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1.  Predicting Local Dengue Transmission in Guangzhou, China, through the Influence of Imported Cases, Mosquito Density and Climate Variability 
PLoS ONE  2014;9(7):e102755.
Introduction
Each year there are approximately 390 million dengue infections worldwide. Weather variables have a significant impact on the transmission of Dengue Fever (DF), a mosquito borne viral disease. DF in mainland China is characterized as an imported disease. Hence it is necessary to explore the roles of imported cases, mosquito density and climate variability in dengue transmission in China. The study was to identify the relationship between dengue occurrence and possible risk factors and to develop a predicting model for dengue’s control and prevention purpose.
Methodology and Principal Findings
Three traditional suburbs and one district with an international airport in Guangzhou city were selected as the study areas. Autocorrelation and cross-correlation analysis were used to perform univariate analysis to identify possible risk factors, with relevant lagged effects, associated with local dengue cases. Principal component analysis (PCA) was applied to extract principal components and PCA score was used to represent the original variables to reduce multi-collinearity. Combining the univariate analysis and prior knowledge, time-series Poisson regression analysis was conducted to quantify the relationship between weather variables, Breteau Index, imported DF cases and the local dengue transmission in Guangzhou, China. The goodness-of-fit of the constructed model was determined by pseudo-R2, Akaike information criterion (AIC) and residual test. There were a total of 707 notified local DF cases from March 2006 to December 2012, with a seasonal distribution from August to November. There were a total of 65 notified imported DF cases from 20 countries, with forty-six cases (70.8%) imported from Southeast Asia. The model showed that local DF cases were positively associated with mosquito density, imported cases, temperature, precipitation, vapour pressure and minimum relative humidity, whilst being negatively associated with air pressure, with different time lags.
Conclusions
Imported DF cases and mosquito density play a critical role in local DF transmission, together with weather variables. The establishment of an early warning system, using existing surveillance datasets will help to control and prevent dengue in Guangzhou, China.
doi:10.1371/journal.pone.0102755
PMCID: PMC4097061  PMID: 25019967
2.  De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae) 
Parasites & Vectors  2014;7:314.
Background
Anopheles sinensis is the major malaria vector in China and Southeast Asia. Vector control is one of the most effective measures to prevent malaria transmission. However, there is little transcriptome information available for the malaria vector. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to build a transcriptome dataset for functional genomics analysis by large-scale RNA sequencing (RNA-seq).
Methods
To provide a more comprehensive and complete transcriptome of An. sinensis, eggs, larvae, pupae, male adults and female adults RNA were pooled together for cDNA preparation, sequenced using the Illumina paired-end sequencing technology and assembled into unigenes. These unigenes were then analyzed in their genome mapping, functional annotation, homology, codon usage bias and simple sequence repeats (SSRs).
Results
Approximately 51.6 million clean reads were obtained, trimmed, and assembled into 38,504 unigenes with an average length of 571 bp, an N50 of 711 bp, and an average GC content 51.26%. Among them, 98.4% of unigenes could be mapped onto the reference genome, and 69% of unigenes could be annotated with known biological functions. Homology analysis identified certain numbers of An. sinensis unigenes that showed homology or being putative 1:1 orthologues with genomes of other Dipteran species. Codon usage bias was analyzed and 1,904 SSRs were detected, which will provide effective molecular markers for the population genetics of this species.
Conclusions
Our data and analysis provide the most comprehensive transcriptomic resource and characteristics currently available for An. sinensis, and will facilitate genetic, genomic studies, and further vector control of An. sinensis.
doi:10.1186/1756-3305-7-314
PMCID: PMC4105132  PMID: 25000941
Anopheles sinensis; Transcriptome; RNA-Seq; Codon usage bias; Simple sequence repeat; Malaria; Vector control
3.  Immunization against Multidrug-Resistant Acinetobacter baumannii Effectively Protects Mice in both Pneumonia and Sepsis Models 
PLoS ONE  2014;9(6):e100727.
Objective
Acinetobacter baumannii is considered the prototypical example of a multi- or pan- drug-resistant bacterium. It has been increasingly implicated as a major cause of nosocomial and community-associated infections. This study proposed to evaluate the efficacy of immunological approaches to prevent and treat A. baumannii infections.
Methods
Mice were immunized with outer membrane vesicles (OMVs) prepared from a clinically isolated multidrug-resistant strain of A. baumannii. Pneumonia and sepsis models were used to evaluate the efficacy of active and passive immunization with OMVs. The probable effective mechanisms and the protective potential of clonally distinct clinical isolates were investigated in vitro using an opsonophagocytic assay.
