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1.  Elevated C1orf63 expression is correlated with CDK10 and predicts better outcome for advanced breast cancers: a retrospective study 
BMC Cancer  2015;15:548.
Background
Chromosome 1 open reading frame 63 (C1orf63) is located on the distal short arm of chromosome 1, whose allelic loss has been observed in several human cancers. C1orf63 has been reported to be up-regulated in IL-2-starved T lymphocytes, which suggests it might be involved in cell cycle control, a common mechanism for carcinogenesis. Here we investigated the expression and clinical implication of C1orf63 in breast cancer.
Methods
Paraffin-embedded specimens, clinicopathological features and follow-up data of the breast cancer patients were collected. Publicly available microarray and RNA-seq datasets used in this study were downloaded from ArrayExpress of EBI and GEO of NCBI. KM plotter tool was also adopted. The expression of C1orf63 and CDK10, one known cell cycle-dependent tumor suppressor in breast cancer, was assessed by immunohistochemistry. Western blotting was performed to detect C1orf63 protein in human breast cancer cell lines, purchased from the Culture Collection of the Chinese Academy of Sciences, Shanghai.
Results
In a group of 12 human breast tumors and their matched adjacent non-cancerous tissues, C1orf63 expression was observed in 7 of the 12 breast tumors, but not in the 12 adjacent non-cancerous tissues (P < 0.001). Similar results were observed of C1orf63 mRNA expression both in breast cancer and several other cancers, including lung cancer, prostate cancer and hepatocellular carcinoma. In another group of 182 breast cancer patients, C1orf63 expression in tumors was not correlated with any clinicopathological features collected in this study. Survival analyses showed that there was no significant difference of overall survival (OS) rates between the C1orf63 (+) group and the C1orf63 (−) group (P = 0.145). However, the analyses of KM plotter displayed a valid relationship between C1orf63 and RFS (relapse free survival)/OS (P < 0.001; P = 0.007). Notablely, in breast cancers with advanced TNM stages (III ~ IV) among these 182 patients, C1orf63 expression was an independent prognostic factor predicting better clinical outcome (HR: 0.41; 95 % CI: 0.17 ~ 0.97; P = 0.042). Additionally, we found that CDK10 mRNA expression was positively correlated with C1orf63, which was consistent with the relationship of protein expression between C1orf63 and CDK10 (rs = 0.391; P < 0.001).
Conclusions
Compared to adjacent non-cancerous tissues, C1orf63 expression was elevated in tumor tissues. However, C1orf63 predicts better prognosis for breast cancers with advanced TNM stage, and the underlying mechanism is unknown. In addition, C1orf63 is correlated with the cell cycle related gene, CDK10.
doi:10.1186/s12885-015-1569-2
PMCID: PMC4513615  PMID: 26209438
C1orf63; CDK10; Overall survival; TNM stage
2.  The Relationship between Depression and Asthma: A Meta-Analysis of Prospective Studies 
PLoS ONE  2015;10(7):e0132424.
Background
Previous studies have suggested that asthmatic patients often have comorbid depression; however, temporal associations remain unclear.
Objectives
To determine whether depression predicts asthma and, conversely, whether asthma predicts depression.
Methods
A literature search was conducted without language restrictions using Pubmed, Embase, Cochrane and PsycINFO for studies published before January, 2015. Papers referenced by the obtained articles were also reviewed. Only comparative prospective studies with reported risk estimates of the association between depression and asthma were included. In order to investigate whether one of these conditions was predictive of the other, studies were excluded if enrolled participants had pre-existing depression or asthma. A random-effects model was used to calculate the pooled risk estimates for two outcomes: depression predicting asthma and asthma predicting depression.
Results
Seven citations, derived from 8 cohort studies, met our inclusion criteria. Of these, six studies reported that depression predicted incident adult-onset asthma, including 83684 participants and 2334 incident cases followed for 8 to 20 years. Conversely, two studies reported that asthma predicted incident depression. These studies involved 25566 participants and 2655 incident cases followed for 10 and 20 years, respectively. The pooled adjusted relative risks (RRs) of acquiring asthma associated with baseline depression was 1.43 (95% CI, 1.28–1.61) (P<0.001). The adjusted RRs for acquiring depression associated with baseline asthma was 1.23 (95% CI, 0.72–2.10) (P = 0.45).
Conclusions
Depression was associated with a 43% increased risk of developing adult-onset asthma. However, asthma did not increase the risk of depression based on limited studies. Further prospective studies ascertaining the true association between asthma and subsequent risk of depression are warranted.
doi:10.1371/journal.pone.0132424
PMCID: PMC4510436  PMID: 26197472
3.  The Murine Norovirus Core Subgenomic RNA Promoter Consists of a Stable Stem-Loop That Can Direct Accurate Initiation of RNA Synthesis 
Journal of Virology  2014;89(2):1218-1229.
