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- 2017
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In: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Journal article (peer-reviewed)
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| 6. |
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Overview of the JET results
- 2015
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In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 55:10
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Journal article (peer-reviewed)
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| 11. |
- Leebens-Mack, James H., et al.
(author)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Journal article (peer-reviewed)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 12. |
- Wang, Li-San, et al.
(author)
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Rarity of the Alzheimer Disease-Protective APP A673T Variant in the United States.
- 2015
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In: JAMA neurology. - : American Medical Association (AMA). - 2168-6157 .- 2168-6149. ; 72:2
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Journal article (peer-reviewed)abstract
- Recently, a rare variant in the amyloid precursor protein gene (APP) was described in a population from Iceland. This variant, in which alanine is replaced by threonine at position 673 (A673T), appears to protect against late-onset Alzheimer disease (AD). We evaluated the frequency of this variant in AD cases and cognitively normal controls to determine whether this variant will significantly contribute to risk assessment in individuals in the United States.
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| 13. |
- Breves, J. P., et al.
(author)
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Hepatic insulin-like growth factor binding protein (igfbp) responses to food restriction in Atlantic salmon smolts
- 2016
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In: General and Comparative Endocrinology. - : Elsevier BV. - 0016-6480. ; 233, s. 79-87
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Journal article (peer-reviewed)abstract
- The growth hormone (Gh)/insulin-like growth-factor (Igf) system plays a central role in the regulation of growth in fishes. However, the roles of Igf binding proteins (Igfbps) in coordinating responses to food availability are unresolved, especially in anadromous fishes preparing for seaward migration. We assayed plasma Gh, Igf1, thyroid hormones and cortisol along with igfbp mRNA levels in fasted and fed Atlantic salmon (Salmo solar). Fish were fasted for 3 or 10 days near the peak of smoltification (late April to early May). Fasting reduced plasma glucose by 3 days and condition factor by 10 days. Plasma Gh, cortisol, and thyroxine (T-4) were not altered in response to fasting, whereas Igf1 and 3,5,3'-triiodo-L-thyronine (T-3) were slightly higher and lower than controls, respectively. Hepatic igfbp1b1, -1b2, -2a,-2b1 and -2b2 mRNA levels were not responsive to fasting, but there were marked increases in igfbp1a1 following 3 and 10 days of fasting. Fasting did not alter hepatic igf1 or igf2; however, muscle igf1 was diminished by 10 days of fasting. There were no signs that fasting compromised branchial ionoregulatory functions, as indicated by unchanged Na+/K+-ATPase activity and ion pump/transporter mRNA levels. We conclude that dynamic hepatic igfbp1a1 and muscle igf1 expression participate in the modulation of Gh/Igf signaling in smolts undergoing catabolism.
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| 14. |
- Breves, J. P., et al.
(author)
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Variation in branchial expression among insulin-like growth-factor binding proteins (igfbps) during Atlantic salmon smoltification and seawater exposure
- 2017
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In: BMC Physiology. - : Springer Science and Business Media LLC. - 1472-6793. ; 17:1
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Journal article (peer-reviewed)abstract
- Background: In preparation for migration from freshwater to marine habitats, Atlantic salmon (Salmo salar L.) undergo smoltification, a transformation that includes the acquisition of hyposmoregulatory capacity. The growth hormone (Gh)/insulin-like growth-factor (Igf) axis promotes the development of branchial ionoregulatory functions that underlie ion secretion. Igfs interact with a suite of Igf binding proteins (Igfbps) that modulate hormone activity. In Atlantic salmon smolts, igfbp4,-5a,-5b1,-5b2,-6b1 and-6b2 transcripts are highly expressed in gill. We measured mRNA levels of branchial and hepatic igfbps during smoltification (March, April, and May), desmoltification (July) and following seawater (SW) exposure in March and May. We also characterized parallel changes in a broad suite of osmoregulatory (branchial Na+/K+-ATPase (Nka) activity, Na + /K + /2Cl - cotransporter 1 (nkcc1) and cystic fibrosis transmembrane regulator 1 (cftr1) transcription) and endocrine (plasma Gh and Igf1) parameters. Results: Indicative of smoltification, we observed increased branchial Nka activity, nkcc1 and cftr1 transcription in May. Branchial igfbp6b1 and -6b2 expression increased coincidentally with smoltification. Following a SW challenge in March, igfbp6b1 showed increased expression while igfbp6b2 exhibited diminished expression. igfbp5a,-5b1 and-5b2 mRNA levels did not change during smolting, but each had lower levels following a SW exposure in March. Conclusions: Salmonids express an especially large suite of igfbps. Our data suggest that dynamic expression of particular igfbps accompanies smoltification and SW challenges; thus, transcriptional control of igfbps may provide a mechanism for the local modulation of Igf activity in salmon gill. © 2017 The Author(s).
