| 1. |
- Murari, A., et al.
(författare)
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A control oriented strategy of disruption prediction to avoid the configuration collapse of tokamak reactors
- 2024
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Ingår i: Nature Communications. - 2041-1723 .- 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- The objective of thermonuclear fusion consists of producing electricity from the coalescence of light nuclei in high temperature plasmas. The most promising route to fusion envisages the confinement of such plasmas with magnetic fields, whose most studied configuration is the tokamak. Disruptions are catastrophic collapses affecting all tokamak devices and one of the main potential showstoppers on the route to a commercial reactor. In this work we report how, deploying innovative analysis methods on thousands of JET experiments covering the isotopic compositions from hydrogen to full tritium and including the major D-T campaign, the nature of the various forms of collapse is investigated in all phases of the discharges. An original approach to proximity detection has been developed, which allows determining both the probability of and the time interval remaining before an incoming disruption, with adaptive, from scratch, real time compatible techniques. The results indicate that physics based prediction and control tools can be developed, to deploy realistic strategies of disruption avoidance and prevention, meeting the requirements of the next generation of devices.
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| 8. |
- Azevedo, Flavio, et al.
(författare)
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Social and moral psychology of COVID-19 across 69 countries
- 2023
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Ingår i: Scientific Data. - : NATURE PORTFOLIO. - 2052-4463. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The COVID-19 pandemic has affected all domains of human life, including the economic and social fabric of societies. One of the central strategies for managing public health throughout the pandemic has been through persuasive messaging and collective behaviour change. To help scholars better understand the social and moral psychology behind public health behaviour, we present a dataset comprising of 51,404 individuals from 69 countries. This dataset was collected for the International Collaboration on Social & Moral Psychology of COVID-19 project (ICSMP COVID-19). This social science survey invited participants around the world to complete a series of moral and psychological measures and public health attitudes about COVID-19 during an early phase of the COVID-19 pandemic (between April and June 2020). The survey included seven broad categories of questions: COVID-19 beliefs and compliance behaviours; identity and social attitudes; ideology; health and well-being; moral beliefs and motivation; personality traits; and demographic variables. We report both raw and cleaned data, along with all survey materials, data visualisations, and psychometric evaluations of key variables.
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| 9. |
- Van Bavel, Jay J., et al.
(författare)
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National identity predicts public health support during a global pandemic
- 2022
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Ingår i: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Understanding collective behaviour is an important aspect of managing the pandemic response. Here the authors show in a large global study that participants that reported identifying more strongly with their nation reported greater engagement in public health behaviours and support for public health policies in the context of the pandemic. Changing collective behaviour and supporting non-pharmaceutical interventions is an important component in mitigating virus transmission during a pandemic. In a large international collaboration (Study 1, N = 49,968 across 67 countries), we investigated self-reported factors associated with public health behaviours (e.g., spatial distancing and stricter hygiene) and endorsed public policy interventions (e.g., closing bars and restaurants) during the early stage of the COVID-19 pandemic (April-May 2020). Respondents who reported identifying more strongly with their nation consistently reported greater engagement in public health behaviours and support for public health policies. Results were similar for representative and non-representative national samples. Study 2 (N = 42 countries) conceptually replicated the central finding using aggregate indices of national identity (obtained using the World Values Survey) and a measure of actual behaviour change during the pandemic (obtained from Google mobility reports). Higher levels of national identification prior to the pandemic predicted lower mobility during the early stage of the pandemic (r = -0.40). We discuss the potential implications of links between national identity, leadership, and public health for managing COVID-19 and future pandemics.
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| 10. |
- Abrams, M. B., et al.
(författare)
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A Standards Organization for Open and FAIR Neuroscience : the International Neuroinformatics Coordinating Facility
- 2021
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Ingår i: Neuroinformatics. - : Springer Nature. - 1539-2791 .- 1559-0089.
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Tidskriftsartikel (refereegranskat)abstract
- There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.
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| 11. |
- Barquinero, J-F., et al.