ABSTRACT
All members of the Caliciviridae family of viruses produce a subgenomic RNA during infection. The subgenomic RNA typically encodes only the major and minor capsid proteins, but in murine norovirus (MNV), the subgenomic RNA also encodes the VF1 protein, which functions to suppress host innate immune responses. To date, the mechanism of norovirus subgenomic RNA synthesis has not been characterized. We have previously described the presence of an evolutionarily conserved RNA stem-loop structure on the negative-sense RNA, the complementary sequence of which codes for the viral RNA-dependent RNA polymerase (NS7). The conserved stem-loop is positioned 6 nucleotides 3′ of the start site of the subgenomic RNA in all caliciviruses. We demonstrate that the conserved stem-loop is essential for MNV viability. Mutant MNV RNAs with substitutions in the stem-loop replicated poorly until they accumulated mutations that revert to restore the stem-loop sequence and/or structure. The stem-loop sequence functions in a noncoding context, as it was possible to restore the replication of an MNV mutant by introducing an additional copy of the stem-loop between the NS7- and VP1-coding regions. Finally, in vitro biochemical data suggest that the stem-loop sequence is sufficient for the initiation of viral RNA synthesis by the recombinant MNV RNA-dependent RNA polymerase, confirming that the stem-loop forms the core of the norovirus subgenomic promoter.
IMPORTANCE Noroviruses are a significant cause of viral gastroenteritis, and it is important to understand the mechanism of norovirus RNA synthesis. Here we describe the identification of an RNA stem-loop structure that functions as the core of the norovirus subgenomic RNA promoter in cells and in vitro. This work provides new insights into the molecular mechanisms of norovirus RNA synthesis and the sequences that determine the recognition of viral RNA by the RNA-dependent RNA polymerase.
doi:10.1128/JVI.02432-14
PMCID: PMC4300638  PMID: 25392209
4.  Pathogenicity and Complete Genome Characterization of Fowl Adenoviruses Isolated from Chickens Associated with Inclusion Body Hepatitis and Hydropericardium Syndrome in China 
PLoS ONE  2015;10(7):e0133073.
In this study, we determined and genetically characterized three fowl adenoviruses isolated from chickens with inclusion body hepatitis (IBH) and hydropericardium syndrome (HPS) in China and assessed their pathogenicity. The full genome of HBQ12, BJH13 and JSJ13 was found to be 44,081, 43,966 and 43,756 nucleotides long, respectively. Sequence alignment and phylogenetic analysis revealed that strain HBQ12 and BJH13 were clustered together belonging to fowl adenoviruses D species and serotyped as FAdV-11, whereas strain JSJ13 was classified into fowl adenoviruses C species and serotyped as FAdV-4. To our knowledge, this is the first report of FAdV-4 strain circulating in China. The pathogenicity test showed that mortality for chickens infected with HBQ12 and JSJ13 within 21 days post infection (dpi) was 8.6% and 28.6%, respectively. Necropsy displayed mild or severe hepatitis and hydropericardium at 3 and 5 dpi as well as dead chickens. Viral DNA was detected in almost all tissues sampled from dead chickens. These results revealed that fowl adenovirus strains HBQ12 and JSJ13 are capable of causing IBH and HPS in chickens, indicating that preventive measures against FAdV infection on poultry farms should be implemented in China.
doi:10.1371/journal.pone.0133073
PMCID: PMC4500579  PMID: 26167857
5.  Toxoplasma gondii Pneumonia in an Immunocompetent Individual 
doi:10.1097/MAJ.0000000000000496
PMCID: PMC4495860  PMID: 26110745
Toxoplasma gondii; shortness of breath and fever; compound sulfamethoxazole; clindamycin phosphate
6.  Quantitative and qualitative analysis of the novel antitumor 1,3,4-oxadiazole derivative (GLB) and its metabolites using HPLC-UV and UPLC-QTOF-MS 
Scientific Reports  2015;5:11906.
Fructose-based 3-acetyl-2,3-dihydro-1,3,4-oxadiazole (GLB) is a novel antitumor agent and belongs to glycosylated spiro-heterocyclic oxadiazole scaffold derivative. This research first reported a simple, specific, sensitive and stable high performance liquid chromatography -ultraviolet detector (HPLC-UV) method for the quantitative determination of GLB in plasma. In this method, the chromatographic separation was achieved with a reversed phase C18 column. The calibration curve for GLB was linear at 300 nm. The lower limit of quantification was 10 ng/mL. The precision, accuracy and stability of the method were validated adequately. This method was successfully applied to the pharmacokinetic study in rats for detection of GLB after oral administration. Moreover, the structures of parent compound GLB and its two major metabolites M1 and M2 were identified in plasma using an ultra performance liquid chromatography- electrospray ionization-quadrupole-time of flight- mass spectrometry (UPLC-ESI-QTOF-MS) method. Our results indicated that the di-hydroxylation (M1) and hydroxylation (M2) of GLB are the major metabolites. In conclusion, the present study provided valuable information on an analytical method for the determination of GLB and its metabolites in rats, can be used to support further developing of this antitumor agent.
doi:10.1038/srep11906
PMCID: PMC4493701  PMID: 26148672
7.  Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD 
PLoS ONE  2015;10(7):e0130736.
