| 1. |
- Schael, S, et al.
(författare)
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Precision electroweak measurements on the Z resonance
- 2006
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Ingår i: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454
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Forskningsöversikt (refereegranskat)abstract
- We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
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| 2. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 3. |
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| 4. |
- 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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| 5. |
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| 6. |
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| 7. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 8. |
- Ding, Li, et al.
(författare)
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Somatic mutations affect key pathways in lung adenocarcinoma
- 2008
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 455:7216, s. 1069-1075
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Tidskriftsartikel (refereegranskat)abstract
- Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.
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| 9. |
- Kamba, S., et al.
(författare)
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Magnetodielectric effect and optic soft mode behaviour in quantum paraelectric EuTiO3 ceramics
- 2007
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Ingår i: Europhysics letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 80:2, s. 27002-
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Tidskriftsartikel (refereegranskat)abstract
- Infrared reflectivity and time-domain terahertz transmission spectra of EuTiO3 ceramics revealed a polar optic phonon at 6-300K whose softening is fully responsible for the recently observed quantum paraelectric behaviour. Even if our EuTiO3 ceramics show lower permittivity than the single crystal due to a reduced density and/ or small amount of secondary pyrochlore Eu2Ti2O7 phase, we confirmed a magnetic field dependence of the permittivity, also slightly smaller than in single crystal. An attempt to reveal the soft phonon dependence at 1.8K on the magnetic field up to 13T remained below the accuracy of our infrared reflectivity experiment.
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| 10. |
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| 11. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 12. |
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| 13. |
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| 14. |
- Chen, D. R., et al.
(författare)
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Band-rejection fiber filter and fiber sensor based on a Bragg fiber of transversal resonant structure
- 2008
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Ingår i: Optics Express. - 1094-4087. ; 16:21, s. 16489-16495
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Tidskriftsartikel (refereegranskat)abstract
- We propose a novel band-rejection fiber filter based on a Bragg fiber of transversal resonant structure, which can also be used as a fiber sensor. Defect layers are introduced in the periodic high/low index structure in the cladding of the Bragg fiber. Coupling between the core mode and the defect mode results in large confinement loss for some resonant wavelengths inside the band gap of the Bragg fiber. A segment of the Bragg fiber of transversal resonant structure can be used as a band-rejection fiber filter, whose characteristics are mainly determined by the defect layer. The loss peak wavelength of the Bragg fiber is dependent on the refractive index and the thickness of the defect layer which indicates its applications of refractive index and strain sensing.
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| 15. |
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| 16. |
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| 17. |
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| 18. |
- Large, DJ, et al.
(författare)
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The influence of climate, hydrology and permafrost on Holocene peat accumulation at 3500 m on the eastern Qinghai-Tibetan plateau
- 2009
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 28:27-28, s. 3303-3314
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Tidskriftsartikel (refereegranskat)abstract
- Peatland of the eastern Qinghai–Tibetan Plateau lies at the convergence of the East Asian and Indian monsoon systems in eastern Asia. To understand the evolution of this peatland and its potential to provide new insights into the Holocene evolution of the East Asian monsoon a 6 m peat core was collected from the undisturbed central part of a peat deposit near Hongyuan. The age-depth profile was determined using 16 14C-AMS age dates, the peat analysed for a range of environmental variables including carbon, nitrogen and hydrogen concentration, bulk density, δ13C and the associated spring water analysed for hydrogen and oxygen isotopes. The age-depth profile of the recovered peat sequence covers the period from 9.6 to 0.3 kyr BP and is linear indicating that the conditions governing productivity and decay varied little over the Holocene. Using changes in carbon density, organic carbon content and its δ13C, cold dry periods of permafrost characterised by low density and impeded surface drainage were identified. The low δ18O and δD values of the spring water emanating around the peat deposit, down to −13.8 and −102‰ (VSMOW), respectively, with an inverse relationship between electrical conductivity and isotopic composition indicate precipitation under colder and drier conditions relative to the present day. In view of the current annual mean air temperature of 1 °C this suggests conditions in the past have been conducive to permafrost. Inferred periods of permafrost correspond to independently recognised cold periods in other Holocene records from across China at 8.6, 8.2–7.8, 5.6–4.2, 3.1 and 1.8–1.5 kyr BP. The transition to a cold dry climate appears to be more rapid than the subsequent recovery and cold dry periods at Hongyuan are of longer duration than equivalent cold dry periods over central and eastern China. Light–dark banding peat on a scale of 15–30 years from 9.6 to 5.5 kyr BP may indicate a strong influence of decadal oscillations possibly the Pacific Decadal Oscillation and a potential link between near simultaneous climatic changes in the northwest Pacific, ENSO, movement of the Intertropical Convergence Zone and the East Asian Monsoon.
