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Negative Rate (negative + rate)
Kinds of Negative Rate Selected AbstractsDetecting New Forms of Network Intrusion Using Genetic ProgrammingCOMPUTATIONAL INTELLIGENCE, Issue 3 2004Wei Lu How to find and detect novel or unknown network attacks is one of the most important objectives in current intrusion detection systems. In this paper, a rule evolution approach based on Genetic Programming (GP) for detecting novel attacks on networks is presented and four genetic operators, namely reproduction, mutation, crossover, and dropping condition operators, are used to evolve new rules. New rules are used to detect novel or known network attacks. A training and testing dataset proposed by DARPA is used to evolve and evaluate these new rules. The proof of concept implementation shows that a rule generated by GP has a low false positive rate (FPR), a low false negative rate and a high rate of detecting unknown attacks. Moreover, the rule base composed of new rules has high detection rate with low FPR. An alternative to the DARPA evaluation approach is also investigated. [source] Applications and statistical properties of minimum significant difference-based criterion testing in a toxicity testing program,ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2000Qin Wang Abstract As a follow up to the recommendations of the September 1995 SETAC Pellston Workshop on Whole Effluent Toxicity (WET) on test methods and appropriate endpoints, this paper will discuss the applications and statistical properties of using a statistical criterion of minimum significant difference (MSD). We examined the upper limits of acceptable MSDs as acceptance criterion in the case of normally distributed data. The implications of this approach are examined in terms of false negative rate as well as false positive rate. Results indicated that the proposed approach has reasonable statistical properties. Reproductive data from short-term chronic WET test with Ceriodaphnia dubia tests were used to demonstrate the applications of the proposed approach. The data were collected by the North Carolina Department of Environment, Health, and Natural Resources (Raleigh, NC, USA) as part of their National Pollutant Discharge Elimination System program. [source] A comparison of diagnostic efficacies among different reagent strips and automated cell count in spontaneous bacterial peritonitisJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 5 2010Rungsun Rerknimitr Abstract Background:, Currently, decision to give antibiotics in spontaneous bacterial peritonitis (SBP) suspected patient depends mainly on the result of manual cell count, which requires significant waiting period. Recently, many reports on the efficacies of reagent strips and a few reports of automated cell count are available but there has been no direct comparison study. Aims:, This prospective study was to assess the diagnostic efficacies of different reagent strips (Aution, Multistix, Combur) and automated cell count. Methods and Results:, A total of 250 paracenteses were performed. There were 40 specimens obtained from patients with clinical suspicion for SBP, the rest were obtained from non SBP suspected patients. Thirty specimens from 250 samples (12%) were diagnosed as SBP by manual cell count. Automated system provided higher value for SBP diagnosis in all parameters (sensitivity, specificity, PPV, NPV, and accuracy; 87.5,99.1%) whereas the strip tests provided lower number in all parameters (80,98.6%). Multistix provided the lowest sensitivity (80%). The false negative rates by Aution, Multistix, Combur tests and automated cell count were 10%, 20%, 10% and 3.3%, respectively. By lowering the cut off for SBP diagnosis with the automated system to 200 cells/mm3, there was no false negative. Conclusions:, Comparing to reagent strips, automated cell count is a better screening tool for SBP diagnosis because it provides higher validity scores and a lower false negative rate. However, the discrepancy of cell count reading may occur, we suggest using a lower cut off for SBP diagnosis by the automated system. [source] Assessment of obesity in children and adolescents: synthesis of recent systematic reviews and clinical guidelinesJOURNAL OF HUMAN NUTRITION & DIETETICS, Issue 3 2010J. J. Reilly Abstract This review summarises recent systematic reviews and evidence-based guidelines that deal with the issue of how best to diagnose or define obesity in children and adolescents. A recent