A New Test Statistic Based on Shrunken Sample Variance for Identifying Differentially Expressed Genes in Small Microarray Experiments

Choosing an appropriate statistic and precisely evaluating the false discovery rate (FDR) are both essential for devising an effective method for identifying differentially expressed genes in microarray data. The t-type score proposed by Pan et al. (2003) succeeded in suppressing false positives by controlling the underestimation of variance but left the overestimation uncontrolled. For controlling the overestimation, we devised a new test statistic (variance stabilized t-type score) by placing shrunken sample variances of the James-Stein type in the denominator of the t-type score. Since the relative superiority of the mean and median FDRs was unclear in the widely adopted Significance Analysis of Microarrays (SAM), we conducted simulation studies to examine the performance of the variance stabilized t-type score and the characteristics of the two FDRs. The variance stabilized t-type score was generally better than or at least as good as the t-type score, irrespective of the sample size and proportion of differentially expressed genes. In terms of accuracy, the median FDR was superior to the mean FDR when the proportion of differentially expressed genes was large. The variance stabilized t-type score with the median FDR was applied to actual colorectal cancer data and yielded a reasonable result

Estimating the False Discovery Rate Using Mixed Normal Distribution for Identifying Differentially Expressed Genes in Microarray Data Analysis

The recent development of DNA microarray technology allows us to measure simultaneously the expression levels of thousands of genes and to identify truly correlated genes with anticancer drug response (differentially expressed genes) from many candidate genes. Significance Analysis of Microarray (SAM) is often used to estimate the false discovery rate (FDR), which is an index for optimizing the identifiability of differentially expressed genes, while the accuracy of the estimated FDR by SAM is not necessarily confirmed. We propose a new method for estimating the FDR assuming a mixed normal distribution on the test statistic and examine the performance of the proposed method and SAM using simulated data. The simulation results indicate that the accuracy of the estimated FDR by the proposed method and SAM, varied depending on the experimental conditions. We applied both methods to actual data comprised of expression levels of 12,625 genes of 10 responders and 14 non-responders to docetaxel for breast cancer. The proposed method identified 280 differentially expressed genes correlated with docetaxel response using a cut-off value for achieving FDR <0.01 to prevent false-positive genes, although 92 genes were previously thought to be correlated with docetaxel response ones

Synthesis of the entire carbon framework of the kedarcidin chromophore aglycon

In advanced studies directed toward the total synthesis of the kedarcidin chromophore, we have successfully achieved the late-stage installation of the nine-membered diyne ring in the presence of the highly functionalised ansamacrocyclic bridge

High Prevalence of Dysplastic Development of Sacral Vertebral Arches in Pediatric Enuresis

Purpose This is the first report to compare 3-dimensional computed tomography (3D-CT) images between pediatric patients with enuresis and children without lower urinary tract symptoms who underwent pelvic CT for other reasons. Methods Forty-seven children (33 boys and 14 girls) with primary enuresis underwent 3D-CT of sacrococcygeal bones. The control group consisted of 138 children (78 boys and 60 girls) who underwent pelvic CT for other reasons. First, we determined the presence or absence of unfused sacral arches at the L4-S3 levels in both cohorts. Subsequently, we compared the fusion of sacral arches in age- and sex-matched children from these 2 groups. Results Dysplastic sacral arches, characterized by lack of fusion at 1 or more levels of the S1–3 arches, were observed in nearly all patients in the enuresis group. In the control group (n=138), 54 of 79 children over 10 years old (68%) exhibited fused sacral arches at 3 S1–3 levels. All 11 control children under 4 years old displayed at least 2 unfused sacral arches at the S1–3 levels. In a comparative study of age- and sex-matched patients with enuresis and control children aged 5 to 13 years (n=32 for each group, with 21 boys and 11 girls; mean age, 8.0±2.2 years [range, 5–13 years]), only 1 patient (3%) in the enuresis group exhibited fusion of all S1–3 arches. In contrast, 20 of 32 control group participants (63%) had 3 fused sacral arches (P<0.0001). Conclusions Sacral vertebral arches typically fuse by the age of 10 years. However, in this study, children with enuresis exhibited a significantly elevated prevalence of unfused sacral arches, suggesting that dysplastic development of sacral vertebral arches may play a pathological role in enuresis

