| 1. |
- Prusti, T., et al.
(författare)
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The Gaia mission
- 2016
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 595
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Tidskriftsartikel (refereegranskat)abstract
- Gaia is a cornerstone mission in the science programme of the European Space Agency (ESA). The spacecraft construction was approved in 2006, following a study in which the original interferometric concept was changed to a direct-imaging approach. Both the spacecraft and the payload were built by European industry. The involvement of the scientific community focusses on data processing for which the international Gaia Data Processing and Analysis Consortium (DPAC) was selected in 2007. Gaia was launched on 19 December 2013 and arrived at its operating point, the second Lagrange point of the Sun-Earth-Moon system, a few weeks later. The commissioning of the spacecraft and payload was completed on 19 July 2014. The nominal five-year mission started with four weeks of special, ecliptic-pole scanning and subsequently transferred into full-sky scanning mode. We recall the scientific goals of Gaia and give a description of the as-built spacecraft that is currently (mid-2016) being operated to achieve these goals. We pay special attention to the payload module, the performance of which is closely related to the scientific performance of the mission. We provide a summary of the commissioning activities and findings, followed by a description of the routine operational mode. We summarise scientific performance estimates on the basis of in-orbit operations. Several intermediate Gaia data releases are planned and the data can be retrieved from the Gaia Archive, which is available through the Gaia home page.
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| 2. |
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| 3. |
- Cossarizza, A., et al.
(författare)
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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
- 2019
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Ingår i: European Journal of Immunology. - : Wiley. - 0014-2980 .- 1521-4141. ; 49:10, s. 1457-1973
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Tidskriftsartikel (refereegranskat)abstract
- These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
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| 4. |
- Wortman, J. R., et al.
(författare)
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The 2008 update of the Aspergillus nidulans genome annotation: A community effort
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46, s. S2-S13
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Tidskriftsartikel (refereegranskat)abstract
- The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. (C) 2009 Elsevier Inc. All rights reserved.
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| 5. |
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| 6. |
- Lønborg, C., et al.
(författare)
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A global database of dissolved organic matter (DOM) concentration measurements in coastal waters (CoastDOM v1)
- 2024
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Ingår i: Earth System Science Data. - : Copernicus Publications. - 1866-3508 .- 1866-3516. ; 16:2, s. 1107-1119
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Tidskriftsartikel (refereegranskat)abstract
- Measurements of dissolved organic carbon (DOC), nitrogen (DON), and phosphorus (DOP) concentrations are used to characterize the dissolved organic matter (DOM) pool and are important components ofbiogeochemical cycling in the coastal ocean. Here, we present the first edition of a global database (CoastDOMv1; available at https://doi.org/10.1594/PANGAEA.964012, Lønborg et al., 2023) compiling previously published and unpublished measurements of DOC, DON, and DOP in coastal waters. These data are complementedby hydrographic data such as temperature and salinity and, to the extent possible, other biogeochemical variables(e.g. chlorophyll a, inorganic nutrients) and the inorganic carbon system (e.g. dissolved inorganic carbon andtotal alkalinity). Overall, CoastDOM v1 includes observations of concentrations from all continents. However,most data were collected in the Northern Hemisphere, with a clear gap in DOM measurements from the SouthernHemisphere. The data included were collected from 1978 to 2022 and consist of 62 338 data points for DOC,20 356 for DON, and 13 533 for DOP. The number of measurements decreases progressively in the sequenceDOC > DON > DOP, reflecting both differences in the maturity of the analytical methods and the greater focuson carbon cycling by the aquatic science community. The global database shows that the average DOC concentration in coastal waters (average ± standard deviation (SD): 182±314 µmolC L−1; median: 103 µmolC L−1) is13-fold higher than the average coastal DON concentration (13.6 ± 30.4 µmol N L−1; median: 8.0 µmol N L−1),which is itself 39-fold higher than the average coastal DOP concentration (0.34 ± 1.11 µmol P L−1; median:0.18 µmol P L−1). This dataset will be useful for identifying global spatial and temporal patterns in DOM and willhelp facilitate the reuse of DOC, DON, and DOP data in studies aimed at better characterizing local biogeochemical processes; closing nutrient budgets; estimating carbon, nitrogen, and phosphorous pools; and establishing abaseline for modelling future changes in coastal waters.
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| 7. |
- Gjestvang, D., et al.
(författare)
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Examination of how properties of a fissioning system impact isomeric yield ratios of the fragments
- 2023
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Ingår i: Physical Review C. - : American Physical Society. - 2469-9985 .- 2469-9993. ; 108:6
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Tidskriftsartikel (refereegranskat)abstract
- The population of isomeric states in the prompt decay of fission fragments-so-called isomeric yield ratios (IYRs)-is known to be sensitive to the angular momentum J that the fragment emerged with, and may therefore contain valuable information on the mechanism behind the fission process. In this work, we investigate how changes in the fissioning system impact the measured IYRs of fission fragments to learn more about what parameters affect angular momentum generation. To enable this, a new technique for measuring IYRs is first demonstrated. It is based on the time of arrival of discrete gamma rays, and has the advantage that it enables the study of the IYR as a function of properties of the partner nucleus. This technique is used to extract the IYR of 134Te, strongly populated in actinide fission, from the three different fissioning systems: 232Th(n, f), 238U(n, f), at two different neutron energies, as well as 252Cf(sf). The impacts of changing the fissioning system, the compound nuclear excitation energy, the minimum J of the binary partner, and the number of neutrons emitted on the IYR of 134Te are determined. The decay code TALYS is used in combination with the fission simulation code FREYA to calculate the primary fragment angular momentum from the IYR. We find that the IYR of 134Te has a slope of 0.004 +/- 0.002 with increase in compound nucleus (CN) mass. When investigating the impact on the IYR of increased CN excitation energy, we find no change with an energy increase similar to the difference between thermal and fast fission. By varying the mass of the partner fragment emerging with 134Te, it is revealed that the IYR of 134Te is independent of the total amount of prompt neutrons emitted from the fragment pair. This indicates that neutrons carry minimal angular momentum away from the fission fragments. Comparisons with the FREYA+TALYS simulations reveal that the average angular momentum in 134Te following 238U(n, f) is 6.0 h over bar . This is not consistent with the value deduced from recent CGMF calculations. Finally, the IYR sensitivity to the angular momentum of the primary fragment is discussed. These results are not only important to help understanding the underlying mechanism in nuclear fission, but can also be used to constrain and benchmark fission models, and are relevant to the gamma -ray heating problem of reactors.
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| 8. |
- Djoussé, L, et al.
(författare)
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Interaction of normal and expanded CAG repeat sizes influences age at onset of Huntington disease.
