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author:("Zhang, jinhua")
1.  Discovery of co-occurring driver pathways in cancer 
BMC Bioinformatics  2014;15(1):271.
Background
It has been widely realized that pathways rather than individual genes govern the course of carcinogenesis. Therefore, discovering driver pathways is becoming an important step to understand the molecular mechanisms underlying cancer and design efficient treatments for cancer patients. Previous studies have focused mainly on observation of the alterations in cancer genomes at the individual gene or single pathway level. However, a great deal of evidence has indicated that multiple pathways often function cooperatively in carcinogenesis and other key biological processes.
Results
In this study, an exact mathematical programming method was proposed to de novo identify co-occurring mutated driver pathways (CoMDP) in carcinogenesis without any prior information beyond mutation profiles. Two possible properties of mutations that occurred in cooperative pathways were exploited to achieve this: (1) each individual pathway has high coverage and high exclusivity; and (2) the mutations between the pair of pathways showed statistically significant co-occurrence. The efficiency of CoMDP was validated first by testing on simulated data and comparing it with a previous method. Then CoMDP was applied to several real biological data including glioblastoma, lung adenocarcinoma, and ovarian carcinoma datasets. The discovered co-occurring driver pathways were here found to be involved in several key biological processes, such as cell survival and protein synthesis. Moreover, CoMDP was modified to (1) identify an extra pathway co-occurring with a known pathway and (2) detect multiple significant co-occurring driver pathways for carcinogenesis.
Conclusions
The present method can be used to identify gene sets with more biological relevance than the ones currently used for the discovery of single driver pathways.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-271) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2105-15-271
PMCID: PMC4133618  PMID: 25106096
2.  Spectrum of LKB1, EGFR, and KRAS Mutations in Chinese Lung Adenocarcinomas 
Introduction
Somatic LKB1 mutations are found in lung adenocarcinomas at different frequencies in Caucasian and East Asian (Japanese and Korean) populations. This study was designed to characterize the frequency of LKB1 mutations, their relationship to EGFR and KRAS mutations, and their associated clinicopathologic characteristics in Chinese patients.
Methods
Two hundred thirty-nine lung adenocarcinomas consecutively collected from October 2007 to July 2009 were dissected into 3 to 4 small (3 mm) pieces for histopathological analyses of tumor content. Genomic DNA and/or cDNA from 86 samples with more than 70% tumor content were used for sequencing of LKB1 (exons 1–9), EGFR (exons 18–21), and KRAS (exon 2). LKB1 germline mutation status was determined by sequencing of genomic DNA from matched histologically distant lung tissues that are histologically normal.
Results
6.9% of lung adenocarcinomas harbored LKB1 somatic mutations. A total of 10.5% of patients had an LKB1 germline polymorphism, F354L. Interestingly, in two of these patients, tumors displayed loss of heterozygosity at this allele. EGFR kinase domain and KRAS mutations were found in 66.3% and 2.3% of Chinese lung adenocarcinomas, respectively. Concurrent LKB1 and EGFR somatic mutations were observed in one patient. Both KRAS-mutant tumors harbored LKB1 mutations.
Conclusions
These data provide important clinical and molecular characteristics of lung adenocarcinomas from Chinese patients.
doi:10.1097/JTO.0b013e3181e05016
PMCID: PMC4009449  PMID: 20559149
Chinese lung adenocarcinoma; LKB1; EGFR; KRAS; Mutation
3.  Clinical Research of Traditional Chinese Medicine Needs to Develop Its Own System of Core Outcome Sets 
Currently, quality issues concerning clinical research of traditional Chinese medicine (TCM) have come into the spotlight. It has been recognized that poorly-devised research methodology largely restricted the development of clinical research in TCM. The choice of appropriate outcome measurements is key to the success of clinical research; however, the current procedure for outcomes selection in clinical research of TCM is problematic due to the underdevelopment of clinical methodology. Under this circumstance, we propose the introduction to the concept of Core Outcome Set (COS) and discuss the feasibility of developing a COS system that caters for clinical studies in TCM, in the hope that the outcome evaluation system could be up to international standards.
doi:10.1155/2013/202703
PMCID: PMC3838829  PMID: 24312133
4.  Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data 
BMC Systems Biology  2013;7(Suppl 2):S4.
Motivation
Understanding the molecular mechanisms underlying cancer is an important step for the effective diagnosis and treatment of cancer patients. With the huge volume of data from the large-scale cancer genomics projects, an open challenge is to distinguish driver mutations, pathways, and gene sets (or core modules) that contribute to cancer formation and progression from random passengers which accumulate in somatic cells but do not contribute to tumorigenesis. Due to mutational heterogeneity, current analyses are often restricted to known pathways and functional modules for enrichment of somatic mutations. Therefore, discovery of new pathways and functional modules is a pressing need.
