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A bootstrap-based regression method for comprehensive discovery of differential gene expressions: An application to the osteoporosis study

A common purpose of microarray experiments is to study the variation in gene expression across the categories of an experimental factor such as tissue types and drug treatments. However, it is not uncommon that the studied experimental factor is a quantitative variable rather than categorical variable. Loss of information would occur by comparing gene-expression levels between groups that are factitiously defined according to the quantitative threshold values of an experimental factor. Additionally, lack of control for some sensitive clinical factors may bring serious false positive or negative findings.In the present study, we described a bootstrap-based regression method for analyzing gene-expression data from the non-categorical microarray experiments. To illustrate the utility of this method, we applied it to our recent gene-expression study of circulating monocytes in subjects with a wide range of variations in bone mineral density (BMD). This method allows a comprehensive discovery of gene expressions associated with osteoporosis-related traits while controlling other common confounding factors such as height, weight and age. Several genes identified in our study are involved in osteoblast and osteoclast functions and bone remodeling and/or menopause-associated estrogen-dependent pathways, which provide important clues to understand the etiology of osteoporosis. Availability: SAS code is available from the authors upon request. © 2011 Elsevier Masson SAS.postprin

Improved performance of pentacene OTFTs with HfLaO gate dielectric by using fluorination and nitridation

Pentacene organic thin-film transistors (OTFTs) with fluorinated high-κ HfLaO as gate insulator were fabricated. The dielectrics were prepared by sputtering method and then annealed in N 2 or NH 3 at 400 °C. Subsequently, the dielectrics were treated by fluorine plasma for different durations (100, 300, and 900 s). The N 2 and NH 3-annealed OTFTs with a 100-s plasma treatment achieve a carrier mobility of 0.62 and 0.66 cm 2V̇s, respectively, which are higher than those of the OTFTs without plasma treatment (0.22 and 0.41 cm 2V̇s). Moreover, the plasma-treated OTFTs realize better 1/f noise characteristics than those without plasma treatment. The improved performance is due to passivation of the dielectric surface by plasma-induced fluorine incorporation. However, for longer time (300 and 900 s) of plasma treatment, the performance of the OTFTs deteriorates in terms of carrier mobility and 1/f noise characteristics due to increased plasma-induced damage of the dielectric surface. The morphology of the pentacene film grown on the HfLaO gate insulator was characterized by SEM. It reveals that the pentacene film has larger grain size and smoother surface on the HfLaO dielectric (for both annealing gases) with 100-s plasma treatment than the others (0, 300, and 900 s). Finally, AFM characterization of the HfLaO film also confirms the damaging effect of excessive plasma treatment on the dielectric. © 2012 IEEE.published_or_final_versio

Low-voltage polymer thin-film transistors with high-k HfTiO gate dielectric annealed in NH3 or N2

OTFTs with P3HT as organic semiconductor and HfTiO as gate dielectric have been studied in this work. The HfTiO dielectric film was prepared by RF sputtering of Hf and DC sputtering of Ti at room temperature. Subsequently, the dielectric film was annealed in an NH3 or N2 ambient at 200 °C. Then a layer of OTS was deposited by spin-coating method to improve the surface characteristics of the gate dielectric. Afterwards, P3HT was deposited by spin-coating method. The OTFTs were characterized by I-V measurement and 1/f noise measurement. The OTFT with gate dielectric annealed in NH3 displays higher carrier mobility, smaller threshold voltage, smaller sub-threshold swing, and lower 1/f noise level than the OTFT annealed in N2. Moreover, the HfTiO dielectric film annealed in NH3 shows higher dielectric constant. In summary, HfTiO film annealed in NH 3 at low temperature is a promising candidate to act as the gate dielectric of high-quality low-voltage OTFTs. ©2009 IEEE.published_or_final_versionThe IEEE International Conference of Electron Devices and Solid-State Circuits (EDSSC 2009), Xi'an, China, 25-27 December 2009. In Proceedings of EDSSC, 2009, p. 201-20

