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1.  Aquaporin3 Is Required for FGF-2-Induced Migration of Human Breast Cancers 
PLoS ONE  2013;8(2):e56735.
Purpose
The aquaporin (AQP) family consists of a number of small integral membrane proteins that transport water and glycerol. AQPs are critical for trans-epithelial fluid transport. Recent reports demonstrated that AQPs, particularly AQP1 and AQP5, are expressed in high grade tumor cells of a variety of tissue origins, and that AQPs are involved in cell migration and metastasis. Based on this background, we examined whether AQP3, another important member of the AQP family, could facilitate cell migration in human breast cancers.
Methods
Potential role of AQP3 was examined using two representative breast cancer cell lines (MDA-MB-231 and Bcap-37). Briefly, AQP3 expression was inhibited with a lentivirus construct that stably expressed shRNA against the AQP3 mRNA. AQP3 expression inhibition was verified with Western blot. Cell migration was examined using a wound scratch assay in the presence of fibroblast growth factor-2 (FGF-2). In additional experiments, AQP3 was inhibited by CuSO4. Fibroblast growth factor receptor (FGFR) kinase inhibitor PD173074, PI3K inhibitor LY294002, and MEK1/2 inhibitor PD98059 were used to dissect the molecular mechanism of FGF-2 induced AQP3 expression.
Results
FGF-2 treatment increased AQP3 expression and induced cell migration in a dose dependent manner. Silencing AQP3 expression by a lentiviral shRNA inhibited FGF-2 induced cell migration. CuSO4, a water transport inhibitor selective for AQP3, also suppressed FGF-2-induced cell migration. The FGFR kinase inhibitor PD173074, significantly inhibited FGF-2-induced AQP3 expression and cell migration. The PI3K inhibitor LY294002 and MEK1/2 inhibitor PD98059 inhibited, but not fully blocked, FGF-2-induced AQP3 expression and cell migration.
Conclusions
AQP3 is required for FGF-2-induced cell migration in cultured human breast cancer cells. Our findings also suggest the importance of FGFR-PI3K and FGFR-ERK signaling in FGF-2-induced AQP3 expression. In summary, our findings suggest a novel function of AQP3 in cell migration and metastasis of breast cancers.
doi:10.1371/journal.pone.0056735
PMCID: PMC3585269  PMID: 23468877
2.  Peripheral Immune Cell Gene Expression Changes in Advanced Non-Small Cell Lung Cancer Patients Treated with First Line Combination Chemotherapy 
PLoS ONE  2013;8(2):e57053.
Introduction
Increasing evidence has shown that immune surveillance is compromised in a tumor-promoting microenvironment for patients with non-small cell lung cancer (NSCLC), and can be restored by appropriate chemotherapy.
Methods
To test this hypothesis, we analyzed microarray gene expression profiles of peripheral blood mononuclear cells from 30 patients with newly-diagnosed advanced stage NSCLC, and 20 age-, sex-, and co-morbidity-matched healthy controls. All the patients received a median of four courses of chemotherapy with cisplatin and gemcitabine for a 28-day cycle as first line treatment.
Results
Sixty-nine differentially expressed genes between the patients and controls, and 59 differentially expressed genes before and after chemotherapy were identified. The IL4 pathway was significantly enriched in both tumor progression and chemotherapy signatures. CXCR4 and IL2RG were down-regulated, while DOK2 and S100A15 were up-regulated in the patients, and expressions of all four genes were partially or totally reversed after chemotherapy. Real-time quantitative RT-PCR for the four up-regulated (S100A15, DOK2) and down-regulated (TLR7, TOP1MT) genes in the patients, and the six up-regulated (TLR7, CRISP3, TOP1MT) and down-regulated (S100A15, DOK2, IL2RG) genes after chemotherapy confirmed the validity of the microarray results. Further immunohistochemical analysis of the paraffin-embedded lung cancer tissues identified strong S100A15 nuclear staining not only in stage IV NSCLC as compared to stage IIIB NSCLC (p = 0.005), but also in patients with stable or progressive disease as compared to those with a partial response (p = 0.032). A high percentage of S100A15 nuclear stained cells (HR 1.028, p = 0.01) was the only independent factor associated with three-year overall mortality.
Conclusions
Our results suggest a potential role of the IL4 pathway in immune surveillance of advanced stage NSCLC, and immune potentiation of combination chemotherapy. S100A15 may serve as a potential biomarker for tumor staging, and a predictor of poor prognosis in NSCLC.
doi:10.1371/journal.pone.0057053
PMCID: PMC3581559  PMID: 23451142
3.  Sequential Oxygenation Index and Organ Dysfunction Assessment within the First 3 Days of Mechanical Ventilation Predict the Outcome of Adult Patients with Severe Acute Respiratory Failure 
The Scientific World Journal  2013;2013:413216.