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| 15. |
- Shefferson, Richard P., et al.
(author)
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Drivers of vegetative dormancy across herbaceous perennial plant species
- 2018
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In: Ecology Letters. - : WILEY. - 1461-023X .- 1461-0248. ; 21:5, s. 724-733
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Journal article (peer-reviewed)abstract
- Vegetative dormancy, that is the temporary absence of aboveground growth for 1year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life-history costs of sprouting, and of dormancy. Short-lived and mycoheterotrophic species have higher proportions of dormant plants than long-lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.
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| 16. |
- Breves, J. P., et al.
(author)
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In vivo effects of 17α-ethinylestradiol, 17β-estradiol and 4-nonylphenol on insulin-like growth-factor binding proteins (igfbps) in Atlantic salmon
- 2018
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In: Aquatic Toxicology. - : Elsevier BV. - 0166-445X. ; 203, s. 28-39
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Journal article (peer-reviewed)abstract
- Feminizing endocrine disrupting compounds (EDCs) affect the growth and development of teleost fishes. The major regulator of growth performance, the growth hormone (Gh)/insulin-like growth-factor (Igf) system, is sensitive to estrogenic compounds and mediates certain physiological and potentially behavioral consequences of EDC exposure. Igf binding proteins (Igfbps) are key modulators of Igf activity, but their alteration by EDCs has not been examined. We investigated two life-stages (fry and smolts) of Atlantic salmon (Salmo salar), and characterized how the Gh/Igf/Igfbp system responded to waterborne 17α-ethinylestradiol (EE2), 17β-estradiol (E2) and 4-nonylphenol (NP). Fry exposed to EE2 and NP for 21 days had increased hepatic vitellogenin (vtg) mRNA levels while hepatic estrogen receptor α (erα), gh receptor (ghr), igf1 and igf2 mRNA levels were decreased. NP-exposed fry had reduced body mass and total length compared to controls. EE2 and NP reduced hepatic igfbp1b1, -2a, -2b1, -4, -5b2 and -6b1, and stimulated igfbp5a. In smolts, hepatic vtg mRNA levels were induced following 4-day exposures to all three EDCs, while erα only responded to EE2 and E2. EDC exposures did not affect body mass or fork length; however, EE2 diminished plasma Gh and Igf1 levels in parallel with reductions in hepatic ghr and igf1. In smolts, EE2 and E2 diminished hepatic igfbp1b1, -4 and -6b1, and stimulated igfbp5a. There were no signs of compromised ionoregulation in smolts, as indicated by unchanged branchial ion pump/transporter mRNA levels. We conclude that hepatic igfbps respond (directly and/or indirectly) to environmental estrogens during two key life-stages of Atlantic salmon, and thus may modulate the growth and development of exposed individuals.
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| 17. |
- Büntgen, Ulf, et al.
