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1.  Analysis of Surface EMG Baseline for Detection of Hidden Muscle Activity 
Journal of neural engineering  2014;11(1):016011.
This study explored the feasibility of detecting hidden muscle activity in surface electromyogram (EMG) baseline.
Power spectral density (PSD) analysis and multi-scale entropy (MSE) analysis were used respectively. Both analyses were applied to computer simulations of surface EMG baseline with presence (representing activity data) or absence (representing reference data) of hidden muscle activity, as well as surface electrode array EMG baseline recordings of healthy control and amyotrophic lateral sclerosis (ALS) subjects.
Main results
Although the simulated reference data and the activity data yielded no distinguishable difference in the time domain, they demonstrated a significant difference in the frequency and signal complexity domains with the PSD and MSE analyses. For a comparison using pooled data, such a difference was also observed when the PSD and MSE analyses were applied to surface electrode array EMG baseline recordings of healthy control and ALS subjects, which demonstrated no distinguishable difference in the time domain. Compared with the PSD analysis, the MSE analysis appeared to be more sensitive for detecting the difference in surface EMG baselines between the two groups.
The findings implied presence of hidden muscle activity in surface EMG baseline recordings from the ALS subjects. To promote the presented analysis as a useful diagnostic or investigatory tool, future studies are necessary to assess the pathophysiological nature or origins of the hidden muscle activity, as well as the baseline difference at the individual subject level.
PMCID: PMC4230535  PMID: 24445526
2.  Identification of Locally Advanced Rectal Cancer with Low Risk of Local Recurrence 
PLoS ONE  2015;10(1):e0117141.
The routine application of neoadjuvant chemoradiotherapy for T3N0 rectal cancer remains controversial. The aim of this study was to use clinical, Magnetic resonance imaging, and pathological parameters to identify a subgroup of patients with low risk of local recurrence who might be precluded from neoadjuvant chemoradiotherapy.
We retrospectively reviewed a prospectively maintained database of consecutive rectal cancer patients who underwent curative resection. 166 pathologic confirmed T3N0 rectal cancer patients with tumor located 5–12cm above the anal verge and preoperative circumferential resection margin>1mm were included in analysis. The primary outcomes measured were3- and 5-year local recurrence rates.
Local recurrence was demonstrated during follow-up in 5 patients; the actuarial overall 3- and 5-year local recurrence rates were 2.5% and 3.4%, respectively. Inadequate sampling of lymph nodes (≤12) was associated with higher local recurrence (P = 0.03) in this group of patients.
For upper and middle T3N0 rectal cancer with preoperative circumferential resection margin>1mm, local recurrence rate after total mesorectal excision is low and surgery alone may be enough for this group of patients.
PMCID: PMC4309455  PMID: 25629521
3.  Sexual and Reproductive Health Knowledge, Contraception Uptake, and Factors Associated with Unmet Need for Modern Contraception among Adolescent Female Sex Workers in China 
PLoS ONE  2015;10(1):e0115435.
In China, policy and social taboo prevent unmarried adolescents from accessing sexual and reproductive health (SRH) services. Research is needed to determine the SRH needs of highly disadvantaged groups, such as adolescent female sex workers (FSWs). This study describes SRH knowledge, contraception use, pregnancy, and factors associated with unmet need for modern contraception among adolescent FSWs in Kunming, China.
A cross-sectional study using a one-stage cluster sampling method was employed to recruit adolescents aged 15 to 20 years, and who self-reported having received money or gifts in exchange for sex in the past 6 months. A semi-structured questionnaire was administered by trained peer educators or health workers. Multivariable logistic regression was conducted to determine correlates of low knowledge and unmet need for modern contraception.
SRH knowledge was poor among the 310 adolescents surveyed; only 39% had heard of any long-acting reversible contraception (implant, injection or IUD). Despite 98% reporting not wanting to get pregnant, just 43% reported consistent condom use and 28% currently used another form of modern contraception. Unmet need for modern contraception was found in 35% of adolescents, and was associated with having a current non-paying partner, regular alcohol use, and having poorer SRH knowledge. Past abortion was common (136, 44%). In the past year, 76% had reported a contraception consultation but only 27% reported ever receiving SRH information from a health service.
This study demonstrated a low level of SRH knowledge, a high unmet need for modern contraception and a high prevalence of unintended pregnancy among adolescent FSWs in Kunming. Most girls relied on condoms, emergency contraception, or traditional methods, putting them at risk of unwanted pregnancy. This study identifies an urgent need for Chinese adolescent FSWs to be able to access quality SRH information and effective modern contraception.
PMCID: PMC4307985  PMID: 25625194
4.  A Multicenter, Randomized Clinical Trial Comparing the Three-Weekly Docetaxel Regimen plus Prednisone versus Mitoxantone plus Prednisone for Chinese Patients with Metastatic Castration Refractory Prostate Cancer 
PLoS ONE  2015;10(1):e0117002.
