PATO: Pangenome Analysis Toolkit.

MOTIVATION: We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment. RESULTS: PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20-30× times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Finally, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R. AVAILABILITYAND IMPLEMENTATION: The source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Relevance of cutoff on a 4th generation ELISA performance in the false positive rate during HIV diagnostic in a low HIV prevalence setting.

BACKGROUND: Despite the high specificity of fourth-generation enzyme immunoassays (4th-gen-EIA) for screening during HIV diagnosis, their positive predictive value is low in populations with low HIV prevalence. Thus, screening should be optimized to reduce false positive results. OBJECTIVES: The influence of sample cutoff (S/CO) values by a 4th-gen-EIA with the false positive rate during the routine HIV diagnosis in a low HIV prevalence population was evaluated. STUDY DESIGN: A total of 30,201 sera were tested for HIV diagnosis using Abbott Architect® HIV-Ag/Ab-Combo 4th-gen-EIA at a hospital in Spain during 17 months. Architect S/CO values were recorded, comparing the HIV-1 positive results following Architect interpretation (S/CO≥1) with the final HIV-1 diagnosis by confirmatory tests (line immunoassay, LIA and/or nucleic acid test, NAT). ROC curve was also performed. RESULTS: Among the 30,201 HIV performed tests, 256 (0.85%) were positive according to Architect interpretation (S/CO≥1) but only 229 (0.76%) were definitively HIV-1 positive after LIA and/or NAT. Thus, 27 (10.5%) of 256 samples with S/CO≥1 by Architect were false positive diagnose. The false positive rate decreased when the S/CO ratio increased. All 19 samples with S/CO ≤10 were false positives and all 220 with S/CO>50 true HIV-positives. The optimal S/CO cutoff value provided by ROC curves was 32.7. No false negative results were found. CONCLUSIONS: We show that very low S/CO values during HIV-1 screening using Architect can result HIV negative after confirmation by LIA and NAT. The false positive rate is reduced when S/CO increases.

Assessment of occupational exposure to extremely low frequency magnetic fields in hospital personnel.

It has been proposed that chronic exposure to extremely low frequency (ELF) magnetic fields (MF) in occupational environments could represent a risk factor for a number of disorders. Medical and technical workers in hospitals have been reported to be exposed to relatively strong ELF fields. The present work aims to characterize exposure to MF in the 5 Hz to 2 kHz frequency range in a large hospital through both instantaneous environmental measurements and personal monitoring of workers. The study was conducted in different working environments of a hospital with about 4400 employees, many of them working at two or more different work stations and consequently, exposed to MF levels that were expected to be unevenly distributed in space and time. The results indicate that: (1) The dominant frequency at the studied environments was 50 Hz (average 90.8 ± 6% of the total B value); (2) The best descriptive information on a worker's exposure is obtained from personal monitoring of volunteer workers; (3) The arithmetic averages of exposure levels obtained from the monitoring ranged from 0.03 ± 0.01 µT in nurses to 0.39 ± 0.13 µT in physiotherapists; and (4) The description of the MF environment through spot measurements in the workplace, although coherent with the data from personal monitoring, might not adequately estimate MF exposure in some professional categories.