| 1. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 3. |
- Buchanan, E. M., et al.
(author)
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The Psychological Science Accelerator's COVID-19 rapid-response dataset
- 2023
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In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 10:1
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Journal article (peer-reviewed)abstract
- In response to the COVID-19 pandemic, the Psychological Science Accelerator coordinated three large-scale psychological studies to examine the effects of loss-gain framing, cognitive reappraisals, and autonomy framing manipulations on behavioral intentions and affective measures. The data collected (April to October 2020) included specific measures for each experimental study, a general questionnaire examining health prevention behaviors and COVID-19 experience, geographical and cultural context characterization, and demographic information for each participant. Each participant started the study with the same general questions and then was randomized to complete either one longer experiment or two shorter experiments. Data were provided by 73,223 participants with varying completion rates. Participants completed the survey from 111 geopolitical regions in 44 unique languages/dialects. The anonymized dataset described here is provided in both raw and processed formats to facilitate re-use and further analyses. The dataset offers secondary analytic opportunities to explore coping, framing, and self-determination across a diverse, global sample obtained at the onset of the COVID-19 pandemic, which can be merged with other time-sampled or geographic data.
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| 4. |
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| 5. |
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| 6. |
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| 7. |
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| 8. |
- Hartley, Philippa, et al.
(author)
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SKA Science Data Challenge 2: analysis and results
- 2023
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In: Monthly Notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 523:2, s. 1967-1993
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Journal article (peer-reviewed)abstract
- The Square Kilometre Array Observatory (SKAO) will explore the radio sky to new depths in order to conduct transformational science. SKAO data products made available to astronomers will be correspondingly large and complex, requiring the application of advanced analysis techniques to extract key science findings. To this end, SKAO is conducting a series of Science Data Challenges, each designed to familiarize the scientific community with SKAO data and to drive the development of new analysis techniques. We present the results from Science Data Challenge 2 (SDC2), which invited participants to find and characterize 233 245 neutral hydrogen (H i) sources in a simulated data product representing a 2000 h SKA-Mid spectral line observation from redshifts 0.25-0.5. Through the generous support of eight international supercomputing facilities, participants were able to undertake the Challenge using dedicated computational resources. Alongside the main challenge, 'reproducibility awards' were made in recognition of those pipelines which demonstrated Open Science best practice. The Challenge saw over 100 participants develop a range of new and existing techniques, with results that highlight the strengths of multidisciplinary and collaborative effort. The winning strategy - which combined predictions from two independent machine learning techniques to yield a 20 per cent improvement in overall performance - underscores one of the main Challenge outcomes: that of method complementarity. It is likely that the combination of methods in a so-called ensemble approach will be key to exploiting very large astronomical data sets.
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| 9. |
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| 10. |
- Needham, E. J., et al.
(author)
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Brain injury in COVID-19 is associated with dysregulated innate and adaptive immune responses
- 2022
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In: Brain. - : Oxford University Press (OUP). - 0006-8950 .- 1460-2156. ; 145:11, s. 4097-4107
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Journal article (peer-reviewed)abstract
- COVID-19 is associated with neurological complications including stroke, delirium and encephalitis. Furthermore, a post-viral syndrome dominated by neuropsychiatric symptoms is common, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of COVID-19 severity. We investigated the dynamics of, and relationship between, serum markers of brain injury [neurofilament light (NfL), glial fibrillary acidic protein (GFAP) and total tau] and markers of dysregulated host response (autoantibody production and cytokine profiles) in 175 patients admitted with COVID-19 and 45 patients with influenza. During hospitalization, sera from patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependent manner, with evidence of ongoing active brain injury at follow-up 4 months later. These biomarkers were associated with elevations of pro-inflammatory cytokines and the presence of autoantibodies to a large number of different antigens. Autoantibodies were commonly seen against lung surfactant proteins but also brain proteins such as myelin associated glycoprotein. Commensurate findings were seen in the influenza cohort. A distinct process characterized by elevation of serum total tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses unlike NfL and GFAP. These results demonstrate that brain injury is a common consequence of both COVID-19 and influenza, and is therefore likely to be a feature of severe viral infection more broadly. The brain injury occurs in the context of dysregulation of both innate and adaptive immune responses, with no single pathogenic mechanism clearly responsible. Needham et al. reveal elevations in blood biomarkers of brain injury in patients hospitalised with COVID-19. The changes, which were severity-dependent, were associated with dysregulated immune responses including increases in pro-inflammatory cytokines and autoantibodies. Ongoing active brain injury could still be seen months after infection.
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| 11. |
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| 12. |
- Jacobsson, Jesper, 1984-, et al.
