| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
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| 3. |
- 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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| 4. |
- Hamann, M., et al.
(författare)
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Scenarios of Good Anthropocenes in southern Africa
- 2020
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Ingår i: Futures. - : Elsevier BV. - 0016-3287 .- 1873-6378. ; 118
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Tidskriftsartikel (refereegranskat)abstract
- In the rapidly changing and uncertain world of the Anthropocene, positive visions of the future could play a crucial role in catalysing deep social-ecological transformations to help guide humanity towards more sustainable and equitable futures. This paper presents the outcomes from a novel visioning process designed to elicit creative and inspirational future scenarios for southern Africa. The approach based scenario development on seeds of good Anthropocenes, i.e. existing initiatives or technologies that represent current, local-scale innovations for sustainability. A selection of seeds was used to create four distinct, positive visions in a participatory workshop process. Common themes that independently emerged in all four visions were i) decentralized governance and decision-making; ii) a strong emphasis on equity and empathy; iii) high levels of connectedness between people; and iv) a reinforced, respectful relationship with nature. The visions mainly differ in the extent of fusion between people and technology in everyday life, and how much nature plays a role in defining the human experience. The narratives presented here describe worlds that have undergone a more significant paradigm shift towards shared human values and stewardship of resources than is explored in most other ambient narratives for the region. These Good Anthropocene scenarios therefore demonstrate more radical, previously unimagined ways of thinking about sustainability futures on the African continent and beyond.
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| 5. |
- Holmes, Emily A., et al.
(författare)
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Multidisciplinary research priorities for the COVID-19 pandemic : a call for action for mental health science
- 2020
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Ingår i: Lancet psychiatry. - 2215-0374 .- 2215-0366. ; 7:6, s. 547-560
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Tidskriftsartikel (refereegranskat)abstract
- The coronavirus disease 2019 (COVID-19) pandemic is having a profound effect on all aspects of society, including mental health and physical health. We explore the psychological, social, and neuroscientific effects of COVID-19 and set out the immediate priorities and longer-term strategies for mental health science research. These priorities were informed by surveys of the public and an expert panel convened by the UK Academy of Medical Sciences and the mental health research charity, MQ: Transforming Mental Health, in the first weeks of the pandemic in the UK in March, 2020. We urge UK research funding agencies to work with researchers, people with lived experience, and others to establish a high level coordination group to ensure that these research priorities are addressed, and to allow new ones to be identified over time. The need to maintain high-quality research standards is imperative. International collaboration and a global perspective will be beneficial. An immediate priority is collecting high-quality data on the mental health effects of the COVID-19 pandemic across the whole population and vulnerable groups, and on brain function, cognition, and mental health of patients with COVID-19. There is an urgent need for research to address how mental health consequences for vulnerable groups can be mitigated under pandemic conditions, and on the impact of repeated media consumption and health messaging around COVID-19. Discovery, evaluation, and refinement of mechanistically driven interventions to address the psychological, social, and neuroscientific aspects of the pandemic are required. Rising to this challenge will require integration across disciplines and sectors, and should be done together with people with lived experience. New funding will be required to meet these priorities, and it can be efficiently leveraged by the UK's world-leading infrastructure. This Position Paper provides a strategy that may be both adapted for, and integrated with, research efforts in other countries.
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| 6. |
- Hutchison, Zoe L., et al.
(författare)
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A modelling evaluation of electromagnetic fields emitted by buried subsea power cables and encountered by marine animals : Considerations for marine renewable energy development
- 2021
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Ingår i: Renewable energy. - : Elsevier BV. - 0960-1481 .- 1879-0682. ; 177, s. 72-81
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Tidskriftsartikel (refereegranskat)abstract
- The expanding marine renewable energy industry will increase the prevalence of electromagnetic fields (EMFs) from power cables in coastal waters. Assessments of environmental impacts are required within licensing/permitting processes and increased prevalence of cables will increase questions concerning EMF emissions and potential cumulative impacts. It is presumed that protecting a cable by burial, may also mitigate EMF emissions and potential impacts on species. Focussing on a bundled high voltage direct current (HVDC) transmission cable, we use computational and interpretive models to explore the influence of cable properties and burial depth on the DC magnetic field (DC-MF) potentially encountered by receptive species. Greater cable pair separation increased the deviations from the geomagnetic field and while deeper burial reduced the deviations, the DC-MF was present at intensities perceivable by receptive species. An animal moving along a cable route may be exposed to variable EMFs due to varied burial depth and that combined with an animal's position in the water column determines the distance from source and EMF exposure. Modelling contextually realistic scenarios would improve assessments of potential effects. We suggest developers and cable industries make cable properties and energy transmission data available, enabling realistic modelling and environmental assessment supporting future developments.
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| 7. |
- Jeong, WooSeok, et al.
(författare)
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Automation of Active Space Selection for Multireference Methods via Machine Learning on Chemical Bond Dissociation
- 2020
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Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 16:4, s. 2389-2399
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Tidskriftsartikel (refereegranskat)abstract
- Predicting and understanding the chemical bond is one of the major challenges of computational quantum chemistry. Kohn-Sham density functional theory (KS-DFT) is the most common method, but approximate density functionals may not be able to describe systems where multiple electronic configurations are equally important. Multiconfigurational wave functions, on the other hand, can provide a detailed understanding of the electronic structures and chemical bonds of such systems. In the complete active space self-consistent field (CASSCF) method, one performs a full configuration interaction calculation in an active space consisting of active electrons and active orbitals. However, CASSCF and its variants require the selection of these active spaces. This choice is not black box; it requires significant experience and testing by the user, and thus active space methods are not considered particularly user-friendly and are employed only by a minority of quantum chemists. Our goal is to popularize these methods by making it easier to make good active space choices. We present a machine learning protocol that performs an automated selection of active spaces for chemical bond dissociation calculations of main group diatomic molecules. The protocol shows high prediction performance for a given target system as long as a properly correlated system is chosen for training. Good active spaces are correctly predicted with a considerably better success rate than random guess (larger than 80% precision for most systems studied). Our automated machine learning protocol shows that a "black-box" mode is possible for facilitating and accelerating the large-scale calculations on multireference systems where single-reference methods such as KS-DFT cannot be applied.