Results
In this study, we propose a novel method to identify Mutated Core Modules in Cancer (iMCMC) without any prior information other than cancer genomic data from patients with tumors. This is a network-based approach in which three kinds of data are integrated: somatic mutations, copy number variations (CNVs), and gene expressions. Firstly, the first two datasets are merged to obtain a mutation matrix, based on which a weighted mutation network is constructed where the vertex weight corresponds to gene coverage and the edge weight corresponds to the mutual exclusivity between gene pairs. Similarly, a weighted expression network is generated from the expression matrix where the vertex and edge weights correspond to the influence of a gene mutation on other genes and the Pearson correlation of gene mutation-correlated expressions, respectively. Then an integrative network is obtained by further combining these two networks, and the most coherent subnetworks are identified by using an optimization model. Finally, we obtained the core modules for tumors by filtering with significance and exclusivity tests. We applied iMCMC to the Cancer Genome Atlas (TCGA) glioblastoma multiforme (GBM) and ovarian carcinoma data, and identified several mutated core modules, some of which are involved in known pathways. Most of the implicated genes are oncogenes or tumor suppressors previously reported to be related to carcinogenesis. As a comparison, we also performed iMCMC on two of the three kinds of data, i.e., the datasets combining somatic mutations with CNVs and secondly the datasets combining somatic mutations with gene expressions. The results indicate that gene expressions or CNVs indeed provide extra useful information to the original data for the identification of core modules in cancer.
Conclusions
This study demonstrates the utility of our iMCMC by integrating multiple data sources to identify mutated core modules in cancer. In addition to presenting a generally applicable methodology, our findings provide several candidate pathways or core modules recurrently perturbed in GBM or ovarian carcinoma for further studies.
doi:10.1186/1752-0509-7-S2-S4
PMCID: PMC3851989  PMID: 24565034
5.  Rapid Method for the Determination of 5-Hydroxymethylfurfural and Levulinic Acid Using a Double-Wavelength UV Spectroscopy 
The Scientific World Journal  2013;2013:506329.
This study reports on a rapid method for the determination of levulinic acid (LA) and 5-hydroxymethylfurfural (HMF) in acid hydrolyze system of glucose based on UV spectroscopy. It was found that HMF and LA have a maximum absorption at the wavelengths of 284 nm and 266 nm, respectively, in a water medium, and the absorptions of HMF and LA at 284 nm and 266 nm follow Beer's law very well. However, it was found that a major spectral interference species will arise in the quantification of HMF and LA; nonetheless, this interference can be eliminated through the absorption treatment of charcoal. Therefore, both HMF and LA can be quantified with a double-wavelength technique. The repeatability of the method had a relative standard deviation of less than 4.47% for HMF and 2.25% for LA; the limit of quantification (LOQ) was 0.017 mmol/L for HMF and 4.68 mmol/L for LA, and the recovery ranged from 88% to 116% for HMF and from 94% to 105% for LA. The present method is simple, rapid, and accurate. It is suitable to use in the research of the preparation of HMF and LA in biorefinery area.
doi:10.1155/2013/506329
PMCID: PMC3817645  PMID: 24228006
6.  Qi-Shen-Yi-Qi Dripping Pills for the Secondary Prevention of Myocardial Infarction: A Randomised Clinical Trial 
Background. Several types of drugs have been recommended for the secondary prevention of myocardial infarction (MI). However, these conventional strategies have several limitations, such as low adherence, high cost, and side effects during long time use. Novel approaches to this problem are still needed. This trial aimed to test the effectiveness and safety of Qi-Shen-Yi-Qi Dripping Pills (QSYQ), a multi-ingredient Chinese patent medicine, for the secondary prevention of MI. Methods and Findings. A total of 3505 eligible patients were randomly assigned to QSYQ group (1746 patients) or aspirin group (1759). Patients took their treatments for 12 months. The final follow-up visit took place 6 months after the end of the trial drugs. The 12-month and 18-month estimated incidences of the primary outcome were 2.98% and 3.67%, respectively, in the QSYQ group. The figures were 2.96% and 3.81% in the aspirin group. No significant difference was identified between the groups. Conclusions. This trial did not show significant difference of primary and secondary outcomes between aspirin and QSYQ in patients who have had an MI. Though inconclusive, the result suggests that QSYQ has similar effects to aspirin in the secondary prevention of MI.
doi:10.1155/2013/738391
PMCID: PMC3725842  PMID: 23935677
7.  Experimental Certification of Random Numbers via Quantum Contextuality 
Scientific Reports  2013;3:1627.