Effects of annealing temperature and gas on pentacene OTFTs with HfLaO as gate dielectric

Pentacene organic thin-film transistors (OTFTs) with high-κ HfLaO as gate insulator were fabricated. HfLaO film was prepared by sputtering method. To improve the film quality, the dielectric was annealed in N 2, NH 3, or O 2 at two temperatures, i.e., 200 °C and 400 °C, respectively. The I-V characteristics of the OTFTs and C-V characteristics of corresponding organic capacitors were measured. The OTFTs could operate at a low operating voltage of below 5 V, and the dielectric constant of the HfLaO film could be above ten. For all the annealing gases, the OTFTs annealed at 400 °C achieved higher carrier mobility than their counterparts annealed at 200 °C (with the one annealed in NH 3 at 400 °C showing the highest carrier mobility of 0.45 cm 2/ V·s), which could be supported by SEM images which indicate that pentacene tended to form larger grains on HfLaO annealed at 400 °C than on that annealed at 200 °C. The C-V measurement of the organic capacitors indicated that the localized charge density in the organic semiconductor/oxide was lower for the 400 °C annealing than for the 200 °C annealing. Furthermore, through the characterization of gate current leakage, HfLaO film annealed at 400 °C achieved much smaller leakage than that annealed at 200 °C. Since the maximum processing temperature of ITO glass substrates is around 400 °C , this study shows that 400 °C is suitable for the annealing of HfLaO film in high-performance OTFTs on glass substrate. © 2011 IEEE.published_or_final_versio

Effects of different annealing gases on pentacene OTFT with HfLaO gate dielectric

Pentacene organic thin-film transistors (OTFTs) with HfLaO high-kappa gate dielectric were fabricated. The dielectric was prepared by a sputtering method and then annealed in N2,NH3,O2, or NO at 400°C. The carrier mobility of the NH3-annealed OTFT could reach 0.59 cm2/V̇s, which is higher than those of the other three devices. Moreover, the NH3-annealed OTFT obtained the smallest subthreshold swing of 0.26 V/dec among them. Furthermore,1/f noise measurement indicated that the NH3-annealed OTFT achieved the smallest 1/f noise. All these should be attributed to the improved interface between the gate dielectric and the organic semiconductor associated with the passivation effects of the NH3 annealing on the dielectric surface. © 2010 IEEE.published_or_final_versio

Composition of gut microbiota in infants in China and global comparison

published_or_final_versio

Conformal symmetry of the critical 3D Ising model inside a sphere

We perform Monte-Carlo simulations of the three-dimensional Ising model at the critical temperature and zero magnetic field. We simulate the system in a ball with free boundary conditions on the two dimensional spherical boundary. Our results for one and two point functions in this geometry are consistent with the predictions from the conjectured conformal symmetry of the critical Ising model.We are grateful to Slava Rychkov for useful discussions and for suggesting this work. The research leading to these results has received funding from the [European Union] Seventh Framework Programme [FP7-People-2010-IRSES] and [FP7/2007-2013] under grant agreements No 269217, 317089 and No 247252, and from the grant CERN/FP/123599/2011. Centro de Física do Porto is partially funded by the Foundation for Science and Technology of Portugal (FCT). J.V.P.L. acknowledges funding from projecto Operacional Regional do Norte, within Quadro de Referência Estratégico Nacional (QREN) and through Fundo Europeu de Desenvolvimento Regional (FEDER), Ref. NORTE-07-0124-FEDER- 00003

