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1.  A Graphic Method for Identification of Novel Glioma Related Genes 
BioMed Research International  2014;2014:891945.
Glioma, as the most common and lethal intracranial tumor, is a serious disease that causes many deaths every year. Good comprehension of the mechanism underlying this disease is very helpful to design effective treatments. However, up to now, the knowledge of this disease is still limited. It is an important step to understand the mechanism underlying this disease by uncovering its related genes. In this study, a graphic method was proposed to identify novel glioma related genes based on known glioma related genes. A weighted graph was constructed according to the protein-protein interaction information retrieved from STRING and the well-known shortest path algorithm was employed to discover novel genes. The following analysis suggests that some of them are related to the biological process of glioma, proving that our method was effective in identifying novel glioma related genes. We hope that the proposed method would be applied to study other diseases and provide useful information to medical workers, thereby designing effective treatments of different diseases.
doi:10.1155/2014/891945
PMCID: PMC4094879  PMID: 25050377
2.  Disulfiram targeting lymphoid malignant cell lines via ROS-JNK activation as well as Nrf2 and NF-kB pathway inhibition 
Background
Disulfiram (DS), an anti-alcoholism drug, demonstrates strong antitumor activity in a copper (Cu)-dependent manner. This study investigates the cytotoxicity of DS/Cu complex in lymphoid malignant cell lines in vitro and in vivo.
Method
Raji cells were subjected to different treatments and thereafter MTT assay, flow cytometry were used to determine IC50 and apoptotic status. We also tested the cytotoxicity of DS/Cu in acute lymphoblastic leukemia cell line Molt4 in vitro. In vivo experiments were also performed to demonstrate the anticancer efficacy of DS/Cu in Raji cells xenografted nude mice.
Results
In combination with a low concentration (1 μM) of Cu2+, DS induced cytotoxicity in Raji cells with an IC50 of 0.085 ± 0.015 μM and in Molt4 cells with an IC50 of 0.435 ± 0.109 μM. The results of our animal experiments also showed that the mean tumor volume in DS/Cu-treated mice was significantly smaller than that in DS or control group, indicating that DS/Cu inhibits the proliferation of Raji cells in vivo. DS/Cu also induced apoptosis in 2 lymphoid malignant cell lines. After exposure to DS (3.3 μM)/Cu (1 μM) for 24 hours, apoptosis was detected in 81.03 ± 7.91% of Raji cells. DS/Cu induced significant apoptosis in a concentration-dependent manner with the highest apoptotic proportion (DS/Cu: 89.867 ± 4.69%) at a concentration of 2 μM in Molt4 cells. After 24 h exposure, DS/Cu inhibits Nrf2 expression. Flow cytometric analysis shows that DS/Cu induced ROS generation. DS/Cu induced phosphorylation of JNK and inhibits p65 expression as well as Nrf2 expression both in vitro and in vivo. N-acetyl-L-cysteine (NAC), an antioxidant, can partially attenuate DS/Cu complex-induced apoptosis and block JNK activation in vitro. In addition, NAC is able to restore Nrf2 nuclear translocation and p65 expression.
Conclusion
Our study manifests that DS/Cu complex targets lymphoid malignant cells in vitro and in vivo. Generation of ROS might be one of core steps in DS/Cu induced apoptosis. Moreover, ROS-related activation of JNK pathway and inhibition of NF-κB and Nrf2 may also contribute to the DS/Cu induced apoptosis.
doi:10.1186/1479-5876-12-163
PMCID: PMC4075939  PMID: 24915933
Disulfiram; Nrf2; NF-κB; JNK; Apoptosis
3.  Ameloblastic carcinoma: An analysis of 12 cases with a review of the literature 
Oncology Letters  2014;8(2):914-920.
The diagnosis of ameloblastic carcinoma is often difficult and the optimal treatment methods remain controversial. The current study retrospectively investigated the optimal diagnosis and treatment methods of 12 ameloblastic carcinoma patients at the West China Hospital of Stomatology, Sichuan University (Chengdu, China), and 20 patients selected from the PubMed database, were reviewed. The clinical features, diagnosis and outcome of the different treatments were evaluated. Ameloblastic carcinoma occurred in 12 out of a total of 538 ameloblastoma patients; the majority were of the primary type. Of the 538 ameloblastoma patients, 294 were male, 244 were female with a male to female ratio of 1.2:1. The predilection age is 20–30 years, which accounts for 40% of the total. In total, 461 cases were in the mandible and 77 were located in the maxilla. The cure rate of the primary type and the recurrence rate of the secondary type tumors were higher in the patients from the West China Hospital of Stomatology compared with those reported in the literature. In particular, a case with a long-term survival of 30 years is presented, which is considered to be relatively rare. The evolution of the clinical course has experienced three stages: Ameloblastoma (1978) followed by metastatic ameloblastoma (2000) and finally ameloblastic carcinoma (2008). To avoid recurrence, wide local excision with postoperative radiation therapy is required. While novel therapeutic regimens should also be considered as appropriate, including carbon ion therapy and Gamma Knife stereotactic radiosurgery. However, controlled studies with larger groups of patients are required to increase the accuracy of results.
doi:10.3892/ol.2014.2230
PMCID: PMC4081393  PMID: 25013517
ameloblastic carcinoma; diagnosis; treatment; radiotherapy
4.  A population of Nestin expressing progenitors in the cerebellum exhibits increased tumorigenicity 
Nature neuroscience  2013;16(12):10.1038/nn.3553.
