| 1. |
- Abdallah, J., et al.
(author)
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Mechanical construction and installation of the ATLAS tile calorimeter
- 2013
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In: Journal of Instrumentation. - 1748-0221. ; 8, s. T11001-
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Journal article (peer-reviewed)abstract
- This paper summarises the mechanical construction and installation of the Tile Calorimeter for the ATLAS experiment at the Large Hadron Collider in CERN, Switzerland. The Tile Calorimeter is a sampling calorimeter using scintillator as the sensitive detector and steel as the absorber and covers the central region of the ATLAS experiment up to pseudorapidities +/- 1.7. The mechanical construction of the Tile Calorimeter occurred over a period of about 10 years beginning in 1995 with the completion of the Technical Design Report and ending in 2006 with the installation of the final module in the ATLAS cavern. During this period approximately 2600 metric tons of steel were transformed into a laminated structure to form the absorber of the sampling calorimeter. Following instrumentation and testing, which is described elsewhere, the modules were installed in the ATLAS cavern with a remarkable accuracy for a structure of this size and weight.
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| 2. |
- Abdallah, J., et al.
(author)
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The optical instrumentation of the ATLAS Tile Calorimeter
- 2013
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In: Journal of Instrumentation. - 1748-0221. ; 8, s. P01005-
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Journal article (peer-reviewed)abstract
- The Tile Calorimeter, covering the central region of the ATLAS experiment up to pseudorapidities of +/-1.7, is a sampling device built with scintillating tiles that alternate with iron plates. The light is collected in wave-length shifting (WLS) fibers and is read out with photomultipliers. In the characteristic geometry of this calorimeter the tiles lie in planes perpendicular to the beams, resulting in a very simple and modular mechanical and optical layout. This paper focuses on the procedures applied in the optical instrumentation of the calorimeter, which involved the assembly of about 460,000 scintillator tiles and 550,000 WLS fibers. The outcome is a hadronic calorimeter that meets the ATLAS performance requirements, as shown in this paper.
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| 3. |
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| 4. |
- Hudson, Lawrence N., et al.
(author)
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The PREDICTS database : a global database of how local terrestrial biodiversity responds to human impacts
- 2014
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In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:24, s. 4701-4735
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Journal article (peer-reviewed)abstract
- Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
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| 5. |
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| 6. |
- Hudson, Thomas J., et al.
(author)
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International network of cancer genome projects
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998
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Journal article (peer-reviewed)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
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| 7. |
- Bruggmann, P., et al.
(author)
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Historical epidemiology of hepatitis C virus (HCV) in selected countries
- 2014
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In: Journal of Viral Hepatitis. - Hoboken : Wiley-Blackwell. - 1352-0504 .- 1365-2893. ; 21, s. 5-33
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Journal article (peer-reviewed)abstract
- Chronic infection with hepatitis C virus (HCV) is a leading indicator for liver disease. New treatment options are becoming available, and there is a need to characterize the epidemiology and disease burden of HCV. Data for prevalence, viremia, genotype, diagnosis and treatment were obtained through literature searches and expert consensus for 16 countries. For some countries, data from centralized registries were used to estimate diagnosis and treatment rates. Data for the number of liver transplants and the proportion attributable to HCV were obtained from centralized databases. Viremic prevalence estimates varied widely between countries, ranging from 0.3% in Austria, England and Germany to 8.5% in Egypt. The largest viremic populations were in Egypt, with 6358000 cases in 2008 and Brazil with 2106000 cases in 2007. The age distribution of cases differed between countries. In most countries, prevalence rates were higher among males, reflecting higher rates of injection drug use. Diagnosis, treatment and transplant levels also differed considerably between countries. Reliable estimates characterizing HCV-infected populations are critical for addressing HCV-related morbidity and mortality. There is a need to quantify the burden of chronic HCV infection at the national level.
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| 8. |
- Razavi, H., et al.
(author)
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The present and future disease burden of hepatitis C virus (HCV) infection with today's treatment paradigm
- 2014
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In: Journal of Viral Hepatitis. - Hoboken : Wiley-Blackwell. - 1352-0504 .- 1365-2893. ; 21:Suppl. 1, s. 34-59
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Journal article (peer-reviewed)abstract
- The disease burden of hepatitis C virus (HCV) is expected to increase as the infected population ages. A modelling approach was used to estimate the total number of viremic infections, diagnosed, treated and new infections in 2013. In addition, the model was used to estimate the change in the total number of HCV infections, the disease progression and mortality in 2013-2030. Finally, expert panel consensus was used to capture current treatment practices in each country. Using today's treatment paradigm, the total number of HCV infections is projected to decline or remain flat in all countries studied. However, in the same time period, the number of individuals with late-stage liver disease is projected to increase. This study concluded that the current treatment rate and efficacy are not sufficient to manage the disease burden of HCV. Thus, alternative strategies are required to keep the number of HCV individuals with advanced liver disease and liver-related deaths from increasing.
