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1.  Establishment and ultrasound characteristics of atherosclerosis in rhesus monkey 
BioMedical Engineering OnLine  2015;14(Suppl 1):S13.
Background
Atherosclerosis is one of the main risk factors cause acute cerebral-cardio vascular diseases. It's of great significance to establish an atherosclerosis animal model that can mimic the characteristics and nature course of human patients. Therefore, a rhesus monkey model was induced by high-fat diet to monitor their lipid profile and intima-media thickness (IMT) of artery walls and study atherosclerosis progression.
Methods
Fifty male rhesus monkeys were enrolled in this study. All of these monkeys were aged 7 to 14 years with BMI >30 kg/m2. They were fed with high-fat diet containing 10% of fat for the first 48 weeks. Use ultrasound to measure the IMT at bilateral common carotid arteries and their bifurcations and aorta (AO) of the monkeys, and screen out the individuals with thickened IMT for the next phase. In the next 48 weeks, some of these monkeys (n = 4) were fed with standard diet containing 3% fat. Meanwhile the other monkeys (n = 5) were fed with high-fat diet for another 48 weeks. Their serum lipid level was monitored and arterial IMT was also determined periodically.
Results
Serum lipid level of all 50 monkeys elevated after fed with high-fat diet for the first 48 weeks. IMT thickening at right common carotid bifurcation and aorta (AO) was thickened in 9 monkeys. Furthermore, 4 of these 9 monkeys were fed with standard diet and other 5 monkeys were fed with high-fat diet in the following 48 weeks. The serum lipid level of the 4 monkeys recovered and their IMT at RBIF and AO did not progress. However, the lipid level of other 5 monkeys remained high, and their IMT thickening of AO progressed, and plaques and calcification focuses were found at the anterior wall of aorta near the bifurcation of common iliac artery.
Conclusions
After high-fat diet induction for 96 weeks, serum lipid levels of rhesus monkeys elevated significantly, which subsequently caused IMT thickening and plaques formation. When IMT thickening occurred, further vascular injury may be prevented by reducing diet fat content. Our study indicates that vascular injury of high-fat diet induced rhesus monkey is similar to that of human in position and progression.
doi:10.1186/1475-925X-14-S1-S13
PMCID: PMC4306102  PMID: 25602196
2.  PharmGKB summary: very important pharmacogene information for cytochrome P450, family 2, subfamily C, polypeptide 8 
Pharmacogenetics and genomics  2013;23(12):721-728.
doi:10.1097/FPC.0b013e3283653b27
PMCID: PMC4038626  PMID: 23962911
CYP2C8; CYP2C8*3; metabolism; pharmacogenetics; pharmacogenomics; pharmGKB
3.  GW4064, a farnesoid X receptor agonist, upregulates adipokine expression in preadipocytes and HepG2 cells 
World Journal of Gastroenterology : WJG  2014;20(42):15727-15735.
AIM: To investigate the effect of GW4064 on the expression of adipokines and their receptors during differentiation of 3T3-L1 preadipocytes and in HepG2 cells.
METHODS: The mRNA expression of farnesoid X receptor (FXR), peroxisome proliferator-activated receptor-gamma 2 (PPAR-γ2), adiponectin, leptin, resistin, adiponectin receptor 1 (AdipoR1), adiponectin receptor 2 (AdipoR2), and the long isoform of leptin receptor (OB-Rb) and protein levels of adiponectin, leptin, and resistin were determined using fluorescent real-time PCR and enzyme linked immunosorbent assay, respectively, on days 0, 2, 4, 6, and 8 during the differentiation of 3T3-L1 preadipocytes exposed to GW4064. Moreover, mRNA expression of AdipoR2 and OB-Rb was also examined using fluorescent real-time PCR at 0, 12, 24, and 48 h in HepG2 cells treated with GW4064.
RESULTS: The mRNA expression of FXR, PPAR-γ2, adiponectin, leptin, resistin, AdipoR1, AdipoR2, and OB-Rb and protein levels of adiponectin, leptin, and resistin increased along with differentiation of 3T3-L1 preadipocytes (P < 0.05 for all). The mRNA expression of FXR, PPAR-γ2, adiponectin, leptin, and AdipoR2 in 3T3-L1 preadipocytes, and AdipoR2 and OB-Rb in HepG2 cells was significantly increased after treatment with GW4064, when compared with the control group (P < 0.05 for all). A similar trend was observed for protein levels of adipokines (including adiponectin, leptin and resistin). However, the expression of resistin, AdipoR1, and OB-Rb in 3T3-L1 cells did not change after treatment with GW4064.
