| 1. |
- Borgstrom, F, et al.
(author)
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The cost-effectiveness of risedronate in the treatment of osteoporosis: an international perspective
- 2006
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In: Osteoporosis International. - : Springer Science and Business Media LLC. - 1433-2965 .- 0937-941X. ; 17:7, s. 996-1007
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Journal article (peer-reviewed)abstract
- Introduction: Risedronate, a bisphosphonate for treatment and prevention of osteoporosis, has been shown in several clinical trials to reduce the risk of fractures in postmenopausal women with osteoporosis. The cost-effectiveness of risedronate treatment has previously been evaluated within different country settings using different model and analysis approaches. The objective of this study was to assess the cost-effectiveness of risedronate in postmenopausal women in four European countries-Sweden, Finland, Spain, and Belgium-by making use of the same modelling framework and analysis setup. Methods: A previously developed Markov cohort model for the evaluation of osteoporosis treatments was used to estimate the cost-effectiveness of risedronate treatment. For each country, the model was populated with local mortality, fracture incidence, and cost data. Hip fractures, clinical vertebral fractures, and wrist fractures were included in the model. Results: The incremental cost per quality-adjusted life years (QALY) gained from a 5-year intervention with risedronate compared to "no intervention" in 70-year-old women at the threshold of osteoporosis [T-score = -2.5 based on National Health and Nutrition Examination Survey (NHANES) III data] and previous vertebral fracture was estimated to be E860, E19,532, E11,782, and E32,515 in Sweden, Finland, Belgium, and Spain, respectively. Among 70-year-old women at the threshold of osteoporosis without previous fracture the estimated cost per QALY gained ranged from E21,148 (Sweden) to E80,100 (Spain). The differences in cost-effectiveness between countries are mainly explained by different costs (fracture and treatment costs), fracture risks, and discount rates. Based on cost per QALY gained threshold values found in the literature, the study results indicated risedronate to be cost effective in the treatment of elderly women with established osteoporosis in all the included countries. Conclusions: At a hypothetical threshold value of E40,000 per QALY gained, the results in this study indicate that risedronate is a cost-effective treatment in elderly women at the threshold of osteoporosis (i.e., a T-score of -2.5) with prevalent vertebral fractures in Sweden, Finland, Belgium, and Spain.
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| 2. |
- Caleman, Carl, et al.
(author)
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Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
- 2015
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In: Optics Express. - 1094-4087. ; 23:2, s. 1213-1231
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Journal article (peer-reviewed)abstract
- In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.
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| 3. |
- 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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| 4. |
- Dawod, Ibrahim, et al.
(author)
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Anisotropic melting of ice induced by ultrafast non-thermal heating
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Other publication (other academic/artistic)abstract
- Water and ice are routinely studied with X-rays to reveal their diverse structures and anomalous properties. We employ a hybrid collisional-radiative/molecular dynamics method to explore how femtosecond X-ray pulses interact with hexagonal ice. We find that ice makes a phase transition into a crystalline plasma where its initial structure is maintained up to tens of femtoseconds. The ultrafast melting process occurs anisotropically, where different geometric configurations of the structure melt on different time scales. The transient state and anisotropic melting of crystals can be captured by X-ray diffraction, which impacts any study of crystalline structures probed by femtosecond X-ray lasers.
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| 5. |
- Ekeberg, Tomas, et al.