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| 8. |
- King, Carina, et al.
(författare)
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COVID-19—a very visible pandemic
- 2020
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Ingår i: The Lancet. - : Elsevier. - 0140-6736 .- 1474-547X. ; 396:10248, s. 15-15
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Tidskriftsartikel (refereegranskat)
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| 9. |
- King, Martin D., et al.
(författare)
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The reaction of oleic acid monolayers with gas-phase ozone at the air water interface : the effect of sub-phase viscosity, and inert secondary components
- 2020
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : ROYAL SOC CHEMISTRY. - 1463-9076 .- 1463-9084. ; 22:48, s. 28032-28044
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Tidskriftsartikel (refereegranskat)abstract
- Organic films that form on atmospheric particulate matter change the optical and cloud condensation nucleation properties of the particulate matter and consequently have implications for modern climate and climate models. The organic films are subject to attack from gas-phase oxidants present in ambient air. Here we revisit in greater detail the oxidation of a monolayer of oleic acid by gas-phase ozone at the air-water interface as this provides a model system for the oxidation reactions that occur at the air-water interface of aqueous atmospheric aerosol. Experiments were performed on monolayers of oleic acid at the air-liquid interface at atmospherically relevant ozone concentrations to investigate if the viscosity of the sub-phase influences the rate of the reaction and to determine the effect of the presence of a second component within the monolayer, stearic acid, which is generally considered to be non-reactive towards ozone, on the reaction kinetics as determined by neutron reflectometry measurements. Atmospheric aerosol can be extremely viscous. The kinetics of the reaction were found to be independent of the viscosity of the sub-phase below the monolayer over a range of moderate viscosities, eta/eta water = 1.0-7.2, demonstrating no involvement of aqueous sub-phase oxidants in the rate determining step. The kinetics of oxidation of monolayers of pure oleic acid were found to depend on the surface coverage with different behaviour observed above and below a surface coverage of oleic acid of similar to 1 x 10(18) molecule m(-2). Atmospheric aerosol are typically complex mixtures, and the presence of an additional compound in the monolayer that is inert to direct ozone oxidation, stearic acid, did not significantly change the reaction kinetics. It is demonstrated that oleic acid monolayers at the air-water interface do not leave any detectable material at the air-water interface, contradicting the previous work published in this journal which the authors now believe to be erroneous. The combined results presented here indicate that the kinetics, and thus the atmospheric chemical lifetime for unsaturated surface active materials at the air-water interface to loss by reaction with gas-phase ozone, can be considered to be independent of other materials present at either the air-water interface or in the aqueous sub-phase.
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| 10. |
- Lantero Rodriguez, Juan, et al.
(författare)
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Plasma p-tau181 accurately predicts Alzheimer's disease pathology at least 8years prior to post-mortem and improves the clinical characterisation of cognitive decline.
- 2020
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Ingår i: Acta neuropathologica. - : Springer Science and Business Media LLC. - 1432-0533 .- 0001-6322. ; 140:3, s. 267-278
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Tidskriftsartikel (refereegranskat)abstract
- The neuropathological confirmation of amyloid-β (Aβ) plaques and tau neurofibrillary tangles (NFT) remains the gold standard for a definitive diagnosis of Alzheimer's disease (AD). Nowadays, the in vivo diagnosis of AD is greatly aided by both cerebrospinal fluid (CSF) and positron emission tomography (PET) biomarkers. Although highly accurate, their broad implementation is restricted by high cost, limited accessibility and invasiveness. We recently developed a high-performance, ultrasensitive immunoassay for the quantification of tau phosphorylated at threonine-181 (p-tau181) in plasma, which identifies AD pathophysiology with high accuracy. However, it remains unclear whether plasma p-tau181, measured years before the death, can predict the eventual neuropathological confirmation of AD, and successfully discriminates AD from non-AD dementia pathologies. We studied a unique cohort of 115 individuals with longitudinal blood collections with clinical evaluation at 8, 4 and 2years prior to neuropathological assessment at death. The results demonstrate that plasma p-tau181 associates better with AD neuropathology and Braak staging than a clinical diagnosis 8years before post-mortem. Moreover, while all patients had a diagnosis of AD dementia during life, plasma p-tau181 proved to discriminate AD from non-AD pathologies with high accuracy (AUC=97.4%, 95% CI=94.1-100%) even 8years before death. Additionally, the longitudinal trajectory of plasma p-tau181 was assessed in all patients. We found that the main increases in plasma p-tau181 occurred between 8 and 4years prior to death in patients with AD neuropathology and later plateauing. In contrast, non-AD pathologies and controls exhibited minor, albeit significant, increases in p-tau181 up until death. Overall, our study demonstrates that plasma p-tau181 is highly predictive and specific of AD neuropathology years before post-mortem examination. These data add further support for the use of plasma p-tau181 to aid clinical management in primary care and recruitment for clinical trials.
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