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Internal Validation (internal + validation)
Selected AbstractsInternal Validation of the AmpFlSTR YfilerÔ Amplification Kit for Use in Forensic CaseworkJOURNAL OF FORENSIC SCIENCES, Issue 1 2008Ann Marie Gross M.S. Abstract:, Y-chromosomal short-tandem repeat (Y-STR) amplification has been used in forensic casework at the Bureau of Criminal Apprehension (BCA) Forensic Science Laboratory since 2003. At that time, two separate amplifications were required to type the SWGDAM recommended loci (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439). The YfilerÔ kit coamplifies these loci as well as DYS437, DYS448, DYS456, DYS458, DYS635, and Y GATA H4. The YfilerÔ kit was validated following the internal validations outlined in the SWGDAM revised validation guidelines. Our studies show that 0.125 ng of male DNA will generate a complete 17 locus profile and that as little as 0.06 ng of male DNA yields an average of nine loci. In the male,male mixtures, a complete profile from the minor component was detected up to 1:5 ratio; most of the alleles of the minor component were detected at a 1:10 ratio and more than half the alleles of the minor component were detected at a 1:20 ratio. Complete YSTR profiles were obtained when 500 pg male DNA was mixed with female DNA at ratios up to 1:1000. At ratios of 1:5000 and 1:10,000 (male DNA to female DNA) inhibition of the YSTR amplification was evident. The YSTR results obtained for the adjudicated case samples gave significantly more probative information than the autosomal results. Our studies demonstrate that the YfilerÔ kit is extremely sensitive, does not exhibit cross-reactivity with female DNA, successfully types male DNA in the presence of overwhelming amounts of female DNA and is successful in typing actual forensic samples from adjudicated cases. [source] Medication Quantification Scale Version III: Internal Validation of Detriment Weights Using a Chronic Pain PopulationPAIN PRACTICE, Issue 1 2008Michael Gallizzi MS ,,Abstract Introduction: We report an internal validation of the Medication Quantification Scale (MQS III) using a chronic pain population. The MQS was designed as a methodology of quantifying different drug regimens in 1992, updated in 1998 (MQS II), and again updated in 2003 (MQS III) using "detriment" weights determined by surveying physician members of the American Pain Society. The MQS has been used as a unitary clinical and research outcome. Methods: A retrospective chart review was collected from 400 patients in an interdisciplinary outpatient chronic pain clinic. A linear regression equation was developed using the patients' composite MQS III score, and those values were used in a Pearson correlation analysis. Results: The correlation between the subjects' computed regression detriment weights and the corresponding MQS III detriment weights yielded a significant result (r = 0.962, P < 0.01; two-tailed). Discussion: Our chronic pain sample-derived detriment weights did differ in some drug classes from that of the physician consensus, most notably the selective serotonin reuptake inhibitor, Opioid Schedule II, and NSAID class detriment. It is necessary to periodically resurvey large groups of physicians in order to control and modify the detriment weights of our categories in light of new information about detrimental effects (eg, COX-2 inhibitors), or to accommodate medical or political changes in prescribing habits (eg, more liberal opioid prescribing in the later years). This work suggests it may also be important to assess patients' perspective on detriment, as well as statistical and empiric use patterns.,, [source] Are Mechanistic and Statistical QSAR Approaches Really Different?MOLECULAR INFORMATICS, Issue 6-7 2010MLR Studies on 158 Cycloalkyl-Pyranones Abstract Two parallel approaches for quantitative structure-activity relationships (QSAR) are predominant in literature, one guided by mechanistic methods (including read-across) and another by the use of statistical methods. To bridge the gap between these two approaches and to verify their main differences, a comparative study of mechanistically relevant and statistically relevant QSAR models, developed on a case study of 158 cycloalkyl-pyranones, biologically active on inhibition (Ki) of HIV protease, was performed. Firstly, Multiple Linear Regression (MLR) based models were developed starting from a limited amount of molecular descriptors which were widely proven to have mechanistic interpretation. Then robust and predictive MLR models were developed on the same set using two different statistical approaches unbiased of input descriptors. Development of models based on Statistical I method was guided by stepwise addition of descriptors while Genetic Algorithm based selection of descriptors was used for the Statistical II. Internal validation, the standard error of the estimate, and Fisher's significance test were performed for both the statistical models. In addition, external validation was performed for Statistical II model, and Applicability Domain was verified as normally practiced in this approach. The relationships between the activity and the important descriptors selected in all the models were analyzed and compared. It is concluded that, despite the different type and number of input descriptors, and the applied descriptor selection tools or the algorithms used for developing the