(författare)
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RENEB Inter-Laboratory Comparison 2021 : The FISH-Based Translocation Assay
- 2023
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Ingår i: Radiation Research. - 0033-7587 .- 1938-5404. ; 199:6, s. 583-590
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Tidskriftsartikel (refereegranskat)abstract
- Translocation analysis using fluorescence in situ hybridization (FISH) is the method of choice for dose assessment in case of chronic or past exposures to ionizing radiation. Although it is a widespread technique, unlike dicentrics, the number of FISH-based inter-laboratory comparisons is small. For this reason, although the current Running the European Network of Biological and Physical retrospective Dosimetry (RENEB) inter-laboratory comparison 2021 was designed as a fast response to a real emergency scenario, it was considered a good opportunity to perform an inter-laboratory comparison using the FISH technique to gain further experience. The Bundeswehr Institute of Radiobiology provided peripheral blood samples from one healthy human volunteer. Three test samples were irradiated with blinded doses of 0, 1.2, and 3.5 Gy, respectively. Samples were then sent to the seven participating laboratories. The FISH technique was applied according to the standard procedure of each laboratory. Both, the frequency of translocations and the estimated dose for each sample were sent to the coordinator using a special scoring sheet for FISH. All participants sent their results in due time. However, although it was initially requested to send the results based on the full analysis, evaluating 500 equivalent cells, most laboratories only sent the results based on triage, with a smaller number of analyzed cells. In the triage analysis, there was great heterogeneity in the number of equivalent cells scored. On the contrary, for the full analysis, this number was more homogeneous. For all three samples, one laboratory showed outlier yields compared to the other laboratories. Excluding these results, in the triage analysis, the frequency of translocations in sample no. 1 ranged from 0 to 0.013 translocations per cell, and for samples no. 2 and no. 3 the genomic mean frequency were 0.27 +/- 0.03 and 1.47 +/- 0.14, with a coefficient of variation of 0.29 and 0.23 respectively. Considering only results obtained in the triage analysis for sample no. 1, all laboratories, except one, classified this sample as the non-irradiated one. For sample no. 2, excluding the outlier value, the mean reported dose was 1.74 +/- 0.16 Gy indicating a mean deviation of about 0.5 Gy to the delivered dose of 1.2 Gy. For sample no. 3 the mean dose estimated was 4.21 +/- 0.21 Gy indicating a mean deviation of about 0.7 Gy to the delivered dose of 3.5 Gy. In the frame of RENEB, this is the second FISH-based inter-laboratory comparison. The whole exercise was planned as a response to an emergency, therefore, a triage analysis was requested for all the biomarkers except for FISH. Although a full analysis was initially requested for FISH, most of the laboratories reported only a triage-based result. The main reason is that it was not clearly stated what was required before starting the exercise. Results show that most of the laboratories successfully discriminated unexposed and irradiated samples from each other without any overlap. A good agreement in the observed frequencies of translocations was observed but there was a tendency to overestimate the delivered doses. Efforts to improve the harmonization of this technique and subsequent exercises to elucidate the reason for this trend should be promoted.
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| 12. |
- Olahova, M., et al.
(författare)
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POLRMT mutations impair mitochondrial transcription causing neurological disease
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- While >300 disease-causing variants have been identified in the mitochondrial DNA (mtDNA) polymerase gamma, no mitochondrial phenotypes have been associated with POLRMT, the RNA polymerase responsible for transcription of the mitochondrial genome. Here, we characterise the clinical and molecular nature of POLRMT variants in eight individuals from seven unrelated families. Patients present with global developmental delay, hypotonia, short stature, and speech/intellectual disability in childhood; one subject displayed an indolent progressive external ophthalmoplegia phenotype. Massive parallel sequencing of all subjects identifies recessive and dominant variants in the POLRMT gene. Patient fibroblasts have a defect in mitochondrial mRNA synthesis, but no mtDNA deletions or copy number abnormalities. The in vitro characterisation of the recombinant POLRMT mutants reveals variable, but deleterious effects on mitochondrial transcription. Together, our in vivo and in vitro functional studies of POLRMT variants establish defective mitochondrial transcription as an important disease mechanism. POLRMT is key for transcription of the mitochondrial genome, yet has not been implicated in mitochondrial disease to date. Here, the authors identify mutations in POLRMT in individuals with mitochondrial disease-related phenotypes and characterise underlying defects in mitochondrial transcription.
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| 13. |
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| 14. |
- Abend, M., et al.
