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1.  An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data 
Analytica chimica acta  2013;806:10.1016/j.aca.2013.10.050.
It is common that imbalanced datasets are often generated from high-throughput screening (HTS). For a given dataset without taking into account the imbalanced nature, most classification methods tend to produce high predictive accuracy for the majority class, but significantly poor performance for the minority class. In this work, an efficient algorithm, GLMBoost, coupled with Synthetic Minority Over-sampling TEchnique (SMOTE) is developed and utilized to overcome the problem for several imbalanced datasets from PubChem BioAssay. By applying the proposed combinatorial method, those data of rare samples (active compounds), for which usually poor results are generated, can be detected apparently with high balanced accuracy (Gmean). As a comparison with GLMBoost, Random Forest (RF) combined with SMOTE is also adopted to classify the same datasets. Our results show that the former (GLMBoost + SMOTE) not only exhibits higher performance as measured by percentage correct classification for the rare samples (Sensitivity) and Gmean, but also demonstrates greater computational efficiency than the latter (RF + SMOTE). Therefore, we hope that the proposed combinatorial algorithm based on GLMBoost and SMOTE could be extensively used to tackle the imbalanced classification problem.
doi:10.1016/j.aca.2013.10.050
PMCID: PMC3884825  PMID: 24331047
High-throughput screening; Under-sampling; Over-sampling; PubChem; Imbalanced classification
2.  Risk factor analysis of perioperative mortality after ruptured bleeding in hepatocellular carcinoma 
World Journal of Gastroenterology : WJG  2014;20(40):14921-14926.
AIM: To discuss strategies and prognosis for the emergency treatment of ruptured bleeding in primary hepatocellular carcinoma.
METHODS: The retrospective analysis was performed by examining the emergency treatment experiences of 60 cases of ruptured bleeding in primary hepatocellular carcinoma. The treatment methods included surgical tumour resection, transcatheter arterial embolization (TAE) and non-surgical treatment. Univariate and multivariate analyses were performed to identify the risk factors that impacted 30-d mortality in the research groups.
RESULTS: The 30-d mortality of all patients was 28.3% (n = 17). The univariate analysis showed that Child-Pugh C level liver function, shock, massive blood transfusion and large tumour volume were risk factors that influenced 30-d mortality. The multivariate analysis showed that shock and massive blood transfusion were independent risk factors that impacted the 30-d mortality of surgical resection. As for the TAE patients, larger tumour volume was a risk factor towards prognosis.
CONCLUSION: Radical resection and TAE therapy would achieve better results in carefully selected ruptured hepatocellular tumours.
doi:10.3748/wjg.v20.i40.14921
PMCID: PMC4209555  PMID: 25356052
Hepatocellular carcinoma; Spontaneous rupture; Liver resection
3.  Did you notice the tibial nutrient artery when applying external fixation? 
International Orthopaedics  2013;37(10):2089-2090.
doi:10.1007/s00264-013-2062-7
PMCID: PMC3779580  PMID: 23949093
Tibial nutrient artery; External fixator
4.  Microparticles: new light shed on the understanding of venous thromboembolism 
Acta Pharmacologica Sinica  2014;35(9):1103-1110.
Microparticles are small membrane fragments shed primarily from blood and endothelial cells during either activation or apoptosis. There is mounting evidence suggesting that microparticles perform a large array of biological functions and contribute to various diseases. Of these disease processes, a significant link has been established between microparticles and venous thromboembolism. Advances in research on the role of microparticles in thrombosis have yielded crucial insights into possible mechanisms, diagnoses and therapeutic targets of venous thromboembolism. In this review, we discuss the definition and properties of microparticles and venous thromboembolism, provide a synopsis of the evidence detailing the contributions of microparticles to venous thromboembolism, and propose potential mechanisms, by which venous thromboembolism occurs. Moreover, we illustrate a possible role of microparticles in cancer-related venous thromboembolism.
doi:10.1038/aps.2014.73
PMCID: PMC4155535  PMID: 25152025
microparticle; blood cell; endothelial cell; venous thromboembolism; intercellular communication; inflammation; cancer
5.  QTug.sau-3B Is a Major Quantitative Trait Locus for Wheat Hexaploidization 
G3: Genes|Genomes|Genetics  2014;4(10):1943-1953.
