| 21. |
- Jolma, A, et al.
(author)
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Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
- 2010
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 20:6, s. 861-873
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Journal article (peer-reviewed)abstract
- The genetic code—the binding specificity of all transfer-RNAs—defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the ∼1400 human transcription factors (TFs). We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing. The method is optimized for analysis of large numbers of TFs in parallel through the use of affinity-tagged proteins, barcoded selection oligonucleotides, and multiplexed sequencing. Data are analyzed by a new bioinformatic platform that uses the hundreds of thousands of sequencing reads obtained to control the quality of the experiments and to generate binding motifs for the TFs. The described technology allows higher throughput and identification of much longer binding profiles than current microarray-based methods. In addition, as our method is based on proteins expressed in mammalian cells, it can also be used to characterize DNA-binding preferences of full-length proteins or proteins requiring post-translational modifications. We validate the method by determining binding specificities of 14 different classes of TFs and by confirming the specificities for NFATC1 and RFX3 using ChIP-seq. Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers.
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| 22. |
- Kapilashrami, Mukes, et al.
(author)
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Soft X-ray characterization of Zn1-xSnxOy electronic structure for thin film photovoltaics
- 2012
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 14:29, s. 10154-10159
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Journal article (peer-reviewed)abstract
- Zinc tin oxide (Zn1-xSnxOy) has been proposed as an alternative buffer layer material to the toxic, and light narrow-bandgap CdS layer in CuIn1-x,GaxSe2 thin film solar cell modules. In this present study, synchrotron-based soft X-ray absorption and emission spectroscopies have been employed to probe the densities of states of intrinsic ZnO, Zn1-xSnxOy and SnOx thin films grown by atomic layer deposition. A distinct variation in the bandgap is observed with increasing Sn concentration, which has been confirmed independently by combined ellipsometry-reflectometry measurements. These data correlate directly to the open circuit potentials of corresponding solar cells, indicating that the buffer layer composition is associated with a modification of the band discontinuity at the CIGS interface. Resonantly excited emission spectra, which express the admixture of unoccupied O 2p with Zn 3d, 4s, and 4p states, reveal a strong suppression in the hybridization between the O 2p conduction band and the Zn 3d valence band with increasing Sn concentration.
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| 23. |
- Liu, Tie, et al.
(author)
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Effects of high magnetic fields on solidification microstructure of Al-Si alloys
- 2011
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In: Journal of Materials Science. - : Springer Science and Business Media LLC. - 0022-2461 .- 1573-4803. ; 46:6, s. 1628-1634
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Journal article (peer-reviewed)abstract
- The effects of high magnetic fields on the solidification microstructure of Al-Si alloys were investigated. Al-7.2 wt%Si and Al-11.8 wt%Si alloys were solidified in various high magnetic fields at different cooling rates. The secondary dendrite arm spacing (SDAS) of the primary Al dendrites and the lamellar spacing (LS) of the eutectics were measured. It was found that the application of a high magnetic field could decrease the SDAS of the primary Al dendrites in Al-7.2 wt% Si alloys and the LS of the eutectics in Al-11.8 wt% Si alloys. The effects of the high magnetic field on the SDAS decreased with increasing cooling rate. The decrease in the SDAS and LS can be attributed to the decrease of the solute diffusivity in the liquid ahead of the solid/liquid interface during the growth of the dendrite and eutectic. This decrease is caused by the high magnetic field which can damp the convection and avoid its contributions to the diffusion.
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| 24. |
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| 25. |
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| 26. |
- Rodriguez Lorenzo, Andres, et al.
