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1.  Radiofrequency ablation of hepatocellular carcinoma in difficult locations: Strategies and long-term outcomes 
AIM: To investigate the treatment strategies and long-term outcomes of radiofrequency ablation (RFA) of hepatocellular carcinoma (HCC) in difficult locations and to compare the results with non-difficult HCC.
METHODS: From 2004 to 2012, a total of 470 HCC patients underwent ultrasound-guided percutaneous RFA. Among these HCC patients, 382 with tumors located ≤ 5 mm from a major vessel/bile duct (n = 87), from peripheral important structures (n = 232) or from the liver capsule (n = 63) were regarded as difficult cases. There were 331 male patients and 51 female patients, with an average age of 55.3 ± 10.1 years old. A total of 235 and 147 patients had Child-Pugh class A and class B liver function, respectively. The average tumor size was 3.4 ± 1.2 cm. Individual treatment strategies were developed to treat these difficult cases. During the same period, 88 HCC patients with tumors that were not in difficult locations served as the control group. In the control group, 74 patients were male, and 14 patients were female, with an average age of 57.4 ± 11.8 years old. Of these, 62 patients and 26 patients had Child-Pugh class A and class B liver function, respectively. Regular follow-up after RFA was performed to assess treatment efficacy. Survival results were generated from Kaplan-Meier estimates, and multivariate analysis was performed using the Cox regression model.
RESULTS: Early tumor necrosis rate in the difficult group was similar to that in the control group (97.6% vs 94.3%, P = 0.080). The complication rate in the difficult group was significantly higher than that in the control group (4.9% vs 0.8%, P = 0.041). The follow-up period ranged from 6 to 116 mo, with an average of 28 ± 22.4 mo. Local progression rate in the difficult group was significantly higher than that in the control group (12.7% vs 7.1%, P = 0.046). However, the 1-, 3-, 5-, and 7-year overall survival rates in the difficult group were not significantly different from those in the control group (84.3%, 54.4%, 41.2%, and 29.9% vs 92.5%, 60.3%, 43.2%, and 32.8%, respectively, P = 0.371). Additionally, a multivariate analysis revealed that tumor location was not a significant risk factor for survival.
CONCLUSION: There was no significant difference in long-term overall survival between the two groups even though the local progression rate was higher in the difficult group.
doi:10.3748/wjg.v21.i5.1554
PMCID: PMC4316097  PMID: 25663774
Radiofrequency ablation; Ultrasound guidance; Hepatocellular carcinoma; Difficult location; Long-term outcome
2.  Molecular characterization and copy number of SMN1, SMN2 and NAIP in Chinese patients with spinal muscular atrophy and unrelated healthy controls 
Background
Spinal muscular atrophy (SMA) is caused by SMN1 dysfunction, and the copy number of SMN2 and NAIP can modify the phenotype of SMA. The aim of this study was to analyze the copy numbers and gene structures of SMA-related genes in Chinese SMA patients and unrelated healthy controls.
Methods
Forty-two Chinese SMA patients and two hundred and twelve unrelated healthy Chinese individuals were enrolled in our study. The copy numbers and gene structures of SMA-related genes were measured by MLPA assay.
Results
We identified a homozygous deletion of SMN1 in exons 7 and 8 in 37 of 42 patients (88.1%); the other 5 SMA patients (11.9%) had a single copy of SMN1 exon 8. The proportions of the 212 unrelated healthy controls with different copy numbers for the normal SMN1 gene were 1 copy in 4 individuals (1.9%), 2 copies in 203 (95.7%) and 3 copies in 5 (2.4%). Three hybrid SMN genes and five genes that lack partial sequences were found in SMA patients and healthy controls. Distributions of copy numbers for normal SMN2 and NAIP were significantly different (P < 0.001) in people with and without SMA.
Conclusion
The copy numbers and gene structures of SMA-related genes were different in Chinese SMA patients and healthy controls.
doi:10.1186/s12891-015-0457-x
PMCID: PMC4328246
Chinese; MLPA; SMA; Gene copy number
3.  Intracellular CD24 disrupts the ARF–NPM interaction and enables mutational and viral oncogene-mediated p53 inactivation 
Nature Communications  2015;6:5909.
CD24 is overexpressed in nearly 70% human cancers, whereas TP53 is the most frequently mutated tumour-suppressor gene that functions in a context-dependent manner. Here we show that both targeted mutation and short hairpin RNA (shRNA) silencing of CD24 retard the growth, progression and metastasis of prostate cancer. CD24 competitively inhibits ARF binding to NPM, resulting in decreased ARF, increase MDM2 and decrease levels of p53 and the p53 target p21/CDKN1A. CD24 silencing prevents functional inactivation of p53 by both somatic mutation and viral oncogenes, including the SV40 large T antigen and human papilloma virus 16 E6-antigen. In support of the functional interaction between CD24 and p53, in silico analyses reveal that TP53 mutates at a higher rate among glioma and prostate cancer samples with higher CD24 mRNA levels. These data provide a general mechanism for functional inactivation of ARF and reveal an important cellular context for genetic and viral inactivation of TP53.
