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1.  An atlas of DNA methylomes in porcine adipose and muscle tissues 
Nature communications  2012;3:850.
It is evident that epigenetic factors, especially DNA methylation, play essential roles in obesity development. Using pig as a model, here we investigated the systematic association between DNA methylation and obesity. We sampled eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generated 1,381 gigabases (Gb) of sequence data from 180 methylated DNA immunoprecipitation (MeDIP) libraries, and provided a genome-wide DNA methylation map as well as a gene expression map for adipose and muscle studies. The analysis showed global similarity and difference among breeds, sexes and anatomic locations, and identified the differentially methylated regions (DMRs). The DMRs in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth.
doi:10.1038/ncomms1854
PMCID: PMC3508711  PMID: 22617290
2.  Genome-Wide Mapping of DNA Methylation in Chicken 
PLoS ONE  2011;6(5):e19428.
Cytosine DNA methylation is an important epigenetic modification termed as the fifth base that functions in diverse processes. Till now, the genome-wide DNA methylation maps of many organisms has been reported, such as human, Arabidopsis, rice and silkworm, but the methylation pattern of bird remains rarely studied. Here we show the genome-wide DNA methylation map of bird, using the chicken as a model organism and an immunocapturing approach followed by high-throughput sequencing. In both of the red jungle fowl and the avian broiler, DNA methylation was described separately for the liver and muscle tissue. Generally, chicken displays analogous methylation pattern with that of animals and plants. DNA methylation is enriched in the gene body regions and the repetitive sequences, and depleted in the transcription start site (TSS) and the transcription termination site (TTS). Most of the CpG islands in the chicken genome are kept in unmethylated state. Promoter methylation is negatively correlated with the gene expression level, indicating its suppressive role in regulating gene transcription. This work contributes to our understanding of epigenetics in birds.
doi:10.1371/journal.pone.0019428
PMCID: PMC3088676  PMID: 21573164
3.  Nrf2 Deficiency in Dendritic Cells Enhances the Adjuvant Effect of Ambient Ultrafine Particles on Allergic Sensitization 
Journal of innate immunity  2013;5(6):543-554.
Particulate matter (PM) is an important risk factor for asthma. Generation of oxidative stress by PM is a major mechanism of its health effects. Transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) mediates antioxidant and phase II enzymes and is essential in protecting against oxidative stress and lung inflammation. We have previously shown that ambient ultrafine particles (UFP) could exert a potent adjuvant effect on allergic sensitization to ovalbumin (OVA) in mice. We hypothesized that Nrf2 deficiency in dendritic cells (DC) could enhance the adjuvant potential of UFP on allergic sensitization. We show that the adjuvant effect of intranasally instilled UFP is significantly enhanced in Nrf2 knockout (Nrf2-/-) mice compared with their wild-type (Nrf2+/+) counterparts. Under resting conditions Nrf2-/- DC displayed an intrinsic predilection to a T-helper 2 (Th2)-favoring cytokine profile characterized by low level of IL-12p70 and high level of IL-6 as compared to Nrf2+/+ DC. Adoptive transfer of OVA/UFP-treated Nrf2-/- DC provoked a more severe allergic inflammation in the lung than Nrf2+/+ DC in the same treatment group. We conclude that Nrf2 deficiency in DC may promote a constitutive immune-polarizing cytokine milieu, which we propose may have contributed to the augmented adjuvant effect of UFP on allergic sensitization.
doi:10.1159/000347060
PMCID: PMC3932311  PMID: 23595026
Nrf2; Dendritic cell; Adjuvant; Allergic sensitization; Lung inflammation; Ultrafine particles; IL-12p70; IL-6; T-helper 2
4.  Reversal of Ischemic Cardiomyopathy with Sca-1+ Stem Cells Modified with Multiple Growth Factors 
PLoS ONE  2014;9(4):e93645.
Background
We hypothesized that bone marrow derived Sca-1+ stem cells (BM Sca-1+) transduced with multiple therapeutic cytokines with diverse effects will induce faster angiomyogenic differentiation in the infarcted myocardium.