Objective. To determine early predictors of outcomes of adult patients with severe acute respiratory failure. Method. 100 consecutive adult patients with severe acute respiratory failure were evaluated in this retrospective study. Data including comorbidities, Sequential Organ Failure Assessment (SOFA) score, Acute Physiological Assessment and Chronic Health Evaluation II (APACHE II) score, PaO2, FiO2, PaO2/FiO2, PEEP, mean airway pressure (mPaw), and oxygenation index (OI) on the 1st and the 3rd day of mechanical ventilation, and change in OI within 3 days were recorded. Primary outcome was hospital mortality; secondary outcome measure was ventilator weaning failure. Results. 38 out of 100 (38%) patients died within the study period. 48 patients (48%) failed to wean from ventilator. Multivariate analysis showed day 3 OI (P = 0.004) and SOFA (P = 0.02) score were independent predictors of hospital mortality. Preexisting cerebrovascular accident (CVA) (P = 0.002) was the predictor of weaning failure. Results from Kaplan-Meier method demonstrated that higher day 3 OI was associated with shorter survival time (log-Rank test, P < 0.001). Conclusion. Early OI (within 3 days) and SOFA score were predictors of mortality in severe acute respiratory failure. In the future, prospective studies measuring serial OIs in a larger scale of study cohort is required to further consolidate our findings.
doi:10.1155/2013/413216
PMCID: PMC3588184  PMID: 23476133
4.  Old flies have a robust central oscillator but weaker behavioral rhythms that can be improved by genetic and environmental manipulations 
Aging cell  2012;11(3):428-438.
Summary
Sleep:wake cycles break down with age, but the causes of this degeneration are not clear. Using a Drosophila model we addressed the contribution of circadian mechanisms to this aged-induced deterioration. We found that in old flies free-running circadian rhythms (behavioral rhythms assayed in constant darkness) have a longer period and an unstable phase before they eventually degenerate. Surprisingly, rhythms are weaker in light:dark cycles and the circadian-regulated morning peak of activity is diminished under these conditions. On a molecular level, aging results in reduced amplitude of circadian clock gene expression in peripheral tissues. However, oscillations of the clock protein PERIOD (PER) are robust and synchronized among different clock neurons, even in very old, arrhythmic flies. To improve rhythms in old flies, we manipulated environmental conditions, which can have direct effects on behavior, and also tested a role for molecules that act downstream of the clock. Coupling temperature cycles with a light:dark schedule or reducing expression of protein kinase A (PKA) improved behavioral rhythms and consolidated sleep. Our data demonstrate that a robust molecular time-keeping mechanism persists in the central pacemaker of aged flies, and reducing PKA can strengthen behavioral rhythms.
doi:10.1111/j.1474-9726.2012.00800.x
PMCID: PMC3353743  PMID: 22268765
Aging; Behavioral rhythms; Circadian clock; Period; Sleep; PKA
5.  Natural Variation in the Drosophila melanogaster Clock Gene Period Modulates Splicing of Its 3′-Terminal Intron and Mid-Day Siesta 
PLoS ONE  2012;7(11):e49536.
Drosophila melanogaster exhibits circadian (≅24 hr) regulated morning and evening bouts of activity that are separated by a mid-day siesta. Increases in daily ambient temperature are accompanied by a progressively longer mid-day siesta and delayed evening activity. Presumably, this behavioral plasticity reflects an adaptive response that endows D. melanogaster with the ability to temporally optimize daily activity levels over a wide range of physiologically relevant temperatures. For example, the shift in activity towards the cooler nighttime hours on hot days might minimize the risks associated with exposure to mid-day heat, whereas on cold days activity is favored during the warmer daytime hours. These temperature-induced shifts in the distribution of daily activity are partly based on the thermal sensitive splicing of an intron found in the 3′ untranslated region (UTR) of the circadian clock gene termed period (per). As temperature decreases, splicing of this 3′-terminal intron (termed dmpi8) is gradually increased, which is causally linked to a shorter mid-day siesta. Herein we identify several natural polymorphisms in the per 3′ UTR from wild-caught populations of flies originating along the east coast of the United States. Two non-intronic closely spaced single nucleotide polymorphisms (SNPs) modulate dmpi8 splicing efficiency, with the least efficiently spliced version associated with a longer mid-day siesta, especially at lower temperatures. Although these SNPs modulate the splicing efficiency of dmpi8 they have little to no effect on its thermal responsiveness, consistent with the notion that the suboptimal 5′ and 3′ splice sites of the dmpi8 intron are the primary cis-acting elements mediating temperature regulation. Our results demonstrate that natural variations in the per gene can modulate the splicing efficiency of the dmpi8 intron and the daily distribution of activity, providing natural examples for the involvement of dmpi8 splicing in the thermal adaptation of behavioral programs in D. melanogaster.
doi:10.1371/journal.pone.0049536
PMCID: PMC3496713  PMID: 23152918
6.  Robust Markers Reflecting Phylogeny and Taxonomy of Rhizobia 
PLoS ONE  2012;7(9):e44936.
Genomic ANI (Average Nucleotide Identity) has been found to be able to replace DNA-DNA hybridization in prokaryote taxonomy. The ANI of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ANI. This allowed us to identify three housekeeping genes (SMc00019-truA-thrA) whose ANI reflected the intraspecies and interspecies genomic ANI among rhizobial strains, revealing an ANI gap (≥2%) between the inter- and intra-species comparisons. The intraspecies (96%) and interspecies (94%) ANI boundaries calculated from three genes (SMc00019-truA-thrA) provided a criterion for bacterial species definition and confirmed 621/629 of known interspecies relationships within Bradyrhizobium, Mesorhizobium, Sinorhizobium and Rhizobium. Some widely studied strains should be renamed. The SMc00019-truA-thrA ANI also correlates well with the genomic ANI of strains in Agrobacterium, Methylobacterium, Ralstonia, Rhodopseudomonas, Cupriavidus and Burkholderia, suggesting their wide applicability in other bacteria.
doi:10.1371/journal.pone.0044936
PMCID: PMC3444505  PMID: 23028691
7.  Factors Predicting Ventilator Dependence in Patients with Ventilator-Associated Pneumonia 
The Scientific World Journal  2012;2012:547241.
