College of Medical Genetics and Genomics (ACMG). However, the performance of clinical exome methods for reporting small subsets of genes has not been previously reported. METHODS In this study, 57 exome data sets performed as clinical (n = 12) or research (n = 45) tests were retrospectively analyzed. Exome sequencing data was examined for adequacy in the detection of potentially pathogenic variant locations in the 56 genes described in the ACMG incidental findings recommendation. All exons of the 56 genes were examined for adequacy of sequencing coverage. In addition, nucleotide positions annotated in HGMD (Human Gene Mutation Database) were examined. RESULTS The 56 ACMG genes have 18 336 nucleotide variants annotated in HGMD. None of the 57 exome data sets possessed a HGMD variant. The clinical exome test had inadequate coverage for &gt;50% of HGMD variant locations in 7 genes. Six exons from 6 different genes had consistent failure across all 3 test methods; these exons had high GC content (76%–84%). CONCLUSIONS The use of clinical exome sequencing for the interpretation and reporting of subsets of genes requires recognition of the substantial possibility of inadequate depth and breadth of sequencing coverage at clinically relevant locations. Inadequate depth of coverage may contribute to false-negative clinical exome results.

scholarly journals A Statistical Comparison of the Blossom Blight Forecasts of MARYBLYT and Cougarblight with Receiver Operating Characteristic Curve Analysis

2007 ◽  
Vol 97 (9) ◽  
pp. 1164-1176 ◽  
Author(s):  
M. M. Dewdney ◽  
A. R. Biggs ◽  
W. W. Turechek
Keyword(s):  
Receiver Operating Characteristic ◽  
Roc Curve ◽  
Fire Blight ◽  
Operating Characteristic ◽  
Curve Analysis ◽  
Data Sets ◽  
Risk Threshold ◽  
Geographic Regions ◽  
Pairwise Contrasts ◽  
Receiver Operating

Blossom blight forecasting is an important aspect of fire blight, caused by Erwinia amylovora, management for both apple and pear. A comparison of the forecast accuracy of two common fire blight forecasters, MARYBLYT and Cougarblight, was performed with receiver operating characteristic (ROC) curve analysis and 243 data sets. The rain threshold of Cougarblight was analyzed as a separate model termed Cougarblight and rain. Data were used as a whole and then grouped into geographic regions and cultivar susceptibilities. Frequency distributions of cases and controls, orchards or regions (depending on the data set), with and without observed disease, respectively, in all data sets overlapped. MARYBLYT, Cougarblight, and Cougarblight and rain all predicted blossom blight infection better than chance (P = 0.05). It was found that the blossom blight forecasters performed equivalently in the geographic regions of the east and west coasts of North America and moderately susceptible cultivars based on the 95% confidence intervals and pairwise contrasts of the area under the ROC curve. Significant differences (P < 0.05) between the forecasts of Cougarblight and MARYBLYT were found with pairwise contrasts in the England and very susceptible cultivar data sets. Youden's index was used to determine the optimal cutpoint of both forecasters. The greatest sensitivity and specificity for MARYBLYT coincided with the use of the highest risk threshold for predictions of infection; with Cougarblight, there was no clear single risk threshold across all data sets.

Serum miR-21 and miR-26a Levels Negatively Correlate with Severity of Cirrhosis in Patients with Chronic Hepatitis B

MicroRNA ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 86-92 ◽  
Author(s):  
Shili Jiang ◽  
Wei Jiang ◽  
Ying Xu ◽  
Xiaoning Wang ◽  
Yongping Mu ◽  
...  
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis B ◽  
Chronic Hepatitis B ◽  
Operating Characteristic ◽  
Characteristic Curve ◽  
Curve Analysis ◽  
Pugh Class ◽  
Operating Characteristic Curve ◽  
Class C ◽  
Circulating Levels

