| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Amora-Nogueira, Leonardo, et al.
(författare)
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Linking centennial scale anthropogenic changes and sedimentary records as lessons for urban coastal management
- 2023
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Ingår i: Science of the Total Environment. - : ELSEVIER. - 0048-9697 .- 1879-1026. ; 902
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Tidskriftsartikel (refereegranskat)abstract
- Coastal eutrophication and urban flooding are increasingly important components of global change. Although increased seawater renewal by barrier openings and channelizing are common mitigation measures in coastal lagoons worldwide, their effects on these ecosystems are not fully understood. Here, we evaluated the re-lationships between human interventions in the watershed, artificial connections to the sea, and the sediment burial rates in an urban coastal lagoon (Maric & PRIME;a lagoon, Southeastern Brazil). Sediment accretion along with nutrient and carbon burial rates were determined in two sediment cores representing the past-120 years (210Pb dating) and associated with anthropogenic changes as indicated by historical records and geoinformation ana-lyses. Lagoon infilling and eutrophication, expressed by the average sediment accretion, TP, TN, and OC burial rates, respectively, increased-9-18, 13-15, 11-14 and 11-12-fold from the earliest (<1950) to the most recent (2000-2017) period. These multi-proxy records confirm mechanistic links between deforestation, urbanization, and untreated sewage discharges. In addition, our findings reveal artificial connections to the sea may contribute to lagoonal eutrophication and infilling, particularly when not integrated with sewage treatment and forest conservation or reforestation in the watershed. Therefore, increased seawater renewal by physical interventions commonly considered as mitigation measures may in contrast cause severe degradation in coastal lagoons, causing harmful consequences that should be not neglected when implementing management practices.
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| 3. |
- Tiegs, Scott D., et al.
(författare)
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Global patterns and drivers of ecosystem functioning in rivers and riparian zones
- 2019
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Ingår i: Science Advances. - Washington : American Association of Advancement in Science. - 2375-2548. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.
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| 4. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 5. |
- Bruneau, Anne, et al.
(författare)
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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification
- 2024
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Ingår i: PhytoKeys. - 1314-2011 .- 1314-2003. ; 240, s. 1-552
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Tidskriftsartikel (refereegranskat)abstract
- Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Cera-tonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.
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| 6. |
- Chagas, Vinicius S., et al.
(författare)
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RTNduals an R/Bioconductor package for analysis of co-regulation and inference of dual regulons
- 2019
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 35:24, s. 5357-5358
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Tidskriftsartikel (refereegranskat)abstract
- MOTIVATION: Transcription factors (TFs) are key regulators of gene expression, and can activate or repress multiple target genes, forming regulatory units, or regulons. Understanding downstream effects of these regulators includes evaluating how TFs cooperate or compete within regulatory networks. Here we present RTNduals, an R/Bioconductor package that implements a general method for analyzing pairs of regulons. RESULTS: RTNduals identifies a dual regulon when the number of targets shared between a pair of regulators is statistically significant. The package extends the RTN (Reconstruction of Transcriptional Networks) package, and uses RTN transcriptional networks to identify significant co-regulatory associations between regulons. The Supplementary Information reports two case studies for TFs using the METABRIC and TCGA breast cancer cohorts. AVAILABILITY AND IMPLEMENTATION: RTNduals is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNduals/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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| 7. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Measurement and assignment of double-resonance transitions to the 8900-9100- cm-1 levels of methane
- 2021
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 103:2
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Tidskriftsartikel (refereegranskat)abstract
- Optical-optical double-resonance spectroscopy with a continuous wave pump and frequency comb probe allows measurement of sub-Doppler transitions to highly excited molecular states over a wide spectral range with high frequency accuracy. We report on assessment and characterization of sub-Doppler double-resonance transitions in methane measured using a 3.3-μm continuous wave optical parametric oscillator as a pump and a 1.67-μm frequency comb as a probe. The comb spectra were recorded using a Fourier transform spectrometer with comb-mode-limited resolution. With the pump tuned to nine different transitions in the ν3 fundamental band, we detected 36 ladder-type transitions to the 3ν3 overtone band region, and 18 V-type transitions to the 2ν3 overtone band. We describe in detail the experimental approach and the pump stabilization scheme, which currently limits the frequency accuracy of the measurement. We present the data analysis procedure used to extract the frequencies and intensities of the probe transitions for parallel and perpendicular relative pump-probe polarization. We compare the center frequencies and relative intensities of the ladder-type transitions to theoretical predictions from the TheoReTS and ExoMol line lists, demonstrating good agreement with TheoReTS.
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| 8. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Sub-Doppler Double-Resonance Spectroscopy of Methane Using a Frequency Comb Probe
- 2021
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 126:6
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Tidskriftsartikel (refereegranskat)abstract
- We report the first measurement of sub-Doppler molecular response using a frequency comb by employing the comb as a probe in optical-optical double-resonance spectroscopy. We use a 3.3 μm continuous wave pump and a 1.67 μm comb probe to detect sub-Doppler transitions to the 2ν3 and 3ν3 bands of methane with ∼1.7 MHz center frequency accuracy. These measurements provide the first verification of the accuracy of theoretical predictions from highly vibrationally excited states, needed to model the high-temperature spectra of exoplanets. Transition frequencies to the 3ν3 band show good agreement with the TheoReTS line list.
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| 9. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Sub-doppler double-resonance spectroscopy of methane using a frequency comb probe
- 2020
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Ingår i: Conference on Lasers and Electro-Optics. - : Optica Publishing Group (formerly OSA). - 9781943580767 - 9781728144184
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Konferensbidrag (refereegranskat)abstract
- We use a 3.3 µm continuous wave optical parametric oscillator as a pump and a 1.67 µm frequency comb as a probe to record 36 sub-Doppler double-resonance transitions in the 3v3 band of methane (including 26 previously unreported) with ~1.5 MHz center frequency accuracy.
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| 10. |
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