| 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. |
- Chen, Zhishan, et al.
(författare)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 3. |
- Feng, Zhiwei, et al.
(författare)
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On the scheduling of fault-tolerant time-sensitive networking with IEEE 802.1CB
- 2024
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Ingår i: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0070 .- 1937-4151. ; 43:6, s. 1715-1728
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Tidskriftsartikel (refereegranskat)abstract
- Time-sensitive networking (TSN) has become the most popular technique in modern safety-critical automotive and industrial automation networks by providing deterministic transmission policies. However, the data of TSN messages may be affected by transient faults. IEEE 802.1CB, a reliability standard in TSN, protects against such faults by providing disjoint redundant routes for each stream. However, the unique assumption may present a new challenge, i.e., an inadequate number of redundant routes that may negatively impact stream scheduling. This article presents an offline fault-tolerant TSN scheduling approach that considers such impacts for real-time streams (such as time-trigger (TT) and audio video bridging (AVB) streams). Specifically, we intend to calculate the minimum upper bound number of disjoint routes required for each stream to meet the reliability requirements, subsequently enhancing the network's schedulability. We also propose a service degradation function for AVB streams when the network is under heavy load caused by redundant transmissions of TT streams. This function will maintain schedulability and reliability for AVB streams. Experiments with small- and large-scale synthetic networks show the efficiency.
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| 4. |
- Geng, Yuhan, et al.
(författare)
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In Situ All-Fiber Remote Gas Sensing Strategy Based on Anti-Resonant Hollow-Core Fiber and Middle-Hole Eccentric-Core Fiber
- 2024
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Ingår i: Photonics. - : Multidisciplinary Digital Publishing Institute (MDPI). - 2304-6732. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- Laser absorption spectroscopy for gas sensing basically employs an air pump located at the gas cell probe to draw in ambient gases, and the on-site gas sample is subsequently delivered for laboratory non-real-time analysis. In this study, an in situ all-fiber remote gas sensing strategy is proposed. The anti-resonant hollow-core fiber (AR-HCF) is used as the sensing fiber, and a 20 m middle-hole eccentric-core fiber (MH-ECF) is used as the conducting fiber. The remote ambient gases can be inhaled into the AR-HCF as a result of the negative pressure transmitted through the MH-ECF when pumping gas at the interface of the MH-ECF. Since the real-time monitoring of greenhouse gas emissions in industrial processes holds immense significance in addressing global climate change, the detection of CO2 is achieved with the TDLAS-WMS method, and the gas sensing performance of an all-fiber remote gas sensing structure (RGS) is experimentally validated. The response time t90 under the pumping condition is about 456 s, which is about 30 times faster than that of free diffusion. Allan deviation results for more than one hour of continuous monitoring indicate that the lowest detection limit for the all-fiber RGS is 0.0373% when the integration time is 184 s. The all-fiber remote gas sensing strategy also possesses the benefits of being applicable to multiplex, hazardous gas environment passive monitoring.
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| 5. |
- Huang, Haiping, et al.
(författare)
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An Efficient Signature Scheme Based on Mobile Edge Computing in the NDN-IoT Environment
- 2021
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Ingår i: IEEE Transactions on Computational Social Systems. - : IEEE. - 2329-924X. ; 8:5, s. 1108-1120
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Tidskriftsartikel (refereegranskat)abstract
- Named data networking (NDN) is an emerging information-centric networking paradigm, in which the Internet of Things (IoT) achieves excellent scalability. Recent literature proposes the concept of NDN-IoT, which maximizes the expansion of IoT applications by deploying NDN in the IoT. In the NDN, the security is built into the network by embedding a public signature in each data package to verify the authenticity and integrity of the content. However, signature schemes in the NDN-IoT environment are facing several challenges, such as signing security challenge for resource-constrained IoT end devices (EDs) and verification efficiency challenge for NDN routers. This article mainly studies the data package authentication scheme in the package-level security mechanism. Based on mobile edge computing (MEC), an efficient certificateless group signature scheme featured with anonymity, unforgeability, traceability, and key escrow resilience is proposed. The regional and edge architecture is utilized to solve the device management problem of IoT, reducing the risks of content pollution attacks from the data source. By offloading signature pressure to MEC servers, the contradiction between heavy overhead and shortage of ED resources is avoided. Moreover, the verification efficiency in NDN router is much improved via batch verification in the proposed scheme. Both security analysis and experimental simulations show that the proposed MEC-based certificateless group signature scheme is provably secure and practical.
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| 6. |
- Wu, Ziqian, et al.
(författare)
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Identification of Functional Modules and Key Pathways Associated with Innervation in Graft Bone-CGRP Regulates the Differentiation of Bone Marrow Mesenchymal Stem Cells via p38 MAPK and Wnt6/β-Catenin
- 2023
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Ingår i: Stem cells international. - : Hindawi Publishing Corporation. - 1687-966X .- 1687-9678. ; 2023
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Tidskriftsartikel (refereegranskat)abstract
- Bone resorption occurs after bone grafting, however, contemporaneous reconstruction of the innervation of the bone graft is a potential treatment to maintain the bone mass of the graft. The innervation of bone is an emerging research topic. To understand the potential molecular mechanisms of bone innervation after bone grafting, we collected normal iliac bone tissue as well as bone grafts with or without innervation from nine patients 1 year after surgery and performed RNA sequencing. We identified differentially expressed genes) from these samples and used the gene ontology and Kyoto Encyclopedia of Genes and Genomes databases for functional enrichment and signaling pathway analysis. In parallel, we established protein-protein interaction networks to screen functional modules. Based on bioinformatic results, we validated in vitro the osteogenic differentiation potential of rat bone marrow mesenchymal stem cells (BMMSCs) after calcitonin gene-related peptide (CGRP) stimulation and the expression of p38 MAPK and Wnt6/β-catenin pathways during osteogenesis. Our transcriptome analysis of bone grafts reveals functional modules and signaling pathways of innervation which play a vital role in the structural and functional integration of the bone graft. Simultaneously, we demonstrate that CGRP regulates the differentiation of BMMSCs through p38 MAPK and Wnt6/β-catenin.
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| 7. |
- Xue, Yuhan, et al.
(författare)
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Computational insights into the different catalytic activities of CYP3A4 and CYP3A5 toward schisantherin E
- 2019
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Ingår i: Chemical Biology and Drug Design. - : Blackwell Publishing. - 1747-0277 .- 1747-0285. ; 93:5, s. 854-864
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Tidskriftsartikel (refereegranskat)abstract
- The cytochromes CYP3A4 and CYP3A5 share 84% sequence identity, but they exhibit different catalytic activities toward some substrates. Schisantherin E (SE) was recently identified as a selective substrate of CYP3A5, which exhibited catalytic efficiency that was more than 23 times higher than CYP3A4. At present, however, the structural determinants responsible for the different catalytic activities of the two enzymes toward SE have not been fully understood. In this study, a combination of molecular docking, molecular dynamic simulations, and binding free energy calculation was performed on the CYP3A4/CYP3A5-SE systems to investigate the issue. The results demonstrate that Ser119 in CYP3A4 and Glu374 in CYP3A5 formed direct hydrogen bonding with SE, respectively. Additionally, one water molecule located between the B-C loop and the I helix mediated different hydrogen-bonding networks between CYP3A4/3A5 and SE. The residue differences (Phe/Leu108 and Leu/Phe210) triggered the distinct conformational changes of the Phe-cluster residues, especially Phe213 and Phe215, which formed stronger hydrophobic interactions with SE in CYP3A5. The calculated binding free energies were consistent with the experimental results.
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