| 1. |
- Abdesselam, A., et al.
(författare)
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The ATLAS semiconductor tracker end-cap module
- 2007
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 575:3, s. 353-389
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Tidskriftsartikel (refereegranskat)abstract
- The challenges for the tracking detector systems at the LHC are unprecedented in terms of the number of channels, the required read-out speed and the expected radiation levels. The ATLAS Semiconductor Tracker. (SCT) end-caps have a total of about 3 million electronics channels each reading out every 25 ns into its own on-chip 3.3 mu s buffer. The highest anticipated dose after 10 years operation is 1.4x10(14) cm(-2) in units of 1 MeV neutron equivalent (assuming the damage factors scale with the non-ionising energy loss). The forward tracker has 1976 double-sided modules, mostly of area similar to 70 cm(2), each having 2 x 768 strips read out by six ASICs per side. The requirement to achieve an average perpendicular radiation length of 1.5% X-0, while coping with up to 7 W dissipation per module (after irradiation), leads to stringent constraints on the thermal design. The additional requirement of 1500e(-) equivalent noise charge (ENC) rising to only 1800e(-) ENC after irradiation, provides stringent design constraints on both the high-density Cu/Polyimide flex read-out circuit and the ABCD3TA read-out ASICs. Finally, the accuracy of module assembly must not compromise the 16 mu m (r phi) resolution perpendicular to the strip directions or 580 mu m radial resolution coming from the 40 mrad front-back stereo angle. A total of 2210 modules were built to the tight tolerances and specifications required for the SCT. This was 234 more than the 1976 required and represents a yield of 93%. The component flow was at times tight, but the module production rate of 40-50 per week was maintained despite this. The distributed production was not found to be a major logistical problem and it allowed additional flexibility to take advantage of where the effort was available, including any spare capacity, for building the end-cap modules. The collaboration that produced the ATLAS SCT end-cap modules kept in close contact at all times so that the effects of shortages or stoppages at different sites could be rapidly resolved.
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| 2. |
- Abdesselam, A., et al.
(författare)
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The barrel modules of the ATLAS semiconductor tracker
- 2006
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 568:2, s. 642-671
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes the silicon microstrip modules in the barrel section of the SemiConductor Tracker (SCT) of the ATLAS experiment at the CERN Large Hadron Collider (LHC). The module requirements, components and assembly techniques are given, as well as first results of the module performance on the fully assembled barrels that make up the detector being installed in the ATLAS experiment.
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| 3. |
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| 4. |
- Wilson, J. A., et al.
(författare)
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The optical links of the ATLAS SemiConductor tracker
- 2007
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 2, s. 1-28
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Tidskriftsartikel (refereegranskat)abstract
- Optical links are used for the readout of the 4088 silicon microstrip modules that make up the SemiConductor Tracker of the ATLAS experiment at the CERN Large Hadron Collider (LHC). The optical link requirements are reviewed, with particular emphasis on the very demanding environment at the LHC. The on-detector components have to operate in high radiation levels for 10 years, with no maintenance, and there are very strict requirements on power consumption, material and space. A novel concept for the packaging of the on-detector optoelectronics has been developed to meet these requirements. The system architecture, including its redundancy features, is explained and the critical on-detector components are described. The results of the extensive Quality Assurance performed during all steps of the assembly are discussed.
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| 5. |
- Saito, T. R., et al.
(författare)
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Studies of three-and four-body hypernuclei with heavy-ion beams, nuclear emulsions and machine learning
- 2023
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Ingår i: Journal of Physics, Conference Series. - : Institute of Physics (IOP). - 1742-6588 .- 1742-6596. ; 2586
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Tidskriftsartikel (refereegranskat)abstract
- Interests on few-body hypernuclei have been increased by recent results of experiments employing relativistic heavy ion beams. Some of the experiments have revealed that the lifetime of the lightest hypernucleus, hypertriton, is significantly shorter than 263 ps which is expected by considering the hypertriton to be a weakly-bound system. The STAR collaboration has also measured the hypertriton binding energy, and the deduced value is contradicting to its formerly known small binding energy. These measurements have indicated that the fundamental physics quantities of the hypertriton such as its lifetime and binding energy have not been understood, therefore, they have to be measured very precisely. Furthermore, an unprecedented Lambda nn bound state observed by the HypHI collaboration has to be studied in order to draw a conclusion whether or not such a bound state exists. These three-body hypernuclear states are studied by the heavy-ion beam data in the WASA-FRS experiment and by analysing J-PARC E07 nuclear emulsion data with machine learning.
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| 6. |
- Sekiya, R., et al.
