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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 3. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 4. |
- He, G. S., et al.
(författare)
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Multifocus Structures of Ultrashort Self-Focusing Laser Beam Observed in a Three-Photon Fluorescent Medium
- 2009
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Ingår i: IEEE Journal of Quantum Electronics. - : Institute of Electrical and Electronics Engineers (IEEE). - 0018-9197 .- 1558-1713. ; 45:7, s. 816-824
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Tidskriftsartikel (refereegranskat)abstract
- Self-focusing effect and multifocus structures of an ultrashort (similar to 160-fs) pulsed laser beam of similar to 1.3-mu m wavelength are investigated in several organic liquids. The intensity-dependent self-focusing formation and multifocus structures of the infrared (IR) laser beam were directly observed in a three-photon active fluorescent dye solution cell, in which a high contrast image of the spatial structure of the self-focusing beam can be obtained due to the cubic dependence of the fluorescence intensity on the local IR laser intensity. By combining this dye solution cell with another cell filled with various transparent organic liquids, the contributions of these tested liquids to the observed self-focusing effect are elucidated. The numerical simulations for this type of self-focusing behavior are presented, based on the assumption that the major contribution to the observed self-focusing is the nonlinear refractive-index change of the solvent due to electronic-cloud distortion. The simulation results are in fairly good agreement with the experimental results.
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| 5. |
- Kang, Fengwen, et al.
(författare)
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Spectral Tuning, Stabilities under External Exposures, and Spontaneous Enhancement of Emission Intensity in Grown-into-Glass All-Inorganic Metal Halide Perovskite Nanocrystals
- 2023
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Ingår i: Laser and Photonics Reviews. - : Wiley. - 1863-8880 .- 1863-8899. ; 17:1
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Tidskriftsartikel (refereegranskat)abstract
- Herein, the grown-into-glass (GIG) CsPbBr3:Ln3+ (Ln = La, Lu) nanocrystals (NCs) are designed and fabricated using an in situ nanocrystallization method. It is shown that a substitution of Pb2+ sites with Ln3+ ions leads to a blueshift of emission position induced by an increase of the bandgap of CsPbBr3. Additionally, the GIG-samples are found to feature excellent photoluminescent (PL) properties after being immersed respectively in water for 300 days at room temperature, boiling water for 12 h, and corrosive environments for 24 h, as well as recoverable PL intensity either after several cycles of heat-cooling experiments or after being continuously exposed to a 405 nm laser irradiation. Besides, a spontaneous enhancement of 20-25% of emission intensity during the 1-2.5 hours' stage of a 405 nm laser irradiation, attributed to the radiative recombination of charge carriers that can be de-trapped from trapping levels upon the laser light irradiation and that then spontaneously reinforces the emission intensity, is observed in the GIG-CsPbBr3:Ln3+ NCs. Finally, a white light-emitting prototype, with a CIE chromaticity coordinate at (0.4110, 0.3706), a color rendering index of 89 and a correlated color temperature of 3363 K is realized by combining the GIG-CsPbBr3 NCs, YAG:Ce and CaWO4:Eu phosphors.
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| 6. |
- Riddle, Nicole C, et al.
(författare)
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Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
- 2011
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 21:2, s. 147-163
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Tidskriftsartikel (refereegranskat)abstract
- Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifications and chromosomal proteins. As anticipated, the pericentric heterochromatin and chromosome 4 are on average enriched for the "silencing" marks H3K9me2, H3K9me3, HP1a, and SU(VAR)3-9, and are generally depleted for marks associated with active transcription. The locations of the euchromatin-heterochromatin borders identified by these marks are similar in animal tissues and most cell lines, although the amount of heterochromatin is variable in some cell lines. Combinatorial analysis of chromatin patterns reveals distinct profiles for euchromatin, pericentric heterochromatin, and the 4th chromosome. Both silent and active protein-coding genes in heterochromatin display complex patterns of chromosomal proteins and histone modifications; a majority of the active genes exhibit both "activation" marks (e.g., H3K4me3 and H3K36me3) and "silencing" marks (e.g., H3K9me2 and HP1a). The hallmark of active genes in heterochromatic domains appears to be a loss of H3K9 methylation at the transcription start site. We also observe complex epigenomic profiles of intergenic regions, repeated transposable element (TE) sequences, and genes in the heterochromatic extensions. An unexpectedly large fraction of sequences in the euchromatic chromosome arms exhibits a heterochromatic chromatin signature, which differs in size, position, and impact on gene expression among cell types. We conclude that patterns of heterochromatin/euchromatin packaging show greater complexity and plasticity than anticipated. This comprehensive analysis provides a foundation for future studies of gene activity and chromosomal functions that are influenced by or dependent upon heterochromatin.
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| 7. |
- Whitehouse, Daniel P., et al.
