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1.  Nonparametric ROC Summary Statistics for Correlated Diagnostic Marker Data 
Statistics in medicine  2012;32(13):2209-2220.
We propose efficient nonparametric statistics to compare medical imaging modalities in multi-reader multi-test data and to compare markers in longitudinal ROC data. The proposed methods are based on the weighted area under the ROC curve which includes the area under the curve and the partial area under the curve as special cases. The methods maximize the local power for detecting the difference between imaging modalities. The asymptotic results of the proposed methods are developed under a complex correlation structure. Our simulation studies show that the proposed statistics result in much better powers than existing statistics. We applied the proposed statistics to an endometriosis diagnosis study.
doi:10.1002/sim.5654
PMCID: PMC3578098  PMID: 23055248
ROC curve; Optimal weights; Wilcoxon statistics; Correlated data
2.  Epstein-Barr Virus (EBV) Infection in Chinese Children: A Retrospective Study of Age-Specific Prevalence 
PLoS ONE  2014;9(6):e99857.
Background
Epstein-Barr Virus (EBV) is a globally prevalent herpesvirus associated with infectious mononucleosis and many malignancies. The survey on EBV prevalence appears to be important to study EBV-related diseases and determine when to administer prophylactic vaccine. The purpose of this retrospective study was to collect baseline information about the prevalence of EBV infection in Chinese children.
Methodology/Principal Finding
We collected 1778 serum samples from healthy children aged 0 to 10, who were enrolled in conventional health and nutrition examinations without any EBV-related symptom in 2012 and 2013 in North China (n = 973) and South China (n = 805). We detected four EBV-specific antibodies, i.e., anti-VCA-IgG and IgM, anti-EBNA-IgG and anti-EA-IgG, by ELISA, representing all of the phases of EBV infection. The overall EBV seroprevalence in samples from North and South China were 80.78% and 79.38% respectively. The EBV seropositivity rates dropped slightly at age 2, and then increased gradually with age. The seroprevalence became stabilized at over 90% after age 8. In this study, the seroprevalence trends between North and South China showed no difference (P>0.05), and the trends of average antibody concentrations were similar as well (P>0.05).
Conclusions/Significance
EBV seroprevalence became more than 50% before age 3 in Chinese children, and exceed 90% after age 8. This study can be helpful to study the relationship between EBV and EBV-associated diseases, and supportive to EBV vaccine development and implementation.
doi:10.1371/journal.pone.0099857
PMCID: PMC4051769  PMID: 24914816
3.  Metastasis, Risk Factors and Prognostic Significance of Splenic Hilar Lymph Nodes in Gastric Adenocarcinoma 
PLoS ONE  2014;9(6):e99650.
Background
The metastatic rate and risk factors of splenic hilar (No.10) lymph nodes (LNs) in gastric adenocarcinoma were still variable and uncertain, and the prognostic significance of No.10 LNs was also controversial. The aim of this retrospective study was to analyze the metastatic rate, risk factors and prognostic significance of No.10 LNs in gastric adenocarcinoma.
Methods
From August 2007 to December 2011, 205 patients who were diagnosed with primary gastric adenocarcinoma and underwent total or proximal gastrectomy plus No.10 LNs dissection in West China Hospital were enrolled. Clinicopathological features and survival outcomes were retrospectively analyzed.
Results
Mean numbers of harvested LNs and metastatic LNs were 34.8±12.6 (15–73) and 8.7±10.8 (0–67), respectively. The proportion of cases with positive No.10 LNs was 8.8% (18/205). In all 204 dissected No.10 LNs, 47 LNs (23.0%) were metastatic. In 52.2% (107/205) patients, the dissected splenic hilar tissues were histologically determined as only fat tissues but without LNs structure. Histological evidence of LNs structure was found in 98 (47.8%) patients with 18.4% (18/98) metastatic No.10 LNs. In multivariate logistic regression analysis, metastasis of No.10 LNs was significantly correlated with No.4sa LNs (p = 0.010) and pN stage (p = 0.012). Regarding survival analysis, 199 (97.1%) patients were followed up (0.6–74.8 months). In all patients with R0 resection, metastatic No.10 LNs caused significantly worse prognosis both in Kaplan-Meier (p = 0.006) and Cox regression analysis (p = 0.031).
Conclusions
Although the metastatic rate of No.10 LNs was 8.8%, dissection of No.10 LNs might be meaningful due to the poor prognosis of positive cases. And attentions should be also paid to its correlated factors including pN stage and No.4sa LNs.
doi:10.1371/journal.pone.0099650
PMCID: PMC4051839  PMID: 24915065
4.  Stromal Cell-Derived Factor-1 Receptor CXCR4-Overexpressing Bone Marrow Mesenchymal Stem Cells Accelerate Wound Healing by Migrating into Skin Injury Areas 
Cellular Reprogramming  2013;15(3):206-215.
