| 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. |
- Meng, Long, et al.
(författare)
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Dynamic Response of 6MW Spar Type Floating Offshore Wind Turbine by Experiment and Numerical Analyses
- 2020
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Ingår i: China Ocean Engineering. - : Springer Science and Business Media LLC. - 0890-5487 .- 2191-8945. ; 34:5, s. 608-620
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Tidskriftsartikel (refereegranskat)abstract
- The floating offshore wind turbine (FOWT) is widely used for harvesting marine wind energy. Its dynamic responses under offshore wind and wave environment provide essential reference for the design and installation. In this study, the dynamic responses of a 6MW Spar type FOWT designed for the water depth of 100 m are investigated by means of the wave tank experiment and numerical analysis. A scaled model is manufactured for the experiment at a ratio of 65.3, while the numerical model is constructed on the open-source platform FAST (Fatigue, Aerodynamics, Structures, and Turbulence). Still water tests, wind-induced only tests, wave-induced only tests and combined wind-wave-current tests are all conducted experimentally and numerically. The accuracy of the experimental set-up as well as the loading generation has been verified. Surge, pitch and heave motions are selected to analyze and the numerical results agree well with the experimental values. Even though results obtained by using the FOWT calculation model established in FAST software show some deviations from the test results, the trends are always consistent. Both experimental and numerical studies demonstrate that they are reliable for the designed 6MW Spar type FOWT.
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| 3. |
- Xie, Yuan, et al.
(författare)
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Key molecular alterations in endothelial cells in human glioblastoma uncovered through single-cell RNA sequencing
- 2021
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Ingår i: JCI Insight. - : American Society For Clinical Investigation. - 2379-3708. ; 6:15
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Tidskriftsartikel (refereegranskat)abstract
- Passage of systemically delivered pharmacological agents into the brain is largely blocked by the blood-brain-barrier (BBB), an organotypic specialization of brain endothelial cells (ECs). Tumor vessels in glioblastoma (GBM), the most common malignant brain tumor in humans, are abnormally permeable, but this phenotype is heterogeneous and may differ between the tumor's center and invasive front. Here, through single-cell RNA sequencing (scRNA-seq) of freshly isolated ECs from human glioblastoma and paired tumor peripheral tissues, we have constructed a molecular atlas of human brain ECs providing unprecedented molecular insight into the heterogeneity of the human BBB and its molecular alteration in glioblastoma. We identified 5 distinct EC phenotypes representing different states of EC activation and BBB impairment, and associated with different anatomical locations within and around the tumor. This unique data resource provides key information for designing rational therapeutic regimens and optimizing drug delivery.
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| 4. |
- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 5. |
- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 6. |
- Berne, Olivier, et al.
(författare)
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PDRs4All : A JWST Early Release Science Program on Radiative Feedback from Massive Stars
- 2022
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Ingår i: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 134:1035
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Tidskriftsartikel (refereegranskat)abstract
- Massive stars disrupt their natal molecular cloud material through radiative and mechanical feedback processes. These processes have profound effects on the evolution of interstellar matter in our Galaxy and throughout the universe, from the era of vigorous star formation at redshifts of 1-3 to the present day. The dominant feedback processes can be probed by observations of the Photo-Dissociation Regions (PDRs) where the far-ultraviolet photons of massive stars create warm regions of gas and dust in the neutral atomic and molecular gas. PDR emission provides a unique tool to study in detail the physical and chemical processes that are relevant for most of the mass in inter- and circumstellar media including diffuse clouds, proto-planetary disks, and molecular cloud surfaces, globules, planetary nebulae, and star-forming regions. PDR emission dominates the infrared (IR) spectra of star-forming galaxies. Most of the Galactic and extragalactic observations obtained with the James Webb Space Telescope (JWST) will therefore arise in PDR emission. In this paper we present an Early Release Science program using the MIRI, NIRSpec, and NIRCam instruments dedicated to the observations of an emblematic and nearby PDR: the Orion Bar. These early JWST observations will provide template data sets designed to identify key PDR characteristics in JWST observations. These data will serve to benchmark PDR models and extend them into the JWST era. We also present the Science-Enabling products that we will provide to the community. These template data sets and Science-Enabling products will guide the preparation of future proposals on star-forming regions in our Galaxy and beyond and will facilitate data analysis and interpretation of forthcoming JWST observations.