(författare)
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RENEB Inter-Laboratory Comparison 2021 : The Gene Expression Assay
- 2023
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Ingår i: Radiation Research. - 0033-7587 .- 1938-5404. ; 199:6, s. 598-615
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Tidskriftsartikel (refereegranskat)abstract
- Early and high-throughput individual dose estimates are essential following large-scale radiation exposure events. In the context of the Running the European Network for Biodosimetry and Physical Dosimetry (RENEB) 2021 exercise, gene expression assays were conducted and their corresponding performance for dose-assessment is presented in this publication. Three blinded, coded whole blood samples from healthy donors were exposed to 0, 1.2 and 3.5 Gy X-ray doses (240 kVp, 1 Gy/min) using the X-ray source Yxlon. These exposures correspond to clinically relevant groups of unexposed, low dose (no severe acute health effects expected) and high dose exposed individuals (requiring early intensive medical health care). Samples were sent to eight teams for dose estimation and identification of clinically relevant groups. For quantitative reverse transcription polymerase chain reaction (qRT-PCR) and microarray analyses, samples were lysed, stored at 20°C and shipped on wet ice. RNA isolations and assays were run in each laboratory according to locally established protocols. The time-to-result for both rough early and more precise later reports has been documented where possible. Accuracy of dose estimates was calculated as the difference between estimated and reference doses for all doses (summed absolute difference, SAD) and by determining the number of correctly reported dose estimates that were defined as ±0.5 Gy for reference doses <2.5 Gy and ±1.0 Gy for reference doses >3 Gy, as recommended for triage dosimetry. We also examined the allocation of dose estimates to clinically/diagnostically relevant exposure groups. Altogether, 105 dose estimates were reported by the eight teams, and the earliest report times on dose categories and estimates were 5 h and 9 h, respectively. The coefficient of variation for 85% of all 436 qRT-PCR measurements did not exceed 10%. One team reported dose estimates that systematically deviated several-fold from reported dose estimates, and these outliers were excluded from further analysis. Teams employing a combination of several genes generated about two-times lower median SADs (0.8 Gy) compared to dose estimates based on single genes only (1.7 Gy). When considering the uncertainty intervals for triage dosimetry, dose estimates of all teams together were correctly reported in 100% of the 0 Gy, 50% of the 1.2 Gy and 50% of the 3.5 Gy exposed samples. The order of dose estimates (from lowest to highest) corresponding to three dose categories (unexposed, low dose and highest exposure) were correctly reported by all teams and all chosen genes or gene combinations. Furthermore, if teams reported no exposure or an exposure >3.5 Gy, it was always correctly allocated to the unexposed and the highly exposed group, while low exposed (1.2 Gy) samples sometimes could not be discriminated from highly (3.5 Gy) exposed samples. All teams used FDXR and 78.1% of correct dose estimates used FDXR as one of the predictors. Still, the accuracy of reported dose estimates based on FDXR differed considerably among teams with one team's SAD (0.5 Gy) being comparable to the dose accuracy employing a combination of genes. Using the workflow of this reference team, we performed additional experiments after the exercise on residual RNA and cDNA sent by six teams to the reference team. All samples were processed similarly with the intention to improve the accuracy of dose estimates when employing the same workflow. Re-evaluated dose estimates improved for half of the samples and worsened for the others. In conclusion, this inter-laboratory comparison exercise enabled (1) identification of technical problems and corrections in preparations for future events, (2) confirmed the early and high-throughput capabilities of gene expression, (3) emphasized different biodosimetry approaches using either only FDXR or a gene combination, (4) indicated some improvements in dose estimation with FDXR when employing a similar methodology, which requires further research for the final conclusion and (5) underlined the applicability of gene expression for identification of unexposed and highly exposed samples, supporting medical management in radiological or nuclear scenarios.
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| 15. |
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| 16. |
- Debowska, M, et al.
(författare)
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Association between Biomarkers of Mineral and Bone Metabolism and Removal of Calcium and Phosphate in Hemodialysis
- 2020
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Ingår i: Blood purification. - : S. Karger AG. - 1421-9735 .- 0253-5068. ; 49:1-2, s. 71-78
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Tidskriftsartikel (refereegranskat)abstract
- <b><i>Background:</i></b> A significant drop of serum phosphate and calcium removal or loading during hemodialysis induce reactions in mineral and bone remodeling that may inversely affect phosphate and calcium removal during dialysis. <b><i>Objectives:</i></b> We aimed to analyze the interdependencies between biomarkers of mineral and bone metabolism and removal of phosphate and calcium during hemodialysis, as this complex relationship is not fully understood. <b><i>Methods:</i></b> Three subsequent hemodialysis sessions during a 1-week treatment cycle with interdialytic periods of 2–2-3 days were monitored in 25 anuric patients. Calcium and phosphate concentrations were measured in serum before, at 1, 2, and 3 h, at the end, and 45 min after each session and in the outlet dialysate every 30 min. Biomarkers associated with mineral and bone metabolism: parathyroid hormone (PTH 1–34 and PTH 1–84), calcitonin, 25(OH)-vitamin D, fetuin-A, osteopontin, osteocalcin 1–43/49, and intact osteocalcin were assayed once in each patient before the midweek hemodialysis session. <b><i>Results:</i></b> Post-dialytic and intra-dialytic serum phosphate of midweek hemodialysis session and phosphate mass removed within 1 week correlated positively with serum PTH (0.40 < rho <0.46, <i>p</i> value <0.05). Higher concentration of serum PTH was associated with an increased level of osteocalcin. Pre-dialytic, post-dialytic, average for treatment time and average weekly concentrations of ionized calcium in serum correlated positively with serum osteocalcin. Serum osteocalcin and osteopontin levels were associated with the masses of total and ionized calcium, respectively, removed during 3 hemodialysis sessions. <b><i>Conclusions:</i></b> During hemodialysis, phosphate removal was associated with serum PTH, whereas calcium kinetics was influenced by serum osteocalcin and osteopontin. These results demonstrate that active processes involving biomarkers of mineral and bone metabolism are affected by the phosphate and calcium kinetics already within 4 h hemodialysis sessions.
