| 1. |
- Chapman, H N, et al.
(author)
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Coherent imaging at FLASH
- 2009
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In: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 186:1, s. 012051-
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Journal article (peer-reviewed)abstract
- We have carried out high-resolution single-pulse coherent diffractive imaging at the FLASH free-electron laser. The intense focused FEL pulse gives a high-resolution low-noise coherent diffraction pattern of an object before that object turns into a plasma and explodes. In particular we are developing imaging of biological specimens beyond conventional radiation damage resolution limits, developing imaging of ultrafast processes, and testing methods to characterize and perform single-particle imaging.
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| 2. |
- Hajkova, V., et al.
(author)
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X-ray laser-induced ablation of lead compounds
- 2011
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In: DAMAGE TO VUV, EUV, AND X-RAY OPTICS III. - : SPIE.
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Conference paper (peer-reviewed)abstract
- The recent commissioning of a X-ray free-electron laser triggered an extensive research in the area of X-ray ablation of high-Z, high-density materials. Such compounds should be used to shorten an effective attenuation length for obtaining clean ablation imprints required for the focused beam analysis. Compounds of lead (Z=82) represent the materials of first choice. In this contribution, single-shot ablation thresholds are reported for PbWO(4) and PbI(2) exposed to ultra-short pulses of extreme ultraviolet radiation and X-rays at FLASH and LCLS facilities, respectively. Interestingly, the threshold reaches only 0.11 J/cm(2) at 1.55 nm in lead tungstate although a value of 0.4 J/cm(2) is expected according to the wavelength dependence of an attenuation length and the threshold value determined in the XUV spectral region, i.e., 79 mJ/cm(2) at a FEL wavelength of 13.5 nm. Mechanisms of ablation processes are discussed to explain this discrepancy. Lead iodide shows at 1.55 nm significantly lower ablation threshold than tungstate although an attenuation length of the radiation is in both materials quite the same. Lower thermal and radiation stability of PbI(2) is responsible for this finding.
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| 3. |
- Andreasson, Jakob, et al.
(author)
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Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser
- 2011
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In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 83:1, s. 016403-
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Journal article (peer-reviewed)abstract
- Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 1017 W/cm2 were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 1016 W/cm2. This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.
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| 4. |
- Barbateskovic, Marija, et al.
(author)
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A new tool to assess Clinical Diversity In Meta-analyses (CDIM) of interventions
- 2021
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In: Journal of Clinical Epidemiology. - : Elsevier BV. - 0895-4356 .- 1878-5921. ; 135, s. 29-41
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Journal article (peer-reviewed)abstract
- Objective: To develop and validate Clinical Diversity In Meta-analyses (CDIM), a new tool for assessing clinical diversity between trials in meta-analyses of interventions. Study design and setting: The development of CDIM was based on consensus work informed by empirical literature and expertise. We drafted the CDIM tool, refined it, and validated CDIM for interrater scale reliability and agreement in three groups. Results: CDIM measures clinical diversity on a scale that includes four domains with 11 items overall: setting (time of conduct/country development status/units type); population (age, sex, patient inclusion criteria/baseline disease severity, comorbidities); interventions (intervention intensity/strength/duration of intervention, timing, control intervention, cointerventions); and outcome (definition of outcome, timing of outcome assessment). The CDIM is completed in two steps: first two authors independently assess clinical diversity in the four domains. Second, after agreeing upon scores of individual items a consensus score is achieved. Interrater scale reliability and agreement ranged from moderate to almost perfect depending on the type of raters. Conclusion: CDIM is the first tool developed for assessing clinical diversity in meta-analyses of interventions. We found CDIM to be a reliable tool for assessing clinical diversity among trials in meta-analysis.
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| 5. |
- Bogan, M. J., et al.