Abstract
Stromal cell-derived factor-1 (SDF-1) and its membrane receptor C-X-C chemokine receptor type 4 (CXCR4) are involved in the homing and migration of multiple stem cell types, neovascularization, and cell proliferation. This study investigated the hypothesis that bone marrow–derived mesenchymal stem cells (BMSCs) accelerate skin wound healing in the mouse model by overexpression of CXCR4 in BMSCs. We compared SDF-1 expression and skin wound healing times of BALB/c mice, severe combined immunodeficiency (SCID) mice, and immune system–deficient nude mice after 60Co radiation–induced injury of their bone marrow. The occurrence of transplanted adenovirus-transfected CXCR4-overexpressing male BMSCs in the wound area was compared with the occurrence of untransfected male BALB/c BMSCs in 60Co-irradiated female mice skin wound healing areas by Y chromosome marker analyses. The wound healing time of BALB/c mice was 14.00±1.41 days, whereas for the nude and SCID mice it was 17.16±1.17 days and 19.83±0.76 days, respectively. Male BMSCs could be detected in the surrounding areas of 60Co-irradiated female BALB/c mice wounds, and CXCR4-overexpressing BMSCs accelerated the wound healing time. CXCR4-overexpressing BMSCs migrate in an enhanced manner to skin wounds in a SDF-1–expression-dependent manner, thereby reducing the skin wound healing time.
doi:10.1089/cell.2012.0046
PMCID: PMC3666362  PMID: 23713431
5.  Information Dissemination Analysis of Different Media towards the Application for Disaster Pre-Warning 
PLoS ONE  2014;9(5):e98649.
Knowing the information dissemination mechanisms of different media and having an efficient information dissemination plan for disaster pre-warning plays a very important role in reducing losses and ensuring the safety of human beings. In this paper we established models of information dissemination for six typical information media, including short message service (SMS), microblogs, news portals, cell phones, television, and oral communication. Then, the information dissemination capability of each medium concerning individuals of different ages, genders, and residential areas was simulated, and the dissemination characteristics were studied. Finally, radar graphs were used to illustrate comprehensive assessments of the six media; these graphs show directly the information dissemination characteristics of all media. The models and the results are essential for improving the efficiency of information dissemination for the purpose of disaster pre-warning and for formulating emergency plans which help to reduce the possibility of injuries, deaths and other losses in a disaster.
doi:10.1371/journal.pone.0098649
PMCID: PMC4039515  PMID: 24878739
6.  The Interface between Methyltransferase and Polymerase of NS5 Is Essential for Flavivirus Replication 
The flavivirus NS5 harbors both a methyltransferase (MTase) and an RNA-dependent RNA polymerase (RdRP). Both enzyme activities of NS5 are critical for viral replication. Recently, the full-length NS5 crystal structure of Japanese encephalitis virus reveals a conserved MTase-RdRP interface that features two conserved components: a six-residue hydrophobic network and a GTR sequence. Here we showed for the first time that these key interface components are essential for flavivirus replication by various reverse genetics approaches. Interestingly, some replication-impaired variants generated a common compensatory NS5 mutation outside the interface (L322F), providing novel routes to further explore the crosstalk between MTase and RdRP.
Author Summary
Flaviviruses, such as Japanese encephalitis virus (JEV) and dengue virus 1-4 (DENV1-4), are important arthropod-borne pathogens causing major public health threats worldwide. For example, JEV is the most common cause of viral encephalitis in eastern and southern Asia, affecting over 50,000 patients, and leads to 15,000 deaths annually. DENV is responsible for an estimated 50 million cases of dengue fever and over 450,000 cases of life-threatening dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS) each year. Currently, there is no effective antiviral therapeutics available for flaviviruses. Non-structural protein 5 (NS5) is a multifunctional, viral protein that contains a methyltransferase (MTase) and an RNA-dependent RNA polymerase (RdRP). Both MTase and RdRP are required for replication of the viral genome. A conserved interface between MTase and RdRP was first identified in the full-length NS5 crystal structure of JEV. In this study we used the infectious clones of both JEV and DENV-2 to perform functional mutagenesis analyses and demonstrated for the first time that the recently identified conserved interface between MTase and RdRP is critical for viral replication. In a replicon system, we also confirmed that mutations within the conserved interface greatly affect viral RNA replication during viral infection. Our functional validation of the conserved MTase-RdRP interface consolidated its potential as a novel target for anti-flavivirus drug development.
doi:10.1371/journal.pntd.0002891
PMCID: PMC4031075  PMID: 24852307
7.  No Chemopreventive Effect of Nonsteroidal Anti-Inflammatory Drugs on Nonmelanoma Skin Cancer: Evidence from Meta-Analysis 
PLoS ONE  2014;9(5):e96887.
Background
Nonmelanoma skin cancer (NMSC),which includes squamous cell carcinoma (SCC) and basal cell carcinoma (BCC), is the most common form of cancer, and its incidence is increasing. Nonsteroidal anti-inflammatory drugs (NSAIDs) have been reported to be chemopreventive for NMSC. However, the results from published studies were controversial.
Methods
We searched the PubMed and Embase databases for relevant studies. Moreover, relevant reviews regarding the use of NSAIDs for NMSC patients were examined for potential inclusive studies. To measure the effects of NSAIDs, the relative risk (RR) was analyzed.
Results
A Total of 8 studies were included in our meta-analysis. We found that NSAIDs use was not associated with a reduced risk of SCC or BCC under the random effects model (pooled RR  =  0.86, 95% CI, 0.73–1.02, P  =  0.085; pooled RR  =  0.94, 95% CI 0.85–1.04, P  =  0.266; respectively).
