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| 2. |
- 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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| 3. |
- Carter, Jodi M., et al.
(author)
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Distinct spatial immune microlandscapes are independently associated with outcomes in triple-negative breast cancer
- 2023
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14
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Journal article (peer-reviewed)abstract
- The utility of spatial immunobiomarker quantitation in prognostication and therapeutic prediction is actively being investigated in triple-negative breast cancer (TNBC). Here, with high-plex quantitative digital spatial profiling, we map and quantitate intraepithelial and adjacent stromal tumor immune protein microenvironments in systemic treatment-naive (female only) TNBC to assess the spatial context in immunobiomarker-based prediction of outcome. Immune protein profiles of CD45-rich and CD68-rich stromal microenvironments differ significantly. While they typically mirror adjacent, intraepithelial microenvironments, this is not uniformly true. In two TNBC cohorts, intraepithelial CD40 or HLA-DR enrichment associates with better outcomes, independently of stromal immune protein profiles or stromal TILs and other established prognostic variables. In contrast, intraepithelial or stromal microenvironment enrichment with IDO1 associates with improved survival irrespective of its spatial location. Antigen-presenting and T-cell activation states are inferred from eigenprotein scores. Such scores within the intraepithelial compartment interact with PD-L1 and IDO1 in ways that suggest prognostic and/or therapeutic potential. This characterization of the intrinsic spatial immunobiology of treatment-naive TNBC highlights the importance of spatial microenvironments for biomarker quantitation to resolve intrinsic prognostic and predictive immune features and ultimately inform therapeutic strategies for clinically actionable immune biomarkers.
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| 4. |
- Chen, Xiaowen, et al.
(author)
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Multi-bit Transient Fault Control for NoC Links Using 2D Fault Coding Method
- 2016
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In: 2016 TENTH IEEE/ACM INTERNATIONAL SYMPOSIUM ON NETWORKS-ON-CHIP (NOCS). - : IEEE. - 9781467390309
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Conference paper (peer-reviewed)abstract
- In deep nanometer scale, Network-on-Chip (NoC) links are more prone to multi-bit transient fault. Conventional ECC techniques brings heavy area, power, and timing overheads when correcting and detecting multiple transient faults. Therefore, a cost-effective ECC technique, named 2D fault coding method, is adopted to overcome the multi-bit transient fault issue of NoC links. Its key innovation is that the wires of a link are treated as its matrix appearance and light-weight Parity Check Coding (PCC) is performed on the matrix's two dimensions (horizontal matrix rows and vertical matrix columns). Horizontal PCCs and vertical PCCs work together to find the faults' position and then correct them by simply inverting them. The procedure of using the 2D fault coding method to protect a NoC link is proposed, its correction and detection capability is analyzed, and its hardware implementation is carried out. Comparative experiments show that the proposal can largely reduce the ECC hardware cost, have much higher fault detection coverage, maintain almost zero silent fault percentages, and have higher fault correction percentages normalized under the same area, demonstrating that it is cost-effective and suitable to the multi-bit transient fault control for NoC links.
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| 5. |
- Shu, Xiang, et al.
(author)
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Evaluation of associations between genetically predicted circulating protein biomarkers and breast cancer risk
- 2020
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In: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 146:8, s. 2130-2138
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Journal article (peer-reviewed)abstract
- A small number of circulating proteins have been reported to be associated with breast cancer risk, with inconsistent results. Herein, we attempted to identify novel protein biomarkers for breast cancer via the integration of genomics and proteomics data. In the Breast Cancer Association Consortium (BCAC), with 122,977 cases and 105,974 controls of European descendants, we evaluated the associations of the genetically predicted concentrations of >1,400 circulating proteins with breast cancer risk. We used data from a large-scale protein quantitative trait loci (pQTL) analysis as our study instrument. Summary statistics for these pQTL variants related to breast cancer risk were obtained from the BCAC and used to estimate odds ratios (OR) for each protein using the inverse-variance weighted method. We identified 56 proteins significantly associated with breast cancer risk by instrumental analysis (false discovery rate <0.05). Of these, the concentrations of 32 were influenced by variants close to a breast cancer susceptibility locus (ABO, 9q34.2). Many of these proteins, such as insulin receptor, insulin-like growth factor receptor 1 and other membrane receptors (OR: 0.82–1.18, p values: 6.96 × 10−4–3.28 × 10−8), are linked to insulin resistance and estrogen receptor signaling pathways. Proteins identified at other loci include those involved in biological processes such as alcohol and lipid metabolism, proteolysis, apoptosis, immune regulation and cell motility and proliferation. Consistent associations were observed for 22 proteins in the UK Biobank data (p < 0.05). The study identifies potential novel biomarkers for breast cancer, but further investigation is needed to replicate our findings.