Background and Objective: Accurately evaluating the severity of liver cirrhosis is essential for clinical decision making and disease management. This study aimed to evaluate the value of circulating levels of microRNA (miR)-26a and miR-21 as novel noninvasive biomarkers in detecting severity of cirrhosis in patients with chronic hepatitis B. </P><P> Methods: Thirty patients with clinically diagnosed chronic hepatitis B-related cirrhosis and 30 healthy individuals were selected. The serum levels of miR-26a and miR-21 were quantified by qRT-PCR. Receiver operating characteristic curve analysis was performed to evaluate the sensitivity and specificity of the miRNAs for detecting the severity of cirrhosis. Results: Serum miR-26a and miR-21 levels were found to be significantly downregulated in patients with severe cirrhosis scored at Child-Pugh class C in comparison to healthy controls (miR-26a p<0.01, and miR-21 p<0.001, respectively). The circulating miR-26a and miR-21 levels in patients were positively correlated with serum albumin concentration but negatively correlated with serum total bilirubin concentration and prothrombin time. Receiver operating characteristic curve analysis revealed that both serum miR-26a and miR-21 levels were associated with a high diagnostic accuracy for patients with cirrhosis scored at Child-Pugh class C (miR-26a Cut-off fold change at ≤0.4, Sensitivity: 84.62%, Specificity: 89.36%, P<0.0001; miR-21 Cut-off fold change at ≤0.6, Sensitivity: 84.62%, Specificity: 78.72%, P<0.0001). Our results indicate that the circulating levels of miR-26a and miR-21 are closely related to the extent of liver decompensation, and the decreased levels are capable of discriminating patients with cirrhosis at Child-Pugh class C from the whole cirrhosis cases.

A validated novel preoperative index to predict the extent of intraperitoneal contamination in patients with acute abdominal pathology: A cohort study

2019 ◽  
Vol 30 (7-8) ◽  
pp. 221-228
Author(s):  
Shahab Hajibandeh ◽  
Shahin Hajibandeh ◽  
Nicholas Hobbs ◽  
Jigar Shah ◽  
Matthew Harris ◽  
...  
Keyword(s):  
Receiver Operating Characteristic Curve ◽  
Receiver Operating Characteristic ◽  
Operating Characteristic ◽  
Validation Cohort ◽  
Characteristic Curve ◽  
Curve Analysis ◽  
Emergency Laparotomy ◽  
Contamination Index ◽  
Operating Characteristic Curve ◽  
Receiver Operating

Aims To investigate whether an intraperitoneal contamination index (ICI) derived from combined preoperative levels of C-reactive protein, lactate, neutrophils, lymphocytes and albumin could predict the extent of intraperitoneal contamination in patients with acute abdominal pathology. Methods Patients aged over 18 who underwent emergency laparotomy for acute abdominal pathology between January 2014 and October 2018 were randomly divided into primary and validation cohorts. The proposed intraperitoneal contamination index was calculated for each patient in each cohort. Receiver operating characteristic curve analysis was performed to determine discrimination of the index and cut-off values of preoperative intraperitoneal contamination index that could predict the extent of intraperitoneal contamination. Results Overall, 468 patients were included in this study; 234 in the primary cohort and 234 in the validation cohort. The analyses identified intraperitoneal contamination index of 24.77 and 24.32 as cut-off values for purulent contamination in the primary cohort (area under the curve (AUC): 0.73, P < 0.0001; sensitivity: 84%, specificity: 60%) and validation cohort (AUC: 0.83, P < 0.0001; sensitivity: 91%, specificity: 69%), respectively. Receiver operating characteristic curve analysis also identified intraperitoneal contamination index of 33.70 and 33.41 as cut-off values for feculent contamination in the primary cohort (AUC: 0.78, P < 0.0001; sensitivity: 87%, specificity: 64%) and validation cohort (AUC: 0.79, P < 0.0001; sensitivity: 86%, specificity: 73%), respectively. Conclusions As a predictive measure which is derived purely from biomarkers, intraperitoneal contamination index may be accurate enough to predict the extent of intraperitoneal contamination in patients with acute abdominal pathology and to facilitate decision-making together with clinical and radiological findings.

