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| 2. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
- 2019
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 2019:2
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Tidskriftsartikel (refereegranskat)abstract
- Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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| 3. |
- Fripiat, F., et al.
(författare)
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Macro-nutrient concentrations in Antarctic pack ice: Overall patterns and overlooked processes
- 2017
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Ingår i: Elementa. - : University of California Press. - 2325-1026. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Antarctic pack ice is inhabited by a diverse and active microbial community reliant on nutrients for growth. Seeking patterns and overlooked processes, we performed a large-scale compilation of macro-nutrient data (hereafter termed nutrients) in Antarctic pack ice (306 ice-cores collected from 19 research cruises). Dissolved inorganic nitrogen and silicic acid concentrations change with time, as expected from a seasonally productive ecosystem. In winter, salinity-normalized nitrate and silicic acid concentrations (C∗) in sea ice are close to seawater concentrations (Cw), indicating little or no biological activity. In spring, nitrate and silicic acid concentrations become partially depleted with respect to seawater (C∗ < Cw), commensurate with the seasonal build-up of ice microalgae promoted by increased insolation. Stronger and earlier nitrate than silicic acid consumption suggests that a significant fraction of the primary productivity in sea ice is sustained by flagellates. By both consuming and producing ammonium and nitrite, the microbial community maintains these nutrients at relatively low concentrations in spring. With the decrease in insolation beginning in late summer, dissolved inorganic nitrogen and silicic acid concentrations increase, indicating imbalance between their production (increasing or unchanged) and consumption (decreasing) in sea ice. Unlike the depleted concentrations of both nitrate and silicic acid from spring to summer, phosphate accumulates in sea ice (C∗ > Cw). The phosphate excess could be explained by a greater allocation to phosphorus-rich biomolecules during ice algal blooms coupled with convective loss of excess dissolved nitrogen, preferential remineralization of phosphorus, and/or phosphate adsorption onto metal-organic complexes. Ammonium also appears to be efficiently adsorbed onto organic matter, with likely consequences to nitrogen mobility and availability. This dataset supports the view that the sea ice microbial community is highly efficient at processing nutrients but with a dynamic quite different from that in oceanic surface waters calling for focused future investigations. Copyright © 2017 The Author(s).
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- Anzellini, S., et al.
(författare)
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Phase diagram of calcium at high pressure and high temperature
- 2018
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Ingår i: Physical Review Materials. - : American Physical Society. - 2475-9953. ; 2:8
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Tidskriftsartikel (refereegranskat)abstract
- Resistively heated diamond-anvil cells have been used together with synchrotron x-ray diffraction to investigate the phase diagram of calcium up to 50 GPa and 800 K. The phase boundaries between the Ca-I (fcc), Ca-II (bcc), and Ca-III (simple cubic, sc) phases have been determined at these pressure-temperature conditions, and the ambient temperature equation of state has been generated. The equation of state parameters at ambient temperature have been determined from the experimental compression curve of the observed phases by using third-order Birch-Murnaghan and Vinet equations. A thermal equation of state was also determined for Ca-I and Ca-II by combining the room-temperature Birch-Murnaghan equation of state with a Berman-type thermal expansion model.
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| 5. |
- Georgakis, Marios K., et al.
(författare)
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Age at menopause and duration of reproductive period in association with dementia and cognitive function : A systematic review and meta-analysis
- 2016
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Ingår i: Psychoneuroendocrinology. - : Elsevier BV. - 0306-4530 .- 1873-3360. ; 73, s. 224-243
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Forskningsöversikt (refereegranskat)abstract
- Introduction: The preponderance of dementia among postmenopausal women compared with same-age men and the female sex hormones neuroprotective properties support a tentative role of their deficiency in the dementia pathogenesis. Methods: Pairs of independent reviewers screened 12,323 publications derived from a search strategy for MEDLINE to identify articles investigating the association of age at menopause/reproductive period with (i) dementia and (ii) cognitive function; a snowball of eligible articles and reviews was conducted and authors were contacted for additional information. Random-effect models were used for the meta analysis. Results: Age at menopause (13 studies; 19,449 participants) and reproductive period (4 studies; 9916 participants) in the highest categories were not associated with odds of dementia (effect size [ES]: 0.97 [0.78-1.21]) and Alzheimer's disease (ES: 1.06 [0.71-1.58]). Significant heterogeneity was however noted in both analyses (12: 63.3%, p = 0.003 and 12: 72.6%, p = 0.01, respectively). Subgroup analyses by outcome assessment, study design, level of adjustment and study quality did not materially change the findings. In 9/13 studies assessing cognitive function, advanced age at menopause/longer reproductive period was significantly associated with better cognitive performance/lower decline. Due to statistical differences, no meta-analysis was possible for cognitive function. Conclusions: Existing evidence does not support an association between indices of prolonged exposure to female hormones and lower dementia risk. There are indications, however, for better cognitive performance and delayed cognitive decline, supporting a link between female hormone deficiency and cognitive aging. Current literature limitations, indicated by the heterogeneous study-set, point towards research priorities in this clinically relevant area.
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| 6. |
- Rojo, R, et al.
(författare)
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Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 3215-
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Tidskriftsartikel (refereegranskat)abstract
- The proliferation, differentiation and survival of mononuclear phagocytes depend on signals from the receptor for macrophage colony-stimulating factor, CSF1R. The mammalian Csf1r locus contains a highly conserved super-enhancer, the fms-intronic regulatory element (FIRE). Here we show that genomic deletion of FIRE in mice selectively impacts CSF1R expression and tissue macrophage development in specific tissues. Deletion of FIRE ablates macrophage development from murine embryonic stem cells. Csf1rΔFIRE/ΔFIRE mice lack macrophages in the embryo, brain microglia and resident macrophages in the skin, kidney, heart and peritoneum. The homeostasis of other macrophage populations and monocytes is unaffected, but monocytes and their progenitors in bone marrow lack surface CSF1R. Finally, Csf1rΔFIRE/ΔFIRE mice are healthy and fertile without the growth, neurological or developmental abnormalities reported in Csf1r−/− rodents. Csf1rΔFIRE/ΔFIRE mice thus provide a model to explore the homeostatic, physiological and immunological functions of tissue-specific macrophage populations in adult animals.
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