- 2003
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Ingår i: American Journal of Medical Genetics. Part A. - : Wiley. - 1552-4825 .- 1552-4833. ; 119A:3, s. 279-82
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Tidskriftsartikel (refereegranskat)abstract
- Huntington disease (HD) is a neurodegenerative disorder caused by the abnormal expansion of CAG repeats in the HD gene on chromosome 4p16.3. Past studies have shown that the size of expanded CAG repeat is inversely associated with age at onset (AO) of HD. It is not known whether the normal Huntington allele size influences the relation between the expanded repeat and AO of HD. Data collected from two independent cohorts were used to test the hypothesis that the unexpanded CAG repeat interacts with the expanded CAG repeat to influence AO of HD. In the New England Huntington Disease Center Without Walls (NEHD) cohort of 221 HD affected persons and in the HD-MAPS cohort of 533 HD affected persons, we found evidence supporting an interaction between the expanded and unexpanded CAG repeat sizes which influences AO of HD (P = 0.08 and 0.07, respectively). The association was statistically significant when both cohorts were combined (P = 0.012). The estimated heritability of the AO residual was 0.56 after adjustment for normal and expanded repeats and their interaction. An analysis of tertiles of repeats sizes revealed that the effect of the normal allele is seen among persons with large HD repeat sizes (47-83). These findings suggest that an increase in the size of the normal repeat may mitigate the expression of the disease among HD affected persons with large expanded CAG repeats.
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| 9. |
- Nene, Vishvanath, et al.
(författare)
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Genome sequence of Aedes aegypti, a major arbovirus vector.
- 2007
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 316:5832, s. 1718-23
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Tidskriftsartikel (refereegranskat)abstract
- We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
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| 10. |
- Wichert, R., et al.
(författare)
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Mucus Detachment by Host Metalloprotease Meprin beta Requires Shedding of Its Inactive Pro-form, which Is Abrogated by the Pathogenic Protease RgpB
- 2017
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 21:8, s. 2090-2103
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Tidskriftsartikel (refereegranskat)abstract
- The host metalloprotease meprin beta is required for mucin 2 (MUC2) cleavage, which drives intestinal mucus detachment and prevents bacterial over-growth. To gain access to the cleavage site in MUC2, meprin b must be proteolytically shed from epithelial cells. Hence, regulation of meprin b shedding and activation is important for physiological and pathophysiological conditions. Here, we demonstrate that meprin b activation and shedding are mutually exclusive events. Employing ex vivo small intestinal organoid and cell culture experiments, we found that ADAM-mediated shedding is restricted to the inactive pro-form of meprin beta and is completely inhibited upon its conversion to the active form at the cell surface. This strict regulation of meprin beta activity can be overridden by pathogens, as demonstrated for the bacterial protease Arg-gingipain (RgpB). This secreted cysteine protease potently converts membrane-bound meprin beta into its active form, impairing meprin beta shedding and its function as a mucus-detaching protease.
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| 11. |
- Giblin, S. R., et al.
(författare)
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Pauling Entropy, Metastability, and Equilibrium in Dy2Ti2O7 Spin Ice
- 2018
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 121:6
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Tidskriftsartikel (refereegranskat)abstract
- Determining the fate of the Pauling entropy in the classical spin ice material Dy2Ti2O7 with respect to the third law of thermodynamics has become an important test case for understanding the existence and stability of ice-rule states in general. The standard model of spin ice-the dipolar spin ice model-predicts an ordering transition at T approximate to 0.15 K, but recent experiments by Pomaranski et al. suggest an entropy recovery over long timescales at temperatures as high as 0.5 K, much too high to be compatible with the theory. Using neutron scattering and specific heat measurements at low temperatures and with long timescales ( 0.35 K/10(6) s and 0.5 K/10(5) s, respectively) on several isotopically enriched samples, we find no evidence of a reduction of ice-rule correlations or spin entropy. High-resolution simulations of the neutron structure factor show that the spin correlations remain well described by the dipolar spin ice model at all temperatures. Furthermore, by careful consideration of hyperfine contributions, we conclude that the original entropy measurements of Ramirez et al. are, after all, essentially correct: The short-time relaxation method used in that study gives a reasonably accurate estimate of the equilibrium spin ice entropy due to a cancellation of contributions.
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| 12. |
- Gonzalez, J. M., et al.
(författare)
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Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)
- 2008
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 105:25, s. 8724-8729
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhoclopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhoclopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.
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| 13. |
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| 14. |
- Ljungman, S., et al.
(författare)
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Factors associated with time to first dialysis-associated peritonitis episode: Data from the Peritonitis Prevention Study (PEPS)
- 2023
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Ingår i: Peritoneal Dialysis International. - 0896-8608. ; 43:3, s. 241-251
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Peritonitis remains a potentially serious complication of peritoneal dialysis (PD) treatment. It is therefore important to identify risk factors in order to reduce the incidence of peritonitis. The aim of the present analysis was to identify factors associated with time to first peritonitis episode. Methods: Incident PD patients from 57 centres in Europe participated in the prospective randomised controlled Peritonitis Prevention Study (PEPS) from 2010 to 2015. Peritonitis-free, self-care PD patients >= 18 years were randomised to a retraining or a control group and followed for 1-36 months after PD initiation. The association of biochemical, clinical and prescription data with time to first peritonitis episode was studied. Results: A first peritonitis episode was experienced by 33% (223/671) of participants. Univariable Cox proportional hazard regression showed a strong association between the time-updated number of PD bags connected per 24 h (PD bags/24 h) and time to first peritonitis episode (HR 1.35; 95% confidence interval (CI) 1.17-1.57), even after inclusion of PD modalities in the same model. Multivariable Cox regression revealed that the factors independently associated with time to first peritonitis episode included age (HR 1.16 per 10 years; 95% CI 1.05-1.28), PD bags/24 h (HR 1.32; 95% CI 1.13-1.54), serum albumin >35 g/L (HR 1.39; 95% CI 1.06-1.82) and body weight per 10 kg (HR 1.10; 95% CI 1.01-1.19). Conclusion: This study of incident PD patients indicates that older age, greater number of PD bags connected/24 h, higher body weight and hypoalbuminaemia are independently associated with a shorter time to first peritonitis episode.
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| 15. |
- Ljungman, Susanne, 1942, et al.
(författare)
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Retraining for prevention of peritonitis in peritoneal dialysis patients: A randomized controlled trial
- 2020
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Ingår i: Peritoneal Dialysis International. - : SAGE Publications. - 0896-8608 .- 1718-4304. ; 40:2, s. 141-152
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Tidskriftsartikel (refereegranskat)abstract
- Background: Peritonitis is more common in peritoneal dialysis (PD) patients nonadherent to the PD exchange protocol procedures than in compliant patients. We therefore investigated whether regular testing of PD knowledge with focus on infection prophylaxis could increase the time to first peritonitis (primary outcome) and reduce the peritonitis rate in new PD patients. Methods: This physician-initiated, open-label, parallel group trial took place at 57 centers in Sweden, Denmark, Norway, Finland, Estonia, Latvia, the Netherlands, and the United Kingdom from 2010 to 2015. New peritonitis-free PD patients were randomized using computer-generated numbers 1 month after the start of PD either to a control group (n = 331) treated according to center routines or to a retraining group (n = 340), which underwent testing of PD knowledge and skills at 1, 3, 6, 12, 18, 24, 30, and 36 months after PD start, followed by retraining if the goals were not achieved. Results: In all, 74% of the controls and 80% of the retraining patients discontinued the study. The groups did not differ significantly regarding cumulative incidence of first peritonitis adjusted for competing risks (kidney transplantation, transfer to hemodialysis and death; hazard ratio 0.84; 95% confidence interval (CI) 0.65-1.09) nor regarding peritonitis rate per patient year (relative risk 0.93; 95% CI 0.75-1.16). Conclusions: In this randomized controlled trial, we were unable to demonstrate that regular, targeted testing and retraining of new PD patients increased the time to first peritonitis or reduced the rate of peritonitis, as the study comprised patients with a low risk of peritonitis, was underpowered, open to type 1 statistical error, and contamination between groups.
