| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Cotter, Chris, et al.
(author)
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Piloting a programme tool to evaluate malaria case investigation and reactive case detection activities : results from 3 settings in the Asia Pacific
- 2017
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In: Malaria Journal. - : Springer Science and Business Media LLC. - 1475-2875. ; 16
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Journal article (peer-reviewed)abstract
- Background: Case investigation and reactive case detection (RACD) activities are widely-used in low transmission settings to determine the suspected origin of infection and identify and treat malaria infections nearby to the index patient household. Case investigation and RACD activities are time and resource intensive, include methodologies that vary across eliminating settings, and have no standardized metrics or tools available to monitor and evaluate them. Methods: In response to this gap, a simple programme tool was developed for monitoring and evaluating (M&E) RACD activities and piloted by national malaria programmes. During the development phase, four modules of the RACD M&E tool were created to assess and evaluate key case investigation and RACD activities and costs. A pilot phase was then carried out by programme implementers between 2013 and 2015, during which malaria surveillance teams in three different settings (China, Indonesia, Thailand) piloted the tool over a period of 3 months each. This study describes summary results of the pilots and feasibility and impact of the tool on programmes. Results: All three study areas implemented the RACD M&E tool modules, and pilot users reported the tool and evaluation process were helpful to identify gaps in RACD programme activities. In the 45 health facilities evaluated, 71.8% (97/135; min 35.3-max 100.0%) of the proper notification and reporting forms and 20.0% (27/135; min 0.0-max 100.0%) of standard operating procedures (SOPs) were available to support malaria elimination activities. The tool highlighted gaps in reporting key data indicators on the completeness for malaria case reporting (98.8%; min 93.3-max 100.0%), case investigations (65.6%; min 61.8-max 78.4%) and RACD activities (70.0%; min 64.7-max 100.0%). Evaluation of the SOPs showed that knowledge and practices of malaria personnel varied within and between study areas. Average monthly costs for conducting case investigation and RACD activities showed variation between study areas (min USD $844.80-max USD $2038.00) for the malaria personnel, commodities, services and other costs required to carry out the activities. Conclusion: The RACD M&E tool was implemented in the three pilot areas, identifying key gaps that led to impacts on programme decision making. Study findings support the need for routine M&E of malaria case reporting, case investigation and RACD activities. Scale-up of the RACD M&E tool in malaria-eliminating settings will contribute to improved programme performance to the high level that is required to reach elimination.
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| 3. |
- Huang, Kun, et al.
(author)
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Enhanced peak growth of global vegetation and its key mechanisms
- 2018
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In: Nature Ecology and Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 2:12, s. 1897-1905
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Journal article (peer-reviewed)abstract
- The annual peak growth of vegetation is critical in characterizing the capacity of terrestrial ecosystem productivity and shaping the seasonality of atmospheric CO2 concentrations. The recent greening of global lands suggests an increasing trend of terrestrial vegetation growth, but whether or not the peak growth has been globally enhanced still remains unclear. Here, we use two global datasets of gross primary productivity (GPP) and a satellite-derived Normalized Difference Vegetation Index (NDVI) to characterize recent changes in annual peak vegetation growth (that is, GPPmax and NDVImax). We demonstrate that the peak in the growth of global vegetation has been linearly increasing during the past three decades. About 65% of the NDVImax variation is evenly explained by expanding croplands (21%), rising CO2 (22%) and intensifying nitrogen deposition (22%). The contribution of expanding croplands to the peak growth trend is substantiated by measurements from eddy-flux towers, sun-induced chlorophyll fluorescence and a global database of plant traits, all of which demonstrate that croplands have a higher photosynthetic capacity than other vegetation types. The large contribution of CO2 is also supported by a meta-analysis of 466 manipulative experiments and 15 terrestrial biosphere models. Furthermore, we show that the contribution of GPPmax to the change in annual GPP is less in the tropics than in other regions. These multiple lines of evidence reveal an increasing trend in the peak growth of global vegetation. The findings highlight the important roles of agricultural intensification and atmospheric changes in reshaping the seasonality of global vegetation growth.
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| 4. |
- Huang, Yuanyuan, et al.
(author)
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Hidden spin polarization in the centrosymmetric Mo S2 crystal revealed via elliptically polarized terahertz emission
- 2020
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In: Physical Review B. - 2469-9950. ; 102:8
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Journal article (peer-reviewed)abstract
- The spin polarization in centrosymmetric molybdenum disulfide (MoS2) bulk crystal is recorded by helicity dependent photocurrent exposed as elliptically polarized terahertz (THz) emission. We assign this observation to hidden spin polarization due to the local Dresselhaus effect induced by the molybdenum atomic site asymmetry. This spin polarization induces ultrafast optically controlled circular photogalvanic current that results in elliptically polarized THz emission. Furthermore, this THz radiation exhibits a helicity dependent bleaching effect under opposite circularly polarized excitations due to the spin relaxation. Our results demonstrate the viability of all-optical control of hidden spin polarization in two-dimensional materials and propose the applicability of the THz emission spectroscopy as a sensitive and contactless method to study spintronic physics in two-dimensional materials.
