Statistically, the concentration of antibodies against parasites decreases with the duration of infection. This can result in false-negative outcomes of diagnostic tests for subjects with old infections. When a property of seronegative and seropositive subjects is compared under these circumstances, the statistical tests can detect no difference between these two groups of subjects, despite the fact that they differ. When the effect of the infection has a cumulative character and subjects with older infections are affected to a greater degree, we may even get paradoxical results of the comparison - the seropositive subjects have, on average, a higher value of certain traits despite the infection having a negative effect on those traits. A permutation test for the contaminated data implemented, e.g. in the program Treept or available as a comprehensibly commented R function at https://github.com/costlysignalling/Permutation_test_for_contaminated_data, can be used to reveal and to eliminate the effect of false negatives. A Monte Carlo simulation in the program R showed that our permutation test is a conservative test - it could provide false negative, but not false positive, results if the studied population contains no false-negative subjects. A new R version of the test was expanded by skewness analysis, which helps to estimate the proportion of false-negative subjects based on the assumption of equal data skewness in groups of healthy and infected subjects. Based on the results of simulations and our experience with empirical studies we recommend the usage of a permutation test for contaminated data whenever seronegative and seropositive individuals are compared.

• Keywords
• Case-control studies, Epidemiology, Randomisation tests, Sensitivity, Serology, Specificity, Toxoplasma,
• MeSH
• Biology * methods   MeSH
• Precision Medicine * methods   MeSH
• Humans MeSH
• DNA Mutational Analysis * methods   standards   MeSH
• Sensitivity and Specificity MeSH
• Software * MeSH
• Case-Control Studies MeSH
• Computational Biology methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Cytomegalovirus (CMV) is the herpetic virus, which infects 45-100% people worldwide. Many reports suggest that CMV could impair cognitive functions of infected subjects. Here we searched for indices of effects of CMV on infected subjects' intelligence and knowledge. The Intelligence Structure Test I-S-T 2000 R was used to compare IQ of 148 CMV-infected and 135 CMV-free university students. Infected students expressed higher intelligence. Paradoxically, their IQ decreased with decreasing concentration of anti-CMV antibodies, which can be used, statistically, as a proxy of the time passed from the moment of infection in young subjects when the age of subjects is statistically controlled. The paradox of seemingly higher intelligence of CMV infected subjects could be explained by the presence of the subpopulation of about 5-10% CMV-positive individuals in the population of "CMV-negative students". These false negative subjects had probably not only the oldest infections and therefore the lowest concentration of anamnestic antibodies, but also the lowest intelligence among the infected students. Prevalence of CMV infection in all countries is very high, approaching sometimes 90%. Therefore, the total impact of CMV on human intelligence may be large.

• MeSH
• Biomarkers MeSH
• Cytomegalovirus Infections epidemiology   psychology   virology   MeSH
• Cytomegalovirus * MeSH
• Intelligence MeSH
• Intelligence Tests MeSH
• Cognition * MeSH
• Humans MeSH
• Public Health Surveillance MeSH
• Students * MeSH
• Case-Control Studies MeSH
• Models, Theoretical MeSH
• Universities * MeSH
• Health Knowledge, Attitudes, Practice MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Retracted Publication MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Biomarkers MeSH

BACKGROUND: Despite the medical importance of trichomoniasis, little is known about the genetic relatedness of Trichomonas vaginalis strains with similar biological characteristics. Furthermore, the distribution of endobionts such as mycoplasmas or Trichomonas vaginalis virus (TVV) in the T. vaginalis metapopulation is poorly characterised. RESULTS: We assayed the relationship between 20 strains of T. vaginalis from 8 countries using the Random Amplified Polymorphic DNA (RAPD) analysis with 27 random primers. The genealogical tree was constructed and its bootstrap values were computed using the program FreeTree. Using the permutation tail probability tests we found that the topology of the tree reflected both the pattern of resistance to metronidazole (the major anti-trichomonal drug) (p < 0.01) and the pattern of infection of strains by mycoplasmas (p < 0.05). However, the tree did not reflect pattern of virulence, geographic origin or infection by TVV. Despite low bootstrap support for many branches, the significant clustering of strains with similar drug susceptibility suggests that the tree approaches the true genealogy of strains. The clustering of mycoplasma positive strains may be an experimental artifact, caused by shared RAPD characters which are dependent on the presence of mycoplasma DNA. CONCLUSIONS: Our results confirmed both the suitability of the RAPD technique for genealogical studies in T. vaginalis and previous conclusions on the relatedness of metronidazol resistant strains. However, our studies indicate that testing analysed strains for the presence of endobionts and assessment of the robustness of tree topologies by bootstrap analysis seem to be obligatory steps in such analyses.

• MeSH
• Species Specificity MeSH
• Phenotype MeSH
• Phylogeny MeSH
• Humans MeSH
• Mycoplasma genetics   isolation & purification   MeSH
• Mycoplasma Infections genetics   MeSH
• Mice, Inbred C57BL MeSH
• Mice MeSH
• Polymorphism, Genetic genetics   MeSH
• DNA, Protozoan genetics   MeSH
• RNA Viruses genetics   isolation & purification   MeSH
• Random Amplified Polymorphic DNA Technique methods   MeSH
• Trichomonas Vaginitis genetics   MeSH
• Trichomonas vaginalis genetics   microbiology   pathogenicity   virology   MeSH
• Virulence genetics   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Mice MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Names of Substances
• DNA, Protozoan MeSH