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| 6. |
- Wei, Wendong, et al.
(author)
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Embodied greenhouse gas emissions from building China's large-scale power transmission infrastructure
- 2021
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In: Nature Sustainability. - : NATURE RESEARCH. - 2398-9629. ; 4:8, s. 739-747
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Journal article (peer-reviewed)abstract
- China has built the world's largest power transmission infrastructure by consuming massive volumes of greenhouse gas-(GHG-) intensive products such as steel. A quantitative analysis of the carbon implications of expanding the transmission infrastructure would shed light on the trade-offs among three connected dimensions of sustainable development, namely, climate change mitigation, energy access and infrastructure development. By collecting a high-resolution inventory, we developed an assessment framework of, and analysed, the GHG emissions caused by China's power transmission infrastructure construction during 1990-2017. We show that cumulative embodied GHG emissions have dramatically increased by more than 7.3 times those in 1990, reaching 0.89 GtCO(2)-equivalent in 2017. Over the same period, the gaps between the well-developed eastern and less-developed western regions in China have gradually narrowed. Voltage class, transmission-line length and terrain were important factors that influenced embodied GHG emissions. We discuss measures for the mitigation of GHG emissions from power transmission development that can inform global low-carbon infrastructure transitions.
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| 7. |
- Yang, Jiabao, et al.
(author)
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Overcome Low Intrinsic Conductivity of NiOx Through Triazinyl Modification for Highly Efficient and Stable Inverted Perovskite Solar Cells
- 2022
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In: Solar RRL. - : John Wiley & Sons. - 2367-198X. ; 6:9
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Journal article (peer-reviewed)abstract
- Nickel oxide (NiOx) is a promising hole transport material in inverted organic-inorganic metal halide perovskite solar cells. However, its low intrinsic conductivity hinders its further improvement in device performance. Here, we employ a trimercapto-s-triazine trisodium salt (TTTS) as a chelating agent of Ni2+ in the NiOx layer to improve its conductivity. Due to the electron-deficient triazine ring, the TTTS complexes with Ni2+ in NiOx via a strong Ni2+-N coordination bond and increases the ratio of Ni3+:Ni2+. The increased Ni3+ concentration adjusts the band structure of NiOx, thus enhancing hole density and mobility, eventually improving the intrinsic conductivity of NiOx. As a result, the device with TTTS modification displays a champion power conversion efficiency (PCE) of 22.81%. The encapsulated device based on a modified-NiOx layer maintains 94% of its initial power output at the maximum power point and continuous one-sun illumination for 1000 h at 45 degrees C. In addition, the unencapsulated target devices also maintain 92% at 60 +/- 5% relative humidity and 25 degrees C in the air for 5000 h; and 91% at 85 degrees C in a nitrogen atmosphere for 1000 h. The research provides an effective strategy to enhance PCE and stability of inverted PSCs via modifying NiOx films with triazine molecule.
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| 8. |
- Yang, Yaohua, et al.
(author)
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Genetically Predicted Levels of DNA Methylation Biomarkers and Breast Cancer Risk : Data From 228 951 Women of European Descent
- 2020
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 112:3, s. 295-304
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Journal article (peer-reviewed)abstract
- BACKGROUND: DNA methylation plays a critical role in breast cancer development. Previous studies have identified DNA methylation marks in white blood cells as promising biomarkers for breast cancer. However, these studies were limited by low statistical power and potential biases. Using a new methodology, we investigated DNA methylation marks for their associations with breast cancer risk. METHODS: Statistical models were built to predict levels of DNA methylation marks using genetic data and DNA methylation data from HumanMethylation450 BeadChip from the Framingham Heart Study (n = 1595). The prediction models were validated using data from the Women's Health Initiative (n = 883). We applied these models to genomewide association study (GWAS) data of 122 977 breast cancer patients and 105 974 controls to evaluate if the genetically predicted DNA methylation levels at CpG sites (CpGs) are associated with breast cancer risk. All statistical tests were two-sided. RESULTS: Of the 62 938 CpG sites CpGs investigated, statistically significant associations with breast cancer risk were observed for 450 CpGs at a Bonferroni-corrected threshold of P less than 7.94 × 10-7, including 45 CpGs residing in 18 genomic regions, that have not previously been associated with breast cancer risk. Of the remaining 405 CpGs located within 500 kilobase flaking regions of 70 GWAS-identified breast cancer risk variants, the associations for 11 CpGs were independent of GWAS-identified variants. Integrative analyses of genetic, DNA methylation, and gene expression data found that 38 CpGs may affect breast cancer risk through regulating expression of 21 genes. CONCLUSION: Our new methodology can identify novel DNA methylation biomarkers for breast cancer risk and can be applied to other diseases.
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