final model, the mechanistical and statistical approach are comparable to each other in terms of quality and also for mechanistic interpretability of modelling descriptors. Agreement can be observed between these two approaches and the better result could be a consensus prediction from both the models. [source] Recommendations for the Assessment and Reporting of Multivariable Logistic Regression in Transplantation LiteratureAMERICAN JOURNAL OF TRANSPLANTATION, Issue 7 2010A. C. Kalil Multivariable logistic regression is an important method to evaluate risk factors and prognosis in solid organ transplant literature. We aimed to assess the quality of this method in six major transplantation journals. Eleven analytical criteria and four documentation criteria were analyzed for each selected article that used logistic regression. A total of 106 studies (6%) out of 1,701 original articles used logistic regression analyses from January 1, 2005 to January 1, 2006. The analytical criteria and their respective reporting percentage among the six journals were: Linearity (25%); Beta coefficient (48%); Interaction tests (19%); Main estimates (98%); Ovefitting prevention (84%); Goodness-of-fit (3.8%); Multicolinearity (4.7%); Internal validation (3.8%); External validation (8.5%). The documentation criteria were reported as follows: Selection of independent variables (73%); Coding of variables (9%); Fitting procedures (49%); Statistical program (65%). No significant differences were found among different journals or between general versus subspecialty journals with respect to reporting quality. We found that the report of logistic regression is unsatisfactory in transplantation journals. Because our findings may have major consequences for the care of transplant patients and for the design of transplant clinical trials, we recommend a practical solution for the use and reporting of logistic regression in transplantation journals. [source] SCALES: a large-scale assessment model of soil erosion hazard in Basse-Normandie (northern-western France)EARTH SURFACE PROCESSES AND LANDFORMS, Issue 8 2010P. Le Gouée Abstract The cartography of erosion risk is mainly based on the development of models, which evaluate in a qualitative and quantitative manner the physical reproduction of the erosion processes (CORINE, EHU, INRA). These models are mainly semi-quantitative but can be physically based and spatially distributed (the Pan-European Soil Erosion Risk Assessment, PESERA). They are characterized by their simplicity and their applicability potential at large temporal and spatial scales. In developing our model SCALES (Spatialisation d'éChelle fine de l'ALéa Erosion des Sols/large-scale assessment and mapping model of soil erosion hazard), we had in mind several objectives: (1) to map soil erosion at a regional scale with the guarantee of a large accuracy on the local level, (2) to envisage an applicability of the model in European oceanic areas, (3) to focus the erosion hazard estimation on the level of source areas (on-site erosion), which are the agricultural parcels, (4) to take into account the weight of the temporality of agricultural practices (land-use concept). Because of these objectives, the nature of variables, which characterize the erosion factors and because of its structure, SCALES differs from other models. Tested in Basse-Normandie (Calvados 5500,km2) SCALES reveals a strong predisposition of the study area to the soil erosion which should require to be expressed in a wet year. Apart from an internal validation, we tried an intermediate one by comparing our results with those from INRA and PESERA. It appeared that these models under estimate medium erosion levels and differ in the spatial localization of areas with the highest erosion risks. SCALES underlines here the limitations in the use of pedo-transfer functions and the interpolation of input data with a low resolution. One must not forget however that these models are mainly focused on an interregional comparative approach. Therefore the comparison of SCALES data with those of the INRA and PESERA models cannot result on a convincing validation of our model. For the moment the validation is based on the opinion of local experts, who agree with the qualitative indications delivered by our cartography. An external validation of SCALES is foreseen, which will be based on a thorough inventory of erosion signals in areas with different hazard levels. Copyright © 2010 John Wiley & Sons, Ltd. [source] Development and internal validation of a nomogram predicting extracapsular extension in radical prostatectomy specimensINTERNATIONAL JOURNAL OF UROLOGY, Issue 3 2010Naoya Satake Objectives: To present a nomogram predicting the side-specific probability of extracapsular extension (ECE) in radical prostatectomy (RP) specimens. Methods: Three hundred and fifty-four patients with T1c-T3a prostate cancer undergoing RP were included in the analysis. A receiver operating characteristic (ROC) analysis was carried out to evaluate the predictive values of each clinical and pathological factor, separately and in combination. Based on logistic regression analysis, a nomogram predicting the side-specific probability of ECE was developed. Results: Overall, 146 (40%) of 354 patients and 165 (23%) of 708 lobes had ECE pathologically. The areas under the ROC curve (AUC) of the standard features, such as serum PSA, clinical stage and