Results
Intramuscular immunization with OMVs rapidly produced high levels of OMV-specific IgG antibodies, and subsequent intranasal challenge with A. baumannii elicited mucosal IgA and IgG responses. Both active and passive immunization protected the mice from challenges with homologue bacteria in a sepsis model. Bacterial burden in bronchoalveolar lavage fluids (BALF), lung, and spleen, inflammatory cell infiltration in BALF and lung, and inflammatory cytokine accumulation in BALF was significantly suppressed in the pneumonia model by both active and passive immunization strategies. The antisera from immunized mice presented with significant opsonophagocytic activities in a dose-dependent manner against not only homologous strains but also five of the other six clonally distinct clinical isolates.
Conclusions
Utilizing immunological characteristics of outer membrane proteins to elevate protective immunity and circumvent complex multidrug-resistance mechanisms might be a viable approach to effectively control A. baumannii infections.
doi:10.1371/journal.pone.0100727
PMCID: PMC4067354  PMID: 24956279
4.  Nuclear Factor One B regulates neural stem cell differentiation and axonal projection of corticofugal neurons 
During development of the cerebral cortex, neural stem cells divide to expand the progenitor pool and generate basal progenitors, outer radial glia and cortical neurons. As these newly born neurons differentiate, they must properly migrate toward their final destination in the cortical plate, project axons to appropriate targets, and develop dendrites. However, a complete understanding of the precise genetic mechanisms regulating these steps is lacking. Here we show that a member of the nuclear factor one (NFI) family of transcription factors, NFIB, is essential for many of these processes in mice. We performed a detailed analysis of NFIB expression during cortical development, and investigated defects in cortical neurogenesis, neuronal migration and differentiation in NfiB−/− brains. We found that NFIB is strongly expressed in radial glia and corticofugal neurons throughout cortical development. However, in NfiB−/− cortices, radial glia failed to generate outer radial glia, subsequently resulting in a loss of late basal progenitors. In addition, corticofugal neurons showed a severe loss of axonal projections, while late-born cortical neurons displayed defects in migration and ectopically expressed the early-born neuronal marker, CTIP2. Furthermore, gene expression analysis, by RNA-sequencing, revealed a misexpression of genes that regulate the cell cycle, neuronal differentiation and migration in NfiB−/− brains. Together these results demonstrate the critical functions of NFIB in regulating cortical development.
doi:10.1002/cne.23373
PMCID: PMC4058429  PMID: 23749646
NFIB; radial glia; outer radial glia; basal progenitors; neuronal migration; neurogenesis
5.  Study on Typhoon Characteristic Based on Bridge Health Monitoring System 
The Scientific World Journal  2014;2014:204675.
Through the wind velocity and direction monitoring system installed on Jiubao Bridge of Qiantang River, Hangzhou city, Zhejiang province, China, a full range of wind velocity and direction data was collected during typhoon HAIKUI in 2012. Based on these data, it was found that, at higher observed elevation, turbulence intensity is lower, and the variation tendency of longitudinal and lateral turbulence intensities with mean wind speeds is basically the same. Gust factor goes higher with increasing mean wind speed, and the change rate obviously decreases as wind speed goes down and an inconspicuous increase occurs when wind speed is high. The change of peak factor is inconspicuous with increasing time and mean wind speed. The probability density function (PDF) of fluctuating wind speed follows Gaussian distribution. Turbulence integral scale increases with mean wind speed, and its PDF does not follow Gaussian distribution. The power spectrum of observation fluctuating velocity is in accordance with Von Karman spectrum.
doi:10.1155/2014/204675
PMCID: PMC4070361  PMID: 25003137
6.  Peroxisome Proliferator–Activated Receptor Alpha Expression Changes in Human Pregnant Myometrium 
Reproductive Sciences  2013;20(6):654-660.
