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1.  A genetic contribution from the Far East into Ashkenazi Jews via the ancient Silk Road 
Scientific Reports  2015;5:8377.
Contemporary Jews retain a genetic imprint from their Near Eastern ancestry, but obtained substantial genetic components from their neighboring populations during their history. Whether they received any genetic contribution from the Far East remains unknown, but frequent communication with the Chinese has been observed since the Silk Road period. To address this issue, mitochondrial DNA (mtDNA) variation from 55,595 Eurasians are analyzed. The existence of some eastern Eurasian haplotypes in eastern Ashkenazi Jews supports an East Asian genetic contribution, likely from Chinese. Further evidence indicates that this connection can be attributed to a gene flow event that occurred less than 1.4 kilo-years ago (kya), which falls within the time frame of the Silk Road scenario and fits well with historical records and archaeological discoveries. This observed genetic contribution from Chinese to Ashkenazi Jews demonstrates that the historical exchange between Ashkenazim and the Far East was not confined to the cultural sphere but also extended to an exchange of genes.
doi:10.1038/srep08377
PMCID: PMC4323646  PMID: 25669617
2.  ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism 
BMC Plant Biology  2015;15:19.
Background
Oil crop seeds are important sources of fatty acids (FAs) for human and animal nutrition. Despite their importance, there is a lack of an essential bioinformatics resource on gene transcription of oil crops from a comparative perspective. In this study, we developed ocsESTdb, the first database of expressed sequence tag (EST) information on seeds of four large-scale oil crops with an emphasis on global metabolic networks and oil accumulation metabolism that target the involved unigenes.
Description
A total of 248,522 ESTs and 106,835 unigenes were collected from the cDNA libraries of rapeseed (Brassica napus), soybean (Glycine max), sesame (Sesamum indicum) and peanut (Arachis hypogaea). These unigenes were annotated by a sequence similarity search against databases including TAIR, NR protein database, Gene Ontology, COG, Swiss-Prot, TrEMBL and Kyoto Encyclopedia of Genes and Genomes (KEGG). Five genome-scale metabolic networks that contain different numbers of metabolites and gene–enzyme reaction–association entries were analysed and constructed using Cytoscape and yEd programs. Details of unigene entries, deduced amino acid sequences and putative annotation are available from our database to browse, search and download. Intuitive and graphical representations of EST/unigene sequences, functional annotations, metabolic pathways and metabolic networks are also available. ocsESTdb will be updated regularly and can be freely accessed at http://ocri-genomics.org/ocsESTdb/.
Conclusion
ocsESTdb may serve as a valuable and unique resource for comparative analysis of acyl lipid synthesis and metabolism in oilseed plants. It also may provide vital insights into improving oil content in seeds of oil crop species by transcriptional reconstruction of the metabolic network.
Electronic supplementary material
The online version of this article (doi:10.1186/s12870-014-0399-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12870-014-0399-8
PMCID: PMC4312456  PMID: 25604238
Database; Expressed sequence tag; Metabolic network; Oil crop seeds
3.  Meta-analysis of the efficacy of probiotics in Helicobacter pylori eradication therapy 
World Journal of Gastroenterology : WJG  2014;20(47):18013-18021.
AIM: To evaluate the role of probiotics in the standard triple Helicobacter pylori therapy.
METHODS: In this meta-analysis, we investigated the efficacy of probiotics in a standard triple H. pylori therapy in adults. Searches were mainly conducted in MEDLINE/PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials. Fourteen studies met our criteria, and the quality of these studies was assessed using the Jadad scale. We used STATA version 12.0 to extract data and to calculate the odds ratios (ORs), which are presented with the corresponding 95% confidence intervals (CIs). The data are presented as forest plots.
RESULTS: The pooled ORs for the eradication rates calculated by intention-to-treat analysis and per-protocol analysis in the probiotic group vs the control group were 1.67 (95%CI: 1.38-2.02) and 1.68 (95%CI: 1.35-2.08), respectively, using the fixed-effects model. The sensitivity of the Asian studies was greater than that of the Caucasian studies (Asian: OR = 1.78, 95%CI: 1.40-2.26; Caucasian: OR = 1.48, 95%CI: 1.06-2.05). The pooled OR for the incidence of total adverse effects was significantly lower in the probiotic group (OR = 0.49, 95%CI: 0.26-0.94), using the random effects model, with significant heterogeneity (I2 = 85.7%). The incidence of diarrhea was significantly reduced in the probiotic group (OR = 0.21, 95%CI: 0.06-0.74), whereas the incidence of taste disorders, metallic taste, vomiting, nausea, and epigastric pain did not differ significantly between the probiotic group and the control group.
