| 1. |
- Abelev, Betty, et al.
(author)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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In: Journal of High Energy Physics. - 1029-8479. ; :11
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Journal article (peer-reviewed)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 2. |
- Abelev, Betty, et al.
(author)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
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In: Journal of High Energy Physics. - 1029-8479. ; :7
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Journal article (peer-reviewed)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 3. |
- Abelev, Betty, et al.
(author)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Journal article (peer-reviewed)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 4. |
- Seibert, M. Marvin, et al.
(author)
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Single mimivirus particles intercepted and imaged with an X-ray laser
- 2011
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 470:7332, s. 78-81
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Journal article (peer-reviewed)abstract
- X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions(1-4). Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma(1). The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval(2). Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a noncrystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source(5). Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
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| 5. |
- Chapman, Henry N, et al.
(author)
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Femtosecond X-ray protein nanocrystallography.
- 2011
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7
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Journal article (peer-reviewed)abstract
- X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200nm to 2μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
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| 6. |
- Ho, Joshua W. K., et al.
(author)
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Comparative analysis of metazoan chromatin organization
- 2014
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 512:7515, s. 449-U507
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Journal article (peer-reviewed)abstract
- Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms(1-3). Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths(4,5). To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.
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| 7. |
- Bernhard, Juerg, et al.
(author)
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Clinical Benefit Response in Pancreatic Cancer Trials Revisited
- 2014
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In: Oncology Research and Treatment. - : S. Karger AG. - 2296-5270 .- 2296-5262. ; 37:1-2, s. 42-48
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Journal article (peer-reviewed)abstract
- Objectives: Clinical benefit response (CBR), based on changes in pain, Karnofsky performance status, and weight, is an established palliative endpoint in trials for advanced gastrointestinal cancer. We investigated whether CBR is associated with survival, and whether CBR reflects a wide-enough range of domains to adequately capture patients' perception. Methods: CBR was prospectively evaluated in an international phase III chemotherapy trial in patients with advanced pancreatic cancer (n = 311) in parallel with patient-reported outcomes (PROs). Results: The median time to treatment failure was 3.4 months (range: 0-6). The majority of the CBRs (n = 39) were noted in patients who received chemotherapy for at least 5 months. Patients with CBR (n = 62) had longer survival than non-responders (n = 182) (hazard ratio = 0.69; 95% confidence interval: 0.51-0.94; p = 0.013). CBR was predicted with a sensitivity and specificity of 77-80% by various combinations of 3 mainly physical PROs. A comparison between the duration of CBR (n = 62, median = 8 months, range = 4-31) and clinically meaningful improvements in the PROs (n = 100-116; medians = 9-11 months, range = 4-24) showed similar intervals. Conclusion: CBR is associated with survival and mainly reflects physical domains. Within phase III chemotherapy trials for advanced gastrointestinal cancer, CBR can be replaced by a PRO evaluation, without losing substantial information but gaining complementary information.
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| 8. |
- Bjarnason, Elizabeth, et al.
(author)
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Integrating Requirements Engineering with Software Development - A Research Abstract
- 2012
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In: ICB Research Reports. - 1860-2770. ; :46
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Conference paper (peer-reviewed)abstract
- Software development companies operating in market-driven domains need to deliver new and appealing software products at an increasing rate in order to stay competitive. This requires fast and efficient development of software for which the requirements are based on ever-changing market demands. Agile development claims to achieve increased development efficiency by performing the requirements engineering (RE) activities concurrently with design, planning and testing in an integrated fashion. However, coordination and communication is often reported as a challenge both for agile and for traditional RE practices. Increased insight into the factors affected by integrating RE may allow tailoring the degree of RE integration to suit specific project context, e.g. size, rate of requirements change, domain etc., and thereby support increased efficiency in software development. The aim of this research is to develop methods for assessing the level of RE integration and techniques for improving the integration of requirements. The research is performed in collaboration with industry and the developed methods and techniques will be empirically evaluated in an industrial setting.
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| 9. |
- Gonzalez-Acuna, Daniel, et al.