Peroxisome proliferator–activated receptor alpha (PPARα) has been demonstrated to exhibit anti-inflammatory activities that are hypothesized to play a key role in labor suppression and maintenance of uterine quiescence. The aim of this study was to identify pregnancy- and labor-associated changes in PPARα in human myometrium. For this investigation, human myometrium was obtained from premenopausal women, and the study participants were categorized into the following 4 groups: nonpregnant (NP; n = 10), preterm not in labor (PNL; n = 10, gestation range 20-35 weeks), term not in labor (TNL; n = 20, gestation range 37-41 weeks), and term in labor (TL; n = 20, gestation range 37-41 weeks). Immunohistochemistry was used to locate and confirm the expression of PPARα. Relative quantitative real-time polymerase chain reaction (PCR) and Western blotting were employed to study the expression of anti-inflammatory PPARα and proinflammatory interleukin 1β (IL-1β). Immunohistochemistry indicated that PPARα was located in the nucleus of uterine smooth muscle cells. Compared to other groups, in PNL group, the PPARα messenger RNA (mRNA) and protein increased significantly. Decreased PPARα mRNA and protein expressions in myometrium were associated with labor while IL-1β increased remarkably. There were negative correlations between PPARα and IL-1β on mRNA (r = −.765, P < .01) and protein (r = −.624, P < .01) levels analyzed using Pearson test. In conclusion, human pregnancy is associated with changes in expression of PPARα and IL-1β in myometrium. The changes observed suggest that PPARα may play a role in maintaining pregnancy or initiating labor through inhibiting the expression of IL-1β in human myometrium.
doi:10.1177/1933719112461187
PMCID: PMC3713545  PMID: 23144166
pregnancy; myometrium; labor onset; peroxisome proliferator–activated receptor alpha; interleukin 1β
7.  Use of lipolanthionine peptide, a toll-like receptor 2 inhibitor, enhances transdermal delivery efficiency 
Molecular Medicine Reports  2014;10(2):593-598.
The transdermal delivery system (TDS) is able to obtain a systemic therapeutic effect by administration through the skin, which has low side effects and is able to maintain a sustained blood concentration. However, due to the barrier presented by the stratum corneum, numerous drugs have poor percutaneous permeability. Therefore, the improvement of skin permeability is key to TDS. The main method of promoting transdermal absorption is through the usage of penetration enhancers. Dimethyl sulfoxide (DMSO) is a commonly used penetration enhancer, which has anti-inflammatory analgesic effects and is able to penetrate the skin. Retinoic acid (RA) and lipolanthionine peptide (LP) may also benefit the permeation efficiency of TDS. Therefore, the present study examined the function of DMSO, RA and LP as penetration enhancers in TDS. Firstly, the optimum concentration of DMSO was confirmed by detecting the expression of the LacZ gene in vitro. Secondly, different combinations of LP, RA and DMSO were applied to mouse skin to analyze the penetration enhancer combination with the greatest efficacy. All the animals were divided into five groups: The RA + LP + DMSO + pORF-LacZ group, the RA + DMSO + pORF-LacZ group, the LP + DMSO + pORF-LacZ group, the DMSO + pORF-LacZ group and the control group. Skin was soaked in combinations of LP, RA and DMSO for seven days and then the pORF-LacZ plasmids were daubed onto the skin once daily three days. On the 11th day, all the animals were sacrificed by cervical dislocation and the skin and blood samples were collected. The blood samples were used to detect the expression of the LacZ gene by quantitative polymerase chain reaction and the skin samples were used to detect the expression of claudin-4 and zonula occluden-1 (ZO-1) proteins by immunohistochemistry and western blot analysis. The results demonstrated that the combination of LP, RA and DMSO exhibited the greatest transdermal delivery efficiency, which verified that RA and LP were able to increase the penetration effects. Following treatment with LP, the symptoms of dermal edema were relieved and the capillaries contracted, which suggested that LP was a safe and effective penetration enhancer able to reduce the side-effects caused by DMSO. The present study provides a guideline for the synthesis of novel penetration enhancers.
doi:10.3892/mmr.2014.2251
PMCID: PMC4094769  PMID: 24858729
toll-like receptor 2; lipolanthionine peptide; retinoic acid; dimethyl sulfoxide; transdermal delivery system
8.  Hypertrophy of Ligamentum Flavum in Lumbar Spine Stenosis Is Associated with Increased miR-155 Level 
Disease Markers  2014;2014:786543.
