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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.  Inhibition of human high affinity copper importer Ctr1 orthologous in the nervous system of Drosophila ameliorates Aβ42-induced alzheimer’s disease-like symptoms 
Neurobiology of aging  2013;34(11):2604-2612.
Disruption of copper homeostasis has been implicated in Alzheimer’s disease (AD) during the last two decades; however, whether copper is a friend or a foe is controversial. Within a genetically tractable Drosophila AD model, we manipulated the expression of human high affinity copper importer orthologous in Drosophila to explore the in vivo roles of copper ions in the development of AD. We found that inhibition of Ctr1C expression by RNAi in Aβ-expressing flies significantly reduced copper accumulation in the brains of the flies as well as ameliorating neurodegeneration, enhancing climbing ability and prolonging lifespan. Interestingly, Ctr1C inhibition led to a significant increase in higher molecular weight Aβ42 forms in brain lysates, while it was accompanied by a trend of decreased expression of amyloid-β degradation proteases (including NEP1-3 and IDE) with age and reduced Cu-Aβ interaction-induced oxidative stress in Ctr1C RNAi flies. Similar results were obtained from inhibiting another copper importer Ctr1B and overexpressing a copper exporter DmATP7 in the nervous system of AD flies. These results imply that copper may play a causative role in developing AD, as either Aβ oligomers or aggregates were less toxic in a reduced copper environment or one with less copper binding. Early manipulation of brain copper uptake can have a great effect on Aβ pathology.
doi:10.1016/j.neurobiolaging.2013.05.029
PMCID: PMC3770863  PMID: 23827522
Alzheimer's disease; Drosophila; Copper; Amyloid-β; Neurodegeneration; High affinity copper importer; Ctr1; DmATP7
3.  Neuromyelitis optica spectrum disorders without and with autoimmune diseases 
BMC Neurology  2014;14:162.
Background
Neuromyelitis optica spectrum disorder (NMOSD) can coexist with non-organ-specific or organ-specific autoimmune diseases. The aim of this study was to investigate and compare the features between NMOSD without and with autoimmune diseases, and NMOSD with non-organ-specific and organ-specific autoimmune diseases.
Methods
One hundred and fifty five NMOSD patients without autoimmune diseases (n = 115) and with autoimmune diseases (n = 40) were enrolled. NMOSD with autoimmune diseases were divided by organ-specific autoimmune diseases. The clinical, laboratory and magnetic resonance imaging features between two groups were assessed.
Results
Motor deficit was less frequent in NMOSD patients with non-organ-specific autoimmune diseases (p = 0.024). Cerebrospinal fluid white blood cell and protein, serum C-reactive protein and immunoglobulin G were lower in NMOSD patients without autoimmune diseases, while several autoantibodies seropositivity and thyroid indexes were significantly higher in NMOSD patients with autoimmune diseases (p < 0.05). No difference was found in other clinical and laboratory characteristics between different NMOSD subtypes (p > 0.05). NMOSD patients with autoimmune diseases had higher brain abnormalities than NMOSD without autoimmune diseases (p < 0.001).
Conclusions
The characteristics between NMOSD without and with autoimmune diseases were similar. NMOSD with autoimmune diseases have high frequency of brain abnormalities.
doi:10.1186/s12883-014-0162-7
PMCID: PMC4236652  PMID: 25135481
Neuromyelitis optica; Neuromyelitis optica spectrum disorder; Non-organ-specific autoimmune diseases; Organ-specific autoimmune diseases; Autoantibodies; Magnetic resonance imaging
4.  Automated White Matter Hyperintensity Detection in Multiple Sclerosis Using 3D T2 FLAIR 
White matter hyperintensities (WMH) seen on T2WI are a hallmark of multiple sclerosis (MS) as it indicates inflammation associated with the disease. Automatic detection of the WMH can be valuable in diagnosing and monitoring of treatment effectiveness. T2 fluid attenuated inversion recovery (FLAIR) MR images provided good contrast between the lesions and other tissue; however the signal intensity of gray matter tissue was close to the lesions in FLAIR images that may cause more false positives in the segment result. We developed and evaluated a tool for automated WMH detection only using high resolution 3D T2 fluid attenuated inversion recovery (FLAIR) MR images. We use a high spatial frequency suppression method to reduce the gray matter area signal intensity. We evaluate our method in 26 MS patients and 26 age matched health controls. The data from the automated algorithm showed good agreement with that from the manual segmentation. The linear correlation between these two approaches in comparing WMH volumes was found to be Y = 1.04X + 1.74  (R2 = 0.96). The automated algorithm estimates the number, volume, and category of WMH.
doi:10.1155/2014/239123
PMCID: PMC4130152  PMID: 25136355
5.  Spatio-temporal mapping of variation potentials in leaves of Helianthus annuus L. seedlings in situ using multi-electrode array 
Scientific Reports  2014;4:5435.