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| 16. |
- Nguyen, M. Q., et al.
(författare)
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Assessing the content validity of the Manchester–Oxford Foot Questionnaire in surgically treated ankle fracture patients : a qualitative study
- 2023
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Ingår i: Journal of Orthopaedic Surgery and Research. - : BioMed Central (BMC). - 1749-799X. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Roughly 10% of fractures in adults are ankle fractures. These injuries are found in both sexes and present with different fracture characteristics. The treatment varies with the patients’ biology and fracture type, and the goals are to restore stability, prevent pain and maintain ankle function. Clinicians generally use outcomes like assessment of radiography, pain level, or function. The use of patient-reported outcome measures is increasing, and the Manchester–Oxford Foot Questionnaire (MOXFQ) has been shown to have good measurement properties when validated in patients with foot and ankle disorders. However, the instrument has not been validated for ankle fracture patients. This study aims to assess the content validity of the items in MOXFQ in surgically treated ankle fracture patients. Methods: A qualitative deductive design was used to investigate patients’ response process of the MOXFQ. Individual interviews were conducted using cognitive interviewing based on the theoretical framework of the 4-step model by Tourangeau. Adult patients that were surgically treated for an ankle fracture between four weeks and 18 months were purposively sampled, and interviews followed a semi-structured interview guide. The predetermined categories were comprehension, retrieval, judgement, and response. Results: Seventeen respondents (65% females) were interviewed. Respondents’ age ranged from 27 to 76 years. Some of the respondents in the early recovery phase were limited by post-operative restrictions and did not find the items in the walking/standing domain relevant. Respondents that were allowed weight-bearing as tolerated (WBAT) were able to recall relevant information for most items. Respondents with time since surgery more than 12 months had less pain and remembered fewer relevant episodes in the recall period. Items in the social interaction domain contained ambiguous questions and were generally considered less important by respondents. The summary index score lacked important concepts in measuring overall quality of life. Conclusions: Pain was a central concept in the post-operative recovery of ankle fracture patients. The MOXFQ-subscales for pain and walking/standing had acceptable content validity in patients that were allowed WBAT. The social interaction-subscale and the summary index score had insufficient content validity for this patient population.
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| 17. |
- Uter, W., et al.
(författare)
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The epidemic of methylisothiazolinone contact allergy in Europe : follow-up on changing exposures
- 2020
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Ingår i: Journal of the European Academy of Dermatology and Venereology. - : Wiley. - 0926-9959 .- 1468-3083. ; 34:2, s. 333-339
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Tidskriftsartikel (refereegranskat)abstract
- Background: Methylisothiazolinone (MI) has caused an unprecedented epidemic of contact allergy in Europe and elsewhere. Subsequently, regulatory action has been taken, at least in Europe, aiming at reducing risk of MI sensitization. Objective: To follow-up on the prevalence of contact allergy to MI in consecutively patch tested patients and assess the spectrum of products containing MI or methylchloroisothiazolinone (MCI)/MI in patients positive to MI which elicited current allergic contact dermatitis. Methods: A cross-sectional survey was performed in 2016 and 2017, including all adult patients patch tested with the baseline series (including MI 0.2% aq.) between 1 May and 31 October at 14 centres in 11 European countries. Patients with positive reactions (+ to +++) to MI were further examined regarding history, clinical characteristics and eliciting products, which were categorized into 34 types and 4 classes (leave-on, rinse-off, household, occupational). The results were compared with the reference year 2015. Results: A total of 317 patients, n = 202 of 4278 tested in 2016 (4.72%) and n = 115 of 3879 tested in 2017 (2.96%), had positive reactions to MI; the previous result from 2015 was 5.97% (P < 0.0001). The share of currently relevant contact allergy among all positive reactions declined significantly as well (P = 0.0032). Concerning product classes, a relative decline of leave-on and a relative increase of rinse-off and household products was noted. Conclusion: The prevalence of MI contact allergy decreased by 50% from 2015 to 2017. As a consequence of regulation, the share of cosmetics products (leave-on in particular) eliciting allergic contact dermatitis is decreasing. The chosen method of analysing causative products in sensitized patients has proven useful to monitor effects of intervention.
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| 18. |
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| 19. |
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| 20. |
- Landsverk, Ole J. B., et al.
(författare)
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Antibody-secreting plasma cells persist for decades in human intestine
- 2017
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Ingår i: Journal of Experimental Medicine. - NewYork, USA : Rockefeller University Press. - 0022-1007 .- 1540-9538. ; 214:2, s. 309-317
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Tidskriftsartikel (refereegranskat)abstract
- Plasma cells (PCs) produce antibodies that mediate immunity after infection or vaccination. In contrast to PCs in the bone marrow, PCs in the gut have been considered short lived. In this study, we studied PC dynamics in the human small intestine by cell-turnover analysis in organ transplants and by retrospective cell birth dating measuring carbon-14 in genomic DNA. We identified three distinct PC subsets: a CD19(+) PC subset was dynamically exchanged, whereas of two CD19(-) PC subsets, CD45(+) PCs exhibited little and CD45(-) PCs no replacement and had a median age of 11 and 22 yr, respectively. Accumulation of CD45(-) PCs during ageing and the presence of rotavirus-specific clones entirely within the CD19(-) PC subsets support selection and maintenance of protective PCs for life in human intestine.
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| 21. |
- Pan, W. H., et al.
(författare)
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Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
- 2018
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Ingår i: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Background: The interplay of epigenetic processes and the intestinal microbiota may play an important role in intestinal development and homeostasis. Previous studies have established that the microbiota regulates a large proportion of the intestinal epithelial transcriptome in the adult host, but microbial effects on DNA methylation and gene expression during early postnatal development are still poorly understood. Here, we sought to investigate the microbial effects on DNA methylation and the transcriptome of intestinal epithelial cells (IECs) during postnatal development. Methods: We collected IECs from the small intestine of each of five 1-, 4-and 12 to 16-week-old mice representing the infant, juvenile, and adult states, raised either in the presence or absence of a microbiota. The DNA methylation profile was determined using reduced representation bisulfite sequencing (RRBS) and the epithelial transcriptome by RNA sequencing using paired samples from each individual mouse to analyze the link between microbiota, gene expression, and DNA methylation. Results: We found that microbiota-dependent and -independent processes act together to shape the postnatal development of the transcriptome and DNA methylation signatures of IECs. The bacterial effect on the transcriptome increased over time, whereas most microbiota-dependent DNA methylation differences were detected already early after birth. Microbiota-responsive transcripts could be attributed to stage-specific cellular programs during postnatal development and regulated gene sets involved primarily immune pathways and metabolic processes. Integrated analysis of the methylome and transcriptome data identified 126 genomic loci at which coupled differential DNA methylation and RNA transcription were associated with the presence of intestinal microbiota. We validated a subset of differentially expressed and methylated genes in an independent mouse cohort, indicating the existence of microbiota-dependent " functional" methylation sites which may impact on long-term gene expression signatures in IECs. Conclusions: Our study represents the first genome-wide analysis of microbiota-mediated effects on maturation of DNA methylation signatures and the transcriptional program of IECs after birth. It indicates that the gut microbiota dynamically modulates large portions of the epithelial transcriptome during postnatal development, but targets only a subset of microbially responsive genes through their DNA methylation status.
