| 1. |
- 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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| 2. |
- 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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| 3. |
- Berndt, Sonja, I, et al.
(författare)
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Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes
- 2022
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Ingår i: Leukemia. - : Springer Nature. - 0887-6924 .- 1476-5551. ; 36:12, s. 2835-2844
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Tidskriftsartikel (refereegranskat)abstract
- Lymphoma risk is elevated for relatives with common non-Hodgkin lymphoma (NHL) subtypes, suggesting shared genetic susceptibility across subtypes. To evaluate the extent of mutual heritability among NHL subtypes and discover novel loci shared among subtypes, we analyzed data from eight genome-wide association studies within the InterLymph Consortium, including 10,629 cases and 9505 controls. We utilized Association analysis based on SubSETs (ASSET) to discover loci for subsets of NHL subtypes and evaluated shared heritability across the genome using Genome-wide Complex Trait Analysis (GCTA) and polygenic risk scores. We discovered 17 genome-wide significant loci (P < 5 × 10−8) for subsets of NHL subtypes, including a novel locus at 10q23.33 (HHEX) (P = 3.27 × 10−9). Most subset associations were driven primarily by only one subtype. Genome-wide genetic correlations between pairs of subtypes varied broadly from 0.20 to 0.86, suggesting substantial heterogeneity in the extent of shared heritability among subtypes. Polygenic risk score analyses of established loci for different lymphoid malignancies identified strong associations with some NHL subtypes (P < 5 × 10−8), but weak or null associations with others. Although our analyses suggest partially shared heritability and biological pathways, they reveal substantial heterogeneity among NHL subtypes with each having its own distinct germline genetic architecture.
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| 4. |
- Costello, David M., et al.
(författare)
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Global patterns and controls of nutrient immobilization on decomposing cellulose in riverine ecosystems
- 2022
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Ingår i: Global Biogeochemical Cycles. - : John Wiley & Sons. - 0886-6236 .- 1944-9224. ; 36:3
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Tidskriftsartikel (refereegranskat)abstract
- Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature. Collectively, we demonstrated that exogenous nutrient supply and immobilization are critical control points for decomposition of organic matter.
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| 5. |
- Cunha, Jose M. V., et al.
(författare)
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High-Performance and Industrially Viable Nanostructured SiOx Layers for Interface Passivation in Thin Film Solar Cells
- 2021
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Ingår i: Solar RRL. - : John Wiley & Sons. - 2367-198X. ; 5:3
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Tidskriftsartikel (refereegranskat)abstract
- Herein, it is demonstrated, by using industrial techniques, that a passivation layer with nanocontacts based on silicon oxide (SiOx) leads to significant improvements in the optoelectronical performance of ultrathin Cu(In,Ga)Se-2 (CIGS) solar cells. Two approaches are applied for contact patterning of the passivation layer: point contacts and line contacts. For two CIGS growth conditions, 550 and 500 degrees C, the SiOx passivation layer demonstrates positive passivation properties, which are supported by electrical simulations. Such positive effects lead to an increase in the light to power conversion efficiency value of 2.6% (absolute value) for passivated devices compared with a nonpassivated reference device. Strikingly, both passivation architectures present similar efficiency values. However, there is a trade-off between passivation effect and charge extraction, as demonstrated by the trade-off between open-circuit voltage (V-oc) and short-circuit current density (J(sc)) compared with fill factor (FF). For the first time, a fully industrial upscalable process combining SiOx as rear passivation layer deposited by chemical vapor deposition, with photolithography for line contacts, yields promising results toward high-performance and low-cost ultrathin CIGS solar cells with champion devices reaching efficiency values of 12%, demonstrating the potential of SiOx as a passivation material for energy conversion devices.
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| 6. |
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| 7. |
- Englund, Oskar, et al.
(författare)
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Multifunctional perennial production systems for bioenergy: performance and progress
- 2020
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Ingår i: Wiley Interdisciplinary Reviews. - : Wiley. - 2041-8396 .- 2041-840X.
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Tidskriftsartikel (refereegranskat)abstract
- As the global population increases and becomes more affluent, biomass demands for food and biomaterials will increase. Demand growth is further accelerated by the implementation of climate policies and strategies to replace fossil resources with biomass. There are, however, concerns about the size of the prospective biomass demand and the environmental and social consequences of the corresponding resource mobilization, especially concerning impacts from the associated land-use change. Strategically integrating perennials into landscapes dominated by intensive agriculture can, for example, improve biodiversity, reduce soil erosion and nutrient emissions to water, increase soil carbon, enhance pollination, and avoid or mitigate flooding events. Such ?multifunctional perennial production systems? can thus contribute to improving overall land-use sustainability, while maintaining or increasing overall biomass productivity in the landscape. Seven different cases in different world regions are here reviewed to exemplify and evaluate (a) multifunctional production systems that have been established to meet emerging bioenergy demands, and (b) efforts to identify locations where the establishment of perennial crops will be particularly beneficial. An important barrier towards wider implementation of multifunctional systems is the lack of markets, or policies, compensating producers for enhanced ecosystem services and other environmental benefits. This deficiency is particularly important since prices for fossil-based fuels are low relative to bioenergy production costs. Without such compensation, multifunctional perennial production systems will be unlikely to contribute to the development of a sustainable bioeconomy.