(author)
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Cooling and societal change during the Late Antique Little Ice Age from 536 to around 660 AD
- 2016
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In: Nature Geoscience. - 1752-0894 .- 1752-0908. ; 9:3, s. 231-236
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Journal article (peer-reviewed)abstract
- Climatic changes during the first half of the Common Era have been suggested to play a role in societal reorganizations in Europe and Asia. In particular, the sixth century coincides with rising and falling civilizations, pandemics, human migration and political turmoil. Our understanding of the magnitude and spatial extent as well as the possible causes and concurrences of climate change during this period is, however, still limited. Here we use tree-ring chronologies from the Russian Altai and European Alps to reconstruct summer temperatures over the past two millennia. We find an unprecedented, long-lasting and spatially synchronized cooling following a cluster of large volcanic eruptions in 536, 540 and 547 AD, which was probably sustained by ocean and sea-ice feedbacks, as well as a solar minimum. We thus identify the interval from 536 to about 660 AD as the Late Antique Little Ice Age. Spanning most of the Northern Hemisphere, we suggest that this cold phase be considered as an additional environmental factor contributing to the establishment of the Justinian plague, transformation of the eastern Roman Empire and collapse of the Sasanian Empire, movements out of the Asian steppe and Arabian Peninsula, spread of Slavic-speaking peoples and political upheavals in China.
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| 18. |
- Büntgen, Ulf, et al.
(author)
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Reply to 'Limited Late Antique cooling'
- 2017
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In: Nature Geoscience. - : Springer Science and Business Media LLC. - 1752-0894 .- 1752-0908. ; 10:4, s. 243-243
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Journal article (other academic/artistic)
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| 19. |
- Emgard, J, et al.
(author)
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MAIT Cells Are Major Contributors to the Cytokine Response in Group A Streptococcal Toxic Shock Syndrome
- 2019
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 116:51, s. 25923-25931
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Journal article (peer-reviewed)abstract
- Streptococcal toxic shock syndrome (STSS) is a rapidly progressing, life-threatening, systemic reaction to invasive infection caused by group A streptococci (GAS). GAS superantigens are key mediators of STSS through their potent activation of T cells leading to a cytokine storm and consequently vascular leakage, shock, and multiorgan failure. Mucosal-associated invariant T (MAIT) cells recognize MR1-presented antigens derived from microbial riboflavin biosynthesis and mount protective innate-like immune responses against the microbes producing such metabolites. GAS lack de novo riboflavin synthesis, and the role of MAIT cells in STSS has therefore so far been overlooked. Here we have conducted a comprehensive analysis of human MAIT cell responses to GAS, aiming to understand the contribution of MAIT cells to the pathogenesis of STSS. We show that MAIT cells are strongly activated and represent the major T cell source of IFNγ and TNF in the early stages of response to GAS. MAIT cell activation is biphasic with a rapid TCR Vβ2-specific, TNF-dominated response to superantigens and a later IL-12- and IL-18-dependent, IFNγ-dominated response to both bacterial cells and secreted factors. Depletion of MAIT cells from PBMC resulted in decreased total production of IFNγ, IL-1β, IL-2, and TNFβ. Peripheral blood MAIT cells in patients with STSS expressed elevated levels of the activation markers CD69, CD25, CD38, and HLA-DR during the acute compared with the convalescent phase. Our data demonstrate that MAIT cells are major contributors to the early cytokine response to GAS, and are therefore likely to contribute to the pathological cytokine storm underlying STSS.
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| 20. |
- Finzell, Thomas, et al.
(author)
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A Detailed Observational Analysis of V1324 Sco, the Most Gamma-Ray-luminous Classical Nova to Date
- 2018
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 852:2
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Journal article (peer-reviewed)abstract
- It has recently been discovered that some, if not all, classical novae emit GeV gamma-rays during outburst, but the mechanisms involved in the production ofgamma-rays are still not well understood. We present here a comprehensive multiwavelength data set - from radio to X-rays - for the most gamma-ray-luminous classical nova to date, V1324 Sco. Using this data set, we show that V1324 Sco is a canonical dusty Fe ii-type nova, with a maximum ejecta velocity of 2600 km s-1 and an ejecta mass of a few × 10-5 M⊙. There is also evidence for complex shock interactions, including a double-peaked radio light curve which shows high brightness temperatures at early times. To explore why V1324 Sco was so gamma-ray luminous, we present a model of the nova ejecta featuring strong internal shocks and find that higher gamma-ray luminosities result from higher ejecta velocities and/or mass-loss rates. Comparison of V1324 Sco with other gamma-ray-detected novae does not show clear signatures of either, and we conclude that a larger sample of similarly well-observed novae is needed to understand the origin and variation of gamma-rays in novae.
