| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Lin, Xiaojing, et al.
(author)
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Metal-enriched Neutral Gas Reservoir around a Strongly Lensed Low-mass Galaxy at z = 4 Identified by JWST/NIRISS and VLT/MUSE
- 2023
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In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 944:2
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Journal article (peer-reviewed)abstract
- Direct observations of low-mass, low-metallicity galaxies at z ≳ 4 provide an indispensable opportunity for detailed inspection of the ionization radiation, gas flow, and metal enrichment in sources similar to those that reionized the universe. Combining the James Webb Space Telescope (JWST), Very Large Telescope/MUSE, and Atacama Large Millimeter/submillimeter Array, we present detailed observations of a strongly lensed, low-mass (≈107.6 M ⊙) galaxy at z = 3.98 (also see Vanzella et al.). We identify strong narrow nebular emission, including C iv λ λ1548, 1550, He ii λ1640, O iii] λ λ1661, 1666, [Ne iii] λ3868, [O ii] λ3727, and the Balmer series of hydrogen from this galaxy, indicating a metal-poor H ii region (≲0.12 Z ⊙) powered by massive stars. Further, we detect a metal-enriched damped Lyα system (DLA) associated with the galaxy with the H i column density of N H I ≈ 1021.8 cm−2. The metallicity of the associated DLA may reach the supersolar metallicity (≳Z ⊙). Moreover, thanks to JWST and gravitational lensing, we present the resolved UV slope (β) map at the spatial resolution of ≈100 pc at z = 4, with steep UV slopes reaching β ≈ −2.5 around three star-forming clumps. Combining with low-redshift analogs, our observations suggest that low-mass, low-metallicity galaxies, which dominate reionization, could be surrounded by a high covering fraction of the metal-enriched, neutral-gaseous clouds. This implies that the metal enrichment of low-mass galaxies is highly efficient, and further supports that in low-mass galaxies, only a small fraction of ionizing radiation can escape through the interstellar or circumgalactic channels with low-column-density neutral gas.
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| 3. |
- Lin, Qing-Fang, et al.
(author)
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A stable aluminosilicate zeolite with intersecting three-dimensional extra-large pores
- 2021
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6575, s. 1605-1608
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Journal article (peer-reviewed)abstract
- Zeolites are crystalline porous materials with important industrial applications, including uses in catalytic and adsorption-separation processes. Access into and out of their inner confined space, where adsorption and reactions occur, is limited by their pore apertures. Stable multidimensional zeolites with larger pores able to process larger molecules are in demand in the fine chemical industry and for the oil processing on which the world still relies for fuels. Currently known extra-large-pore zeolites display poor stability and/or lack pore multidimensionality, limiting their usefulness. We report ZEO-1, a robust, fully connected aluminosilicate zeolite with mutually intersecting three-dimensional extra-large plus three-dimensional large pores. ZEO-1 is stable up to 1000 degrees C, has an extraordinary specific surface area (1000 square meters per gram), and shows potential as a catalytic cracking catalyst.
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| 4. |
- Zhao, Kunsong, et al.
(author)
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DeepInfer : Deep Type Inference from Smart Contract Bytecode
- 2023
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In: Proceedings Of The 31St Acm Joint Meeting European Software Engineering Conference And Symposium On The Foundations Of Software Engineering, Esec/Fse 2023. - : Association for Computing Machinery (ACM). ; , s. 745-757
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Conference paper (peer-reviewed)abstract
- Smart contracts play an increasingly important role in Ethereum platform. It provides various functions implementing numerous services, whose bytecode runs on Ethereum Virtual Machine. To use services by invoking corresponding functions, the callers need to know the function signatures. Moreover, such signatures provide crucial information for many downstream applications, e.g., identifying smart contracts, fuzzing, detecting vulnerabilities, etc. However, it is challenging to infer function signatures from the bytecode due to a lack of type information. Existing work solving this problem depended heavily on limited databases or hardcoded heuristic patterns. However, these approaches are hard to be adapted to semantic differences in distinct languages and various compiler versions when developing smart contracts. In this paper, we propose a novel framework DeepInfer that first leverages deep learning techniques to automatically infer function signatures and returns. The novelties of DeepInfer are: 1) DeepInfer lifts the byte-code into the Intermediate Representation (IR) to preserve code semantics; 2) DeepInfer extracts the type-related knowledge (e.g., critical data flows, constant values, and control flow graphs) from the IR to recover function signatures and returns. We conduct experiments on Solidity and Vyper smart contracts and the results show that DeepInfer performs faster and more accurate than existing tools, while being immune to changes in different languages and various compiler versions.
