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1.  qFibrosis: A fully-quantitative innovative method incorporating histological features to facilitate accurate fibrosis scoring in animal model and chronic hepatitis B patients 
Journal of hepatology  2014;61(2):260-269.
Background & Aims
There is increasing need for accurate assessment of liver fibrosis/cirrhosis. We aimed to develop qFibrosis, a fully-automated assessment method combining quantification of histopathological architectural features, to address unmet needs in core biopsy evaluation of fibrosis in chronic hepatitis B (CHB) patients.
Methods
qFibrosis was established as a combined index based on 87 parameters of architectural features. Images acquired from 25 Thioacetamide-treated rat samples and 162 CHB core biopsies were used to train and test qFibrosis and to demonstrate its reproducibility. qFibrosis scoring was analyzed employing Metavir and Ishak fibrosis staging as standard references, and collagen proportionate area (CPA) measurement for comparison.
Results
qFibrosis faithfully and reliably recapitulates Metavir fibrosis scores, as it can identify differences between all stages in both animal samples (p <0.001) and human biopsies (p <0.05). It is robust to sampling size, allowing for discrimination of different stages in samples of different sizes (area under the curve (AUC): 0.93–0.99 for animal samples: 1–16 mm2; AUC: 0.84–0.97 for biopsies: 10–44 mm in length). qFibrosis can significantly predict staging underestimation in suboptimal biopsies (<15 mm) and under- and over-scoring by different pathologists (p <0.001). qFibrosis can also differentiate between Ishak stages 5 and 6 (AUC: 0.73, p = 0.008), suggesting the possibility of monitoring intra-stage cirrhosis changes. Best of all, qFibrosis demonstrates superior performance to CPA on all counts.
Conclusions
qFibrosis can improve fibrosis scoring accuracy and throughput, thus allowing for reproducible and reliable analysis of efficacies of anti-fibrotic therapies in clinical research and practice.
doi:10.1016/j.jhep.2014.02.015
PMCID: PMC4278959  PMID: 24583249
Liver fibrosis assessment; qFibrosis; Chronic hepatitis B; Liver biopsy; Image analysis
2.  Transcriptome analysis of food habit transition from carnivory to herbivory in a typical vertebrate herbivore, grass carp Ctenopharyngodon idella 
BMC Genomics  2015;16(1):15.
Background
Although feeding behavior and food habit are ecologically and economically important properties, little is known about formation and evolution of herbivory. Grass carp (Ctenopharyngodon idella) is an ecologically appealing model of vertebrate herbivore, widely cultivated in the world as edible fish or as biological control agents for aquatic weeds. Grass carp exhibits food habit transition from carnivory to herbivory during development. However, currently little is known about the genes regulating the unique food habit transition and the formation of herbivory, and how they could achieve higher growth rates on plant materials, which have a relatively poor nutritional quality.
Results
We showed that grass carp fed with duckweed (modeling fish after food habit transition) had significantly higher relative length of gut than fish before food habit transition or those fed with chironomid larvae (fish without transition). Using transcriptome sequencing, we identified 10,184 differentially expressed genes between grass carp before and after transition in brain, liver and gut. By eliminating genes potentially involved in development (via comparing fish with or without food habit transition), we identified changes in expression of genes involved in cell proliferation and differentiation, appetite control, circadian rhythm, and digestion and metabolism between fish before and after food habit transition. Up-regulation of GHRb, Egfr, Fgf, Fgfbp1, Insra, Irs2, Jak, STAT, PKC, PI3K expression in fish fed with duckweed, consistent with faster gut growth, could promote the food habit transition. Grass carp after food habit transition had increased appetite signal in brain. Altered expressions of Per, Cry, Clock, Bmal2, Pdp, Dec and Fbxl3 might reset circadian phase of fish after food habit transition. Expression of genes involved in digestion and metabolism were significantly different between fish before and after the transition.
Conclusions
We suggest that the food habit transition from carnivory to herbivory in grass carp might be due to enhanced gut growth, increased appetite, resetting of circadian phase and enhanced digestion and metabolism. We also found extensive alternative splicing and novel transcript accompanying food habit transition. These differences together might account for the food habit transition and the formation of herbivory in grass carp.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1217-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1217-x
PMCID: PMC4307112  PMID: 25608568
Food habit transition; Carnivory; Herbivory; Grass carp; Transcriptome sequencing
3.  Rs1800625 in the receptor for advanced glycation end products gene predisposes to sepsis and multiple organ dysfunction syndrome in patients with major trauma 
Critical Care  2015;19(1):6.
