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1.  Evaluation of the Lymphocyte Trafficking Drug FTY720 in Vaginal Tissues 
Journal of medical primatology  2013;42(2):89-100.
Background
FTY720 is an immunomodulatory agent that reduces lymphocytes in peripheral tissues and circulation. Such agents may be effective as vaginal microbicides for HIV prevention. Systemic or vaginal application of FTY720 may reduce lymphocyte concentrations in genital tissues, reducing HIV target cell numbers.
Methods
Five female pigtail macaques received topical vaginal gel FTY720 (n=2), intravenous (IV) FTY720 (n=2), or placebo gel (n=1) in this pilot study. Circulating and mucosal lymphocytes and genital mucosa, cytokines, and tissue histology were analyzed to document topical and IV FTY720 effects.
Results
Topical and IV FTY720 appeared to decrease levels of cervicovaginal IL-8, IL-1ra, and genital inflammatory cells. Small sample size precluded statistical analysis. Topical administration had no overt adverse effects.
Conclusion
This study introduces FTY720 as an immunomodulatory agent for the vaginal mucosa, compares topical effects to those of IV administration, and provides the basis for future studies involving FTY720 for HIV prevention.
doi:10.1111/jmp.12033
PMCID: PMC3594332  PMID: 23311598
Genital; nonhuman primates; topical gel; HIV
2.  Inhibition of protein kinase CK2 reduces CYP24A1 expression and enhances 1,25-dihydroxyvitamin D3 anti-tumor activity in human prostate cancer cells 
Cancer research  2013;73(7):2289-2297.
Vitamin D has broad range of physiological functions and anti-tumor effects. 24-hydroxylase, encoded by the CYP24A1 gene, is the key enzyme for degrading many forms of vitamin D including the most active form, 1,25D3. Inhibition of CYP24A1 enhances 1,25D3 anti-tumor activity. In order to isolate regulators of CYP24A1 expression in prostate cancer cells, we established a stable prostate cancer cell line PC3 with CYP24A1 promoter driving luciferase expression to screen a small molecular library for compounds that inhibit CYP24A1 promoter activity. From this screening, we identified, 4,5,6,7-tetrabromobenzimidazole (TBBz), a protein kinase CK2 selective inhibitor as a disruptor of CYP24A1 promoter activity. We show that TBBz inhibits CYP24A1 promoter activity induced by 1,25D3 in prostate cancer cells. In addition, TBBz downregulates endogenous CYP24A1 mRNA level in TBBz treated PC3 cells. Furthermore, siRNA-mediated CK2 knockdown reduces 1,25D3 induced CYP24A1 mRNA expression in PC3 cells. These results suggest that CK2 contributes to 1,25D3 mediated target gene expression. Lastly, inhibition of CK2 by TBBz or CK2 siRNA significantly enhanced 1,25D3 mediated anti-proliferative effect in vitro and in vivo in a xenograft model. In summary, our findings reveal that protein kinase CK2 is involved in the regulation of CYP24A1 expression by 1,25D3 and CK2 inhibitor enhances 1,25D3 mediated anti-tumor effect.
doi:10.1158/0008-5472.CAN-12-4119
PMCID: PMC3618587  PMID: 23358686
1,25-dihydroxyvitamin D3; CYP24A1; protein kinase CK2; prostate cancer
3.  Machine-learning prediction of cancer survival: a retrospective study using electronic administrative records and a cancer registry 
BMJ Open  2014;4(3):e004007.
Objectives
Using the prediction of cancer outcome as a model, we have tested the hypothesis that through analysing routinely collected digital data contained in an electronic administrative record (EAR), using machine-learning techniques, we could enhance conventional methods in predicting clinical outcomes.
Setting
A regional cancer centre in Australia.
Participants
Disease-specific data from a purpose-built cancer registry (Evaluation of Cancer Outcomes (ECO)) from 869 patients were used to predict survival at 6, 12 and 24 months. The model was validated with data from a further 94 patients, and results compared to the assessment of five specialist oncologists. Machine-learning prediction using ECO data was compared with that using EAR and a model combining ECO and EAR data.
Primary and secondary outcome measures
Survival prediction accuracy in terms of the area under the receiver operating characteristic curve (AUC).
Results
The ECO model yielded AUCs of 0.87 (95% CI 0.848 to 0.890) at 6 months, 0.796 (95% CI 0.774 to 0.823) at 12 months and 0.764 (95% CI 0.737 to 0.789) at 24 months. Each was slightly better than the performance of the clinician panel. The model performed consistently across a range of cancers, including rare cancers. Combining ECO and EAR data yielded better prediction than the ECO-based model (AUCs ranging from 0.757 to 0.997 for 6 months, AUCs from 0.689 to 0.988 for 12 months and AUCs from 0.713 to 0.973 for 24 months). The best prediction was for genitourinary, head and neck, lung, skin, and upper gastrointestinal tumours.