Methods and Results
BM Sca-1+ were purified from transgenic male mice expressing GFP. Plasmids encoding for select quartet of growth factors, i.e., human IGF-1, VEGF, SDF-1α and HGF were prepared and used for genetic modification of Sca-1+ cells (GFSca-1+). Scramble transfected cells (ScSca-1+) were used as a control. RT-PCR and western blotting showed significantly higher expression of the growth factors in GFSca-1+. Besides the quartet of the therapeutic growth factors, PCR based growth factor array showed upregulation of multiple angiogenic and prosurvival factors such as Ang-1, Ang-2, MMP9, Cx43, BMP2, BMP5, FGF2, and NGF in GFSca-1+ (p<0.01 vs ScSca-1+). LDH and TUNEL assays showed enhanced survival of GFSca-1+ under lethal anoxia (p<0.01 vs ScSca-1+). MTS assay showed significant increased cell proliferation in GFSca-1+ (p<0.05 vs ScSca-1+). For in vivo study, female mice were grouped to receive the intramyocardial injection of 15 μl DMEM without cells (group-1) or containing 2.5×105 ScSca-1+ (group-2) or GFSca-1+ (group-3) immediately after coronary artery ligation. As indicated by Sry gene, a higher survival of GFSca-1+ in group-3 on day4 (2.3 fold higher vs group-2) was observed with massive mobilization of stem and progenitor cells (cKit+, Mdr1+, Cxcr4+ cells). Heart tissue sections immunostained for actinin and Cx43 at 4 weeks post engraftment showed extensive myofiber formation and expression of gap junctions. Immunostaining for vWF showed increased blood vessel density in both peri-infarct and infarct regions in group-3. Infarct size was attenuated and the global heart function was improved in group-3 as compared to group-2.
Conclusions
Administration of BM Sca-1+ transduced with multiple genes is a novel approach to treat infarcted heart for its regeneration.
doi:10.1371/journal.pone.0093645
PMCID: PMC3976296  PMID: 24705272
5.  Calcium Channel Autoantibodies Predicted Sudden Cardiac Death and All-Cause Mortality in Patients with Ischemic and Nonischemic Chronic Heart Failure 
Disease Markers  2014;2014:796075.
The purpose of this study was to evaluate whether CC-AAbs levels could predict prognosis in CHF patients. A total of 2096 patients with CHF (841 DCM patients and 1255 ICM patients) and 834 control subjects were recruited. CC-AAbs were detected and the relationship between CC-AAbs and patient prognosis was analyzed. During a median follow-up time of 52 months, there were 578 deaths. Of these, sudden cardiac death (SCD) occurred in 102 cases of DCM and 121 cases of ICM. The presence of CC-AAbs in patients was significantly higher than that of controls (both P < 0.001). Multivariate analysis revealed that positive CC-AAbs could predict SCD (HR 3.191, 95% CI 1.598–6.369 for DCM; HR 2.805, 95% CI 1.488–5.288 for ICM) and all-cause mortality (HR 1.733, 95% CI 1.042–2.883 for DCM; HR 2.219, 95% CI 1.461–3.371 for ICM) in CHF patients. A significant association between CC-AAbs and non-SCD (NSCD) was found in ICM patients (HR = 1.887, 95% CI 1.081–3.293). Our results demonstrated that the presence of CC-AAbs was higher in CHF patients versus controls and corresponds to a higher incidence of all-cause death and SCD. Positive CC-AAbs may serve as an independent predictor for SCD and all-cause death in these patients.
doi:10.1155/2014/796075
PMCID: PMC3966345
6.  The effects of a tourniquet used in total knee arthroplasty: a meta-analysis 
Background
The purpose of this research is to evaluate the effects of a tourniquet in total knee arthroplasty (TKA).
Methods
The study was done by randomized controlled trials (RCTs) on the effects of a tourniquet in TKA. All related articles which were published up to June 2013 from Medline, Embase, and Cochrane Central Register of Controlled Trails were identified. The methodological quality of the included studies was assessed by the Physiotherapy Evidence Database (PEDro) scale. The meta-analysis was performed using Cochrane RevMan software version 5.1.
Results
Thirteen RCTs that involved a total of 689 patients with 689 knees were included in the meta-analysis, which were divided into two groups. The tourniquet group included 351 knees and the non-tourniquet group included 338 knees. The meta-analysis showed that using a tourniquet in TKA could reduce intraoperative blood loss (weighted mean difference (WMD), -198.21; 95% confidence interval (CI), -279.82 to -116.60; P < 0.01) but did not decrease the calculated blood loss (P = 0.80), which indicates the actual blood loss. Although TKA with a tourniquet could save the operation time for 4.57 min compared to TKA without a tourniquet (WMD, -4.57; 95% CI, -7.59 to -1.56; P < 0.01), it had no clinical significance. Meanwhile, the use of tourniquet could not reduce the possibility of blood transfusion (P > 0.05). Postoperative knee range of motion (ROM) in tourniquet group was 10.41° less than that in the non-tourniquet group in early stage (≤10 days after surgery) (WMD, -10.41; 95% CI, -16.41 to -4.41; P < 0.01). Moreover, the use of a tourniquet increased the risk of either thrombotic events (risk ratio (RR), 5.00; 95% CI, 1.31 to 19.10; P = 0.02) or non-thrombotic complications (RR, 2.03; 95% CI, 1.12 to 3.67; P = 0.02).
Conclusions
TKA without a tourniquet was superior to TKA with a tourniquet in thromboembolic events and the other related complications. There were no significant differences between the two groups in the actual blood loss. TKA with a tourniquet might hinder patients' early postoperative rehabilitation exercises.
doi:10.1186/1749-799X-9-13
PMCID: PMC3973857  PMID: 24602486
Tourniquet; Total knee arthroplasty; Blood loss; Complications
7.  GABRA2 MARKERS MODERATE THE SUBJECTIVE EFFECTS OF ALCOHOL 
Addiction biology  2012;18(2):357-369.