It is generally believed that cerebellar granule neurons originate exclusively from granule neuron precursors (GNPs) in the external germinal layer (EGL). Here we identify a rare population of neuronal progenitors in mouse developing cerebellum that expresses Nestin. Although Nestin is widely considered a marker for multipotent stem cells, these Nestin-expressing progenitors (NEPs) are committed to the granule neuron lineage. Unlike conventional GNPs, which reside in the outer EGL and proliferate extensively, NEPs reside in the deep part of the EGL and are quiescent. Expression profiling reveals that NEPs are distinct from GNPs, and in particular, express markedly reduced levels of genes associated with DNA repair. Consistent with this, upon aberrant activation of Sonic hedgehog (Shh) signaling, NEPs exhibit more severe genomic instability and give rise to tumors more efficiently than GNPs. These studies identify a novel progenitor for cerebellar granule neurons and a novel cell of origin for medulloblastoma.
doi:10.1038/nn.3553
PMCID: PMC3845444  PMID: 24141309
5.  In situ precipitation: a novel approach for preparation of iron-oxide magnetoliposomes 
Background
Conventional methods of preparing magnetoliposomes are complicated and inefficient. A novel approach for magnetoliposomes preparation was investigated in the study reported here.
Methods
FeCl3/FeCl2 solutions were hydrated with lipid films to obtain liposome-encapsulated iron ions by ultrasonic dispersion. Non-encapsulated iron ions were removed by dialysis. NH3 · H2O was added to the system to adjust the pH to a critical value. Four different systems were prepared. Each was incubated at a different temperature for a different length of time to facilitate the permeation of NH3 · H2O into the inner phase of the liposomes and the in situ formation of magnetic iron-oxide cores in the liposomes. Single-factor analysis and orthogonal-design experiments were applied to determinate the effects of alkalization pH, temperature, duration, and initial Fe concentration on encapsulation efficiency and drug loading.
Results
The magnetoliposomes prepared by in situ precipitation had an average particle size of 168±14 nm, zeta potential of −26.2±1.9 mV and polydispersity index of 0.23±0.06. The iron-oxide cores were confirmed as Fe3O4 by X-ray diffraction and demonstrated a superparamagnetic response. Encapsulation efficiency ranged from 3% to 22%, while drug loading ranged from 0.2 to 1.58 mol Fe/mol lipid. The optimal conditions for in situ precipitation were found to be an alkalization pH of 12, temperature of 60°C, time of 60 minutes, and initial Fe concentration of 100 mM Fe3+ + 50 mM Fe2+.
Conclusion
In situ precipitation could be a simple and efficient approach for the preparation of iron-oxide magnetoliposomes.
doi:10.2147/IJN.S59859
PMCID: PMC4043714  PMID: 24920898
magnetoliposomes; in situ precipitation; iron oxide; alkalization; permeability
6.  Efficient 18F labeling of cysteine containing peptides and proteins using the tetrazine-trans-cyclooctene ligation 
Molecular imaging  2013;12(2):121-128.
18F PET has a number of attributes that make it clinically attractive, including nearly 100% positron efficiency, very high specific radioactivity, and short half-life of ~110 min. However, the short half-life of 18F and the poor nucleophilicity of fluoride introduce challenges for the incorporation of 18F into complex molecules. Recently, the tetrazine-trans-cyclooctene ligation has been introduced as a novel 18F labeling method that proceeds with fast reaction rates without catalysis. Herein, we report an efficient method for 18F-labeling of free cysteines of peptides and proteins based on sequential ligation with a bifunctional tetrazinyl-maleimide and an 18F-labeled trans-cyclooctene. The newly developed method was tested for site specific labeling of both c(RGDyC) peptide and VEGF-SH protein. Starting with 4 mCi of 18F-trans-cyclooctene and only 10 μg of tetrazine-RGD (80–100 μM) or 15 μg of tetrazine-VEGF (6.0 μM), 18F labeled RGD peptide and VEGF protein could be obtained within five minutes in 95% yield and 75% yield, respectively. The obtained tracers were then evaluated in mice. In conclusion, a highly efficient method has been developed for site-specific 18F labeling of cysteine containing peptides and proteins. The special characteristics of the tetrazine-trans-cyclooctene ligation provide unprecedented opportunities to synthesize 18F-labeled probes with high specific activity for PET applications.
PMCID: PMC4027965  PMID: 23415400
18F; tetrazine-trans-cyclooctene; PET; Protein labeling; Maleimide
7.  Adenine Nucleotide Translocase 1 Deficiency Results in Dilated Cardiomyopathy With Defects in Myocardial Mechanics, Histopathological Alterations, and Activation of Apoptosis 
Objectives
The aim of this study was to test the hypothesis that chronic mitochondrial energy deficiency causes dilated cardiomyopathy, we characterized the hearts of age-matched young and old adenine nucleotide translocator (ANT)1 mutant and control mice.