Damaging thermal stimuli trigger long-lasting variation potentials (VPs) in higher plants. Owing to limitations in conventional plant electrophysiological recording techniques, recorded signals are composed of signals originating from all of the cells that are connected to an electrode. This limitation does not enable detailed spatio-temporal distributions of transmission and electrical activities in plants to be visualised. Multi-electrode array (MEA) enables the recording and imaging of dynamic spatio-temporal electrical activities in higher plants. Here, we used an 8 × 8 MEA with a polar distance of 450 μm to measure electrical activities from numerous cells simultaneously. The mapping of the data that were recorded from the MEA revealed the transfer mode of the thermally induced VPs in the leaves of Helianthus annuus L. seedlings in situ. These results suggest that MEA can enable recordings with high spatio-temporal resolution that facilitate the determination of the bioelectrical response mode of higher plants under stress.
doi:10.1038/srep05435
PMCID: PMC4069705  PMID: 24961469
6.  Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis 
BMC Genomics  2014;15(1):363.
Background
Amycolatopsis orientalis is the type species of the genus and its industrial strain HCCB10007, derived from ATCC 43491, has been used for large-scale production of the vital antibiotic vancomycin. However, to date, neither the complete genomic sequence of this species nor a systemic characterization of the vancomycin biosynthesis cluster (vcm) has been reported. With only the whole genome sequence of Amycolatopsis mediterranei available, additional complete genomes of other species may facilitate intra-generic comparative analysis of the genus.
Results
The complete genome of A. orientalis HCCB10007 comprises an 8,948,591-bp circular chromosome and a 33,499-bp dissociated plasmid. In total, 8,121 protein-coding sequences were predicted, and the species-specific genomic features of A. orientalis were analyzed in comparison with that of A. mediterranei. The common characteristics of Amycolatopsis genomes were revealed via intra- and inter-generic comparative genomic analyses within the domain of actinomycetes, and led directly to the development of sequence-based Amycolatopsis molecular chemotaxonomic characteristics (MCCs). The chromosomal core/quasi-core and non-core configurations of the A. orientalis and the A. mediterranei genome were analyzed reciprocally, with respect to further understanding both the discriminable criteria and the evolutionary implementation. In addition, 26 gene clusters related to secondary metabolism, including the 64-kb vcm cluster, were identified in the genome. Employing a customized PCR-targeting-based mutagenesis system along with the biochemical identification of vancomycin variants produced by the mutants, we were able to experimentally characterize a halogenase, a methyltransferase and two glycosyltransferases encoded in the vcm cluster. The broad substrate spectra characteristics of these modification enzymes were inferred.
Conclusions
This study not only extended the genetic knowledge of the genus Amycolatopsis and the biochemical knowledge of vcm-related post-assembly tailoring enzymes, but also developed methodology useful for in vivo studies in A. orientalis, which has been widely considered as a barrier in this field.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-363) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-363
PMCID: PMC4048454  PMID: 24884615
Amycolatopsis orientalis; Complete genome sequencing; Molecular taxonomic characteristics; Vancomycin biosynthesis
7.  Comparison of form-deprived myopia and lens-induced myopia in guinea pigs 
AIM
To study the efficacy difference between form-deprived myopia (FDM) and lens-induced myopia (LIM), the degree of myopia, axial length and pathological changes of the posterior sclera from guinea pigs were evaluated.
METHODS
Four-week pigmented guinea pigs were randomly assigned into 3 groups, including normal control (n=6), FDM group with monocular cover (n=11) and LIM group with monocular -7D lens treatment (n=11). FDM group was form-deprived while LIM group was lens-induced for 14 d. Refractive error and axial length were measured prior to and post treatment, respectively. Morphological changes of sclera were examined using both light and electronic microscopes.
RESULTS
After 14d treatment, refractive errors for FDM group and LIM group were -3.05±0.71D and -2.12±1.29D, respectively, which were significantly more myopic than that of normal controls and fellow control eyes (P<0.01). As for axial length, it was 7.93±0.03 mm for FDM group and 7.89±0.06 mm for LIM group, which were significantly longer than both normal and fellow controls (P<0.01). With respect to both refractory error and axial length, the differences between FDM group and LIM group were not significant (P>0.05). Under light microscope, both FDM group and LIM group showed thinned sclera, disarrangement of fibrosis and enlarged disassociation between fibers. Consistently, ultrastructural examination showed degenerated fibroblasts and thinned fibers in posterior sclera.
