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Search: WFRF:(Zhang Shuyu)

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1.
  • Beal, Jacob, et al. (author)
  • Robust estimation of bacterial cell count from optical density
  • 2020
  • In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
  • 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.
  • Shi, Tingting, et al. (author)
  • The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees
  • 2024
  • 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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3.
  • Liu, Shuyu, et al. (author)
  • Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome
  • 2022
  • In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:2
  • 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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4.
  • Zhang, Shuyu, et al. (author)
  • Moisture Sources and Pathways of Annual Maximum Precipitation in the Lancang-Mekong River Basin
  • 2024
  • In: GEOPHYSICAL RESEARCH LETTERS. - 0094-8276 .- 1944-8007. ; 51:6
  • Journal article (peer-reviewed)abstract
    • Recent extremely heavy precipitation has led to substantial economic losses and affected millions of residences in the Lancang-Mekong River Basin (LMRB). This study analyzed the spatial-temporal characteristics of the annual maximum precipitation (R1X) of the LMRB and identified the moisture sources and pathways conducive to R1Xs using a Lagrangian back trajectory model. Results show that India Ocean and Bay of Bengal (IO/BOB), local evapotranspiration, and West Pacific Ocean and East China (WP/EC) are the three main moisture transport pathways of the R1Xs in LMRB, contributing 68.3%, 20.4% and 11.3% of the trajectories, respectively. R1Xs in the downstream eastern area are affected by tropical cyclones bringing large amounts of moisture from the WP/EC. As tropical cyclones shifted northward under climate change impact, more extreme precipitation occurred over the LMRB due to moisture coming from WP/EC, but those from the IO/BOB had decreased because of the slowdown of flows across the Equator. Recent extremely heavy precipitation has led to more frequent floods, storm surges, and other natural hazards in the Lancang-Mekong River Basin, resulting in substantial economic losses and affecting millions of residences. This study used annual maximum precipitation to represent the extreme precipitation and analyzed its spatial-temporal characteristics and the moisture sources and pathways. Results show that the extreme precipitation of the upstream region mainly occurred in July, while that of the downstream region mainly occurred in August-September. The moisture pathways of the historical extreme precipitation were identified using a physical-based model, and are classified into three clusters using a machine-learning model. West Pacific Ocean and East China, local evapotranspiration, and Indian Ocean and Bay of Bengal (IO/BOB) are the three moisture transport pathways with contributions of 68.3%, 20.4%, and 11.3% to the total pathways. The tropical cyclones bring large amounts of moisture and mainly affect R1Xs in the downstream eastern area. Tropical cyclones shifted northward under climate change impact, and more extreme precipitation occurred over the LMRB due to moisture coming from the West Pacific Ocean and East China, but those from the IO and BOB had decreased because of the slowdown of flows across the Equator. The timing of the annual maximum precipitation of the Lancang-Mekong River Basin (LMRB) varies from July to September The extreme precipitation of the LMRB mainly received moisture from the Indian Ocean to the West Pacific Ocean Tropical cyclones will bring more extreme precipitation to the LMRB under climate change
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5.
  • Buitelaar, Jan K, et al. (author)
  • A comparison of North American versus non-North American ADHD study populations.
  • 2006
  • In: European Child & Adolescent Psychiatry. - : Springer Science and Business Media LLC. - 1018-8827 .- 1435-165X. ; 15:3, s. 177-181
  • Journal article (peer-reviewed)abstract
    • Few large, prospective clinical studies in Europe have assessed the validity and applicability of research methods used to study ADHD in North America. To assess comparability of study populations, we examined baseline patient characteristics from a group of North American studies against those of a large European/African/Australian study. All studies used identical diagnostic assessments and inclusion criteria, with ADHD diagnosis and the presence of comorbid psychiatric conditions confirmed using the KSADS-PL. Raters were trained and assessed to ensure uniform diagnostic and symptom severity rating standards. Six hundred and four patients (mean age = 10.2 years) enrolled in the non-North American study, and 665 patients (mean age = 10.4 years) enrolled in the North American study. The proportion of girls was higher in the North American studies (29.2% vs. 10.4%, p < 0.001). In both groups, most patients had a positive family history of ADHD and previous stimulant treatment. Fewer had the inattentive subtype of ADHD, and mean severity was slightly higher in the non-North American study. Results demonstrate that, when a uniform set of rigorous, standardized diagnostic criteria are used by skilled clinicians, the patient populations identified are generally similar. This supports the practice of generalizing results from treatment studies across geographies.