Background
ANTs export mitochondrial adenosine triphosphate into the cytosol and have a role in the regulation of the intrinsic apoptosis pathway. Mitochondrial energy deficiency has been hypothesized, on the basis of indirect evidence, to be a factor in the pathophysiology of dilated cardiomyopathies. Ant1 inactivation should limit adenosine triphosphate for contraction and calcium transport, thereby resulting in early cardiac dysfunction with later dilation and heart failure.
Methods
We conducted a multiyear study of 73 mutant (Ant1−/−) and 57 control (Ant1+/+) mice, between the ages of 2 and 21 months. Hearts were characterized by cardiac anatomy, echocardiographic imaging with velocity vector analysis, histopathology, and apoptosis assays.
Results
The Ant1−/− mice developed a distinctive concentric dilated cardiomyopathy, characterized by substantial myocardial hypertrophy and ventricular dilation, with cardiac function declining earlier in age as compared to control mice. Left ventricular circumferential, radial, and rotational mechanics were reduced even in the younger mutants with preserved systolic function. Histopathologic analysis demonstrated increased myocyte hypertrophy, fibrosis, and calcification in the mutant mice as compared with control mice. Furthermore, increased cytoplasmic cytochrome c levels and caspase 3 activation were observed in the mutant mice.
Conclusions
Our results demonstrate that mitochondrial energy deficiency is sufficient to cause dilated cardiomyopathy, confirming that energy defects are a factor in this disease. Energy deficiency initially leads to early mechanical dysfunction before a decline in left ventricular systolic function. Chronic energy deficiency with age then leads to heart failure. Our results now allow us to use the Ant1−/− mouse model for testing new therapies for ANT1 mutant patients.
doi:10.1016/j.jcmg.2010.06.018
PMCID: PMC4023693  PMID: 21232697
adenine nucleotide translocator; aging; apoptosis; cardiomyopathy; mitochondria
8.  Excimer Laser Phototherapeutic Keratectomy for the Treatment of Clinically Presumed Fungal Keratitis 
Journal of Ophthalmology  2014;2014:963287.
This retrospective study was to evaluate treatment outcomes of excimer laser phototherapeutic keratectomy (PTK) for clinically presumed fungal keratitis. Forty-seven eyes of 47 consecutive patients underwent manual superficial debridement and PTK. All corneal lesions were located in the anterior stroma and were resistant to medication therapy for at least one week. Data were collected by a retrospective chart review with at least six months of follow-up data available. After PTK, infected corneal lesions were completely removed and the clinical symptoms resolved in 41 cases (87.2%). The mean ablation depth was 114.39 ± 45.51 μm and diameter of ablation was 4.06 ± 1.07 mm. The mean time for healing of the epithelial defect was 8.8 ± 5.6 days. Thirty-four eyes (82.9%) showed an improvement in best spectacle-corrected visual acuity of two or more lines. PTK complications included mild to moderate corneal haze, hyperopic shift, irregular astigmatism, and thinning cornea. Six eyes (12.8%) still showed progressed infection, and conjunctival flap covering, amniotic membrane transplantation, or penetrating keratoplasty were given. PTK is a valuable therapeutic alternative for superficial infectious keratitis. It can effectively eradicate lesions, hasten reepithelialization, and restore and preserve useful visual function. However, the selection of surgery candidates should be conducted carefully.
doi:10.1155/2014/963287
PMCID: PMC4033497  PMID: 24891945
9.  The prognostic effect of perineural invasion in esophageal squamous cell carcinoma 
BMC Cancer  2014;14:313.
Background
Perineural invasion (PNI) is correlated with adverse survival in several malignancies, but its significance in esophageal squamous cell carcinoma (ESCC) remains to be clearly defined. The objective of this study was to determine the association between PNI status and clinical outcomes.
Methods
We retrospectively evaluated the PNI of 433 patients with ESCC treated with surgery between 2000 and 2007 at a single academic center. The resulting data were analyzed using Spearman’s rank correlation, the Kaplan-Meier method, Cox proportional hazards regression modeling and Harrell’s concordance index (C-index).
Results
PNI was identified in 209 of the 433 (47.7%) cases of ESCC. The correlation analysis demonstrated that PNI in ESCC was significantly correlated with tumor differentiation, infiltration depth, pN classification and stage (P < 0.05). The five-year overall survival rate was 0.570 for PNI-negative tumors versus 0.326 for PNI-positive tumors. Patients with PNI-negative tumors exhibited a 1.7-fold increase in five-year recurrence-free survival compared with patients with PNI-positive tumors (0.531 v 0.305, respectively; P < 0.0001). In the subset of patients with node-negative disease, PNI was evaluated as a prognostic predictor as well (P < 0.05). In the multivariate analysis, PNI was an independent prognostic factor for overall survival (P = 0.027). The C-index estimate for the combined model (PNI, gender and pN status) was a significant improvement on the C-index estimate of the clinicopathologic model alone (0.739 v 0.706, respectively).