(författare)
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Search for η'-mesic nuclei in 12C(p, dp) reaction with the WASA detector at GSI-FRS
- 2024
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Ingår i: Nuovo cimento della societa italiana de fisica. C, Geophysics and space physics. - : Società Italiana di Fisica. - 1124-1896 .- 1826-9885. ; 47:4
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Tidskriftsartikel (refereegranskat)abstract
- We conducted an experimental search for η′-mesic nuclei, bound systems of an η′ meson and a nucleus, in 12C(p, dp) reactions. We measured the missing mass in the (p, d) reaction to obtain the mass spectrum of the reaction product near the η′ emission threshold. Forward-emitted deuterons were momentum-analyzed in the FRS of GSI. We installed a nearly 4π detector WASA near the 12C target to effectively select formation and decay of the η′-mesic nuclei. We are presently finalizing the analysis.
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| 7. |
- Jakosky, B. M., et al.
(författare)
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The Mars Atmosphere and Volatile Evolution (MAVEN) Mission
- 2015
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Ingår i: Space Science Reviews. - : Springer Science and Business Media LLC. - 0038-6308 .- 1572-9672. ; 195:1-4, s. 3-48
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Forskningsöversikt (refereegranskat)abstract
- The MAVEN spacecraft launched in November 2013, arrived at Mars in September 2014, and completed commissioning and began its one-Earth-year primary science mission in November 2014. The orbiter's science objectives are to explore the interactions of the Sun and the solar wind with the Mars magnetosphere and upper atmosphere, to determine the structure of the upper atmosphere and ionosphere and the processes controlling it, to determine the escape rates from the upper atmosphere to space at the present epoch, and to measure properties that allow us to extrapolate these escape rates into the past to determine the total loss of atmospheric gas to space through time. These results will allow us to determine the importance of loss to space in changing the Mars climate and atmosphere through time, thereby providing important boundary conditions on the history of the habitability of Mars. The MAVEN spacecraft contains eight science instruments (with nine sensors) that measure the energy and particle input from the Sun into the Mars upper atmosphere, the response of the upper atmosphere to that input, and the resulting escape of gas to space. In addition, it contains an Electra relay that will allow it to relay commands and data between spacecraft on the surface and Earth.
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| 8. |
- Saito, T. R., et al.
(författare)
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The WASA-FRS project at GSI and its perspective
- 2023
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Ingår i: Nuclear Instruments and Methods in Physics Research Section B. - : Elsevier. - 0168-583X .- 1872-9584. ; 542, s. 22-25
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Tidskriftsartikel (refereegranskat)abstract
- A novel technique to study bound states of exotic hadrons in subatomic nuclei, such as hypernuclei and mesic nuclei, has been developed by employing the Fragment Separator FRS and the WASA central detector at GSI. Two experiments, S447 for studying light hypernuclei, especially hypertriton and a Ann bound state, and S490 for searching for ri' mesic-nuclei, were recently performed. Data analyses are currently in progress, and light charged particles such as protons and x & PLUSMN; are clearly observed and identified in the both experiments. For S447, light nuclear fragments that can also be residual nuclei from decays of hypernuclei of interests have been analysed by the FRS, and a momentum resolution, Ap/p, of 5 x 10-4 has been achieved. Further data analyses are to be completed. The WASA-FRS project will be continued and extended with the FRS at FAIR Phase 0, and upgrading of the WASA magnet and detectors is currently in progress. Furthermore, construction of a larger detector system with the Super-FRS at FAIR Phase 1 is also under consideration.
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| 9. |
- Tanaka, Y. K., et al.
(författare)
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WASA-FRS EXPERIMENTS IN FAIR PHASE-0 AT GSI
- 2023
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Ingår i: ACTA PHYSICA POLONICA B PROCEEDINGS SUPPLEMENT. - : Jagiellonian University.
-
Konferensbidrag (refereegranskat)abstract
- We have developed a new and unique experimental setup integrating the central part of the Wide Angle Shower Apparatus (WASA) into the Fragment Separator (FRS) at GSI. This combination opens up possibilities of new experiments with high-resolution spectroscopy at forward 0 and measurements of light decay particles with nearly full solid-angle acceptance in coincidence. The first series of the WASA-FRS experiments have been successfully carried out in 2022. The developed experimental setup and two physics experiments performed in 2022 including the status of the preliminary data analysis are introduced.
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| 10. |
- Brusaferri, L., et al.