(author)
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An open-access database and analysis tool for perovskite solar cells based on the FAIR data principles
- 2022
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In: Nature Energy. - : Springer Nature. - 2058-7546. ; 7:1, s. 107-115
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Journal article (peer-reviewed)abstract
- Large datasets are now ubiquitous as technology enables higher-throughput experiments, but rarely can a research field truly benefit from the research data generated due to inconsistent formatting, undocumented storage or improper dissemination. Here we extract all the meaningful device data from peer-reviewed papers on metal-halide perovskite solar cells published so far and make them available in a database. We collect data from over 42,400 photovoltaic devices with up to 100 parameters per device. We then develop open-source and accessible procedures to analyse the data, providing examples of insights that can be gleaned from the analysis of a large dataset. The database, graphics and analysis tools are made available to the community and will continue to evolve as an open-source initiative. This approach of extensively capturing the progress of an entire field, including sorting, interactive exploration and graphical representation of the data, will be applicable to many fields in materials science, engineering and biosciences.
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| 13. |
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| 14. |
- Jones, Benedict C, et al.
(author)
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To which world regions does the valence-dominance model of social perception apply?
- 2021
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In: Nature Human Behaviour. - : Springer Science and Business Media LLC. - 2397-3374. ; 5:1, s. 159-169
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Journal article (peer-reviewed)abstract
- Over the past 10 years, Oosterhof and Todorov's valence-dominance model has emerged as the most prominent account of how people evaluate faces on social dimensions. In this model, two dimensions (valence and dominance) underpin social judgements of faces. Because this model has primarily been developed and tested in Western regions, it is unclear whether these findings apply to other regions. We addressed this question by replicating Oosterhof and Todorov's methodology across 11 world regions, 41 countries and 11,570 participants. When we used Oosterhof and Todorov's original analysis strategy, the valence-dominance model generalized across regions. When we used an alternative methodology to allow for correlated dimensions, we observed much less generalization. Collectively, these results suggest that, while the valence-dominance model generalizes very well across regions when dimensions are forced to be orthogonal, regional differences are revealed when we use different extraction methods and correlate and rotate the dimension reduction solution. PROTOCOL REGISTRATION: The stage 1 protocol for this Registered Report was accepted in principle on 5 November 2018. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.7611443.v1 .
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| 15. |
- Hall, C. Michael, et al.
(author)
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Denying bogus skepticism in climate change and tourism research.
- 2015
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In: Tourism Management. - : Elsevier BV. - 0261-5177 .- 1879-3193. ; 47, s. 352-356
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Journal article (peer-reviewed)abstract
- This final response to the two climate change denial papers by Shani and Arad further highlights the inaccuracies, misinformation and errors in their commentaries. The obfuscation of scientific research and the consensus on anthropogenic climate change may have significant long-term negative consequences for better understanding the implications of climate change and climate policy for tourism and create confusion and delay in developing and implementing tourism sector responses.
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| 16. |
- Hall, C. Michael, et al.
(author)
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No time for smokescreen skepticism : A rejoinder to Shani and Arad
- 2015
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In: Tourism Management. - : Elsevier BV. - 0261-5177 .- 1879-3193. ; 47, s. 341-347
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Journal article (peer-reviewed)abstract
- Shani and Arad (2014) claimed that tourism scholars tend to endorse the most pessimistic assessments regarding climate change, and that anthropogenic climate change was a "fashionable" and "highly controversial scientific topic". This brief rejoinder provides the balance that is missing from such climate change denial and skepticism studies on climate change and tourism. Recent research provides substantial evidence that reports on anthropogenic climate change are accurate, and that human-induced greenhouse gas emissions, including from the tourism industry, play a significant role in climate change. Some positive net effects may be experienced by some destinations in the short-term, but in the long-term all elements of the tourism system will be impacted. The expansion of tourism emissions at a rate greater than efficiency gains means that it is increasingly urgent that the tourism sector acknowledge, accept and respond to climate change. Debate on tourism-related adaptation and mitigation measures is to be encouraged and welcomed. Climate change denial is not.
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| 17. |
- Needham, Edward J, et al.
(author)
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Complex Autoantibody Responses Occur following Moderate to Severe Traumatic Brain Injury.
- 2021
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In: Journal of immunology. - : The American Association of Immunologists. - 1550-6606 .- 0022-1767. ; 207:1, s. 90-100
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Journal article (peer-reviewed)abstract
- Most of the variation in outcome following severe traumatic brain injury (TBI) remains unexplained by currently recognized prognostic factors. Neuroinflammation may account for some of this difference. We hypothesized that TBI generated variable autoantibody responses between individuals that would contribute to outcome. We developed a custom protein microarray to detect autoantibodies to both CNS and systemic Ags in serum from the acute-phase (the first 7 d), late (6-12 mo), and long-term (6-13 y) intervals after TBI in human patients. We identified two distinct patterns of immune response to TBI. The first was a broad response to the majority of Ags tested, predominantly IgM mediated in the acute phase, then IgG dominant at late and long-term time points. The second was responses to specific Ags, most frequently myelin-associated glycopeptide (MAG), which persisted for several months post-TBI but then subsequently resolved. Exploratory analyses suggested that patients with a greater acute IgM response experienced worse outcomes than predicted from current known risk factors, suggesting a direct or indirect role in worsening outcome. Furthermore, late persistence of anti-MAG IgM autoantibodies correlated with raised serum neurofilament light concentrations at these time points, suggesting an association with ongoing neurodegeneration over the first year postinjury. Our results show that autoantibody production occurs in some individuals following TBI, can persist for many years, and is associated with worse patient outcome. The complexity of responses means that conventional approaches based on measuring responses to single antigenic targets may be misleading.