Conclusions
PNI can function as an independent prognostic factor of outcomes in ESCC patients, and the PNI status in primary ESCC specimens should be considered for therapy stratification.
doi:10.1186/1471-2407-14-313
PMCID: PMC4016635  PMID: 24886020
Perineural invasion; Prognosis; Esophageal squamous cell carcinoma
10.  Protective effect of Xin Mai Jia ultrafiltration extract on human umbilical vein endothelial cell injury induced by hydrogen peroxide and the effect on the NO-cGMP signaling pathway 
The aim of the present study was to evaluate the protective effect of the ultrafiltration extract of Xin Mai Jia (XMJ) on a human umbilical vein endothelial cell (HUVEC) injury model induced by hydrogen peroxide (H2O2), by providing experimental data to investigate the mechanism and efficacy underlying the therapeutic effects on atherosclerosis. HUVECs were first injured by H2O2 and then varying final concentrations of the Chinese herb extract were added. Effects of the XMJ extract on morphology, activity, monolayer permeability, biochemical indicators, cytokines, endothelial nitric oxide synthase (eNOS) protein content and eNOS gene expression in the HUVECs were analyzed. H2O2 significantly promoted HUVEC injury. The XMJ ultrafiltration extract significantly improved the morphological changes in the injured HUVECs. In addition, XMJ treatment increased cell activity and decreased monolayer permeability. The expression levels of intracellular adhesion molecule-1, vascular adhesion molecule-1, interleukin-1 and -6 and nuclear factor-κB decreased, while the expression levels of matrix metalloproteinase-2 and tissue inhibitor of metalloproteinase-2 increased with XMJ administration. Increased levels of nitric oxide (NO), eNOS protein and eNOS gene expression were also observed. Therefore, the XMJ ultrafiltration extract exhibits marked anti-inflammatory effects and antioxidant abilities. These properties significantly inhibited the H2O2-induced injury of HUVECs, which may be associated with the NO-cyclic guanosine monophosphate signaling pathway.
doi:10.3892/etm.2014.1700
PMCID: PMC4061210  PMID: 24944594
Xin Mai Jia; human umbilical vein endothelial cell; hydrogen peroxide; atherosclerosis
11.  A High-Sensitivity Current Sensor Utilizing CrNi Wire and Microfiber Coils 
Sensors (Basel, Switzerland)  2014;14(5):8423-8429.
We obtain an extremely high current sensitivity by wrapping a section of microfiber on a thin-diameter chromium-nickel wire. Our detected current sensitivity is as high as 220.65 nm/A2 for a structure length of only 35 μm. Such sensitivity is two orders of magnitude higher than the counterparts reported in the literature. Analysis shows that a higher resistivity or/and a thinner diameter of the metal wire may produce higher sensitivity. The effects of varying the structure parameters on sensitivity are discussed. The presented structure has potential for low-current sensing or highly electrically-tunable filtering applications.
doi:10.3390/s140508423
PMCID: PMC4063069  PMID: 24824372
microfiber; current sensor; sensitivity; chrome-nickel wire
12.  Genome-Wide Linkage Analysis and Association Study Identifies Loci for Polydactyly in Chickens 
G3: Genes|Genomes|Genetics  2014;4(6):1167-1172.
Polydactyly occurs in some chicken breeds, but the molecular mechanism remains incompletely understood. Combined genome-wide linkage analysis and association study (GWAS) for chicken polydactyly helps identify loci or candidate genes for the trait and potentially provides further mechanistic understanding of this phenotype in chickens and perhaps other species. The linkage analysis and GWAS for polydactyly was conducted using an F2 population derived from Beijing-You chickens and commercial broilers. The results identified two QTLs through linkage analysis and seven single-nucleotide polymorphisms (SNPs) through GWAS, associated with the polydactyly trait. One QTL located at 35 cM on the GGA2 was significant at the 1% genome-wise level and another QTL at the 1% chromosome-wide significance level was detected at 39 cM on GGA19. A total of seven SNPs, four of 5% genome-wide significance (P < 2.98 × 10−6) and three of suggestive significance (5.96 × 10−5) were identified, including two SNPs (GGaluGA132178 and Gga_rs14135036) in the QTL on GGA2. Of the identified SNPs, the eight nearest genes were sonic hedgehog (SHH), limb region 1 homolog (mouse) (LMBR1), dipeptidyl-peptidase 6, transcript variant 3 (DPP6), thyroid-stimulating hormone, beta (TSHB), sal-like 4 (Drosophila) (SALL4), par-6 partitioning defective 6 homolog beta (Caenorhabditis elegans) (PARD6B), coenzyme Q5 (COQ5), and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, etapolypeptide (YWHAH). The GWAS supports earlier reports of the importance of SHH and LMBR1 as regulating genes for polydactyly in chickens and other species, and identified others, most of which have not previously been associated with limb development. The genes and associated SNPs revealed here provide detailed information for further exploring the molecular and developmental mechanisms underlying polydactyly.
doi:10.1534/g3.114.011338
PMCID: PMC4065260  PMID: 24752238
chicken; polydactyly; linkage analysis; GWAS; candidate genes
13.  Investigation of Antimicrobial Resistance in Escherichia coli and Enterococci Isolated from Tibetan Pigs 
PLoS ONE  2014;9(4):e95623.
Objectives
This study investigated the antimicrobial resistance of Escherichia coli and enterococci isolated from free-ranging Tibetan pigs in Tibet, China, and analyzed the influence of free-ranging husbandry on antimicrobial resistance.