Meiotic nonreduction resulting in unreduced gametes is thought to be the predominant mechanism underlying allopolyploid formation in plants. Until now, however, its genetic base was largely unknown. The allohexaploid crop common wheat (Triticum aestivum L.), which originated from hybrids of T. turgidum L. with Aegilops tauschii Cosson, provides a model to address this issue. Our observations of meiosis in pollen mother cells from T. turgidum×Ae. tauschii hybrids indicated that first division restitution, which exhibited prolonged cell division during meiosis I, was responsible for unreduced gamete formation. A major quantitative trait locus (QTL) for this trait, named QTug.sau-3B, was detected on chromosome 3B in two T. turgidum×Ae. tauschii haploid populations. This QTL is situated between markers Xgwm285 and Xcfp1012 and covered a genetic distance of 1 cM in one population. QTug.sau-3B is a haploid-dependent QTL because it was not detected in doubled haploid populations. Comparative genome analysis indicated that this QTL was close to Ttam-3B, a collinear homolog of tam in wheat. Although the relationship between QTug.sau-3B and Ttam requires further study, high frequencies of unreduced gametes may be related to reduced expression of Ttam in wheat.
doi:10.1534/g3.114.013078
PMCID: PMC4199700  PMID: 25128436
allopolyploidy; CYCA1;2/TAM; first division restitution; unreduced gametes; Triticum aestivum
6.  MicroRNA-induced pluripotent stem cells 
Cell stem cell  2010;7(1):31-35.
doi:10.1016/j.stem.2010.06.011
PMCID: PMC4121883  PMID: 20621047
microRNA (miRNA); Reprogramming; Induced Pluripotent stem (iPS) cells; Embryonic Stem cells
7.  Radix Astragali Improves Dysregulated Triglyceride Metabolism and Attenuates Macrophage Infiltration in Adipose Tissue in High-Fat Diet-Induced Obese Male Rats through Activating mTORC1-PPARγ Signaling Pathway 
PPAR Research  2014;2014:189085.
Increased levels of free fatty acids (FFAs) and hypertriglyceridemia are important risk factors for cardiovascular disease. The effective fraction isolated from radix astragali (RA) has been reported to alleviate hypertriglyceridemia. The mechanism of this triglyceride-lowering effect of RA is unclear. Here, we tested whether activation of the mTORC1-PPARγ signaling pathway is related to the triglyceride-lowering effect of RA. High-fat diet-induced obese (DIO) rats were fed a high-fat diet (40% calories from fat) for 9-10 weeks, and 4 g/kg/d RA was administered by gavage. RA treatment resulted in decreased fasting triglyceride levels, FFA concentrations, and adipocyte size. RA treated rats showed improved triglyceride clearance and fatty acid handling after olive oil overload. RA administration could also decrease macrophage infiltration and expression of MCP-1 and TNFα, but it may also increase the expression of PPARγ in epididymal adipose tissue from RA treated rats. Consistently, expressions of PPARγ and phospho-p70S6K were increased in differentiated 3T3-L1 adipocytes treated with RA. Moreover, RA couldnot upregulate the expression of PPARγ at the presence of rapamycin. In conclusion, the mTORC1-PPARγ signaling pathway is a potential mechanism through which RA exerts beneficial effects on the disturbance of triglyceride metabolism and dysfunction of adipose tissue in DIO rats.
doi:10.1155/2014/189085
PMCID: PMC4000987  PMID: 24817881
8.  Analyzing and modeling rheological behavior of liver fibrosis in rats using shear viscoelastic moduli*  
The process of liver fibrosis changes the rheological properties of liver tissue. This study characterizes and compares liver fibrosis stages from F0 to F4 in rats in terms of shear viscoelastic moduli. Here two viscoelastic models, the Zener model and Voigt model, were applied to experimental data of rheometer tests and then values of elasticity and viscosity were estimated for each fibrosis stage. The results demonstrate that moderate fibrosis (≤F2) has a good correlation with liver viscoelasticity. The mean Zener elasticity E 1 increases from (0.452±0.094) kPa (F0) to (1.311±0.717) kPa (F2), while the mean Voigt elasticity E increases from (0.618±0.089) kPa (F0) to (1.701±0.844) kPa (F2). The mean Zener viscosity increases from (3.499±0.186) Pa·s (F0) to (4.947±1.811) Pa·s (F2) and the mean Voigt viscosity increases from (3.379±0.316) Pa·s (F0) to (4.625±1.296) Pa·s (F2). Compared with viscosity, the elasticity shows smaller variations at stages F1 and F2 no matter what viscoelastic model is used. Therefore, the estimated elasticity is more effective than viscosity for differentiating the fibrosis stages from F0 to F2.
