Displaying publications 161 - 180 of 245 in total

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  1. Saokaew S, Kositamongkol C, Charatcharoenwitthaya P, Srivanichakorn W, Washirasaksiri C, Chaiyakunapruk N, et al.
    Medicine (Baltimore), 2020 Dec 11;99(50):e23619.
    PMID: 33327335 DOI: 10.1097/MD.0000000000023619
    Over half of metabolic syndrome (MetS) patients have nonalcoholic fatty liver disease (NAFLD). To prevent its complications, standard routine screening is required, but the human-resource and budgetary implications need to be taken into consideration. This study compared the performances of 4 noninvasive scoring systems in predicting NAFLD in MetS patients. They were the fatty liver index, hepatic steatosis index, lipid accumulation product index, and nonalcoholic fatty liver disease in metabolic syndrome patients scoring system (NAFLD-MS).Scores were determined for 499 MetS patients, including 249 patients in a type 2 diabetes mellitus (T2DM) subgroup. Ultrasonography was used to diagnose NAFLD. The accuracies and performance of the scoring systems were analyzed using published cutoff values, and comparisons were made of their areas under receiver operating characteristic curves, sensitivities, specificities, positive and negative predictive values, and likelihood ratios.NAFLD was detected in 68% of the MetS patients and 77% of the MetS patients with T2DM. According to the areas under receiver operating characteristic curves, fatty liver index and hepatic steatosis index provided better performances in predicting NAFLD. NAFLD-MS provided the highest specificity of 99% among the MetS patients as a whole, and it provided even better accuracy with similar performance when applied to the subgroup of MetS patients with T2DM. The maximum cost avoidance from unnecessary ultrasonography was also reported by using NAFLD-MS. In terms of simplicity and ease of calculation, the lipid accumulation product index and NAFLD-MS are preferred.All 4 scoring systems proved to be acceptable for predicting NAFLD among MetS and T2DM patients in settings where the availability of ultrasonography is limited. NAFLD-MS provided the highest specificity and cost avoidance, and it is simple to use. All 4 systems can help clinicians decide further investigations.
    Matched MeSH terms: ROC Curve
  2. Banneheke H, Fernandopulle R, Gunasekara U, Barua A, Fernando N, Wickremasinghe R
    Trop Biomed, 2015 Jun;32(2):192-7.
    PMID: 26691246
    Wet mount microscopy is the most commonly used diagnostic method for trichomoniasis in clinical diagnostic services all over the world including Sri Lanka due to its availability, simplicity and is relatively inexpensive. However, Trichomonas culture and PCR are the gold standard tests. Unfortunately, neither the culture nor PCR is available for the diagnosis of trichomoniasis in Sri Lanka. Thus, it is important to validate the wet mount microscopy as it is the only available diagnostic test and has not been validated to date in Sri Lanka. The objective was to evaluate the validity and reliability of wet mount microscopy against gold standard Trichomonas culture among clinic based population of reproductive age group women in Western province, Sri Lanka. Women attending hospital and institutional based clinics were enrolled. They were interviewed and high vaginal swabs were taken for laboratory diagnosis by culture and wet mount microscopy. There were 601 participants in the age group of 15-45 years. Wet mount microscopy showed 68% sensitivity, 100% specificity, 100% positive (PPV) and 98% negative predictive values (NPV) (P=0.001, kappa=0.803) respectively against the gold standard culture. The area under the ROC curve was 0.840. Sensitivity of wet mount microscopy is low. However it has high validity and reliability as a specific diagnostic test for trichomoniasis. If it is to be used among women of reproductive age group in Western province, Sri Lanka, a culture method could be adopted as a second test to confirm the negative wet mount for symptomatic patients.
    Matched MeSH terms: ROC Curve
  3. Trutnovsky G, Kamisan Atan I, Ulrich D, Martin A, Dietz HP
    Acta Obstet Gynecol Scand, 2016 Dec;95(12):1411-1417.
    PMID: 27622984 DOI: 10.1111/aogs.13018
    INTRODUCTION: The study aimed to analyze the relation between the degree of puborectalis muscle trauma and subjective symptoms and objective findings of pelvic organ prolapse (POP), comparing two continuous scoring systems with a discrete scoring system for translabial ultrasound imaging.

