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| 2. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)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. |
- Angelopoulus, M., et al.
(author)
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Physical properties of sea ice cores from site MCS_FYI measured on legs 1 to 3 of the MOSAiC expedition.
- 2022
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In: PANGAEA.
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Other publication (other academic/artistic)abstract
- We present sea ice temperature and salinity data from first-year ice (FYI) and second-year ice (SYI) relevant to the temporal development of sea ice permeability and brine drainage efficiency from the early growth phase in October 2019 to the onset of spring warming in May 2020. Our dataset was collected in the central Arctic Ocean during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) Expedition in 2019 to 2020. MOSAiC was an international transpolar drift expedition in which the German icebreaker RV Polarstern anchored into an ice floe to gain new insights into Arctic climate over a full annual cycle. In October 2019, RV Polarstern moored to an ice floe in the Siberian sector of the Arctic at 85 degrees north and 137 degrees east to begin the drift towards the North Pole and the Fram Strait via the Transpolar Drift Stream. The data presented here were collected during the first three legs of the expedition, so all the coring activities took place on the same floe. The end dates of legs 1, 2, and 3 were 13 December, 24 February, and 4 June, respectively. The dataset contributed to a baseline study entitled, Deciphering the properties of different Arctic ice types during the growth phase of the MOSAiC floes: Implications for future studies. The study highlights downward directed gas pathways in FYI and SYI by inferring sea ice permeability and potential brine release from several time series of temperature and salinity measurements. The physical properties presented in this paper lay the foundation for subsequent analyses on actual gas contents measured in the ice cores, as well as air-ice and ice-ocean gas fluxes. Sea ice cores were collected with a Kovacs Mark II 9 cm diameter corer. To measure ice temperatures, about 4.5 cm deep holes were drilled into the core (intervals varied by site and leg) . The temperatures were measured by a digital thermometer within minutes after the cores were retrieved. The ice cores were placed into pre-labelled plastic sleeves sealed at the bottom end. The ice cores were transported to RV Polarstern and stored in a -20 degrees Celsius freezer. Each of the cores was sub-sampled, melted at room temperature, and processed for salinity within one or two days. The practical salinity was estimated by measuring the electrical conductivity and temperature of the melted samples using a WTW Cond 3151 salinometer equipped with a Tetra-Con 325 four-electrode conductivity cell. The practical salinity represents the the salinity estimated from the electrical conductivity of the solution. The dataset also contains derived variables, including sea ice density, brine volume fraction, and the Rayleigh number.
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| 4. |
- Angelopoulus, M., et al.
(author)
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Physical properties of sea ice cores from site MCS-SYI measured on legs 1 to 3 of the MOSAiC expedition
- 2022
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In: PANGAEA.
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Other publication (other academic/artistic)abstract
- We present sea ice temperature and salinity data from first-year ice (FYI) and second-year ice (SYI) relevant to the temporal development of sea ice permeability and brine drainage efficiency from the early growth phase in October 2019 to the onset of spring warming in May 2020. Our dataset was collected in the central Arctic Ocean during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) Expedition in 2019 to 2020. MOSAiC was an international transpolar drift expedition in which the German icebreaker RV Polarstern anchored into an ice floe to gain new insights into Arctic climate over a full annual cycle. In October 2019, RV Polarstern moored to an ice floe in the Siberian sector of the Arctic at 85 degrees north and 137 degrees east to begin the drift towards the North Pole and the Fram Strait via the Transpolar Drift Stream. The data presented here were collected during the first three legs of the expedition, so all the coring activities took place on the same floe. The end dates of legs 1, 2, and 3 were 13 December, 24 February, and 4 June, respectively. The dataset contributed to a baseline study entitled, Deciphering the properties of different Arctic ice types during the growth phase of the MOSAiC floes: Implications for future studies. The study highlights downward directed gas pathways in FYI and SYI by inferring sea ice permeability and potential brine release from several time series of temperature and salinity measurements. The physical properties presented in this paper lay the foundation for subsequent analyses on actual gas contents measured in the ice cores, as well as air-ice and ice-ocean gas fluxes. Sea ice cores were collected with a Kovacs Mark II 9 cm diameter corer. To measure ice temperatures, about 4.5 cm deep holes were drilled into the core (intervals varied by site and leg) . The temperatures were measured by a digital thermometer within minutes after the cores were retrieved. The ice cores were placed into pre-labelled plastic sleeves sealed at the bottom end. The ice cores were transported to RV Polarstern and stored in a -20 degrees Celsius freezer. Each of the cores was sub-sampled, melted at room temperature, and processed for salinity within one or two days. The practical salinity was estimated by measuring the electrical conductivity and temperature of the melted samples using a WTW Cond 3151 salinometer equipped with a Tetra-Con 325 four-electrode conductivity cell. The practical salinity represents the the salinity estimated from the electrical conductivity of the solution. The dataset also contains derived variables, including sea ice density, brine volume fraction, and the Rayleigh number.