CONCLUSION: The FXR agonist through regulating, at least partially, the expression of adipokines and their receptors could offer an innovative way for counteracting the progress of metabolic diseases such as nonalcoholic fatty liver disease.
doi:10.3748/wjg.v20.i42.15727
PMCID: PMC4229537  PMID: 25400456
Farnesoid X receptor; Adipokines; Adipokine receptors; 3T3-L1 cells; HepG2 cells; Nonalcoholic fatty liver disease
4.  Effects of fentanyl anesthesia and sufentanil anesthesia on regulatory T cells frequencies 
Background: CD4+CD25+Foxp3+ regulatory T cells (Tregs) can inhibit anti-tumor immune responses and opioids were also immunosuppressive. We set out to compare the effects of sufentanil and fentanyl on Tregs frequencies both in vitro and in breast cancer (BC) patients undergoing eradicative operation. Methods: PBMCs from 12 BC patients were activated in vitro in the presence of fentanyl or sufentanil. The percentage of Tregs was detected by flow cytometry after seven days culture. Other 38 patients who underwent eradicative operation were prospectively randomized to sufentanil anesthesia and fentanyl anesthesia. Blood samples were collected for Tregs quantification by flow cytometry analysis and for Foxp3 mRNA expression by RT-PCR, at 10 min before anesthesia (D0), 24h (D1), and 168 h (D7) after the operation respectively. Results: Activation of PBMCs in the presence of either fentanyl or sufentanil increased the Tregs number, and the effect of sufentanil was more significant under the same analgesic effect with fentanyl. In the 38 operated cases, both the Tregs frequencies and Foxp3 mRNA expression on D1 decreased in comparison to those on D0, but then recovered on D7. By comparing SF and F group, there ware no significant differences in Tregs frequencies and Foxp3 mRNA expression on D0, D1 and D7. Conclusion: With the same analgesic potency, sufentanil is more powerful in increasing the Tregs quantity than fentanyl in vitro. But there are no significant differences as to Tregs frequencies between sufentanil anesthesia and fentanyl anesthesia perioperatively. Further studies are needed to determine the differences in the Tregs function and long-term outcome of these patients.
PMCID: PMC4270602  PMID: 25550807
CD4+CD25+Foxp3+ regulatory T cell; breast cancer; recurrence; fentanyl; sufentanil
5.  Diagnosis of primary pulmonary T- cell/histiocyte-rich large B cell lymphoma with tissue eosinophilia via clinicopathological observation and molecular assay 
Diagnostic Pathology  2014;9(1):188.
Background
Primary pulmonary lymphoma (PPL) is rare and easily misdiagnosed because of the lack of typical clinical features. It most commonly involves elderly patients aged between 60 and 70 years, and pathological diagnosis depends mainly on chest surgery rather than bronchial mucosal biopsy. Via percutaneous needle aspiration biopsy of the lung of a 33-year-old woman, which had distinct tissue eosinophilia, we diagnosed a rare case of rapidly growing large B cell lymphoma.
Methods
Bronchial mucosal biopsy and computed tomography–guided percutaneous needle aspiration biopsy were performed to determine the nature of the lesion, and we identified its immunophenotype using immunohistochemistry. We used BIOMED-2 gene rearrangement PCR to determine lymphocyte clonality; laser microdissection was used to confirm the clonality of suspicious malignant lymphocytes.
Results
Morphologically, the lesion was composed of a large number of eosinophilic cells and a few lymphoid cells. Immunohistochemical staining revealed a few CD1α-positive cells, but they were S-100–negative. The small lymphoid cells predominantly expressed CD3; the large lymphoid cells expressed CD20 and some scattered large lymphoid cells expressed Pax5. However, molecular studies confirmed clonal immunoglobulin heavy chain (IGH)-D gene rearrangement in Pax5–positive large B lymphocytes.