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| 18. |
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| 19. |
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| 20. |
- Duffy, J. Emmett, et al.
(author)
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Toward a Coordinated Global Observing System for Seagrasses and Marine Macroalgae
- 2019
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In: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 6
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Research review (peer-reviewed)abstract
- In coastal waters around the world, the dominant primary producers are benthic macrophytes, including seagrasses and macroalgae, that provide habitat structure and food for diverse and abundant biological communities and drive ecosystem processes. Seagrass meadows and macroalgal forests play key roles for coastal societies, contributing to fishery yields, storm protection, biogeochemical cycling and storage, and important cultural values. These socio-economically valuable services are threatened worldwide by human activities, with substantial areas of seagrass and macroalgal forests lost over the last half-century. Tracking the status and trends in marine macrophyte cover and quality is an emerging priority for ocean and coastal management, but doing so has been challenged by limited coordination across the numerous efforts to monitor macrophytes, which vary widely in goals, methodologies, scales, capacity, governance approaches, and data availability. Here, we present a consensus assessment and recommendations on the current state of and opportunities for advancing global marine macrophyte observations, integrating contributions from a community of researchers with broad geographic and disciplinary expertise. With the increasing scale of human impacts, the time is ripe to harmonize marine macrophyte observations by building on existing networks and identifying a core set of common metrics and approaches in sampling design, field measurements, governance, capacity building, and data management. We recommend a tiered observation system, with improvement of remote sensing and remote underwater imaging to expand capacity to capture broad-scale extent at intervals of several years, coordinated with strati fied in situ sampling annually to characterize the key variables of cover and taxonomic or functional group composition, and to provide ground-truth. A robust networked system of macrophyte observations will be facilitated by establishing best practices, including standard protocols, documentation, and sharing of resources at all stages of work flow, and secure archiving of open-access data. Because such a network is necessarily distributed, sustaining it depends on close engagement of local stakeholders and focusing on building and long-term maintenance of local capacity, particularly in the developing world. Realizing these recommendations will producemore effective, efficient, and responsive observing, a more accurate global picture of change in vegetated coastal systems, and stronger international capacity for sustaining observations.
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| 21. |
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| 22. |
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| 23. |
- Hutchinson, Peter J, et al.
(author)
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Consensus statement from the 2014 International Microdialysis Forum
- 2015
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In: Intensive Care Medicine. - : Springer Science and Business Media LLC. - 0342-4642 .- 1432-1238. ; 41:9, s. 1517-1528
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Journal article (peer-reviewed)abstract
- Microdialysis enables the chemistry of the extracellular interstitial space to be monitored. Use of this technique in patients with acute brain injury has increased our understanding of the pathophysiology of several acute neurological disorders. In 2004, a consensus document on the clinical application of cerebral microdialysis was published. Since then, there have been significant advances in the clinical use of microdialysis in neurocritical care. The objective of this review is to report on the International Microdialysis Forum held in Cambridge, UK, in April 2014 and to produce a revised and updated consensus statement about its clinical use including technique, data interpretation, relationship with outcome, role in guiding therapy in neurocritical care and research applications.
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| 24. |
- Moshontz, Hannah, et al.
(author)
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The Psychological Science Accelerator: Advancing Psychology Through a Distributed Collaborative Network
- 2018
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In: Advances in Methods and Practices in Psychological Science. - : SAGE Publications. - 2515-2459 .- 2515-2467. ; 1:4, s. 501-515
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Journal article (peer-reviewed)abstract
- Concerns about the veracity of psychological research have been growing. Many findings in psychological science are based on studies with insufficient statistical power and nonrepresentative samples, or may otherwise be limited to specific, ungeneralizable settings or populations. Crowdsourced research, a type of large-scale collaboration in which one or more research projects are conducted across multiple lab sites, offers a pragmatic solution to these and other current methodological challenges. The Psychological Science Accelerator (PSA) is a distributed network of laboratories designed to enable and support crowdsourced research projects. These projects can focus on novel research questions or replicate prior research in large, diverse samples. The PSA’s mission is to accelerate the accumulation of reliable and generalizable evidence in psychological science. Here, we describe the background, structure, principles, procedures, benefits, and challenges of the PSA. In contrast to other crowdsourced research networks, the PSA is ongoing (as opposed to time limited), efficient (in that structures and principles are reused for different projects), decentralized, diverse (in both subjects and researchers), and inclusive (of proposals, contributions, and other relevant input from anyone inside or outside the network). The PSA and other approaches to crowdsourced psychological science will advance understanding of mental processes and behaviors by enabling rigorous research and systematic examination of its generalizability.