(författare)
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The pandemic brain: Neuroinflammation in non-infected individuals during the COVID-19 pandemic
- 2022
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Ingår i: Brain, Behavior, and Immunity. - : Elsevier BV. - 0889-1591. ; 102, s. 89-97
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Tidskriftsartikel (refereegranskat)abstract
- While COVID-19 research has seen an explosion in the literature, the impact of pandemic-related societal and lifestyle disruptions on brain health among the uninfected remains underexplored. However, a global increase in the prevalence of fatigue, brain fog, depression and other “sickness behavior”-like symptoms implicates a possible dysregulation in neuroimmune mechanisms even among those never infected by the virus. We compared fifty-seven ‘Pre-Pandemic’ and fifteen ‘Pandemic’ datasets from individuals originally enrolled as control subjects for various completed, or ongoing, research studies available in our records, with a confirmed negative test for SARS-CoV-2 antibodies. We used a combination of multimodal molecular brain imaging (simultaneous positron emission tomography / magnetic resonance spectroscopy), behavioral measurements, imaging transcriptomics and serum testing to uncover links between pandemic-related stressors and neuroinflammation. Healthy individuals examined after the enforcement of 2020 lockdown/stay-at-home measures demonstrated elevated brain levels of two independent neuroinflammatory markers (the 18 kDa translocator protein, TSPO, and myoinositol) compared to pre-lockdown subjects. The serum levels of two inflammatory markers (interleukin-16 and monocyte chemoattractant protein-1) were also elevated, although these effects did not reach statistical significance after correcting for multiple comparisons. Subjects endorsing higher symptom burden showed higher TSPO signal in the hippocampus (mood alteration, mental fatigue), intraparietal sulcus and precuneus (physical fatigue), compared to those reporting little/no symptoms. Post-lockdown TSPO signal changes were spatially aligned with the constitutive expression of several genes involved in immune/neuroimmune functions. This work implicates neuroimmune activation as a possible mechanism underlying the non-virally-mediated symptoms experienced by many during the COVID-19 pandemic. Future studies will be needed to corroborate and further interpret these preliminary findings. © 2022 Elsevier Inc.
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| 11. |
- Bates, R. L., et al.
(författare)
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The ATLAS SCT grounding and shielding concept and implementation
- 2012
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 7, s. P03005-
-
Tidskriftsartikel (refereegranskat)abstract
- This paper describes the design and implementation of the grounding and shielding system for the ATLAS SemiConductor Tracker (SCT). The mitigation of electromagnetic interference and noise pickup through power lines is the critical design goal as they have the potential to jeopardize the electrical performance. We accomplish this by adhering to the ATLAS grounding rules, by avoiding ground loops and isolating the different subdetectors. Noise sources are identified and design rules to protect the SCT against them are described. A rigorous implementation of the design was crucial to achieve the required performance. This paper highlights the location, connection and assembly of the different components that affect the grounding and shielding system: cables, filters, cooling pipes, shielding enclosure, power supplies and others. Special care is taken with the electrical properties of materials and joints. The monitoring of the grounding system during the installation period is also discussed. Finally, after connecting more than four thousand SCT modules to all of their services, electrical, mechanical and thermal within the wider ATLAS experimental environment, dedicated tests show that noise pickup is minimised.
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| 12. |
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| 13. |
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| 14. |
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| 15. |
- Siepielski, Adam M., et al.
(författare)
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Precipitation drives global variation in natural selection
- 2017
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 355:6328, s. 959-962
-
Tidskriftsartikel (refereegranskat)abstract
- Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation-natural selection-are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By showing that selection was influenced by climate variation, our results indicate that climate change may cause widespread alterations in selection regimes, potentially shifting evolutionary trajectories at a global scale.
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| 16. |
- Siepielski, Adam M, et al.
(författare)
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Response to Comment on "Precipitation drives global variation in natural selection"
- 2018
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 359:6374
-
Tidskriftsartikel (refereegranskat)abstract
- The comment by Myers-Smith and Myers focuses on three main points: (i) the lack of a mechanistic explanation for climate-selection relationships, (ii) the appropriateness of the climate data used in our analysis, and (iii) our focus on estimating climate-selection relationships across (rather than within) taxonomic groups. We address these critiques in our response.
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| 17. |
- Bonnet, Timothee, et al.
(författare)
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Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 376:6596, s. 1012-1016
-
Tidskriftsartikel (refereegranskat)abstract
- The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.
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| 18. |
- Caruso, Christina M., et al.