CD69 is a TGF-β/1α,25-dihydroxyvitamin D3 target gene in monocytes

CD69 is a transmembrane lectin that can be expressed on most hematopoietic cells. In monocytes, it has been functionally linked to the 5-lipoxygenase pathway in which the leukotrienes, a class of highly potent inflammatory mediators, are produced. However, regarding CD69 gene expression and its regulatory mechanisms in monocytes, only scarce data are available. Here, we report that CD69 mRNA expression, analogous to that of 5-lipoxygenase, is induced by the physiologic stimuli transforming growth factor-β (TGF-β) and 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) in monocytic cells. Comparison with T- and B-cell lines showed that the effect was specific for monocytes. CD69 expression levels were increased in a concentration-dependent manner, and kinetic analysis revealed a rapid onset of mRNA expression, indicating that CD69 is a primary TGF-β/1α,25(OH)2D3 target gene. PCR analysis of different regions of the CD69 mRNA revealed that de novo transcription was initiated and proximal and distal parts were induced concomitantly. In common with 5-lipoxygenase, no activation of 0.7 kb or ~2.3 kb promoter fragments by TGF-β and 1α,25(OH)2D3 could be observed in transient reporter assays for CD69. Analysis of mRNA stability using a transcription inhibitor and a 3′UTR reporter construct showed that TGF-β and 1α,25(OH)2D3 do not influence CD69 mRNA stability. Functional knockdown of Smad3 clearly demonstrated that upregulation of CD69 mRNA, in contrast to 5-LO, depends on Smad3. Comparative studies with different inhibitors for mitogen activated protein kinases (MAPKs) revealed that MAPK signalling is involved in CD69 gene regulation, whereas 5-lipoxygenase gene expression was only partly affected. Mechanistically, we found evidence that CD69 gene upregulation depends on TAK1-mediated p38 activation. In summary, our data indicate that CD69 gene expression, conforming with 5-lipoxygenase, is regulated monocyte-specifically by the physiologic stimuli TGF-β and 1α,25(OH)2D3 on mRNA level, although different mechanisms account for the upregulation of each gene

Disparities and risks of sexually transmissible infections among men who have sex with men in China: a meta-analysis and data synthesis.

BACKGROUND: Sexually transmitted infections (STIs), including Hepatitis B and C virus, are emerging public health risks in China, especially among men who have sex with men (MSM). This study aims to assess the magnitude and risks of STIs among Chinese MSM. METHODS: Chinese and English peer-reviewed articles were searched in five electronic databases from January 2000 to February 2013. Pooled prevalence estimates for each STI infection were calculated using meta-analysis. Infection risks of STIs in MSM, HIV-positive MSM and male sex workers (MSW) were obtained. This review followed the PRISMA guidelines and was registered in PROSPERO. RESULTS: Eighty-eight articles (11 in English and 77 in Chinese) investigating 35,203 MSM in 28 provinces were included in this review. The prevalence levels of STIs among MSM were 6.3% (95% CI: 3.5-11.0%) for chlamydia, 1.5% (0.7-2.9%) for genital wart, 1.9% (1.3-2.7%) for gonorrhoea, 8.9% (7.8-10.2%) for hepatitis B (HBV), 1.2% (1.0-1.6%) for hepatitis C (HCV), 66.3% (57.4-74.1%) for human papillomavirus (HPV), 10.6% (6.2-17.6%) for herpes simplex virus (HSV-2) and 4.3% (3.2-5.8%) for Ureaplasma urealyticum. HIV-positive MSM have consistently higher odds of all these infections than the broader MSM population. As a subgroup of MSM, MSW were 2.5 (1.4-4.7), 5.7 (2.7-12.3), and 2.2 (1.4-3.7) times more likely to be infected with chlamydia, gonorrhoea and HCV than the broader MSM population, respectively. CONCLUSION: Prevalence levels of STIs among MSW were significantly higher than the broader MSM population. Co-infection of HIV and STIs were prevalent among Chinese MSM. Integration of HIV and STIs healthcare and surveillance systems is essential in providing effective HIV/STIs preventive measures and treatments. TRIAL REGISTRATION: PROSPERO NO: CRD42013003721