To explore the feasibility and efficacy of docetaxel plus prednisone for Chinese population with metastatic castration refractory prostate cancer (mCRPC).
Patients and methods
A total of 228 patients recruited from 15 centers were randomized to receive 10 cycles of D3P arm (docetaxel: 75 mg/m2, intravenous infusion, every three weeks; Prednisone 10mg orally given daily) or M3P arm (mitoxantrone: 12 mg/m2, intravenous infusion, every three weeks; Prednisone 10mg orally given daily). Primary end point was overall survival, and secondary end points were events progression-free survival (PFS), response rate, response duration. Quality of life (QoL) was also assessed in both treatment groups.
The median overall survival was 21.88 months in D3P arm and 13.67 months in M3P arm (P = 0.0011, hazard ratio = 0.63, 95% confidence interval, 0.46–0.86). Subgroup analysis was consistent with the results of overall analysis. Events progression-free survival (pain, PSA, tumor and disease) were significantly improved in D3P arm compared with M3P arm. PSA response rate was 35.11% for patients treated by D3P arm and 19.39% for M3P arm (P = 0.0155). Pain response rate was higher in D3P arm (61.11%, P = 0.0011) than in M3P (23.08%) arm. No statistical differences were found between D3P arm and M3P arm for QoL, tumor response rate and response duration of PSA and pain. The tolerability and overall safety of D3P arm were generally comparable to that of M3P arm.
Compared with M3P arm, D3P arm significantly prolonged overall survival for the Chinese patients with mCRPC and improved the response rate for PSA and pain.
Trial Registration NCT00436839
PMCID: PMC4307981  PMID: 25625938
5.  The Hypoxic Response Contributes to Altered Gene Expression and Pre-Capillary Pulmonary Hypertension in Patients with Sickle Cell Disease 
Circulation  2014;129(16):1650-1658.
We postulated that the hypoxic response in sickle cell disease (SCD) contributes to altered gene expression and pulmonary hypertension, a complication associated with early mortality.
Methods and Results
To identify genes regulated by the hypoxic response and not other effects of chronic anemia, we compared expression variation in peripheral blood mononuclear cells from 13 SCD subjects with hemoglobin SS genotype and 15 Chuvash polycythemia subjects (VHLR200W homozygotes with constitutive up-regulation of hypoxia inducible factors in the absence of anemia or hypoxia). At 5% false discovery rate, 1040 genes exhibited >1.15 fold change in both conditions; 297 were up-regulated and 743 down-regulated including MAPK8 encoding a mitogen-activated protein kinase important for apoptosis, T-cell differentiation and inflammatory responses. Association mapping with a focus on local regulatory polymorphisms in 61 SCD patients identified expression quantitative trait loci (eQTL) for 103 of these hypoxia response genes. In a University of Illinois SCD cohort the A allele of a MAPK8 eQTL, rs10857560, was associated with pre-capillary pulmonary hypertension defined as mean pulmonary artery pressure ≥25 and pulmonary capillary wedge pressure ≤15 mm Hg at right heart catheterization (allele frequency=0.66; OR=13.8, P=0.00036, n=238). This association was confirmed in an independent Walk-PHaSST cohort (allele frequency=0.65; OR=11.3, P=0.0025, n=519). The homozygous AA genotype of rs10857560 was associated with decreased MAPK8 expression and present in all 14 identified pre-capillary pulmonary hypertension cases among the combined 757 patients.
Our study demonstrates a prominent hypoxic transcription component in SCD and a MAPK8 eQTL associated with pre-capillary pulmonary hypertension.
PMCID: PMC4287376  PMID: 24515990
sickle cell disease; MAPK8; hypoxic response; expression quantitative trait loci; association mapping; pre-capillary pulmonary hypertension
6.  Glycyrrhetinic acid induces G1-phase cell cycle arrest in human non-small cell lung cancer cells through endoplasmic reticulum stress pathway 
International Journal of Oncology  2015;46(3):981-988.