CONCLUSION: Supplementary probiotic preparations during standard triple H. pylori therapy may improve the eradication rate, particularly in Asian patients, and the incidence of total adverse effects.
doi:10.3748/wjg.v20.i47.18013
PMCID: PMC4273153  PMID: 25548501
Helicobacter pylori; Eradication; Probiotics; Meta-analysis; Adult
4.  Detection of Leptospira-Specific Antibodies Using a Recombinant Antigen-Based Enzyme-Linked Immunosorbent Assay 
We produced three highly purified recombinant antigens rLipL32, rLipL41, and rLigA-Rep (leptospiral immunoglobulin-like A repeat region) for the detection of Leptospira-specific antibodies in an enzyme-linked immunosorbent assay (ELISA). The performance of these recombinant antigens was evaluated using 121 human sera. Among them, 63 sera were microscopic agglutination test (MAT)-confirmed positive sera from febrile patients in Peru, 22 sera were indigenous MAT-negative febrile patient sera, and 36 sera were from patients with other febrile diseases from Southeast Asia, where leptospirosis is also endemic. Combining the results of immunoglobulin M (IgM) and IgG detection from these three antigens, the overall sensitivity is close to 90% based on the MAT. These results suggest that an ELISA using multiple recombinant antigens may be used as an alternative method for the detection of Leptospira-specific antibodies.
doi:10.4269/ajtmh.13-0041
PMCID: PMC3854885  PMID: 24166046
5.  De Novo Transcriptome Sequence Assembly and Identification of AP2/ERF Transcription Factor Related to Abiotic Stress in Parsley (Petroselinum crispum) 
PLoS ONE  2014;9(9):e108977.
Parsley is an important biennial Apiaceae species that is widely cultivated as herb, spice, and vegetable. Previous studies on parsley principally focused on its physiological and biochemical properties, including phenolic compound and volatile oil contents. However, little is known about the molecular and genetic properties of parsley. In this study, 23,686,707 high-quality reads were obtained and assembled into 81,852 transcripts and 50,161 unigenes for the first time. Functional annotation showed that 30,516 unigenes had sequence similarity to known genes. In addition, 3,244 putative simple sequence repeats were detected in curly parsley. Finally, 1,569 of the identified unigenes belonged to 58 transcription factor families. Various abiotic stresses have a strong detrimental effect on the yield and quality of parsley. AP2/ERF transcription factors have important functions in plant development, hormonal regulation, and abiotic response. A total of 88 putative AP2/ERF factors were identified from the transcriptome sequence of parsley. Seven AP2/ERF transcription factors were selected in this study to analyze the expression profiles of parsley under different abiotic stresses. Our data provide a potentially valuable resource that can be used for intensive parsley research.
doi:10.1371/journal.pone.0108977
PMCID: PMC4182582  PMID: 25268141
6.  CarrotDB: a genomic and transcriptomic database for carrot 
Carrot (Daucus carota L.) is an economically important vegetable worldwide and is the largest source of carotenoids and provitamin A in the human diet. Given the importance of this vegetable to humans, research and breeding communities on carrot should obtain useful genomic and transcriptomic information. The first whole-genome sequences of ‘DC-27’ carrot were de novo assembled and analyzed. Transcriptomic sequences of 14 carrot genotypes were downloaded from the Sequence Read Archive (SRA) database of National Center for Biotechnology Information (NCBI) and mapped to the whole-genome sequence before assembly. Based on these data sets, the first Web-based genomic and transcriptomic database for D. carota (CarrotDB) was developed (database homepage: http://apiaceae.njau.edu.cn/car rotdb). CarrotDB offers the tools of Genome Map and Basic Local Alignment Search Tool. Using these tools, users can search certain target genes and simple sequence repeats along with designed primers of ‘DC-27’. Assembled transcriptomic sequences along with fragments per kilobase of transcript sequence per millions base pairs sequenced information (FPKM) information of 14 carrot genotypes are also provided. Users can download de novo assembled whole-genome sequences, putative gene sequences and putative protein sequences of ‘DC-27’. Users can also download transcriptome sequence assemblies of 14 carrot genotypes along with their FPKM information. A total of 2826 transcription factor (TF) genes classified into 57 families were identified in the entire genome sequences. These TF genes were embedded in CarrotDB as an interface. The ‘GERMPLASM’ part of CarrotDB also offers taproot photos of 45 carrot genotypes and a table containing accession numbers, names, countries of origin and colors of cortex, phloem and xylem parts of taproots corresponding to each carrot genotype. CarrotDB will be continuously updated with new information.
Database URL: http://apiaceae.njau.edu.cn/carrotdb/
doi:10.1093/database/bau096
PMCID: PMC4178371  PMID: 25267795
7.  Effective Extraction and Assembly Methods for Simultaneously Obtaining Plastid and Mitochondrial Genomes 
PLoS ONE  2014;9(9):e108291.