The changes in the microbial community structure during acute exacerbations of severe chronic obstructive pulmonary disease (COPD) in hospitalized patients remain largely uncharacterized. Therefore, further studies focused on the temporal dynamics and structure of sputum microbial communities during acute exacerbation of COPD (AECOPD) would still be necessary. In our study, the use of molecular microbiological techniques provided insight into both fungal and bacterial diversities in AECOPD patients during hospitalization. In particular, we examined the structure and varieties of lung microbial community in 6 patients with severe AECOPD by amplifying 16S rRNA V4 hyper-variable and internal transcribed spacer (ITS) DNA regions using barcoded primers and the Illumina sequencing platform. Sequence analysis showed 261 bacterial genera representing 20 distinct phyla, with an average number of genera per patient of >157, indicating high diversity. Acinetobacter, Prevotella, Neisseria, Rothia, Lactobacillus, Leptotrichia, Streptococcus, Veillonella, and Actinomyces were the most commonly identified genera, and the average total sequencing number per sputum sample was >10000 18S ITS sequences. The fungal population was typically dominated by Candia, Phialosimplex, Aspergillus, Penicillium, Cladosporium and Eutypella. Our findings highlight that COPD patients have personalized structures and varieties in sputum microbial community during hospitalization periods.
doi:10.1371/journal.pone.0130736
PMCID: PMC4493005  PMID: 26147303
8.  Knockout of the adp gene related with colonization in Bacillus nematocida B16 using customized transcription activator-like effectors nucleases 
Microbial Biotechnology  2015;8(4):681-692.
Bacillus nematocida B16 is able to dominate in the intestines of the worm Caenorhabditis elegans in ‘Trojan horse’ pathogenic mechanism. The adp is one candidate gene which potentially play a vital role in the colonization from our previous random mutagenesis screening results. To analyse the functional role of this gene, we constructed the adp knockout mutant through customized transcription activator-like effectors nucleases (TALEN), which has been successfully used in yeasts, nematodes, zebrafish and human pluripotent cells. Here, we first time report this knockout method in bacteria on this paper. Bioassay experiments demonstrated that the adp knockout mutant of B16 showed considerably lower colonization activity, reduced numbers of intestines and less than 80% nematocidal activity compared with the wild-type strain when infected for 48 h. However, no obvious change on proteolytic activity was observed in the mutant. Conversely, the complementation of adp gene restored most of the above deficient phenotypes. These results indicated that the adp gene was involved in surface adhesion and played a comparatively important role in colonizing host nematodes. Moreover, TALENs successfully disrupt target genes in bacteria.
doi:10.1111/1751-7915.12282
PMCID: PMC4476823  PMID: 25912819
9.  Preparation of Graphene-Modified Acupuncture Needle and Its Application in Detecting Neurotransmitters 
Scientific Reports  2015;5:11627.
We report a unique nanosensing platform by combining modern nanotechnology with traditional acupuncture needle to prepare graphene-modified acupuncture needle (G-AN), and using it for sensitive detection of neurotransmitters via electrochemistry. An electrochemical deposition method was employed to deposit Au nanoparticles (AuNPs) on the tip surface of the traditional acupuncture needle, while the other part of the needle was coated with insulation paste. Subsequently, the G-AN was obtained by cyclic voltammetry reduction of a graphene oxide solution on the surface of the AuNPs. To investigate the sensing property of the G-AN, pH dependence was measured by recording the open circuit potential in the various pH buffer solutions ranging from 2.0 to 10.0. What’s more, the G-AN was further used for detection of dopamine (DA) with a limit of detection of 0.24 μM. This novel G-AN exhibited a good sensitivity and selectivity, and could realize direct detection of DA in human serum.
doi:10.1038/srep11627
PMCID: PMC4481527  PMID: 26112773
10.  Modular Isotopomer Synthesis of γ-Hydroxybutyric Acid for a Quantitative Analysis of Metabolic Fates 
ACS Chemical Biology  2014;9(8):1706-1711.
Herein we report a study combining metabolomics and mass isotopomer analysis used for investigation of the biochemical fate of γ-hydroxybutyric acid (GHB). Using various 13C incorporation labeling patterns into GHB, we have discovered that GHB is catabolized by previously unknown processes that include (i) direct β-oxidation to acetyl-CoA and glycolate, (ii) α-oxidation to 3-hydroxypropionyl-CoA and formate, and (iii) cleavage of C-4 to yield 3-hydroxypropionate and CO2. We further utilized the unique attributes of our labeling patterns and the resultant isotopomers to quantitate relative flux down the identified pathways.
doi:10.1021/cb500380b
PMCID: PMC4136706  PMID: 24933109
11.  CT imaging of ovarian yolk sac tumor with emphasis on differential diagnosis 
Scientific Reports  2015;5:11000.