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| 17. |
- Endesfelder, D., et al.
(författare)
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What We Have Learned from RENEB Inter-Laboratory Comparisons Since 2012 With Focus on ILC 2021
- 2023
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Ingår i: Radiation Research. - 0033-7587 .- 1938-5404. ; 199:6, s. 616-627
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Tidskriftsartikel (refereegranskat)abstract
- Inter-laboratory exercises are important tools within the European network for biological dosimetry and physical retrospective dosimetry (RENEB) to validate and improve the performance of member laboratories and to ensure an operational network with high quality standards for dose estimations in case of a large-scale radiological or nuclear event. In addition to the RENEB inter-laboratory comparison 2021, several inter-laboratory comparisons have been performed in the frame of RENEB for a number of assays in recent years. This publication gives an overview of RENEB inter-laboratory comparisons for biological dosimetry assays in the past and a final summary of the challenges and lessons learnt from the RENEB inter-laboratory comparison 2021. In addition, the dose estimates of all RENEB inter-laboratory comparisons since 2013 that have been conducted for the dicentric chromosome assay, the most established and applied assay, are compared and discussed.
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| 18. |
- Waldner, L., et al.
(författare)
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The 2019-2020 EURADOS WG10 and RENEB Field Test of Retrospective Dosimetry Methods in a Small-Scale Incident Involving Ionizing Radiation
- 2021
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Ingår i: Radiation Research. - 0033-7587 .- 1938-5404. ; 195:3, s. 253-264
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Tidskriftsartikel (refereegranskat)abstract
- With the use of ionizing radiation comes the risk of accidents and malevolent misuse. When unplanned exposures occur, there are several methods which can be used to retrospectively reconstruct individual radiation exposures; biological methods include analysis of aberrations and damage of chromosomes and DNA, while physical methods rely on luminescence (TL/OSL) or EPR signals. To ensure the quality and dependability of these methods, they should be evaluated under realistic exposure conditions. In 2019, EURADOS Working Group 10 and RENEB organized a field test with the purpose of evaluating retrospective dosimetry methods as carried out in potential real-life exposure scenarios. A 1.36 TBq 192Ir source was used to irradiate anthropomorphic phantoms in different geometries at doses of several Gy in an outdoor open-air geometry. Materials intended for accident dosimetry (including mobile phones and blood) were placed on the phantoms together with reference dosimeters (LiF, NaCl, glass). The objective was to estimate radiation exposures received by individuals as measured using blood and fortuitous materials, and to evaluate these methods by comparing the estimated doses to reference measurements and Monte Carlo simulations. Herein we describe the overall planning, goals, execution and preliminary outcomes of the 2019 field test. Such field tests are essential for the development of new and existing methods. The outputs from this field test include useful experience in terms of planning and execution of future exercises, with respect to time management, radiation protection, and reference dosimetry to be considered to obtain relevant data for analysis.
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| 19. |
- Wisniewski, K., et al.
(författare)
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Overlapping stimulation of subthalamic nucleus and dentato-rubro-thalamic tract in Parkinson's disease after deep brain stimulation
- 2024
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Ingår i: Acta Neurochirurgica. - : Springer. - 0001-6268 .- 0942-0940. ; 166:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundDeep brain stimulation (DBS) of the subthalamic nucleus (STN) reduces tremor, rigidity, and akinesia. According to the literature, the dentato-rubro-thalamic tract (DRTt) is verified target for DBS in essential tremor; however, its role in the treatment of Parkinson's disease is only vaguely described. The aim of our study was to identify the relationship between symptom alleviation in PD patients and the distance of the DBS electrode electric field (EF) to the DRTt.MethodsA single-center retrospective analysis of patients (N = 30) with idiopathic Parkinson's disease (PD) who underwent DBS between November 2018 and January 2020 was performed. DRTt and STN were visualized using diffusion-weighted imaging (DWI) and tractography protocol of magnetic resonance (MR). The EF was calculated and compared with STN and course of DRTt. Evaluation of patients before and after surgery was performed with use of UPDRS-III scale. The association between distance from EF to DRTt and clinical outcomes was examined. To confirm the anatomical variation between DRTt and STN observed in tractography, white matter dissection was performed with the Klingler technique on ten human brains.ResultsPatients with EF overlapping STN and DRTt benefited from significant motor symptoms improvement. Anatomical findings confirmed the presence of population differences in variability of the DRTt course and were consistent with the DRTt visualized by MR.ConclusionsDRTt proximity to STN, the main target in PD DBS surgery, confirmed by DWI with tractography protocol of MR combined with proper predefined stimulation parameters may improve efficacy of DBS-STN.