Methods
A total of 232 fecal samples were collected from Tibetan pigs, and the disk diffusion method was used to examine their antimicrobial resistance. Broth microdilution and agar dilution methods were used to determine minimum inhibitory concentrations for antimicrobial agents for which disks were not commercially available.
Results
A total of 129 E. coli isolates and 84 Enterococcus isolates were recovered from the fecal samples. All E. coli isolates were susceptible to amoxicillin/clavulanic acid, and 40.4% were resistant to tetracycline. A small number of isolates were resistant to florfenicol (27.9%), ampicillin (27.9%), sulfamethoxazole/trimethoprim (19.4%), nalidixic acid (19.4%), streptomycin (16.2%) and ceftiofur (10.9%), and very low resistance rates to ciprofloxacin (7.8%), gentamicin (6.9%), and spectinomycin (2.3%) were observed in E. coli. All Enterococcus isolates, including E. faecium, E. faecalis, E. hirae, and E. mundtii, were susceptible to amoxicillin/clavulanic acid and vancomycin, but showed high frequencies of resistance to oxacillin (92.8%), clindamycin (82.1%), tetracycline (64.3%), and erythromycin (48.8%). Resistance rates to florfenicol (17.9%), penicillin (6.0%), ciprofloxacin (3.6%), levofloxacin (1.2%), and ampicillin (1.2%) were low. Only one high-level streptomycin resistant E. faecium isolate and one high-level gentamicin resistant E. faecium isolate were observed. Approximately 20% and 70% of E. coli and Enterococcus isolates, respectively, were defined as multidrug-resistant.
Conclusions
In this study, E. coli and Enterococcus isolated from free-ranging Tibetan pigs showed relatively lower resistance rates than those in other areas of China, where more intensive farming practices are used. These results also revealed that free-range husbandry and absence of antibiotic use could decrease the occurrence of antimicrobial resistance to some extent.
doi:10.1371/journal.pone.0095623
PMCID: PMC3991701  PMID: 24748326
14.  Probing circulating tumor cells in microfluidics 
Lab on a chip  2013;13(4):602-609.
Circulating tumor cells (CTCs) are important targets for study as we strive to better understand, diagnose, and treat cancers. However, CTCs are found in blood at extremely low concentrations; this makes isolation, enrichment, and characterization of CTCs technically challenging. Recently, the development of CTC separation devices has grown rapidly in both academia and industry. Part of this development effort centered on microfluidic platforms, exploiting the advantages of microfluidics to improve CTC separation performance and device integration. In this Focus article, we highlight some of the recent work in microfluidic CTC separation and detection systems and discuss our appraisal of what the field should do next.
doi:10.1039/c2lc90148j
PMCID: PMC3990734  PMID: 23306378
15.  TCMSP: a database of systems pharmacology for drug discovery from herbal medicines 
Background
Modern medicine often clashes with traditional medicine such as Chinese herbal medicine because of the little understanding of the underlying mechanisms of action of the herbs. In an effort to promote integration of both sides and to accelerate the drug discovery from herbal medicines, an efficient systems pharmacology platform that represents ideal information convergence of pharmacochemistry, ADME properties, drug-likeness, drug targets, associated diseases and interaction networks, are urgently needed.
Description
The traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) was built based on the framework of systems pharmacology for herbal medicines. It consists of all the 499 Chinese herbs registered in the Chinese pharmacopoeia with 29,384 ingredients, 3,311 targets and 837 associated diseases. Twelve important ADME-related properties like human oral bioavailability, half-life, drug-likeness, Caco-2 permeability, blood-brain barrier and Lipinski’s rule of five are provided for drug screening and evaluation. TCMSP also provides drug targets and diseases of each active compound, which can automatically establish the compound-target and target-disease networks that let users view and analyze the drug action mechanisms. It is designed to fuel the development of herbal medicines and to promote integration of modern medicine and traditional medicine for drug discovery and development.
Conclusions
The particular strengths of TCMSP are the composition of the large number of herbal entries, and the ability to identify drug-target networks and drug-disease networks, which will help revealing the mechanisms of action of Chinese herbs, uncovering the nature of TCM theory and developing new herb-oriented drugs. TCMSP is freely available at http://sm.nwsuaf.edu.cn/lsp/tcmsp.php.
doi:10.1186/1758-2946-6-13
PMCID: PMC4001360  PMID: 24735618
TCM; Systems pharmacology; Drug discovery; ADME
16.  TCMSP: a database of systems pharmacology for drug discovery from herbal medicines 
Background
Modern medicine often clashes with traditional medicine such as Chinese herbal medicine because of the little understanding of the underlying mechanisms of action of the herbs. In an effort to promote integration of both sides and to accelerate the drug discovery from herbal medicines, an efficient systems pharmacology platform that represents ideal information convergence of pharmacochemistry, ADME properties, drug-likeness, drug targets, associated diseases and interaction networks, are urgently needed.
