| 1. |
- Ren, Luyao, et al.
(författare)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
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Tidskriftsartikel (refereegranskat)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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| 2. |
- Lu, Yahua, et al.
(författare)
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Engineer Nanoscale Defects into Selective Channels : MOF-Enhanced Li+ Separation by Porous Layered Double Hydroxide Membrane
- 2023
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Ingår i: Nano-Micro Letters. - 2311-6706. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) membrane-based ion separation technology has been increasingly explored to address the problem of lithium resource shortage, yet it remains a sound challenge to design 2D membranes of high selectivity and permeability for ion separation applications. Zeolitic imidazolate framework functionalized modified layered double hydroxide (ZIF-8@MLDH) composite membranes with high lithium-ion (Li+) permeability and excellent operational stability were obtained in this work by in situ depositing functional ZIF-8 nanoparticles into the nanopores acting as framework defects in MLDH membranes. The defect-rich framework amplified the permeability of Li+, and the site-selective growth of ZIF-8 in the framework defects bettered its selectivity. Specifically speaking, the ZIF-8@MLDH membranes featured a high permeation rate of Li+ up to 1.73 mol m−2 h−1 and a desirable selectivity of Li+/Mg2+ up to 31.9. Simulations supported that the simultaneously enhanced selectivity and permeability of Li+ are attributed to changes in the type of mass transfer channels and the difference in the dehydration capacity of hydrated metal cations when they pass through nanochannels of ZIF-8. This study will inspire the ongoing research of high-performance 2D membranes through the engineering of defects.
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| 3. |
- Lu, Yahua, et al.
(författare)
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Heterostructure membranes of high permeability and stability assembled from MXene and modified layered double hydroxide nanosheets
- 2023
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Ingår i: Journal of Membrane Science. - 0376-7388 .- 1873-3123. ; 688
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Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) MXene-based lamellar membranes play transformative roles in membrane filtration technology. Their practical use in water treatment is however hindered by several hurdles, e.g., unfavorable swelling due to weak interactions between adjacent MXene nanosheets, tortuous diffusion pathways of layered stacking, and the intrinsic aquatic oxidation-prone nature of MXene. Herein, nanoporous 2D/2D heterostructure membranes are elaborately constructed via solution-phase assembly of oppositely charged MXene and modified layered double hydroxide (MLDH) nanosheets. As a multifunctional component, positively charged holey MLDH nanosheets were first tailor-made to serve simultaneously as a binder, spacer and surface-modifier; next they were intercalated into negatively charged MXene lamella to enhance structural stability and mass transfer of membranes. As a result, the as-prepared MLDH@MXene heterostructure membranes successfully break the persistent trade-off between high permeability and selectivity while mitigating the common drawbacks in 2D MXene-based lamellar membranes, e.g., swelling issues, restacking problems, and vulnerable chemical stability. Noticeably, at an operating pressure of 4 bar and a feed solution of 100 ppm of Congo red, the heterostructure membranes enable a threefold jump in permeability (332.7 +/- 20 L m(-2) h(-1 )bar(-1)) when compared to the pristine MXene membrane (119.3 +/- 18 L m(-2 )h(-1) bar(-1)), and better operational stability without compromising the rejection.
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