| 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. |
- Allentoft, Morten E., et al.
(författare)
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Population genomics of post-glacial western Eurasia
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625:7994, s. 301-311
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Tidskriftsartikel (refereegranskat)abstract
- Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
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| 3. |
- Søgaard Jørgensen, Peter, et al.
(författare)
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Coevolutionary Governance of Antibiotic and Pesticide Resistance
- 2020
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Ingår i: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 35:6, s. 484-494
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Forskningsöversikt (refereegranskat)abstract
- Development of new biocides has dominated human responses to evolution of antibiotic and pesticide resistance. Increasing and uniform biocide use, the spread of resistance genes, and the lack of new classes of compounds indicate the importance of navigating toward more sustainable coevolutionary dynamics between human culture and species that evolve resistance. To inform this challenge, we introduce the concept of coevolutionary governance and propose three priorities for its implementation: (i) new norms and mental models for lowering use, (ii) diversifying practices to reduce directional selection, and (iii) investment in collective action institutions to govern connectivity. We highlight the availability of solutions that facilitate broader sustainable development, which for antibiotic resistance include improved sanitation and hygiene, strong health systems, and decreased meat consumption.
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| 4. |
- Carriere, Yves, et al.
(författare)
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Governing evolution : A socioecological comparison of resistance management for insecticidal transgenic Bt crops among four countries
- 2020
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Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 49:1, s. 1-16
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Forskningsöversikt (refereegranskat)abstract
- Cooperative management of pest susceptibility to transgenic Bacillus thuringiensis (Bt) crops is pursued worldwide in a variety of forms and to varying degrees of success depending on context. We examine this context using a comparative socioecological analysis of resistance management in Australia, Brazil, India, and the United States. We find that a shared understanding of resistance risks among government regulators, growers, and other actors is critical for effective governance. Furthermore, monitoring of grower compliance with resistance management requirements, surveillance of resistance, and mechanisms to support rapid implementation of remedial actions are essential to achieve desirable outcomes. Mandated resistance management measures, strong coordination between actors, and direct linkages between the group that appraises resistance risks and growers also appear to enhance prospects for effective governance. Our analysis highlights factors that could improve current governance systems and inform other initiatives to conserve susceptibility as a contribution to the cause of public good.
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| 5. |
- Högås, Marcus, 1991-
(författare)
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Was Einstein Wrong? : Theoretical and observational constraints on massive gravity
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- For more than a century, Einstein's theory of general relativity has described gravitational phenomena with astonishing precision. However, for the theory to fit observations we need to add two elusive substances: dark energy and dark matter. Together they add up to 95% of the energy budget of the Universe. Yet, we do not know what these substances are. Another question mark is the expansion rate of the Universe; two incompatible values are obtained depending on the measuring method. These problems (dark energy, dark matter, and the expansion rate) belong to the big questions within gravity today and they may be interpreted as signs that general relativity is not the final theory for gravity. As an alternative, in this thesis we analyze an extended theory of gravity called bimetric gravity. In general relativity (GR), gravity is massless which means that gravitational waves propagate at the speed of light. Hence, a natural extension is to consider theories where gravity has a mass. This is precisely what bimetric gravity achieves. The theoretical consistency of this theory is firmly established but it is also crucial to test if the theory agrees with observations. In fact, in this theory there are two types of gravitational waves/fields, one massless as in GR but also one massive. When observing gravitational phenomena, we observe a mix of the two. Depending on the mixing and on the mass of the massive field, observational signatures appear for example on cosmological scales, in gravitational wave events or on solar-system scales. Until recently the phenomenology of the full theory was still uncharted, and an important question was if all observational tests could be satisfied at the same time. To address this, we devised a unified framework that enables straightforward comparison between constraints from different probes, without being restricted to a particular region of the parameter space. The result is that bimetric gravity is compatible with observations and even fit data slightly better than GR. Together with the fact that the dark energy can be explained by the interaction between the two gravitational fields, we have shown that the theory is a viable dark energy candidate. At the same time, the observational data provides a substantial restriction on the parameter space that excludes many of the popular models in the literature – an important result in and of itself.A longstanding issue within this theory has been to predict the growth of structure while avoiding exponential instabilities. Here, we propose a simple model which solves the full, nonlinear equations of motion, which can be used to calculate the growth of structure, without any instabilities. We also describe our work towards a framework for calculating the process of gravitational collapse in this theory where we manage to solve the equations numerically for a short time interval. The results indicate that the gravitational collapse proceeds as in general relativity, assuming that the initial conditions are similar.Future work is needed to decide whether bimetric gravity can solve any of the other big questions within gravity today, such as the discrepant expansion rate of the Universe. In this thesis, we show that it is an observationally viable dark energy candidate that exhibits novel gravitational features. In short, gravity can be massive.