(författare)
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Relationship of admission blood proteomic biomarkers levels to lesion type and lesion burden in traumatic brain injury : A CENTER-TBI study
- 2022
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Ingår i: EBioMedicine. - : Elsevier. - 2352-3964. ; 75
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Tidskriftsartikel (refereegranskat)abstract
- Background: We aimed to understand the relationship between serum biomarker concentration and lesion type and volume found on computed tomography (CT) following all severities of TBI.Methods: Concentrations of six serum biomarkers (GFAP, NFL, NSE, S100B, t-tau and UCH-L1) were measured in samples obtained <24 hours post-injury from 2869 patients with all severities of TBI, enrolled in the CENTER-TBI prospective cohort study (NCT02210221). Imaging phenotypes were defined as intraparenchymal haemorrhage (IPH), oedema, subdural haematoma (SDH), extradural haematoma (EDH), traumatic subarachnoid haemorrhage (tSAH), diffuse axonal injury (DAI), and intraventricular haemorrhage (IVH). Multivariable polynomial regression was performed to examine the association between biomarker levels and both distinct lesion types and lesion volumes. Hierarchical clustering was used to explore imaging phenotypes; and principal component analysis and k-means clustering of acute biomarker concentrations to explore patterns of biomarker clustering.Findings: 2869 patient were included, 68% (n=1946) male with a median age of 49 years (range 2-96). All severities of TBI (mild, moderate and severe) were included for analysis with majority (n=1946, 68%) having a mild injury (GCS 13-15). Patients with severe diffuse injury (Marshall III/IV) showed significantly higher levels of all measured biomarkers, with the exception of NFL, than patients with focal mass lesions (Marshall grades V/VI). Patients with either DAI+IVH or SDH+IPH+tSAH, had significantly higher biomarker concentrations than patients with EDH. Higher biomarker concentrations were associated with greater volume of IPH (GFAP, S100B, t-tau;adj r2 range:0·48-0·49; p<0·05), oedema (GFAP, NFL, NSE, t-tau, UCH-L1;adj r2 range:0·44-0·44; p<0·01), IVH (S100B;adj r2 range:0.48-0.49; p<0.05), Unsupervised k-means biomarker clustering revealed two clusters explaining 83·9% of variance, with phenotyping characteristics related to clinical injury severity.Interpretation: Interpretation: Biomarker concentration within 24 hours of TBI is primarily related to severity of injury and intracranial disease burden, rather than pathoanatomical type of injury.
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| 8. |
- Yan, Ming, et al.
(författare)
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An in vitro study of vascular endothelial toxicity of CdTe quantum dots
- 2011
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Ingår i: Toxicology. - : Elsevier. - 0300-483X .- 1879-3185. ; 282:3, s. 94-103
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Tidskriftsartikel (refereegranskat)abstract
- Quantum dots (QDs), as novel bioimaging and drug delivery agents, are generally introduced into vascular system by injection, and thus directly exposed to vascular endothelial cells (ECs). However, the adverse effects of QDs on ECs are poorly understood. In this study, employing human umbilical vein ECs (HUVECs), we investigated the potential vascular endothelial toxicity of mercaptosuccinic acid (MSA)-capped CdTe QDs in vitro. In the experiment, water-soluble and pH stable CdTe QDs were synthesized; and the cell viability assays showed that CdTe QDs (0.1-100 mu g/mL) dose-dependently decreased the cell viability of HUVECs, indicating CdTe QDs induced significant endothelial toxicity. The flow cytometric and immunofluorescence results revealed that 10 mu g/mL CdTe QDs elicited significant oxidative stress, mitochondrial network fragmentation as well as disruption of mitochondrial membrane potential (Delta psi(m)); whereas ROS scavenger could protect HUVECs from QDs-induced mitochondrial dysfunction. Moreover, upon 24h exposure to 10 mu g/mL CdTe QDs, the apoptotic HUVECs dramatically increased by 402.01%, accompanied with alternative expression of apoptosis proteins, which were upregulation of Bax, down-regulation of Bcl-2, release of mitochondrial cytochrome c and cleavage of caspase-9/caspase-3. These results suggested that CdTe QDs could not only impair mitochondria but also exert endothelial toxicity through activation of mitochondrial death pathway and induction of endothelial apoptosis. Our results provide strong evidences of the direct toxic effects of QDs on human vascular ECs, and reveal that exposure to QDs is a significant risk for the development of cardiovascular diseases. These results also provide helpful guidance on the future safe use and manipulation of QDs to make them more suitable tools in nanomedicine.
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| 9. |
- Yang, Fengmei, et al.
(författare)
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Li2FePO4F and its metal-doping for Li-ion batteries : an ab initio study
- 2014
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Ingår i: RSC Advances. - : Royal Society of Chemistry (RSC). - 2046-2069. ; 4:91, s. 50195-50201
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Tidskriftsartikel (refereegranskat)abstract
- The electrochemical properties of three isotopic Li2FePO4F compounds, as cathode materials under different space groups Pbcn, P (1) over bar and Pnma were investigated using first principle calculations. Their structures and average open circuit voltages for step delithiation reactions were explored, and the results are in good agreement with the reported experimental data. We estimate the substitution effect of Fe by Co in Pnma-Li2FePO4F. The substitution of Fe by Co in Li2Fe1-xCoxPO4F may enhance the discharge potential of the materials, and the rate of its volume change during the redox process is between 0.6% and 2.1%. Furthermore, from the projected density of states for Li2Fe0.5Co0.5PO4F, we found strong hybridization for Fe-3d and Co-3d bands near the Fermi level, which implies that the Co-doped Li2Fe1-xCoxPO4F may possess better electronic conductivity than the pure phase.
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