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| 8. |
- Hambrecht, George, et al.
(författare)
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Archaeological sites as Distributed Long-term Observing Networks of the Past (DONOP)
- 2020
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Ingår i: Quaternary International. - : Elsevier BV. - 1040-6182 .- 1873-4553. ; 549, s. 218-226
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Tidskriftsartikel (refereegranskat)abstract
- Archaeological records provide a unique source of direct data on long-term human-environment interactions and samples of ecosystems affected by differing degrees of human impact. Distributed long-term datasets from archaeological sites provide a significant contribution to establish local, regional, and continental-scale environmental baselines and can be used to understand the implications of human decision-making and its impacts on the environment and the resources it provides for human use. Deeper temporal environmental baselines are essential for resource and environmental managers to restore biodiversity and build resilience in depleted ecosystems. Human actions are likely to have impacts that reorganize ecosystem structures by reducing diversity through processes such as niche construction. This makes data from archaeological sites key assets for the management of contemporary and future climate change scenarios because they combine information about human behavior, environmental baselines, and biological systems. Sites of this kind collectively form Distributed Long-term Observing Networks of the Past (DONOP), allowing human behavior and environmental impacts to be assessed over space and time. Behavioral perspectives are gained from direct evidence of human actions in response to environmental opportunities and change. Baseline perspectives are gained from data on species, landforms, and ecology over timescales that long predate our typically recent datasets that only record systems already disturbed by people. Biological perspectives can also provide essential data for modern managers wanting to understand and utilize past diversity (i.e., trophic and/or genetic) as a way of revealing, and potentially correcting, weaknesses in our contemporary wild and domestic animal populations.
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| 9. |
- Jackson, Chelsea L., et al.
(författare)
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Diagnostic and prognostic implications of a three-antibody molecular subtyping algorithm for non-muscle invasive bladder cancer
- 2022
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Ingår i: Journal of Pathology: Clinical Research. - : Wiley. - 2056-4538. ; 8:2, s. 143-154
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Tidskriftsartikel (refereegranskat)abstract
- Intrinsic molecular subtypes may explain marked variation between bladder cancer patients in prognosis and response to therapy. Complex testing algorithms and little attention to more prevalent, early-stage (non-muscle invasive) bladder cancers (NMIBCs) have hindered implementation of subtyping in clinical practice. Here, using a three-antibody immunohistochemistry (IHC) algorithm, we identify the diagnostic and prognostic associations of well-validated proteomic features of basal and luminal subtypes in NMIBC. By IHC, we divided 481 NMIBCs into basal (GATA3−/KRT5+) and luminal (GATA3+/KRT5 variable) subtypes. We further divided the luminal subtype into URO (p16 low), URO-KRT5+ (KRT5+), and genomically unstable (GU) (p16 high) subtypes. Expression thresholds were confirmed using unsupervised hierarchical clustering. Subtypes were correlated with pathology and outcomes. All NMIBC cases clustered into the basal/squamous (basal) or one of the three luminal (URO, URO-KRT5+, and GU) subtypes. Although uncommon in this NMIBC cohort, basal tumors (3%, n = 16) had dramatically higher grade (100%, n = 16, odds ratio [OR] = 13, relative risk = 3.25) and stage, and rapid progression to muscle invasion (median progression-free survival = 35.4 months, p = 0.0001). URO, the most common subtype (46%, n = 220), showed rapid recurrence (median recurrence-free survival [RFS] = 11.5 months, p = 0.039) compared to its GU counterpart (29%, n = 137, median RFS = 16.9 months), even in patients who received intravesical immunotherapy (p = 0.049). URO-KRT5+ tumors (22%, n = 108) were typically low grade (66%, n = 71, OR = 3.7) and recurred slowly (median RFS = 38.7 months). Therefore, a simple immunohistochemical algorithm can identify clinically relevant molecular subtypes of NMIBC. In routine clinical practice, this three-antibody algorithm may help clarify diagnostic dilemmas and optimize surveillance and treatment strategies for patients.
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| 10. |
- Jandrić, Petar, et al.
(författare)
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Teaching in the Age of Covid-19
- 2020
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Ingår i: Postdigital Science and Education. - : Springer Science and Business Media LLC. - 2524-4868 .- 2524-485X. ; 2:3, s. 1069-1230
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- A collection of 84 author's testimonies and workspace photographs between 18 March and 5 May 2020.
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