Objectives. To determine risk factors associated with ventilator dependence in patients with ventilator-associated pneumonia (VAP). Study Design. A retrospective study was conducted at Chang Gung Memorial Hospital, Kaohsiung, from January 1, 2007 to January 31, 2008. Methods. This study evaluated 163 adult patients (aged ≥18 years). Eligibility was evaluated according to the criterion for VAP, Sequential Organ Failure Assessment (SOFA) score, Acute Physiological Assessment and Chronic Health Evaluation II (APACHE II) score. Oxygenation index, underlying comorbidities, septic shock status, previous tracheostomy status, and factors related to pneumonia were collected for analysis. Results. Of the 163 VAP patients in the study, 90 patients survived, yielding a mortality rate of 44.8%. Among the 90 surviving patients, only 36 (40%) had been weaned off ventilators at the time of discharge. Multivariate logistic regression analysis was used to identify underlying factors such as congestive cardiac failure (P = 0.009), initial high oxygenation index value (P = 0.04), increased SOFA scores (P = 0.01), and increased APACHE II scores (P = 0.02) as independent predictors of ventilator dependence. Results from the Kaplan-Meier method indicate that initial therapy with antibiotics could increase the ventilator weaning rate (log Rank test, P < 0.001). Conclusions. Preexisting cardiopulmonary function, high APACHE II and SOFA scores, and high oxygenation index were the strongest predictors of ventilator dependence. Initial empiric antibiotic treatment can improve ventilator weaning rates at the time of discharge.
doi:10.1100/2012/547241
PMCID: PMC3417186  PMID: 22919335
8.  Reinstitution of Mechanical Ventilation within 14 Days as a Poor Predictor in Prolonged Mechanical Ventilation Patients following Successful Weaning 
The Scientific World Journal  2012;2012:957126.
Although many parameters were investigated about weaning and mortality in critical patients in intensive units, no studies have yet investigated predictors in prolonged mechanical ventilation (PMV) patients following successful weaning. A cohort of 142 consecutive PMV patients with successful weaning in our respiratory care center was enrolled in this study. Successful weaning is defined as a patient having smooth respiration for more than 5 days after weaning. The results showed as follows: twenty-seven patients (19%) had the reinstitution within 14 days, and 115 patients (81%) had the reinstitution beyond 14 days. Renal disease RIFLE-LE was associated with the reinstitution within 14 days (P = 0.006). One year mortality rates showed significant difference between the two groups (85.2% in the reinstitution within 14 days group versus 53.1% in the reinstitution beyond 14 days; P < 0.001). Kaplan-Meier analysis showed that age ≥70 years (P = 0.04), ESRD (P = 0.02), and the reinstitution within 14 days (P < 0.001) were associated with one-year mortality. Cox proportional hazards regression model showed that only the reinstitution within 14 days was the independent predictor for mortality (P < 0.001). In conclusion, the reinstitution within 14 days was a poor predictor for PMV patients after successful weaning.
doi:10.1100/2012/957126
PMCID: PMC3417172  PMID: 22924030
9.  Effect of epimedium pubescen flavonoid on bone mineral status and bone turnover in male rats chronically exposed to cigarette smoke 
Background
Epimedii herba is one of the most frequently used herbs in formulas that are prescribed for the treatment of osteoporosis in China and its main constituent is Epimedium pubescen flavonoid (EPF). However, it is unclear whether EPF during chronic exposure to cigarette smoke may have a protective influence on the skeleton. The present study investigated the effect of EPF on bone mineral status and bone turnover in a rat model of human relatively high exposure to cigarette smoke.
Methods
Fifty male Wistar rats were randomized into five groups: controls, passive smoking groups and passive smoking rats administered EPF at three dosage levels (75, 150 or 300 mg/kg/day) in drinking water for 4 months. A rat model of passive smoking was prepared by breeding male rats in a cigarette-smoking box. Bone mineral content (BMC), bone mineral density (BMD), bone turnover markers, bone histomorphometric parameters and biomechanical properties were examined.
Results
Smoke exposure decreased BMC and BMD, increased bone turnover (inhibited bone formation and stimulated its resorption), affected bone histomorphometry (increased trabecular separation and osteoclast surface per bone surface; decreased trabecular bone volume, trabecular thickness, trabecular number, cortical thickness, bone formation rate and osteoblast surface per bone surface), and reduced mechanical properties. EPF supplementation during cigarette smoke exposure prevented smoke-induced changes in bone mineral status and bone turnover.