    MATERIAL AND METHODS: In this retrospective observational study the records of patients attending a tertiary urogynecological unit between January 2012 and December 2014 were analyzed. POP assessment included a standardized interview, clinical examination using Pelvic Organ Prolapse Quantification and four-dimensional translabial ultrasound. Puborectalis muscle trauma was assessed with tomographic ultrasound imaging using two continuous scoring systems and a previously established discrete system. Receiver operating characteristics and adjusted odds ratios were used for comparison of scoring systems in predicting symptoms and signs of POP.

    RESULTS: Of 1258 women analyzed, 52.6% complained of prolapse symptoms. On ultrasound imaging, 65.7% of women had sonographically significant POP. Complete avulsion was diagnosed in 25.3% of women, being unilateral in 13.9% and bilateral in 11.4%. A maximum score in the 6-point and the 12-point tomographic ultrasound imaging scale increased the odds for a diagnosis of any significant POP on ultrasound by 4.4 and 4.8 times, respectively, compared with 4.6 times for the discrete diagnosis of bilateral avulsion. For all avulsion scoring systems the relation was strongest for cystocele and uterine prolapse.

    CONCLUSIONS: A continuous avulsion scoring system based on tomographic findings does not provide superior performance for the prediction of subjective symptoms and objective findings of prolapse compared with a discrete diagnostic system of unilateral or bilateral avulsion.

    Matched MeSH terms: ROC Curve
  4. Raffiz M, Abdullah JM
    Am J Emerg Med, 2017 Jan;35(1):150-153.
    PMID: 27852525 DOI: 10.1016/j.ajem.2016.09.044
    INTRODUCTION: Bedside ultrasound measurement of optic nerve sheath diameter (ONSD) is emerging as a non-invasive technique to evaluate and predict raised intracranial pressure (ICP). It has been shown in previous literature that ONSD measurement has good correlation with surrogate findings of raised ICP such as clinical and radiological findings suggestive of raised ICP.

    OBJECTIVES: The objective of the study is to find a correlation between sonographic measurements of ONSD value with ICP value measured via the gold standard invasive intracranial ICP catheter, and to find the cut-off value of ONSD measurement in predicting raised ICP, along with its sensitivity and specificity value.

    METHODS: A prospective observational study was performed using convenience sample of 41 adult neurosurgical patients treated in neurosurgical intensive care unit with invasive intracranial pressure monitoring placed in-situ as part of their clinical care. Portable SonoSite ultrasound machine with 7 MHz linear probe were used to measure optic nerve sheath diameter using the standard technique. Simultaneous ICP readings were obtained directly from the invasive monitoring.

    RESULTS: Seventy-five measurements were performed on 41 patients. The non-parametric Spearman correlation test revealed a significant correlation at the 0.01 level between the ICP and ONSD value, with correlation coefficient of 0.820. The receiver operating characteristic curve generated an area under the curve with the value of 0.964, and with standard error of 0.22. From the receiver operating characteristic curve, we found that the ONSD value of 5.205 mm is 95.8% sensitive and 80.4% specific in detecting raised ICP.

    CONCLUSIONS: ONSD value of 5.205 is sensitive and specific in detecting raised ICP. Bedside ultrasound measurement of ONSD is readily learned, and is reproducible and reliable in predicting raised ICP. This non-invasive technique can be a useful adjunct to the current invasive intracranial catheter monitoring, and has wide potential clinical applications in district hospitals, emergency departments and intensive care units.