Background
In conventional approaches to plastid and mitochondrial genome sequencing, the sequencing steps are performed separately; thus, plastid DNA (ptDNA) and mitochondrial DNA (mtDNA) should be prepared independently. However, it is difficult to extract pure ptDNA and mtDNA from plant tissue. Following the development of high-throughput sequencing technology, many researchers have attempted to obtain plastid genomes or mitochondrial genomes using high-throughput sequencing data from total DNA. Unfortunately, the huge datasets generated consume massive computing and storage resources and cost a great deal, and even more importantly, excessive pollution reads affect the accuracy of the assembly. Therefore, it is necessary to develop an effective method that can generate base sequences from plant tissue and that is suitable for all plant species. Here, we describe a highly effective, low-cost method for obtaining plastid and mitochondrial genomes simultaneously.
Results
First, we obtained high-quality DNA employing Partial Concentration Extraction. Second, we evaluated the purity of the DNA sample and determined the sequencing dataset size employing Vector Control Quantitative Analysis. Third, paired-end reads were obtained using a high-throughput sequencing platform. Fourth, we obtained scaffolds employing Two-step Assembly. Finally, we filled in gaps using specific methods and obtained complete plastid and mitochondrial genomes. To ensure the accuracy of plastid and mitochondrial genomes, we validated the assembly using PCR and Sanger sequencing. Using this method,we obtained complete plastid and mitochondrial genomes with lengths of 153,533 nt and 223,412 nt separately.
Conclusion
A simple method for extracting, evaluating, sequencing and assembling plastid and mitochondrial genomes was developed. This method has many advantages: it is timesaving, inexpensive and reproducible and produces high-quality sequence. Furthermore, this method can produce plastid and mitochondrial genomes simultaneously and be used for other plant species. Due to its simplicity and extensive applicability, this method will support research on plant cytoplasmic genomes.
doi:10.1371/journal.pone.0108291
PMCID: PMC4177114  PMID: 25251391
8.  Low-magnitude high-frequency loading, by whole-body vibration, accelerates early implant osseointegration in ovariectomized rats 
Molecular Medicine Reports  2014;10(6):2835-2842.
Osteoporosis deteriorates jaw bone quality and may compromise early implant osseointegration and early implant loading. The influence of low-magnitude, high-frequency (LMHF) vibration on peri-implant bone healing and implant integration in osteoporotic bones remains poorly understood. LMHF loading via whole-body vibration (WBV) for 8 weeks has previously been demonstrated to significantly enhance bone-to-implant contact, peri-implant bone fraction and implant mechanical properties in osteoporotic rats. In the present study, LMHF loading by WBV was performed in osteoporotic rats, with a loading duration of 4 weeks during the early stages of bone healing. The results indicated that 4-week LMHF loading by WBV partly reversed the negative effects of osteoporosis and accelerated early peri-implant osseointegration in ovariectomized rats.
doi:10.3892/mmr.2014.2597
PMCID: PMC4227418  PMID: 25270245
low-magnitude high-frequency loading; whole-body vibration; osteoporosis; dental implants; osseointegration; rat
9.  Activation of Dormant Secondary Metabolite Production by Introducing Neomycin Resistance into the Deep-Sea Fungus, Aspergillus versicolor ZBY-3 
Marine Drugs  2014;12(8):4326-4352.
A new ultrasound-mediated approach has been developed to introduce neomycin-resistance to activate silent pathways for secondary metabolite production in a bio-inactive, deep-sea fungus, Aspergillus versicolor ZBY-3. Upon treatment of the ZBY-3 spores with a high concentration of neomycin by proper ultrasound irradiation, a total of 30 mutants were obtained by single colony isolation. The acquired resistance of the mutants to neomycin was confirmed by a resistance test. In contrast to the ZBY-3 strain, the EtOAc extracts of 22 of the 30 mutants inhibited the human cancer K562 cells, indicating that these mutants acquired a capability to produce antitumor metabolites. HPLC-photodiode array detector (PDAD)-UV and HPLC-electron spray ionization (ESI)-MS analyses of the EtOAc extracts of seven bioactive mutants and the ZBY-3 strain indicated that diverse secondary metabolites have been newly produced in the mutant extracts in contrast to the ZBY-3 extract. The followed isolation and characterization demonstrated that six metabolites, cyclo(d-Pro-d-Phe) (1), cyclo(d-Tyr-d-Pro) (2), phenethyl 5-oxo-l-prolinate (3), cyclo(l-Ile-l-Pro) (4), cyclo(l-Leu-l-Pro) (5) and 3β,5α,9α-trihydroxy-(22E,24R)-ergosta-7,22-dien-6-one (6), were newly produced by the mutant u2n2h3-3 compared to the parent ZBY-3 strain. Compound 3 was a new compound; 2 was isolated from a natural source for the first time, and all of these compounds were also not yet found in the metabolites of other A. versicolor strains. Compounds 1–6 inhibited the K562 cells, with inhibition rates of 54.6% (1), 72.9% (2), 23.5% (3), 29.6% (4), 30.9% (5) and 51.1% (6) at 100 μg/mL, and inhibited also other human cancer HL-60, BGC-823 and HeLa cells, to some extent. The present study demonstrated the effectiveness of the ultrasound-mediated approach to activate silent metabolite production in fungi by introducing acquired resistance to aminoglycosides and its potential for discovering new compounds from silent fungal metabolic pathways. This approach could be applied to elicit the metabolic potentials of other fungal isolates to discover new compounds from cryptic secondary metabolites.