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| 20. |
- Wojcik-Gargula, A., et al.
(författare)
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Studies on the behaviour of titanium activation foils during long-term exposure at the JET tokamak
- 2022
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Ingår i: Fusion engineering and design. - : Elsevier BV. - 0920-3796 .- 1873-7196. ; 177, s. 113056-
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Tidskriftsartikel (refereegranskat)abstract
- Titanium activation foils for neutron studies were exposed inside the JET tokamak vessel during the entire 15 months long experimental campaign with deuterium fuelling. Afterwards, it was found that the structure of some foils was only slightly affected, while others were totally or partly disintegrated into dust: flakes and powder. The analyses indicated that defects produced in materials by cutting during the sample preparation eventually lead to the degradation of the titanium crystal structure upon the exposure in JET to neutral particles including hydrogen. In some cases, a passive oxide layer on the foil surface effectively prevented the access of hydrogen, and by this protected the metal against partial or complete transformation into the titanium hydride powder.
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| 21. |
- Bahr, A., et al.
(författare)
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High-temperature oxidation resistance of ternary and quaternary Cr-(Mo)-Si-B2-z coatings-Influence of Mo addition
- 2023
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Ingår i: Surface & Coatings Technology. - : Elsevier. - 0257-8972 .- 1879-3347. ; 468
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Tidskriftsartikel (refereegranskat)abstract
- The Si-based alloying of transition metal diborides is a promising strategy to improve their limited oxidation resistance in high-temperature environments. In this study, we investigate the oxidation resistance of ternary and quaternary Cr-(Mo)-Si-B2-z coatings sputter-deposited from alloyed CrB2/TMSi2 targets (TM = Cr, Mo). The asdeposited Cr-(Mo)-Si-B2-z coatings are stabilized in the single-phased hexagonal AlB2-structure, except the high-Si containing Cr0.26Mo0.11Si0.24B0.39 presenting amorphous character. The Mo-containing Cr-Mo-Si-B2-z films exhibit relatively high hardness compared to their ternary Cr-Si-B2-z counterparts, obtaining up to 26 GPa due to the formation of (Cr,Mo)B-2 solid solutions. The Si-alloying in ternary and quaternary coatings provides oxidation resistance up to 1200 degrees C, owing to the formation of highly protective double-layered scales consisting of SiO2 with a Cr2O3 layer on top, inhibiting oxygen inward diffusion. The quaternary Cr0.31Mo0.07Si0.15B0.47 coating is distinguished by superior oxidation resistance with lower porosity and void formation compared to the ternary Cr0.37Si0.16B0.47. Mo proved to be the key element for the higher stability and enhanced oxidation resistance due to the evolution of the MoSi2 phase at similar to 600 degrees C. This phase formation controls the Si diffusion and mobility within the microstructure, thus reducing the porosity and governing the Si supply to form SiO2 scale. The quaternary Cr0.31Mo0.07Si0.15B0.47 coating maintained an oxidation resistance up to 30 h at 1200 degrees C by forming a 2.5 mu m dense amorphous Si-based oxide scale with a thin Cr2O3 on top.
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| 22. |
- Bahr, A., et al.
(författare)
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Non-reactive HiPIMS deposition of NbCx thin films : Effect of the target power density on structure-mechanical properties
- 2022
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Ingår i: Surface & Coatings Technology. - : Elsevier. - 0257-8972 .- 1879-3347. ; 444
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Tidskriftsartikel (refereegranskat)abstract
- The exceptional mechanical properties of transition metal carbide coatings are known to be governed by the carbon content and its morphological distribution. Here, we verify the influence of the target peak power density on the chemical composition, microstructure, and mechanical properties of NbCx coatings grown by non-reactive high-power impulse magnetron sputtering (HiPIMS). By tuning the pulse parameters, the power density can be increased from 0.11 to 1.48 kW/cm2 leading to a decrease in the C/Nb ratio from 1.52 to 0.99 within the films - proven by combined elastic backscattering and time-of-flight elastic recoil detection analysis. This decrease in the C/Nb ratio is accompanied by microstructural changes from nanocomposite morphologies with an average grain size of 6.6 +/- 2.5 nm at 0.13 kW/cm2 into more columnar structures with an average column width of 65.2 +/- 18.7 nm at 1.48 kW/cm2. Independent from the C/Nb ratio, all films exhibit a single face-centered cubic structure. The mechanical properties correlate with the enhanced growth behavior dominated by ions at higher peak power densities and the varied C/Nb ratios. A maximum in hardness and fracture toughness of H = 38.7 +/- 3.6 GPa and KIc = 2.78 +/- 0.13 MPa center dot m1/2 (at 3.2 GPa residual compressive stress), is obtained for the nearly stoichiometric NbC coating exhibiting C/Nb ratio of 1.06.