(author)
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Single-shot femtosecond x-ray diffraction from randomly oriented ellipsoidal nanoparticles
- 2010
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In: Physical Review Special Topics - Accelerators and Beams. - 1098-4402. ; 13:9, s. 094701-
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Journal article (peer-reviewed)abstract
- Coherent diffractive imaging of single particles using the single-shot "diffract and destroy" approach with an x-ray free electron laser (FEL) was recently demonstrated. A high-resolution low-noise coherent diffraction pattern, representative of the object before it turns into a plasma and explodes, results from the interaction of the FEL with the particle. Iterative phase retrieval algorithms are used to reconstruct two-dimensional projection images of the object from the recorded intensities alone. Here we describe the first single-shot diffraction data set that mimics the data proposed for obtaining 3D structure from identical particles. Ellipsoidal iron oxide nanoparticles (250 nm x 50 nm) were aerosolized and injected through an aerodynamic lens stack into a soft x-ray FEL. Particle orientation was not controlled with this injection method. We observed that, at the instant the x-ray pulse interacts with the particle, a snapshot of the particle's orientation is encoded in the diffraction pattern. The results give credence to one of the technical concepts of imaging individual nanometer and subnanometer-sized objects such as single molecules or larger clusters of molecules using hard x-ray FELs and will be used to help develop robust algorithms for determining particle orientations and 3D structure.
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| 6. |
- Darmadi, Iwan, 1990, et al.
(author)
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Rationally Designed PdAuCu Ternary Alloy Nanoparticles for Intrinsically Deactivation-Resistant Ultrafast Plasmonic Hydrogen Sensing
- 2019
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In: ACS Sensors. - : American Chemical Society (ACS). - 2379-3694. ; 4:5, s. 1424-1432
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Journal article (peer-reviewed)abstract
- Hydrogen sensors are a prerequisite for the implementation of a hydrogen economy due to the high flammability of hydrogen-air mixtures. They are to comply with the increasingly stringent requirements set by stakeholders, such as the automotive industry and manufacturers of hydrogen safety systems, where sensor deactivation is a severe but widely unaddressed problem. In response, we report intrinsically deactivation-resistant nanoplasmonic hydrogen sensors enabled by a rationally designed ternary PdAuCu alloy nanomaterial, which combines the identified best intrinsic attributes of the constituent binary Pd alloys. This way, we achieve extraordinary hydrogen sensing metrics in synthetic air and poisoning gas background, simulating real application conditions. Specifically, we find a detection limit in the low ppm range, hysteresis-free response over 5 orders of magnitude hydrogen pressure, subsecond response time at room temperature, long-term stability, and, as the key, excellent resistance to deactivating species like carbon monoxide, notably without application of any protective coatings. This constitutes an important step forward for optical hydrogen sensor technology, as it enables application under demanding conditions and provides a blueprint for further material and performance optimization by combining and concerting intrinsic material assets in multicomponent nanoparticles. In a wider context, our findings highlight the potential of rational materials design through alloying of multiple elements for gas sensor development, as well as the potential of engineered metal alloy nanoparticles in nanoplasmonics and catalysis.
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| 7. |
- de Kloe, Gerdien E, et al.
(author)
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Surface Plasmon Resonance Biosensor Based Fragment Screening Using Acetylcholine Binding Protein Identifies Ligand Efficiency Hot Spots (LE Hot Spots) by Deconstruction of Nicotinic Acetylcholine Receptor α7 Ligands
- 2010
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In: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 53:19, s. 7192-7201
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Journal article (peer-reviewed)abstract
- The soluble acetylcholine binding protein (AChBP) is a homologue of the ligand-binding domain of the nicotinic acetylcholine receptors (nAChR). To guide future fragment-screening using surface plasmon resonance (SPR) biosensor technology as a label-free, direct binding, biophysical screening assay, a focused fragment library was generated based on deconstruction of a set of α7 nAChR selective quinuclidine containing ligands with nanomolar affinities. The interaction characteristics of the fragments and the parent compounds with AChBP were evaluated using an SPR biosensor assay. The data obtained from this direct binding assay correlated well with data from the reference radioligand displacement assay. Ligand efficiencies for different (structural) groups of fragments in the library were correlated to binding with distinct regions of the binding pocket, thereby identifying ligand efficiency hot spots (LE hot spots). These hot spots can be used to identity the most promising hit fragments in a large scale fragment library screen.