Conclusion
From the included studies, we found no statistically significant chemopreventive effect on NMSC of NSAIDs. This finding warrants more prospective studies evaluating the relationship between NSAIDs and NMSC.
doi:10.1371/journal.pone.0096887
PMCID: PMC4020781  PMID: 24828489
8.  Redox-filled Carbon-Fiber Microelectrodes for Single-Cell Exocytosis 
Electroanalysis  2013;25(9):2151-2158.
Carbon-fiber microelectrodes (CFEs) are the primary electroanalytical tool in single-cell exocytosis and in-vivo studies. Here we report a new study on the kinetic properties of electrolyte-filled CFEs in single-cell measurements and demonstrate that the addition of outer sphere redox species, such as Fe(CN)63− and Ru(NH3)63+, in the backfill electrolyte solution can greatly enhance the kinetic response of CFEs. We show that at 750 mV, a voltage normally applied for detection of dopamine, the presence of fast outer sphere redox species in the backfilling solution significantly enhances the kinetic response of CFEs toward fast dopamine detection at single PC12 cells. Moreover, we also demonstrate that the use of Fe(CN)63− in the backfilling solution has enabled direct measurement of dopamine at applied voltages as low as 200 mV. This kinetic enhancement is believed to be due to faster electron-transfer kinetics on the coupling pole as compared to the sluggish reduction of oxygen. We anticipate that such redox-filled CFE ultramicroelectrodes will find many useful applications in single cell exocytosis and in-vivo sensing.
doi:10.1002/elan.201300255
PMCID: PMC4018834  PMID: 24833889
9.  Wnt/β-Catenin Pathway Regulates Cementogenic Differentiation of Adipose Tissue-Deprived Stem Cells in Dental Follicle Cell-Conditioned Medium 
PLoS ONE  2014;9(5):e93364.
The formation and attachment of new cementum is crucial for periodontium regeneration. Tissue engineering is currently explored to achieve complete, reliable and reproducible regeneration of the periodontium. The capacity of multipotency and self-renewal makes adipose tissue-deprived stem cells (ADSCs) an excellent cell source for tissue regeneration and repair. After rat ADSCs were cultured in dental follicle cell-conditioned medium (DFC-CM) supplemented with DKK-1, an inhibitor of the Wnt pathway, followed by 7 days of induction, they exhibited several phenotypic characteristics of cementoblast lineages, as indicated by upregulated expression levels of CAP, ALP, BSP and OPN mRNA, and accelerated expression of BSP and CAP proteins. The Wnt/β-catenin signaling pathway controls differentiation of stem cells by regulating the expression of target genes. Cementoblasts share phenotypical features with osteoblasts. In this study, we demonstrated that culturing ADSCs in DFC-CM supplemented with DKK-1 results in inhibition of β-catenin nuclear translocation and down-regulates TCF-4 and LEF-1 mRNA expression levels. We also found that DKK-1 could promote cementogenic differentiation of ADSCs, which was evident by the up-regulation of CAP, ALP, BSP and OPN gene expressions. On the other hand, culturing ADSCs in DFC-CM supplemented with 100 ng/mL Wnt3a, which activates the Wnt/β-catenin pathway, abrogated this effect. Taken together, our study indicates that the Wnt/β-catenin signaling pathway plays an important role in regulating cementogenic differentiation of ADSCs cultured in DFC-CM. These results raise the possibility of using ADSCs for periodontal regeneration by modifying the Wnt/β-catenin pathway.
doi:10.1371/journal.pone.0093364
PMCID: PMC4012947  PMID: 24806734
10.  Prognostic Significance of the Neutrophil-to-Lymphocyte Ratio in Primary Liver Cancer: A Meta-Analysis 
PLoS ONE  2014;9(5):e96072.
The neutrophil-to-lymphocyte ratio (NLR) is a useful biomarker that reflects systemic inflammation responses. However, the prognostic value of the NLR in patients with primary liver cancer (PLC) remains controversial. We performed a meta-analysis of 26 studies (comprising 4,461 patients) to evaluate the association between the pre-treatment NLR and clinical outcomes of overall survival (OS) and disease-free survival (DFS) in patients with PLC. The correlation between NLR and tumor characteristics or other inflammation-related parameters was also assessed. Data were synthesized using the random-effects model of DerSimonian and Laird, and the hazard ratio (HR) or odds ratio (OR) with 95% confidence interval (CI) was used to estimate effect size. Our analysis indicated that a high NLR predicted poor OS (HR, 2.102; 95% CI: 1.741–2.538) and DFS (HR, 2.474; 95% CI: 1.855–3.300) for PLC. A high NLR was associated with the presence of tumor vascular invasion (OR: 1.889, 95% CI: 1.487–2.400; p<0.001) and an elevated alpha-fetoprotein level (OR: 1.536; 95% CI: 1.152–2.048; p = 0.003). Thus, we conclude that a high NLR indicates a poor prognosis for patients with PLC and may also be predictive for PLC invasion and metastasis. Subgroup analysis suggested that the predictive role of NLR in cholangiocarcinoma is limited, and a further large study to confirm these findings is warranted.
doi:10.1371/journal.pone.0096072
PMCID: PMC4008563  PMID: 24788770
11.  Live birth after fresh embryo transfer vs elective embryo cryopreservation/frozen embryo transfer in women with polycystic ovary syndrome undergoing IVF (FreFro-PCOS): study protocol for a multicenter, prospective, randomized controlled clinical trial 
Trials  2014;15:154.