systematic review showed that parents typically fail to recognise obesity in their children and adolescents, and a good deal of other evidence suggests that health professionals under-diagnose obesity in children and adolescents when using informal methods based on observation. There is therefore a need for practical, objective, methods that both identify the fattest children and adolescents adequately, and identify those who are at greatest risk of the ,co-morbidities' of obesity. A large body of consistent evidence shows that a high body mass index (BMI) for age and sex identifies the fattest children adequately, with low,moderate false negative rate and a low false positive rate. Furthermore, children and adolescents at high BMI for age are at much greater risk of the co-morbidities of obesity. A recent systematic review found that the use of BMI for age with national reference data and cut-off points (such as the 95th percentile to define obesity) was superior to the Cole,International Obesity Task Force international approach for defining obesity based on BMI for age. The same systematic review also found no evidence that use of waist circumference for age improved the diagnosis of obesity, or the cardio-metabolic co-morbidities of obesity, in children and adolescents. Recent systematic reviews are therefore supportive of current guidelines that recommend percentile-based cut-offs relative to national reference data to (e.g. BMI at or above the 95th or 98th percentile in the UK) to define obesity for clinical applications in children and adolescents. [source] Assessment of referral patterns for CT KUB in a tertiary settingJOURNAL OF MEDICAL IMAGING AND RADIATION ONCOLOGY, Issue 6 2009H Jo Summary The purpose of this study was to assess the referral patterns and the use of unenhanced renal tract CT (CT KUB) for investigating patients presenting with clinically suspected renal colic. We retrospectively reviewed 500 consecutive CT KUB studies requested for suspected renal colic carried out at a single institution between December 2006 and July 2007. Follow-up radiology reports and discharge summaries on the hospital clinical Intranet were also reviewed. Studies were analysed for characteristics including patient demographics, referring clinical team, time of referral, final diagnosis and requirement for further imaging. The majority of requests were from Emergency (ED) or Urology Departments (49%, 245 out of 500, and 37%, 186 out of 500, respectively). The positive rate for urolithiasis was 67% (337 out of 500), the negative rate was 25% (123 out of 500), and 8% (40 out of 500) of patients had alternative significant findings. Female patients were more likely to have a negative study than male patients (35 versus 20%, P < 0.0001) and more likely to have alternative significant pathology (12 versus 6%, P < 0.0001). Patients referred by specialities other than Urology and ED were more likely to be female and have a negative or alternative finding (P < 0.0001). CT KUB is a widely used first method of investigation for patients with suspected renal colic with a high positive predictive value allowing rapid diagnosis and intervention. However, given the high rate of negative or alternative findings on CT KUB in young women, especially those referred by specialities other than ED or Urology, ultrasound should be considered as an alternative imaging method to minimise unnecessary radiation exposure. [source] Genome-wide association studies and the genetic dissection of complex traits,AMERICAN JOURNAL OF HEMATOLOGY, Issue 8 2009Paola Sebastiani The availability of affordable high throughput technology for parallel genotyping has opened the field of genetics to genome-wide association studies (GWAS), and in the last few years hundreds of articles reporting results of GWAS for a variety of heritable traits have been published. What do these results tell us? Although GWAS have discovered a few hundred reproducible associations, this number is underwhelming in relation to the huge amount of data produced, and challenges the conjecture that common variants may be the genetic causes of common diseases. We argue that the massive amount of genetic data that result from these studies remains largely unexplored and unexploited because of the challenge of mining and modeling enormous data sets, the difficulty of using nontraditional computational techniques and the focus of accepted statistical analyses on controlling the false positive rate rather than limiting the false