| 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. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 3. |
- Fu, Qiliang, 1986-, et al.
(författare)
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Transparent plywood as a load-bearing and luminescent biocomposite
- 2018
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Ingår i: Composites Science And Technology. - : Elsevier. - 0266-3538 .- 1879-1050. ; 164, s. 296-303
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Tidskriftsartikel (refereegranskat)abstract
- Transparent wood (TW) structures in research studies were either thin and highly anisotropic or thick and isotropic but weak. Here, transparent plywood (TPW) laminates are investigated as load-bearing biocomposites with tunable mechanical and optical performances. Structure-property relationships are analyzed. The plies of TPW were laminated with controlled fiber directions and predetermined stacking sequence in order to control the directional dependence of modulus and strength, which would give improved properties in the weakest direction. Also, the angular dependent light scattering intensities were investigated and showed more uniform distribution. Luminescent TPW was prepared by incorporation of quantum dots (QDs) for potential lighting applications. TPW can be designed for large-scale use where multiaxial load-bearing performance is combined with new optical functionalities.
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| 4. |
- Li, Yuanyuan, et al.
(författare)
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Towards centimeter thick transparent wood through interface manipulation
- 2018
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry. - 2050-7488 .- 2050-7496. ; 6:3, s. 1094-1101
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Tidskriftsartikel (refereegranskat)abstract
- Transparent wood is an attractive structural material for energy-saving buildings due to its high optical transmittance, good thermal insulation, and high toughness. However, thick highly transparent wood is challenging to realize. In the current work, highly transparent wood (1.5 mm) with a transmittance of 92%, close to that of pure PMMA (95%), is demonstrated. The high transmittance was realized by interface manipulation through acetylation of wood template. Both experiments and electromagnetic modeling support that the improved transmittance is mainly due to elimination of interface debonding gap. By applying this method, a centimeter-thick transparent wood structure was obtained. The transparent wood could be used as a substrate for an optically tunable window by laminating a polymer dispersed liquid crystal (PDLC) film on top. The techniques demonstrated are a step towards the replacement of glass in smart windows and smart buildings.
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| 5. |
- Lobov, Gleb S., et al.
(författare)
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Electric field induced optical anisotropy of P3HT nanofibers in a liquid solution
- 2015
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Ingår i: Optical Materials Express. - : Optical Society of America. - 2159-3930. ; 5:11, s. 2642-2647
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Tidskriftsartikel (refereegranskat)abstract
- The nanofiber morphology of regioregular Poly-3- hexylthiophene (P3HT) is a 1D crystalline structure organized by π - π stacking of the backbone chains. In this study, we report the impact of electric field on the orientation and optical properties of P3HT nanofibers dispersed in liquid solution. We demonstrate that alternating electric field aligns nanofibers, whereas static electric field forces them to migrate towards the cathode. The alignment of nanofibers introduces anisotropic optical properties, which can be dynamically manipulated until the solvent has evaporated. Time resolved spectroscopic measurements revealed that the electro-optical response time decreases significantly with the magnitude of applied electric field. Thus, for electric field 1.3 V ·μm-1 the response time was measured as low as 20 ms, while for 0.65 V ·μm-1 it was 110-150 ms. Observed phenomenon is the first mention of P3HT supramolecules associated with electrooptical effect. Proposed method provides real time control over the orientation of nanofibers, which is a starting point for a novel practical implementation. With further development P3HT nanofibers can be used individually as an anisotropic solution or as an active component in a guest-host system.
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| 6. |
- Soltanmoradi, Reyhaneh, et al.
(författare)
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Multi-resonator structure based on continuous silver thin films for transparent conductors
- 2014
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 105:6, s. 061110-
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Tidskriftsartikel (refereegranskat)abstract
- A type of metal-dielectric multilayered structures is investigated theoretically and experimentally for achieving optical transparency with a high electrical conductivity. The structure in our demonstrated case comprises of two coupled metal-dielectric-metal planar optical resonators with metal-layer thicknesses near to its skin depth. Simulations show that the maximum transmittance for visible light can easily reach 90% for silver-based structures. Experimentally, the sample fabricated exhibits a transmission window with a bandwidth of 150 nm and a maximum transmittance of 76% around 643 nm wavelength at normal incidence. Its sheet resistance is measured to be less than 10 Omega/square, much smaller than that of common indium-tin-oxide films. Transparent conductors functioning for blue light and even for the whole visible light are also shown to be theoretically possible. Owing to their simple fabrication procedure as well as design flexibility, such a layered structure can serve as a compelling alternative as transparent conductors for optoelectronic devices, especially for liquid-crystal displays and light-emitting diodes.
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| 7. |
- Yu, X., et al.