P53 is a tumour suppressor that is frequently mutated or downregulated in cancer. Here, Wang et al. show that CD24, a molecule frequently overexpressed in cancer, promotes p53 degradation by disrupting a regulatory ARF–MDM2 interaction, and silencing CD24 prevents the downregulation of p53.
doi:10.1038/ncomms6909
PMCID: PMC4300525  PMID: 25600590
4.  Nerve regeneration and elastin formation within poly(glycerol sebacate)-based synthetic arterial grafts one-year post-implantation in a rat model 
Biomaterials  2013;35(1):10.1016/j.biomaterials.2013.09.081.
The objective of this study was to evaluate the long term performance of cell-free vascular grafts made from a fast-degrading elastic polymer. We fabricated small arterial grafts from microporous tubes of poly(glycerol sebacate) (PGS) reinforced with polycaprolactone (PCL) nanofibers on the outer surface. Grafts were interpositioned in rat abdominal aortas and characterized at 1 year post-implant. Grafts remodeled into “neoarteries” (regenerated arteries) with similar gross appearance to native rat aortas. Neoarteries mimic arterial tissue architecture with a confluent endothelium and media and adventita-like layers. Patent vessels (80%) showed no significant stenosis, dilation, or calcification. Neoarteries contain nerves and have the same amount of mature elastin as native arteries. Despite some differences in matrix organization, regenerated arteries had similar dynamic mechanical compliance to native arteries in vivo. Neoarteries responded to vasomotor agents, albeit with different magnitude than native aortas. These data suggest that an elastic vascular graft that resorbs quickly has potential to improve the performance of vascular grafts used in small arteries. This design may also promote constructive remodeling in other soft tissues.
doi:10.1016/j.biomaterials.2013.09.081
PMCID: PMC3882022  PMID: 24119457
5.  Depletion of extracellular signal-regulated kinase 1 in mice with cardiomyopathy caused by lamin A/C gene mutation partially prevents pathology before isoenzyme activation 
Human Molecular Genetics  2013;23(1):1-11.
Mutations in the lamin A/C gene (LMNA) encoding A-type nuclear lamins cause dilated cardiomyopathy with variable muscular dystrophy. These mutations enhance mitogen-activated protein kinase signaling in the heart and pharmacological inhibition of extracellular signal-regulated kinase (ERK) 1 and 2 improves cardiac function in LmnaH222P/H222P mice. In the current study, we crossed mice lacking ERK1 to LmnaH222P/H222P mice and examined cardiac performance and survival. Male LmnaH222P/H222P/Erk1−/− mice lacking ERK1 had smaller left ventricular end systolic diameters and increased fractional shortening (FS) at 16 weeks of age than LmnaH222P/H222P/Erk1+/+ mice. Their mean survival was also significantly longer. However, the improved cardiac function was abrogated at 20 weeks of age concurrent with an increased activity of ERK2. LmnaH222P/H222P/Erk1−/− mice treated with an inhibitor of ERK1/2 activation had smaller left ventricular diameters and increased FS at 20 weeks of age. These results provide genetic evidence that ERK1 and ERK2 contribute to the development of cardiomyopathy caused by LMNA mutations and reveal interplay between these isoenzymes in maintaining a combined pathological activity in heart.
doi:10.1093/hmg/ddt387
PMCID: PMC3857940  PMID: 23933734
6.  A novel C19MC amplified cell line links Lin28/let-7 to mTOR signaling in embryonal tumor with multilayered rosettes 
Neuro-Oncology  2013;16(1):62-71.
Background
Embryonal tumor with multilayered rosettes (ETMR) is an aggressive central nervous system primitive neuroectodermal tumor (CNS-PNET) variant. ETMRs have distinctive histology, amplification of the chromosome 19 microRNA cluster (C19MC) at chr19q13.41-42, expression of the RNA binding protein Lin28, and dismal prognosis. Functional and therapeutic studies of ETMR have been limited by a lack of model systems.
Methods
We have established a first cell line, BT183, from a case of ETMR and characterized its molecular and cellular features. LIN28 knockdown was performed in BT183 to examine the potential role of Lin28 in regulating signaling pathway gene expression in ETMR. Cell line findings were corroborated with immunohistochemical studies in ETMR tissues. A drug screen of 73 compounds was performed to identify potential therapeutic targets.
