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| 2. |
- Garcia-Benito, R., et al.
(författare)
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CALIFA, the Calar Alto Legacy Integral Field Area survey III. Second public data release
- 2015
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 576:A135
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes the Second Public Data Release (DR2) of the Calar Alto Legacy Integral Field Area (CALIFA) survey. The data for 200 objects are made public, including the 100 galaxies of the First Public Data Release (DR1). Data were obtained with the integral-field spectrograph PMAS /PPak mounted on the 3.5 m telescope at the Calar Alto observatory. Two different spectral setups are available for each galaxy, (i) a low-resolution V500 setup covering the wavelength range 3745-7500 angstrom with a spectral resolution of 6.0 angstrom (FWHM); and (ii) a medium-resolution V1200 setup covering the wavelength range 3650-4840 angstrom with a spectral resolution of 2.3 angstrom (FWHM). The sample covers a redshift range between 0.005 and 0.03, with a wide range of properties in the color-magnitude diagram, stellar mass, ionization conditions, and morphological types. All the cubes in the data release were reduced with the latest pipeline, which includes improved spectrophotometric calibration, spatial registration, and spatial resolution. The spectrophotometric calibration is better than 6% and the median spatial resolution is 2 4. In total, the second data release contains over 1.5 million spectra.
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| 3. |
- Frassl, Marieke A., et al.
(författare)
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Ten simple rules for collaboratively writing a multi-authored paper
- 2018
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Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 14:11
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Science is increasingly done in large teams, making it more likely that papers will be written by several authors from different institutes, disciplines, and cultural backgrounds. A small number of “Ten simple rules” papers have been written on collaboration and on writing but not on combining the two. Collaborative writing with multiple authors has additional challenges, including varied levels of engagement of coauthors, provision of fair credit through authorship or acknowledgements, acceptance of a diversity of work styles, and the need for clear communication. Miscommunication, a lack of leadership, and inappropriate tools or writing approaches can lead to frustration, delay of publication, or even the termination of a project.To provide insight into collaborative writing, we use our experience from the Global Lake Ecological Observatory Network (GLEON) to frame 10 simple rules for collaboratively writing a multi-authored paper. We consider a collaborative multi-authored paper to have three or more people from at least two different institutions. A multi-authored paper can be a result of a single discrete research project or the outcome of a larger research program that includes other papers based on common data or methods. The writing of a multi-authored paper is embedded within a broader context of planning and collaboration among team members. Our recommended rules include elements of both the planning and writing of a paper, and they can be iterative, although we have listed them in numerical order. It will help to revisit the rules frequently throughout the writing process. With the 10 rules outlined below, we aim to provide a foundation for writing multi-authored papers and conducting exciting and influential science.
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| 4. |
- Serabyn, E, et al.
(författare)
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The W. M. Keck Observatory infrared vortex coronagraph and a first image of HIP79124 B
- 2017
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 153:1, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- An optical vortex coronagraph has been implemented within the NIRC2 camera on the Keck II telescope and used to carry out on-sky tests and observations. The development of this new L′-band observational mode is described, and an initial demonstration of the new capability is presented: a resolved image of the low-mass companion to HIP 79124, which had previously been detected by means of interferometry. With HIP 79124 B at a projected separation of 186.5 mas, both the small inner working angle of the vortex coronagraph and the related imaging improvements were crucial in imaging this close companion directly. Due to higher Strehl ratios and more relaxed contrasts in L′ band versus H band, this new coronagraphic capability will enable high-contrast, small-angle observations of nearby young exoplanets and disks on a par with those of shorter-wavelength extreme adaptive optics coronagraphs.
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| 5. |
- Andersson, Martin G. I., et al.
(författare)
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Effects of sterilization on dissolved organic carbon (DOC) composition and bacterial utilization of DOC from lakes
- 2018
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Ingår i: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 82:2, s. 199-208
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Tidskriftsartikel (refereegranskat)abstract
- Sterilization of dissolved organic carbon (DOC) is an essential step in research on interactions between DOC and organisms, for example where the effect of different microbial communities on DOC is studied or vice versa. However, few studies have gone beyond acknowledging that sterilization of DOC influences its characteristics. Here, we aimed to provide further knowledge that enables scientists to better tailor their sterilization methods to their research question. To meet this aim, we conducted a sterilization experiment with DOC from 4 boreal lakes treated with 4 sterilization methods, i.e. 2 filtrations (0.2 µm, 0.1 µm) and 2 autoclaving approaches (single and double autoclaving with a single pH adjustment). Quantity and spectroscopic properties of DOC, before and after sterilization, were studied, and DOC was further tested as a substrate for bacterial growth. We found that the filtration methods better preserved the different DOC measures. In contrast, autoclaving caused major inconsistent shifts in both qualitative and quantitative measures of DOC, as well as an increase of the maximum abundance of bacteria in growth experiments. Nonetheless, there remains a trade-off between retaining the quality of DOC and achieving sterile conditions. Therefore, the sterilization method of choice should be guided by the scientific question at hand.