negative rate. In this article, we will review the common approach to analysis of GWAS data and then discuss options to learn more from these data. We will use examples from our ongoing studies of sickle cell anemia and also GWAS in multigenic traits. Am. J. Hematol., 2009. © 2009 Wiley-Liss, Inc. [source] A cost effectiveness analysis of omitting radiography in diagnosis of acute bronchiolitis,PEDIATRIC PULMONOLOGY, Issue 2 2009Jean Hai Ein Yong MASc Abstract Objective To carry out a cost-effectiveness analysis of omitting chest radiography in the diagnosis of infant bronchiolitis. Hypothesis Omitting chest radiographs in the diagnosis of typical bronchiolitis was expected to reduce costs without adversely affecting the detection rate of alternate diseases. Study Design An economic evaluation was conducted using clinical and health resources. Emergency department (ED) physicians provided diagnoses pre- and post-radiography as well as a management plan. The primary outcome was the diagnostic accuracy (false-negative rate) of alternate diagnoses with and without X-ray. The incremental costs of omitting radiography in comparison to routine radiography per patient were assessed from a health system perspective. Patient Selection We studied 265 infants, 2,23 months old, presenting at the ED with typical bronchiolitis. Patients with pre-existing conditions or radiographs were omitted from the study. Methodology Expected costs to the health care system of including and excluding chest radiographs were compared, including costs associated with misdiagnosis. Results All alternate diagnoses (two cases) were missed by ED physicians pre- and post-radiography, resulting in a 100% false negative rate. The specificity in detecting alternate diseases was 96.6% pre-radiography and 88.6% post-radiography. Of the 17 cases of coexistent pneumonia, 88% were missed pre-radiography and 59% post-radiography, with respective false positive rates of 10.5% and 16.1%. Omission of routine chest radiograph saved CDN $59 per patient, primarily due to savings in radiography and hospitalization costs. The economic benefit persisted after the inpatient length of stay, ED overhead and radiograph costs were varied. Conclusion For infants with typical bronchiolitis, omitting radiography is cost saving without compromising diagnostic accuracy of alternate diagnoses and of associated pneumonia. Pediatr Pulmonol. 2009; 44:122,127. © 2009 Wiley-Liss, Inc. [source] Quantitative proteomics of intracellular Porphyromonas gingivalisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 23 2007Qiangwei Xia Abstract Whole-cell quantitative proteomic analyses were conducted to investigate the change from an extracellular to intracellular lifestyle for Porphyromonas gingivalis, a Gram-negative intracellular pathogen associated with periodontal disease. Global protein abundance data for P. gingivalis strain ATCC 33277 internalized for 18,h within human gingival epithelial cells and controls exposed to gingival cell culture medium were obtained at sufficient coverage to provide strong evidence that these changes are profound. A total of 385 proteins were overexpressed in internalized P. gingivalis relative to controls; 240 proteins were shown to be underexpressed. This represented in total about 28% of the protein encoding ORFs annotated for this organism, and slightly less than half of the proteins that were observed experimentally. Production of several proteases, including the classical virulence factors RgpA, RgpB, and Kgp, was decreased. A separate validation study was carried out in which a 16-fold dilution of the P. gingivalis proteome was compared to the undiluted sample in order to assess the quantitative false negative rate (all ratios truly alternative). Truly null (no change) abundance ratios from technical replicates were used to assess the rate of quantitative false positives over the entire proteome. A global comparison between the direction of abundance change observed and previously published bioinformatic gene pair predictions for P. gingivalis will assist with future studies of P. gingivalis gene regulation and operon prediction. [source] The Use of Stereotaxic Core Biopsy and Stereotaxic Aspiration Biopsy as Diagnostic Tools in the Evaluation of Mammary CalcificationTHE BREAST JOURNAL, Issue 6 2000Joan F. Cangiarella MD Abstract: We compared stereotaxic fine needle aspiration biopsy (SFNA) with stereotaxic core needle biopsy (SCB) in the evaluation of radiographically clustered mammary