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1.  Cassava genome from a wild ancestor to cultivated varieties 
Nature Communications  2014;5:5110.
Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
Cassava is a major source of food in tropical and subtropical regions. Here the authors sequence the genomes of wild and domesticated cassava varieties and identify genes that have been selected for and against during the evolution and domestication of this economically important crop.
doi:10.1038/ncomms6110
PMCID: PMC4214410  PMID: 25300236
3.  Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data 
PLoS ONE  2014;9(6):e98855.
Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. Simulation study shows HighMap can create a linkage map with three times as many markers as ordering-only methods while offering more accurate marker orders and stable genetic distances. Using HighMap, we constructed a common carp linkage map with 10,004 markers. The singleton rate was less than one-ninth of that generated by JoinMap4.1. Its total map distance was 5,908 cM, consistent with reports on low-density maps. HighMap is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL studies. HighMap is available at http://highmap.biomarker.com.cn/.
doi:10.1371/journal.pone.0098855
PMCID: PMC4048240  PMID: 24905985
4.  Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx) 
Science (New York, N.Y.)  2009;326(5951):433-436.
A single–base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ∼16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.
doi:10.1126/science.1176620
PMCID: PMC3951477  PMID: 19713493
5.  Three-dimensional conformal radiotherapy with concurrent chemotherapy for postoperative recurrence of esophageal squamous cell carcinoma: clinical efficacy and failure pattern 
Background
To assess the therapeutic outcome and failure pattern of three-dimensional conformal radiotherapy (3D-CRT)-based concurrent chemoradiotherapy (CCRT) for recurrence of esophageal squamous cell carcinoma (SCC) after radical surgery.
Methods
Treatment outcome and failure pattern were retrospectively evaluated in 83 patients with localized cervical and thoracic recurrences after radical surgery for thoracic esophageal SCC. All patients were treated with 3DCRT-based CCRT (median radiation dose 60 Gy), in which 39 received concurrent cisplatin plus 5-fluorouracil (PF), and 44 received concurrent docetaxel plus cisplatin (TP). Treatment response was evaluated at 1–3 months after CCRT.
Results
With a median follow-up of 34 months (range, 2–116 months), the 3-year overall survival (OS) of all the patients was 51.8% and the median OS time was 43.0 months. The overall tumor response rate was 75.9% (63/83), with a complete remission (CR) rate of 44.6% (37/83). In univariate analysis, tumor response after CCRT (p = 0.000), recurrence site (p = 0.028) and concurrent chemotherapy (p = 0.090) showed a trend favoring better OS. Multivariate analysis revealed that tumor response after CCRT (p = 0.000) and concurrent chemotherapy (p = 0.010) were independent predictors of OS. Forty-seven patients had progressive diseases after CCRT, 27 had local failure (27/47, 57.4%), 18 had distant metastasis (18/47, 38.3%) and 2 had both local and distant failures (2/47, 4.3%).
Conclusions
3DCRT-based CCRT is effective in postoperatively recurrent esophageal SCC. Patients that obtained complete remission after CCRT appeared to achieve long-term OS and might benefit from concurrent TP regimen. Local and distant failures remained high and prospective studies are needed to validate these factors.
doi:10.1186/1748-717X-8-241
PMCID: PMC3816598  PMID: 24139225
Esophageal squamous cell carcinoma; Postoperative recurrence; Concurrent chemoradiotherapy
6.  Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data 
PLoS ONE  2013;8(8):e71152.
Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.
doi:10.1371/journal.pone.0071152
PMCID: PMC3743905  PMID: 23967161
7.  Epithelial Mesenchymal Transition Is Required for Acquisition of Anoikis Resistance and Metastatic Potential in Adenoid Cystic Carcinoma 
PLoS ONE  2012;7(12):e51549.