biopsy Gleason sum on each side, in predicting side-specific probability of ECE were 0.624, 0.627, and 0.747, respectively. When these three features were combined, AUC increased to 0.773 which was not significantly different from 0.791 of maximum percent of cancer alone (P = 0.613) and significantly enhanced by including maximum percent of cancer on each side, 0.799 (P = 0.022). The resulting nomogram was internally validated and had excellent calibration. Conclusions: The accuracy in predicting ECE is increased by combining standard clinical factors (clinical stage, serum PSA, highest Gleason score) and biopsy features, such as maximum percent of cancer in the cores. The developed nomogram is helpful when deciding whether or not neurovascular bundles can be preserved. [source] Science learning in a leisure settingJOURNAL OF RESEARCH IN SCIENCE TEACHING, Issue 2 2010John H. Falk Abstract Most people visit a science center in order to satisfy specific leisure-related needs; needs which may or may not actually include science learning. Falk proposed that an individual's identity-related motivations provide a useful lens through which to understand adult free-choice science learning in leisure settings. Over a 3-year period the authors collected in-depth data on a random sample of visitors to a large recently opened, hands-on, interactive science center; collecting information on why people visited, what they did within the science center, what they knew about the subject presented upon entering and exiting, and what each individual's long-term self-perceptions of their own learning was. Presented is a qualitative analysis of visitor interviews collected roughly 2 years after the initial visit. Although there was evidence for a range of science learning outcomes, outcomes did appear to be strongly influenced by visitor's entering identity-related motivations. However, the data also suggested that not only were the motivational goals of a science center visit important in determining outcomes, so too were the criteria by which visitors judged satisfaction of those goals; in particular whether goal satisfaction required external or merely internal validation. The implications for future informal science education research and practice are discussed. © 2009 Wiley Periodicals, Inc. J Res Sci Teach 47:194,212, 2010 [source] Principles of QSAR models validation: internal and externalMOLECULAR INFORMATICS, Issue 5 2007Paola Gramatica Abstract The recent REACH Policy of the European Union has led to scientists and regulators to focus their attention on establishing general validation principles for QSAR models in the context of chemical regulation (previously known as the Setubal, nowadays, the OECD principles). This paper gives a brief analysis of some principles: unambiguous algorithm, Applicability Domain (AD), and statistical validation. Some concerns related to QSAR algorithm reproducibility and an example of a fast check of the applicability domain for MLR models are presented. Common myths and misconceptions related to popular techniques for verifying internal predictivity, particularly for MLR models (for instance cross-validation, bootstrap), are commented on and compared with commonly used statistical techniques for external validation. The differences in the two validating approaches are highlighted, and evidence is presented that only models that have been validated externally, after their internal validation, can be considered reliable and applicable for both external prediction and regulatory purposes. [source] Medication Quantification Scale Version III: Internal Validation of Detriment Weights Using a Chronic Pain PopulationPAIN PRACTICE, Issue 1 2008Michael Gallizzi MS ,,Abstract Introduction: We report an internal validation of the Medication Quantification Scale (MQS III) using a chronic pain population. The MQS was designed as a methodology of quantifying different drug regimens in 1992, updated in 1998 (MQS II), and again updated in 2003 (MQS III) using "detriment" weights determined by surveying physician members of the American Pain Society. The MQS has been used as a unitary clinical and research outcome. Methods: A retrospective chart review was collected from 400 patients in an interdisciplinary outpatient chronic pain clinic. A linear regression equation was developed using the patients' composite MQS III score, and those values were used in a Pearson correlation analysis. Results: The correlation between the subjects' computed regression detriment weights and the corresponding MQS III detriment weights yielded a significant result (r = 0.962, P < 0.01; two-tailed). Discussion: Our chronic pain sample-derived detriment weights did differ in some drug classes from that of the physician consensus, most notably the selective serotonin reuptake inhibitor, Opioid Schedule II, and NSAID class detriment. It is necessary to periodically resurvey large groups of physicians in order to control and modify the detriment weights of our categories in light of new information about detrimental effects (eg, COX-2 inhibitors), or to accommodate medical or political changes in prescribing habits (eg, more liberal opioid prescribing in the later years). This work suggests it may also be important to assess patients' perspective on detriment, as well as statistical and empiric use patterns.,, [source] Protein profiling in pathology: Analysis and evaluation of 239 frozen