| 1. |
- Bott, Lukas Thomas, et al.
(författare)
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Coulomb dissociation of O-16 into He-4 and C-12
- 2023
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Ingår i: NUCLEAR PHYSICS IN ASTROPHYSICS - X, NPA-X 2022. - : EDP Sciences. - 2100-014X. ; 279
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Konferensbidrag (refereegranskat)abstract
- We measured the Coulomb dissociation of O-16 into He-4 and C-12 within the FAIR Phase-0 program at GSI Helmholtzzentrum fur Schwerionenforschung Darmstadt, Germany. From this we will extract the photon dissociation cross section O-16(alpha,gamma)C-12, which is the time reversed reaction to C-12(alpha,gamma)O-16. With this indirect method, we aim to improve on the accuracy of the experimental data at lower energies than measured so far. The expected low cross section for the Coulomb dissociation reaction and close magnetic rigidity of beam and fragments demand a high precision measurement. Hence, new detector systems were built and radical changes to the (RB)-B-3 setup were necessary to cope with the high-intensity O-16 beam. All tracking detectors were designed to let the unreacted O-16 ions pass, while detecting the C-12 and He-4.
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| 2. |
- Andresen, Louise C., 1974, et al.
(författare)
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Shifting Impacts of Climate Change: Long-Term Patterns of Plant Response to Elevated CO2, Drought, and Warming Across Ecosystems
- 2016
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Ingår i: Large-Scale Ecology: Model Systems to Global Perspectives. - : Elsevier. - 9780081009352 ; , s. 437-473
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Bokkapitel (refereegranskat)abstract
- Field experiments that expose terrestrial ecosystems to climate change factors by manipulations are expensive to maintain, and typically only last a few years. Plant biomass is commonly used to assess responses to climate treatments and to predict climate change impacts. However, response to the treatments might be considerably different between the early years and a decade later. The aim of this data analysis was to develop and apply a method for evaluating changes in plant biomass responses through time, in order to provide a firm basis for discussing how the ‘short-term’ response might differ from the ‘long-term’ response. Across 22 sites situated in the northern hemisphere, which covered three continents, and multiple ecosystems (grasslands, shrublands, moorlands, forests, and deserts), we evaluated biomass datasets from long-term experiments with exposure to elevated CO2 (eCO2), warming, or drought. We developed methods for assessing biomass response patterns to the manipulations using polynomial and linear (piecewise) model analysis and linked the responses to sitespecific variables such as temperature and rainfall. Polynomial patterns across sites indicated changes in response direction over time under eCO2, warming, and drought. In addition, five distinct pattern types were confirmed within sites: ‘no response’, ‘delayed response’, ‘directional response’, ‘dampening response’, and ‘altered response’ patterns. We found that biomass response direction was as likely to change over time as it was to be consistent, and therefore suggest that climate manipulation experiments should be carried out over timescales covering both short- and long-term responses, in order to realistically assess future impacts of climate change.
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| 3. |
- Aquila, Andrew, et al.
(författare)
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Time-resolved protein nanocrystallography using an X-ray free-electron laser
- 2012
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Ingår i: Optics Express. - 1094-4087. ; 20:3, s. 2706-2716
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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| 4. |
- Chapman, Henry N, et al.
(författare)
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Femtosecond X-ray protein nanocrystallography.
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7
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Tidskriftsartikel (refereegranskat)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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| 5. |
- Ekeberg, Tomas, et al.
(författare)
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Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
- 2016
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.
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| 6. |
- Ekeberg, Tomas, 1983-, et al.
(författare)
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Three-dimensional structure determination with an X-ray laser
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus.
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| 7. |
- Gorkhover, Tais, et al.
(författare)
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Femtosecond and nanometre visualization of structural dynamics in superheated nanoparticles
- 2016
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Ingår i: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 10:2, s. 93-97
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Tidskriftsartikel (refereegranskat)abstract
- The ability to observe ultrafast structural changes in nanoscopic samples is essential for understanding non-equilibrium phenomena such as chemical reactions, matter under extreme conditions, ultrafast phase transitions and intense light-matter interactions. Established imaging techniques are limited either in time or spatial resolution and typically require samples to be deposited on a substrate, which interferes with the dynamics. Here, we show that coherent X-ray diffraction images from isolated single samples can be used to visualize femtosecond electron density dynamics. We recorded X-ray snapshot images from a nanoplasma expansion, a prototypical non-equilibrium phenomenon. Single Xe clusters are superheated using an intense optical laser pulse and the structural evolution of the sample is imaged with a single X-ray pulse. We resolved ultrafast surface softening on the nanometre scale at the plasma/vacuum interface within 100 fs of the heating pulse. Our study is the first time-resolved visualization of irreversible femtosecond processes in free, individual nanometre-sized samples.
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| 8. |
- Johansson, Linda C, 1983, et al.