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| 5. |
- Li, Haiyan, et al.
(author)
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Fragmentation inside proton-transfer-reaction-based mass spectrometers limits the detection of ROOR and ROOH peroxides
- 2022
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In: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 15:6, s. 1811-1827
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Journal article (peer-reviewed)abstract
- Proton transfer reaction (PTR) is a commonly applied ionization technique for mass spectrometers, in which hydronium ions (H3O+) transfer a proton to analytes with higher proton affinities than the water molecule. This method has most commonly been used to quantify volatile hydrocarbons, but later-generation PTR instruments have been designed for better throughput of less volatile species, allowing detection of more functionalized molecules as well. For example, the recently developed Vocus PTR time-of-flight mass spectrometer (PTR-TOF) has been shown to agree well with an iodide-adduct-based chemical ionization mass spectrometer (CIMS) for products with 3-5 O atoms from oxidation of monoterpenes (C10H16). However, while several different types of CIMS instruments (including those using iodide) detect abundant signals also at dimeric species, believed to be primarily ROOR peroxides, no such signals have been observed in the Vocus PTR even though these compounds fulfil the condition of having higher proton affinity than water. More traditional PTR instruments have been limited to volatile molecules as the inlets have not been designed for transmission of easily condensable species. Some newer instruments, like the Vocus PTR, have overcome this limitation but are still not able to detect the full range of functionalized products, suggesting that other limitations need to be considered. One such limitation, well-documented in PTR literature, is the tendency of protonation to lead to fragmentation of some analytes. In this work, we evaluate the potential for PTR to detect dimers and the most oxygenated compounds as these have been shown to be crucial for forming atmospheric aerosol particles. We studied the detection of dimers using a Vocus PTR-TOF in laboratory experiments, as well as through quantum chemical calculations. Only noisy signals of potential dimers were observed during experiments on the ozonolysis of the monoterpene alpha-pinene, while a few small signals of dimeric compounds were detected during the ozonolysis of cyclohexene. During the latter experiments, we also tested varying the pressures and electric fields in the ionization region of the Vocus PTR-TOF, finding that only small improvements were possible in the relative dimer contributions. Calculations for model ROOR and ROOH systems showed that most of these peroxides should fragment partially following protonation. With the inclusion of additional energy from the ion-molecule collisions driven by the electric fields in the ionization source, computational results suggest substantial or nearly complete fragmentation of dimers. Our study thus suggests that while the improved versions of PTR-based mass spectrometers are very powerful tools for measuring hydrocarbons and their moderately oxidized products, other types of CIMS are likely more suitable for the detection of ROOR and ROOH species.
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| 6. |
- Li, Linjie, et al.
(author)
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Gas-to-Particle Partitioning of Products from Ozonolysis of Δ3-Carene and the Effect of Temperature and Relative Humidity
- 2024
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In: JOURNAL OF PHYSICAL CHEMISTRY A. - 1089-5639 .- 1520-5215. ; 128:5, s. 918-928
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Journal article (peer-reviewed)abstract
- Formation of oxidized products from Delta(3)-carene (C10H16) ozonolysis and their gas-to-particle partitioning at three temperatures (0, 10, and 20 degrees C) under dry conditions (<2% RH) and also at 10 degrees C under humid (78% RH) conditions were studied using a time-of-flight chemical ionization mass spectrometer (ToF-CIMS) combined with a filter inlet for gases and aerosols (FIGAERO). The Delta(3)-carene ozonolysis products detected by the FIGAERO-ToF-CIMS were dominated by semivolatile organic compounds (SVOCs). The main effect of increasing temperature or RH on the product distribution was an increase in fragmentation of monomer compounds (from C-10 to C-7 compounds), potentially via alkoxy scission losing a C-3 group. The equilibrium partitioning coefficient estimated according to equilibrium partitioning theory shows that the measured SVOC products distribute more into the SOA phase as the temperature decreases from 20 to 10 and 0 degrees C and for most products as the RH increases from <2 to 78%. The temperature dependency of the saturation vapor pressure (above an assumed liquid state), derived from the partitioning method, also allows for a direct way to obtain enthalpy of vaporization for the detected species without accessibility of authentic standards of the pure substances. This method can provide physical properties, beneficial for, e.g., atmospheric modeling, of complex multifunctional oxidation products.
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| 7. |
- Luo, Yiqi, et al.