Description
The traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) was built based on the framework of systems pharmacology for herbal medicines. It consists of all the 499 Chinese herbs registered in the Chinese pharmacopoeia with 29,384 ingredients, 3,311 targets and 837 associated diseases. Twelve important ADME-related properties like human oral bioavailability, half-life, drug-likeness, Caco-2 permeability, blood-brain barrier and Lipinski’s rule of five are provided for drug screening and evaluation. TCMSP also provides drug targets and diseases of each active compound, which can automatically establish the compound-target and target-disease networks that let users view and analyze the drug action mechanisms. It is designed to fuel the development of herbal medicines and to promote integration of modern medicine and traditional medicine for drug discovery and development.
Conclusions
The particular strengths of TCMSP are the composition of the large number of herbal entries, and the ability to identify drug-target networks and drug-disease networks, which will help revealing the mechanisms of action of Chinese herbs, uncovering the nature of TCM theory and developing new herb-oriented drugs. TCMSP is freely available at http://sm.nwsuaf.edu.cn/lsp/tcmsp.php.
doi:10.1186/1758-2946-6-13
PMCID: PMC4001360  PMID: 24735618
TCM; Systems pharmacology; Drug discovery; ADME
17.  High expression of NEDD9 predicts adverse outcomes of colorectal cancer patients 
NEDD9, a member of Crk-associated substrate (CAS) family, is highly expressed in multiple cancer types and involved cancer cell adhesion, migration, invasion. The prognostic value of NEDD9 has not been evaluated before. The aim of this study was to evaluate the association between NEDD9 expression and survival in colorectal cancer (CRC) patients. NEDD9 expression was analyzed by immunohistochemistry in 92 patients with CRC. Patients were followed-up annually by telephone or at outpatient clinic. The results revealed that high expression of NEDD9 in 68/92 CRC samples, compared with 12/92 normal tissues (P<0.01). Correlation analysis showed high level of expression of NEDD9 was significantly correlated with advanced TNM stage (P=0.014), pT grade (P=0.009), pN (P=0.013) and pM status (P=0.047). Patients with a higher NEDD9 expression had a significantly shorter overall survival (OS) (P<0.01). The multivariate analysis revealed that NEDD9 expression could serve as an independent predictive factor of OS. Our finding demonstrated the potential value of NEDD9 expression level as a prognostic molecular marker and a target for new therapies for CRC patients.
PMCID: PMC4069898  PMID: 24966970
NEDD9; colorectal cancer; immunohistochemistry; EMT; prognosis
18.  Abnormal promoter methylation of multiple tumor suppressor genes in human bronchial epithelial malignant cells 
Biomedical Reports  2014;2(4):525-528.
Carcinoma of the lung is the leading cause of cancer-related mortality worldwide. In order to understand the pathogenesis of radiation-induced lung cancer, we adopted a model of transformed human bronchial epithelial cells (BEP2D) induced by α-particles. Methylation-specific polymerase chain reaction was performed to detect aberrant promoter methylation of multiple tumor suppressor genes, including p14ARF, p16INK4a, O6-methylguanine-DNA methyltransferase, glutathione S-transferase P1 and death-associated protein kinase genes in the BEP2D cell line and its malignant transformant, the BERP35T1 cell line. Our results demonstrated the distinctive methylation pattern for these tumor suppressor genes in radiation-induced malignant cells, as compared to their wild-type counterparts. Our study revealed epigenetic signatures for the characterization of radiation-mediated carcinogenesis and it may facilitate early diagnosis of patients at high risk for lung cancer.
doi:10.3892/br.2014.268
PMCID: PMC4051483  PMID: 24944801
lung cancer; carcinogenesis; DNA methylation; tumor suppressor genes
19.  Primary Prevention of Macroangiopathy in Patients With Short-Duration Type 2 Diabetes by Intensified Multifactorial Intervention 
Diabetes Care  2013;36(4):978-984.
OBJECTIVE
To explore whether intensified, multifactorial intervention could prevent macrovascular disease in patients with recently diagnosed type 2 diabetes.
RESEARCH DESIGN AND METHODS
A total of 150 type 2 diabetic patients, with disease duration of <1 year and without clinical arteriosclerotic disease or subclinical atherosclerotic signs confirmed by ultrasonographic scanning of three conducting arteries, were randomized into an intensive intervention group and a conventional intervention group. They then received intensive, multifactorial intervention or conventional intervention over 7 years of follow-up. The patients’ common carotid intima-media thicknesses (CC-IMTs) were measured every year. The primary outcome was the time to the first occurrence of CC-IMTs ≥1.0 mm and/or development of atherosclerosis plaques in the carotid artery. The secondary outcome was clinical evidence of cardiovascular disease.
RESULTS
A total of 70 patients in the intensive group and 68 patients in the conventional group completed the 7-year follow-up. Subclinical macrovascular (primary) outcomes occurred in seven cases in the intensive group and 22 cases in the conventional group for a cumulative prevalence of 10.00 and 32.35%, respectively (P < 0.05). No significant differences between the two groups were observed regarding the secondary outcome.
