| 1. |
- Lazaridis, Iosif, et al.
(författare)
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Ancient human genomes suggest three ancestral populations for present-day Europeans
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7518, s. 409-
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Tidskriftsartikel (refereegranskat)abstract
- We sequenced the genomes of a similar to 7,000-year-old farmer from Germany and eight similar to 8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes(1-4) with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians(3), who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had similar to 44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
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| 2. |
- Lehman, Joel, et al.
(författare)
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The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities
- 2020
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Ingår i: Artificial Life. - : MIT Press - Journals. - 1530-9185 .- 1064-5462. ; 26:2, s. 274-306
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Tidskriftsartikel (refereegranskat)abstract
- Evolution provides a creative fount of complex and subtle adaptations that often surprise the scientists who discover them. However, the creativity of evolution is not limited to the natural world: Artificial organisms evolving in computational environments have also elicited surprise and wonder from the researchers studying them. The process of evolution is an algorithmic process that transcends the substrate in which it occurs. Indeed, many researchers in the field of digital evolution can provide examples of how their evolving algorithms and organisms have creatively subverted their expectations or intentions, exposed unrecognized bugs in their code, produced unexpectedly adaptations, or engaged in behaviors and outcomes, uncannily convergent with ones found in nature. Such stories routinely reveal surprise and creativity by evolution in these digital worlds, but they rarely fit into the standard scientific narrative. Instead they are often treated as mere obstacles to be overcome, rather than results that warrant study in their own right. Bugs are fixed, experiments are refocused, and one-off surprises are collapsed into a single data point. The stories themselves are traded among researchers through oral tradition, but that mode of information transmission is inefficient and prone to error and outright loss. Moreover, the fact that these stories tend to be shared only among practitioners means that many natural scientists do not realize how interesting and lifelike digital organisms are and how natural their evolution can be. To our knowledge, no collection of such anecdotes has been published before. This article is the crowd-sourced product of researchers in the fields of artificial life and evolutionary computation who have provided first-hand accounts of such cases. It thus serves as a written, fact-checked collection of scientifically important and even entertaining stories. In doing so we also present here substantial evidence that the existence and importance of evolutionary surprises extends beyond the natural world, and may indeed be a universal property of all complex evolving systems.
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| 3. |
- Palkopoulou, Eleftheria, et al.
(författare)
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A comprehensive genomic history of extinct and living elephants
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 115:11, s. E2566-E2574
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Tidskriftsartikel (refereegranskat)abstract
- Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an similar to 120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for similar to 500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.
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| 4. |
- Edwards, Robert A., et al.
(författare)
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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
- 2019
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Ingår i: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 4:10, s. 1727-1736
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Tidskriftsartikel (refereegranskat)abstract
- Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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| 5. |
- Zona, Donatella, et al.
(författare)
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Earlier snowmelt may lead to late season declines in plant productivity and carbon sequestration in Arctic tundra ecosystems
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Arctic warming is affecting snow cover and soil hydrology, with consequences for carbon sequestration in tundra ecosystems. The scarcity of observations in the Arctic has limited our understanding of the impact of covarying environmental drivers on the carbon balance of tundra ecosystems. In this study, we address some of these uncertainties through a novel record of 119 site-years of summer data from eddy covariance towers representing dominant tundra vegetation types located on continuous permafrost in the Arctic. Here we found that earlier snowmelt was associated with more tundra net CO2 sequestration and higher gross primary productivity (GPP) only in June and July, but with lower net carbon sequestration and lower GPP in August. Although higher evapotranspiration (ET) can result in soil drying with the progression of the summer, we did not find significantly lower soil moisture with earlier snowmelt, nor evidence that water stress affected GPP in the late growing season. Our results suggest that the expected increased CO2 sequestration arising from Arctic warming and the associated increase in growing season length may not materialize if tundra ecosystems are not able to continue sequestering CO2 later in the season.
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| 6. |
- Bjermer, Leif, et al.