Ovarian yolk sac tumors (YSTs) are rare neoplasms. No radiological study has been done to compare the imaging findings between this type of tumor and other ovarian tumors. Here we analyzed the CT findings of 11 pathologically proven ovarian YSTs and compared their imaging findings with 18 other types of ovarian tumors in the same age range. Patient age, tumor size, tumor shape, ascites and metastasis of two groups did not differ significantly (P > 0.05). A mixed solid-cystic nature, intratumoral hemorrhage, marked enhancement and dilated intratumoral vessel of two groups differed significantly (P < 0.05). The area under the ROC curve of four significant CT features was 0.679, 0.707, 0.705, and 1.000, respectively. Multivariate logistic regression analysis identified two independent signs of YST: intratumoral hemorrhage and marked enhancement. Our results show that certain suggestive CT signs that may be valuable for improving the accuracy of imaging diagnosis of YST and may be helpful in distinguishing YST from other ovarian tumors.
doi:10.1038/srep11000
PMCID: PMC4466583  PMID: 26074455
12.  Complex epilepsy phenotype extraction from narrative clinical discharge summaries 
Epilepsy is a common serious neurological disorder with a complex set of possible phenotypes ranging from pathologic abnormalities to variations in electroencephalogram. This paper presents a system called Phenotype Exaction in Epilepsy (PEEP) for extracting complex epilepsy phenotypes and their correlated anatomical locations from clinical discharge summaries, a primary data source for this purpose. PEEP generates candidate phenotype and anatomical location pairs by embedding a named entity recognition method, based on the Epilepsy and Seizure Ontology, into the National Library of Medicine's MetaMap program. Such candidate pairs are further processed using a correlation algorithm. The derived phenotypes and correlated locations have been used for cohort identification with an integrated ontology-driven visual query interface. To evaluate the performance of PEEP, 400 de-identified discharge summaries were used for development and an additional 262 were used as test data. PEEP achieved a micro-averaged precision of 0.924, recall of 0.931, and F1-measure of 0.927 for extracting epilepsy phenotypes. The performance on the extraction of correlated phenotypes and anatomical locations shows a micro-averaged F1-measure of 0.856 (Precision: 0.852, Recall: 0.859). The evaluation demonstrates that PEEP is an effective approach to extracting complex epilepsy phenotypes for cohort identification.
doi:10.1016/j.jbi.2014.06.006
PMCID: PMC4464795  PMID: 24973735
Epilepsy; Information Extraction; Cohort Identification
13.  Electrophysiological Signal Analysis and Visualization using Cloudwave for Epilepsy Clinical Research 
Epilepsy is the most common serious neurological disorder affecting 50–60 million persons worldwide. Electrophysiological data recordings, such as electroencephalogram (EEG), are the gold standard for diagnosis and pre-surgical evaluation in epilepsy patients. The increasing trend towards multi-center clinical studies require signal visualization and analysis tools to support real time interaction with signal data in a collaborative environment, which are cannot be supported by traditional desktop-based standalone applications. As part of the Prevention and Risk Identification of SUDEP Mortality (PRISM) project, we have developed a Web-based electrophysiology data visualization and analysis platform called Cloudwave using highly scalable open source cloud computing infrastructure. Cloudwave is integrated with the PRISM patient cohort identification tool called MEDCIS (Multi-modality Epilepsy Data Capture and Integration System). The Epilepsy and Seizure Ontology (EpSO) underpins both Cloudwave and MEDCIS to support query composition and result retrieval. Cloudwave is being used by clinicians and research staff at the University Hospital - Case Medical Center (UH-CMC) Epilepsy Monitoring Unit (EMU) and will be progressively deployed at four EMUs in the United States and the United Kingdom as part of the PRISM project.
PMCID: PMC4451213  PMID: 23920671
SUDEP; Electrophysiological signal analysis; EEG monitoring; EEG Signal analysis; Multi-modal seizure data; EDF; Epileptic events; Epilepsy and Seizure ontology
14.  Comparative analysis of a novel disease phenotype network based on clinical manifestations 
Systems approaches to analyzing disease phenotype networks in combination with protein functional interaction networks have great potential in illuminating disease pathophysiological mechanisms. While many genetic networks are readily available, disease phenotype networks remain largely incomplete. In this study, we built a large-scale Disease Manifestation Network (DMN) from 50,543 highly accurate disease-manifestation semantic relationships in the United Medical Language System (UMLS). Our new phenotype network contains 2305 nodes and 373,527 weighted edges to represent the disease phenotypic similarities. We first compared DMN with the networks representing genetic relationships among diseases, and demonstrated that the phenotype clustering in DMN reflects common disease genetics. Then we compared DMN with a widely-used disease phenotype network in previous gene discovery studies, called mimMiner, which was extracted from the textual descriptions in Online Mendelian Inheritance in Man (OMIM). We demonstrated that DMN contains different knowledge from the existing phenotype data source. Finally, a case study on Marfan syndrome further proved that DMN contains useful information and can provide leads to discover unknown disease causes. Integrating DMN in systems approaches with mimMiner and other data offers the opportunities to predict novel disease genetics. We made DMN publicly available at nlp/case.edu/public/data/DMN.