Glycyrrhetinic acid (GA) is a natural compound extracted from liquorice, which is often used in traditional Chinese medicine. The purpose of the present study was to investigate the antitumor effect of GA in human non-small cell lung cancer (NSCLC), and its underlying mechanisms in vitro. We have shown that GA suppressed the proliferation of A549 and NCI-H460 cells. Flow cytometric analysis showed that GA arrested cell cycle in G0/G1 phase without inducing apoptosis. Western blot analysis indicated that GA mediated G1-phase cell cycle arrest by upregulation of cyclin-dependent kinase inhibitors (CKIs) (p18, p16, p27 and p21) and inhibition of cyclins (cyclin-D1, -D3 and -E) and cyclin-dependent kinases (CDKs) (CDK4, 6 and 2). GA also maintained pRb phosphorylation status, and inhibited E2F transcription factor 1 (E2F-1) in both cell lines. GA upregulated the unfolded proteins, Bip, PERK and ERP72. Accumulation of unfolded proteins in the endoplasmic reticulum (ER) triggered the unfolded protein response (UPR), which could be the mechanism by which GA inhibited cell proliferation in NSCLC cells. GA then coordinated the induction of ER chaperones, which decreased protein synthesis and induced cell cycle arrest in the G1 phase. This study provides experimental evidence to support the development of GA as a chemotherapeutic agent for NSCLC.
PMCID: PMC4324580  PMID: 25573651
glycyrrhetinic acid; cell cycle arrest; ER stress; NSCLC
7.  Generating rats with conditional alleles using CRISPR/Cas9 
Cell Research  2013;24(1):122-125.
PMCID: PMC3879705  PMID: 24296780
8.  A Novel Technique for Muscle Onset Detection Using Surface EMG Signals without Removal of ECG Artifacts 
Physiological measurement  2013;35(1):45-54.
Surface electromyogram (EMG) signal from trunk muscles is often contaminated by electrocardiogram (ECG) artifacts. This study presents a novel method for muscle activity onset detection by processing surface EMG against ECG artifacts. The method does not require removal of ECG artifacts from raw surface EMG signals. Instead, it applies the sample entropy (SampEn) analysis to highlight EMG activity and suppress ECG artifacts in the signal complexity domain. A SampEn threshold can then be determined for detection of muscle activity. The performance of the proposed method was examined with different SampEn analysis window lengths, using a series of combinations of “clean” experimental EMG and ECG recordings over a wide range of signal to noise ratios (SNRs) from −10 dB to 10 dB. For all the examined SNRs, the window length of 128 ms yielded the best performance among all the tested lengths. Compared with the conventional amplitude thresholding and integrated profile methods, the SampEn analysis based method achieved significantly better performance, demonstrated as the shortest average latency or error among the three methods (p<0.001 for any of the examined SNRs except 10 dB).
PMCID: PMC4035355  PMID: 24345857
9.  Iron deficiency modifies gene expression variation induced by augmented hypoxia sensing 
Blood cells, molecules & diseases  2013;52(1):10.1016/j.bcmd.2013.07.016.
In congenital Chuvash polycythemia (CP), VHLR200W homozygosity leads to elevated hypoxia inducible factor (HIF) levels at normoxia. CP is often treated by phlebotomy resulting in iron deficiency, permitting us to examine the separate and synergistic effects of iron deficiency and HIF signaling on gene expression. We compared peripheral blood mononuclear cell gene expression profiles of eight VHLR200W homozygotes with 17 wildtype individuals with normal iron status and found 812 up-regulated and 2120 down-regulated genes at false discovery rate 0.05. Among differential genes we identified three major gene regulation modules involving induction of innate immune responses, alteration of carbohydrate and lipid metabolism, and down-regulation of cell proliferation, stress-induced apoptosis and T-cell activation. These observations suggest molecular mechanisms for previous observations in CP of lower blood sugar without increased insulin and low oncogenic potential. Studies including 16 additional VHLR200W homozygotes with low ferritin indicated that iron deficiency enhanced the induction effect of VHLR200W for 50 genes including hemoglobin synthesis loci but suppressed the effect for 107 genes enriched for HIF-2 targets. This pattern is consistent with potentiation of HIF-1α protein stability by iron deficiency but a trend for down-regulation of HIF-2α translation by iron deficiency overriding an increase in HIF-2α protein stability.
PMCID: PMC3852195  PMID: 23993337
10.  Complementary Roles of Squamous Cell Carcinoma Antigen and 18F-FDG PET/CT in Suspected Recurrence of Cervical Squamous Cell Cancer 
Journal of Cancer  2015;6(3):287-291.