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| 7. |
- Calabrese, Claudia, et al.
(författare)
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Genomic basis for RNA alterations in cancer
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
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Tidskriftsartikel (refereegranskat)abstract
- Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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| 8. |
- Chen, Chenlin, et al.
(författare)
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Experimental and kinetic modeling study of laminar burning velocity enhancement by ozone additive in NH3+O2+N2 and NH3+CH4/C2H6/C3H8+air flames
- 2023
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Ingår i: Proceedings of the Combustion Institute. - : Elsevier BV. - 1540-7489. ; 39:4, s. 4237-4246
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Tidskriftsartikel (refereegranskat)abstract
- Ammonia (NH3) is regarded as a promising future carbon-free fuel but needs to overcome drawbacks including extremely low burning velocity in practical combustion apparatus. In this study, ozone (O3) additive is used to elucidate one of the mechanisms of potential flame enhancement method based on plasma-assisted combustion. The effects of ozone addition on the laminar burning velocity of premixed NH3/(35%O2/65%N2) and NH3+ CH4/C2H6/C3H8+air flames over a wide range of equivalence ratios were investigated experimentally and numerically. Blending NH3 with hydrocarbons can decrease the ignition energy and increase the burning velocities of the whole mixture, which may contribute to developing ammonia co-fired mechanisms with varied complex fuels and validating the feasibility of NH3 using strategies in real applications. Measurements were conducted at atmospheric conditions using the Heat Flux method. For NH3/(35%O2/65%N2) flames, a significant increase was found on the fuel-lean side. Experimental data showed that maximum enhancement reaches 15.34% at π=0.6 with 5000 ppm O3 additive. For NH3+CH4/C2H6/C3H8+air blended flames, the enhancement effect was much more profound under off-stoichiometric conditions, being 1.5-4 times higher than that under near-stoichiometric conditions. A 28-step O3 related kinetic sub-mechanism was integrated with five selected NH3-oxidation mechanisms to simulate the burning velocities of NH3/(35%O2/65%N2) flames and CEU-Mech for NH3+CH4/C2H6/C3H8+air flames. Simulation results show improved agreement with the experimental data, especially for fuel-rich conditions as NH3 blending ratio xNH3 increases from 0 to 0.9. Each of the NH3/CH4/air, NH3/C2H6/air and NH3/C3H8/air cases fits well between experimental data and numerical results with varied NH3-fuel blending ratios. Detailed kinetic analyses adopting the CEU-NH3-Mech integrated with O3 sub-mechanism were carried out and revealed that active radicals such as HNO, which are rapidly produced due to high O concentration from O3 decomposing in the pre-heating zone, interfered with the ammonia-fuel chemistry and thus evidently promoted the overall combustion process.
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| 9. |
- Chen, Zhiwen, et al.
(författare)
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Interface engineering of NiS@MoS2 core-shell microspheres as an efficient catalyst for hydrogen evolution reaction in both acidic and alkaline medium
- 2021
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Ingår i: Journal of Alloys and Compounds. - : ELSEVIER SCIENCE SA. - 0925-8388 .- 1873-4669. ; 853
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Tidskriftsartikel (refereegranskat)abstract
- Electrochemical splitting of water is one of the most reliable and effective ways for the sustainable production of pure hydrogen on a large scale, while the core of this technology lies in the development of highly active non-noble-metal-based electrocatalysts to lower the large dynamic overpotentials of electrode materials. Here, an interface engineering strategy is demonstrated to construct an efficient and stable catalyst based on NiS@MoS2 core-shell hierarchical microspheres for the hydrogen evolution reactions (HER). The ultrathin MoS2 nanosheets in-situ grow on the surface of NiS hierarchical micro-sized spheres constructed by porous nanoplates, endowing the composites with rich interfaces, well-exposed electroactive edges, high structural porosity and fast transport channels. These advantages are favorable for the improvement of catalytic sites and the transport of catalysis-relevant species. More importantly, the intimate contact between MoS2 nanosheets and NiS nanoplates synergistically favors the chemical sorption of hydrogen intermediates, thereby reducing the reaction barrier and accelerating the HER catalytic process. As a result, the optimized NiS@MoS2 catalyst manifests impressive HER activity and durability, with a low overpotential of 208 mV in 0.5 M H2SO4 and 146 mV in 1.0 M KOH at 10 mA cm(-2), respectively. This work not only provides an effective way to construct core-shell hierarchical microspheres but also a multiscale strategy to regulate the electronic structure of heterostructured materials for energy-related applications. (C) 2020 Elsevier B.V. All rights reserved.