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| 9. |
- Wedemeyer, H., et al.
(author)
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Strategies to manage hepatitis C virus (HCV) disease burden
- 2014
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In: Journal of Viral Hepatitis. - Hoboken : Wiley-Blackwell. - 1352-0504 .- 1365-2893. ; 21, s. 60-89
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Journal article (peer-reviewed)abstract
- The number of hepatitis C virus (HCV) infections is projected to decline while those with advanced liver disease will increase. A modeling approach was used to forecast two treatment scenarios: (i) the impact of increased treatment efficacy while keeping the number of treated patients constant and (ii) increasing efficacy and treatment rate. This analysis suggests that successful diagnosis and treatment of a small proportion of patients can contribute significantly to the reduction of disease burden in the countries studied. The largest reduction in HCV-related morbidity and mortality occurs when increased treatment is combined with higher efficacy therapies, generally in combination with increased diagnosis. With a treatment rate of approximately 10%, this analysis suggests it is possible to achieve elimination of HCV (defined as a >90% decline in total infections by 2030). However, for most countries presented, this will require a 3-5 fold increase in diagnosis and/or treatment. Thus, building the public health and clinical provider capacity for improved diagnosis and treatment will be critical.
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| 10. |
- Cryan, J P, et al.
(author)
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Molecular frame Auger electron energy spectrum from N2
- 2012
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In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 45:5, s. 055601-
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Journal article (peer-reviewed)abstract
- Here we present the first angle-resolved, non-resonant (normal) Auger spectra for impulsively aligned nitrogen molecules. We have measured the angular pattern of Auger electron emission following K -shell photoionization by 1.1 keV photons from the Linac Coherent Light Source (LCLS). Using strong-field-induced molecular alignment to make molecular frame measurements is equally effective for both repulsive and quasi-bound final states. The capability to resolve Auger emission angular distributions in the molecular frame of reference provides a new tool for spectral assignments in congested Auger electron spectra that takes advantage of the symmetries of the final diction states. Based on our experimental results and theoretical predictions, we propose the assignment of the spectral features in the Auger electron spectrum.
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| 11. |
- Sutton, M. A., et al.
(author)
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Towards a climate-dependent paradigm of ammonia emission and deposition
- 2013
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In: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 1471-2970 .- 0962-8436. ; 368:1621
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Journal article (peer-reviewed)abstract
- Existing descriptions of bi-directional ammonia (NH3) land-atmosphere exchange incorporate temperature and moisture controls, and are beginning to be used in regional chemical transport models. However, such models have typically applied simpler emission factors to upscale the main NH3 emission terms. While this approach has successfully simulated the main spatial patterns on local to global scales, it fails to address the environment-and climate-dependence of emissions. To handle these issues, we outline the basis for a new modelling paradigm where both NH3 emissions and deposition are calculated online according to diurnal, seasonal and spatial differences in meteorology. We show how measurements reveal a strong, but complex pattern of climatic dependence, which is increasingly being characterized using ground-based NH3 monitoring and satellite observations, while advances in process-based modelling are illustrated for agricultural and natural sources, including a global application for seabird colonies. A future architecture for NH3 emission-deposition modelling is proposed that integrates the spatio-temporal interactions, and provides the necessary foundation to assess the consequences of climate change. Based on available measurements, a first empirical estimate suggests that 5 degrees C warming would increase emissions by 42 per cent (28-67%). Together with increased anthropogenic activity, global NH3 emissions may increase from 65 (45-85) Tg N in 2008 to reach 132 (89-179) Tg by 2100.
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| 12. |
- Trigo, M., et al.
(author)
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Fourier-transform inelastic X-ray scattering from time- and momentum-dependent phonon-phonon correlations
- 2013
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In: Nature Physics. - 1745-2473. ; 9:12, s. 790-794
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Journal article (peer-reviewed)abstract
- The macroscopic characteristics of a material are determined by its elementary excitations, which dictate the response of the system to external stimuli. The spectrum of excitations is related to fluctuations in the density-density correlations and is typically measured through frequency-domain neutron(1) or X-ray(2-4) scattering. Time-domain measurements of these correlations could yield a more direct way to investigate the excitations of solids and their couplings both near to and far from equilibrium. Here we show that we can access large portions of the phonon dispersion of germanium by measuring the diffuse scattering from femtosecond X-ray free-electron laser pulses. A femtosecond optical laser pulse slightly quenches the vibrational frequencies, producing pairs of high-wavevector phonons with opposite momenta. These phonons manifest themselves as time-dependent coherences in the displacement correlations(5) probed by the X-ray scattering. As the coherences are preferentially created in regions of strong electron-phonon coupling, the time-resolved approach is a natural spectroscopic tool for probing low-energy collective excitations in solids, and their microscopic interactions.