Background
Individual differences in subjective responses to alcohol (SR) are moderated by genetic variants and may be risk factors for the development of alcohol use disorders. Variation in the GABAA α2 receptor subunit gene (GABRA2) has been associated with alcohol dependence (AD). Therefore, we examined whether individual differences in SR, which reflect sensitivity to the effects of alcohol, are associated with variation in GABRA2.
Methods
Sixty-nine healthy subjects (21–30 yr) underwent a laboratory-based within-session, cumulative oral alcohol dosing procedure, achieving a mean peak blood alcohol level of 100.4 mg/dL (SE =2.5). Subjective assessments were obtained throughout the session, including ascending and descending limbs of the alcohol curve. We genotyped single nucleotide polymorphisms (SNPs) across the chromosome 4 region spanning GABRA2 and analyzed the effect of genotype and haplotypes on subjective responses to alcohol. Population substructure was characterized through the use of ancestry informative markers.
Results
Individual SNP analysis demonstrated that carriers of the minor alleles for SNPs rs279858, rs279844, rs279845, rs279826, rs279828 and rs279836 had lower “Negative” alcohol effects scores than individuals homozygous for the common allele at each SNP (p=0.0060, p=0.0035, p=0.0045, p=0.0043, p=0.0037, p=0.0061, respectively). Haplotype effects of block 1 showed concordant results with SNPs in this block (p=0.0492 and p=0.0150 for haplotypes 1 and 4, respectively). The minor alleles for several of these SNPs have previously been associated with AD.
Conclusions
Our findings provide further evidence that variation within GABRA2 is associated with attenuated negative responses to alcohol, a known risk factor for vulnerability to alcohol use disorders.
doi:10.1111/j.1369-1600.2012.00457.x
PMCID: PMC3402582  PMID: 22501025
Alcoholism; Alcohol Dependence; GABA; GABRA2; Subjective Response
8.  Hydrolyzed protein supplementation improves protein content and peroxidation of skeletal muscle by adjusting the plasma amino acid spectrums in rats after exhaustive swimming exercise: a pilot study 
Background
This study was designed to evaluate the effects of hydrolyzed protein supplementation upon skeletal muscle total protein and peroxidation in rats following exhaustive swimming exercise.
Methods
Twenty-four rats were randomized to 4 experimental groups (n = 6 per group): control group fed standard diet without exercise (SD), exercise (EX), exercise plus standard diet for 72 hours (EX + SD), and exercise plus standard diet supplemented with hydrolyzed protein (2 g/kg/d) for 72 hours (EX + HP). Immediately following exercise, the EX group was euthanized for collecting plasma and skeletal muscle samples. The EX + SD and EX + HP groups were fed their respective diets for 72 hour still plasma and skeletal muscle collection. Skeletal muscle samples were used to measure levels of total protein (TP), malondialdehyde (MDA), and protein carbonyl (PC). Plasma samples were used to analyze the amino acids spectrum.
Results
Compared with the EX + SD, EX + HP presented the significantly increased TP (P = 0.02) and decreased MDA and PC levels (P = 0.035). MDA was negatively correlated with the methionine levels. Moreover, EX + HP maintained higher levels of plasmaleucine, isoleucine, and methionine than EX + SD, which may be associated with the increased skeletal muscle TP levels observed (P < 0.05).
Conclusions
These results collectively suggest that hydrolyzed protein supplementation can improve skeletal muscle TP and ameliorate peroxidation damage in rats subjected to exhaustive exercise stress, which may be, at least in part, related with the maintenance of plasma leucine, isoleucine, and methionine levels.
doi:10.1186/1550-2783-11-5
PMCID: PMC3945952  PMID: 24565110
Protein hydrolysates; Oxidative stress; Amino acid spectrum; Physical training
9.  High-Level Recombinant Human Lysozyme Expressed in Milk of Transgenic Pigs Can Inhibit the Growth of Escherichia coli in the Duodenum and Influence Intestinal Morphology of Sucking Pigs 
PLoS ONE  2014;9(2):e89130.