    Matched MeSH terms: ROC Curve
  5. Tan JR, Tan KS, Yong FL, Armugam A, Wang CW, Jeyaseelan K, et al.
    PLoS One, 2017;12(2):e0172131.
    PMID: 28199366 DOI: 10.1371/journal.pone.0172131
    Ischemic stroke is a major cause of mortality and morbidity globally. Among the ischemic stroke subtypes, cardioembolic stroke is with poor functional outcome (Modified Rankin score ≥ 2). Early diagnosis of cardioembolic stroke will prove beneficial. This study examined the microRNAs targeting cluster of differentiation 46 (CD46), a potential biomarker for cardioembolic stroke. CD46 mRNA level was shown to be differentially expressed (p < 0.001) between cardioembolic stroke (median = 1.32) and non-cardioembolic stroke subtypes (large artery stroke median = 5.05; small vessel stroke median = 6.45). Bioinformatic search showed that miR-19a, -20a, -185 and -374b were found to target CD46 mRNA and further verified by luciferase reporter assay. The levels of miRNAs targeting CD46 were significantly reduced (p < 0.05) in non-cardioembolic stroke patients (large artery stroke median: miR-19a = 0.63, miR-20a = 0.42, miR-185 = 0.32, miR-374b = 0.27; small artery stroke median: miR-19a = 0.07, miR-20a = 0.06, miR-185 = 0.07, miR-374b = 0.05) as compared to cardioembolic stroke patients (median: miR-19a = 2.69, miR-20a = 1.36, miR-185 = 1.05, miR-374b = 1.23). ROC curve showed that the miRNAs could distinguish cardioembolic stroke from non-cardioembolic stroke with better AUC value as compared to CD46. Endogenous expression of CD46 in Human Umbilical Vein Endothelial Cells (HUVECs) were found to be regulated by miR-19a and miR-20a. Thus implicating that miR-19a and -20a may play a role in pathogenesis of cardioembolic stroke, possibly via the endothelial cells.
    Matched MeSH terms: ROC Curve
  6. Chuah KH, Wan Yusoff WNI, Sthaneshwar P, Nik Mustapha NR, Mahadeva S, Chan WK
    Liver Int, 2019 07;39(7):1315-1324.
    PMID: 30825254 DOI: 10.1111/liv.14084
    INTRODUCTION: MACK-3 (combination of hoMa, Ast and CK18) was reported to be a good biomarker for the diagnosis of fibrotic non-alcoholic steatohepatitis (NASH). However, there is no external validation to date.

    AIM: To evaluate the accuracy of MACK-3 for the diagnosis of fibrotic NASH.

    METHODOLOGY: Consecutive adult non-alcoholic fatty liver disease (NAFLD) patients who had liver biopsy in a university hospital were included. MACK-3 was calculated using the online calculator using the following variables: fasting glucose, fasting insulin, aspartate aminotransferase (AST) and cytokeratin 18 (CK18). MACK-3 cut-offs ≤0.134 and ≥0.550 were used to predict absence and presence of fibrotic NASH, respectively. Histopathological examination of liver biopsy specimen was reported according to the NASH Clinical Research Network Scoring System.

    RESULTS: Data for 196 subjects were analysed. MACK-3 was good for diagnosis of fibrotic NASH (area under receiver-operating characteristics curve [AUROC] 0.80), comparable to the Fibrosis-4 index (FIB4) and the NAFLD fibrosis score (NFS) and superior to the BARD score and CK18. MACK-3 was good for diagnosis of active NASH (AUROC 0.81) and was superior to other blood fibrosis tests. The overall accuracy, percentage of subjects in grey zone, sensitivity, specificity, positive predictive value and negative predictive value of MACK-3 for diagnosis of fibrotic NASH was 79.1%, 46.9%, 100%, 43.8%, 43.1% and 100%, respectively, while for diagnosis of active NASH was 90.0%, 39.3%, 84.2%, 81.4%, 88.9% and 74.5%, respectively.

    CONCLUSION: MACK-3 is promising as a non-invasive test for active NASH and fibrotic NASH and may be useful to identify patients who need more aggressive intervention.

    Matched MeSH terms: ROC Curve
  7. Abdullah SN, Sanderson GF, Husni MA, Maddess T
    PMID: 32034583 DOI: 10.1007/s10633-020-09750-7
    PURPOSE: To compare two forms of perimetry that use large contrast-modulated grating stimuli in terms of: their relative diagnostic power, their independent diagnostic information about glaucoma and their utility for mfVEPs. We evaluated a contrast-threshold mfVEP in normal controls using the same stimuli as one of the tests.

    METHODS: We measured psychophysical contrast thresholds in one eye of 16 control subjects and 19 patients aged 67.8 ± 5.65 and 71.9 ± 7.15, respectively, (mean ± SD). Patients ranged in disease severity from suspects to severe glaucoma. We used the 17-region FDT-perimeter C20-threshold program and a custom 9-region test (R9) with similar visual field coverage. The R9 stimuli scaled their spatial frequencies with eccentricity and were modulated at lower temporal frequencies than C20 and thus did not display a clear spatial frequency-doubling (FD) appearance. Based on the overlapping areas of the stimuli, we transformed the C20 results to 9 measures for direct comparison with R9. We also compared mfVEP-based and psychophysical contrast thresholds in 26 younger (26.6 ± 7.3 y, mean ± SD) and 20 older normal control subjects (66.5 ± 7.3 y) control subjects using the R9 stimuli.