Purpose: To assess the clinical value of FDG PET/CT and evaluate the complementary roles of serum squamous cell carcinoma antigen (SCCAg) and FDG PET/CT in the diagnosis of suspected recurrent of cervical squamous cell cancer. Methods: Serum SCCAg levels were retrospectively reviewed in patients previously treated for cervical squamous cell carcinoma, who had suspected recurrence of cervical cancer and who had undergone FDG PET/CT scans. The clinical impact of elevated SCCAg (>1.5 ng/ml) and negative SCCAg (≤1.5 ng/ml) levels were analyzed based on the results of PET/CT and final diagnosis. Results: The overall patient-based sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of PET/CT for the detection of tumor recurrence or malignancy were 100% (86/86), 80.8% (21/26), 95.5% (107/112), 94.5% (86/91) and 100% (21/21), respectively. Of the 112 patients included in this study, recurrence or malignancy was detected by PET/CT in 62 of the 64 patients with elevated SCCAg, compared to 24 of the 48 patients with negative SCCAg levels. The overall patient-based PPV, NPV, sensitivity and accuracy of SCCAg for the detection of tumor recurrence or malignancy were 96.9% (62/64), 50% (24/48), 72.1% (62/86) and 76.8% (86/112), respectively. The five false-positive PET/CT results were all associated with patients with negative SCCAg levels. The PPV of positive PET/CT-associated elevated SCCAg for the detection of tumor recurrence or malignancy was 100% (62/62). The NPV of negative SCCAg-associated negative PET/CT was 100% (19/19). Conclusions: Serum SCCAg evaluation and FDG PET/CT imaging can be complementary techniques in cases of suspected recurrent cervical squamous cancer. Positive PET/CT with elevated SCCAg can predict recurrence. Although PET/CT cannot confidently be deferred due to a negative SCCAg test, the possibility of a false-positive PET/CT in those cases may have diagnostic importance.
PMCID: PMC4317765  PMID: 25663947
Squamous cell carcinoma antigen; Cervical squamous cancer; Recurrence; FDG PET/CT; False positive
11.  Clinical Treatment of Orthostatic Hypotension after Spinal Cord Injury with Standing Training Coupled with a Remote Monitoring System 
The treatment for orthostatic hypotension (OH) after spinal cord injury (SCI) is an important part of rehabilitation in late-stage SCI. Electric uprise bed training is a relatively commonly used method in treating OH, and how to carry out uprise bed training safely and effectively is an urgent problem. In the early stage of SCI, we used a remote monitoring system to monitor the whole process of uprise bed training, and we explored a safe and efficient method of electric uprise bed training.
The experimental group consisted of 36 patients diagnosed with orthostatic hypotension (OH) after SCI and who received training with an electric uprise bed coupled with remote monitoring system, and the control group of 18 subjects who used a traditional training method.
There were no differences in baseline data between the 2 groups. There were no severe symptoms during training in the experimental group, but 3 patients had severe symptoms in the control group. Among the 32 enrolled subjects reaching upright training status within 30 days (17 subjects in the experimental group and 15 subjects in the control group), time interval of training from horizontal position to erect position in the experimental group was 18.00±3.12 days and 21.40±4.95 days in the control group. Time interval in the experimental group was significantly less than in the control group. However, among all 36 subjects, by combining results of follow-up, there was no significant difference of time interval of training from horizontal position to erect position between the experimental group and the control group. In the experimental group 90.52% of patients finished training compared to 78.19% in the control group (P<0.01). After training, values of OCs and OCd of the experimental group were lower than in the control group. There was no significant difference between groups in number of re-diagnosed OH.
Implementation of training with electric uprise bed coupled with remote monitoring system is generally safe for patients with OH after SCI. For patients who could reach standing training status within 30 days, implementation can improve efficiency of training by shortening time interval of training from horizontal position to erect position. It can increase orthostatic blood pressure change during position change.
PMCID: PMC4280052  PMID: 25529992
Blood Pressure; Electrocardiography; Hypotension, Orthostatic; Spinal Cord Injuries
12.  HPLC determination and clinical significance of serum prednisone in patients with nephrotic syndrome 
Aim: A rapid protocol is necessary to determine the serum concentrations of prednisone. Methods: The HP1100 high-performance liquid chromatographic (HPLC) system was employed. The HP Lichrosphere C8 column (250 mm × 4 mm, i.d., 5 μm particle size) was used. The mobile phase was methanol, tetrahydrofuran and water in the ratio 25:25:50. The flow rate was 1.0 ml/min. The sample was monitored by UV absorbance at 240 nm. Acetanilide was used as the internal standard, and methanol was added into the serum for depositing the protein. Results: The chromatography was effective and was not interfered with by the serum components. Good linearity was observed, within the range of 10-500 μg/L for prednisone, and the detection limit was 5 μg/L. The serum concentrations of prednisone between the nephrotic syndrome (NS) group and the control group were significantly different (P < 0.05), while there was no significant difference between the females and males of the NS group (P > 0.05). The serum ncentration of prednisone in the steroid-resistant group was lower than that in the steroid-sensitive group (P < 0.05). Conclusions: HPLC is a practical and reliable method to determine the serum concentration of prednisone with high accuracy, precision, linearity and repeatability.
PMCID: PMC4307511  PMID: 25664064
Drug monitoring; HPLC; prednisone
13.  The Possible Impact of Vaccination for Seasonal Influenza on Emergence of Pandemic Influenza via Reassortment 
PLoS ONE  2014;9(12):e114637.