CONCLUSION
Following two weeks of myopia induction in guinea pigs, with regard to the degree of myopia, axial length and pathological alterations, there was no significant difference between FDM and LIM models. Therefore, FDM and LIM are equally effective and useful as a model of experimental myopia and guinea pigs are ideal animals for induction of experimental myopia because their high sensitivity to both form-deprivation and lens-induction.
doi:10.3980/j.issn.2222-3959.2014.02.10
PMCID: PMC4003077  PMID: 24790865
form-deprived myopia; lens-induced myopia; pathology
8.  Graded Encoding of Food Odor Value in the Drosophila Brain 
The Journal of Neuroscience  2013;33(40):15693-15704.
Odors are highly evocative, yet how and where in the brain odors derive meaning remains unknown. Our analysis of the Drosophila brain extends the role of a small number of hunger-sensing neurons to include food-odor value representation. In vivo two-photon calcium imaging shows the amplitude of food odor-evoked activity in neurons expressing Drosophila neuropeptide F (dNPF), the neuropeptide Y homolog, strongly correlates with food-odor attractiveness. Hunger elevates neural and behavioral responses to food odors only, although food odors that elicit attraction in the fed state also evoke heightened dNPF activity in fed flies. Inactivation of a subset of dNPF-expressing neurons or silencing dNPF receptors abolishes food-odor attractiveness, whereas genetically enhanced dNPF activity not only increases food-odor attractiveness but promotes attraction to aversive odors. Varying the amount of presented odor produces matching graded neural and behavioral curves, which can function to predict preference between odors. We thus demonstrate a possible motivationally scaled neural “value signal” accessible from uniquely identifiable cells.
doi:10.1523/JNEUROSCI.2605-13.2013
PMCID: PMC3787495  PMID: 24089477
9.  Curcumin suppresses tumor necrosis factor-α-induced matrix metalloproteinase-2 expression and activity in rat vascular smooth muscle cells via the NF-κB pathway 
The aim of the present study was to investigate the inhibitory effect of curcumin on tumor necrosis factor (TNF)-α-induced cell migration and matrix metalloproteinase (MMP)-2 expression and activity in rat vascular smooth muscle cells (VSMCs), in order to identify whether the effects are mediated by the nuclear factor (NF)-κB signaling pathway. The VSMCs cells were pretreated with curcumin prior to stimulation with TNF-α. Reverse transcription-polymerase chain reaction and western blot analysis were used to determine the MMP-2 mRNA and protein expression levels in TNF-α-stimulated VSMCs. Activity levels of MMP-2 were measured using a gelatin zymography assay. Intracellular reactive oxygen species (ROS) generation was also analyzed. Curcumin was found to suppress the TNF-α-stimulated migration of VSMCs. In addition, curcumin inhibited the TNF-α-induced induction of MMP-2 activity and expression. Curcumin also decreased ROS generation in TNF-α-stimulated VSMCs. Signal transduction experiments indicated that TNF-α-induced MMP-2 expression in VSMCs was partly reversed with the application of an NF-κB inhibitor (BAY11-7082). In addition, western blot analysis revealed that curcumin reduced NF-κB p65 protein expression in TNF-α-stimulated VSMCs at the concentration of 20 and 40 μM. Therefore, these observations indicated that curcumin suppressed TNF-α-stimulated VSMC migration and partially prevented TNF-α-induced MMP-2 expression and activity in VSMCs via the NF-κB pathway.
doi:10.3892/etm.2014.1647
PMCID: PMC4043596  PMID: 24926361
curcumin; tumor necrosis factor-α; nuclear factor-κB; matrix metalloproteinase-2
10.  Draft genome sequence of Bacillus amyloliquefaciens HB-26 
Standards in Genomic Sciences  2014;9(3):775-782.
Bacillus amyloliquefaciens HB-26, a Gram-positive bacterium was isolated from soil in China. SDS-PAGE analysis showed this strain secreted six major protein bands of 65, 60, 55, 34, 25 and 20 kDa. A bioassay of this strain reveals that it shows specific activity against P. brassicae and nematode. Here we describe the features of this organism, together with the draft genome sequence and annotation. The 3,989,358 bp long genome (39 contigs) contains 4,001 protein-coding genes and 80 RNA genes.
doi:10.4056/sigs.4978673
PMCID: PMC4149015  PMID: 25197462
Bacillus amyloliquefaciens HB-26; The Next-Generation sequencing; Plasmodiophora brassicae
11.  Anticipation, anti-glaucoma drug treatment response and phenotype of a Chinese family with glaucoma caused by the Pro370Leu myocilin mutation 
AIM
To describe the anticipation and anti-glaucoma drugs response of a Chinese family with juvenile-onset open angle glaucoma (JOAG) caused by the Pro370Leu myocilin (MYOC) mutation.