Conclusions
Machine learning applied to information from a disease-specific (cancer) database and the EAR can be used to predict clinical outcomes. Importantly, the approach described made use of digital data that is already routinely collected but underexploited by clinical health systems.
doi:10.1136/bmjopen-2013-004007
PMCID: PMC3963101  PMID: 24643167
Cancer; Survival; Prediction; Machine Learning; Electronic Medical Record
4.  Risk stratification using data from electronic medical records better predicts suicide risks than clinician assessments 
BMC Psychiatry  2014;14:76.
Background
To date, our ability to accurately identify patients at high risk from suicidal behaviour, and thus to target interventions, has been fairly limited. This study examined a large pool of factors that are potentially associated with suicide risk from the comprehensive electronic medical record (EMR) and to derive a predictive model for 1–6 month risk.
Methods
7,399 patients undergoing suicide risk assessment were followed up for 180 days. The dataset was divided into a derivation and validation cohorts of 4,911 and 2,488 respectively. Clinicians used an 18-point checklist of known risk factors to divide patients into low, medium, or high risk. Their predictive ability was compared with a risk stratification model derived from the EMR data. The model was based on the continuation-ratio ordinal regression method coupled with lasso (which stands for least absolute shrinkage and selection operator).
Results
In the year prior to suicide assessment, 66.8% of patients attended the emergency department (ED) and 41.8% had at least one hospital admission. Administrative and demographic data, along with information on prior self-harm episodes, as well as mental and physical health diagnoses were predictive of high-risk suicidal behaviour. Clinicians using the 18-point checklist were relatively poor in predicting patients at high-risk in 3 months (AUC 0.58, 95% CIs: 0.50 – 0.66). The model derived EMR was superior (AUC 0.79, 95% CIs: 0.72 – 0.84). At specificity of 0.72 (95% CIs: 0.70-0.73) the EMR model had sensitivity of 0.70 (95% CIs: 0.56-0.83).
Conclusion
Predictive models applied to data from the EMR could improve risk stratification of patients presenting with potential suicidal behaviour. The predictive factors include known risks for suicide, but also other information relating to general health and health service utilisation.
doi:10.1186/1471-244X-14-76
PMCID: PMC3984680  PMID: 24628849
Suicide risk; Electronic medical record; Predictive models
5.  Encapsulation of MnO Nanocrystals in Electrospun Carbon Nanofibers as High-Performance Anode Materials for Lithium-Ion Batteries 
Scientific Reports  2014;4:4229.
A novel and controllable approach is developed for the synthesis of MnO nanocrystals embedded in carbon nanofibers (MnO/CNFs) through an electrospinning process. The as-formed MnO/CNFs have a porous structure with diameters of 100–200 nm and lengths up to several millimeters. When used as an anode material for lithium-ion batteries, the resulting MnO/CNFs exhibit superior electrochemical performances with high specific capacity, good cyclability, and excellent rate capability. The unique porous carbon nanofibers (PCNFs) can not only improve the contact area between the electrode and the electrolyte, but also alleviate the impact of the large volume effect of MnO during the electrochemical cycling. It is expected that the present synthetic strategy can be extended to synthesize other nanostructured oxides encapsulated in carbon nanofibers for extensive energy transfer and storage applications.
doi:10.1038/srep04229
PMCID: PMC3944319  PMID: 24598639
6.  Mebendazole Reduces Vascular Smooth Muscle Cell Proliferation and Neointimal Formation Following Vascular Injury in Mice 
PLoS ONE  2014;9(2):e90146.
Mebendazole is an antihelminthic drug that exerts its effects via interference with microtubule function in parasites. To determine the utility of mebendazole as a potential treatment for vascular diseases involving proliferation of vascular smooth muscle cells, the effects of mebendazole on vascular smooth muscle cell proliferation were tested in vitro and in a mouse model of arterial injury. In vitro, mebendazole inhibited proliferation and migration of murine vascular smooth muscle cells and this was associated with altered intracellular microtubule organization. To determine in vivo effects of mebendazole following vascular injury, femoral arterial wire injury was induced in wild-type mice treated with either mebendazole or placebo control. Compared with placebo-treated mice, mebendazole-treated mice formed less neointima at the site of injury. Mebendazole is effective at inhibiting vascular smooth muscle cell proliferation and migration, and neointimal formation following arterial injury in mice.
doi:10.1371/journal.pone.0090146
PMCID: PMC3937425  PMID: 24587248
7.  A Geovisual Analytic Approach to Understanding Geo-Social Relationships in the International Trade Network 
PLoS ONE  2014;9(2):e88666.