One pathway through which pandemic influenza strains might emerge is reassortment from coinfection of different influenza A viruses. Seasonal influenza vaccines are designed to target the circulating strains, which intuitively decreases the prevalence of coinfection and the chance of pandemic emergence due to reassortment. However, individual-based analyses on 2009 pandemic influenza show that the previous seasonal vaccination may increase the risk of pandemic A(H1N1) pdm09 infection. In view of pandemic influenza preparedness, it is essential to understand the overall effect of seasonal vaccination on pandemic emergence via reassortment.
Methods and Findings
In a previous study we applied a population dynamics approach to investigate the effect of infection-induced cross-immunity on reducing such a pandemic risk. Here the model was extended by incorporating vaccination for seasonal influenza to assess its potential role on the pandemic emergence via reassortment and its effect in protecting humans if a pandemic does emerge. The vaccination is assumed to protect against the target strains but only partially against other strains. We find that a universal seasonal vaccine that provides full-spectrum cross-immunity substantially reduces the opportunity of pandemic emergence. However, our results show that such effectiveness depends on the strength of infection-induced cross-immunity against any novel reassortant strain. If it is weak, the vaccine that induces cross-immunity strongly against non-target resident strains but weakly against novel reassortant strains, can further depress the pandemic emergence; if it is very strong, the same kind of vaccine increases the probability of pandemic emergence.
Two types of vaccines are available: inactivated and live attenuated, only live attenuated vaccines can induce heterosubtypic immunity. Current vaccines are effective in controlling circulating strains; they cannot always help restrain pandemic emergence because of the uncertainty of the oncoming reassortant strains, however. This urges the development of universal vaccines for prevention of pandemic influenza.
PMCID: PMC4262424  PMID: 25494180
14.  A Chitin-Like Component on Sclerotic Cells of Fonsecaea pedrosoi Inhibits Dectin-1-Mediated Murine Th17 Development by Masking β-Glucans 
PLoS ONE  2014;9(12):e114113.
Fonsecaea pedrosoi (F. pedrosoi), a major agent of chromoblastomycosis, has been shown to be recognized primarily by C-type lectin receptors (CLRs) in a murine model of chromoblastomycosis. Specifically, the β-glucan receptor, Dectin-1, mediates Th17 development and consequent recruitment of neutrophils, and is evidenced to have the capacity to bind to saprophytic hyphae of F. pedrosoi in vitro. However, when embedded in tissue, most etiological agents of chromoblastomycosis including F. pedrosoi will transform into the sclerotic cells, which are linked to the greatest survival of melanized fungi in tissue. In this study, using immunocompetent and athymic (nu/nu) murine models infected subcutaneously or intraperitoneally with F. pedrosoi, we demonstrated that T lymphocytes play an active role in the resolution of localized footpad infection, and there existed a significantly decreased expression of Th17-defining transcription factor Rorγt and inefficient recruitment of neutrophils in chronically infected spleen where the inoculated mycelium of F. pedrosoi transformed into the sclerotic cells. We also found that Dectin-1-expressing histocytes and neutrophils participated in the enclosure of transformed sclerotic cells in the infectious foci. Furthermore, we induced the formation of sclerotic cells in vitro, and evidenced a significantly decreased binding capacity of human or murine-derived Dectin-1 to the induced sclerotic cells in comparison with the saprophytic mycelial forms. Our analysis of β-glucans-masking components revealed that it is a chitin-like component, but not the mannose moiety on the sclerotic cells, that interferes with the binding of β-glucans by human or murine Dectin-1. Notably, we demonstrated that although Dectin-1 contributed to the development of IL-17A-producing CD3+CD4+ murine splenocytes upon in vitro-stimulation by saprophytic F. pedrosoi, the masking effect of chitin components partly inhibited Dectin-1-mediated Th17 development upon in vitro-stimulation by induced sclerotic cells. Therefore, these findings extend our understanding of the chronicity of chromoblastomycosis.
PMCID: PMC4260783  PMID: 25490199
15.  Abundance and Diversity of Bacterial Nitrifiers and Denitrifiers and Their Functional Genes in Tannery Wastewater Treatment Plants Revealed by High-Throughput Sequencing 
PLoS ONE  2014;9(11):e113603.
Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs) due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB) amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.
PMCID: PMC4242629  PMID: 25420093
16.  Surface Plasmon-Polariton Mediated Red Emission from Organic Light-Emitting Devices Based on Metallic Electrodes Integrated with Dual-Periodic Corrugation 
Scientific Reports  2014;4:7108.