doi:10.3390/md12084326
PMCID: PMC4145319  PMID: 25076061
Aspergillus versicolor ZBY-3; deep-sea fungus; neomycin resistance; ultrasound; antitumor activity; secondary metabolite production
10.  Glioma-Associated Antigen HEATR1 Induces Functional Cytotoxic T Lymphocytes in Patients with Glioma 
Journal of Immunology Research  2014;2014:131494.
A2B5+ glioblastoma (GBM) cells have glioma stem-like cell (GSC) properties that are crucial to chemotherapy resistance and GBM relapse. T-cell-based antigens derived from A2B5+ GBM cells provide important information for immunotherapy. Here, we show that HEAT repeat containing 1 (HEATR1) expression in GBM tissues was significantly higher than that in control brain tissues. Furthermore, HEATR1 expression in A2B5+ U87 cells was higher than that in A2B5−U87 cells (P = 0.016). Six peptides of HEATR1 presented by HLA-A∗02 were selected for testing of their ability to induce T-cell responses in patients with GBM. When peripheral blood mononuclear cells from healthy donors (n = 6) and patients with glioma (n = 33) were stimulated with the peptide mixture, eight patients with malignant gliomas had positive reactivity with a significantly increased number of responding T-cells. The peptides HEATR1682–690, HEATR11126–1134, and HEATR1757–765 had high affinity for binding to HLA-A∗02:01 and a strong capacity to induce CTL response. CTLs against HEATR1 peptides were capable of recognizing and lysing GBM cells and GSCs. These data are the first to demonstrate that HEATR1 could induce specific CTL responses targeting both GBM cells and GSCs, implicating that HEATR1 peptide-based immunotherapy could be a novel promising strategy for treating patients with GBM.
doi:10.1155/2014/131494
PMCID: PMC4121097  PMID: 25126583
11.  Cardiac Troponin T (TNNT2) Mutations in Chinese Dilated Cardiomyopathy Patients 
BioMed Research International  2014;2014:907360.
Background. Dilated cardiomyopathy (DCM) is one of the leading causes of heart failure with high morbidity and mortality. Although more than 40 genes have been reported to cause DCM, the role of genetic testing in clinical practice is not well defined. Mutations in the troponin T (TNNT2) gene represent an important subset of known disease-causing mutations associated with DCM. Therefore, the aim of the present study was to determine the genetic variations in TNNT2 and the associations of those variations with DCM in Chinese patients. Methods. An approximately 4 kb fragment of the TNNT2 gene was isolated from 103 DCM patients and 192 healthy controls and was analyzed by DNA sequence analysis for genetic variations. Results. A total of 6 TNNT2 mutations were identified in 99 patients, including a G321T missense mutation (Leu84Phe) and 5 novel intronic mutations. Alleles of two novel SNPs (c.192 + 353 C>A, OR = 0.095, 95% CI: 0.013–0.714, P = 0.022; c.192 + 463 G>A, OR = 0.090, 95% CI: 0.012–0.675, P = 0.019) and SNP rs3729843 (OR = 1.889, 95% CI: 1.252–2.852; P = 0.002) were significantly correlated with DCM. Conclusions. These results suggest that the missense mutation (Leu84Phe) and two novel SNPs (c.192 + 353 C>A, c.192 + 463 G>A) in TNNT2 gene might be associated with DCM in the Chinese population.
doi:10.1155/2014/907360
PMCID: PMC4109665  PMID: 25110706
12.  Temporal scaling in information propagation 
Scientific Reports  2014;4:5334.
For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.
doi:10.1038/srep05334
PMCID: PMC4061555  PMID: 24939414
13.  Detecting Deep Divergence in Seventeen Populations of Tea Geometrid (Ectropis obliqua Prout) in China by COI mtDNA and Cross-Breeding 
PLoS ONE  2014;9(6):e99373.