METHODS
Fifteen members of a three-generation Chinese family with JOAG were recruited to this study. They all underwent ophthalmic common examinations. Patients suspected to have JOAG got an assessment of visual field and optical coherence tomography. Intraocular pressures (IOPs) of four patients were measured at 8, 10, 12, 14, 17 o'clock respectively after using anti-glaucoma drugs. Mutation screening of all MYOC gene coding exons of the participants was performed by using direct sequencing of PCR products.
RESULTS
Clinical examinations and pedigree analysis revealed eight family members were suffered from JOAG. Apparent genetics anticipation phenomenon was observed in this family. Their clinical features included elevated IOP of 35-55mmHg, loss of visual field, thinning of retinal nerve fiber layer, and glaucomatous optic disc damage. Noticeably, their intraocular pressure levels could be controlled within normal range at 8 and 10 o'clock by anti-glaucoma drugs, but their IOPs would elevate >21mmHg after 12 o'clock. Seven patients received trabeculectomy produced thin-walled, pale, and saccate filtering blebs maintaining lower intraocular pressure efficiently. Mutation screening indentified a heterozygous C→T missense mutation in the MYOC gene at position 1 109 in exon 3, corresponding to a substitution of a highly conserved proline to leucine at codon 370 in the olfactomedin domain of MYOC.
CONCLUSION
The clinical characteristics of JOAG in this family were 1) genetics anticipation; 2) high IOP; 3) temporay response to anti-glaucoma drugs; 4) filtering surgery produced thin-walled and saccate filtering blebs, helping maintain lower IOP.
doi:10.3980/j.issn.2222-3959.2014.01.08
PMCID: PMC3949457  PMID: 24634862
phenotype; anticipation; anti-glaucoma drugs; myocilin
12.  The effect of ROCK-1 activity change on the adhesive and invasive ability of Y79 retinoblastoma cells 
BMC Cancer  2014;14:89.
Background
Retinoblastoma (Rb) is the most common intraocular tumor in childhood worldwide. It is a deadly pediatric eye cancer. The main cause of death in Rb patients is intracranial and systemic metastasis. ROCK is the main downstream effector of Ras-homologous (Rho) family of GTPases which are involved in many cellular functions, such as cell proliferation, invasion and metastasis. Overexpression of ROCK promotes invasion and metastasis of many solid tumors. However, the effect of ROCK in Rb is largely unknown.
Methods
ROCK-1 and ROCK-2 mRNA expression in Y79 cell lines were examined by RT-PCR. Protein expression in the Y79 cell line were examined by western blot analyses. ROCK-1 and ROCK-2 siRNA were transfected into Y79 cells with Lipofectamine 2000. Cell proliferation was evaluated by CCK-8 assay after exposure to ROCK inhibitor (Y-27632). We examined the effect of ROCK inhibitors (Y-27632, ROCK-1 and ROCK-2 siRNA) on Y79 cell adhesive capacity by cell adhesion assay. Cell invasion assay through matrigel was used to study the effect of ROCK inhibitors on Y79 cell invasive capacity.
Results
The expression of mRNA of ROCK-1 was more than that of ROCK-2 in the Y79 cell line. The protein expression levels of ROCK-1 and ROCK-2 were downregulated in the cells transfected with siRNA. Y-27632 treatment didn’t lead to any changes of Y79 cells proliferation. Adhesive ability of Y79 cells was enhanced following Y-27632 or ROCK-1 siRNA treatment. The invasive capacity of Y79 cells showed an inverse relationship with increasing Y-27632 concentration. Invasiveness of Y79 cells also decreased in Y79 cells transfected with ROCK-1 siRNA. However, there was no change in adhesive ability or invasive capacity in Y79 cells transfected with siRNA against ROCK-2.
Conclusions
The findings of this study demonstrate that ROCK-1 protein plays a key role in regulating metastasis and invasion of Y79 cells, suggesting that the ROCK-1 dependent pathway may be a potential target for therapy of Rb.
doi:10.1186/1471-2407-14-89
PMCID: PMC3931292  PMID: 24528629
Adhesion; Invasion; Retinoblastoma; ROCK
13.  Neurochemical phenotype and function of endomorphin 2-immunopositive neurons in the myenteric plexus of the rat colon 
The distribution and activity of endomorphins (EMs), which are endogenous μ-opioid receptor (MOR) ligands in the gastrointestinal tract (GI), are yet to be elucidated. The current study aimed to shed light on this topic. EM2 was expressed in the enteric neurons in the myenteric plexus of the mid-colon. Of the EM2-immunoreactive (EM2-IR) neurons, 53 ± 4.6%, 26 ± 4.5%, 26 ± 2.8% and 49 ± 4.2% displayed immunopositive staining for choline acetyl transferase (ChAT), substance P (SP), vasoactive intestinal peptide (VIP) and nitric oxide synthetase (NOS), respectively. A bath application of EM2 (2 μM) enhanced spontaneous contractile amplitude and tension, which were reversed by β-FNA (an antagonist of MOR) but not NG-nitro-L-arginine methyl ether (L-NAME, a non-selective inhibitor of NOS) or VIP6-28 (an antagonist of the VIP receptor) in the colonic strips. EM2 significantly suppressed inhibitory junction potentials (IJPs) in 14 of the 17 examined circular muscle cells, and this effect was not antagonized by preincubation in L-NAME. EM2 was widely expressed in interneurons and motor neurons in the myenteric plexus and presynaptically inhibited fast IJPs, thereby enhancing spontaneous contraction and tension in the colonic smooth muscle.
