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- 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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- Chng, Kern Rei, et al.
(author)
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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
- 2020
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In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 26, s. 941-951
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Journal article (peer-reviewed)abstract
- Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections. Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.
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- Wei, Yangjun, et al.
(author)
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Design of an industrial chemical looping gasification system
- 2022
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In: Fuel. - : Elsevier BV. - 0016-2361. ; 330
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Journal article (peer-reviewed)abstract
- A design methodology for an industrial Chemical Looping Gasification (CLG) unit is proposed, including the reactor system, oxygen carrier, solid fuel, key parameters, mass and energy balance, reactor dimension, and emissions. To determine a reactor system for CLG, the first design step is to choose between four types of systems and their applicability. The selection of a circulating material and a particle size of the oxygen carrier and the solid fuel is discussed. Determination of the key operating parameters comprises oxygen-to-fuel ratio, steam-to-fuel ratio, charging/discharging of the oxygen carrier and the conversion difference between an air reactor and a fuel reactor, their temperatures, velocities in each reactor, and cyclone efficiency. As design basis, the mass and energy balance of the system is computed based on the distribution of syngas composition and oxygen transportation over the system. It is not critical to obtain an adequate circulation for a CLG unit. But to satisfy the heat balance, oxygen transport and reasonable efficiency of syngas production at the same time makes CLG technology challenging. More work is needed for the introduced design items in the case of commercial-scale units.
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