Hypertrophy of ligamentum flavum (LF) contributes to lumbar spinal stenosis (LSS) and is caused mainly by fibrosis. Recent data indicate that miR-155 plays a crucial role in the pathogenesis of different fibrotic diseases. This study aimed to test the hypothesis that miR-155 exerts effects on LF thickness by regulating collagen expression. We found that LF thickness and the expression of collagen I and, collagen III were higher in LF from LSS patients than in LF from lumbar disc herniation (LDH) patients (P < 0.01). The expression of miR-155 was significantly higher in LF from LSS group than in LF from LDH group (P < 0.01). miR-155 level was positively correlated with LF thickness (r = 0.958, P < 0.01), type I collagen level (r = 0.825, P < 0.01), and type III collagen level (r = 0.827, P < 0.01). miR-155 mimic increased mRNA and protein expression of collagen I and collagen III in fibroblasts isolated from LF, while miR-155 sponge decreased mRNA and protein expression of collagen I and III in fibroblasts. In conclusions, miR-155 is a fibrosis-associated miRNA and may play important role in the pathogenesis of LF hypertrophy.
doi:10.1155/2014/786543
PMCID: PMC4052175  PMID: 24963214
9.  Microsurgical Techniques Used to Construct the Vascularized and Neurotized Tissue Engineered Bone 
BioMed Research International  2014;2014:281872.
The lack of vascularization in the tissue engineered bone results in poor survival and ossification. Tissue engineered bone can be wrapped in the soft tissue flaps which are rich in blood supply to complete the vascularization in vivo by microsurgical technique, and the surface of the bone graft can be invaded with new vascular network. The intrinsic vascularization can be induced via a blood vessel or an arteriovenous loop located centrally in the bone graft by microsurgical technique. The peripheral nerve especially peptidergic nerve has effect on the bone regeneration. The peptidergic nerve can be used to construct the neurotized tissue engineered bone by implanting the nerve fiber into the center of bone graft. Thus, constructing a highly vascularized and neurotized tissue engineered bone according with the theory of biomimetics has become a useful method for repairing the large bone defect. Many researchers have used the microsurgical techniques to enhance the vascularization and neurotization of tissue engineered bone and to get a better osteogenesis effect. This review aims to summarize the microsurgical techniques mostly used to construct the vascularized and neurotized tissue engineered bone.
doi:10.1155/2014/281872
PMCID: PMC4036431  PMID: 24900962
10.  Ten Simple Rules for Internship in a Pharmaceutical Company 
PLoS Computational Biology  2014;10(5):e1003600.
doi:10.1371/journal.pcbi.1003600
PMCID: PMC4014388  PMID: 24811706
11.  Numb Promotes Cell Proliferation and Correlates with Poor Prognosis in Hepatocellular Carcinoma 
PLoS ONE  2014;9(4):e95849.
Background
Numb is an evolutionary conserved protein that plays critical roles in cell fate determination, cell adhesion, cell migration and a number of signaling pathways, but evidence for a substantial involvement of Numb in HCC has remained unclear. The present study was aimed to investigate the clinical and prognostic significance of Numb and its role in hepatocellular carcinoma (HCC).
Methodology
The expression of Numb was detected in 107 cases of clinical paraffin-embedded hepatocellular carcinoma tissues,5 matched paris of fresh tissues and six hepatocellular cell lines by immunohistochemistry with clinicopathological analyses,RT-PCR or Western blot. Moreover, loss of function and gain of function assays were performed to evaluate the effect of Numb on cell proliferation in vitro.
Conclusions
We found that Numb was obviously up-regulated in HCC tissues and cell lines (p<0.05). The Numb up-regulation correlated significantly with poor prognosis, and Numb status was identified as an independent prognostic factor. Over-expression of Numb increased proliferation in SMMC-7721 and BEL-7402 cells, while knock-down of Numb showed the opposite effect. Our study indicates that Numb up-regulation significantly correlates with cell proliferation and poor prognosis in hepatocellular carcinoma patients. It may be a useful biomarker for therapeutic strategy in hepatocellular carcinoma treatment.
doi:10.1371/journal.pone.0095849
PMCID: PMC4000222  PMID: 24770339
12.  Predictive Models of Diffusive Nanoparticle Transport in 3-Dimensional Tumor Cell Spheroids 
The AAPS Journal  2013;15(3):816-831.
The rapidly evolving nanotechnology field highlights the need of better understanding the relationship between nanoparticle (NP) properties and NP transport in solid tumors. The present study tested the hypothesis that the diffusive transport and spatial distribution of NP can be predicted based on the following parameters: interstitial NP diffusivity, NP–cell interaction parameters (cell surface binding capacity, rate constants of association, dissociation, and internalization). We (a) established the models and equations; (b) experimentally measured, in monolayer pharynx FaDu cells, the model parameters for three NP formulations (negatively charged polystyrene beads, near-neutral liposomes, and positively charged liposomes, with respective diameter of 20, 110, and 130 nm); and (c) used the models and parameters to simulate NP diffusion in 3-dimensional (3D) systems. We next measured the NP concentration–depth profiles in tumor cell spheroids, an avascular 3D system, and found good agreement between model-simulated and experimental data in spheroids for the negative and neutral NP (>90% predicted data points at three NP concentrations and three treatment times were within the 95% confidence intervals of experimental data). Model performance was inferior for positive liposomes containing a fusogenic lipid. The present study demonstrated the possibility of using in vitro NP–cell biointerface data in monolayer cultures with in silico studies to predict the NP diffusive transport and concentration–time–depth profiles in 3D systems, as functions of NP concentrations and treatment times. Extending this approach to include convective transport may yield a cost-effective means to predict the NP delivery and residence in solid tumors.