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| 5. |
- Zhou, Yueting, et al.
(author)
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Self-calibrated NICE-OHMS based on an asymmetric signal : theoretical analysis and experimental validation
- 2023
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In: Optics Express. - : Optical Society of America. - 1094-4087. ; 31:17, s. 27830-27842
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Journal article (peer-reviewed)abstract
- As an ultra-sensitive detection technique, the noise-immune cavity enhanced optical heterodyne molecular spectroscopy (NICE-OHMS) technique has great potential for assessment of the concentration of trace gases. To determine gas concentrations at the ppt or lower level with high accuracy, it is desirable that the technique exhibits self-calibration (or calibration-free) capabilities. Although being sensitive, NICE-OHMS has so far not demonstrated any such ability. To remedy this, this paper provides a self-calibrated realization of NICE-OHMS that is based on a switching of the feedback target of the DeVoe-Brewer (DVB) locking procedure from the modulation frequency of the frequency modulation spectroscopy (FMS) to the cavity length, which creates an asymmetrical signal whose form and size can be used to unambiguously assess the gas concentration. A comprehensive theoretical model for self-calibrated NICE-OHMS is established by analyzing the shift of cavity modes caused by intracavity absorption, demonstrating that gas absorption information can be encoded in both the laser frequency and the NICE-OHMS signal. To experimentally verify the methodology, we measure a series of dispersion signals under different levels of absorbance using a built experimental setup. An instrument factor and the partial pressure are obtained by fitting the measured signal through theoretical expressions. Our results demonstrate that fitted values are more accurate for higher partial pressures than for lower. To improve on the accuracy at low partial pressures, it is shown that the instrument factor obtained by fitting the signal at large partial pressures (in this case, above 7.8 µTorr) can be set to a fixed value for all fits. By this, the partial pressures can be assessed with a relative error below 0.65%. This technique has the potential to enable calibration-free ultra-sensitive gas detection.
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| 6. |
- Chen, Fei-Jian, et al.
(author)
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Structure-direction towards the new large pore zeolite NUD-3
- 2021
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In: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 57:2, s. 191-194
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Journal article (peer-reviewed)abstract
- The new zeolite NUD-3 possesses a three-dimensional system of large pore channels that is topologically identical to those of ITQ-21 and PKU-14. However, the three zeolites have distinctly different frameworks: a particular single 4-membered ring inside the denser portion of the zeolite is missing in PKU-14, disordered in ITQ-21 and fully ordered in NUD-3. We document these differences and use molecular simulations to unravel the mechanism by which a particular structure directing agent dication, 1,1′-(1,2-phenylenebis(methylene))bis(3-methylimidazolium), is able to orient this inner ring.
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| 7. |
- Chen, Zhang, et al.
(author)
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Making monolayer graphene photoluminescent by electron-beam-activated fluorination approach
- 2023
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In: Applied Surface Science. - : Elsevier. - 0169-4332 .- 1873-5584. ; 608
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Journal article (peer-reviewed)abstract
- The past one and half decades have witnessed a tremendous development of graphene electronics, and the key to the success of graphene is its exceptional properties. The lacking of an inherent bandgap endows graphene with excellent electrical properties but considerably limits its applications in light-emitting and high-performance graphene-based devices. Herein, an approach for the direct writing of semiconducting and photoluminescent fluorinated graphene (C4F) patterns on monolayer graphene by an optimized electron-beam-activated fluorination technique is reported. A series of characterization approaches, such as atomic force microscopy, X-ray photoelectron spectroscopy and Raman spectroscopy were used to demonstrate the successful preparation of C4F for maskless lithography. Specially, a sharp and strong photoluminescence located at the purple light range of ∼380 nm was observed in C4F, demonstrating a desirable semiconducting nature, and the bandgap was further confirmed by follow-up electrical measurements, where the C4F filed-effect transistor exhibited a p-type semiconductor behavior and significantly enhanced on/off ratio. Therefore, this work provides a novel technique for the fabrication of graphene devices for promising electronic and optoelectronic applications, but also opens a route towards the tailoring and engineering of electronic properties of graphene.
