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1.  Decrease of Urinary Nerve Growth Factor but Not Brain-Derived Neurotrophic Factor in Patients with Interstitial Cystitis/Bladder Pain Syndrome Treated with Hyaluronic Acid 
PLoS ONE  2014;9(3):e91609.
Aims
To investigate urinary nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) levels in interstitial cystitis/bladder pain syndrome (IC/BPS) patients after hyaluronic acid (HA) therapy.
Methods
Thirty-three patients with IC/BPS were prospectively studied; a group of 45 age-matched healthy subjects served as controls. All IC/BPS patients received nine intravesical HA instillations during the 6-month treatment regimen. Urine samples were collected for measuring urinary NGF and BDNF levels at baseline and 2 weeks after the last HA treatment. The clinical parameters including visual analog scale (VAS) of pain, daily frequency nocturia episodes, functional bladder capacity (FBC) and global response assessment (GRA) were recorded. Urinary NGF and BDNF levels were compared between IC/BPS patients and controls at baseline and after HA treatment.
Results
Urinary NGF, NGF/Cr, BDNF, and BDNF/Cr levels were significantly higher in IC/BPS patients compared to controls. Both NGF and NGF/Cr levels significantly decreased after HA treatment. Urinary NGF and NGF/Cr levels significantly decreased in the responders with a VAS pain reduction by 2 (both p < 0.05) and the GRA improved by 2 (both p < 0.05), but not in non-responders. Urinary BDNF and BDNF/Cr did not decrease in responders or non-responders after HA therapy.
Conclusions
Urinary NGF, but not BDNF, levels decreased significantly after HA therapy; both of these factors remained higher than in controls even after HA treatment. HA had a beneficial effect on IC/BPS, but it was limited. The reduction of urinary NGF levels was significant in responders, with a reduction of pain and improved GRA.
doi:10.1371/journal.pone.0091609
PMCID: PMC3948883  PMID: 24614892
2.  Who purchases cigarettes from cheaper sources in China? Findings from the ITC China Survey 
Tobacco control  2013;23(0 1):i97-i101.
Objective
The availability of cigarettes from cheaper sources constitutes a major challenge to public health throughout the world, including China, because it may counteract price-based tobacco control policies. The goal of this study was to identify factors associated with purchasing cigarettes from cheaper sources among adult smokers in China.
Methods
Data were analyzed from Waves 1–3 of the International Tobacco Control China Survey, conducted in 2006–2009 among adult smokers in six cities in China (N=7,980). One survey question asked, “In the last six months, have you purchased cheaper cigarettes than you can get from local stores for economic reasons?” We examined whether sociodemographic factors and smoking intensity were associated with purchasing cigarettes from cheaper sources using the general estimating equations (GEE) model. Sociodemographic factors considered were gender, age, marital status, monthly household income, education, employment status, and city of residence.
Results
15.6% of smokers reported purchasing cigarettes from cheaper sources. After controlling for other covariates, the associations of the behavior of purchasing cigarettes from cheaper sources with age (AOR=1.49, 95% CI=1.17–3.92 for age 18–24 compared to age 55+) and with income (AOR=2.93, 95%CI=2.27–3.79 for low income compared to high income) were statistically significant, but there was no statistically significant relationship with smoking intensity.
Conclusions
Our findings indicate that young and low income smokers are more likely than older and high income smokers to purchase cigarettes from cheaper sources in China. Tobacco control policies that reduce the availability of cigarettes from cheaper sources could have an impact on reducing cigarette consumption among young and low income smokers in China.
doi:10.1136/tobaccocontrol-2013-051040
PMCID: PMC3931911  PMID: 24078076
Cheaper sources; Smoking; China; Taxation; Income
3.  Association of gyrA/B mutations and resistance levels to fluoroquinolones in clinical isolates of Mycobacterium tuberculosis 
To evaluate the association between mutations in the genes gyrA/B and resistance levels to fluoroquinolones in clinical isolates of Mycobacterium tuberculosis, a total of 80 ofloxacin-resistant isolates collected in 2009 by the Shanghai Municipal Centers for Disease Control and Prevention were studied. The minimum inhibitory concentration (MIC) of ofloxacin, moxifloxacin and gatifloxacin for each isolate was determined using the microscopic observation drug susceptibility assay. Sequencing was used to identify mutations in the quinolone resistance-determining region (QRDR) of the gyrA and gyrB genes. In total, 68 isolates had mutations in gyrA, three isolates had mutations in gyrB, six isolates had mutations in both gyrA and gyrB, and three isolates had no mutations. Two common mutations in gyrA, the D94G and D94N mutations, were associated with higher-level resistance to all three fluoroquinolones than two other common mutations (A90V and D94A). Understanding the relationship between MICs and mutations in ofloxacin-resistant isolates will facilitate the optimization of the use of new-generation fluoroquinolones to treat patients with ofloxacin-resistant tuberculosis (TB).
doi:10.1038/emi.2014.21
PMCID: PMC3974338
fluoroquinolones; MICs; M. tuberculosis; mutations
4.  An Assessment of Health Risks and Mortality from Exposure to Secondhand Smoke in Chinese Restaurants and Bars 
PLoS ONE  2014;9(1):e84811.