    RESULTS: The best intraclass correlations between R9/C20 thresholds were for the central and outer regions: 0.82 ± 0.05 (mean ± SD, p ≤ 0.0001). The areas under receiver operator characteristic plots for C20 and R9 were as high as 0.99 ± 0.012 (mean ± SE). Canonical correlation analysis (CCA) showed significant correlation (r = 0.638, p = 0.029) with 1 dimension of the C20 and R9 data, suggesting that the lower and higher temporal frequency tests probed the same neural mechanism(s). Low signal quality made the contrast-threshold mfVEPs non-viable. The resulting mfVEP thresholds were limited by noise to artificially high contrasts, which unlike the psychophysical versions, were not correlated with age.

    CONCLUSION: The lower temporal frequency R9 stimuli had similar diagnostic power to the FDT-C20 stimuli. CCA indicated the both stimuli drove similar neural mechanisms, possibly suggesting no advantage of FD stimuli for mfVEPs. Given that the contrast-threshold mfVEPs were non-viable, we used the present and published results to make recommendations for future mfVEP tests.

    Matched MeSH terms: ROC Curve
  8. Tan PC, Aziz AZ, Ismail IS, Omar SZ
    Clin Biochem, 2012 Oct;45(15):1192-6.
    PMID: 22659058 DOI: 10.1016/j.clinbiochem.2012.05.025
    OBJECTIVES: To evaluate gamma-glutamyltransferase (GGT), alanine transaminases (ALT) and aspartate transaminases (AST) levels and prevalent gestational diabetes mellitus (GDM).
    DESIGN AND METHODS: Random plasma glucose, GGT, ALT and AST and the 50-g glucose challenge test were done on antenatal women followed by diagnostic 3-point 75-g oral glucose tolerance test within two weeks. GDM was diagnosed by ADA (2011) criteria.
    RESULTS: The GDM rate was 12.2% (319/2610). Mean GGT level was higher in GDM women, 18 ± 12 vs. 16 ± 11 IU/L; P=0.03. The risk for GDM was higher for women in the highest GGT quartile band compared to the lowest: RR 1.35 95%CI 1.0-1.8; P=0.04. However, after adjustment for confounders, GGT was no longer associated with GDM. There was no correlation between ALT and AST levels and GDM.
    CONCLUSIONS: Liver transaminases do not predict GDM in contrast to type 2 diabetes.
    Matched MeSH terms: ROC Curve
  9. Quek KF, Chua CB, Razack AH, Low WY, Loh CS
    Int J Urol, 2005 Jan;12(1):39-45.
    PMID: 15661053 DOI: 10.1111/j.1442-2042.2004.00988.x
    The purpose of the present study was to validate the Mandarin version of the International Prostate Symptom Score (Mand-IPSS) in a Malaysian population.
    Matched MeSH terms: ROC Curve
  10. Goh AY, Abdel-Latif Mel-A, Lum LC, Abu-Bakar MN
    Intensive Care Med, 2003 Jan;29(1):97-102.
    PMID: 12528029 DOI: 10.1007/s00134-002-1534-9
    Objective: Lack of direct access to tertiary pediatric intensive care services in rural hospitals may be associated with poorer outcome among critically ill children. Inter-hospital transport by non-specialized teams may also lead to increased morbidity and even mortality. We therefore studied the outcome of children with different accessibility to tertiary pediatric care in Malaysia.

    Methods: We prospectively compared the Pediatric Risk of Mortality (PRISM II) adjusted standardized mortality ratio (SMR), unanticipated deaths and length of stay of 131 patients transported from rural hospitals (limited access) with 215 transferred from the casualty wards or other in-hospital wards (direct access) to a tertiary pediatric ICU.

    Results: The transported patients were younger than the in-hospital patients (median age 1.0 versus 6.0 months, p=0.000) and were more likely to have respiratory diseases. Other baseline characteristics did not differ significantly. Differences in access to tertiary intensive care from community hospitals was associated with an extended median length of stay (4.0 versus 2.0 days, p=0.000) but did not affect SMR (0.92 versus 0.84, rate ratio 1.09, 95% CI 0.57-2.01; p=0.348) or percentage of unexpected deaths (4.8% versus 2.8%, p=0.485). The adjusted odds ratio for mortality (1.7, 95% CI 0.7-4.3) associated with transfer was not statistically significant (p=0.248).