Background
Polycystic ovary syndrome (PCOS) patients are at increased risk of pregnancy complications, which may impair pregnancy outcome. Transfer of fresh embryos after superovulation may lead to abnormal implantation and placentation and further increase risk for pregnancy loss and complications. Some preliminary data suggest that elective embryo cryopreservation followed by frozen–thawed embryo transfer into a hormonally primed endometrium could result in a higher clinical pregnancy rate than that achieved by fresh embryo transfer.
Methods/Design
This study is a multicenter, prospective, randomized controlled clinical trial (1:1 treatment ratio of fresh vs. elective frozen embryo transfers).. A total of 1,180 infertile PCOS patients undergoing the first cycle of in vitro fertilization (IVF) or intracytoplasmic sperm injection will be enrolled and randomized into two parallel groups. Participants in group A will undergo fresh embryo transfer on day 3 after oocyte retrieval, and participants in group B will undergo elective embryo cryopreservation after oocyte retrieval and frozen–thawed embryo transfer in programmed cycles. The primary outcome is the live birth rate. Our study is powered at 80 to detect an absolute difference of 10 at the significance level of 0.01 based on a two-sided test.
Discussion
We hypothesize that elective embryo cryopreservation and frozen–thawed embryo transfer will reduce the incidence of pregnancy complications and increase the live birth rate in PCOS patients who need IVF to achieve pregnancy.
Trial registration
ClinicalTrials.gov Identifier: NCT01841528
doi:10.1186/1745-6215-15-154
PMCID: PMC4022358  PMID: 24885793
Frozen–thawed embryo transfer; In vitro fertilization; Live birth; Polycystic ovarian syndrome
12.  The role of heat shock proteins in inflammatory injury induced by cold stress in chicken hearts 
Cell Stress & Chaperones  2013;18(6):773-783.
The aim of this study was to investigate the effects of cold stress on the expression levels of heat shock proteins (Hsps90, 70, 60, 40, and 27) and inflammatory factors (iNOS, COX-2, NF-κB, TNF-α, and PTGEs) and oxidative indexes in hearts of chickens. Two hundred forty 15-day-old male chickens were randomly divided into 12 groups and kept at the temperature of 12 ± 1 °C for acute and chronic cold stress. There were one control group and five treatment groups for acute cold stress, three control groups, and three treatment groups for chronic cold stress. After cold stress, malondialdehyde level increased in chicken heart; the activity of superoxide dismutase and glutathione peroxidase in the heart first increased and then decreased. The inflammatory factors mRNA levels were increased in cold stress groups relative to control groups. The histopathological analysis showed that heart tissues were seriously injured in the cold stress group. Additionally, the mRNA levels of Hsps (70, 60, 40, and 27) increased significantly (P < 0.05) in the cold stress groups relative to the corresponding control group. Meanwhile, the mRNA level and protein expression of Hsp90 decreased significantly (P < 0.05) in the stress group, and showed a gradually decreasing tendency. These results suggested that the levels of inflammatory factors and Hsps expression levels in heart tissues can be influenced by cold stress. Hsps commonly played an important role in the protection of the heart after cold stress.
doi:10.1007/s12192-013-0429-8
PMCID: PMC3789878  PMID: 23636703
Cold stress; Heat shock proteins; Inflammatory injury; Chicken heart
13.  Synthesis and screening of 3-MA derivatives for autophagy inhibitors 
Autophagy  2013;9(4):595-603.
Autophagy is a conserved degradation process, which plays important pathophysiological roles. The lack of effective inhibitors of autophagy has been an obstacle in both basic research and understanding the physiological role of autophagy in disease manifestation. The most widely used inhibitor, 3-methyladenine (3-MA), is poorly soluble at room temperature and is effective only at high concentrations. In this study, we synthesized a library of small compounds by chemically modifying 3-MA and screened this library for autophagy inhibitors. Three 3-MA derivatives generated through this approach showed improved solubility and effectiveness in inhibiting autophagy. We demonstrated that chemical modification of an existing autophagy inhibitor is an effective method to generate improved autophagy inhibitors.
doi:10.4161/auto.23641
PMCID: PMC3627673  PMID: 23412639
autophagy; inhibitor; 3-MA; synthesis; derivatives
14.  Regulation of G-protein signaling via Gnas is required to regulate proximal tubular growth in the Xenopus pronephros 
Developmental biology  2013;376(1):31-42.