The world has become a complex set of geo-social systems interconnected by networks, including transportation networks, telecommunications, and the internet. Understanding the interactions between spatial and social relationships within such geo-social systems is a challenge. This research aims to address this challenge through the framework of geovisual analytics. We present the GeoSocialApp which implements traditional network analysis methods in the context of explicitly spatial and social representations. We then apply it to an exploration of international trade networks in terms of the complex interactions between spatial and social relationships. This exploration using the GeoSocialApp helps us develop a two-part hypothesis: international trade network clusters with structural equivalence are strongly ‘balkanized’ (fragmented) according to the geography of trading partners, and the geographical distance weighted by population within each network cluster has a positive relationship with the development level of countries. In addition to demonstrating the potential of visual analytics to provide insight concerning complex geo-social relationships at a global scale, the research also addresses the challenge of validating insights derived through interactive geovisual analytics. We develop two indicators to quantify the observed patterns, and then use a Monte-Carlo approach to support the hypothesis developed above.
doi:10.1371/journal.pone.0088666
PMCID: PMC3928244  PMID: 24558409
8.  Regulation of Motility, Invasion and Metastatic Potential of Squamous Cell Carcinoma by 1,25D3 
Cancer  2012;119(3):563-574.
BACKGROUND
1,25D3, the active metabolite of vitamin D, has been shown to exhibit broad spectrum anti-tumor activity in xenograft animal models. However, its activity against metastatic disease has not been extensively investigated.
METHODS
Squamous cell carcinoma (SCC) or 1,25D3-resistant variant SCC-DR cells were treated with 1,25D3. Actin organization was examined by immunofluorescence assay. Cell migration was assessed by “wound” healing and chemotactic migration assay. Cell invasion was assessed by Matrigel-based invasion assay and in situ zymography. MMP-2 and MMP-9 expression and secretion was examined by immunoblot analysis and ELISA, respectively. E-cadherin expression was assessed by flow cytometry, immunoblot analysis and immunohistochemistry. Knockdown of E-cadherin was achieved by siRNA. Experimental metastasis mouse model was done by intravenous injection of tumor cells. Lung tumor development was assessed by magnetic resonance imaging, gross observation and histology.
RESULTS
SCC cellular morphology and actin organization were altered by 10 nM of 1,25D3. 1,25D3 inhibited SCC cell motility and invasion, which was associated with reduced expression and secretion of MMP-2 and MMP-9. 1,25D3 promoted the expression of E-cadherin. These findings were not observed in SCC-DR cells. Knock down of E-cadherin rescued 1,25D3-inhibited cell migration. Intravenous injection of SCC or SCC-DR cells resulted in the establishment of extensive pulmonary lesions in saline-treated C3H mice. Treatment with 1,25D3 resulted in a marked reduction in the formation of lung tumor colonies in animals injected with SCC but not SCC-DR cells.
CONCLUSIONS
1,25D3 suppresses SCC cell motility, invasion and metastasis, partially through the promotion of E-cadherin-mediated cell-cell adhesion.
doi:10.1002/cncr.27531
PMCID: PMC3485450  PMID: 22833444
1; 25D3; SCC; E-cadherin; motility; invasion; metastasis
9.  Improving Learning Performance with Happiness by Interactive Scenarios 
The Scientific World Journal  2014;2014:807347.
Recently, digital learning has attracted a lot of researchers to improve the problems of learning carelessness, low learning ability, lack of concentration, and difficulties in comprehending the logic of math. In this study, a digital learning system based on Kinect somatosensory system is proposed to make children and teenagers happily learn in the course of the games and improve the learning performance. We propose two interactive geometry and puzzle games. The proposed somatosensory games can make learners feel curious and raise their motivation to find solutions for boring problems via abundant physical expressions and interactive operations. The players are asked to select particular operation by gestures and physical expressions within a certain time. By doing so, the learners can feel the fun of game playing and train their logic ability before they are aware. Experimental results demonstrate that the proposed somatosensory system can effectively improve the students' learning performance.
doi:10.1155/2014/807347
PMCID: PMC3914601  PMID: 24558331
10.  Wide-field optical detection of nanoparticles using on-chip microscopy and self-assembled nanolenses 
Nature photonics  2013;7(3):10.1038/nphoton.2012.337.
The direct observation of nanoscale objects is a challenging task for optical microscopy because the scattering from an individual nanoparticle is typically weak at optical wavelengths. Electron microscopy therefore remains one of the gold standard visualization methods for nanoparticles, despite its high cost, limited throughput and restricted field-of-view. Here, we describe a high-throughput, on-chip detection scheme that uses biocompatible wetting films to self-assemble aspheric liquid nanolenses around individual nanoparticles to enhance the contrast between the scattered and background light. We model the effect of the nanolens as a spatial phase mask centred on the particle and show that the holographic diffraction pattern of this effective phase mask allows detection of sub-100 nm particles across a large field-of-view of >20 mm2. As a proof-of-concept demonstration, we report on-chip detection of individual polystyrene nanoparticles, adenoviruses and influenza A (H1N1) viral particles.
doi:10.1038/nphoton.2012.337
PMCID: PMC3866034  PMID: 24358054
11.  Mortality among Methadone Maintenance Clients in China: A Six-Year Cohort Study 
PLoS ONE  2013;8(12):e82476.
Objective
To assess the overall mortality of methadone maintenance treatment (MMT) clients in China and its associated factors.
Methods
A total of 1,511 MMT clients, all of whom enrolled in China's first eight MMT clinics between March and December 2004, were included in this cohort study and followed for approximately six years, until June 2010. Mortality and its predictors were examined using Cox proportional hazards regression models.