Results
The BT183 line maintains C19MC amplification, expresses C19MC-encoded microRNAs, and is tumor initiating. ETMRs, including BT183, have high LIN28 expression and low let-7 miRNA expression, and show evidence of mTOR pathway activation. LIN28 knockdown increases let-7 expression and decreases expression of IGF/PI3K/mTOR pathway components. Pharmacologic inhibition of the mTOR pathway reduces BT183 cell viability.
Conclusions
BT183 retains key genetic and histologic features of ETMR. In ETMR, Lin28 is not only a diagnostic marker but also a regulator of genes involved in growth and metabolism. Our findings indicate that inhibitors of the IGF/PI3K/mTOR pathway may be promising novel therapies for these fatal embryonal tumors. As the first patient-derived cell line of these rare tumors, BT183 is an important, unique reagent for investigating ETMR biology and therapeutics.
doi:10.1093/neuonc/not162
PMCID: PMC3870842  PMID: 24311633
ETMR; ETANTR; C19MC; Lin28; mTOR
7.  ROBUST REVERSE ENGINEERING OF DYNAMIC GENE NETWORKS UNDER SAMPLE SIZE HETEROGENEITY 
Simultaneously reverse engineering a collection of condition-specific gene networks from gene expression microarray data to uncover dynamic mechanisms is a key challenge in systems biology. However, existing methods for this task are very sensitive to variations in the size of the microarray samples across different biological conditions (which we term sample size heterogeneity in network reconstruction), and can potentially produce misleading results that can lead to incorrect biological interpretation. In this work, we develop a more robust framework that addresses this novel problem. Just like microarray measurements across conditions must undergo proper normalization on their magnitudes before entering subsequent analysis, we argue that networks across conditions also need to be “normalized” on their density when they are constructed, and we provide an algorithm that allows such normalization to be facilitated while estimating the networks. We show the quantitative advantages of our approach on synthetic and real data. Our analysis of a hematopoietic stem cell dataset reveals interesting results, some of which are confirmed by previously validated results.
PMCID: PMC3939316  PMID: 24297553
gene network reconstruction; dynamic; sample size heterogeneity
8.  The effects of situated learning and health knowledge involvement on health communications 
Reproductive Health  2014;11(1):93.
Background
Many patients use websites, blogs, or online social communities to gain health knowledge, information about disease symptoms, and disease diagnosis opinions. The purpose of this study is to use the online platform of blogs to explore whether the framing effect of information content, situated learning of information content, and health knowledge involvement would affect health communication between doctors and patients and further explore whether this would increase patient willingness to seek treatment.
Methods
This study uses a survey to collect data from patient subjects who have used online doctor blogs or patients who have discussed medical information with doctors on blogs. The number of valid questionnaire samples is 278, and partial least square is used to conduct structural equation model analysis.
Results
Research results show that situated learning and health knowledge involvement have a positive effect on health communication. The negative framing effect and health knowledge involvement would also affect the patient’s intention to seek medical help. In addition, situated learning and health knowledge involvement would affect the intention to seek medical help through communication factors.
Conclusions
Blogs are important communication channels between medical personnel and patients that allow users to consult and ask questions without time limitations and enable them to obtain comprehensive health information.
doi:10.1186/1742-4755-11-93
PMCID: PMC4297390  PMID: 25542070
Framing effects; Situated learning; Health knowledge involvement; Health communication; Visiting a doctor
9.  Identifying cooperative transcription factors in yeast using multiple data sources 
BMC Systems Biology  2014;8(Suppl 5):S2.
Background
Transcriptional regulation of gene expression is usually accomplished by multiple interactive transcription factors (TFs). Therefore, it is crucial to understand the precise cooperative interactions among TFs. Various kinds of experimental data including ChIP-chip, TF binding site (TFBS), gene expression, TF knockout and protein-protein interaction data have been used to identify cooperative TF pairs in existing methods. The nucleosome occupancy data is not yet used for this research topic despite that several researches have revealed the association between nucleosomes and TFBSs.
Results
In this study, we developed a novel method to infer the cooperativity between two TFs by integrating the TF-gene documented regulation, TFBS and nucleosome occupancy data. TF-gene documented regulation and TFBS data were used to determine the target genes of a TF, and the genome-wide nucleosome occupancy data was used to assess the nucleosome occupancy on TFBSs. Our method identifies cooperative TF pairs based on two biologically plausible assumptions. If two TFs cooperate, then (i) they should have a significantly higher number of common target genes than random expectation and (ii) their binding sites (in the promoters of their common target genes) should tend to be co-depleted of nucleosomes in order to make these binding sites simultaneously accessible to TF binding. Each TF pair is given a cooperativity score by our method. The higher the score is, the more likely a TF pair has cooperativity. Finally, a list of 27 cooperative TF pairs has been predicted by our method. Among these 27 TF pairs, 19 pairs are also predicted by existing methods. The other 8 pairs are novel cooperative TF pairs predicted by our method. The biological relevance of these 8 novel cooperative TF pairs is justified by the existence of protein-protein interactions and co-annotation in the same MIPS functional categories. Moreover, we adopted three performance indices to compare our predictions with 11 existing methods' predictions. We show that our method performs better than these 11 existing methods in identifying cooperative TF pairs in yeast. Finally, the cooperative TF network constructed from the 27 predicted cooperative TF pairs shows that our method has the power to find cooperative TF pairs of different biological processes.
