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  1. Free, publicly-accessible full text available January 1, 2024
  2. As countries look toward re-opening of economic activities amidst the ongoing COVID-19 pandemic, ensuring public health has been challenging. While contact tracing only aims to track past activities of infected users, one path to safe reopening is to develop reliable spatiotemporal risk scores to indicate the propensity of the disease. Existing works which aim at developing risk scores either rely on compartmental model-based reproduction numbers (which assume uniform population mixing) or develop coarse-grain spatial scores based on reproduction number (R0) and macro-level density-based mobility statistics. Instead, in this article, we develop a Hawkes process-based technique to assign relatively fine-grain spatial and temporal risk scores by leveraging high-resolution mobility data based on cell-phone originated location signals. While COVID-19 risk scores also depend on a number of factors specific to an individual, including demography and existing medical conditions, the primary mode of disease transmission is via physical proximity and contact. Therefore, we focus on developing risk scores based on location density and mobility behaviour. We demonstrate the efficacy of the developed risk scores via simulation based on real-world mobility data. Our results show that fine-grain spatiotemporal risk scores based on high-resolution mobility data can provide useful insights and facilitate safe re-opening.
    Free, publicly-accessible full text available June 30, 2023
  3. Free, publicly-accessible full text available May 16, 2023
  4. Abstract Investigating the length scales of granules could help understand the dynamics of granules in the photosphere. In this work, we detected and identified granules in an active region near disk center observed at wavelength of TiO (7057 Å) by the 1.6 m Goode Solar Telescope (GST). By a detailed analysis of the size distribution and flatness of granules, we found a critical size that divides the granules in motions into two regimes: convection and turbulence. The length scales of granules with sizes larger than 600 km follow Gauss function and demonstrate “flat” in flatness, which reveal that these granules are dominated by convection. Those with sizes smaller than 600 km follow power-law function and behave power-law tendency in flatness, which indicate that the small granules are dominated by turbulence. Hence, for the granules in active regions, they are originally convective in large length scale, and directly become turbulent once their sizes turn to small, likely below the critical size of 600 km. Comparing with the granules in quiet regions, they evolve with the absence of the mixing motions of convection and turbulence. Such a difference is probably caused by the interaction between fluid motions and strong magnetic fields inmore »active regions. The strong magnetic fields make high magnetic pressure which creates pressure walls and slows down the evolution of convective granules. Such walls cause convective granules extending to smaller sizes on one hand, and cause wide intergranular lanes on the other hand. The small granules isolated in such wide intergranular lanes are continually sheared, rotated by strong downflows in surroundings and hereby become turbulent.« less
    Free, publicly-accessible full text available July 15, 2023
  5. Free, publicly-accessible full text available January 1, 2023
  6. Free, publicly-accessible full text available February 1, 2023
  7. Symplasmicly connected cells called sieve elements form a network of tubes in the phloem of vascular plants. Sieve elements have essential functions as they provide routes for photoassimilate distribution, the exchange of developmental signals, and the coordination of defense responses. Nonetheless, they are the least understood main type of plant cells. They are extremely sensitive, possess a reduced endomembrane system without Golgi apparatus, and lack nuclei and translation machineries, so that transcriptomics and similar techniques cannot be applied. Moreover, the analysis of phloem exudates as a proxy for sieve element composition is marred by methodological problems. We developed a simple protocol for the isolation of sieve elements from leaves and stems of Nicotiana tabacum at sufficient amounts for large-scale proteome analysis. By quantifying the enrichment of individual proteins in purified sieve element relative to bulk phloem preparations, proteins of increased likelyhood to function specifically in sieve elements were identified. To evaluate the validity of this approach, yellow fluorescent protein constructs of genes encoding three of the candidate proteins were expressed in plants. Tagged proteins occurred exclusively in sieve elements. Two of them, a putative cytochrome b561/ferric reductase and a reticulon-like protein, appeared restricted to segments of the endoplasmic reticulum (ER)more »that were inaccessible to green fluorescent protein dissolved in the ER lumen, suggesting a previously unknown differentiation of the endomembrane system in sieve elements. Evidently, our list of promising candidate proteins ( SI Appendix , Table S1 ) provides a valuable exploratory tool for sieve element biology.« less
    Free, publicly-accessible full text available January 4, 2023
  8. Free, publicly-accessible full text available February 1, 2023
  9. Introduction Widespread problems of psychological distress have been observed in many countries following the outbreak of COVID-19, including Australia. What is lacking from current scholarship is a national-scale assessment that tracks the shifts in mental health during the pandemic timeline and across geographic contexts. Methods Drawing on 244 406 geotagged tweets in Australia from 1 January 2020 to 31 May 2021, we employed machine learning and spatial mapping techniques to classify, measure and map changes in the Australian public’s mental health signals, and track their change across the different phases of the pandemic in eight Australian capital cities. Results Australians’ mental health signals, quantified by sentiment scores, have a shift from pessimistic (early pandemic) to optimistic (middle pandemic), reflected by a 174.1% (95% CI 154.8 to 194.5) increase in sentiment scores. However, the signals progressively recessed towards a more pessimistic outlook (later pandemic) with a decrease in sentiment scores by 48.8% (95% CI 34.7 to 64.9). Such changes in mental health signals vary across capital cities. Conclusion We set out a novel empirical framework using social media to systematically classify, measure, map and track the mental health of a nation. Our approach is designed in a manner that can readily bemore »augmented into an ongoing monitoring capacity and extended to other nations. Tracking locales where people are displaying elevated levels of pessimistic mental health signals provide important information for the smart deployment of finite mental health services. This is especially critical in a time of crisis during which resources are stretched beyond normal bounds.« less
    Free, publicly-accessible full text available January 1, 2023
  10. Abstract

    Protein fold recognition is a critical step toward protein structure and function prediction, aiming at providing the most likely fold type of the query protein. In recent years, the development of deep learning (DL) technique has led to massive advances in this important field, and accordingly, the sensitivity of protein fold recognition has been dramatically improved. Most DL-based methods take an intermediate bottleneck layer as the feature representation of proteins with new fold types. However, this strategy is indirect, inefficient and conditional on the hypothesis that the bottleneck layer’s representation is assumed as a good representation of proteins with new fold types. To address the above problem, in this work, we develop a new computational framework by combining triplet network and ensemble DL. We first train a DL-based model, termed FoldNet, which employs triplet loss to train the deep convolutional network. FoldNet directly optimizes the protein fold embedding itself, making the proteins with the same fold types be closer to each other than those with different fold types in the new protein embedding space. Subsequently, using the trained FoldNet, we implement a new residue–residue contact-assisted predictor, termed FoldTR, which improves protein fold recognition. Furthermore, we propose a new ensemblemore »DL method, termed FSD_XGBoost, which combines protein fold embedding with the other two discriminative fold-specific features extracted by two DL-based methods SSAfold and DeepFR. The Top 1 sensitivity of FSD_XGBoost increases to 74.8% at the fold level, which is ~9% higher than that of the state-of-the-art method. Together, the results suggest that fold-specific features extracted by different DL methods complement with each other, and their combination can further improve fold recognition at the fold level. The implemented web server of FoldTR and benchmark datasets are publicly available at http://csbio.njust.edu.cn/bioinf/foldtr/.

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