Results
A total of 154 deaths were observed within 5,391 person-years (PY) of follow-up for an all-cause mortality rate of 28.6 per 1,000 PY. The leading causes of death were drug overdose (33.8%), HIV/AIDS-unrelated disease (21.4%), and HIV/AIDS (16.9%). The all-cause mortality rate of clients engaged in MMT for one year or less was roughly three times that of clients who stayed in MMT for four years or more (14.0 vs. 4.6, p<0.0001), HIV-positive subjects was nearly four times mortality rate than that of HIV-negative individuals (28.1 vs.6.8, p<0.0001). ART-naive HIV-positive subjects had approximately two times higher mortality rate than those receiving ART (31.2 vs. 17.3, <0.0001). After adjusting for confounding variables, we found that being male (HR = 1.63, CI: 1.03–2.57, p = 0.0355) and being HIV-positive (HR = 5.16, CI: 3.70–7.10, p<0.0001) were both associated with higher risk of death whereas increased durations of methadone treatment were associated with a lower risk of death (HR = 0.26, CI: 0.18–0.38, p<0.0001 for two to three years, HR = 0.08, CI: 0.05–0.14, p<0.0001 for four or more years).
Conclusion
Overall mortality was high among MMT clients in China. Specific interventions aimed at decreasing mortality among MMT clients are needed. Our study supports the need for keeping client at MMT longer and for expanding ART coverage and suggests the potential benefits of integrated MMT and ART services for drug users in China.
doi:10.1371/journal.pone.0082476
PMCID: PMC3861403  PMID: 24349294
12.  Toward giga-pixel nanoscopy on a chip: a computational wide-field look at the nano-scale without the use of lenses 
Lab on a chip  2013;13(11):10.1039/c3lc50222h.
The development of lensfree on-chip microscopy in the past decade has opened up various new possibilities for biomedical imaging across ultra-large fields of view using compact, portable, and cost-effective devices. However, until recently, its ability to resolve fine features and detect ultra-small particles has not rivalled the capabilities of the more expensive and bulky laboratory-grade optical microscopes. In this Frontier Review, we highlight the developments over the last two years that have enabled computational lensfree holographic on-chip microscopy to compete with and, in some cases, surpass conventional bright-field microscopy in its ability to image nano-scale objects across large fields of view, yielding giga-pixel phase and amplitude images. Lensfree microscopy has now achieved a numerical aperture as high as 0.92, with a spatial resolution as small as 225 nm across a large field of view e.g., >20 mm2. Furthermore, the combination of lensfree microscopy with self-assembled nanolenses, forming nano-catenoid minimal surfaces around individual nanoparticles has boosted the image contrast to levels high enough to permit bright-field imaging of individual particles smaller than 100 nm. These capabilities support a number of new applications, including, for example, the detection and sizing of individual virus particles using field-portable computational on-chip microscopes.
doi:10.1039/c3lc50222h
PMCID: PMC3813829  PMID: 23592185
13.  Obesity-Induced Endothelial Dysfunction Is Prevented by Deficiency of P-Selectin Glycoprotein Ligand-1 
Diabetes  2012;61(12):3219-3227.
Endothelial dysfunction precedes atherosclerosis and represents an important link between obesity and cardiovascular events. Strategies designed to prevent endothelial dysfunction may therefore reduce the cardiovascular complications triggered by obesity. We tested the hypothesis that deficiency of P-selectin glycoprotein ligand-1 (Psgl-1) would improve the endothelial dysfunction associated with obesity. Psgl-1-deficient (Psgl-1−/−) and wild-type (Psgl-1+/+) mice were fed standard chow or a high-fat, high-sucrose diet (diet-induced obesity [DIO]) for 10 weeks. DIO increased mesenteric perivascular adipose tissue (mPVAT) macrophage content and vascular oxidative stress in Psgl-1+/+ mice but not in Psgl-1−/− mice. Pressure myography using mesenteric arteries demonstrated that relaxation responses to acetylcholine were significantly impaired in DIO Psgl-1+/+ mice, whereas DIO Psgl-1−/− mice were protected from endothelial dysfunction with similar relaxation responses to Psgl-1+/+ or Psgl-1−/− mice fed standard chow. The superoxide scavenger 4-hydroxy-2,2,6,6-tetramethylpiperidinyloxy (TEMPOL) partially recovered impaired endothelial function induced by DIO. A neutralizing Psgl-1 antibody was also effective in preventing endothelial dysfunction and reducing mPVAT macrophage content induced by DIO. These results indicate that obesity in mice leads to PVAT inflammation and endothelial dysfunction that is prevented by Psgl-1 deficiency. Psgl-1 inhibition may be a useful treatment strategy for targeting vascular disease associated with obesity.
doi:10.2337/db12-0162
PMCID: PMC3501858  PMID: 22891216
14.  Effectiveness of interferon-gamma release assays for differentiating intestinal tuberculosis from Crohn’s disease: A meta-analysis 
AIM: To investigate the clinical usefulness of interferon-gamma release assays (IGRAs) in the differential diagnosis of intestinal tuberculosis (ITB) from Crohn’s disease (CD) by meta-analysis.
