| 1. |
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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Heinze, Karolin, et al.
(author)
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Validated biomarker assays confirm ARID1A loss is confounded with MMR deficiency, CD8 TIL infiltration, and provides no independent prognostic value in endometriosis-associated ovarian carcinomas.
- 2021
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In: The Journal of pathology. - : Wiley. - 1096-9896 .- 0022-3417. ; 256:4, s. 388-401
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Journal article (peer-reviewed)abstract
- ARID1A (BAF250a) is a component of the SWI/SNF chromatin modifying complex, plays an important tumour suppressor role, and is considered prognostic in several malignancies. However, in ovarian carcinomas there are contradictory reports on its relationship to outcome, immune response, and correlation with clinicopathological features. We assembled a series of 1,623 endometriosis-associated ovarian carcinomas, including 1,078 endometrioid (ENOC) and 545 clear cell (CCOC) ovarian carcinomas through combining resources of the Ovarian Tumor Tissue Analysis (OTTA) Consortium, the Canadian Ovarian Unified Experimental Resource (COEUR), local, and collaborative networks. Validated immunohistochemical surrogate assays for ARID1A mutations were applied to all samples. We investigated associations between ARID1A loss/mutation, clinical features, outcome, CD8+ tumour-infiltrating lymphocytes (CD8+ TIL), and DNA mismatch repair deficiency (MMRd). ARID1A loss was observed in 42% of CCOC and 25% of ENOC. We found no associations between ARID1A loss and outcomes, stage, age, or CD8+ TIL status in CCOC. Similarly, we found no association with outcome or stage in endometrioid cases. In ENOC, ARID1A loss was more prevalent in younger patients (p=0.012), and associated with MMRd (p<0.001), and presence of CD8+ TIL (p=0.008). Consistent with MMRd being causative of ARID1A mutations, in a subset of ENOC we also observed an association between ARID1A loss-of-function mutation as a result of small indels (p=0.035, versus single nucleotide variants). In ENOC, the association between ARID1A loss, CD8+ TIL, and age, appears confounded by MMRd status. Although this observation does not explicitly rule out a role for ARID1A influence on CD8+ TIL infiltration in ENOC, given current knowledge regarding MMRd, it seems more likely that effects are dominated by the hypermutation phenotype. This large dataset with consistently applied biomarker assessment now provides a benchmark for the prevalence of ARID1A loss-of-function mutations in endometriosis-associated ovarian cancers and brings clarity to the prognostic significance. This article is protected by copyright. All rights reserved.
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| 3. |
- Abazajian, Kevork, et al.
(author)
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CMB-S4 : Forecasting Constraints on Primordial Gravitational Waves
- 2022
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 926:1
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Journal article (peer-reviewed)abstract
- CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
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| 4. |
- Lee, Seunghyun, et al.
(author)
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Plasmonic polymer nanoantenna arrays for electrically tunable and electrode-free metasurfaces
- 2023
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In: Journal of Materials Chemistry A. - : ROYAL SOC CHEMISTRY. - 2050-7488 .- 2050-7496. ; 11:40, s. 21569-21576
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Journal article (peer-reviewed)abstract
- Electrically tunable metasurfaces and interrelated nanofabrication techniques are essential for metasurface-based optoelectronic applications. We present a nanofabrication method suitable for various types of plasmonic polymer metasurfaces including inverted arrays of nanoantennas. Inverted metasurfaces are of particular interest since the metasurface itself can work as an electrode due to its interconnected nature, which enables electrical control without adopting an additional electrode. In comparison with inverted nanodisk arrays that support relatively weak resonance features, we show that inverted nanorod arrays can possess stronger resonances, even comparable with those of nanorod arrays. The origin of plasmon resonances in inverted arrays is systematically investigated using finite-difference time-domain (FDTD) simulations. Further, we demonstrate electrically tunable electrode-free metasurface devices using polymer inverted nanorod arrays, which can operate in the full spectral range of the material including the mid-infrared region. Electrically tunable and electrode-free metasurfaces using plasmonic polymer inverted nanoantenna arrays can operate across the entire spectral range of the material, including the mid-infrared region.
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| 5. |
- Chen, Shangzhi, et al.
(author)
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Conductive polymer nanoantennas for dynamic organic plasmonics
- 2020
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In: Nature Nanotechnology. - London : Nature Publishing Group. - 1748-3387 .- 1748-3395. ; 15
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Journal article (peer-reviewed)abstract
- Being able to dynamically shape light at the nanoscale is oneof the ultimate goals in nano-optics1. Resonant light–matterinteraction can be achieved using conventional plasmonicsbased on metal nanostructures, but their tunability is highlylimited due to a fixed permittivity2. Materials with switchablestates and methods for dynamic control of light–matterinteraction at the nanoscale are therefore desired. Here weshow that nanodisks of a conductive polymer can supportlocalized surface plasmon resonances in the near-infraredand function as dynamic nano-optical antennas, with their resonancebehaviour tunable by chemical redox reactions. Theseplasmons originate from the mobile polaronic charge carriersof a poly(3,4-ethylenedioxythiophene:sulfate) (PEDOT:Sulf)polymer network. We demonstrate complete and reversibleswitching of the optical response of the nanoantennasby chemical tuning of their redox state, which modulatesthe material permittivity between plasmonic and dielectricregimes via non-volatile changes in the mobile chargecarrier density. Further research may study different conductivepolymers and nanostructures and explore their usein various applications, such as dynamic meta-optics andreflective displays.
