[show abstract][hide abstract] ABSTRACT: This paper proposes a new method for estimating sparse precision matrices in
the high dimensional setting. This procedure applies a novel Sparse Column-wise
Inverse Operator (SCIO) to modified sample covariance matrices. We establish
the convergence rates of this procedure under various matrix norms. Under the
Frobenius norm loss, we prove theoretical guarantees on using cross validation
to pick data-driven tunning parameters. Another important advantage of this
estimator is its efficient computation for large-scale problems, using a
path-following coordinate descent algorithm we provide. Numerical merits of our
estimator are also illustrated using simulated and real datasets. In
particular, this method is found to perform favorably on analyzing an HIV brain
tissue dataset and an ADHD resting fMRI dataset.
[show abstract][hide abstract] ABSTRACT: A role for the angiotensin-converting enzyme (ACE) gene has been suggested in the aetiology of type 2 diabetes (T2DM). However, results have been inconsistent. In this study, we performed a meta-analysis to further clarify the association between ACE I/D polymorphism and T2DM risk in a Chinese population.
PubMed, EMBASE, CNKI and Wan Fang Data were searched for eligible studies. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using a fixed-effects model or random-effects model.
: A total of 41 studies (4708 cases and 5368 controls) for the association between ACE I/D polymorphism and T2DM in a Chinese population were identified. The pooled ORs for the association between ACE I/D polymorphism and T2DM risk were not statistically significant under all genetic models (co-dominant model: DD vs. II: OR = 1.17, 95% CI 0.97-1.42 and ID vs. II: OR = 1.01, 95% CI 0.93-1.10; dominant model: OR = 1.06, 95% CI 0.94-1.19; multiplicative model: OR = 1.08, 95% CI 0.98-1.18). Although a marginally significant association was observed under a recessive model (OR = 1.17, 95% CI 1.00-1.36), robustness of this estimate could not be established under additional sensitivity analyses.
: The meta-analysis presented in this study indicated that ACE I/D polymorphism may not be associated with the risk of T2DM in the Chinese population.
Journal of Renin-Angiotensin-Aldosterone System 03/2012; 13(3):372-8. · 2.29 Impact Factor
[show abstract][hide abstract] ABSTRACT: Lysozyme is an important component of the immune response against bacteria that is characterized by its ability to break down bacterial cell-walls. We constructed a high-quality cDNA library from mantle tissue of adult Japanese scallop (Mizuhopecten yessoensis). The EST which is high homology with g-type lysozyme genes of other species was found in the cDNA library. In the present study, the complete express sequence of g-type lysozyme genes from Japanese scallop (designated as MyLysoG) was directly obtained by PCR. The complete sequence of MyLysoG cDNA consisted of a 5' untranslated region (UTR) of 25 bp, an open reading frame (ORF) of 606 bp, and a 3' UTR of 100 bp with one polyadenylation signal (AATAAA). The deduced amino acids of MyLysoG were 201 amino acids with a putative signal peptide of 18 amino acid residues. It shared the sequence similarity and the common structure features with the g-type lysozyme from other species. Quantitative reverse trancriptase real-time PCR (qRT-PCR) assay demonstrated that mRNA transcripts of g-type lysozyme could be detected in various tissues of unchallenged scallop, and the highest expression of MyLysoG was detected in hepatopancreas tissue. The temporal expression of MyLysoG in hemolymph after Vibrio anguillarum challenge was up-regulated and reached the maximum level at 3h post stimulation, and then dropped back to the original level even lower than the control group. Furthermore, a 978 bp of 5'-flanking sequence of MyLysoG was identified by genome walking, and several potential transcription factor binding sites (TFBS) were detected in the putative promoter region. One part of the MyLysoG promoter region contains nine sites of SNPs and three sites of insert-deletion (indel) polymorphisms, and these mutations were found organize into two haplotypes. The two haplotypes were associated with different TFBS. The haplotypes could be selected to analyze the transcriptional-level control of scallop g-type lysozyme gene and the scallop immune system.
Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 02/2012; 162(1-3):34-43. · 1.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: Catfish is one of the most important aquaculture species in America (as well as in Asia and Africa). In recent years, the production of catfish has suffered massive financial losses due to pathogen spread and breakouts. Innate immunity plays a crucial role in increasing resistance to pathogenic organisms and has generated increasing interest in the past few years. This review summarizes the current understanding of innate immune-related genes in catfish, including pattern recognition receptors, antimicrobial peptides, complements, lectins, cytokines, transferrin and gene expression profiling using microarrays and next generation sequencing technologies. This review will benefit the understanding of innate immune system in catfish and further efforts in studying the innate immune-related genes in fish.