Conclusion
Our method is effective in identifying cooperative TF pairs in yeast. Many of our predictions are validated by the literature, and our method outperforms 11 existing methods. We believe that our study will help biologists to understand the mechanisms of transcriptional regulation in eukaryotic cells.
doi:10.1186/1752-0509-8-S5-S2
PMCID: PMC4305981  PMID: 25559499
transcription factor cooperativity; nucleosome; transcription factor binding site; yeast
10.  A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae 
BMC Systems Biology  2014;8(Suppl 5):S9.
Background
Defining a measure for regulatory similarity (RS) of two genes is an important step toward identifying co-regulated genes. To date, transcription factor binding sites (TFBSs) have been widely used to measure the RS of two genes because transcription factors (TFs) binding to TFBSs in promoters is the most crucial and well understood step in gene regulation. However, existing TFBS-based RS measures consider the relation of a TFBS to a gene as a Boolean (either 'presence' or 'absence') without utilizing the information of TFBS locations in promoters.
Results
Functional TFBSs of many TFs in yeast are known to have a strong positional preference to occur in a small region in the promoters. This biological knowledge prompts us to develop a novel RS measure that exploits the TFBS location information. The performances of different RS measures are evaluated by the fraction of gene pairs that are co-regulated (validated by literature evidence) by at least one common TF under different RS scores. The experimental results show that the proposed RS measure is the best co-regulation indicator among the six compared RS measures. In addition, the co-regulated genes identified by the proposed RS measure are also shown to be able to benefit three co-regulation-based applications: detecting gene co-function, gene co-expression and protein-protein interactions.
Conclusions
The proposed RS measure provides a good indicator for gene co-regulation. Besides, its good performance reveals the importance of the location information in TFBS-based RS measures.
doi:10.1186/1752-0509-8-S5-S9
PMCID: PMC4305988  PMID: 25560196
11.  FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis 
Cell Research  2014;24(12):1403-1419.
The role of Fat Mass and Obesity-associated protein (FTO) and its substrate N6-methyladenosine (m6A) in mRNA processing and adipogenesis remains largely unknown. We show that FTO expression and m6A levels are inversely correlated during adipogenesis. FTO depletion blocks differentiation and only catalytically active FTO restores adipogenesis. Transcriptome analyses in combination with m6A-seq revealed that gene expression and mRNA splicing of grouped genes are regulated by FTO. M6A is enriched in exonic regions flanking 5′- and 3′-splice sites, spatially overlapping with mRNA splicing regulatory serine/arginine-rich (SR) protein exonic splicing enhancer binding regions. Enhanced levels of m6A in response to FTO depletion promotes the RNA binding ability of SRSF2 protein, leading to increased inclusion of target exons. FTO controls exonic splicing of adipogenic regulatory factor RUNX1T1 by regulating m6A levels around splice sites and thereby modulates differentiation. These findings provide compelling evidence that FTO-dependent m6A demethylation functions as a novel regulatory mechanism of RNA processing and plays a critical role in the regulation of adipogenesis.
doi:10.1038/cr.2014.151
PMCID: PMC4260349  PMID: 25412662
N6-methyladenosine (m6A); METTL3; FTO; mRNA splicing; adipogenesis
12.  Large-Scale Synthesis of Gold Nanorods through Continuous Secondary Growth 
Gold nanorods (GNRs) exhibit a tunable longitudinal surface plasmon resonance (LSPR) that depends on the GNR aspect ratio (AR). Independently controlling the AR and size of GNRs remains challenging but is important because the scattering intensity strongly depends on the GNR size. Here, we report a secondary (seeded) growth procedure, wherein continuous addition of ascorbic acid (AA) to a stirring solution of GNRs, stabilized by cetyltrimethylammonium bromide (CTAB) and synthesized by a common GNR growth procedure, deposits the remaining (~70%) of the Au precursor onto the GNRs. The growth phase of GNR synthesis is often performed without stirring, since stirring has been believed to reduce the yield of rod-shaped nanoparticles, but we report that stirring coupled with continuous addition of AA during secondary growth allows improved control over the AR and size of GNRs. After a common primary GNR growth procedure, the LSPR of GNRs is ~820 nm, which can be tuned between ~700–880 nm during secondary growth by adjusting the rate of AA addition or adding benzyldimethylhexadecylammonium chloride hydrate (BDAC). This approach for secondary growth can also be used with primary GNRs of different ARs to achieve different LSPRs and can likely be extended to nanoparticles of different shapes and other metals.