Human adenoid cystic carcinoma (ACC) is characterized by diffused invasion of the tumor into adjacent organs and early distant metastasis. Anoikis resistance and epithelial mesenchymal transition (EMT) are considered prerequisites for cancer cells to metastasize. Exploring the relationship between these processes and their underlying mechanism of action is a promising way to better understand ACC tumors. We initially established anoikis-resistant sublines of ACC cells; the variant cells revealed a mesenchymal phenotype through Slug-mediated EMT-like transformation and displayed enhanced metastatic potential both in vitro and in vivo. Suppression of EMT by knockdown of Slug significantly impaired anoikis resistance, migration, and invasion of the variant cells. With overexpression of Slug and Twist, we determined that induction of EMT in normal ACC cells could prevent anoikis, albeit partially. These findings strongly suggest that EMT is indispensable in anoikis resistance, at least in ACC cells. Furthermore, we found that the EGFR/PI3K/Akt pathway acts as the common regulator for EMT-like transformation and anoikis resistance, as confirmed by their specific inhibitors. Gefitinib and LY294003 restored the sensibilities of anoikis-resistant cells to anoikis and simultaneously impaired their metastatic potential. In addition, the results from our in vivo model of metastasis suggest that pretreatment with gefitinib promotes mouse survival by alleviating pulmonary metastasis. Most importantly, immunohistochemistry of human ACC specimens showed a correlation between the overexpression of Slug and EGFR staining. This study has demonstrated that Slug-mediated EMT-like transformation is required by human ACC cells to achieve anoikis resistance and their metastatic potential. Targeting the EGFR/PI3K/Akt pathway holds potential as a preventive strategy against distant metastasis of ACC.
doi:10.1371/journal.pone.0051549
PMCID: PMC3522696  PMID: 23272116
8.  Optimization of fatty alcohol biosynthesis pathway for selectively enhanced production of C12/14 and C16/18 fatty alcohols in engineered Escherichia coli 
Background
With the increasing stress from oil price and environmental pollution, aroused attention has been paid to the microbial production of chemicals from renewable sources. The C12/14 and C16/18 alcohols are important feedstocks for the production of surfactants and detergents, which are widely used in the most respected consumer detergents, cleaning products and personal care products worldwide. Though bioproduction of fatty alcohols has been carried out in engineered E. coli, several key problems have not been solved in earlier studies, such as the quite low production of C16/18 alcohol, the lack of optimization of the fatty alcohol biosynthesis pathway, and the uncharacterized performance of the engineered strains in scaled-up system.
Results
We improved the fatty alcohol production by systematically optimizing the fatty alcohol biosynthesis pathway, mainly targeting three key steps from fatty acyl-acyl carrier proteins (ACPs) to fatty alcohols, which are sequentially catalyzed by thioesterase, acyl-coenzyme A (CoA) synthase and fatty acyl-CoA reductase. By coexpression of thioesterase gene BTE, acyl-CoA synthase gene fadD and fatty acyl-CoA reductase gene acr1, 210.1 mg/L C12/14 alcohol was obtained. A further optimization of expression level of BTE, fadD and acr1 increased the C12/14 alcohol production to 449.2 mg/L, accounting for 75.0% of the total fatty alcohol production (598.6 mg/L). In addition, by coexpression of thioesterase gene ‘tesA, acyl-CoA synthase gene fadD and fatty acyl-CoA reductase gene FAR, 101.5 mg/L C16/18 alcohol was obtained, with C16/18 alcohol accounting for 89.2% of the total fatty alcohol production.
Conclusions
To our knowledge, this is the first report on selective production of C12/14 and C16/18 alcohols by microbial fermentation. This work achieved high-specificity production of both C12/14 and C16/18 alcohols. The encouraging 598.6 mg/L of fatty alcohols represents the highest titer reported so far. In addition, the 101.5 mg/L 89.2% C16/18 alcohol suggests an important breakthrough in C16/18 alcohol production. A more detailed optimization of the expression level of fatty alcohol biosynthesis pathway may contribute to a further improvement of fatty alcohol production.
doi:10.1186/1475-2859-11-65
PMCID: PMC3439321  PMID: 22607313
Fatty alcohol; Escherichia coli; Pathway optimization; Selective production; Fermentation
9.  First Report on Co-Occurrence Knockdown Resistance Mutations and Susceptibility to Beta-Cypermethrin in Anopheles sinensis from Jiangsu Province, China 
PLoS ONE  2012;7(1):e29242.