Conclusion
The results suggest that EPF can prevent the adverse effects of smoke exposure on bone by stimulating bone formation and inhibiting bone turnover and bone resorption.
doi:10.1186/1471-2474-13-105
PMCID: PMC3480917  PMID: 22713117
Smoking; Epimedium pubescen flavonoid; Bone mineral density; Bone mineral content; Bone turnover; Bone histomorphometry
10.  Concomitant Pulmonary Tuberculosis in Hospitalized Healthcare-Associated Pneumonia in a Tuberculosis Endemic Area: A Multi-center Retrospective Study 
PLoS ONE  2012;7(5):e36832.
Background
In tuberculosis (TB) endemic areas, Mycobacterium tuberculosis is an important but easily misdiagnosed pathogen in community-acquired pneumonia (CAP). However, the occurrence of concomitant pulmonary tuberculosis (PTB) in hospitalized healthcare-associated pneumonia (HCAP) has never been investigated.
Methods and Findings
Seven hundred and one hospitalized HCAP and 934 hospitalized CAP patients from six medical centers in Taiwan were included in this nationwide retrospective study. Concomitant PTB was defined as active PTB diagnosed within 60 days of admission due to HCAP or CAP. The predictors for concomitant PTB and the impact of PTB on the outcomes of pneumonia were investigated. Among the enrolled subjects, 21/701 (3%) of the HCAP patients and 25/934 (2.7%) of the CAP patients were documented to have concomitant PTB. In multivariate analysis, a history of previous anti-TB treatment (OR = 5.84, 95% CI: 2.29–20.37 in HCAP; OR = 3.33, 95% CI: 1.09–10.22 in CAP) and escalated pneumonia severity index (PSI) scores (OR = 1.014, 95% CI: 1.002–1.026, in HCAP; OR = 1.013, 95% CI: 1.001–1.026, in CAP) were independent predictors for concomitant PTB in both CAP and HCAP patients. Regarding treatment outcomes, HCAP patients with concomitant PTB were associated with more acute respiratory failure within 48 hours of admission (47.6% vs. 22.6%, p = 0.008), higher intensive care unit admission rate (61.9% vs. 35.7%, p = 0.014), longer hospitalization (39.6±34.1 vs. 23.7±27 days, p = 0.009), and higher in-hospital mortality (47.6% vs. 26.3%, p = 0.03) than those without concomitant PTB. Exposure to certain groups of antibiotics for the treatment of pneumonia was not associated with the occurrence of concomitant PTB.
Conclusions
In HCAP patients, the occurrence of concomitant PTB is comparable with that in CAP patients and associated with higher PSI scores, more acute respiratory failure, and higher in-hospital mortality.
doi:10.1371/journal.pone.0036832
PMCID: PMC3358294  PMID: 22629334
11.  Epidermal Growth Factor Gene Polymorphism and Risk of Hepatocellular Carcinoma: A Meta-Analysis 
PLoS ONE  2012;7(3):e32159.
Background
Hepatocarcinogenesis is a complex process that may be influenced by many factors, including polymorphism in the epidermal growth factor (EGF) gene. Previous work suggests an association between the EGF 61*A/G polymorphism (rs4444903) and susceptibility to hepatocellular carcinoma (HCC), but the results have been inconsistent. Therefore, we performed a meta-analysis of several studies covering a large population to address this controversy.
Methods
PubMed, EMBASE, Google Scholar and the Chinese National Knowledge Infrastructure databases were systematically searched to identify relevant studies. Data were abstracted independently by two reviewers. A meta-analysis was performed to examine the association between EGF 61*A/G polymorphism and susceptibility to HCC. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated.
Results
Eight studies were chosen in this meta-analysis, involving 1,304 HCC cases (1135 Chinese, 44 Caucasian and 125 mixed) and 2,613 controls (1638 Chinese, 77 Caucasian and 898 mixed). The EGF 61*G allele was significantly associated with increased risk of HCC based on allelic contrast (OR = 1.29, 95% CI = 1.16–1.44, p<0.001), homozygote comparison (OR = 1.79, 95% CI = 1.39–2.29, p<0.001) and a recessive genetic model (OR = 1.34, 95% CI = 1.16–1.54, p<0.001), while patients carrying the EGF 61*A/A genotype had significantly lower risk of HCC than those with the G/A or G/G genotype (A/A vs. G/A+G/G, OR = 0.66, 95% CI = 0.53–0.83, p<0.001).
Conclusion
The 61*G polymorphism in EGF is a risk factor for hepatocarcinogenesis while the EGF 61*A allele is a protective factor. Further large and well-designed studies are needed to confirm this conclusion.
doi:10.1371/journal.pone.0032159
PMCID: PMC3293888  PMID: 22403631
12.  Biodiversity and Biogeography of Rhizobia Associated with Soybean Plants Grown in the North China Plain ▿ †  
Applied and Environmental Microbiology  2011;77(18):6331-6342.
As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera Sinorhizobium and Bradyrhizobium, including four novel groups, with S. fredii (68.28%) as the dominant group. The phylogeny of symbiotic genes nodC and nifH defined four lineages among the isolates associated with Sinorhizobium fredii, Bradyrhizobium elkanii, B. japonicum, and B. yuanmingense, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns: Sinorhizobium spp. were superdominant in sampling sites with alkaline-saline soils, while Bradyrhizobium spp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.
doi:10.1128/AEM.00542-11
PMCID: PMC3187167  PMID: 21784912
13.  Expression of T-helper-associated cytokines in patients with type 2 diabetes mellitus with retinopathy 
Molecular Vision  2012;18:219-226.