The intrinsic unpredictability of measurements in quantum mechanics can be used to produce genuine randomness. Here, we demonstrate a random number generator where the randomness is certified by quantum contextuality in connection with the Kochen-Specker theorem. In particular, we generate random numbers from measurements on a single trapped ion with three internal levels, and certify the generated randomness by showing a bound on the minimum entropy through observation of violation of the Klyachko-Can-Binicioglu-Shumovsky (KCBS) inequality. Concerning the test of the KCBS inequality, we close the detection efficiency loophole for the first time and make it relatively immune to the compatibility loophole. In our experiment, we generate 1 × 105 random numbers that are guaranteed to have 5.2 × 104 bits of minimum entropy with a 99% confidence level.
doi:10.1038/srep01627
PMCID: PMC4070742  PMID: 23568082
8.  The carbohydrate-binding module of xylanase from Nonomuraea flexuosa decreases its non-productive adsorption on lignin 
Background
The enzymatic hydrolysis step converting lignocellulosic materials into fermentable sugars is recognized as one of the major limiting steps in biomass-to-ethanol process due to the low efficiency of enzymes and their cost. Xylanases have been found to be important in the improvement of the hydrolysis of cellulose due to the close interaction of cellulose and xylan. In this work, the effects of carbohydrate-binding module (CBM family II) of the xylanase 11 from Nonomuraea flexuosa (Nf Xyn11) on the adsorption and hydrolytic efficiency toward isolated xylan and lignocellulosic materials were investigated.
Results
The intact family 11 xylanase of N. flexuosa clearly adsorbed on wheat straw and lignin, following the Langmuir-type isotherm. The presence of the CBM in the xylanase increased the adsorption and hydrolytic efficiency on insoluble oat spelt xylan. But the presence of the CBM did not increase adsorption on pretreated wheat straw or isolated lignin. On the contrary, the CBM decreased the adsorption of the core protein to lignin containing substrates, indicating that the CBM of N. flexuosa xylanase did not contribute to the non-productive adsorption.
Conclusion
The CBM of the N. flexuosa xylanase was shown to be a xylan-binding module, which had low affinity on cellulose. The CBM of the N. flexuosa xylanase reduced the non-specific adsorption of the core protein to lignin and showed potential for improving the hydrolysis of lignocellulosic materials to platform sugars.
doi:10.1186/1754-6834-6-18
PMCID: PMC3577619  PMID: 23363927
Carbohydrate binding module; Xylanase; Adsorption; Xylan
9.  Acute Inhibition of GTP Cyclohydrolase 1 Uncouples Endothelial Nitric Oxide Synthase and Elevates Blood Pressure 
Hypertension  2008;52(3):484-490.
GTP cyclohydrolase 1 (GTPCH1) is the rate-limiting enzyme in de novo synthesis of tetrahydrobiopterin (BH4), an essential cofactor for endothelial nitric oxide synthase (eNOS) dictating at least partly, the balance of nitric oxide (NO) and superoxide (O2•−) produced by this enzyme. The aim of this study was to determine the effect of acute inhibition of GTPCH1 on BH4, eNOS function, and blood pressure in vivo. Exposure of bovine or mouse aortic endothelial cells to GTPCH1 inhibitors (DAHP or NAS) or GTPCH1- siRNA significantly reduced BH4 and NO levels, but increased superoxide (O2•−) levels. This increase was abolished by sepiapterin (BH4 precursor) or L-NAME (non-selective NOS inhibitor). Incubation of isolated murine aortas with DAHP or NAS impaired acetylcholine-induced endothelium-dependent relaxation, but not endothelium-independent relaxation. Aortas from GTPCH1 siRNA-injected mice, but not their control-siRNA injected counterparts, also exhibited impaired endothelium-dependent relaxation. BH4 reduction induced by GTPCH1 siRNA injection was associated with increased aortic levels of O2•−, 3-nitrotyrosine, and adhesion molecules (ICAM1 and VCAM1) as well as a significantly elevated systolic, diastolic, and mean blood pressure in C57BL6 mice. GTPCH1 siRNA was unable to elicit these effects in eNOS−/− mice. Sepiapterin supplementation, which had no effect on high blood pressure in eNOS−/− mice, partially reversed GTPCH1 siRNA-induced elevation of blood pressure in wild type mice. In conclusion, GTPCH1 via BH4 maintains normal blood pressure and endothelial function in vivo by preserving NO synthesis by eNOS.
doi:10.1161/HYPERTENSIONAHA.108.112094
PMCID: PMC3523107  PMID: 18645049
Hypertension; Nitric Oxide; Superoxide Anions; Endothelial Nitric Oxide Synthase; Tetrahydrobiopterin; GTP-cyclohydrolase 1; Oxidative Stress
11.  A review of the species of Rhynchopsilopa Hendel from China (Diptera, Ephydridae) 
ZooKeys  2012;23-42.
Species of the shore-fly genus Rhynchopsilopa Hendel from China are reviewed. Four new species (Rhynchopsilopa guangdongensis sp. n., Rhynchopsilopa huangkengensis sp. n., Rhynchopsilopa jinxiuensis sp. n., Rhynchopsilopa shixingensis sp. n.) and two previously known species, Rhynchopsilopa longicornis (Okada) and Rhynchopsilopa magnicornis Hendel, are described or redescribed. A key to the species hitherto known from China is presented.
doi:10.3897/zookeys.216.3224
PMCID: PMC3426893  PMID: 22936876
Diptera; Ephydridae; Rhynchopsilopa; new species; China
12.  The expression and clinical significance of PI3K, pAkt and VEGF in colon cancer 
Oncology Letters  2012;4(4):763-766.
