Shuxiang Li

Capital Medical University

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Anna R. Panchenko

Queen's University

Jidong Jia

Beijing Friendship Hospital

Weijia Duan

National Clinical Research Center for Digestive Diseases

Xiaojuan Ou

National Clinical Research Center for Digestive Diseases

Hong You

Beijing Friendship Hospital

Sha Chen

Sichuan University

Tingting Lv

Beijing Tsinghua Chang Gung Hospital

Xiaoliang Sun

Soochow University

Yunhui Peng

Central China Normal University

Xinyan Zhao

Capital Medical University

Cooperative Institutions

Chinese Academy of Sciences

Capital Medical University

Soochow University

Beijing Friendship Hospital

National Clinical Research Center for Digestive Diseases

Nanjing Medical University

University of Chinese Academy of Sciences

Chinese Academy of Medical Sciences & Peking Union Medical College

Zhejiang University

Peking University

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Research progress in mucosal adjuvants for influenza vaccines

Int J Biologicals (2017)

Shuxiang Li

Current influenza vaccines mainly include intramuscular inactivated vaccines and intranasal attenuated live vaccines. Antigen-specific mucosal immune response is important for preventing influenza spread via respiratory transmission. Available data show that both vaccines have inevitable limitations. In order to solve this problem, in-depth studies on mucosal adjuvant influenza vaccines are needed. In this paper, the mucosal adjuvants used in influenza vaccines entered clinical trial are reviewed. Key words: Influenza vaccines; Adjuvants, immunologic; Immunity, mucosal

Mucosal Immunity

Antibody response

10.3760/cma.j.issn.1673-4211.2017.04.005

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Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency

Biomolecules (2019)

Jingqian Liu Syukri Shukor Shuxiang Li Alfred Tamayo Lorenzo Tosi

Multiplexed cloning of long DNA sequences is a valuable technique in many biotechnology applications, such as long-read genome sequencing and the creation of open reading frame (ORF) libraries. Long-adapter single-stranded oligonucleotide (LASSO) probes have shown promise as a tool to clone long DNA fragments. LASSO probes are molecular inversion probes (MIP) engineered with an adapter region of user-defined length, flanked between template-specific probe sequences. Herein, we demonstrate that the adapter length is a key feature of LASSO that influences the efficiency of gene capture and cloning. Furthermore, we applied a model based on Monte Carlo molecular simulation in order to study the relationship between the long-adapter length of LASSO and capture enrichment. Our results suggest that the adapter length is a factor that contributes to the free energy of target–probe interaction, thereby determining the efficiency of capture. The results indicate that LASSOs with extremely long adapters cannot capture the targets well. They also suggest that targets of different lengths may prefer adapters of different lengths.

Adapter (computing)

10.3390/biom9050199

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Homology Modeling and Screening of New 14α-Demethylase Inhibitor (DMI) Fungicides Based on Optimized Expression of CYP51 from Ustilago maydis in Escherichia coli

Journal of Agricultural and Food Chemistry (2010)

Rui Han Jianhua Zhang Shuxiang Li Shufen Cao Hui Geng

Ustilago maydis infection is a serious disease affecting corn crops worldwide. Sterol 14α-demethylase (CYP51) is one of the key enzymes of sterol biosynthesis and an effective target of antifungal drugs. To further study the interaction between CYP51 and drugs and exploit more specific 14α-demethylase inhibitor (DMI) fungicides for U. maydis, in this study homology modeling of CYP51 from U. maydis (UmCYP51) templated as the eukaryotic orthologues (the human CYP51) and screening of new DMI fungicides based on optimized expression were carried out for the first time. In addition, XF-113 and ZST-4 were screened by analyzing the spectral characteristics between the purified UmCYP51-35 and fungicides. These results provide a theoretical basis and new ideas for efficient design and development of new antifungal drugs.

Ustilago

Demethylase

Homology

10.1021/jf103243m

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The quadcode and its arithmetic

Communications of the ACM (1987)

Shuxiang Li Murray H. Loew

The quadcode is a hierarchical data structure for describing digital images. It has the following properties: (1) straightforward representation of dimension, size, and the relationship between an image and its subsets; (2) explicit description of geometric properties, such as location, distance, and adjacency; and (3) ease of conversion from and to raster representation. The quadcode has applications to computer graphics and image processing because of its ability to focus on selected subsets of the data and to allow utilization of multiple resolutions in different parts of the image. A related approach is the quadtree. Samet recently presented a thorough survey of the literature in that field [ 7 ]. Gargantini [ 2 ] and Abel and Smith [ 1 ] presented linear quadtrees and linear locational keys that are efficient labeling techniques for quadtrees. In those papers the geometric concepts of the image are discussed by using the tree as an interpretive medium, and the approaches and procedures are based on traversal of the nodes in the tree. In this paper we present the quadcode system, which is a direct description of the image, and discuss the geometric concepts in terms of the coded images themselves.