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| 8. |
- Gao, Zihao Rei, et al.
(author)
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Dication Containing Three Aromatic Ring Structure-Directs toward a Chiral Zeolite, Spans Three Cavities, and Effectively Traps Water
- 2022
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In: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 34:7, s. 3197-3205
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Journal article (peer-reviewed)abstract
- The chiral zeolite STW has been synthesized using a large dication containing three aromatic rings (two imidazolium moieties plus a benzene one). The integrity of the occluded organics is proven by 1H and 13C liquid NMR of the zeolite dissolved in HF/D2O. Molecular simulations strongly suggest that each aromatic ring is located in a different cavity so that each dication crosses two medium pore 10-membered-ring (MR) windows. This is confirmed by Rietveld refinement against synchrotron powder X-ray diffraction data, which suggests that there is also trapped water in the cavities, explaining a significant excess of H found in this material. The presence of water is very soundly confirmed by Fourier-transform infrared experiments, which also show that this water cannot leave the zeolite even after heating at 180 °C under vacuum. Molecular simulations allow us to conclude that this is due to the blockage of the 10 and 8MR windows by the occluded organics. The peculiar situation of an organic structure-directing agent spanning three cavities has important implications for the structure-direction concept that are briefly discussed. Several chiral derivatives of this dication have also been studied, and their possibility to enantioselectively direct the crystallization of STW has been analyzed.
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| 9. |
- Gao, Zihao Rei, et al.
(author)
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HPM-14 : A New Germanosilicate Zeolite with Interconnected Extra-Large Pores Plus Odd-Membered and Small Pores
- 2021
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In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 60:7, s. 3438-3442
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Journal article (peer-reviewed)abstract
- HPM-14 is a new extra-large pore zeolite synthesized using imidazolium-based organic structure-directing agents (SDAs), fluoride anions, and germanium and silicon as tetrahedral components of the framework. Owing to the presence of stacking disorder, the structure elucidation of HPM-14 was challenging, and different techniques were necessary to clarify the details of the structure and to understand the nature of the disorder. The structure has been solved by three-dimensional electron-diffraction technique (3D ED) and consists of an intergrowth of two polymorphs possessing a three-dimensional channel system, including an extra-large pore opened through windows made up of sixteen tetrahedral atoms (16-membered ring, 16MR) as well as two additional sets of odd-membered (9MR) and small (8MR) pores. The intergrowth has been studied by scanning transmission electron microscopy (C-s-STEM) and powder X-ray diffraction simulations (DIFFaX), which show a large predominance of the monoclinic polymorph A.
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| 10. |
- Gao, Zihao Rei, et al.
(author)
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HPM-16, a Stable Interrupted Zeolite with a Multidimensional Mixed Medium-Large Pore System Containing Supercages
- 2021
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In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 60:37, s. 20249-20252
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Journal article (peer-reviewed)abstract
- HPM-16 is a highly porous germanosilicate zeolite with an interrupted framework that contains a three-dimensional system of 12+10x10(12)x12+10-membered ring (MR) pores. The 10(12) MR pore in the b direction is a 10 MR pore with long 12 MR stretches forming 30 angstrom long tubular supercages. Along one direction the 10 MR pores are fused, meaning that the separation between adjacent pores consists of a single tetrahedron that is, additionally, connected to only three additional tetrahedra (a Q(3)). These fused pores are thus decorated by T-OH groups along the whole diffusion path, creating a hydrophilic region embedded in an otherwise essentially hydrophobic environment. The structure is built from highly porous 12x12x12 MR uninterrupted layers that are connected to each other through Q(3) producing a second system of 10x10x10 MR pores. This zeolite can be extensively degermanated yielding a material with high thermal stability, despite its interrupted nature.
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