    Conclusions: The outcome of critically ill children transferred from community hospitals did not differ from that of those who develop ICU needs in the wards of a tertiary center, despite being transported by non-specialized teams. Outcome was not affected by initial inaccessibility to intensive care if the children finally received care in a tertiary center.
    Matched MeSH terms: ROC Curve
  11. Aziz F, Malek S, Ibrahim KS, Raja Shariff RE, Wan Ahmad WA, Ali RM, et al.
    PLoS One, 2021;16(8):e0254894.
    PMID: 34339432 DOI: 10.1371/journal.pone.0254894
    BACKGROUND: Conventional risk score for predicting short and long-term mortality following an ST-segment elevation myocardial infarction (STEMI) is often not population specific.

    OBJECTIVE: Apply machine learning for the prediction and identification of factors associated with short and long-term mortality in Asian STEMI patients and compare with a conventional risk score.

    METHODS: The National Cardiovascular Disease Database for Malaysia registry, of a multi-ethnic, heterogeneous Asian population was used for in-hospital (6299 patients), 30-days (3130 patients), and 1-year (2939 patients) model development. 50 variables were considered. Mortality prediction was analysed using feature selection methods with machine learning algorithms and compared to Thrombolysis in Myocardial Infarction (TIMI) score. Invasive management of varying degrees was selected as important variables that improved mortality prediction.

    RESULTS: Model performance using a complete and reduced variable produced an area under the receiver operating characteristic curve (AUC) from 0.73 to 0.90. The best machine learning model for in-hospital, 30 days, and 1-year outperformed TIMI risk score (AUC = 0.88, 95% CI: 0.846-0.910; vs AUC = 0.81, 95% CI:0.772-0.845, AUC = 0.90, 95% CI: 0.870-0.935; vs AUC = 0.80, 95% CI: 0.746-0.838, AUC = 0.84, 95% CI: 0.798-0.872; vs AUC = 0.76, 95% CI: 0.715-0.802, p < 0.0001 for all). TIMI score underestimates patients' risk of mortality. 90% of non-survival patients are classified as high risk (>50%) by machine learning algorithm compared to 10-30% non-survival patients by TIMI. Common predictors identified for short- and long-term mortality were age, heart rate, Killip class, fasting blood glucose, prior primary PCI or pharmaco-invasive therapy and diuretics. The final algorithm was converted into an online tool with a database for continuous data archiving for algorithm validation.

    CONCLUSIONS: In a multi-ethnic population, patients with STEMI were better classified using the machine learning method compared to TIMI scoring. Machine learning allows for the identification of distinct factors in individual Asian populations for better mortality prediction. Ongoing continuous testing and validation will allow for better risk stratification and potentially alter management and outcomes in the future.

    Matched MeSH terms: ROC Curve
  12. ASCI Practice Guideline Working Group, Beck KS, Kim JA, Choe YH, Sim KH, Hoe J, et al.
    Korean J Radiol, 2017 Nov-Dec;18(6):871-880.
    PMID: 29089819 DOI: 10.3348/kjr.2017.18.6.871
    In 2010, the Asian Society of Cardiovascular Imaging (ASCI) provided recommendations for cardiac CT and MRI, and this document reflects an update of the 2010 ASCI appropriate use criteria (AUC). In 2016, the ASCI formed a new working group for revision of AUC for noninvasive cardiac imaging. A major change that we made in this document is the rating of various noninvasive tests (exercise electrocardiogram, echocardiography, positron emission tomography, single-photon emission computed tomography, radionuclide imaging, cardiac magnetic resonance, and cardiac computed tomography/angiography), compared side by side for their applications in various clinical scenarios. Ninety-five clinical scenarios were developed from eight selected pre-existing guidelines and classified into four sections as follows: 1) detection of coronary artery disease, symptomatic or asymptomatic; 2) cardiac evaluation in various clinical scenarios; 3) use of imaging modality according to prior testing; and 4) evaluation of cardiac structure and function. The clinical scenarios were scored by a separate rating committee on a scale of 1-9 to designate appropriate use, uncertain use, or inappropriate use according to a modified Delphi method. Overall, the AUC ratings for CT were higher than those of previous guidelines. These new AUC provide guidance for clinicians choosing among available testing modalities for various cardiac diseases and are also unique, given that most previous AUC for noninvasive imaging include only one imaging technique. As cardiac imaging is multimodal in nature, we believe that these AUC will be more useful for clinical decision making.
    Matched MeSH terms: ROC Curve
  13. Ng SC, Abu Samah F, Helmy K, Sia KK
    Med J Malaysia, 2017 10;72(5):286-290.
    PMID: 29197884 MyJurnal
    OBJECTIVE: To compare FEV1/FEV6 to the standard spirometry (FEV1/FVC) as a screening tool for COPD.