doi:10.1631/jzus.B1300121
PMCID: PMC3989156  PMID: 24711358
Biological mechanics; Rheological properties; Liver fibrosis; Viscoelasticity; Shear modulus; Elasticity; Viscosity; Zener model; Voigt model
9.  Mutational Spectrum of the NKX2-5 Gene in Patients with Lone Atrial Fibrillation 
Atrial fibrillation (AF) is the most common form of sustained cardiac arrhythmia in humans and is responsible for substantial morbidity and mortality worldwide. Emerging evidence indicates that abnormal cardiovascular development is involved in the pathogenesis of AF. In this study, the coding exons and splice sites of the NKX2-5 gene, which encodes a homeodomain-containing transcription factor essential for cardiovascular genesis, were sequenced in 146 unrelated patients with lone AF as well as the available relatives of the mutation carriers. A total of 700 unrelated ethnically matched healthy individuals used as controls were genotyped. The disease-causing potential of the identified NKX2-5 variations was predicted by MutationTaster and PolyPhen-2. The functional characteristics of the mutant NKX2-5 proteins were analyzed using a dual-luciferase reporter assay system. As a result, two heterozygous NKX2-5 mutations, including a previously reported p.E21Q and a novel p.T180A mutation, were identified in two families with AF transmitted in an autosomal dominant pattern. The mutations co-segregated with AF in the families with complete penetrance. The detected substitutions, which altered the amino acids highly conserved evolutionarily across species, were absent in 700 control individuals and were both predicted to be causative. Functional analyses demonstrated that the NKX2-5 mutants were associated with significantly decreased transcriptional activity compared with their wild-type counterpart. The findings expand the spectrum of NKX2-5 mutations linked to AF and provide additional evidence that dysfunctional NKX2-5 may confer vulnerability to AF, suggesting the potential benefit for the early prophylaxis and personalized treatment of AF.
doi:10.7150/ijms.8407
PMCID: PMC4003540  PMID: 24782644
Atrial fibrillation; Transcription factor; NKX2-5; Molecular genetics; Mutation.
10.  Tai Chi Chuan optimizes the functional organization of the intrinsic human brain architecture in older adults 
Whether Tai Chi Chuan (TCC) can influence the intrinsic functional architecture of the human brain remains unclear. To examine TCC-associated changes in functional connectomes, resting-state functional magnetic resonance images were acquired from 40 older individuals including 22 experienced TCC practitioners (experts) and 18 demographically matched TCC-naïve healthy controls, and their local functional homogeneities across the cortical mantle were compared. Compared to the controls, the TCC experts had significantly greater and more experience-dependent functional homogeneity in the right post-central gyrus (PosCG) and less functional homogeneity in the left anterior cingulate cortex (ACC) and the right dorsal lateral prefrontal cortex. Increased functional homogeneity in the PosCG was correlated with TCC experience. Intriguingly, decreases in functional homogeneity (improved functional specialization) in the left ACC and increases in functional homogeneity (improved functional integration) in the right PosCG both predicted performance gains on attention network behavior tests. These findings provide evidence for the functional plasticity of the brain’s intrinsic architecture toward optimizing locally functional organization, with great implications for understanding the effects of TCC on cognition, behavior and health in aging population.
