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Evolutionary de Rham-Hodge method [article]

Jiahui Chen, Rundong Zhao, Yiying Tong, Guo-Wei Wei
2019 arXiv   pre-print
The de Rham-Hodge theory is a landmark of the 20^th Century's mathematics and has had a great impact on mathematics, physics, computer science, and engineering. This work introduces an evolutionary de Rham-Hodge method to provide a unified paradigm for the multiscale geometric and topological analysis of evolving manifolds constructed from a filtration, which induces a family of evolutionary de Rham complexes. While the present method can be easily applied to close manifolds, the emphasis is
more » ... en to more challenging compact manifolds with 2-manifold boundaries, which require appropriate analysis and treatment of boundary conditions on differential forms to maintain proper topological properties. Three sets of unique evolutionary Hodge Laplacian operators are proposed to generate three sets of topology-preserving singular spectra, for which the multiplicities of zero eigenvalues correspond to exactly the persistent Betti numbers of dimensions 0, 1, and 2. Additionally, three sets of non-zero eigenvalues further reveal both topological persistence and geometric progression during the manifold evolution. Extensive numerical experiments are carried out via the discrete exterior calculus to demonstrate the utility and usefulness of the proposed method for data representation and shape analysis.
arXiv:1912.12388v1 fatcat:fonugxo6kjgf3o4vz7qmgkompm

FUIM: Fuzzy Utility Itemset Mining [article]

Shicheng Wan, Wensheng Gan, Xu Guo, Jiahui Chen, Unil Yun
2021 arXiv   pre-print
Because of usefulness and comprehensibility, fuzzy data mining has been extensively studied and is an emerging topic in recent years. Compared with utility-driven itemset mining technologies, fuzzy utility mining not only takes utilities (e.g., profits) into account, but also considers quantities of items in each transaction for discovering high fuzzy utility itemsets (HFUIs). Thus, fuzziness can be regard as a key criterion to select high-utility itemsets, while the exiting algorithms are not
more » ... fficient enough. In this paper, an efficient one-phase algorithm named Fuzzy-driven Utility Itemset Miner (FUIM) is proposed to find out a complete set of HFUIs effectively. In addition, a novel compact data structure named fuzzy-list keeps the key information from quantitative transaction databases. Using fuzzy-list, FUIM can discover HFUIs from transaction databases efficiently and effectively. Both completeness and correctness of the FUIM algorithm are proved by five theorems. At last, substantial experiments test three terms (runtime cost, memory consumption, and scalability) to confirm that FUIM considerably outperforms the state-of-the-art algorithms.
arXiv:2111.00307v1 fatcat:q4nshoag3zfyzee7r2bkupdeci

Mutations strengthened SARS-CoV-2 infectivity [article]

Jiahui Chen, Rui Wang, Menglun Wang, Guo-Wei Wei
2020 arXiv   pre-print
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is a major concern in coronavirus disease 2019 (COVID-19) prevention and economic reopening. However, rigorous determination of SARS-COV-2 infectivity is essentially impossible owing to its continuous evolution with over 13752 single nucleotide polymorphisms (SNP) variants in six different subtypes. We develop an advanced machine learning algorithm based on the algebraic topology to quantitatively evaluate the binding
more » ... ity changes of SARS-CoV-2 spike glycoprotein (S protein) and host angiotensin-converting enzyme 2 (ACE2) receptor following the mutations. Based on mutation-induced binding affinity changes, we reveal that five out of six SARS-CoV-2 subtypes have become either moderately or slightly more infectious, while one subtype has weakened its infectivity. We find that SARS-CoV-2 is slightly more infectious than SARS-CoV according to computed S protein-ACE2 binding affinity changes. Based on a systematic evaluation of all possible 3686 future mutations on the S protein receptor-binding domain (RBD), we show that most likely future mutations will make SARS-CoV-2 more infectious. Combining sequence alignment, probability analysis, and binding affinity calculation, we predict that a few residues on the receptor-binding motif (RBM), i.e., 452, 489, 500, 501, and 505, have very high chances to mutate into significantly more infectious COVID-19 strains.
arXiv:2005.14669v1 fatcat:cyctuf22cbf6dhfuwnhbcskltu

MLIMC: Machine learning-based implicit-solvent Monte Carlo [article]

