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1.  IL-1β mediates MCP-1 induction by Wnt5a in gastric cancer cells 
BMC Cancer  2014;14:480.
Both Wnt5a overexpression and macrophage infiltration have been implicated in inflammation and cancer. The aim of this study is to reveal the involvement of Wnt5a in macrophage recruitment in gastric cancer.
mRNA expression in gastric cancer tissues and cells was investigated by real-time PCR. Protein secretion by gastric cancer cells was determined by ELISA. PcDNA3.1-Wnt5a expression vector and Wnt5a siRNA vector were used to overexpress and silence Wnt5a expression in gastric cells, respectively. Macrophage migration was analyzed by transwell, and macrophage cytoskeleton was stained with FITC-phalloidin.
Wnt5a was overexpressed in gastric cancer tissues, and correlated with monocyte chemotactic protein 1 (MCP-1) and interleukin 1β (IL-1β), respectively. In gastric cancer cells, Wnt5a induced MCP-1 expression, which was mediated by IL-1β. Conditioned medium from gastric cancer cells transfected with Wnt5a stimulated macrophage chemotaxis and cytoskeletal changes via MCP-1, which were suppressed by recombinant IL-1 receptor antagonist (rIL-1Ra).
These results suggest that Wnt5a is involved in macrophage recruitment by upregulating MCP-1, and IL-1Ra may be used to inhibit macrophage recruitment in gastric cancer.
PMCID: PMC4086280  PMID: 24993819
2.  Hyperoside, a Flavonoid Compound, Inhibits Proliferation and Stimulates Osteogenic Differentiation of Human Osteosarcoma Cells 
PLoS ONE  2014;9(7):e98973.
Osteosarcoma, one of the most common malignant bone tumours, is generally considered a differentiation disease caused by genetic and epigenetic disruptions in the terminal differentiation of osteoblasts. Novel therapies based on the non-cytotoxic induction of cell differentiation-responsive pathways could represent a significant advance in treating osteosarcoma; however, effective pharmaceuticals to induce differentiation are lacking. In the present study, we investigated the effect of hyperoside, a flavonoid compound, on the osteoblastic differentiation of U2OS and MG63 osteosarcoma cells in vitro. Our results demonstrated that hyperoside inhibits the proliferation of osteosarcoma cells by inducing G0/G1 arrest in the cell cycle, without causing obvious cell death. Cell migration assay further suggested that hyperoside could inhibit the invasion potential of osteosarcoma cells. Additionally, osteopontin and runt-related transcription factor 2 protein levels and osteocalcin activation were upregulated dramatically in hyperoside-treated osteosarcoma cells, suggesting that hyperoside may stimulates osteoblastic differentiation in osteosarcoma cells. This differentiation was accompanied by the activation of transforming growth factor (TGF)-β and bone morphogenetic protein-2, suggesting that the hyperoside-induced differentiation involves the TGF-β signalling pathway. To our knowledge, this study is the first to evaluate the differentiation effect of hyperoside in osteosarcoma cells and assess the possible potential for hyperoside treatment as a future therapeutic approach for osteosarcoma differentiation therapy.
PMCID: PMC4077650  PMID: 24983940
3.  Nrf2 Signaling Contributes to the Neuroprotective Effects of Urate against 6-OHDA Toxicity 
PLoS ONE  2014;9(6):e100286.
Mounting evidence shows that urate may become a biomarker of Parkinson's disease (PD) diagnosis and prognosis and a neuroprotectant candidate for PD therapy. However, the cellular and molecular mechanisms underlying its neuroprotective actions remain poorly understood.
In this study, we showed that urate pretreatment protected dopaminergic cell line (SH-SY5Y and MES23.5) against 6-hydroxydopamine (6-OHDA)- and hydrogen peroxide- induced cell damage. Urate was found to be accumulated into SH-SY5Y cells after 30 min treatment. Moreover, urate induced NF-E2-related factor 2 (Nrf2) accumulation by inhibiting its ubiquitinationa and degradation, and also promoted its nuclear translocation; however, it did not modulate Nrf2 mRNA level or Kelch-like ECH-associated protein 1 (Keap1) expression. In addition, urate markedly up-regulated the transcription and protein expression of γ-glutamate-cysteine ligase catalytic subunit (γ-GCLC) and heme oxygenase-1 (HO-1), both of which are controlled by Nrf2 activity. Furthermore, Nrf2 knockdown by siRNA abolished the intracellular glutathione augmentation and the protection exerted by urate pretreatment.