doi:10.3389/fnagi.2014.00074
PMCID: PMC4029006  PMID: 24860494
functional homogeneity; Tai Chi Chuan; meditation; aerobic exercise; executive function
11.  Nickel trafficking system responsible for urease maturation in Helicobacter pylori 
Helicobacter pylori (H. pylori) is a common human pathogen responsible for various gastric diseases. This bacterium relies on the production of urease and hydrogenase to inhabit the acidic environment of the stomach. Nickel is an essential cofactor for urease and hydrogenase. H. pylori has to uptake sufficient nickel ions for the maturation of urease, and on the other way, to prevent the toxic effects of excessive nickel ions. Therefore, H. pylori has to strike a delicate balance between the import of nickel ions, its efficient intracellular storage, and delivery to nickel-dependent metalloenzymes when required. The assembly and maturation of the urease enzyme is a complex and timely ordered process, requiring various regulatory, uptake, chaperone and accessory proteins. In this review, we focus on several nickel trafficking proteins involved in urease maturation: NikR, NixA, HypAB, UreEFGH, HspA, Hpn and Hpnl. The work will deepen our understanding of how this pathogenic bacterium adapts to severe habitant environments in the host.
doi:10.3748/wjg.v19.i45.8211
PMCID: PMC3857443  PMID: 24363511
Urease; Histidine-rich protein; NikR; NixA; Helicobacter pylori
12.  A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28-let-7 pathway 
Nature  2013;497(7448):244-248.
The pluripotency factor Lin28 blocks the expression of let-7 microRNAs (miRNAs) in undifferentiated cells during development and functions as an oncogene in a subset of cancers1. Lin28 binds to let-7 precursor RNAs and recruits 3′ terminal uridylyl transferases (TUTases) to selectively inhibit let-7 biogenesis2–4. Uridylated pre-let-7 is refractory to processing by Dicer and is rapidly degraded by an unknown ribonuclease5. Here we identify Dis3l2 as the 3′-5′ exonuclease responsible for the decay of uridylated pre-let-7. Biochemical reconstitution assays reveal that 3′ oligouridylation stimulates Dis3l2 activity in vitro, and knockdown of Dis3l2 in mouse embryonic stem cells leads to the stabilization of pre-let-7. Our study establishes 3′ oligouridylation as an RNA decay signal for Dis3l2 and identifies the first physiological RNA substrate of this novel exonuclease that is mutated in the Perlman syndrome of fetal overgrowth and predisposition to Wilms’ tumor6.
doi:10.1038/nature12119
PMCID: PMC3651781  PMID: 23594738
Dis3l2; exonuclease; uridylation; Lin-28; Lin28; let-7; microRNA (miRNA); TUTase; Embryonic Stem Cells
13.  Efficacy and safety of combination therapy with vildagliptin and metformin versus metformin up-titration in Chinese patients with type 2 diabetes mellitus: study design and rationale of the vision study 
Background and aim
Limitations of the currently recommended stepwise treatment pathway for type 2 diabetes mellitus (T2DM), especially the failure of monotherapies to maintain good glycemic control, have prompted use of early, more aggressive combination therapies.
The VISION study is designed to explore the efficacy and safety of vildagliptin as an add-on to metformin therapy compared with up-titration of metformin monotherapy in Chinese patients with T2DM.
Methods
VISION, a 24-week, phase 4, prospective, randomized, multicenter, open-label, parallel-group study, will include 3312 Chinese T2DM patients aged ≥18 years who are inadequately controlled (6.5% >HbA1c ≤9%) by metformin (750–1000 mg/day). Eligible patients will be randomized to receive either vildagliptin plus metformin or up-titration of metformin monotherapy (5:1). Patients will also be subgrouped (1:1:1:1) based on their age and body mass index (BMI): <60 years and <24 kg/m2; <60 years and ≥24 kg/m2; ≥60 years and <24 kg/m2; and ≥60 years and ≥24 kg/m2.
Conclusion
The VISION study will test the hypothesis that early use of combination therapy with vildagliptin and metformin will provide good glycemic control and will be better tolerated than up-titration of metformin monotherapy. The study will also correlate these benefits with age and BMI.
doi:10.1186/1475-2840-12-118
PMCID: PMC3766124  PMID: 23958390
VISION study; Vildagliptin; Type 2 diabetes; Study design; DPP-IV inhibitors
14.  Glycemic control among patients in China with type 2 diabetes mellitus receiving oral drugs or injectables 
BMC Public Health  2013;13:602.