scholarly journals Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform

2020 ◽  
Author(s):  
William A Freyman ◽  
Kimberly F McManus ◽  
Suyash S Shringarpure ◽  
Ethan M Jewett ◽  
Katarzyna Bryc ◽  
...  
Keyword(s):  
Isolation By Distance ◽  
False Negative ◽  
Segment Length ◽  
Data Sets ◽  
Haplotype Sharing ◽  
Binary File ◽  
Inference Algorithms ◽  
Out Of Sample ◽  
Massive Scale ◽  
Burrows Wheeler Transform

Abstract Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer (DTC) genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows-Wheeler transform (TPBWT) to make fast IBD estimates robust to genotype and phasing errors. Using haplotype data simulated over pedigrees with realistic genotyping and phasing errors we show that the TPBWT outperforms other state-of-the-art IBD inference algorithms in terms of speed and accuracy. For each phase-aware method, we explore the false positive and false negative rates of inferring IBD by segment length and characterize the types of error commonly found. Our results highlight the fragility of most phased IBD inference methods; the accuracy of IBD estimates can be highly sensitive to the quality of haplotype phasing. Additionally we compare the performance of the TPBWT against a widely used phase-free IBD inference approach that is robust to phasing errors. We introduce both in-sample and out-of-sample TPBWT-based IBD inference algorithms and demonstrate their computational efficiency on massive-scale datasets with millions of samples. Furthermore we describe the binary file format for TPBWT-compressed haplotypes that results in fast and efficient out-of-sample IBD computes against very large cohort panels. Finally, we demonstrate the utility of the TPBWT in a brief empirical analysis exploring geographic patterns of haplotype sharing within Mexico. Hierarchical clustering of IBD shared across regions within Mexico reveals geographically structured haplotype sharing and a strong signal of isolation by distance. Our software implementation of the TPBWT is freely available for non-commercial use in the code repository https://github.com/23andMe/phasedibd.

scholarly journals AB0644 EVALUATION OF MONOCYTE TO HIGH-DENSITY LIPOPROTEIN RATIO AND CAROTID INTIMA MEDIA THICKNESS IN GOUT PATIENTS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1355.1-1355
Author(s):  
C. Kadiyoran ◽  
A. Kucuk ◽  
H. Aydemir ◽  
A. U. Uslu
Keyword(s):  
High Density Lipoprotein ◽  
Operating Characteristic ◽  
Characteristic Curve ◽  
Density Lipoprotein ◽  
Intima Media Thickness ◽  
Carotid Intima Media Thickness ◽  
Curve Analysis ◽  
High Density ◽  
Media Thickness ◽  
Operating Characteristic Curve