doi:10.3389/fnana.2014.00149
PMCID: PMC4267282  PMID: 25565974
endomorphin-2; myenteric plexus; μ-opioid receptor; inhibitory neuromuscular transmission; colonic motility
14.  Fluorous Metal-Organic Frameworks with Enhanced Stability and High H2/CO2 Storage Capacities 
Scientific Reports  2013;3:3312.
A new class of metal-organic frameworks (MOFs) has been synthesized by ligand-functionalization strategy. Systematic studies of their adsorption properties were performed at low and high pressure. Importantly, when fluorine was introduced into the framework via the functionalization, both the framework stabilities and adsorption capacities towards H2/CO2 were enhanced significantly. This consequence can be well interpreted by theoretical studies of these MOFs structures. In addition, one of these MOFs TKL-107 was used to fabricate mixed matrix membranes, which exhibit great potential for the application of CO2 separation.
doi:10.1038/srep03312
PMCID: PMC3837364  PMID: 24264725
15.  Clinical Significance of the Genetic Landscape of Pancreatic Cancer and Implications for Identification of Potential Long Term Survivors 
Purpose
Genetic alterations of KRAS, CDKN2A, TP53 and SMAD4 are the most frequent events in pancreatic cancer. We determined the extent to which these four alterations are coexistent in the same carcinoma, and their impact on patient outcome.
Experimental Design
Pancreatic cancer patients who underwent an autopsy were studied (n=79). Matched primary and metastasis tissues were evaluated for intragenic mutations in KRAS, CDKN2A and TP53 and immunolabeled for CDKN2A, TP53 and SMAD4 protein products. The number of altered driver genes in each carcinoma was correlated to clinicopathologic features. Kaplan-Meier estimates were used to determine median disease free and overall survival, and a Cox proportional hazards model used to compare risk factors.
Results
The number of genetically altered driver genes in a carcinoma was variable, with only 29 patients (37%) having an alteration in all four genes analyzed. The number of altered driver genes was significantly correlated with disease free survival (p=0.008), overall survival (p=0.041) and metastatic burden at autopsy (p=0.002). On multivariate analysis, the number of driver gene alterations in a pancreatic carcinoma remained independently associated with overall survival (p=0.046). Carcinomas with only one to two driver alterations were enriched for those patients with the longest survival (median 23 months, range 1–53).
Conclusions
Determinations of the status of the four major driver genes in pancreatic cancer, and specifically the extent to which they are coexistent in an individual patients cancer, provides distinct information regarding disease progression and survival that is independent of clinical stage and treatment status.
doi:10.1158/1078-0432.CCR-12-1215
PMCID: PMC3500447  PMID: 22991414
16.  Evaluation of a partial optic nerve crush model in rats 
This study was performed to determine whether a partial optic nerve crush (PONC) model in rats is effective and reliable for the study of optic nerve protection and regeneration. Bilateral superior colliculus (SC) retrograde 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate (DiI) labeling of retinal ganglion cells (RGCs; n=3) and unilateral SC retrograde labeling of RGCs (n=3) were performed in adult Sprague-Dawley (SD) rats and the results were compared with the bilateral and unilateral SC retrograde-labeled RGCs. Another 40 adult SD rats, three days after bilateral SC retrograde DiI labeling of RGCs underwent crushing with a non-invasive vascular clip (40 gram power) 1 mm behind the right optic nerve head for 5, 10 and 30 sec (n=10 each), and a sham-operated control group (n=10) was used as a control. The retinas of all 40 rats were flattened by four radial cuts, mounted vitreal side-up on gelatin-coated slides, and the number of labeled RGCs was counted in four distinct regions per retinal quadrant at three different eccentricities of 1/6, 3/6 and 5/6 of the retinal radius three days later. Bilateral SC retrograde DiI injection labeled the majority of normal RGCs, while unilateral SC injections only labeled a small part of the RGCs; the majority of RGCs were not labeled. In the mild crush (5 sec) injury group, the bilateral SC retrograde DiI injection labeled the majority of RGCs. The RGC densities at 1/6, 3/6 and 5/6 of the retinal radius showed no significant difference compared with the RGC densities at the corresponding region of the retinal radius in the sham-operated control group (P=0.734, 0.461, 0.273, respectively). In the moderate crush injury (10 sec) group, the number of labeled RGCs was significantly lower compared to that of the sham-operated control group, and the RGC densities at 1/6, 3/6, 5/6 of the retinal radius were significantly lower compared to the RGC densities at the corresponding retinal radius in the sham-operated control group (P<0.001). In the severe crush injury (30 sec) group the number of labeled RGCs was significantly decreased, and the labeled RGCs were not observed in the region at 5/6 of the retinal radius. The RGC densities at 1/6 and 3/6 of the retinal radius were significantly lower compared to the RGC densities at the corresponding retinal radius region in the sham-operated control group (P<0.001). Compared with the mild and severe optic nerve crush injury models, the moderate crush injury model is more suitable for the study of optic nerve damage and regeneration.
