| 1. |
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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. |
- 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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| 4. |
- Varju, Katalin, et al.
(författare)
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Reconstruction of attosecond pulse trains using an adiabatic phase expansion
- 2005
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Ingår i: Physical Review Letters. - 1079-7114. ; 95:24
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Tidskriftsartikel (refereegranskat)abstract
- We propose a new method to reconstruct the electric field of attosecond pulse trains. The phase of the high-order harmonic emission electric field is Taylor expanded around the maximum of the laser pulse envelope in the time domain and around the central harmonic in the frequency domain. Experimental measurements allow us to determine the coefficients of this expansion and to characterize the radiation with attosecond accuracy over a femtosecond time scale. The method gives access to pulse-to-pulse variations along the train, including the timing, the chirp, and the attosecond carrier envelope phase.
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| 5. |
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| 6. |
- Kovacev, M, et al.
(författare)
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Extreme ultraviolet fourier-transform spectroscopy with high order harmonics
- 2005
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Ingår i: Physical Review Letters. - 1079-7114. ; 95:22
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate a new scheme for extreme ultraviolet (xuv) Fourier-transform spectroscopy based on the generation of two phase-locked high-harmonic beams. It allows us to measure for the first time interferograms at wavelengths as short as 90 nm, and open the perspective of performing high-resolution Fourier-transform absorption spectroscopy in the xuv. Our measurements also demonstrate that a precise control of the relative phase of harmonic pulses can be obtained with an accuracy on an attosecond time scale, of importance for future xuv pump-xuv probe attosecond spectroscopy.
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| 7. |
- Szatmari, Peter, et al.
(författare)
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Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
- 2007
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:3, s. 319-328
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Tidskriftsartikel (refereegranskat)abstract
- Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,168 families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.
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| 8. |
- Bergman, Peder, 1961-, et al.
(författare)
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Improved SiC Epitaxial Material for Bipolar Applications
- 2008
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Ingår i: Proc. of MRS Spring Meeting 2008. ; , s. D05-
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Konferensbidrag (refereegranskat)abstract
- Epitaxial growth on Si-face nominally on-axis 4H-SiC substrates has been performed using horizontal Hot-wall chemical vapor deposition system. The formation of 3C inclusions is one of the main problem with growth on on-axis Si-face substrates. In situ surface preparation, starting growth parameters and growth temperature are found to play a vital role in the epilayer polytype stability. High quality epilayers with 100% 4H-SiC were obtained on full 2″ substrates. Different optical and structural techniques were used to characterize the material and to understand the growth mechanisms. It was found that the replication of the basal plane dislocation from the substrate into the epilayer can be eliminated through growth on on-axis substrates. Also, no other kind of structural defects were found in the grown epilayers. These layers have also been processed for simple PiN structures to observe any bipolar degradation. More than 70% of the diodes showed no forward voltage drift during 30 min operation at 100 A/cm2.
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| 9. |
- Birney, Ewan, et al.
(författare)
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Prepublication data sharing
- 2009
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7261, s. 168-170
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Tidskriftsartikel (refereegranskat)abstract
- Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.
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| 10. |
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| 11. |
- Cornelissen, Johannes H C, et al.
(författare)
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Global negative vegetation feedback to climate warming responses of leaf litter decomposition rates in cold biomes
- 2007
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 10:7, s. 619-627
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Tidskriftsartikel (refereegranskat)abstract
- Whether climate change will turn cold biomes from large long-term carbon sinks into sources is hotly debated because of the great potential for ecosystem-mediated feedbacks to global climate. Critical are the direction, magnitude and generality of climate responses of plant litter decomposition. Here, we present the first quantitative analysis of the major climate-change-related drivers of litter decomposition rates in cold northern biomes worldwide.Leaf litters collected from the predominant species in 33 global change manipulation experiments in circum-arctic-alpine ecosystems were incubated simultaneously in two contrasting arctic life zones. We demonstrate that longer-term, large-scale changes to leaf litter decomposition will be driven primarily by both direct warming effects and concomitant shifts in plant growth form composition, with a much smaller role for changes in litter quality within species. Specifically, the ongoing warming-induced expansion of shrubs with recalcitrant leaf litter across cold biomes would constitute a negative feedback to global warming. Depending on the strength of other (previously reported) positive feedbacks of shrub expansion on soil carbon turnover, this may partly counteract direct warming enhancement of litter decomposition.