    METHODS: This cross-sectional study was conducted at Hospital Tuanku Fauziah, Perlis, Malaysia from August 2015 to April 2016. FEV1/FEV6 and FEV1/FVC results of 117 subjects were analysed. Demographic data and spirometric variables were tabulated. A scatter plot graph with Spearman's correlation was constructed for the correlation between FEV1/FEV6 and FEV1/FVC. The sensitivity, specificity, positive and negative predictive values of FEV1/FEV6 were determined with reference to the gold standard of FEV1/FVC ratio <0.70. Receiver-operator characteristic (ROC) curve analysis and Kappa statistics were used to determine the FEV1/FEV6 ratio in predicting an FEV1/FVC ratio <0.70.

    RESULTS: Spearman's correlation with r = 0.636 (P<0.001) was demonstrated. The area under the ROC curve was 0.862 (95% confidence interval [CI]: 0.779 - 0.944, P<0.001). The FEV1/FEV6 cut-off with the greatest sum of sensitivity and specificity was 0.75. FEV1/FEV6 sensitivity, specificity, positive and negative predictive values were 93.02%, 67.74%, 88.89% and 77.78% respectively. There was substantial agreement between the two diagnostic cut-offs (κ = 0.634; 95% CI: 0.471 - 0.797, P<0.001) CONCLUSIONS: The FEV1/FEV6 ratio can be considered to be a good alternative to the FEV1/FVC ratio for screening of COPD. Larger multicentre study and better education on spirometric techniques can validate similar study outcome and establish reference values appropriate to the population being studied.

    Matched MeSH terms: ROC Curve
  14. Shukeri WFWM, Ralib AM, Abdulah NZ, Mat-Nor MB
    J Crit Care, 2018 Feb;43:163-168.
    PMID: 28903084 DOI: 10.1016/j.jcrc.2017.09.009
    PURPOSE: To derive a prediction equation for 30-day mortality in sepsis using a multi-marker approach and compare its performance to the Sequential Organ Failure Assessment (SOFA) score.

    METHODS: This study included 159 septic patients admitted to an intensive care unit. Leukocytes count, procalcitonin (PCT), interleukin-6 (IL-6), and paraoxonase (PON) and arylesterase (ARE) activities of PON-1 were assayed from blood obtained on ICU presentation. Logistic regression was used to derive sepsis mortality score (SMS), a prediction equation describing the relationship between biomarkers and 30-day mortality.

    RESULTS: The 30-day mortality rate was 28.9%. The SMS was [еlogit(p)/(1+еlogit(p))]×100; logit(p)=0.74+(0.004×PCT)+(0.001×IL-6)-(0.025×ARE)-(0.059×leukocytes count). The SMC had higher area under the receiver operating characteristic curve (95% Cl) than SOFA score [0.814 (0.736-0.892) vs. 0.767 (0.677-0.857)], but is not statistically significant. When the SMS was added to the SOFA score, prediction of 30-day mortality improved compared to SOFA score used alone [0.845 (0.777-0.899), p=0.022].

    CONCLUSIONS: A sepsis mortality score using baseline leukocytes count, PCT, IL-6 and ARE was derived, which predicted 30-day mortality with very good performance and added significant prognostic information to SOFA score.

    Matched MeSH terms: ROC Curve
  15. Low JZB, Khang TF, Tammi MT
    BMC Bioinformatics, 2017 12 28;18(Suppl 16):575.
    PMID: 29297307 DOI: 10.1186/s12859-017-1974-4
    BACKGROUND: In current statistical methods for calling differentially expressed genes in RNA-Seq experiments, the assumption is that an adjusted observed gene count represents an unknown true gene count. This adjustment usually consists of a normalization step to account for heterogeneous sample library sizes, and then the resulting normalized gene counts are used as input for parametric or non-parametric differential gene expression tests. A distribution of true gene counts, each with a different probability, can result in the same observed gene count. Importantly, sequencing coverage information is currently not explicitly incorporated into any of the statistical models used for RNA-Seq analysis.