(author)
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Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
- 2016
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In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
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Journal article (peer-reviewed)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. |
- Jönsson, H. Olof, 1985-
(author)
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Femtosecond Dynamics in Water and Biological Materials with an X-Ray Laser
- 2016
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Licentiate thesis (other academic/artistic)abstract
- Using high intensity ultrashort pulses from X-ray free electron lasers to investigate soft matter is a recent and successful development. The last decade has seen the development of new variant of protein crystallography with femtosecond dynamics, and single particle imaging with atomic resolution is on the horizon. The work presented here is part of the effort to explain what processes influence the capability to achieve high resolution information in these techniques. Non-local thermal equilibrium plasma continuum modelling is used to predict signal changes as a function of pulse duration, shape and energy. It is found that ionization is the main contributor to radiation damage in certain photon energy and intensity ranges, and diffusion depending on heating is dominant in other scenarios. In femtosecond protein crystallography, self-gating of Bragg diffraction is predicted to quench the signal from the latest parts of an X-ray pulse. At high intensities ionization is dominant and the last part of the pulse will contain less information at low resolution. At lower intensities, displacement will dominate and high resolution information will be gated first. Temporal pulse shape is also an important factor. The difference between pulse shapes is most prominent at low photon energy in the form of a general increase or decrease in signal, but the resolution dependance is most prominent at high energies. When investigating the X-ray scattering from water a simple diffusion model can be replaced by a molecular dynamics simulation, which predicts structural changes in water on femtosecond timescales. Experiments performed at LCLS are presented that supports the simulation results on structural changes that occur in the solvent during the exposure.
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| 7. |
- Jönsson, H. Olof, et al.
(author)
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Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
- 2017
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In: IUCrJ. - 2052-2525. ; 4:6, s. 778-784
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Journal article (peer-reviewed)abstract
- Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.
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| 8. |
- Jönsson, H. Olof, et al.
(author)
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Simulations of Radiation Damage as a Function of the Temporal Pulse Profile in Femtosecond X-ray Protein Crystallography
- 2015
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In: Journal of Synchrotron Radiation. - 0909-0495 .- 1600-5775. ; 22:2, s. 256-266
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Journal article (peer-reviewed)abstract
- Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10$\sp 4$ to 10$\sp 7$Jcm$\sp $-$2$ with photon energies from 2 to 12keV, up to 100fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.
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| 9. |
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| 10. |
- Kassemeyer, Stephan, et al.
(author)
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Femtosecond free-electron laser x-ray diffraction data sets for algorithm development
- 2012
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In: Optics Express. - 1094-4087. ; 20:4, s. 4149-4158
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Journal article (peer-reviewed)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. |
- Lee, Yu-Jen, et al.
(author)
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Spatio-temporal dynamics of impulse responses to figure motion in optic flow neurons
- 2015
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
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Journal article (peer-reviewed)abstract
- White noise techniques have been used widely to investigate sensory systems in both vertebrates and invertebrates. White noise stimuli are powerful in their ability to rapidly generate data that help the experimenter decipher the spatio-temporal dynamics of neural and behavioral responses. One type of white noise stimuli, maximal length shift register sequences (m-sequences), have recently become particularly popular for extracting response kernels in insect motion vision. We here use such m-sequences to extract the impulse responses to figure motion in hoverfly lobula plate tangential cells (LPTCs). Figure motion is behaviorally important and many visually guided animals orient towards salient features in the surround. We show that LPTCs respond robustly to figure motion in the receptive field. The impulse response is scaled down in amplitude when the figure size is reduced, but its time course remains unaltered. However, a low contrast stimulus generates a slower response with a significantly longer time-to-peak and half-width. Impulse responses in females have a slower time-to-peak than males, but are otherwise similar. Finally we show that the shapes of the impulse response to a figure and a widefield stimulus are very similar, suggesting that the figure response could be coded by the same input as the widefield response.
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| 12. |
- Nass, Karol, et al.
(author)
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Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
- 2015
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In: Journal of Synchrotron Radiation. - 0909-0495 .- 1600-5775. ; 22:2, s. 225-238
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Journal article (peer-reviewed)abstract
- Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe–4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe–4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.
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| 13. |
- Wells, Daniel J., et al.
(author)
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Observations of phase changes in monoolein during high viscous injection
- 2022
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In: Journal of Synchrotron Radiation. - : International Union Of Crystallography. - 0909-0495 .- 1600-5775. ; 29:3, s. 602-614
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Journal article (peer-reviewed)abstract
- Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.
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| 14. |
- Östlin, Christofer, et al.
(author)
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Reproducibility of Single Protein Explosions Induced by X-ray Lasers
- 2018
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In: Physical Chemistry, Chemical Physics - PCCP. - 1463-9076 .- 1463-9084. ; 20:18, s. 12381-12389
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Journal article (peer-reviewed)abstract
- Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems – four polypeptides with different amounts of surface bound water – were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.
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