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| 6. |
- Arrázola, Macarena S., et al.
(författare)
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Axonal degeneration is mediated by necroptosis activation
- 2019
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Ingår i: The Journal of Neuroscience. - 0270-6474. ; 39:20, s. 3832-3844
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Tidskriftsartikel (refereegranskat)abstract
- Axonal degeneration, which contributes to functional impairment in several disorders of the nervous system, is an important target for neuroprotection. Several individual factors and subcellular events have been implicated in axonal degeneration, but researchers have so far been unable to identify an integrative signaling pathway activating this self-destructive process. Through pharmacological and genetic approaches, we tested whether necroptosis, a regulated cell-death mechanism implicated in the pathogenesis of several neurodegenerative diseases, is involved in axonal degeneration. Pharmacological inhibition of the necroptotic kinase RIPK1 using necrostatin-1 strongly delayed axonal degeneration in the peripheral nervous system and CNS of wild-type mice of either sex and protected in vitro sensory axons from degeneration after mechanical and toxic insults. These effects were also observed after genetic knock-down of RIPK3, a second key regulator of necroptosis, and the downstream effector MLKL (Mixed Lineage Kinase Domain-Like). RIPK1 inhibition prevented mitochondrial fragmentation in vitro and in vivo, a typical feature of necrotic death, and inhibition of mitochondrial fission by Mdivi also resulted in reduced axonal loss in damaged nerves. Furthermore, electrophysiological analysis demonstrated that inhibition of necroptosis delays not only the morphological degeneration of axons, but also the loss of their electrophysiological function after nerve injury. Activation of the necroptotic pathway early during injury-induced axonal degeneration was made evident by increased phosphorylation of the downstream effector MLKL. Our results demonstrate that axonal degeneration proceeds by necroptosis, thus defining a novel mechanistic framework in the axonal degenerative cascade for therapeutic interventions in a wide variety of conditions that lead to neuronal loss and functional impairment.
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| 8. |
- Catalán, Núria, 1985-, et al.
(författare)
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Behind the Scenes : mechanisms Regulating Climatic Patterns of Dissolved Organic Carbon Uptake in Headwater Streams
- 2018
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Ingår i: Global Biogeochemical Cycles. - : American Geophysical Union (AGU). - 0886-6236 .- 1944-9224. ; 32:10, s. 1528-1541
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Tidskriftsartikel (refereegranskat)abstract
- Large variability in dissolved organic carbon (DOC) uptake rates has been reported for headwater streams, but the causes of this variability are still not well understood. Here we assessed acetate uptake rates across 11 European streams comprising different ecoregions by using whole-reach pulse acetate additions. We evaluated the main climatic and biogeochemical drivers of acetate uptake during two seasonal periods. Our results show a minor influence of sampling periods but a strong effect of climate and dissolved organic matter (DOM) composition on acetate uptake. In particular, mean annual precipitation explained half of the variability of the acetate uptake velocities (Vf(Acetate)) across streams. Temperate streams presented the lowest Vf(Acetate), together with humic-like DOM and the highest stream respiration rates. In contrast, higher Vf(Acetate) were found in semiarid streams, with protein-like DOM, indicating a dominance of reactive, labile compounds. This, together with lower stream respiration rates and molar ratios of DOC to nitrate, suggests a strong C limitation in semiarid streams, likely due to reduced inputs from the catchment. Overall, this study highlights the interplay of climate and DOM composition and its relevance to understand the biogeochemical mechanisms controlling DOC uptake in streams. Plain Language Summary Headwater streams receive and degrade organic carbon and nutrients from the surrounding catchments. That degradation can be assessed by measuring the uptake of simple compounds of carbon or nitrogen such as acetate or nitrate. Here we determine the variability in acetate and nitrate uptake rates across headwater streams and elucidate the mechanisms behind that variability. The balance between nutrients, the composition of the organic materials present in the streams, and the climatic background is at interplay.