doi:10.1208/s12248-013-9478-2
PMCID: PMC3691442  PMID: 23605950
3-dimensional tumors; computational models; diffusional transport; nanoparticle; solid tumors
13.  A carbon nanofiber based biosensor for simultaneous detection of dopamine and serotonin in the presence of ascorbic acid 
Biosensors & bioelectronics  2012;42:434-438.
A biosensor based on an array of vertically aligned carbon nanofibers (CNFs) grown by plasma enhanced chemical vapor deposition is found to be effective for the simultaneous detection of dopamine (DA) and serotonin (5-HT) in the presence of excess ascorbic acid (AA). The CNF electrode outperforms the conventional glassy carbon electrode (GCE) for both selectivity and sensitivity. Using differential pulse voltammetry (DPV), three distinct peaks are seen for the CNF electrode at 0.13 V, 0.45 V, and 0.70 V for the ternary mixture of AA, DA, and 5-HT. In contrast, the analytes are indistinguishable in a mixture using a GCE. For the CNF electrode, the detection limits are 50 nM for DA and 250 nM for 5-HT.
doi:10.1016/j.bios.2012.10.080
PMCID: PMC3746014  PMID: 23228495
Biosensor; Dopamine; Serotonin; Carbon nanofiber; Nanoelectrode array
14.  Isolation and Characterization of New Phenolic Compounds with Estrogen Biosynthesis-Inhibiting and Antioxidation Activities from Broussonetia papyrifera Leaves 
PLoS ONE  2014;9(4):e94198.
Broussonetia papyrifera leaves (BPL) as a traditional Chinese medicine are also used in livestock feed for stimulating reproduction, adipose tissue and muscle development; however, the mechanism of their action is still unknown. Through estrogen biosynthesis-guided fractionation in human ovarian granulosa-like KGN cells, five new phenolic glycosides, broussoside A–E(1–5), along with fifteen known dietary phenolic compounds, were isolated from the n-butanol extract of BPL, and their structures were elucidated on the basis of NMR spectra analysis and chemical evidence. New compounds 3, 4, 5 and the known compounds 9 and 10 were found to potently inhibit estrogen biosynthesis in KGN cells. In addition, compounds 9, 17, 18, and 20 showed strong antioxidant activity against ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt) and DPPH (1, 1′-diphenyl -2-picryl-hydrazyl radical) assays. These findings suggest that BPL may improve meat quality through the regulation of estrogen biosynthesis. Furthermore, they may be useful for the discovery of potential aromatase modulators from natural products. Finally, they could be considered as a new source for natural antioxidants.
doi:10.1371/journal.pone.0094198
PMCID: PMC3979757  PMID: 24714659
15.  Asexuality Development among Middle Aged and Older Men 
PLoS ONE  2014;9(3):e92794.
Objectives
To assess erectile function in middle-aged and older men with asexuality status and further analyze their specific reasons for this condition.
Subjects and Methods
Men who had regular sexual intercourse attempts (sex frequency≥1 time per month) were classified into mild erectile dysfunction (ED), moderate to severe ED and non-ED according to International Index of Erectile Function-5, and men having no sexual intercourse attempts for at least 6 months were defined as having an asexuality status. The risk factors associated with ED were collected in a sample of 1,531 Chinese men aged 40 to 80 years, and the self-report reasons for asexuality were recorded in asexual cohort individually. Comparative analyses and multivariate regression models were conducted among these groups.
Results
The prevalence rates of ED and asexuality status were 49.9% and 37.2%. The asexuality status group had higher risk factors than the moderate to severe ED group in terms of old age (age≥65, adjusted odds ratio (OR) 17.69 versus (Vs.) 7.19), diabetes (crude OR: 2.40 Vs. 2.36) and hypertension (crude OR: 1.78 Vs. 1.72). The specific reasons for the asexuality status were “erectile difficulty” (52.9%), “do not care about sexuality” (53.5%)”, “no longer necessary to have sexuality at this age” (47.7%), “severe stress” (44.4%), “severe fatigue” (26.3%) and “masturbation” (26.9%).