Introduction
The receptor for advanced glycation end products (RAGE) is a transmembrane receptor of the immunoglobulin superfamily, it plays pivotal roles in the pathogenesis of sepsis in several ways. Our previous study showed that rs1800625 (−429T/C) revealed a strong clinical relevance with sepsis morbidity rate and multiple organ dysfunction syndrome (MODS) in patients with major trauma. In this study, we enlarged the sample size, added two validation populations and examined the expression of RAGE on the surface of peripheral leukocytes to ex vivo lipopolysaccharide (LPS) stimulation in subjects with different genotypes.
Methods
Rs1800625 was genotyped using pyrosequencing in 837 Chinese Han patients with major trauma in Chongqing. We then validated the clinical relevance in 340 Zhejiang and 347 Yunnan patients. The expression of RAGE on the surface of peripheral blood mononuclear cells was measured by flow cytometric analysis.
Results
The results indicated that rs1800625 was significantly associated with sepsis morbidity rate and MODS in patients with major trauma in the Chongqing, Zhejiang and Yunnan districts. Patients with CC genotype had lower sepsis morbidity rate and MODS after major trauma. Furthermore, patients with CC genotype had significantly higher RAGE expression (P = 0.009).
Conclusions
The rs1800625 polymorphism is a functional single nucleotide polymorphism and confers host susceptibility to sepsis and MODS in patients with major trauma.
doi:10.1186/s13054-014-0727-2
PMCID: PMC4310192  PMID: 25572180
4.  Overexpression of copper/zinc superoxide dismutase from mangrove Kandelia candel in tobacco enhances salinity tolerance by the reduction of reactive oxygen species in chloroplast 
Na+ uptake and transport in Kandelia candel and antioxidative defense were investigated under rising NaCl stress from 100 to 300 mM. Salinized K. candel roots had a net Na+ efflux with a declined flux rate during an extended NaCl exposure. Na+ buildup in leaves enhanced H2O2 levels, superoxide dismutase (SOD) activity, and increased transcription of CSD gene encoding a Cu/Zn SOD. Sequence and subcellular localization analyses have revealed that KcCSD is a typical Cu/Zn SOD in chloroplast. The transgenic tobacco experimental system was used as a functional genetics model to test the effect of KcCSD on salinity tolerance. KcCSD-transgenic lines were more Na+ tolerant than wild-type (WT) tobacco in terms of lipid peroxidation, root growth, and survival rate. In the latter, 100 mM NaCl led to a remarkable reduction in chlorophyll content and a/b ratio, decreased maximal chlorophyll a fluorescence, and photochemical efficiency of photosystem II. NaCl stress in WT resulted from H2O2 burst in chloroplast. Na+ injury to chloroplast was less pronounced in KcCSD-transgenic plants due to upregulated antioxidant defense. KcCSD-transgenic tobacco enhanced SOD activity by an increment in SOD isoenzymes under 100 mM NaCl stress from 24 h to 7 day. Catalase activity rose in KcCSD overexpressing tobacco plants. KcCSD-transgenic plants better scavenged NaCl-elicited reactive oxygen species (ROS) compared to WT ones. In conclusion, K. candel effectively excluded Na+ in roots during a short exposure; and increased CSD expression to reduce ROS in chloroplast in a long-term and high saline environment.
doi:10.3389/fpls.2015.00023
PMCID: PMC4302849  PMID: 25657655
Kandelia candel; Na+ flux; superoxide anion; hydrogen peroxide; salt; catalase; superoxide dismutase
5.  Intercropping Enhances Productivity and Maintains the Most Soil Fertility Properties Relative to Sole Cropping 
PLoS ONE  2014;9(12):e113984.
Yield and nutrient acquisition advantages are frequently found in intercropping systems. However, there are few published reports on soil fertility in intercropping relative to monocultures. A field experiment was therefore established in 2009 in Gansu province, northwest China. The treatments comprised maize/faba bean, maize/soybean, maize/chickpea and maize/turnip intercropping, and their correspoding monocropping. In 2011 (the 3rd year) and 2012 (the 4th year) the yields and some soil chemical properties and enzyme activities were examined after all crop species were harvested or at later growth stages. Both grain yields and nutrient acquisition were significantly greater in all four intercropping systems than corresponding monocropping over two years. Generally, soil organic matter (OM) did not differ significantly from monocropping but did increase in maize/chickpea in 2012 and maize/turnip in both years. Soil total N (TN) did not differ between intercropping and monocropping in either year with the sole exception of maize/faba bean intercropping receiving 80 kg P ha−1 in 2011. Intercropping significantly reduced soil Olsen-P only in 2012, soil exchangeable K in both years, soil cation exchangeable capacity (CEC) in 2012, and soil pH in 2012. In the majority of cases soil enzyme activities did not differ across all the cropping systems at different P application rates compared to monocrops, with the exception of soil acid phosphatase activity which was higher in maize/legume intercropping than in the corresponding monocrops at 40 kg ha−1 P in 2011. P fertilization can alleviate the decline in soil Olsen-P and in soil CEC to some extent. In summary, intercropping enhanced productivity and maintained the majority of soil fertility properties for at least three to four years, especially at suitable P application rates. The results indicate that maize-based intercropping may be an efficient cropping system for sustainable agriculture with carefully managed fertilizer inputs.
doi:10.1371/journal.pone.0113984
PMCID: PMC4259307  PMID: 25486249
6.  Pulsed laser deposition of single-crystalline Cu7In3/CuIn0.8Ga0.2Se2 core/shell nanowires 
Nanoscale Research Letters  2014;9(1):650.
