| 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. |
- Wang, Xin, et al.
(author)
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Organic nanocrystals induced surface passivation towards high-efficiency and stable perovskite solar cells
- 2021
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In: Nano Energy. - : ELSEVIER. - 2211-2855 .- 2211-3282. ; 89
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Journal article (peer-reviewed)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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| 3. |
- Xiao, Wenming, et al.
(author)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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In: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Journal article (peer-reviewed)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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| 4. |
- Alipoormazandarani, Niloofar, et al.
(author)
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Functional Lignin Nanoparticles with Tunable Size and Surface Properties : Fabrication, Characterization, and Use in Layer-by-Layer Assembly
- 2021
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In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 13:22, s. 26308-26317
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Journal article (peer-reviewed)abstract
- Lignin is the richest source of renewable aromatics and has immense potential for replacing synthetic chemicals. The limited functionality of lignin is, however, challenging for its potential use, which motivates research for creating advanced functional lignin-derived materials. Here, we present an aqueous-based acid precipitation method for preparing functional lignin nanoparticles (LNPs) from carboxy-methylated or carboxy-pentylated lignin. We observe that the longer grafted side chains of carboxy-pentylated lignin allow for the formation of larger LNPs. The functional nanoparticles have high tolerance against salt and aging time and well-controlled size distribution with R-h <= 60 nm over a pH range of 5-11. We further investigate the layer-by-layer (LbL) assembly of the LNPs and poly(allylamine hydrochloride) (PAH) using a stagnation point adsorption reflectometry (SPAR) and quartz crystal microbalance with dissipation (QCM-D). Results demonstrate that LNPs made of carboxypentylated lignin (i.e., PLNPs with the adsorbed mass of 3.02 mg/m(2)) form a more packed and thicker adlayer onto the PAH surface compared to those made of carboxymethylated lignin (i.e., CLNPs with the adsorbed mass of 2.51 mg/m(2)). The theoretical flux, J, and initial rate of adsorption, (d Gamma/dt)(0), analyses confirm that 22% of PLNPs and 20% of CLNPs arriving at the PAH surface are adsorbed. The present study provides a feasible platform for engineering LNPs with a tunable size and adsorption behavior, which can be adapted in hionanomaterial production.
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| 5. |
- Ling, Chen, et al.
(author)
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A comprehensive consumption-based carbon accounting framework for power system towards low-carbon transition
- 2024
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In: Renewable & sustainable energy reviews. - : Elsevier Ltd. - 1364-0321 .- 1879-0690. ; 206
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Journal article (peer-reviewed)abstract
- Nearly 40 % current global annual energy-related CO2 emissions come from the fossil fuel-dominated power sector. Accurately accounting for carbon emissions in power systems from the consumption-based perspective is crucial for achieving the low-carbon power transition. Consumption-based carbon accounting has emerged as a major research focus, which aids in the implementation of targeted measures such as low-carbon demand response and dispatch. Choosing an appropriate method to account carbon emission needs thorough consideration of characteristics of various methods. There still lacks a systematic review that concludes the essence and application status of these methods, as well as comparing their advantages and disadvantages. To address this gap, a consumption-based carbon accounting framework for power systems is proposed. This framework groups four typical methods into two perspectives: Attributional methods and consequential methods. The principles, calculation approaches, and research application status of these methods are comprehensively summarized in a transparent, integrated and comparative manner, which makes progress in two critical limitations: (i) temporal and spatial granularity, and (ii) consideration of the actual topology and operational constraints of the power grid. As improvements in the transparency and quality of electricity data and expansion of application scenarios, the flexibility and applicability of the framework will continue to improve to achieve the unity of efficiency and fairness. The proposed framework can serve as a valuable guide to conducting research and exploration on low-carbon energy management, policy and regulatory decisions and to inform the development of effective strategies for the low-carbon transition of power systems.
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| 6. |
- Ren, Luyao, et al.
(author)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- 2023
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In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
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Journal article (peer-reviewed)abstract
- BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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| 7. |
- Wang, Youqing, et al.
(author)
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Using Period Analysis to Timely Assess and Predict 5-Year Relative Survival for Liver Cancer Patients From Taizhou, Eastern China
- 2022
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In: Frontiers in Oncology. - : Frontiers Media SA. - 2234-943X. ; 12
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Journal article (peer-reviewed)abstract
- Introduction: While timely assessment of long-term survival for patients with liver cancer is essential for the evaluation of early detection and screening programs of liver cancer, those data are extremely scarce in China. We aimed to timely and accurately assess long-term survival for liver cancer patients in eastern China.Methods: Patients diagnosed with liver cancer during 2004-2018 from four cancer registries with high-quality data from Taizhou, eastern China, were included. The period analysis was used to calculate the 5-year relative survival (RS) for overall and the stratification by sex, age at diagnosis, and region. The projected 5-year RS of liver cancer patients during 2019-2023 was also assessed using a model-based period analysis.Results: The overall 5-year RS for patients with liver cancer during 2014-2018 reached 32.4%, being 29.3% for men and 36.1% for women. The 5-year RS declined along with aging, decreasing from 38.2% for age <45 years to 18.8% for age >74 years, while the 5-year RS for urban area was higher compared to rural area (36.8% vs. 29.3%). The projected overall 5-year RS of liver cancer patients could reach 41.4% during the upcoming period 2019-2023.Conclusions: We provided, for first time in China using the period analysis, the most up-to-date 5-year RS for patients with liver cancer from Taizhou, eastern China, and also found that the 5-year RS for liver cancer patients have improved greatly during 2004-2018, which has important implications for the timely evaluation of early detection and screening programs for patients with liver cancer in eastern China.
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| 8. |
- Zhang, Lixiu, et al.
(author)
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Advances in the Application of Perovskite Materials
- 2023
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In: NANO-MICRO LETTERS. - : SHANGHAI JIAO TONG UNIV PRESS. - 2311-6706. ; 15:1
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Research review (peer-reviewed)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. |
- Dong, Jiajun, et al.
(author)
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Decompression-Induced Diamond Formation from Graphite Sheared under Pressure
- 2020
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In: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 124:6
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Journal article (peer-reviewed)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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| 10. |
- Fang, Li Tai, et al.
(author)
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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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In: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Journal article (peer-reviewed)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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