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| 21. |
- Kitagawa, M, et al.
(author)
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Dual blockade of the lipid kinase PIP4Ks and mitotic pathways leads to cancer-selective lethality
- 2017
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8:1, s. 2200-
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Journal article (peer-reviewed)abstract
- Achieving robust cancer-specific lethality is the ultimate clinical goal. Here, we identify a compound with dual-inhibitory properties, named a131, that selectively kills cancer cells, while protecting normal cells. Through an unbiased CETSA screen, we identify the PIP4K lipid kinases as the target of a131. Ablation of the PIP4Ks generates a phenocopy of the pharmacological effects of PIP4K inhibition by a131. Notably, PIP4Ks inhibition by a131 causes reversible growth arrest in normal cells by transcriptionally upregulating PIK3IP1, a suppressor of the PI3K/Akt/mTOR pathway. Strikingly, Ras activation overrides a131-induced PIK3IP1 upregulation and activates the PI3K/Akt/mTOR pathway. Consequently, Ras-transformed cells override a131-induced growth arrest and enter mitosis where a131’s ability to de-cluster supernumerary centrosomes in cancer cells eliminates Ras-activated cells through mitotic catastrophe. Our discovery of drugs with a dual-inhibitory mechanism provides a unique pharmacological strategy against cancer and evidence of cross-activation between the Ras/Raf/MEK/ERK and PI3K/AKT/mTOR pathways via a Ras˧PIK3IP1˧PI3K signaling network.
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| 22. |
- McCormick, S. D., et al.
(author)
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The evolutionary consequences for seawater performance and its hormonal control when anadromous Atlantic salmon become landlocked
- 2019
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Journal article (peer-reviewed)abstract
- Populations of anadromous fish have become landlocked in relatively recent geological history (< 14,000 years), but the evolutionary impacts of this altered lifecycle on traits underlying seawater performance have not been established. In order to examine the effects of relaxed selection on seawater traits, anadromous and landlocked Atlantic salmon were reared under identical conditions and examined for differences in seawater performance and its underlying physiological and endocrine control during the time of spring downstream migration. Salinity tolerance, survival and initial growth in seawater were greater in anadromous than in landlocked salmon. Abundance of the seawater isoform of gill Na+/K+-ATPase increased in spring in both strains but was greater in anadromous salmon. Hormones associated with seawater acclimation (adrenocorticotropic hormone, cortisol and growth hormone) increased in spring in both strains but were higher in anadromous salmon, whereas plasma thyroid hormones did not differ. Hypothalamic urotensin I mRNA levels also increased in spring and were higher in the anadromous strain. The results provide evidence that salinity tolerance and associated physiological traits are regulated by seasonal stimulation of the hypothalamic-pituitaryinterrenal axis, and that relaxed selection on seawater entry traits has decreased this stimulation in landlocked salmon.
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| 23. |
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| 24. |
- Nyqvist, Daniel, et al.
(author)
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Downstream migration and multiple dam passage by Atlantic salmon smolts
- 2017
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In: North American Journal of Fisheries Management. - : Taylor & Francis. - 0275-5947 .- 1548-8675. ; 4:37, s. 816-828
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Journal article (peer-reviewed)abstract
- The purpose of this study was to investigate behavior and survival of radio-tagged wild and hatchery-reared landlocked Atlantic Salmon Salmo salar smolts as they migrated past three hydropower dams equipped with fish bypass solutions in the Winooski River, Vermont. Among hatchery-reared smolts, those released early were more likely to initiate migration and did so after less delay than those released late. Once migration was initiated, however, the late-released hatchery smolts migrated at greater speeds. Throughout the river system, hatchery-reared fish performed similarly to wild fish. Dam passage rates varied between the three dams and was highest at the dam where unusually high spill levels occurred throughout the study period. Of the 50 fish that did migrate downstream, only 10% managed to reach the lake. Migration success was low despite the presence of bypass solutions, underscoring the need for evaluations of remedial measures; simply constructing a fishway is not synonymous with providing fish passage.
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