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| 5. |
- Salganik, E., et al.
(author)
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Temporal evolution of under-ice meltwater layers and false bottoms and their impact on summer Arctic sea ice mass balance
- 2023
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In: Elementa: Science of the Anthropocene. - 2325-1026. ; 11:1
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Journal article (peer-reviewed)abstract
- Low-salinity meltwater from Arctic sea ice and its snow cover accumulates and creates under-ice meltwater layers below sea ice. These meltwater layers can result in the formation of new ice layers, or false bottoms, at the interface of this low-salinity meltwater and colder seawater. As part of the Multidisciplinary drifting Observatory for the Study of the Arctic Climate (MOSAiC), we used a combination of sea ice coring, temperature profiles from thermistor strings and underwater multibeam sonar surveys with a remotely operated vehicle (ROV) to study the areal coverage and temporal evolution of under-ice meltwater layers and false bottoms during the summer melt season from mid-June until late July. ROV surveys indicated that the areal coverage of false bottoms for a part of the MOSAiC Central Observatory (350 by 200 m2) was 21%. Presence of false bottoms reduced bottom ice melt by 7-8% due to the local decrease in the ocean heat flux, which can be described by a thermodynamic model. Under-ice meltwater layer thickness was larger below first-year ice and thinner below thicker second-year ice. We also found that thick ice and ridge keels confined the areas in which under-ice meltwater accumulated, preventing its mixing with underlying seawater. While a thermodynamic model could reproduce false bottom growth and melt, it could not describe the observed bottom melt rates of the ice above false bottoms. We also show that the evolution of under-ice meltwaterlayer salinity below first-year ice is linked to brine flushing from the above sea ice and accumulating in the meltwater layer above the false bottom. The results of this study aid in estimating the contribution of underice meltwater layers and false bottoms to the mass balance and salt budget for Arctic summer sea ice.
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| 7. |
- Saegerman, Claude, et al.
(author)
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First Expert Elicitation of Knowledge on Possible Drivers of Observed Increasing Human Cases of Tick-Borne Encephalitis in Europe
- 2023
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In: Viruses. - : MDPI AG. - 1999-4915. ; 15:3
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Journal article (peer-reviewed)abstract
- Tick-borne encephalitis (TBE) is a viral disease endemic in Eurasia. The virus is mainly transmitted to humans via ticks and occasionally via the consumption of unpasteurized milk products. The European Centre for Disease Prevention and Control reported an increase in TBE incidence over the past years in Europe as well as the emergence of the disease in new areas. To better understand this phenomenon, we investigated the drivers of TBE emergence and increase in incidence in humans through an expert knowledge elicitation. We listed 59 possible drivers grouped in eight domains and elicited forty European experts to: (i) allocate a score per driver, (ii) weight this score within each domain, and (iii) weight the different domains and attribute an uncertainty level per domain. An overall weighted score per driver was calculated, and drivers with comparable scores were grouped into three terminal nodes using a regression tree analysis. The drivers with the highest scores were: (i) changes in human behavior/activities; (ii) changes in eating habits or consumer demand; (iii) changes in the landscape; (iv) influence of humidity on the survival and transmission of the pathogen; (v) difficulty to control reservoir(s) and/or vector(s); (vi) influence of temperature on virus survival and transmission; (vii) number of wildlife compartments/groups acting as reservoirs or amplifying hosts; (viii) increase of autochthonous wild mammals; and (ix) number of tick species vectors and their distribution. Our results support researchers in prioritizing studies targeting the most relevant drivers of emergence and increasing TBE incidence.
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| 8. |
- São Pedro, Mariana N., et al.
