| 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. |
- Dong, Jiajun, et al.
(författare)
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Decompression-Induced Diamond Formation from Graphite Sheared under Pressure
- 2020
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 124:6
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Tidskriftsartikel (refereegranskat)abstract
- Graphite is known to transform into diamond under dynamic compression or under combined high pressure and high temperature, either by a concerted mechanism or by a nucleation mechanism. However, these mechanisms fail to explain the recently reported discovery of diamond formation during ambient temperature compression combined with shear stress. Here we report a new transition pathway for graphite to diamond under compression combined with shear, based on results from both theoretical simulations and advanced experiments. In contrast to the known model for thermally activated diamond formation under pressure, the shear-induced diamond formation takes place during the decompression process via structural transitions. At a high pressure with large shear, graphite transforms into ultrastrong sp3 phases whose structures depend on the degree of shear stress. These metastable sp3 phases transform into either diamond or graphite upon decompression. Our results explain several recent experimental observations of low-temperature diamond formation. They also emphasize the importance of shear stress for diamond formation, providing new insight into the graphite-diamond transformation mechanism.
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| 3. |
- Fang, Li Tai, et al.
(författare)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Tidskriftsartikel (refereegranskat)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 4. |
- Tun, Yan Kyaw, et al.
(författare)
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Collaborative Computing Services at Ground, Air, and Space : An Optimization Approach
- 2024
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Ingår i: IEEE Transactions on Vehicular Technology. - : Institute of Electrical and Electronics Engineers (IEEE). - 0018-9545 .- 1939-9359. ; 73:1, s. 1491-1496
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Tidskriftsartikel (refereegranskat)abstract
- Multi-access edge computing (MEC)-enabled integrated space-air-ground networks have drawn much attention recently, as they can provide communication and computing services to wireless devices in areas that lack terrestrial base stations (TBSs). They could make it possible for battery-powered Internet of Things (IoT) devices to offload their computation tasks to MEC-enabled unmanned aerial vehicles (UAVs) assisted aerial networks and low earth orbit (LEO) satellites and thus reduce their energy consumption and allow them to complete the execution of tasks on time. However, due to the limited computation capacity of the MEC servers at UAVs and satellites, an efficient offloading decision and computation resource allocation scheme is essential. Therefore, this paper investigates the problem of minimizing the latency experienced by the wireless devices in the MEC-enabled integrated space-air-ground network by optimizing the offloading decision while assuring the energy constraints of both devices and UAVs. The problem is proved to be a non-convex problem, and the block successive upper-bound minimization (BSUM) method is proposed as a solution. Finally, extensive simulation results are presented to exhibit the effectiveness of the BSUM algorithm in solving the proposed problem.
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| 5. |
- Wang, Xin, et al.
(författare)
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Organic nanocrystals induced surface passivation towards high-efficiency and stable perovskite solar cells
- 2021
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Ingår i: Nano Energy. - : ELSEVIER. - 2211-2855 .- 2211-3282. ; 89
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Tidskriftsartikel (refereegranskat)abstract
- Surface passivation has played a critical role for efficient and stable perovskite solar cells by reducing surface defects, promoting charge transport, and preventing the penetration of degrading agents. State-of-the-art passivation approaches mainly rely on the formation of a two-dimensional (2D) perovskite layer or the deposition of an ultrathin layer based on the molecular design. Here, we demonstrated a novel nanocrystal-pinning passivation by dripping 2-bromoethyltrimethylammonium bromide (BETAB) colloidal solution onto perovskite films. Theoretical simulation and kinds of experimental results confirm that BETAB nanocrystals can effectively reduce the defect density of perovskite films. Impressively, the resulting FA1-xMAxPbI3 based planar devices exhibit a champion power conversion efficiency (PCE) of 23.04% (certified: 22.10%) with a voltage loss of only 390 mV. Besides, the BETAB nanocrystals could simultaneously increase the hydrophobic property of perovskite films and prevent the reaction and formation of 2D perovskites during device operation. Correspondingly, the resulted devices exhibit excellent stability under moisture, heating, and operational tracking conditions.
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| 6. |
- Xiao, Wenming, et al.
(författare)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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| 7. |
- Yang, Xigui, et al.