doi:10.1016/j.jbi.2014.09.007
PMCID: PMC4452018  PMID: 25277758
Ontology; Disease phenotype network; Network analysis
15.  Construction of a Quadruple Auxotrophic Mutant of an Industrial Polyploid Saccharomyces cerevisiae Strain by Using RNA-Guided Cas9 Nuclease 
Applied and Environmental Microbiology  2014;80(24):7694-7701.
Industrial polyploid yeast strains harbor numerous beneficial traits but suffer from a lack of available auxotrophic markers for genetic manipulation. Here we demonstrated a quick and efficient strategy to generate auxotrophic markers in industrial polyploid yeast strains with the RNA-guided Cas9 nuclease. We successfully constructed a quadruple auxotrophic mutant of a popular industrial polyploid yeast strain, Saccharomyces cerevisiae ATCC 4124, with ura3, trp1, leu2, and his3 auxotrophies through RNA-guided Cas9 nuclease. Even though multiple alleles of auxotrophic marker genes had to be disrupted simultaneously, we observed knockouts in up to 60% of the positive colonies after targeted gene disruption. In addition, growth-based spotting assays and fermentation experiments showed that the auxotrophic mutants inherited the beneficial traits of the parental strain, such as tolerance of major fermentation inhibitors and high temperature. Moreover, the auxotrophic mutants could be transformed with plasmids containing selection marker genes. These results indicate that precise gene disruptions based on the RNA-guided Cas9 nuclease now enable metabolic engineering of polyploid S. cerevisiae strains that have been widely used in the wine, beer, and fermentation industries.
doi:10.1128/AEM.02310-14
PMCID: PMC4249234  PMID: 25281382
16.  Different Dynamic Patterns of β-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity 
PLoS ONE  2015;10(5):e0126712.
The adverse impact of antibiotics on the gut microbiota has attracted extensive interest, particularly due to the development of microbiome research techniques in recent years. However, a direct comparison of the dynamic effects of various types of antibiotics using the same animal model has not been available. In the present study, we selected six antibiotics from four categories with the broadest clinical usage, namely, β-lactams (Ceftriaxone Sodium, Cefoperazone/Sulbactam and meropenem), quinolones (ofloxacin), glycopeptides (vancomycin), and macrolides (azithromycin), to treat BALB/c mice. Stool samples were collected during and after the administration of antibiotics, and microbial diversity was analyzed through Illumina sequencing and bioinformatics analyses using QIIME. Both α and β diversity analyses showed that ceftriaxone sodium, cefoperazone/sulbactam, meropenem and vancomycin changed the gut microbiota dramatically by the second day of antibiotic administration whereas the influence of ofloxacin was trivial. Azithromycin clearly changed the gut microbiota but much less than vancomycin and the β-lactams. In general, the community changes induced by the three β-lactam antibiotics showed consistency in inhibiting Papillibacter, Prevotella and Alistipes while inducing massive growth of Clostridium. The low diversity and high Clostridium level might be an important cause of Clostridium difficile infection after usage of β-lactams. Vancomycin was unique in that it inhibited Firmicutes, mainly the genus Clostridium. On the other hand, it induced the growth of Escherichia and effect lasted for months afterward. Azithromycin and meropenem induced the growth of Enterococcus. These findings will be useful for understanding the potential adverse effects of antibiotics on the gut microbiome and ensuring their better usage.
doi:10.1371/journal.pone.0126712
PMCID: PMC4430517  PMID: 25970622
17.  Glutathionylated 4-hydroxy-2-(E)-alkenal enantiomers in rat organs and its contributions towards the disposal of 4-hydroxy-2-(E)-nonenal in rat liver 
The major route for elimination of 4-hydroxy-2-(E)-nonenal (4-HNE) has long been considered to be through glutathionylation and eventual excretion as a mercapturic acid conjugate. To better quantitate the glutathionylation process, we developed a sensitive LC-MS/MS method for the detection of glutathione (GSH) conjugates of 4-hydroxy-2-(E)-alkenal enantiomers having carbon skeleton of C-5 to C-12. The newly developed method enabled us to quantify 4-hydroxy-2-(E)-alkenal-glutathione diastereomers in various organs, i.e. liver, heart and brain. We identified the addition of iodoacetic acid as a critical step during sample preparation to avoid an overestimation of glutathione-alkenal conjugation. Specifically, we found that in the absence of a quenching step reduced GSH and 4-hydroxy-2-(E)-alkenals react very rapidly during the extraction and concentration steps of sample preparation. Rat liver perfused with d11-4-hydroxy-2-(E)-nonenal (d11-4-HNE) revealed enantioselective conjugation with GSH and transportation out of the liver. In the d11-4-HNE perfused rat livers, the amount of d11-(S)-4-HNE-GSH released from the rat liver is higher than the d11-(R)-4-HNE-GSH, and more d11-(R)-4-HNE-GSH than d11-(S)-4-HNE-GSH remained in the perfused liver tissues. Overall, the glutathionylation pathway was found to account for only 8.7% of the disposition of 4-HNE, whereas catabolism to acetyl-CoA, propionyl-CoA, and formate represented the major detoxification pathway.