Background:The aim of this study is to investigate, evaluation of monocyte to high density liporotein ratio and carotid intima media thickness in gout patients.Objectives:Gout disease is an autoinflammatory disease caused by the accumulation of monosodium urate crystals (MSU) in tissues and organs due to hyperuricemia (1). It is a common cause of arthritis due to the changes in lifestyle and eating habits. The effects of the inflammatory process and hyperuricemia in gout are not limited to the joints, but are associated with increased atherosclerosis and cardiovascular disease (1,2) Monocyte to high-density lipoprotein cholesterol ratio (MHR) is a systemic inflammatory marker and has recently been used quite widely for the evaluation of inflammation in cardiovascular disorders (3,4).Methods:Fourty eight patients who were evaluated in the rheumatology clinic with an arthritis attack and diagnosed with Gout, and 48 healthy individuals whose age, gender and body mass index were matched were included in our study. Basic laboratory and biochemical parameters of the period when gout patients were asymptomatic were examined. Carotid intima-media thickness (CIMT), which is a non-invasive procedure due to its widespread use, was used as a marker.Results:MHR and CIMT values were 18.22 ± 9.01 and 0.76 ± 0.11 mm in patients with gout. In the control group, it was 13.62 ± 4.48 and 0.65 ± 0.13 (p = 0.002, p <0.0001, respectively). When evaluated within the study group, it was found that there was a positive correlation between MHR and CIMT (r = 0.253, p = 0.013), and according to linear regression analysis, there was an independent relationship between MHR and CIMT (beta [β] = 0.293, p = 0.049). When assessing Gout patients in the study population, a cutoff value of 13.85 with sensitivity of 66 %, specificity of 53 %, and p = 0.011 (area under curve: 0.650, 95% confidence interval 0.540-0.760), was observed according to receiver-operating characteristic curve analysis (Figure 1).Figure 1.Receiver-operating characteristic curve analysis.Conclusion:This study showed us that MHR can be an inexpensive and easily accessible marker that can be used in the evaluation of atherosclerotic lesions. We think that studies with larger number of patients are needed on this subject.References:[1]Çukurova S, Pamuk ON, Unlu Ercument, Pamuk GE, Cakir NE. Subclinical atherosclerosis in gouty arthritis patients: a comparative study. Rheumatol Int. 2012 Jun; 3 2(6): 1769-73.[2]Choi HK, Curhan G. Independent impact of gout on mortality and risk for coronary heart disease. Circulation 2007 Aug 21; 116 (8): 894-900.[3]McAdams-DeMarco MA, Maynard JW, Coresh J, Baer AN.Anemia and the onset of gout in a population-based cohort of adults: Atherosclerosis Risk in Communities study. Arthritis Res Ther. 2012 Aug 20; 14(4): R193.[4]Enhos A, Cosansu K, Huyut MA, Turna F, Karacop E, Bakshaliyev N, Nadir A, Ozdemir R, Uluganyan M. Assessment of the Relationship between Monocyte to High-Density Lipoprotein Ratio and Myocardial Bridge. Arq Bras Cardiol. 2019 Jan;112(1):12-17.Disclosure of Interests:None declared.

scholarly journals Presepsin values and prognostic nutritional index predict mortality in intensive care unit patients with sepsis: a pilot study

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yuichiro Shimoyama ◽  
Osamu Umegaki ◽  
Noriko Kadono ◽  
Toshiaki Minami
Keyword(s):  
Multivariate Analysis ◽  
Roc Curve ◽  
Operating Characteristic ◽  
Prognostic Nutritional Index ◽  
Early Mortality ◽  
Curve Analysis ◽  
Rank Test ◽  
Roc Curve Analysis ◽  
Log Rank Test ◽  
Nutritional Index

Abstract Objective Sepsis is a major cause of mortality for critically ill patients. This study aimed to determine whether presepsin values can predict mortality in patients with sepsis. Results Receiver operating characteristic (ROC) curve analysis, Log-rank test, and multivariate analysis identified presepsin values and Prognostic Nutritional Index as predictors of mortality in sepsis patients. Presepsin value on Day 1 was a predictor of early mortality, i.e., death within 7 days of ICU admission; ROC curve analysis revealed an AUC of 0.84, sensitivity of 89%, and specificity of 77%; and multivariate analysis showed an OR of 1.0007, with a 95%CI of 1.0001–1.0013 (p = 0.0320).

Diagnostic Value of CD4/CD8 in Scrub Typhus

2021 ◽  
Author(s):  
Kangkang Hong ◽  
Ziping Shu ◽  
Laodong Li ◽  
Yu Zhong ◽  
Weiqian Chen ◽  
...  
Keyword(s):  
Hiv Infection ◽  
Bloodstream Infection ◽  
Operating Characteristic ◽  
Scrub Typhus ◽  
Characteristic Curve ◽  
Community Acquired Pneumonia ◽  
Curve Analysis ◽  
Control Groups ◽  
Infection Group ◽  
Operating Characteristic Curve