Single-crystalline Cu7In3/CuIn0.8Ga0.2Se2 (CI/CIGS) core/shell nanowires are fabricated by pulsed laser deposition with Ni nanoparticles as catalyst. The CI/CIGS core/shell nanowires are made up of single-crystalline CI cores surrounded by single-crystalline CIGS shells. The CI/CIGS nanowires are grown at a considerably low temperature (350°C ~ 450°C) by vapor-liquid-solid mode combined with vapor-solid mode. The distribution density of the nanowires increases with the increasing of the deposition duration, and the substrate temperature determines the lengths of the nanowires. The U-V absorption spectra of the CIGS thin films with and without the CI/CIGS core/shell nanowires demonstrate that the CI/CIGS nanowires can remarkably enhance the absorption of CIGS thin films in the spectrum range of 300 to 900 nm.
PACS
61.46. + w; 61.41.e; 81.15.Fg; 81.07.b
doi:10.1186/1556-276X-9-650
PMCID: PMC4266518  PMID: 25520597
Pulsed laser deposition; Nickel catalyst; CuIn0.8Ga0.2Se2; core/shell nanowires; Light absorption
7.  Development of aminoglycoside and β-lactamase resistance among intestinal microbiota of swine treated with lincomycin, chlortetracycline, and amoxicillin 
Lincomycin, chlortetracycline, and amoxicillin are commonly used antimicrobials for growth promotion and infectious disease prophylaxis in swine production. In this study, we investigated the shifts and resistance development among intestinal microbiota in pregnant sows before and after lincomycin, chlortetracycline, and amoxicillin treatment by using phylogenetic analysis, bacterial enumeration, and PCR. After the antimicrobial treatment, shifts in microbial community, an increased proportion of resistant bacteria, and genes related to antimicrobial resistance as compared to the day before antimicrobial administration (day 0) were observed. Importantly, a positive correlation between antimicrobial resistance gene expression in different categories, especially those encoding aminoglycoside and β-lactamase and antimicrobial resistance, was observed. These findings demonstrate an important role of antimicrobial usage in animals in the development of antimicrobial resistance, and support the notion that prudent use of antimicrobials in swine is needed to reduce the risk of the emergence of multi-drug resistant zoonotic pathogens.
doi:10.3389/fmicb.2014.00580
PMCID: PMC4219486  PMID: 25408688
culture-independent method; qPCR; antimicrobial-resistant genes; 16S rRNA; Bacterial Enumeration
8.  LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma  
Gut  2014;63(11):1700-1710.
Background
Oesophageal cancer is one of the most deadly forms of cancer worldwide. Long non-coding RNAs (lncRNAs) are often found to have important regulatory roles.
Objective
To assess the lncRNA expression profile of oesophageal squamous cell carcinoma (OSCC) and identify prognosis-related lncRNAs.
Method
LncRNA expression profiles were studied by microarray in paired tumour and normal tissues from 119 patients with OSCC and validated by qRT-PCR. The 119 patients were divided randomly into training (n=60) and test (n=59) groups. A prognostic signature was developed from the training group using a random Forest supervised classification algorithm and a nearest shrunken centroid algorithm, then validated in a test group and further, in an independent cohort (n=60). The independence of the signature in survival prediction was evaluated by multivariable Cox regression analysis.
Results
LncRNAs showed significantly altered expression in OSCC tissues. From the training group, we identified a three-lncRNA signature (including the lncRNAs ENST00000435885.1, XLOC_013014 and ENST00000547963.1) which classified the patients into two groups with significantly different overall survival (median survival 19.2 months vs >60 months, p<0.0001). The signature was applied to the test group (median survival 21.5 months vs >60 months, p=0.0030) and independent cohort (median survival 25.8 months vs >48 months, p=0.0187) and showed similar prognostic values in both. Multivariable Cox regression analysis showed that the signature was an independent prognostic factor for patients with OSCC. Stratified analysis suggested that the signature was prognostic within clinical stages.