Purpose
Recent studies showed that immunological mechanisms were involved in the pathogenesis of diabetic retinopathy (DR). T-helper (Th) cells play an important role in chronic inflammatory disorders and autoimmune diseases. Whether Th cells participate in the pathogenesis of DR remains unclear.
Methods
To evaluate the role of Th cells in the pathogenesis of type 2 diabetes mellitus with retinopathy, the concentrations of interferon (IFN)-γ, interleukin (IL)-1β, IL-2, IL-4, IL-5, IL-6, IL-9, IL-10, IL-12 p70, IL-13, IL-17A, IL-22, and tumor necrosis factor (TNF)-α in the serum of 29 patients with type 2 diabetes mellitus and 30 normal controls were measured with FlowCytomix Technology. IL-22 levels in unstimulated and stimulated peripheral blood mononuclear cells (PBMCs) were examined with enzyme-linked immunosorbent assay.
Results
We found that the mean IL-22 serum levels were slightly lower in diabetic patients than in normal controls. The IL-22 level of PBMCs was significantly elevated in patients with proliferative diabetic retinopathy compared with the level in patients with non-proliferative diabetic retinopathy, patients with non-DR, and healthy controls. Additionally, the IL-22 serum and PBMC levels were positively correlated with the duration of diabetes. Serum levels of other associated cytokines showed no significant change in diabetic patients compared to controls.
Conclusions
These results indicate a possible role of Th22 cells in DR, and IL-22 may be involved more in the pathogenesis of proliferative diabetic retinopathy than in other stages of DR.
PMCID: PMC3272054  PMID: 22312190
14.  COL1A2 polymorphic markers confer an increased risk of neovascular age-related macular degeneration in a Han Chinese population 
Molecular Vision  2012;18:1787-1793.
Purpose
We have previously documented that neovascular age-related macular degeneration (nAMD) and polypoidal choroidal vasculopathy (PCV) have multiple different clinical and genetic characteristics. In this study, we investigated the association of rs42524 in the alpha-2 type I collagen (COL1A2) gene, which has been identified as a risk variant for intracranial aneurysm, with nAMD and PCV in a Han Chinese population.
Methods
The study prospectively recruited 195 patients with PCV, 136 patients with nAMD, and 181 control individuals. We genotyped the rs42524 polymorphism of COL1A2 using the Multiplex SNaPshot System and direct DNA sequencing. Genotype and allele frequencies were evaluated with PLINK software.
Results
The rs42524 polymorphism was modestly significantly associated with nAMD [minor allele: G, p(allelic)=0.04253, odds ratio=0.5285 (95% confidence interval: 0.2832–0.9866)], but not with PCV [minor allele: G, p(allelic)=0.4164, odds ratio=1.2110 (95% confidence interval: 0.7631–1.9210)]. The pvalues for the additive model were significant for nAMD but not for the dominant or recessive models. None of the models for PCV were statistically significant. The size of our sample cohort resulted in a post hoc power of more than 80% to detect associations of rs42524 with nAMD and PCV.
Conclusions
The rs42524 polymorphism is a risk allele for nAMD in a Han Chinese population. rs42524 in COL1A2 confers different levels of susceptibility to nAMD and PCV.
PMCID: PMC3398488  PMID: 22815632
15.  An efficient method of addressing ectopic beats: new insight into data preprocessing of heart rate variability analysis*  
Heart rate variability (HRV) analysis is affected by ectopic beats. An efficient method was proposed to deal with the ectopic beats. The method was based on trend correlation of the heart timing signal. Predictor of R-R interval (RRI) value at ectopic beat time was constructed by the weight calculation and the slope estimation of preceding normal RRI. The type of ectopic beat was detected and replaced by the predictor of RRI. The performance of the simulated signal after ectopic correction was tested by the standard value using power spectrum density (PSD) estimation, whereas the results of clinical data with ectopic beats were compared with the adjacent ectopic-free data. The result showed the frequency indexes after ectopy corrected had less error than other methods with the test of simulated signal and clinical data. It indicated our method could improve the PSD estimation in HRV analysis. The method had advantages of high accuracy and real time properties to recover the sinus node modulation.
doi:10.1631/jzus.B1000392
PMCID: PMC3232430  PMID: 22135146
Frequency domain; Ectopic beat; Heart rate variability (HRV); Power spectrum density
16.  Clinical management of gastric cancer: results of a multicentre survey 
BMC Cancer  2011;11:369.
Background
The National Comprehensive Cancer Network clinical practice guidelines in oncology-gastric cancer guidelines have been widely used to provide appropriate recommendations for the treatment of patients with gastric cancer. The aim of this study was to examine the adherence of surgical oncologists, medical oncologists, and radiation oncologists' to the recommended guidelines.
Methods
A questionnaire asking the treatment options for gastric cancer cases was sent to 394 Chinese oncology specialists, including surgical oncologists, medical oncologists, and radiation oncologists working in hospitals joined in The Western Cooperative Gastrointestinal Oncology Group of China. The questionnaire involved a series of clinical scenarios regarding the interpretation of surgery, neoadjuvant, adjuvant, and advanced treatment planning of gastric cancer.
