| 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. |
- Fan, Zhouzhou, et al.
(author)
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Changes in Plant Rhizosphere Microbial Communities under Different Vegetation Restoration Patterns in Karst and Non-karst Ecosystems
- 2019
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
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Journal article (peer-reviewed)abstract
- Understanding how patterns of recovery and geological conditions affect microbial communities is important for determining the stability of karst ecosystems. Here, we investigated the diversity and composition of microorganisms in karst and non-karst environments under natural restoration and artificial rehabilitation conditions. The results showed no significant differences in soil microbial diversity, but the microbial communities associated with geological conditions and tree species differed significantly. Variation partitioning analysis (VPA) showed that a total of 77.3% of the variation in bacteria and a total of 69.3% of the variation in fungi could be explained by vegetation type and geological background. There were significant differences in six bacterial classes (Actinobacteria, Alphaproteobacteria, Ktedonobacteria, TK10, Gammaproteobacteria, and Anaerolineae) and nine fungal classes (Eurotiomycetes, Agaricomycetes, unclassified _p_Ascomycota, Sordariomycetes, Tremellomycetes, norank_k_Fungi, Pezizomycetes, Leotiomycetes and Archaeorhizomycetes) among the soils collected from six plots. A Spearman correlation heatmap showed that the microbial community was affected by the major soil properties. Principal coordinates analysis indicated that the microbial community of Pinus yunnanensis in the artificial forest, which was established for the protection of the environment was most similar to that in the natural secondary forest in the karst ecosystem. These findings further our understanding of microbial responses to vegetation restoration and geological conditions.
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| 3. |
- Huang, Letian, et al.
(author)
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A Lifetime-aware Mapping Algorithm to Extend MTTF of Networks-on-Chip
- 2018
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In: 2018 23rd Asia and South Pacific Design Automation Conference Proceedings (ASP-DAC). - : Institute of Electrical and Electronics Engineers (IEEE). - 9781509006021 ; , s. 147-152
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Conference paper (peer-reviewed)abstract
- Fast aging of components has become one of the major concerns in Systems-on-Chip with further scaling of the submicron technology. This problem accelerates when combined with improper working conditions such as unbalanced components' utilization. Considering the mapping algorithms in the Networks-on-Chip domain, some routers/links might be frequently selected for mapping while others are underutilized. Consequently, the highly utilized components may age faster than others which results in disconnecting the related cores from the network. To address this issue, we propose a mapping algorithm, called lifetime-aware neighborhood allocation (LaNA), that takes the aging of components into account when mapping applications. The proposed method is able to balance the wear-out of NoC components, and thus extending the service time of NoC. We model the lifetime as a resource consumed over time and accordingly define the lifetime budget metric. LaNA selects a suitable node for mapping which has the maximum lifetime budget. Experimental results show that the lifetime-aware mapping algorithm could improve the minimal MTTF of NoC around 72.2%, 58.3%, 46.6% and 48.2% as compared to NN, CoNA, WeNA and CASqA, respectively.
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| 4. |
- Jiang, Shuyan, et al.
(author)
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Optimizing Dynamic Mapping Techniques for On-Line NoC Test
- 2018
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In: 2018 23RD ASIA AND SOUTH PACIFIC DESIGN AUTOMATION CONFERENCE (ASP-DAC). - : IEEE. - 9781509006021 ; , s. 227-232
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Conference paper (peer-reviewed)abstract
- With the aggressive scaling of submicron technology, intermittent faults are becoming one of the limiting factors in achieving a high reliability in Network-on-Chip (NoC). Increasing test frequency is necessary to detect intermittent faults, which in turn interrupts the execution of applications. On the other hand, the main goal of traditional mapping algorithms is to allocate applications to the NoC platform, ignoring about the test requirement. In this paper, we propose a novel testing-aware mapping algorithm (TAMA) for NoC, targeting intermittent faults on the paths between crossbars. In this approach, the idle links are identified and the components between two crossbars are tested when the application is mapped to the platform. The components can be tested if there is enough time from when the application leaves the platform and a new application enters it. The mapping algorithm is tuned to give a higher priority to the tested paths in the next application mapping. This leaves enough time to test the links and the belonging components that have not been tested in the expected time. Experiment results show that the proposed testing-aware mapping algorithm leads to a significant improvement over FF, NN, CoNA, and WeNA.
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| 5. |
- Jiang, Shuyan, et al.