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| 23. |
- Cowan-Turner, Daniel, et al.
(författare)
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Sequencing complex plants on a budget: The development of Kalanchoë blossfeldiana as a C3, CAM comparative tool
- 2024
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Ingår i: Plants, People, Planet. - : WILEY. - 2572-2611.
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Tidskriftsartikel (refereegranskat)abstract
- Despite the increasing number of well-studied plant species with well-annotated genomes across plant life, there are few densely sampled genera with more than a couple of genome sequences representing the diversity of whole genera. Here, we develop an economic approach to full-genome sequencing that could be used to sequence many species within a genus. We made use of the Nanopore rapid sequencing kit to assist in plant genome assembly, dramatically reducing the cost. Here we applied this method to cost-effectively develop genomic resources for Kalancho & euml; blossfeldiana, a commercially important ornamental, in which Crassulacean Acid Metabolism (CAM), a water-conserving mode of photosynthesis can be induced. We present a physiological and biochemical characterisation of Kalanchoe blossfeldiana with its nuclear and chloroplastic genome and a comparative C3, CAM dusk transcriptome. We apply this approach to a complex tetraploid genome, making use of a relative species for chromosomal scaffolding to reduce assembly ploidy, we provide a resource for future gene expression studies. We highlight its limitations, e.g. the need for deeper sequencing to accurately resolve genome structure and haplotypes without using a relative species for scaffolding. T he study demonstrates the merits of K. blossfeldiana as a comparative system for studying C3 and CAM within a plant and has identified substantial changes in the dusk transcriptome between young C3 and mature CAM K. blossfeldiana leaves in response to age-induced CAM, and shows that in the absence of abiotic stress, CAM induction still involves the engagement of drought and abscisic acid (ABA) response pathways.
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| 24. |
- Dey, J., et al.
(författare)
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Helical magnetic structure of epitaxial films of nanolaminated Mn2GaC MAX phase
- 2023
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 108:5
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Tidskriftsartikel (refereegranskat)abstract
- Nanolaminated Mn2GaC epitaxial films crystallizing in the hexagonal structure belong to the family of MAX phase compounds and display complex magnetic interactions. While the critical temperature of the order-disorder transition is 507 K, at around 214 K this compound undergoes a first-order phase transition with the magnetic structure below the transition point not being fully resolved. Previous studies indicated a noncollinear spin arrangement, but a specific magnetic structure could not be defined. In this work we present the results of 69Ga, 71Ga, and 55Mn NMR experiments performed at 4.2 K in an external in-plane magnetic field up to 1 T. The in-depth analysis of the experimental results shows a helical magnetic structure consisting of the ferromagnetically coupled Mn-C-Mn slabs that are twisted across the Ga layer by 167.2 degrees with respect to the next Mn-C-Mn slab. As a result, the magnetic structure presents a spiral propagating along the out-of-plane direction (hexagonal c axis) with a pitch of around 14 lattice constants.
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| 25. |
- Dey, J., et al.
(författare)
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Non-collinear magnetic structure of the MAX phase Mn2GaC epitaxial films inferred from zero-field NMR study (CE-5:L05)
- 2023
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Ingår i: Ceramics International. - : ELSEVIER SCI LTD. - 0272-8842 .- 1873-3956. ; 49:14, s. 24235-24238
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Tidskriftsartikel (refereegranskat)abstract
- Zero-field NMR investigations on the 69Ga, 71Ga, and 55Mn nuclei have been performed at 4.2 K on a 100 nm thick epitaxial Mn2GaC(0001) MAX phase film grown on a MgO(111) substrate. This nano-laminated structure consists of ferromagnetic Mn-C-Mn stacks interleaved with monolayers of gallium. A resolved quadrupolar structure of the observed gallium resonances is a fingerprint of a well-defined crystal field confirming high crystal quality. The nuclei of non-magnetic gallium atoms are shown to experience the transferred hyperfine magnetic field of 15.75 T (& PLUSMN;0.05 T), which is due to polarization of their 4s electron shell by the magnetic moments of manganese neighbors, evidencing the presence of an uncompensated ferromagnetic moment within the manganese sublattice. The average magnetic moment of manganese was found to be around 2 & mu;B, strongly contrasting with the reported remnant magnetization of only 0.3 & mu;B. Moreover, the 55Mn NMR spectrum in-dicates the presence of magnetically non-equivalent manganese sites within this structure. The observed features of the 69,71Ga and 55Mn NMR spectra cannot be reconciled with any of the hitherto proposed collinear ar-rangements of manganese moments and suggest their non-collinear arrangement across a gallium layer. Nevertheless a more advanced study is required to elucidate the detailed nature of magnetic structure in this material.