(författare)
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What Are the Environmental Determinants of Phenotypic Selection? : A Meta-analysis of Experimental Studies
- 2017
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 190:3, s. 363-376
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Tidskriftsartikel (refereegranskat)abstract
- Although many selection estimates have been published, the environmental factors that cause selection to vary in space and time have rarely been identified. One way to identify these factors is by experimentally manipulating the environment and measuring selection in each treatment. We compiled and analyzed selection estimates from experimental studies. First, we tested whether the effect of manipulating the environment on selection gradients depends on taxon, trait type, or fitness component. We found that the effect of manipulating the environment was larger when selection was measured on life-history traits or via survival. Second, we tested two predictions about the environmental factors that cause variation in selection. We found support for the prediction that variation in selection is more likely to be caused by environmental factors that have a large effect on mean fitness but not for the prediction that variation is more likely to be caused by biotic factors. Third, we compared selection gradients from experimental and observational studies. We found that selection varied more among treatments in experimental studies than among spatial and temporal replicates in observational studies, suggesting that experimental studies can detect relationships between environmental factors and selection that would not be apparent in observational studies.
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| 19. |
- Lawler, M., et al.
(författare)
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The European Code of Cancer Practice
- 2021
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Ingår i: Journal of Cancer Policy. - : Elsevier BV. - 2213-5383. ; 28
-
Tidskriftsartikel (refereegranskat)abstract
- There are considerable disparities between the quality of cancer care and clinical outcomes for cancer patients in different European countries, regions, hospitals and communities. These have persisted despite the introduction of many European and National Cancer Plans, an extensive portfolio of clinical guidelines and the existence of evidence based guidelines for the good practice in planning cancer healthcare systems. We describe the European Code of Cancer Practice which is a citizen and patient-centred accessible widely disseminated statement of the core requirements for good clinical cancer practice. The Code sets out 10 key overarching Rights of what a patient should expect from their healthcare system each supported by a plain language explanation. The Rights highlight the importance of equal access to affordable and optimal cancer care, good quality information about an individual patient's disease and treatment and about the quality and outcomes of the cancer service they will use. Specialised multidisciplinary cancer care teams, shared decision-making, research and innovation, a focus on quality of life, the integration of supportive and palliative care within oncology are all emphasised. There is a need for a systematic approach to supporting cancer survivors with a survivorship care plan including their rehabilitation, reintegration into society and return to work where appropriate without discrimination. The Code has been co-produced by a team of cancer patients, patient advocates and cancer professionals to bridge the gap between clinical guidelines, healthcare policies and patients' everyday experience. It is robustly evidence-based and supported by a comprehensive review of the medical literature and evidence for good clinical practice. The Code is strongly endorsed by Europe's professional and patient cancer organisations and the European Commission.
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| 20. |
- Buker, P., et al.
(författare)
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DO3SE modelling of soil moisture to determine ozone flux to forest trees
- 2012
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 12:12, s. 5537-5562
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Tidskriftsartikel (refereegranskat)abstract
- The DO3SE (Deposition of O-3 for Stomatal Exchange) model is an established tool for estimating ozone (O-3) deposition, stomatal flux and impacts to a variety of vegetation types across Europe. It has been embedded within the EMEP (European Monitoring and Evaluation Programme) photochemical model to provide a policy tool capable of relating the flux-based risk of vegetation damage to O-3 precursor emission scenarios for use in policy formulation. A key limitation of regional flux-based risk assessments has been the assumption that soil water deficits are not limiting O-3 flux due to the unavailability of evaluated methods for modelling soil water deficits and their influence on stomatal conductance (g(sto)), and subsequent O-3 flux. This paper describes the development and evaluation of a method to estimate soil moisture status and its influence on g(sto) for a variety of forest tree species. This DO3SE soil moisture module uses the Penman-Monteith energy balance method to drive water cycling through the soil-plant-atmosphere system and empirical data describing g(sto) relationships with pre-dawn leaf water status to estimate the biological control of transpiration. We trial four different methods to estimate this biological control of the transpiration stream, which vary from simple methods that relate soil water content or potential directly to g(sto), to more complex methods that incorporate hydraulic resistance and plant capacitance that control water flow through the plant system. These methods are evaluated against field data describing a variety of soil water variables, g(sto) and transpiration data for Norway spruce (Picea abies), Scots pine (Pinus sylvestris), birch (Betula pendula), aspen (Populus tremuloides), beech (Fagus sylvatica) and holm oak (Quercus ilex) collected from ten sites across Europe and North America. Modelled estimates of these variables show consistency with observed data when applying the simple empirical methods, with the timing and magnitude of soil drying events being captured well across all sites and reductions in transpiration with the onset of drought being predicted with reasonable accuracy. The more complex methods, which incorporate hydraulic resistance and plant capacitance, perform less well, with predicted drying cycles consistently underestimating the rate and magnitude of water loss from the soil. A sensitivity analysis showed that model performance was strongly dependent upon the local parameterisation of key model drivers such as the maximum g(sto), soil texture, root depth and leaf area index. The results suggest that the simple modelling methods that relate g(sto) directly to soil water content and potential provide adequate estimates of soil moisture and influence on g(sto) such that they are suitable to be used to assess the potential risk posed by O-3 to forest trees across Europe.