The increasing prevalence of insecticide resistance in Anopheles sinensis, a major vector of malaria in Jiangsu province in eastern China, threatens to compromise the successful use of insecticides in malaria control strategies. It is therefore vital to understand the insecticide resistance status of An. sinensis in the region. This study examined the nucleotide diversity of the para-sodium channel and knockdown resistance (kdr) in five field populations of adult An. sinensis mosquitoes collected in Jiangsu province, identifying the L1014F and L1014C substitutions for the first time. Competitive polymerase chain reaction (PCR) amplification of specific allele (cPASA) and polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) for resistance diagnosis were developed and validated. Comparing the results with direct sequencing revealed that the PCR-RFLP method was more sensitive and specific whereas the cPASA method was more convenient and suitable. The significant positive correlation between kdr allele frequency and bioassay-based resistance phenotype demonstrates that the frequency of L1014F and L1014C substitutions in the kdr gene provides a useful molecular marker for monitoring beta-cypermethrin resistance in natural populations of An. sinensis. Our results point to the L1014F substitution as the key mutation associated with beta-cypermethrin resistance. The high resistance and mutation frequency detected in the five populations also suggest cross-resistance with other pyrethroids may occur in An. sinensis, highlighting the need for further surveys to map insecticide resistance in China and the adoption of a rational management of insecticide application for resistance management and mosquito vector control.
doi:10.1371/journal.pone.0029242
PMCID: PMC3260143  PMID: 22272229
10.  Chinese Culture, Homosexuality Stigma, Social Support and Condom Use: A Path Analytic Model 
Stigma research and action  2011;1(1):27-35.
Purpose
The objective of this study was to examine the interrelationships among individualism, collectivism, homosexuality-related stigma, social support, and condom use among Chinese homosexual men.
Methods
A cross-sectional study using the respondent-driven sampling approach was conducted among 351 participants in Shenzhen, China. Path analytic modeling was used to analyze the interrelationships.
Results
The results of path analytic modeling document the following statistically significant associations with regard to homosexuality: (1) higher levels of vertical collectivism were associated with higher levels of public stigma [β (standardized coefficient) = 0.12] and self stigma (β = 0.12); (2) higher levels of vertical individualism were associated with higher levels self stigma (β = 0.18); (3) higher levels of horizontal individualism were associated with higher levels of public stigma (β = 0.12); (4) higher levels of self stigma were associated with higher levels of social support from sexual partners (β = 0.12); and (5) lower levels of public stigma were associated with consistent condom use (β = −0.19).
Conclusions
The findings enhance our understanding of how individualist and collectivist cultures influence the development of homosexuality-related stigma, which in turn may affect individuals’ decisions to engage in HIV-protective practices and seek social support. Accordingly, the development of HIV interventions for homosexual men in China should take the characteristics of Chinese culture into consideration.
doi:10.5463/sra.v1i1.16
PMCID: PMC3124705  PMID: 21731850
collectivism; HIV/AIDS; homosexuality; individualism
11.  CADgene: a comprehensive database for coronary artery disease genes 
Nucleic Acids Research  2010;39(Database issue):D991-D996.