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| 25. |
- Muller, Joanne, et al.
(author)
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The use of principle component analyses in characterising trace and major elemental distribution in a 55 kyr peat deposit in tropical Australia: Implications to paleoclimate
- 2008
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In: Geochimicia et Cosmochimica Acta. ; 72, s. 449-463
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Journal article (peer-reviewed)abstract
- The Lynch's Crater peat deposit in NE-Australia is a sensitive environmental archive located in the tropical Southern Hemisphere. This unique deposit illustrates that local and regional changes had a profound effect on the local Australian ecosystem over the past 55 kyr. To obtain a proxy of past climate changes, trace and major element geochemistry analyses were applied to a 13 m peat core from the crater. Principle component analysis (PCA) was used to identify the main factors that control elemental distribution in the peat and to add interpretative strength to the geochemical behavior of selected major and trace elements. For example, Sc, Al, Cu, and Pb were found to be related to increased erosion of the basin soils, and from this, several periods of significant flux from atmospheric input and/or terrigenous run-off were identified. Geochemically mobile elements during rock weathering and pedogenesis, such as Mg, Ca, and Sr helped to identify the peat ombrotrophic-minerotrophic boundary at ~1.5 m depth and offered important information about fluxes of these nutrients to the mire and their dynamics within the deposit. Arsenic and V comparisons between the peat record (high concentrations in some peat sections) and in local basin rocks (very low concentrations), suggested the presence of a long range, atmospheric dust source early in the formation of the mire. The Lynch's Crater peat record presents a continuous record of environmental change in tropical Australia and contributes new understanding to geochemical processes in peatlands.
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| 26. |
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| 27. |
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| 28. |
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| 29. |
- Coles, J. B., et al.
(author)
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Bandwidth-efficient phase modulation techniques for Stimulated Brillouin Scattering suppression in fiber optic parametric amplifiers
- 2010
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In: Optics Express. - 1094-4087 .- 1094-4087. ; 18:17, s. 18138-18150
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Journal article (peer-reviewed)abstract
- Two novel bandwidth efficient pump-dithering Stimulated Brillouin Scattering (SBS) suppression techniques are introduced. The techniques employ a frequency-hopped chirp and an RF noise source to impart phase modulation on the pumps of a two pump Fiber Optical Parametric Amplifier (FOPA). The effectiveness of the introduced techniques is confirmed by measurements of the SBS threshold increase and the associated improvements relative to the current state of the art. Additionally, the effect on the idler signal integrity is presented as measured following amplification from a two pump FOPA employing both techniques. The measured 0.8 dB penalty with pumps dithered by an RF noise source, after accruing 160ps/nm of dispersion with 38 dB conversion gain in a two-pump FOPA is the lowest reported to date.
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| 30. |
- Dickens, Alex Mountfort, et al.
(author)
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Serum Metabolites Associated with Computed TomographyFindings after Traumatic Brain Injury
- 2018
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In: Journal of Neurotrauma. - : Mary Ann Liebert. - 0897-7151 .- 1557-9042. ; 35:22, s. 2673-2683
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Journal article (peer-reviewed)abstract
- There is a need to rapidly detect patients with traumatic brain injury (TBI) who require head computed tomography (CT). Given the energy crisis in the brain following TBI, we hypothesized that serum metabolomics would be a useful tool for developing a set of biomarkers to determine the need for CT and to distinguish between different types of injuries observed. Logistic regression models using metabolite data from the discovery cohort (n=144, Turku, Finland) were used to distinguish between patients with traumatic intracranial findings and negative findings on head CT. The resultant models were then tested in the validation cohort (n=66, Cambridge, UK). The levels of glial fibrillary acidic protein and ubiquitin C-terminal hydrolase-L1 were also quantified in the serum from the same patients. Despite there being significant differences in the protein biomarkers in patients with TBI, the model that determined the need for a CT scan validated poorly (AUC=0.64: Cambridge patients). However, using a combination of six metabolites (two amino acids, three sugar derivatives and one ketoacid) it was possible to discriminate patients with intracranial abnormalities on CT and patients with a normal CT (AUC=0.77 in Turku patients and AUC=0.73 in Cambridge patients). Furthermore, a combination of three metabolites could distinguish between diffuse brain injuries and mass lesions (AUC=0.87 in Turku patients and AUC=0.68 in Cambridge patients). This study identifies a set of validated serum polar metabolites, which associate with the need for a CT scan. Additionally, serum metabolites can also predict the nature of the brain injury. These metabolite markers may prevent unnecessary CT scans, thus reducing the cost of diagnostics and radiation load.