Onchocercomas in Guatemala, with Special Reference to Appearance of New Nodules and Parasite Content

To determine the rate of appearance of new nodules during a specified period, a follow-up study on onchocercomas that had been removed was carried out in San Vicente Pacaya, Guatemala, between June 1976 and April 1977. Incidence rate, or rate of nodules appearing in initially negative subjects, was studied in relation to the degree of endemicity. Rates in a period of 7?8 months in high, medium, and low endemic areas were 0.231, 0.083, and 0.022, respectively. The rate of nodule appearance in persons nodulectomized, or rate of nodules appearing in subjects who were surgically rendered negative during the first survey, was 45.3%, 36.4%, and 4.5% in those areas. The highest rate of nodule appearance was observed in patients with microfilariae in both the skin and nodules, followed by patients with either microfilariae or nodules. In highly endemic areas, new nodules appeared in 13.2% of persons without microfilariae or nodules, while in low endemic areas even patients with nodules earlier were less likely to have developed new ones. The performance of the nodulectomy teams (brigadas) was evaluated by confirming the worms in nodules. By gross examination alone, about 6% of nodules removed by brigadas did not contain worms. Nodules containing worms were examined for microfilariae to clarify their role as a source of microfilariae. Microfilariae were not detected in some of these nodules, especially in small ones. In contrast, microfilariae emerged from 80% of those larger than 10 mm. Number of worms per nodule, their sex, and the fecundity of female worms were examined by a collagenase technique. The average number of worms per nodule was 0.6 males and 1.2 females. The highest burden in any one nodule was seven worms, four females and three males. Most nodules had one female and either one male worm or none. Intrauterine microfilariae were found in most females from nodules shared with a male, while solitary females were not gravid. Solitary females were likely to be found in small nodules and large nodules were more likely to include both sexes

Focal choroidal excavation in eyes with central serous chorioretinopathy.

[Purpose]To study the prevalence and 3-dimensional (3-D) tomographic features of focal choroidal excavations in eyes with central serous chorioretinopathy (CSC) using swept-source optical coherence tomography (OCT). [Design]Prospective, cross-sectional study. [Methods]We examined 116 consecutive eyes with CSC with a prototype 3-D swept-source OCT. 3-D images of the shape of the macular area, covering 6 × 6 mm2, were reconstructed by segmentation of the outer surface of the retinal pigment epithelium (RPE). [Results]The 3-D swept-source OCT detected focal choroidal excavations in 9 eyes (7.8%). The 3-D scanning protocol, coupled with en face scans, allowed for clear visualization of the excavation morphology. In 5 eyes with focal excavations, unusual choroidal tissue was found beneath the excavation, bridging the bottom of the excavation and the outer choroidal boundary. Additionally, 3 of those 5 eyes showed a suprachoroidal space below the excavation, as if the outer choroidal boundary is pulled inward by this bridging tissue. The focal choroidal excavations were located within fluorescein leakage points and areas of choroidal hyperpermeability. Eyes with focal choroidal excavations were more myopic (−4.42 ± 2.92 diopters) than eyes without excavations (−0.27 ± 1.80 diopters, P = .001). Subfoveal choroidal thickness was significantly thinner (301.3 ± 60.1 μm) in eyes with focal excavations than in eyes without the excavations (376.6 ± 104.8 μm, P = .036). [Conclusions]Focal choroidal excavations were present in 7.8% of eyes with CSC. In these eyes, focal choroidal excavations may have formed from RPE retraction caused by focal scarring of choroidal connective tissue

Efficient construction of the kedarcidin chromophore ansamacrolide

The streamlined assembly of the ansamacrolide framework of the kedarcidin chromophore via an efficient atropselective Sonogashira coupling step is described. To this end, two newly improved practical syntheses of the cyclopentene and dine fragments have been developed, which feature 0.2 mol % catalytic loadings for an RCM step and i-PrMgCl/CH2I2 as a new entry to gem-disubstituted epoxides from ketones, both being applicable to 49-g scales