| 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. |
- Cabrera Arteaga, Javier, 1992-, et al.
(författare)
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Superoptimization of WebAssembly bytecode
- 2020
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Ingår i: Conference Companion of the 4th International Conference on Art, Science, and Engineering of Programming. - Portugal : Aakar Books.
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Konferensbidrag (refereegranskat)abstract
- Motivated by the fast adoption of WebAssembly, we propose the first functional pipeline to support the superoptimization of WebAssembly bytecode. Our pipeline works over LLVM and Souper. We evaluate our superoptimization pipeline with 12 programs from the Rosetta code project. Our pipeline improves the code section size of 8 out of 12 programs. We discuss the challenges faced in superoptimization of WebAssembly with two case studies.
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| 3. |
- 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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| 4. |
- Gharibi, Arash, et al.
(författare)
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Tunable transient evolutional behaviours of a four-level atomic vapour and the application to photonic logic gates
- 2009
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Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 42:5, s. 055502-
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Tidskriftsartikel (refereegranskat)abstract
- The evolutional optical behaviours (turn-on dynamics) of a four-level N-configuration atomic system are considered based on the transient solution to the equations of motion of atomic probability amplitudes. It is shown that the quantum interference between the signal and control fields can lead to the controllable absorption and transparency properties of the atomic vapour. One of the most remarkable properties of the present scheme is that the absorption (or transmittance) of the probe light in the atomic vapour depends on the intensity ratio of the signal field to the control field, and thus the tunable optical features (transparency or opaqueness to the probe light) can be realized by tuning the quantum interferences between the signal and control fields. The present mechanism can be applicable to designs of some new photonic and quantum optical devices such as logic and functional devices as well as optical switches. Two typical photonic logic gates (NOT and NOR gates) designed based on the tunable four-level optical responses are presented as illustrative examples.
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| 5. |
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| 6. |
- Gu, Jian, et al.
(författare)
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Multimodal Representation for Neural Code Search
- 2021
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Ingår i: 2021 IEEE international conference on software maintenance and evolution (ICSME 2021). - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 483-494
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Konferensbidrag (refereegranskat)abstract
- Semantic code search is about finding semantically relevant code snippets for a given natural language query. In the state-of-the-art approaches, the semantic similarity between code and query is quantified as the distance of their representation in the shared vector space. In this paper, to improve the vector space, we introduce tree-serialization methods on a simplified form of AST and build the multimodal representation for the code data. We conduct extensive experiments using a single corpus that is large-scale and multi-language: CodeSearchNet. Our results show that both our tree-serialized representations and multimodal learning model improve the performance of code search. Last, we define intuitive quantification metrics oriented to the completeness of semantic and syntactic information of the code data, to help understand the experimental findings.
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| 7. |
- Gu, Jian, et al.
(författare)
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Visualizing Material Processing via Photoexcitation-Controlled Organic-Phase Aggregation-Induced Emission
- 2021
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Ingår i: RESEARCH. - : American Association for the Advancement of Science (AAAS). - 2639-5274. ; 2021
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Tidskriftsartikel (refereegranskat)abstract
- Aggregation-induced emission (AIE) has been much employed for visualizing material aggregation and self-assembly. However, water is generally required for the preparation of the AIE aggregates, the operation of which limits numerous material processing behaviors. Employing hexathiobenzene-based small molecules, monopolymers, and block copolymers as different material prototypes, we herein achieve AIE in pure organic phases by applying a nonequilibrium strategy, photoexcitation-controlled aggregation. This strategy enabled a dynamic change of molecular conformation rather than chemical structure upon irradiation, leading to a continuous aggregation-dependent luminescent enhancement (up to similar to 200-fold increase of the luminescent quantum yield) in organic solvents. Accompanied by the materialization of the nonequilibrium strategy, photoconvertible self-assemblies with a steady-state characteristic can be achieved upon organic solvent processing. The visual monitoring with the luminescence change covered the whole solution-to-film transition, as well as the in situ photoprocessing of the solid-state materials.
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| 8. |
- Gu, Song, et al.