Conclusions
Men with an asexual status suffer from higher risk factors for ED than men with moderate to severe ED. The majority of this asexual status could be attributed to a full ED, although the reasons for this transient asexuality also involved sexual attitudes and interests, sexual partners and masturbation.
doi:10.1371/journal.pone.0092794
PMCID: PMC3965446  PMID: 24667838
16.  The taxonomic accounts of the genus Symmorphus Wesmael (Hymenoptera, Vespidae, Eumeninae) from China, with descriptions of three new species 
ZooKeys  2014;9-26.
In this study, we recognize and review a total of 19 species of the genus Symmorphus Wesmael from China. We also provide a key to these species. Three new species are described and illustrated, namely Symmorphus (Symmorphus) tianchiensis Li & Chen, sp. n., S. (S.) cavatus Li & Chen, sp. n., and S. (S.) nigriclypeus Li & Chen, sp. n. The following four species are newly recorded from China: Symmorphus (S.) fuscipes (Herrich-Schaeffer), S. (S.) lucens (Kostylev), S. (S.) sublaevis Kostylev, and S. (S.) violaceipennis Giordani Soika. In addition, we map the species geographical distributions in China of these 19 species. Type specimens of these three new species are deposited in Chongqing Normal University and Yunnan Agricultural University.
doi:10.3897/zookeys.389.7045
PMCID: PMC3974429  PMID: 24715771
Hymenoptera; Vespidae; Eumeninae; Symmorphus; new species; China
17.  Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex 
Neural Development  2014;9:6.
Background
The genetic programs required for development of the cerebral cortex are under intense investigation. However, non-coding DNA elements that control the expression of developmentally important genes remain poorly defined. Here we investigate the regulation of Fezf2, a transcription factor that is necessary for the generation of deep-layer cortical projection neurons.
Results
Using a combination of chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) we mapped the binding of four deep-layer-enriched transcription factors previously shown to be important for cortical development. Building upon this we characterized the activity of three regulatory regions around the Fezf2 locus at multiple stages throughout corticogenesis. We identified a promoter that was sufficient for expression in the cerebral cortex, and enhancers that drove reporter gene expression in distinct forebrain domains, including progenitor cells and cortical projection neurons.
Conclusions
These results provide insight into the regulatory logic controlling Fezf2 expression and further the understanding of how multiple non-coding regulatory domains can collaborate to control gene expression in vivo.
doi:10.1186/1749-8104-9-6
PMCID: PMC4008173  PMID: 24618363
Fezf2; Enhancer; Promoter; Cerebral cortex; Gene regulation; Transcription
18.  The de novo Transcriptome and Its Analysis in the Worldwide Vegetable Pest, Delia antiqua (Diptera: Anthomyiidae) 
G3: Genes|Genomes|Genetics  2014;4(5):851-859.
The onion maggot Delia antiqua is a major insect pest of cultivated vegetables, especially the onion, and a good model to investigate the molecular mechanisms of diapause. To better understand the biology and diapause mechanism of the insect pest species, D. antiqua, the transcriptome was sequenced using Illumina paired-end sequencing technology. Approximately 54 million reads were obtained, trimmed, and assembled into 29,659 unigenes, with an average length of 607 bp and an N50 of 818 bp. Among these unigenes, 21,605 (72.8%) were annotated in the public databases. All unigenes were then compared against Drosophila melanogaster and Anopheles gambiae. Codon usage bias was analyzed and 332 simple sequence repeats (SSRs) were detected in this organism. These data represent the most comprehensive transcriptomic resource currently available for D. antiqua and will facilitate the study of genetics, genomics, diapause, and further pest control of D. antiqua.
doi:10.1534/g3.113.009779
PMCID: PMC4025484  PMID: 24615268
onion maggot; high-throughput RNA sequencing; de novo assembly; codon usage bias; simple sequence repeat
19.  Cheap, Gram-Scale Fabrication of BN Nanosheets via Substitution Reaction of Graphite Powders and Their Use for Mechanical Reinforcement of Polymers 
Scientific Reports  2014;4:4211.