(författare)
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Polarized Raman study of aligned multiwalled carbon nanotubes arrays under high pressure
- 2015
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:49, s. 27759-27767
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Tidskriftsartikel (refereegranskat)abstract
- Tuning the intertube interaction and the topological structure of carbon nanotubes by the application of pressure may obviously affect their properties such as optical and electronic properties. However, characterizing such changes is still challenging. Here, we performed polarized Raman scattering studies on aligned multiwalled carbon nanotube arrays (MWNTAs). Unlike researchers from the previous literature, we found that the MWNTAs exhibit a polarization dependence similar to that of isolated single walled carbon nanotubes at ambient conditions. Upon compression, the polarization dependence weakens gradually with increasing pressure up to ∼20 GPa, which has been discussed in terms of pressure-induced enhancement of intertube interactions. At around 20 GPa, the depolarization effect vanishes, which can be explained by the formation of interlinked sp3 bonding in the MWNTAs. Our results show that polarized Raman spectroscopy is an efficient method to explore not only intertube interaction but also structural transition changes in MWNTs, which overcome the difficulty that MWNTs have no obvious fingerprints like those of single-walled carbon nanotubes in the study of structural transformations.
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| 8. |
- Zhang, Lixiu, et al.
(författare)
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Advances in the Application of Perovskite Materials
- 2023
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Ingår i: NANO-MICRO LETTERS. - : SHANGHAI JIAO TONG UNIV PRESS. - 2311-6706. ; 15:1
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Forskningsöversikt (refereegranskat)abstract
- Nowadays, the soar of photovoltaic performance of perovskite solar cells has set off a fever in the study of metal halide perovskite materials. The excellent optoelectronic properties and defect tolerance feature allow metal halide perovskite to be employed in a wide variety of applications. This article provides a holistic review over the current progress and future prospects of metal halide perovskite materials in representative promising applications, including traditional optoelectronic devices (solar cells, light-emitting diodes, photodetectors, lasers), and cutting-edge technologies in terms of neuromorphic devices (artificial synapses and memristors) and pressure-induced emission. This review highlights the fundamentals, the current progress and the remaining challenges for each application, aiming to provide a comprehensive overview of the development status and a navigation of future research for metal halide perovskite materials and devices.
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| 9. |
- Zhao, Yongmei, et al.
(författare)
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Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study
- 2021
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- With the rapid advancement of sequencing technologies, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best practices in cancer mutation detection using NGS and the need for standard reference data sets for systematically measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples and generated whole-genome (WGS) and whole-exome sequencing (WES) data using sixteen library protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.
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| 10. |
- Zou, Luyao, et al.
(författare)
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Energy Efficient Leaderless Softwarized UAV Network: Joint Intelligent User Association and Resource Allocation Design
- 2023
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Ingår i: Proceedings of IEEE/IFIP Network Operations and Management Symposium 2023, NOMS 2023. - : Institute of Electrical and Electronics Engineers (IEEE).
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Konferensbidrag (refereegranskat)abstract
- Unmanned aerial vehicles (UAVs) have been conceived as an available solution to substitute terrestrial base stations (TBSs) to provide downloading services for user equipment (i.e. mobile devices) that have difficulty communicating directly with TBSs. However, the mobility of user equipment (UE) and the random nature of the number of UE will cause several challenges including 1) the hardness of determining optimal user association and UAV resource (i.e., bandwidth and transmit power) allocation decision, 2) the burden of network function maintenance owing to the necessity of shutting down the entire system. Therefore, in this article, joint user association and resource allocation are designed for a software-defined network (SDN)-adopted leaderless softwarized UAV network, where each UAV is regarded as a flying SDN controller to enhance the control ability of the considered network. The purpose is to maximize energy efficiency (EE) with satisfying the quality of service (QoS). To this end, a joint method based on hierarchical agglomerative clustering (HAGC) and multi-agent deep deterministic policy gradient (MADDPG) is proposed. Specifically, the HAGC approach is utilized to determine the optimal MDs association with UAVs. Afterward, MADDPG approach is leveraged to obtain the best policy for resource allocation, aiming to achieve the maximum EE. Finally, the effectiveness of the proposed method is confirmed by the evaluation results.
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