Our findings demonstrated that urate treatment may result in Nrf2-targeted anti-oxidant genes transcription and expression by reducing Nrf2 ubiquitination and degradation and promoting its nuclear translocation, and thus offer neuroprotection on dopaminergic cells against oxidative stresses.
PMCID: PMC4069024  PMID: 24959672
4.  Cry1 and Tef gene polymorphisms are associated with Major Depressive Disorder in the Chinese population 
Journal of affective disorders  2013;157:100-103.
Accumulating evidences indicate that circadian abnormalities lead to sleep disorder, neurodegenerative diseases and depression. We have reported that the polymorphisms of a clock-related gene, Tef, contributed to the risk of sleep disturbances and depression in Parkinson disease. The objective of the present study was to examine whether the three clock genes we previous studied are associated with major depressive disorder (MDD) in the Chinese population.
105 subjects with MDD and 485 control subjects participated in this case-control study. Demographics, Mini-mental Status Examination (MMSE), and Hamilton rating scale for depression (HAMD) were obtained in all subjects. Genotypes of SNPs (single nucleotide polymorphism) of Cry1 rs2287161, Cry2 rs10838524 and Tef rs738499 was screened by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).
MDD cases had a significantly higher frequency carrying the C allele and CC genotype in Cry1 rs2287161 and the T allele and TT genotype in Tef rs738499 than controls.
The sample size of MDD group was relatively small.
The polymorphisms of Cry1 rs2287161 and Tef rs738499 are associated to MDD.
PMCID: PMC4058073  PMID: 24581835
Major Depressive Disorder; Circadian rhythm; Clock genes; Cry1; Tef
6.  Automatic Lung Tumor Segmentation on PET/CT Images Using Fuzzy Markov Random Field Model 
The combination of positron emission tomography (PET) and CT images provides complementary functional and anatomical information of human tissues and it has been used for better tumor volume definition of lung cancer. This paper proposed a robust method for automatic lung tumor segmentation on PET/CT images. The new method is based on fuzzy Markov random field (MRF) model. The combination of PET and CT image information is achieved by using a proper joint posterior probability distribution of observed features in the fuzzy MRF model which performs better than the commonly used Gaussian joint distribution. In this study, the PET and CT simulation images of 7 non-small cell lung cancer (NSCLC) patients were used to evaluate the proposed method. Tumor segmentations with the proposed method and manual method by an experienced radiation oncologist on the fused images were performed, respectively. Segmentation results obtained with the two methods were similar and Dice's similarity coefficient (DSC) was 0.85 ± 0.013. It has been shown that effective and automatic segmentations can be achieved with this method for lung tumors which locate near other organs with similar intensities in PET and CT images, such as when the tumors extend into chest wall or mediastinum.
PMCID: PMC4058834  PMID: 24987451
7.  Identification of Influenza A/H7N9 Virus Infection-Related Human Genes Based on Shortest Paths in a Virus-Human Protein Interaction Network 
BioMed Research International  2014;2014:239462.
The recently emerging Influenza A/H7N9 virus is reported to be able to infect humans and cause mortality. However, viral and host factors associated with the infection are poorly understood. It is suggested by the “guilt by association” rule that interacting proteins share the same or similar functions and hence may be involved in the same pathway. In this study, we developed a computational method to identify Influenza A/H7N9 virus infection-related human genes based on this rule from the shortest paths in a virus-human protein interaction network. Finally, we screened out the most significant 20 human genes, which could be the potential infection related genes, providing guidelines for further experimental validation. Analysis of the 20 genes showed that they were enriched in protein binding, saccharide or polysaccharide metabolism related pathways and oxidative phosphorylation pathways. We also compared the results with those from human rhinovirus (HRV) and respiratory syncytial virus (RSV) by the same method. It was indicated that saccharide or polysaccharide metabolism related pathways might be especially associated with the H7N9 infection. These results could shed some light on the understanding of the virus infection mechanism, providing basis for future experimental biology studies and for the development of effective strategies for H7N9 clinical therapies.
PMCID: PMC4052153  PMID: 24955349
8.  Dysfunction of Affective Network in Post Ischemic Stroke Depression: A Resting-State Functional Magnetic Resonance Imaging Study 
BioMed Research International  2014;2014:846830.
