| 1. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 2. |
- Fenstermacher, M.E., et al.
(författare)
-
DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy
- 2022
-
Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:4
-
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.
|
|
| 3. |
- Wang, Bo-Yao, et al.
(författare)
-
Nonlinear bandgap opening behavior of BN co-doped graphene
- 2016
-
Ingår i: Carbon. - : Elsevier. - 0008-6223 .- 1873-3891. ; 107, s. 857-864
-
Tidskriftsartikel (refereegranskat)abstract
- We have demonstrated a nonlinear behavior for the bandgap opening of doped graphene by controlling the concentration of B and N co-dopants. X-ray absorption and emission spectra reveal that the bandgap increases from 0 to 0.6 eV as the concentration of BN dopants is increased from 0 to 6%, while the bandgap closes when the doping concentration becomes 56%. This nonlinear behavior of bandgap opening of the BN-doped graphene depending on the BN concentrations is consistent with the valenceband photoemission spectroscopic measurements. The spatially resolved B, N and C K-edge scanning transmission x-ray microscopy and their x-ray absorption near- edge structure spectra all support the scenario of the development of h-BN-like domains at high concentrations of BN. Ab initio calculation, by taking into account of the strong correlation between the bandgap and the geometry/concentration of the dopant, has been performed with various BN-dopant nano-domains embedded in the graphene monolayer to verify the unique bandgap behavior. Based on the experimental measurements and ab initio calculation, we propose the progressive formation of a phase-separated zigzag-edged BN domain from BN quantum dots with increasing BN-dopant concentration to explain the extraordinary nonlinear behavior of bandgap opening of BN-doped graphene sheets. This study reveals a new way to engineer the bandgap of low-dimensional systems.
|
|
| 4. |
- Yu, Shujun, et al.
(författare)
-
Macroscopic, Spectroscopic, and Theoretical Investigation for the Interaction of Phenol and Naphthol on Reduced Graphene Oxide
- 2017
-
Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 51:6, s. 3278-3286
-
Tidskriftsartikel (refereegranskat)abstract
- Interaction of phenol and naphthol with reduced graphene oxide (rGO), and their competitive behavior on rGO were examined by batch experiments, spectroscopic analysis and theoretical calculations. The batch sorption showed that the removal percentage of phenol or naphthol on rGO in bisolute systems was significantly lower than those of phenol or naphthol in single-solute systems. However, the overall sorption capacity of rGO in bisolute system was higher than single-solute system, indicating that the rGO was a very suitable material for the simultaneous elimination of organic pollutants from aqueous solutions. The interaction mechanism was mainly pi-pi interactions and hydrogen bonds, which was evidenced by FTIR, Raman and theoretical calculation. FTIR and Raman showed that a blue shift of C=C and -OH stretching modes and the enhanced intensity ratios of I-D/I-G after phenols sorption. The theoretical calculation indicated that the total hydrogen bond numbers, diffusion constant and solvent accessible surface area of naphthol were higher than those of phenol, indicating higher sorption affinity of rGO for naphthol as compared to phenol. These findings were valuable for elucidating the interaction mechanisms between phenols and graphene-based materials, and provided an essential start in simultaneous removal of organics from wastewater.
|
|
| 5. |
- Brownstein, Catherine A., et al.
(författare)
-
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
-
Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
-
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.
|
|
| 6. |
- Gu, Song, et al.
(författare)
-
Gaze Estimation via a Differential Eyes' Appearances Network with a Reference Grid
- 2021
-
Ingår i: ENGINEERING. - : Elsevier BV. - 2095-8099. ; 7:6, s. 777-786
-
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.
|
|
| 7. |
- Gu, Song, et al.
(författare)
-
Online Video Object Segmentation via Boundary-Constrained Low-Rank Sparse Representation
- 2019
-
Ingår i: IEEE Access. - : Institute of Electrical and Electronics Engineers (IEEE). - 2169-3536. ; 7, s. 53520-53533
-
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.
|
|
| 8. |
- Huang, Xing, et al.
(författare)
-
Semiconducting Conjugated Coordination Polymer with High Charge Mobility Enabled by "4+2" Phenyl Ligands
- 2023
-
Ingår i: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 145:4, s. 2430-2438
-
Tidskriftsartikel (refereegranskat)abstract
- Electrically conductive coordination polymers and metal-organic frameworks are attractive emerging electroactive materials for (opto-)electronics. However, developing semiconducting coordination polymers with high charge carrier mobility for devices remains a major challenge, urgently requiring the rational design of ligands and topological networks with desired electronic structures. Herein, we demonstrate a strategy for synthesizing high-mobility semiconducting conjugated coordination polymers (c-CPs) utilizing novel conjugated ligands with D2h symmetry, namely, "4 + 2" phenyl ligands. Compared with the conventional phenyl ligands with C6h symmetry, the reduced symmetry of the "4 + 2" ligands leads to anisotropic coordination in the formation of c-CPs. Consequently, we successfully achieve a single-crystalline three-dimensional (3D) c-CP Cu4DHTTB (DHTTB = 2,5-dihydroxy-1,3,4,6-tetrathiolbenzene), containing orthogonal ribbon-like pi-d conjugated chains rather than 2D conjugated layers. DFT calculation suggests that the resulting Cu4DHTTB exhibits a small band gap (similar to 0.2 eV), strongly dispersive energy bands near the Fermi level with a low electron-hole reduced effective mass (similar to 0.2m0*). Furthermore, the four-probe method reveals a semiconducting behavior with a decent conductivity of 0.2 S/cm. Thermopower measurement suggests that it is a p-type semiconductor. Ultrafast terahertz photoconductivity measurements confirm Cu4DHTTB's semiconducting nature and demonstrate the Drude-type transport with high charge carrier mobilities up to 88 +/- 15 cm2 V-1 s-1, outperforming the conductive 3D coordination polymers reported till date. This molecular design strategy for constructing high-mobility semiconducting c-CPs lays the foundation for achieving high-performance c-CP-based (opto-)electronics.
|
|
| 9. |
- Jinzhi, Lu, 1988-, et al.
(författare)
-
A Domain-specific Modeling Approach Supporting Tool-chain Development with Bayesian Network Models
- 2019
-
Ingår i: Integrated Computer-Aided Engineering. - : IOS Press. - 1069-2509 .- 1875-8835. ; 27:2, s. 153-171
-
Tidskriftsartikel (refereegranskat)abstract
- Constructing and evaluating a comprehensive tool-chain with commercial off-the-shelf and proprietary tools for the deployment of model-based systems engineering (MBSE) is a challenging and complex task. Specifically, the lack of early assessment during tool-chain development has led to increased research and development costs when unexpected features are developed or poor decisions are made. In this paper, a domain-specific modeling (DSM) approach is proposed to support decision-makings during tool-chain design and to facilitate quantitative assessment of tool-chain features at early-phases. Using this approach, different views of tool-chains are first formalized under a DSM framework. Then the DSM models are transformed to Bayesian network models for supporting the quantitative assessment of related tools in order to analyze the whole tool-chains’ features. In the case study, the approach is verified by comparing two MBSE tool-chains for an auto-braking system design. The results indicate that the DSM approach enhances the understanding of tool-chain concepts, promotes the efficiency of MBSE tool-chain development, and verifies the tool-chain in early development phases using a quantitative approach.
|
|
| 10. |
|
|