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| 8. |
- Geitmann, Matthis, et al.
(author)
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Interaction kinetic and structural dynamic analysis of ligand binding to acetylcholine-binding protein
- 2010
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In: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 49:37, s. 8143-8154
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Journal article (peer-reviewed)abstract
- The mechanism of agonist interactions with Cys-loop ligand-gated ion channels has been studied using the acetylcholine-binding protein (AChBP) from Lymnaea stagnalis as a model protein, and acetylcholine, nicotine, epibatidine and a series of substituted quinuclidines as ligands. A biosensor-based assay for direct interaction studies of immobilized AChBP and small molecule ligands was developed. It allowed the characterization of the interaction kinetics of the ligands and the structural dynamics of the protein. The interactions with AChBP were very sensitive to variations in the experimental conditions and showed several types of complexities. These could be resolved into two types of ligand-induced secondary effects with different kinetics, representing fast and slow conformational changes. The data could be rationalized in a mechanistic model and a structural interpretation of the interaction was obtained by molecular modelling involving induced-fit and loop flexibility simulations. The data suggests that AChBP exhibits ligand-induced structural dynamics, as expected for the ligand gating mechanism of Cys-loop receptors. It shows that the formation of the initial encounter complex between AChBP and ligands is very rapid, in accordance with the functional characteristics required of neurotransmission. These developed procedures will enable further exploration of the mechanism of Cys-loop receptor function and the identification of specific ligands suitable for pharmacological use.
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| 9. |
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| 10. |
- Heywood, W. E., et al.
(author)
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Cerebrospinal fluid neurofilament light chain levels in CLN2 disease patients treated with enzyme replacement therapy normalise after two years on treatment
- 2022
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In: F1000Research. - : F1000 Research Ltd. - 2046-1402. ; 10
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Journal article (peer-reviewed)abstract
- Classic late infantile neuronal ceroid lipofuscinosis (CLN2 disease) is caused by a deficiency of tripeptidyl-peptidase-1. In 2017, the first CLN2 enzyme replacement therapy (ERT) cerliponase alfa (Brineura) was approved by the FDA and EMA. The CLN2 disease clinical rating scale (CLN2 CRS) was developed to monitor loss of motor function, language and vision as well as frequency of generalised tonic clonic seizures. Using CLN2 CRS in an open label clinical trial it was shown that Brineura slowed down the progression of CLN2 symptoms. Neurofilament light chain (NfL) is a protein highly expressed in myelinated axons. An increase of cerebrospinal fluid (CSF) and blood NfL is found in a variety of neuroinflammatory, neurodegenerative, traumatic, and cerebrovascular diseases. We analysed CSF NfL in CLN2 patients treated with Brineura to establish whether it can be used as a possible biomarker of response to therapy. Newly diagnosed patients had CSF samples collected and analysed at first treatment dose and up to 12 weeks post-treatment to look at acute changes. Patients on a compassionate use programme who were already receiving ERT for approximately 1yr had CSF samples collected and NfL analysed over the following 1.3 years (2.3 years post-initiation of ERT) to look at long-term changes. All newly diagnosed patients we investigated with classical late infantile phenotype had high NfL levels >2000 pg/ml at start of treatment. No significant change was observed in NfL up to 12 weeks post-treatment. After one year of ERT, two out of six patients still had high NfL levels, but all patients showed a continued decrease, and all had low NfL levels after two years on ERT. NfL levels appear to correspond and predict improved clinical status of patients on ERT and could be useful as a biomarker to monitor neurodegeneration and verify disease modification in CLN2 patients on ERT. © 2022 Iwan K et al.