We demonstrate an effective approach to realize excitation and outcoupling of the SPP modes associated with both cathode/organic and anode/organic interfaces in OLEDs by integrating dual-periodic corrugation. The dual-periodic corrugation consists of two set gratings with different periods. The light trapped in the SPP modes associated with both top and bottom electrode/organic interfaces are efficiently extracted from the OLEDs by adjusting appropriate periods of two set corrugations, and a 29% enhancement in the current efficiency has been obtained.
PMCID: PMC4236905  PMID: 25407776
17.  A cytosolic glucose-6-phosphate dehydrogenase gene, ScG6PDH, plays a positive role in response to various abiotic stresses in sugarcane 
Scientific Reports  2014;4:7090.
As one of the key enzymes in the oxidative pentose phosphate pathway, glucose-6-phosphate dehydrogenase (G6PDH) plays a role in response to abiotic stresses and pathogenesis. Here, a full-length cDNA was obtained, designed as ScG6PDH from sugarcane. The ScG6PDH gene is 1,646 bp long with a 1,524-bp long ORF encoding 507 amino acid residues. Analysis of a phylogenetic tree indicated that this gene is a member of the cytosolic G6PDH gene family, which is consistent with results from a subcellular localization experiment. Based on a real-time quantitative RT-PCR performed under salt, drought, heavy metal (CdCl2) and low temperature (4°C) treatments, the transcription levels of the ScG6PDH gene were higher compared with transcription levels where these treatments were not imposed, suggesting a positive response of this gene to these environmental stresses. Furthermore, G6PDH activity was stimulated under 4°C, CdCl2, NaCl and PEG treatments, but the increments varied with treatment and sampling time, implying positive response to abiotic stresses, similar to the transcript of the G6PDH gene. Ion conductivity measurements and a histochemical assay provided indirect evidence of the involvement of the ScG6PDH gene in defense reactions to the above-mentioned abiotic stresses.
PMCID: PMC4235309  PMID: 25404472
18.  Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array 
PeerJ  2014;2:e660.
Genetic admixture has been utilized as a tool for identifying loci associated with complex traits and diseases in recently admixed populations such as African Americans. In particular, admixture mapping is an efficient approach to identifying genetic basis for those complex diseases with substantial racial or ethnic disparities. Though current advances in admixture mapping algorithms may utilize the entire panel of SNPs, providing ancestry-informative markers (AIMs) that can differentiate parental populations and estimate ancestry proportions in an admixed population may particularly benefit admixture mapping in studies of limited samples, help identify unsuitable individuals (e.g., through genotyping the most informative ancestry markers) before starting large genome-wide association studies (GWAS), or guide larger scale targeted deep re-sequencing for determining specific disease-causing variants. Defining panels of AIMs based on commercial, high-throughput genotyping platforms will facilitate the utilization of these platforms for simultaneous admixture mapping of complex traits and diseases, in addition to conventional GWAS. Here, we describe AIMs detected based on the Shannon Information Content (SIC) or Fst for African Americans with genome-wide coverage that were selected from ∼2.3 million single nucleotide polymorphisms (SNPs) covered by the Affymetrix Axiom Pan-African array, a newly developed genotyping platform optimized for individuals of African ancestry.
PMCID: PMC4226639  PMID: 25392759
Admixture mapping; Single nucleotide polymorphism; Pan-African array; Ancestry-informative marker; African American
19.  Overexpression of platelet-derived growth factor receptor alpha promotes tumor progression and indicates poor prognosis in hepatocellular carcinoma 
Oncotarget  2014;5(21):10307-10317.
Dysregulation of platelet-derived growth factor receptor alpha (PDGFRα) has been documented in various cancers. However, its role in hepatocellular carcinoma (HCC) remains unknown. We and others have examined that upregulation of PDGFRα might be involved in hepatocarcinogenesis. Here, we report that PDGFRα plays a critical role in HCC progression and prognosis. The expression of PDGFRα was markedly higher in human HCC compared to adjacent liver tissues. Although PDGFRA mRNA was decreased in HCC, PDGF-A mRNA was dramatically increased in HCC. Overexpression of PDGFRα was strongly correlated with microvessel density (MVD) of HCC (p<0.05), as well as macroscopic vascular invasion of the tumors (p<0.05). HCC patients with high PDGFRα expression displayed a shorter overall survival and a higher recurrence rate than those with low PDGFRα expression (p<0.05, respectively). Additionally, stable overexpression of PDGFRα in hepatoma cells promoted cell proliferation, migration, invasion and epithelial-mesenchymal transition in vitro. Similarly, an in vivo assay showed that PDGFRα overexpression in hepatoma cells exhibited remarkably tumorigenic potential in tumor size and weight in vivo, which displayed markedly elevated MVD than controls. Thus, our study provided the evidence that PDGFRα may serve as a candidate prognostic marker and a novel therapeutic target for HCC.