doi:10.1016/j.freeradbiomed.2014.02.008
PMCID: PMC4040968  PMID: 24556413
4-hydroxy-2-(E)-alkenal; 4-hydroxy-2-(E)-nonenal; rat organs; rat liver; LC-MS/MS; glutathione conjugate
18.  High-Density Lipoprotein Prevents Endoplasmic Reticulum Stress-Induced Downregulation of Liver LOX-1 Expression 
PLoS ONE  2015;10(4):e0124285.
Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a specific cell-surface receptor for oxidized-low-density lipoprotein (ox-LDL). The impact of high-density lipoprotein (HDL) on endoplasmic reticulum (ER) stress-mediated alteration of the LOX-1 level in hepatocytes remains unclear. We aimed to investigate the impact on LOX-1 expression by tunicamycin (TM)-induced ER stress and to determine the effect of HDL on TM-affected LOX-1 expression in hepatic L02 cells. Overexpression or silencing of related cellular genes was conducted in TM-treated cells. mRNA expression was evaluated using real-time polymerase chain reaction (PCR). Protein expression was analyzed by western blot and immunocytochemistry. Lipid uptake was examined by DiI-ox-LDL, followed by flow cytometric analysis. The results showed that TM induced the upregulation of ER chaperone GRP78, downregulation of LOX-1 expression, and lipid uptake. Knock down of IRE1 or XBP-1 effectively restored LOX-1 expression and improved lipid uptake in TM-treated cells. HDL treatment prevented the negative impact on LOX-1 expression and lipid uptake induced by TM. Additionally, 1–10 μg/mL HDL significantly reduced the GRP78, IRE1, and XBP-1 expression levels in TM-treated cells. Our findings reveal that HDL could prevent the TM-induced reduction of LOX-1 expression via inhibiting the IRE1/XBP-1 pathway, suggesting a new mechanism for beneficial roles of HDL in improving lipid metabolism.
doi:10.1371/journal.pone.0124285
PMCID: PMC4414515  PMID: 25923692
19.  A New Myco-Heterotrophic Genus, Yunorchis, and the Molecular Phylogenetic Relationships of the Tribe Calypsoeae (Epidendroideae, Orchidaceae) Inferred from Plastid and Nuclear DNA Sequences 
PLoS ONE  2015;10(4):e0123382.
We identified a new holomycotrophic orchid that is related to the myco-heterotrophic Calypsoeae. Because chloroplast genes are primarily lacking or are highly divergent, key morphological characters are either reduced or lost from many myco-heterotrophs, and the phylogenetic relationships of weakly supported paraphyletic Calypsoeae within Epidendroideae have been poorly understood in previous molecular systematic studies. Using chloroplast rbcL, psaB, and matK and nuclear Xdh and ITS sequences, we determined the circumscription and systematic positions of the new orchid and the tribe. The results indicate that the epidendroid taxa include most of the clades that are successively sister to the grade of clades representing previously recognized tribes. Calypsoeae comprising four well-supported clades with 12 genera (except for the previous temporarily placed Wullschlaegelia) is supported as a monophyletic and sister clade to Epidendreae (excluding Coeliinae). The new orchid is nested in Calypsoeae and is a sister to Dactylostalix and/or Calypso. This new holomycotrophic orchid presents a subumbel inflorescence that grows underground, and flower with a long pedicel reputing the ground to open and two fragments at the base of the hook, which are obviously morphologically different from those of Calypsoeae. To accommodate this species in the current generic circumscription, a new genus Yunorchis was created.
doi:10.1371/journal.pone.0123382
PMCID: PMC4406536  PMID: 25902264
20.  Prostatic arterial embolization for the treatment of lower urinary tract symptoms due to large (>80 mL) benign prostatic hyperplasia: results of midterm follow-up from Chinese population 
BMC Urology  2015;15:33.
Background
Currently, large prostate size (>80 mL) of benign prostatic hyperplasia (BPH) still pose technical challenges for surgical treatment. This prospective study was designed to explore the safety and efficacy of prostatic arterial embolization (PAE) as an alternative treatment for patients with lower urinary tract symptoms (LUTS) due to largeBPH.