Conclusions
This is the first recorded case of T- cell/histiocyte-rich large B cell lymphoma with tissue eosinophilia of the lung. It highlights the unusual morphological features of PPL that might be mistaken for eosinophilic granuloma or parasitic infection. In addition, IGH and T cell receptor gene rearrangement play important roles in differentiating rare B cell lymphoma from lung space–occupying lesions with abundant eosinophils or T cell infiltration.
Virtual Slides
The virtual slide(s) for this article can be found here: http://med.motic.com/MoticGallery/Slides/AC5C9A6F-46EC-4C71-A448-1312F6900C65?user=2C69F0D6-A478-4A2B-ABF0-BB36763E8025
doi:10.1186/s13000-014-0188-6
PMCID: PMC4207321  PMID: 25273521
Primary pulmonary lymphoma; B cell lymphoma; Tissue eosinophilia; Gene rearrangement
6.  The Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for SLCO1B1 and simvastatin-induced myopathy: 2014 update 
Simvastatin is among the most commonly used prescription medications for cholesterol reduction. A single coding SNP, rs4149056T>C, in SLCO1B1 increases systemic exposure to simvastatin and the risk of muscle toxicity. We summarize evidence from the literature supporting this association and provide therapeutic recommendations for simvastatin based on SLCO1B1 genotype. This document is an update to the 2012 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for SLCO1B1 and simvastatin-induced myopathy.
doi:10.1038/clpt.2014.125
PMCID: PMC4169720  PMID: 24918167
pharmacogenetics; pharmacogenomics; myalgias; rhabdomyolysis; CPIC; SLCO1B1; simvastatin
7.  Etoposide pathway 
Pharmacogenetics and genomics  2009;19(7):552-553.
doi:10.1097/FPC.0b013e32832e0e7f
PMCID: PMC4164627  PMID: 19512958
etoposide; pathway; pharmacogenetics; pharmacogenomics; pharmGKB
8.  PharmGKB, an Integrated Resource of Pharmacogenomic Data and Knowledge 
The PharmGKB (http://www.pharmgkb.org) is a publicly available online resource that aims to facilitate understanding on how genetic variation contributes to variation in drug response. It is not only a repository of pharmacogenomics primary data, but also provides fully curated knowledge including drug pathways, annotated pharmacogene summaries and relationships amongst genes, drugs and diseases. This unit describes how to navigate the PharmGKB website to retrieve detailed information on genes and important variants, as well as their relationship to drugs and diseases. It also includes protocols on our drug-centered pathway, annotated pharmacogene summaries and our web services for downloading the underlying data. Workflow on how to use PharmGKB to facilitate design of the pharmacogenomic study is also described in this unit.
doi:10.1002/0471250953.bi1407s23
PMCID: PMC4153752  PMID: 18819074
Database; pharmacogenomics; pharmacogenetics; drug response; genetic variation; pathway analysis; SNP; polymorphisms; study design
9.  Platinum pathway 
Pharmacogenetics and genomics  2009;19(7):563-564.
doi:10.1097/FPC.0b013e32832e0ed7
PMCID: PMC4153753  PMID: 19525887
anticancer; drug response; pathway; pharmacogenomics; platinum
10.  Effect of ERK1/2 Signaling Pathway in Electro-Acupuncture – Mediated Up-Regulation of Heme Oxygenase-1 in Lungs of Rabbits with Endotoxic Shock 
Background
The anti-oxidative and anti-inflammatory activities of electro-acupuncture (EA), a traditional clinical method, are widely accepted, but its mechanisms are not yet well defined. In this study, we investigated the role of extracellular signal-regulated kinases1/2 (ERK1/2) pathways on electro-acupuncture – mediated up-regulation of heme oxygenase-1 (HO-1) in rabbit lungs injured by LPS-induced endotoxic shock.
Material/Methods
Seventy rabbits were randomly divided into 7 groups: group C, group M, group D, group SEAM, group EAM, group EAMPD, and group PD98059. Male New England white rabbits were given EA treatment on both sides once a day on days 1–5, and then received LPS to replicate the experimental model of injured lung induced by endotoxic shock. Then, they were killed by exsanguination at 6 h after LPS administration. The blood samples were collected for serum examination, and the lungs were removed for pathology examination, determination of wet-to-dry weight ratio, MDA content, SOD activity, serum tumor necrosis factor-α, determination of HO-1 protein and mRNA expression, and determination of ERK1/2 protein.
