Simple, defensible sample sizes based on cost efficiency

Summary .   The conventional approach of choosing sample size to provide 80% or greater power ignores the cost implications of different sample size choices. Costs, however, are often impossible for investigators and funders to ignore in actual practice. Here, we propose and justify a new approach for choosing sample size based on cost efficiency, the ratio of a study's projected scientific and/or practical value to its total cost. By showing that a study's projected value exhibits diminishing marginal returns as a function of increasing sample size for a wide variety of definitions of study value, we are able to develop two simple choices that can be defended as more cost efficient than any larger sample size. The first is to choose the sample size that minimizes the average cost per subject. The second is to choose sample size to minimize total cost divided by the square root of sample size. This latter method is theoretically more justifiable for innovative studies, but also performs reasonably well and has some justification in other cases. For example, if projected study value is assumed to be proportional to power at a specific alternative and total cost is a linear function of sample size, then this approach is guaranteed either to produce more than 90% power or to be more cost efficient than any sample size that does. These methods are easy to implement, based on reliable inputs, and well justified, so they should be regarded as acceptable alternatives to current conventional approaches.     

Collagen phagocytosis is regulated by the guanine nucleotide exchange factor Vav2

Collagen phagocytosis is a crucial alpha2beta1-integrin-dependent process that mediates extracellular matrix remodeling by fibroblasts. We showed previously that after initial contact with collagen, activated Rac1 accelerates collagen phagocytosis but the Rac guanine nucleotide exchange factors (GEFs) that regulate Rac are not defined. We examined here the GEFs that regulate collagen phagocytosis in mouse fibroblasts. Collagen binding enhanced Rac1 activity (5-20 min) but not Cdc42 or RhoA activity. Analysis of collagen bead-associated proteins showed enrichment with Vav2, which correlated temporally with increased Rac1 activity. Knockdown of Vav2 prevented Rac activation, recruitment of Rac1 to collagen bead binding sites, and collagen bead binding, but knockdown of Sos-1 or beta-Pix had no effect on Rac activation or collagen binding. Vav2 was associated with the nucleotide-free Rac1 mutant (G15ARac1) after collagen binding. Collagen bead binding promoted phosphorylation of Vav2, which temporally correlated with Rac1 activation and which required Src kinase activity. Blockage of Src activity prevented collagen bead-induced Rac activation and collagen bead binding. Collectively these data indicate that Vav2 regulates the Rac1 activity associated with the binding step of collagen phagocytosis.     

Exploring gene-environment interactions in Parkinson’s disease

The objective of this study was to explore combined effects of four candidate susceptibility genes and two exposures on Parkinson’s disease (PD) risk; namely, α-synuclein (SNCA) promoter polymorphism REP1, microtubule-associated protein tau (MAPT) H1/H2 haplotypes, apolipoprotein E (APOE) ε2/ε3/ε4 polymorphism, ubiquitin carboxy-terminal esterase L1 (UCHL1) S18Y variant, cigarette smoking and caffeinated coffee consumption. 932 PD patients and 664 control subjects from the NeuroGenetics Research Consortium, with complete data on all six factors, were studied. Uniform protocols were used for diagnosis, recruitment, data collection and genotyping. A logistic regression model which included gene-exposure interactions was applied. Likelihood ratio tests (LRTs) were used for significance testing and Bayesian inference was used to estimate odds ratios (ORs). MAPT (P = 0.007), SNCA REP1 (P = 0.012), smoking (P = 0.001), and coffee (P = 0.011) were associated with PD risk. Two novel interactions were detected: APOE with coffee (P = 0.005), and REP1 with smoking (P = 0.021). While the individual main effects were modest, each yielding OR < 1.6, the effects were cumulative, with some combinations reaching OR = 12.6 (95% CI: 5.9–26.8). This study provides evidence for the long-held notion that PD risk is modulated by cumulative and interactive effects of genes and exposures. Furthermore, the study demonstrates that while interaction studies are useful for exploring risk relationships that might otherwise go undetected, results should be interpreted with caution because of the inherent loss of power due to multiple testing. The novel findings of this study that warrant replication are the evidence for interaction of coffee with APOE, and of smoking with REP1 on PD risk. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A role for decorin in the remodeling of myocardial infarction.

Because the small leucine-rich proteoglycan decorin has been implicated in regulation of collagen fibrillogenesis leading to proper extracellular matrix assembly, we hypothesized it could play a key role in cardiac fibrosis following myocardial infarction. In this study we ligated the left anterior descending coronary artery in wildtype and decorin-null mice to produce large infarcts in the anterior wall of the left ventricle. At early stages post-coronary occlusion the myocardial infarction size did not appreciably differ between the two genotypes. However, we found a wider distribution of collagen fibril sizes with less organization and loose packing in mature scar from decorin-null mice. Thus, we tested the hypothesis that these abnormal collagen fibrils would adversely affect post-infarction mechanics and ventricular remodeling. Indeed, scar size, right ventricular remote hypertrophy, and left ventricular dilatation were greater in decorin-null animals compared with wildtype littermates 14 days after acute myocardial infarction. Echocardiography revealed depressed left ventricular systolic function between 4 and 8 weeks post-ischemia in the decorin-null animals. These changes indicate that decorin is required for the proper fibrotic evolution of myocardial infarctions, and that its absence leads to abnormal scar tissue formation. This might contribute to aneurysmal ventricular dilatation, remote hypertrophy, and depressed ventricular function.     