Objective. Previous studies have demonstrated that stroke characteristics and social and psychological factors jointly contribute to the development of poststroke depression (PSD). The purpose of this study was to identify altered functional connectivity (FC) of the affective network (AN) in patients with PSD and to explore the correlation between FC and the severity of PSD. Materials and Methods. 26 PSD patients, 24 stroke patients without depression, and 24 age-matched normal controls underwent the resting-state functional MRI (fMRI) scanning. The bilateral anterior cingulated cortices (ACCs) were selected as regions of interest (ROIs). FC was calculated and compared among the three groups. The association between FC and Hamilton Depression Rate Scale (HDRS) scores of PSD group was investigated. Results. The FC of the AN was disrupted in PSD patients compared to stroke patients without depression and normal controls. Moreover, the left orbital part of inferior frontal gyrus which indicated altered FC was significantly correlated with HDRS scores in PSD patients. Conclusions. Dysfunction of the affective network may be one of the reasons of the development of PSD.
PMCID: PMC4053214  PMID: 24963485
9.  Limitations of real-world treatment with atorvastatin monotherapy for lowering LDL-C in high-risk cardiovascular patients in the US 
Guidelines endorse statin therapy for lowering low-density lipoprotein cholesterol (LDL-C) to recommended levels, in patients with cardiovascular disease (CVD) risk, if needed, after lifestyle changes. Atorvastatin is a common statin with greater LDL-C lowering efficacy than most other statins; its availability in generic form will likely increase its use. This study assessed attainment of guideline-recommended LDL-C levels in high-risk CVD patients treated with atorvastatin monotherapy.
Analyses of two retrospective US cohorts of patients who received a prescription for atorvastatin monotherapy between January 1, 2008 and December 31, 2010 (index date defined as first prescription date) in the GE Centricity Electronic Medical Record (EMR) (N=10,693) and Humana Medicare (N=16,798) databases. Eligible patients were ≥18 years, diagnosed with coronary heart disease or atherosclerotic vascular disease, with ≥1 LDL-C measurement between 3 months and 1 year postindex date, and continuously enrolled for 1 year prior to and following the index date.
Of the eligible patients, 21.8%, 29.6%, 29.9%, and 18.7% (GE Centricity EMR) and 25.4%, 32.9%, 27.8%, and 14.0% (Humana Medicare) received 10, 20, 40, and 80 mg doses of atorvastatin, respectively. The mean ± standard deviation (SD) follow-up LDL-C levels were 2.1±0.8 mmol/L (83±30 mg/dL) and 2.3±0.8 mmol/L (88±31 mg/dL) for the GE Centricity EMR and Humana Medicare cohorts, respectively. Regardless of dose, only 28.3%–34.8% of patients had LDL-C levels <1.8 mmol/L (<70 mg/dL), and 72.0%–78.0% achieved LDL-C <2.6 mmol/L (<100 mg/dL) in both cohorts. As many as 41% and 13% of patients had LDL-C levels ≥0.5 mmol/L (≥20 mg/dL) above LDL-C 1.8 mmol/L (70 mg/dL) and 2.6 mmol/L (100 mg/dL), respectively, in both cohorts; these percentages were generally similar across atorvastatin doses.
In this real-world US setting, a large number of high-risk CVD patients did not attain guideline-recommended LDL-C levels with atorvastatin monotherapy. More than 65% of the patients had LDL-C levels >1.8 mmol/L (>70 mg/dL), and of these, 30%–40% had LDL-C levels ≥0.5 mmol/L (≥20 mg/dL) above this, regardless of dose. This suggests that more effective lipid-lowering strategies, such as statin uptitration, switching to a higher efficacy statin, and/or combination therapy, may be required to achieve optimal LDL-C lowering in high-risk patients.
PMCID: PMC4008284  PMID: 24851051
statin therapy; managed-care; lipid-lowering therapy
10.  Identification of Novel and Conserved MicroRNAs Related to Drought Stress in Potato by Deep Sequencing 
PLoS ONE  2014;9(4):e95489.
MicroRNAs (miRNAs) are a group of small, non-coding RNAs that play important roles in plant growth, development and stress response. There have been an increasing number of investigations aimed at discovering miRNAs and analyzing their functions in model plants (such as Arabidopsis thaliana and rice). In this research, we constructed small RNA libraries from both polyethylene glycol (PEG 6,000) treated and control potato samples, and a large number of known and novel miRNAs were identified. Differential expression analysis showed that 100 of the known miRNAs were down-regulated and 99 were up-regulated as a result of PEG stress, while 119 of the novel miRNAs were up-regulated and 151 were down-regulated. Based on target prediction, annotation and expression analysis of the miRNAs and their putative target genes, 4 miRNAs were identified as regulating drought-related genes (miR811, miR814, miR835, miR4398). Their target genes were MYB transcription factor (CV431094), hydroxyproline-rich glycoprotein (TC225721), quaporin (TC223412) and WRKY transcription factor (TC199112), respectively. Relative expression trends of those miRNAs were the same as that predicted by Solexa sequencing and they showed a negative correlation with the expression of the target genes. The results provide molecular evidence for the possible involvement of miRNAs in the process of drought response and/or tolerance in the potato plant.