The tea geometrid (Ectropis obliqua Prout, Lepidoptera: Geometridae) is a dominant chewing insect endemic in most tea-growing areas in China. Recently some E. obliqua populations have been found to be resistant to the nucleopolyhedrovirus (EoNPV), a host-specific virus that has so far been found only in E. obliqua. Although the resistant populations are morphologically indistinguishable from susceptible populations, we conducted a nationwide collection and examined the genetic divergence in the COI region of the mtDNA in E. obliqua. Phylogenetic analyses of mtDNA in 17 populations revealed two divergent clades with genetic distance greater than 3.7% between clades and less than 0.7% within clades. Therefore, we suggest that E. obliqua falls into two distinct groups. Further inheritance analyses using reciprocal single-pair mating showed an abnormal F1 generation with an unbalanced sex ratio and the inability to produce fertile eggs (or any eggs) through F1 self-crossing. These data revealed a potential cryptic species complex with deep divergence and reproductive isolation within E. obliqua. Uneven distribution of the groups suggests a possible geographic effect on the divergence. Future investigations will be conducted to examine whether EoNPV selection or other factors prompted the evolution of resistance.
doi:10.1371/journal.pone.0099373
PMCID: PMC4051655  PMID: 24915522
14.  Nine New and Five Known Polyketides Derived from a Deep Sea-Sourced Aspergillus sp. 16-02-1 
Marine Drugs  2014;12(6):3116-3137.
Nine new C9 polyketides, named aspiketolactonol (1), aspilactonols A–F (2–7), aspyronol (9) and epiaspinonediol (11), were isolated together with five known polyketides, (S)-2-(2′-hydroxyethyl)-4-methyl-γ-butyrolactone (8), dihydroaspyrone (10), aspinotriol A (12), aspinotriol B (13) and chaetoquadrin F (14), from the secondary metabolites of an Aspergillus sp. 16-02-1 that was isolated from a deep-sea sediment sample. Structures of the new compounds, including their absolute configurations, were determined by spectroscopic methods, especially the 2D NMR, circular dichroism (CD), Mo2-induced CD and Mosher’s 1H NMR analyses. Compound 8 was isolated from natural sources for the first time, and the possible biosynthetic pathways for 1–14 were also proposed and discussed. Compounds 1–14 inhibited human cancer cell lines, K562, HL-60, HeLa and BGC-823, to varying extents.
doi:10.3390/md12063116
PMCID: PMC4071568  PMID: 24871461
Aspergillus sp. 16-02-1; fungal strain from deep sea sediment; aspiketolactonol; aspilactonol; aspyronol; lactone; epiaspinonediol; polyketide; structure; cytotoxicity
15.  Procalcitonin and C-reactive protein in urinary tract infection diagnosis 
BMC Urology  2014;14:45.
Background
Urinary infections are a common type of pediatric disease, and their treatment and prognosis are closely correlated with infection location. Common clinical manifestations and laboratory tests are insufficient to differentiate between acute pyelonephritis and lower urinary tract infection. This study was conducted to explore a diagnostic method for upper and lower urinary tract infection differentiation.
Methods
The diagnostic values of procalcitonin (PCT) and C-reactive protein (CRP) were analyzed using the receiver operating characteristic curve method for upper and lower urinary tract infection differentiation. PCT was determined using chemiluminescent immunoassay.
Results
The PCT and CRP values in children with acute pyelonephritis were significantly higher than those in children with lower urinary tract infection (3.90 ± 3.51 ng/ml and 68.17 ± 39.42 mg/l vs. 0.48 ± 0.39 ng/ml and 21.39 ± 14.92 mg/l). The PCT values were correlated with the degree of renal involvement, whereas the CRP values failed to show such a significant correlation. PCT had a sensitivity of 90.47% and a specificity of 88% in predicting nephropathia, whereas CRP had sensitivity of 85.71% and a specificity of 48%.
Conclusions
Both PCT and CRP can be used for upper and lower urinary tract infection differentiation, but PCT has higher sensitivity and specificity in predicting pyelonephritis than CRP. PCT showed better results than CRP. PCT values were also correlated with the degree of renal involvement.
doi:10.1186/1471-2490-14-45
PMCID: PMC4074860  PMID: 24886302
Urinary tract infections; Acute pyelonephritis; Receiver operating characteristic curve; Procalcitonin
16.  Plasma NT pro-BNP, hs-CRP and big-ET levels at admission as prognostic markers of survival in hospitalized patients with dilated cardiomyopathy: a single-center cohort study 
Background
Circulating N-terminal pro-B-type natriuretic peptide (NT pro-BNP), high- sensitivity C-reactive protein (hs-CRP) and big endothelin (big-ET) have been shown to be increased in heart failure and to contribute to both hemodynamic deterioration and cardiovascular remodeling. Here, we examined the prognostic value of the three neurohormones at admission in a population of hospitalized patients with dilated cardiomyopathy (DCM).