Coronary artery disease (CAD) is a complex, multifactorial disease and a leading cause of mortality world wide. Over the past decades, great efforts have been made to elucidate the underlying genetic basis of CAD and massive data have been accumulated. To integrate these data together and to provide a useful resource for researchers, we developed the CADgene, a comprehensive database for CAD genes. We manually extracted CAD-related evidence for more than 300 candidate genes for CAD from over 1300 publications of genetic studies. We classified these candidate genes into 12 functional categories based on their roles in CAD. For each gene, we extracted detailed information from related studies (e.g. the size of case–control, population, SNP, odds ratio, P-value, etc.) and made useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein–protein interactions and others. Besides the statistical number of studies for each gene, CADgene also provides tools to search and show the most frequently studied candidate genes. In addition, CADgene provides cumulative data from 11 publications of CAD-related genome-wide association studies. CADgene has a user-friendly web interface with multiple browse and search functions. It is freely available at http://www.bioguo.org/CADgene/.
doi:10.1093/nar/gkq1106
PMCID: PMC3013698  PMID: 21045063
12.  LPS-induced down-regulation of signal regulatory protein α contributes to innate immune activation in macrophages 
The Journal of Experimental Medicine  2007;204(11):2719-2731.
Activation of the mitogen-activated protein kinases (MAPKs) and nuclear factor κB (NF-κB) cascades after Toll-like receptor (TLR) stimulation contributes to innate immune responses. Signal regulatory protein (SIRP) α, a member of the SIRP family that is abundantly expressed in macrophages, has been implicated in regulating MAPK and NF-κB signaling pathways. In addition, SIRPα can negatively regulate the phagocytosis of host cells by macrophages, indicating an inhibitory role of SIRPα in innate immunity. We provide evidences that SIRPα is an essential endogenous regulator of the innate immune activation upon lipopolysaccharide (LPS) exposure. SIRPα expression was promptly reduced in macrophages after LPS stimulation. The decrease in SIRPα expression levels was required for initiation of LPS-induced innate immune responses because overexpression of SIRPα reduced macrophage responses to LPS. Knockdown of SIRPα caused prolonged activation of MAPKs and NF-κB pathways and augmented production of proinflammatory cytokines and type I interferon (IFN). Mice transferred with SIRPα-depleted macrophages were highly susceptible to endotoxic shock, developing multiple organ failure and exhibiting a remarkable increase in mortality. SIRPα may accomplish this mainly through its association and sequestration of the LPS signal transducer SHP-2. Thus, SIRPα functions as a biologically important modulator of TLR signaling and innate immunity.
doi:10.1084/jem.20062611
PMCID: PMC2118489  PMID: 17954568
13.  A Re-evaluation of CD22 Expression by Human Lung Cancer 
Cancer research  2014;74(1):263-271.
CD22 is a transmembrane glycoprotein expressed by mature B cells. It inhibits signal transduction by the B cell receptor and its co-receptor CD19. Recently it was reported that most human lung cancer cells and cell lines express CD22 making it an important new lung cancer therapeutic target (Can Res 72:5556, 2012). The objective of our studies was to independently validate these results with the goal of testing the efficacy of our CD22 immunotoxins on lung cancer cell lines. As determined by qRT-PCR analysis, we found that levels of CD22 mRNA in a panel of human lung cancer cell lines were 200–60,000- fold lower than those observed in the human CD22+ Burkitt’s lymphoma cells, Daudi. Using flow cytometry with a panel of CD22 monoclonal antibodies and Western blot analyses, we could not detect surface or intracellular expression of CD22 protein in a panel of lung cancer cell lines. In addition, the in vitro proliferation of the lung tumor cell lines was not affected by CD22 antibodies or our highly potent anti-CD22 immunotoxin. By contrast, CD22+ Daudi cells expressed high levels of CD22 mRNA and protein and were sensitive to our CD22 immunotoxin. Importantly, primary non-small cell lung cancers from over 250 patient specimens did not express detectable levels of CD22 protein as assessed by immunohistochemistry. We conclude that CD22 is not expressed at measurable levels on the surface of lung cancer cells and that these cells can not be killed by anti-CD22 immunotoxins.
doi:10.1158/0008-5472.CAN-13-1436
PMCID: PMC3903042  PMID: 24395821
lung cancer; CD22 expression
14.  Nosocomial Infection in Adult Admissions with Hematological Malignancies Originating from Different Lineages: A Prospective Observational Study 
PLoS ONE  2014;9(11):e113506.