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| 12. |
- Fuller, Jessica, et al.
(författare)
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Genetic Dissection Reveals Diabetes Loci Proximal to the Gimap5 Lymphopenia Gene.
- 2009
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Ingår i: Physiological Genomics. - : American Physiological Society. - 1094-8341 .- 1531-2267. ; 38, s. 89-97
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Tidskriftsartikel (refereegranskat)abstract
- Congenic DRF.(f/f) rats are protected from type 1 diabetes (T1D) by 34 Mb of F344 DNA introgressed proximal to the Gimap5 lymphopenia gene. To dissect the genetic factor(s) that confer protection from T1D in the DRF.(f/f) rat line, DRF.(f/f) rats were crossed to inbred BBDR or DR.(lyp/lyp) rats to generate congenic sublines that were genotyped, monitored for T1D and positional candidate genes sequenced. All (100%) DR.(lyp/lyp) rats developed T1D by 83 days of age. Reduction of the DRF.(f/f) F344 DNA fragment by 26 Mb (42.52 Mb-68.51 Mb) retained complete T1D protection. Further dissection revealed that a 2 Mb interval of F344 DNA (67.41-70.17 Mb) (Region 1) resulted in 47% protection and significantly delayed onset (p<0.001 compared to DR.(lyp/lyp)). Retaining <1 Mb of F344 DNA at the distal end (76.49-76.83 Mb) (Region 2) resulted in 28% protection and also delayed onset (p<0.001 compared to DR.(lyp/lyp)). Comparative analysis of diabetes frequency in the DRF.(f/f) congenic sublines further refined the RNO4 Region 1 interval to approximately 670 Kb and Region 2 to the 340 Kb proximal to Gimap5. All congenic DRF.(f/f) sublines were prone to low-grade pancreatic mononuclear cell infiltration around ducts and vessels but less than 20% of islets in non-diabetic rats showed islet infiltration. Coding sequence analysis revealed TCR Vbeta 8E, 12 and 13 as candidate genes in Region 1 and Znf467 and Atp6v0e2 as candidate genes in Region 2. Our results show that spontaneous T1D is controlled by at least two genetic loci 7 Mb apart on rat chromosome 4. Key words: Type 1 diabetes, BB rat, T cell receptor, autoimmune.
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| 13. |
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| 14. |
- Johnsson, Per, et al.
(författare)
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Attosecond electron wave packet dynamics in strong laser fields
- 2005
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Ingår i: Physical Review Letters. - 1079-7114. ; 95:1, s. 1-013001
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Tidskriftsartikel (refereegranskat)abstract
- We use a train of sub-200 attosecond extreme ultraviolet (XUV) pulses with energies just above the ionization threshold in argon to create a train of temporally localized electron wave packets. We study the energy transfer from a strong infrared (IR) laser field to the ionized electrons as a function of the delay between the XUV and IR fields. When the wave packets are born at the zero crossings of the IR field, a significant amount of energy (similar to 20 eV) is transferred from the field to the electrons. This results in dramatically enhanced above-threshold ionization in conditions where the IR field alone does not induce any significant ionization. Because both the energy and duration of the wave packets can be varied independently of the IR laser, they are valuable tools for studying and controlling strong-field processes.
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| 15. |
- Lindgren, Cecilia M, et al.
(författare)
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Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.
- 2009
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Ingår i: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 5:6, s. e1000508-
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Tidskriftsartikel (refereegranskat)abstract
- To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9x10(-11)) and MSRA (WC, P = 8.9x10(-9)). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8)). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.
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| 16. |
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| 17. |
- Morlens, AS, et al.