Quadtree

Representation

Adjacency list

Digital geometry

10.1145/28569.28573

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Giant magnetoresistance in Fe/Ag multilayers and its anomalous temperature dependence

Physical review. B, Condensed matter (1995)

Chengtao Yu Shuxiang Li Wuyan Lai Minglang Yan Yizhong Wang

The observation of giant magnetoresistance (GMR) effect in sputtered Fe/Ag multilayers is presented. The observed maximum GMR amounts to -7.3% at 1.5 K. The amplitude of the GMR oscillates with variation of Ag thickness, and the oscillation period is about 11 \AA{}. The origin of the GMR in these Fe/Ag multilayers is believed to lie mainly in the interface. The GMR effect contains contributions either arising from the antiferromagnetic coupled magnetization in the neighboring Fe layer or superparamagneticlike spins at the interface. An anomalous temperature dependence of magnetoresistance is reported and it is attributed to the suppression of thermal excitations of superparamagneticlike spins by applied magnetic field, which results in a reduction of the GMR effect with decreasing temperature. In addition, the specific field dependence of the magnetoresistance curve with respect to temperature is also accounted for by the contribution from those arising from superparamagneticlike spins at the interface, which could be easily quenched at low temperature, leading to the observation of a decreasing tendency of saturation field with decreasing temperature.

Saturation (graph theory)

10.1103/physrevb.52.1123

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Two-loop planar master integrals for NNLO QCD corrections to W-pair production in quark-antiquark annihilation

arXiv (Cornell University) (2024)

Wen-Jie He Zhang Ren-You L. Han Yi Jiang Zhe Li

The planar two-loop scalar Feynman integrals contributing to the massive NNLO QCD corrections for $W$-boson pair production via quark-antiquark annihilation can be classified into three family branches, each of which is reduced to a distinct set of master integrals (MIs), totaling $27$, $45$ and $15$, respectively. These MIs are analytically calculated using the method of differential equations, with solutions expanded as Taylor series in the dimensional regulator $\epsilon$. For the first two family branches, the differential systems can be successfully transformed into canonical form by adopting appropriate bases of MIs. This enables the MIs of these family branches to be expressed either as Goncharov polylogarithms (GPLs) or as one-fold integrals over GPLs, up to $\mathcal{O}(\epsilon^4)$. In contrast, the differential system for the third family branch can only be cast into a form linear in $\epsilon$ due to the presence of elliptic integrals. The solution to this linear-form differential system is expressed in an iterated form owing to the strictly lower-triangular structure of the coefficient matrices at $\epsilon = 0$. Our analytic expressions for these MIs are verified with high accuracy against the numerical results from the \texttt{AMFlow} package.

Annihilation

Pair production

10.48550/arxiv.2409.08879

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[The assessing tools of the treatment planning in X-knife].

PubMed (2002)

Guangming Li Shuxiang Li

The treatment planning can directly decide the treatment effect of X-knife. This paper presents some qualitative and quantitative tools assessing the treatment planning, mainly they are the isodose curve, dose-wash, volume dose and dose volume histogram.

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Antihypertensive activity of recombinant peptide IYPR expressed in Escherichia coli as inclusion bodies

Protein Expression and Purification (2012)

Liurong Huang Haile Ma Yunliang Li Shuxiang Li

Inclusion bodies

10.1016/j.pep.2012.02.004

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Natural Neighbor Algorithm for Breast Cancer Diagnosis

Journal of Physics Conference Series (2019)

Shuxiang Li Lijun Yang Pei-yu Chen Cheng Yang

Abstract Machine learning to diagnose breast cancer is an important, real-world medical problem. As one of the most popular machine learning algorithm, K-Nearest Neighbors (KNN) algorithm is widely used in breast cancer classification and can provide high classification accuracy and effective diagnostic capabilities. However, selection of parameter K is still an unsolved problem for K-Nearest Neighbors (KNN). To address the problem, we introduce a novel neighbor form, Natural Neighbor (NaN), which is obtained adaptively by its search algorithm. We firstly use a noise filter, which called edited natural neighbor algorithm (ENaN), to eliminate the noises and global outliers of Wisconsin’s breast cancer prognosis dataset. Then, cleaned data set and natural neighbor algorithm are used to construct a new non parameter diagnostic system. The main advantages of the proposed algorithm are that it does not need any parameters and can maintain high classification accuracy. Experiments show that the classification accuracy of proposed method is similar to the highest classification accuracy obtained by traditional K-Nearest Neighbors algorithm with different K values.

Nearest-neighbor chain algorithm

Statistical classification

10.1088/1742-6596/1395/1/012003

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Registration of serial tissue section images.

PubMed (2001)

Zhexing Liu Wu Dong Shuxiang Li Jiang Gui-ping Yu Zhang

OBJECTIVE: This study aims to tackle the problem of image registration during computer-assisted three-dimensional (3D) reconstruction of serial tissue sections. METHODS: We proposed segmentation-counting algorithm for computerized image registration on the basis of joint histogram. This approach utilizes thresholding of the 2 images to be registered, and the criterion function is defined as the counting in a specific region of the joint histogram. The registration parameters can be obtained by optimizing the criterion function. RESULTS: In the trial application of this approach in image registration for the serial tissue sections of mouse wse embryos, a more efficient result was achieved. CONCLUSION: The method can rapidly accomplish the image registration task for serial tissue sections with simpler calculation processes.

Image registration

Image histogram

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