Conclusions
Our results suggest that the three-lncRNA signature is a new biomarker for the prognosis of patients with OSCC, enabling more accurate prediction of survival.
doi:10.1136/gutjnl-2013-305806
PMCID: PMC4215280  PMID: 24522499
Oesophageal Cancer
9.  Illumina Amplicon Sequencing of 16S rRNA Tag Reveals Bacterial Community Development in the Rhizosphere of Apple Nurseries at a Replant Disease Site and a New Planting Site 
PLoS ONE  2014;9(10):e111744.
We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant) and a new planting site (NewPlant) in Beijing. Dwarfing apple nurseries of ‘Fuji’/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil) and from the new planting site (NewSoil) was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant). More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria). The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition.
doi:10.1371/journal.pone.0111744
PMCID: PMC4216118  PMID: 25360786
10.  A Preclinical Study Combining the DNA Repair Inhibitor Dbait with Radiotherapy for the Treatment of Melanoma1 
Neoplasia (New York, N.Y.)  2014;16(10):835-844.
Melanomas are highly radioresistant tumors, mainly due to efficient DNA double-strand break (DSB) repair. Dbait (which stands for DNA strand break bait) molecules mimic DSBs and trap DNA repair proteins, thereby inhibiting repair of DNA damage induced by radiation therapy (RT). First, the cytotoxic efficacy of Dbait in combination with RT was evaluated in vitro in SK28 and 501mel human melanoma cell lines. Though the extent of RT-induced damage was not increased by Dbait, it persisted for longer revealing a repair defect. Dbait enhanced RT efficacy independently of RT doses. We further assayed the capacity of DT01 (clinical form of Dbait) to enhance efficacy of “palliative” RT (10 × 3 Gy) or “radical” RT (20 × 3 Gy), in an SK28 xenografted model. Inhibition of repair of RT-induced DSB by DT01 was revealed by the significant increase of micronuclei in tumors treated with combined treatment. Mice treated with DT01 and RT combination had significantly better tumor growth control and longer survival compared to RT alone with the “palliative” protocol [tumor growth delay (TGD) by 5.7-fold; median survival: 119 vs 67 days] or the “radical” protocol (TGD by 3.2-fold; median survival: 221 vs 109 days). Only animals that received the combined treatment showed complete responses. No additional toxicity was observed in any DT01-treated groups. This preclinical study provides encouraging results for a combination of a new DNA repair inhibitor, DT01, with RT, in the absence of toxicity. A first-in-human phase I study is currently under way in the palliative management of melanoma in-transit metastases (DRIIM trial).
doi:10.1016/j.neo.2014.08.008
PMCID: PMC4212251  PMID: 25379020
DNA-PK, DNA-dependent kinase; DSB, double-strand break; PARP, poly-adenyl-ribose polymerase; RT, radiation therapy; SSB, single-strand break; TGD, tumor growth delay
11.  Effects of Grazing Regimes on Plant Traits and Soil Nutrients in an Alpine Steppe, Northern Tibetan Plateau 
PLoS ONE  2014;9(9):e108821.
Understanding the impact of grazing intensity on grassland production and soil fertility is of fundamental importance for grassland conservation and management. We thus compared three types of alpine steppe management by studying vegetation traits and soil properties in response to three levels of grazing pressure: permanent grazing (M1), seasonal grazing (M2), and grazing exclusion (M3) in the alpine steppe in Xainza County, Tibetan Plateau. The results showed that community biomass allocation did not support the isometric hypothesis under different grassland management types. Plants in M1 had less aboveground biomass but more belowground biomass in the top soil layer than those in M2 and M3, which was largely due to that root/shoot ratios of dominant plants in M1 were far greater than those in M2 and M3. The interramet distance and the tiller size of the dominant clonal plants were greater in M3 than in M1 and M2, while the resprouting from rhizome buds did not differ significantly among the three greezing regimes. Both soil bulk density and soil available nitrogen in M3 were greater than in M1 at the 15–30 cm soil depth (P = 0.05). Soil organic carbon and soil total nitrogen were greater in M3 than in M1 and M2 (P = 0.05). We conclude that the isometric hypothesis is not supported in this study and fencing is a helpful grassland management in terms of plant growth and soil nutrient retention in alpine steppe. The extreme cold, scarce precipitation and short growing period may be the causation of the unique plant and soil responses to different management regimes.
doi:10.1371/journal.pone.0108821
PMCID: PMC4182571  PMID: 25268517
12.  Novel structural phases and superconductivity of iridium telluride under high pressures 
Scientific Reports  2014;4:6433.