(author)
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Selection of the recipient vein in microvascular flap reconstruction of the lower extremity : analysis of 362 free-tissue transfers
- 2011
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In: Journal of Plastic, Reconstructive & Aesthetic Surgery. - : Elsevier BV. - 1748-6815 .- 1878-0539. ; 64:5, s. 649-655
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Journal article (peer-reviewed)abstract
- Venous insufficiency is the most common cause of re-exploration in free-tissue transfers to the lower extremity. There is currently no consensus regarding the best approach to recipient vein selection. This study was designed to evaluate whether the type of venous system or the number of recipient veins would impact flap outcomes after microsurgical lower-extremity reconstruction. A retrospective study was conducted in 362 free-tissue transfers for lower-extremity reconstruction between 2003 and 2008. Flap outcomes were evaluated according to the selection of recipient vein system and number of veins. The deep venous system (80.4%) was more frequently selected than the superficial venous system (12.1%) or the combination of both systems (7.5%). In addition, one vein (65.5%) was more commonly used for anastomosis than two veins (34.5%). A total of 26 flaps (7.2%) presented with postoperative venous insufficiency. Male patients, composite defects including bones and the use of bone flaps presented higher rates of venous insufficiency with statistical significance. However, no significant differences were found among the different groups related to the age of patients, co-morbidities, aetiology, location of the defects or timing of reconstruction after trauma. The superficial venous system group was associated with a higher rate of venous insufficiency and partial flap loss compared with the deep venous system group (p = 0.036 and 0.018, respectively). One-vein-anastomosis flaps were associated with statistically significant fewer complete flap failure in comparison with two-vein-anastomosis flaps (p = 0.014). In conclusion, the assessment of recipient vein parameters by surgeon's experience is the best predictor of flap outcome in lower-extremity reconstruction. In our cohort of patients, the deep venous system was more reliable than the superficial venous system, but the use of more than one vein for anastomosis did not correlate with better flap outcomes.
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| 27. |
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| 28. |
- Sun, Yongfu, et al.
(author)
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Fabrication of flexible and freestanding zinc chalcogenide single layers
- 2012
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 3, s. 1057-
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Journal article (peer-reviewed)abstract
- Inorganic graphene analogues (IGAs) are a conceptually new class of materials with attractive applications in next-generation flexible and transparent nanodevices. However, their species are only limited to layered compounds, and the difficulty in extension to non-layered compounds hampers their widespread applicability. Here we report the fabrication of large-area freestanding single layers of non-layered ZnSe with four-atomic thickness, using a strategy involving a lamellar hybrid intermediate. Their surface distortion, revealed by means of synchrotron radiation X-ray absorption fine structure spectroscopy, is shown to give rise to a unique electronic structure and an excellent structural stability, thus determining an enhanced solar water splitting efficiency and photostability. The ZnSe single layers exhibit a photocurrent density of 2.14 mA cm(-2) at 0.72 V versus Ag/AgCl under 300 W Xe lamp irradiation, 195 times higher than that of bulk counterpart. This work opens the door for extending atomically thick IGAs to non-layered compounds and holds promise for a wealth of innovative applications.
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| 29. |
- Tang, Ting-Ting, et al.
(author)
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Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
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Journal article (peer-reviewed)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
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| 30. |
- Wu, Ming-Chung, et al.
(author)
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Photo-Kelvin probe force microscopy for photocatalytic performance characterization of single filament of TiO2 nanofiber photocatalysts
- 2013
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In: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 1:18, s. 5715-5720
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Journal article (peer-reviewed)abstract
- This is an in-depth study on the photocatalytic performance characterization for single filament of TiO2 nanofiber photocatalysts by the novel photo-Kelvin probe force microscopy technique (photo-KPFM) and first principles calculations. Three kinds of TiO2 nanofibers: anatase TiO2 nanofibers (anatase TiO2 NFs), nitrogen doped TiO2 nanofibers (N-TiO2 NFs), and nitrogen doped TiO2 nanofibers decorated with platinum nanoparticles (N-TiO2-Pt NFs) were investigated. The N-TiO2-Pt NFs exhibit the largest negative photo surface potential shift (-182 mV) as compared to anatase TiO2 NFs (-29 mV). The first-principles calculations based on density functional theory (CASTEP simulation software) indicate that the significant photo surface potential shift obtained by adding nitrogen and platinum into TiO2 NFs is induced by two mechanisms: (1) enhancement in absorbance to increase exciton generation and (2) decreased charge recombination to increase surface charge. These changes in the photo surface potential of various TiO2 nanofibers are closely correlated with their photocatalytic activity. Thus, this novel photo-KPFM provides a useful technique to easily monitor the photocatalytic capability of materials in the development of high performance photocatalysts.
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