(author)
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Testing aware dynamic mapping for path-centric network-on-chip test
- 2019
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In: Integration. - : Elsevier. - 0167-9260 .- 1872-7522. ; 67, s. 134-143
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Journal article (peer-reviewed)abstract
- With the aggressive scaling of submicron technology, intermittent faults are becoming one of the limiting factors in achieving high reliability in Network-on-Chip (NoC). Increasing test frequency is necessary to detect intermittent faults, which in turn interrupts the execution of applications. On the other hand, the primary goal of traditional mapping algorithms is to allocate applications to the NoC platform, ignoring the test requirement. In this paper, we propose a novel testing-aware mapping algorithm (TAMA) for NoC, targeting intermittent faults on the paths between crossbars. In this approach, the idle paths are identified, and the components between two crossbars are tested when the application is mapped to the platform. The components can be tested if there is enough time from the time when the application leaves the platform to the time when a new application enters it. The mapping algorithm is tuned to give a higher priority to the tested paths in the next application mapping, which leaves enough time to test the links and the belonging components that have not been tested in the expected time. Experiment results show that the proposed testing-aware mapping algorithm leads to a significant improvement over FF(Fiexitrst Free), NN(Nearest Neighbor), CoNA(Contiguous Neighborhood Allocation), and WeNA(Weighted-based Neighborhood Allocation).
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| 6. |
- Liu, Shuyu, et al.
(author)
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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome
- 2022
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In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:2
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Journal article (peer-reviewed)abstract
- Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.
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| 7. |
- Ma, Mengnan, et al.
(author)
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Summer regional climate simulations over Tibetan Plateau: from gray zone to convection permitting scale
- 2022
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In: Climate Dynamics. - : Springer Science and Business Media LLC. - 0930-7575 .- 1432-0894.
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Journal article (peer-reviewed)abstract
- The Tibetan Plateau (TP) is often referred to as ‘the Third Pole’ and plays an essential role in the global climate. However, it remains challenging for most global and regional models to realistically simulate the characteristics of climate over the TP. In this study, two Weather Research and Forecasting model (WRF) experiments using spectral nudging with gray-zone (GZ9) and convection-permitting (CP3) resolution are conducted for summers from 2009 to 2018. The surface air temperature (T2m) and precipitation from the two simulations and the global reanalysis ERA5 are evaluated against in-situ observations. The results show that ERA5 has a general cold bias over southern TP, especially in maximum T2m (Tmax), and wet bias over whole TP. Both experiments can successfully capture the spatial pattern and daily variation of T2m and precipitation, though cold bias for temperature and dry bias for precipitation exist especially over the regions south of 35° N. Compared with ERA5, the added value of the two WRF experiments is mainly reflected in the reduced cold bias especially for Tmax with more improvement found in CP3 and the reduced wet bias. However, the ability of the convection-permitting WRF experiment in improving the simulation of precipitation seems limited when compared to the gray-zone WRF experiment, which may be related to the biases in physical parameterization and lack of representativeness of station observation. Further investigation into surface radiation budget reveals that the underestimation of net shortwave radiation contributes a lot to the cold bias of T2m over the southeastern TP in GZ9 which is improved in CP3. Compared with GZ9, CP3 shows that larger specific humidity at low-level (mid-high level) coexists with more precipitation (clouds) over the southern TP. This improvement is achieved by better depiction of topographic details, underlying surface and atmospheric processes, land–atmosphere interactions and so on, leading to stronger northward water vapor transport (WVT) in CP3, providing more water vapor for precipitation at surface and much wetter condition in the mid-high level.
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| 8. |
- Niu, Xiaorui, et al.
(author)
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On the sensitivity of seasonal and diurnal precipitation to cumulus parameterization over CORDEX-EA-II
- 2020
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In: Climate Dynamics. - : Springer Science and Business Media LLC. - 0930-7575 .- 1432-0894. ; 54, s. 373-393
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Journal article (peer-reviewed)abstract
- The ability of the Weather Research and Forecasting (WRF) model in simulating the seasonal and diurnal cycles of rainfall over the Coordinated Regional Climate Downscaling Experiment East Asia Phase II (CORDEX-EA-II) domain is validated against the Tropical Rainfall Measuring Mission (TRMM) datasets. A focus is placed on the role of convective parameterization (CP) schemes. A set of numerical experiments at a 25km resolution for 1998–2009, using six different CPs, is performed to evaluate the physics-dependency of simulation results. All CPs simulate realistic summer mean precipitation and its northward propagation, with the best performance in the Simplified Arakawa-Schubert (SAS). The biases in the seasonal evolution of rainfall are related to the deficiency in simulated low-level winds and the northward propagation of the cyclonic vorticity. The simulated earlier peak time in other CPs is delayed by about 1–2h by the Kain-Fritsch with a modified trigger function (KFMT), although this scheme shows a disadvantage in the magnitude. The performance of different CPs in simulating diurnal rainfall cycles is dependent on regions, and none of them performs better than the others for all the sub-regions. The initiation of simulated convection is weakly physics-dependent. However, the timing and magnitude of stratiform precipitation differ among the six experiments. A furtheranalysisshows that the dry biases over the lower Yangtze River basin are a result of the weakened southwesterly water vapor transport, while the excessive afternoon rainfall in the Kain-Fritsch (KF) simulation is attributed to the largest positive perturbation in the lower level atmosphere, especially the enhanced vertical transport of humidity.
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| 9. |
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| 10. |
- Shi, Tingting, et al.
(author)
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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees
- 2024
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In: Molecular Plant. - : Elsevier. - 1674-2052 .- 1752-9867. ; 17:5, s. 725-746
-
Journal article (peer-reviewed)abstract
- Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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