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| 6. |
- Chen, Shangzhi, et al.
(author)
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Unraveling vertical inhomogeneity in vapour phase polymerized PEDOT:Tos films
- 2020
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In: Journal of Materials Chemistry A. - : Royal Society of Chemistry. - 2050-7488 .- 2050-7496. ; 8, s. 18726-18734
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Journal article (peer-reviewed)abstract
- The conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) forms a promising alternative to conventional inorganic conductors, where deposition of thin films via vapour phase polymerization (VPP) has gained particular interest owing to high electrical conductivity within the plane of the film. The conductivity perpendicular to the film is typically much lower, which may be related not only to preferential alignment of PEDOT crystallites but also to vertical stratification across the film. In this study, we reveal non-linear vertical microstructural variations across VPP PEDOT:Tos thin films, as well as significant differences in doping level between the top and bottom surfaces. The results are consistent with a VPP mechanism based on diffusion-limited transport of polymerization precursors. Conducting polymer films with vertical inhomogeneity may find applications in gradient-index optics, functionally graded thermoelectrics, and optoelectronic devices requiring gradient doping.
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| 7. |
- Kang, Evan S. H., et al.
(author)
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Hybrid plasmonic metasurfaces
- 2019
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In: Journal of Applied Physics. - : American Institute of Physics. - 0021-8979 .- 1089-7550. ; 126:14
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Journal article (peer-reviewed)abstract
- Plasmonic metasurfaces based on ensembles of distributed metallic nanostructures can absorb, scatter, and in other ways shape light at the nanoscale. Forming hybrid plasmonic metasurfaces by combination with other materials opens up for new research directions and novel applications. This perspective highlights some of the recent advancements in this vibrant research field. Particular emphasis is put on hybrid plasmonic metasurfaces comprising organic materials and on concepts related to switchable surfaces, light-to-heat conversion, and hybridized light-matter states based on strong coupling.
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| 8. |
- Kang, Evan S. H., et al.
(author)
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Organic Anisotropic Excitonic Optical Nanoantennas
- 2022
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In: Advanced Science. - : Wiley. - 2198-3844 .- 2198-3844. ; 9:23
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Journal article (peer-reviewed)abstract
- Optical nanoantennas provide control of light at the nanoscale, which makes them important for diverse areas ranging from photocatalysis and flat metaoptics to sensors and biomolecular tweezing. They have traditionally been limited to metallic and dielectric nanostructures that sustain plasmonic and Mie resonances, respectively. More recently, nanostructures of organic J-aggregate excitonic materials have been proposed capable of also supporting nanooptical resonances, although their advance has been hampered from difficulty in nanostructuring. Here, the authors present the realization of organic J-aggregate excitonic nanostructures, using nanocylinder arrays as model system. Extinction spectra show that they can sustain both plasmon-like resonances and dielectric resonances, owing to the material providing negative and large positive permittivity regions at the different sides of its exciton resonance. Furthermore, it is found that the material is highly anisotropic, leading to hyperbolic and elliptic permittivity regions. Nearfield analysis using optical simulation reveals that the nanostructures therefore support hyperbolic localized surface exciton resonances and elliptic Mie resonances, neither of which has been previously demonstrated for this type of material. The anisotropic nanostructures form a new type of optical nanoantennas, which combined with the presented fabrication process opens up for applications such as fully organic excitonic metasurfaces.
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| 9. |
- Kang, Evan S. H., et al.