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| 19. |
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| 20. |
- Perez-Martinez, Pablo, et al.
(författare)
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Association between glucokinase regulatory protein (GCKR) and apolipoprotein A5 (APOA5) gene polymorphisms and triacylglycerol concentrations in fasting, postprandial, and fenofibrate-treated states
- 2009
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Ingår i: American Journal of Clinical Nutrition. - : Elsevier BV. - 1938-3207 .- 0002-9165. ; 89:1, s. 391-399
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Tidskriftsartikel (refereegranskat)abstract
- Background: Hypertriglyceridemia is a risk factor for cardiovascular disease. Variation in the apolipoprotein A5 (APOA5) and glucokinase regulatory protein (GCKR) genes has been associated with fasting plasma triacylglycerol. Objective: We investigated the combined effects of the GCKR rs780094C -> T, APOA5 -1131T -> C, and APOA5 56C -> G single nucleotide polymorphisms (SNPs) on fasting triacylglycerol in several independent populations and the response to a high-fat meal and fenofibrate interventions. Design: We used a cross-sectional design to investigate the association with fasting triacylglycerol in 8 populations from America, Asia, and Europe (n = 7730 men and women) and 2 intervention studies in US whites (n = `1061) to examine postprandial triacylglycerol after a high-fat meal and the response to fenofibrate. We defined 3 combined genotype groups: 1) protective (homozygous for the wild-type allele for all 3 SNPs); 2) intermediate (any mixed genotype not included in groups 1 and 3); and 3) risk (carriers of the variant alleles at both genes). Results: Subjects within the risk group had significantly higher fasting triacylglycerol and a higher prevalence of hypertriglyceridemia than did subjects in the protective group across all populations. Moreover, subjects in the risk group had a greater postprandial triacylglycerol response to a high-fat meal and greater fenofibrate-induced reduction of fasting triacylglycerol than did the other groups, especially among persons with hypertriglyceridemia. Subjects with the intermediate genotype had intermediate values (P for trend < 0.001). Conclusions: SNPs in GCKR and APOA5 have an additive effect on both fasting and postprandial triacylglycerol and contribute to the interindividual variability in response to fenofibrate treatment. Am J Clin Nutr 2009;89:391-9. Clin Nutr 2009; 89: 391-9.
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| 21. |
- Petzelt, J., et al.
(författare)
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Grain boundary and size effect on the dielectric, infrared and Raman response of SrTiO3 nanograin ceramics
- 2008
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Ingår i: Ferroelectrics (Print). - : Informa UK Limited. - 0015-0193 .- 1563-5112. ; 363, s. 227-244
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Tidskriftsartikel (refereegranskat)abstract
- The recently revealed giant grain size effect on dielectric properties in undoped SrTiO3 ceramics (J. Petzelt et al., J. Phys.: Con dens. Matter 19, 196222 (2007) and references therein), was extended to smaller grains of 80 nm mean grain size. Like for previously studied ceramics with larger grain size, in addition to dielectric permittivity also the infrared and Raman responses were studied and discussed. It was shown that the reduced effective permittivity is fully accounted for by the infrared soft mode behaviour and, similar to single crystals and other ceramics studied, no dielectric dispersion appears below the THz frequency range. The rather universal (independent of the grain size and sintering process) double dead layer structure was proposed to be responsible for the observed changes in the infrared and Raman spectra, allowing the grain core to keep the single crystal dielectric function. The outer dead layer shell (obviously charged due to an oxygen deficit) is very thin (similar to 1 nm) having frequency and temperature independent low permittivity (similar to 10) and is responsible for the static permittivity suppression. The inner layer of only slightly distorted perovskite structure is polar with local polarization normal to grain boundaries gradually decreasing towards the grain centre. This polarization and/or the thickness of the polar layers, which compensate the charged grain boundaries, appear to increase on decreasing temperature, particularly below the structural phase transition. Its nature is still not fully understood. In agreement with our previous suggestions, from the Raman data it con be also concluded that in the low-temperature tetragonal phase of all SrTiO3 ceramics, the local tetragonal axes tend perpendicular to the grain boundaries and the tetragonality is strongly reduced compared to single crystals.
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| 22. |
- Shen, G. X., et al.