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6.
  • Buitelaar, Jan K, et al. (author)
  • A prospective, multicenter, open-label assessment of atomoxetine in non-North American children and adolescents with ADHD.
  • 2004
  • In: European Child & Adolescent Psychiatry. - : Springer Science and Business Media LLC. - 1018-8827 .- 1435-165X. ; 13:4, s. 249-257
  • Journal article (peer-reviewed)abstract
    • OBJECTIVE: The aim of this study was to study treatment response to atomoxetine in a large, multicenter study of non-North American patients with ADHD. METHODS: A total of 604 children and adolescents with ADHD were enrolled in a 10-week open-label trial with atomoxetine prior to randomization to a double-blind relapse prevention phase at 33 sites in the United Kingdom, continental Europe, Israel, South Africa, and Australia. All patients had ADHD symptom severity at least 1.5 standard deviations above United States age and gender norms for their diagnostic subtype as measured by the investigator-scored ADHD Rating Scale (ADHD RS). Outcomes were assessed by analysis of change in the ADHD RS; functional and psychosocial outcomes were assessed using the Child Health Questionnaire (CHQ). RESULTS: At endpoint, ADHD RS total scores decreased by an average of 56.7%, and 69% of patients were rated as having no or minimal symptoms. Significant improvement was observed in psychosocial and functional outcomes. Discontinuations attributed to adverse events were < 4%. CONCLUSION: These open-label data, gathered in an international setting, add to our knowledge of the value of atomoxetine in treating ADHD symptoms, as well as its safety and tolerability.
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7.
  • Buitelaar, Jan K, et al. (author)
  • A randomized, double-blind study of continuation treatment for attention-deficit/hyperactivity disorder after 1 year.
  • 2007
  • In: Biological Psychiatry. - : Elsevier BV. - 0006-3223. ; 61:5, s. 694-699
  • Journal article (peer-reviewed)abstract
    • BACKGROUND: The efficacy of atomoxetine in maintaining symptom response following 1 year of treatment was assessed in children and adolescents (n = 163) with DSM-IV defined attention-deficit/hyperactivity disorder (ADHD). METHODS: Subjects had previously responded to atomoxetine acutely and had completed 1 year of double-blind atomoxetine treatment. They were then randomly assigned in double-blind fashion to continued atomoxetine or placebo substitution for 6 months. RESULTS: Atomoxetine was superior to placebo in preventing relapse (Wilcoxon test, p = .008) and in maintaining symptom response (ADHD Rating Scale IV score, p < .001). Among subjects assigned to discontinuation, the magnitude of symptom return was generally to a level of severity less than that observed at study entry. CONCLUSIONS: Following 1 year of treatment with atomoxetine, continued treatment over the ensuing 6 months was associated with superior outcomes compared with placebo substitution. However, there was considerable variability between individuals in the magnitude of symptom return after drug discontinuation, suggesting that some subjects treated with atomoxetine for a year with good results may consolidate gains made during drug treatment and could benefit from a medication-free trial to assess the need for ongoing drug treatment.
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8.
  • Michelson, David, et al. (author)
  • Relapse prevention in pediatric patients with ADHD treated with atomoxetine: a randomized, double-blind, placebo-controlled study.