Background
The prevalence of type 2 diabetes mellitus (T2DM) is increasing rapidly among Chinese adults, and limited data are available on T2DM management and the status of glycemic control in China. We assessed the efficacy of oral antidiabetes drugs (OADs), glucagon-like peptide-1 (GLP-1) receptor agonists, and insulin for treatment of T2DM across multiple regions in China.
Methods
This was a multicenter, cross-sectional survey of outpatients conducted in 606 hospitals across China. Data from all the patients were collected between April and June, 2011.
Results
A total of 238,639 patients were included in the survey. Eligible patients were treated with either OADs alone (n=157,212 [65.88%]), OADs plus insulin (n=80,973 [33.93%]), or OADs plus GLP-1 receptor agonists (n=454 [0.19%]). The OAD monotherapy, OAD + insulin, and OAD + GLP-1 receptor agonist groups had mean glycosylated hemoglobin (HbA1c) levels (±SD) of 7.67% (±1.58%), 8.21% (±1.91%), and 7.80% (±1.76%), respectively. Among those three groups, 34.63%, 26.21%, and 36.12% met the goal of HbA1c <7.0%, respectively. Mean HbA1c and achievement of A1c <7.0% was related to the duration of T2DM.
Conclusions
Less than one third of the patients had achieved the goal of HbA1c <7.0%. Glycemic control decreased and insulin use increased with the duration of diabetes.
doi:10.1186/1471-2458-13-602
PMCID: PMC3729491  PMID: 23800082
China; GLP-1 receptor agonists; HbA1c; Insulin; Oral antidiabetes drugs (OADs); Type 2 diabetes mellitus
15.  Experimental Research on the Dam-Break Mechanisms of the Jiadanwan Landslide Dam Triggered by the Wenchuan Earthquake in China 
The Scientific World Journal  2013;2013:272363.
Dam breaks of landslide dams are always accompanied by large numbers of casualties, a large loss of property, and negative influences on the downstream ecology and environment. This study uses the Jiadanwan landslide dam, created by the Wenchuan earthquake, as a case study example. Several laboratory experiments are carried out to analyse the dam-break mechanism of the landslide dam. The different factors that impact the dam-break process include upstream flow, the boulder effect, dam size, and channel discharge. The development of the discharge channel and the failure of the landslide dam are monitored by digital video and still cameras. Experimental results show that the upstream inflow and the dam size are the main factors that impact the dam-break process. An excavated discharge channel, especially a trapezoidal discharge channel, has a positive effect on reducing peak flow. The depth of the discharge channel also has a significant impact on the dam-break process. The experimental results are significant for landslide dam management and flood disaster prevention and mitigation.
doi:10.1155/2013/272363
PMCID: PMC3690269  PMID: 23844387
16.  Can Taichi Reshape the Brain? A Brain Morphometry Study 
PLoS ONE  2013;8(4):e61038.
Although research has provided abundant evidence for Taichi-induced improvements in psychological and physiological well-being, little is known about possible links to brain structure of Taichi practice. Using high-resolution MRI of 22 Tai Chi Chuan (TCC) practitioners and 18 controls matched for age, sex and education, we set out to examine the underlying anatomical correlates of long-term Taichi practice at two different levels of regional specificity. For this purpose, parcel-wise and vertex-wise analyses were employed to quantify the difference between TCC practitioners and the controls based on cortical surface reconstruction. We also adopted the Attention Network Test (ANT) to explore the effect of TCC on executive control. TCC practitioners, compared with controls, showed significantly thicker cortex in precentral gyrus, insula sulcus and middle frontal sulcus in the right hemisphere and superior temporal gyrus and medial occipito-temporal sulcus and lingual sulcus in the left hemisphere. Moreover, we found that thicker cortex in left medial occipito-temporal sulcus and lingual sulcus was associated with greater intensity of TCC practice. These findings indicate that long-term TCC practice could induce regional structural change and also suggest TCC might share similar patterns of neural correlates with meditation and aerobic exercise.
doi:10.1371/journal.pone.0061038
PMCID: PMC3621760  PMID: 23585869
17.  The genetic study utility of a hexaploid wheat DH population with non-recombinant A- and B-genomes 
SpringerPlus  2013;2:131.