doi:10.1021/cm402277y
PMCID: PMC3883054  PMID: 24415848
gold; silver; nanorods; seeded growth; surface plasmon resonance
13.  Conventional empirical law reverses in the phase transitions of 122-type iron-based superconductors 
Scientific Reports  2014;4:7172.
Phase transition of solid-state materials is a fundamental research topic in condensed matter physics, materials science and geophysics. It has been well accepted and widely proven that isostructural compounds containing different cations undergo same pressure-induced phase transitions but at progressively lower pressures as the cation radii increases. However, we discovered that this conventional law reverses in the structural transitions in 122-type iron-based superconductors. In this report, a combined low temperature and high pressure X-ray diffraction (XRD) measurement has identified the phase transition curves among the tetragonal (T), orthorhombic (O) and the collapsed-tetragonal (cT) phases in the structural phase diagram of the iron-based superconductor AFe2As2 (A = Ca, Sr, Eu, and Ba). The cation radii dependence of the phase transition pressure (T → cT) shows an opposite trend in which the compounds with larger ambient radii cations have a higher transition pressure.
doi:10.1038/srep07172
PMCID: PMC4241531  PMID: 25417655
14.  Alveolar Type II Epithelial Cell Dysfunction in Rat Experimental Hepatopulmonary Syndrome (HPS) 
PLoS ONE  2014;9(11):e113451.
The hepatopulmonary syndrome (HPS) develops when pulmonary vasodilatation leads to abnormal gas exchange. However, in human HPS, restrictive ventilatory defects are also observed supporting that the alveolar epithelial compartment may also be affected. Alveolar type II epithelial cells (AT2) play a critical role in maintaining the alveolar compartment by producing four surfactant proteins (SPs, SP-A, SP-B, SP-C and SP-D) which also facilitate alveolar repair following injury. However, no studies have evaluated the alveolar epithelial compartment in experimental HPS. In this study, we evaluated the alveolar epithelial compartment and particularly AT2 cells in experimental HPS induced by common bile duct ligation (CBDL). We found a significant reduction in pulmonary SP production associated with increased apoptosis in AT2 cells after CBDL relative to controls. Lung morphology showed decreased mean alveolar chord length and lung volumes in CBDL animals that were not seen in control models supporting a selective reduction of alveolar airspace. Furthermore, we found that administration of TNF-α, the bile acid, chenodeoxycholic acid, and FXR nuclear receptor activation (GW4064) induced apoptosis and impaired SP-B and SP-C production in alveolar epithelial cells in vitro. These results imply that AT2 cell dysfunction occurs in experimental HPS and is associated with alterations in the alveolar epithelial compartment. Our findings support a novel contributing mechanism in experimental HPS that may be relevant to humans and a potential therapeutic target.
doi:10.1371/journal.pone.0113451
PMCID: PMC4242631  PMID: 25419825
15.  Rare ocular features in a case of Kabuki syndrome (Niikawa-Kuroki syndrome) 
BMC Ophthalmology  2014;14(1):143.
Background
Kabuki syndrome is a multi-system disorder with peculiar facial features, and ophthalmic abnormalities are frequently involved. This case report of a child with Kabuki syndrome describes two new previously unreported ophthalmic conditions.
Case presentation
A 3-year-old Taiwanese boy with Kabuki syndrome had a short stature, spinal dysraphism, intellectual disability and typical facial features. Ophthalmic findings which have been previously reported in the literature and in this patient, included ptosis, esotropia, coloboma of the iris, retina, choroid and optic disc, and microcornea. The newly identified ophthalmic features in this patient included colobomatous microphthalmos and a dysplastic and elevated disc without central cupping. The genetic analysis identified an MLL2 gene mutation.
Conclusion
The presentations of a dysplastic disc and colobomatous microphthalmia are rarely reported in patients with Kabuki syndrome, but these ophthalmic abnormalities may affect vision. Detailed ophthalmic evaluations in children with Kabuki syndrome are advised.
doi:10.1186/1471-2415-14-143
PMCID: PMC4251844  PMID: 25421742
Kabuki syndrome; Colobomatous microphthalmia; Optic disc dysplasia; MLL2 gene mutation
16.  Lens Subluxation after Plasmin and SF6 Injections in Rabbit Eyes 
PLoS ONE  2014;9(11):e112957.