Background PI3K/Akt signaling has been shown to be activated in a variety of cancers. However, the correlation between Akt activation and VEGF expression is unclear in colon cancer tissues. This study aimed to investigate the expression and predictive value of phosphorylated Akt (pAkt) and VEGF in colon cancer tissues. The expression of PI3K, pAkt and VEGF was detected by immunohistochemical staining in 60 samples of colon cancer tissues and their corresponding adjacent normal colon tissues. In addition, the correlations between the expression levels of the 3 proteins and the clinicopathological parameters of the colon cancer cases were analyzed. The positive rates of PI3K, pAkt and VEGF expression were 71.7% (43/60), 68.3% (41/60) and 61.7% (37/60) in colon cancer, respectively, which were significantly higher than in adjacent normal colon tissues (P<0.001). Correlation analyses showed that PI3K expression was not significantly associated with the gender or age of the patients, tumor size or differentiation (P>0.05), but was closely associated with serous coat infiltration and lymphatic metastasis of colon cancer (P<0.05). Neither pAkt nor VEGF expression were significantly associated with the gender or age of the patients, or tumor differentiation (P>0.05), but were closely associated with tumor size, serous coat infiltration and lymphatic metastasis of colon cancer (P<0.05). In addition, the expression levels of Pl3K and pAkt were positively correlated with that of VEGF in colon cancer tissues (P<0.05). Our data show a positive correlation between PI3K/Akt activation and VEGF expression in colon cancer tissues and indicate that pAkt is an independent prognostic marker for colon cancer patients.
doi:10.3892/ol.2012.822
PMCID: PMC3506699  PMID: 23205098
colon cancer; PI3K/Akt; VEGF; angiogenesis; prognosis
13.  Structural and Functional Difference of Pheromone Binding Proteins in Discriminating Chemicals in the Gypsy Moth, Lymantria Dispar 
Pheromone-binding proteins (PBPs) of the gypsy moth, Lymantria dispar L., play an important role in olfaction. Here structures of PBPs were first built by Homology Modeling, and each model of PBPs had seven α-helices and a large hydrophobic cavity including 25 residues for PBP1 and 30 residues for PBP2. Three potential semiochemicals were first screened by CDOCKER program based on the PBP models and chemical database. These chemicals were Palmitic acid n-butyl ester (Pal), Bis(3,4-epoxycyclohexylmethyl) adipate (Bis), L-trans-epoxysuccinyl-isoleucyl-proline methyl ester propylamide (CA-074). The analysis of chemicals docking the proteins showed one hydrogen bond was established between the residues Lys94 and (+)-Disparlure ((+)-D), and л-л interactions were present between Phe36 of PBP1 and (+)-D. The Lys94 of PBP1 formed two and three hydrogen bonds with Bis and CA-074, respectively. There was no residue of PBP2 interacting with these four chemicals except Bis forming one hydrogen bond with Lys121. After simulating the conformational changes of LdisPBPs at pH7.3 and 5.5 by constant pH molecular dynamics simulation in implicit solvent, the N-terminal sequences of PBPs was unfolded, only having five α-helices, and PBP2 had larger binding pocket at 7.3 than PBP1. To investigate the changes of α-helices at different pH, far-UV and near-UV circular dichroism showed PBPs consist of α-helices, and the tertiary structures of PBP1 and PBP2 were influenced at pH7.3 and 5.5. The fluorescence binding assay indicated that PBP1 and PBP2 have similarly binding affinity to (+)-D at pH 5.5 and 7.3, respectively. At pH 5.5, the dissociation constant of the complex between PBP1 and 2-decyl-1-oxaspiro [2.2] pentane (OXP1) was 0.68±0.01μM, for (+)-D was 5.32±0.11μM, while PBP2 with OXP1 and (+)-D were 1.88±0.02μM and 5.54±0.04μM, respectively. Three chemicals screened had higher affinity to PBP1 than (+)-D except Pal at pH5.5, and had lower affinity than (+)-D at pH7.3. To PBP2, these chemicals had lower affinity than the sex pheromone except Bis at pH 5.5 and pH 7.3. Only PBP1 had higher affinity with Sal than the sex pheromone at pH 5.5. Therefore, the structures of PBP1 and PBP2 had different changes at pH5.5 and 7.3, showing different affinity to chemicals. This study helps understanding the role of PBPs as well as in developing more efficient chemicals for pest control.