(author)
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Matrix Approach to Land Carbon Cycle Modeling
- 2022
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In: Journal of Advances in Modeling Earth Systems. - 1942-2466. ; 14:7
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Research review (peer-reviewed)abstract
- Land ecosystems contribute to climate change mitigation by taking up approximately 30% of anthropogenically emitted carbon. However, estimates of the amount and distribution of carbon uptake across the world's ecosystems or biomes display great uncertainty. The latter hinders a full understanding of the mechanisms and drivers of land carbon uptake, and predictions of the future fate of the land carbon sink. The latter is needed as evidence to inform climate mitigation strategies such as afforestation schemes. To advance land carbon cycle modeling, we have developed a matrix approach. Land carbon cycle models use carbon balance equations to represent carbon exchanges among pools. Our approach organizes this set of equations into a single matrix equation without altering any processes of the original model. The matrix equation enables the development of a theoretical framework for understanding the general, transient behavior of the land carbon cycle. While carbon input and residence time are used to quantify carbon storage capacity at steady state, a third quantity, carbon storage potential, integrates fluxes with time to define dynamic disequilibrium of the carbon cycle under global change. The matrix approach can help address critical contemporary issues in modeling, including pinpointing sources of model uncertainty and accelerating spin-up of land carbon cycle models by tens of times. The accelerated spin-up liberates models from the computational burden that hinders comprehensive parameter sensitivity analysis and assimilation of observational data to improve model accuracy. Such computational efficiency offered by the matrix approach enables substantial improvement of model predictions using ever-increasing data availability. Overall, the matrix approach offers a step change forward for understanding and modeling the land carbon cycle.
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| 8. |
- Tao, Feng, et al.
(author)
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Convergence in simulating global soil organic carbon by structurally different models after data assimilation
- 2024
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In: Global Change Biology. - 1354-1013 .- 1365-2486. ; 30:5
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Journal article (peer-reviewed)abstract
- Current biogeochemical models produce carbon–climate feedback projections with large uncertainties, often attributed to their structural differences when simulating soil organic carbon (SOC) dynamics worldwide. However, choices of model parameter values that quantify the strength and represent properties of different soil carbon cycle processes could also contribute to model simulation uncertainties. Here, we demonstrate the critical role of using common observational data in reducing model uncertainty in estimates of global SOC storage. Two structurally different models featuring distinctive carbon pools, decomposition kinetics, and carbon transfer pathways simulate opposite global SOC distributions with their customary parameter values yet converge to similar results after being informed by the same global SOC database using a data assimilation approach. The converged spatial SOC simulations result from similar simulations in key model components such as carbon transfer efficiency, baseline decomposition rate, and environmental effects on carbon fluxes by these two models after data assimilation. Moreover, data assimilation results suggest equally effective simulations of SOC using models following either first-order or Michaelis–Menten kinetics at the global scale. Nevertheless, a wider range of data with high-quality control and assurance are needed to further constrain SOC dynamics simulations and reduce unconstrained parameters. New sets of data, such as microbial genomics-function relationships, may also suggest novel structures to account for in future model development. Overall, our results highlight the importance of observational data in informing model development and constraining model predictions.
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| 9. |
- Tao, Feng, et al.
(author)
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Microbial carbon use efficiency promotes global soil carbon storage
- 2023
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In: Nature. - 0028-0836 .- 1476-4687. ; 618:7967, s. 981-985
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Journal article (peer-reviewed)abstract
- Soils store more carbon than other terrestrial ecosystems. How soil organic carbon (SOC) forms and persists remains uncertain, which makes it challenging to understand how it will respond to climatic change. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.
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| 10. |
- Thomsen, Ditte, et al.
(author)
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The effect of temperature and relative humidity on secondary organic aerosol formation from ozonolysis of Δ3-carene
- 2024
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In: Environmental Science: Atmospheres. - 2634-3606. ; 4:1, s. 88-103
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Journal article (peer-reviewed)abstract
- This study investigates the effects of temperature and relative humidity (RH) on the formation of secondary organic aerosol (SOA) from Δ3-carene, a prevalent monoterpene in boreal forests. Dark ozonolysis experiments of 10 ppb Δ3-carene were conducted in the Aarhus University Research on Aerosol (AURA) atmospheric simulation chamber at temperatures of 0, 10, and 20 °C. Under dry conditions (RH < 2%), the SOA formation in terms of both particle number and mass concentration shows minimal temperature dependence. This is in contrast to previous findings at higher initial concentrations and suggests an effect of VOC loading for Δ3-carene. Interestingly, the mass fraction of key oxidation products (cis-3-caric acid, cis-3-caronic acid) exhibit a temperature dependence suggesting continuous condensation at lower temperatures, while evaporation and further reactions over time become more favourable at higher temperatures. The oxygen-to-carbon ratios in the particle phase and the occurrence of highly oxygenated organic molecules (HOM) in the gas phase show modest increases with higher temperatures. Predictions from the Aerosol Dynamics and Gas- and Particle-Phase Chemistry Kinetic Multilayer Model (ADCHAM) agrees with the experimental results regarding both physical particle properties and aerosol composition considering the experimental uncertainties. At high RH (∼80%, 10 °C), a considerable increase in the particle nucleation rate and particle number concentration is observed compared to experiments under dry conditions. This is likely due to enhanced particle nucleation resulting from more stable cluster formation of water and inorganics at increased RH. However, RH does not affect the particle mass concentration.
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