Lysozyme is often used as a feed additive and acts as an antimicrobial protein that enhances immune function and defends against pathogenic bacteria in pigs. In this study, we genetically added recombinant human lysozyme (rhLZ) to sow milk by somatic cell nuclear transfer and investigated whether the presence of recombinant human lysozyme can influence intestinal microbiota and mophology in sucking pigs. We generated transgenic cloned pigs and the first-generation hybrids (F1) produced high levels of rhLZ in milk. The average concentration of rhLZ was 116.34±24.46 mg/L in the milk of F1 sows, which was 1500-fold higher than that of the native pig lysozyme. In vitro, it was demonstrated that rhLZ in milk of transgenic pigs had enzyme levels at 92,272±26,413 U/mL. In a feeding experiment, a total of 40 newborn piglets were nursed by four transgenic sows and four sibling non-transgenic sows (F1), with five piglets per gilt. The piglets were allowed to nurse for 21 days and the sow milk was the only source of nutrition for the piglets. All piglets were slaughtered on postnatal day 22. Six types of bacteria were cultured and analyzed to detect the impact of rhLZ on gut microbiota. The number of Escherichia coli in the duodenum of piglets reared by transgenic sows was significantly decreased (p<0.001) and their villus height to crypt depth ratio in the intestine were increased due to the significant decrease of crypt depth in the duodenum, jejunum, and ileum (p<0.001). Together, we successfully generated rhLZ transgenic cloned pigs and elevated lysozyme level in nuring piglets. The results of the feeding experiments demonstrated that rhLZ-enhanced milk can inhibit the growth of E. coli in the duodenum and positively influence intestinal morphology without adversely affecting weight gain or piglet growth.
doi:10.1371/journal.pone.0089130
PMCID: PMC3931683  PMID: 24586544
10.  Immunotoxicological Evaluation of Corn Genetically Modified with Bacillus thuringiensis Cry1Ah Gene by a 30-Day Feeding Study in BALB/c Mice 
PLoS ONE  2014;9(2):e78566.
This study was to investigate the immunotoxicological potential of corn genetically modified (GM) with Bacillus thuringiensis (Bt) Cry1Ah gene in BALB/c mice. Female BALB/c mice were randomly assigned to one of the four groups: the negative control group, the parental corn group, the GM corn group and the positive control group with 10 mice per group. Mice in the GM corn group and the parental corn group were fed with diets containing 70% corresponding corn for 30 days. Mice in the negative control group and the positive control group were fed with AIN93G diet, administered with saline or 200 mg/kg of cyclophosphamide (CY) via intraperitoneal injection 24 h before the termination of the study, respectively. At the end of the study, the immunotoxicological effects of the GM corn were evaluated through immunopathology parameters including body and organ weights, hematology and clinical chemistry parameters, histological examination, peripheral blood lymphocytes phenotype; humoral immunity including antibody plaque-forming cell, serum immunoglobulin, cytokine and half hemolysis value; cellular immunity such as mitogen-induced splenocyte proliferation, cytotoxic T-lymphocyte reaction, delayed-type hypersensitivity reaction; non-specific immunity including phagocytic activities of phagocytes, natural killer cell activity. A single dose of cyclophosphamide (200 mg/kg bw) was found to have significant adverse effects on immunopathology, cellular immunity, and humoral immunity in mice. The corn genetically modified with Bt Cry1Ah gene is considered consistent with the parental corn in terms of immunopathology, humoral immunity, cellular immunity and non-specific immunity. No adverse immunotoxicological effects of GM corn with Bt Cry1Ah gene were found when feeding mice for 30 days.
doi:10.1371/journal.pone.0078566
PMCID: PMC3919699  PMID: 24520311
11.  Predicting Treatment Outcomes and Responder Subsets in Scleroderma-related Interstitial Lung Disease 
Arthritis and rheumatism  2011;63(9):2797-2808.
Objectives
To identify baseline characteristics of patients with Scleroderma-Related Interstitial Lung Disease (SSc-ILD) which predict the most favorable response to a 12-month treatment with oral cyclophosphamide (CYC).
Methods
Regression analyses were retrospectively applied to the Scleroderma Lung Study data in order to identify baseline characteristics that correlated with the absolute change in %-predicted Forced Vital Capacity (FVC) and the placebo-adjusted change in %-predicted FVC over time (the CYC treatment effect).
Results
Completion of the CYC arm of the Scleroderma Lung Study was associated with a placebo-adjusted improvement in %-predicted FVC of 2.11% at 12 months which increased to 4.16% when patients were followed for another 6 months (p=0.014). Multivariate regression analyses identified the maximal severity of reticular infiltrates on baseline high-resolution computerized tomography (HRCT), the modified Rodnan Skin Score (mRSS), and Mahler's Baseline Dyspnea Index (BDI) as independent correlates of treatment response. When patients were stratified based on whether 50% or more of any lung zone was involved by reticular infiltrates on HRCT and/or the presence of a mRSS of at least 23, a subgroup emerged with an average CYC treatment effect of 4.73% at 12 months and 9.81% at 18 months (p<0.001). Conversely, there was no treatment effect (−0.58%) in patients with less severe HRCT findings and a lower mRSS.
Conclusions
A retrospective analysis of the Scleroderma Lung Study identified the severity of reticular infiltrates on baseline HRCT and the baseline mRSS as patient features that might predict responsiveness to CYC therapy.
doi:10.1002/art.30438
PMCID: PMC3910296  PMID: 21547897
12.  MicroRNA 181 Suppresses Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection by Targeting PRRSV Receptor CD163 
Journal of Virology  2013;87(15):8808-8812.
