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- Breitbarth, E., et al.
(author)
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Iron biogeochemistry across marine systems : progress from the past decade
- 2010
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In: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 7:3, s. 1075-1097
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Journal article (peer-reviewed)abstract
- Based on an international workshop (Gothenburg, 14-16 May 2008), this review article aims to combine interdisciplinary knowledge from coastal and open ocean research on iron biogeochemistry. The major scientific findings of the past decade are structured into sections on natural and artificial iron fertilization, iron inputs into coastal and estuarine systems, colloidal iron and organic matter, and biological processes. Potential effects of global climate change, particularly ocean acidification, on iron biogeochemistry are discussed. The findings are synthesized into recommendations for future research areas
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| 7. |
- Breitbarth, Eike, et al.
(author)
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Iron biogeochemistry across marine systems – progress from the past decade
- 2010
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In: Biogeosciences. - 1726-4170. ; 7, s. 1075-1097
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Research review (peer-reviewed)abstract
- Based on an international workshop (Gothenburg, 14–16 May 2008), this review article aims to combine interdisciplinary knowledge from coastal and open ocean research on iron biogeochemistry. The major scientific findings of the past decade are structured into sections on natural and artificial iron fertilization, iron inputs into coastal and estuarine systems, colloidal iron and organic matter, and biological processes. Potential effects of global climate change, particularly ocean acidification, on iron biogeochemistry are discussed. The findings are synthesized into recommendations for future research areas.
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| 8. |
- Riazifar, M., et al.
(author)
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Stem Cell-Derived Exosomes as Nanotherapeutics for Autoimmune and Neurodegenerative Disorders
- 2019
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In: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 13:6, s. 6670-6688
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Journal article (peer-reviewed)abstract
- To dissect therapeutic mechanisms of transplanted stem cells and develop exosome-based nanotherapeutics in treating autoimmune and neurodegenerative diseases, we assessed the effect of exosomes secreted from human mesenchymal stem cells (MSCs) in treating multiple sclerosis using an experimental autoimmune encephalomyelitis (EAE) mouse model. We found that intravenous administration of exosomes produced by MSCs stimulated by IFN (IFN-Exo) (i) reduced the mean clinical score of EAE mice compared to PBS control, (ii) reduced demyelination, (iii) decreased neuroinflammation, and (iv) upregulated the number of CD4+CD25+FOXP3+ regulatory T cells (Tregs) within the spinal cords of EAE mice. Co-culture of IFN-Exo with activated peripheral blood mononuclear cells (PBMCs) cells in vitro reduced PBMC proliferation and levels of pro-inflammatory Th1 and Th17 cytokines including IL-6, IL-12p70, IL-17AF, and IL-22 yet increased levels of immunosuppressive cytokine indoleamine 2,3-dioxygenase. IFN-Exo could also induce Tregs in vitro in a murine splenocyte culture, likely mediated by a third-party accessory cell type. Further, IFN-Exo characterization by deep RNA sequencing suggested that IFN-Exo contains anti-inflammatory RNAs, where their inactivation partially hindered the exosomes potential to induce Tregs. Furthermore, we found that IFN-Exo harbors multiple anti-inflammatory and neuroprotective proteins. These results not only shed light on stem cell therapeutic mechanisms but also provide evidence that MSC-derived exosomes can potentially serve as cell-free therapies in creating a tolerogenic immune response to treat autoimmune and central nervous system disorders. © 2019 American Chemical Society.
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| 9. |
- Bermudez, Rafael, et al.
(author)
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Long-Term Conditioning to Elevated pCO(2) and Warming Influences the Fatty and Amino Acid Composition of the Diatom Cylindrotheca fusiformis
- 2015
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
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Journal article (peer-reviewed)abstract
- The unabated rise in anthropogenic CO2 emissions is predicted to strongly influence the ocean's environment, increasing the mean sea-surface temperature by 4 degrees C and causing a pH decline of 0.3 units by the year 2100. These changes are likely to affect the nutritional value of marine food sources since temperature and CO2 can influence the fatty (FA) and amino acid (AA) composition of marine primary producers. Here, essential amino (EA) and polyunsaturated fatty (PUFA) acids are of particular importance due to their nutritional value to higher trophic levels. In order to determine the interactive effects of CO2 and temperature on the nutritional quality of a primary producer, we analyzed the relative PUFA and EA composition of the diatom Cylindrotheca fusiformis cultured under a factorial matrix of 2 temperatures (14 and 19 degrees C) and 3 partial pressures of CO2 (180, 380, 750 mu atm) for >250 generations. Our results show a decay of similar to 3% and similar to 6% in PUFA and EA content in algae kept at a pCO(2) of 750 mu atm (high) compared to the 380 mu atm (intermediate) CO2 treatments at 14 degrees C. Cultures kept at 19 degrees C displayed a similar to 3% lower PUFA content under high compared to intermediate pCO(2), while EA did not show differences between treatments. Algae grown at a pCO(2) of 180 mu atm (low) had a lower PUFA and AA content in relation to those at intermediate and high CO2 levels at 14 degrees C, but there were no differences in EA at 19 degrees C for any CO2 treatment. This study is the first to report adverse effects of warming and acidification on the EA of a primary producer, and corroborates previous observations of negative effects of these stressors on PUFA. Considering that only similar to 20% of essential biomolecules such as PUFA (and possibly EA) are incorporated into new biomass at the next trophic level, the potential impacts of adverse effects of ocean warming and acidification at the base of the food web may be amplified towards higher trophic levels, which rely on them as source of essential biomolecules.
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| 10. |
- Boyd, P. W., et al.
