| 1. |
- Ablikim, M., et al.
(författare)
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Measurements of (XcJ)-> K+K-K+K- decays
- 2006
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 642:3, s. 197-202
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Tidskriftsartikel (refereegranskat)abstract
- Using 14M psi(2S) events taken with the BESII detector, chi(cJ) -> 2(K+K-) decays are studied. For the four-kaon final state, the branching fractions are B(chi(c0,1,2) ->.2(K+K-)) = (3.48 +/- 0.23 +/- 0.47) x 10(-3), (0.70 +/- 0.13 +/- 0.10) x 10(-3), and (2.17 +/- 0.20 +/- 0.31) x 10(-3). For the phi K+K- final state, the branching fractions, which are measured for the first time, are B(chi(c0,1,2) -> phi K+K-) = (1.03 +/- 0.22 +/- 0.15) x 10(-3), (0.46 +/- 0.16 +/- 0.06) x 10(-3), and (1.67 +/- 0.26 +/- 0.24) x 10(-4). For the phi phi final state, B(chi(c0,2) -> phi phi) = (0.94 +/- 0.21 +/- 0.13) x 10(-3) and (1.70 +/- 0.30 +/- 0.25) x 10(-3).
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| 2. |
- 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. - 1061-4036 .- 1546-1718. ; 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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| 3. |
- Karlsson, Göran, et al.
(författare)
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Gene expression profiling demonstrates that TGF-{beta}1 signals exclusively through receptor complexes involving Alk5 and identifies targets of TGF-{beta} signaling.
- 2005
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Ingår i: Physiological Genomics. - : American Physiological Society. - 1094-8341 .- 1531-2267. ; 21:3, s. 396-403
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Tidskriftsartikel (refereegranskat)abstract
- Transforming growth factor-β 1 (TGF-β) regulates cellular functions like proliferation, differentiation, and apoptosis. On the cell surface, TGF-β binds to receptor complexes consisting of TGF-β receptor type II (Tβ RII) and activin-like kinase receptor-5 (Alk5), and the downstream signaling is transduced by Smad and MAPK proteins. Recent data have shown that alternative receptor combinations aside from the classical pairing of Tβ RII/Alk5 can be relevant for TGF-β signaling. We have screened for alternative receptors for TGF-β and also for gene targets of TGF-β signaling, by performing functional assays and microarray analysis in murine embryonic fibroblast (MEF) cell lines lacking Alk5. Data from TGF-β-stimulated Alk5(-/-) cells show them to be completely unaffected by TGF-β. Additionally, 465 downstream targets of Alk5 signaling were identified when comparing Alk5(-/-) or TGF-β-stimulated Alk5(+/+) MEFs with unstimulated Alk5(+/+) cells. Our results demonstrate that, in MEFs, TGF-β signals exclusively through complexes involving Alk5, and give insight to its downstream effector genes.
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| 4. |
- Krogh, Morten, et al.
(författare)
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Analysis of DIGE data using a linear mixed model allowing for protein-specific dye effects
- 2007
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 7:23, s. 4235-4244
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Tidskriftsartikel (refereegranskat)abstract
- Abstract in UndeterminedDifferential in-gel electrophoresis (DIGE) experiments allow three protein samples to be run per gel. The three samples are labeled with the spectrally resolvable fluorescent dyes, Cy2, Cy3, and Cy5, respectively. Here, we show that protein-specific dye effects exist, and we present a linear mixed model for analysis of DIGE data which takes dye effects into account. A Java implementation of the model, called DIGEanalyzer, is freely available at http://bioinfo.thep.lu.se/digeanalyzer.html. Three DIGE experiments from our laboratory, with 173, 64, and 24 gels, respectively, were used to quantify and verify the dye effects. DeCyder 5.0 and 6.5 were used for spot detection and matching. The fractions of proteins with a statistically significant (0.001 level) dye effect were 19, 34, and 23%, respectively. The fractions of proteins with a dye effect above 1.4-fold change were 1, 4, and 6%, respectively. The median magnitude of the dye effect was 1.07-fold change for Cy5 versus Cy3 and 1.16-fold change for Cy3 versus Cy2. The maximal dye effect was a seven-fold change. The dye effects of spots corresponding to the same protein tend to be similar within each of the three experiments, and to a smaller degree across experiments.
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| 5. |
- Li, Jiachen, et al.