METHODS: A systematic search of English language studies was performed. We searched the following databases: Medline, Embase, Web of Science and the Cochrane Library. The Standards for Reporting Diagnostic Accuracy initiative and Quality Assessment for Studies of Diagnostic Accuracy tool were used to assess the methodological quality of the studies. Sensitivity, specificity, and other measures of the accuracy of IGRAs in the differential diagnosis of ITB from CD were pooled and analyzed using random-effects models. Receiver operating characteristic curves were applied to summarize overall test performance. Two reviewers independently judged study eligibility while screening the citations.
RESULTS: Five studies met the inclusion criteria. The average inter-rater agreement between the two reviewers for items in the quality checklist was 0.95. Analysis of IGRAs for the differential diagnosis of ITB from CD produced summary estimates as follows: sensitivity, 0.74 (95%CI: 0.68-0.80); specificity, 0.87 (95%CI: 0.82-0.90); positive likelihood ratio, 5.98 (95%CI: 3.79-9.43); negative likelihood ratio, 0.28 (95%CI: 0.18-0.43); and diagnostic odds ratio, 26.21 (95%CI: 14.15-48.57). The area under the curve was 0.92. The evaluation of publication bias was not significant (P = 0.235).
CONCLUSION: Although IGRAs are not sensitive enough, they provide good specificity for the accurate diagnosis of ITB, which may be helpful in the differential diagnosis of ITB from CD.
doi:10.3748/wjg.v19.i44.8133
PMCID: PMC3848163  PMID: 24307809
Intestinal tuberculosis; Crohn’s disease; Interferon-gamma; Meta-analysis
15.  Formation of Nanofoam carbon and re-emergence of Superconductivity in compressed CaC6 
Scientific Reports  2013;3:3331.
Pressure can tune material's electronic properties and control its quantum state, making some systems present disconnected superconducting region as observed in iron chalcogenides and heavy fermion CeCu2Si2. For CaC6 superconductor (Tc of 11.5 K), applying pressure first Tc increases and then suppresses and the superconductivity of this compound is eventually disappeared at about 18 GPa. Here, we report a theoretical finding of the re-emergence of superconductivity in heavily compressed CaC6. The predicted phase III (space group Pmmn) with formation of carbon nanofoam is found to be stable at wide pressure range with a Tc up to 14.7 K at 78 GPa. Diamond-like carbon structure is adhered to the phase IV (Cmcm) for compressed CaC6 after 126 GPa, which has bad metallic behavior, indicating again departure from superconductivity. Re-emerged superconductivity in compressed CaC6 paves a new way to design new-type superconductor by inserting metal into nanoporous host lattice.
doi:10.1038/srep03331
PMCID: PMC3840379  PMID: 24276612
16.  Tooth Loss and Head and Neck Cancer: A Meta-Analysis of Observational Studies 
PLoS ONE  2013;8(11):e79074.
Backgroud
Epidemiological studies have shown that tooth loss is associated with risk of head and neck cancer (HNC); however, the results were inconsistent. Therefore, we conducted a meta-analysis to ascertain the relationship between tooth loss and HNC.
Methods
We searched for relevant observational studies that tested the association between tooth loss and risk of HNC from PubMed and were conducted up to January 30, 2013. Data from the eligible studies were independently extracted by two authors. The meta-analysis was performed using the Comprehensive Meta-Analysis 2.2 software. Sensitivity and subgroup analyses were conducted to evaluate the influence of various inclusions. Publication bias was also detected.
Results
Ten articles involving one cohort and ten case-control studies were yielded. Based on random-effects meta-analysis, an association between tooth loss and HNC risk was identified [increased risk of 29% for 1 to 6 teeth loss (OR = 1.29, 95% CI = 0.52–3.20, p = 0.59), 58% for 6 to 15 teeth loss (OR = 1.58, 95% CI = 1.08–2.32, p = 0.02), 63% for 11+ teeth loss (OR = 1.63, 95% CI = 1.23–2.14, p<0.001), 72% for 15+ teeth loss (OR = 1.72, 95% CI = 1.26–2.36, p<0.001), and 89% for 20+ teeth loss (OR = 1.89, 95% CI = 1.27–2.80, p<0.001)]. The sensitivity analysis shows that the result was robust, and publication bias was not detected.
Conclusions
Based on the current evidence, tooth loss is probably a significant and dependent risk factor of HNC, which may have a dose-response effect. People who lost six or more teeth should pay attention to symptoms of HNC, and losing 11 teeth or 15 teeth may be the threshold.
doi:10.1371/journal.pone.0079074
PMCID: PMC3829962  PMID: 24260154
17.  Identification and characterization of microRNAs involved in growth of blunt snout bream (Megalobrama amblycephala) by Solexa sequencing 
BMC Genomics  2013;14:754.