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| 6. |
- Jaromin, Anna, et al.
(författare)
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Liposomal formulation of a new antifungal hybrid compound provides protection against Candida auris in the ex vivo skin colonization model.
- 2024
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Ingår i: Antimicrobial Agents and Chemotherapy. - 1098-6596. ; 68:1
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Tidskriftsartikel (refereegranskat)abstract
- The newly emerged pathogen, Candida auris, presents a serious threat to public health worldwide. This multidrug-resistant yeast often colonizes and persists on the skin of patients, can easily spread from person to person, and can cause life-threatening systemic infections. New antifungal therapies are therefore urgently needed to limit and control both superficial and systemic C. auris infections. In this study, we designed a novel antifungal agent, PQA-Az-13, that contains a combination of indazole, pyrrolidine, and arylpiperazine scaffolds substituted with a trifluoromethyl moiety. PQA-Az-13 demonstrated antifungal activity against biofilms of a set of 10 different C. auris clinical isolates, representing all four geographical clades distinguished within this species. This compound showed strong activity, with MIC values between 0.67 and 1.25 µg/mL. Cellular proteomics indicated that PQA-Az-13 partially or completely inhibited numerous enzymatic proteins in C. auris biofilms, particularly those involved in both amino acid biosynthesis and metabolism processes, as well as in general energy-producing processes. Due to its hydrophobic nature and limited aqueous solubility, PQA-Az-13 was encapsulated in cationic liposomes composed of soybean phosphatidylcholine (SPC), 1,2-dioleoyloxy-3-trimethylammonium-propane chloride (DOTAP), and N-(carbonyl-methoxypolyethylene glycol-2000)-1,2-distearoyl- sn-glycero-3-phosphoethanolamine, sodium salt (DSPE-PEG 2000), and characterized by biophysical and spectral techniques. These PQA-Az-13-loaded liposomes displayed a mean size of 76.4 nm, a positive charge of +45.0 mV, a high encapsulation efficiency of 97.2%, excellent stability, and no toxicity to normal human dermal fibroblasts. PQA-Az-13 liposomes demonstrated enhanced antifungal activity levels against both C. auris in in vitro biofilms and ex vivo skin colonization models. These initial results suggest that molecules like PQA-Az-13 warrant further study and development.
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| 7. |
- Lang, Justin J., et al.
(författare)
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Top 10 International Priorities for Physical Fitness Research and Surveillance Among Children and Adolescents : A Twin-Panel Delphi Study
- 2023
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Ingår i: Sports Medicine. - New Zealand : Adis International Ltd.. - 0112-1642 .- 1179-2035. ; 53:2, s. 549-564
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Tidskriftsartikel (refereegranskat)abstract
- Background The measurement of physical fitness has a history that dates back nearly 200 years. Recently, there has been an increase in international research and surveillance on physical fitness creating a need for setting international priorities that could help guide future efforts. Objective This study aimed to produce a list of the top 10 international priorities for research and surveillance on physical fitness among children and adolescents. Methods Using a twin-panel Delphi method, two independent panels consisting of 46 international experts were identified (panel 1 = 28, panel 2 = 18). The panel participants were asked to list up to five priorities for research or surveillance (round 1), and then rated the items from their own panel on a 5-point Likert scale of importance (round 2). In round 3, experts were asked to rate the priorities identified by the other panel. Results There was strong between-panel agreement (panel 1: r(s) = 0.76, p < 0.01; panel 2: r(s) = 0.77, p < 0.01) in the priorities identified. The list of the final top 10 priorities included (i) "conduct longitudinal studies to assess changes in fitness and associations with health". This was followed by (ii) "use fitness surveillance to inform decision making", and (iii) "implement regular and consistent international/national fitness surveys using common measures". Conclusions The priorities identified in this study provide guidance for future international collaborations and research efforts on the physical fitness of children and adolescents over the next decade and beyond.