(författare)
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A combined computational and experimental approach predicts thrombin adsorption to zeolites
- 2023
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Ingår i: Colloids and Surfaces B. - : Elsevier BV. - 0927-7765 .- 1873-4367. ; 221, s. 113007-
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Tidskriftsartikel (refereegranskat)abstract
- Robust protein-nanomaterial surface analysis is important, but also a challenge. Thrombin plays an important role in the coagulant activity of protein corona mediated by Ca2+ ion exchanged zeolites. However, the mech-anism for this modulation remains unresolved. In this study, we proposed a combined computational and experimental approach to determine the adsorbed sites and orientations of thrombin binding to Ca2+-exchanged LTA-type (CaA) zeolite. Specifically, fourteen ensembles of simulated annealing molecular dynamics (SAMD) simulations and experimental surface residues microenvironment analysis were used to reduce the starting orientations needed for further molecular dynamics (MD) simulations. The combined MD simulations and pro -coagulant activity characterization also reveal the consequent corresponding deactivation of thrombin on CaA zeolite. It is mainly caused by two aspects: (1) the secondary structure of thrombin can change after its adsorption on the CaA zeolite. (2) The positively charged area of thrombin mediates the preferential interaction between thrombin and CaA zeolite. Some thrombin substrate sites are thus blocked by zeolite after its adsorption. This study not only provides a promising method for characterizing the protein-nanoparticle interaction, but also gives an insight into the design and application of zeolite with high procoagulant activity.
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| 6. |
- Liu, Yingchun, et al.
(författare)
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Multiclass discovery in array data
- 2004
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Background A routine goal in the analysis of microarray data is to identify genes with expression levels that correlate with known classes of experiments. In a growing number of array data sets, it has been shown that there is an over-abundance of genes that discriminate between known classes as compared to expectations for random classes. Therefore, one can search for novel classes in array data by looking for partitions of experiments for which there are an over-abundance of discriminatory genes. We have previously used such an approach in a breast cancer study. Results We describe the implementation of an unsupervised classification method for class discovery in microarray data. The method allows for discovery of more than two classes. We applied our method on two published microarray data sets: small round blue cell tumors and breast tumors. The method predicts relevant classes in the data sets with high success rates. Conclusions We conclude that the proposed method is accurate and efficient in finding biologically relevant classes in microarray data. Additionally, the method is useful for quality control of microarray experiments. We have made the method available as a computer program.
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| 7. |
- Liu, Yingchun, et al.
(författare)
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Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis
- 2007
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1474-7596 .- 1465-6906. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- Gene expression signatures consisting of tens to hundreds of genes have been found to be informative for different biological states. Recently, many computational methods have been proposed for biological interpretation of such signatures. However, there is a lack of methods for identifying cell signaling pathways whose deregulation result in an observed expression signature. We present a strategy for identifying such signaling pathways and evaluate the strategy using six human and mouse gene expression signatures.
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| 8. |
- Liu, Yingchun
(författare)
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Statistical and Functional Analysis of Genomic and Proteomic Data
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- High-throughput technologies have led to an explosion in the availability of data at the genome scale. Such data provide important information about cellular processes and causes of human diseases, as well as for drug discovery. Deciphering the biologically relevant results from these data requires comprehensive analytical methods. In this dissertation, we present methods for gene and protein expression data analysis. Our major contributions include a method for differential in-gelelectrophoresis data analysis capable of removing protein-specific dye bias in the data, a method for finding unknown biological groups using expression data, and a method for identifying active and inactive signaling pathways in a gene expression signature based on the enrichment of downstream target genes of pathways.
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| 9. |
- Wang, Yamin, et al.
(författare)
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Reductive Decomposition of Solvents and Additives toward Solid-Electrolyte Interphase Formation in Lithium-Ion Battery
- 2020
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 124:17, s. 9099-9108
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Tidskriftsartikel (refereegranskat)abstract
- The solid-electrolyte interphase (SEI) formed through the reductive decomposition of solvent molecules plays a crucial role in the stability and durability of lithium-ion batteries. Here, we investigate the initial process of SEI formation through reactive force field-molecular dynamics (ReaxFF-MD) simulations and density functional theory (DFT) calculations. ReaxFF-MD is used as a simulation protocol to predict the evolution of SEI components, and products are obtained in good agreement with the experimental results. DFT calculations are then used to model the reaction center. We find that one-electron reduction induces the similar breaking of the C-O bond in solvent ethylene carbonate (EC) and additive fluoroethylene carbonate (FEC). When another electron is added, EC decomposition produces gas CO + alkylcarbonate or ethylene (C2H4) + carbonate (CO32-), whereas FEC decomposition generates lithium fluoride (LiF) and vinylene carbonate (VC) in addition to CO + alkylcarbonate. LiF and VC could also be regarded as important electrolyte additives to improve battery performance. The reduction on FEC moiety/molecule is more energetically favorable than that on the corresponding EC moiety/molecule. This knowledge on the decomposition products at the atomic scale well correlate with available experiments, and theory provides useful guidelines and structural motifs for interpretations of future SEI-related experiments.
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