Introduction
Smoking is generally not regulated in restaurants or bars in China, or the restrictions are not fully implemented if there are any, while the related hazard health effects are not recognized by the majority of the Chinese population.
Objectives
This study aims to assess the excess health risks and mortality attributed to secondhand smoke (SHS) exposure in restaurants and bars for both servers and patrons to provide necessary evidence for advancing tobacco control in this microenvironment.
Methods
Two approaches were used for the assessment. One is a continuous approach based on existing field measurements and Repace and Lowrey’s dose-response model, and the other is a categorical approach based on exposure or not and epidemiological studies.
Results
Based on the continuous approach, servers were estimated to have a lifetime excess risk (LER) of lung cancer death (LCD) of 730 to 1,831×10−6 for working five days a week for 45 years in smoking restaurants and 1,862 to 8,136×10−6 in smoking bars, and patrons could have a LER of LCD of 47 to 117×10−6 due to visiting smoking restaurants for an average of 13 minutes a day for 60 years, and 119 to 522×10−6 due to visiting smoking bars. The categorical approach estimated that SHS exposure in restaurants and bars alone caused 84 LCD and 57 ischemic heart disease (IHD) deaths among nonsmoking servers and 1,2419 LCDs and 1,689 IHD deaths among the nonsmoking patron population.
Conclusions
SHS exposure in restaurants and bars alone can impose high lifetime excess risks of lung cancer death and ischemic heart disease deaths to both servers and patrons, and can cause a significant number of deaths each year in China. These health risks and deaths can be prevented by banning smoking in restaurants and bars and effectively implementing these smoking bans.
doi:10.1371/journal.pone.0084811
PMCID: PMC3885645  PMID: 24416289
5.  Identification and characterization of CBL and CIPK gene families in canola (Brassica napus L.) 
BMC Plant Biology  2014;14:8.
Background
Canola (Brassica napus L.) is one of the most important oil-producing crops in China and worldwide. The yield and quality of canola is frequently threatened by environmental stresses including drought, cold and high salinity. Calcium is a ubiquitous intracellular secondary messenger in plants. Calcineurin B-like proteins (CBLs) are Ca2+ sensors and regulate a group of Ser/Thr protein kinases called CBL-interacting protein kinases (CIPKs). Although the CBL-CIPK network has been demonstrated to play crucial roles in plant development and responses to various environmental stresses in Arabidopsis, little is known about their function in canola.
Results
In the present study, we identified seven CBL and 23 CIPK genes from canola by database mining and cloning of cDNA sequences of six CBLs and 17 CIPKs. Phylogenetic analysis of CBL and CIPK gene families across a variety of species suggested genome duplication and diversification. The subcellular localization of three BnaCBLs and two BnaCIPKs were determined using green fluorescence protein (GFP) as the reporter. We also demonstrated interactions between six BnaCBLs and 17 BnaCIPKs using yeast two-hybrid assay, and a subset of interactions were further confirmed by bimolecular fluorescence complementation (BiFC). Furthermore, the expression levels of six selected BnaCBL and 12 BnaCIPK genes in response to salt, drought, cold, heat, ABA, methyl viologen (MV) and low potassium were examined by quantitative RT-PCR and these CBL or CIPK genes were found to respond to multiple stimuli, suggesting that the canola CBL-CIPK network may be a point of convergence for several different signaling pathways. We also performed a comparison of interaction patterns and expression profiles of CBL and CIPK in Arabidospsis, canola and rice, to examine the differences between orthologs, highlighting the importance of studying CBL-CIPK in canola as a prerequisite for improvement of this crop.
Conclusions
Our findings indicate that CBL and CIPK family members may form a dynamic complex to respond to different abiotic or hormone signaling. Our comparative analyses of the CBL-CIPK network between canola, Arabidopsis and rice highlight functional differences and the necessity to study CBL-CIPK gene functions in canola. Our data constitute a valuable resource for CBL and CPK genomics.
doi:10.1186/1471-2229-14-8
PMCID: PMC3890537  PMID: 24397480
Abiotic stress; Brassica napus; CBL; CIPK
6.  Value of multidetector computed tomography in the diagnosis of mucosa-associated lymphoid tissue-lymphomas in the parotid gland: A case report and review of the literature 
Oncology Letters  2013;7(3):781-786.
The present study aimed to review the multidetector computed tomography (MDCT) imaging features of eight mucosa-associated lymphoid tissue (MALT)-lymphoma cases of the parotid gland and to explore the diagnostic value of MDCT. A total of eight patients with pathologically confirmed MALT-lymphomas of the parotid gland underwent pre-operative MDCT plain and dual-phase scans. The changes in the CT values and enhancement patterns of the tumors were assessed. Quantitative analysis was performed to determine the CT value changes of the tumors in the various enhanced phases compared with the plain scan. The MALT-lymphomas of the parotid gland exhibited even density isodense or hyperdense nodules, with occasional calcification and necrosis. The dual-phase scan of the MALT-lymphomas revealed a pattern of lower or moderate enhancement, circumambient enhancement or delayed enhancement. The MALT-lymphomas were closely associated with Sjögre’s syndrome and demonstrated malignant features and isodense or hyperdense nodules and lower or moderate enhancement on the CT scans.
doi:10.3892/ol.2013.1769
PMCID: PMC3919924  PMID: 24520295
parotid gland; mucosa-associated lymphoid tissue lymphomas; computer tomography; enhancement
7.  Effect of Tetrandrine against Candida albicans Biofilms 
PLoS ONE  2013;8(11):e79671.