(author)
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Health evaluation of wild gentoo penguins (Pygoscelis papua) in the Antarctic Peninsula
- 2013
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In: Polar Biology. - : Springer Science and Business Media LLC. - 0722-4060 .- 1432-2056. ; 36:12, s. 1749-1760
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Journal article (peer-reviewed)abstract
- Historically wildlife conservation was based on habitat protection and exploitation control. Only recently have diseases been considered an important issue. However, pathogens are usually described during or after disease outbreaks, but to determine which pathogens may be emerging, surveys of wildlife health are critical in a given time. This study deals with the health status of gentoo penguins Pygoscelis papua in two localities at the Antarctica Peninsula and one at Ardley Island off the South Shetland Islands. Cloacal swaps, fresh fecal samples, ectoparasites, and blood smears were collected. We examined and dissected 14 penguin corpses found dead. Fecal samples were positive for Campylobacter, Escherichia coli and in the carcasses four endoparasitic species were found: Diphyllobothrium sp. and Parorchites zederi, Corynosoma shackletoni and Stegophorus adeliae. The tick Ixodes uriae occurred in five of the examined penguins, and the louse Austrogoniodes gressitti on six birds. From the colony grounds, we collected 1,184 I. uriae. We recorded antibiotic-resistant bacteria, such as E. coli, in ecosystems where gentoo penguins breed. Cloacal samples (300) were negative for Chlamydia, as well as for Salmonella, Campylobacter, E. coli, Newcastle and Influenza viruses.
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| 10. |
- Ruhi, Albert, et al.
(author)
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Change in biological traits and community structure of macroinvertebrates through primary succession in a man-made Swedish wetland
- 2012
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In: Freshwater Science. - : University of Chicago Press. - 2161-9565 .- 2161-9549. ; 31:1, s. 22-37
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Journal article (peer-reviewed)abstract
- We investigated the successional development of a benthic macrofaunal community in Kalmar Dämme, a man-made wetland in southeastern Sweden, over a 13-y period after construction (1997–2009). We assessed primary succession by monitoring changes in species composition, biological traits, and community structure. Predictable successional changes occurred, and the structure of the community was complex at the advanced phase. Three successional phases were observed, each with typifying species. At the advanced phase, dominant biological traits shifted to favor animals with longer life-cycle durations, aerial dispersal strategies, and certain feeding types (i.e., filter-feeders, fine sediment collectors, predators, and parasites). We selected the Coleoptera assemblage to represent the macroinvertebrate community in an evaluation of the extent to which man-made wetlands in different age classes (<3 y and ≥10 y) were similar to natural wetlands (>50 y). No significant differences in Coleoptera assemblages were found between natural wetlands and man-made wetlands ≥10 y. However, man-made wetlands ≥10 y had significantly higher coleopteran species richness than natural and man-made wetlands <3 y because of the convergence of pioneering species persisting from early successional stages with representative specialized taxa from natural wetlands. Our results suggest that 10 y may be sufficient time for the macrofaunal communities of man-made wetlands to resemble those of natural wetlands.
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| 11. |
- Ruhi, Albert Vidal, et al.
(author)
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How do early successional patterns in man-made wetlands differ between cold temperate and Mediterranean regions?
- 2012
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In: Limnologica. - : Elsevier BV. - 0075-9511 .- 1873-5851. ; 42:4, s. 328-339
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Journal article (peer-reviewed)abstract
- The early stages of succession in newly created wetlands should be impacted by the region in which the wetland is located, since climate may have filtered the dominant biological strategies of the taxa leading this process and may condition their dynamics. We studied the early successional patterns of macroinvertebrates within man made ponds, located in cold temperate (Scandinavian Peninsula) and Mediterranean regions (Iberian Peninsula), during the first three years following their creation. We predicted (1) non random subsets of the regional species pool (deterministic assembly) guiding the successional process in cold temperate wetlands, and random (stochastic) assembly in the Mediterranean region; (2) higher successional rates in Mediterranean ponds than in the cold temperate ponds, with contrary episodes of highest and lowest change throughout the year; and (3) a significant difference in the composition of biological traits between regions, due to the dominance of traits adapted to hydrological variability in the Mediterranean region. Hypotheses on community structure (1) and the composition of dominant biological traits (3) were mostly supported - deterministic assembly mechanisms in the cold temperate ponds and stochastic assembly in the Mediterranean ponds; and a dominance of different biological traits between regions, explained by the need to overcome hydrological disturbances in the Mediterranean ponds. The dynamics of succession (2) were explained by climatic factors in the cold temperate region but not in the Mediterranean ponds. We suggest that the intrinsic hydrological variability of Mediterranean lentic systems may be a major factor driving community changes in man-made wetlands in this region. In order to generalize the observed patterns, we performed a meta-analysis of the temporal trends of taxonomic distinctness parameters of other successional studies across a latitudinal gradient in Europe, which supported the differences we had observed between latitudinal extremes.
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| 12. |
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| 13. |
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