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| 11. |
- Iwan, B., et al.
(author)
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Modeling of soft X-ray induced ablation in solids
- 2011
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In: DAMAGE TO VUV, EUV, AND X-RAY OPTICS III. - : SPIE.
-
Conference paper (peer-reviewed)abstract
- Powerful free electron lasers (FELs) operating in the soft X-ray regime are offering new possibilities for creating and probing materials under extreme conditions. We describe here simulations to model the interaction of a focused FEL pulse with metallic solids (niobium, vanadium, and their deuterides) at 13.5 nm wavelength (92 eV) with peak intensities between 10(15) to 10(18) W/cm(2) and a fixed pulse length of 15 femtoseconds (full width at half maximum). The interaction of the pulse with the metallic solids was modeled with a non-local thermodynamic equilibrium code that included radiation transfer. The calculations also made use of a self-similar isothermal fluid model for plasma expansion into vacuum. We find that the time-evolution of the simulated critical charge density in the sample results in a critical depth that approaches the observed crater depths in an earlier experiment performed at the FLASH free electron laser in Hamburg. The results show saturation in the ablation process at intensities exceeding 10(16) W/cm(2). Furthermore, protons and deuterons with kinetic energies of several keV have been measured, and these concur with predictions from the plasma expansion model. The results indicate that the temperature of the plasma reached almost 5 million K after the pulse has passed.
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| 12. |
- Iwan, Bianca S, et al.
(author)
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TOF-OFF : A method for determining focal positions in tightly focused free-electron laser experiments by measurement of ejected ions
- 2011
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In: High Energy Density Physics. - : Elsevier BV. - 1574-1818. ; 7:4, s. 336-342
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Journal article (peer-reviewed)abstract
- Pulse intensities greater than 1017 Watt/cm2 were reached at the FLASH soft X-ray laser in Hamburg, Germany, using an off-axis parabolic mirror to focus 15 fs pulses of 5–70 μJ energy at 13.5 nm wavelength to a micron-sized spot. We describe the interaction of such pulses with niobium and vanadium targets and their deuterides. The beam produced craters in the solid targets, and we measured the kinetic energy of ions ejected from these craters. Ions with several keV kinetic energy were observed from craters approaching 5 μm in depth when the sample was at best focus. We also observed the onset of saturation in both ion acceleration and ablation with pulse intensities exceeding 1016 W/cm2, when the highest detected ion energies and the crater depths tend to saturate with increasing intensity. A general difficulty in working with micron and sub-micron focusing optics is finding the exact focus of the beam inside a vacuum chamber. Here we propose a direct method to measure the focal position to a resolution better than the Rayleigh length. The method is based on the correlation between the energies of ejected ions and the physical dimensions of the craters. We find that the focus position can be quickly determined from the ion time-of-flight (TOF) data as the target is scanned through the expected focal region. The method does not require external access to the sample or venting the vacuum chamber. Profile fitting employed to analyze the TOF data can extend resolution beyond the actual scanning step size.
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| 13. |
- Nelson, A. J., et al.
(author)
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Soft x-ray free electron laser microfocus for exploring matter under extreme conditions
- 2009
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In: Optics Express. - 1094-4087. ; 17:20, s. 18271-18278
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Journal article (peer-reviewed)abstract
- We have focused a beam (BL3) of FLASH (Free-electron LASer in Hamburg: lambda = 13.5 nm, pulse length 15 fs, pulse energy 10-40 mu J, 5Hz) using a fine polished off-axis parabola having a focal length of 270 mm and coated with a Mo/Si multilayer with an initial reflectivity of 67% at 13.5 nm. The OAP was mounted and aligned with a picomotor controlled six-axis gimbal. Beam imprints on poly(methyl methacrylate) -PMMA were used to measure focus and the focused beam was used to create isochoric heating of various slab targets. Results show the focal spot has a diameter of <= 1 mu m. Observations were correlated with simulations of best focus to provide further relevant information.