(author)
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Real-time detection of mAb aggregates in an integrated downstream process
- 2023
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In: Biotechnology and Bioengineering. - 0006-3592. ; 120:10, s. 2989-3000
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Journal article (peer-reviewed)abstract
- The implementation of continuous processing in the biopharmaceutical industry is hindered by the scarcity of process analytical technologies (PAT). To monitor and control a continuous process, PAT tools will be crucial to measure real-time product quality attributes such as protein aggregation. Miniaturizing these analytical techniques can increase measurement speed and enable faster decision-making. A fluorescent dye (FD)-based miniaturized sensor has previously been developed: a zigzag microchannel which mixes two streams under 30 s. Bis-ANS and CCVJ, two established FDs, were employed in this micromixer to detect aggregation of the biopharmaceutical monoclonal antibody (mAb). Both FDs were able to robustly detect aggregation levels starting at 2.5%. However, the real-time measurement provided by the microfluidic sensor still needs to be implemented and assessed in an integrated continuous downstream process. In this work, the micromixer is implemented in a lab-scale integrated system for the purification of mAbs, established in an ÄKTA™ unit. A viral inactivation and two polishing steps were reproduced, sending a sample of the product pool after each phase directly to the microfluidic sensor for aggregate detection. An additional UV sensor was connected after the micromixer and an increase in its signal would indicate that aggregates were present in the sample. The at-line miniaturized PAT tool provides a fast aggregation measurement, under 10 min, enabling better process understanding and control.
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| 9. |
- Van Wijk, Rob C., 1991-, et al.
(author)
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Anti‐tuberculosis effect of isoniazid scales accurately from zebrafish to humans
- 2020
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In: British Journal of Pharmacology. - : Wiley. - 0007-1188 .- 1476-5381. ; 177:24, s. 5518-5533
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Journal article (peer-reviewed)abstract
- Background and purposeThere is a strong need for innovation in anti-tuberculosis drug development. The zebrafish larva is an attractive disease model in tuberculosis research. To translate pharmacological findings to higher vertebrates, including humans, the internal exposure of drugs needs to be quantified and linked to observed response.Experimental approachIn zebrafish studies, drugs are commonly dissolved in the external water, posing a challenge to quantify internal exposure. We developed experimental methods to quantify internal exposure, including nano-scale blood sampling, and to quantify the bacterial burden, using automated fluorescence imaging analysis, with isoniazid as paradigm compound. We used pharmacokinetic-pharmacodynamic modelling to quantify the exposure-response relationship responsible for the antibiotic response. To translate isoniazid response to humans, the quantitative exposure-response relationship in zebrafish was linked to simulated concentration-time profiles in humans, and two quantitative translational factors on sensitivity to isoniazid and stage of infection were included.Key resultsBlood concentration was only 20% of the external drug concentration. The bacterial burden increased exponentially and an isoniazid dose corresponding to 15 mg·L-1internal concentration (minimum inhibitory concentration) lead to bacteriostasis of the mycobacterial infection in the zebrafish. The concentration-effect relationship was quantified, and based on that relationship and the translational factors, the isoniazid response was translated to humans, which correlated well with observed data.Conclusions and implicationsThis proof-of-concept confirms the potential of the zebrafish larvae as tuberculosis disease model in translational pharmacology, and contributes to innovative anti-tuberculosis drug development which is strongly needed.
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| 10. |
- Watson-Parris, D., et al.
(author)
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ClimateBench v1.0 : A Benchmark for Data-Driven Climate Projections
- 2022
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In: Journal of Advances in Modeling Earth Systems. - 1942-2466. ; 14:10
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Journal article (peer-reviewed)abstract
- Many different emission pathways exist that are compatible with the Paris climate agreement, and many more are possible that miss that target. While some of the most complex Earth System Models have simulated a small selection of Shared Socioeconomic Pathways, it is impractical to use these expensive models to fully explore the space of possibilities. Such explorations therefore mostly rely on one-dimensional impulse response models, or simple pattern scaling approaches to approximate the physical climate response to a given scenario. Here we present ClimateBench-the first benchmarking framework based on a suite of Coupled Model Intercomparison Project, AerChemMIP and Detection-Attribution Model Intercomparison Project simulations performed by a full complexity Earth System Model, and a set of baseline machine learning models that emulate its response to a variety of forcers. These emulators can predict annual mean global distributions of temperature, diurnal temperature range and precipitation (including extreme precipitation) given a wide range of emissions and concentrations of carbon dioxide, methane and aerosols, allowing them to efficiently probe previously unexplored scenarios. We discuss the accuracy and interpretability of these emulators and consider their robustness to physical constraints such as total energy conservation. Future opportunities incorporating such physical constraints directly in the machine learning models and using the emulators for detection and attribution studies are also discussed. This opens a wide range of opportunities to improve prediction, robustness and mathematical tractability. We hope that by laying out the principles of climate model emulation with clear examples and metrics we encourage engagement from statisticians and machine learning specialists keen to tackle this important and demanding challenge.
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