Scrub typhus is often misdiagnosed in febrile patients, leading to antibiotic abuse and multiple complications. We conducted a retrospective record review at the Fourth Affiliated Hospital of Guangxi Medical University in China. Data were collected on 52 patients with a confirmed diagnosis of scrub typhus and complete clinical data. In addition, data were collected on 52 patients with bloodstream infection, 25 patients with HIV infection, 112 patients with common community-acquired pneumonia (CCAP), and 36 patients with severe community-acquired pneumonia (SCAP) to serve as control groups. The peripheral blood CD4 and CD8 counts, CD4/CD8 ratio, C-reactive protein, procalcitonin, alanine aminotransferase, aspartate aminotransferase, creatinine, and β2 microglobulin levels; and the white blood cell count and neutrophil percentage were compared between the scrub typhus and the control groups. The value of these biomarkers in the diagnosis of scrub typhus was assessed using receiver–operating characteristic curve analysis. The scrub typhus group had a significantly lower CD4 count and CD4/CD8 ratio than the bloodstream infection, CCAP, and SCAP groups, and a significantly greater CD4 count and CD4/CD8 ratio than the HIV infection group. In contrast, the scrub typhus group had a significantly greater CD8 count than the bloodstream infection and CCAP and SCAP groups, and it had a lower level of CD8 than the HIV infection group. The areas under the curve of CD4/CD8 were more than 0.93 in the receiver–operating characteristic curve analysis. These findings suggest that the CD4/CD8 ratio is a useful ancillary test for diagnosing scrub typhus.

Predictors of thermal increase in magnetic resonance–guided focused ultrasound treatment for essential tremor: histogram analysis of skull density ratio values for 1024 elements

2021 ◽  
pp. 1-6
Author(s):  
Ken Iijima ◽  
Hajime Yokota ◽  
Toshio Yamaguchi ◽  
Masayuki Nakano ◽  
Takahiro Ouchi ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Operating Characteristic ◽  
Focused Ultrasound ◽  
Characteristic Curve ◽  
Density Ratio ◽  
Predictive Ability ◽  
Curve Analysis ◽  
Regression Analyses ◽  
Multivariate Logistic Regression ◽  
Operating Characteristic Curve

OBJECTIVE Sufficient thermal increase capable of generating thermocoagulation is indispensable for an effective clinical outcome in patients undergoing magnetic resonance–guided focused ultrasound (MRgFUS). The skull density ratio (SDR) is one of the most dominant predictors of thermal increase prior to treatment. However, users currently rely only on the average SDR value (SDRmean) as a screening criterion, although some patients with low SDRmean values can achieve sufficient thermal increase. The present study aimed to examine the numerical distribution of SDR values across 1024 elements to identify more precise predictors of thermal increase during MRgFUS. METHODS The authors retrospectively analyzed the correlations between the skull parameters and the maximum temperature achieved during unilateral ventral intermediate nucleus thalamotomy with MRgFUS in a cohort of 55 patients. In addition, the numerical distribution of SDR values was quantified across 1024 elements by using the skewness, kurtosis, entropy, and uniformity of the SDR histogram. Next, the authors evaluated the correlation between the aforementioned indices and a peak temperature > 55°C by using univariate and multivariate logistic regression analyses. Receiver operating characteristic curve analysis was performed to compare the predictive ability of the indices. The diagnostic performance of significant factors was also assessed. RESULTS The SDR skewness (SDRskewness) was identified as a significant predictor of thermal increase in the univariate and multivariate logistic regression analyses (p < 0.001, p = 0.013). Moreover, the receiver operating characteristic curve analysis indicated that the SDRskewness exhibited a better predictive ability than the SDRmean, with area under the curve values of 0.847 and 0.784, respectively. CONCLUSIONS The SDRskewness is a more accurate predictor of thermal increase than the conventional SDRmean. The authors suggest setting the SDRskewness cutoff value to 0.68. SDRskewness may allow for the inclusion of treatable patients with essential tremor who would have been screened out based on the SDRmean exclusion criterion.

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