Model study of ATP and ADP buffering, transport of Ca(2+) and Mg(2+), and regulation of ion pumps in ventricular myocyte.

We extended the model of the ventricular myocyte by Winslow et al. (Circ. Res 1999, 84:571-586) by incorporating equations for Ca(2+) and Mg(2+) buffering and transport by ATP and ADP and equations for MgATP regulation of ion transporters (Na(+)-K(+) pump, sarcolemmal and sarcoplasmic Ca(2+) pumps). The results indicate that, under normal conditions, Ca(2+) binding by low-affinity ATP and diffusion of CaATP may affect the amplitude and time course of intracellular Ca(2+) signals. The model also suggests that a fall in ATP/ADP ratio significantly reduces sarcoplasmic Ca(2+) content, increases diastolic Ca(2+), lowers systolic Ca(2+), increases Ca(2+) influx through L-type channels, and decreases the efficiency of the Na(+)/Ca(2+) exchanger in extruding Ca(2+) during periodic voltage-clamp stimulation. The analysis suggests that the most important reason for these changes during metabolic inhibition is the down-regulation of the sarcoplasmic Ca(2+)-ATPase pump by reduced diastolic MgATP levels. High Ca(2+) concentrations developed near the membrane might have a greater influence on Mg(2+), ATP, and ADP concentrations than that of the lower Ca(2+) concentrations in the bulk myoplasm. The model predictions are in general agreement with experimental observations measured under normal and pathological conditions.     

Topographically generated fronts, very nearshore oceanography and the distribution and settlement of mussel larvae and barnacle cyprids

Flow patterns adjacent to shore may prevent or aid shorewardmigration of benthic invertebrate larvae. We hypothesized thata front at the mouth of Sunset Bay, Oregon, prevents shorewarddispersal of larvae, significantly altering settlement of mussellarvae and barnacle cyprids. Settlement was measured at threesets of moorings (three moorings per site) distributed acrossthe front at Sunset Bay. From 6 July to 4 September 2000, sampleswere collected roughly every other day. Concurrently, we madevertical zooplankton tows adjacent to each mooring site andcollected physical oceanographic data. During upwelling-favorablewinds, the front was always present at the bay mouth, separatingsignificantly cooler, saltier and denser offshore water fromthat within the bay. During downwelling winds, the front brokedown and we found no significant difference in the surface physicaloceanographic parameters across the bay mouth. During upwelling,the concentration of mussel larvae was higher seaward of thefront than landward, but there was no significant differencein concentration during downwelling, suggesting that the frontmay act as a barrier to the shoreward dispersal of mussels.Mussel settlement was too low and sporadic to allow statisticalanalysis. There was no difference in cyprid concentrations acrossthe bay mouth whether the front was present or not. Cyprid settlementwas, however, nearly an order of magnitude lower at mooringsseaward of the front than at those landward. A significant cross-correlationwas found between settlement at the offshore mooring and tidalrange (r = 0.464, lag = 0 days) and between settlement at themid and inner moorings and downwelling winds (r = 0.532 midbay, r = 0.532 inner bay, lag = 0 days). Seaward of the front,settlement varied with tidal range, while landward of the front,most settlement occurred as brief pulses during downwellingwinds, periods when the front was not present. We found largedifferences in the distribution of cyprids, and mussel larvaeand cyprid settlement relative to the front; larval distributionsand settlement varied with upwelling versus downwelling windsand was due to differences in the very nearshore (i.e. within100–1000 m of shore) coastal oceanography.     

Relationship between c-Kit expression and proliferation in acute myeloblastic leukemia cell lines

We have proposed that the transmembrane receptor encoded by the c-Kit protooncogene and its ligand play an important role in regulating the proliferation of blasts cells in acute myeloblastic leukemia (AML). To test this hypothesis, immunobeads were used to separate blasts from three Kit-expression positive cell lines into strongly Kit-protein positive and weakly Kit-protein positive fractions. The strongly positive fraction had greater proliferative potential than the weakly positive fraction as assessed both by colony-formation in methylcellulose and growth of clonogenic cells in suspension. The reproducibility of the percentage of each blast population found in the strongly and weakly positive fractions provided evidence that Kit-protein expression is regulated. Kinetic experiments provided evidence for reversible transitions between strong and weak Kit protein expression. Thus regulated expression of the Kit receptor may be a mechanism for controlling blast cell growth in culture. © 1993 Wiley-Liss, Inc.     

The effect of follicular fluid hormones on oocyte recovery after ovarian stimulation: FSH level predicts oocyte recovery

Background  

Ovarian stimulation for assisted reproductive technology (ART) overcomes the physiologic process to develop a single dominant follicle. However, following stimulation, egg recovery rates are not 100%. The objective of this study is to determine if the follicular fluid hormonal environment is associated with oocyte recovery.