tissue biopsies for diagnosis of B-cell lymphomasPROTEOMICS - CLINICAL APPLICATIONS, Issue 5 2010Corine Jansen Abstract Purpose: We determined the potential value of protein profiling of tissue samples by assessing how precise this approach enables discrimination of B-cell lymphoma from reactive lymph nodes, and how well the profiles can be used for lymphoma classification. Experimental design: Protein lysates from lymph nodes (n=239) from patients with the diagnosis of reactive hyperplasia (n=44), follicular lymphoma (n=63), diffuse large B-cell lymphoma (n=43), mantle cell lymphoma (n=47), and chronic lymphocytic leukemia/small lymphocytic B-cell lymphoma (n=42) were analysed by SELDI-TOF MS. Data analysis was performed by (i) classification and regression tree-based analysis and (ii) binary and polytomous logistic regression analysis. Results: After internal validation by the leave-one-out principle, both the classification and regression tree and logistic regression classification correctly identified the majority of the malignant (87 and 96%, respectively) and benign cases (73 and 75%, respectively). Classification was less successful since approximately one-third of the cases of each group were misclassified according to the histological classification. However, an additional mantle cell lymphoma case that was misclassified as chronic lymphocytic leukemia/small lymphocytic B-cell lymphoma initially was identified based on the protein profile. Conclusions and clinical relevance: SELDI-TOF MS protein profiling allows for reliable identification of the majority of malignant lymphoma cases; however, further validation and testing robustness in a diagnostic setting is needed. [source] Circulating tumour-associated plasma DNA represents an independent and informative predictor of prostate cancerBJU INTERNATIONAL, Issue 3 2006FELIX K.-H. OBJECTIVE To investigate whether preoperative plasma levels of free DNA can discriminate between men with localized prostate cancer and benign prostatic hyperplasia (BPH). PATIENTS AND METHODS In all, 161 referred patients suspicious for prostate cancer either by an elevated prostate-specific antigen (PSA) level and/or abnormal digital rectal examination (DRE) were included in this prospective study. Peripheral plasma was taken before prostate biopsy and genomic DNA was extracted from the plasma using the a commercial kit and a vacuum chamber. After controlling for age, PSA level, the percentage free/total (f/t) PSA and prostate volume, the median prostate cancer plasma DNA concentration served as diagnostic threshold in uni- and multivariate logistic regression models. Multivariate models were subjected to 200 bootstraps for internal validation and to reduce over-fit bias. RESULTS Subgroups consisted of 142 men with clinically localized prostate cancer and 19 with BPH. The median plasma concentration of cell-free DNA was 267 ng/mL in men with BPH vs 709 ng/mL in men with prostate cancer. In univariate analyses, plasma DNA concentration was a statistically significant and informative predictor (P = 0.032 and predictive accuracy 0.643). In multivariate analyses, it remained statistically significant after controlling for age, tPSA, f/tPSA and prostate volume, increasing the predictive accuracy by 5.6%. CONCLUSIONS Our data suggest that plasma DNA level is a highly accurate and informative predictor in uni- and multivariate models for the presence of prostate cancer on needle biopsy. The predictive accuracy was substantially increased by adding plasma DNA level. However, larger-scale studies are needed to further confirm its clinical impact on prostate cancer detection. [source] Internal Validation of the AmpFlSTR YfilerÔ Amplification Kit for Use in Forensic CaseworkJOURNAL OF FORENSIC SCIENCES, Issue 1 2008Ann Marie Gross M.S. Abstract:, Y-chromosomal short-tandem repeat (Y-STR) amplification has been used in forensic casework at the Bureau of Criminal Apprehension (BCA) Forensic Science Laboratory since 2003. At that time, two separate amplifications were required to type the SWGDAM recommended loci (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439). The YfilerÔ kit coamplifies these loci as well as DYS437, DYS448, DYS456, DYS458, DYS635, and Y GATA H4. The YfilerÔ kit was validated following the internal validations outlined in the SWGDAM revised validation guidelines. Our studies show that 0.125 ng of male DNA will generate a complete 17 locus profile and that as little as 0.06 ng of male DNA yields an average of nine loci. In the male,male mixtures, a complete profile from the minor component was detected up to 1:5 ratio; most of the alleles of the minor component were detected at a 1:10 ratio and more than half the alleles of the minor component were detected at a 1:20 ratio. Complete YSTR profiles were obtained when 500 pg male DNA was mixed with female DNA at ratios up to 1:1000. At ratios of 1:5000 and 1:10,000 (male DNA to female DNA) inhibition of the YSTR amplification was evident. The YSTR results obtained for the adjudicated case samples gave significantly more probative information than the autosomal results. Our studies demonstrate that the YfilerÔ kit is extremely sensitive, does not exhibit cross-reactivity with female DNA, successfully types male DNA in the presence of overwhelming amounts of female DNA and is successful in typing actual forensic samples from adjudicated cases. [source] | |||||||||||||