Augmentation of Transcriptomic Data for Improved Classification of Patients with Respiratory Diseases of Viral Origin.

To better understand the molecular basis of respiratory diseases of viral origin, high-throughput gene-expression data are frequently taken by means of DNA microarray or RNA-seq technology. Such data can also be useful to classify infected individuals by molecular signatures in the form of machine-learning models with genes as predictor variables. Early diagnosis of patients by molecular signatures could also contribute to better treatments.

Correcting the Estimation of Viral Taxa Distributions in Next-Generation Sequencing Data after Applying Artificial Neural Networks.

Estimating the taxonomic composition of viral sequences in a biological samples processed by next-generation sequencing is an important step in comparative metagenomics. Mapping sequencing reads against a database of known viral reference genomes, however, fails to classify reads from novel viruses whose reference sequences are not yet available in public databases. Instead of a mapping approach, and in order to classify sequencing reads at least to a taxonomic level, the performance of artificial neural networks and other machine learning models was studied.

The impact on accuracy and cost of ligase chain reaction testing by pooling urine specimens for the diagnosis of Chlamydia trachomatis infections.

Background And Objectives: Nucleic acid amplification testing is the most accurate approach to diagnosing Chlamydia trachomatis infections. Our objective was to compare the accuracy and cost savings of pooling urines as opposed to individual testing.

Study Design: Strategies of pooling urine specimens into groups of four (4x pool) or eight (8x pool) followed by testing the positive pools individually were compared to individual specimen testing to determine if significant cost savingS could be realized without compromising the sensitivity and specificity of the LCx C.

Impact of reference standard sensitivity on accuracy of rapid antigen detection assays and a leukocyte esterase dipstick for diagnosis of Chlamydia trachomatis infection in first-void urine specimens from men.

A total of 128 previously frozen first-void urine (FVU) specimens from selected asymptomatic men were centrifuged and tested by three Chlamydia trachomatis rapid antigen detection tests and with a leukocyte esterase (LE) dipstick. When the results were compared to those of a reference standard of positivity determined by the Chlamydiazyme enzyme immunoassay as confirmed by a blocking assay, the sensitivities of the Testpack Chlamydia (Abbott), Clearview Chlamydia (Unipath), and Surecell Chlamydia (Kodak) tests and the LE dipstick test were 76.4, 76.

Multiplex PCR for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Genitourinary specimens.

We developed a multiplex PCR (M-PCR) assay for the simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae. M-PCR employed C. trachomatis-specific primers KL1-KL2 and N.