As one of the most important two-dimensional (2D) materials, BN nanosheets attracted intensive interest in the past decade. Although there are many methods suitable for the preparation of BN sheets, finding a cheap and nontoxic way for their mass and high-quality production is still a challenge. Here we provide a highly effective and cheap way to synthesize gram-scale-level well-structured BN nanosheets from many common graphite products as source materials. Single-crystalline multi-layered BN sheets have a mean lateral size of several hundred nanometers and a thickness ranging from 5 nm to 40 nm. Cathodoluminescence (CL) analysis shows that the structures exhibit a near band-edge emission and a broad emission band from 300 nm to 500 nm. Utilization of nanosheets for the reinforcement of polymers revealed that the Young's modulus of BN/PMMA composite had increased to 1.56 GPa when the BN's fraction was only 2 wt.%, thus demonstrating a 20% gain compared to a blank PMMA film. It suggests that the BN nanosheet is an ideal mechanical reinforcing material for polymers. In addition, this easy and nontoxic substitution method may provide a universal route towards high yields of other 2D materials.
doi:10.1038/srep04211
PMCID: PMC3936228  PMID: 24572725
20.  RANKL Expression in Periodontal Disease: Where Does RANKL Come from? 
BioMed Research International  2014;2014:731039.
Periodontitis is an inflammatory disease characterized by periodontal pocket formation and alveolar bone resorption. Periodontal bone resorption is induced by osteoclasts and receptor activator of nuclear factor-κB ligand (RANKL) which is an essential and central regulator of osteoclast development and osteoclast function. Therefore, RANKL plays a critical role in periodontal bone resorption. In this review, we have summarized the sources of RANKL in periodontal disease and explored which factors may regulate RANKL expression in this disease.
doi:10.1155/2014/731039
PMCID: PMC3955606  PMID: 24719884
21.  Ultra-Flexibility and Unusual Electronic, Magnetic and Chemical Properties of Waved Graphenes and Nanoribbons 
Scientific Reports  2014;4:4198.
Two-dimensional materials have attracted increasing attention because of their particular properties and potential applications in next-generation nanodevices. In this work, we investigate the physical and chemical properties of waved graphenes/nanoribbons based on first-principles calculations. We show that waved graphenes are compressible up to a strain of 50% and ultra-flexible because of the vanishing in-plane stiffness. The conductivity of waved graphenes is reduced due to charge decoupling under high compression. Our analysis of pyramidalization angles predicts that the chemistry of waved graphenes can be easily controlled by modulating local curvatures. We further demonstrate that band gaps of armchair waved graphene nanoribbons decrease with the increase of compression if they are asymmetrical in geometry, while increase if symmetrical. For waved zigzag nanoribbons, their anti-ferromagnetic states are strongly enhanced by increasing compression. The versatile functions of waved graphenes enable their applications in multi-functional nanodevices and sensors.
doi:10.1038/srep04198
PMCID: PMC3935201  PMID: 24569444
22.  Association of interleukin-10 promoter polymorphisms and corresponding plasma levels with susceptibility to laryngeal squamous cell carcinoma 
Oncology Letters  2014;7(5):1721-1727.
Interleukin (IL)-10 is critically involved in tumorigenesis. In the present study, the association between the IL-10 −1082/−819/−592 promoter polymorphisms, the plasma IL-10 levels and the risk of laryngeal squamous cell carcinoma (LSCC) was investigated in a prospective, case-control study. In total, 146 patients with LSCC, 61 with vocal leukoplakia and 119 healthy controls were genotyped for the IL-10 gene (IL-10 −1082 A/G, −819 T/C and −592 A/C) using pyrosequencing, and their plasma IL-10 levels were analyzed by ELISA. The patients with LSCC had a significantly higher frequency of AC at position −592 and −819 (OR, 1.82 and P=0.024) compared with the control, and a higher frequency of AG at position −1082 (OR, 2.20 and P=0.037). The patients with advanced LSCC had a significantly higher frequency of AG+GG at position −1082 compared with those with early-stage LSCC (OR, 3.13 and P=0.008 vs. OR, 2.06 and P=0.068). The patients with lymph node metastasis had a significantly higher frequency of AG+GG at position −1082 compared with the patients with no lymph node metastasis (OR, 2.97 and P=0.048 vs. OR, 2.23 and P=0.035). In addition, the patients with high frequencies of each genotype polymorphism had high plasma IL-10 concentrations. The present study indicates that the IL-10 −1082/−819/−592 promoter polymorphisms and corresponding high plasma IL-10 concentrations are associated with LSCC, and that variations in genotype distribution and plasma IL-10 concentrations may be associated with the stage and the lymph node metastasis status of LSCC.
doi:10.3892/ol.2014.1914
PMCID: PMC3997667  PMID: 24765208
laryngeal squamous cell carcinoma; vocal leukoplakia; cytokines; polymorphism; interleukin-10
23.  The Association of HMGB1 Gene with the Prognosis of HCC 
PLoS ONE  2014;9(2):e89097.