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| 31. |
- Hadjigeorgiou, E., et al.
(author)
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A systematic review into expert knowledge elicitation methods for emerging food and feed risk identification
- 2022
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In: Food Control. - : Elsevier BV. - 0956-7135 .- 1873-7129. ; 136, s. 108848-
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Research review (peer-reviewed)abstract
- An emerging risk results "... from a newly identified hazard to which a significant exposure may occur, or from an unexpected new or increased significant exposure and/or susceptibility to a known hazard". In the field of emerging food and feed risks, expert knowledge elicitation methodologies represent important tools for identifying and addressing data gaps associated with emerging risk identification, particularly under conditions of risk uncertainty and/or ambiguity. A systematic review was conducted to identify expert knowledge elicitation methods which have been used in the context of emerging food and feed risks. The primary research questions were which existing expert knowledge elicitation methodologies have been used to study emerging food and feed risks? and what contexts or situations have been studied using expert knowledge elicitation methodologies in relation to emerging food and feed-related risks? Three databases were searched: Web of Science Core Collection, Scopus, and Google Scholar. Searches covered all studies published from 1998 onwards. A total of 59 studies were included in the review following the application of the inclusion and exclusion criteria. Given the heterogeneity of the included studies, a thematic analysis was applied to assess these papers in relation to the research questions. There was no one expert knowledge elicitation method consistently adopted for the identification of a specific type of emerging food and feed risk. Method triangulation was observed in 23 studies and was reported to improve the validity of results in 15 of these. Most published research considered emerging risks associated with societal controversy ("ambiguous risks"). Although the use of methodological triangulation appears to be helpful in relation to understanding emerging food and feed risks, future research into the development of a harmonised framework will enable the identification, processing, and evaluation of emerging food risks in a systemic way which can facilitate comparative analysis and harmonise mitigation strategies to address emerging risks and their drivers.
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| 32. |
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| 33. |
- Huijben, Jilske A., et al.
(author)
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Development of a quality indicator set to measure and improve quality of ICU care for patients with traumatic brain injury
- 2019
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In: Critical Care. - : BioMed Central. - 1364-8535 .- 1466-609X. ; 23
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Journal article (peer-reviewed)abstract
- Background: We aimed to develop a set of quality indicators for patients with traumatic brain injury (TBI) in intensive care units (ICUs) across Europe and to explore barriers and facilitators for implementation of these quality indicators.Methods: A preliminary list of 66 quality indicators was developed, based on current guidelines, existing practice variation, and clinical expertise in TBI management at the ICU. Eight TBI experts of the Advisory Committee preselected the quality indicators during a first Delphi round. A larger Europe-wide expert panel was recruited for the next two Delphi rounds. Quality indicator definitions were evaluated on four criteria: validity (better performance on the indicator reflects better processes of care and leads to better patient outcome), feasibility (data are available or easy to obtain), discriminability (variability in clinical practice), and actionability (professionals can act based on the indicator). Experts scored indicators on a 5-point Likert scale delivered by an electronic survey tool.Results. The expert panel consisted of 50 experts from 18 countries across Europe, mostly intensivists (N=24, 48%) and neurosurgeons (N=7, 14%). Experts agreed on a final set of 42 indicators to assess quality of ICU care: 17 structure indicators, 16 process indicators, and 9 outcome indicators. Experts are motivated to implement this finally proposed set (N=49, 98%) and indicated routine measurement in registries (N=41, 82%), benchmarking (N=42, 84%), and quality improvement programs (N=41, 82%) as future steps. Administrative burden was indicated as the most important barrier for implementation of the indicator set (N=48, 98%).Conclusions: This Delphi consensus study gives insight in which quality indicators have the potential to improve quality of TBI care at European ICUs. The proposed quality indicator set is recommended to be used across Europe for registry purposes to gain insight in current ICU practices and outcomes of patients with TBI. This indicator set may become an important tool to support benchmarking and quality improvement programs for patients with TBI in the future.
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| 34. |
- Kwon, J. Y., et al.
