Power and sample size calculations for longitudinal studies estimating a main effect of a time-varying exposure

Existing study design formulas for longitudinal studies have assumed that the exposure is time-invariant. We derived sample size formulas for studies comparing rates of change by exposure when the exposure varies with time within a subject, focusing on observational studies where this variation is not controlled by the investigator. Two scenarios are considered, one assuming that the effect of exposure on the response is acute and the other assuming that it is cumulative. We show that accurate calculations can often be obtained by providing the intraclass correlation of exposure and the exposure prevalence at each time point. When comparing rates of change, studies with a time-varying exposure are, in general, less efficient than studies with a time-invariant one. We provide a public access program to perform the calculations described in the paper (http://www.hsph.harvard.edu/faculty/spiegelman/optitxs.html).Research supported, in part, by NIH grant CA0651

An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease

Cyanophage genomes frequently possess the psbA gene, encoding the D1 polypeptide of photosystem II. This protein is believed to maintain host photosynthetic capacity during infection and enhance phage fitness under high-light conditions. Although the first documented cyanophage-encoded psbA gene contained a group I intron, this feature has not been widely reported since, despite a plethora of new sequences becoming available. In this study, we show that in cyanophage S-PM2, this intron is spliced during the entire infection cycle. Furthermore, we report the widespread occurrence of psbA introns in marine metagenomic libraries, and with psbA often adjacent to a homing endonuclease (HE). Bioinformatic analysis of the intergenic region between psbA and the adjacent HE gene F-CphI in S-PM2 showed the presence of an antisense RNA (asRNA) connecting these two separate genetic elements. The asRNA is co-regulated with psbA and F-CphI, suggesting its involvement with their expression. Analysis of scaffolds from global ocean survey datasets shows this asRNA to be commonly associated with the 3′ end of cyanophage psbA genes, implying that this potential mechanism of regulating marine ‘viral’ photosynthesis is evolutionarily conserved. Although antisense transcription is commonly found in eukaryotic and increasingly also in prokaryotic organisms, there has been no indication for asRNAs in lytic phages so far. We propose that this asRNA also provides a means of preventing the formation of mobile group I introns within cyanophage psbA genes

Prevalence of renal stones in an Italian urban population: a general practice-based study

Kidney stones represent a common condition characterized by significant morbidity and economic costs. The epidemiology of kidney stones is not completely understood and may vary substantially based on geographic, socioeconomic and clinical factors; the present study aims at defining the prevalence and diagnostic patterns of kidney stones in a cohort representative of the general population in Florence, Italy. A sample of 1,543 adult subjects, all Caucasians, was randomly selected from a population of over 25,000 subjects followed by 22 general practitioners (GPs). Subjects were administered a questionnaire requesting the patient's age and sex, any history of kidney stones and/or colics and the prescription of kidney ultrasound (US) examination. GPs data-bases were also interrogated. Crude and adjusted prevalence proportions and ratios (PRs) with corresponding 95\ua0% confidence intervals (CIs) were computed. Furthermore, the association between the practice pattern of each physician with respect to US prescription and the prevalence of kidney stones was investigated. The overall prevalence of kidney stones was 7.5\ua0% (95\ua0% confidence interval 6.2, 8.9\ua0%), increasing with age until 55-60\ua0years and then decreasing. About 50\ua0% reported recurrent disease. There were no significant differences in prevalence among males and females. GPs who tended to prescribe more US examinations were more likely to have more patients with kidney stones (adjusted PR 1.80, 95\ua0% CI 1.11, 2.94; p\ua0=\ua00.020). The present study confirms both the high prevalence and the regional variability of kidney stones. Practice patterns may be involved in such variability

Bovine Leukemia Virus: An Exogenous RNA Oncogenic Virus?

Short term cultures of bovine leukemic lymphocytes release virus particles with biochemical properties of RNA oncogenic viruses. These particles, tentatively called bovine leukemia virus (BLV), have a high molecular weight RNA reverse transcriptase complex and a density of 1.155 g/ml in sucrose solutions. Molecular hybridizations between BLV [3H] cDNA and several viral RNAs show that BLV is not related to Mason Pfizer monkey virus, simian sarcoma associated virus, feline leukemia virus, or avian myeloblastosis virus. These results were confirmed by hybridization between BLV 70S RNA and [3H] cDNA synthesized in the various viruses tested. The high preference of BLV reverse transcriptase for Mg++ as the divalent cation suggests that BLV might be an atypical mammalian leukemogenic 'type C' virus. DNA DNA hybridization studies using BLV [3H] cDNA as a probe strongly suggest that the DNA of bovine leukemic cells contains viral sequences that cannot be detected in normal bovine DNA.SCOPUS: ar.jinfo:eu-repo/semantics/publishe