Search results for "false positive"
showing 10 items of 64 documents
Reducing False Node Failure Predictions in HPC
2019
Future HPC applications must be able to scale to thousands of compute nodes, while running for several days. The increased runtime and node count inconveniently raises the probability of hardware failures that may interrupt computations. Scientists must therefore protect their simulations against hardware failures. This is typically done using frequent checkpoint& restart, which may have significant overheads. Consequently, the frequency in which checkpoints are taken should be minimized. Predicting hardware failures ahead of time is a promising approach to address this problem, but has remaining issues like false alarms at large scales. In this paper, we introduce the probability of unnece…
Exudate-based diabetic macular edema detection in fundus images using publicly available datasets
2010
International audience; Diabetic macular edema (DME) is a common vision threatening complication of diabetic retinopathy. In a large scale screening environment DME can be assessed by detecting exudates (a type of bright lesions) in fundus images. In this work, we introduce a new methodology for diagnosis of DME using a novel set of features based on colour, wavelet decomposition and automatic lesion segmentation. These features are employed to train a classifier able to automatically diagnose DME through the presence of exudation. We present a new publicly available dataset with ground-truth data containing 169 patients from various ethnic groups and levels of DME. This and other two publi…
First trimester biochemical screening for Down's syndrome in singleton pregnancies conceived by assisted reproduction
2005
BACKGROUND: Serum biochemical markers [free betahCG (fbetahCG); pregnancy-associated plasma protein-A (PAPP-A)] used in first trimester Down's syndrome screening have not been fully investigated in pregnancies achieved by assisted reproduction techniques. We present data on pregnancies conceived by all types of assisted reproduction techniques, including pregnancies following ovum donation (OD) and a large sample by ICSI. METHODS: First trimester Down's syndrome screening was performed in 1054 normal singleton pregnancies: natural conception (n = 498), ovulation induction (OS, n = 97), IVF (n = 47), ICSI (n = 222) and OD (n = 190). RESULTS: No differences in maternal levels of fbetahCG and …
Detection of 9-Tetrahydrocannabinol and Amphetamine-Type Stimulants in Oral Fluid Using the Rapid Stat Point-of-Collection Drug-Testing Device
2010
The Rapid Stat assay, a point-of-collection drug-testing device for detection of amphetamines, cannabinoids, cocaine, opiates, methadone, and benzodiazepines in oral fluid, was evaluated for cannabis and amphetamine-type stimulants. The Rapid Stat tests (n = 134) were applied by police officers in routine traffic checks. Oral fluid and blood samples were analyzed using gas chromatography-mass spectrometry (GC-MS) for Delta(9)-tetrahydrocannabinol, amphetamine, methamphetamine, methylenedioxymethamphetamine, methylenedioxyethylamphetamine, and methylenedioxyamphetamine. The comparison of GC-MS analysis of oral fluid with the Rapid Stat results for cannabis showed a sensitivity of 85%, a spec…
Application of the Morris method for screening the influential parameters of fuzzy controllers applied to wastewater treatment plants
2011
In this paper,we evaluate the application of a sensitivity analysis to help fine-tuning a fuzzy controller for a biological nitrogen and phosphorus removal (BNPR) plant. TheMorris Screeningmethod is proposed and evaluated as a prior step to obtain the parameter significance ranking. First, an iterative procedure has been performed in order to find out the proper repetition number of the elementary effects (r) of the method. The optimal repetition number found in this study (r = 60) is in direct contrast to previous applications of the Morris method, which usually use low repetition number, e.g. r = 10 ~ 20. Working with a non-proper repetition number (r) could lead to Type I error (identify…
On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing
2013
One of the most used techniques to study structural variation at a genome level is paired-end mapping (PEM). PEM has the advantage of being able to detect balanced events, such as inversions and translocations. However, inversions are still quite difficult to predict reliably, especially from high-throughput sequencing data. We simulated realistic PEM experiments with different combinations of read and library fragment lengths, including sequencing errors and meaningful base-qualities, to quantify and track down the origin of false positives and negatives along sequencing, mapping, and downstream analysis. We show that PEM is very appropriate to detect a wide range of inversions, even with …
Confidence-based Somatic Mutation Evaluation and Prioritization
2012
Next generation sequencing (NGS) has enabled high throughput discovery of somatic mutations. Detection depends on experimental design, lab platforms, parameters and analysis algorithms. However, NGS-based somatic mutation detection is prone to erroneous calls, with reported validation rates near 54% and congruence between algorithms less than 50%. Here, we developed an algorithm to assign a single statistic, a false discovery rate (FDR), to each somatic mutation identified by NGS. This FDR confidence value accurately discriminates true mutations from erroneous calls. Using sequencing data generated from triplicate exome profiling of C57BL/6 mice and B16-F10 melanoma cells, we used the exist…
General Principles for the Detection of Modified Nucleotides in RNA by Specific Reagents.
2021
Epitranscriptomics heavily rely on chemical reagents for the detection, quantification, and localization of modified nucleotides in transcriptomes. Recent years have seen a surge in mapping methods that use innovative and rediscovered organic chemistry in high throughput approaches. While this has brought about a leap of progress in this young field, it has also become clear that the different chemistries feature variegated specificity and selectivity. The associated error rates, e.g., in terms of false positives and false negatives, are in large part inherent to the chemistry employed. This means that even assuming technically perfect execution, the interpretation of mapping results issuin…
Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases.
2021
Abstract Background Exome sequencing (ES) has become the most powerful and cost‐effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%–40% in solo‐ES and 50% in trio‐ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES. Methods We pooled six (Agilent‐CRE‐v2–100X) or five parental DNA (TWIST‐HCE–70X) aiming to detect allelic balance around 8–10% for heterozygous status. The strategies were applied as second‐tier (74 individuals after negative solo‐ES) and first‐tier approaches (324 individuals without previous ES). Results The allelic balance of parental‐pool v…
Detection of mammalian carcinogens with an immunological DNA synthesis-inhibition test.
1992
There is a close relationship between genotoxicity, mutagenicity and carcinogenicity. But the controversy of which short-term test system best recognizes human carcinogens is still going on. Currently, the Salmonella gene mutation assay ('Ames test') is the most widely used test for the screening of mutagens. However, many in vitro tests hold unsatisfactory validity data, presumably because of the inability of present short-term tests to detect non-genotoxic carcinogens, which are increasingly being brought into focus in the discussions of genesis of cancer. One principle often neglected in this context is the property of genotoxic agents to inhibit replicative DNA synthesis in (proliferati…