Background
Nosocomial infection (NI) causes prolonged hospital stays, increased healthcare costs, and higher mortality among patients with hematological malignancies (HM). However, few studies have compared the incidence of NI according to the HM lineage.
Objective
To compare the incidence of NI according to the type of HM lineage, and identify the risk factors for NI.
Methods
This prospective observational study monitored adult patients with HM admitted for >48 hours to the General Hospital of the People's Liberation Army during 2010–2013. Attack rates and incidences of NI were compared, and multivariable logistic regression was used to control for confounding effects.
Results
This study included 6,613 admissions from 1,922 patients. During these admissions, 1,023 acquired 1,136 NI episodes, with an attack rate of 15.47% and incidence of 9.6‰ (95% CI: 9.1–10.2). Higher rates and densities of NIs were observed among myeloid neoplasm (MN) admissions, compared to lymphoid neoplasm (LN) admissions (28.42% vs. 11.00%, P<0.001 and 11.4% vs. 8.4‰, P<0.001). NI attack rates in acute myeloid leukemia (AML) and myelodysplastic/myeloproliferative neoplasm (MDS/MPN) were higher than those in MDS (30.69% vs. 20.19%, P<0.001; 38.89% vs. 20.19%, P = 0.003). Attack rates in T/NK-cell neoplasm and B-cell neoplasm were higher than those in Hodgkin lymphoma (15.04% vs. 3.65%; 10.94% vs. 3.65%, P<0.001). Multivariable regression analysis indicated prolonged hospitalization, presence of central venous catheterization, neutropenia, current stem cell transplant, infection on admission, and old age were independently associated with higher NI incidence. After adjusting for these factors, MN admissions still had a higher risk of infection (odds ratio 1.34, 95% CI: 1.13–1.59, P<0.001).
Conclusion
Different NI attack rates were observed for HM from different lineages, with MN lineages having a higher attack rate and incidence than LN lineages. Special attention should be paid to MN admissions, especially AML and MDS/MPN admissions, to control NI incidence.
doi:10.1371/journal.pone.0113506
PMCID: PMC4240653  PMID: 25415334
15.  Immuno-phenotypes and prognosis of acute leukemia in elderly patients 
Objective: This study is to provide reliable experimental treatment options for the diagnosis of acute leukemia, prognosis analysis and the detection of minimal residual disease. We observed the bone marrow CD123/CD117/CD34/HLA-DR antigen expression in 64 elderly patients with acute leukemia (AL). Methods: The immune phenotypes of 64 elderly AL patients were detected and the correlations of CD123, HLA-DR, CD34 and CD117 expression with the leukemia cell morphology were analyzed. The cell genetics, molecular biology and the prognostic stratification were compared based on flow cytometry. Results: In CDl23-positive patients, the complete remission (CR) rate was 21.5%. In CDl23-negative patients, the CR rate was 59.1%. The CR rate was 21.9% in HLA-DR-positive patients and 43.8% in HLA-DR-negative patients. The CR rate was 24.0% in CD34-positive patients and 41.1% in CD34-negative patients. The CR rate was 29.0% in CD117-positive patients and 42.3% in CD117-negative patients. The CR rate was 34.4% in CD38-positive patients and 0.00% in CD38-negative patients. Conclusions: These results suggest that CD123+, CD117+, CD34+, and HLA-DR+ are the factors related with the poor prognosis of elderly patients with acute leukemia.
PMCID: PMC4238529  PMID: 25419423
Acute leukemia; CD123; elderly patients; flow cytometry
16.  Asymptomatic, Mild, and Severe Influenza A(H7N9) Virus Infection in Humans, Guangzhou, China 
Emerging Infectious Diseases  2014;20(9):1535-1540.
doi:10.3201/eid2009.140424
PMCID: PMC4178418  PMID: 25148539
avian influenza; influenza; influenza A(H7N9); H7N9; surveillance; person-to-person transmission; asymptomatic infection; viruses; respiratory infections; human; China
17.  Reliable management of post-esophagectomy anastomotic fistula with endoscopic trans-fistula negative pressure drainage 
Background
A gastroesophageal anastomotic fistula remains a potentially life-threatening post-esophagectomy complication. To promote fistula closure, we developed a modified endoscopic method of trans-fistula drainage with persistent negative pressure. In this study, we aimed to evaluate the efficacy of this endoscopic therapy.