Methods and results
This cohort study was undertaken in 622 hospitalized patients with DCM in Fuwai Hospital from January 2005 to September 2011 (female 26.5%, 51.4 ± 14.6 years old). Standard demographics, echocardiography and routine blood samples were obtained shortly after admission. NT pro-BNP, hs-CRP and big-ET were measured, and their concentrations in relation to all-cause mortality were assessed through a mean follow-up of 2.6 ± 1.6 years. Kaplan-Meier curves showed that the all-cause mortality rates were higher in patients with NT pro-BNP > 2247 pmol/L compared to patients with NT pro-BNP < 2247 pmol/L (11.9% vs 34.8%, log-rank χ2 = 35.588, P < 0.001), in patients with hs-CRP > 3.90 mg/L compared to patients with hs-CRP < 3.90 mg/L (12.8% vs 33.6%, log-rank χ2 = 39.662, P < 0.001) and in patients with big-ET > 0.95 pmol/L compared to patients with big-ET <0.95 pmol/L (12.5% vs 31.0%, log-rank χ2 = 17.890, P < 0.001). High circulating concentrations of NT pro-BNP (HR 2.217, 95% CI 1.015-4.846, P = 0.046) and hs-CRP (HR 1.922, 95% CI 1.236-2.988, P = 0.004), but not big-ET, in addition to left atrial diameter and fasting blood glucose, were independent predictors of the outcome defined as all-cause mortality.
Conclusions
In a large population of patients with DCM, the circulating concentrations of NT pro-BNP and hs-CRP, but not big-ET, were independent markers of all-cause mortality.
doi:10.1186/1471-2261-14-67
PMCID: PMC4041639  PMID: 24885051
Dilated cardiomyopathy; NT pro-BNP; Hs-CRP; Big-endothelin; Prognosis
17.  Effect of Heparin on Prevention of Flap Loss in Microsurgical Free Flap Transfer: A Meta-Analysis 
PLoS ONE  2014;9(4):e95111.
The effectiveness of heparin for thromboprophylaxis during microvascular free flap transfer is uncertain. The purpose of this meta-analysis was to determine the effect of heparin on the prevention of flap loss in microsurgical free flap transfer.A search of PubMed, Cochrane databases, and Google Scholar using combinations of the search terms heparin, free flap, flap loss, free tissue transfer was conducted on March 15, 2013. Inclusion criteria were: 1) Prospective randomized trials. 2) Retrospective, non-randomized studies. 3) Patients received free tissue transfer. Flap loss rate was used to evaluate treatment efficacy. Odds ratios (ORs) with 95% confidence intervals (CI) were calculated and compared between therapies. Four studies meet the criteria for analysis and were included. Two studiescompared aspirin and heparin, and the ORs of the 2 studies were 1.688 and 2.087. The combined OR of 2.003 (95% CI 0.976–4.109, p = 0.058) did not indicate any significant difference between heparin and aspirin therapies. Two studiescompared high and low doses of dalteparin/heparin therapies, and the ORs of the 2 studies were 4.691 and 11.00. The combined OR of 7.810 (95% CI 1.859–32.808, p = 0.005) revealed a significant difference indicating that high dose dalteparin or heparin therapy is associated with a greater flap loss rate than low dose therapy. Heparin and aspirin prophylaxis are associated with similar flap loss rates after free flap transfer, and high dose dalteparin or heparin therapy is associated with a greater flap loss rate than low dose therapy.
doi:10.1371/journal.pone.0095111
PMCID: PMC3994018  PMID: 24751924
18.  The influence of herbal medicine ursolic acid on the uptake of rosuvastatin mediated by OATP1B1*1a and *5 
Chinese herbal medicines such as hawthorn, salvia, etc., are frequently combined with statins so as to treat cardiovascular diseases more effectively. Chinese herbal medicines contain many kinds of active components, which may have drug–drug interactions with statins. This study aims to explore the effect and mechanism by which ursolic acid affects OATP1B1-mediated transport of rosuvastatin. This study will explore the effect of ursolic acid on OAPT1B1-mediated transport of rosuvastatin in the different cell systems. Given the genetic polymorphisms of OATP1B1, simultaneously, this study will further explore the effect of ursolic acid on OATP1B1 (521T>C)-mediated transport of rosuvastatin. When the concentration of ursolic acid was 1.8 and 18 µM, it showed that ursolic acid significantly inhibits the uptake of rosuvastatin in both OATP1B1*1a-HEK 293T cells and OATP1B1*5-HEK 293T cells. The reduction of OATP1B1*1a transport of rosuvastatin were 34.60 ± 2.99 and 66.08 ± 1.83 %, and for OATP1B1*5 were 34.27 ± 7.08 % and 66.95 ± 1.14 %. Inhibitory parameters of IC50 were 6.25 ± 0.42 and 6.07 ± 0.57 µM, respectively. This study suggests that ursolic acid can affect the uptake of rosuvastatin in hepatocytes by inhibiting the transport of OATP1B1, and gene mutation of OATP1B1 may cause different effects on its transport of rosuvastatin.
doi:10.1007/s13318-014-0187-8
PMCID: PMC4142139  PMID: 24736980
Rosuvastatin; Ursolic acid; OATP1B1; Transporter
20.  The Role of Lung Ultrasound in Diagnosis of Respiratory Distress Syndrome in Newborn Infants 
Iranian Journal of Pediatrics  2014;24(2):147-154.