(författare)
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Design and characterization of extreme-ultraviolet broadband mirrors for attosecond science
- 2006
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Ingår i: Optics Letters. - 0146-9592. ; 31:10, s. 1558-1560
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Tidskriftsartikel (refereegranskat)abstract
- A novel multilayer mirror was designed and fabricated based on a recently developed three-material technology aimed both at reaching reflectivities of about 20% and at controlling dispersion over a bandwidth covering photon energies between 35 and 50 eV. The spectral phase upon reflection was retrieved by measuring interferences in a two-color ionization process using high-order harmonics produced from a titanium: sapphire laser. We demonstrate the feasibility of designing and characterizing phase-controlled broadband optics in the extreme-ultraviolet domain, which should facilitate the manipulation of attosecond pulses for applications.
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| 18. |
- Petri, Michelle, et al.
(författare)
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Systemic lupus international collaborating clinics renal activity/response exercise - Development of a renal activity score and renal response index
- 2008
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Ingår i: Arthritis and Rheumatism. - : Wiley. - 1529-0131 .- 0004-3591. ; 58:6, s. 1784-1788
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Tidskriftsartikel (refereegranskat)abstract
- Objective. To develop a measure of renal activity in systemic lupus erythematosus and use it to develop a renal response index. Methods. Abstracted data from the medical records of 215 patients with lupus nephritis were sent to 8 nephrologists and 29 rheumatologists for rating. Seven nephrologists and 22 rheumatologists completed the ratings. Each physician rated each patient visit with respect to renal disease activity (none, mild, moderate, or severe). Using the most commonly selected rating for each patient as the gold standard, stepwise regression modeling was performed to identify the variables most related to renal disease activity, and these variables were then used to create an activity score. This activity score could then be applied to 2 consecutive visits to define a renal response index. Results. The renal activity score was computed as follows: proteinuria 0.5-1 gm/day (3 points), proteinuria >1-3 gm/day (5 points), proteinuria >3 gm/day (11 points), urine red blood cell count > 10/high-power field (3 points), and urine white blood cell count >10/high-power field (I point). The chance-adjusted agreement between the renal response index derived from the activity score applied to the paired visits and the plurality physician response rating was 0.69 (95% confidence interval 0.59-0.79). Conclusion. Ratings derived from this index for rating of renal response showed reasonable agreement with physician ratings in a pilot study. The index will require further refinement, testing, and validation. A data-driven approach to create renal activity and renal response indices will be useful in both clinical care and research settings.
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| 19. |
- Pinay, Gilles, et al.
(författare)
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Patterns of denitrification rates in European alluvial soils under various hydrological regimes
- 2007
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Ingår i: Freshwater Biology. - 0046-5070 .- 1365-2427. - 0046-5070 ; 52:2, s. 252-266
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Tidskriftsartikel (refereegranskat)abstract
- 1. Denitrification in floodplain soils is one of the main biological processes emitting and reducing nitrous oxide, a greenhouse gas, and the main process responsible for the buffering capacity of riparian zones against diffuse nitrate pollution. 2. The aim of this study was to measure denitrification rates under a wide range of current climatic conditions and hydrological regimes in Europe (from latitude 64 degrees N to latitude 42 degrees N and from longitude 2 degrees W to longitude 25 degrees E), in order to determine the response patterns of this microbial process under different climatic and hydrological conditions, and to identify denitrification proxies robust enough to be used at the European scale. 3. Denitrification activity was significant in all the floodplain soils studied whatever the latitude. However, we found an increase in rates of an order of magnitude from high to mid latitudes. Maximum rates (above 30 g N m(-2) month(-1)) were measured in the maritime conditions of the Trent floodplain. These rates are similar to mineralisation rates measured in alluvial soils and of the same order of magnitude as the amount of N stored in herbaceous plants in alluvial soils. 4. We used Multivariate Adaptative Regression Splines to relate the response variable denitrification with five relevant predictors, namely soil moisture, temperature, silt plus clay, nitrate content and herbaceous plant biomass. 5. Soil moisture, temperature, and nitrate were the three main control variables of microbial denitrification in alluvial soils in decreasing order of importance. 6. The model developed for denitrification with interaction effects outperformed a pure additive model. Soil moisture was involved in all interactions, emphasising its importance in predicting denitrification. 7. These results are discussed in the context of scenarios for future change in European hydrological regimes.
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| 20. |
- Rich, Rebecca L., et al.