Jiahui Chen, Weihua Geng, Guo-Wei Wei
2021 arXiv   pre-print
Monte Carlo (MC) methods are important computational tools for molecular structure optimizations and predictions. When solvent effects are explicitly considered, MC methods become very expensive due to the large degree of freedom associated with the water molecules and mobile ions. Alternatively implicit-solvent MC can largely reduce the computational cost by applying a mean field approximation to solvent effects and meanwhile maintains the atomic detail of the target molecule. The two most
more » ... lar implicit-solvent models are the Poisson-Boltzmann (PB) model and the Generalized Born (GB) model in a way such that the GB model is an approximation to the PB model but is much faster in simulation time. In this work, we develop a machine learning-based implicit-solvent Monte Carlo (MLIMC) method by combining the advantages of both implicit solvent models in accuracy and efficiency. Specifically, the MLIMC method uses a fast and accurate PB-based machine learning (PBML) scheme to compute the electrostatic solvation free energy at each step. We validate our MLIMC method by using a benzene-water system and a protein-water system. We show that the proposed MLIMC method has great advantages in speed and accuracy for molecular structure optimization and prediction.
arXiv:2109.12100v1 fatcat:7bq3tp3i2jeebcxhimezba6sgy

Review of COVID-19 Antibody Therapies [article]

Jiahui Chen, Kaifu Gao, Rui Wang, Duc Duy Nguyen, Guo-Wei Wei
2020 arXiv   pre-print
Under the global health emergency caused by coronavirus disease 2019 (COVID-19), efficient and specific therapies are urgently needed. Compared with traditional small-molecular drugs, antibody therapies are relatively easy to develop and as specific as vaccines in targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and thus attract much attention in the past few months. This work reviews seven existing antibodies for SARS-CoV-2 spike (S) protein with three-dimensional (3D)
more » ... ructures deposited in the Protein Data Bank. Five antibody structures associated with SARS-CoV are evaluated for their potential in neutralizing SARS-CoV-2. The interactions of these antibodies with the S protein receptor-binding domain (RBD) are compared with those of angiotensin-converting enzyme 2 (ACE2) and RBD complexes. Due to the orders of magnitude in the discrepancies of experimental binding affinities, we introduce topological data analysis (TDA), a variety of network models, and deep learning to analyze the binding strength and therapeutic potential of the aforementioned fourteen antibody-antigen complexes. The current COVID-19 antibody clinical trials, which are not limited to the S protein target, are also reviewed.
arXiv:2006.10584v1 fatcat:nwq32rkfmnbh5eqrh7rvoe56bq

Identification and evolution of C4 photosynthetic pathway genes in plants

Weiping Shi, Linqi Yue, Jiahui Guo, Jianming Wang, Xiangyang Yuan, Shuqi Dong, Jie Guo, Pingyi Guo
2020 BMC Plant Biology  
NADP-malic enzyme (NAPD-ME), and pyruvate orthophosphate dikinase (PPDK) are important enzymes that participate in C4 photosynthesis. However, the evolutionary history and forces driving evolution of these genes in C4 plants are not completely understood. We identified 162 NADP-ME and 35 PPDK genes in 25 species and constructed respective phylogenetic trees. We classified NADP-ME genes into four branches, A1, A2, B1 and B2, whereas PPDK was classified into two branches in which monocots were in
more » ... branch I and dicots were in branch II. Analyses of selective pressure on the NAPD-ME and PPDK gene families identified four positively selected sites, including 94H and 196H in the a5 branch of NADP-ME, and 95A and 559E in the e branch of PPDK at posterior probability thresholds of 95%. The positively selected sites were located in the helix and sheet regions. Quantitative RT-PCR (qRT-PCR) analyses revealed that expression levels of 6 NADP-ME and 2 PPDK genes from foxtail millet were up-regulated after exposure to light. This study revealed that positively selected sites of NADP-ME and PPDK evolution in C4 plants. It provides information on the classification and positive selection of plant NADP-ME and PPDK genes, and the results should be useful in further research on the evolutionary history of C4 plants.
doi:10.1186/s12870-020-02339-x pmid:32228460 pmcid:PMC7106689 fatcat:gcnq3ux2rfgsdldzw25s53kkmq

Test-retest reliability of functional connectivity networks during naturalistic fMRI paradigms [article]