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| 21. |
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| 22. |
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| 23. |
- Azzoni, Emanuele, et al.
(författare)
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The onset of circulation triggers a metabolic switch required for endothelial to hematopoietic transition
- 2021
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 37:11
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Tidskriftsartikel (refereegranskat)abstract
- Hematopoietic stem cells (HSCs) emerge during development from the vascular wall of the main embryonic arteries. The onset of circulation triggers several processes that provide critical external factors for HSC generation. Nevertheless, it is not fully understood how and when the onset of circulation affects HSC emergence. Here we show that in Ncx1−/− mouse embryos devoid of circulation the HSC lineage develops until the phenotypic pro-HSC stage. However, these cells reside in an abnormal microenvironment, fail to activate the hematopoietic program downstream of Runx1, and are functionally impaired. Single-cell transcriptomics shows that during the endothelial-to-hematopoietic transition, Ncx1−/− cells fail to undergo a glycolysis to oxidative phosphorylation metabolic switch present in wild-type cells. Interestingly, experimental activation of glycolysis results in decreased intraembryonic hematopoiesis. Our results suggest that the onset of circulation triggers metabolic changes that allow HSC generation to proceed.
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| 24. |
- Charlton, D. G., et al.
(författare)
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System tests of radiation hard optical links for the ATLAS semiconductor tracker
- 2000
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - 0168-9002 .- 1872-9576. ; 443:03-feb, s. 430-446
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Tidskriftsartikel (refereegranskat)abstract
- A prototype optical data and Timing Trigger and Control transmission system based on LEDs and PIN-diodes has been constructed. The system would be suitable in terms of radiation hardness and radiation length for use in the ATLAS SemiConductor Tracker. Bit error rate measurements were performed for the data links and for the links distributing the Timing, Trigger and Control data from the counting room to the front-end modules. The effects of cross-talk between the emitters and receivers were investigated. The advantages of using Vertical Cavity Surface Emitting Lasers (VCSELs) instead of LEDs are discussed.
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| 25. |
- Collins, Catherine M., et al.
(författare)
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Molecular cloning and expression analysis of two distinct beta-glucosidase genes, bg1 and aven1, with very different biological roles from the thermophilic, saprophytic fungus Talaromyces emersonii
- 2007
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Ingår i: Mycological Research. - : Elsevier BV. - 0953-7562 .- 1469-8102. ; 111, s. 840-849
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Tidskriftsartikel (refereegranskat)abstract
- Recent sequencing of a number of fungal genomes has revealed the presence of multiple putative beta-glucosidases. Here, we report the cloning of two beta-glucosidase genes (bg1 and aven1), which have very different biological functions and represent two of a number of beta-glucosidases from Talaromyces emersonii. The bg1 gene, encoding a putative intracellular beta-glucosidase, shows significant similarity to other fungal glucosidases from glycosyl hydrolase family 1, known to be involved in cellulose degradation. Solka floc, methyl-xylose, gentiobiose, beech wood xylan, and lactose induced expression of bg1, whereas glucose repressed expression. A second beta-glucosidase gene isolated from T. emersonii, aueni, encodes a putative avenacinase, an enzyme that deglucosylates the anti-fungal saponin, avenacin, rendering it less toxic to the fungus. This gene displays high homology with other fungal saponin-hydrolysing enzymes and beta-glucosidases within GH3. A putative secretory signal peptide of 21 amino acids was identified at the N-terminus of the predicted aven1 protein sequence suggesting that this enzyme is extracellular. Furthermore, T. emersonii cultivated on oat plant biomass was shown to deglucosylate avenacin. The presence of the avenacinase transcript was confirmed by RT-PCR on RNA extracted from mycelia grown in the presence of avenacin. The expression pattern of aven1 on various carbon sources was distinctly different from that of bg1. Only methyl-xylose and gentiobiose induced transcription of aven1. Gentiobiose induces synthesis of a number of cellulase genes by T. emersonii and it may be a possible candidate for the natural cellulase inducer observed in Penicillium purpurogenum. This work represents the first report of an avenacinase gene from a thermophilic, saprophytic fungal source, and suggests that this gene is not exclusive to plant pathogens.
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| 26. |
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| 27. |
- de Villemereuil, Pierre, et al.
(författare)
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Fluctuating optimum and temporally variable selection on breeding date in birds and mammals
- 2020
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 117:50, s. 31969-31978
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Tidskriftsartikel (refereegranskat)abstract
- Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and auto-correlation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.
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| 28. |
- Doughty, Tyler, 1987, et al.
(författare)
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Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology.