Abstract
Objective
The aim of this study was to evaluate the value of lung ultrasound in the diagnosis of respiratory distress syndrome (RDS) in newborn infants.
Methods
From March 2012 to May 2013, 100 newborn infants were divided into two groups: RDS group (50 cases) and control group (50 cases). According to the findings of chest x-ray, there were 10 cases of grade II RDS, 15 grade III cases, and 25 grade IV cases in RDS group. Lung ultrasound was performed at bedside by a single expert. The ultrasound indexes observed in this study included pleural line, A-line, B-line, lung consolidation, air bronchograms, bilateral white lung, interstitial syndrome, lung sliding, lung pulse etc.
Findings
In all of the infants with RDS, lung ultrasound consistently showed generalized consolidation with air bronchograms, bilateral white lung or interstitial syndrome, pleural line abnormalities, A-line disappearance, pleural effusion, lung pulse, etc. The simultaneous demonstration of lung consolidation, pleural line abnormalities and bilateral white lung, or lung consolidation, pleural line abnormalities and A-line disappearance co-exists with a sensitivity and specificity of 100% for the diagnosis of neonatal RDS.
Conclusion
This study indicates that using an ultrasound to diagnose neonatal RDS is accurate and reliable tool. A lung ultrasound has many advantages over other techniques. Ultrasound is non-ionizing, low-cost, easy to operate, and can be performed at bedside, making this technique ideal for use in NICU.
PMCID: PMC4268833  PMID: 25535532
Lung Ultrasound; Respiratory Distress Syndrome; Newborn
21.  Pattern of cerebral hyperperfusion in Alzheimer’s disease and amnestic mild cognitive impairment using voxel-based analysis of 3D arterial spin-labeling imaging: initial experience 
Purpose
A three-dimensional (3D) continuous pulse arterial spin labeling (ASL) technique was used to investigate cerebral blood flow (CBF) changes in patients with Alzheimer’s disease (AD), amnestic mild cognitive impairment (aMCI), and age- and sex-matched healthy controls.
Materials and methods
Three groups were recruited for comparison, 24 AD patients, 17 MCI patients, and 21 age- and sex-matched control subjects. Three-dimensional ASL scans covering the entire brain were acquired with a 3.0 T magnetic resonance scanner. Spatial processing was performed with statistical parametric mapping 8. A second-level one-way analysis of variance analysis (threshold at P<0.05) was performed on the preprocessed ASL data. An average whole-brain CBF for each subject was also included as group-level covariates for the perfusion data, to control for individual CBF variations.
Results
Significantly increased CBF was detected in bilateral frontal lobes and right temporal subgyral regions in aMCI compared with controls. When comparing AD with aMCI, the major hyperperfusion regions were the right limbic lobe and basal ganglia regions, including the putamen, caudate, lentiform nucleus, and thalamus, and hypoperfusion was found in the left medial frontal lobe, parietal cortex, the right middle temporo-occipital lobe, and particularly, the left anterior cingulate gyrus. We also found decreased CBF in the bilateral temporo-parieto-occipital cortices and left limbic lobe in AD patients, relative to the control group. aMCI subjects showed decreased blood flow in the left occipital lobe, bilateral inferior temporal cortex, and right middle temporal cortex.
Conclusion
Our results indicated that ASL provided useful perfusion information in AD disease and may be used as an appealing alternative for further pathologic and neuropsychological studies, especially of compensatory mechanisms for cerebral hypoperfusion.
doi:10.2147/CIA.S58879
PMCID: PMC3971940  PMID: 24707173
Alzheimer’s disease; amnestic mild cognitive impairment; perfusion image; arterial spin labeling
22.  Personal Exposure to Household Particulate Matter, Household Activities and Heart Rate Variability among Housewives 
PLoS ONE  2014;9(3):e89969.
Background
The association between indoor air pollution and heart rate variability (HRV) has been well-documented. Little is known about effects of household activities on indoor air quality and HRV alteration. To investigate changes in HRV associated with changes in personal exposure to household particulate matter (PM) and household activities.
Methods
We performed 24-h continuous monitoring of electrocardiography and measured household PM exposure among 50 housewives. The outcome variables were log10-transformed standard deviation of normal-to-normal (NN) intervals (SDNN) and the square root of the mean of the sum of the squares of differences between adjacent NN intervals (r-MSSD). Household PM was measured as the mass concentration of PM with an aerodynamic diameter <2.5 µm (PM2.5). We used mixed-effects models to examine the association between household PM2.5 exposure and log10-transformed HRV indices.