doi:10.3892/etm.2012.619
PMCID: PMC3503534  PMID: 23181107
optic nerve; partial crush injury model; retinal ganglion cells
17.  MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples 
Bioinformatics  2013;29(20):2529-2538.
Motivation: High-throughput sequencing of mRNA (RNA-Seq) has led to tremendous improvements in the detection of expressed genes and reconstruction of RNA transcripts. However, the extensive dynamic range of gene expression, technical limitations and biases, as well as the observed complexity of the transcriptional landscape, pose profound computational challenges for transcriptome reconstruction.
Results: We present the novel framework MITIE (Mixed Integer Transcript IdEntification) for simultaneous transcript reconstruction and quantification. We define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data and show how to find the optimal solution using Mixed Integer Programming. MITIE can (i) take advantage of known transcripts, (ii) reconstruct and quantify transcripts simultaneously in multiple samples, and (iii) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction. We present an extensive study based on realistic simulated RNA-Seq data. When compared with state-of-the-art approaches, MITIE proves to be significantly more sensitive and overall more accurate. Moreover, MITIE yields substantial performance gains when used with multiple samples. We applied our system to 38 Drosophila melanogaster modENCODE RNA-Seq libraries and estimated the sensitivity of reconstructing omitted transcript annotations and the specificity with respect to annotated transcripts. Our results corroborate that a well-motivated objective paired with appropriate optimization techniques lead to significant improvements over the state-of-the-art in transcriptome reconstruction.
Availability: MITIE is implemented in C++ and is available from http://bioweb.me/mitie under the GPL license.
Contact: Jonas_Behr@web.de and raetsch@cbio.mskcc.org
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btt442
PMCID: PMC3789545  PMID: 23980025
18.  Transcriptome/Degradome-Wide Identification of R. glutinosa miRNAs and Their Targets: The Role of miRNA Activity in the Replanting Disease 
PLoS ONE  2013;8(7):e68531.
Rehmannia glutinosa, a traditional Chinese medicine herb, is unable to grow normally in a soil where the same species has recently been cultivated. The biological basis of this so called “replanting disease” is unknown, but it may involve the action of microRNAs (miRNAs), which are known to be important regulators of plant growth and development. High throughput Solexa/Illumina sequencing was used to generate a transcript library of the R. glutinosa transcriptome and degradome in order to identify possible miRNAs and their targets implicated in the replanting disease. A total of 87,665 unigenes and 589 miRNA families (17 of which have not been identified in plants to date) was identified from the libraries made from a first year (FP) and a second year (SP) crop. A comparison between the FP and SP miRNAs showed that the abundance of eight of the novel and 295 of the known miRNA families differed between the FP and SP plants. Sequencing of the degradome sampled from FP and SP plants led to the identification of 165 transcript targets of 85 of the differentially abundant miRNA families. The interaction of some of these miRNAs with their target(s) is likely to form an important part of the molecular basis of the replanting disease of R. glutinosa.
doi:10.1371/journal.pone.0068531
PMCID: PMC3702588  PMID: 23861915
19.  Thrombin promotes epithelial ovarian cancer cell invasion by inducing epithelial-mesenchymal transition 
Journal of Gynecologic Oncology  2013;24(3):265-272.
Objective
Over-expression of thrombin in ovarian cancer cells is associated with poor prognosis. In this study, we investigated the role of thrombin in inducing epithelial-mesenchymal transition (EMT) in SKOV3 epithelial ovarian cancer cells.
Methods
After thrombin treatment SKOV3 cells were subjected to western blots, reverse-transcription PCR, and enzyme-linked immunosorbent assay to quantify EMT-related proteins, mRNA expression of SMAD2, DKK1, and sFRP1, and the secretion of matrix metalloproteinases (MMPs) and cytokines. Meanwhile, invasion ability was evaluated using transwell assays.