Purpose
To investigate the rate of lens subluxation following plasmin and/or SF6 injections in eyes, and whether a subsequent elevated level of vascular endothelial growth factor (VEGF) and vitreous tap would aggravate subluxation.
Methods
Four groups of rabbits were used. Group 1 received an intravitreal injection (IVI) of plasmin and SF6 in the right eye; group 2 received an IVI of plasmin in the right eye; group 3 received an IVI of SF6 in the right eye; and group 4 received an IVI of balanced salt solution in the right eye. After treatment, IVIs of VEGF were given and vitreous tap was performed three times, followed by clinical observation of lens subluxation and scanning electronic microscope evaluation of the zonular fibers.
Results
After IVIs of plasmin and SF6, and VEGF and vitreous tap had been performed one to three times, lens subluxation was noted in 0%, 43%, 71%, 71%, and 86% of the eyes in group 1. After IVIs of plasmin, VEGF, and vitreous tap had been performed one to three times, lens subluxation was noted in 11%, 22%, 44%, 44%, and 67% of the eyes in group 2. The eyes in group 3 and 4 did not show signs of lens subluxation after VEGF IVIs and vitreous tap. Histology confirmed zonular fiber damage in the eyes treated with plasmin.
Conclusions
The incidence of lens subluxation increased following plasmin injections in the eyes, and this was aggravated by the subsequent high VEGF level in the eyes and vitreous tapping. Zonular fibers were disrupted following plasmin treatment. These effects should be kept in mind when using plasmin enzymes in patients with vitreoretinal abnormalities.
doi:10.1371/journal.pone.0112957
PMCID: PMC4232556  PMID: 25397749
17.  Enhancement of oral bioavailability of cyclosporine A: comparison of various nanoscale drug-delivery systems 
A variety of nanoscale delivery systems have been shown to enhance the oral absorption of poorly water-soluble and poorly permeable drugs. However, the performance of these systems has seldom been evaluated simultaneously. The aim of this study was to compare the bioavailability enhancement effect of lipid-based nanocarriers with poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) to highlight the importance of the lipid composition, with cyclosporine A (CyA) as a model drug. CyA-loaded PLGA NPs, nanostructured lipid carriers (NLCs), and self-microemulsifying drug-delivery systems (SMEDDS) were prepared. The particle size of PLGA NPs (182.2±12.8 nm) was larger than that of NLCs (89.7±9.0 nm) and SMEDDS (26.9±1.9 nm). All vehicles are charged negatively. The entrapment efficiency of PLGA NPs and NLCs was 87.6%±1.6% and 80.3%±0.6%, respectively. In vitro release tests indicated that the cumulative release of CyA was lower than 4% from all vehicles, including Sandimmun Neoral®, according to the dialysis method. Both NLCs and SMEDDS showed high relative oral bioavailability, 111.8% and 73.6%, respectively, after oral gavage administration to beagle dogs, which was not statistically different from commercial Sandimmun Neoral®. However, PLGA NPs failed to achieve efficient absorption, with relative bioavailability of about 22.7%. It is concluded that lipid-based nanoscale drug-delivery systems are superior to polymeric NPs in enhancing oral bioavailability of poorly water-soluble and poorly permeable drugs.
doi:10.2147/IJN.S72560
PMCID: PMC4218918  PMID: 25378925
cyclosporine A; PLGA nanoparticle; nanostructured lipid carrier; self-microemulsifying drug-delivery systems; bioavailability
18.  Bacterial Communities in Semen from Men of Infertile Couples: Metagenomic Sequencing Reveals Relationships of Seminal Microbiota to Semen Quality 
PLoS ONE  2014;9(10):e110152.
Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA), Atypical, and leukocytes). Computer-assisted semen analysis (CASA) was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%), Pseudomonas (9.85%), Prevotella (8.51%) and Gardnerella (4.21%). The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6%) were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.
doi:10.1371/journal.pone.0110152
PMCID: PMC4207690  PMID: 25340531
19.  Prognostic Role of Common MicroRNA Polymorphisms in Cancers: Evidence from a Meta-Analysis 
PLoS ONE  2014;9(10):e106799.
Background
The morbidity and mortality of cancer increase remarkably every year. It's a heavy burden for family and society. The detection of prognostic biomarkers can help to improve the theraputic effect and prolong the lifetime of patients. microRNAs have an influential role in cancer prognosis. The results of articles discussing the relationship between microRNA polymorphisms and cancer prognosis are inconsistent.