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| 26. |
- Gisslander, Karl, et al.
(författare)
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Data quality and patient characteristics in European ANCA-associated vasculitis registries : data retrieval by federated querying
- 2023
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Ingår i: Annals of the Rheumatic Diseases. - 0003-4967. ; 83:1, s. 112-120
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Tidskriftsartikel (refereegranskat)abstract
- Objectives This study aims to describe the data structure and harmonisation process, explore data quality and define characteristics, treatment, and outcomes of patients across six federated antineutrophil cytoplasmic antibody-associated vasculitis (AAV) registries. Methods Through creation of the vasculitis-specific Findable, Accessible, Interoperable, Reusable, VASCulitis ontology, we harmonised the registries and enabled semantic interoperability. We assessed data quality across the domains of uniqueness, consistency, completeness and correctness. Aggregated data were retrieved using the semantic query language SPARQL Protocol and Resource Description Framework Query Language (SPARQL) and outcome rates were assessed through random effects meta-analysis. Results A total of 5282 cases of AAV were identified. Uniqueness and data-type consistency were 100% across all assessed variables. Completeness and correctness varied from 49%-100% to 60%-100%, respectively. There were 2754 (52.1%) cases classified as granulomatosis with polyangiitis (GPA), 1580 (29.9%) as microscopic polyangiitis and 937 (17.7%) as eosinophilic GPA. The pattern of organ involvement included: lung in 3281 (65.1%), ear-nose-throat in 2860 (56.7%) and kidney in 2534 (50.2%). Intravenous cyclophosphamide was used as remission induction therapy in 982 (50.7%), rituximab in 505 (17.7%) and pulsed intravenous glucocorticoid use was highly variable (11%-91%). Overall mortality and incidence rates of end-stage kidney disease were 28.8 (95% CI 19.7 to 42.2) and 24.8 (95% CI 19.7 to 31.1) per 1000 patient-years, respectively. Conclusions In the largest reported AAV cohort-study, we federated patient registries using semantic web technologies and highlighted concerns about data quality. The comparison of patient characteristics, treatment and outcomes was hampered by heterogeneous recruitment settings.
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| 27. |
- Glechner, T., et al.
(författare)
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Influence of the non-metal species on the oxidation kinetics of Hf, HfN, HfC, and HfB2 coatings
- 2021
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Ingår i: Materials & design. - : Elsevier. - 0264-1275 .- 1873-4197. ; 211
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Tidskriftsartikel (refereegranskat)abstract
- The influence of the non-metal species on the oxidation resistance of transition metal ceramic based thin films is still unclear. For this purpose, we thoroughly investigated the oxide scale formation of a metal (Hf), carbide (HFC0.96), nitride (HfB1.5), and boride (HfB2.3) coating grown by physical vapor deposition. The non-metal species decisively affect the onset temperature of oxidation, ranging between 550 degrees C for HfC0.96 to 840 degrees C for HfN1.5. HfB2.3 and HfN1.5 obtain the slowest oxide scale kinetic following a parabolic law with k(p) values of 4.97.10(-10) and 5.66.10(-11) kg(2) m(-4) s(-1) at 840 degrees C, respectively. A characteristic feature for the oxide scale on Hf coatings, is a columnar morphology and a substantial oxygen inward diffusion. HfC0.96 reveals an ineffective oxycarbide based scale, whereas HfN(1.5 )features a scale with globular HfO2 grains. HfB(2.3 )exhibits a layered scale with a porous boron rich region on top, followed by a highly dense and crystalline HfO2 beneath. Furthermore, HfB(2.3 )presents a hardness of 47.7 +/- 2.7 GPa next to an exceptional low inward diffusion of oxygen during oxidation. This study showcases the strong influence of the non-metallic bonding partner despite the same metallic basis, as well as the huge potential for HfB2 based coatings also for oxidative environments.
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| 28. |
- Hudak, O. E., et al.