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| 8. |
- Renk, Janina J., 1990-
(författare)
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Delving in the Dark : Searching for Signatures of Non-Standard Physics in Cosmological and Astrophysical Observables
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The dark sectors of our Universe, dark matter and dark energy, together constitute about 96 % of the total energy content of the Universe. To date, we only have observational evidence for their existence. What is still lacking is a complete theoretical framework consistent with all observational data to embed a dark matter particle or component into the standard models of particle physics and cosmology, as well as an explanation for the nature or origin of dark energy.Since the discovery of these dark components decades ago, a variety of different theories have been proposed to overcome the shortcomings of our current standard models. To assess the viability of these non-standard theories, they ideally should be tested against all relevant available datasets. In this thesis, I show two examples of how cosmological and astrophysical observables are used to constrain or even rule out non-standard cosmological models. Further, I present the first software tool that provides a general framework to test non-standard physics with global fits to data from particle physics and cosmology simultaneously.The first example is minimally coupled covariant Galileons, a modification of General Relativity to explain dark energy without the need for a fine-tuned cosmological constant. I demonstrate how the combination of constraints arising from the integrated Sachs-Wolf effect and the propagation speed of gravitational waves can rule out all three branches of the theory.The second example shows how the existence and parameter space of cosmic superstrings can be constrained. These are the hypothesised fundamental building blocks of Type IIb Superstring theory, stretched out to cosmological scales during the phase of inflation. The theory can be tested through the unique microlensing signature of cosmic superstrings when crossing the line of sight of an observer monitoring a point-like source. I show how, based on simulations, we can estimate the expected detection rates from observations of distant Type Ia Supernovae and stars in Andromeda; from these estimates I assess the implications for the theory.Finally, I present CosmoBit, a new module for the Global and Modular Beyond-Standard Model Inference Tool (GAMBIT). \gambit allows the user to test a variety of extensions to the Standard Model of particle physics against data from, e.g. collider searches, dark matter direct and indirect detection experiments, as well as laboratory measurements of neutrino properties. CosmoBit augments this with the inclusion of cosmological likelihoods. This addition opens up the possibility to test a given model against data from, e.g. the Big Bang Nucleosynthesis proceeding minutes after the Big Bang, probes of the Cosmic Microwave Background ~ 380,000 years later, and (laboratory) measurements from the present day, 13.8 billion years after the Big Bang. Including measurements that span several different epochs and orders of magnitude in energy, the combination of CosmoBit with other GAMBIT modules provides a promising tool for shedding light on the dark sectors of the Universe.
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| 9. |
- Xu, Johanna, 1989, et al.
(författare)
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Effect of tension during stabilization on carbon fiber multifunctionality for structural battery composites
- 2023
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Ingår i: Carbon. - : Elsevier BV. - 0008-6223. ; 209
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Tidskriftsartikel (refereegranskat)abstract
- Here we demonstrate carbon fibers with tailorable multifunctional properties for energy storage composites. Carbon fibers made from the same precursor but with different processing tensions are investigated. The applied tension during the stabilization/oxidation stage of fiber manufacturing determines the microstructure and the resulting mechanical and electrochemical performance. Understanding of the interconnected effects enables tailoring of fibers to function as electrodes in structural battery composites. The study reveals that both amorphous and crystalline phases affect the electrochemical capacity, as higher capacity is achieved by larger d-spacing as well as higher void content. Further, the study confirms the trade-off between high tensile strength and high electrochemical capacity that needs to be taken into consideration when designing multifunctional carbon fibers.
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