PMCID: PMC3991665  PMID: 24748226
11.  In vitro catabolism of quercetin by human fecal bacteria and the antioxidant capacity of its catabolites 
Food & Nutrition Research  2014;58:10.3402/fnr.v58.23406.
Part of quercetin flows into the colon after escaping the absorption of the small intestine and will be degraded by colonic microbiota. The catabolites in the colon partially determine the physiological activity of quercetin.
Seven gut bacteria isolated from human feces were utilized to in vitro ferment quercetin. Their catabolites were analyzed with high-performance liquid chromatography and mass spectrometry, and the antioxidant activities of their fermented broths were compared with that of quercetin.
One metabolite, 3,4-dihydroxyphenylacetic acid, was produced by both C. perfringens and B. fragilis transforming quercetin. No other metabolites were detected in the other fermented broths. The antioxidant activities of all strains fermenting quercetin reached the highest values at the concentration of 1 mg/mL quercetin in broth; the fermented products of C. perfringens and B. fragilis presented stronger activities than those of other strains at most concentrations of quercetin in broth. Additionally, all of the fermented broths presented a decline of the antioxidant activities compared to quercetin. Therefore, the antioxidant activity of quercetin will be lost when it reaches the human colon because of the gut bacterial fermentation.
This is the first study to report that quercetin can be degraded by C. perfringens and B. fragilis and transformed to the same metabolite, 3,4-dihydroxyphenylacetic acid, and that antioxidant activities decline when quercetin is fermented by seven gut bacteria.
PMCID: PMC3991839  PMID: 24765061
quercetin; gut bacteria; catabolites; antioxidant activity
12.  Endocardial focal activation originating from Purkinje fibers plays a role in the maintenance of long duration ventricular fibrillation 
Croatian Medical Journal  2014;55(2):121-127.
To determine the role of repetitive endocardial focal activations and Purkinje fibers in the maintenance of long duration ventricular fibrillation (LDVF, VF>1 minute) in canine hearts in vivo.
The study was conducted in electrophysiological laboratory of Shanghai Ruijin hospital from July 2010 to August 2012. A 64-electrode basket was introduced through a carotid artery into the left ventricle (LV) of 11 beagle dogs for global endocardial electrical mapping. In the Lugol’s solution group (n = 5), the subendocardium was ablated by washing with Lugol’s solution. In the control group, (n = 6) saline was used for ablation. Before and after saline or Lugol ablation, we determined QRS duration and QT/QTc interval in sinus rhythm (SR). We also measured the activation rates in the first 2 seconds of each minute during 7 minutes of VF for each group. If VF terminated spontaneously in less than 7 minutes, the VF segments used in activation rate analysis were reduced accordingly.
At the beginning of VF there was no difference between the groups in the activation rate. However, after 1 minute of LDVF the Lugol’s solution group had significantly slower activation rate than the control group. In the control group, all episodes of LDVF (6/6) were successfully sustained for 7 minutes, while in the Lugol’s solution group 4/5 episodes of LDVF spontaneously terminated before 7 minutes (4.8 ± 1.4 minutes) (P = 0.015). In the control group, at 5.1 ± 1.3 minutes of LDVF, a successive, highly organized focal LV endocardial activation pattern was observed. During this period, activations partly arose in PF and spread to the working ventricular myocardium. Mapping analysis showed that these events were consistent with repetitive endocardial focal activations. No evidence of similar focal activations was observed in the Lugol’s solution group.
Repetitive endocardial focal activations in the LV endocardium may be associated with activation of subendocardial PFs. This mechanism may play an important role in the maintenance of LDVF.
PMCID: PMC4009712  PMID: 24778098
13.  Prediction of Multi-Type Membrane Proteins in Human by an Integrated Approach 
PLoS ONE  2014;9(3):e93553.