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| 10. |
- Chown, Ryan, et al.
(författare)
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PDRs4All: IV. An embarrassment of riches: Aromatic infrared bands in the Orion Bar
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 685
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Tidskriftsartikel (refereegranskat)abstract
- Context. Mid-infrared observations of photodissociation regions (PDRs) are dominated by strong emission features called aromatic infrared bands (AIBs). The most prominent AIBs are found at 3.3, 6.2, 7.7, 8.6, and 11.2 µm. The most sensitive, highest-resolution infrared spectral imaging data ever taken of the prototypical PDR, the Orion Bar, have been captured by JWST. These high-quality data allow for an unprecedentedly detailed view of AIBs. Aims. We provide an inventory of the AIBs found in the Orion Bar, along with mid-IR template spectra from five distinct regions in the Bar: the molecular PDR (i.e. the three H2 dissociation fronts), the atomic PDR, and the H II region. Methods. We used JWST NIRSpec IFU and MIRI MRS observations of the Orion Bar from the JWST Early Release Science Program, PDRs4All (ID: 1288). We extracted five template spectra to represent the morphology and environment of the Orion Bar PDR. We investigated and characterised the AIBs in these template spectra. We describe the variations among them here. Results. The superb sensitivity and the spectral and spatial resolution of these JWST observations reveal many details of the AIB emission and enable an improved characterization of their detailed profile shapes and sub-components. The Orion Bar spectra are dominated by the well-known AIBs at 3.3, 6.2, 7.7, 8.6, 11.2, and 12.7 µm with well-defined profiles. In addition, the spectra display a wealth of weaker features and sub-components. The widths of many AIBs show clear and systematic variations, being narrowest in the atomic PDR template, but showing a clear broadening in the H II region template while the broadest bands are found in the three dissociation front templates. In addition, the relative strengths of AIB (sub-)components vary among the template spectra as well. All AIB profiles are characteristic of class A sources as designated by Peeters (2022, A&A, 390, 1089), except for the 11.2 µm AIB profile deep in the molecular zone, which belongs to class B11.2. Furthermore, the observations show that the sub-components that contribute to the 5.75, 7.7, and 11.2 µm AIBs become much weaker in the PDR surface layers. We attribute this to the presence of small, more labile carriers in the deeper PDR layers that are photolysed away in the harsh radiation field near the surface. The 3.3/11.2 AIB intensity ratio decreases by about 40% between the dissociation fronts and the H II region, indicating a shift in the polycyclic aromatic hydrocarbon (PAH) size distribution to larger PAHs in the PDR surface layers, also likely due to the effects of photochemistry. The observed broadening of the bands in the molecular PDR is consistent with an enhanced importance of smaller PAHs since smaller PAHs attain a higher internal excitation energy at a fixed photon energy. Conclusions. Spectral-imaging observations of the Orion Bar using JWST yield key insights into the photochemical evolution of PAHs, such as the evolution responsible for the shift of 11.2 µm AIB emission from class B11.2 in the molecular PDR to class A11.2 in the PDR surface layers. This photochemical evolution is driven by the increased importance of FUV processing in the PDR surface layers, resulting in a “weeding out” of the weakest links of the PAH family in these layers. For now, these JWST observations are consistent with a model in which the underlying PAH family is composed of a few species: the so-called ‘grandPAHs’.
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