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| 29. |
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| 30. |
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| 31. |
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| 32. |
- Matsson, Pär, et al.
(författare)
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Discovery of regulatory elements in human ATP-binding cassette transporters through expression quantitative trait mapping
- 2012
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Ingår i: The Pharmacogenomics Journal. - : Springer Science and Business Media LLC. - 1470-269X .- 1473-1150. ; 12, s. 214-226
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Tidskriftsartikel (refereegranskat)abstract
- ATP-binding cassette (ABC) membrane transporters determine the disposition of many drugs, metabolites and endogenous compounds. Coding region variation in ABC transporters is the cause of many genetic disorders, but much less is known about the genetic basis and functional outcome of ABC transporter expression level variation. We used genotype and mRNA transcript level data from human lymphoblastoid cell lines to assess population and gender differences in ABC transporter expression, and to guide the discovery of genomic regions involved in transcriptional regulation. Nineteen of 49 ABC genes were differentially expressed between individuals of African, Asian and European descent, suggesting an important influence of race on expression level of ABC transporters. Twenty-four significant associations were found between transporter transcript levels and proximally located genetic variants. Several of the associations were experimentally validated in reporter assays. Through influencing ABC expression levels, these single-nucleotide polymorphisms may affect disease susceptibility and response to drugs.
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| 33. |
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| 34. |
- Nicholson, Anna M., et al.
(författare)
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Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium
- 2018
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Ingår i: Cell Stem Cell. - : CELL PRESS. - 1934-5909 .- 1875-9777. ; 22:6, s. 909-918.e8
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the means and timing by which mutations become fixed in the human colonic epithelium by visualizing somatic clones and mathematical inference. Fixation requires two sequential steps. First, one of approximately seven active stem cells residing within each colonic crypt has to be mutated. Second, the mutated stem cell has to replace neighbors to populate the entire crypt in a process that takes several years. Subsequent clonal expansion due to crypt fission is infrequent for neutral mutations (around 0.7% of all crypts undergo fission in a single year). Pro-oncogenic mutations subvert both stem cell replacement to accelerate fixation and clonal expansion by crypt fission to achieve high mutant allele frequencies with age. The benchmarking of these behaviors allows the advantage associated with different gene-specific mutations to be compared irrespective of the cellular mechanisms by which they are conferred.
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| 35. |
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| 36. |
- Prencipe, Maria, et al.
(författare)
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Relationship Between Serum Response Factor and Androgen Receptor in Prostate Cancer
- 2015
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Ingår i: The Prostate. - : Wiley. - 0270-4137. ; 75:15, s. 1704-1717
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND. Serum response factor (SRF) is an important transcription factor in castrate-resistant prostate cancer (CRPC). Since CRPC is associated with androgen receptor (AR) hypersensitivity, we investigated the relationship between SRF and AR. MATERIALS AND METHODS. Transcriptional activity was assessed by luciferase assay. Cell proliferation was measured by MTT and flow cytometry. Protein expression in patients was assessed by immunohistochemistry. RESULTS. To investigate AR involvement in SRF response to androgen, AR expression was down-regulated using siRNA. This resulted in the abrogation of SRF induction post-DHT. Moreover, DHT stimulation failed to induce SRF transcriptional activity in AR-negative PC346 DCC cells, which was only restored following AR over-expression. Next, SRF expression was down-regulated by siRNA, resulting in AR increased transcriptional activity in castrate-resistant LNCaP Abl cells but not in the parental LNCaP. This negative feedback loop in the resistant cells was confirmed by immunohistochemistry which showed a negative correlation between AR and SRF expression in CRPC bone metastases and a positive correlation in androgen-naive prostatectomies. Cell proliferation was next assessed following SRF inhibition, demonstrating that SRF inhibition is more effective than AR inhibition in castrate-resistant cells. CONCLUSION. Our data support SRF as a promising therapeutic target in combination with current treatments. (C) 2015 Wiley Periodicals, Inc.
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| 37. |
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| 38. |
- Tamblyn, R, et al.