PMCID: PMC4279374  PMID: 25333264
Platelet-derived growth factor receptor alpha; Hepatocellular carcinoma; survival; metastasis; CD31
20.  CCR7 Regulates Cell Migration and Invasion through JAK2/STAT3 in Metastatic Squamous Cell Carcinoma of the Head and Neck 
BioMed Research International  2014;2014:415375.
Squamous cell carcinoma of the head and neck (SCCHN) frequently involves metastasis at diagnosis. Our previous research has demonstrated that CCR7 plays a key role in regulating SCCHN metastasis, and this process involves several molecules, such as PI3K/cdc42, pyk2, and Src. In this study, the goals are to identify whether JAK2/STAT3 also participates in CCR7's signal network, its relationship with other signal pathways, and its role in SCCHN cell invasion and migration. The results showed that stimulation of CCL19 could induce JAK2/STAT3 phosphorylation, which can be blocked by Src and pyk2 inhibitors. After activation, STAT3 was able to promote low expression of E-cadherin and had no effect on vimentin. This JAk2/STAT3 pathway not only mediated CCR7-induced cell migration but also mediated invasion speed. The immunohistochemistry results also showed that the phosphorylation of STAT3 was correlated with CCR7 expression in SCCHN, and CCR7 and STAT3 phosphorylation were all associated with lymph node metastasis. In conclusion, JAk2/STAT3 plays a key role in CCR7 regulating SCCHN metastasis.
PMCID: PMC4227331  PMID: 25405202
21.  A Versatile Two-Step CRISPR- and RMCE-Based Strategy for Efficient Genome Engineering in Drosophila 
G3: Genes|Genomes|Genetics  2014;4(12):2409-2418.
The development of clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) technologies promises a quantum leap in genome engineering of model organisms. However, CRISPR-mediated gene targeting reports in Drosophila melanogaster are still restricted to a few genes, use variable experimental conditions, and vary in efficiency, questioning the universal applicability of the method. Here, we developed an efficient two-step strategy to flexibly engineer the fly genome by combining CRISPR with recombinase-mediated cassette exchange (RMCE). In the first step, two sgRNAs, whose activity had been tested in cell culture, were co-injected together with a donor plasmid into transgenic Act5C-Cas9, Ligase4 mutant embryos and the homologous integration events were identified by eye fluorescence. In the second step, the eye marker was replaced with DNA sequences of choice using RMCE enabling flexible gene modification. We applied this strategy to engineer four different locations in the genome, including a gene on the fourth chromosome, at comparably high efficiencies. Our data suggest that any fly laboratory can engineer their favorite gene for a broad range of applications within approximately 3 months.
PMCID: PMC4267936  PMID: 25324299
Drosophila; CRISPR/Cas9; homologous recombination; RMCE; muscle
22.  α-Naphthoflavone modulates inflammatory response in adipocytes-macrophages interaction through NFκB signaling 
Objective: Our previous study demonstrated that α-naphthoflavone (α-NF) inhibits mouse 3T3-L1 pre-adipocytes differentiation via PPARγ, a key transcription factor in adipogenesis. Due to the critical role of inflammation in adipogenesis, we speculated that the suppression role of α-NF in adipogenesis might involve in modulation of cytokines secretion raised by adipocyte differentiation cocktail. Therefore, the present study aims to investigate the role of α-NF in modulating of inflammatory response during adipocytes differentiation and adipocyte-macrophage interaction. Methods: Conditioned medium from different doses of α-NF treated 10-day differentiated 3T3-L1 adipocytes were collected to culture RAW264.7 macrophages. Conditioned medium from activated macrophages and α-NF pre-treated macrophage were used to investigate the effects of α-NF in adipocytes differentiation. Cultured cells and medium were harvested for RT-PCR, Western blot and ELISA. Results: α-NF dose-dependently decreased TNF-α and IL-6 and increased IL-10 expression induced by IDM (Insulin, dexamethasone, isobutylmethylxanthine) in 3T3-L1 pre-adipocytes. Conditioned medium from α-NF treated 3T3-L1 differentiated cells inhibited inflammatory response in mouse macrophage cell line RAW264.7 in contrast to IDM control medium. NFĸB activation elicited by IDM was suppressed by α-NF in a dose-response manner. Consequently, decreased TNF-α and increased IL-10 secretion, downstream targets of NFĸB signaling pathway, were observed with α-NF in macrophages. Finally, Conditioned medium from α-NF pre-treated, LPS-activated macrophages ameliorated the suppression of 3T3-L1 adipogenesis by LPS activated macrophages. Conclusion: Our results suggest that α-NF regulates inflammation response in both adipocytes and macrophages and adipocyte-macrophage interaction which contributes to pre-adipocyte differentiation.