(författare)
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Gaze Estimation via a Differential Eyes' Appearances Network with a Reference Grid
- 2021
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Ingår i: ENGINEERING. - : Elsevier BV. - 2095-8099. ; 7:6, s. 777-786
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Tidskriftsartikel (refereegranskat)abstract
- A person's eye gaze can effectively express that person's intentions. Thus, gaze estimation is an important approach in intelligent manufacturing to analyze a person's intentions. Many gaze estimation methods regress the direction of the gaze by analyzing images of the eyes, also known as eye patches. However, it is very difficult to construct a person-independent model that can estimate an accurate gaze direction for every person due to individual differences. In this paper, we hypothesize that the difference in the appearance of each of a person's eyes is related to the difference in the corresponding gaze directions. Based on this hypothesis, a differential eyes' appearances network (DEANet) is trained on public datasets to predict the gaze differences of pairwise eye patches belonging to the same individual. Our proposed DEANet is based on a Siamese neural network (SNNet) framework which has two identical branches. A multi-stream architecture is fed into each branch of the SNNet. Both branches of the DEANet that share the same weights extract the features of the patches; then the features are concatenated to obtain the difference of the gaze directions. Once the differential gaze model is trained, a new person's gaze direction can be estimated when a few calibrated eye patches for that person are provided. Because person specific calibrated eye patches are involved in the testing stage, the estimation accuracy is improved. Furthermore, the problem of requiring a large amount of data when training a person-specific model is effectively avoided. A reference grid strategy is also proposed in order to select a few references as some of the DEANet's inputs directly based on the estimation values, further thereby improving the estimation accuracy. Experiments on public datasets show that our proposed approach outperforms the state-of-the-art methods.
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| 9. |
- Gu, Song, et al.
(författare)
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Online Video Object Segmentation via Boundary-Constrained Low-Rank Sparse Representation
- 2019
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Ingår i: IEEE Access. - : Institute of Electrical and Electronics Engineers (IEEE). - 2169-3536. ; 7, s. 53520-53533
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Tidskriftsartikel (refereegranskat)abstract
- Graphcut-based algorithm is adopted in many video object segmentation systems because different terms can be probabilistically fused together in a framework. Constructing spatio-temporal coherences is an important stage in segmentation systems. However, many steps are involved when computing a key term with good discriminative power. If the cascade steps are adopted, the inaccurate output of the previous step will definitely affect the next step, leading to inaccurate segmentation. In this paper, a key term that is computed by a single framework referred to as boundary-constrained low-rank sparse representation (BCLRSR) is proposed to achieve the accurate segmentation. By treating the elements as linear combinations of dictionary templates, low-rank sparse optimization is adopted to achieve the spatio-temporal saliency. For adding the spatial information to the low-rank sparse model, a boundary constraint is adopted in the framework as a Laplacian regularization. A BCLRSR saliency is then obtained by the represented coefficients, which measure the similarity between the elements in the current frame and the ones in the dictionary. At last, the object is segmented by minimizing the energy function, which is formalized by the spatio-temporal coherences. The experiments on some public datasets show that our proposed algorithm outperforms the state-of-the-art methods.
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| 10. |
- Wang, Yan-Zhao, et al.
(författare)
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Pairing Effects on Bubble Nuclei
- 2019
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Ingår i: Chinese Physics Letters. - : IOP PUBLISHING LTD. - 0256-307X .- 1741-3540. ; 36:3
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Tidskriftsartikel (refereegranskat)abstract
- In the framework of the Skyrme-Hartree-Fock-Bogoliubov approach with the SkT interaction, the pairing effects on the proton bubble structures of Ar-46 and( 206)Hg are discussed. In calculations, three kinds of pairing forces (volume, surface and mixed pairing interactions) are used. For Ar-46, it is shown that the bubble structure with the volume pairing is almost the same as that with the mixed pairing. The bubble with the surface pairing is less pronounced than those with the volume and mixed pairings. Analyzing the density distributions and occupation probabilities of the proton s states and the quasi-degeneracy between the proton 2s(1/2) and 1d(3/2) orbitals, we explain the difference between the bubble structure with the surface pairing and those with the volume and mixed pairings. For Hg-206, it is seen that the proton density distribution with the surface pairing is different from those with the volume and mixed pairings in the whole region of the radial distance. In addition, it is found that the bubbles with the three pairing forces are different from each other and the least pronounced bubble is obtained with the surface pairing. Thus the selection of the pairing force is important for the study of the nuclear bubble structure.
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