(författare)
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Lipidic phase membrane protein serial femtosecond crystallography.
- 2012
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Ingår i: Nature methods. - : Springer Science and Business Media LLC. - 1548-7105 .- 1548-7091. ; 9:3, s. 263-265
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.
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| 9. |
- Kaja, Magdalena, et al.
(författare)
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Resonant laser ionization of neptunium: investigation on excitation schemes and the first ionization potential
- 2024
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Ingår i: EUROPEAN PHYSICAL JOURNAL D. - 1434-6060 .- 1434-6079. ; 78:5
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Tidskriftsartikel (refereegranskat)abstract
- The atomic structure of neptunium (Np) was investigated by two-step resonance ionization spectroscopy. The study involved exploring ground-state transitions as well as following transitions to high-lying states just below the ionization potential (IP) or auto-ionizing states above the IP. That resulted in the identification of two-step ionization schemes, suitable for trace analysis and nuclear structure investigations. The lifetimes of two excited states located at 25,342.48 cm(-1) and 25,277.64 cm(-1) were determined as 230(12) ns and 173(9) ns, respectively. Because of the absence of Rydberg series in wide-ranging spectra recorded, the first IP was determined through the field ionization of high-lying, weakly-bound states using a well-controlled static electric field. By applying the saddle-point model, an IP value of 50,535.54(15) cm(-1) [6.265608(19) eV] was derived. This value agrees with the current literature value of 50,535(2) cm(-1), while providing a more than ten times higher precision.
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| 10. |
- Kassemeyer, Stephan, et al.
(författare)
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Femtosecond free-electron laser x-ray diffraction data sets for algorithm development
- 2012
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Ingår i: Optics Express. - 1094-4087. ; 20:4, s. 4149-4158
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Tidskriftsartikel (refereegranskat)abstract
- We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.
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| 11. |
- Koopmann, Rudolf, et al.
(författare)
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In vivo protein crystallization opens new routes in structural biology
- 2012
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 9:3, s. 259-262
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Tidskriftsartikel (refereegranskat)abstract
- Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
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| 12. |
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| 13. |
- Kuepper, Jochen, et al.
(författare)
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X-Ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser
- 2014
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 112:8, s. 083002-
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Tidskriftsartikel (refereegranskat)abstract
- We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e.g., structural-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules.
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| 14. |
- Loh, N. Duane, et al.
(författare)
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Sensing the wavefront of x-ray free-electron lasers using aerosol spheres
- 2013
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Ingår i: Optics Express. - 1094-4087. ; 21:10, s. 12385-12394
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Tidskriftsartikel (refereegranskat)abstract
- Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 1021 W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.
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| 15. |
- Lomb, Lukas, et al.
(författare)
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Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser
- 2011
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 84:21, s. 214111-1-214111-6
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
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| 16. |
- Maschler, Julia, et al.
(författare)
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Links across ecological scales: Plant biomass responses to elevated CO2
- 2022
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 28:21, s. 6115-6134
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Tidskriftsartikel (refereegranskat)abstract
- The degree to which elevated CO2 concentrations (e[CO2]) increase the amount of carbon (C) assimilated by vegetation plays a key role in climate change. However, due to the short-term nature of CO2 enrichment experiments and the lack of reconciliation between different ecological scales, the effect of e[CO2] on plant biomass stocks remains a major uncertainty in future climate projections. Here, we review the effect of e[CO2] on plant biomass across multiple levels of ecological organization, scaling from physiological responses to changes in population-, community-, ecosystem-, and global-scale dynamics. We find that evidence for a sustained biomass response to e[CO2] varies across ecological scales, leading to diverging conclusions about the responses of individuals, populations, communities, and ecosystems. While the distinct focus of every scale reveals new mechanisms driving biomass accumulation under e[CO2], none of them provides a full picture of all relevant processes. For example, while physiological evidence suggests a possible long-term basis for increased biomass accumulation under e[CO2] through sustained photosynthetic stimulation, population-scale evidence indicates that a possible e[CO2]-induced increase n mortality rates might potentially outweigh the effect of increases in plant growth rates on biomass levels. Evidence at the global scale may indicate that e[CO2] has contributed to increased biomass cover over recent decades, but due to the difficulty to disentangle the effect of e[CO2] from a variety of climatic and land-use-related drivers of plant biomass stocks, it remains unclear whether nutrient limitations or other ecological mechanisms operating at finer scales will dampen the e[CO2] effect over time. By exploring these discrepancies, we identify key research gaps in our understanding of the effect of e[CO2] on plant biomass and highlight the need to integrate knowledge across scales of ecological organization so that large-scale modeling can represent the finer-scale mechanisms needed to constrain our understanding of future terrestrial C storage.
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| 17. |
- Neumann, Johannes Tobias, et al.