High-mobility group box 1 protein (HMGB1) is an evolutionarily ancient and critical regulator of cell death and survival. HMGB1 is a chromatin-associated nuclear protein molecule that triggers extracellular damage. The expression of HMGB1 has been reported in many types of cancers, but the role of HMGB1 in hepato cellular carcinoma (HCC) is unknown.The aim of this study was to analyze the roles of HMGB1 in HCC progression using HCC clinical samples. We also investigated the clinical outcomes of HCC samples with a special focus on HMBG1 expression. In an immunohistochemical study conducted on 208 cases of HCC, HMGB1 had high expression in 134 cases(64.4%).The HMGB1 expression level did not correlate with any clinicopathological parameters, except alpha fetoprotein (AFP) (p = 0.041) and CLIP stage (p = 0.007). However, survival analysis showed that the group with HMBG1 overexpression had a significantly shorter overall survival time than the group with a down-regulatedexpression of HMBG1 (HR = 0.568, CI (0.398, 0.811), p = 0.002). Multivariate analysis showed that HMGB1 expression was a significant and independent prognostic parameter (HR = 0.562, CI (0.388, 0.815), p = 0.002) for HCC patients. The ability of proliferation, migration and invasion of HCC cells was suppressed with the disruption of endogenous HMGB1 using small interfering RNAs. On the other hand, the ability of proliferation, migration and invasion of HCC cells was strengthened when the expression endogenous HMGB1 was enhanced using HMGB1 DNA. HMGB1 expression may be a novel and independent predictor for the prognosis of HCC patients. The overexpression of HMGB1 in HCC could be a novel, effective, and supplementary biomarker for HCC, since it plays a vital role in the progression of HCC.
doi:10.1371/journal.pone.0089097
PMCID: PMC3929653  PMID: 24586525
24.  A Modeling and Experiment Framework for the Emergency Management in AHC Transmission 
Emergency management is crucial to finding effective ways to minimize or even eliminate the damage of emergent events, but there still exists no quantified method to study the events by computation. Statistical algorithms, such as susceptible-infected-recovered (SIR) models on epidemic transmission, ignore many details, thus always influencing the spread of emergent events. In this paper, we first propose an agent-based modeling and experiment framework to model the real world with the emergent events. The model of the real world is called artificial society, which is composed of agent model, agent activity model, and environment model, and it employs finite state automata (FSA) as its modeling paradigm. An artificial campus, on which a series of experiments are done to analyze the key factors of the acute hemorrhagic conjunctivitis (AHC) transmission, is then constructed to illustrate how our method works on the emergency management. Intervention measures and optional configurations (such as the isolation period) of them for the emergency management are also given through the evaluations in these experiments.
doi:10.1155/2014/897532
PMCID: PMC3947678  PMID: 24693330
25.  Interleukin-10 Inhibits Bone Resorption: A Potential Therapeutic Strategy in Periodontitis and Other Bone Loss Diseases 
BioMed Research International  2014;2014:284836.
Periodontitis and other bone loss diseases, decreasing bone volume and strength, have a significant impact on millions of people with the risk of tooth loss and bone fracture. The integrity and strength of bone are maintained through the balance between bone resorption and bone formation by osteoclasts and osteoblasts, respectively, so the loss of bone results from the disruption of such balance due to increased resorption or/and decreased formation of bone. The goal of therapies for diseases of bone loss is to reduce bone loss, improve bone formation, and then keep healthy bone density. Current therapies have mostly relied on long-term medication, exercise, anti-inflammatory therapies, and changing of the life style. However there are some limitations for some patients in the effective treatments for bone loss diseases because of the complexity of bone loss. Interleukin-10 (IL-10) is a potent anti-inflammatory cytokine, and recent studies have indicated that IL-10 can contribute to the maintenance of bone mass through inhibition of osteoclastic bone resorption and regulation of osteoblastic bone formation. This paper will provide a brief overview of the role of IL-10 in bone loss diseases and discuss the possibility of IL-10 adoption in therapy of bone loss diseases therapy.
doi:10.1155/2014/284836
PMCID: PMC3947664  PMID: 24696846

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