Candida albicans is the most common human fungal pathogen and has a high propensity to develop biofilms that are resistant to traditional antifungal agents. In this study, we investigated the effect of tetrandrine (TET) on growth, biofilm formation and yeast-to-hypha transition of C. albicans. We characterized the inhibitory effect of TET on hyphal growth and addressed its possible mechanism of action. Treatment of TET at a low concentration without affecting fungal growth inhibited hyphal growth in both liquid and solid Spider media. Real-time RT-PCR revealed that TET down-regulated the expression of hypha-specific genes ECE1, ALS3 and HWP1, and abrogated the induction of EFG1 and RAS1, regulators of hyphal growth. Addition of cAMP restored the normal phenotype of the SC5314 strain. These results indicate that TET may inhibit hyphal growth through the Ras1p-cAMP-PKA pathway. In vivo, at a range of concentrations from 4 mg/L to 32 mg/L, TET prolonged the survival of C. albicans-infected Caenorhabditis elegans significantly. This study provides useful information for the development of new strategies to reduce the incidence of C. albicans biofilm-associated infections.
doi:10.1371/journal.pone.0079671
PMCID: PMC3832530  PMID: 24260276
8.  Increased Pro-Inflammatory Cytokines, C-Reactive Protein and Nerve Growth Factor Expressions in Serum of Patients with Interstitial Cystitis/Bladder Pain Syndrome 
PLoS ONE  2013;8(10):e76779.
Objective
The etiology and pathogenesis of interstitial cystitis/bladder pain syndrome (IC/BPS) are unclear. Chronic inflammation is considered the main pathology of IC/BPS. This study measured the serum c-reactive protein (CRP), nerve growth factor (NGF) and pro-inflammatory cytokine/chemokine interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, and IL-8 expression in patients with IC/BPS to elucidate the involvement of systemic inflammation in IC/BPS.
Methods
Serum samples were collected from 30 IC/BPS patients and 26 control subjects. The concentrations of serum nerve growth factor (NGF), IL-1β, IL-6, TNF-α, and IL-8 were quantified using a bead-based, human serum adipokine panel kit. Serum C-reactive protein (CRP) was also assessed. Differences of serum CRP, NGF, IL-1β, IL-6, TNF-α, and IL-8 levels between the IC/BPS patients and controls were compared, and correlations between CRP and pro-inflammatory cytokines and chemokine were also evaluated.
Results
The results showed that CRP level (p = 0.031), NGF (p = 0.015) and pro-inflammatory cytokines/chemokine IL-1β, IL-6, TNF-α, and IL-8 levels were significantly higher in the patients with IC/BPS than among controls (all p<0.001). Significant associations were observed between IL-1β and IL-8 (p<0.001), IL-6 and CRP (p = 0.01), IL-6 and IL-8 (p = 0.02), and IL-6 and TNF-α (p = 0.03).
Conclusion
Increased pro-inflammatory cytokines/chemokine (IL-1β, IL-6, TNF-α, and IL-8) expression in the sera of IC/BPS patients implies not only mast cell activation, but also that other inflammatory mediators play important roles in the pathogenesis of IC/BPS. Thus, for some patients, IC/BPS is considered a chronic inflammatory disease.
doi:10.1371/journal.pone.0076779
PMCID: PMC3798602  PMID: 24146927
10.  Increased Serum Adipokines Implicate Chronic Inflammation in the Pathogenesis of Overactive Bladder Syndrome Refractory to Antimuscarinic Therapy 
PLoS ONE  2013;8(10):e76706.
Objectives
Recent studies have shown that chronic inflammation is involved in overactive bladder (OAB) syndrome. OAB could be a subtype of neurogenic inflammation. This pilot study investigated serum adipokine levels in patients with OAB refractory to antimuscarinic therapy.
Methods
Thirty consecutive patients with OAB-dry (n = 16) or OAB-wet (n = 14) refractory to previous antimuscarinic treatment were prospectively enrolled in this study, a group of 26 normal subjects without lower urinary tract symptoms served as controls. Concentrations of serum C-reactive protein (CRP), nerve growth factor (NGF), and adipokines including interleukins ([IL], IL-1β, IL-6, IL-8), tumor necrosis factor (TNF)-α, monocyte chemotactic protein (MCP)-1, insulin, and leptin were quantified using a bead-based human serum adipokine panel B kit. Data were analyzed using the LX 200 platform. Patients were further classified as having dry or wet OAB and having medical diseases or not. The serum CRP, NGF, and adipokine levels were compared between OAB patients and the controls, and between OAB subgroups.