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| 13. |
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| 14. |
- Glownia, James M., et al.
(author)
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Time-resolved pump-probe experiments at the LCLS
- 2010
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In: Optics Express. - 1094-4087. ; 18:17, s. 17620-17630
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Journal article (peer-reviewed)abstract
- The first time-resolved x-ray/optical pump-probe experiments at the SLAC Linac Coherent Light Source (LCLS) used a combination of feedback methods and post-analysis binning techniques to synchronize an ultrafast optical laser to the linac-based x-ray laser. Transient molecular nitrogen alignment revival features were resolved in time-dependent x-ray-induced fragmentation spectra. These alignment features were used to find the temporal overlap of the pump and probe pulses. The strong-field dissociation of x-ray generated quasi-bound molecular dications was used to establish the residual timing jitter. This analysis shows that the relative arrival time of the Ti:Sapphire laser and the x-ray pulses had a distribution with a standard deviation of approximately 120 fs. The largest contribution to the jitter noise spectrum was the locking of the laser oscillator to the reference RF of the accelerator, which suggests that simple technical improvements could reduce the jitter to better than 50 fs.
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| 15. |
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| 16. |
- Cryan, James P., et al.
(author)
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Auger Electron Angular Distribution of Double Core-Hole States in the Molecular Reference Frame
- 2010
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 105:8, s. 083004-
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Journal article (peer-reviewed)abstract
- The Linac Coherent Light Source free electron laser is a source of high brightness x rays, 2×1011 photons in a ∼5 fs pulse, that can be focused to produce double core vacancies through rapid sequential ionization. This enables double core vacancy Auger electron spectroscopy, an entirely new way to study femtosecond chemical dynamics with Auger electrons that probe the local valence structure of molecules near a specific atomic core. Using 1.1 keV photons for sequential x-ray ionization of impulsively aligned molecular nitrogen, we observed a rich single-site double core vacancy Auger electron spectrum near 413 eV, in good agreement with ab initio calculations, and we measured the corresponding Auger electron angle dependence in the molecular frame.
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| 17. |
- Fuchs, M.a b, et al.
(author)
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Nonlinear X-ray compton scattering
- 2014
-
Conference paper (other academic/artistic)abstract
- We use XFEL pulses to observe the most fundamental nonlinear X-ray-matter interaction: nonlinear Compton scattering. In contrast to theoretical predictions, we measure an anonymous and yet to be explained red-shift in the observed photon energy.
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| 18. |
- Vieno, M., et al.
(author)
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Modelling surface ozone during the 2003 heat-wave in the UK
- 2010
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 10:16, s. 7963-7978
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Journal article (peer-reviewed)abstract
- The EMEP4UK modelling system is a high resolution (5x5 km(2)) application of the EMEP chemistry-transport model, designed for scientific and policy studies in the UK. We demonstrate the use and performance of the EMEP4UK system through the study of ground-level ozone (O-3) during the extreme August 2003 heat-wave. Meteorology is generated by the Weather Research and Forecast (WRF) model, nudged every six hours with reanalysis data. We focus on SE England, where hourly average O-3 reached up to 140 ppb during the heat-wave. EMEP4UK accurately reproduces elevated O-3 and much of its day-to-day variability during the heat-wave. Key O-3 precursors, nitrogen dioxide and isoprene, are less well simulated, but show generally accurate diurnal cycles and concentrations to within a factor of similar to 2-3 of observations. The modelled surface O-3 distribution has an intricate spatio-temporal structure, governed by a combination of meteorology, emissions and photochemistry. A series of sensitivity runs with the model are used to explore the factors that influenced O-3 levels during the heat-wave. Various factors appear to be important on different days and at different sites. Ozone imported from outside the model domain, especially the south, is very important on several days during the heat-wave, contributing up to 85 ppb. The effect of dry deposition is also important on several days. Modelled isoprene concentrations are generally best simulated if isoprene emissions are changed from the base emissions: typically doubled, but elevated by up to a factor of five on one hot day. We found that accurate modelling of the exact positions of nitrogen oxide and volatile organic compound plumes is crucial for the successful simulation of O-3 at a particular time and location. Variations in temperature of +/- 5 K were found to have impacts on O-3 of typically less than +/- 10 ppb.
