| 1. |
- Brownstein, Catherine A., et al.
(author)
-
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
-
In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
-
Journal article (peer-reviewed)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
|
|
| 2. |
- Dong, Bin, et al.
(author)
-
Substrate-, Wavelength-, and Time-Dependent Plasmon-Assisted Surface Catalysis Reaction of 4-Nitrobenzenethiol Dimerizing to p,p '-Dimercaptoazobenzene on Au, Ag, and Cu Films
- 2011
-
In: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 27:17, s. 10677-10682
-
Journal article (peer-reviewed)abstract
- In this article, we experimentally investigate the substrate, wavelength, and time dependence of the plasmon-assisted surface-catalyzed dimerization of 4-nitrobenzenethiol to form p,p'-dimercaptoazobenzene on Au, Ag, and Cu films. We provide direct experimental evidence that surface plasmon resonance plays the most important role in these surface-catalyzed reactions. It is found that the reaction is strongly dependent on the substrate, the wavelength of the laser, and the reaction timescales. Our experimental results revealed that optimal experimental conditions can be rationally chosen to control (accelerate or restrain) this reaction. The experimental results are also confirmed by theoretical calculations.
|
|
| 3. |
- Fu, Jianxin, et al.
(author)
-
Loss of intestinal core 1-derived O-glycans causes spontaneous colitis in mice.
- 2011
-
In: The Journal of clinical investigation. - 1558-8238. ; 121:4, s. 1657-66
-
Journal article (peer-reviewed)abstract
- Mucin-type O-linked oligosaccharides (O-glycans) are primary components of the intestinal mucins that form the mucus gel layer overlying the gut epithelium. Impaired expression of intestinal O-glycans has been observed in patients with ulcerative colitis (UC), but its role in the etiology of this disease is unknown. Here, we report that mice with intestinal epithelial cell-specific deficiency of core 1-derived O-glycans, the predominant form of O-glycans, developed spontaneous colitis that resembled human UC, including massive myeloid infiltrates and crypt abscesses. The colitis manifested in these mice was also characterized by TNF-producing myeloid infiltrates in colon mucosa in the absence of lymphocytes, supporting an essential role for myeloid cells in colitis initiation. Furthermore, induced deletion of intestinal core 1-derived O-glycans caused spontaneous colitis in adult mice. These data indicate a causal role for the loss of core 1-derived O-glycans in colitis. Finally, we detected a biosynthetic intermediate typically exposed in the absence of core 1 O-glycan, Tn antigen, in the colon epithelium of a subset of UC patients. Somatic mutations in the X-linked gene that encodes core 1 β1,3-galactosyltransferase-specific chaperone 1 (C1GALT1C1, also known as Cosmc), which is essential for core 1 O-glycosylation, were found in Tn-positive epithelia. These data suggest what we believe to be a new molecular mechanism for the pathogenesis of UC.
|
|
| 4. |
- Guan, Xiaowei, et al.
(author)
-
Ultrasmall Directional Coupler and Disk-resonantor Based on Nano-scale Silicon Hybrid Plasmonic Waveguides
- 2012
-
In: 2012 Asia Communications And Photonics Conference (ACP). - Washington, D.C. : OSA. - 9781467362740 ; , s. AS2H.4-
-
Conference paper (peer-reviewed)abstract
- Nanophotonic integrated devices based on nano-scale silicon hybrid plasmonic waveguides have been demonstrated experimentally, including directional couplers and disk-resonators. The temperature-dependence of the hybrid plasmonic disk-resonators is also characterized.
|
|
| 5. |
- Sun, Mengtao, et al.
(author)
-
The pH-Controlled Plasmon-Assisted Surface Photocatalysis Reaction of 4-Aminothiophenol to p,p '-Dimercaptoazobenzene on Au, Ag, and Cu Colloids
- 2011
-
In: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 115:19, s. 9629-9636
-
Journal article (peer-reviewed)abstract
- In this paper, we report experimentally and theoretically a surface photocatalysis reaction of 4-aminothiophenol (PATP) to p,p'-dimercaptoazobenzene (DMAB) on Au, Ag, and Cu colloids. Surface enhanced Raman scattering (SEAS) spectra of PATP on Au and Cu colloids are significantly different from the normal Raman spectrum of PATP powder. Quantum chemical calculations reveal that PATP on Au and Cu colloids is converted to DMAB by a surface photocatalysis reaction, and all the strongly enhanced Raman peaks are the symmetric Ag vibrational mode by surface plasmon. The pH value effects on surface photocatalysis reaction were also investigated experimentally. It is found that plasmon-assisted surface photocatalysis reaction can be efficiently controlled by different pH values. The possibility of protonation of PATP adsorbed on Au and Ag nanoparticles at pH 3 is investigated theoretically. The molecular mechanism is proposed for controlling surface photocatalysis reaction by pH values.
|
|