Results
The results revealed that after EA treatment, expression of HO-1and ERK1/2 was slightly increased compared to those in other groups, accompanied with less severe lung injury as indicated by lower index of lung injury score, lower wet-to-dry weight ratio, MDA content, and serum tumor necrosis factor-α levels, and greater SOD activity (p<0.05 for all). After pretreatment with ERK1/2 inhibitor PD98059, the effect of EA treatment and expression of HO-1 were suppressed (p<0.05 for all).
Conclusions
After electro-acupuncture stimulation at ST36 and BL13, severe lung injury during endotoxic shock was attenuated. The mechanism may be through up-regulation of HO-1, mediated by the signal transductions of ERK1/2 pathways. Thus, the regulation of ERK1/2 pathways via electro-acupuncture may be a therapeutic strategy for endotoxic shock.
doi:10.12659/MSM.890736
PMCID: PMC4144948  PMID: 25139460
Acupuncture; Acute Lung Injury; Mitogen-Activated Protein Kinase 1
11.  Role of Nrf2/ARE Pathway in Protective Effect of Electroacupuncture against Endotoxic Shock-Induced Acute Lung Injury in Rabbits 
PLoS ONE  2014;9(8):e104924.
NF-E2 related factor 2 (Nrf2) is a major transcription factor and acts as a key regulator of antioxidant genes to exogenous stimulations. The aim of current study was to determine whether Nrf2/ARE pathway is involved in the protective effect of electroacupuncture on the injured lung in a rabbit model of endotoxic shock. A dose of lipopolysaccharide (LPS) 5 mg/kg was administered intravenously to replicate the model of acute lung injury induced by endotoxic shock. Electroacupuncture pretreatment was handled bilaterally at Zusanli and Feishu acupoints for five consecutive days while sham electroacupuncture punctured at non-acupoints. Fourty anesthetized New England male rabbits were randomized into normal control group (group C), LPS group (group L), electroacupuncture + LPS group (group EL) and sham electroacupuncture + LPS (group SEL). At 6 h after LPS administration, the animals were sacrificed and the blood samples were collected for biochemical measurements. The lungs were removed for calculation of wet-to-dry weight ratios (W/D), histopathologic examination, determination of heme oxygenase (HO)-1 protein and mRNA, Nrf2 total and nucleoprotein, as well as Nrf2 mRNA expression, and evaluation of the intracellular distribution of Nrf2 nucleoprotein. LPS caused extensive morphologic lung damage, which was lessened by electroacupuncture treatment. Besides, lung W/D ratios were significantly decreased, the level of malondialdehyde was inhibited, plasma levels of TNF-α and interleukin-6 were decreased, while the activities of superoxide dismutase, glutathione peroxidase and catalase were enhanced in the electroacupucnture treated animals. In addition, electroacupuncture stimulation distinctly increased the expressions of HO-1 and Nrf2 protein including Nrf2 total protein and nucleoprotein as well as mRNA in lung tissue, while these effects were blunted in the sham electroacupuncture group. We concluded that electroacupuncture treatment at ST36 and BL13 effectively attenuates lung injury in a rabbit model of endotoxic shock through activation of Nrf2/ARE pathway and following up-regulation of HO-1 expression.
doi:10.1371/journal.pone.0104924
PMCID: PMC4130631  PMID: 25115759
12.  Tai Chi for Improvement of Motor Function, Balance and Gait in Parkinson's Disease: A Systematic Review and Meta-Analysis 
PLoS ONE  2014;9(7):e102942.
Background
Recently, several studies assessed the effectiveness of Tai Chi for Parkinson's disease (PD), but the role of Tai Chi in the management of PD remained controversial. Therefore, the purpose of this systematic review is to evaluate the evidence on the efficacy of Tai Chi for PD.
Methods
Six English and Chinese electronic databases, up to April 2014, were searched to identify relevant studies. The risk of bias in eligible studies was assessed by Cochrane Collaboration's tools. The primary outcomes were motor function, balance and gait in individuals with PD. Standardized mean difference (SMD) and 95% confidence intervals (CI) of random-effect model were calculated. And heterogeneity was assessed based on the I2statistic.