We previously showed that microRNA 181 (miR-181) can inhibit PRRSV replication by directly targeting its genomic RNA. Here, we report that miR-181 can downregulate the PRRSV receptor CD163 in blood monocytes and porcine alveolar macrophages (PAMs) through targeting the 3′ untranslated region (UTR) of CD163 mRNA. Downregulation of CD163 leads to the inhibition of PRRSV entry into PAMs and subsequently suppresses PRRSV infection. Our findings indicate that delivery of miR-181 can be used as antiviral therapy against PRRSV infection.
doi:10.1128/JVI.00718-13
PMCID: PMC3719804  PMID: 23740977
13.  The Genome of the Netherlands: design, and project goals 
Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent–offspring trios include adult individuals ranging in age from 19 to 87 years (mean=53 years; SD=16 years) from birth cohorts 1910–1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14–15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.
doi:10.1038/ejhg.2013.118
PMCID: PMC3895638  PMID: 23714750
whole-genome sequence; trio-design; population genetics
14.  Inhibition of the K+ Channel KCa3.1 Reduces TGF-β1-Induced Premature Senescence, Myofibroblast Phenotype Transition and Proliferation of Mesangial Cells 
PLoS ONE  2014;9(1):e87410.
Objective
KCa3.1 channel participates in many important cellular functions. This study planned to investigate the potential involvement of KCa3.1 channel in premature senescence, myofibroblast phenotype transition and proliferation of mesangial cells.
Methods & Materials
Rat mesangial cells were cultured together with TGF-β1 (2 ng/ml) and TGF-β1 (2 ng/ml) + TRAM-34 (16 nM) separately for specified times from 0 min to 60 min. The cells without treatment served as controls. The location of KCa3.1 channels in mesangial cells was determined with Confocal laser microscope, the cell cycle of mesangial cells was assessed with flow cytometry, the protein and mRNA expression of KCa3.1, α-smooth muscle actin (α-SMA) and fibroblast-specific protein-1 (FSP-1) were detected with Western blot and RT-PCR. One-way analysis of variance (ANOVA) and Student-Newman-Keuls-q test (SNK-q) were used to do statistical analysis. Statistical significance was considered at P<0.05.
Results
Kca3.1 channels were located in the cell membranes and/or in the cytoplasm of mesangial cells. The percentage of cells in G0-G1 phase and the expression of Kca3.1, α-SMA and FSP-1 were elevated under the induction of TGF-β1 when compared to the control and decreased under the induction of TGF-β1+TRAM-34 when compared to the TGF-β1 induced (P<0.05 or P<0.01).
Conclusion
Targeted disruption of KCa3.1 inhibits TGF-β1-induced premature aging, myofibroblast-like phenotype transdifferentiation and proliferation of mesangial cells.
doi:10.1371/journal.pone.0087410
PMCID: PMC3905019  PMID: 24489911
15.  Decreased Dissolution of ZnO by Iron Doping Yields Nanoparticles with Reduced Toxicity in the Rodent Lung and Zebrafish Embryos 
ACS nano  2011;5(2):1223-1235.
We have recently shown that the dissolution of ZnO nanoparticles and Zn2+ shedding leads to a series of sub-lethal and lethal toxicological responses at cellular level that can be alleviated by iron-doping. Iron-doping changes the particle matrix and slows the rate of particle dissolution. To determine whether iron doping of ZnO also leads to lesser toxic effects in vivo, toxicity studies were performed in rodent and zebrafish models. First, we synthesized a fresh batch of ZnO nanoparticles doped with 1–10 wt % of Fe. These particles were extensively characterized to confirm their doping status, reduced rate of dissolution in an exposure medium and reduced toxicity in a cellular screen. Subsequent studies compared the effects of undoped to doped particles in the rat lung, mouse lung and the zebrafish embryo. The zebrafish studies looked at embryo hatching and mortality rates as well as the generation of morphological defects, while the endpoints in the rodent lung included an assessment of inflammatory cell infiltrates, LDH release and cytokine levels in the bronchoalveolar lavage fluid. Iron doping, similar to the effect of the metal chelator, DTPA, interfered in the inhibitory effects of Zn2+ on zebrafish hatching. In the oropharyngeal aspiration model in the mouse, iron doping was associated with decreased polymorphonuclear cell counts and IL-6 mRNA production. Doped particles also elicited decreased heme oxygenase 1 expression in the murine lung. In the intratracheal instillation studies in the rat, Fe-doping was associated with decreased polymorphonuclear cell counts, LDH and albumin levels. All considered, the above data show that Fe-doping is a possible safe design strategy for preventing ZnO toxicity in animals and the environment.