In the kidney, proximal tubules are very important for the reabsorption of water, ions and organic solutes from the primary urine. They are composed of highly specialized epithelial cells that are characterized by an elaborate apical brush border to increase transport efficiency. Using the pronephric kidney of Xenopus laevis we discovered that the G-protein modulator cholera toxin resulted in a dramatic reduction of the proximal tubular size. This phenotype was accompanied by changes in the cytoarchitecture characterized by ectopic expression of the distal tubular marker 4A6 and an impairment of yolk platelet degradation. In addition, cholera toxin caused edema formation. However, this phenotype was not due to kidney defects, but rather due to impaired vasculature development. Based on experiments with antisense morpholino oligomers as well as pharmacological agonists and antagonists, we could show that the complex phenotype of cholera toxin in the pronephric kidney was caused by the hyperactivation of a single G-protein alpha subunit, Gnas. This—in turn—caused elevated cAMP levels, triggered a Rapgef4-dependent signaling cassette and perturbed exo- and endocytosis. This perturbation of the secretory pathway by Ctx was not only observed in Xenopus embryos. Also, in a human proximal tubular cell line, cholera toxin or a Rapgef4-specific agonist increased uptake and decreased secretion of FITC-labeled Albumin. Based on these data we propose that the Gnas/cAMP/Rapgef4 pathway regulates the signals inducing the proliferation of proximal tubules to acquire their final organ size.
doi:10.1016/j.ydbio.2013.01.017
PMCID: PMC3767149  PMID: 23352791
Cholera toxin; Endocytosis; Exocytosis; Pronephric kidney; Xenopus; Yolk degradation
15.  The Effects of the CCR6/CCL20 Biological Axis on the Invasion and Metastasis of Hepatocellular Carcinoma 
Chemokines and their receptors have recently been shown to play major roles in cancer metastasis. Chemokine receptor 6 (CCR6) and its ligand, CCL20, were highly expressed in a variety of human cancers. In our present study, we aimed to clarify whether CCR6/CCL20 was correlated with the migration of hepatocellular carcinoma (HCC). RT-PCR and Western blot results showed that CCR6 was overexpressed in different invasive potential HCC cell lines (p < 0.05), while the expression of CCL20 had no obvious difference (p > 0.05). CCR6 was suppressed by siRNA in HCCLM6, and then the biological behaviors of HCCLM6 cells were observed. The results showed that the CCR6/CCL20 biological axis increased the capacity of proliferation and adhesion, as well as the chemotactic migration and the level of cytokines related to degraded extracellular matrix. In conclusion, these findings indicate that CCR6 indeed participates in regulating the migration and invasion of HCC, and it might become a prognostic factor of HCC.
doi:10.3390/ijms15046441
PMCID: PMC4013639  PMID: 24743888
CCR6; CCL20; hepatocellular carcinoma; metastasis
16.  A new mosaic pattern in glioma vascularization: exogenous endothelial progenitor cells integrating into the vessels containing tumor-derived endothelial cells 
Oncotarget  2014;5(7):1955-1968.
Emerging evidence suggests that glioma stem-like cells (GSCs) transdifferentiating into vascular endothelial cells (ECs) possibly contributes to tumor resistance to antiangiogenic therapy. Endothelial progenitor cells (EPCs), showing active migration and incorporation into neovasculature of glioma, may be a good vehicle for delivering genes to target GSCs transdifferentiation. Here, we found a new mosaic pattern that exogenous EPCs integrated into the vessels containing the tumor-derived ECs in C6 glioma rat model. Further, we evaluated the effect of these homing EPCs on C6 glioma cells transdifferentiation. The transdifferentiation frequency of C6 glioma cells and the expressions of key factors on GSCs transdifferentiation, i.e. HIF-1α, Notch1, and Flk1 in gliomas with or without EPCs transplantation showed no significant difference. Additionally, magnetic resonance imaging could track the migration and incorporation of EPCs into glioma in vivo, which was confirmed by Prussian blue staining. The number of magnetically labeled EPCs estimated from T2 maps correlated well with direct measurements of labeled cell counts by flow cytometry. Taken together, our findings may provide a rational base for the future application of EPCs as a therapeutic and imaging probe to overcome antiangiogenic resistance for glioma and monitor the efficacy of this treatment.
PMCID: PMC4039108  PMID: 24722469
endothelial progenitor cells; C6 glioma cells; glioma; angiogenesis; magnetic resonance imaging
17.  Regulation of transplanted mesenchymal stem cells by the lung progenitor niche in rats with chronic obstructive pulmonary disease 
Respiratory Research  2014;15(1):33.
Background
Stem cell transplantation is a promising method for the treatment of chronic obstructive pulmonary disease (COPD), and mesenchymal stem cells (MSCs) have clinical potential for lung repair/regeneration. However, the rates of engraftment and differentiation are generally low following MSC therapy for lung injury. In previous studies, we constructed a pulmonary surfactant-associated protein A (SPA) suicide gene system, rAAV-SPA-TK, which induced apoptosis in alveolar epithelial type II (AT II) cells and vacated the AT II cell niche. We hypothesized that this system would increase the rates of MSC engraftment and repair in COPD rats.
Methods
The MSC engraftment rate and morphometric changes in lung tissue in vivo were investigated by in situ hybridization, hematoxylin and eosin staining, Masson’s trichrome staining, immunohistochemistry, and real-time PCR. The expression of hypoxia inducible factor (HIF-1α) and stromal cell-derived factor-1 (SDF-1), and relationship between HIF-1α and SDF-1 in a hypoxic cell model were analyzed by real-time PCR, western blotting, and enzyme-linked immunosorbent assay.