Jiahui Wang, Yudan Ren, Xintao Hu, Vinh Thai Nguyen, Lei Guo, Junwei Han, Christine Cong Guo
2016 bioRxiv   pre-print
Some have been found to be effective, such as not regressing out global signals (Guo, et al., 2012; Liao, et al., 2013) , using wavelet processing (Guo, et al., 2012) , or requiring eyes fixation (Patriat  ...  ., 2007; Guo, et al., 2012; Li, et al., 2012; Patriat, et al., 2013; Telesford, et al., 2010; Wang, et al., 2011) . C . C . G u o . , J .  ... 
doi:10.1101/087197 fatcat:k5fy6pgbxjgtrk4dcwfjxyghsq

Chondrocyte ferroptosis contribute to the progression of osteoarthritis

Xudong Yao, Kai Sun, Shengnan Yu, Jiahui Luo, Jiachao Guo, Jiamin Lin, Genchun Wang, Zhou Guo, Yaping Ye, Fengjing Guo
2021 Journal of Orthopaedic Translation  
Osteoarthritis (OA) is a complex process comprised of mechanical load, inflammation, and metabolic factors. It is still unknown that if chondrocytes undergo ferroptosis during OA and if ferroptosis contribute to the progression of OA. In our study, we use Interleukin-1 Beta (IL-1β) to simulate inflammation and ferric ammonium citrate (FAC) to simulate the iron overload in vitro. Also, we used the surgery-induced destabilized medial meniscus (DMM) mouse model to induce OA in vivo. We verify
more » ... ptosis by its definition that defined by the Nomenclature Committee on Cell Death with both in vitro and in vivo model. We observed that both IL-1β and FAC induced reactive oxygen species (ROS), and lipid ROS accumulation and ferroptosis related protein expression changes in chondrocytes. Ferrostatin-1, a ferroptosis specific inhibitor, attenuated the cytotoxicity, ROS and lipid-ROS accumulation and ferroptosis related protein expression changes induced by IL-1β and FAC and facilitated the activation of Nrf2 antioxidant system. Moreover, erastin, the most classic inducer of ferroptosis, promoted matrix metalloproteinase 13 (MMP13) expression while inhibited type II collagen (collagen II) expression in chondrocytes. At last, we proved that intraarticular injection of ferrostatin-1 rescued the collagen II expression and attenuated the cartilage degradation and OA progression in mice OA model. In summary, our study firstly proved that chondrocytes underwent ferroptosis under inflammation and iron overload condition. Induction of ferroptosis caused increased MMP13 expression and decreased collagen II expression in chondrocytes. Furthermore, inhibition of ferroptosis, by intraarticular injection of ferrostatin-1, in our case, seems to be a novel and promising option for the prevention of OA. The translation potential of this article is that we first indicated that chondrocyte ferroptosis contribute to the progression of osteoarthritis which provides a novel strategy in the prevention of OA.
doi:10.1016/ pmid:33376672 pmcid:PMC7750492 fatcat:aq5z4n763nez3oov6u75xtn53a

Graph and Hodge Laplacians: Similarity and Difference [article]

Emily Ribando-Gros, Rui Wang, Jiahui Chen, Yiying Tong, Guo-Wei Wei
2022 arXiv   pre-print
As key subjects in spectral geometry and spectral graph theory respectively, the Hodge Laplacian and the graph Laplacian share similarities in their realization of vector calculus, through the gradient, curl, and divergence, and by revealing the topological dimension and geometric shape of data. These similarities are reflected in the popular usage of "Hodge Laplacians on graphs" in the literature. However, these Laplacians are intrinsically different in their domains of definitions and
more » ... ility to specific data formats, hindering any in-depth comparison of the two approaches. To bring the graph Laplacian and Hodge Laplacian on an equal footing for manifolds with boundary, we introduce Boundary-Induced Graph (BIG) Laplacians using tools from Discrete Exterior Calculus (DEC). BIG Laplacians are defined on discrete domains with appropriate boundary conditions to characterize the topology and shape of data. The similarities and differences of the graph Laplacian, BIG Laplacian, and Hodge Laplacian are examined. Through an Eulerian representation of 3D domains as level-set functions on regular grids, we show experimentally the conditions for the convergence of BIG Laplacian eigenvalues to those of the Hodge Laplacian for elementary shapes.
arXiv:2204.12218v1 fatcat:dlc3azyyjzgeled2wxqjno3wbu