Results
The serum concentrations of CRP, NGF, IL-1β, IL-6, IL-8, and TNF-α in OAB-dry and OAB-wet patients were significantly higher than among the controls. There was no significant difference in adipokine levels between OAB-dry and OAB-wet, or between OAB patients with and without medical diseases. Serum CRP and NGF levels were significantly higher only in OAB-wet or OAB patients with medical diseases than among controls. The MCP-1 levels, on the other hand, were significantly higher in OAB-dry or OAB patients with disease, than the controls.
Conclusions
Both OAB-dry and OAB-wet patients showed increased serum CRP, NGF, and adipokine levels compared with the controls, suggesting chronic inflammation of the bladder involving both peripheral and central mechanisms in all OAB patients refractory to antimuscarinic therapy. The increased serum adipokine levels were not relevant to medical diseases.
doi:10.1371/journal.pone.0076706
PMCID: PMC3788120  PMID: 24098552
11.  Biomass and Its Allocation in Relation to Temperature, Precipitation, and Soil Nutrients in Inner Mongolia Grasslands, China 
PLoS ONE  2013;8(7):e69561.
Aim
Understanding and predicting ecosystem functioning such as biomass accumulation requires an accurate assessment of large-scale patterns of biomass distribution and partitioning in relation to climatic and soil environments.
Methods
We sampled above- and belowground biomass from 26 sites spanning 1500 km in Inner Mongolian grasslands, compared the difference in aboveground, belowground biomass and below-aboveground biomass ratio (AGB, BGB, and B/A, respectively) among meadow steppe, typical steppe, and desert steppe types. The relationships between AGB, BGB, B/A and climatic and soil environments were then examined.
Results
We found that AGB and BGB differed significantly among three types of grasslands while B/A did not differ. Structural equation model analyses indicated that mean annual precipitation was the strongest positive driver for AGB and BGB. AGB was also positively associated with soil organic carbon, whereas B/A was positively associated with total soil nitrogen.
Conclusions
These results indicated that precipitation positively influence plant production in Inner Mongolian grasslands. Contrary to the prediction from the optimal partitioning hypothesis, biomass allocation to belowground increased with soil total nitrogen, suggesting that more productive sites may increase belowground allocation as an adaptive strategy to potentially high fire frequencies.
doi:10.1371/journal.pone.0069561
PMCID: PMC3723834  PMID: 23936045
12.  Methylation levels at IGF2 and GNAS DMRs in infants born to preeclamptic pregnancies 
BMC Genomics  2013;14:472.
Background
Offspring of pregnancy complicated with preeclampsia are at high risk for hypertension, stroke and possibly obesity. The mechanisms behind the association of intrauterine exposure to preeclampsia and high risk of health problems in the later life remain largely unknown. The aims of the current investigation were to determine the changes in DNA methylation at IGF2 and GNAS DMR in offspring of preeclamptic pregnancy and to explore the possible mechanisms underlying the association between maternal preeclampsia and high risk for health problems in the later life of their offspring.
Results
Umbilical cord blood was taken from infants born to women of preeclampsia (n=56), gestational hypertension (n=23) and normal pregnancy (n=81). DNA methylation levels of IGF2 and GNAS DMR were determined by Massarray quantitative methylation analysis. Methylation levels at IGF2 DMR were significantly lower in preeclampsia than normal pregnancy. The average methylation level at IGF2 DMR was significantly correlated with preeclampsia even after birth weight, maternal age, gestational age at delivery and fetal gender were adjusted. The difference in methylation level was not significantly different between mild and severe preeclampsia. The methylation level at GNAS DMR was not significantly correlated with birth weight, maternal age, gestational age at delivery, fetal gender, preeclampsia or gestational hypertension.
Conclusions
We concluded preeclampsia induced a decrease in methylation level at IGF 2 DMR, and this might be among the mechanisms behind the association between intrauterine exposure to preeclampsia and high risk for metabolic diseases in the later life of the infants.
doi:10.1186/1471-2164-14-472
PMCID: PMC3723441  PMID: 23844573
Preeclampsia; Offspring; DNA methylation; IGF2; GNAS; Metabolic diseases
13.  Effectiveness of a Smoke-Free Policy in Lowering Secondhand Smoke Concentrations in Offices in China 
Objective
To examine the secondhand smoke (SHS) exposure level in Chinese office buildings and to evaluate the effectiveness of a smoke-free policy in reducing SHS exposure.
Methods
Survey of smoking policies and measurement of SHS level in 14 office buildings from 10 provinces in China.
Results
Smoking in the building significantly elevated the SHS concentrations both in offices with at least one smoker and in offices with no smokers. In one building that recently adopted a smoke-free policy, the nicotine concentrations decreased significantly after the policy was enacted. Enactment of a smoking policy was effective in reducing SHS exposure in the buildings.
Conclusions
Nonsmoking office workers in China were exposed to significant levels of SHS at work; both the central and local governments should realize the need to legislate against workplace smoking.
doi:10.1097/JOM.0b013e3181638640
PMCID: PMC3685721  PMID: 18469626
14.  Identification and analysis of MKK and MPK gene families in canola (Brassica napus L.) 
BMC Genomics  2013;14:392.