Results
rAAV-SPA-TK transfection increased the recruitment of MSCs but induced pulmonary fibrosis in COPD rats. HIF-1α and SDF-1 expression were enhanced after rAAV-SPA-TK transfection. Hypoxia increased the expression of HIF-1α and SDF-1 in the hypoxic cell model, and SDF-1 expression was augmented by HIF-1α under hypoxic conditions.
Conclusions
Vacant AT II cell niches increase the homing and recruitment of MSCs to the lung in COPD rats. MSCs play an important role in lung repair and promote collagen fiber deposition after induction of secondary damage in AT II cells by rAAV-SPA-TK, which involves HIF-1α and SDF-1 signaling.
doi:10.1186/1465-9921-15-33
PMCID: PMC3987841  PMID: 24661402
Chronic obstructive pulmonary disease; Mesenchymal stem cells; Alveolar epithelial type II cells; Niche
18.  Various applications of TALEN- and CRISPR/Cas9-mediated homologous recombination to modify the Drosophila genome 
Biology Open  2014;3(4):271-280.
ABSTRACT
Modifying the genomes of many organisms is becoming as easy as manipulating DNA in test tubes, which is made possible by two recently developed techniques based on either the customizable DNA binding protein, TALEN, or the CRISPR/Cas9 system. Here, we describe a series of efficient applications derived from these two technologies, in combination with various homologous donor DNA plasmids, to manipulate the Drosophila genome: (1) to precisely generate genomic deletions; (2) to make genomic replacement of a DNA fragment at single nucleotide resolution; and (3) to generate precise insertions to tag target proteins for tracing their endogenous expressions. For more convenient genomic manipulations, we established an easy-to-screen platform by knocking in a white marker through homologous recombination. Further, we provided a strategy to remove the unwanted duplications generated during the “ends-in” recombination process. Our results also indicate that TALEN and CRISPR/Cas9 had comparable efficiency in mediating genomic modifications through HDR (homology-directed repair); either TALEN or the CRISPR/Cas9 system could efficiently mediate in vivo replacement of DNA fragments of up to 5 kb in Drosophila, providing an ideal genetic tool for functional annotations of the Drosophila genome.
doi:10.1242/bio.20147682
PMCID: PMC3988796  PMID: 24659249
Drosophila; TALEN; CRISPR/Cas9; Homologous recombination; Targeted genomic modification
19.  Statins for the Prevention of Stroke: A Meta-Analysis of Randomized Controlled Trials 
PLoS ONE  2014;9(3):e92388.
Background
Stroke is a frequently encountered clinical event that has a detrimental impact on the quality of life. Evidence has increasingly shown that statins can substantially reduce the risk of coronary heart disease. However, it remains to be determined whether statins are definitively effective in preventing stroke.
Methods
We systematically searched the PubMed, Embase, and Central databases for studies that compared the effects of statins and placebo in patients at high risk for stroke. The outcome measures were overall incidence of stroke, incidence of fatal stroke, and incidence of hemorrhagic stroke.
Results
Eighteen randomized controlled trials satisfied all the inclusion criteria for the meta-analysis. The analysis revealed that statins reduced the overall incidence of stroke than placebo (odds ratio [OR]: 0.80; 95% confidence interval [CI]: 0.74–0.87; P<0.00001). In particular, statins showed efficacy in reducing the incidence of fatal stroke (OR: 0.90; 95% CI: 0.67–1.21; P = 0.47) and hemorrhagic stroke (OR: 0.87; 95% CI: 0.60–1.25; P = 0.45). On the contrary, they were found to increase the overall incidence of stroke (OR: 1.12; 95% CI: 0.89–1.41; P = 0.32) and fatal stroke (OR: 1.37; 95% CI: 0.93–2.03; P = 0.11) in renal transplant recipients and patients undergoing regular hemodialysis.
Conclusion
The results of this analysis suggest that statins may be beneficial in reducing the overall incidence of stroke and they may decrease the risk of fatal stroke and hemorrhagic stroke. However, statins should be used with caution in patients with a history of renal transplantation, regular hemodialysis, transient ischemic attack, or stroke. Further analyses should focus on multicentre, double-blind, placebo-controlled randomized trials with data stratification according to the nature of primary diseases and dose–effect relationship, to clarify the benefits of statins in protection against stroke.
doi:10.1371/journal.pone.0092388
PMCID: PMC3958535  PMID: 24643199
20.  Metabolic flux responses to genetic modification for shikimic acid production by Bacillus subtilis strains 
Background
Shikimic acid (SA) is a key chiral starting molecule for the synthesis of the neuramidase inhibitor GS4104 against viral influenza. Microbial production of SA has been extensively investigated in Escherichia coli, and to a less extent in Bacillus subtilis. However, metabolic flux of the high SA-producing strains has not been explored. In this study, we constructed with genetic manipulation and further determined metabolic flux with 13C-labeling test of high SA-producing B. subtilis strains.