(författare)
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Dual bronchodilator therapy as first-line treatment in maintenance-naïve patients with symptomatic copd : A pre-specified analysis of the emax trial
- 2021
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Ingår i: International Journal of COPD. - 1176-9106. ; 16, s. 1939-1956
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Limited prospective evidence is available to guide selection of first-line maintenance therapy in patients with COPD. This pre-specified analysis of the EMAX trial explored the efficacy and safety of dual-versus mono-bronchodilator therapy in maintenance-naïve and maintenance-treated patients. Methods: The 24-week EMAX trial evaluated lung function, symptoms (including rescue medication use), exacerbations, and safety with umeclidinium/vilanterol, umeclidinium, and salmeterol in symptomatic patients at low exacerbation risk who were not receiving inhaled corticosteroids. Maintenance-naïve and maintenance-treated subgroups were defined by maintenance bronchodilator use 30 days before screening. Results: The analysis included 749 (31%) maintenance-naïve and 1676 (69%) maintenance-treated patients. For both subgroups, improvements from baseline in trough FEV1 at Week 24 (primary endpoint) were greater with umeclidinium/vilanterol versus umeclidinium (mean difference [95% CI]; maintenance-naïve: 44 mL [1, 87]; maintenance-treated: 77 mL [50, 104]), and salmeterol (maintenance-naïve: 128 mL [85, 171]; maintenance-treated: 145 mL [118, 172]), and in rescue medication inhalations/day over 24 weeks versus umeclidinium (maintenance-naïve: −0.44 [−0.73, −0.16]; maintenance-treated: −0.28 [−0.45, −0.12]) and salmeterol (maintenance-naïve: −0.37 [−0.66, −0.09]; maintenance-treated: −0.25 [−0.41, −0.08]). In maintenance-naïve patients, umeclidinium/vilanterol numerically improved scores at Week 24 for Transition Dyspnea Index versus umeclidinium (0.37 [−0.21, 0.96]) and versus salmeterol (0.47 [−0.10, 1.05]) and Evaluating Respiratory Symptoms–COPD versus umeclidinium (−0.26 [−1.04, 0.53]) and versus salmeterol (−0.58 [−1.36, 0.20]), with similar improvements seen in maintenance-treated patients. All treatments were well tolerated across both subgroups. Conclusion: Similar to maintenance-treated patients, maintenance-naïve patients receiving umeclidinium/vilanterol showed greater improvements in lung function and symptoms com-pared with patients receiving umeclidinium or salmeterol. These findings provide support for the consideration of dual bronchodilator treatment in symptomatic maintenance-naïve patients with COPD.
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| 7. |
- Bjermer, Leif H., et al.
(författare)
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Efficacy and Safety of Umeclidinium/Vilanterol in Current and Former Smokers with COPD : A Prespecified Analysis of The EMAX Trial
- 2021
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Ingår i: Advances in Therapy. - : Springer Science and Business Media LLC. - 0741-238X .- 1865-8652. ; 38:9, s. 4815-4835
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Smoking may reduce the efficacy of inhaled corticosteroids (ICS) in patients with chronic obstructive pulmonary disease (COPD), but its impact on bronchodilator efficacy is unclear. This analysis of the EMAX trial explored efficacy and safety of dual- versus mono-bronchodilator therapy in current or former smokers with COPD. Methods: The 24-week EMAX trial evaluated lung function, symptoms, health status, exacerbations, clinically important deterioration, and safety with umeclidinium/vilanterol, umeclidinium, and salmeterol in symptomatic patients at low exacerbation risk who were not receiving ICS. Current and former smoker subgroups were defined by smoking status at screening. Results: The