Results
Analysis of 358 respondents (91%) showed variations between each specialization and from the recommended guidelines in the management approaches to specific clinical scenarios. The majority of specialists admitted that less than 50% of patients received multidisciplinary evaluation before treatment. The participants gave different responses to questions involving adjuvant, neoadjuvant, and advanced settings, compared to the recommended guidelines.
Conclusions
These results highlight the heterogeneity of the treatment of gastric cancer. Surgical oncologists, medical oncologists, and radiation oncologists are not adhering to the recommended guidelines.
doi:10.1186/1471-2407-11-369
PMCID: PMC3224384  PMID: 21864355
17.  Exon 6 variants carried on systemic lupus erythematosus (SLE) risk haplotypes modulate IRF5 function 
Autoimmunity  2010;44(2):82-89.
Interferon response factor 5 (IRF5) regulates innate immune responses to viral infection. IRF5 genetic variants have been shown to be strongly associated with risk for systemic lupus erythematosus (SLE). Functional roles of IRF5 exon 6 structural variants that occur as part of a SLE risk-associated haplotype, including a 30-bp in/del (in/del-10) and a 48-bp splice-site variant (SV-16), have not been established. In this study, we used IRF5 deficient cells overexpressing human IRF5 variants to investigate the roles of exon 6 in/del-10 and SV-16 in regulation of the apoptosis response, nuclear translocation, and ability to transactivate IRF5 responsive cytokines. We found that expression of IRF5 isoforms including either SV-16 or in/del-10 confers ability of IRF5 to impair the apoptotic response and correlates with reduced capacity for IRF5 nuclear translocation in MEFs after a DNA-damaging stimulus treatment. Interestingly, the presence or absence of both SV-16 and in/del-10 results in abrogation of both the anti-apoptotic and enhanced nuclear translocation effects of IRF5 expression. Only cells expressing IRF5 bearing SV-16 show increased IL-6 production upon LPS stimulation. MEFs expressing hIRF5 variants containing in/del-10 showed no significant difference from the control; however, cells carrying hIRF5 lacking both SV-16 and in/del-10 showed reduced IL-6 production. Our overall findings suggest that exon 6 SV-16 is more potent than in/del-10 for IRF5-driven resistance to apoptosis and promotion of cytokine production; however, in/del-10 co-expression can neutralize these effects of SV-16.
doi:10.3109/08916934.2010.491842
PMCID: PMC3104271  PMID: 20695768
SLE; IRF5 variants; exon 6; apoptosis; nuclear translocation
18.  Association Between a Functional Variant Downstream of TNFAIP3 and Systemic Lupus Erythematosus 
Nature genetics  2011;43(3):253-258.
Systemic Lupus Erythematosus (SLE, OMIM 152700) is an autoimmune disease characterized by self-reactive antibodies resulting in systemic inflammation and organ failure. TNFAIP3, encoding the ubiquitin-modifying enzyme A20, is an established susceptibility locus for SLE. By fine mapping and genomic resequencing in ethnically diverse populations we fully characterized the TNFAIP3 risk haplotype and isolated a novel TT>A polymorphic dinucleotide associated with SLE in subjects of European (P = 1.58 × 10−8; odds ratio (OR) = 1.70) and Korean (P = 8.33 × 10−10; OR = 2.54) ancestry. This variant, located in a region of high conservation and regulatory potential, bound a nuclear protein complex comprised of NF-κB subunits with reduced avidity. Furthermore, compared with the non-risk haplotype, the haplotype carrying this variant resulted in reduced TNFAIP3 mRNA and A20 protein expression. These results establish this TT>A variant as the most likely functional polymorphism responsible for the association between TNFAIP3 and SLE.
doi:10.1038/ng.766
PMCID: PMC3103780  PMID: 21336280
19.  Mouse Prkar1a haploinsufficiency leads to an increase in tumors in the Trp53+/− or Rb1+/− backgrounds and chemically induced skin papillomas by dysregulation of the cell cycle and Wnt signaling 
Human Molecular Genetics  2010;19(8):1387-1398.
PRKAR1A inactivation leads to dysregulated cAMP signaling and Carney complex (CNC) in humans, a syndrome associated with skin, endocrine and other tumors. The CNC phenotype is not easily explained by the ubiquitous cAMP signaling defect; furthermore, Prkar1a+/− mice did not develop skin and other CNC tumors. To identify whether a Prkar1a defect is truly a generic but weak tumorigenic signal that depends on tissue-specific or other factors, we investigated Prkar1a+/− mice when bred within the Rb1+/− or Trp53+/− backgrounds, or treated with a two-step skin carcinogenesis protocol. Prkar1a+/− Trp53+/− mice developed more sarcomas than Trp53+/− mice (P < 0.05) and Prkar1a+/− Rb1+/− mice grew more (and larger) pituitary and thyroid tumors than Rb1+/− mice. All mice with double heterozygosity had significantly reduced life-spans compared with their single-heterozygous counterparts. Prkar1a+/− mice also developed more papillomas than wild-type animals. A whole-genome transcriptome profiling of tumors produced by all three models identified Wnt signaling as the main pathway activated by abnormal cAMP signaling, along with cell cycle abnormalities; all changes were confirmed by qRT–PCR array and immunohistochemistry. siRNA down-regulation of Ctnnb1, E2f1 or Cdk4 inhibited proliferation of human adrenal cells bearing a PRKAR1A-inactivating mutation and Prkar1a+/− mouse embryonic fibroblasts and arrested both cell lines at the G0/G1 phase of the cell cycle. In conclusion, Prkar1a haploinsufficiency is a relatively weak tumorigenic signal that can act synergistically with other tumor suppressor gene defects or chemicals to induce tumors, mostly through Wnt-signaling activation and cell cycle dysregulation, consistent with studies in human neoplasms carrying PRKAR1A defects.