Results
B. subtilis 1A474 had a mutation in SA kinase gene (aroI) and accumulated 1.5 g/L of SA. Overexpression of plasmid-encoded aroA, aroB, aroC or aroD in B. subtilis revealed that aroD had the most significantly positive effects on SA production. Simultaneous overexpression of genes for 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (aroA) and SA dehydrogenase (aroD) in B. subtilis BSSA/pSAAroA/pDGSAAroD resulted in SA production of 3.2 g/L. 13C-Metabolic flux assay (MFA) on the two strains BSSA/pHCMC04/pDG148-stu and BSSA/pSAAroA/pDGSAAroD indicated the carbon flux from glucose to SA increased to 4.6% in BSSA/pSAAroA/pDGSAAroD from 1.9% in strain BSSA/pHCMC04/pDG148-stu. The carbon flux through tricarboxylic acid cycle significantly reduced, while responses of the pentose phosphate pathway and the glycolysis to high SA production were rather weak, in the strain BSSA/pSAAroA/pDGSAAroD. Based on the results from MFA, two potential targets for further optimization of SA production were identified. Experiments on genetic deletion of phosphoenoylpyruvate kinase gene confirmed its positive influence on SA production, while the overexpression of the transketolase gene did not lead to increase in SA production.
Conclusion
Of the genes involved in shikimate pathway in B. subtilis, aroD exerted most significant influence on SA accumulation. Overexpression of plasmid-encoded aroA and aroD doubled SA production than its parent strain. MFA revealed metabolic flux redistribution among phosphate pentose pathway, glycolysis, TCA cycle in the low and high SA-producing B. subtilis strains. The high SA producing strain BSSA/pSAAroA/pDGSAAroD had increased carbon flux into shikimate pathway and reduced flux into TCA cycle.
doi:10.1186/1475-2859-13-40
PMCID: PMC4003833  PMID: 24628944
Shikimic acid production; Shikimate pathway; Bacillus subtilis; Metabolic flux assay (MFA); aroA; aroD; tkt; pyk
21.  Monothiol glutaredoxins and A-type proteins: Partners in Fe-S cluster trafficking 
Monothiol glutaredoxins (Grxs) are proposed to function in Fe-S cluster storage and delivery, based on their ability to exist as apo monomeric forms and dimeric forms containing a subunit-bridging [Fe2S2]2+ cluster, and to accept [Fe2S2]2+ clusters from primary scaffold proteins. In addition yeast cytosolic monothiol Grxs interact with Fra2 (Fe repressor of activation-2), to form a heterodimeric complex with a bound [Fe2S2]2+ cluster that plays a key role in iron sensing and regulation of iron homeostasis. In this work, we report on in vitro UV-visible CD studies of cluster transfer between homodimeric monothiol Grxs and members of the ubiquitous A-type class of Fe-S cluster carrier proteins (NifIscA and SufA). The results reveal rapid, unidirectional, intact and quantitative cluster transfer from the [Fe2S2]2+ cluster-bound forms of A. thaliana GrxS14, S. cerevisiae Grx3, and A. vinelandii Grx-nif homodimers to A. vinelandii NifIscA and from A. thaliana GrxS14 to A. thaliana SufA1. Coupled with in vivo evidence for interaction between monothiol Grxs and A-type Fe-S cluster carrier proteins, the results indicate that these two classes of proteins work together in cellular Fe-S cluster trafficking. However, cluster transfer is reversed in the presence of Fra2, since the [Fe2S2]2+ cluster-bound heterodimeric Grx3/Fra2 complex can be formed by intact [Fe2S2]2+ cluster transfer from NifIscA. The significance of these results for Fe-S cluster biogenesis or repair and the cellular regulation of the Fe-S cluster status are discussed.
doi:10.1039/c2dt32263c
PMCID: PMC3578507  PMID: 23292141
22.  Intestinal obstruction due to migration of a thermometer from bladder to abdominal cavity: A case report 
Intraperitoneal foreign bodies such as retained surgical instruments can cause intestinal obstruction. However, intestinal obstruction due to transmural migration of foreign bodies has rarely been reported. Here, we report a case of intestinal obstruction due to a clinical thermometer which migrated from the bladder into the abdominal cavity. A 45-year-old man was admitted to our hospital with a one-year history of recurrent lower abdominal cramps. Two days before admission, the abdominal cramps aggravated. Intestinal obstruction was confirmed with upright abdominal radiography and computerized tomography scan which showed dilation of the small intestines and a thermometer in the abdominal cavity. Then laparotomy was performed. A scar was observed at the fundus of the bladder and a thermometer was adhering to the small bowels and mesentery which resulted in intestinal obstruction. Abdominal cramps were eliminated and defecation and flatus recovered soon after removal of the thermometer.
doi:10.3748/wjg.v20.i9.2426
PMCID: PMC3942848  PMID: 24605042
Intestinal obstruction; Foreign body; Thermometer; Transmural migration; Bladder
23.  New Coxsackievirus B4 Genotype Circulating in Inner Mongolia Autonomous Region, China 
PLoS ONE  2014;9(3):e90379.