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| 14. |
- Nugroho, Ferry, 1986, et al.
(author)
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Metal–polymer hybrid nanomaterials for plasmonic ultrafast hydrogen detection
- 2019
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In: Nature Materials. - : Springer Science and Business Media LLC. - 1476-4660 .- 1476-1122. ; 18:5, s. 489-495
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Journal article (peer-reviewed)abstract
- Hydrogen–air mixtures are highly flammable. Hydrogen sensors are therefore of paramount importance for timely leak detection during handling. However, existing solutions do not meet the stringent performance targets set by stakeholders, while deactivation due to poisoning, for example by carbon monoxide, is a widely unsolved problem. Here we present a plasmonic metal–polymer hybrid nanomaterial concept, where the polymer coating reduces the apparent activation energy for hydrogen transport into and out of the plasmonic nanoparticles, while deactivation resistance is provided via a tailored tandem polymer membrane. In concert with an optimized volume-to-surface ratio of the signal transducer uniquely offered by nanoparticles, this enables subsecond sensor response times. Simultaneously, hydrogen sorption hysteresis is suppressed, sensor limit of detection is enhanced, and sensor operation in demanding chemical environments is enabled, without signs of long-term deactivation. In a wider perspective, our work suggests strategies for next-generation optical gas sensors with functionalities optimized by hybrid material engineering.
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| 15. |
- Retra, Kim, et al.
(author)
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Development of surface plasmon resonance biosensor assays for primary and secondary screening of acetylcholine binding protein ligands
- 2010
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In: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 407:1, s. 58-64
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Journal article (peer-reviewed)abstract
- Surface plasmon resonance (SPR) biosensors recently gained an important place in drug discovery. Here we present a primary and secondary SPR biosensor screening methodology. The primary screening method is based on a direct binding assay with covalent immobilized drug target proteins. For the secondary screening method, a sequential competition assay has been developed where the captured protein is first exposed to an unknown test compound, followed directly by an exposure to a high-molecular-weight reporter ligand. Using the high-molecular-weight reporter ligand to probe the remaining free binding site on the sensor, a significant signal enhancement is obtained. Furthermore, this assay format allows the validation of the primary direct binding assay format, efficiently revealing false positive data. As a model system, acetylcholine binding protein (AChBP), which is a soluble model protein for neuronal nicotinic acetylcholine receptors, has been used. The secondary assay is lower in throughput than the primary assay; however, the signal-to-noise ratio is two times higher compared with the direct assay, and it has a z' factor of 0.96. Using both assays, we identified the compound tacrine as a ligand for AChBP.
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| 16. |
- Sangeorzan, Irina, et al.