Methods
We conduct a meta-analysis of 19 publications concerning the association of four common polymorphisms, mir-146a rs2910164, mir-149 rs2292832, mir-196a2 rs11614913 and mir-499 rs3746444, with cancer prognosis. Pooled Hazard Ratios with 95% Confidence Intervals for the relationship between four genetic polymorphisms and Overall Survival, Recurrence-free Survival, Disease-free survival, recurrence are calculated. Subgroup analysis by population and type of tumor are conducted.
Results
GG genotype of mir-146a may be the protective factor for overall survival, especially in Caucasian population. C-containing genotypes of mir-196a2 act as a risk role for overall survival. The same result exists in Asian population, in Non-Small Cell Lung Cancer and digestive cancer. The patients with C allele of mir-149 have a better overall survival, especially in Non-Small Cell Lung Cancer. No significant results are obtained for mir-499 polymorphisms.
Conclusions
Genetic polymorphisms in mir-146a, mir-196a2 and mir-149 may be associated with overall survival. This effect varies with different types of cancer. Genetic polymorphism in mir-499 may have nothing to do with cancer prognosis.
doi:10.1371/journal.pone.0106799
PMCID: PMC4206268  PMID: 25337946
20.  Dax1 and Nanog act in parallel to stabilize mouse embryonic stem cells and induced pluripotency 
Nature Communications  2014;5:5042.
Nanog expression is heterogeneous and dynamic in embryonic stem cells (ESCs). However, the mechanism for stabilizing pluripotency during the transitions between Nanoghigh and Nanoglow states is not well understood. Here we report that Dax1 acts in parallel with Nanog to regulate mouse ESC (mESCs) identity. Dax1 stable knockdown mESCs are predisposed towards differentiation but do not lose pluripotency, whereas Dax1 overexpression supports LIF-independent self-renewal. Although partially complementary, Dax1 and Nanog function independently and cannot replace one another. They are both required for full reprogramming to induce pluripotency. Importantly, Dax1 is indispensable for self-renewal of Nanoglow mESCs. Moreover, we report that Dax1 prevents extra-embryonic endoderm (ExEn) commitment by directly repressing Gata6 transcription. Dax1 may also mediate inhibition of trophectoderm differentiation independent or as a downstream effector of Oct4. These findings establish a basal role of Dax1 in maintaining pluripotency during the state transition of mESCs and somatic cell reprogramming.
The transcription factor Dax1 is often used as an embryonic stem cell (ESC) marker. Here the authors show that Dax1 acts in parallel to the pluripotency transcription factor Nanog in the maintenance of mouse ESC pluripotency and is required for full somatic cell reprogramming.
doi:10.1038/ncomms6042
PMCID: PMC4205889  PMID: 25284313
21.  Correlated changes in structure and viscosity during gelatinization and gelation of tapioca starch granules 
IUCrJ  2014;1(Pt 6):418-428.
Melting of the semicrystalline structure of native tapioca starch granules is correlated to solution viscosity for elucidating gelatinization and gelation processes.
Melting of native tapioca starch granules in aqueous pastes upon heating is observed in situ using simultaneous small- and wide-angle X-ray scattering (SAXS/WAXS) and solution viscometry. Correlated structure and viscosity changes suggest closely associated amylose and amylopectin chains in the semicrystalline layers, and the release of amylose chains for enhanced solution viscosity occurs largely after melting of the semicrystalline structure. Before melting, WAXS results reveal mixed crystals of A- and B-types (∼4:1 by weight), whereas SAXS results indicate that the semicrystalline layers are composed of lamellar blocklets of ca 43 nm domain size, with polydisperse crystalline (≃7.5 nm) and amorphous (≃1.1 nm) layers alternatively assembled into a lamellar spacing of ≃8.6 nm with 20% polydispersity. Upon melting, the semicrystalline lamellae disintegrate into disperse and molten amylopectin nanoclusters with dissolved and partially untangled amylose chains in the aqueous matrix which leads to increased solution viscosity. During subsequent cooling, gelation starts at around 347 K; successively increased solution viscosity coincides with the development of nanocluster aggregation to a fractal dimension ≃2.3 at 303 K, signifying increasing intercluster association through collapsed amylose chains owing to decreased solvency of the aqueous medium with decreasing temperature.
doi:10.1107/S2052252514019137
PMCID: PMC4224460  PMID: 25485122
tapioca starch granules; gelatinization; gelation; SAXS/WAXS; viscosity
22.  Thymic epithelial tumors: a clinicopathologic study of 249 cases from a single institution 
The WHO histological classification for thymic epithelial tumors of 2004 edition is widely used, but its prognostic value is still controversial. In the present study we collected 249 Chinese patients with thymic epithelial tumors from West China Hospital of Sichuan University since 1999-2009 to assess the prognosis relating to tumor stages, histological classifications, MG and adjuvant therapy. There were 18 cases of type A (7.2%), 97 of type AB (39.0%), 22 of type B1 (8.8%), 63 of type B2 (25.3%), 16 of type B3 (6.5%) thymomas and 33 of thymic carcinomas (13.3%). According to the Massaoka staging, there were 107 patients in stage I (43%), 73 patients in stage II (29.3%), 50 patients in stage III (20.1%) and 19 in stage IV (7.6%). 101 patients (40.6%) complicated with MG, the incidence of MG was highest in type B3 thymomas, then in B2, none of thymic carcinomas complicated with MG. Cox regression analysis showed the Masaoka stage was the most important prognostic factor. Besides of staging, WHO histological classification was also an independent prognostic factor. The age, gender, MG and adjuvant therapy have no significant influence to the prognosis of the patients.