Results
7 randomized controlled trials and 1 non-randomized controlled trial were eligible. The aggregated results suggested that Tai Chi showed beneficial effects in improving motor function (SMD, −0.57; 95% CI −1.11 to −0.04; p = 0.03), balance (SMD, 1.22; 95% CI 0.80 to 1.65; p<0.00001) and functional mobility (SMD, 1.06; 95% CI 0.68 to 1.44; p<0.00001) in patients with PD, but not in improving gait velocity (SMD, −0.02; 95% CI −0.58 to 0.54; p = 0.94), step length (SMD, −0.00; 95% CI −0.57 to 0.56; p = 0.99), or gait endurance (SMD, 0.53; 95% CI −0.07 to 1.12; p = 0.08). Comparing with other active therapies, however, Tai Chi only showed better effects in improving balance (SMD, 0.74; 95% CI 0.38 to 1.10; p<0.0001).
Conclusion
Tai Chi should be a valid complementary and alternative therapy for PD, especially in improving motor function and balance. However, more studies with long follow-up are warrant to confirm the current finding of Tai Chi for PD.
doi:10.1371/journal.pone.0102942
PMCID: PMC4105461  PMID: 25047456
13.  Relationships of Biomass with Environmental Factors in the Grassland Area of Hulunbuir, China 
PLoS ONE  2014;9(7):e102344.
Many studies have focused on the relationship between vegetation biomass and environmental factors in grassland. However, several questions remain to be answered, especially with regards to the spatial pattern of vegetation biomass. Thus, the distributed mechanism will be explored in the present study. Here, plant biomass was measured at 23 sites along a transect survey during the peak growing season in 2006. The data were analyzed with a classification and regression tree (CART) model. The structural equation modeling (SEM) was conducted to explicitly evaluate the both direct and indirect effects of these critical environmental elements on vegetation biomass. The results demonstrated that mean annual temperature (MAT) affected aboveground biomass (AGB) scored at −0.811 (P<0.05). The direct effect of MAT on belowground biomass (BGB) was −0.490 (P<0.05). The results were determined by SEM. Our results indicate that AGB and BGB in semi-arid ecosystems is strongly affected by precipitation and temperature. Future work shall attempt to take into account the integrated effects of precipitation and temperature. Meanwhile, partitioning the influences of environmental variations and vegetation types are helpful in illuminating the internal mechanism of biomass distribution.
doi:10.1371/journal.pone.0102344
PMCID: PMC4102509  PMID: 25032808
14.  DDB2 Suppresses Tumorigenicity by Limiting the Cancer Stem Cell Population in Ovarian Cancer 
Molecular cancer research : MCR  2014;12(5):784-794.
Ovarian cancer is an extremely aggressive disease associated with a high percentage of tumor recurrence and chemotherapy resistance. Understanding the underlying mechanism of tumor relapse is crucial for effective therapy of ovarian cancer. DNA damage-binding protein 2 (DDB2) is a DNA repair factor mainly involved in nucleotide excision repair. Here, a novel role was identified for DDB2 in the tumorigenesis of ovarian cancer cells and the prognosis of patients with ovarian cancer. Overexpressing DDB2 in human ovarian cancer cells suppressed its capability to recapitulate tumors in athymic nude mice. Mechanistic investigation demonstrated that DDB2 is able to reduce the cancer stem cell (CSC) population characterized with high aldehyde dehydrogenase activity in ovarian cancer cells, probably through disrupting the self-renewal capacity of CSCs. Low DDB2 expression correlates with poor outcomes among patients with ovarian cancer, as revealed from the analysis of publicly available gene expression array datasets. Given the finding that DDB2 protein expression is low in ovarian tumor cells, enhancement of DDB2 expression is a promising strategy to eradicate CSCs and would help to halt ovarian cancer relapse.
doi:10.1158/1541-7786.MCR-13-0638
PMCID: PMC4096129  PMID: 24574518
15.  A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12 
PLoS ONE  2014;9(7):e98628.
