Higher-order least squares: assessing partial goodness of fit of linear causal models

We introduce a simple diagnostic test for assessing the overall or partial goodness of fit of a linear causal model with errors being independent of the covariates. In particular, we consider situations where hidden confounding is potentially present. We develop a method and discuss its capability to distinguish between covariates that are confounded with the response by latent variables and those that are not. Thus, we provide a test and methodology for partial goodness of fit. The test is based on comparing a novel higher-order least squares principle with ordinary least squares. In spite of its simplicity, the proposed method is extremely general and is also proven to be valid for high-dimensional settings.</p

Supporting_information.docx – Supplemental material for A study on human serum albumin corona formed on photoluminescent carbon dots

Supplemental material, Supporting_information.docx for A study on human serum albumin corona formed on photoluminescent carbon dots by Peng Wang, Ming Yuan, Na Li and Feng Zhang in Journal of Chemical Research</p

Statistical Significance of Clustering using Soft Thresholding

<div><p>Clustering methods have led to a number of important discoveries in bioinformatics and beyond. A major challenge in their use is determining which clusters represent important underlying structure, as opposed to spurious sampling artifacts. This challenge is especially serious, and very few methods are available, when the data are very high in dimension. Statistical Significance of Clustering (SigClust) is a recently developed cluster evaluation tool for high dimensional low sample size data. An important component of the SigClust approach is the very definition of a single cluster as a subset of data sampled from a multivariate Gaussian distribution. The implementation of SigClust requires the estimation of the eigenvalues of the covariance matrix for the null multivariate Gaussian distribution. We show that the original eigenvalue estimation can lead to a test that suffers from severe inflation of type-I error, in the important case where there are a few very large eigenvalues. This paper addresses this critical challenge using a novel likelihood based soft thresholding approach to estimate these eigenvalues, which leads to a much improved SigClust. Major improvements in SigClust performance are shown by both mathematical analysis, based on the new notion of Theoretical Cluster Index, and extensive simulation studies. Applications to some cancer genomic data further demonstrate the usefulness of these improvements.</p></div

Table_1_Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions.xlsx

Pseudomonas aeruginosa is a common cause of urinary tract infections by strains that are often multidrug resistant, representing a major challenge to the world’s health care system. This microorganism has a highly adaptable metabolism that allows it to colonize many environments, including the urinary tract. In this work, we have characterized the metabolic strategies used by stationary phase P. aeruginosa cells cultivated in urine-like media to understand the adaptations used by this microorganism to survive and produce disease. Our proteomics results show that cells rely on the Entner-Duodoroff pathway, pentose phosphate pathway, the Krebs cycle/ glyoxylate shunt and the aerobic oxidative phosphorylation to survive in urine-like media and other conditions. A deep characterization of the oxidative phosphorylation showed that the respiratory rate of stationary phase cells is increased 3–4 times compared to cells in the logarithmic phase of growth, indicating that the aerobic metabolism plays critical roles in the stationary phase of cells grown in urine like media. Moreover, the data show that respiratory complex III, succinate dehydrogenase and the NADH dehydrogenase NQR have important functions and could be used as targets to develop new antibiotics against this bacterium.</p

MRNA levels of DNA repair enzymes are decreased in aged retinal pigment epithelium and choroid

Comparisons of the mRNA levels of DNA repair enzymes: OGG1 (), MYH (), TDG () and NTH1 (), in mouse retinal pigment epithelium (RPE) and choroid at different ages 18s mRNA was used as internal standard for normalization. The expression levels of OGG1 were decreased at 18 month (p=0.01, n=6), but showed no difference at 12 month (p=0.73, n=6) and at 24 month (p=0.07, n=6) as compared with the 4 month group (n=5) (). The expression levels of MYH were decreased at 18 month (p=0.001, n=6) and at 24 month (p=0.007, n=6), but showed no difference at 12 month (p=0.87, n=6), compared with the 4 month group (). The expression levels of TDG were decreased at 18 month (p0.05, n=6; Panel ). Values are the mean ±SEM.<p><b>Copyright information:</b></p><p>Taken from "Increased mitochondrial DNA damage and down-regulation of DNA repair enzymes in aged rodent retinal pigment epithelium and choroid"</p><p></p><p>Molecular Vision 2008;14():644-651.</p><p>Published online 04 Apr 2008</p><p>PMCID:PMC2288587.</p><p></p

Data_Sheet_2_Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions.PDF

Pseudomonas aeruginosa is a common cause of urinary tract infections by strains that are often multidrug resistant, representing a major challenge to the world’s health care system. This microorganism has a highly adaptable metabolism that allows it to colonize many environments, including the urinary tract. In this work, we have characterized the metabolic strategies used by stationary phase P. aeruginosa cells cultivated in urine-like media to understand the adaptations used by this microorganism to survive and produce disease. Our proteomics results show that cells rely on the Entner-Duodoroff pathway, pentose phosphate pathway, the Krebs cycle/ glyoxylate shunt and the aerobic oxidative phosphorylation to survive in urine-like media and other conditions. A deep characterization of the oxidative phosphorylation showed that the respiratory rate of stationary phase cells is increased 3–4 times compared to cells in the logarithmic phase of growth, indicating that the aerobic metabolism plays critical roles in the stationary phase of cells grown in urine like media. Moreover, the data show that respiratory complex III, succinate dehydrogenase and the NADH dehydrogenase NQR have important functions and could be used as targets to develop new antibiotics against this bacterium.</p