International Journal of Molecular Sciences 01/2012; 13(11):14172-202. · 2.46 Impact Factor
[show abstract][hide abstract] ABSTRACT: Loss of fluid shear stress (ischemia) to the lung endothelium causes endothelial plasma membrane depolarization via ATP-sensitive K(+) (K(ATP)) channel closure, initiating a signaling cascade that leads to NADPH oxidase (NOX2) activation and ROS production. Since wortmannin treatment significantly reduces ROS production with ischemia, we investigated the role of phosphoinositide 3-kinase (PI3K) in shear-associated signaling. Pulmonary microvascular endothelial cells in perfused lungs subjected to abrupt stop of flow showed membrane depolarization and ROS generation. Stop of flow in flow-adapted mouse pulmonary microvascular endothelial cells in vitro resulted in the activation of PI3K and Akt as well as ROS generation. ROS generation in the lungs in situ was almost abolished by the PI3K inhibitor wortmannin and the PKC inhibitor H7. The combination of the two (wortmannin and H7) did not have a greater effect. Activation of NOX2 was greatly diminished by wortmannin, knockout of Akt1, or dominant negative PI3K, whereas membrane depolarization was unaffected. Ischemia-induced Akt activation (phosphorylation) was not observed with K(ATP) channel-null cells, which showed minimal changes in membrane potential with ischemia. Activation of Akt was similar to wild-type cells in NOX2-null cells, which do not generate ROS with ischemia. Cromakalim, a K(ATP) channel agonist, prevented both membrane depolarization and Akt phosphorylation with ischemia. Thus, Akt1 phosphorylation follows cell membrane depolarization and precedes the activation of NOX2. These results indicate that PI3K/Akt and PKC serve as mediators between endothelial cell membrane depolarization and NOX2 assembly.
[show abstract][hide abstract] ABSTRACT: To determine the effect of transfection of enhanced green fluorescent protein (EGFP) on neuron-like differentiation of rat mesenchymal stem cells (rMSC) with plasmid vector.
In vitro cultured rMSC was transfected with plasmid vector containing EGFP, and its surface marker and differentiation neuron-like cells were detected. Results There was no significant difference in the morphology and surface markers between the EGFP-rMSC and rMSC. The cell surface markers of EGFP-rMSC including expression of CD44(+),CD11b (-) and CD45(-) remained similar to those of rMSC. EGFP-rMSC presented the differentiated potential to neuron-like cells. There was no statistical difference in the positive ratio of neuron-like differentiation between the EGFP-rMSC and rMSC (P> 0.05).
EGFP does not affect the neuron-like differentiation potential of rMSC, and can be used as the trace marker in the study of differentiation potential of rMSC.
Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences 12/2011; 36(12):1183-8.
[show abstract][hide abstract] ABSTRACT: The Japanese scallop Mizuhopecten yessoensis is one of the most important aquaculture mollusca in Japan and China. In the present study, a high-quality cDNA library of the Japanese scallop was constructed from the kidney tissue. A total of 2919 expressed sequence tags longer than 100 bp were generated from this library. A cluster of 1440 unique sequences, which consisted of 258 contigs and 1182 singletons, was revealed. Based on blast searches, 882 (61.3%) genes had significant (E-value <1e–5) matches to known sequences in public databases. Among them, >70 genes were involved in stress response, immunity and apoptosis. These results expanded our knowledge of the genetics and physiology of the Japanese scallop, and provided a useful resource for gene discovery for further research of this species.
Aquaculture Research 03/2010; 41(11):1602 - 1613. · 1.42 Impact Factor
[show abstract][hide abstract] ABSTRACT: Bubble-size distributions influence the behavior of multiphase systems, but are not readily measured directly using probes. The chord lengths may be transformed into bubble sizes by modeling the bubble shapes as ellipsoids. Previous research on the transformation of chord-length data into bubble-size distributions using a numerical backward transformation revealed an instability problem. This problem was overcome by transforming the chord-length data to a local bubble-size distribution directly by using a Parzen window function and summing to yield the whole distribution. The best estimate of the local bubble-size density distribution depends on the Parzen window width that was chosen by proposing a measure of performance. An empirical relationship was also offered to determine the best Parzen window width. Chord lengths were generated using the example of a Rayleigh bubble-size distribution and Monte-Carlo simulation. The window approach transformed the chord lengths back into the bubble-size distribution with good agreement.
[show abstract][hide abstract] ABSTRACT: The probability relationships between bubble sizes and chord lengths in an heterogeneously bubbling system have been analyzed. A forward transform of chord length distribution for a given bubble size density distribution affecting the probe under a heterogeneously bubbling condition has been demonstrated. Three backward transform techniques, an analytical, a general, and a numerical, have been developed to infer bubble sizes from the chord length data in heterogeneously bubbling system. Both the analytical and the general backward transforms were based on the representation of the bubble population density function as a product of two functions which depend on bubble size and chord length. The techniques were tested and compared using Monte-Carlo simulations.
Chemical Engineering Science. 03/1998; 53(6):1267–1276.
[show abstract][hide abstract] ABSTRACT: Bubble behavior in fluidized beds may have a profound effect on other aspects of bed hydrodynamics. Submersible probes are often used to study the local bubble properties in these systems. Generally, the axes of the pierced bubbles need not be aligned with the vertical axis of the bed. This matter is further complicated by the fact that there is a distribution of bubble size. Therefore, data interpretation of probe signals should be performed carefully to yield bubble size distribution information. In this paper an analytic data interpretation technique in closed form has been presented based on the assumption that the bubble rise velocity depends on bubble size (usually the velocity increases as the square root of the linear size). A method employing a non-parametric approach to infer the bubble size distribution from the probe time signals (pierced time durations) without need for information about the nature of the pierced time duration distribution has also been described. A statistical data transformation approach for obtaining the average bubble size and the standard deviation of the local bubble size distribution has been established. Monte-Carlo simulations have been conducted to demonstrate the correctness of these techniques.