Transition metal selenide and telluride have recently receive considerable attention due to their possible structural relation to ferropnictide. Pressure is often used as an efficient way to modify the crystal or electronic structure that in many cases lead to new material states of interest. Here we search the structures of IrTe2 up to 150 GPa using crystal structure prediction techniques combining with ab initio calculations. Three new stable phases under high pressures are predicted, and their electronic structure properties, phonon spectra, and electron-phonon couplings are also investigated. Significant reconstructions of band structures and Fermi surfaces are found in these new phases. Calculated results show that while the C2/m-2 phase has bad metal behavior and very weak electron-phonon coupling, the and I4/mmm phases have relatively higher electron-phonon coupling up to ~ 1.5 and 0.7, respectively. The variable-composition searching have been performed, newly compounds with different stoichiometries, such as IrTe3, IrTe, and Ir3Te, are predicted to be thermodynamically and dynamically stable at high pressures. The pressure range investigated here is accessible in the diamond anvil cell experiments, thus our results might stimulate further experimental studies.
doi:10.1038/srep06433
PMCID: PMC4170196  PMID: 25242541
13.  An NN-Based SRD Decomposition Algorithm and Its Application in Nonlinear Compensation 
Sensors (Basel, Switzerland)  2014;14(9):17353-17375.
In this study, a neural network-based square root of descending (SRD) order decomposition algorithm for compensating for nonlinear data generated by sensors is presented. The study aims at exploring the optimized decomposition of data 1.00,0.00,0.00 and minimizing the computational complexity and memory space of the training process. A linear decomposition algorithm, which automatically finds the optimal decomposition of N subparts and reduces the training time to 1N and memory cost to 1N, has been implemented on nonlinear data obtained from an encoder. Particular focus is given to the theoretical access of estimating the numbers of hidden nodes and the precision of varying the decomposition method. Numerical experiments are designed to evaluate the effect of this algorithm. Moreover, a designed device for angular sensor calibration is presented. We conduct an experiment that samples the data of an encoder and compensates for the nonlinearity of the encoder to testify this novel algorithm.
doi:10.3390/s140917353
PMCID: PMC4208228  PMID: 25232912
decomposition algorithm; data amount; Fourier neural network; nonlinear errors compensation
14.  Association of UGT1A1 Variants and Hyperbilirubinemia in Breast-Fed Full-Term Chinese Infants 
PLoS ONE  2014;9(8):e104251.
A retrospective case control study of breast-fed full-term infants was carried out to determine whether variants in Uridine Diphosphate Glucuronosyl Transferase 1A1 (UGT1A1) and Heme Oxygenase-1 (HMOX1) were associated with neonatal hyperbilirubinemia. Eight genetic variants of UGT1A1 and 3 genetic variants of HMOX1 were genotyped in 170 hyperbilirubinemic newborns and 779 controls. Five significant associations with breast-fed hyperbilirubinemia were detected after adjusting for gender, birth season, birth weight, delivery mode, gestational age and False Discovery Rate (FDR) correction: the dominant effect of rs887829 (c-364t) (Odds Ratio (OR): 0.55; 95% Confidence Interval (CI): 0.34–0.89; p = 0.014), the additive effect of (TA)n repeat (OR: 0.59; 95%CI: 0.38–0.91; p = 0.017), the dominant effect of rs4148323 (Gly71Arg, G211A) (OR: 2.02; 95%CI: 1.44–2.85; p = 5.0×10−5), the recessive effect of rs6717546 (g+914a) (OR: 0.30; 95%CI: 0.11–0.83; p = 0.021) and rs6719561 (t+2558c) (OR: 0.38; 95%CI: 0.20–0.75; p = 0.005). Neonates carrying the minor allele of rs887829 (TA)n repeat had significantly lower peak bilirubin than wild types, while the minor allele carriers of rs4148323 had significantly higher peak bilirubin than wild types. No association was found in HMOX1. Our findings added to the understanding of the significance of UGT1A1 in association with neonatal hyperbilirubinemia in East Asian population. Additional studies were required to investigate the mechanisms of the protective effects.
doi:10.1371/journal.pone.0104251
PMCID: PMC4125195  PMID: 25102181
15.  Postoperative radiotherapy to stabilize a tumor embolus in clear cell renal cell carcinoma: A case report 
Oncology Letters  2014;8(4):1856-1858.
Superior vena cava (SVC) syndrome results from clear cell renal cell carcinoma and is a challenge in clinical practice due to its pathological complexity and a lack of research data. The current study presents a 49-year-old female with symptoms of exertional dyspnea and increased fatigue, which had persisted for 15 months, as well as bilateral edema in the lower limbs for two days. A transesophageal echocardiogram demonstrated a right atrial mass originating from the inferior vena cava (IVC; size, 14×8 cm) that caused a tricuspid inflow obstruction. Following a partial resection of the thrombus, a clear cell renal cell carcinoma was identified by histological examination. The patient received intensity-modulated radiation therapy following refusal of other therapeutic methods. The eleven-month follow-up indicated that the tumor on the kidney and IVC was stable. Intensity-modulated radiation therapy may be beneficial to patients with clear cell renal cell carcinoma and SVC syndrome. However, additional studies are required to obtain further data regarding the treatment of this syndrome.
doi:10.3892/ol.2014.2421
PMCID: PMC4156207  PMID: 25202425
intensity modulated radiation therapy; clear cell renal cell carcinoma; tricuspid inflow obstruction
16.  Estimating the burden of acute gastrointestinal illness in the community in Gansu Province, northwest China, 2012–2013 
BMC Public Health  2014;14(1):787.