Methods
A total of 117 patients with prostates >80 mL were included in the study; all were failure of medical treatment and unsuited for surgery. PAE was performed using combination of 50-μm and 100-μm particles in size, under local anaesthesia by a unilateral femoral approach. Clinical follow-up was performed using the international prostate symptoms score (IPSS), quality of life (QoL), peak urinary flow (Qmax), post-void residual volume (PVR), international index of erectile function short form (IIEF-5), prostatic specific antigen (PSA) and prostatic volume (PV) measured by magnetic resonance (MR) imaging, at 1, 3, 6 and every 6 months thereafter.
Results
The prostatic artery origins in this study population were different from previously published results. PAE was technically successful in 109 of 117 patients (93.2%). Follow-up data were available for the 105 patients with a mean follow-up of 24 months. The clinical improvements in IPSS, QoL, Qmax, PVR, and PV at 1, 3, 6, 12, and 24 months was 94.3%, 94.3%, 93.3%, 92.6%, and 91.7%, respectively. The mean IPSS (pre-PAE vs post-PAE 26.0 vs 9.0; P < .0.01), the mean QoL (5.0 vs 3.0; P < 0.01), the mean Qmax (8.5 vs 14.5; P < 0.01), the mean PVR (125.0 vs 40.0; P < 0.01), and PV (118.0 vs 69.0, with a mean reduction of 41.5%; P < 0.01 ) at 24-month after PAE were significantly different with respect to baseline. The mean IIEF-5 was not statistically different from baseline. No major complications were noted.
Conclusions
PAE is a safe and effective treatment method for patients with LUTS due to large volume BPH. PAE may play an important role in patients in whom medical therapy has failed, who are not candidates for open surgery or TURP or refuse any surgical treatment.
doi:10.1186/s12894-015-0026-5
PMCID: PMC4403829  PMID: 25887036
Angiography; Benign prostatic hyperplasia (BPH); Lower urinary tract symptoms (LUTS); Prostatic artery embolization (PAE)
21.  Gαq Protein Carboxyl Terminus Imitation Polypeptide GCIP-27 Improves Cardiac Function in Chronic Heart Failure Rats 
PLoS ONE  2015;10(3):e0121007.
Background
Gαq protein carboxyl terminus imitation polypeptide (GCIP)-27 has been shown to alleviate pathological cardiomyocyte hypertrophy induced by various factors. Pathological cardiac hypertrophy increases the morbidity and mortality of cardiovascular diseases while it compensates for poor heart function. This study was designed to investigate the effects of GCIP-27 on heart function in rats with heart failure induced by doxorubicin.
Methods and Results
Forty-eight rats were randomly divided into the following six groups receiving vehicle (control), doxorubicin (Dox), losartan (6 mg/kg, i.g.) and three doses of GCIP-27 (10, 30, 90 μg/kg; i.p., bid), respectively. Heart failure was induced by Dox, which was administered at a 20 mg/kg cumulative dose. After 10 weeks of treatment, we observed that GCIP-27 (30, 90 μg/kg) significantly increased ejection fraction, fraction shortening, stroke volume and sarcoplasmic reticulum Ca2+ ATPase activity of Dox-treated hearts. Additionally, GCIP-27 decreased myocardial injury, heart weight index and left ventricular weight index, fibrosis and serum cardiac troponin-I concentration in Dox-treated mice. Immunohistochemistry, western blotting and real-time PCR experiments indicated that GCIP-27 (10–90 μg/kg) could markedly upregulate the protein expression of myocardial α-myosin heavy chain (MHC), Bcl-2, protein kinase C (PKC) ε and phosphorylated extracellular signal-regulated kinase (p-ERK) 1/2 as well as the mRNA expression of α-MHC, but downregulated the expression of β-MHC, Bax and PKC βII, and the mRNA expression levels of β-MHC in Dox-treated mice. It was also found that GCIP-27 (30, 90 μg/L) decreased cell size and protein content of cardiomyocytes significantly in vitro by comparison of Dox group.
Conclusions
GCIP-27 could effectively ameliorate heart failure development induced by Dox. PKC–ERK1/2 signaling might represent the underlying mechanism of the beneficial effects of GCIP-27.
doi:10.1371/journal.pone.0121007
PMCID: PMC4379177  PMID: 25822412
23.  Prognostic Value of Classifying Parapharyngeal Extension in Nasopharyngeal Carcinoma Based on Magnetic Resonance Imaging 
BioMed Research International  2015;2015:749515.