Results
After controlling for potential confounders, an interquartile range change in household PM2.5 with 1- to 4-h mean was associated with 1.25–4.31% decreases in SDNN and 0.12–3.71% decreases in r-MSSD. Stir-frying, cleaning with detergent and burning incense may increase household PM2.5 concentrations and modify the effects of household PM2.5 on HRV indices among housewives.
Conclusions
Indoor PM2.5 exposures were associated with decreased SDNN and r-MSSD among housewives, especially during stir-frying, cleaning with detergent and burning incense.
doi:10.1371/journal.pone.0089969
PMCID: PMC3940710  PMID: 24594880
23.  Safety and efficacy of intravenous esmolol before prospective electrocardiogram-triggered high-pitch spiral acquisition for computed tomography coronary angiography 
Background
In order to acquire a high quality image with a low radiation dose, prospective electrocardiogram (ECG)-triggered computed tomography coronary angiography (CTCA) requires a stable heart rate (HR) < 65 beats/min. Esmolol has the advantage of reducing HR. The objective of this article is to assess the value of intravenous esmolol treatment before prospective ECG-triggered high-pitch spiral acquisition for CTCA.
Methods
From March 2013 to June 2013, 313 patients underwent prospective ECG-triggered CTCA. Two hundred and thirty two of them received esmolol before angiography. We retrospectively analyzed clinical characteristics, esmolol dose, radiation exposure dose, and the change in HR and blood pressure in these 232 patients.
Results
A total of 232 patients with a HR > 65 beats/min before CTCA examination received intravenous esmolol treatment (mean dose of 57.26 ± 15.39 mg). The mean initial HR (HR1), slowest HR (HR2), and the HR 30 min after HR2 (HR3) were 75.06 ± 5.59, 60.75 ± 4.00, and 75.54 ± 5.96 beats/min, respectively (HR1 vs. HR2, P < 0.0001; HR1 vs. HR3, P = 0.377). The mean time from esmolol administration to HR2 was 24.25 ± 4.97 s and the mean effective radiation dose was 2.28 ± 0.02 mSv.
Conclusions
HR could be rapidly controlled at an optimum level with intravenous esmolol before prospective ECG-triggered high-pitch spiral acquisition for CTCA. Consequently, the patients received a very low radiation dose.
doi:10.3969/j.issn.1671-5411.2014.01.011
PMCID: PMC3981982  PMID: 24748880
Esmolol; Electrocardiogram; Coronary angiography; Heart rate
24.  A New QTL for Plant Height in Barley (Hordeum vulgare L.) Showing No Negative Effects on Grain Yield 
PLoS ONE  2014;9(2):e90144.
Introduction
Reducing plant height has played an important role in improving crop yields. The success of a breeding program relies on the source of dwarfing genes. For a dwarfing or semi-dwarfing gene to be successfully used in a breeding program, the gene should have minimal negative effects on yield and perform consistently in different environments.
Methods
In this study, 182 doubled haploid lines, generated from a cross between TX9425 and Naso Nijo, were grown in six different environments to identify quantitative trait loci (QTL) controlling plant height and investigate QTL × environments interaction.
Results
A QTL for plant was identified on 7H. This QTL showed no significant effects on other agronomic traits and yield components and consistently expressed in the six environments. A sufficient allelic effect makes it possible for this QTL to be successfully used in breeding programs.
doi:10.1371/journal.pone.0090144
PMCID: PMC3938599  PMID: 24587247
25.  Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis 
Genome Biology  2014;15(2):R39.
Background
Sesame, Sesamum indicum L., is considered the queen of oilseeds for its high oil content and quality, and is grown widely in tropical and subtropical areas as an important source of oil and protein. However, the molecular biology of sesame is largely unexplored.
Results
Here, we report a high-quality genome sequence of sesame assembled de novo with a contig N50 of 52.2 kb and a scaffold N50 of 2.1 Mb, containing an estimated 27,148 genes. The results reveal novel, independent whole genome duplication and the absence of the Toll/interleukin-1 receptor domain in resistance genes. Candidate genes and oil biosynthetic pathways contributing to high oil content were discovered by comparative genomic and transcriptomic analyses. These revealed the expansion of type 1 lipid transfer genes by tandem duplication, the contraction of lipid degradation genes, and the differential expression of essential genes in the triacylglycerol biosynthesis pathway, particularly in the early stage of seed development. Resequencing data in 29 sesame accessions from 12 countries suggested that the high genetic diversity of lipid-related genes might be associated with the wide variation in oil content. Additionally, the results shed light on the pivotal stage of seed development, oil accumulation and potential key genes for sesamin production, an important pharmacological constituent of sesame.
Conclusions
As an important species from the order Lamiales and a high oil crop, the sesame genome will facilitate future research on the evolution of eudicots, as well as the study of lipid biosynthesis and potential genetic improvement of sesame.
doi:10.1186/gb-2014-15-2-r39
PMCID: PMC4053841  PMID: 24576357

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