  • 2004
  • In: Journal of the American Academy of Child and Adolescent Psychiatry. - 0890-8567. ; 43:7, s. 896-904
  • Journal article (peer-reviewed)abstract
    • OBJECTIVE: Attention-deficit/hyperactivity disorder (ADHD) is typically treated over extended periods; however, few placebo-controlled, long-term studies of efficacy have been reported. METHOD: In a global multicenter study, children and adolescents who responded to an initial 12-week, open-label period of treatment with atomoxetine, a nonstimulant treatment for ADHD, were randomized to continued atomoxetine treatment or placebo for 9 months under double-blind conditions. RESULTS: A total of 416 patients completed acute atomoxetine treatment and were randomized. At end point, atomoxetine was superior to placebo in preventing relapse defined as a return to 90% of baseline symptom severity (proportion relapsing: atomoxetine 65 of 292 [22.3%], placebo 47 of 124 [37.9%], p =.002). The proportion of patients with a 50% worsening in symptoms post-randomization was also lower on atomoxetine (atomoxetine 83 of 292 [28.4%], placebo 59 of 124 [47.6%], p <.001). Compared with patients in the placebo group, atomoxetine-treated patients had superior psychosocial functioning at end point. Discontinuations for adverse events were low in both groups, and tolerability was similar to that observed in acute treatment trials. CONCLUSIONS: In patients who responded favorably to 12 weeks of initial treatment, atomoxetine was superior to placebo in maintaining response for the ensuing 9 months. This result supports the value of maintenance treatment with atomoxetine in patients with ADHD who respond to initial treatment.
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9.
  • Wang, Qin, et al. (author)
  • Genetic susceptibility to diabetic kidney disease is linked to promoter variants of XOR
  • 2023
  • In: NATURE METABOLISM. - 2522-5812. ; 5, s. 607-625
  • Journal article (peer-reviewed)abstract
    • The lifetime risk of kidney disease in people with diabetes is 10-30%, implicating genetic predisposition in the cause of diabetic kidney disease (DKD). Here we identify an expression quantitative trait loci (QTLs) in the cis-acting regulatory region of the xanthine dehydrogenase, or xanthine oxidoreductase (Xor), a binding site for C/EBP beta, to be associated with diabetes-induced podocyte loss in DKD in male mice. We examine mouse inbred strains that are susceptible (DBA/2J) and resistant (C57BL/6J) to DKD, as well as a panel of recombinant inbred BXD mice, to map QTLs. We also uncover promoter XOR orthologue variants in humans associated with high risk of DKD. We introduced the risk variant into the 5 '-regulatory region of XOR in DKD-resistant mice, which resulted in increased Xor activity associated with podocyte depletion, albuminuria, oxidative stress and damage restricted to the glomerular endothelium, which increase further with type 1 diabetes, high-fat diet and ageing. Therefore, differential regulation of Xor contributes to phenotypic consequences with diabetes and ageing. Wang et al. identify a promoter variant in xanthine oxidoreductase associated with diabetic kidney disease through increased podocyte depletion and glomerular injury.
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10.
  • Zhang, Xu, et al. (author)
  • Connectivity, permeability and flow channelization in fractured karst reservoirs: A numerical investigation based on a two-dimensional discrete fracture-cave network model
  • 2022
  • In: Advances in Water Resources. - : Elsevier BV. - 0309-1708 .- 1872-9657. ; 161, s. 104142-104142
  • Journal article (peer-reviewed)abstract
    • Fractured karst reservoirs play a significant role in hydrocarbon reserves and groundwater storage. They often exhibit complex multiscale heterogeneities involving pores, fractures and caves, whose length scales range from microns to tens or hundreds of meters. Thus, the study of fractured karst reservoirs is faced with a significant unresolved challenge in quantitatively characterizing the geometrical connectivity and hydraulic conductivity as well as their interrelationships in such strongly heterogeneous, multicomponent systems. In this paper, we propose an analytical formulation to characterize the connectivity of discrete fracture-cave networks building upon the excluded area concept of the percolation theory. By implementing a state-of-the-art computational model solving coupled Navier-Stokes (free flow) and Darcy (porous media flow) equations, we numerically derive the permeability of a fractured and karstified porous media, such that the relationship between the connectivity and permeability is further explored. The high-fidelity numerical model also permits us to elucidate the process of flow channelization within the fracture-cave network. The results show that the fracture-cave network connectivity correlates to the permeability via a power law scaling for connected systems. Significant flow channeling occurs around the percolation threshold where the flow is dominated by a limited number of preferential pathways. Caves play a crucial role in the flow due to the fact that caves could globally enhance the network connectivity and locally serve as hotspots for high fluid velocity. Finally, a semi-analytical permeability model for fractured karst reservoirs is developed. The results of our research and insights obtained have important implications for understanding the subsurface fluid flow in fractured karst reservoirs.
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