Membrane proteins were found to be involved in various cellular processes performing various important functions, which are mainly associated to their types. However, it is very time-consuming and expensive for traditional biophysical methods to identify membrane protein types. Although some computational tools predicting membrane protein types have been developed, most of them can only recognize one kind of type. Therefore, they are not as effective as one membrane protein can have several types at the same time. To our knowledge, few methods handling multiple types of membrane proteins were reported. In this study, we proposed an integrated approach to predict multiple types of membrane proteins by employing sequence homology and protein-protein interaction network. As a result, the prediction accuracies reached 87.65%, 81.39% and 70.79%, respectively, by the leave-one-out test on three datasets. It outperformed the nearest neighbor algorithm adopting pseudo amino acid composition. The method is anticipated to be an alternative tool for identifying membrane protein types. New metrics for evaluating performances of methods dealing with multi-label problems were also presented. The program of the method is available upon request.
PMCID: PMC3968155  PMID: 24676214
14.  Interaction of sleep quality and sleep duration on impaired fasting glucose: a population-based cross-sectional survey in China 
BMJ Open  2014;4(3):e004436.
To explore the interactions of sleep quality and sleep duration and their effects on impaired fasting glucose (IFG) in Chinese adults.
Cross-sectional survey.
Community-based investigation in Xuzhou, China.
15 145 Chinese men and women aged 18–75 years old who fulfilled the inclusion criteria.
Primary and secondary outcome measures
The Pittsburgh Sleep Quality Index was used to produce sleep quality categories of good, common and poor. Fasting blood glucose levels were assessed for IFG. Sleep duration was measured by average hours of sleep per night, with categories of <6, 6–8 and >8 h. The products of sleep and family history of diabetes, obesity and age were added to the logistic regression model to evaluate the addictive interaction and relative excess risk of interaction (RERI) on IFG. The attributable proportion (AP) of the interaction and the synergy index (S) were applied to evaluate the additive interaction of two factors. Bootstrap measures were used to calculate 95% CI of RERI, AP and S.
The prevalence of IFG was greatest in those with poor sleep quality and short sleep duration (OR 6.37, 95% CI 4.66 to 8.67; p<0.001) compared with those who had good sleep quality and 6–8 h sleep duration, after adjusting for confounders. After adjusting for potential confounders RERI, AP and S values (and their 95% CI) were 1.69 (0.31 to 3.76), 0.42 (0.15 to 0.61) and 2.85 (2.14 to 3.92), respectively, for the interaction between poor sleep quality and short sleep duration, and 0.78 (0.12 to 1.43), 0.61 (0.26 to 0.87) and −65 (−0.94 to −0.27) for the interaction between good sleep quality and long sleep duration.
The results suggest that there are additive interactions between poor sleep quality and short sleep duration.
PMCID: PMC3963090  PMID: 24625639
Diabetes & Endocrinology; Epidemiology
15.  Isolation and Identification of Quercetin Degrading Bacteria from Human Fecal Microbes 
PLoS ONE  2014;9(3):e90531.
Quercetin has a wide range of biological properties. The gut microflora can often modulate its biological activity and their potential health effects. There still is a lack of information about gut bacteria involving in this process. The strains of gut microbes from human feces that can transform quercetin were isolated and identified by in vitro fermentation. The results showed that Escherichia coli, Stretococcus lutetiensis, Lactobacillus acidophilus, Weissella confusa, Enterococcus gilvus, Clostridium perfringens and Bacteroides fragilis have the various ability of degrading quercetin. Among them, C. perfringens and B. fragilis were discovered to have the strongest ability of degrading quercetin. Additionally, quercetin can't inhibit the growth of C. perfringens. In conclusion, many species of gut microbiota can degrade quercetin, but their ability are different.
PMCID: PMC3942438  PMID: 24594786
16.  DLC1-dependent parathyroid hormone–like hormone inhibition suppresses breast cancer bone metastasis 
The Journal of Clinical Investigation  2014;124(4):1646-1659.
Bone metastasis is a frequent complication of breast cancer that is often accelerated by TGF-β signaling; however, little is known about how the TGF-β pathway is regulated during bone metastasis. Here we report that deleted in liver cancer 1 (DLC1) is an important regulator of TGF-β responses and osteolytic metastasis of breast cancer cells. In murine models, breast cancer cells lacking DLC1 expression exhibited enhanced capabilities of bone metastasis. Knockdown of DLC1 in cancer cells promoted bone metastasis, leading to manifested osteolysis and accelerated death in mice, while DLC1 overexpression suppressed bone metastasis. Activation of Rho-ROCK signaling in the absence of DLC1 mediated SMAD3 linker region phosphorylation and TGF-β–induced expression of parathyroid hormone–like hormone (PTHLH), leading to osteoclast maturation for osteolytic colonization. Furthermore, pharmacological inhibition of Rho-ROCK effectively reduced PTHLH production and breast cancer bone metastasis in vitro and in vivo. Evaluation of clinical breast tumor samples revealed that reduced DLC1 expression was linked to elevated PTHLH expression and organ-specific metastasis to bone. Overall, our findings define a stroma-dependent paradigm of Rho signaling in cancer and implicate Rho–TGF-β crosstalk in osteolytic bone metastasis.