Background
Blunt snout bream (Megalobrama amblycephala) is an economically important fish species in the Chinese freshwater polyculture system for its delicacy and high economic value. MicroRNAs (miRNAs) play important roles in regulation of almost all biological processes in eukaryotes. Although previous studies have identified thousands of miRNAs from many species, little information is known for miRNAs of M. amblycephala. To investigate functions of miRNAs associated with growth of M. amblycephala, we adopted the Solexa sequencing technology to sequence two small RNA libraries prepared from four growth related tissues (brain, pituitary, liver and muscle) of M. amblycephala using individuals with relatively high and low growth rates.
Results
In this study, we have identified 347 conserved miRNAs (belonging to 123 families) and 22 novel miRNAs in M. amblycephala. Moreover, we observed sequence variants and seed edits of the miRNAs. Of the 5,166 single nucleotide substitutions observed in two libraries, the most abundant were G-to-U (15.9%), followed by U-to-C (12.1%), G-to-A (11.2%), and A to G (11.2%). Subsequently, we compared the expression patterns of miRNAs in the two libraries (big-size group with high growth rate versus small-size group with low growth rate). Results indicated that 27 miRNAs displayed significant differential expressions between the two libraries (p < 0.05). Of these, 16 were significantly up-regulated and 11 were significantly down-regulated in the big-size group compared to the small-size group. Furthermore, stem-loop RT-PCR was applied to validate and profile the expression of the differentially expressed miRNAs in ten tissues, and the result revealed that the conserved miRNAs expressed at higher levels than the novel miRNAs, especially in brain, liver and muscle. Also, targets prediction of differentially expressed miRNAs and KEGG pathway analysis suggested that differentially expressed miRNAs are involved in growth and metabolism, signal transduction, cell cycle, neural development and functions.
Conclusions
The present study provides the first large-scale characterization of miRNAs in M. amblycephala and miRNA profile related to different growth performances. The discovery of miRNA resource from this study is expected to contribute to a better understanding of the miRNAs roles playing in regulating the growth biological processes and the study of miRNA function and phenotype-associated miRNA identification in fish.
doi:10.1186/1471-2164-14-754
PMCID: PMC3827868  PMID: 24188211
18.  Osteogenic potentials of osteophytes in the cervical spine compared with patient matched bone marrow stromal cells 
Indian Journal of Orthopaedics  2013;47(6):565-571.
Background:
Osteophytes that form adjacent to degenerated disc have osteogeic potential. Studies suggest that their formation is associated with mesenchymal precursors arising from the chondrosynovial junction. This study is aimed to determine the cellular aging and osteogenic differentiation potential of osteophyte-derived mesenchymal cells (oMSCs) when compared to patient-matched bone marrow stromal cells (bMSCs).
Materials and Methods:
oMSCs and bMSCs were isolated from tissue samples during anterior cervical discectomy and fusion surgery. Extensive expansion of cell cultures was performed and early and late passage cells (P4 and P9, respectively) were used to study cell senescence and telomerase activity. Furthermore, osteogenic differentiation was applied to detect their osteogenic capacity.
Results:
The proliferation capacity of oMSCs in culture was superior to that of bMSCs and these cells readily underwent osteogenic differentiation. Our results showed that oMSCs had higher telomerase activity in late passages compared with bMSCs, although there was no significant difference in the telomerase activity in the early passages in either cell types. The telomerase activity was detectable only in early passage oMSCs and not in bMSCs.
Conclusions:
Our results indicate that oMSCs retain a level of telomerase activity in vitro, which may account for the relatively greater longevity of these cells, compared to bMSCs. Furthermore, when compared to bMSCs, oMSCs maintained a higher proliferative capacity and the same osteogenic capacity, which may offer new insights of tissue formation.
doi:10.4103/0019-5413.121579
PMCID: PMC3868137  PMID: 24379461
Cervical spine; mesenchymal stromal cells; osteogenesis; osteophyte; telomerase activity
19.  Haploinsufficiency of E-selectin ligand-1 is Associated with Reduced Atherosclerotic Plaque Macrophage Content while Complete Deficiency Leads to Early Embryonic Lethality in Mice 
Atherosclerosis  2012;224(2):363-367.
E-selectin-1 (ESL-1), also known as golgi complex-localized glycoprotein-1 (GLG1), homocysteine-rich fibroblast growth factor receptor (CGR-1), and latent transforming growth factor-β complex protein 1 (LTCP-1), is a multifunctional protein with widespread tissue distribution. To determine the functional consequences of ESL-1 deficiency, mice were generated carrying an ESL-1 gene trap. After backcrossing to C57BL6/J for 6 generations, mice heterozygous for the gene trap (ESL-1+/-) were intercrossed to produce ESL-1-/- mice, however ESL-1-/- mice were not viable, even at embryonic day E10.5. To determine the effect of heterozygous ESL-1 deficiency on atherosclerosis, apolipoprotein E deficient (ApoE-/-), ESL-1+/- mice were generated and fed western diet. Compared to ApoE-/-, ESL-1++ mice, atherosclerotic lesions from ApoE-/-, ESL-1+/- contained more collagen and fewer macrophages, suggesting increased plaque stability. In conclusion, heterozygous deficiency of ESL-1 is associated with features of increased atherosclerotic plaque stability while complete deficiency of ESL-1 leads to embryonic lethality.