analysis included 1203 (50%) current smokers and 1221 (50%) former smokers. Both subgroups demonstrated greater improvements from baseline in trough FEV1 at week 24 (primary endpoint) with umeclidinium/vilanterol versus umeclidinium (least squares [LS] mean difference, mL [95% CI]; current: 84 [50, 117]; former: 49 [18, 80]) and salmeterol (current: 165 [132, 198]; former: 117 [86, 148]) and larger reductions in rescue medication inhalations/day over 24 weeks versus umeclidinium (LS mean difference [95% CI]; current: − 0.42 [− 0.63, − 0.20]; former: − 0.25 − 0.44, − 0.05]) and salmeterol (current: − 0.28 [− 0.49, − 0.06]; former: − 0.29 [− 0.49, − 0.09]). Umeclidinium/vilanterol increased the odds (odds ratio [95% CI]) of clinically significant improvement at week 24 in Transition Dyspnea Index versus umeclidinium (current: 1.54 [1.16, 2.06]; former: 1.32 [0.99, 1.75]) and salmeterol (current: 1.37 (1.03, 1.82]; former: 1.60 [1.20, 2.13]) and Evaluating Respiratory Symptoms–COPD versus umeclidinium (current: 1.54 [1.13, 2.09]; former: 1.50 [1.11, 2.04]) and salmeterol (current: 1.53 [1.13, 2.08]; former: 1.53 [1.12, 2.08]). All treatments were well tolerated in both subgroups. Conclusions: In current and former smokers, umeclidinium/vilanterol provided greater improvements in lung function and symptoms versus umeclidinium and salmeterol, supporting consideration of dual-bronchodilator therapy in symptomatic patients with COPD regardless of their smoking status.
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| 8. |
- He, Liyuan, et al.
(författare)
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Dynamics of Fungal and Bacterial Biomass Carbon in Natural Ecosystems: Site-level Applications of the CLM-Microbe Model
- 2021
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Ingår i: Journal of Advances in Modeling Earth Systems. - 1942-2466. ; 13:2
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Tidskriftsartikel (refereegranskat)abstract
- Explicitly representing microbial processes has been recognized as a key improvement to Earth system models for the realistic projections of soil carbon (C) and climate dynamics. The CLM‐Microbe model builds upon the CLM4.5 and explicitly represents two major soil microbial groups, fungi and bacteria. Based on the compiled time‐series data of fungal (FBC) and bacterial (BBC) biomass C from nine biomes, we parameterized and validated the CLM‐Microbe model, and further conducted sensitivity analysis and uncertainty analysis for simulating C cycling. The model performance was evaluated with mean absolute error (MAE), root mean square error (RMSE), and coefficient of determination (R2) for relative change in FBC and BBC. The CLM‐Microbe model is able to reasonably capture the seasonal dynamics of FBC and BBC across biomes, particularly for tropical/subtropical forest, temperate broadleaf forest, and grassland, with MAE < 0.49 for FBC and <0.36 for BBC and RMSE <0.52 FBC and <0.39 for BBC, while R2 values are relatively smaller in some biomes (e.g., shrub) due to small sample sizes. We found good consistencies between simulated and observed FBC (R2=0.70, P<0.001) and BBC (R2=0.26, P<0.05) on average across biomes, but the model is not able to fully capture the large variation in observed FBC and BBC. Sensitivity analysis shows the most critical parameters are turnover rate, carbon‐to‐nitrogen ratio of fungi and bacteria, and microbial assimilation efficiency. This study confirms that the explicit representation of soil microbial mechanisms enhances model performance in simulating C variables such as heterotrophic respiration and soil organic C density. The further application of the CLM‐Microbe model would deepen our understanding of microbial contributions to the global C cycle.
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| 9. |
- He, Liyuan, et al.