(author)
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Patient-Reported Outcomes Measurement in Radiation Oncology: Interpretation of Individual Scores and Change over Time in Clinical Practice
- 2022
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In: Current Oncology. - : MDPI AG. - 1198-0052 .- 1718-7729. ; 29:5, s. 3093-3103
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Journal article (peer-reviewed)abstract
- Tools for measuring patients' perceived health and quality of life, such as patient-reported outcome measures (PROMs), inform clinical decisions for patients requiring radiation therapy. However, there may be inconsistencies in how patients interpret and respond to PROMs due to cultural, environmental, personal, or experiential factors. Differential item functioning (DIF) and response shift (RS) refer to differences in the meaning of PROMs between patients or over time (respectively). DIF and RS can threaten the accurate interpretation and use of PROMs, potentially resulting in erroneous conclusions about effectiveness, and flawed individual-level clinical decision-making. Given the empirical evidence of DIF and RS, we aim to review clinical implications and solutions for addressing DIF and RS by providing vignettes from collaborative examinations with workshop participants, as well as the literature. By making these methodological concepts accessible and relevant, for practice, clinicians may feel more confident to ask clarifying questions of patients when PROM scores and the contextual patient information do not align. PROM scores need to be interpreted via dialogue with the patient to avoid misinterpretation due to DIF and RS, which could diminish patient-clinician communication and impede shared decision-making. This work is part of an interdisciplinary knowledge translation initiative focused on the interpretation of PROM scores by clinically-oriented audiences.
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| 35. |
- Mohammad, Rizgar Hassan, et al.
(author)
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Isolation and characterisation of 13 pterosins and pterosides from bracken (Pteridium aquilinum (L.) Kuhn) rhizome
- 2016
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In: Phytochemistry. - : Elsevier BV. - 0031-9422 .- 1873-3700. ; 128, s. 82-94
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Journal article (peer-reviewed)abstract
- Systematic phytochemical investigations of the underground rhizome of Pteridium aquilinum (L.) Kuhn (Dennstaedtiaceae) afforded thirty-five pterosins and pterosides. By detailed analysis of one- and two-dimensional nuclear magnetic resonance spectroscopy, circular dichroism (CD) and high-resolution mass spectrometric data, thirteen previously undescribed pterosins and pterosides have been identified. Interestingly, for the first time 12-O-beta-D-glucopyranoside substituted pterosins, rhedynosides C and D, and the sulfate-containing pterosin, rhedynosin H, alongside the two known compounds, histiopterosin A and (2S)-pteroside A2, were isolated from the rhizomes of subsp. aquilinum of bracken. In addition, six-membered cyclic ether pterosins and pterosides, rhedynosin A and rhedynoside A, are the first examples of this type of pterosin-sesquiterpenoid. Additionally, the three previously reported compounds (rhedynosin I, (2S)-2-hydroxymethylpterosin E and (2S)-12-hydroxypterosin A) were obtained for the first time from plants as opposed to mammalian metabolic products. Single crystal X-ray diffraction analysis was applied to the previously undescribed compounds (2R)-rhedynoside B, (2R)pteroside B and (2S)-pteroside K, yielding the first crystal structures for pterosides, and three known pterosins, (2S)-pterosin A, trans-pterosin C and cis-pterosin C. Rhedynosin C is the only example of the cyclic lactone pterosins with a keto group at position C-14. Six selected pterosins ((2S)-pterosin A, (2R)pterosin B and trans-pterosin C) and associated glycosides ((2S)-pteroside A, (2R)-pteroside B and pterbside Z) were assessed for their anti -diabetic activity using an intestinal glucose uptake assay; all were found to be inactive at 300 mu M.
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| 36. |
- Oresic, Matej, 1967-, et al.
(author)
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Human Serum Metabolites Associate With Severity and Patient Outcomes in Traumatic Brain Injury
- 2016
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In: EBioMedicine. - : Elsevier. - 2352-3964. ; 12, s. 118-126
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Journal article (peer-reviewed)abstract
- Traumatic brain injury (TBI) is a major cause of death and disability worldwide, especially in children and young adults. TBI is an example of a medical condition where there are still major lacks in diagnostics and outcome prediction. Here we apply comprehensive metabolic profiling of serum samples from TBI patients and controls in two independent cohorts. The discovery study included 144 TBI patients, with the samples taken at the time of hospitalization. The patients were diagnosed as severe (sTBI; n=22), moderate (moTBI; n=14) or mild TBI (mTBI; n=108) according to Glasgow Coma Scale. The control group (n=28) comprised of acute orthopedic non-brain injuries. The validation study included sTBI (n=23), moTBI (n=7), mTBI (n=37) patients and controls (n=27). We show that two medium-chain fatty acids (decanoic and octanoic acids) and sugar derivatives including 2,3-bisphosphoglyceric acid are strongly associated with severity of TBI, and most of them are also detected at high concentrations in brain microdialysates of TBI patients. Based on metabolite concentrations from TBI patients at the time of hospitalization, an algorithm was developed that accurately predicted the patient outcomes (AUC=0.84 in validation cohort). Addition of the metabolites to the established clinical model (CRASH), comprising clinical and computed tomography data, significantly improved prediction of patient outcomes. The identified 'TBI metabotype' in serum, that may be indicative of disrupted blood-brain barrier, of protective physiological response and altered metabolism due to head trauma, offers a new venue for the development of diagnostic and prognostic markers of broad spectrum of TBIs. (C) 2016 Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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| 37. |
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| 38. |
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| 39. |
- Zielinski, Brian L., et al.