Purpose. To subclassify parapharyngeal extension in nasopharyngeal carcinoma (NPC) and investigate its prognostic value and staging categories based on magnetic resonance imaging (MRI). Methods and Materials. Data from 1504 consecutive NPC patients treated with definitive-intent radiotherapy were analyzed retrospectively. Sites of parapharyngeal extension were defined by MRI. Overall survival (OS), local relapse-free survival (LRFS), and distant metastasis-free survival (DMFS) were calculated by the Kaplan-Meier method and compared with the log-rank test. Hazard consistency and hazard discrimination were determined by multivariate analysis with Cox proportional hazards models. Results. 1104 patients (73.4%) had parapharyngeal extension; 1.7–63.8% had involvement of various anatomic sites. The hazard ratio for death was significantly higher with extensive parapharyngeal extension (lateral pterygoid muscle of masticator space and beyond or parotid space) than with mild extension (medial pterygoid muscle of masticator space, or carotid, prestyloid, and prevertebral or retropharyngeal space). OS, LRFS, and DMFS with extensive parapharyngeal extension were similar to those in T4 disease; OS, LRFS, and DMFS with mild parapharyngeal extension were significantly higher than in those T3 disease (all P ≤ 0.015). Conclusions. Parapharyngeal extension in NPC should be subclassified as mild or extensive, which should be regarded as stages T2 and T4 diseases, respectively.
doi:10.1155/2015/749515
PMCID: PMC4391645  PMID: 25883973
24.  Design and Implementation of a Comprehensive Web-based Survey for Ovarian Cancer Survivorship with an Analysis of Prediagnosis Symptoms via Text Mining 
Cancer Informatics  2015;13(Suppl 3):113-123.
Ovarian cancer (OvCa) is the most lethal gynecologic disease in the United States, with an overall 5-year survival rate of 44.5%, about half of the 89.2% for all breast cancer patients. To identify factors that possibly contribute to the long-term survivorship of women with OvCa, we conducted a comprehensive online Ovarian Cancer Survivorship Survey from 2009 to 2013. This paper presents the design and implementation of our survey, introduces its resulting data source, the OVA-CRADLE™ (Clinical Research Analytics and Data Lifecycle Environment), and illustrates a sample application of the survey and data by an analysis of prediagnosis symptoms, using text mining and statistics. The OVA-CRADLE™ is an application of our patented Physio-MIMI technology, facilitating Web-based access, online query and exploration of data. The prediagnostic symptoms and association of early-stage OvCa diagnosis with endometriosis provide potentially important indicators for future studies in this field.
doi:10.4137/CIN.S14034
PMCID: PMC4373720  PMID: 25861211
survey; design; database; informatics; CRADLE™ (Clinical Research Analytics and Data Lifecycle Environment); early diagnosis; ovarian cancer; endometriosis; prediagnosis symptoms; text mining; correspondence analysis; (CART) Classification and Regression Tree; Random Forest
25.  Effect of oral melatonin and wearing earplugs and eye masks on nocturnal sleep in healthy subjects in a simulated intensive care unit environment: which might be a more promising strategy for ICU sleep deprivation? 
Critical Care  2015;19(1):124.
Introduction
Sleep deprivation is common in critically ill patients in the intensive care unit (ICU). Noise and light in the ICU and the reduction in plasma melatonin play the essential roles. The aim of this study was to determine the effect of simulated ICU noise and light on nocturnal sleep quality, and compare the effectiveness of melatonin and earplugs and eye masks on sleep quality in these conditions in healthy subjects.
Methods
This study was conducted in two parts. In part one, 40 healthy subjects slept under baseline night and simulated ICU noise and light (NL) by a cross-over design. In part two, 40 subjects were randomly assigned to four groups: NL, NL plus placebo (NLP), NL plus use of earplugs and eye masks (NLEE) and NL plus melatonin (NLM). 1 mg of oral melatonin or placebo was administered at 21:00 on four consecutive days in NLM and NLP. Earplugs and eye masks were made available in NLEE. The objective sleep quality was measured by polysomnography. Serum was analyzed for melatonin levels. Subjects rated their perceived sleep quality and anxiety levels.
Results
Subjects had shorter total sleep time (TST) and rapid eye movement (REM) sleep, longer sleep onset latency, more light sleep and awakening, poorer subjective sleep quality, higher anxiety level and lower serum melatonin level in NL night (P <0.05). NLEE had less awakenings and shorter sleep onset latency (P <0.05). NLM had longer TST and REM and shorter sleep onset latency (P <0.05). Compared with NLEE, NLM had fewer awakenings (P = 0.004). Both NLM and NLEE improved perceived sleep quality and anxiety level (P = 0.000), and NLM showed better than NLEE in perceived sleep quality (P = 0.01). Compared to baseline night, the serum melatonin levels were lower in NL night at every time point, and the average maximal serum melatonin concentration in NLM group was significantly greater than other groups (P <0.001).
Conclusions
Compared with earplugs and eye masks, melatonin improves sleep quality and serum melatonin levels better in healthy subjects exposed to simulated ICU noise and light.
Trial registration
Chinese Clinical Trial Registry ChiCTR-IPR-14005458. Registered 10 November 2014.
doi:10.1186/s13054-015-0842-8
PMCID: PMC4365553  PMID: 25887528

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