| 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. |
- Fenstermacher, M.E., et al.
(författare)
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DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy
- 2022
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:4
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Tidskriftsartikel (refereegranskat)abstract
- DIII-D physics research addresses critical challenges for the operation of ITER and the next generation of fusion energy devices. This is done through a focus on innovations to provide solutions for high performance long pulse operation, coupled with fundamental plasma physics understanding and model validation, to drive scenario development by integrating high performance core and boundary plasmas. Substantial increases in off-axis current drive efficiency from an innovative top launch system for EC power, and in pressure broadening for Alfven eigenmode control from a co-/counter-I p steerable off-axis neutral beam, all improve the prospects for optimization of future long pulse/steady state high performance tokamak operation. Fundamental studies into the modes that drive the evolution of the pedestal pressure profile and electron vs ion heat flux validate predictive models of pedestal recovery after ELMs. Understanding the physics mechanisms of ELM control and density pumpout by 3D magnetic perturbation fields leads to confident predictions for ITER and future devices. Validated modeling of high-Z shattered pellet injection for disruption mitigation, runaway electron dissipation, and techniques for disruption prediction and avoidance including machine learning, give confidence in handling disruptivity for future devices. For the non-nuclear phase of ITER, two actuators are identified to lower the L-H threshold power in hydrogen plasmas. With this physics understanding and suite of capabilities, a high poloidal beta optimized-core scenario with an internal transport barrier that projects nearly to Q = 10 in ITER at ∼8 MA was coupled to a detached divertor, and a near super H-mode optimized-pedestal scenario with co-I p beam injection was coupled to a radiative divertor. The hybrid core scenario was achieved directly, without the need for anomalous current diffusion, using off-axis current drive actuators. Also, a controller to assess proximity to stability limits and regulate β N in the ITER baseline scenario, based on plasma response to probing 3D fields, was demonstrated. Finally, innovative tokamak operation using a negative triangularity shape showed many attractive features for future pilot plant operation.
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| 3. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 4. |
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| 5. |
- Li, Xing-Yu, et al.
(författare)
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Comparative Study of Dayside Pulsating Auroras Induced by Ultralow-Frequency Waves
- 2023
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Ingår i: Universe. - : MDPI AG. - 2218-1997. ; 9:6
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Tidskriftsartikel (refereegranskat)abstract
- Pulsating auroras are usually observed with ultralow-frequency (ULF) waves in the Pc 3-5 band (period 10-600 s). These auroras are thought to result from interactions between energetic electrons and chorus waves, but their relationship with ULF waves remains an open question. In this study, we investigated this question by conducting a comparative study on two ULF wave events with pulsating auroras observed near the magnetic footprints. Conjugate observations from the Magnetospheric Multiscale mission and the Chinese Yellow River Station were used. In both events, lower-band chorus waves were observed, which were suggested to be connected with the auroral pulsations by wavelet analysis. The intensity of these waves oscillates at the period of the ULF waves, but the physics laid behind them differs by events. During the event of 22 January 2019, compressional ULF waves changed the threshold for the whistler anisotropy instability periodically, affecting the emission of chorus waves. In the event on 10 January 2016, poloidal ULF waves modulated the chorus wave generation by regulating electron temperature anisotropy through drift resonance. ULF waves in these events may originate from perturbations in the solar wind. We highlight the role of ULF waves in the solar wind-magnetosphere-ionosphere coupling, which requires further study.
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| 6. |
- Li, Xing Yu, et al.
(författare)
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Ion Acceleration and Corresponding Bounce Echoes Induced by Electric Field Impulses: MMS Observations
- 2024
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Ingår i: Journal of Geophysical Research - Space Physics. - : American Geophysical Union (AGU). - 2169-9380 .- 2169-9402. ; 129:2
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Tidskriftsartikel (refereegranskat)abstract
- Dayside magnetosphere interactions are essential for energy and momentum transport between the solar wind and the magnetosphere. In this study, we investigate a new phenomenon within this regime. Sudden enhancements of ion fluxes followed by repeating dropouts and recoveries were observed by Magnetospheric Multiscale on 5 November 2016, which is the very end of the recovery phase from a moderate geomagnetic storm. These repetitive flux variations display energy-dispersive characteristics with periods relevant to ion bounce motion, suggesting they are corresponding echoes. Alongside the flux variations, bipolar electric field impulses originating from external sources were detected. We traced the source region of the initial injection and found it is located near the spacecraft's position. To elucidate the underlying physics, a test-particle simulation is conducted. The results reveal that radial transport resulting from impulse-induced acceleration can give rise to these echoes. Observations demonstrate dayside magnetosphere interactions are more common than we previously considered, which warrants further research.
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| 7. |
- Li, Ziyao, et al.