(författare)
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Coupling coefficient of two-core microstructured optical fiber
- 2006
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Ingår i: Optics Communications. - : Elsevier. - 0030-4018 .- 1873-0310. ; 260:1, s. 164-169
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, coupled-mode theory is applied to a two-core microstructured optical fiber for the first time to calculate the coupling coefficients for different fiber structures by employing a simple effective index model approach. The dependence of the mode coupling properties upon the geometrical parameters of the two-core structures (air-hole arrangement, hole size, and pitch size) and wavelength are evaluated systematically. The effective index coupled-mode theory is compared with the finite-element method based super-mode theory in details and the results show good agreement. The coupling characteristics are proven to be insensitive to the longitudinal strain by considering the photoelastic effects.
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| 8. |
- Chen, Hui
(författare)
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Light Scattering Effects in Transparent Wood Biocomposites
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Transparent wood (TW) shows interesting optical properties and offers a sustainable alternative to petroleum-based polymer glasses. The influence of the TW internal structure (e.g. fiber alignment, volume fraction of cellulose, lignin content, defects from preparation process) on the optical properties is poorly understood, which limits its use in various applications. It is also true for transparent cellulose biocomposites in general. In this thesis, eco-friendly TW biocomposites are investigated. The work focuses on experimental characterization, structure-optical property relationships and possibilities to quantify such relationships. TWs made of delignified wood substrates with longitudinal direction of the tree parallel to the specimen surface are prepared. Relationships between anisotropic scattering and fiber alignment are studied by scattering angle measurement. Anisotropic photons distributions are compared between two fiber directions and various sample thicknesses. Next, attenuation coefficients (related to the anisotropic diffusion coefficients and absorption coefficient) for TWs are obtained by combining the photon diffusion equation with total transmittance measurements. The results indicate strong influence from the air gaps between wood substrate phase and polymer in the lumen pores on the scattering. Beside the airgaps between wood substrate and polymer, refractive index mismatch between polymer and wood substrate strongly influences the scattering. Thus, immersion liquid method (based on the total transmittance measurement) combined with a light transmission model (based on Fresnel reflection theory) is applied to estimate the refractive index of the delignified wood substrate. This facilitates TW design (i.e. the proper polymer selection for various applications) and modelling of the optical properties of delignified wood based transparent materials. Finally, extinction coefficients, Rayleigh scattering and absorption coefficients of TW are extracted from photon budget measurements combined with a light diffusion model developed. With higher volume fraction of cellulose, all these parameters are increased, although polymer-cellulose refractive index mismatch is the dominating factor controlling transmittance. The strong forward scattering in TW is analysed, and Rayleigh scattering has a strong effect on haze. The influence of lignin content on the absorption coefficient is also discussed.
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| 9. |
- Chen, Hui, et al.
(författare)
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Refractive index of delignified wood for transparent biocomposites
- 2020
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Ingår i: RSC Advances. - 2046-2069. ; 10, s. 40719-40724
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Tidskriftsartikel (refereegranskat)abstract
- Refractive index (RI) determination for delignified wood templates is vital for transparent wood composite fabrication. Reported RIs in the literature are based on either single plant fibers or wood powder, measured by the immersion liquid method (ILM) combined with mathematical fitting. However, wood structure complexity and the physical background of the fitting were not considered. In this work, RIs of delignified wood templates were measured by the ILM combined with a light transmission model developed from the Fresnel reflection/refraction theory for composite materials. The RIs of delignified balsa wood are 1.536 ± 0.006 and 1.525 ± 0.008 at the wavelength of 589 nm for light propagating perpendicular and parallel to the wood fiber direction, respectively. For delignified birch wood, corresponding values are 1.537 ± 0.005 and 1.529 ± 0.006, respectively. The RI data for delignified wood scaffolds are important for tailoring optical properties of transparent wood biocomposites, and also vital in optical properties investigations by theoretical modelling of complex light propagation in transparent wood and related composites. The developed light transmission model in combination with the immersion liquid method can be used to determine the RI of complex porous or layered solid materials and composites.
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| 10. |
- Chen, Hui, et al.
(författare)
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Thickness Dependence of Optical Transmittance of Transparent Wood : Chemical Modification Effects
- 2019
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Ingår i: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 11:38, s. 35451-35457
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Tidskriftsartikel (refereegranskat)abstract
- Transparent wood (TW) is an emerging optical material combining high optical transmittance and haze for structural applications. Unlike nonscattering absorbing media, the thickness dependence of light transmittance for TW is complicated because optical losses are also related to increased photon path length from multiple scattering. In the present study, starting from photon diffusion equation, it is found that the angle-integrated total light transmittance of TW has an exponentially decaying dependence on sample thickness. The expression reveals an attenuation coefficient which depends not only on the absorption coefficient but also on the diffusion coefficient. The total transmittance and thickness were measured for a range of TW samples, from both acetylated and nonacetylated balsa wood templates, and were fitted according to the derived relationship. The fitting gives a lower attenuation coefficient for the acetylated TW compared to the nonacetylated one. The lower attenuation coefficient for the acetylated TW is attributed to its lower scattering coefficient or correspondingly lower haze. The attenuation constant resulted from our model hence can serve as a singular material parameter that facilitates cross-comparison of different sample types, at even different thicknesses, when total optical transmittance is concerned. The model was verified with two other TWs (ash and birch) and is in general applicable to other scattering media.
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