(författare)
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The chloroplast protease subunit ClpP4 is a substrate of the E3 ligase AtCHIP and plays an important role in chloroplast function
- 2007
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Ingår i: Plant Journal. - 0960-7412. ; 49:2, s. 228-237
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Tidskriftsartikel (refereegranskat)abstract
- Animal CHIP proteins are chaperone-dependent E3 ubiquitin ligases that physically interact with Hsp70, Hsp90 and proteasome, promoting degradation of a selective group of non-native or damaged proteins in animal cells. The plant CHIP-like protein, AtCHIP, also plays important roles in protein turnover metabolism. AtCHIP interacts with a proteolytic subunit, ClpP4, of the chloroplast Clp protease in vivo, and ubiquitylates ClpP4 in vitro. The steady-state level of ClpP4 is reduced in AtCHIP-overexpressing plants under high-intensity light conditions, suggesting that AtCHIP targets ClpP4 for degradation and thereby regulates the Clp proteolytic activity in chloroplasts under certain stress conditions. Overexpression of ClpP4 in Arabidopsis leads to chlorotic phenotypes in transgenic plants, and chloroplast structures in the chlorotic tissues of ClpP4-overexpressing plants are abnormal and largely devoid of thylakoid membranes, suggesting that ClpP4 plays a critical role in chloroplast structure and function. As AtCHIP is a cytosolic protein that has been shown to play an important role in regulating an essential chloroplast protease, this research provides new insights into the regulatory networks controlling protein turnover catabolism in chloroplasts.
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| 23. |
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| 24. |
- Shen, M. H., et al.
(författare)
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Detection of copy number changes at the NF1 locus with improved high-resolution array CGH
- 2007
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Ingår i: Clinical Genetics. - : Wiley. - 0009-9163 .- 1399-0004. ; 72:3, s. 238-244
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Tidskriftsartikel (refereegranskat)abstract
- Neurofibromatosis type 1 (NF1) is a common autosomal dominant disease caused by various types of mutations in the NF1 gene. We have previously developed a locus-specific DNA microarray for detection of copy number changes at the NF1 locus by comparative genomic hybridization (CGH) analysis. The original array contains 183 probes pooled from 444 polymerase chain reaction (PCR) products. In the current work, we have used 493 probes derived from single PCR products (200-998 bp in size) to construct a higher resolution array with a smaller average probe size for molecular diagnosis of NF1. This has improved the average resolution from 12.6 kb in the previous array to 4.5 kb in the current version. The performance of the newly constructed microarray was validated with 14 well-characterized NF1 mutations for CGH analysis. These mutations represent deletions from ∼7 kb to over 2 Mb in size. Using this array, we examined a total of 55 NF1 patients for copy number changes at the NF1 locus, detecting deletions in four of them. These results demonstrate that a locus-specific microarray constructed from single PCR products can efficiently detect copy number changes at the NF1 locus, providing a simple method for the molecular diagnosis of NF1.
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| 25. |
- Straat, K, et al.
(författare)
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Activation of telomerase by human cytomegalovirus
- 2009
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 101:7, s. 488-497
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Tidskriftsartikel (refereegranskat)
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| 26. |
- Wood, Laura D, et al.
(författare)
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The genomic landscapes of human breast and colorectal cancers.
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 318:5853, s. 1108-1113
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Tidskriftsartikel (refereegranskat)abstract
- Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalog the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene "mountains" and a much larger number of gene "hills" that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.
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| 27. |
- Wu, Xifeng, et al.
(författare)
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Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer.
- 2009
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:9, s. 991-5
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Tidskriftsartikel (refereegranskat)abstract
- We conducted a genome-wide association study on 969 bladder cancer cases and 957 controls from Texas. For fast-track validation, we evaluated 60 SNPs in three additional US populations and validated the top SNP in nine European populations. A missense variant (rs2294008) in the PSCA gene showed consistent association with bladder cancer in US and European populations. Combining all subjects (6,667 cases, 39,590 controls), the overall P-value was 2.14 x 10(-10) and the allelic odds ratio was 1.15 (95% confidence interval 1.10-1.20). rs2294008 alters the start codon and is predicted to cause truncation of nine amino acids from the N-terminal signal sequence of the primary PSCA translation product. In vitro reporter gene assay showed that the variant allele significantly reduced promoter activity. Resequencing of the PSCA genomic region showed that rs2294008 is the only common missense SNP in PSCA. Our data identify rs2294008 as a new bladder cancer susceptibility locus.
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