Methods
Between June and November 2013, five male patients with post-surgical esophageal leakages who had undergone trans-fistula drainage therapy were treated with the modified endoscopic trans-fistula negative pressure drainage (E-TNPD) method. We placed a nasogastric silicone tube into the paraesophageal cavity through the fistula and accomplished drainage of the infected effusion with continuous negative pressure, resulting in shrinkage of the para-anastomotic cavity and eventual fistula closure. We withdrew the trans-fistula drainage when there were no signs of leakage, as confirmed by esophagography. Final closure was confirmed by esophagography before the patient was allowed to begin oral intake.
Results
E-TNPD was successful in all five patients. The median duration of drainage until tube removal was 34 days (range: 18 to 81 days). The duration for Cases 1 to 4 was 18 to 28 days. Case 5 suffered from multiple separate leaks at the anastomotic site and the gastric conduit. Complete restoration was achieved in 81 days for this patient. We found that in general, the earlier that trans-fistula drainage was established, the shorter the duration of hospitalization until complete defect closure.
Conclusions
E-TNPD provided reliable and convenient management of post-surgical gastroesophageal anastomotic fistula and esophageal perforation. This method promoted fistula closure and prevented unnecessary repeated endoscopic examinations, extra equipment and expense.
doi:10.1186/1477-7819-12-240
PMCID: PMC4119058  PMID: 25078091
anastomotic fistula; esophagectomy; endoscopic management
18.  Determination of the Total Mass of Antioxidant Substances and Antioxidant Capacity per Unit Mass in Serum Using Redox Titration 
Objective. Total antioxidant capacity in serum is determined by the total mass of antioxidant substances and the antioxidant capacity per unit mass (average activity). The purpose of this study was to develop a method to determine the mass of antioxidant substances and average activity in human serum. Methods. Specimens of serum were collected from 100 subjects each from two different age groups: over 75 years old and 20–40 years old. The test serum was diluted into a series of concentrations, following which standard oxidation agents (KMnO4 for potassium permanganate method and I2 for iodimetry) were added to each concentration of serum, and the absorbance of the mixture (optical density, OD) was measured. The OD value and logarithm of dilution factor (lgT) at the end of the titration were obtained, from which the lgT could be considered as mass of antioxidant substances (M). Total antioxidant capacity (Ta) was calculated with the equation Ta = 100/(OD1 + 2 ∗ OD2 + 2 ∗ OD3 + 2 ∗ OD4 + OD5), and average activity (A) was calculated as A = Ta/M. Results. The potassium permanganate method generated similar results to the iodimetric method. Compared with the younger group, total antioxidant capacity in the over-75-year age group was found to be significantly reduced, along with a decrease in the mass of antioxidant substances and average activity levels in human serum. Conclusions. The approach described in this paper is suitable for determining the average activity and mass of antioxidant substances in human serum.
doi:10.1155/2014/928595
PMCID: PMC4129143  PMID: 25140122
19.  Enantioselective Metabolism of Quizalofop-Ethyl in Rat 
PLoS ONE  2014;9(6):e101052.