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| 19. |
- Ziegler, JC, et al.
(author)
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Orthographic depth and its impact on universal predictors of reading: a cross-language investigation
- 2010
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In: Psychological science. - : SAGE Publications. - 1467-9280 .- 0956-7976. ; 21:4, s. 551-559
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Journal article (peer-reviewed)abstract
- Alphabetic orthographies differ in the transparency of their letter-sound mappings, with English orthography being less transparent than other alphabetic scripts. The outlier status of English has led scientists to question the generality of findings based on English-language studies. We investigated the role of phonological awareness, memory, vocabulary, rapid naming, and nonverbal intelligence in reading performance across five languages lying at differing positions along a transparency continuum (Finnish, Hungarian, Dutch, Portuguese, and French). Results from a sample of 1,265 children in Grade 2 showed that phonological awareness was the main factor associated with reading performance in each language. However, its impact was modulated by the transparency of the orthography, being stronger in less transparent orthographies. The influence of rapid naming was rather weak and limited to reading and decoding speed. Most predictors of reading performance were relatively universal across these alphabetic languages, although their precise weight varied systematically as a function of script transparency.
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| 20. |
- Parreira, P., et al.
(author)
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Atomic force microscopy measurements reveal multiple bonds between Helicobacter pylori blood group antigen binding adhesin and Lewis b ligand
- 2014
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 11:101, s. UNSP 20141040-
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Journal article (peer-reviewed)abstract
- The strength of binding between the Helicobacter pylori blood group antigen-binding adhesin (BabA) and its cognate glycan receptor, the Lewis b blood group antigen (Leb), was measured by means of atomic force microscopy. High-resolution measurements of rupture forces between single receptor-ligand pairs were performed between the purified BabA and immobilized Leb structures on self-assembled monolayers. Dynamic force spectroscopy revealed two similar but statistically different bond populations. These findings suggest that the BabA may form different adhesive attachments to the gastric mucosa in ways that enhance the efficiency and stability of bacterial adhesion.
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| 21. |
- Parreira, P., et al.
(author)
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Bioengineered surfaces promote specific protein-glycan mediated binding of the gastric pathogen Helicobacter pylori
- 2013
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In: Acta biomaterialia. - : Elsevier BV. - 1878-7568 .- 1742-7061. ; 9:11, s. 8885-8893
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Journal article (peer-reviewed)abstract
- Helicobacter pylori colonizes the gastric mucosa of half of the worlds population and persistent infection is related with an increase in the risk of gastric cancer. Adhesion of H. pylori to the gastric epithelium, which is essential for infection, is mediated by bacterial adhesin proteins that recognize specific glycan structures (Gly-R) expressed in the gastric mucosa. The blood group antigen binding adhesin (BabA) recognizes difucosylated antigens such as Lewis B (Le(b)), while the sialic acid binding adhesin (SabA) recognizes sialylated glycoproteins and glycolipids, such as sialyl-Lewis x (sLe(x)). This work aimed to investigate whether these Gly-Rs (Le(b) and sLe(x)) can attract and specifically bind H. pylori after immobilization on synthetic surfaces (self-assembled monolayers (SAMs) of alkanethiols on gold). Functional bacterial adhesion assays for (Gly-R)-SAMs were performed using H. pylori strains with different adhesin protein profiles. The results demonstrate that H. pylori binding to surfaces occurs via interaction between its adhesins and cognate (Gly-R)-SAMs and bound H. pylori maintains its characteristic rod-shaped morphology only during conditions of specific adhesin-glycan binding. These results offer new insights into innovative strategies against H. pylori infection based on the scavenging of bacteria from the stomach using specific H. pylori chelating biomaterials.
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| 22. |
- Wetterskog, Daniel, 1978, et al.