(author)
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Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume
- 2016
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:9
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Journal article (peer-reviewed)abstract
- The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 mu m size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as silicon became limiting. Expression of these genes, including carbonic anhydrase and transporters for nitrate and phosphate, were found to reflect the physiological status and biogeochemistry of river plume environments. These relatively stable patterns of eukaryotic transcript abundance occurred over modest spatiotemporal scales, with similarity observed in sample duplicates collected up to 2.45 km in space and 120 minutes in time. These results confirm the use of metatranscriptomics as a valuable tool to understand and predict microbial community function.
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| 40. |
- Anh, TNH, et al.
(author)
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Dendritic cell functional properties in a three-dimensional tissue model of human lung mucosa
- 2012
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In: American journal of physiology. Lung cellular and molecular physiology. - : American Physiological Society. - 1522-1504 .- 1040-0605. ; 302:2, s. L226-L237
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Journal article (peer-reviewed)abstract
- In lung tissue, dendritic cells (DC) are found in close association with the epithelial cell layer, and there is evidence of DC regulation by the epithelium; that epithelial dysfunction leads to overzealous immune cell activation. However, dissecting basic mechanisms of DC interactions with epithelial cells in human tissue is difficult. Here, we describe a method to generate a three-dimensional organotypic model of the human airway mucosa in which we have implanted human DC. The model recapitulates key anatomical and functional features of lung mucosal tissue, including a stratified epithelial cell layer, deposition of extracellular matrix proteins, and the production of tight junction and adherence junction proteins. Labeling of fixed tissue model sections and imaging of live tissue models also revealed that DC distribute in close association with the epithelial layer. As functional properties of DC may be affected by the local tissue microenvironment, this system provides a tool to study human DC function associated with lung mucosal tissue. As an example, we report that the lung tissue model regulates the capacity of DC to produce the chemokines CCL17, CCL18, and CCL22, leading to enhanced CCL18 expression and reduced CCL17 and CCL22 expression. This novel tissue model thus provides a tool well suited for a wide range of studies, including those on the regulation of DC functional properties within the local tissue microenvironment during homeostasis and inflammatory reactions.
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| 41. |
- Barker, Roger A., et al.
(author)
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GDNF and Parkinson's Disease : Where Next? A Summary from a Recent Workshop
- 2020
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In: Journal of Parkinson's Disease. - 1877-7171. ; 10:3, s. 875-891
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Journal article (peer-reviewed)abstract
- The concept of repairing the brain with growth factors has been pursued for many years in a variety of neurodegenerative diseases including primarily Parkinson's disease (PD) using glial cell line-derived neurotrophic factor (GDNF). This neurotrophic factor was discovered in 1993 and shown to have selective effects on promoting survival and regeneration of certain populations of neurons including the dopaminergic nigrostriatal pathway. These observations led to a series of clinical trials in PD patients including using infusions or gene delivery of GDNF or the related growth factor, neurturin (NRTN). Initial studies, some of which were open label, suggested that this approach could be of value in PD when the agent was injected into the putamen rather than the cerebral ventricles. In subsequent double-blind, placebo-controlled trials, the most recent reporting in 2019, treatment with GDNF did not achieve its primary end point. As a result, there has been uncertainty as to whether GDNF (and by extrapolation, related GDNF family neurotrophic factors) has merit in the future treatment of PD. To critically appraise the existing work and its future, a special workshop was held to discuss and debate this issue. This paper is a summary of that meeting with recommendations on whether there is a future for this therapeutic approach and also what any future PD trial involving GDNF and other GDNF family neurotrophic factors should consider in its design.
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| 42. |
- Biganzoli, L., et al.
(author)
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The requirements of a specialist breast centre
- 2020
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In: Breast. - : Elsevier BV. - 0960-9776 .- 1532-3080. ; 51, s. 65-84
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Journal article (peer-reviewed)abstract
- This article is an update of the requirements of a specialist breast centre, produced by EUSOMA and endorsed by ECCO as part of Essential Requirements for Quality Cancer Care (ERQCC) programme, and ESMO. To meet aspirations for comprehensive cancer control, healthcare organisations must consider the requirements in this article, paying particular attention to multidisciplinarity and patient-centred pathways from diagnosis, to treatment, to survivorship. The centrepiece of this article is the requirements section, comprising definitions; multidisciplinary structure; minimum case, procedure and staffing volumes; and detailed descriptions of the skills of, and resources needed by, members and specialisms in the multidisciplinary team in a breast centre. These requirements are positioned within narrative on European breast cancer epidemiology, the standard of care, challenges to delivering this standard, and supporting evidence, to enable a broad audience to appreciate the importance of establishing these requirements in specialist breast centres. (C) 2020 The Authors. Published by Elsevier Ltd.