doi:10.1016/j.atherosclerosis.2012.08.009
PMCID: PMC3659783  PMID: 22939356
leukocyte; selectins; macrophage; atherosclerosis; endothelium
20.  Leptin‐Induced Endothelial Dysfunction Is Mediated by Sympathetic Nervous System Activity 
Background
The adipocyte‐derived hormone leptin is elevated in obesity and may contribute to vascular risk associated with obesity. The mechanism(s) by which leptin affects vascular disease is unclear, although leptin has been shown to increase sympathetic activity. The aim of this study was to investigate the effect of leptin treatment on endothelial function and the role of the local sympathetic nervous system in mediating these effects.
Methods and Results
Recombinant leptin was administered to C57BL6/J mice every other day for 1 week. Mesenteric arteriole myography revealed that leptin treatment caused significant impairment of endothelium‐dependent vasorelaxation. Although leptin alone did not raise aortic blood pressure, leptin treatment augmented the blood pressure response to angiotensin II. The effects of leptin on mesenteric arteriolar function and aortic blood pressure response to angiotensin II were neutralized following sympathetic denervation to the mesenteric vasculature. The superoxide scavenger TEMPOL was also effective in preventing the effects of leptin on endothelial dysfunction.
Conclusions
Leptin causes endothelial dysfunction and enhances the effects of angiotensin II on blood pressure. These effects of leptin are mediated by sympathetic nervous system activation and superoxide and may contribute to vascular stiffness and hypertension in obesity.
doi:10.1161/JAHA.113.000299
PMCID: PMC3835232  PMID: 24042086
ganglionectomy; hypertension; nervous system; obesity; superoxide
21.  Field-Portable Pixel Super-Resolution Colour Microscope 
PLoS ONE  2013;8(9):e76475.
Based on partially-coherent digital in-line holography, we report a field-portable microscope that can render lensfree colour images over a wide field-of-view of e.g., >20 mm2. This computational holographic microscope weighs less than 145 grams with dimensions smaller than 17×6×5 cm, making it especially suitable for field settings and point-of-care use. In this lensfree imaging design, we merged a colorization algorithm with a source shifting based multi-height pixel super-resolution technique to mitigate ‘rainbow’ like colour artefacts that are typical in holographic imaging. This image processing scheme is based on transforming the colour components of an RGB image into YUV colour space, which separates colour information from brightness component of an image. The resolution of our super-resolution colour microscope was characterized using a USAF test chart to confirm sub-micron spatial resolution, even for reconstructions that employ multi-height phase recovery to handle dense and connected objects. To further demonstrate the performance of this colour microscope Papanicolaou (Pap) smears were also successfully imaged. This field-portable and wide-field computational colour microscope could be useful for tele-medicine applications in resource poor settings.
doi:10.1371/journal.pone.0076475
PMCID: PMC3785454  PMID: 24086742
22.  Simultaneous splicing of multiple DNA fragments in one PCR reaction 
Background
Rapid and simultaneous splicing of multiple DNA fragments is frequently required in many recombinant DNA projects. However, former overlap extension PCRs, the most common methods for splicing DNA fragments, are not really simultaneous fusing of multiple DNA fragments.
Results
We performed an optimized method which allowed simultaneous splicing of multiple DNA fragments in one PCR reaction. Shorter outermost primers were prior mixed with other PCR components at the same time. A sequential thermo cycling program was adopted for overlap extension reaction and amplification of spliced DNA. Annealing temperature was relatively higher in the overlap extension reaction stage than in the fused DNA amplification. Finally we successfully harvested target PCR products deriving from fusion of two to seven DNA fragments after 5–10 cycles for overlap extension reaction and then 30 cycles for fused DNA amplification.
Conclusions
Our method provides more rapid, economical and handy approach to accurately splice multiple DNA fragments. We believe that our simultaneous splicing overlap extension PCR can be used to fuse more than seven DNA fragments as long as the DNA polymerase can match.
doi:10.1186/1480-9222-15-9
PMCID: PMC3847634  PMID: 24015676
Simultaneous splicing; Multiple DNA fragments; Overlap extension PCR
23.  Type I Interferons Modulate Vascular Function, Repair, Thrombosis and Plaque Progression in Murine Models of Lupus and Atherosclerosis 
Arthritis and rheumatism  2012;64(9):2975-2985.
Objectives
Patients with systemic lupus erythematosus (SLE) have a striking increase in atherothrombotic cardiovascular disease (CVD), not explained by the Framingham risk equation. In vitro studies indicate that type-I Interferons (IFNs) may play prominent roles in increased CV risk in SLE. However, the in vivo relevance of these findings, with regards to the development of CVD, has not been characterized. We examined the role of type-I IFNs in endothelial dysfunction, aberrant vascular repair, and atherothrombosis in murine models of lupus and atherosclerosis.