Background
Eukaryotic mitogen-activated protein kinase (MAPK/MPK) signaling cascades transduce and amplify environmental signals via three types of reversibly phosphorylated kinases to activate defense gene expression. Canola (oilseed rape, Brassica napus) is a major crop in temperate regions. Identification and characterization of MAPK and MAPK kinases (MAPKK/MKK) of canola will help to elucidate their role in responses to abiotic and biotic stresses.
Results
We describe the identification and analysis of seven MKK (BnaMKK) and 12 MPK (BnaMPK) members from canola. Sequence alignments and phylogenetic analyses of the predicted amino acid sequences of BnaMKKs and BnaMPKs classified them into four different groups. We also examined the subcellular localization of four and two members of BnaMKK and BnaMPK gene families, respectively, using green fluorescent protein (GFP) and, found GFP signals in both nuclei and cytoplasm. Furthermore, we identified several interesting interaction pairs through yeast two-hybrid (Y2H) analysis of interactions between BnaMKKs and BnaMPKs, as well as BnaMPK and BnaWRKYs. We defined contiguous signaling modules including BnaMKK9-BnaMPK1/2-BnaWRKY53, BnaMKK2/4/5-BnaMPK3/6-BnaWRKY20/26 and BnaMKK9-BnaMPK5/9/19/20. Of these, several interactions had not been previously described in any species. Selected interactions were validated in vivo by a bimolecular fluorescence complementation (BiFC) assay. Transcriptional responses of a subset of canola MKK and MPK genes to stimuli including fungal pathogens, hormones and abiotic stress treatments were analyzed through real-time RT-PCR and we identified a few of BnaMKKs and BnaMPKs responding to salicylic acid (SA), oxalic acid (OA), Sclerotinia sclerotiorum or other stress conditions. Comparisons of expression patterns of putative orthologs in canola and Arabidopsis showed that transcript expression patterns were generally conserved, with some differences suggestive of sub-functionalization.
Conclusions
We identified seven MKK and 12 MPK genes from canola and examined their phylogenetic relationships, transcript expression patterns, subcellular localization, and protein-protein interactions. Not all expression patterns and interactions were conserved between canola and Arabidopsis, highlighting the limitations of drawing inferences about crops from model species. The data presented here provide the first systematic description of MKK-MPK-WRKY signaling modules in canola and will further improve our understanding of defense responses in general and provide a basis for future crop improvement.
doi:10.1186/1471-2164-14-392
PMCID: PMC3701561  PMID: 23758924
Abiotic stress; Biotic stress; Brassica napus; MKK; MPK; Sclerotinia sclerotiorum; WRKY
15.  Bifactor Item Response Theory Model of Acute Stress Response 
PLoS ONE  2013;8(6):e65291.
Background
Better understanding of acute stress responses is important for revision of DSM-5. However, the latent structure and relationship between different aspects of acute stress responses haven’t been clarified comprehensively. Bifactor item response model may help resolve this problem.
Objective
The purpose of this study is to develop a statistical model of acute stress responses, based on data from earthquake rescuers using Acute Stress Response Scale (ASRS). Through this model, we could better understand acute stress responses comprehensively, and provide preliminary information for computerized adaptive testing of stress responses.
Methods
Acute stress responses of earthquake rescuers were evaluated using ASRS, and state/trait anxiety were assessed using State-trait Anxiety Inventory (STAI). A hierarchical item response model (bifactor model) was used to analyze the data. Additionally, we tested this hierarchical model with model fit comparisons with one-dimensional and five-dimensional models. The correlations among acute stress responses and state/trait anxiety were compared, based on both the five-dimensional and bifactor models.
Results
Model fit comparisons showed bifactor model fit the data best. Item loadings on general and specific factors varied greatly between different aspects of stress responses. Many symptoms (40%) of physiological responses had positive loadings on general factor, and negative loadings on specific factor of physiological responses, while other stress responses had positive loadings on both general and specific factors. After extracting general factor of stress responses using bifactor analysis, significant positive correlations between physiological responses and state/trait anxiety (r = 0.185/0.112, p<0.01) changed into negative ones (r = −0.177/−0.38, p<0.01).
Conclusion
Our results demonstrated bifactor structure of acute stress responses, and positive and negative correlations between physiological responses and stress responses suggested physiological responses could have negative feedback on severity of stress responses. This finding has not been convincingly demonstrated in previous research.