    RESULTS: We developed a fast Bayesian method which uses the sequencing coverage information determined from the concentration of an RNA sample to estimate the posterior distribution of a true gene count. Our method has better or comparable performance compared to NOISeq and GFOLD, according to the results from simulations and experiments with real unreplicated data. We incorporated a previously unused sequencing coverage parameter into a procedure for differential gene expression analysis with RNA-Seq data.

    CONCLUSIONS: Our results suggest that our method can be used to overcome analytical bottlenecks in experiments with limited number of replicates and low sequencing coverage. The method is implemented in CORNAS (Coverage-dependent RNA-Seq), and is available at https://github.com/joel-lzb/CORNAS .

    Matched MeSH terms: ROC Curve
  16. Goonasegaran AR, Nabila FN, Shuhada NS
    Singapore Med J, 2012 Jun;53(6):403-8.
    PMID: 22711041
    Body mass index (BMI) has limited diagnostic performance due to its inability to discriminate between fat and lean mass. This study was conducted to compare the effectiveness of body fat percentage (BFP) against BMI in defining body composition.
    Matched MeSH terms: ROC Curve
  17. Tan TL, Ahmad NS, Nasuruddin DN, Ithnin A, Tajul Arifin K, Zaini IZ, et al.
    PLoS One, 2016;11(3):e0152065.
    PMID: 27003588 DOI: 10.1371/journal.pone.0152065
    INTRODUCTION: Early diagnosis of sepsis and bacterial infection is imperative as treatment relies on early antibiotic administration. There is a need to develop new biomarkers to detect patients with sepsis and bacterial infection as early as possible, thereby enabling prompt antibiotic treatment and improving the survival rate.

    METHODS: Fifty-one adult patients with suspected bacterial sepsis on admission to the Emergency Department (ED) of a teaching hospital were included into the study. All relevant cultures and serology tests were performed. Serum levels for Group II Secretory Phospholipase A2 (sPLA2-IIA) and CD64 were subsequently analyzed.

    RESULTS AND DISCUSSION: Sepsis was confirmed in 42 patients from a total of 51 recruited subjects. Twenty-one patients had culture-confirmed bacterial infections. Both biomarkers were shown to be good in distinguishing sepsis from non-sepsis groups. CD64 and sPLA2-IIA also demonstrated a strong correlation with early sepsis diagnosis in adults. The area under the curve (AUC) of both Receiver Operating Characteristic curves showed that sPLA2-IIA was better than CD64 (AUC = 0.93, 95% confidence interval (CI) = 0.83-0.97 and AUC = 0.88, 95% CI = 0.82-0.99, respectively). The optimum cutoff value was 2.13μg/l for sPLA2-IIA (sensitivity = 91%, specificity = 78%) and 45 antigen bound cell (abc) for CD64 (sensitivity = 81%, specificity = 89%). In diagnosing bacterial infections, sPLA2-IIA showed superiority over CD64 (AUC = 0.97, 95% CI = 0.85-0.96, and AUC = 0.95, 95% CI = 0.93-1.00, respectively). The optimum cutoff value for bacterial infection was 5.63μg/l for sPLA2-IIA (sensitivity = 94%, specificity = 94%) and 46abc for CD64 (sensitivity = 94%, specificity = 83%).

    CONCLUSIONS: sPLA2-IIA showed superior performance in sepsis and bacterial infection diagnosis compared to CD64. sPLA2-IIA appears to be an excellent biomarker for sepsis screening and for diagnosing bacterial infections, whereas CD64 could be used for screening bacterial infections. Both biomarkers either alone or in combination with other markers may assist in decision making for early antimicrobial administration. We recommend incorporating sPLA2-IIA and CD64 into the diagnostic algorithm of sepsis in ED.

    Matched MeSH terms: ROC Curve
  18. Bates T, Kennedy M, Diajil A, Goodson M, Thomson P, Doran E, et al.
    Cancer Epidemiol Biomarkers Prev, 2016 Jun;25(6):927-35.
    PMID: 27197272 DOI: 10.1158/1055-9965.EPI-15-0949
    BACKGROUND: Oral squamous cell carcinoma (OSCC) is a global healthcare problem associated with poor clinical outcomes. Early detection is key to improving patient survival. OSCC may be preceded by clinically recognizable lesions, termed oral potentially malignant disorders (OPMD). As histologic assessment of OPMD does not accurately predict their clinical behavior, biomarkers are required to detect cases at risk of malignant transformation. Epidermal growth factor receptor gene copy number (EGFR GCN) is a validated biomarker in lung non-small cell carcinoma. We examined EGFR GCN in OPMD and OSCC to determine its potential as a biomarker in oral carcinogenesis.