To study the D-genome of the wild wheat relative Aegilops tauschii Cosson at the hexaploid level, we developed a synthetic doubled-haploid (DH) hexaploid wheat population, SynDH3. This population was derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from a cross between Triticum turgidum ssp. dicoccon PI377655 and A. tauschii ssp. strangulata AS66 × ssp. tauschii AS87. SynDH3 is a diploidization-hexaploid DH population containing recombinant D chromosomes from two different A. tauschii genotypes, with A and B chromosomes from T. turgidum being homogenous across the entire population. Using this population, we constructed a genetic map. Of the 440 markers used to construct the map, 421 (96%) were assigned to 12 linkage groups; these included 346 Diversity Arrays Technology (DArT) and 75 simple sequence repeat (SSR) markers. The total map length of the seven D chromosomes spanned 916.27 cM, with an average length of 130.90 cM per chromosome and an average distance between markers of 3.47 cM. Seven segregation distortion regions were detected on seven linkage groups. Out of 50 markers shared with those on a common wheat map, 37 showed a consistent order. The utility of the diploidization-hexaploid DH population for mapping qualitative trait genes was confirmed using the dominant glaucousness-inhibiting gene W2I as an example.
Electronic supplementary material
The online version of this article (doi:10.1186/2193-1801-2-131) contains supplementary material, which is available to authorized users.
doi:10.1186/2193-1801-2-131
PMCID: PMC3618880  PMID: 23577301
Allopolyploid; Aegilops tauschii; Doubled-haploid; Segregation distortion
18.  Systematic Angle Random Walk Estimation of the Constant Rate Biased Ring Laser Gyro 
Sensors (Basel, Switzerland)  2013;13(3):2750-2762.
An actual account of the angle random walk (ARW) coefficients of gyros in the constant rate biased rate ring laser gyro (RLG) inertial navigation system (INS) is very important in practical engineering applications. However, no reported experimental work has dealt with the issue of characterizing the ARW of the constant rate biased RLG in the INS. To avoid the need for high cost precise calibration tables and complex measuring set-ups, the objective of this study is to present a cost-effective experimental approach to characterize the ARW of the gyros in the constant rate biased RLG INS. In the system, turntable dynamics and other external noises would inevitably contaminate the measured RLG data, leading to the question of isolation of such disturbances. A practical observation model of the gyros in the constant rate biased RLG INS was discussed, and an experimental method based on the fast orthogonal search (FOS) for the practical observation model to separate ARW error from the RLG measured data was proposed. Validity of the FOS-based method was checked by estimating the ARW coefficients of the mechanically dithered RLG under stationary and turntable rotation conditions. By utilizing the FOS-based method, the average ARW coefficient of the constant rate biased RLG in the postulate system is estimated. The experimental results show that the FOS-based method can achieve high denoising ability. This method estimate the ARW coefficients of the constant rate biased RLG in the postulate system accurately. The FOS-based method does not need precise calibration table with high cost and complex measuring set-up, and Statistical results of the tests will provide us references in engineering application of the constant rate biased RLG INS.
doi:10.3390/s130302750
PMCID: PMC3658711  PMID: 23447008
rate biased technique; ring laser gyro; fast orthogonal search; Allan variance
19.  Relationship between Oxidant/Antioxidant Markers and Severity of Microalbuminuria in the Early Stage of Nephropathy in Type 2 Diabetic Patients 
Journal of Diabetes Research  2013;2013:232404.
A wide range of microalbuminuria cutoff values are currently used for diagnosing the early stage of nephropathy in type 2 diabetes (T2D). This study analyzed the relationships between oxidant and antioxidant markers of nephropathy and the severity of microalbuminuria. The study included 50 healthy controls (Group 1), 50 diabetic patients with no nephropathy (Group 2), 50 diabetic patients with nephropathy and a urinary albumin excretion (UAE) of 30–200 mg/24 h (Group 3), and 50 diabetic patients with UAE 200–300 mg/24 h (Group 4). Serum nitrotyrosine, conjugated dienes, 8-hydroxy-2′-deoxyguanosine (8-OHdG), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC) levels were determined. Oxidative stress is increased in the early stage of nephropathy in patients with T2D. There was a significant correlation between the extent of microalbuminuria and markers of oxidative stress. Multiple linear regression analysis identified lipid oxidative stress as a possible independent marker for evaluating the degree of renal damage in diabetic nephropathy. Stratifying microalbuminuria values during the early stage of nephropathy might be an important factor in facilitating earlier and more specific interventions.