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| 9. |
- Catalán, Núria, 1985-, et al.
(författare)
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Effects of beaver impoundments on dissolved organic matter quality and biodegradability in boreal riverine systems
- 2017
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Ingår i: Hydrobiologia. - : Springer Science and Business Media LLC. - 0018-8158 .- 1573-5117. ; 793:1, s. 135-148
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Tidskriftsartikel (refereegranskat)abstract
- Beaver impoundments modify the structure of river reaches and lead to changes in ecosystem function and biogeochemical processes. Here, we assessed the changes in dissolved organic matter (DOM) quality and the biodegradation patterns in a set of beaver systems across Sweden. As the effect of beaver impoundments might be transient and local, we compared DOM quality and biodegradability of both pond and upstream sections of differentially aged beaver systems. Newly established dams shifted the sources and DOM biodegradability patterns. In particular, humic-like DOM, most likely leached from surrounding soils, characterized upstream sections of new beaver impoundments. In contrast, autochthonous and processed compounds, with both higher biodegradation rates and a broader spectrum of reactivities, differentiated DOM in ponds. DOM in recently established ponds seemed to be more humic and less processed compared to older ponds, but system idiosyncrasies determined by catchment particularities influenced this ageing effect.
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| 10. |
- Hampton, Stephanie E., et al.
(författare)
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Ecology under lake ice
- 2017
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 20:1, s. 98-111
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Forskningsöversikt (refereegranskat)abstract
- Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer ‘growing seasons’. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.
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| 11. |
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| 13. |
- Ramnarine, Timothy J. S., et al.
(författare)
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Population Genetic and Functional Analysis of a cis-Regulatory Polymorphism in the Drosophila melanogaster Metallothionein A gene
- 2019
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- Although gene expression can vary extensively within and among populations, the genetic basis of this variation and the evolutionary forces that maintain it are largely unknown. In Drosophila melanogaster, a 49-bp insertion/deletion (indel) polymorphism in the Metallothionein A (MtnA) gene is associated with variation in MtnA expression and oxidative stress tolerance. To better understand the functional and evolutionary significance of this polymorphism, we investigated it in several worldwide populations. In a German population, the deletion was present at a high and stable frequency over multiple seasons and years, and was associated with increased MtnA expression. There was, however, no evidence that the polymorphism was maintained by overdominant, seasonally fluctuating, or sexually antagonistic selection. The deletion was rare in a population from the species' ancestral range in sub-Saharan Africa and is likely the result of non-African admixture, suggesting that it spread to high frequency following the species' out-of-Africa expansion. Using data from a North American population, we found that the deletion was associated with MtnA expression and tolerance to oxidative stress induced by menadione sodium bisulfite. Our results are consistent with the deletion being selectively favored in temperate populations due to the increased MtnA expression and oxidative stress tolerance that it confers.
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| 14. |
- Reggiani, M, et al.
(författare)
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Discovery of a point-like source and a third spiral arm in the transition disk around the Herbig Ae star MWC 758
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 611
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Tidskriftsartikel (refereegranskat)abstract
- Context. Transition disks offer the extraordinary opportunity to look for newly born planets and to investigate the early stages of planet formation. Aims. In this context we observed the Herbig A5 star MWC 758 with the L'-band vector vortex coronagraph installed in the near-infrared camera and spectrograph NIRC2 at the Keck II telescope, with the aim of unveiling the nature of the spiral structure by constraining the presence of planetary companions in the system. Methods. Our high-contrast imaging observations show a bright (Delta L' = 7.0 +/- 0.3 mag) point-like emission south of MWC 758 at a deprojected separation of similar to 20 au (r = 0 ''.111 +/- 0 ''.004) from the central star. We also recover the two spiral arms (southeast and northwest), already imaged by previous studies in polarized light, and discover a third arm to the southwest of the star. No additional companions were detected in the system down to 5 Jupiter masses beyond 0 ''.6 from the star. Results. We propose that the bright L'-band emission could be caused by the presence of an embedded and accreting protoplanet, although the possibility of it being an asymmetric disk feature cannot be excluded. The spiral structure is probably not related to the protoplanet candidate, unless on an inclined and eccentric orbit, and it could be due to one (or more) yet undetected planetary companions at the edge of or outside the spiral pattern. Future observations and additional simulations will be needed to shed light on the true nature of the point-like source and its link with the spiral arms.
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