CONCLUSIONS
Primary prevention of macrovascular diseases can be achieved through intensified, multifactorial intervention in patients with short-duration type 2 diabetes. Type 2 diabetic patients should undergo intensive multifactorial interventions with individual targets for the prevention of macrovascular diseases.
doi:10.2337/dc12-0227
PMCID: PMC3609518  PMID: 23230099
20.  Anterior capsulotomy improves persistent developmental stuttering with a psychiatric disorder: a case report and literature review 
Stuttering is characterized by disrupted fluency of verbal expression, and occurs mostly in children. Persistent developmental stuttering (PDS) may occur in adults. Reports of the surgical management of PDS are limited. Here we present the case of a 28-year-old man who had had PDS since the age of 7 years, was diagnosed with depression and anxiety disorder at the age of 24 years, and had physical concomitants. He underwent a bilateral anterior capsulotomy 4 years after the diagnosis. Over one year of follow-up, his physical concomitants resolved, and significant improvements in his psychiatric disorders and PDS were observed. To the best of our knowledge, this is the first report of simultaneous improvement in a patient’s PDS and psychiatric disorder after a bilateral anterior capsulotomy.
doi:10.2147/NDT.S58984
PMCID: PMC3979796  PMID: 24729709
persistent developmental stuttering; psychiatric disorders; anterior capsulotomy
21.  The Cytokines IL-21 and GM-CSF have Opposing Regulatory Roles in the Apoptosis of Conventional Dendritic Cells 
Immunity  2013;38(3):514-527.
Interleukin-21 (IL-21) has broad actions on T- and B-cells, but its actions in innate immunity are poorly understood. Here we show that IL-21 induced apoptosis of conventional dendritic cells (cDCs) via STAT3 and Bim, and this was inhibited by granulocyte-macrophage colony-stimulating factor (GM-CSF). ChIP-Seq analysis revealed genome-wide binding competition between GM-CSF-induced STAT5 and IL-21-induced STAT3. Expression of IL-21 in vivo decreased cDC numbers, and this was prevented by GM-CSF. Moreover, repetitive α-galactosylceramide injection of mice induced IL-21 but decreased GM-CSF production by natural killer T (NKT) cells, correlating with decreased cDC numbers. Furthermore, adoptive-transfer of wild-type CD4+ T cells caused more severe colitis with increased DCs and interferon (IFN)-γ producing CD4+ T cells in Il21r−/−Rag2−/− mice (which lack T cells and have IL-21-unresponsive DCs) than in Rag2−/− mice. Thus, IL-21 and GM-CSF exhibit cross-regulatory actions on gene regulation and apoptosis, regulating cDC numbers and thereby the magnitude of the immune response.
doi:10.1016/j.immuni.2013.02.011
PMCID: PMC3705920  PMID: 23453633
IL-21; GM-CSF; apoptosis; dendritic cells
22.  VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions 
Copy number variations (CNVs) constitute a major source of genetic variations in human populations and have been reported to be associated with complex diseases. Methods have been developed for detecting CNVs and testing CNV associations in genome-wide association studies (GWAS) based on SNP arrays. Commonly used two-step testing procedures work well only for long CNVs while direct CNV association testing methods work only for recurrent CNVs. Assuming that short CNVs disrupting any part of a given genomic region increase disease risk, we developed a variable threshold exact test (VTET) for testing disease associations of CNVs randomly distributed in the genome using intensity data from SNP arrays. By extensive simulations, we found that VTET outperformed two-step testing procedures based on existing CNV calling algorithms for short CNVs and that the performance of VTET was robust to the length of the genomic region. In addition, VTET had a comparable performance with CNVtools for testing the association of recurrent CNVs. Thus, we expect VTET to be useful for testing disease associations of both recurrent and randomly distributed CNVs using existing GWAS data. We applied VTET to a lung cancer GWAS and identified a genome-wide significant region on chromosome 18q22.3 for lung squamous cell carcinoma.
doi:10.3389/fgene.2014.00053
PMCID: PMC3957064  PMID: 24672538
copy number varination; variable threshold exact test; genome-wide association study; interval-based association test; lung cancer CNV analysis
23.  Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History 
Molecular Biology and Evolution  2014;31(6):1475-1489.
Macaques are the most widely distributed nonhuman primates and used as animal models in biomedical research. The availability of full-genome sequences from them would be essential to both biomedical and primate evolutionary studies. Previous studies have reported whole-genome sequences from rhesus macaque (Macaca mulatta) and cynomolgus macaque (M. fascicularis, CE), both of which belong to the fascicularis group. Here, we present a 37-fold coverage genome sequence of the Tibetan macaque (M. thibetana; TM). TM is an endemic species to China belonging to the sinica group. On the basis of mapping to the rhesus macaque genome, we identified approximately 11.9 million single-nucleotide variants), of which 3.9 million were TM specific, as assessed by comparison two Chinese rhesus macaques (CR) and two CE genomes. Some genes carried TM-specific homozygous nonsynonymous variants (TSHNVs), which were scored as deleterious in human by both PolyPhen-2 and SIFT (Sorting Tolerant From Intolerant) and were enriched in the eye disease genes. In total, 273 immune response and disease-related genes carried at least one TSHNV. The heterozygosity rates of two CRs (0.002617 and 0.002612) and two CEs (0.003004 and 0.003179) were approximately three times higher than that of TM (0.000898). Polymerase chain reaction resequencing of 18 TM individuals showed that 29 TSHNVs exhibited high allele frequencies, thus confirming their low heterozygosity. Genome-wide genetic divergence analysis demonstrated that TM was more closely related to CR than to CE. We further detected unusual low divergence regions between TM and CR. In addition, after applying statistical criteria to detect putative introgression regions (PIRs) in the TM genome, up to 239,620 kb PIRs (8.84% of the genome) were identified. Given that TM and CR have overlapping geographical distributions, had the same refuge during the Middle Pleistocene, and show similar mating behaviors, it is highly likely that there was an ancient introgression event between them. Moreover, demographic inferences revealed that TM exhibited a similar demographic history as other macaques until 0.5 Ma, but then it maintained a lower effective population size until present time. Our study has provided new insight into the macaque evolutionary history, confirming hybridization events between macaque species groups based on genome-wide data.