doi:10.1093/hmg/ddq014
PMCID: PMC2846157  PMID: 20080939
20.  Application and comparison of scoring indices to predict outcomes in patients with healthcare-associated pneumonia 
Critical Care  2011;15(1):R32.
Introduction
Healthcare-associated pneumonia (HCAP) is a relatively new category of pneumonia. It refers to infections that occur prior to hospital admission in patients with specific risk factors following contact or exposure to a healthcare environment. There is currently no scoring index to predict the outcomes of HCAP patients. We applied and compared different community acquired pneumonia (CAP) scoring indices to predict 30-day mortality and 3-day and 14-day intensive care unit (ICU) admission in patients with HCAP.
Methods
We conducted a retrospective cohort study based on an inpatient database from six medical centers, recruiting a total of 444 patients with HCAP between 1 January 2007 and 31 December 2007. Pneumonia severity scoring indices including PSI (pneumonia severity index), CURB 65 (confusion, urea, respiratory rate, blood pressure, age 65), IDSA/ATS (Infectious Diseases Society of America/American Thoracic Society), modified ATS rule, SCAP (severe community acquired pneumonia), SMART-COP (systolic blood pressure, multilobar involvement, albumin, respiratory rate, tachycardia, confusion, oxygenation, pH), SMRT-CO (systolic blood pressure, multilobar involvement, respiratory rate, tachycardia, confusion, oxygenation), and SOAR (systolic blood pressure, oxygenation, age, respiratory rate) were calculated for each patient. Patient characteristics, co-morbidities, pneumonia pathogen culture results, length of hospital stay (LOS), and length of ICU stay were also recorded.
Results
PSI (>90) has the highest sensitivity in predicting mortality, followed by CURB-65 (≥2) and SCAP (>9) (SCAP score (area under the curve (AUC): 0.71), PSI (AUC: 0.70) and CURB-65 (AUC: 0.66)). Compared to PSI, modified ATS, IDSA/ATS, SCAP, and SMART-COP were easy to calculate. For predicting ICU admission (Day 3 and Day 14), modified ATS (AUC: 0.84, 0.82), SMART-COP (AUC: 0.84, 0.82), SCAP (AUC: 0.82, 0.80) and IDSA/ATS (AUC: 0.80, 0.79) performed better (statistically significant difference) than PSI, CURB-65, SOAR and SMRT-CO.
Conclusions
The utility of the scoring indices for risk assessment in patients with healthcare-associated pneumonia shows that the scoring indices originally designed for CAP can be applied to HCAP.
doi:10.1186/cc9979
PMCID: PMC3222068  PMID: 21247444
21.  The Role of TLR2, TRL3, TRL4, and TRL9 Signaling in the Pathogenesis of Autoimmune Disease in a Retinal Autoimmunity Model 
Activation of Toll-like receptors during microbial infection plays an important role in the pathogenesis of autoimmune diseases such as uveitis.
Purpose.
Induction of tissue-specific experimental autoimmune diseases involves the use of complete Freund adjuvant containing Mycobacterium tuberculosis, whose recognition by the innate immune system depends on Toll-like receptors (TLRs) that signal through the adaptor molecule MyD88. The authors' previous study showed that MyD88−/− mice, but not TLR2−/−, TLR4−/−, or TLR9−/− mice, were resistant to experimental autoimmune uveitis (EAU).
Methods.
The EAU induction in mice deficient in TLR3 or mice double deficient in TLR2+4, TLR2+9, and TLR4+9 was examined and the role of the TLR agonists in the adjuvant effect involved in the induction of EAU was assessed.
Results.
TLR3-deficient and TLR2+4, TLR2+9, and TLR4+9 double-deficient mice were as susceptible to EAU as their control littermates. However, in mice immunized with a low-dose EAU regimen, TLR4 agonist lipopolysaccharide (LPS) enhanced EAU scores, delayed-type hypersensitivity responses, and antigen-specific T-cell proliferation. Antigen-specific IL-17 and IFN-γ production by T lymphocytes was markedly increased in the LPS-treated group. The effects of LPS on EAU were abolished by treatment with an LPS deactivator polymyxin B. Inclusion of agonists for TLR2, TRL3, or TRL9 in immunization also enhanced EAU scores.
Conclusions.
These results suggest that signaling of TLR2, TRL3, TRL4, and TRL9 is highly redundant in the adjuvant effect needed to induce EAU and that diverse microbial infections may contribute to the pathogenesis of diseases such as uveitis.
doi:10.1167/iovs.09-4754
PMCID: PMC2891468  PMID: 20107166
22.  SERPING1 polymorphisms in polypoidal choroidal vasculopathy 
Molecular Vision  2010;16:231-239.