    METHODS: EGFR GCN was examined by in situ hybridization (ISH) in biopsies from 78 patients with OPMD and 92 patients with early-stage (stages I and II) OSCC. EGFR ISH signals were scored by two pathologists and a category assigned by consensus. The data were correlated with patient demographics and clinical outcomes.

    RESULTS: OPMD with abnormal EGFR GCN were more likely to undergo malignant transformation than diploid cases. EGFR genomic gain was detected in a quarter of early-stage OSCC, but did not correlate with clinical outcomes.

    CONCLUSION: These data suggest that abnormal EGFR GCN has clinical utility as a biomarker for the detection of OPMD destined to undergo malignant transformation. Prospective studies are required to verify this finding. It remains to be determined if EGFR GCN could be used to select patients for EGFR-targeted therapies.

    IMPACT: Abnormal EGFR GCN is a potential biomarker for identifying OPMD that are at risk of malignant transformation. Cancer Epidemiol Biomarkers Prev; 25(6); 927-35. ©2016 AACR.

    Matched MeSH terms: ROC Curve
  19. Duell EJ, Lujan-Barroso L, Sala N, Deitz McElyea S, Overvad K, Tjonneland A, et al.
    Int J Cancer, 2017 Sep 01;141(5):905-915.
    PMID: 28542740 DOI: 10.1002/ijc.30790
    Noninvasive biomarkers for early pancreatic ductal adenocarcinoma (PDAC) diagnosis and disease risk stratification are greatly needed. We conducted a nested case-control study within the Prospective Investigation into Cancer and Nutrition (EPIC) cohort to evaluate prediagnostic microRNAs (miRs) as biomarkers of subsequent PDAC risk. A panel of eight miRs (miR-10a, -10b, -21-3p, -21-5p, -30c, -106b, -155 and -212) based on previous evidence from our group was evaluated in 225 microscopically confirmed PDAC cases and 225 controls matched on center, sex, fasting status and age/date/time of blood collection. MiR levels in prediagnostic plasma samples were determined by quantitative RT-PCR. Logistic regression was used to model levels and PDAC risk, adjusting for covariates and to estimate area under the receiver operating characteristic curves (AUC). Plasma miR-10b, -21-5p, -30c and -106b levels were significantly higher in cases diagnosed within 2 years of blood collection compared to matched controls (all p-values <0.04). Based on adjusted logistic regression models, levels for six miRs (miR-10a, -10b, -21-5p, -30c, -155 and -212) overall, and for four miRs (-10a, -10b, -21-5p and -30c) at shorter follow-up time between blood collection and diagnosis (≤5 yr, ≤2 yr), were statistically significantly associated with risk. A score based on the panel showed a linear dose-response trend with risk (p-value = 0.0006). For shorter follow-up (≤5 yr), AUC for the score was 0.73, and for individual miRs ranged from 0.73 (miR-212) to 0.79 (miR-21-5p).
    Matched MeSH terms: ROC Curve
  20. Al-Faris AQ, Ngah UK, Isa NA, Shuaib IL
    J Digit Imaging, 2014 Feb;27(1):133-44.
    PMID: 24100762 DOI: 10.1007/s10278-013-9640-5
    In this paper, an automatic computer-aided detection system for breast magnetic resonance imaging (MRI) tumour segmentation will be presented. The study is focused on tumour segmentation using the modified automatic seeded region growing algorithm with a variation of the automated initial seed and threshold selection methodologies. Prior to that, some pre-processing methodologies are involved. Breast skin is detected and deleted using the integration of two algorithms, namely the level set active contour and morphological thinning. The system is applied and tested on 40 test images from the RIDER breast MRI dataset, the results are evaluated and presented in comparison to the ground truths of the dataset. The analysis of variance (ANOVA) test shows that there is a statistically significance in the performance compared to the previous segmentation approaches that have been tested on the same dataset where ANOVA p values for the evaluation measures' results are less than 0.05, such as: relative overlap (p = 0.0002), misclassification rate (p = 0.045), true negative fraction (p = 0.0001) and sum of true volume fraction (p = 0.0001).
    Matched MeSH terms: ROC Curve
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