Omicron (B.1.1.529): Infectivity, vaccine breakthrough, and antibody resistance [article]

Jiahui Chen, Rui Wang, Nancy Benovich Gilby, Guo-Wei Wei
2021 arXiv   pre-print
The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its contagious and vaccine escape mutations. The essential infectivity and antibody resistance of the SARS-CoV-2 variant are determined by its mutations on the spike (S) protein receptor-binding domain (RBD). However, a complete experimental evaluation of Omicron might take weeks or even months. Here, we present a comprehensive quantitative
more » ... sis of Omicron's infectivity, vaccine-breakthrough, and antibody resistance. An artificial intelligence (AI) model, which has been trained with tens of thousands of experimental data points and extensively validated by experimental data on SARS-CoV-2, reveals that Omicron may be over ten times more contagious than the original virus or about twice as infectious as the Delta variant. Based on 132 three-dimensional (3D) structures of antibody-RBD complexes, we unveil that Omicron may be twice more likely to escape current vaccines than the Delta variant. The Food and Drug Administration (FDA)-approved monoclonal antibodies (mAbs) from Eli Lilly may be seriously compromised. Omicron may also diminish the efficacy of mAbs from Celltrion and Rockefeller University. However, its impact on Regeneron mAb cocktail appears to be mild.
arXiv:2112.01318v1 fatcat:fkdvdbx62rgqvbfho4b5jg2wai

Repositioning of 8565 existing drugs for COVID-19 [article]

Kaifu Gao, Duc Duy Nguyen, Jiahui Chen, Rui Wang, Guo-Wei Wei
2020 arXiv   pre-print
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected near 5 million people and led to over 0.3 million deaths. Currently, there is no specific anti-SARS-CoV-2 medication. New drug discovery typically takes more than ten years. Drug repositioning becomes one of the most feasible approaches for combating COVID-19. This work curates the largest available experimental dataset for SARS-CoV-2 or SARS-CoV main protease
more » ... bitors. Based on this dataset, we develop validated machine learning models with relatively low root mean square error to screen 1553 FDA-approved drugs as well as other 7012 investigational or off-market drugs in DrugBank. We found that many existing drugs might be potentially potent to SARS-CoV-2. The druggability of many potent SARS-CoV-2 main protease inhibitors is analyzed. This work offers a foundation for further experimental studies of COVID-19 drug repositioning.
arXiv:2005.10028v1 fatcat:c5deb325vvhvnljfqo2wurhr2a

Review of the mechanisms of SARS-CoV-2 evolution and transmission [article]

Jiahui Chen, Rui Wang, Guo-Wei Wei
2021 arXiv   pre-print
The mechanism of SARS-CoV-2 evolution and transmission is elusive and its understanding, a prerequisite to forecast emerging variants, is of paramount importance. SARS-CoV-2 evolution is driven by the mechanisms at molecular and organism scales and regulated by the transmission pathways at the population scale. In this review, we show that infectivity-based natural selection was discovered as the mechanism for SARS-CoV-2 evolution and transmission in July 2020. In April 2021, we proved beyond
more » ... l doubt that such a natural selection via infectivity-based transmission pathway remained the sole mechanism for SARS-CoV-2 evolution. However, we reveal that antibody-disruptive co-mutations [Y449S, N501Y] debuted as a new vaccine-resistant transmission pathway of viral evolution in highly vaccinated populations a few months ago. Over one year ago, we foresaw that mutations spike protein RBD residues, 452 and 501, would "have high chances to mutate into significantly more infectious COVID-19 strains". Mutations on these residues underpin prevailing SARS-CoV-2 variants Alpha, Beta, Gamma, Delta, Epsilon, Theta, Kappa, Lambda, and Mu at present and are expected to be vital to emerging variants. We anticipate that viral evolution will combine RBD co-mutations at these two sites, creating future variants that are tens of times more infectious than the original SARS-CoV-2. Additionally, two complementary transmission pathways of viral evolution: infectivity and vaccine-resistant, will prolong our battle with COVID-19 for years. We predict that RBD co-mutation [A411S, L452R, T478K], [L452R, T478K, N501Y], [L452R, T478K, E484K, N501Y], [K417N, L452R, T478K], and [P384L, K417N, E484K, N501Y] will have high chances to grow into dominating variants due to their high infectivity and/or strong ability to break through current vaccines, calling for the development of new vaccines and antibody therapies.
arXiv:2109.08148v1 fatcat:zovz34ij4vdtlgtuniddynzikq