Purpose
To investigate whether common genetic variants in the complement component 1 inhibitor gene (serpin peptidase inhibitor, clade G, member 1, SERPING1) are associated with polypoidal choroidal vasculopathy (PCV) in a Chinese Han population.
Methods
DNA samples were obtained from 118 PCV patients and 115 healthy subjects. Data derived from the HapMap project were used to select tag single nucleotide polymorphisms (SNPs) across the extended SERPING1 region. A previously reported age-related macular degeneration-related risk factor (rs2511989) was forcibly included. Genotyping of each tag SNP was performed by PCR restriction fragment length polymorphism and direct DNA sequencing techniques.
Results
Four SNPs for SERPING1, rs2509897, rs1005510, rs11603020, and rs2511989, were chosen as tag SNPs. None of these tag SNPs were associated with PCV, according to the single-SNP association test (p=0.41–0.83). Evaluation of common haplotypes across SERPING1 did not reveal any association with PCV (p=0.49–0.82).
Conclusions
We found no evidence to support the role of any common SERPING1 variants, including the rs2511989 variant, in the susceptibility to PCV in a Chinese Han population.
PMCID: PMC2822549  PMID: 20161815
23.  Digenean parasites of Chinese marine fishes: a list of species, hosts and geographical distribution 
Systematic Parasitology  2009;75(1):1-52.
In the literature, 630 species of Digenea (Trematoda) have been reported from Chinese marine fishes. These belong to 209 genera and 35 families. The names of these species, along with their hosts, geographical distribution and records, are listed in this paper.
doi:10.1007/s11230-009-9211-9
PMCID: PMC2791834  PMID: 20012517
24.  Heme Oxygenase-1 suppresses Hepatitis C Virus replication and increases resistance of hepatocytes to oxidant injury 
Hepatology (Baltimore, Md.)  2008;48(5):1430-1439.
Oxidative injury to hepatocytes occurs as a result of HCV infection and replication. Modulation of host cell antioxidant enzymes such as heme oxygenase-1 (HO-1) may be useful therapeutically to minimize cellular injury, reduce viral replication, and attenuate liver disease. In this report, we evaluated the effects of HO-1 overexpression on HCV replication and hepatocellular injury. Full length (FL) (Con1) or Non-structural (NS) replicons (I 389 NS3-3′) were transfected with complete human HO-1 sequences or empty vector for control. Cell lines overexpressing HO-1 (2-6 fold above basal values) or empty vector were isolated and their HCV RNA synthesis, pro-oxidant levels, and resistance to oxidative injury were assessed. HO-1 overexpression decreased HCV RNA replication in both FL and NS replicons without affecting cellular growth or DNA synthesis. The attenuation of HCV replication was significantly reversed in both replicon systems with HO-1 siRNA knockdown. Both FL and NS replicons that overexpress HO-1 showed reduced prooxidant levels at baseline and increased resistance to oxidant-induced cytotoxicity. HO-1 induction with hemin also markedly decreased HCV replication in both parental FL and NS replicon cell lines. On the other hand, knock-down of HO-1 mRNA by siRNA in parental FL or NS replicons did not significantly affect HCV replication suggesting that less than basal levels of HO-1 had minimal affect on HCV replication.
Conclusion
Overexpression or induction of HO-1 results in decreased HCV replication as well as protection from oxidative damage. These findings suggest a potential role for HO-1 in antiviral therapy and therapeutic protection against hepatocellular injury in HCV infection.
doi:10.1002/hep.22491
PMCID: PMC2587102  PMID: 18972446
Anti-oxidative enzymes; oxidative stress; viral replication; replicons; Huh7 cells
25.  Clinical outcomes in patients with ICU-related pancreatitis 
AIM: To identify risk factors predictive of intensive care unit (ICU) mortality in patients with ventilator-related pancreatitis. The clinical outcomes of patients with ventilator-related pancreatitis were compared with those of patients with pancreatitis-related respiratory failure as well as controls.
METHODS: One hundred and forty-eight patients with respiratory failure requiring mechanical ventilation and concomitant acute pancreatitis were identified from a prospectively collected dataset of 9108 consecutive patients admitted with respiratory failure over a period of five years. Sixty patients met the criteria for ventilator-related pancreatitis, and 88 (control patients), for pancreatitis-related respiratory failure.
RESULTS: Mortality rate in ventilator-related pancreatitis was comparable to that in ICU patients without pancreatitis by case-control methodology (P = 0.544). Multivariate logistic regression analysis identified low PaO2/FiO2 (OR: 1.032, 95% CI: 1.006-1.059, P = 0.016) as an independent risk factor for mortality in patients with ventilator-related pancreatitis. The mortality rate in patients with ventilator-related pancreatitis was lower than that in patients with acute pancreatitis-related respiratory failure (P < 0.001).
CONCLUSION: We found that low PaO2/FiO2 was an independent clinical parameter predictive of ICU mortality in patients with ventilator-related pancreatitis.
doi:10.3748/wjg.15.4938
PMCID: PMC2764973  PMID: 19842226
Acute pancreatitis; Hyperamylasemia; Hyperlipasemia; Mechanical ventilation; Respiratory failure

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