A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.
doi:10.1371/journal.pone.0098628
PMCID: PMC4094432  PMID: 25014030
16.  Isolation and characterization of spliceostatin B, a new analogue of FR901464, from Pseudomonas sp. No. 2663 
The Journal of antibiotics  2013;66(9):555-558.
doi:10.1038/ja.2013.38
PMCID: PMC4067007  PMID: 23652603
cytotoxicity; FR901464; Pseudomonas sp. No. 2663; spliceostatin B
17.  CCND1 G870A polymorphism contributes to the risk of esophageal cancer: An updated systematic review and cumulative meta-analysis 
Biomedical Reports  2014;2(4):549-554.
The common functional cyclin D1 (CCND1) G870A polymorphism may influence the risk of esophageal cancer. However, the conclusions of previous studies have been inconsistent for the association between the CCND1 G870A polymorphism and esophageal cancer risk. A meta-analysis of 11 published case-control studies was performed, including 2,111 patients with esophageal cancer and 3,232 controls, to investigate the association between the CCND1 G870A polymorphism and esophageal cancer risk. The odds ratio (OR) with a 95% confidence interval (CI) was applied to assess the association between the CCND1 G870A polymorphism and esophageal cancer risk. A significant association between the CCND1 G870A polymorphism and esophageal cancer risk was observed for the allele contrast (A vs. G: OR, 1.23; 95% CI, 1.02–1.48; P=0.029), codominant (AA vs. GG: OR, 1.58; 95% CI; 1.06–2.35; P=0.024) and recessive models (AA vs. GG + GA: OR, 1.33, 95% CI, 1.03–1.73; P=0.030). However, in the stratified analysis by ethnicity, study design and pathology, there was no significant association detected in these genetic models. In conclusion, results of the meta-analysis suggested that the CCND1 G870A polymorphism is a potential risk factor in the development of esophageal cancer.
doi:10.3892/br.2014.286
PMCID: PMC4051475  PMID: 24944806
CCND1; polymorphism; esophageal cancer; meta-analysis
18.  Piperlongumine Induces Apoptosis and Synergizes with Cisplatin or Paclitaxel in Human Ovarian Cancer Cells 
Piperlongumine (PL), a natural alkaloid from Piper longum L., possesses the highly selective and effective anticancer property. However, the effect of PL on ovarian cancer cells is still unknown. In this study, we firstly demonstrate that PL selectively inhibited cell growth of human ovarian cancer cells. Furthermore, PL notably induced cell apoptosis, G2/M phase arrest, and accumulation of the intracellular reactive oxidative species (ROS) in a dose- and time-dependent manner. Pretreatment with antioxidant N-acety-L-cysteine could totally reverse the PL-induced ROS accumulation and cell apoptosis. In addition, low dose of PL/cisplatin or paclitaxel combination therapies had a synergistic antigrowth effect on human ovarian cancer cells. Collectively, our study provides new therapeutic potential of PL on human ovarian cancer.
doi:10.1155/2014/906804
PMCID: PMC4034765  PMID: 24895529
19.  A Novel Artificial Bee Colony Algorithm Based on Internal-Feedback Strategy for Image Template Matching 
The Scientific World Journal  2014;2014:906861.
Image template matching refers to the technique of locating a given reference image over a source image such that they are the most similar. It is a fundamental mission in the field of visual target recognition. In general, there are two critical aspects of a template matching scheme. One is similarity measurement and the other is best-match location search. In this work, we choose the well-known normalized cross correlation model as a similarity criterion. The searching procedure for the best-match location is carried out through an internal-feedback artificial bee colony (IF-ABC) algorithm. IF-ABC algorithm is highlighted by its effort to fight against premature convergence. This purpose is achieved through discarding the conventional roulette selection procedure in the ABC algorithm so as to provide each employed bee an equal chance to be followed by the onlooker bees in the local search phase. Besides that, we also suggest efficiently utilizing the internal convergence states as feedback guidance for searching intensity in the subsequent cycles of iteration. We have investigated four ideal template matching cases as well as four actual cases using different searching algorithms. Our simulation results show that the IF-ABC algorithm is more effective and robust for this template matching mission than the conventional ABC and two state-of-the-art modified ABC algorithms do.
doi:10.1155/2014/906861
PMCID: PMC4032671  PMID: 24892107
20.  Genomics-Guided Discovery of Thailanstatins A, B and C as Pre-mRNA Splicing Inhibitors and Antiproliferative Agents from Burkholderia thailandensis MSMB43 
Journal of natural products  2013;76(4):685-693.