PMCID: PMC3973085  PMID: 24590291
17.  Primary tumor regression speed after radiotherapy and its prognostic significance in nasopharyngeal carcinoma: a retrospective study 
BMC Cancer  2014;14:136.
To observe the primary tumor (PT) regression speed after radiotherapy (RT) in nasopharyngeal carcinoma (NPC) and evaluate its prognostic significance.
One hundred and eighty-eight consecutive newly diagnosed NPC patients were reviewed retrospectively. All patients underwent magnetic resonance imaging and fiberscope examination of the nasopharynx before RT, during RT when the accumulated dose was 46–50 Gy, at the end of RT, and 3–4 months after RT.
Of 188 patients, 40.4% had complete response of PT (CRPT), 44.7% had partial response of PT (PRPT), and 14.9% had stable disease of PT (SDPT) at the end of RT. The 5-year overall survival (OS) rates for patients with CRPT, PRPT, and SDPT at the end of RT were 84.0%, 70.7%, and 44.3%, respectively (P < 0.001, hazard ratio [HR] = 2.177, 95% confidence interval [CI] = 1.480-3.202). The 5-year failure-free survival (FFS) and distant metastasis-free survival (DMFS) rates also differed significantly (87.8% vs. 74.3% vs. 52.7%, P = 0.001, HR = 2.148, 95% CI, 1.384-3.333; 91.7% vs. 84.7% vs. 66.1%, P = 0.004, HR = 2.252, 95% CI = 1.296-3.912). The 5-year local relapse–free survival (LRFS) rates were not significantly different (95.8% vs. 86.0% vs. 81.8%, P = 0.137, HR = 1.975, 95% CI, 0.976-3.995). By multivariate analyses, the PT regression speed at the end of RT was the only independent prognostic factor of OS, FFS, and DMFS (P < 0.001, P = 0.001, and P = 0.004, respectively). The 5-year FFS rates for patients with CRPT during RT and CRPT only at the end of RT were 80.2% and 97.1%, respectively (P = 0.033). For patients with persistent PT at the end of RT, the 5-year LRFS rates of patients without and with boost irradiation were 87.1% and 84.6%, respectively (P = 0.812).
PT regression speed at the end of RT was an independent prognostic factor of OS, FFS, and DMFS in NPC patients. Immediate strengthening treatment may be provided to patients with poor tumor regression at the end of RT.
PMCID: PMC3943409  PMID: 24571531
Nasopharyngeal carcinoma; Radiotherapy; Tumor regression; Survival
18.  Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.] 
BMC Genomics  2014;15:78.
Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species.
A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1’ by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei’s genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective.
A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.
PMCID: PMC3930901  PMID: 24472631
Microsatellite marker; SSR development; Polymorphism; Setaria italica
19.  Prediction of Aptamer-Target Interacting Pairs with Pseudo-Amino Acid Composition 
PLoS ONE  2014;9(1):e86729.
Aptamers are oligonucleic acid or peptide molecules that bind to specific target molecules. As a novel and powerful class of ligands, aptamers are thought to have excellent potential for applications in the fields of biosensing, diagnostics and therapeutics. In this study, a new method for predicting aptamer-target interacting pairs was proposed by integrating features derived from both aptamers and their targets. Features of nucleotide composition and traditional amino acid composition as well as pseudo amino acid were utilized to represent aptamers and targets, respectively. The predictor was constructed based on Random Forest and the optimal features were selected by using the maximum relevance minimum redundancy (mRMR) method and the incremental feature selection (IFS) method. As a result, 81.34% accuracy and 0.4612 MCC were obtained for the training dataset, and 77.41% accuracy and 0.3717 MCC were achieved for the testing dataset. An optimal feature set of 220 features were selected, which were considered as the ones that contributed significantly to the interacting aptamer-target pair predictions. Analysis of the optimal feature set indicated several important factors in determining aptamer-target interactions. It is anticipated that our prediction method may become a useful tool for identifying aptamer-target pairs and the features selected and analyzed in this study may provide useful insights into the mechanism of interactions between aptamers and targets.