(författare)
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A global benchmark study using affinity-based biosensors
- 2009
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Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 386:2, s. 194-216
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Tidskriftsartikel (refereegranskat)abstract
- To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
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| 21. |
- ul-Hassan, Jawad, 1974-, et al.
(författare)
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On-axis Homoepitaxy on Full 2- 4H-SiC Wafer for High Power Applications
- 2009
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Ingår i: Materials Science Forum Vols. 615-617. - : Trans Tech Publications. - 9780878493340 ; , s. 133-136
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Konferensbidrag (refereegranskat)abstract
- Homoepitaxial growth has been performed on Si-face nominally on-axis 4H-SiC substrates. Special attention was paid to the surface preparation before starting the growth. Si-face polished surfaces were studied after etching under C-rich, Si-rich and under pure hydrogen ambient conditions. In-situ surface preparation, starting growth parameters and growth temperature are found to play a vital role to maintain the polytype stability in the epilayer. High quality epilayers with 100% 4H-SiC were obtained on full 2” wafer. Complete PiN structure was grown and more than 70% of the diodes showed a stable behavior and the forward voltage drift was less than 0.1 V. Also, a comparison of the electroluminescence images of diodes before and after heavy injection of 125 A/cm2 for 30 min did not show any sign of stacking fault formation in the device active region.
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| 22. |
- Varju, Katalin, et al.
(författare)
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Frequency chirp of harmonic and attosecond pulses
- 2005
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Ingår i: Journal of Modern Optics. - : Informa UK Limited. - 0950-0340 .- 1362-3044. ; 52:2-3, s. 379-394
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Tidskriftsartikel (refereegranskat)abstract
- We study the phase of the atomic polarization in the process of high-order harmonic generation. Its dependence on the laser intensity and the harmonic order induce a frequency variation in time (chirp) respectively of the harmonic pulses and attosecond pulses. We review the recent experimental results on the temporal characterization of the harmonic emission and show that measurements performed using very different techniques (like XFROG and RABITT), probing the phase in different parameter spaces, can be connected through the mixed phase derivatives, demonstrating the common underlying physics
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| 23. |
- Willer, Cristen J., et al.
(författare)
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Six new loci associated with body mass index highlight a neuronal influence on body weight regulation
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:1, s. 25-34
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Tidskriftsartikel (refereegranskat)abstract
- Common variants at only two loci, FTO and MC4R, have been reproducibly associated with body mass index (BMI) in humans. To identify additional loci, we conducted meta-analysis of 15 genome-wide association studies for BMI (n > 32,000) and followed up top signals in 14 additional cohorts (n > 59,000). We strongly confirm FTO and MC4R and identify six additional loci (P < 5 x 10(-8)): TMEM18, KCTD15, GNPDA2, SH2B1, MTCH2 and NEGR1 (where a 45-kb deletion polymorphism is a candidate causal variant). Several of the likely causal genes are highly expressed or known to act in the central nervous system (CNS), emphasizing, as in rare monogenic forms of obesity, the role of the CNS in predisposition to obesity.
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| 24. |
- 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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| 25. |
- Amundadottir, Laufey, et al.
(författare)
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Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer.
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 41, s. 986-990
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Tidskriftsartikel (refereegranskat)abstract
- We conducted a two-stage genome-wide association study of pancreatic cancer, a cancer with one of the lowest survival rates worldwide. We genotyped 558,542 SNPs in 1,896 individuals with pancreatic cancer and 1,939 controls drawn from 12 prospective cohorts plus one hospital-based case-control study. We conducted a combined analysis of these groups plus an additional 2,457 affected individuals and 2,654 controls from eight case-control studies, adjusting for study, sex, ancestry and five principal components. We identified an association between a locus on 9q34 and pancreatic cancer marked by the SNP rs505922 (combined P = 5.37 x 10(-8); multiplicative per-allele odds ratio 1.20; 95% confidence interval 1.12-1.28). This SNP maps to the first intron of the ABO blood group gene. Our results are consistent with earlier epidemiologic evidence suggesting that people with blood group O may have a lower risk of pancreatic cancer than those with groups A or B.
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