Hand, foot, and mouth disease (HFMD) surveillance was initiated in the Inner Mongolia Autonomous Region of China in 2007, a crucial scrutiny for monitoring the prevalence of enterovirus serotypes associated with HFMD patients. However, this surveillance mostly focused on enterovirus 71 (EV-A71) and coxsackievirus A16; therefore, information on other enterovirus serotypes is limited. To identify the other circulating enterovirus serotypes in the HFMD outbreaks in Inner Mongolia in 2010, clinical samples from HFMD patients were investigated. Six coxsackievirus B4 (CVB4) strains were isolated and phylogenetic analyses of VP1 sequences were performed. Full-length genome sequences of two representative CVB4 isolates were acquired and similarity plot and bootscanning analyses were performed. The phylogenetic dendrogram indicated that all CVB4 strains could be divided into 5 genotypes (Genotypes I–V) with high bootstrap support (90–100%). The CVB4 prototype strain (JVB) was the sole member of genotype I. CVB4 strains belonging to genotype II, which were once common in Europe and the Americas, seemingly disappeared and gave way to genotype III and IV strains, which appear to be the dominant circulating strains in the world. All Chinese CVB4 strains belonged to Genotype V, a newly identified genotype supported by a high bootstrap value (100%), and are circulating only in mainland of China. Intertypic recombination occurred in the Chinese CVB4 strains with novel unknown serotype EV-B donor sequences. Two Chinese CVB4 strains had a virulent residue at position 129 of VP1, and one strain also had a virulent residue at position 16 of VP4. Increased surveillance is needed to monitor the emergence of new genetic lineages of enteroviruses in areas that are often associated with large-scale outbreaks. In addition, continued monitoring of enteroviruses by clinical surveillance and genetic characterization should be enhanced.
doi:10.1371/journal.pone.0090379
PMCID: PMC3940859  PMID: 24595311
24.  Streptomyces heilongjiangensis sp. nov., a novel actinomycete that produces borrelidin isolated from the root surface of soybean [Glycine max (L.) Merr] 
A borrelidin-producing actinomycete, designated strain NEAU-W2T, was isolated from the root surface of soybean [Glycine max (L.) Merr] and characterized using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of streptomycetes. The G+C content of the DNA was 66.12 mol%. Analysis of the 16S rRNA gene sequence of strain NEAU-W2T revealed that the strain formed a distinct clade within the 16S rRNA gene sequence phylogenetic tree and showed highest similarity (99.61 %) to Streptomyces neyagawaensis ATCC 27449T. However, the DNA–DNA relatedness between strain NEAU-W2T and S. neyagawaensis ATCC 27449T was 58.51 %. Strain NEAU-W2T could also be differentiated from S. neyagawaensis ATCC 27449T and other Streptomyces species showing high 16S rRNA gene sequence similarity (98–99 %), as well as other borrelidin-producing strains, based on morphological and physiological characteristics. On the basis of its physiological and molecular properties, it is proposed that strain NEAU-W2T represents a novel Streptomyces species, Streptomyces heilongjiangensis sp. nov. The type strain is NEAU-W2T ( = CGMCC 4.7004T  = ATCC BAA-2424T  = DSM 42073T).
doi:10.1099/ijs.0.041483-0
PMCID: PMC3709533  PMID: 22707527
25.  Estrogen receptor α-coupled Bmi1 regulation pathway in breast cancer and its clinical implications 
BMC Cancer  2014;14:122.
Background
Bmi1 has been identified as an important regulator in breast cancer, but its relationship with other signaling molecules such as ERα and HER2 is undetermined.
Methods
The expression of Bmi1 and its correlation with ERα, PR, Ki-67, HER2, p16INK4a, cyclin D1 and pRB was evaluated by immunohistochemistry in a collection of 92 cases of breast cancer and statistically analyzed. Stimulation of Bmi1 expression by ERα or 17β-estradiol (E2) was analyzed in cell lines including MCF-7, MDA-MB-231, ERα-restored MDA-MB-231 and ERα-knockdown MCF-7 cells. Luciferase reporter and chromatin immunoprecipitation assays were also performed.
Results
Immunostaining revealed strong correlation of Bmi1 and ERα expression status in breast cancer. Expression of Bmi1 was stimulated by 17β-estradiol in ERα-positive MCF-7 cells but not in ERα-negative MDA-MB-231 cells, while the expression of Bmi1 did not alter expression of ERα. As expected, stimulation of Bmi1 expression could also be achieved in ERα-restored MDA-MB-231 cells, and at the same time depletion of ERα decreased expression of Bmi1. The proximal promoter region of Bmi1 was transcriptionally activated with co-transfection of ERα in luciferase assays, and the interaction of the Bmi1 promoter with ERα was confirmed by chromatin immunoprecipitation. Moreover, in breast cancer tissues activation of the ERα-coupled Bmi1 pathway generally correlated with high levels of cyclin D1, while loss of its activity resulted in aberrant expression of p16INK4a and a high Ki-67 index, which implied a more aggressive phenotype of breast cancer.
Conclusions
Expression of Bmi1 is influenced by ERα, and the activity of the ERα-coupled Bmi1 signature impacts p16INK4a and cyclin D1 status and thus correlates with the tumor molecular subtype and biologic behavior. This demonstrates the important role which is played by ERα-coupled Bmi1 in human breast cancer.
doi:10.1186/1471-2407-14-122
PMCID: PMC3939403  PMID: 24559156
Bmi1; Estrogen receptor α; p16INK4a; Cyclin D1; Breast cancer

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