microcalcification, a common finding at screening mammography. Over a 4-year period, 181 specimens were obtained from 175 patients who underwent both SFNA and SCB of clustered microcalcification. Aspiration and core biopsies were performed by radiologists at a community-based diagnostic radiology facility. All aspiration smears were air dried, stained on site, and assessed for adequacy by the radiologists, then sent to the cytopathologists at New York University for interpretation. Core biopsy specimens were formalin fixed, paraffin embedded, hematoxylin and eosin stained, and interpreted by surgical pathologists at a community hospital. Of 181 SFNA specimens, 133 (74%) were benign, 18 (10%) were atypical, 13 (7%) were suspicious, and 16 (9%) were malignant. One (0.5%) aspiration biopsy was nondiagnostic. Excisional biopsies were performed after 12 benign SFNAs and in 46 of the 47 cases with an atypical, suspicious, or malignant diagnosis on SFNA. Mammographic follow-up in 111 of the 133 cases (92%) diagnosed as benign showed no radiologic change (mean 29.2 months, range 6,60 months). The false-negative rate for cancer was 4% (6 cases) for SFNA alone. There were no false-positive diagnoses for SFNA. There was one false-positive diagnosis on core biopsy [focal cribriform ductal carcinoma in situ (DCIS)], which at excisional biopsy and correlation with the core biopsy was diagnosed as ductal hyperplasia; the false-negative rate for cancer was 8% (13 cases) for SCB alone. Aspiration biopsy identified calcification in 180 procedures, core needle biopsy revealed calcification in 170. SFNA was superior to SCB for the confirmation of clustered mammary microcalcification (99% versus 94%) and in the identification of cancer associated with microcalcification (false negative rate of 4% versus 8%). Patients with benign findings on stereotaxic aspiration and core biopsy can reasonably be followed mammographically. [source] Bayesian Methods for Predicting Interacting Protein Pairs Using Domain InformationBIOMETRICS, Issue 3 2007Inyoung Kim Summary Protein,protein interactions (PPIs) play important roles in most fundamental cellular processes including cell cycle, metabolism, and cell proliferation. Therefore, the development of effective statistical approaches to predicting protein interactions based on recently available large-scale experimental data is very important. Because protein domains are the functional units of proteins and PPIs are mostly achieved through domain,domain interactions (DDIs), the modeling and analysis of protein interactions at the domain level may be more informative and insightful. However, due to the large number of domains, the number of parameters to be estimated is very large, yet the amount of information for statistical inference is quite limited. In this article we propose a full Bayesian method and a semi-Bayesian method for simultaneously estimating DDI probabilities, the false positive rate, and the false negative rate of high-throughput data through integrating data from several organisms. We also propose a model to associate protein interaction probabilities with domain interaction probabilities that reflects the number of domains in each protein. Our Bayesian methods are compared with the likelihood-based approach (Deng et al., 2002, Genome Research12, 1504,1508; Liu, Liu, and Zhao, 2005, Bioinformatics21, 3279,3285) developed using the expectation maximization algorithm. We show that the full Bayesian method has the smallest mean square error through both simulations and theoretical justification under a special scenario. The large-scale PPI data obtained from high-throughput yeast two-hybrid experiments are used to demonstrate the advantages of the Bayesian approaches. [source] Heel ultrasonography is not a good screening tool for bone loss after kidney and pancreas transplantationCLINICAL TRANSPLANTATION, Issue 5 2004Lynn R Mack-Shipman Abstract:, Background:, Solid organ transplant recipients, particularly simultaneous pancreas kidney recipients, are at high fracture risk. We tested whether quantitative ultrasonography (QUS) of the heel predicts bone mineral density (BMD) by dual energy X-ray absorptiometry (DXA) in solid organ transplant recipients. Methods:, Thirty-eight transplant recipients (22 Female/16 Male) were studied. Spine and hip BMD was measured with a Hologic DXA scanner. ,Stiffness' of the heel was measured with a Lunar Ultrasound densitometer and compared with BMD by DXA. Contributing factors to bone loss