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| 43. |
- Charalambidis, Georgios, et al.
(author)
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A switchable self-assembling and disassembling chiral system based on a porphyrin-substituted phenylalanine-phenylalanine motif
- 2016
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In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 7:12657
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Journal article (peer-reviewed)abstract
- Artificial light-harvesting systems have until now not been able to self-assemble into structures with a large photon capture cross-section that upon a stimulus reversibly can switch into an inactive state. Here we describe a simple and robust FLFL-dipeptide construct to which a meso-tetraphenylporphyrin has been appended and which self-assembles to fibrils, platelets or nanospheres depending on the solvent composition. The fibrils, functioning as quenched antennas, give intense excitonic couplets in the electronic circular dichroism spectra which are mirror imaged if the unnatural FDFD-analogue is used. By slightly increasing the solvent polarity, these light-harvesting fibres disassemble to spherical structures with silent electronic circular dichroism spectra but which fluoresce. Upon further dilution with the nonpolar solvent, the intense Cotton effects are recovered, thus proving a reversible switching. A single crystal X-ray structure shows a head-to-head arrangement of porphyrins that explains both their excitonic coupling and quenched fluorescence.
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| 44. |
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| 45. |
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| 46. |
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| 47. |
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| 48. |
- Kylander, Malin E., et al.
(author)
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A rapid and reliable method for Pb isotopic analysis of peat and lichens by laser ablation-quadrupole-inductively coupled plasma-mass spectrometry for biomonitoring and sample screening
- 2007
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In: Analytica Chimica Acta. - : Elsevier BV. - 0003-2670. ; 582:1, s. 116-124
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Journal article (pop. science, debate, etc.)abstract
- An analytical protocol for rapid and reliable laser ablation-quadrupole (LA-Q)- and multi-collector (MC-) inductively coupled plasma-mass spectrometry (ICP-MS) analysis of Pb isotope ratios (207Pb/206Pb and 208Pb/206Pb) in peats and lichens is developed. This technique is applicable to source tracing atmospheric Pb deposition in biomonitoring studies and sample screening. Reference materials and environmental samples were dry ashed and pressed into pellets for introduction by laser ablation. No binder was used to reduce contamination. LA-MC-ICP-MS internal and external precisions were <1.1% and <0.3%, respectively, on both 207Pb/206Pb and 208Pb/206Pb ratios. LA-Q-ICP-MS internal precisions on 207Pb/206Pb and 208Pb/206Pb ratios were lower with values for the different sample sets <14.3% while external precisions were <2.9%. The level of external precision acquired in this study is high enough to distinguish between most modern Pb sources. LA-MC-ICP-MS measurements differed from thermal ionisation mass spectrometry (TIMS) values by 1% or less while the accuracy obtained using LA-Q-ICP-MS compared to solution MC-ICP-MS was 3.1% or better using a run bracketing (RB) mass bias correction method. Sample heterogeneity and detector switching when measuring 208Pb by Q-ICP-MS are identified as sources of reduced analytical performance.
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| 49. |
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| 50. |
- Pivnenko, M.N., et al.
(author)
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Optical and electro-optical properties of bimesogenic organosiloxane antiferroeletric liquid crystals with molecular tilt approaching 45 degrees
- 2005
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In: Liquid Crystals. - 0267-8292. ; 32, s. 173-181
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Journal article (peer-reviewed)abstract
- We have studied the optical and electro-optical properties of three different bimesogenic siloxane materials. The dimers are symmetrical and the two mesogenic groups are connected by a siloxane unit containing three Si atoms and methylene spacers. The mesogens contain F, Cl and Br substituents, respectively, laterally attached to the phenyl ring lying closest to the chiral centre of the mesogen. These materials each exhibited a broad temperature range antiferroelectric phase and large molecular tilt, which is almost temperature-independent. We have shown that, at low temperatures, the molecular tilt in the antiferroelectric phase is the same as the apparent molecular tilt in the field-induced ferroelectric state and is close to 45°. It was found that the antiferroelectric phase of these compounds, aligned in such way that the dimeric molecules were lying in a plane parallel to the confining substrates, exhibited very low in-plane birefringence. For this reason, samples of the compounds inserted between crossed polarizers in the antiferroelectric state exhibited an extremely dark state, with contrast ratios as high as 1000:1, which did not change noticeably on rotating the sample between the crossed polarizers. It was shown that the optically isotropic siloxane moiety did not contribute to the optical properties, viz. birefringence or tilt angle, but served to enhance the promotion of the antiferroelectric phase and the temperature independent properties. We also showed the existence of a linear electro-optic response in the pretransitional region of the antiferroelectric phase of these compounds over a moderate range of fields.
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