doi:10.1155/2013/232404
PMCID: PMC3647557  PMID: 23671859
20.  Trim71 cooperates with microRNAs to repress Cdkn1a expression and promote embryonic stem cell proliferation 
Nature communications  2012;3:923.
Pluripotent embryonic stem cells (ESCs) have a shortened cell cycle that enables their rapid proliferation. The ESC-specific miR-290 and miR-302 microRNA families promote proliferation whereas let-7 microRNAs inhibit self-renewal and promote cell differentiation. Lin28 suppresses let-7 expression in ESCs. Here, to gain further insight into mechanisms controlling ESC self-renewal we explore the molecular and cellular role of the let-7 target Trim71 (mLin41). We show that Trim71 associates with Argonaute2 (Ago2) and microRNAs and represses expression of Cdkn1a, a cyclin-dependent kinase inhibitor that negatively regulates the G1–S transition. We identify protein domains required for Trim71 association with Ago2, localization to P-bodies, and for repression of reporter mRNAs. Trim71 knockdown prolongs the G1 phase of the cell cycle and slows ESC proliferation, a phenotype that was rescued by depletion of Cdkn1a. Thus, we demonstrate Trim71 is a factor that facilitates the G1–S transition to promote rapid ESC self-renewal.
doi:10.1038/ncomms1909
PMCID: PMC3518406  PMID: 22735451
21.  Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome 
BMC Genetics  2012;13:69.
Background
A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population.
Results
Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B.
Conclusions
A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.
doi:10.1186/1471-2156-13-69
PMCID: PMC3470960  PMID: 22888829
Allopolyploid; Crossability; Doubled haploid; Segregation distortion
22.  Microsatellite Mutation Rate during Allohexaploidization of Newly Resynthesized Wheat 
Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH) populations were made from 241 interspecific F1 haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss.) through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S1 generation (the first generation after chromosome doubling) of the three SynDH populations. Of the 148260 SSR alleles investigated in S1 generation, only one mutation (changed number of repeats) was confirmed with a mutation rate of 6.74 × 10−6. This mutation most likely occurred in the respective F1 hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate.
doi:10.3390/ijms131012533
PMCID: PMC3497285  PMID: 23202911
allopolyploidy; distant hybridization; microsatellite evolution; wheat
23.  Prevalence of overweight and obesity among Chinese Yi nationality: a cross-sectional study 
BMC Public Health  2011;11:919.
Background
Overweight and obesity are considered a serious health problem. There are little data on the prevalence of overweight and obesity among the Yi ethnic group in China. This study aimed to investigate the epidemiologic features of overweight/obesity among Chinese Yi nationality.
Methods
A cross-sectional study, including 1255 subjects aged 20-75 years, was carried out in Liangshan Yi Autonomous Prefecture of Sichuan province from 2007 to 2008. Overweight/overall obesity was defined by World Health Organization (WHO) or the Working Group on Obesity in China.
Results
Overall, the prevalence of overweight and obesity was 19.0% and 2.9%, respectively, based on the WHO definition, while it was 21.0% and 7.4%, respectively, according to the Working Group on Obesity in China, which is similar to data reported in the 2002 Chinese National Nutrition and Health Survey. Urban residents had a significantly higher prevalence of obesity (WHO criteria: 4.3% vs 1.7% p = 0.008; China criteria: 11.4% vs 3.7%, p < 0.001) and overweight (WHO criteria: 28.9% vs 8.9% p < 0.001; China criteria: 31.2% vs 10.4%, p < 0.001) than that in rural residents. Older age, a family history of obesity, higher income, drinking and urban residence were significantly associated with an increased risk of overweight/obesity.