doi:10.1093/molbev/msu104
PMCID: PMC4032132  PMID: 24648498
Tibetan macaque; whole-genome sequencing; SNVs; genetic divergence; introgression; demographic trajectories
24.  Different Biosynthesis Patterns among Flavonoid 3-glycosides with Distinct Effects on Accumulation of Other Flavonoid Metabolites in Pears (Pyrus bretschneideri Rehd.) 
PLoS ONE  2014;9(3):e91945.
Flavonoid biosynthesis profile was clarified by fruit bagging and re-exposure treatments in the green Chinese pear ‘Zaosu’ (Pyrus bretschneideri Rehd.) and its red mutant ‘Red Zaosu’. Two distinct biosynthesis patterns of flavonoid 3-glycosides were found in ‘Zaosu’ pear. By comparison with ‘Red Zaosu’, the biosynthesis of flavonoid 3-galactosides and flavonoid 3-arabinosides were inhibited by bagging and these compounds only re-accumulated to a small degree in the fruit peel of ‘Zaosu’ after the bags were removed. In contrast, the biosynthesis of flavonoid 3-gluctosides and flavonoid 3-rutinosides was reduced by bagging and then increased when the fruits were re-exposed to sunlight. A combination of correlation, multicollinearity test and partial-correlation analyses among major flavonoid metabolites indicated that biosynthesis of each phenolic compound was independent in ‘Zaosu’ pear, except for the positive correlation between flavonoid 3-rutincosides and flavanols. In contrast with the green pear cultivar, almost all phenolic compounds in the red mutant had similar biosynthesis patterns except for arbutin. However, only the biosynthesis of flavonoid 3-galactosides was relatively independent and strongly affected the synthesis of the other phenolic compounds. Therefore, we propose a hypothesis that the strong accumulation of flavonoid 3-galactosides stimulated the biosynthesis of other flavonoid compounds in the red mutant and, therefore, caused systemic variation of flavonoid biosynthesis profiles between ‘Zaosu’ and its red mutant. This hypothesis had been further demonstrated by the enzyme activity of UFGT, and transcript levels of flavonoid biosynthetic genes and been well tested by a stepwise linear regression forecasting model. The gene that encodes flavonoid 3-galacosyltransferase was also identified and isolated from the pear genome.
doi:10.1371/journal.pone.0091945
PMCID: PMC3956819  PMID: 24637788
25.  Effects of different types of hydroxyethyl starch (HES) on microcirculation perfusion and tissue oxygenation in patients undergoing liver surgery 
To compare the effects of hydroxyethyl starch (HES) 130/0.4 and HES 200/0.5, which have different molecular weights and degrees of substitution, on microcirculation perfusion and tissue oxygenation in patients undergoing liver surgery. Thirty patients with an American Society of Anesthesiologists status I/II who were scheduled for liver surgery were randomly divided into two groups: one received an intraoperative HES 130/0.4 infusion equal to the amount of blood loss (HES 130/0.4 group, n=15), and the other received HES 200/0.5 equal to the amount of blood loss (HES 200/0.5 group, n=15). Gastric mucosal perfusion and tissue oxygenation were monitored by measuring the gastric mucosal pH (pHi), which was determined using a carbon dioxide tonometer inserted through a nasogastric tube. Gastric mucosal pHi , hemodynamic parameters, body temperature, and blood gas parameters were recorded upon entering the operating room, before skin incision, one hour and two hours after skin incision, and at the end of surgery. The intraoperative pHi decreased in both groups of patients, but the decline in the HES 130/0.4 group was smaller than that of the HES 200/0.5 group. The pHi of the HES 130/0.4 group was significantly higher than that of the HES 200/0.5 group two hours after skin incision and at the end of surgery (P<0.05). A multivariate analysis showed that the type of colloid used intraoperatively was the only variant that affected pHi (F=0.626, P<0.05). Moreover, there were good correlation between pHi at the end of surgery and the length of postoperative hospital stay (r=-0.536, P<0.05) and the time intervals from surgery to the passage of flatus (r=-0.547, P<0.05). Compared with HES 200/0.5, the use of HES 130/0.4 (with a relatively lower molecular weight and lower degree of substitution) could significantly improve internal organ perfusion and tissue oxygenation in patients undergoing liver surgery with a relatively large amount of blood loss.
PMCID: PMC3992402  PMID: 24753757
Hydroxyethyl starch; gastric mucosa; internal organs; blood loss; surgery

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