doi:10.7150/ijbs.4557
PMCID: PMC3421229  PMID: 22904666
Lymantria dispar; pheromone-binding protein; bioinformatics; discrimination; semiochemicals
14.  LNA real-time PCR probe quantification of hepatitis B virus DNA 
In the present study, we standardized a TaqMan locked nucleic acid (LNA) real-time polymerase chain reaction (PCR) probe for the accurate quantification and detection of hepatitis B virus (HBV) DNA in serum (plasma), and evaluated its methodology. LNA probe technology had a much better detection performance in HBV DNA than the common TaqMan probe. The assay based on the LNA probe had a wider linear detection range, higher sensitivity, stability and amplification efficiency, and a lower concentration of probes than the TaqMan probe. Among the 15 cases with chronic hepatitis B surface antigen (HBsAg) (+) alone, only 4 cases that were detected by TaqMan real-time PCR were negative; however, the same samples were positive by LNA real-time PCR (p<0.05). A positive correlation between viral load measurements for the 35 samples with HBV-positive DNA was detected in both LNA and TaqMan real-time PCR.
doi:10.3892/etm.2011.442
PMCID: PMC3438541  PMID: 22969919
human hepatitis B virus; real-time polymerase chain reaction; probe; locked nucleic acid; TaqMan
15.  The role of acetyl xylan esterase in the solubilization of xylan and enzymatic hydrolysis of wheat straw and giant reed 
Background
Due to the complexity of lignocellulosic materials, a complete enzymatic hydrolysis into fermentable sugars requires a variety of cellulolytic and xylanolytic enzymes. Addition of xylanases has been shown to significantly improve the performance of cellulases and to increase cellulose hydrolysis by solubilizing xylans in lignocellulosic materials. The goal of this work was to investigate the effect of acetyl xylan esterase (AXE) originating from Trichoderma reesei on xylan solubilization and enzymatic hydrolysis of cellulose.
Results
The solubilization of xylan in pretreated wheat straw and giant reed (Arundo donax) by xylanolytic enzymes and the impact of the sequential or simultaneous solubilization of xylan on the hydrolysis of cellulose by purified enzymes were investigated. The results showed that the removal of acetyl groups in xylan by AXE increased the accessibility of xylan to xylanase and improved the hydrolysis of xylan in pretreated wheat straw and giant reed. Solubilization of xylan led to an increased accessibility of cellulose to cellulases and thereby increased the hydrolysis extent of cellulose. A clear synergistic effect between cellulases and xylanolytic enzymes was observed. The highest hydrolysis yield of cellulose was obtained with a simultaneous use of cellulases, xylanase and AXE, indicating the presence of acetylated xylan within the cellulose matrix. Acetylated xylobiose and acetylated xylotriose were produced from xylan without AXE, as confirmed by atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry.
Conclusions
The results in this paper demonstrate that supplementation of xylanase with AXE enhances the solubilization of xylan to some extent and, consequently, increases the subsequent hydrolysis of cellulose. The highest hydrolysis yield was, however, obtained by simultaneous hydrolysis of xylan and cellulose, indicating a layered structure of cellulose and xylan chains in the cell wall substrate. AXE has an important role in the hydrolysis of lignocellulosic materials containing acetylated xylan.
doi:10.1186/1754-6834-4-60
PMCID: PMC3259036  PMID: 22185437
16.  Cochrane Systematic Reviews of Chinese Herbal Medicines: An Overview 
PLoS ONE  2011;6(12):e28696.
Objectives
Our study had two objectives: a) to systematically identify all existing systematic reviews of Chinese herbal medicines (CHM) published in Cochrane Library; b) to assess the methodological quality of included reviews.
Methodology/Principal Findings
We performed a systematic search of the Cochrane Database of Systematic Reviews (CDSR, Issue 5, 2010) to identify all reviews of CHM. A total of fifty-eight reviews were eligible for our study. Twenty-one of the included reviews had at least one Traditional Chinese Medicine (TCM) practitioner as its co-author. 7 reviews didn't include any primary study, the remaining reviews (n = 51) included a median of 9 studies and 936 participants. 50% of reviews were last assessed as up-to-date prior to 2008. The questions addressed by 39 reviews were broad in scope, in which 9 reviews combined studies with different herbal medicines. For OQAQ, the mean of overall quality score (item 10) was 5.05 (95% CI; 4.58-5.52). All reviews assessed the methodological quality of primary studies, 16% of included primary studies used adequate sequence generation and 7% used adequate allocation concealment. Of the 51 nonempty reviews, 23 reviews were reported as being inconclusive, while 27 concluded that there might be benefit of CHM, which was limited by the poor quality or inadequate quantity of included studies. 58 reviews reported searching a median of seven electronic databases, while 10 reviews did not search any Chinese database.
Conclusions
Now CDSR has included large numbers of CHM reviews, our study identified some areas which could be improved, such as almost half of included reviews did not have the participation of TCM practitioners and were not up-to-date according to Cochrane criteria, some reviews pooled the results of different herbal medicines and ignored the searching of Chinese databases.
doi:10.1371/journal.pone.0028696
PMCID: PMC3235143  PMID: 22174870
18.  Thermostable recombinant xylanases from Nonomuraea flexuosa and Thermoascus aurantiacus show distinct properties in the hydrolysis of xylans and pretreated wheat straw 
Background
In the hydrolysis of lignocellulosic materials, thermostable enzymes decrease the amount of enzyme needed due to higher specific activity and elongate the hydrolysis time due to improved stability. For cost-efficient use of enzymes in large-scale industrial applications, high-level expression of enzymes in recombinant hosts is usually a prerequisite. The main aim of the present study was to compare the biochemical and hydrolytic properties of two thermostable recombinant glycosyl hydrolase families 10 and 11 (GH10 and GH11, respectively) xylanases with respect to their potential application in the hydrolysis of lignocellulosic substrates.