Conclusions
The prevalence of overweight/obesity in the Yi nationality is similar to that in Chinese adults 5 years ago. However, urban residents have a much higher prevalence of overweight/obesity than their rural counterparts. Lifestyle and diet patterns associated with socioeconomic status may explain the difference between urban and rural residents. The prevention of overweight/obesity among urban inhabitants deserves more attention in national health education programs.
doi:10.1186/1471-2458-11-919
PMCID: PMC3272001  PMID: 22166070
24.  In Vivo Non Linear Optical (NLO) Imaging in Live Rabbit Eyes Using the Heidelberg Two-Photon Laser Ophthalmoscope 
Experimental eye research  2010;91(2):308-314.
Imaging of non-linear optical (NLO) signals generated from the eye using ultrafast pulsed lasers has been limited to the study of ex vivo tissues because of the use of conventional microscopes with slow scan speeds. The purpose of this study was to evaluate the ability of a novel, high scan rate ophthalmoscope to generate NLO signals using an attached femtosecond laser. NLO signals were generated and imaged in live, anesthetized albino rabbits using a newly designed Heidelberg Two-Photon Laser Ophthalmoscope with attached 25 mW femtosecond laser having a central wavelength of 780 nm, pulsewidth of 75 fs, and a repetition rate of 50 MHz. To assess two-photon excited fluorescent (TPEF) signal generation, cultured rabbit corneal fibroblasts (RCF) were first labeled by Blue-green fluorescent FluoSpheres (1 μm diameter) and then cells were micro-injected into the central cornea. Clumps of RCF cells could be detected by both reflectance and TPEF imaging at 6 hours after injection. By 6 days, RCF containing fluorescent microspheres confirmed by TPEF showed a more spread morphology and had migrated from the original injection site. Overall, this study demonstrates the potential of using NLO microscopy to sequentially detect TPEF signals from live, intact corneas. We conclude that further refinement of the Two-photon laser Ophthalmoscope should lead to the development of an important, new clinical instrument capable of detecting NLO signals from patient corneas.
doi:10.1016/j.exer.2010.06.007
PMCID: PMC2922943  PMID: 20558159
Two-Photon Excited Fluorescence; Microspheres; Rabbit Cornea; Fibroblast; In Vivo Confocal
25.  High incidence of biliary complications in rat liver transplantation: Can we avoid it? 
AIM: To investigate how to reduce the incidence of biliary complications in rat orthotopic liver transplantation.
METHODS: A total of 165 male Wistar rats were randomly divided into three groups: Group A, orthotropic liver transplantation with modified “two-cuff” technique; Group B, bile duct was cut and reconstructed without transplantation; and Group C, only laparotomy was performed. Based on the approaches used for biliary reconstruction, Group A was divided into two sub-groups:A1 (n = 30), duct-duct reconstruction, and A2 (n = 30), duct-duodenum reconstruction. To study the influence of artery reconstruction on bile duct complication, Group B was divided into four sub-groups: B1 (n = 10), duct-duct reconstruction with hepatic artery ligation, B2 (n = 10), duct-duct reconstruction without hepatic artery ligation, B3 (n = 10), duct-duodenum reconstruction with hepatic artery ligation, and B4 (n = 10), duct-duodenum reconstruction without hepatic artery ligation. The samples were harvested 14 d after operation or at the time when significant biliary complication was found.
RESULTS: In Group A, the anhepatic phase was 13.7 ± 1.06 min, and cold ischemia time was 50.5 ± 8.6 min. There was no significant difference between A1 and A2 in the operation duration. The time for biliary reconstruction was almost the same among all groups. The success rate for transplantation was 98.3% (59/60). Significant differences were found in the incidence of biliary complications in Groups A (41.7%), B (27.5%) and C (0%). A2 was more likely to have biliary complications than A1 (50% vs 33.3%). B3 had the highest incidence of biliary complications in Group B.
CONCLUSION: Biliary complications are almost inevitable using the classical “two cuff” techniques, and duct-duodenum reconstruction is not an ideal option in rat orthotopic liver transplantation.
doi:10.3748/wjg.v17.i26.3140
PMCID: PMC3158414  PMID: 21912457
Rat; Liver transplantation; Biliary complication; Animal model

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