Data_Sheet_1_Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions.PDF

Pseudomonas aeruginosa is a common cause of urinary tract infections by strains that are often multidrug resistant, representing a major challenge to the world’s health care system. This microorganism has a highly adaptable metabolism that allows it to colonize many environments, including the urinary tract. In this work, we have characterized the metabolic strategies used by stationary phase P. aeruginosa cells cultivated in urine-like media to understand the adaptations used by this microorganism to survive and produce disease. Our proteomics results show that cells rely on the Entner-Duodoroff pathway, pentose phosphate pathway, the Krebs cycle/ glyoxylate shunt and the aerobic oxidative phosphorylation to survive in urine-like media and other conditions. A deep characterization of the oxidative phosphorylation showed that the respiratory rate of stationary phase cells is increased 3–4 times compared to cells in the logarithmic phase of growth, indicating that the aerobic metabolism plays critical roles in the stationary phase of cells grown in urine like media. Moreover, the data show that respiratory complex III, succinate dehydrogenase and the NADH dehydrogenase NQR have important functions and could be used as targets to develop new antibiotics against this bacterium.</p

Increased levels of deleted mitochondrial DNA in aged retinal pigment epithelium and choroid

Measurements of levels of the PCR products of non-deleted (, not damaged) and deleted (, damaged) mitochondrial DNA (mtDNA) normalized by total mtDNA normalized by total mtDNA were done using the PicoGreen reagent. Each PCR reaction started with 10 ng of genomic DNA (nuclear and mitochondrial) from rat retinal pigment epithelium (RPE) and choroid as a template. There was no difference in the non-deleted mtDNA at 18 month (p=0.02, n=5), 24 month (p=0.06, n=5), and 32 month (p=0.70, n=5), compared with the 4 month group. However, there was a significant increase in deleted mtDNA at 18 month (p=0.003, n=5), 24 month (p<p><b>Copyright information:</b></p><p>Taken from "Increased mitochondrial DNA damage and down-regulation of DNA repair enzymes in aged rodent retinal pigment epithelium and choroid"</p><p></p><p>Molecular Vision 2008;14():644-651.</p><p>Published online 04 Apr 2008</p><p>PMCID:PMC2288587.</p><p></p

Structure growth, stability and adsorption properties of (AgZn₃)_n clusters

Recently, an effective syngas catalyst composed of AgZn3 clusters is reported, in which the CO and H2 generation may occur at the Zn sites and the hollow sites between Ag and Zn. Hence, the atomic model of the AgZn3 is worth established to further investigate the catalytic mechanism. Here, we take advantage of the genetic algorithm with the density functional theory to unbiasedly search configurations of (AgZn3)n (n = 1–6) clusters. It is found that (AgZn3)n clusters evolve from hollow cages to close-packed structures, with Zn atoms gradually occupying the core positions. The Eb and Δ2E analyses show that the (AgZn3)3 has a higher stability than that of its neighbors. The AIMD simulations demonstrate that the (AgZn3)3 shows a favorable stability at 700 K. The molecular orbitals reveal that 21 valence electrons of the (AgZn3)3 fill superatomic orbits resulting in an electronic configuration of 1S21P61D102S21F1. The adsorptions of CO on the bridge sites of (AgZn3)3 are much higher in energy than the top adsorptions, but the red shift of the stretching frequency of C-O is more obvious in the former. Our results are verified that the Zn sites and bridge sites between Ag and Zn are active sites for CO. </p

Alkyl halide/tertiary amine as novel initiators for free radical polymerizations of methyl methacrylate, methyl acrylate and styrene

A series of combinations of alkyl halide with tertiary amine such as ethyl α-bromophenylacetate/tris[2-(dimethylamino)ethyl)]amine (αEBP/Me6TREN), ethyl 2-bromoisobutyrate/triethylamine (EBiB/TEA), and ethyl 2-chloropropionate/N,N,N′,N′,N′′-pentamethyldiethylenetriamine (ECP/PMDETA) have been developed as novel free radical initiators and used for the polymerizations of methyl acrylate (MA), methyl methacrylate (MMA) and styrene (St). The effects of the structure of alkyl halide and tertiary amine on the polymerization of MA were investigated. Gel permeation chromatograph (GPC) and proton nuclear magnetic resonance (1H NMR) have been utilized to analyze the end group of the obtained poly(methyl acrylate). Electron spin resonance (ESR) spectroscopy was employed to identify the structure of the radicals produced by αEBP/Me6TREN, and the results indicated that αEBP reacted with Me6TREN via a single electron transfer (SET) nucleophilic mechanism to produce corresponding ethyl α-phenylacetate radicals which subsequently initiated the polymerization of MA. As both alkyl halide and tertiary amine are commercially available at low cost, non-explosive, and ease of use and storage in comparison with conventional azo, peroxide or persulfate initiators, the combination of alkyl halide and tertiary amine as a free radical initiator is promising for large-scale practical applications.</p