Results
The results indicated a dose- and time-dependent down-regulation of E-cadherin and upregulation of N-cadherin and vimentin in thrombin-treated SKOV3 cells, compared with the thrombin-free control group (p<0.05). There was a dose- and time-dependent increase in the levels of SMAD2 and DKK1 mRNAs and a decrease in the levels of sFRP1 mRNA in thrombin-treated SKOV3 cells compared to control cells (p<0.05). Thrombin-treated SKOV3 cells exhibited increased secretion of MMP-9, MMP-2, interleukin (IL)-8, and IL-6 and increased invasion compared to untreated cells (p<0.05). Thrombin altered the morphology of SKOV3 cells to a spindle-like phenotype. Addition of hirudin to thrombin-treated cells reversed the effects of thrombin.
Conclusion
Thrombin induced EMT and promoted the invasion of SKOV3 cells, possibly via distinct signaling pathways. Hirudin inhibited the effects of thrombin, suggesting that anticoagulant therapy could be a novel therapeutic strategy for ovarian carcinoma.
doi:10.3802/jgo.2013.24.3.265
PMCID: PMC3714465  PMID: 23875077
Epithelial-mesenchymal transition; Epithelial ovarian cancer; Invasion; Thrombin
20.  Ahmed valve implantation for neovascular glaucoma after 23-gauge vitrectomy in eyes with proliferative diabetic retinopathy 
AIM
To report on the outcome of Ahmed glaucoma valve (AGV) implantation for the management of neovascular glaucoma (NVG) after 23-gauge vitrectomy for proliferative diabetic retinopathy (PDR).
METHODS
Twelve medically uncontrolled NVG with earlier 23-gauge vitrectomy for PDR underwent AGV implantation. The control of intraocular pressure (IOP), preoperative and postoperative best-corrected visual acuity, the development of intraoperative and postoperative complications were evaluated during the follow-up.
RESULTS
The mean follow-up was 15.4±4.3 months (9-23 months). Mean preoperative IOP was 49.4±5.1mmHg and mean postoperative IOP at the last visit was 17.5±1.6mmHg. The control of IOP was achieved at the final follow-up visits in all patients, however, 8 of 12 patients still needed anti-glaucoma medication (mean number of medications, 0.8±0.7). The visual acuity improved in nine eyes, and the visual acuity unchanged in three eyes at the final follow-up visits. The complications that occurred were minor hyphema in three eyes, choroid detachment in two eyes, and the minor hyphema and choroid detachments were reabsorbed without any surgical intervention.
CONCLUSION
AGV implantation is a safe and effective procedure that enables successful IOP control and vision preservation in the NVG patients with the history of earlier 23-gauge vitrectomy for PDR.
doi:10.3980/j.issn.2222-3959.2013.03.11
PMCID: PMC3693012  PMID: 23826525
Ahmed glaucoma valve implantation; neovascular glaucoma; proliferative diabetic retinopathy; 23-gauge vitrectomy
21.  Digital sorting of complex tissues for cell type-specific gene expression profiles 
BMC Bioinformatics  2013;14:89.
Background
Cellular heterogeneity is present in almost all gene expression profiles. However, transcriptome analysis of tissue specimens often ignores the cellular heterogeneity present in these samples. Standard deconvolution algorithms require prior knowledge of the cell type frequencies within a tissue or their in vitro expression profiles. Furthermore, these algorithms tend to report biased estimations.
Results
Here, we describe a Digital Sorting Algorithm (DSA) for extracting cell-type specific gene expression profiles from mixed tissue samples that is unbiased and does not require prior knowledge of cell type frequencies.
Conclusions
The results suggest that DSA is a specific and sensitivity algorithm in gene expression profile deconvolution and will be useful in studying individual cell types of complex tissues.
doi:10.1186/1471-2105-14-89
PMCID: PMC3626856  PMID: 23497278
22.  Catalytic activity of nanostructured Au: Scale effects versus bimetallic/bifunctional effects in low-temperature CO oxidation on nanoporous Au 
Summary
The catalytic properties of nanostructured Au and their physical origin were investigated by using the low-temperature CO oxidation as a test reaction. In order to distinguish between structural effects (structure–activity correlations) and bimetallic/bifunctional effects, unsupported nanoporous gold (NPG) samples prepared from different Au alloys (AuAg, AuCu) by selective leaching of a less noble metal (Ag, Cu) were employed, whose structure (surface area, ligament size) as well as their residual amount of the second metal were systematically varied by applying different potentials for dealloying. The structural and chemical properties before and after 1000 min reaction were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The catalytic behavior was evaluated by kinetic measurements in a conventional microreactor and by dynamic measurements in a temporal analysis of products (TAP) reactor. The data reveal a clear influence of the surface contents of residual Ag and Cu species on both O2 activation and catalytic activity, while correlations between activity and structural parameters such as surface area or ligament/crystallite size are less evident. Consequences for the mechanistic understanding and the role of the nanostructure in these NPG catalysts are discussed.
doi:10.3762/bjnano.4.13
PMCID: PMC3596058  PMID: 23503603
AuAg alloy; AuCu alloy; CO oxidation; dynamic studies; kinetics; nanoporous Au (NPG) catalyst; oxygen storage capacity (OSC); temporal analysis of products (TAP)
23.  Effect of Y-27632 on the cultured retinal neurocytes of rats 
AIM
To investigate the effect of Y-27632 on the survival and neurite outgrowth of the cultured retinal neurocytes.