(författare)
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Global biogeography of fungal and bacterial biomass carbon in topsoil
- 2020
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717. ; 151
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Tidskriftsartikel (refereegranskat)abstract
- Bacteria and fungi, representing two major soil microorganism groups, play an important role in global nutrient biogeochemistry. Biogeographic patterns of bacterial and fungal biomass are of fundamental importance for mechanistically understanding nutrient cycling. We synthesized 1323 data points of phospholipid fatty acid-derived fungal biomass C (FBC), bacterial biomass C (BBC), and fungi:bacteria (F:B) ratio in topsoil, spanning 11 major biomes. The FBC, BBC, and F:B ratio display clear biogeographic patterns along latitude and environmental gradients including mean annual temperature, mean annual precipitation, net primary productivity, root C density, soil temperature, soil moisture, and edaphic factors. At the biome level, tundra has the highest FBC and BBC densities at 3684 (95% confidence interval: 1678–8084) mg kg−1 and 428 (237–774) mg kg−1, respectively; desert has the lowest FBC and BBC densities at 16.92 (14.4–19.89) mg kg−1 and 6.83 (6.1–7.65) mg kg−1, respectively. The F:B ratio varies dramatically, ranging from 1.8 (1.6–2.1) in savanna to 8.6 (6.7–11.0) in tundra. An empirical model was developed for the F:B ratio and it is combined with a global dataset of soil microbial biomass C to produce global maps for FBC and BBC in 0–30 cm topsoil. Across the globe, the highest FBC is found in boreal forest and tundra while the highest BBC is in boreal forest and tropical/subtropical forest, the lowest FBC and BBC are in shrub and desert. Global stocks of living microbial biomass C were estimated to be 12.6 (6.6–16.4) Pg C for FBC and 4.3 (0.5–10.3) Pg C for BBC in topsoil. These findings advance our understanding of the global distribution of fungal and bacterial biomass, which facilitates the incorporation of fungi and bacteria into Earth system models. The global maps of bacterial and fungal biomass serve as a benchmark for validating microbial models in simulating the global C cycle under a changing climate.
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| 10. |
- Kerwin, Edward M., et al.
(författare)
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Early and sustained symptom improvement with umeclidinium/vilanterol versus monotherapy in COPD : a post hoc analysis of the EMAX randomised controlled trial
- 2020
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Ingår i: Therapeutic Advances in Respiratory Disease. - : SAGE Publications. - 1753-4658 .- 1753-4666. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: In chronic obstructive pulmonary disease (COPD), both the time needed for patients to gain symptom improvement with long-acting bronchodilator therapy and whether an early response is predictive of a sustained response is unknown. This study aimed to investigate how quickly meaningful symptom responses are seen in patients with COPD with bronchodilator therapy and whether these responses are sustained. Methods: Early MAXimisation of bronchodilation for improving COPD stability (EMAX) was a 24-week, double-blind, double-dummy, parallel-group trial that randomised patients to umeclidinium/vilanterol (UMEC/VI), umeclidinium or salmeterol. Daily Evaluating Respiratory Symptoms in COPD (E-RS:COPD) score and rescue salbutamol use were captured via an electronic diary and analysed initially in 4-weekly periods. Post hoc analyses assessed change from baseline in daily E-RS:COPD score and rescue medication use weekly (Weeks 1–8), and association between E-RS:COPD responder status at Weeks 1–4 and later time points. Results: In the intent-to-treat population (n = 2425), reductions from baseline in E-RS:COPD scores and rescue medication use were apparent from Day 2 with all treatments. Treatment differences for UMEC/VI versus either monotherapy plateaued by Week 4–8 and were sustained at Weeks 21–24; improvements were consistently greater with UMEC/VI. For all treatments, most patients (60–85%) retained their Weeks 1–4 E-RS:COPD responder/non-responder status at Weeks 21−24. Among patients receiving UMEC/VI who were E-RS:COPD responders at Weeks 1–4, 70% were responders at Weeks 21–24. Conclusion: Patients with symptomatic COPD had greater potential for early symptom improvements with UMEC/VI versus either monotherapy. This benefit was generally maintained for 24 weeks. Early monitoring of treatment response can provide clinicians with an early indication of a patient’s likely longer-term response to prescribed bronchodilator treatment and will facilitate appropriate early adjustments in care. Clinical Trial Registration: NCT03034915, 2016-002513-22 (EudraCT Number). The reviews of this paper are available via the supplemental material section.
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