(författare)
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Atomic-level orbital coupling in a tri-metal alloy site enables highly efficient reversible oxygen electrocatalysis
- 2023
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry. - 2050-7488 .- 2050-7496. ; 11:5, s. 2155-2167
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Tidskriftsartikel (refereegranskat)abstract
- Complex multi-metallic alloys with ultra-small sizes have received extensive attention in the fields of Zn-air battery and water splitting, because of their unique advantages including adjustable composition, tailorable active sites, and optimizable electronic structure. In this effort, an atomic-level orbital coupling strategy is presented to effectively regulate the electronic structures of ultra-small tri-metal Fe-Co-Ni nanoalloy particles confined in an N-doped carbon hollow nanobox. As expected, the optimal nanoalloy hybrid material exhibited notable bi-functional catalytic performances toward the oxygen reduction reaction (half-wave potential of 0.902 V) and oxygen evolution reaction (1.589 V at 10 mA cm−2) with a small ΔE of 0.687 V, exceeding the precious-metal-based and many previously reported catalysts. Furthermore, the as-assembled Zn-air device also displayed a superior specific capacity of 894 mA h g−1, a maximal power density of 247 mW cm−2, and impressive durability (over 100 hours). Ultraviolet photoelectron spectroscopy and density functional theory calculations revealed that the electronic structures could be finely tuned and optimized through ternary metal alloying, resulting in a suitable d-band center and advantageous interfacial charge-transfer, which in turn could effectively reduce the involved energy barriers in the electrocatalytic process and significantly boost its intrinsic activity of reversible oxygen catalysis. Thus, this work affords an effective method for the rational creation of bi-functional non-noble-metal-based electrocatalysts for sustainable energy technology.
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| 8. |
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| 9. |
- Grøn, Ole, et al.
(författare)
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Acoustic mapping of submerged stone age sites—A HALD approach
- 2021
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Ingår i: Remote Sensing. - : MDPI AG. - 2072-4292. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- Acoustic response from lithics knapped by humans has been demonstrated to facilitate effective detection of submerged Stone Age sites exposed on the seafloor or embedded within its sediments. This phenomenon has recently enabled the non-invasive detection of several hitherto unknown submerged Stone Age sites, as well as the registration of acoustic responses from already known localities. Investigation of the acoustic-response characteristics of knapped lithics, which appear not to be replicated in naturally cracked lithic pieces (geofacts), is presently on-going through laboratory experiments and finite element (FE) modelling of high-resolution 3D-scanned pieces. Experimental work is also being undertaken, employing chirp sub-bottom systems (reflection seismic) on known sites in marine areas and inland water bodies. Fieldwork has already yielded positive results in this initial stage of development of an optimised Human-Altered Lithic Detection (HALD) method for mapping submerged Stone Age sites. This paper reviews the maritime archaeological perspectives of this promising approach, which potentially facilitates new and improved practice, summarizes existing data, and reports on the present state of development. Its focus is not reflection seismics as such, but a useful resonance phenomenon induced by the use of high-resolution reflection seismic systems.
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| 10. |
- Hu, Rui-Si, et al.
(författare)
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Differential expression of microRNAs and tRNA fragments mediate the adaptation of the liver fluke Fasciola gigantica to its intermediate snail and definitive mammalian hosts
- 2021
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Ingår i: International Journal of Parasitology. - : Elsevier BV. - 0020-7519 .- 1879-0135. ; 51:5, s. 405-414
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Tidskriftsartikel (refereegranskat)abstract
- The tropical liver fluke Fasciola gigantica affects livestock and humans in many Asian countries, large parts of Africa, and parts of Europe. Despite the public health and economic impacts of F. gigantica, understanding of F. gigantica biology and how the complex lifecycle of this liver fluke is transcriptionally regulated remain unknown. Here, we tested the hypothesis that the regulatory small non-coding RNAs (sncRNAs), microRNAs (miRNAs) and tRNA-derived fragments (tRFs) play roles in the adaptation of F. gigantica to its intermediate and definitive hosts. We sequenced sncRNAs of eight lifecycle stages of F. gigantica. In total, 56 miRNAs from 33 conserved families and four Fasciola-specific miRNAs were identified. Expression analysis of miRNAs suggested clear stage-related patterns. By leveraging the existing transcriptomic data, we predicted a miRNA-based regulation of metabolism, transport, growth and developmental processes. Also, by comparing miRNA complement of F. gigantica with that of Fasciola hepatica, we detected a high level of conservation and identified differences in some miRNAs, which can be used to distinguish the two species. Moreover, we found that tRFs at each lifecycle stage were predominantly derived by tRNA-Lys and tRNA-Gly at 50 half sites, but relatively high expression was related to the buffalo-infecting stages. Taken together, we provided a comprehensive overview of the dynamic transcriptional changes of small RNAs that occur during the developmental stages of F. gigantica. This global analysis of F. gigantica lifecycle stages revealed new roles of miRNAs and tRFs in parasite development and will facilitate future research into understanding of fasciolosis pathobiology.
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