METHODS
After the postnatal day 2-3, Sprague-Dawley retinal neurocytes were cultured for 48 hours, the culture media was replaced with serum-free media (control group) and serum-free media contained 30µmol/L Y-27632 (Y-27632 group), and the cells were continually cultured another 48 hours. The cultured retinal neurocytes were identified with anti-neuron specific enolase (NSE) immunocytochemistry. The survival state of those cells was estimated by MTT assay, and the neurite outgrowth of those cells was evaluated by the computerized image-analysis system.
RESULTS
Compared with the control group, the absorbance values of cells survival in Y-27632 group increased 12.90% and 33.33% respectively after 72 and 96 hours culture. Y-27632 had no significant effect on the diameter of cultured retinal neurocytes. Compared with the control group, Y-27632 induced a stable improvement of neurite outgrowth of retinal neurocytes after 72 and 96 hours culture (P=0.001).
CONCLUSION
Y-27632 could promote the survival and neurite outgrowth of the early postnatal cultured retinal neurocytes.
doi:10.3980/j.issn.2222-3959.2013.01.03
PMCID: PMC3580242  PMID: 23550221
Y-27632; retinal neurocytes; cell culture; neurites
24.  Small Cell and Large Cell Neuroendocrine Carcinomas of the Pancreas Are Genetically Similar and Distinct from Well-differentiated Pancreatic Neuroendocrine Tumors 
Poorly differentiated neuroendocrine carcinomas (NEC) of the pancreas are rare malignant neoplasms with a poor prognosis. The aim of this study was to determine the clinicopathologic and genetic features of poorly differentiated NECs and compare them to other types of pancreatic neoplasms. We investigated alterations of KRAS, CDKN2A/p16, TP53, SMAD4/DPC4, DAXX, ATRX, PTEN, Bcl2 and RB1 by immunohistochemistry and/or targeted exomic sequencing in surgically resected specimens of nine small cell NEC, 10 large cell NECs and 11 well-differentiated neuroendocrine tumors (PanNETs) of the pancreas. Abnormal immunolabeling patterns of p53 and Rb were frequent (p53, 18 of 19, 95%; Rb, 14 of 19, 74%) in both small cell and large cell NEC, whereas Smad4/Dpc4, DAXX and ATRX labeling were intact in virtually all of these same carcinomas. Abnormal immunolabeling of p53 and Rb proteins correlated with intragenic mutations in the TP53 and RB1 genes. By contrast, DAXX and ATRX was lost in 45% of PanNETs whereas p53 and Rb immunolabeling was intact in these same cases. Overexpression of Bcl-2 protein was observed in all nine small cell NECs (100%) and in five of 10 (50%) large cell NECs compared to only two of 11 (18%) PanNETs. Bcl-2 overexpression was significantly correlated with higher mitotic rate and Ki-67 labeling index in neoplasms in which it was present. Small cell NECs are genetically similar to large cell NECs, and these genetic changes are distinct from those reported in PanNETs. The finding of Bcl-2 overexpression in poorly differentiated NECs, particularly small cell NEC, suggests that Bcl-2 antagonists/inhibitors may be a viable treatment option for these patients.
doi:10.1097/PAS.0b013e3182417d36
PMCID: PMC3261427  PMID: 22251937
25.  Complete Genome Sequence of a Rabies Virus Isolate from Cattle in Guangxi, Southern China 
Genome Announcements  2013;1(1):e00137-12.
A street rabies virus (RV) isolate, GXHXN, was obtained from brain tissue of rabid cattle in the Guangxi Zhuang Autonomous Region of China in 2009. GXHXN is the first isolate from cattle in China with its entire genome sequenced and is closely related to BJ2011E from horse in Beijing, WH11 from donkey in the Hubei Province, and isolates from dogs in the Guangxi and Fujian Provinces, with homologies of 97.6% to 99.6%. It is more distantly related to isolates from domestic cat, pig, Chinese ferret badger, and vaccine strains, with homologies of 83.1% to 88.0%.
doi:10.1128/genomeA.00137-12
PMCID: PMC3569373  PMID: 23405368

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