Background
Acute gastrointestinal illness (AGI) imposes considerable social and economic burden on low and middle-income countries. This study aimed to estimate the occurrence, distribution, and burden of self-reported AGI in Gansu Province of northwest China, where economic growth rates have lagged far behind those of other regions in China and systematic studies to investigate the burden of AGI are still lacking.
Methods
Twelve-month, retrospective face-to-face surveys were conducted in three sentinel sites between June 2012 and May 2013. Respondents were asked if they had experienced diarrhoea or vomiting in the 28 days prior to the interview.
Results
In total, 2094 interviews were completed. The adjusted monthly prevalence was 8.5% with an incidence rate of 1.16 episodes of AGI per person-year. Healthcare was sought by 73.8% of those reporting illness. Of the cases who visited a doctor, 50.5% submitted a stool sample. The use of antibiotics was reported by 65.6% of the cases and 53.3% took antidiarrhoeals. In the multivariable model, age, household income and sentinel site were significant risk factors of being a case of AGI.
Conclusions
The burden of AGI was considerable in Gansu Province of northwest China. Ongoing research to identify the main causes of AGI is needed for more accurate estimate of the burden of AGI in this region.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2458-14-787) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2458-14-787
PMCID: PMC4246514  PMID: 25086445
18.  A carbon nanotube filled polydimethylsiloxane hybrid membrane for enhanced butanol recovery 
Scientific Reports  2014;4:5925.
The carbon nanotubes (CNTs) filled polydimethylsiloxane (PDMS) hybrid membrane was fabricated to evaluate its potential for butanol recovery from acetone-butanol-ethanol (ABE) fermentation broth. Compared with the homogeneous PDMS membrane, the CNTs filled into the PDMS membrane were beneficial for the improvement of butanol recovery in butanol flux and separation factor. The CNTs acting as sorption-active sites with super hydrophobicity could give an alternative route for mass transport through the inner tubes or along the smooth surface. The maximum total flux and butanol separation factor reached up to 244.3 g/m2·h and 32.9, respectively, when the PDMS membrane filled with 10 wt% CNTs was used to separate butanol from the butanol/water solution at 80°C. In addition, the butanol flux and separation factor increased dramatically as temperature increased from 30°C to 80°C in feed solution since the higher temperature produced more free volumes in polymer chains to facilitate butanol permeation. A similar increase was also observed when butanol titer in solution increased from 10 g/L to 25 g/L. Overall, the CNTs/PDMS hybrid membrane with higher butanol flux and selectivity should have good potential for pervaporation separation of butanol from ABE fermentation broth.
doi:10.1038/srep05925
PMCID: PMC4118185  PMID: 25081019
19.  An Improved Multidimensional MPA Procedure for Bidirectional Earthquake Excitations 
The Scientific World Journal  2014;2014:320756.
Presently, the modal pushover analysis procedure is extended to multidimensional analysis of structures subjected to multidimensional earthquake excitations. an improved multidimensional modal pushover analysis (IMMPA) method is presented in the paper in order to estimate the response demands of structures subjected to bidirectional earthquake excitations, in which the unidirectional earthquake excitation applied on equivalent SDOF system is replaced by the direct superposition of two components earthquake excitations, and independent analysis in each direction is not required and the application of simplified superposition formulas is avoided. The strength reduction factor spectra based on superposition of earthquake excitations are discussed and compared with the traditional strength reduction factor spectra. The step-by-step procedure is proposed to estimate seismic demands of structures. Two examples are implemented to verify the accuracy of the method, and the results of the examples show that (1) the IMMPA method can be used to estimate the responses of structure subjected to bidirectional earthquake excitations. (2) Along with increase of peak of earthquake acceleration, structural response deviation estimated with the IMMPA method may also increase. (3) Along with increase of the number of total floors of structures, structural response deviation estimated with the IMMPA method may also increase.
doi:10.1155/2014/320756
PMCID: PMC4129155  PMID: 25140333
20.  Identification of the Multi-Resistance Gene cfr in Escherichia coli Isolates of Animal Origin 
PLoS ONE  2014;9(7):e102378.