doi:10.1021/nn1028482
PMCID: PMC3900638  PMID: 21250651
ZnO; dissolution; toxicity; iron doping; zebrafish embryo; mouse; rat
16.  Chinese Medicine Shensongyangxin Is Effective for Patients with Bradycardia: Results of a Randomized, Double-Blind, Placebo-Controlled Multicenter Trial 
To evaluate the efficacy and safety of Shensong Yangxin (SSYX) in patients with bradycardia arrhythmias, a randomized, double-blind, and placebo-controlled study was conducted. Patients with bradycardia were randomly assigned to receive either SSYX (trial group, n = 115) or placebo (control group, n = 104) for 4 weeks. ECG, 24-hour continuous ECG recording, echocardiography, and hepatic and renal function were evaluated at baseline and after treatment. Results showed that the average heart rate, the fastest heart rate, and the lowest heart rate in the trial group were all significantly higher than those in the control group at the end of treatment (P < 0.05 or 0.01, resp.). Compared with pretreatment, the average heart rate, the fastest heart rate, and the lowest heart rate in the trial group all increased significantly after treatment (P < 0.05 or 0.01, resp.). Both the efficacy and the symptom scores in the trial group were significantly better than those in the control group after treatment (both having P < 0.01). No severe adverse effects were reported. In conclusion, SSYX treatment significantly increased the heart rate in patients with bradycardia without severe side effects. The exact mechanisms remain to be further explored.
doi:10.1155/2014/605714
PMCID: PMC3914313  PMID: 24527049
17.  Unsafe riding practice among electric bikers in Suzhou, China: an observational study 
BMJ Open  2014;4(1):e003902.
Background
Electric bike (E-bike)-related deaths have been increasing rapidly in China and such injuries may be partly attributable to unsafe riding practice.
Objectives
To describe potentially unsafe riding behaviours among electric bikers (E-bikers) and to investigate factors influencing these practices in China.
Methods
In September 2012, a cross-sectional observation study including a speed measurement component was conducted in Wuzhong (an urban district) and Zhangjiagang (a rural district) of Suzhou, Jiangsu Province, China. Hand-held radar speed metres were used to read travelling speeds of E-bikes and a pro forma observation checklist was used to collect data on road riding practice. Mixed-effect logistic regressions were used to calculate adjusted ORs and 95% CIs for the association between speeding, road rule violations and helmet use and their influencing factors.
Results
Among 800 E-bikes with a speed reading, 70.9% exceeded the designed speed limit of 20 km/h. Among a further 20 647 E-bikers observed, 38.3% did not comply with the road rules when entering intersections; and only 2.2% wore helmets. No regional variation was identified between urban and rural areas. Male E-bikers were associated with more speeding and road rule violations, whereas riding a pedal-equipped E-bike was associated with less road rule violations and less helmet use.
Conclusions
Unsafe riding practices such as speeding, road rule violations and lack of helmet use were commonplace among E-bikers, especially among men. The study findings indicate that measures aimed at improving E-bike safety are required in China.
doi:10.1136/bmjopen-2013-003902
PMCID: PMC3902425  PMID: 24435891
Electric Bike; Cross Sectional Study; Behavior; Risk Factor Research; Driver
18.  Genome-Wide Analysis of DNA Methylation in Five Tissues of Zhikong Scallop, Chlamys farreri 
PLoS ONE  2014;9(1):e86232.
DNA methylation plays a vital role in tissue development and differentiation in eukaryotes. Epigenetic studies have been seldom conducted in the extremely diverse and evolutionarily highly successful bilaterian lineage Mollusca. In the present study, we conducted the genome-wide profiling of DNA methylation for five tissues of a bivalve mollusc, Chlamys farreri using the methylation-sensitive amplification polymorphism (MSAP) technique. The methylation levels were quite similar among tissues, ranging from 20.9% to 21.7%. CG methylation was the dominant type (14.9%–16.5%) in the C. farreri genome, but CHG methylation also accounted for a substantial fraction of total methylation (5.1%–6.3%). Relatively high methylation diversity was observed within tissues. Methylation differentiation between tissues was evaluated and 460 tissue-specific epiloci were identified. Kidney differs from the other tissues in DNA methylation profiles. Our study presents the first look at the tissue-specific DNA methylation patterns in a bivalve mollusc and represents an initial step towards understanding of epigenetic regulatory mechanism underlying tissue development and differentiation in bivalves.
doi:10.1371/journal.pone.0086232
PMCID: PMC3891877  PMID: 24454962
19.  Longitudinal data analysis with non-ignorable missing data 
Statistical methods in medical research  2012;10.1177/0962280212448721.