Results
The xylanases from Nonomuraea flexuosa (Nf Xyn11A) and from Thermoascus aurantiacus (Ta Xyn10A) were purified by heat treatment and gel permeation chromatography. Ta Xyn10A exhibited higher hydrolytic efficiency than Nf Xyn11A toward birchwood glucuronoxylan, insoluble oat spelt arabinoxylan and hydrothermally pretreated wheat straw, and it produced more reducing sugars. Oligosaccharides from xylobiose to xylopentaose as well as higher degree of polymerization (DP) xylooligosaccharides (XOSs), but not xylose, were released during the initial hydrolysis of xylans by Nf Xyn11A, indicating its potential for the production of XOS. The mode of action of Nf Xyn11A and Ta Xyn10A on glucuronoxylan and arabinoxylan showed typical production patterns of endoxylanases belonging to GH11 and GH10, respectively.
Conclusions
Because of its high catalytic activity and good thermostability, T. aurantiacus xylanase shows great potential for applications aimed at total hydrolysis of lignocellulosic materials for platform sugars, whereas N. flexuosa xylanase shows more significant potential for the production of XOSs.
doi:10.1186/1754-6834-4-12
PMCID: PMC3114720  PMID: 21592333
19.  Huangqi Injection (a Traditional Chinese Patent Medicine) for Chronic Heart Failure: A Systematic Review 
PLoS ONE  2011;6(5):e19604.
Background
Chronic heart failure (CHF) is a global public health problem. Therefore, novel and effective drugs that show few side-effects are needed. Early literature studies indicated that Huangqi injection is one of the most commonly used traditional Chinese patent medicines for CHF in China. As a large number of clinical studies has been carried out and published, it is essential to evaluate the effectiveness and safety of Huangqi injection. Therefore, we carried out this systematic review under the support of the framework of the Joint Sino-Italian Laboratory (JoSIL).
Objectives
To evaluate the efficacy and safety of Huangqi injection for CHF according to the available scientific knowledge.
Methods
An extensive search including PubMed, EMBASE, CBM, the Cochrane Library and Chinese literature databases was performed up to July 2008. Clinical trials regarding Huangqi injection for the treatment of CHF were searched for, irrespective of languages. The quality of each trial was assessed according to the Cochrane Reviewers' Handbook 5.0, and RevMan 5.0 provided by the Cochrane Collaboration and STATA 9.2 were used for data analysis.
Results
After selection of 1,205 articles, 62 RCTs and quasi-RCTs conducted in China and published in Chinese journals were included in the review. The methodological quality of the trials was low. In most trials inclusion and exclusion criteria were not specified. Furthermore, only one study evaluated the outcomes for drug efficacy after an adequate period of time. For these reasons and because of the different baseline characteristics we did not conduct a meta-analysis.
Conclusions
Although available studies are not adequate to draw a conclusion on the efficacy and safety of Huangqi injection (a traditional Chinese patent medicine), we hope that our work could provide useful experience on further studies on Huangqi injections. The overall level of TCM clinical research needs to be improved so that the efficacy of TCM can be evaluated by the international community and possibly some TCM can enter into the international market.
doi:10.1371/journal.pone.0019604
PMCID: PMC3089614  PMID: 21573109
20.  Effect of household and village characteristics on financial catastrophe and impoverishment due to health care spending in Western and Central Rural China: A multilevel analysis 
Objective
The study aimed to examine the effect of household and community characteristics on financial catastrophe and impoverishment due to health payment in Western and Central Rural China.
Methods
A household survey was conducted in 2008 in Hebei and Shaanxi provinces and the Inner Mongolia Autonomous Region using a multi-stage sampling technique. Independent variables included village characteristics, household income, chronic illness status, health care use and health spending. A composite contextual variable, named village deprivation, was derived from socio-economic status and availability of health care facilities in each village using factor analysis. Dependent variables were whether household health payment was more than 40% of household's capacity to pay (catastrophic health payment) and whether household per capita income was put under Chinese national poverty line (1067 Yuan income per year) after health spending (impoverishment). Mixed effects logistic regression was used to assess the effect of the independent variables on the two outcomes.
Results
Households with low per capita income, having elderly, hospitalized or chronically ill members, and whose head was unemployed were more likely to incur financial catastrophe and impoverishment due to health expenditure. Both catastrophic and impoverishing health payments increased with increased village deprivation. However, the presence of a village health clinic had no effect on the two outcomes, nor did household enrollment in the New Rural Cooperative Medical Scheme (national health insurance).