Previous study indicated that the multi-resistance gene cfr was mainly found in gram-positive bacteria, such as Staphylococcus and Enterococcus, and was sporadically detected in Escherichia coli. Little is known about the prevalence and transmission mechanism of cfr in E. coli. In this study, the presence of cfr in E. coli isolates collected during 2010–2012 from food-producing animals in Guangdong Province of China was investigated, and the cfr-positive E. coli isolates were characterized by PFGE, plasmid profiling, and genetic environment analysis. Of the 839 E. coli isolates, 10 isolates from pig were cfr positive. All the cfr-positive isolates presented a multi-resistance phenotype and were genetically divergent as determined by PFGE. In 8 out of the 10 strains, the cfr gene was located on plasmids of ∼30 kb. Restriction digestion of the plasmids with EcoRI and sequence hybridization with a cfr-specific probe revealed that the cfr-harboring fragments ranged from 6 to 23 kb and a ∼18 kb cfr-carrying fragment was common for the plasmids that were ∼30 kb. Four different genetic environments of cfr were detected, in which cfr is flanked by two identical copies of IS26, which may loop out the intervening sequence through homologous recombination. Among the 8 plasmids of ∼30 kb, 7 plasmids shared the same genetic environment. These results demonstrate plasmid-carried cfr in E. coli and suggest that transposition and homologous recombination mediated by IS26 might have played a rule in the transfer of the cfr gene in E. coli.
doi:10.1371/journal.pone.0102378
PMCID: PMC4103833  PMID: 25036029
21.  Relationships of Biomass with Environmental Factors in the Grassland Area of Hulunbuir, China 
PLoS ONE  2014;9(7):e102344.
Many studies have focused on the relationship between vegetation biomass and environmental factors in grassland. However, several questions remain to be answered, especially with regards to the spatial pattern of vegetation biomass. Thus, the distributed mechanism will be explored in the present study. Here, plant biomass was measured at 23 sites along a transect survey during the peak growing season in 2006. The data were analyzed with a classification and regression tree (CART) model. The structural equation modeling (SEM) was conducted to explicitly evaluate the both direct and indirect effects of these critical environmental elements on vegetation biomass. The results demonstrated that mean annual temperature (MAT) affected aboveground biomass (AGB) scored at −0.811 (P<0.05). The direct effect of MAT on belowground biomass (BGB) was −0.490 (P<0.05). The results were determined by SEM. Our results indicate that AGB and BGB in semi-arid ecosystems is strongly affected by precipitation and temperature. Future work shall attempt to take into account the integrated effects of precipitation and temperature. Meanwhile, partitioning the influences of environmental variations and vegetation types are helpful in illuminating the internal mechanism of biomass distribution.
doi:10.1371/journal.pone.0102344
PMCID: PMC4102509  PMID: 25032808
22.  Synthesis of 14N and 15N-labeled trityl-nitroxide biradicals with strong spin-spin interaction and improved sensitivity to redox status and oxygen 
The Journal of organic chemistry  2010;75(22):7796-7802.
Simultaneous evaluation redox status and oxygenation in biological systems is of great importance for the understanding of biological functions. Electron paramagnetic resonance spectroscopy coupled with the use of the nitroxide radicals have been an indispensable technique for this application but are still limited by its low oxygen sensitivity, and low EPR resolution in part due to the moderately broad EPR triplet and spin quenching through bioreduction. In this study, we showed that these drawbacks can be overcome through the use of trityl-nitroxide biradicals allowing for the simultaneous measurement of redox status and oxygenation. A new trityl-nitroxide biradical TNN14 composed of a pyrrolidinyl-nitroxide and a trityl, and its isotopically labeled 15N analogue TNN15 were synthesized and characterized. Both biradicals exhibited much stronger spin-spin interaction with J > 400 G than the previous synthesized trityl-nitroxide biradicals TN1 (~160 G) and TN2 (~52 G) with longer linker chain length. The enhanced stability of TNN14 was evaluated using ascorbate as reductant and the effect of different types of cyclodextrins on its stability in the presence of ascorbate was also investigated. Both biradicals are sensitive to redox status, and their corresponding trityl-hydroxylamines resulting from the reduction of the biradicals by ascorbate share the same oxygen sensitivity. Of note is that the 15N-labeled TNN15-H with an EPR doublet exhibits improved EPR signal amplitude as compared to TNN14-H with an EPR triplet. In addition, cyclic voltammetric studies verify the characteristic electrochemical behaviors of the trityl-nitroxide biradicals.
doi:10.1021/jo1016844
PMCID: PMC4073600  PMID: 21028905
23.  Synthesis of trityl radical-conjugated disulfide biradicals for the measurement of thiol concentration 
The Journal of organic chemistry  2011;76(10):3853-3860.