(författare)
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Personalized diagnosis in suspected myocardial infarction
- 2023
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Ingår i: Clinical Research in Cardiology. - : Springer. - 1861-0684 .- 1861-0692. ; 112, s. 1288-1301
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Tidskriftsartikel (refereegranskat)abstract
- Background: In suspected myocardial infarction (MI), guidelines recommend using high-sensitivity cardiac troponin (hscTn)- based approaches. These require fixed assay-specific thresholds and timepoints, without directly integrating clinical information. Using machine-learning techniques including hs-cTn and clinical routine variables, we aimed to build a digital tool to directly estimate the individual probability of MI, allowing for numerous hs-cTn assays.Methods: In 2,575 patients presenting to the emergency department with suspected MI, two ensembles of machine-learning models using single or serial concentrations of six different hs-cTn assays were derived to estimate the individual MI probability ( ARTEMIS model). Discriminative performance of the models was assessed using area under the receiver operating characteristic curve (AUC) and logLoss. Model performance was validated in an external cohort with 1688 patients and tested for global generalizability in 13 international cohorts with 23,411 patients.Results: Eleven routinely available variables including age, sex, cardiovascular risk factors, electrocardiography, and hs-cTn were included in the ARTEMIS models. In the validation and generalization cohorts, excellent discriminative performance was confirmed, superior to hs-cTn only. For the serial hs-cTn measurement model, AUC ranged from 0.92 to 0.98. Good calibration was observed. Using a single hs-cTn measurement, the ARTEMIS model allowed direct rule-out of MI with very high and similar safety but up to tripled efficiency compared to the guideline- recommended strategy.Conclusion We developed and validated diagnostic models to accurately estimate the individual probability of MI, which allow for variable hs-cTn use and flexible timing of resampling. Their digital application may provide rapid, safe and efficient personalized patient care.
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| 18. |
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| 19. |
- Park, Hyung Joo, et al.
(författare)
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Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers
- 2013
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Ingår i: Optics Express. - 1094-4087. ; 21:23, s. 28729-28742
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Tidskriftsartikel (refereegranskat)abstract
- Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.
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| 20. |
- Pearson, Siani, et al.
(författare)
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Accountability for cloud and other future Internet services
- 2012
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Ingår i: 2012 IEEE 4th International Conference on Cloud Computing Technology and Science (CloudCom). - : IEEE. - 9781467345118 - 9781467345095 ; , s. 629-632
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Konferensbidrag (refereegranskat)abstract
- Cloud and IT service providers should act as responsible stewards for the data of their customers and users. However, the current absence of accountability frameworks for distributed IT services makes it difficult for users to understand, influence and determine how their service providers honour their obligations. The A4Cloud project will create solutions to support users in deciding and tracking how their data is used by cloud service providers. By combining methods of risk analysis, policy enforcement, monitoring and compliance auditing with tailored IT mechanisms for security, assurance and redress, A4Cloud aims to extend accountability across entire cloud service value chains, covering personal and business sensitive information in the cloud
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| 21. |
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| 22. |
- Ruebsamen, Thomas, et al.
(författare)
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Security and Privacy Preservation of Evidence in Cloud Accountability Audits
- 2016
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Ingår i: Cloud Computing And Services Science, Closer 2015. - Cham : Springer International Publishing. - 9783319295824 - 9783319295817 ; , s. 95-114
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Konferensbidrag (refereegranskat)abstract
- Cloud accountability audits are promising to strengthen trust in cloud computing by providing reassurance about the processing data in the cloud according to data handling and privacy policies. To effectively automate cloud accountability audits, various distributed evidence sources need to be considered during evaluation. The types of information range from authentication and data access logging to location information, information on security controls and incident detection. Securing that information quickly becomes a challenge in the system design, when the evidence that is needed for the audit is deemed sensitive or confidential information. This means that securing the evidence at-rest as well as in-transit is of utmost importance. In this paper, we present a system that is based on distributed software agents which enables secure evidence collection with the purpose of automated evaluation during cloud accountability audits. We thereby present the integration of Insynd as a suitable cryptographic mechanism for securing evidence. We present our reasoning for choosing Insynd by showing a comparison of Insynd properties with requirements imposed by accountability evidence collection as well as an analysis how security threats are being mitigated by Insynd. We put special emphasis on security and privacy protection in our system analysis.
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| 23. |
- Seibert, M. Marvin, et al.
(författare)
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Single mimivirus particles intercepted and imaged with an X-ray laser
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 470:7332, s. 78-81
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Tidskriftsartikel (refereegranskat)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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| 24. |
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| 25. |
- Yoon, Chun Hong, et al.
(författare)
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Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering
- 2011
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Ingår i: Optics Express. - 1094-4087. ; 19:17, s. 16542-16549
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Tidskriftsartikel (refereegranskat)abstract
- Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.
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