Conclusions
Village deprivation independently increases the risk for financial hardship due to health payment after adjusting for known household-level factors. This suggests that policy makers need to view the individual, household and village as separate units for policy targeting.
doi:10.1186/1478-4505-9-16
PMCID: PMC3080794  PMID: 21466714
21.  Thermostable endoglucanases in the liquefaction of hydrothermally pretreated wheat straw 
Background
Thermostable enzymes have several benefits in lignocellulose processing. In particular, they potentially allow the use of increased substrate concentrations (because the substrate viscosity decreases as the temperature increases), resulting in improved product yields and reduced capital and processing costs. A short pre-hydrolysis step at an elevated temperature using thermostable enzymes aimed at rapid liquefaction of the feedstock is seen as an attractive way to overcome the technical problems (such as poor mixing and mass transfer properties) connected with high initial solid loadings in the lignocellulose to ethanol process.
Results
The capability of novel thermostable enzymes to reduce the viscosity of high-solid biomass suspensions using a real-time viscometric measurement method was investigated. Heterologously expressed enzymes from various thermophilic organisms were compared for their ability to liquefy the lignocellulosic substrate, hydrothermally pretreated wheat straw. Once the best enzymes were identified, the optimal temperatures for these enzymes to decrease substrate viscosity were compared. The combined hydrolytic properties of the thermostable preparations were tested in hydrolysis experiments. The studied mixtures were primarily designed to have good liquefaction potential, and therefore contained an enhanced proportion of the key liquefying enzyme, EGII/Cel5A.
Conclusions
Endoglucanases were shown to have a superior ability to rapidly reduce the viscosity of the 15% (w/w; dry matter) hydrothermally pretreated wheat straw. Based on temperature profiling studies, Thermoascus aurantiacus EGII/Cel5A was the most promising enzyme for biomass liquefaction. Even though they were not optimized for saccharification, many of the thermostable enzyme mixtures had superior hydrolytic properties compared with the commercial reference enzymes at 55°C.
doi:10.1186/1754-6834-4-2
PMCID: PMC3037870  PMID: 21269447
22.  Automatic Cobb Measurement of Scoliosis Based on Fuzzy Hough Transform with Vertebral Shape Prior 
To reduce variability of Cobb angle measurement for scoliosis assessment, a computerized method was developed. This method automatically measured the Cobb angle on spinal posteroanterior radiographs after the brightness and the contrast of the image were adjusted, and the top and bottom of the vertebrae were selected. The automated process started with the edge detection of the vertebra by Canny edge detector. After that, the fuzzy Hough transform was used to find line structures in the vertebral edge images. The lines that fitted to the endplates of vertebrae were identified by selecting peaks in Hough space under the vertebral shape constraints. The Cobb angle was then calculated according to the directions of these lines. A total of 76 radiographs were respectively analyzed by an experienced surgeon using the manual measurement method and by two examiners using the proposed method twice. Intraclass correlation coefficients (ICC) showed high agreement between automatic and manual measurements (ICCs > 0.95). The mean absolute differences between automatic and manual measurements were less than 5°. In the interobserver analyses, ICCs were higher than 0.95, and mean absolute differences were less than 5°. In the intraobserver analyses, ICCs were 0.985 and 0.978, respectively, for each examiner, and mean absolute differences were less than 3°. These results demonstrated the validity and reliability of the proposed method.
doi:10.1007/s10278-008-9127-y
PMCID: PMC3043716  PMID: 18516643
Cobb angle; scoliosis; fuzzy Hough transform (FHT); shape prior; radiograph
23.  JinQi-Jiangtang tablet, a Chinese patent medicine, for pre-diabetes: a randomized controlled trial 
Trials  2010;11:27.
Background
Pre-diabetes is a growing health concern where a large percentage of these patients develop full type 2 diabetes. Effective interventions on pre-diabetes can prevent or delay the occurrence or development of diabetes. Pharmaco-dynamics and pre-clinical of JinQi-Jiangtang tablets (JQJT) suggest that it could be benefit for pre-diabetes.
Methods/Design
Randomized controlled trial (RCT) is implemented in this study. The study term is 24 months (12 months for intervention and 12 months for follow up). Participants are recruited from four cities of China: Beijing, Tianjin, Xi'an and Nanning. Four hundred participants are randomized to treatment group (JQJT tablets) and control group (Placebo); two hundred participants each. People being included in this study must have been diagnosed as pre-diabetes via western medicine criteria and traditional Chinese medicine (TCM) criteria. The end-point indexes include: incidence of diabetes mellitus and reversion rate. Primary outcome indexes include: oral glucose tolerance test; insulin releasing test; glycosylated hemoglobin (HA1c). Secondary outcome indexes include: score of the Short Form 36 Health Survey Questionnaire (SF-36); score of TCM symptoms; blood lipid test. Indexes of safety include: general medical examination; blood and urine regular test; electrocardiogram (ECG), liver function (ALT) and renal function (BUN, Creatinine) test; record of adverse event, such as headache, faint, etc. Qualitative control will be implemented and a number of standard operating processes (SOPs) will be formed throughout the study: laboratory quality control measures; compliance control for researchers and participants; researcher training before study; supervision; investigational drug management and others.
