Window effect in the power spectrum analysis of a galaxy redshift survey

We investigate the effect of the window function on the multipole power spectrum in two different ways. First, we consider the convolved power spectrum including the window effect, which is obtained by following the familiar (FKP) method developed by Feldman, Kaiser and Peacock. We show how the convolved multipole power spectrum is related to the original power spectrum, using the multipole moments of the window function. Second, we investigate the deconvolved power spectrum, which is obtained by using the Fourier deconvolution theorem. In the second approach, we measure the multipole power spectrum deconvolved from the window effect. We demonstrate how to deal with the window effect in these two approaches, applying them to the Sloan Digital Sky Survey (SDSS) luminous red galaxy (LRG) sample.Comment: 22 pages, 11 figures, references adde

L-Arginine treatment may prevent tubulointerstitial nephropathy caused by germanium dioxide

L-Arginine treatment may prevent tubulointerstitial nephropathy caused by germanium dioxide.BackgroundLong-term oral ingestion of germanium dioxide (GeO2) causes progressive renal failure derived from tubulointerstitial nephropathy in humans and animals. The characteristic of GeO2-induced nephropathy is the renal tissue injury persisting for a long time, even after cessation of GeO2 ingestion. However, a treatment that can suppress the long-lasting renal tissue injury has not yet been established.MethodsUsing the methods of immunohistochemistry and reverse transcription-polymerase chain reaction, we examined the expression of ED1-positive cells (macrophages/monocytes), transforming growth factor (TGF)-β1 mRNA and protein and collagen type IV mRNA and protein in the kidneys of rats with GeO2-induced nephropathy. Concomitantly, the effects of L-arginine treatment on their expression was explored in the kidneys of rats with GeO2-induced nephropathy.ResultsChronic administration of GeO2 caused tubulointerstitial nephropathy characterized by leukocyte invasion into the enlarged tubulointerstitial space in rats. The expression of ED1-positive cells, TGF-β1 protein and collagen type IV protein was markedly increased in the tubulointerstitium of the renal cortex from rats with GeO2-induced nephropathy. Similarly, TGF-β1 and collagen type IV mRNA were significantly enhanced in the renal cortex of rats with GeO2-induced nephropathy. A small number of tubulointerstitial cells expressing TGF-β1 protein were also observed in the renal cortex of rats with GeO2-induced nephropathy. However, L-arginine treatment led to a parallel decrease in the expression of ED1-positive cells, TGF-β1 mRNA and collagen type IV mRNA and protein in rats with GeO2-induced nephropathy.ConclusionsIn general, collagen synthesis is driven by TGF-β1 in the fibrotic process associated with a variety of renal disorders. TGF-β1 is secreted by TGF-β1 producing cells such as macrophages, fibroblasts and myofibroblasts. Thus, the present study indicates that the expression of collagen type IV may be mediated by TGF-β1 released from invading macrophages and, to a lesser extent, released from tubulointerstitial cells, presumably fibroblasts and/or myofibroblasts in GeO2-induced nephropathy. L-Arginine treatment inhibits collagen type IV synthesis possibly by suppressing macrophage invasion and the resultant TGF-β1 expression in this nephropathy. L-Arginine treatment may be beneficial in the prevention of tubulointerstitial fibrosis, which is considered to be the terminal stage of GeO2-induced nephropathy

Statistical hypothesis test of factor loading in principal component analysis and its application to metabolite set enrichment analysis

Principal component analysis (PCA) has been widely used to visualize high-dimensional metabolomic data in a two- or three-dimensional subspace. In metabolomics, some metabolites (e.g. top 10 metabolites) have been subjectively selected when using factor loading in PCA, and biological inferences for these metabolites are made. However, this approach is possible to lead biased biological inferences because these metabolites are not objectively selected by statistical criterion. We proposed a statistical procedure to pick up metabolites by statistical hypothesis test of factor loading in PCA and make biological inferences by metabolite set enrichment analysis (MSEA) for these significant metabolites. This procedure depends on the fact that the eigenvector in PCA for autoscaled data is proportional to the correlation coefficient between PC score and each metabolite levels. We applied this approach for two metabolomic data of mice liver samples. 136 of 282 metabolites in first case study and 66 of 275 metabolites in second case study were statistically significant. This result suggests that to set the previously-determined number of metabolites is not appropriate because the number of significant metabolites is different in each study when using factor loading in PCA. Moreover, MSEA was performed for these significant metabolites and significant metabolic pathways can be detected. These results are acceptable when compared with previous biological knowledge. It is essential to select metabolites statistically for making unbiased biological inferences from metabolome data, when using factor loading in PCA. We proposed a statistical procedure to pick up metabolites by statistical hypothesis test of factor loading in PCA and make biological inferences by MSEA for these significant metabolites. We developed an R package mseapca to perform this approach. The “mseapca” package is publicity available on CRAN website

Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis

BACKGROUND: Principal component analysis (PCA) has been widely used to visualize high-dimensional metabolomic data in a two- or three-dimensional subspace. In metabolomics, some metabolites (e.g., the top 10 metabolites) have been subjectively selected when using factor loading in PCA, and biological inferences are made for these metabolites. However, this approach may lead to biased biological inferences because these metabolites are not objectively selected with statistical criteria. RESULTS: We propose a statistical procedure that selects metabolites with statistical hypothesis testing of the factor loading in PCA and makes biological inferences about these significant metabolites with a metabolite set enrichment analysis (MSEA). This procedure depends on the fact that the eigenvector in PCA for autoscaled data is proportional to the correlation coefficient between the PC score and each metabolite level. We applied this approach to two sets of metabolomic data from mouse liver samples: 136 of 282 metabolites in the first case study and 66 of 275 metabolites in the second case study were statistically significant. This result suggests that to set the number of metabolites before the analysis is inappropriate because the number of significant metabolites differs in each study when factor loading is used in PCA. Moreover, when an MSEA of these significant metabolites was performed, significant metabolic pathways were detected, which were acceptable in terms of previous biological knowledge. CONCLUSIONS: It is essential to select metabolites statistically to make unbiased biological inferences from metabolomic data when using factor loading in PCA. We propose a statistical procedure to select metabolites with statistical hypothesis testing of the factor loading in PCA, and to draw biological inferences about these significant metabolites with MSEA. We have developed an R package “mseapca” to facilitate this approach. The “mseapca” package is publicly available at the CRAN website

Palmitate induces reactive oxygen species production and β-cell dysfunction by activating nicotinamide adenine dinucleotide phosphate oxidase through Src signaling.

[Aims/Introduction]Chronic hyperlipidemia impairs pancreatic β-cell function, referred to as lipotoxicity. We have reported an important role of endogenous reactive oxygen species (ROS) overproduction by activation of Src, a non-receptor tyrosine kinase, in impaired glucose-induced insulin secretion (GIIS) from diabetic rat islets. In the present study, we investigated the role of ROS production by Src signaling in palmitate-induced dysfunction of β-cells. [Materials and Methods]After rat insulinoma INS-1D cells were exposed to 0.6 mmol/L palmitate for 24 h (palmitate exposure); GIIS, ROS production and nicotinamide adenine dinucleotide phosphate oxidase (NOX) activity were examined with or without exposure to10 μmol/L 4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP2), a Src inhibitior, for 30 or 60 min. [Results]Exposure to PP2 recovered impaired GIIS and decreased ROS overproduction as a result of palmitate exposure. Palmitate exposure increased activity of NOX and protein levels of NOX2, a pathological ROS source in β-cells. Palmitate exposure increased the protein level of p47phox, a regulatory protein of NOX2, in membrane fraction compared with control, which was reduced by PP2. Transfection of small interfering ribonucleic acid of p47phox suppressed the augmented p47phox protein level in membrane fraction, decreased augmented ROS production and increased impaired GΙIS by palmitate exposure. In addition, exposure to PP2 ameliorated impaired GIIS and decreased ROS production in isolated islets of KK-Ay mice, an obese diabetic model with hyperlipidemia. [Conclusions]Activation of NOX through Src signaling plays an important role in ROS overproduction and impaired GΙIS caused by chronic exposure to palmitate, suggesting a lipotoxic mechanism of β-cell dysfunction of obese mice

解剖体において両側性の星状神経節ブロックは頻繁に硬膜外腔への薬液浸潤を起こす

It is well known that epidural infusion of injectate in association with a C6 paratracheal stellate ganglion block (SGB) leads to negative and/or positive side effects for the patient. However, this associated infusion has not been demonstrated experimentally using cadavers. We found that, in postmortem-fixed cadavers, epidural infusion occurred much more frequently in cases of bilateral SGB than in unilateral SGB. The frequency in the bilateral case (36.1%) was far beyond the two times of the unilateral one (7.7%). The injectate (latex resin, 10 ml for one side) was delivered from the prevertebral deposit into the epidural space by way of the spaces around the C8 and/or T1 spinal nerve roots. Thus, the latex spread around and/or in the brachial plexus usually combined with the epidural infusion. We speculate that the amount of injectate spreading into the prevertebral space in the bilateral injection (total 20 ml) was beyond the hypothetical tentative capacity and that the excess amount made the addional, perineural spread. The present results suggests that, in clinical cases, the frequency of epidural infusion depends on the amount of injectate even in the routine unilateral SGB. However, the cadaveric study did not indicate how much amount is the excess for the living patient

Nicotinamide benefits both mothers and pups in two contrasting mouse models of preeclampsia

Preeclampsia (PE), high blood pressure and protein in the urine in the last third of pregnancy, complicates about 1 in 20 human pregnancies, and it is one of the leading causes of pregnancy-related maternal deaths. The only definitive treatment, induced delivery, invariably results in premature babies. Blood pressure-lowering drugs help, but results in preventing preterm delivery and correcting the fetal growth restriction (FGR) that also occurs in PE have been disappointing. Here we show that feeding high doses of nicotinamide, a vitamin, improves the maternal condition, prolongs pregnancies, and prevents FGR in mice having PE-like conditions due to two contrasting causes. Because nicotinamide benefits both mothers and pups, it merits evaluation for preventing or treating PE in humans

Step-bunching instability of growing interfaces between ice and supercooled water

金沢大学学術メディア創成センターIce-crystal growth in supercooled water is one of the most familiar examples of phase-transition dynamics, playing essential roles in various natural phenomena on Earth. Despite its fundamental importance, the microscopic view at the elementary step level remains elusive. Here, using an advanced optical microscope, we find self-organization of elementary steps during ice-crystal growth, called step-bunching instability (SBI), driven by the competition between step dynamics, interfacial stiffness, and latent heat diffusions. We also find that the SBI transiently induces screw dislocations and resulting spiral growth in the late stage of the growth process. Furthermore, quantitative observations with a two-beam interferometer allow us to obtain insights into the relative importance of the various mechanisms of the step–step interactions. Our finding offers a significant clue to understanding the general mechanism of melt growth beyond ice-crystal growth, inseparably involving several broad research fields, including cryobiological, geophysical, and material branches