were also assessed. Results:, Mean age was 43.1 ± 1.3 yr. Simultaneous pancreas-kidney, kidney, and pancreas alone transplant recipients were assessed. Mean time post-transplantation was 3.0 ± 0.6 yr. Mean DXA spine T-score was ,1.15 ± 0.22 (mean ± SEM) and hip T-score was ,1.22 ± 0.20. There was no difference in mean T-score between women and men at the hip or spine. Mean right heel stiffness T-score was ,0.97 ± 0.25. There was no correlation between QUS and DXA at either the hip or spine in women or men. QUS had a false negative rate for identifying osteopenia or osteoporosis of 17% compared with DXA. The false positive rate for identifying osteopenia was 61%. Conclusions:, The QUS is an unacceptable tool for identifying those at risk for bone loss after kidney or pancreas transplantation. [source] Comparative study: conventional cervical and ThinPrep® Pap tests in a routine clinical settingCYTOPATHOLOGY, Issue 4 2002A. Grace The conventional Papanicolaou smear is associated with variable false positive and false negative rates, difficulties with interpretation and high unsatisfactory and suboptimal rates. Newer fluid-based methods such as the ThinPrep® 2000 system (Cytyc Corp., Boxborough, MA) are said to overcome these difficulties. The aim of this study was to compare the conventional smear with the ThinPrep® method in a busy, routine cytology screening laboratory setting. One thousand split samples were evaluated. Using ThinPrep®, the results showed an increased sensitivity and a dramatic improvement in specimen adequacy, with a combined 17.2% reduction in ,unsatisfactory' and ,suboptimal' reports. Screening time per slide was also reduced to 3,4 min. In conclusion, we report an increase in sensitivity, a reduction in screening time and a dramatic improvement in specimen adequacy with the ThinPrep® method. [source] Evaluation of Three Algorithms to Identify Incident Breast Cancer in Medicare Claims DataHEALTH SERVICES RESEARCH, Issue 5 2007Heather T. Gold Objective. To test the validity of three published algorithms designed to identify incident breast cancer cases using recent inpatient, outpatient, and physician insurance claims data. Data. The Surveillance, Epidemiology, and End Results (SEER) registry data linked with Medicare physician, hospital, and outpatient claims data for breast cancer cases diagnosed from 1995 to 1998 and a 5 percent control sample of Medicare beneficiaries in SEER areas. Study Design. We evaluate the sensitivity and specificity of three algorithms applied to new data compared with original reported results. Algorithms use health insurance diagnosis and procedure claims codes to classify breast cancer cases, with SEER as the reference standard. We compare algorithms by age, stage, race, and SEER region, and explore via logistic regression whether adding demographic variables improves algorithm performance. Principal Findings. The sensitivity of two of three algorithms is significantly lower when applied to newer data, compared with sensitivity calculated during algorithm development (59 and 77.4 percent versus 90 and 80.2 percent, p<.00001). Sensitivity decreases as age increases, and false negative rates are higher for cases with in situ, metastatic, and unknown stage disease compared with localized or regional breast cancer. Substantial variation also exists by SEER registry. There was potential for improvement in algorithm performance when adding age, region, and race to an indicator variable for whether the algorithm determined a subject to be a breast cancer case (p<.00001). Conclusions. Differential sensitivity of the algorithms by SEER region and age likely reflects variation in practice patterns, because the algorithms rely on administrative procedure codes. Depending on the algorithm, 3,5 percent of subjects overall are misclassified in 1998. Misclassification disproportionately affects older women and those diagnosed with in situ, metastatic, or unknown-stage disease. Algorithms should be applied cautiously to insurance claims databases to assess health care utilization outside SEER-Medicare populations because of uneven misclassification of subgroups that may be understudied already. [source] Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2008Julian Vasilescu Abstract We report a simple approach for determining ion score cutoffs that permit the confident identification of ubiquitinated proteins by tandem mass spectrometry (MS/MS). Initial experiments involving the analysis of gel bands containing multi-Ubiquitin