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| 22. |
- Quist-Paulsen, P., et al.
(författare)
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T-cell acute lymphoblastic leukemia in patients 1-45 years treated with the pediatric NOPHO ALL2008 protocol
- 2020
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Ingår i: Leukemia. - : Springer Science and Business Media LLC. - 0887-6924 .- 1476-5551. ; 34:2, s. 347-357
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Tidskriftsartikel (refereegranskat)abstract
- The NOPHO ALL2008 is a population-based study using an unmodified pediatric protocol in patients 1-45 years of age with acute lymphoblastic leukemia. Patients with T-ALL were given a traditional pediatric scheme if fast responding (minimal residual disease (MRD) < 0.1% day 29), or intensive block-based chemotherapy if slow responding (MRD > 0.1% day 29). Both treatment arms included pediatric doses of high-dose methotrexate and asparaginase. If MRD >= 5% on day 29 or >= 0.1% after consolidation, patients were assigned to allogeneic hematopoietic stem cell transplantation. The 5-year overall survival of the 278 T-ALL patients was 0.75 (95% CI 0.69-0.81), being 0.82 (0.74-0.88) for patients 1.0-9.9 years, 0.76 (0.66-0.86) for those 10.0-17.9 years, and 0.65 (0.55-0.75) for the older patients. The risk of death in first remission was significantly higher in adults (12%) compared with the 1-9 years group (4%). The MRD responses in the three age groups were similar, and only a nonsignificant increase in relapse risk was found in adults. In conclusion, an unmodified pediatric protocol in patients 1-45 years is effective in all age groups. The traditional pediatric treatment schedule was safe for all patients, but the intensive block therapy led to a high toxic death rate in adults.
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| 23. |
- Rank, Cecilie U., et al.
(författare)
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Asparaginase-Associated Pancreatitis in Acute Lymphoblastic Leukemia : Results From the NOPHO ALL2008 Treatment of Patients 1-45 Years of Age
- 2020
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Ingår i: Journal of Clinical Oncology. - Alexandria : American Society of Clinical Oncology. - 0732-183X .- 1527-7755. ; 38:2, s. 145-154
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: Asparaginase-associated pancreatitis (AAP) is common in patients with acute lymphoblastic leukemia (ALL), but risk differences across age groups both in relation to first-time AAP and after asparaginase re-exposure have not been explored.PATIENTS AND METHODS: We prospectively registered AAP (n = 168) during treatment of 2,448 consecutive ALL patients aged 1.0-45.9 years diagnosed from July 2008 to October 2018 and treated according to the Nordic Society of Pediatric Hematology and Oncology (NOPHO) ALL2008 protocol.RESULTS: Compared with patients aged 1.0-9.9 years, adjusted AAP hazard ratios (HRa) were associated with higher age with almost identical HRa (1.6; 95% CI, 1.1 to 2.3; P = .02) for adolescents (10.0-17.9 years) and adults (18.0-45.9 years). The day 280 cumulative incidences of AAP were 7.0% for children (1.0-9.9 years: 95% CI, 5.4 to 8.6), 10.1% for adolescents (10.0 to 17.9 years: 95% CI, 7.0 to 13.3), and 11.0% for adults (18.0-45.9 years: 95% CI, 7.1 to 14.9; P = .03). Adolescents had increased odds of both acute (odds ratio [OR], 5.2; 95% CI, 2.1 to 13.2; P = .0005) and persisting complications (OR, 6.7; 95% CI, 2.4 to 18.4; P = .0002) compared with children (1.0-9.9 years), whereas adults had increased odds of only persisting complications (OR, 4.1; 95% CI, 1.4 to 11.8; P = .01). Fifteen of 34 asparaginase-rechallenged patients developed a second AAP. Asparaginase was truncated in 17/21 patients with AAP who subsequently developed leukemic relapse, but neither AAP nor the asparaginase truncation was associated with increased risk of relapse.CONCLUSION: Older children and adults had similar AAP risk, whereas morbidity was most pronounced among adolescents. Asparaginase re-exposure should be considered only for patients with an anticipated high risk of leukemic relapse, because multiple studies strongly indicate that reduction of asparaginase treatment intensity increases the risk of relapse.
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| 24. |
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| 25. |
- Tulstrup, M., et al.
(författare)
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Effects of germ line DHFR and FPGS variants on methotrexate metabolism and relapse of leukemia
- 2020
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 136:10, s. 1161-1168
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Tidskriftsartikel (refereegranskat)abstract
- Methotrexate (MTX) during maintenance therapy is essential for curing acute lymphoblastic leukemia (ALL), but dosing strategies aiming at adequate treatment intensity are challenged by interindividual differences in drug disposition. To evaluate genetic factors associated with MTX metabolism, we performed a genome-wide association study in 447 ALL cases from the Nordic Society for Pediatric Haematology and Oncology ALL2008 study, validating results in an independent set of 196 patients. The intergenic single-nucleotide polymorphism rs1382539, located in a regulatory element of DHFR, was associated with increased levels of short-chain MTX polyglutamates (P = 1.1 x 10(-8)) related to suppression of enhancer activity, whereas rs35789560 in FPGS (p.R466C, P = 5.6 x 10(-9)) was associated with decreased levels of long-chain MTX polyglutamates through reduced catalytic activity. Furthermore, the FPGS variant was linked with increased relapse risk (P = .044). These findings show a genetic basis for interpatient variability in MTX response and could be used to improve future dosing algorithms.
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| 26. |
- Aamodt, A. H., et al.