The pharmacokinetic and distribution of the enantiomers of quizalofop-ethyl and its metabolite quizalofop-acid were studied in Sprague-Dawley male rats. The two pairs of enantiomers were determined using a validated chiral high-performance liquid chromatography method. Animals were administered quizalofop-ethyl at 10 mg kg−1 orally and intravenously. It was found high concentration of quizalofop-acid in the blood and tissues by both intragastric and intravenous administration, and quizalofop-ethyl could not be detected through the whole study which indicated a quick metabolism of quizalofop-ethyl to quizalofop-acid in vivo. In almost all the samples, the concentrations of (+)-quizalofop-acid exceeded those of (−)-quizalofop-acid. Quizalofop-acid could still be detected in the samples even at 120 h except in brain due to the function of blood-brain barrier. Based on a rough calculation, about 8.77% and 2.16% of quizalofop-acid were excreted through urine and feces after intragastric administration. The oral bioavailability of (+)-quizalofop-acid and (−)-quizalofop-acid were 72.8% and 83.6%.
doi:10.1371/journal.pone.0101052
PMCID: PMC4071037  PMID: 24964043
20.  Self-similar erbium-doped fiber laser with large normal dispersion 
Optics letters  2014;39(4):1019-1021.
We report a large normal dispersion erbium-doped fiber laser with self-similar pulse evolution in the gain fiber. The cavity is stabilized by the local nonlinear attractor in the gain fiber through the use of a narrow filter. Experimental results are accounted for by numerical simulations. This laser produces 3.5 nJ pulses, which can be dechirped to 70 fs with an external grating pair.
PMCID: PMC4006903  PMID: 24562267
21.  Plasma Sphingolipids as Potential Indicators of Hepatic Necroinflammation in Patients with Chronic Hepatitis C and Normal Alanine Aminotransferase Level 
PLoS ONE  2014;9(4):e95095.
Accurate estimation of hepatic necroinflammation caused by chronic hepatitis C (CHC) is crucial for prediction of prognosis and design of therapeutic strategy, which is particularly true for CHC patients with normal alanine aminotransferase (ALT) level. Recent studies have shown that sphingolipids have a close relationship with hepatitis C virus infection. The present study aimed to identify plasma sphingolipids related to hepatic necroinflammation. We included 120 treatment-naïve CHC patients and 64/120 had normal ALT levels (<40 U/L). CHC patients who underwent liver biopsies were subjected to Scheuer scoring analysis for scope of hepatic inflammation. Plasma sphingolipids were detected by high-performance liquid chromatography tandem mass spectrometry. Our results showed 44 plasma sphingolipids were detected altogether. Of all detected sphingolipids, hexosylceramide (HexCer) (d18∶1/22∶0) and HexCer (d18∶1/24∶0) showed a significant difference among G0/G1, G2, and G3/G4 (P<0.05). For identifying hepatic necroinflammation (G≥2), after adjusting other factors, the odds ratio (OR) of HexCer (d18∶1/22∶0) reached 1.01 (95% confidence interval [CI]: 1.00–1.02). Furthermore, the area under the curve (AUC) of HexCer (d18∶1/22∶0) was 0.7 (P = 0.01) and approached that of ALT (AUC = 0.78). However, in CHC patients with normal ALT, HexCer (d18∶1/22∶0) was an independent factor (OR: 1.02, 95% CI: 1.01–1.03) to identify the hepatic necroinflammation (G≥2). HexCer (d18∶1/22∶0) not only showed the largest AUC (0.78, P = 0.001), but also exhibited the highest specificity of all indicators. These results indicate that plasma HexCer (d18∶1/22∶0) is a potential indicator to distinguish hepatic necroinflammation in CHC patients. For CHC with normal ALT, the ability of HexCer (d18∶1/22∶0) to distinguish hepatic necroinflammation might be superior to conventional serum indicators.
doi:10.1371/journal.pone.0095095
PMCID: PMC3988168  PMID: 24736528
22.  Hypoxia-Inducible MiR-210 Is an Independent Prognostic Factor and Contributes to Metastasis in Colorectal Cancer 
PLoS ONE  2014;9(3):e90952.