PMCID: PMC4270567  PMID: 25550814
Adipocyte-macrohage interaction; α-NF; condition medium; inflammation
23.  Genetic and epigenetic variants contributing to clofarabine cytotoxicity 
Human Molecular Genetics  2013;22(19):4007-4020.
2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine (Clofarabine), a purine nucleoside analog, is used in the treatment of hematologic malignancies and as induction therapy for stem cell transplantation. The discovery of pharmacogenomic markers associated with chemotherapeutic efficacy and toxicity would greatly benefit the utility of this drug. Our objective was to identify genetic and epigenetic variants associated with clofarabine toxicity using an unbiased, whole genome approach. To this end, we employed International HapMap lymphoblastoid cell lines (190 LCLs) of European (CEU) or African (YRI) ancestry with known genetic information to evaluate cellular sensitivity to clofarabine. We measured modified cytosine levels to ascertain the contribution of genetic and epigenetic factors influencing clofarabine-mediated cytotoxicity. Association studies revealed 182 single nucleotide polymorphisms (SNPs) and 143 modified cytosines associated with cytotoxicity in both populations at the threshold P≤ 0.0001. Correlation between cytotoxicity and baseline gene expression revealed 234 genes at P ≤ 3.98 × 10−6. Six genes were implicated as: (i) their expression was directly correlated to cytotoxicity, (ii) they had a targeting SNP associated with cytotoxicity, and (iii) they had local modified cytosines associated with gene expression and cytotoxicity. We identified a set of three SNPs and three CpG sites targeting these six genes explaining 43.1% of the observed variation in phenotype. siRNA knockdown of the top three genes (SETBP1, BAG3, KLHL6) in LCLs revealed altered susceptibility to clofarabine, confirming relevance. As clofarabine's toxicity profile includes acute kidney injury, we examined the effect of siRNA knockdown in HEK293 cells. siSETBP1 led to a significant change in HEK293 cell susceptibility to clofarabine.
PMCID: PMC3766179  PMID: 23720496
24.  TRIM16 inhibits proliferation and migration through regulation of interferon beta 1 in melanoma cells 
Oncotarget  2014;5(20):10127-10139.
High basal or induced expression of the tripartite motif protein, TRIM16, leads to reduce cell growth and migration of neuroblastoma and skin squamous cell carcinoma cells. However, the role of TRIM16 in melanoma is currently unknown. TRIM16 protein levels were markedly reduced in human melanoma cell lines, compared with normal human epidermal melanocytes due to both DNA methylation and reduced protein stability. TRIM16 knockdown strongly increased cell migration in normal human epidermal melanocytes, while TRIM16 overexpression reduced cell migration and proliferation of melanoma cells in an interferon beta 1 (IFNβ1)-dependent manner. Chromatin immunoprecipitation assays revealed TRIM16 directly bound the IFNβ1 gene promoter. Low level TRIM16 expression in 91 melanoma patient samples, strongly correlated with lymph node metastasis, and, predicted poor patient prognosis in a separate cohort of 170 melanoma patients with lymph node metastasis. The BRAF inhibitor, vemurafenib, increased TRIM16 protein levels in melanoma cells in vitro, and induced growth arrest in BRAF-mutant melanoma cells in a TRIM16-dependent manner. High levels of TRIM16 in melanoma tissues from patients treated with Vemurafenib correlated with clinical response. Our data, for the first time, demonstrates TRIM16 is a marker of cell migration and metastasis, and a novel treatment target in melanoma.
PMCID: PMC4259410  PMID: 25333256
Melanoma; TRIM16; BRAF inhibitor; cell migration; IFNβ1
25.  Responses to crizotinib in a patient with c-ros oncogene 1, receptor tyrosine kinase-positive advanced lung adenocarcinoma: A case report 
Oncology Letters  2014;8(6):2624-2626.
Rearrangements to the c-ros oncogene 1, receptor tyrosine kinase (ROS1) gene are reported in 1–2% of lung adenocarcinomas. These rearrangements are associated with a response to the small-molecule tyrosine kinase inhibitor crizotinib. ROS1 rearrangements can be detected using fluorescence in situ hybridization (FISH), which is considered the gold standard technique in detecting ROS1 rearrangements, and determining whether a patient would respond well to crizotinib treatment. However, FISH is an expensive and time-consuming assay, requiring specialized microscopy equipment and some level of technical expertise. The present report describes the case of a patient with advanced lung adenocarcinoma, who was identified to be negative for ROS-1 rearrangements by FISH, but positive by immunohistochemistry (IHC). The health of the patient improved following treatment with crizotinib. These results indicate that IHC assay could be an alternative option for the detection of ROS1 gene rearrangements.
PMCID: PMC4214434  PMID: 25364439
non-small cell lung cancer; gene rearrangements; receptor tyrosine kinase 1; immunohistochemistry; crizotinib; partial responses

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