(författare)
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Blood neurofilament light concentration at admittance: a potential prognostic marker in COVID-19
- 2021
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Ingår i: Journal of Neurology. - : Springer Science and Business Media LLC. - 0340-5354 .- 1432-1459. ; 268, s. 3574-3583
-
Tidskriftsartikel (refereegranskat)abstract
- Objective To test the hypotheses that blood biomarkers for nervous system injury, serum concentrations of neurofilament light chain protein (NfL) and glial fibrillary acidic protein (GFAp) can serve as biomarkers for disease severity in COVID-19 patients. Methods Forty-seven inpatients with confirmed COVID-19 had blood samples drawn on admission for assessing serum biomarkers of CNS injury by Single molecule array (Simoa), NfL and GFAp. Concentrations of NfL and GFAp were analyzed in relation to symptoms, clinical signs, inflammatory biomarkers and clinical outcomes. We used multivariate linear models to test for differences in biomarker concentrations in the subgroups, accounting for confounding effects. Results In total, 21% (n = 10) of the patients were admitted to an intensive care unit, and the overall mortality rate was 13% (n = 6). Non-survivors had higher serum concentrations of NfL (p < 0.001) upon admission than patients who were discharged alive both in adjusted analyses (p = 2.6 x 10(-7)) and unadjusted analyses (p = 0.001). The concentrations of NfL in non-survivors increased over repeated measurements; whereas, the concentrations in survivors were stable. The GFAp concentration was also significantly higher in non-survivors than survivors (p = 0.02). Conclusion Increased concentrations of NfL and GFAp in COVID-19 patients on admission may indicate increased mortality risk. Measurement of blood biomarkers for nervous system injury can be useful to detect and monitor CNS injury in COVID-19.
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| 27. |
- Andersson, Helena M., et al.
(författare)
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Differences in the inflammatory plasma cytokine response following two elite female soccer games separated by a 72-h recovery
- 2010
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Ingår i: Scandinavian Journal of Medicine and Science in Sports. - Malden, USA : Wiley-Blackwell. - 0905-7188 .- 1600-0838. ; 20:5, s. 740-747
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Tidskriftsartikel (refereegranskat)abstract
- We investigated changes in a large battery of pro- and anti-inflammatory cytokines in elite female soccer players following two 90-min games separated by a 72-h active or passive recovery. Blood samples were taken from 10 players before, within 15-20 min, 21, 45 and 69 h after the first game and within 15-20 min after the second game. The leukocyte count was analyzed, together with several plasma pro- and anti-inflammatory cytokines, using a multiplex bead array system. After the first and second game, the total leukocytes and neutrophils increased significantly. Likewise, increases (P<0.05) in pro-inflammatory cytokines [interleukin (IL)-12, tumor necrosis factor-alpha (TNF-alpha), interferon-gamma (INF-gamma), IL-17], chemokines [monocyte chemotactic protein-1 (MCP-1), IL-8 and monokine induced by gamma interferon (MIG)], anti-inflammatory cytokines (IL-2R, IL-4, IL-5, IL-7, IL-10, IL-13, INF-alpha) and the mixed cytokine IL-6 were observed. Leukocyte and cytokine levels were normalized within 21 h. Active recovery (low-intensity exercises) did not affect the cytokine responses. A dampened cytokine response was observed after the second game as only IL-12, IL-6, MCP-1, IL-8 and MIG increased (P<0.05). In conclusion, a robust pro- and anti-inflammatory cytokine response occurs after the first but not the second soccer game. The implications of the dampened cytokine response in female players after the second game are unknown.
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| 28. |
- Andersson, Helena M., et al.
(författare)
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Neuromuscular fatigue and recovery in elite female soccer : effects of active recovery
- 2008
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Ingår i: Medicine & Science in Sports & Exercise. - : Ovid Technologies (Wolters Kluwer Health). - 0195-9131 .- 1530-0315. ; 40:2, s. 372-380
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: To investigate the time course of recovery from neuromuscular fatigue and some biochemical changes between two female soccer matches separated by an active or passive recovery regime. METHODS: Countermovement jump (CMJ), sprint performance, maximal isokinetic knee flexion and extension, creatine kinase (CK), urea, uric acid, and perceived muscle soreness were measured in 17 elite female soccer players before, immediately after, 5, 21, 45, 51, and 69 h after a first match, and immediately after a second match. Eight players performed active recovery (submaximal cycling at 60% of HRpeak and low-intensity resistance training at < 50% 1RM) 22 and 46 h after the first match. RESULTS: In response to the first match, a significant decrease in sprint performance (-3.0 +/- 0.5%), CMJ (-4.4 +/- 0.8%), peak torque in knee extension (-7.1 +/- 1.9%) and flexion (-9.4 +/- 1.8%), and an increase in CK (+ 152 +/- 28%), urea (15 +/- 2), uric acid (+ 11 +/- 2%), and muscle soreness occurred. Sprint ability was first to return to baseline (5 h) followed by urea and uric acid (21 h), isokinetic knee extension (27 h) and flexion (51 h), CK, and muscle soreness (69 h), whereas CMJ was still reduced at the beginning of the second match. There were no significant differences in the recovery pattern between the active and passive recovery groups. The magnitude of the neuromuscular and biochemical changes after the second match was similar to that observed after the first match. CONCLUSION: The present study reveals differences in the recovery pattern of the various neuromuscular and biochemical parameters in response to a female soccer match. The active recovery had no effects on the recovery pattern of the four neuromuscular and three biochemical parameters.
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| 29. |
- Asghar, Naveed, 1983-, et al.
(författare)
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Transient Expression of Flavivirus Structural Proteins in Nicotiana benthamiana
- 2022
-
Ingår i: Vaccines. - : MDPI. - 2076-393X. ; 10:10
-
Tidskriftsartikel (refereegranskat)abstract
- Flaviviruses are a threat to public health and can cause major disease outbreaks. Tick-borne encephalitis (TBE) is caused by a flavivirus, and it is one of the most important causes of viral encephalitis in Europe and is on the rise in Sweden. As there is no antiviral treatment availa-ble, vaccination remains the best protective measure against TBE. Currently available TBE vaccines are based on formalin-inactivated virus produced in cell culture. These vaccines must be delivered by intramuscular injection, have a burdensome immunization schedule, and may exhibit vaccine failure in certain populations. This project aimed to develop an edible TBE vaccine to trigger a stronger immune response through oral delivery of viral antigens to mucosal surfaces. We demonstrated successful expression and post-translational processing of flavivirus structural pro-teins which then self-assembled to form virus-like particles in Nicotiana benthamiana. We performed oral toxicity tests in mice using various plant species as potential bioreactors and evaluated the immunogenicity of the resulting edible vaccine candidate. Mice immunized with the edible vaccine candidate did not survive challenge with TBE virus. Interestingly, immunization of female mice with a commercial TBE vaccine can protect their offspring against TBE virus infection.
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| 30. |
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| 31. |
- Eekers, Danielle B. P., et al.