MicroRNA-210 (miR-210), the master hypoxamir, plays pleiotropic roles in certain cancers; however, its role in the development of human colorectal cancer remains unclear. Herein, we report that miR-210 is frequently up-regulated in colorectal cancer tissues, with high miR-210 expression significantly correlating with large tumor size, lymph node metastasis, advanced clinical stage and poor prognosis. Functionally, miR-210 overexpression promotes the migration and invasion of colorectal cancer cells. Furthermore, miR-210 can be induced by hypoxia and mediates the hypoxia-induced metastasis of colorectal cancer cells. In addition, vacuole membrane protein 1 (VMP1) is identified as the direct and functional target of miR-210. Thus, miR-210 is a useful biomarker for hypoxic tumor cells and a prognostic factor that plays an essential role in colorectal cancer metastasis.
doi:10.1371/journal.pone.0090952
PMCID: PMC3954583  PMID: 24632577
23.  Spinal Changes of a Newly Isolated Neuropeptide Endomorphin-2 Concomitant with Vincristine-Induced Allodynia 
PLoS ONE  2014;9(2):e89583.
Chemotherapy-induced neuropathic pain (CNP) is the major dose-limiting factor in cancer chemotherapy. However, the neural mechanisms underlying CNP remain unclear. There is increasing evidence implicating the involvement of spinal endomorphin-2 (EM2) in neuropathic pain. In this study, we used a vincristine-evoked rat CNP model displaying mechanical allodynia and central sensitization, and observed a significant decrease in the expression of spinal EM2 in CNP. Also, while intrathecal administration of exogenous EM2 attenuated allodynia and central sensitization, the mu-opioid receptor antagonist β-funaltrexamine facilitated these events. We found that the reduction in spinal EM2 was mediated by increased activity of dipeptidylpeptidase IV, possibly as a consequence of chemotherapy-induced oxidative stress. Taken together, our findings suggest that a decrease in spinal EM2 expression causes the loss of endogenous analgesia and leads to enhanced pain sensation in CNP.
doi:10.1371/journal.pone.0089583
PMCID: PMC3933549  PMID: 24586889
24.  Microbial production of sabinene—a new terpene-based precursor of advanced biofuel 
Background
Sabinene, one kind of monoterpene, accumulated limitedly in natural organisms, is being explored as a potential component for the next generation of aircraft fuels. And demand for advanced fuels impels us to develop biosynthetic routes for the production of sabinene from renewable sugar.
Results
In this study, sabinene was significantly produced by assembling a biosynthetic pathway using the methylerythritol 4-phosphate (MEP) or heterologous mevalonate (MVA) pathway combining the GPP and sabinene synthase genes in an engineered Escherichia coli strain. Subsequently, the culture medium and process conditions were optimized to enhance sabinene production with a maximum titer of 82.18 mg/L. Finally, the fed-batch fermentation of sabinene was evaluated using the optimized culture medium and process conditions, which reached a maximum concentration of 2.65 g/L with an average productivity of 0.018 g h-1 g-1 dry cells, and the conversion efficiency of glycerol to sabinene (gram to gram) reached 3.49%.
Conclusions
This is the first report of microbial synthesis of sabinene using an engineered E. coli strain with the renewable carbon source as feedstock. Therefore, a green and sustainable production strategy has been established for sabinene.
doi:10.1186/1475-2859-13-20
PMCID: PMC3923588  PMID: 24512040
Sabinene; Geranyl diphosphate synthase; Sabinene synthase; Escherichia coli
25.  Application of Butterfly Clos-Network in Network-on-Chip 
The Scientific World Journal  2014;2014:102651.
This paper studied the topology of NoC (Network-on-Chip). By combining the characteristics of the Clos network and butterfly network, a new topology named BFC (Butterfly Clos-network) network was proposed. This topology integrates several modules, which belongs to the same layer but different dimensions, into a new module. In the BFC network, a bidirectional link is used to complete information exchange, instead of information exchange between different layers in the original network. During the routing period, other nondestination nodes can be used as middle stages to transfer data packets to complete the routing mission. Therefore, this topology has the characteristic of multistage. Simulation analyses show that BFC inherits the rich path diversity of Clos network, and it has a better performance than butterfly network in throughput and delay in a quite congested traffic pattern.
doi:10.1155/2014/102651
PMCID: PMC3926393  PMID: 24688357

Results 1-25 (230)