doi:10.1371/journal.pone.0065291
PMCID: PMC3676469  PMID: 23762336
16.  Dietary Intake and Risk for Reflux Esophagitis: A Case-Control Study 
Background. Specific dietary components have been associated with gastroesophageal reflux disease (GERD) in Europe and the United States. However, the relationship between dietary components and GERD in Chinese still remains unclear. Methods. A total of 268 patients who were newly diagnosed as reflux esophagitis (RE) in Outpatient Endoscopy Center of Tongji Hospital were recruited. In addition, 269 sex- and age-matched subjects were also recruited as controls. The body measurements were determined, and the dietary intake during the previous year was evaluated using food frequency questionnaire (FFQ). Stepwise multiple logistic regression analysis was performed to examine the association between nutrients and RE. Results. After adjustment for WC, WHR, total energy intake, and demographics, there were a positive dose-response relationship between RE and calcium, meat, oils, and salt and a negative dose-response relationship between RE and protein, carbohydrate, calories from protein (%), vitamin C, grains and potatoes, fruits, and eggs. Conclusion. High intake of meat, oils, salt, and calcium is associated with an increased risk for RE while high intake of protein, carbohydrate, calories from protein (%), vitamin C, grains and potatoes, fruits, and eggs correlates with a reduced risk for RE.
doi:10.1155/2013/691026
PMCID: PMC3652144  PMID: 23690762
17.  RNA Interference of GADD153 Protects Photoreceptors from Endoplasmic Reticulum Stress-Mediated Apoptosis after Retinal Detachment 
PLoS ONE  2013;8(3):e59339.
Background
Apoptosis of photoreceptors plays a critical role in the vision loss caused by retinal detachment (RD). Pharmacologic inhibition of photoreceptor cell death may prevent RD. This study investigated the role of GADD153 that participates in endoplasmic reticulum (ER) stress-mediated apoptosis of photoreceptor cells after RD.
Methods
Retinal detachment was created in Wistar rats by subretinal injection of hyaluronic acid. The rats were then randomly divided into four groups: normal control group, RD group, GADD153 RNAi group and vehicle group. RNA interference of GADD153 was performed using short hairpin RNA (shRNA). Expressions of GADD153 mRNA and protein were examined by RT-PCR and Western blotting analysis, respectively. GADD153 protein distribution in the retinal cells was observed using immunofluorescence confocal laser scanning microscopy. Apoptosis of retinal cells was determined by TdT-mediated fluorescein-16-dUTP nick-end labeling (TUNEL) assay.
Results
Lentivirus GADD153 shRNA with the most effective silencing effect was chosen for in vivo animal study and was successfully delivered into the retinal tissues. GADD153 mRNA and protein expressions in GADD153 RNAi group were significantly lower than those in the RD group. Silencing of GADD153 by RNAi protected photoreceptors from ER stress-induced apoptosis.
Conclusion
ER stress-mediated pathway is involved in photoreceptor cell apoptosis after RD. GADD153 is a key regulatory molecule regulating ER-stress pathways and plays a crucial role in the apoptosis of photoreceptor cells after RD.
doi:10.1371/journal.pone.0059339
PMCID: PMC3612068  PMID: 23555658
18.  p53 codon 72 polymorphism and breast cancer risk: A meta-analysis 
p53 is a tumor suppressor gene and plays important roles in the etiology of breast cancer. Studies have produced conflicting results concerning the role of p53 codon 72 polymorphism (G>C) on the risk of breast cancer; therefore, a meta-analysis was performed to estimate the association between the p53 codon 72 polymorphism and breast cancer. Screening of the PubMed database was conducted to identify relevant studies. Studies containing available genotype frequencies of the p53 codon 72 polymorphism were selected and a pooled odds ratio (OR) with 95% confidence interval (CI) was used to assess the association. Sixty-one published studies, including 28,539 breast cancer patients and 32,788 controls were identified. The results suggest that variant genotypes are not associated with breast cancer risk (Pro/Pro + Arg/Pro vs. Arg/Arg: OR=1.016, 95% CI=0.931–1.11, P=0.722). The symmetric funnel plot, Egger’s test (P=0.506) and Begg’s test (P=0.921) were all suggestive of the lack of publication bias. This meta-analysis suggests that the p53 codon 72 Pro/Pro + Arg/Pro genotypes are not associated with an increased risk of breast cancer. To validate the association between the p53 codon 72 polymorphism and breast cancer, further studies with larger numbers of participants worldwide are required.
doi:10.3892/etm.2013.1019
PMCID: PMC3671901  PMID: 23737888
p53; meta-analysis; breast cancer
19.  International Prostatic Symptom Score — Voiding/Storage Subscore Ratio in Association with Total Prostatic Volume and Maximum Flow Rate Is Diagnostic of Bladder Outlet-Related Lower Urinary Tract Dysfunction in Men with Lower Urinary Tract Symptoms 
PLoS ONE  2013;8(3):e59176.
Objectives
The aim of this study was to investigate the predictive values of the total International Prostate Symptom Score (IPSS-T) and voiding to storage subscore ratio (IPSS-V/S) in association with total prostate volume (TPV) and maximum urinary flow rate (Qmax) in the diagnosis of bladder outlet-related lower urinary tract dysfunction (LUTD) in men with lower urinary tract symptoms (LUTS).
Methods
A total of 298 men with LUTS were enrolled. Video-urodynamic studies were used to determine the causes of LUTS. Differences in IPSS-T, IPSS-V/S ratio, TPV and Qmax between patients with bladder outlet-related LUTD and bladder-related LUTD were analyzed. The positive and negative predictive values (PPV and NPV) for bladder outlet-related LUTD were calculated using these parameters.