PMCID: PMC3899287  PMID: 24466214
20.  NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse 
Bioinformatics  2012;29(2):295-297.
Summary: Nuclear receptors (NRs) are a class of transcription factors playing important roles in various biological processes. An NR often impacts numerous genes and different NRs share overlapped target networks. To fulfil the need for a database incorporating binding sites of different NRs at various conditions for easy comparison and visualization to improve our understanding of NR binding mechanisms, we have developed NURBS, a database for experimental and predicted nuclear receptor binding sites of mouse (NURBS). NURBS currently contains binding sites across the whole-mouse genome of 8 NRs identified in 40 chromatin immunoprecipitation with massively parallel DNA sequencing experiments. All datasets are processed using a widely used procedure and same statistical criteria to ensure the binding sites derived from different datasets are comparable. NURBS also provides predicted binding sites using NR-HMM, a Hidden Markov Model (HMM) model.
Availability: The GBrowse-based user interface of NURBS is freely accessible at NR-HMM and all results can be downloaded for free at the website.
PMCID: PMC3546791  PMID: 23196988
21.  Cancer Prevention Health Services Research: An Emerging Field 
In October 2009, The University of Texas MD Anderson Cancer Center hosted a symposium, “Future Directions in Cancer Prevention and Control: Workforce Implications for Training, Practice, and Policy.” This article summarizes discussions and an Internet and literature review by the symposium's Health Services Infrastructure Working Group. We agree on the need for the recognition of Cancer Prevention Health Services Research (CP-HSR) as a unified research field. With advances in cancer screening and increased emphasis on preventive services under healthcare reform, there is a growing need for investigators with both cancer prevention and HSR expertise to consider the comparative effectiveness of cancer screening methods, the cost-effectiveness of early detection technologies, and the accessibility of preventive care for individuals at risk of cancer. Defining CP-HSR as a field will provide investigators with credibility and will serve to draw more researchers to the field. Increasing funding to train individuals in CP-HSR will be important to help meet the anticipated demand for investigators with this specialized multidisciplinary expertise.
PMCID: PMC3880141  PMID: 22311693
Cancer prevention; Health service research; Cancer screening; Cost-effectiveness; Comparative effectiveness; Workforce
22.  The Molecular Detection and Clinical Significance of ALK Rearrangement in Selected Advanced Non-Small Cell Lung Cancer: ALK Expression Provides Insights into ALK Targeted Therapy 
PLoS ONE  2014;9(1):e84501.
This study aimed to elucidate clinical significance of anaplastic lymphoma kinase (ALK) rearrangement in selected advanced non-small cell lung cancer (NSCLC), to compare the application of different ALK detection methods, and especially evaluate a possible association between ALK expression and clinical outcomes in crizotinib-treated patients.
ALK status was assessed by fluorescent in situ hybridization (FISH), immunohistochemistry (IHC) and quantitative RT-PCR (qRT-PCR) in 173 selected advanced NSCLC patients. Clinicopathologic data, genotype status and survival outcomes were analyzed. Moreover, the association of ALK expression with clinical outcomes was evaluated in ALK FISH-positive crizotinib-treated patients including two patients with concurrent epidermal growth factor receptor (EGFR) mutation.
The positivity detection rate of ALK rearrangement by FISH, IHC and qRT-PCR was 35.5% (59/166), 35.7% (61/171), and 27.9% (34/122), respectively. ALK rearrangement was observed predominantly in young patients, never or light smokers, and adenocarcinomas, especially with signet ring cell features and poor differentiation. Median progression-free survival (PFS) of crizotinib-treated patients was 7.6 months. The overall survival (OS) of these patients was longer compared with that of crizotinib-naive or wild-type cohorts, but there was no significant difference in OS compared with patients with EGFR mutation. ALK expression did not associate with PFS; but, when ALK expression was analyzed as a dichotomous variable, moderate and strong ALK expression had a decreased risk of death (P = 0.026). The two patients with concomitant EGFR and ALK alterations showed difference in ALK expression, response to EGFR and ALK inhibitors, and overall survival.
Selective enrichment according to clinicopathologic features in NSCLC patients could highly improve the positivity detection rate of ALK rearrangement for ALK-targeted therapy. IHC could provide more clues for clinical trial design and therapeutic strategies for ALK-positive NSCLC patients including patients with double genetic aberration of ALK and EGFR.
PMCID: PMC3880316  PMID: 24404167
23.  A new free-hand pedicle screw placement technique with reference to the supraspinal ligament 
Journal of Biomedical Research  2013;28(1):64-70.