Measurement of thiol concentrations is of great importance for characterizing their critical role in normal metabolism and disease. Low-frequency electron paramagnetic resonance (EPR) spectroscopy and imaging, coupled with the use of exogenous paramagnetic probes, have been indispensable techniques for the in vivo measurement of various physiological parameters owing to the specificity, noninvasiveness and good depth of magnetic field penetration in animal tissues. However, in vivo detection of thiol levels by EPR spectroscopy and imaging is limited due to the need for improved probes. We report the first synthesis of trityl radical-conjugated disulfide biradicals (TSSN and TSST) as paramagnetic thiol probes. The use of trityl radicals in the construction of these biradicals greatly facilitates thiol measurement by EPR spectroscopy since trityls have extraordinary stability in living tissues with single narrow EPR line that enables high sensitivity and resolution for in vivo EPR spectroscopy and imaging. Both biradicals exhibit broad characteristic EPR spectra at room temperature due to their intramolecular spin-spin interaction. Reaction of these biradicals with thiol compounds such as glutathione (GSH) and cysteine results in the formation of trityl monoradicals which exhibit high spectral sensitivity to oxygen. The moderately slow reaction between the biradicals and GSH (k2 ∼ 0.3 M-1s-1 for TSSN and 0.2 M-1s-1 for TSST) allows for in vivo measurement of GSH concentration without altering the redox environment in biological systems. The GSH concentration in rat liver was determined to be 3.49 ± 0.14 mM by TSSN and 3.67 ± 0.24 mM by TSST, consistent with the value (3.71 ± 0.09 mM) determined by the Ellman's reagent. Thus, these trityl-based thiol probes exhibit unique properties enabling measurement of thiols in biological systems and should be of great value for monitoring redox metabolism.
doi:10.1021/jo200265u
PMCID: PMC4073604  PMID: 21488696
24.  Dose Dependent Effects of Reactive Oxygen and Nitrogen Species on the Function of Neuronal Nitric Oxide Synthase 
Reactive nitrogen species (RNS) and oxygen species (ROS) have been reported to modulate the function of nitric oxide synthase (NOS); however, the precise dosedependent effects of specific RNS and ROS on NOS function are unknown. Questions remain unanswered regarding whether pathophysiological levels of RNS and ROS alter NOS function, and if this alteration is reversible. We measured the effects of peroxynitrite (ONOO-), superoxide (O2.-), hydroxyl radical (.OH), and H2O2 on nNOS activity. The results showed that NO production was inhibited in a dose-dependent manner by all four oxidants, but only O2.- and ONOO- were inhibitory at pathophysiological concentrations (≤ 50 μM). Subsequent addition of tetrahydrobiopterin (BH4) fully restored activity after O2.- exposure, while BH4 partially rescued the activity decrease induced by the other three oxidants. Furthermore, treatment with either ONOO- or O2.- stimulated nNOS uncoupling with decreased NO and enhanced O2.- generation. Thus, nNOS is reversibly uncoupled by O2.- (≤ 50 μM), but irreversibly uncoupled and inactivated by ONOO-. Additionally, we observed that the mechanism by which oxidative stress alters nNOS activity involves not only BH4 oxidation, but also nNOS monomerization as well as possible degradation of the heme.
doi:10.1016/j.abb.2008.01.003
PMCID: PMC4073612  PMID: 18201545
neuronal nitric oxide synthase; nitric oxide; superoxide; peroxynitrite; hydroxyl; hydrogen peroxide; dose-dependent; uncoupling; tetrahydrobiopterin; monomerization
25.  Reactive Oxygen and Nitrogen Species Regulate Inducible Nitric Oxide Synthase Function Shifting the Balance of Nitric Oxide and Superoxide Production 
Inducible NOS (iNOS) is induced in diseases associated with inflammation and oxidative stress, and questions remain regarding its regulation. We demonstrate that reactive oxygen / nitrogen species (ROS/RNS) dose-dependently regulate iNOS function. Tetrahydrobiopterin (BH4)-replete iNOS was exposed to increasing concentrations of ROS/RNS and activity was measured with and without subsequent BH4 addition. Peroxynitrite (ONOO−) produced the greatest change in NO generation rate, ~95% decrease, and BH4 only partially restored this loss of activity. Superoxide (O2.−) greatly decreased NO generation, however, BH4 addition restored this activity. Hydroxyl radical (.OH) mildly decreases NO generation in a BH4-dependent manner. iNOS was resistant to H2O2 with only slightly decreased NO generation with up to millimolar concentrations. In contrast to the inhibition of NO generation, ROS enhanced O2.− production from iNOS, while ONOO− had the opposite effect. Thus, ROS promote reversible iNOS uncoupling, while ONOO− induces irreversible enzyme inactivation and decreases both NO and O2.− production.
doi:10.1016/j.abb.2009.11.019
PMCID: PMC4073618  PMID: 19932078
inducible nitric oxide synthase; nitric oxide; superoxide; peroxynitrite; hydroxyl; hydrogen peroxide; dose-dependent; uncoupling; tetrahydrobiopterin; monomerization

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