PMCID: PMC4270607  PMID: 25550813
Thymic epithelial tumors; WHO classification; Masaoka stage; MG; prognostic value
23.  Inhibition Effect of a Custom Peptide on Lung Tumors 
PLoS ONE  2014;9(10):e109174.
Cecropin B is a natural antimicrobial peptide and CB1a is a custom, engineered modification of it. In vitro, CB1a can kill lung cancer cells at concentrations that do not kill normal lung cells. Furthermore, in vitro, CB1a can disrupt cancer cells from adhering together to form tumor-like spheroids. Mice were xenografted with human lung cancer cells; CB1a could significantly inhibit the growth of tumors in this in vivo model. Docetaxel is a drug in present clinical use against lung cancers; it can have serious side effects because its toxicity is not sufficiently limited to cancer cells. In our studies in mice: CB1a is more toxic to cancer cells than docetaxel, but dramatically less toxic to healthy cells.
doi:10.1371/journal.pone.0109174
PMCID: PMC4195615  PMID: 25310698
24.  Molecular evidence for natural hybridization between wild loquat (Eriobotrya japonica) and its relative E. prinoides 
BMC Plant Biology  2014;14(1):275.
Background
Interspecific hybridization has long been recognized as a pivotal process in plant evolution and speciation. It occurs fairly common in the genera of the subtribe Pyrinae. In Eriobotrya, a small tree genus of Pyrinae, E. prinoides var. daduheensis has been recognized as either a variety of E. prinoides, a natural hybrid between E. prinoides and E. japonica, or a variety of E. japonica. However, to date, there has been no convincing evidence on its status.
Results
Four nuclear genes and two chloroplast regions were sequenced in 89 individuals of these three Eriobotrya taxa from two locations where they coexist. A few fixed nucleotide substitutions or gaps were found in each of the investigated nuclear and chloroplast loci between E. japonica and E. prinoides. Of the 35 individuals of E. prinoides var. daduheensis, 33 showed nucleotide additivity of E. japonica and E. prinoides in at least one nuclear gene, and 10 of them harboured nucleotide additivity at all the four nuclear genes. Most haplotypes of E. prinoides var. daduheensis were also shared with those of E. japonica and E. prinoides. In the two chloroplast regions, 28 and 7 individuals were identical with E. japonica and E. prinoides, respectively.
Conclusions
Our study provides compelling evidence for a hybrid status for E. prinoides var. daduheensis. Most hybrid individuals are later-generation hybrids. Both E. japonica and E. prinoides can serve as female parent. Differential adaptation might maintain the species boundary of E. prinoides and E. japonica in the face of hybridization and potential introgression.
doi:10.1186/s12870-014-0275-6
PMCID: PMC4196008  PMID: 25300306
Eriobotrya; Hybridization; Nuclear genes; Chloroplast DNA
25.  JPEG2000 Still Image Coding Quality 
Journal of Digital Imaging  2013;26(5):866-874.
This work demonstrates the image qualities between two popular JPEG2000 programs. Two medical image compression algorithms are both coded using JPEG2000, but they are different regarding the interface, convenience, speed of computation, and their characteristic options influenced by the encoder, quantization, tiling, etc. The differences in image quality and compression ratio are also affected by the modality and compression algorithm implementation. Do they provide the same quality? The qualities of compressed medical images from two image compression programs named Apollo and JJ2000 were evaluated extensively using objective metrics. These algorithms were applied to three medical image modalities at various compression ratios ranging from 10:1 to 100:1. Following that, the quality of the reconstructed images was evaluated using five objective metrics. The Spearman rank correlation coefficients were measured under every metric in the two programs. We found that JJ2000 and Apollo exhibited indistinguishable image quality for all images evaluated using the above five metrics (r > 0.98, p < 0.001). It can be concluded that the image quality of the JJ2000 and Apollo algorithms is statistically equivalent for medical image compression.
doi:10.1007/s10278-013-9603-x
PMCID: PMC3782606  PMID: 23589187
Image compression; JPEG2000; Image quality

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