(author)
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Strong Plasmon-Exciton Coupling with Directional Absorption Features in Optically Thin Hybrid Nanohole Metasurfaces
- 2018
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In: ACS Photonics. - : American Chemical Society (ACS). - 2330-4022. ; 5:10, s. 4046-4064
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Journal article (peer-reviewed)abstract
- Plasmons and excitons can interact to form new hybridized light-matter states, with a multitude of potential applications including optical logic circuits and single-photon switches. Here, we report the first observation of strong coupling based on optically thin plasmonic nanohole films. The absorptive plasmon resonances of these nanohole films lead to suppressed transmission and Fano-shaped extinction peaks. We prepared silver nanohole films by colloidal lithography, which enables large-scale fabrication of nanoholes distributed in a short-range order. When coated with J-aggregate molecules, both extinction and absorption spectra show clear formation of two separated polariton resonances, with vacuum Rabi splitting on the order of 300 meV determined from anticrossing experiments. In accordance with strong coupling theory, the splitting magnitude increases linearly with the square root of molecular concentration. The extinction peak positions are blue-shifted from the absorption polariton positions, as explained by additional Fano interference between the hybridized states and the metal film. This highlights that absorption measurements are important not only to prove strong coupling but also to correctly determine hybridized polariton positions and splitting magnitudes in hybrid plasmonic nanohole systems. The polariton absorption peaks also show strong dependence on illumination direction, as found related to inherent directionality of the plasmonic nanohole metasurface and differences in light interaction with nonhybridized molecules. Importantly, optical simulations could successfully reproduce the experimental results and all coupling features. Furthermore, simulated spatial distribution of the absorption provides additional evidence of strong coupling in the hybrid nanohole system. The work paves the way toward strong coupling applications based on optically thin nanohole systems, as further promoted by the scalable fabrication.
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| 10. |
- Malekian, Bita, et al.
(author)
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Optical Properties of Plasmonic Nanopore Arrays Prepared by Electron Beam and Colloidal Lithography
- 2019
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In: Nanoscale Advances. - : Royal Society of Chemistry. - 2516-0230. ; 1:11, s. 4282-4289
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Journal article (peer-reviewed)abstract
- Solid state nanopores are central structures for many applications. To date, much effort has been spent on controlled fabrication of single nanopores, while relatively little work has focused on large scale fabrication of arrays of nanopores. In this work we show wafer-scale fabrication of plasmonic nanopores in 50 nm thick silicon nitride membranes with one or two 30 nm gold films, using electron beam lithography with a negative resist or a new version of colloidal lithography. Both approaches offer good control of pore diameter (even below 100 nm) and with high yield (>90%) of intact membranes. Colloidal lithography has the advantage of parallel patterning without expensive equipment. Despite its serial nature, electron beam lithography provides high throughput and can make arbitrary array patterns. Importantly, both methods prevent metal from ending up on the membrane pore sidewalls. The new fabrication methods make it possible to compare the optical properties of structurally identical plasmonic nanopore arrays with either long-range order (e-beam) or short-range order (colloidal). The resonance features in the extinction spectrum are very similar for both structures when the pitch is the same as the characteristic spacing in the self-assembled colloidal pattern. Long-range ordering slightly enhances the magnitude of the extinction maximum and blueshift the transmission maximum by tens of nm. Upon reducing the diameter in long-range ordered arrays, the resonance is reduced in magnitude and the transmission maximum is further blue shifted, just like for short-range ordered arrays. These effects are well explained by interpreting the spectra as Fano interference between the grating-type excitation of propagating surface plasmons and the broad transmission via individual pores in the metal film. Furthermore, we find that only the short-range ordered arrays scatter light, which we attribute to the highly limited effective period in the short-range ordered system and the corresponding lack of coherent suppression of scattering via interference effects.
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| 11. |
- Malekian, Bita, 1986, et al.
(author)
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Optical properties of plasmonic nanopore arrays prepared by electron beam and colloidal lithography
- 2019
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In: Nanoscale Advances. - : Royal Society of Chemistry (RSC). - 2516-0230. ; 1:11, s. 4282-4289
-
Journal article (peer-reviewed)abstract
- Solid state nanopores are central structures for many applications. To date, much effort has been spent on controlled fabrication of single nanopores, while relatively little work has focused on large scale fabrication of arrays of nanopores. In this work we show wafer-scale fabrication of plasmonic nanopores in 50 nm thick silicon nitride membranes with one or two 30 nm gold films, using electron beam lithography with a negative resist or a new version of colloidal lithography. Both approaches offer good control of pore diameter (even below 100 nm) and with high yield (>90%) of intact membranes. Colloidal lithography has the advantage of parallel patterning without expensive equipment. Despite its serial nature, electron beam lithography provides high throughput and can make arbitrary array patterns. Importantly, both methods prevent metal from ending up on the membrane pore sidewalls. The new fabrication methods make it possible to compare the optical properties of structurally identical plasmonic nanopore arrays with either long-range order (e-beam) or short-range order (colloidal). The resonance features in the extinction spectrum are very similar for both structures when the pitch is the same as the characteristic spacing in the self-assembled colloidal pattern. Long-range ordering slightly enhances the magnitude of the extinction maximum and blueshift the transmission maximum by tens of nm. Upon reducing the diameter in long-range ordered arrays, the resonance is reduced in magnitude and the transmission maximum is further blue shifted, just like for short-range ordered arrays. These effects are well explained by interpreting the spectra as Fano interference between the grating-type excitation of propagating surface plasmons and the broad transmission via individual pores in the metal film. Furthermore, we find that only the short-range ordered arrays scatter light, which we attribute to the highly limited effective period in the short-range ordered system and the corresponding lack of coherent suppression of scattering by interference effects.
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