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| 2. |
- Kim, Dae-Kyum, et al.
(författare)
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EVpedia: A Community Web Portal for Extracellular Vesicles Research
- 2015
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 31:6, s. 933-939
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. Results: We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research.
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| 3. |
- George, Julie, et al.
(författare)
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Comprehensive genomic profiles of small cell lung cancer
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 47-U73
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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| 4. |
- Kim, O. Y., et al.
(författare)
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Bacterial Protoplast-Derived Nanovesicles as Vaccine Delivery System against Bacterial Infection
- 2015
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 15:1, s. 266-274
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Tidskriftsartikel (refereegranskat)abstract
- The notion that widespread infectious diseases could be best managed by developing potent, adjuvant-free vaccines has resulted in the use of various biological immune-stimulating components as new vaccine candidates. Recently, extracellular vesicles, also known as exosomes and microvesicles in mammalian cells and outer membrane vesicles in Gram-negative bacteria, have gained attention for the next generation vaccine. However, the more invasive and effective the vaccine is in delivery, the more risk it holds for severe immune toxicity. Here, in optimizing the current vaccine delivery system, we designed bacterial protoplast-derived nanovesicles (PDNVs), depleted of toxic outer membrane components to generate a universal adjuvant-free vaccine delivery system. These PDNVs exhibited significantly higher productivity and safety than the currently used vaccine delivery vehicles and induced strong antigen-specific humoral and cellular immune responses. Moreover, immunization with PDNVs loaded with bacterial antigens conferred effective protection against bacterial sepsis in mice. These nonliving nanovesicles derived from bacterial protoplast open up a new avenue for the creation of next generation, adjuvant-free, less toxic vaccines to be used to prevent infectious diseases.
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| 5. |
- Kim, Hwi-Min, et al.
(författare)
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Monolithic integration of self-aligned nanoisland laser with shifted-air-hole waveguide
- 2018
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Ingår i: Optics Express. - : OPTICAL SOC AMER. - 1094-4087. ; 26:10, s. 12569-12578
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Tidskriftsartikel (refereegranskat)abstract
- We report a novel scheme for monolithic integration of a nanoisland laser with a shifted-air-hole waveguide by employing selective etching techniques. An active L3 laser cavity and passive shifted-air-hole waveguide are simultaneously formed through a single fabrication step. In the shifted-air-hole waveguide, the air-hole position is adjusted to be compatible with selective etching. The spectral overlap between the L3 laser resonance and guided mode is achieved by introducing small air holes at the nodes of the shifted-air-hole waveguide. Experiments show that >60% of the light is coupled from the nanoisland laser to the end of the 12-mu m-long waveguide.
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| 7. |
- Nik-Zainal, Serena, et al.
(författare)
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54
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Tidskriftsartikel (refereegranskat)abstract
- We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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| 8. |
- Pramudita, Putu, et al.
(författare)
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Self-aligned nanoislands nanobeam bandedge lasers
- 2017
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Ingår i: Optics Express. - : Optical Society of America. - 1094-4087. ; 25:6, s. 6311-6319
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Tidskriftsartikel (refereegranskat)abstract
- We propose and demonstrate a novel one-dimensional nanobeam bandedge laser constituted by self-aligned nanoisland quantum-well (QW) structures. The formation of self-aligned InGaAsP nanoislands sandwiched between two InP claddings is the result of selective removal of QW through wet-etching processes. By controlling wet-etching time, we show a good spatial and spectral overlap between the dielectric mode and the self-aligned nanoisland structures leads to the realization of nanobeam bandedge lasers with low-threshold operations and high slope efficiencies. Optical characterization results indicate a strong correlation between the size of individual nanoisland and the threshold power of our nanobeam bandedge lasers. We obtain an approximately 81% reduction in the absorbed threshold power as we optimize the size of the nanoislands.
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