Discussion
The aim of this study is to evaluate the effectiveness and safety of JinQi JiangTang (JQJT) tablets for the treatment of patients with pre-diabetes.
Trial registration
Chinese clinical trials register ChiCTR-TRC-00000401
doi:10.1186/1745-6215-11-27
PMCID: PMC2842259  PMID: 20214831
24.  The influence of the rural health security schemes on health utilization and household impoverishment in rural China: data from a household survey of western and central China 
Background
The New Rural Cooperative Medical Scheme (NRCMS, voluntary health insurance) and the Medical Financial Assistance (MFA, financial relief program) were established in 2003 for rural China. The aim of this study was to document their coverage, assess their effectiveness on access to in-patient care and protection against financial catastrophe and household impoverishment due to health spending, and identify the factors predicting impoverishment with and without these schemes.
Methods
A cross-sectional household survey was conducted in 2008 in Hebei and Shaanxi provinces and the Inner Mongolia Autonomous Region using a multi-stage sampling technique. Information on personal demographic characteristics, chronic illness status, health care use, household expenditure, and household health spending were collected by interview.
Results
NRCMS covered 90.8% of the studied individuals and among the designated poor, 7.6% had their premiums paid by MFA. Of those referred for hospitalization in the year prior to the interview, 34.3% failed to comply, mostly (80.2%) owing to financial constraints. There was no significant difference in the unmet need for admission between the insured with NRCMS and the uninsured. Before reimbursement, the incidence of catastrophic health payment (household health spending more than 40% of household's capacity to pay) and medical impoverishment (household per capita income falling below the poverty line due to medical expense) was 14.3% and 8.2%, respectively. NRCMS prevented 9.9% of the households from financial catastrophe and 7.7% from impoverishment, whereas MFA kept just one household from impoverishment and had no effect on financial catastrophe. Household per capita expenditure and household chronic disease proportion (proportion of members of a household with chronic illness) were the most important determinants of the unmet need for admission, risk of being impoverished and the chance of not being saved from impoverishment.
Conclusion
The coverage of NRCMS among the rural population was high but not adequate to improve access to in-patient care and protect against financial catastrophe and household impoverishment due to health payment, especially for the poor and the chronically ill. Furthermore, MFA played almost no such role; therefore, the current schemes need to be improved.
doi:10.1186/1475-9276-9-7
PMCID: PMC2838900  PMID: 20178565
25.  Identification of the Serine 307 of LKB1 as a Novel Phosphorylation Site Essential for Its Nucleocytoplasmic Transport and Endothelial Cell Angiogenesis ▿ †  
Molecular and Cellular Biology  2009;29(13):3582-3596.
LKB1, a master kinase that controls at least 13 downstream protein kinases including the AMP-activated protein kinase (AMPK), resides mainly in the nucleus. A key step in LKB1 activation is its export from the nucleus to the cytoplasm. Here, we identified S307 of LKB1 as a putative novel phosphorylation site which is essential for its nucleocytoplasmic transport. In a cell-free system, recombinant PKC-ζ phosphorylates LKB1 at S307. AMPK-activating agents stimulate PKC-ζ activity and LKB1 phosphorylation at S307 in endothelial cells, hepatocytes, skeletal muscle cells, and vascular smooth muscle cells. Like the kinase-dead LKB1 D194A mutant (mutation of Asp194 to Ala), the constitutively nucleus-localized LKB1 SL26 mutant and the LKB1 S307A mutant (Ser307 to Ala) exhibit a decreased association with STRADα. Interestingly, the PKC-ζ consensus sequence surrounding LKB1 S307 is disrupted in the LKB1 SL26 mutant, thus providing a likely molecular explanation for this mutation causing LKB1 dysfunction. In addition, LKB1 nucleocytoplasmic transport and AMPK activation in response to peroxynitrite are markedly reduced by pharmacological inhibition of CRM1, which normally facilitates nuclear export of LKB1-STRAD complexes. In comparison to the LKB1 wild type, the S307A mutant complexes show reduced association with CRM1. Finally, adenoviral overexpression of wild-type LKB1 suppresses, while the LKB1 S307A mutant increases, tube formation and hydrogen peroxide-enhanced apoptosis in cultured endothelial cells. Taken together, our results suggest that, in multiple cell types the signaling pathways engaged by several physiological stimuli converge upon PKC-ζ-dependent LKB1 phosphorylation at S307, which directs the nucleocytoplasmic transport of LKB1 and consequent AMPK activation.
doi:10.1128/MCB.01417-08
PMCID: PMC2698771  PMID: 19414597

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