(author)
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Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-A review
- 2018
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In: Global Change Biology. - : Wiley. - 1354-1013. ; 24:6, s. 2239-2261
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Journal article (peer-reviewed)abstract
- Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy-making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain processoriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science-based policy formulation.
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| 12. |
- Dingemanse, M., et al.
(author)
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Beyond Single-Mindedness: A Figure-Ground Reversal for the Cognitive Sciences
- 2023
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In: Cognitive Science. - : Wiley. - 0364-0213 .- 1551-6709. ; 47:1
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Journal article (peer-reviewed)abstract
- A fundamental fact about human minds is that they are never truly alone: all minds are steeped in situated interaction. That social interaction matters is recognized by any experimentalist who seeks to exclude its influence by studying individuals in isolation. On this view, interaction complicates cognition. Here, we explore the more radical stance that interaction co-constitutes cognition: that we benefit from looking beyond single minds toward cognition as a process involving interacting minds. All around the cognitive sciences, there are approaches that put interaction center stage. Their diverse and pluralistic origins may obscure the fact that collectively, they harbor insights and methods that can respecify foundational assumptions and fuel novel interdisciplinary work. What might the cognitive sciences gain from stronger interactional foundations? This represents, we believe, one of the key questions for the future. Writing as a transdisciplinary collective assembled from across the classic cognitive science hexagon and beyond, we highlight the opportunity for a figure-ground reversal that puts interaction at the heart of cognition. The interactive stance is a way of seeing that deserves to be a key part of the conceptual toolkit of cognitive scientists.
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| 13. |
- Eckalbar, Walter L., et al.
(author)
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Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes
- 2013
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 14, s. 49-
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Journal article (peer-reviewed)abstract
- Background: The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies. Results: Here we provide an annotation of the A. carolinensis genome based on de novo assembly of deep transcriptomes of 14 adult and embryonic tissues. This revised annotation describes 59,373 transcripts, compared to 16,533 and 18,939 currently for Ensembl and NCBI, and 22,962 predicted protein-coding genes. A key improvement in this revised annotation is coverage of untranslated region (UTR) sequences, with 79% and 59% of transcripts containing 5' and 3' UTRs, respectively. Gaps in genome sequence from the current A. carolinensis build (Anocar2.0) are highlighted by our identification of 16,542 unmapped transcripts, representing 6,695 orthologues, with less than 70% genomic coverage. Conclusions: Incorporation of tissue-specific transcriptome sequence into the A. carolinensis genome annotation has markedly improved its utility for comparative and functional studies. Increased UTR coverage allows for more accurate predicted protein sequence and regulatory analysis. This revised annotation also provides an atlas of gene expression specific to adult and embryonic tissues.
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| 14. |
- García-Mayoral, Ricardo, et al.
(author)
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Modeling of high-Re, incompressible, non-equilibrium, rough-wall boundary layers for naval applications under NATO-AVT349
- 2022
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In: AIAA Science and Technology Forum and Exposition, AIAA SciTech Forum 2022. - Reston, Virginia : American Institute of Aeronautics and Astronautics.
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Conference paper (peer-reviewed)abstract
- This paper discusses the modeling activity of the NATO-STO Research Task Group AVT-349. The aim of this group is to improve the understanding and modeling of boundary layers in the complex flow around water vehicles. As such, the focus is on incompressible, high-Reynolds-number flows that can be subject to non-equilibrium conditions such as strong pressure gradients, three-dimensionality, and surface roughness and heterogeneity. The Task Group has identified a reduced number of simpler problems in which the above conditions can be studied separately and in controlled environments. These include two-dimensional rough-wall boundary layers under both zero and non-zero pressure gradients, two-dimensional smooth-wall boundary layers subject to pressure gradients, and boundary layers around smooth bodies of revolution and three-dimensional obstacles. An experimental and computational data set is being assembled for further analysis and insight into the flow mechanisms involved, as well as the shortcomings of state-of-the-art models. This paper gives an outlook of the modeling effort within the Task Group, as well its different objectives. These include predicting the effect of roughness in equilibrium conditions; assessing the applicability and/or extension of equilibrium models and predictions to non-equilibrium conditions, in particular when outer-layer similarity is lost; the development of near-wall models based on a reduced-order resolvent framework; and the use of machine-aided methods in closure models.
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| 15. |
- Hawkes, Jeffrey A., et al.
(author)
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An international laboratory comparison of dissolved organic matter composition by high resolution mass spectrometry : Are we getting the same answer?
- 2020
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In: Limnology and Oceanography. - : Wiley. - 1541-5856. ; 18:6, s. 235-258
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Journal article (peer-reviewed)abstract
- High-resolution mass spectrometry (HRMS) has become a vital tool for dissolved organic matter (DOM) characterization. The upward trend in HRMS analysis of DOM presents challenges in data comparison and interpretation among laboratories operating instruments with differing performance and user operating conditions. It is therefore essential that the community establishes metric ranges and compositional trends for data comparison with reference samples so that data can be robustly compared among research groups. To this end, four identically prepared DOM samples were each measured by 16 laboratories, using 17 commercially purchased instruments, using positive-ion and negative-ion mode electrospray ionization (ESI) HRMS analyses. The instruments identified similar to 1000 common ions in both negative- and positive-ion modes over a wide range of m/z values and chemical space, as determined by van Krevelen diagrams. Calculated metrics of abundance-weighted average indices (H/C, O/C, aromaticity and m/z) of the commonly detected ions showed that hydrogen saturation and aromaticity were consistent for each reference sample across the instruments, while average mass and oxygenation were more affected by differences in instrument type and settings. In this paper we present 32 metric values for future benchmarking. The metric values were obtained for the four different parameters from four samples in two ionization modes and can be used in future work to evaluate the performance of HRMS instruments.
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