(författare)
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The EPTN consensus-based atlas for CT- and MR-based contouring in neuro-oncology
- 2018
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Ingår i: Radiotherapy and Oncology. - : ELSEVIER IRELAND LTD. - 0167-8140 .- 1879-0887. ; 128:1, s. 37-43
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To create a digital, online atlas for organs at risk (OAR) delineation in neuro-oncology based on high-quality computed tomography (Cr) and magnetic resonance (MR) imaging. Methods: CT and 3 Tesla (3T) MR images (slice thickness 1 mm with intravenous contrast agent) were obtained from the same patient and subsequently fused. In addition, a 7T MR without intravenous contrast agent was obtained from a healthy volunteer. Based on discussion between experienced radiation oncologists, the clinically relevant organs at risk (OARs) to be included in the atlas for neuro-oncology were determined, excluding typical head and neck OARs previously published. The draft atlas was delineated by a senior radiation oncologist, 2 residents in radiation oncology, and a senior neuro-radiologist incorporating relevant available literature. The proposed atlas was then critically reviewed and discussed by European radiation oncologists until consensus was reached. Results: The online atlas includes one CT-scan at two different window settings and one MR scan (3T) showing the OARs in axial, coronal and sagittal view. This manuscript presents the three-dimensional descriptions of the fifteen consensus OARs for neuro-oncology. Among these is a new OAR relevant for neuro-cognition, the posterior cerebellum (illustrated on 7T MR images). Conclusion: In order to decrease inter- and intra-observer variability in delineating OARs relevant for neuro-oncology and thus derive consistent dosimetric data, we propose this atlas to be used in photon and particle therapy. The atlas is available online at w.cancerdata.c and will be updated whenever required.
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| 32. |
- Fabiano, Simone, et al.
(författare)
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On the fundamentals of organic mixed ionic/electronic conductors
- 2023
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Ingår i: Journal of Materials Chemistry C. - : ROYAL SOC CHEMISTRY. - 2050-7526 .- 2050-7534. ; 11:42, s. 14527-14539
-
Tidskriftsartikel (refereegranskat)abstract
- The first Telluride Science meeting (formerly TSRC) on organic mixed ionic and electronic conductors (OMIECs), Oct 3-7, 2022, brought together researchers across the field to understand the fundamental processes and identify out-standing questions related to this exciting class of materials. OMIECs are organic materials that promote the transport of mobile electronic charge carriers while simultaneously supporting ionic transport and ionic-electronic coupling. These properties open up broad areas of applications from energy to bioelectronics. Devices include batteries, supercapacitors, actuators, electrochromic displays, and organic electrochemical transistors (OECTs). They possess the key strengths of traditional organic electronic materials, such as synthetic tunability and low-temperature processing. Despite the recent advances in devices and applications achieved with such materials, many challenges and gaps in understanding remain. These topics hold the key to designing next-generation materials and devices that continue to push the limits of performance and stability and facilitate novel functionality. This perspective aims to summarize the current understanding, conversations, and debates that made this TSRC particularly engaging, enabling new directions and searching for missing pieces of the OMIEC puzzle. This perspective offers insights from discussions conducted during the Telluride Science meeting on organic mixed ionic and electronic conductors, outlining the challenges associated with understanding the behavior of this intriguing materials class.
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| 33. |
- Folkesson, Mattias, 1972-, et al.
(författare)
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Immunohistochemical changes in the expression of HSP27 in exercised human vastus lateralis muscle
- 2008
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Ingår i: Acta Physiologica. - : Blackwell Publishing. - 1748-1708 .- 1748-1716. ; 194:3, s. 215-222
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Tidskriftsartikel (refereegranskat)abstract
- Aim: The role of HSP27 in the adaptive process of skeletal muscle to exercise, especially in humans, is not well understood. The objective of this study was to investigate immunohistochemical changes in HSP27 expression in human vastus lateralis muscle following resistance and endurance exercises.Methods: Two different exercise protocols were used: (1) one-leg ergometer cycling (EC, n = 6) consisting of two 30-min bouts at 40% and 75% of peak oxygen uptake, respectively, and (2) leg extension resistance exercise (RE, n = 9) including 10 sets of eight repetitions at a load corresponding to 70% of one maximal repetition (1RM). Immunohistochemistry using specific monoclonal antibodies was used to determine the location of HSP27 protein in muscle biopsies from human vastus lateralis.Results: Our results show that RE, but not EC, induced a significant appearance of scattered accumulations of HSP27 protein in muscle fibres from five of nine subjects. The number of fibres with accumulation of HSP27 in RE ranged from 0% to 32% with a mean of 6.3% of the total number of fibres.Conclusion: We conclude that this rapid HSP27 protein relocation after RE is an important player in the cellular remodelling of human muscle fibres in response to exercise involving high-force contractions, but not in response to endurance exercises.
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| 34. |
- Golnabi, Amir H., et al.
(författare)
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3-D Microwave Tomography Using the Soft Prior Regularization Technique: Evaluation in Anatomically Realistic MRI-Derived Numerical Breast Phantoms
- 2019
-
Ingår i: IEEE Transactions on Biomedical Engineering. - 0018-9294 .- 1558-2531. ; 66:9, s. 2566-2575
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Fusion of magnetic resonance imaging (MRI) breast images with microwave tomography is accomplished through a soft prior technique, which incorporates spatial information (from MRI), i. e., accurate boundary location of different regions of interest, into the regularization process of the microwave image reconstruction algorithm. Methods: Numerical experiments were completed on a set of three-dimensional (3-D) breast geometries derived from MR breast data with different parenchymal densities, as well as a simulated tumor to evaluate the performance over a range of breast shapes, sizes, and property distributions. Results: When the soft prior regularization technique was applied, both permittivity and conductivity relative root mean square error values decreased by more than 87% across all breast densities, except in two cases where the error decrease was only 55% and 78%. In addition, the incorporation of structural priors increased contrast between tumor and fibroglandular tissue by 59% in permittivity and 192% in conductivity. Conclusion: This study confirmed that the soft prior algorithm is robust in 3-D and can function successfully across a range of complex geometries and tissue property distributions. Significance: This study demonstrates that our microwave tomography is capable of recovering accurate tissue property distributions when spatial information from MRI is incorporated through soft prior regularization.
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| 35. |
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| 36. |
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| 37. |
- Horwath, Oscar, et al.
(författare)
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Isokinetic resistance training combined with eccentric overload improves athletic performance and induces muscle hypertrophy in young ice hockey players.
- 2019
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Ingår i: Journal of Science and Medicine in Sport. - Chatswood : Elsevier. - 1440-2440 .- 1878-1861. ; 22:7, s. 821-826
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: To determine the combined effects of slow isokinetic resistance training and eccentric overload and compare it to traditional resistance training on strength, power, body composition and muscle hypertrophy in young ice hockey players.DESIGN: Experimental, randomized trial.METHODS: Twenty-two resistance-trained ice hockey players (18±1year) were assigned to either isokinetic resistance training and eccentric overload (ISO/ECC; n=11) or traditional resistance training (TRAD; n=11). Participants underwent supervised progressive resistance training for 8 weeks (2-3 sessions/week) involving lower body multiple-joint exercises (heavy squats and explosive jump squats). The ISO/ECC group performed their training using a computerized robotic engine system (1080 Quantum synchro, Sweden), whereas the TRAD group performed the same resistance exercises with isotonic loading. Before and after the intervention, participants were evaluated in 1RM back squat, loaded jump squats, sprint- and jump performance, body composition and muscle thickness using ultrasound measurement.RESULTS: Similar moderate increases in 1RM back squat and power output in the jump squats were found in both the ISO/ECC and TRAD groups (11-17%, P<0.01), whereas only the ISO/ECC group showed improvements in drop jump performance (9.8%, P=0.01). Moreover, similar trivial changes in body composition were observed in both groups, while only the ISO/ECC training group increased muscle thickness in the vastus intermedius (P=0.01) and rectus femoris muscles (P=0.03).CONCLUSIONS: Both modalities effectively increased maximal strength and power output, whereas isokinetic resistance training, combined with eccentric overload, improved drop jump performance and induced greater muscle hypertrophy than traditional training in young ice hockey players. © 2019 Sports Medicine Australia
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| 38. |
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| 39. |
- Knudtzen, F. C., et al.