Results
Of the 298 men, bladder outlet-related LUTD was diagnosed in 167 (56%). We found that IPSS-V/S ratio was significantly higher among those patients with bladder outlet-related LUTD than patients with bladder-related LUTD (2.28±2.25 vs. 0.90±0.88, p<0.001). TPV was similar between the two groups; however, in contrast to patients with bladder-related LUTD, patients with bladder outlet-related LUTD had higher detrusor voiding pressure, lower Qmax values, and greater postvoid residual volumes. The combination of TPV30 ml and Qmax10 ml/sec had a PPV of 68.8% and a NPV of 53.5% for bladder outlet-related LUTD. When IPSS-T12 or IPSS-T15 was considered as an additional criterion, PPV increased to 75.0% and 78.5%, respectively, and the NPV decreased to 50.9% and 50.2%, respectively. When IPSS-V/S>1 or >2 was factored into the equation instead of IPSS-T, PPV were 91.4% and 97.3%, respectively, and NPV were 54.8% and 49.8%, respectively.
Conclusions
Combination of IPSS-T with TPV and Qmax increases the PPV of bladder outlet-related LUTD. Furthermore, including IPSS-V/S>1 or >2 into the equation results in a higher PPV than IPSS-T. IPSS-V/S>1 is a stronger predictor of bladder outlet-related LUTD than IPSS-T.
doi:10.1371/journal.pone.0059176
PMCID: PMC3601066  PMID: 23527124
20.  Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum 
PLoS Pathogens  2013;9(2):e1003204.
Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. We tested these opposing frameworks in two lineages of mutualistic rhizobia, Sinorhizobium fredii and Bradyrhizobium japonicum. To examine genes demonstrably important for host-interactions we coupled the mining of genome sequences to a comprehensive functional screen for type III effector genes, which are necessary for many Gram-negative pathogens to infect their hosts. We demonstrate that the rhizobial type III effector genes exhibit a surprisingly high degree of conservation in content and sequence that is in contrast to those of a well characterized plant pathogenic species. This type III effector gene conservation is particularly striking in the context of the relatively high genome-wide diversity of rhizobia. The evolution of rhizobial type III effectors is inconsistent with the molecular arms race paradigm. Instead, our results reveal that these loci are relatively static in rhizobial lineages and suggest that fitness conflicts between rhizobia mutualists and their host plants have been largely resolved.
Author Summary
Rhizobia are an important group of bacteria that can enter into mutually beneficial symbiotic interactions with legume plants to fix atmospheric nitrogen. However, in order to do so, a complex dialog involving the exchange of chemical and molecular signals must occur between partners. Some species of beneficial rhizobia employ a type III secretion system, a well-characterized virulence mechanism used by pathogens to inject bacterial-encoded type III effector proteins directly into host cells to coerce the host into accommodating the microbe. In this study, we generated draft genome sequences and employed computational as well as experimental methods to identify type III effectors from eight strains representing Sinorhizobium fredii and Bradyrhizobium japonicum. We demonstrate that the type III effector genes of these rhizobial species are highly conserved in content with little diversity between strains. This work is an important step towards understanding the roles for type III secretion systems and their effectors in mutualistic interactions.
doi:10.1371/journal.ppat.1003204
PMCID: PMC3585131  PMID: 23468637
21.  NCK2 Is Significantly Associated with Opiates Addiction in African-Origin Men 
The Scientific World Journal  2013;2013:748979.
Substance dependence is a complex environmental and genetic disorder with significant social and medical concerns. Understanding the etiology of substance dependence is imperative to the development of effective treatment and prevention strategies. To this end, substantial effort has been made to identify genes underlying substance dependence, and in recent years, genome-wide association studies (GWASs) have led to discoveries of numerous genetic variants for complex diseases including substance dependence. Most of the GWAS discoveries were only based on single nucleotide polymorphisms (SNPs) and a single dichotomized outcome. By employing both SNP- and gene-based methods of analysis, we identified a strong (odds ratio = 13.87) and significant (P value = 1.33E − 11) association of an SNP in the NCK2 gene on chromosome 2 with opiates addiction in African-origin men. Codependence analysis also identified a genome-wide significant association between NCK2 and comorbidity of substance dependence (P value = 3.65E − 08) in African-origin men. Furthermore, we observed that the association between the NCK2 gene (P value = 3.12E − 10) and opiates addiction reached the gene-based genome-wide significant level. In summary, our findings provided the first evidence for the involvement of NCK2 in the susceptibility to opiates addiction and further revealed the racial and gender specificities of its impact.
doi:10.1155/2013/748979
PMCID: PMC3603435  PMID: 23533358
22.  Reduced Expression of ZDHHC2 Is Associated with Lymph Node Metastasis and Poor Prognosis in Gastric Adenocarcinoma 
PLoS ONE  2013;8(2):e56366.
Background
Zinc finger, DHHC-type containing 2 (ZDHHC2), originally named as reduced expression associated with metastasis protein (REAM), has been proposed as a putative tumor/metastasis suppressor gene and is often aberrantly decreased in human cancers. However ZDHHC2 expression pattern and its clinical significance have not yet been investigated in gastric adenocarcinoma.