chains with quadrupole time-of-flight and quadrupole ion trap mass spectrometers revealed that standard ion score cutoffs used for database searching were not sufficiently stringent. We also found that false positive and false negative rates (FPR and FNR) varied significantly depending on the cutoff scores used and that appropriate cutoffs could only be determined following a systematic evaluation of false positive rates. When standard cutoff scores were used for the analysis of complex mixtures of ubiquitinated proteins, unacceptably high FPR were observed. Finally, we found that FPR for ubiquitinated proteins are affected by the size of the protein database that is searched. These observations may be applicable for the study of other post-translational modifications. Copyright © 2007 John Wiley & Sons, Ltd. [source] Comparison of conventional FASTA identity searches with the 80 amino acid sliding window FASTA search for the elucidation of potential identities to known allergensMOLECULAR NUTRITION & FOOD RESEARCH (FORMERLY NAHRUNG/FOOD), Issue 8 2007Gregory S. Ladics Abstract Food and Agriculture Organization/World Health Organization (FAO/WHO) recommended that IgE cross-reactivity between a transgenic protein and allergen be considered when there is ,F 35% identity over a sliding "window" of 80 amino acids. Our objective was to evaluate the false positive and negative rates observed using the FAO/WHO versus conventional FASTA analyses. Data used as queries against allergen databases and analyzed to assess false positive rates included: 1102 hypothetical corn ORFs; 907 randomly selected proteins; 89 randomly selected corn proteins; and 97 corn seed proteins. To evaluate false negative rates of both methods: Bet v 1a along with several crossreacting fruit/vegetable allergens and a bean ,-amylase inhibitor were used as queries. Both methods were also evaluated for their ability to detect a putative nonallergenic test protein containing a sequence derived from Ara h 1. FASTA versions 3.3t0 and 3.4t25 were utilized. Data indicate a conventional FASTA analysis produced fewer false positives and equivalent false negative rates. Conventional FASTA versus sliding window derived E scores were generally more significant. Results suggest a conventional FASTA search provides more relevant identity to the query protein and better reflects the functional similarities between proteins. It is recommended that the conventional FASTA analysis be conducted to compare identities of proteins to allergens. [source] Validation of MCADD newborn screeningCLINICAL GENETICS, Issue 2 2009EM Maier Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) represents a potentially fatal fatty acid ,-oxidation disorder. Newborn screening (NBS) by tandem mass spectrometry (MS/MS) has been implemented worldwide, but is associated with unresolved questions regarding population heterogeneity, burden on healthy carriers, cut-off policies, false-positive and negative rates. In a retrospective case-control study, 333 NBS samples showing borderline acylcarnitine patterns but not reaching recall criteria were genotyped for the two most common mutations (c.985A>G/c.199C>T) and compared with genotypes and acylcarnitines of 333 controls, 68 false-positives, and 34 patients. c.985A>G was more frequently identified in the study group and false-positives compared to controls (1:4.3/1:2.3 vs. 1:42), whereas c.199C>T was found more frequently only within the false-positives (1:23). Biochemical criteria were devised to differentiate homozygous (c.985A>G), compound heterozygous (c.985A>G/c.199C>T), and heterozygous individuals. Four false-negatives were identified because our initial algorithm required an elevation of octanoylcarnitine (C8) and three secondary markers in the initial and follow-up sample. The new approach allowed a reduction of false-positives (by defining high cut-offs: 1.4 ,mol/l for C8; 7 for C8/C12) and false-negatives (by sequencing the ACADM gene of few suspicious samples). Our validation strategy is able to differentiate healthy carriers from patients doubling the positive predictive value (42,88%) and to target NBS to MCADD-subsets with potentially higher risk of adverse outcome. It remains controversial, if NBS programs should aim at identifying all subsets of all diseases included. Because the natural course of milder variants cannot be assessed by observational studies, our strategy could serve as a general model for evaluation of MS/MS-based NBS. [source] | ||||||||||||||||