(författare)
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Lyme neuroborreliosis with encephalitis; a systematic literature review and a Scandinavian cohort study
- 2022
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Ingår i: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X. ; 28:5, s. 649-656
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Tidskriftsartikel (refereegranskat)abstract
- Background: Lyme neuroborreliosis (LNB) presenting with encephalitis is rare and scarcely described. Objectives: To describe the available literature on LNB encephalitis and to characterize this patient group through a Scandinavian retrospective cohort study. Data sources: Medline, Embase, Scopus, Cochrane library. Study eligibility criteria: There was no discrimination on study type, time of publication or language. Participants: Review: All articles with definite LNB and confirmed/possible encephalitis. Cohort: LNB cohorts from Denmark, Sweden and Norway 1990–2019 were screened for patients with encephalitis. Methods: Review: Adhering to PRISMA guidelines; two authors extracted reviews and assessed quality of studies. Cohort: Data on demography, symptoms, cerebrospinal fluid findings, differential diagnostic examinations, treatment, residual symptoms, 1-year mortality were registered. Results: Review: 2330 articles screened on title/abstract, 281 full texts, yielding 42 articles (case reports/series or cohort studies), including 45 patients from 18 countries spanning 35 years. Altered mental status ranged from personality changes and confusion to unconsciousness. Common focal symptoms were hemiparesis, ataxia and dysarthria; seven patients had seizures. Median time from symptom onset to hospital was 2 weeks (IQR 2–90 days). Of 38 patients with available follow-up after median 12 months (IQR 5–13), 32 had fully or partially recovered, two had died. Cohort: Thirty-five patients (median age 67 years, IQR 48–76) were included. The encephalitis prevalence was 3.3% (95% CI 2.2–4.4%) among 1019 screened LNB patients. Frequent encephalitis symptoms were confusion, personality changes, aphasia, ataxia. EEGs and neuroimaging showed encephalitis in 93.8% and 20.6%, respectively. Median delay from symptom onset to hospital was 14 days (IQR 7–34), with further 7 days (IQR 3–34) delay until targeted therapy. At follow-up (median 298 days post-treatment; IQR 113–389), 65.6% had residual symptoms. None had died. Conclusions: This study shows that encephalitis is an uncommon, but likely overlooked clinical manifestation of LNB. As the high frequency of residual symptoms may be related to prolonged treatment delay, prompt LNB testing of patients with encephalitis in Borrelia burgdorferi-endemic areas should be considered. © 2021 The Author(s)
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| 40. |
- Langbehn, D, et al.
(författare)
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A new model for prediction of the age of onset and penetrance for Huntington's disease based on CAG length.
- 2004
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Ingår i: Clinical Genetics. - : Wiley. - 0009-9163 .- 1399-0004. ; 65:4, s. 267-277
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Tidskriftsartikel (refereegranskat)abstract
- Huntington's disease (HD) is a neurodegenerative disorder caused by an unstable CAG repeat. For patients at risk, participating in predictive testing and learning of having CAG expansion, a major unanswered question shifts from "Will I get HD?" to "When will it manifest?" Using the largest cohort of HD patients analyzed to date (2913 individuals from 40 centers worldwide), we developed a parametric survival model based on CAG repeat length to predict the probability of neurological disease onset (based on motor neurological symptoms rather than psychiatric onset) at different ages for individual patients. We provide estimated probabilities of onset associated with CAG repeats between 36 and 56 for individuals of any age with narrow confidence intervals. For example, our model predicts a 91% chance that a 40-year-old individual with 42 repeats will have onset by the age of 65, with a 95% confidence interval from 90 to 93%. This model also defines the variability in HD onset that is not attributable to CAG length and provides information concerning CAG-related penetrance rates.
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| 41. |
- Li, Jian-Liang, et al.
(författare)
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A genome scan for modifiers of age at onset in Huntington disease : The HD MAPS study.
- 2003
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 73:3, s. 682-7
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Tidskriftsartikel (refereegranskat)abstract
- Huntington disease (HD) is caused by the expansion of a CAG repeat within the coding region of a novel gene on 4p16.3. Although the variation in age at onset is partly explained by the size of the expanded repeat, the unexplained variation in age at onset is strongly heritable (h2=0.56), which suggests that other genes modify the age at onset of HD. To identify these modifier loci, we performed a 10-cM density genomewide scan in 629 affected sibling pairs (295 pedigrees and 695 individuals), using ages at onset adjusted for the expanded and normal CAG repeat sizes. Because all those studied were HD affected, estimates of allele sharing identical by descent at and around the HD locus were adjusted by a positionally weighted method to correct for the increased allele sharing at 4p. Suggestive evidence for linkage was found at 4p16 (LOD=1.93), 6p21-23 (LOD=2.29), and 6q24-26 (LOD=2.28), which may be useful for investigation of genes that modify age at onset of HD.
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| 42. |
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| 43. |
- Madin, Joshua S., et al.
(författare)
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A synthesis of bacterial and archaeal phenotypic trait data
- 2020
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 7:1
-
Tidskriftsartikel (refereegranskat)abstract
- A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.
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| 44. |
- Mauritsen, Thorsten, et al.
(författare)
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Developments in the MPI-M Earth System Model version 1.2 (MPI-ESM1.2) and Its Response to Increasing CO2
- 2019
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Ingår i: Journal of Advances in Modeling Earth Systems. - 1942-2466. ; 11:4, s. 998-1038
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Tidskriftsartikel (refereegranskat)abstract
- A new release of the Max Planck Institute for Meteorology Earth System Model version 1.2 (MPI-ESM1.2) is presented. The development focused on correcting errors in and improving the physical processes representation, as well as improving the computational performance, versatility, and overall user friendliness. In addition to new radiation and aerosol parameterizations of the atmosphere, several relatively large, but partly compensating, coding errors in the model's cloud, convection, and turbulence parameterizations were corrected. The representation of land processes was refined by introducing a multilayer soil hydrology scheme, extending the land biogeochemistry to include the nitrogen cycle, replacing the soil and litter decomposition model and improving the representation of wildfires. The ocean biogeochemistry now represents cyanobacteria prognostically in order to capture the response of nitrogen fixation to changing climate conditions and further includes improved detritus settling and numerous other refinements. As something new, in addition to limiting drift and minimizing certain biases, the instrumental record warming was explicitly taken into account during the tuning process. To this end, a very high climate sensitivity of around 7 K caused by low-level clouds in the tropics as found in an intermediate model version was addressed, as it was not deemed possible to match observed warming otherwise. As a result, the model has a climate sensitivity to a doubling of CO2 over preindustrial conditions of 2.77 K, maintaining the previously identified highly nonlinear global mean response to increasing CO2 forcing, which nonetheless can be represented by a simple two-layer model.
