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Tidskriftsartikel (refereegranskat)
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- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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- Axfors, Cathrine, et al.
(författare)
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Association between convalescent plasma treatment and mortality in COVID-19 : a collaborative systematic review and meta-analysis of randomized clinical trials
- 2021
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Ingår i: BMC Infectious Diseases. - : BioMed Central (BMC). - 1471-2334. ; 21:1
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Forskningsöversikt (refereegranskat)abstract
- Background: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, ). Methods: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. Results: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I-2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. Conclusions: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care.
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- Alves-Martins, Fernanda, et al.
(författare)
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Drivers of regional and local diversity of Amazonian stream Odonata
- 2019
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Ingår i: Insect Conservation and Diversity. - : Wiley-Blackwell. - 1752-458X .- 1752-4598. ; 12:3, s. 251-261
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Tidskriftsartikel (refereegranskat)abstract
- Large Amazonian rivers may act as dispersal barriers for animals with low dispersal abilities, limiting their distribution to certain interfluves. Consequently, the distribution of these taxa would be less affected by macroclimatic gradients. Conversely, high-dispersal taxa would be less constrained by large rivers and may track suitable climates. We evaluate whether Zygoptera and Anisoptera, two Odonata suborders with different dispersal abilities, show differences in distribution patterns across Amazonian interfluves. We further assess the relative importance of macroclimatic and habitat factors in their community assembly. We used network modularity analyses to identify biogeographic species pools and spatial buffers to define metacommunity species pools. Then, we used structural equationmodels to estimate the relative importance of multi-scale factors on species richness patterns. Zygoptera communities are more similar in species composition within than between interfluves, suggesting that large Amazonian rivers indeed limit the distribution of Zygoptera species. Conversely, the distribution of Anisoptera extends across Amazonian interfluves. Seasonality has a strong positive effect on Zygoptera and Anisoptera richness across scales. In addition, habitat integrity is negatively correlated with the regional species richness and abundance of Anisoptera and positively correlated with Zygoptera local richness. The contrasting effects of habitat integrity on Anisoptera and Zygoptera suggest that the former is favored in open habitats, whereas the latter is so in forests. Despite these differences, both suborders appear to follow similar community assembly mechanisms in Amazonia, with a strong climatic control across scales and an effect of habitat filters on local communities.
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- Calatayud, Joaquín, et al.
(författare)
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Positive associations among rare species and their persistence in ecological assemblages
- 2020
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Ingår i: Nature Ecology & Evolution. - : Nature Publishing Group. - 2397-334X. ; 4:1, s. 40-45
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Tidskriftsartikel (refereegranskat)abstract
- According to the competitive exclusion principle, species with low competitive abilities should be excluded by more efficient competitors; yet, they generally remain as rare species. Here, we describe the positive and negative spatial association networks of 326 disparate assemblages, showing a general organization pattern that simultaneously supports the primacy of competition and the persistence of rare species. Abundant species monopolize negative associations in about 90% of the assemblages. On the other hand, rare species are mostly involved in positive associations, forming small network modules. Simulations suggest that positive interactions among rare species and microhabitat preferences are the most probable mechanisms underpinning this pattern and rare species persistence. The consistent results across taxa and geography suggest a general explanation for the maintenance of biodiversity in competitive environments. Analysing spatial association networks among >300 terrestrial and aquatic assemblages, the authors find that the majority of negative associations involve abundant species. In contrast, rare species form mostly positive associations, potentially explaining their persistence in natural communities.
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- Carrasco-Molina, Tania, et al.
(författare)
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Validation and parametrization of the soil moisture index for stomatal conductance modelling and flux-based ozone risk assessment of Mediterranean plant species
- 2024
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Ingår i: Agricultural and Forest Meteorology. - 0168-1923. ; 354
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Tidskriftsartikel (refereegranskat)abstract
- The Mediterranean region chronically experiences high levels of tropospheric ozone (O3) that can affect the health of vegetation. However, limiting plant growing conditions, such as low soil moisture, may restrict the stomatal phytotoxic ozone dose (POD) absorbed by vegetation, modulating O3 detrimental effects. Atmospheric chemistry transport models that estimate POD for O3 risk assessment of effects on vegetation species, such as the European Monitoring and Evaluation Programme (EMEP), have adopted the soil moisture index (SMI) to consider the influence of soil moisture on POD. The objectives of this study were the parametrization and validation of the SMI effect on stomatal conductance (gs) for improving the POD estimation and O3 risk assessment for different vegetation species under water-limiting growing conditions, using field data collected in Italy and Spain and a literature review. The modelled SMI from EMEP proved to be a good indicator of soil moisture dynamics across sites and years, although it showed a general tendency to overestimate soil moisture availability for plants, particularly in the driest seasons. New parametrizations derived for modelling SMI effects on gs under Mediterranean conditions proposed in this study stress the importance of using species-specific parameters for species showing contrasting water-saving strategies in contrast of the current approach of using a simple relation between SMI and gs for all the species. Furthermore, gs modelling parametrizations based on soil water potential (SWP) were found to be more suitable than SMI for local scale estimation of POD under water-limiting conditions. Further consideration of rooting depth and distribution will be required in the future to determine the soil depth at which the soil moisture should be measured in POD modelling, since these features represent one of the most important uncertainties affecting the estimation of POD that could not be addressed with the present database.
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