We sought to compare the safety and accuracy of a new free-hand pedicle screw placement technique to that of the conventional technique. One hundred fifty-three consecutive adult patients with simple fracture in the thoracic or/and lumbar spine were alternately assigned to either the new free-hand or the conventional group. In the new free-hand technique group, preoperative computerized tomography (CT) images were used to calculate the targeted medial-lateral angle of each pedicle trajectory and the pedicle screw was inserted perpendicular to the correspond-ing supraspinal ligament. In the conventional technique group, the medial-lateral and cranial-caudal angle of each pedicle trajectory was determined by intraoperatively under fluoroscopic guidance. The accuracy rate of pedicle screw placement, the time of intraoperative fluoroscopy, the operating time and the amount of blood loss during operation were respectively compared. All screws were analyzed by using intraoperative radiographs, intraoperative triggered electromyography (EMG) monitoring data, postoperative CT data and clinical outcomes. The accuracy rate of pedicle screw placement in the new free-hand technique group and the conventional technique group was 96.3% and 94.2% (P < 0.05), respectively. The intraoperative fluoroscopy time of the new technique group was less than that of the conventional technique group (5.37 seconds vs. 8.79 seconds, P < 0.05). However, there was no statistical difference in the operating time and the amount of blood loss during operation (P > 0.05). Pedicle screw placement with the free-hand technique which keeps the screw perpendicular to the supraspinal ligament is an accurate, reliable and safe technique to treat simple fracture in the thoracic or lumbar spine.
PMCID: PMC3904177  PMID: 24474966
spine fracture; pedicle screw placement; radiation exposure; supraspinal ligament; anatomy reference
24.  A More Desirable Balanced Polyunsaturated Fatty Acid Composition Achieved by Heterologous Expression of Δ15/Δ4 Desaturases in Mammalian Cells 
PLoS ONE  2013;8(12):e84871.
Arachidonic (ARA), eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids are the most biologically active polyunsaturated fatty acids, but their biosyntheses in mammals are very limited. The biosynthesis of DHA is the most difficult, because this undergoes the Sprecher pathway–a further elongation step from docosapentaenoic acid (DPA), a Δ6-desaturase acting on a C24 fatty acid substrate followed by a peroxisomal chain shortening step. This paper reports the successful heterologous expression of two non-mammalian genes (with modification of codon usage), coding for Euglena gracilis Δ4-desaturase and Siganus canaliculatus Δ4-desaturase respectively, in mammalian cells (HEK293 cell line). Both of the Δ4-desaturases can efficiently function, directly converting DPA into DHA. Moreover, the cooperation of the E. gracilis Δ4-desaturase with C. elegans Δ15-desaturase (able to convert a number of n-6 PUFAs to their corresponding n-3 PUFAs) in transgenic HEK293 cells made a more desirable fatty acid composition – a drastically reduced n-6/n-3 PUFAs ratio and a high level of DHA as well as EPA and ARA. Our findings provide a basis for potential applications of the gene constructs for expression of Δ15/Δ4-desaturases in transgenic livestock to produce such a fatty acid profile in the related products, which certainly will bring benefit to human health.
PMCID: PMC3877351  PMID: 24391980
25.  Maturation of morphology, phenotype and functions of murine bone marrow-derived dendritic cells(DCs) induced by polysaccharide Kureha(PSK) 
Human Vaccines & Immunotherapeutics  2012;8(12):1808-1816.
The aim of this work was to evaluate the influence of protein-bound polysaccharide Kureha(PSK) on murine dendritic cells (DCs). These impacts of PSK on DCs from bone marrow derived DCs(BMDCs) were assessed with inverted phase contrast microscope, conventional scanning electron microscopy (SEM), transmission electron microscopy (TEM) for morphology, fluorescence activated cell sorting (FACS) analysis, cytochemistry assay for key surface molecules, FITC-dextran for phagocytosis, bio-assay and enzyme linked immunosorbent assay (ELISA) for cytokine production. We found that under the influence of PSK, immature DCs changed into mature DCs with decrease of antigens up-taking, simultaneously high expression of key surface molecules of the MHC classII,CD40, CD80, CD86 and CD83 as well as more production of IL-12p70 and tumor necrosis factor α (TNF-α). These data indicate that PSK could markedly promote maturation of DCs and this adjuvant-like activity may have potential therapeutic value in vaccine preparation.
PMCID: PMC3656070  PMID: 23032163
polysaccharide kureha; bone marrow derived DCs; maturation; modulation

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