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| 45. |
- Meaney, Paul M, 1960, et al.
(författare)
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A 4-channel, vector network analyzer microwave imaging prototype based on software defined radio technology
- 2019
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 1089-7623 .- 0034-6748. ; 90:4
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Tidskriftsartikel (refereegranskat)abstract
- We have implemented a prototype 4-channel transmission-based, microwave measurement system built on innovative software defined radio (SDR) technology. The system utilizes the B210 USRP SDR developed by Ettus Research that operates over a 70 MHz-6 GHz bandwidth. While B210 units are capable of being synchronized with each other via coherent reference signals, they are somewhat unreliable in this configuration and the manufacturer recommends using N200 or N210 models instead. For our system, N-series SDRs were less suitable because they are not amenable to RF shielding required for the cross-channel isolation necessary for an integrated microwave imaging system. Consequently, we have configured an external reference that overcame these limitations in a compact and robust package. Our design exploits the rapidly evolving technology being developed for the telecommunications environment for test and measurement tasks with the higher performance specifications required in medical microwave imaging applications. In a larger channel configuration, the approach is expected to provide performance comparable to commercial vector network analyzers at a fraction of the cost and in a more compact footprint.
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| 46. |
- Meaney, Paul M, 1960, et al.
(författare)
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Comments on "Investigation of Histology Region Dielectric Measurements of Heterogeneous Tissues"
- 2020
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Ingår i: IEEE Transactions on Antennas and Propagation. - 0018-926X .- 1558-2221. ; 68:1, s. 615-616
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Tidskriftsartikel (refereegranskat)abstract
- In the article, "Investigation of histology region in dielectric measurements of heterogeneous tissues," by Porter and O'Halloran, the authors utilize a flexible phantom in a layered material dielectric property analysis to quantify the effective sensing volume of a coaxial dielectric probe. Ostensibly, this test has been used by others to characterize the region for which percent variation in the material composition in front of the probe corresponds to percent variation in the computed effective dielectric properties. By employing a compressible material, the authors fail to isolate features that are attributable solely to the probe, itself, and inadvertently incorporate confounding characteristics associated with the compressible nature of the material. The net effect is to exaggerate the probe's sensing volume, which undermines the conclusions drawn from the subsequent tissue dielectric property studies. © 2019 IEEE.
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| 47. |
- Meaney, Paul M, 1960, et al.
(författare)
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Electrical Characterization of Glycerin: Water Mixtures: Implications for Use as a Coupling Medium in Microwave Tomography
- 2017
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Ingår i: IEEE Transactions on Microwave Theory and Techniques. - 0018-9480 .- 1557-9670. ; 65:5, s. 1471-1478
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Tidskriftsartikel (refereegranskat)abstract
- We examine the broadband behavior of complex electrical properties of glycerin and water mixtures over the frequency range of 0.1-25.0 GHz, especially as they relate to using these liquids as coupling media for microwave tomographic imaging. Their combination is unique in that they are mutually miscible over the full range of concentrations, which allows them to be tailored to dielectric property matching for biological tissues. While the resultant mixture properties are partially driven by differences in the inherent low-frequency permittivity of each constituent, relaxation frequency shifts play a disproportionately larger role in increasing the permittivity dispersion while also dramatically increasing the effective conductivity over the frequency range of 1-3 GHz. For the full range of mixture ratios, the relaxation frequency shifts from 17.5 GHz for 0% glycerin to less than 0.1 GHz for 100% glycerin. Of particular interest is the fact that the conductivity stays above 1.0 S/m over the 1-3-GHz range for glycerin mixture ratios (70%-90% glycerin) we use for microwave breast tomography. The high level of attenuation is critical for suppressing unwanted multipath signals. This paper presents a full characterization of these liquids along with a discussion of their benefits and limitations in the context of microwave tomography.
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| 48. |
- Meaney, Paul M, 1960, et al.
(författare)
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Examination of the sensitivity matrix during the iterative reconstruction process for microwave tomography
- 2018
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Ingår i: 2018 IEEE Conference on Antenna Measurements and Applications, CAMA 2018.
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Konferensbidrag (refereegranskat)abstract
- We have reconstructed microwave tomographic images utilizing a Gauss-Newton scheme with a log transformation. While the recovered images are quite good, we have analyzed the behavior of the associated Jacobian, or sensitivity, matrix with respect to how it evolves during the reconstruction process. We found that in general the highest sensitivities are along the periphery of the imaging zone confirming the fact that most algorithms operate best for features nearest the outside. Interestingly, our log transformed algorithm appears to evolve during the reconstruction process to increase its internal sensitivity once the major exterior ones have been resolved. These results provide useful insight into a key driver of the reconstruction process and provide useful tools for assessing different system design criteria.
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| 49. |
- Meaney, Paul M, 1960, et al.
(författare)
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Quasi- Open-Ended Coaxial Dielectric Probe Array for Skin Burn Characterization
- 2019
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Ingår i: 2019 13th European Conference On Antennas And Propagation (EUCAP). - : IEEE. - 9788890701887
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Konferensbidrag (refereegranskat)abstract
- We have developed a planar probe for measuring dielectric properties. It exploits modern circuit board fabrication technologies that effectively construct a quasi-coaxial structure running perpendicular to the board. The feed line is a printed coplanar waveguide which comes in from the side on the top plane. The opening to the bottom behaves exactly like an open-ended coaxial probe. The initial results are comparable to the existing coaxial probes. The geometry of these probes allows them to be fabricated in an array utilizing standard, multi-layer circuit fabrication technology. These probe arrays may prove extremely useful in applications such as tumor margin detection for resected tissue, skin cancer screening and characterizing burns.
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| 50. |
- Meaney, Paul M, 1960, et al.
(författare)
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Two-step reconstruction process for microwave tomography without a priori information
- 2016
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Ingår i: 2016 10th European Conference on Antennas and Propagation, EuCAP 2016. - 2164-3342. - 9788890701863 ; , s. Arti no 7481674-
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Konferensbidrag (refereegranskat)abstract
- While our log transform reconstruction algorithm provides significant advantages over competing algorithms because of its ability to converge to a unique, global solution without utilizing a priori information, the process still requires a modest amount of regularization which naturally tends to smooth the image and sometimes blur important features. We have integrated this overall technique with a novel 2-step reconstruction to produce significantly improved images with respect to feature definition without inducing unwanted artifacts. The critical challenge in this scenario is determining the regularization parameter for the Euclidean distance penalty term in the second step. In this case, because the algorithm is quite fast, the regularization term is computed using a simple linear search. Initial phantom experiment results indicate that targets as small as 5mm diameter are detectable and that the algorithm behaves as an efficient estimator according to standard parameter estimation metrics for a wide range of targets. Results also suggest that there are equally significant improvements in reconstructions from actual patient exams. © 2016 European Association of Antennas and Propagation.
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