(författare)
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Blueschist from the Mariana forearc records long-lived residence of material in the subduction channel
- 2019
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Ingår i: Earth and Planetary Science Letters. - : Elsevier BV. - 0012-821X .- 1385-013X. ; 519, s. 171-181
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Tidskriftsartikel (refereegranskat)abstract
- © 2019 Elsevier B.V. From ca. 50 Ma to present, the western Pacific plate has been subducting under the Philippine Sea plate, forming the oceanic Izu-Bonin-Mariana (IBM) subduction system. It is the only known location where subduction zone products are presently being transported to the surface by serpentinite-mud volcanoes. A large serpentine mud “volcano” forms the South Chamorro Seamount and was successfully drilled by ODP during Leg 195. This returned mostly partially serpentinized harzburgites enclosed in serpentinite muds. In addition, limited numbers of small (1 mm–1 cm) fragments of rare blueschists were also discovered. U–Pb dating of zircon and rutile from one of these blueschist clasts give ages of 51.1 ± 1.2 Ma and 47.5 ± 2.0 Ma, respectively. These are interpreted to date prograde high-pressure metamorphism. Mineral equilibria modelling of the blueschist clast suggests the mineral assemblage formed at conditions of ∼1.6 GPa and ∼590 °C. We interpret that this high-pressure assemblage formed at a depth of ∼50 km within the subduction channel and was subsequently exhumed and entrained into the South Chamorro serpentinite volcano system at depths of ∼27 km. Consequently, we propose that the material erupted from the South Chamarro Seamount may be sampling far greater depths within the Mariana subduction system than previously thought. The apparent thermal gradient implied by the pressure–temperature modelling (∼370 °C/GPa) is slightly warmer than that predicted by typical subduction channel numerical models and other blueschists worldwide. The age of the blueschist suggests it formed during the arc initiation stages of the proto-Izu-Bonin-Mariana arc, with the P–T conditions recording thermally elevated conditions during initial stages of western Pacific plate subduction. This indicates the blueschist had prolonged residence time in the stable forearc as the system underwent east-directed rollback. The Mariana blueschist shows that subduction products can remain entrained in subduction channels for many millions of years prior to exhumation.
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| 39. |
- Tamblyn, R., et al.
(författare)
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Resubduction of lawsonite eclogite within a serpentinite-filled subduction channel
- 2020
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Ingår i: Contributions to Mineralogy and Petrology. - : Springer Science and Business Media LLC. - 0010-7999 .- 1432-0967. ; 175:8
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Tidskriftsartikel (refereegranskat)abstract
- Translating burial and exhumation histories from the petrological and geochronological record of high-pressure assemblages in subduction channels is key to understanding subduction channel processes. Convective return flow, either serpentinite or sediment hosted, has been suggested as a potential mechanism to retrieve rocks from significant depths and exhume them. Numerical modelling predicts that during convective flow, subducted material can be cycled within a serpentinite-filled subduction channel. Geochronological and petrological evidences for such cycling during subduction are preserved in lawsonite eclogite from serpentinite melange in the Southern New England Orogen, eastern Australia. Ar-Ar, Rb-Sr phengite and U-Pb titanite geochronology, supported by phase equilibrium forward modelling and mineral zoning, suggest Cambro-Ordovician eclogite underwent two stages of burial separated by a stage of partial exhumation. The initial subduction of the eclogite at ca. 490 Ma formed porphyroblastic prograde-zoned garnet and lawsonite at approximateP-Tconditions of at least 2.9 GPa and 600 degrees C. Partial exhumation to at least 2.0 GPa and 500 degrees C is recorded by garnet dissolution. Reburial of the eclogite resulted in growth of new Mg-rich garnet rims, growth of new prograde-zoned phengite and recrystallization of titanite atP-Tconditions of approximately 2.7 GPa and 590 degrees C. U-Pb titanite, and Ar-Ar and Rb-Sr phengite ages constrain the timing of reburial to ca. 450 Ma. This was followed by a second exhumation event at approximately 1.9 GPa and 520 degrees C. These conditions fall along a cold approximate geotherm of 230 degrees C/GPa. The inferred changes in pressure suggest the lawsonite eclogite underwent depth cycling within the subduction channel. Geochronological data indicate that partial exhumation and reburial occurred over ca. 50 M y., providing some estimation on the timescales of material convective cycling in the subduction channel.
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| 40. |
- Toombs, A. L., et al.
(författare)
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Supporting the complex social lives of new parents
- 2018
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Ingår i: CHI '18 Proceedings of the 2018 CHI Conference on Human Factors in Computing Systems. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450356206 - 9781450356213
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Konferensbidrag (refereegranskat)abstract
- One of the many challenges of becoming a parent is the shift in one's social life. As HCI researchers have begun to investigate the intersection of sociotechnical system design and parenthood, they have also sought to understand how parents' social lives can be best supported. We build on these strands of research through a qualitative study with new parents regarding the role of digital technologies in their social lives as they transition to parenthood. We demonstrate how sociotechnical systems are entangled in the ways new parents manage their relationships, build (or resist building) new friendships and ad hoc support systems, and navigate the vulnerabilities of parenthood. We discuss how systems designed for new parents can better support the vulnerabilities they internalize, the diverse friendships they desire, and the logistical challenges they experience. We conclude with recommendations for future design and research in this area.