(author)
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Mutation profiling of adenoid cystic carcinomas from multiple anatomical sites identifies mutations in the RAS pathway, but no KIT mutations
- 2013
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In: Histopathology. - : Wiley. - 0309-0167. ; 62:4, s. 543-550
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Journal article (peer-reviewed)abstract
- Aims The majority of adenoid cystic carcinomas (AdCCs), regardless of anatomical site, harbour the MYB–NFIB fusion gene. The aim of this study was to characterize the repertoire of somatic genetic events affecting known cancer genes in AdCCs. Methods and results DNA was extracted from 13 microdissected breast AdCCs, and subjected to a mutation survey using the Sequenom OncoCarta Panel v1.0. Genes found to be mutated in any of the breast AdCCs and genes related to the same canonical molecular pathways, as well as KIT, a proto-oncogene whose protein product is expressed in AdCCs, were sequenced in an additional 68 AdCCs from various anatomical sites by Sanger sequencing. Using the Sequenom MassARRAY platform and Sanger sequencing, mutations in BRAF and HRAS were identified in three and one cases, respectively (breast, and head and neck). KIT, which has previously been reported to be mutated in AdCCs, was also investigated, but no mutations were identified. Conclusions Our results demonstrate that mutations in genes pertaining to the canonical RAS pathway are found in a minority of AdCCs, and that activating KIT mutations are either absent or remarkably rare in these cancers, and unlikely to constitute a driver and therapeutic target for patients with AdCC.
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| 23. |
- Fuhrmann, A., et al.
(author)
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Molecular mechanisms underlying the effects of cyclosporin A and sirolimus on glucose and lipid metabolism in liver, skeletal muscle and adipose tissue in an in vivo rat model
- 2014
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In: Biochemical Pharmacology. - : Elsevier BV. - 0006-2952 .- 1356-1839. ; 88:2, s. 216-228
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Journal article (peer-reviewed)abstract
- Cyclosporin A (CsA) and sirolimus (SRL) are immunosuppressive agents (IAs) associated with dyslipidemia, insulin resistance and new onset diabetes after transplantation (NODAT). However, the molecular mechanisms involved are not fully understood. We investigated the effects of six-week treatment of either CsA or SRL on glucose and lipid metabolism in Wistar rats. The results show that, compared with vehicle-treated rats, SRL-treated rats were significantly lighter starting at week 5. CsA or SRL caused glucose intolerance, increased storage of lipids in the liver and skeletal muscle, and decreased the insulin-stimulated glucose uptake in isolated adipocytes. Furthermore, these agents significantly decreased genes involved in insulin action and glucose uptake, such as, IRS-1, Glut4 and Glut1, and increased genes and/or proteins involved in hepatic lipogenesis and gluconeogenesis, while decreasing them in adipose tissue. After either treatment PGC1 alpha gene expression was down regulated in skeletal muscle, an important player in fatty acid oxidation. Moreover, there was an increase in IL-6 gene expression in adipose tissue in the SRL-treated rats, suggesting stimulation of lipolysis. The results of the present study suggest that CsA and SRL lead to metabolic alterations in liver, muscle and adipose tissue, which may contribute to the development of dyslipidemia and insulin resistance associated with immunosuppressive therapy. (C) 2014 Elsevier Inc. All rights reserved.
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| 24. |
- Hertel, O., et al.
(author)
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Governing processes for reactive nitrogen compounds in the European atmosphere
- 2012
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In: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 9:12, s. 4921-4954
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Research review (peer-reviewed)abstract
- Reactive nitrogen (Nr) compounds have different fates in the atmosphere due to differences in the governing processes of physical transport, deposition and chemical transformation. N r compounds addressed here include reduced nitrogen (NH x : ammonia (NH 3 ) and its reaction product ammonium (NH 4 + )), oxidized nitrogen (NO y : nitrogen monoxide (NO) + nitrogen dioxide (NO 2 ) and their reaction products) as well as organic nitrogen compounds (organic N). Pollution abatement strategies need to take into account the differences in the governing processes of these compounds when assessing their impact on ecosystem services, biodiversity, human health and climate. NO x (NO + NO 2 ) emitted from traffic affects human health in urban areas where the presence of buildings increases the residence time in streets. In urban areas this leads to enhanced exposure of the population to NO x concentrations. NO x emissions generally have little impact on nearby ecosystems because of the small dry deposition rates of NO x . These compounds need to be converted into nitric acid (HNO 3 ) before removal through deposition is efficient. HNO 3 sticks quickly to any surface and is thereby either dry deposited or incorporated into aerosols as nitrate (NO 3 + ). In contrast to NOx compounds, NH 3 has potentially high impacts on ecosystems near the main agricultural sources of NH 3 because of its large ground-level concentrations along with large dry deposition rates. Aerosol phase NH 4 + and NO 3 + contribute significantly to background PM 2.5 and PM 10 (mass of aerosols with an aerodynamic diameter of less than 2.5 and 10 μm, respectively) with an impact on radiation balance as well as potentially on human health. Little is known quantitatively and qualitatively about organic N in the atmosphere, other than that it contributes a significant fraction of wet-deposited N, and is present in both gaseous and particulate forms. Further studies are needed to characterise the sources, air chemistry and removal rates of organic N emissions.
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