Correction of the p-value after multiple tests in a Cox proportional hazard model

We consider a situation which is common in epidemiology, in which several transformations of an explanatory variable are tried in a Cox model and the most significant test is retained. The p-value should then be corrected to take account of the multiplicity of tests. Bonferroni method is often too conservative because the tests may be highly positively correlated. We propose an asymptotically exact correction of the p-value. The method uses the fact that the tests are asymptotically normal to compute numerically the distribution of the maximum of several tests. Counting processes theory is used to derive estimators of the correlations between tests. The method is illustrated by a simulation and an analysis of the relation between concentration of aluminum in drinking water and risk of dementia.

Prevalence of hepatitis C infection and its risk factors in hemodialysis patients in tehran: preliminary report from "the effect of dialysis unit isolation on the incidence of hepatitis C in dialysis patients" project

Hepatitis C virus (HCV) is the most common cause of chronic liver disease in patients with end-stage renal disease. It is more prevalent in hemodialysis (HD) patients than the general population but the exact routes of transmission are not clear. In this study, the current situation of HCV infection was assessed in eleven dialysis centers in Tehran, Iran. A total of 548 patients on maintenance HD with a mean age of 45.4 +/- 16.8 years were studied. Most of the patients were dialysed 3 times/week, each session lasting 4 to 4.5 hours. About 15% of patients had a history of having received peritoneal dialysis prior to maintenance HD and 23.6 of patients had received blood transfusion(s). The most common cause of renal failure was hypertension in 29.7% followed by diabetes mellitus in 23.2%, failed renal transplant in 19.4% and glomerulonephritis in 9.7%. HCV antibodies were measured by ELISA-III. All positive sera were tested for HCV RNA by RT-PCR. Positive HCV antibody tests were present in 19.6% of patients. In these seropositive patients, 48.6% had detectable HCV RNA. Prevalence of HCV antibody seropositivity was not different in patients with or without history of blood transfusion. The prevalence of positive HCV antibody in this study was higher than reports from Europe but lower than other countries in the region. Only 48.6% of seropositive cases were confirmed by PCR, which is lower than expected values. It seems that nosocomial transmission is the main route of infection in Iran.

Analysis of Fgf15 expression pattern in the mouse neural tube

The dynamic process of neural tube regionalization in vertebrates is regulated by the expression of developmental genes which appear in characteristic patterns at neuroepithelial transversal domains, which are called secondary organizers. The molecular code present in these neuroepithelial organizers controls the generation of morphogenetic signals that induce and maintain regional characteristics in the surrounding neuroepithelium. The product of the Fgf8 gene is a secreted protein that has been demonstrated to be the key molecule for the isthmic organizer and is also expressed in two other organizer regions: the zona limitans and the anterior neural ridge. Here we analyze the expression of Fgf15 at different stages of mouse development in relation to Fgf8 and Otx2 expression patterns.

Depolarisation induces rapid and transient formation of intracellular sphingosine-1-phosphate

Formation of sphingosine-1-phosphate (SPP) by sphingosine kinase serves as a signalling pathway for various membrane receptors. Here, we show that membrane depolarisation is another mechanism by which this pathway can be activated. Formation of [(3)H]SPP as well as levels of endogenous SPP were rapidly and transiently increased in PC12 pheochromocytoma cells depolarised with high KCl. Time course and maximum were similar to those induced by bradykinin. Depolarisation-induced SPP production was also observed in RINm5F insulinoma cells, dependent on extracellular Ca(2+) and fully suppressed by verapamil, thus apparently caused by Ca(2+) influx via voltage-gated Ca(2+) channels. Studies with sphingosine kinase inhibitors and overexpression of sphingosine kinase revealed a partial contribution of this pathway to depolarisation-induced noradrenaline release and Ca(2+) increase.

Type IV pilus genes pilA and pilC of Pseudomonas stutzeri are required for natural genetic transformation, and pilA can be replaced by corresponding genes from nontransformable species

Pseudomonas stutzeri lives in terrestrial and aquatic habitats and is capable of natural genetic transformation. After transposon mutagenesis, transformation-deficient mutants were isolated from a P. stutzeri JM300 strain. In one of them a gene which coded for a protein with 75% amino acid sequence identity to PilC of Pseudomonas aeruginosa, an accessory protein for type IV pilus biogenesis, was inactivated. The presence of type IV pili was demonstrated by susceptibility to the type IV pilus-dependent phage PO4, by occurrence of twitching motility, and by electron microscopy. The pilC mutant had no pili and was defective in twitching motility. Further sequencing revealed that pilC is clustered in an operon with genes homologous to pilB and pilD of P. aeruginosa, which are also involved in pilus formation. Next to these genes but transcribed in the opposite orientation a pilA gene encoding a protein with high amino acid sequence identity to pilin, the structural component of type IV pili, was identified. Insertional inactivation of pilA abolished pilus formation, PO4 plating, twitching motility, and natural transformation. The amounts of (3)H-labeled P. stutzeri DNA that were bound to competent parental cells and taken up were strongly reduced in the pilC and pilA mutants. Remarkably, the cloned pilA genes from nontransformable organisms like Dichelobacter nodosus and the PAK and PAO strains of P. aeruginosa fully restored pilus formation and transformability of the P. stutzeri pilA mutant (along with PO4 plating and twitching motility). It is concluded that the type IV pili of the soil bacterium P. stutzeri function in DNA uptake for transformation and that their role in this process is not confined to the species-specific pilin.