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| 41. |
- Veltsos, P., et al.
(författare)
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The genetic architecture of sexually selected traits in two natural populations of Drosophila montana
- 2015
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 115:6, s. 565-572
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the genetic architecture of courtship song and cuticular hydrocarbon traits in two phygenetically distinct populations of Drosophila montana. To study natural variation in these two important traits, we analysed within-population crosses among individuals sampled from the wild. Hence, the genetic variation analysed should represent that available for natural and sexual selection to act upon. In contrast to previous between-population crosses in this species, no major quantitative trait loci (QTLs) were detected, perhaps because the between-population QTLs were due to fixed differences between the populations. Partitioning the trait variation to chromosomes suggested a broadly polygenic genetic architecture of within-population variation, although some chromosomes explained more variation in one population compared with the other. Studies of natural variation provide an important contrast to crosses between species or divergent lines, but our analysis highlights recent concerns that segregating variation within populations for important quantitative ecological traits may largely consist of small effect alleles, difficult to detect with studies of moderate power.
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| 42. |
- Watts, Nick, et al.
(författare)
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The Lancet Countdown on health and climate change : from 25 years of inaction to a global transformation for public health
- 2018
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Ingår i: The Lancet. - : Elsevier. - 0140-6736 .- 1474-547X. ; 391:10120, s. 581-630
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Forskningsöversikt (refereegranskat)abstract
- The Lancet Countdown tracks progress on health and climate change and provides an independent assessment of the health effects of climate change, the implementation of the Paris Agreement, 1 and the health implications of these actions. It follows on from the work of the 2015 Lancet Commission on Health and Climate Change, 2 which concluded that anthropogenic climate change threatens to undermine the past 50 years of gains in public health, and conversely, that a comprehensive response to climate change could be "the greatest global health opportunity of the 21st century". The Lancet Countdown is a collaboration between 24 academic institutions and intergovernmental organisations based in every continent and with representation from a wide range of disciplines. The collaboration includes climate scientists, ecologists, economists, engineers, experts in energy, food, and transport systems, geographers, mathematicians, social and political scientists, public health professionals, and doctors. It reports annual indicators across five sections: climate change impacts, exposures, and vulnerability; adaptation planning and resilience for health; mitigation actions and health co-benefits; economics and finance; and public and political engagement. The key messages from the 40 indicators in the Lancet Countdown's 2017 report are summarised below.
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| 43. |
- Wood, M., et al.
(författare)
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"Protection on that erection?" : Discourses of accountability & compromising participation in digital sexual health
- 2018
-
Ingår i: CHI '18 Proceedings of the 2018 CHI Conference on Human Factors in Computing Systems. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450356206 - 9781450356213
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Konferensbidrag (refereegranskat)abstract
- This paper analyses sexual health workers' 'talk' around their introduction of a digital platform to enhance a regionally managed condom distribution scheme for young people. In examining the discursive resources workers used in framing the sexual health service, their service users and digital technology, we argue that problematic ideologies around young people and sexuality were exercised and reproduced. Workers positioned themselves as the gatekeepers of young people's sexual health, who were in turn constructed as 'mischievous' and 'misguided', with technology having a corruptive role over what was considered to be 'healthy' and 'normal' sexual relationships. We suggest our findings indicate severe challenges in developing community-commissioned platforms alongside service providers, and questions how plausible user participation can be in attempting to conduct collaborative, participatory and engaged work in this context.
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| 44. |
- Zivanovic, Andrej, et al.
(författare)
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Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer
- 2023
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Ingår i: NAR Cancer. - : Oxford University Press. - 2632-8674. ; 5:3
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Tidskriftsartikel (refereegranskat)abstract
- Androgen receptor (AR) inhibition is standard of care for advanced prostate cancer (PC). However, efficacy is limited by progression to castration-resistant PC (CRPC), usually due to AR re-activation via mechanisms that include AR amplification and structural rearrangement. These two classes of AR alterations often co-occur in CRPC tumors, but it is unclear whether this reflects intercellular or intracellular heterogeneity of AR. Resolving this is important for developing new therapies and predictive biomarkers. Here, we analyzed 41 CRPC tumors and 6 patient-derived xenografts (PDXs) using linked-read DNA-sequencing, and identified 7 tumors that developed complex, multiply-rearranged AR gene structures in conjunction with very high AR copy number. Analysis of PDX models by optical genome mapping and fluorescence in situ hybridization showed that AR residing on extrachromosomal DNA (ecDNA) was an underlying mechanism, and was associated with elevated levels and diversity of AR expression. This study identifies co-evolution of AR gene copy number and structural complexity via ecDNA as a mechanism associated with endocrine therapy resistance.
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| 45. |
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