Methodology/Principal Findings
Quantitative Real-Time PCR (qRT-PCR) and immunostaining were performed to detect ZDHHC2 expression in gastric adenocarcinoma, and then the correlation between ZDHHC2 expression and clinicpathologic parameters, and patient survival was analyzed. Compared to the adjacent normal tissues, ZDHHC2 expression was significantly reduced in gastric tumor tissues as shown by qRT-PCR and immunostaining. Low expression of ZDHHC2 was observed in 44.7% (211/472) of gastric adenocarcinoma patients, and was associated significantly with lymph node metastasis (p<0.001) and histological grade (p<0.001). Multivariate Cox regression analysis indicated that ZDHHC2 expression had a significant, independent predictive value for survival of gastric cancer patients (HR = 0.627, p = 0.001).
Conclusions/Significance
Our data suggest that reduced ZDHHC2 expression is associated with lymph node metastasis and independently predicts an unfavorable prognosis in gastric adenocarcinoma patients.
doi:10.1371/journal.pone.0056366
PMCID: PMC3574152  PMID: 23457560
23.  Accurate whole genome sequencing and haplotyping from10-20 human cells 
Nature  2012;487(7406):190-195.
Recent advances in whole genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, Long Fragment Read (LFR) technology, similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ~100 pg of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants (SNVs) were assembled into long haplotype contigs. Removal of false positive SNVs not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 Mb. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.
doi:10.1038/nature11236
PMCID: PMC3397394  PMID: 22785314
24.  Nonparametric Covariate-Adjusted Association Tests Based on the Generalized Kendall’s Tau* 
Identifying the risk factors for comorbidity is important in psychiatric research. Empirically, studies have shown that testing multiple, correlated traits simultaneously is more powerful than testing a single trait at a time in association analysis. Furthermore, for complex diseases, especially mental illnesses and behavioral disorders, the traits are often recorded in different scales such as dichotomous, ordinal and quantitative. In the absence of covariates, nonparametric association tests have been developed for multiple complex traits to study comorbidity. However, genetic studies generally contain measurements of some covariates that may affect the relationship between the risk factors of major interest (such as genes) and the outcomes. While it is relatively easy to adjust these covariates in a parametric model for quantitative traits, it is challenging for multiple complex traits with possibly different scales. In this article, we propose a nonparametric test for multiple complex traits that can adjust for covariate effects. The test aims to achieve an optimal scheme of adjustment by using a maximum statistic calculated from multiple adjusted test statistics. We derive the asymptotic null distribution of the maximum test statistic, and also propose a resampling approach, both of which can be used to assess the significance of our test. Simulations are conducted to compare the type I error and power of the nonparametric adjusted test to the unadjusted test and other existing adjusted tests. The empirical results suggest that our proposed test increases the power through adjustment for covariates when there exist environmental effects, and is more robust to model misspecifications than some existing parametric adjusted tests. We further demonstrate the advantage of our test by analyzing a data set on genetics of alcoholism.
doi:10.1080/01621459.2011.643707
PMCID: PMC3381868  PMID: 22745516
Comorbidity; Environmental factor; Family-based association test; Maximum test statistic; Multiple traits; Ordinal traits
25.  Expression of HGF and Met in Human Tissues of Colorectal Cancers: Biological and Clinical Implications for Synchronous Liver Metastasis 
Background and aims: Synchronous liver metastasis (SLM) remains a significant problem in newly diagnosed colorectal cancer (CRC). The system of hepatocyte growth factor (HGF) and Met plays an important role in cancer invasion and metastasis and is being developed to be targeted drugs. We aimed to investigate the role of HGF/Met in SLM based on a case-matched study and comparison between primary tumors and matched metastases.
Methods: A group of 30 patients with SLM and other two groups of patients without SLM in a hospital database were collected. They were matched into according to clinicopathological factors. 81 patients were included in the study. Their tissues of primary colorectal cancers, lymph nodes and liver metastases were collected to detect HGF and Met expression by immunohistochemistry and RT-PCR.
Results: Expression of HGF and Met at the protein level and the RNA level in primary CRCs with SLM were significantly higher than that in primary colorectal carcinomas without liver metastases (all P value<0.05). Their expression was only related to SLM when concurrent with regional lymph node metastasis (all P value<0.05) but had little influence on SLM without involvement of lymph node metastasis (all P value>0.05). Comparison their expression between primary tumors and matched metastases, major concordance and minor difference existed.
Conclusions: HGF and Met may exert functions in the development of SLM when concurrent with lymph node metastases but had little influence on SLM without lymph node metastasis, further indicating their roles and potential values for a subtype of colorectal cancer metastasis. Major concordance and minor difference exist between primary tumors and matched metastases, which further provides evidence for evaluating the response to their inhibitors based on primary tumors or metastases.
doi:10.7150/ijms.5191
PMCID: PMC3607240  PMID: 23532910
colorectal carcinoma; synchronous liver metastasis; hepatocyte growth factor; Met.

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