A common problem in the longitudinal data analysis is the missing data problem. Two types of missing patterns are generally considered in statistical literature: monotone and non-monotone missing data. Non-monotone missing data occur when study participants intermittently miss scheduled visits, while monotone missing data can be from discontinued participation, loss to follow-up and mortality. Although many novel statistical approaches have been developed to handle missing data in recent years, few methods are available to provide inferences to handle both types of missing data simultaneously. In this article, a latent random effects model is proposed to analyze longitudinal outcomes with both monotone and non-monotone missingness in the context of missing not at random (MNAR). Another significant contribution of this paper is to propose a new computational algorithm for latent random effects models. To reduce the computational burden of high dimensional integration problem in latent random effects models, we develop a new computational algorithm that uses a new adaptive quadrature approach in conjunction with the Taylor series approximation for the likelihood function to simplify the E step computation in the EM algorithm. Simulation study is performed and the data from the Scleroderma lung study are used to demonstrate the effectiveness of this method.
doi:10.1177/0962280212448721
PMCID: PMC3883866  PMID: 22637472
Adaptive quadrature; Missing not at random; Joint model; Scleroderma study
20.  Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing 
BMC Genomics  2014;15:4.
Background
Because few studies exist to describe the unique molecular network regulation behind pig pre-implantation embryonic development (PED), genetic engineering in the pig embryo is limited. Also, this lack of research has hindered derivation and application of porcine embryonic stem cells and porcine induced pluripotent stem cells (iPSCs).
Results
We identified and analyzed the genome wide transcriptomes of pig in vivo-derived and somatic cell nuclear transferred (SCNT) as well as mouse in vivo-derived pre-implantation embryos at different stages using mRNA deep sequencing. Comparison of the pig embryonic transcriptomes with those of mouse and human pre-implantation embryos revealed unique gene expression patterns during pig PED. Pig zygotic genome activation was confirmed to occur at the 4-cell stage via genome-wide gene expression analysis. This activation was delayed to the 8-cell stage in SCNT embryos. Specific gene expression analysis of the putative inner cell mass (ICM) and the trophectoderm (TE) revealed that pig and mouse pre-implantation embryos share regulatory networks during the first lineage segregation and primitive endoderm differentiation, but not during ectoderm commitment. Also, fatty acid metabolism appears to be a unique characteristic of pig pre-implantation embryonic development. In addition, the global gene expression patterns in the pig SCNT embryos were different from those in in vivo-derived pig embryos.
Conclusions
Our results provide a resource for pluripotent stem cell engineering and for understanding pig development.
doi:10.1186/1471-2164-15-4
PMCID: PMC3925986  PMID: 24383959
22.  Novel Approaches for the Accumulation of Oxygenated Intermediates to Multi-Millimolar Concentrations 
Coordination chemistry reviews  2013;257(1):10.1016/j.ccr.2012.06.020.
Metalloenzymes that utilize molecular oxygen as a co-substrate catalyze a wide variety of chemically difficult oxidation reactions. Significant insight into the reaction mechanisms of these enzymes can be obtained by the application of a combination of rapid kinetic and spectroscopic methods to the direct structural characterization of intermediate states. A key limitation of this approach is the low aqueous solubility (< 2 mM) of the co-substrate, O2, which undergoes further dilution (typically by one-third or one-half) upon initiation of reactions by rapid-mixing. This situation imposes a practical upper limit on [O2] (and therefore on the concentration of reactive intermediate(s) that can be rapidly accumulated) of ∼1-1.3 mM in such experiments as they are routinely carried out. However, many spectroscopic methods benefit from or require significantly greater concentrations of the species to be studied. To overcome this problem, we have recently developed two new approaches for the preparation of samples of oxygenated intermediates: (1) direct oxygenation of reduced metalloenzymes using gaseous O2 and (2) the in situ generation of O2 from chlorite catalyzed by the enzyme chlorite dismutase (Cld). Whereas the former method is applicable only to intermediates with half lives of several minutes, owing to the sluggishness of transport of O2 across the gas-liquid interface, the latter approach has been successfully applied to trap several intermediates at high concentration and purity by the freeze-quench method. The in situ approach permits generation of a pulse of at least 5 mM O2 within ∼ 1 ms and accumulation of O2 to effective concentrations of up to ∼ 11 mM (i.e. ∼ 10-fold greater than by the conventional approach). The use of these new techniques for studies of oxygenases and oxidases is discussed.
doi:10.1016/j.ccr.2012.06.020
PMCID: PMC3870000  PMID: 24368870
oxygen; intermediate; ferryl; superoxo; peroxo; iron; non-heme
23.  Conservative treatment of early postoperative small bowel obstruction with obliterative peritonitis 
AIM: To investigate the effect of somatostatin and dexamethasone on early postoperative small bowel obstruction with obliterative peritonitis (EPSBO-OP).
METHODS: This prospective randomized study included 70 patients diagnosed with EPSBO-OP from June 2002 to January 2009. Patients were randomized into two groups: a control group received total parenteral nutrition and nasogastric (NG) tube feeding; and an intervention group received, in addition, somatostatin and dexamethasone treatment. The primary endpoints were time to resolution of bowel obstruction and length of hospital stay, and the secondary endpoints were daily NG output and NG feeding duration, treatment-related complications, postoperative obstruction relapse, and patient satisfaction.