Methods
Lupus-prone New Zealand Mixed-2328 mice (NZM) and atherosclerosis-prone Apolipoprotein-E-knockout mice (ApoE−/−) were compared to mice lacking type-I IFN-receptor (INZM and ApoEIFNR−/−, respectively) in their endothelial vasodilatory function, endothelial progenitor cell (EPC) function, in vivo neoangiogenesis, plaque development and occlusive thrombosis. Similar experiments were performed when NZM and ApoE−/− received an IFN-α-containing or an empty adenovirus.
Results
Loss of type IIFN-receptor signaling improves endothelium-dependent vasorelaxation, lipoprotein parameters, EPC numbers and function and neoangiogenesis in lupus-prone mice, independent of disease activity or gender. Further, acute exposure to IFN-α impairs endothelial vasorelaxation and EPC function in lupus-prone and non-lupus-prone mice. ApoEIFNR−/− mice have decreased atherosclerosis severity and arterial inflammatory infiltrates and increased neoangiogenesis, compared to ApoE−/− mice, while NZM and ApoE−/− mice exposed to IFN-α develop accelerated thrombosis and platelet activation.
Conclusions
These results support the hypothesis that type I-IFNs play key roles in the development of premature CVD in SLE and, potentially, in the general population, through pleiotropic deleterious effects on the vasculature.
doi:10.1002/art.34504
PMCID: PMC3411886  PMID: 22549550
Angiogenesis; atherosclerosis; systemic lupus erythematosus
24.  Reduced Inflammation and CD4 Loss in Acute SHIV Infection During Oral Pre-Exposure Prophylaxis  
The Journal of Infectious Diseases  2012;206(5):770-779.
Background.The impact of pre-exposure prophylaxis (PrEP) with antiretrovirals on breakthrough HIV or SHIV infection is not fully documented. We addressed the hypothesis that SHIVSF162P3 infection despite active PrEP results in altered early immune parameters, compared with untreated infection.
Methods.Eleven rhesus macaques were infected during repeated, rectal, low-dose SHIVSF162P3 exposures while receiving concurrent oral PrEP (Truvada [n = 2] or GS7340 [n = 4]) or as untreated controls (n = 5). We measured SHIV RNA, inflammatory cytokines, CD4 cells, and SHIV-specific and memory T cells until 20 weeks after peak viremia.
Results.SHIV infection during PrEP resulted in 100-fold lower peak viremia and lower IL-15, IL-18, and IL-1Ra levels, compared with controls (P < .05; Wilcoxon rank-sum test). Unlike controls, PrEP-treated macaques showed no significant CD4 cell count reduction during acute infection and developed more SHIV-specific central memory T cells, relative to controls. After in vivo CD8 cell depletion, viral load increased to similar levels, indicating that CD8 cells were critical for viral control in both groups.
Conclusions.PrEP with antiretrovirals has beneficial effects on early SHIV infection even when infection is not prevented. Although long-term immune control could not be examined in this SHIV infection model, our results suggest that PrEP results in improved early disease parameters in breakthrough infections.
doi:10.1093/infdis/jis422
PMCID: PMC3491742  PMID: 22740713
25.  Effect of partial and complete posterior cruciate ligament transection on medial meniscus: A biomechanical evaluation in a cadaveric model 
Indian Journal of Orthopaedics  2013;47(5):493-499.
Background:
The relationship between medial meniscus tear and posterior cruciate ligament (PCL) injury has not been exactly explained. We studied to investigate the biomechanical effect of partial and complete PCL transection on different parts of medial meniscus at different flexion angles under static loading conditions.
Materials and Methods:
Twelve fresh human cadaveric knee specimens were divided into four groups: PCL intact (PCL-I), anterolateral bundle transection (ALB-T), posteromedial bundle transection (PMB-T) and PCL complete transection (PCL-T) group. Strain on the anterior horn, body part and posterior horn of medial meniscus were measured under different axial compressive tibial loads (200-800 N) at 0°, 30°, 60° and 90° knee flexion in each groups respectively.
Results:
Compared with the PCL-I group, the PCL-T group had a higher strain on whole medial meniscus at 30°, 60° and 90° flexion in all loading conditions and at 0° flexion with 400, 600 and 800 N loads. In ALB-T group, strain on whole meniscus increased at 30°, 60° and 90° flexion under all loading conditions and at 0° flexion with 800 N only. PMB-T exihibited higher strain at 0° flexion with 400 N, 600 N and 800 N, while at 30° and 60° flexion with 800 N and at 90° flexion under all loading conditions.
Conclusions:
Partial PCL transection triggers strain concentration on medial meniscus and the effect is more pronounced with higher loading conditions at higher flexion angles.
doi:10.4103/0019-5413.118206
PMCID: PMC3796923  PMID: 24133310
Biomechanics; medial meniscus; posterior cruciate ligament

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