GNSS Spoofing Identification and Smoothing Localization Method for GNSS/Visual SLAM System

Jiahui Song, Haitao Wu, Xiaochen Guo, Dehuai Jiang, Xuqiang Guo, Tong Lv, Hanze Luo
2022 Applied Sciences  
(Xuqiang Guo); Resources, T.L.; Software, X.G. (Xiaochen Guo) and H.L.; Supervision, H.W. and T.L.; Validation, X.G. (Xiaochen Guo) and X.G.  ...  (Xiaochen Guo), D.J. and H.L.; Formal analysis, J.S., X.G. (Xiaochen Guo) and D.J.; Investigation, X.G.(Xuqiang Guo) and T.L.; Methodology, J.S., H.W., D.J. and X.G.  ... 
doi:10.3390/app12031386 fatcat:znvsvub72fdrtd4ouihjlr3api

Characterizing SARS-CoV-2 mutations in the United States [article]

Rui Wang, Jiahui Chen, Kaifu Gao, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei
2020 arXiv   pre-print
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been mutating since it was first sequenced in early January 2020. The genetic variants have developed into a few distinct clusters with different properties. Since the United States (US) has the highest number of viral infected patients globally, it is essential to understand the US SARS-CoV-2. Using genotyping, sequence-alignment, time-evolution, k-means clustering, protein-folding stability, algebraic topology, and network
more » ... eory, we reveal that the US SARS-CoV-2 has four substrains and five top US SARS-CoV-2 mutations were first detected in China (2 cases), Singapore (2 cases), and the United Kingdom (1 case). The next three top US SARS-CoV-2 mutations were first detected in the US. These eight top mutations belong to two disconnected groups. The first group consisting of 5 concurrent mutations is prevailing, while the other group with three concurrent mutations gradually fades out. Our analysis suggests that female immune systems are more active than those of males in responding to SARS-CoV-2 infections. We identify that one of the top mutations, 27964C>T-(S24L) on ORF8, has an unusually strong gender dependence. Based on the analysis of all mutations on the spike protein, we further uncover that three of four US SASR-CoV-2 substrains become more infectious. Our study calls for effective viral control and containing strategies in the US.
arXiv:2007.12692v1 fatcat:jo32hk6tgbeupjabm6ul6o64b4

Mutations Strengthened SARS-CoV-2 Infectivity

Jiahui Chen, Rui Wang, Menglun Wang, Guo-Wei Wei
2020 Journal of Molecular Biology  
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is a major concern in coronavirus disease 2019 (COVID-19) prevention and economic reopening. However, rigorous determination of SARS-COV-2 infectivity is very difficult owing to its continuous evolution with over ten thousand single nucleotide polymorphisms (SNP) variants in many subtypes. We employ an algebraic topology-based machine learning model to quantitatively evaluate the binding free energy changes of SARS-CoV-2
more » ... ike glycoprotein (S protein) and host angiotensin-converting enzyme 2 (ACE2) receptor following mutations. We reveal that the SARS-CoV-2 virus becomes more infectious. Three out of six SARS-CoV-2 sub- types have become slightly more infectious, while other three subtypes have significantly strengthened their infectivity. We also find that SARS-CoV-2 is slightly more infectious than SARS-CoV according to computed S protein-ACE2 binding free energy changes. Based on a systematic evaluation of all possible 3686 future mutations on the S protein receptor-binding domain (RBD), we show that most likely future mutations will make SARS-CoV-2 more infectious. Combining sequence alignment, probability analysis, and binding free energy calculation, we predict that a few residues on the receptor-binding motif (RBM), i.e., 452, 489, 500, 501, and 505, have high chances to mutate into significantly more infectious COVID-19 strains.
doi:10.1016/j.jmb.2020.07.009 pmid:32710986 pmcid:PMC7375973 fatcat:i77wntj4w5dmxd2no6dcmulqye
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