Mining the genome sequence of Burkholderia thailandensis MSMB43 revealed a cryptic biosynthetic gene cluster resembling that of FR901464 (4), a prototype spliceosome inhibitor produced by Pseudomonas sp. No. 2663. Transcriptional analysis revealed a cultivation condition in which a regulatory gene of the cryptic gene cluster is adequately expressed. Consequently, three new compounds, named thailanstatins A (1), B (2) and C (3), were isolated from the fermentation broth of B. thailandensis MSMB43. Thailanstatins are proposed to be biosynthesized by a hybrid polyketide synthase-nonribosomal peptide synthetase pathway. They differ from 4 by lacking an unstable hydroxyl group and by having an extra carboxyl moiety; those differences endow thailanstatins with a significantly greater stability than 4 as tested in phosphate buffer at pH 7.4. In vitro assays showed that thailanstatins inhibit pre-mRNA splicing as potently as 4, with half-maximal inhibitory concentrations in the single to sub µM range. Cell culture assays indicated that thailanstatins also possess potent antiproliferative activities in representative human cancer cell lines, with half-maximal growth inhibitory concentrations in the single nM range. This work provides new chemical entities for research and development, and new structure-activity information for chemical optimization of related spliceosome inhibitors.
doi:10.1021/np300913h
PMCID: PMC3696399  PMID: 23517093
Burkholderia thailandensis MSMB43; genomics-guided discovery; natural product; pre-mRNA splicing inhibitor; thailanstatin
21.  An Improved Artificial Bee Colony Algorithm Based on Balance-Evolution Strategy for Unmanned Combat Aerial Vehicle Path Planning 
The Scientific World Journal  2014;2014:232704.
Unmanned combat aerial vehicles (UCAVs) have been of great interest to military organizations throughout the world due to their outstanding capabilities to operate in dangerous or hazardous environments. UCAV path planning aims to obtain an optimal flight route with the threats and constraints in the combat field well considered. In this work, a novel artificial bee colony (ABC) algorithm improved by a balance-evolution strategy (BES) is applied in this optimization scheme. In this new algorithm, convergence information during the iteration is fully utilized to manipulate the exploration/exploitation accuracy and to pursue a balance between local exploitation and global exploration capabilities. Simulation results confirm that BE-ABC algorithm is more competent for the UCAV path planning scheme than the conventional ABC algorithm and two other state-of-the-art modified ABC algorithms.
doi:10.1155/2014/232704
PMCID: PMC3980870  PMID: 24790555
22.  Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature 
Natural product reports  2013;30(1):108-160.
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
doi:10.1039/c2np20085f
PMCID: PMC3954855  PMID: 23165928
23.  Effect of electroacupuncture at Zusanli (ST36) and Sanyinjiao (SP6) acupoints on adrenocortical function in etomidate anesthesia patients 
Background
We aimed to investigate the effect of electroacupuncture at Zusanli (ST36) and Sanyinjiao (SP6) on adrenocortical function in patients with etomidate anesthesia.
Material/Methods
We randomly divided 80 patients who underwent elective surgery into 4 groups: group etomidate (ETO), group etomidate + electroacupuncture (ETO+EA), group etomidate + sham acupuncture (ETO+SEA), and group propofol (PRO). The patients in group ETO, ETO+EA, and ETO+SEA were induced with etomidate and sufentanil and maintained with intravenous infusion of etomidate and remifentanil. Group PRO was induced with propofol and sufentanil and maintained with propofol and remifentanil. Group ETO+EA received electro-acupuncture stimulation at Zusanli and Sanyinjiao throughout the operation, while group ETO+SEA received electro-acupuncture stimulation at non-acupoints. We recorded the values of MAP, HR, BIS, CVP, cortisol, ACTH, epinephrine, norepinephrine, and arterial blood gas during the perioperative period.
Results
Cortisol concentrations were significantly higher at all times except T0 in group ETO+EA compared with group ETO. The ACTH concentrations were lower in group ETO+EA than that in group ETO at point T3.