RESULTS: Thirty-six patients were allocated to the intervention group and 34 to the control group. No patient needed to undergo surgery. Patients in the intervention group had an earlier resolution of bowel obstruction (22.4 ± 9.1 vs 29.9 ± 10.1 d, P = 0.002). Lower daily NG output (583 ± 208 vs 922 ± 399 mL/d, P < 0.001), shorter duration of NG tube use (16.7 ± 8.8 vs 27.7 ± 9.9 d, P < 0.001), and shorter length of hospital stay (25.8 vs 34.9 d, P = 0.001) were observed in the intervention group. The rate of treatment-related complications (P = 0.770) and relapse of obstruction (P = 0.357) were comparable between the two groups. There were no significant differences in postoperative satisfaction at 1, 2 and 3 years between the two groups.
CONCLUSION: Somatostatin and dexamethasone for EPSBO-OP promote resolution of obstruction and shorten hospital stay, and are safe for symptom control without increasing obstruction relapse.
doi:10.3748/wjg.v19.i46.8722
PMCID: PMC3870520  PMID: 24379592
Dexamethasone; Intestinal obstruction; Parenteral nutrition; Postoperative period; Somatostatin
24.  Changes in Mitochondrial Carriers Exhibit Stress-Specific Signatures in INS-1Eβ-Cells Exposed to Glucose Versus Fatty Acids 
PLoS ONE  2013;8(12):e82364.
Chronic exposure of β-cells to metabolic stresses impairs their function and potentially induces apoptosis. Mitochondria play a central role in coupling glucose metabolism to insulin secretion. However, little is known on mitochondrial responses to specific stresses; i.e. low versus high glucose, saturated versus unsaturated fatty acids, or oxidative stress. INS-1E cells were exposed for 3 days to 5.6 mM glucose, 25 mM glucose, 0.4 mM palmitate, and 0.4 mM oleate. Culture at standard 11.1 mM glucose served as no-stress control and transient oxidative stress (200 µM H2O2 for 10 min at day 0) served as positive stressful condition. Mito-array analyzed transcripts of 60 mitochondrion-associated genes with special focus on members of the Slc25 family. Transcripts of interest were evaluated at the protein level by immunoblotting. Bioinformatics analyzed the expression profiles to delineate comprehensive networks. Chronic exposure to the different metabolic stresses impaired glucose-stimulated insulin secretion; revealing glucotoxicity and lipo-dysfunction. Both saturated and unsaturated fatty acids increased expression of the carnitine/acylcarnitine carrier CAC, whereas the citrate carrier CIC and energy sensor SIRT1 were specifically upregulated by palmitate and oleate, respectively. High glucose upregulated CIC, the dicarboxylate carrier DIC and glutamate carrier GC1. Conversely, it reduced expression of energy sensors (AMPK, SIRT1, SIRT4), metabolic genes, transcription factor PDX1, and anti-apoptotic Bcl2. This was associated with caspase-3 cleavage and cell death. Expression levels of GC1 and SIRT4 exhibited positive and negative glucose dose-response, respectively. Expression profiles of energy sensors and mitochondrial carriers were selectively modified by the different conditions, exhibiting stress-specific signatures.
doi:10.1371/journal.pone.0082364
PMCID: PMC3861392  PMID: 24349266
25.  An initial screening for HIV-associated neurocognitive disorders of HIV-1 infected patients in China 
Journal of neurovirology  2012;18(2):10.1007/s13365-012-0089-y.
HIV-associated neurocognitive disorders (HAND), characterized by cognitive, motor, and behavioral abnormalities, are common among people living with HIV and AIDS. In combined antiretroviral therapy era in Western countries, nearly 40% of HIV-infected patients continue to suffer from HAND, mainly with mild or asymptomatic cognitive impairment. However, the prevalence and the clinical features of HAND in China are still not well known. In this study, a multi-center cross-sectional study was performed to determine the prevalence and clinical features of HAND in 134 HIV-1 infected patients in China. The International HIV Dementia Scale and a neuropsychological test battery were administered for screening and diagnosis HAND. Subjective complaints, CD4 count and viral loads in both blood plasma and cerebrospinal fluid were correlated with diagnosis of HAND. The results showed that the prevalence of HAND was approximately 37% in these patients. CD4 counts at time of sampling were significant lower in the HAND group than in the non-HAND group. But the distribution of the HAND severity did not differ by CD4 count or viral load. The presence of HAND was associated with cognitive and behavior disorder complaints (4.9- and 4.1-fold higher than those without HAND, respectively). The present data suggest that CD4 count and viral load cannot predict the severity of HAND, although the prevalence of HAND is similar to previous report in these patients. Cognitive and behavioral disorder is major complaint rather than cognitive and motor impairment. A larger prospective study is needed to obtain better estimates of HAND in China.
doi:10.1007/s13365-012-0089-y
PMCID: PMC3859527  PMID: 22411002
AIDS; Clinical manifestation; HIV-associated neurocognitive disorders; Prevalence

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