(author)
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Toward Shared Decision-Making in Degenerative Cervical Myelopathy : Protocol for a Mixed Methods Study
- 2023
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In: JMIR Research Protocols. - : JMIR Publications. - 1929-0748. ; 12
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Journal article (peer-reviewed)abstract
- Background: Health care decisions are a critical determinant in the evolution of chronic illness. In shared decision-making (SDM), patients and clinicians work collaboratively to reach evidence-based health decisions that align with individual circumstances, values, and preferences. This personalized approach to clinical care likely has substantial benefits in the oversight of degenerative cervical myelopathy (DCM), a type of nontraumatic spinal cord injury. Its chronicity, heterogeneous clinical presentation, complex management, and variable disease course engenders an imperative for a patient-centric approach that accounts for each patient's unique needs and priorities. Inadequate patient knowledge about the condition and an incomplete understanding of the critical decision points that arise during the course of care currently hinder the fruitful participation of health care providers and patients in SDM. This study protocol presents the rationale for deploying SDM for DCM and delineates the groundwork required to achieve this.Objective: The study's primary outcome is the development of a comprehensive checklist to be implemented upon diagnosis that provides patients with essential information necessary to support their informed decision-making. This is known as a core information set (CIS). The secondary outcome is the creation of a detailed process map that provides a diagrammatic representation of the global care workflows and cognitive processes involved in DCM care. Characterizing the critical decision points along a patient's journey will allow for an effective exploration of SDM tools for routine clinical practice to enhance patient-centered care and improve clinical outcomes.Methods: Both CISs and process maps are coproduced iteratively through a collaborative process involving the input and consensus of key stakeholders. This will be facilitated by Myelopathy.org, a global DCM charity, through its Research Objectives and Common Data Elements for Degenerative Cervical Myelopathy community. To develop the CIS, a 3-round, web-based Delphi process will be used, starting with a baseline list of information items derived from a recent scoping review of educational materials in DCM, patient interviews, and a qualitative survey of professionals. A priori criteria for achieving consensus are specified. The process map will be developed iteratively using semistructured interviews with patients and professionals and validated by key stakeholders.Results: Recruitment for the Delphi consensus study began in April 2023. The pilot-testing of process map interview participants started simultaneously, with the formulation of an initial baseline map underway.Conclusions: This protocol marks the first attempt to provide a starting point for investigating SDM in DCM. The primary work centers on developing an educational tool for use in diagnosis to enable enhanced onward decision-making. The wider objective is to aid stakeholders in developing SDM tools by identifying critical decision junctures in DCM care. Through these approaches, we aim to provide an exhaustive launchpad for formulating SDM tools in the wider DCM community.
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| 17. |
- Thomas, H., et al.
(author)
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Explosions of Xenon Clusters in Ultraintense Femtosecond X-Ray Pulses from the LCLS Free Electron Laser
- 2012
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 108:13
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Journal article (peer-reviewed)abstract
- Explosions of large Xe clusters (< N > similar to 11 000) irradiated by femtosecond pulses of 850 eV x-ray photons focused to an intensity of up to 1017 W/cm(2) from the Linac Coherent Light Source were investigated experimentally. Measurements of ion charge-state distributions and energy spectra exhibit strong evidence for the formation of a Xe nanoplasma in the intense x-ray pulse. This x-ray produced Xe nanoplasma is accompanied by a three-body recombination and hydrodynamic expansion. These experimental results appear to be consistent with a model in which a spherically exploding nanoplasma is formed inside the Xe cluster and where the plasma temperature is determined by photoionization heating.
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| 18. |
- Timneanu, Nicusor, et al.
(author)
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Fragmentation of clusters and recombination induced by intense and ultrashort X-ray laser pulses
- 2013
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In: Damage To Vuv, Euv, And X-Ray Optics Iv; And Euv And X-Ray Optics. - : SPIE - International Society for Optical Engineering.
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Conference paper (peer-reviewed)abstract
- Understanding the ultrafast dynamics of matter under extreme conditions is relevant for structural studies and plasma physics with X-ray lasers. We used the pulses from free-electron lasers (FLASH in Hamburg and LCLS in Stanford) to trigger X-ray induced explosions in atomic atoms (Xe) and molecular clusters (CH4 and CD4). The explosion dynamics depends on cluster size and the intensity of the X-ray pulse, and a transition from Coulomb explosion to hydrodynamic expansion is expected with increasing size and increasing pulse intensity. In methane clusters experiments at FLASH, the time-of-flight spectrometry shows the appearance of molecular adducts which are the result of molecular recombination between ions and molecules. The recombination depends on the cluster size and the expansion mechanism and becomes significant in larger clusters. In Xenon cluster experiments at the LCLS, measurements of the ion charge states in clusters suggest a formation of Xe nanoplasma which expands hydrodynamically. The dominance of low charge states of Xe is due to three-body recombination processes involving electron and Xe ions, and it depends on the X-ray intensity and nanoplasma formation.
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