Conclusions
Electroacupuncture at ST 36 and SP 6 can mitigate the adrenal cortical inhibition induced by etomidate and can reduce the secretion of catecholamines during surgery.
doi:10.12659/MSM.890111
PMCID: PMC3958570  PMID: 24621826
Electroacupuncture; Cortisol; ACTH; Catecholamines; Etomidate
24.  Is there a role of TNFR1 in acute lung injury cases associated with extracorporeal circulation?*  
The signaling pathway for tumor necrosis factor-α (TNF-α) and its receptors is up-regulated during extracorporeal circulation (ECC), and recruits blood neutrophil into the lung tissue, which results in acute lung injury (ALI). In this study, we evaluated the role of tumor necrosis factor receptor 1 (TNFR1) in ECC-induced ALI by blocking TNF-α binding to TNFR1 with CAY10500. Anesthetized Sprague-Dawley (SD) rats were pretreated intravenously with phosphate buffered saline (PBS) or vehicle (0.3 ml ethanol IV) or CAY10500, and then underwent ECC for 2 h. The oxygenation index (OI) and pulmonary inflammation were assessed after ECC. OI was significantly decreased, while TNF-α and neutrophil in bronchoalveolar lavage fluid (BALF) and plasma TNF-α increased after ECC. Pretreatment of CAY10500 decreased plasma TNF-α level, but did not decrease TNF-α levels and neutrophil counts in BALF or improve OI. Lung histopathology showed significant alveolar congestion, infiltration of the leukocytes in the airspace, and increased thickness of the alveolar wall in all ECC-treated groups. CAY10500 pretreatment slightly reduced leukocyte infiltration in lungs, but did not change the wet/dry ratio in the lung tissue. Blocking TNF-α binding to TNFR1 by CAY10500 intravenously slightly mitigates pulmonary inflammation, but cannot improve the pulmonary function, indicating the limited role of TNFR1 pathway in circulating inflammatory cell in ECC-induced ALI.
doi:10.1631/jzus.B1300147
PMCID: PMC3955915  PMID: 24599692
Extracorporeal circulation (ECC); Acute lung injury (ALI); Tumor necrosis factor receptor 1 (TNFR1); Tumor necrosis factor-α (TNF-α)
25.  Dysplastic Nodules with Glypican-3 Positive Immunostaining: A Risk for Early Hepatocellular Carcinoma 
PLoS ONE  2014;9(1):e87120.
Glypican-3 (GPC3) has been reported to be a novel serum and histochemical marker for HCC. The positivity or negativity for GPC3 in hepatic precancerous lesions, such as dysplastic nodules (DN), has also been described. Moreover, our previous studies have demonstrated that some DN in liver cirrhosis represent monoclonal hyperplasia, and confirmed their neoplastic nature. However, additional studies must be performed to investigate further the relationship between DN with GPC3 positivity and HCC. Thus, we first investigated the expression of GPC3 in 136 HCC and 103 small DN (less than 1 cm in diameter) by immunohistochemical staining and determined the clonality of 81 DN from female patients using X-chromosome inactivation mosaicism and polymorphism of androgen receptor (AR) gene. Then we examined these samples for chromosomal loss of heterozygosity (LOH) at 11 microsatellite polymorphism sites. The results demonstrated that GPC3 immunoreactivity was detected in 103 of 136 HCC (75.7%) and 19 of 103 DN (18.4%), and the positive ratio correlated with HBsAg positivity. Clonality assays showed that 15 GPC3-positive DN from female patients, including 12 high-grade DN (HGDN), and 28 (42.4%) of 66 GPC3-negative DN, were monoclonal. In addition, among 19 GPC3-positive DN, chromosomal LOH was found at loci D6S1008 (100%, 19/19), D8S262 (52.6%, 10/19) and D11S1301 (57.9%, 11/19). However, the LOH frequency in GPC3-negative DN was 5.95% (5/84), 23.8% (20/84), and 4.76% (4/84) in three loci, respectively. Thus, we concluded that GPC3-positive DN, especially GPC3-positive HGDN, was really a late premalignant lesion of HCC.
doi:10.1371/journal.pone.0087120
PMCID: PMC3909016  PMID: 24498024

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