(författare)
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Improved corrosion resistance of cathodic arc evaporated Al0.7Cr0.3_xVxN coatings in NaCl-rich media
- 2023
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Ingår i: Corrosion Science. - : Elsevier BV. - 0010-938X .- 1879-0496. ; 221
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Tidskriftsartikel (refereegranskat)abstract
- The corrosion resistance of cathodic arc evaporated Al0.7Cr0.3_xVxN coatings with a vanadium content up to 22.3 at% has been electrochemically tested in a 0.1 M NaCl-solution. Significant improvement in the open porosity and corrosion rate was observed for coatings with higher V-contents, due to a denser and more refined coating morphology. Further reduction in the open porosity rate was achieved through an annealing step in air at 700 degrees C. Here, the formation of an AlVO4 top-oxide and underlying oxygen-rich V-depletion zone provides additional sealing of the coating surface, whilst reducing the corrosion current density to a final 1.59 x 10_9 A/cm2.
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| 29. |
- Kirnbauer, A., et al.
(författare)
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Mechanical properties and thermal stability of reactively sputtered multi-principal-metal Hf-Ta-Ti-V-Zr nitrides
- 2020
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Ingår i: Surface & Coatings Technology. - : ELSEVIER SCIENCE SA. - 0257-8972 .- 1879-3347. ; 389
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Tidskriftsartikel (refereegranskat)abstract
- Crystalline (Hf,Ta,Ti,V,Zr)N nitride thin films, with a high-entropy metal-sublattice, were synthesized at 440 degrees C by reactive magnetron sputtering using an equimolar Hf-Ta-Ti-V-Zr-compound target. The coatings are single-phase fcc structured mono-nitrides for N-2/(Ar + N-2) flow-rate-ratios (f(N2)) between 30 and 45%. For higher f(N2) a small fraction of a second phase (next to the fcc matrix) can be detected by X-ray diffraction (XRD) and selected area electron diffraction (SAED). All coatings studied (prepared with f(N2) between 30 and 60%) show similar chemical compositions and hardness (H) values between 30.0 and 34.0 GPa with indentation moduli of similar to 460 GPa. Atom probe tomography (APT) indicates a homogenous distribution of all elements within our fcc-(Hf,Ta,Ti,V,Zr)N even after vacuum-annealing at 1300 degrees C. While H decreased from 32.5 to 28.1 GPa by this annealing treatment, the coating is still single-phase fcc structured with a defect density (expressed by XRD and SAED features, transmission electron microscopy contrast, and grain sizes) comparable to the as-deposited state. Only after vacuum-annealing at 1500 degrees C, XRD and APT reveal the formation of hexagonal structured (Ta,V)(2)N. The onset of nitrogen-loss - detected by thermogravimetric analysis - is similar to 1350 degrees C. Based on our results we can conclude that the sluggish diffusion within our fcc-(Hf,Ta,Ti,V,Zr)N warrants the single-phase fcc structure up to 1300 degrees C, although ab initio based calculations would suggest the lower-entropy products [fcc-(Hf,Zr)N, fcc-(Ta,V)N, and fcc-TiN] and [fcc-(Hf,Zr)N and fcc-(Ta,Ti,V)N] to be energetically more stable up to 1302 K.
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| 30. |
- McDevitt, Allan D., et al.
(författare)
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Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe
- 2022
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:3, s. 993-1006
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Tidskriftsartikel (refereegranskat)abstract
- Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.
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| 31. |
- Mendoza-Revilla, Javier, et al.
(författare)
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Disentangling Signatures of Selection Before and After European Colonization in Latin Americans
- 2022
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:4
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Tidskriftsartikel (refereegranskat)abstract
- Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.
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| 32. |
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| 33. |
- Wójcik, Natalia A., et al.
(författare)
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Mechanism of hopping conduction in Be-Fe-Al-Te-O semiconducting glasses and glass-ceramics
- 2022
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Ingår i: Journal of Materials Science. - : Springer Nature. - 0022-2461 .- 1573-4803. ; 57, s. 1633-1647
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Tidskriftsartikel (refereegranskat)abstract
- Electrical properties of beryllium-alumino-tellurite glasses and glass-ceramics doped with iron ions were studied using impedance spectroscopy. The conductivity was measured over a wide frequency range from 10 mHz to 1 MHz and the temperature range from 213 to 473 K. The D.C. conductivity values showed a correlation with the Fe-ion concentration and ratio of iron ions on different valence states in the samples. On the basis of Jonscher universal dielectric response the temperature dependence of conductivity parameters were determined and compared to theoretical models collected by Elliott. In glasses, the conduction process was found to be due to the overlap polaron tunneling while in glass-ceramics the quantum mechanical tunneling between semiconducting crystallites of iron oxides is proposed. The D.C. conductivity was found not to follow Arrhenius relation. The Schnakenberg model was used to analyze the conductivity behavior and the polaron hopping energy and disorder energy were estimated. Additionally, the correlation between alumina dissolution and basicity of the melts was observed.
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