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PHISDetector:A Tool to Detect Diverse In Silico Phage–host Interaction Signals for Virome Studies

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Genomics, Proteomics & Bioinformatics 2022年第3期20卷 508-523页

作者： Fengxia Zhou Rui gan Fan Zhang Chunyan Ren Ling yu yu Si Zhiwei Huang HIT Center for Life Sciences School of Life Science and TechnologyHarbin Institute of TechnologyHarbin 150080China Department of Hematology/oncology Boston Children’s HospitalHarvard Medical SchoolBostonMA 02115USA

Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel ***-microbe interactions leave diverse signals in bacterial and phage genomic sequences,defined as phage-host interaction signals(PHISs),which include clustered regularly interspaced short palindromic repeats(CRISPR)targeting,prophage,and protein-protein interaction *** the present study,we developed a novel tool phage-host interaction signal detector(PHISDetector)to predict phage-host interactions by detecting and integrating diverse in silico PHISs,and scoring the probability of phage-host interactions using machine learning models based on PHIS *** evaluated the performance of PHISDetector on multiple benchmark datasets and application *** tested on a dataset of 758 annotated phage-host pairs,PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels,respectively,outperforming other phage-host prediction *** applied to 125,842 metagenomic viral contigs(mVCs)derived from 3042 geographically diverse samples,a detection rate of 54.54% could be ***,PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant(MDR)bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health(NIH)Human Microbiome Project(HMP).The PHISDetector can be run either as a web server(http://***/PHISDetector/)for general users to study individual inputs or as a stand-alone version(https://***/HITImmunologyLab/PHISDetector)to process massive phage contigs from virome studies.

关键词： Phage-host interaction Virome CRISPR Prophage Machine learning

Enhanced Adhesion Properties of Polymer-Metal Interfaces via Nano-injection Molding: A Study on Molecular Kinematic Mechanisms

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Chinese Journal of Polymer Science 2023年第6期41卷 981-993,I0012页

作者： hong-Chen Li Dong-Lei Liu Xin Luo Tian yuan Kai Zhan Jing gan School of Advanced Manufacturing Nanchang UniversityNanchang 330031China

Nano-injection molding enables the formation of nano-scale anchors to connect heterogeneous material surfaces to achieve the required mechanical *** this work,polyphenylene sulfide(PPS),aluminum(Al),copper(Cu),and iron(Fe)were selected as candidate polymer and metal *** kinds of polymer-metal interfacial models with pyramidal nano-slots were *** molecular dynamics simulations were launched to investigate the adhesion properties and molecular kinematic mechanisms of heterogeneous interfaces in nanoinjection *** showed that the wall-slipping behavior of PPS at the interface slot was obvious,it was easy to form multiple-anchorpoints in the central area of substrates,and these anchor points were easily slipping along the wall,different from the de Gennes *** atomic lattice and atomic band gap of metal affected the adhesion *** BCC lattice of Fe was more suitable for nano-injection molding process than the FCC lattice of Al and *** filling rate,interfacial energy,the tensile and shear failures data revealed that the interfacial adhesion performances decreased according to the following order,Fe-PPS,Cu-PPS and Al-PPS components,respectively,and the interface failure mode was closely related to the stress loading mode.

关键词： injection interfacial lattice

Characteristics of strong earthquake evolution around the eastern boundary faults of the Sichuan-yunnan rhombic block

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Science China Earth Sciences 2011年第11期54卷 1716-1729页

作者： CHENG Jia LIU Jie gan WeiJun yu HuaiZhong LI gang China Earthquake Network Center Beijing 100045 China State Key Laboratory of Earthquake Dynamics Institute of Geology China Earthquake Administration Beijing 100029 China

Based on the existing materials of fault segmentation,characteristic earthquakes,and their empirical relationships,we calculated the parameters of the fault segments,such as length,width,magnitudes of characteristic earthquakes,*** by GPS velocity field,the slip rates of these fault segments in depth were inversed using the 3-D half-space elastic dislocation *** not all of the recurrence periods and co-seismic displacements of characteristic earthquakes are known,we selected the fault segments with these two parameters known and calculated the accumulation rate of average co-seismic displacement,which shows the faults' slip rate in seismogenic ***,the slip rate in depth was compared with that in seismogenic layer,the relationship between them was obtained,and this relationship was used to get the recurrence periods and co-seismic displacements of all fault *** the studies above,we calculated the co-seismic deformation field of all the earthquakes larger than M s 6.8 from AD 1700 one by one and inversed the potential displacement in the co-seismic deformation ***,we divided the potential displacement by the slip rate from GPS inversion to get the influences of these fault segments,added the influences into the elapsed time of the characteristic earthquakes,and obtained the earthquake hazard degree of all the segments we studied in the form of the ratio of elapsed time to recurrence period;so,we name the ratio as the Impending Earthquake Risk (IER).Historical earthquake cases show that the fault segment is in safety when the IER is less than 1 but in danger after the IER becomes larger than *** 2009,the IER is larger than 1 on the following segments,1.35 on the Tagong segment of Xianshuihe fault,1 on the Menggu-Dongchuan segment,1.04 on the Dongchuan-Xundian segment,and 1.09 on the Yiliang-Chengjiang segment of Xiaojiang fault.

关键词： eastern boundary faults of Sichuan-yunnan rhombic block fault segment characteristic earthquake recurrence period earthquake Interaction Impending Earthquake Risk

Correlation Between CCG Polymorphisms and CAG Repeats During Germline Transmission in Chinese Patients with Huntington’s Disease

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Neuroscience Bulletin 2020年第7期36卷 811-814页

作者： hong-Rong Cheng Xiao-Yan Li Hui-Li yu Miao Xu Yan-Bin Zhang Shi-Rui gan hong-Lei Li Zhi-Ying Wu Department of Neurology and Research Center of Neurology in the Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of MedicineHangzhou 310009China Department of Neurology and Institute of Neurology Huashan HospitalShanghai Medical CollegeFudan UniversityShanghai 200040China Department of Neurology First Affiliated HospitalFujian Medical UniversityFuzhou 350005China Joint Institute for Genetics and Genome Medicine between Zhejiang University and the University of Toronto Zhejiang UniversityHangzhou 310058China

Dear Editor,Huntington’s disease (HD) is an autosomal dominant neurodegenerative disease characterized by movement disorder,progressive dementia,and psychiatric and behavioral *** is caused by unstable expanded CAG t... 详细信息

关键词： Huntington unstable CAG

A Scheme for Verifying the Integrity of Outsourced Data

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China Communications 2015年第11期12卷 188-195页

作者： WANG Xiaoming yu Fang LIN Yanchun gan Qingqing WU Daini Department of Computer Science Jinan University

Unauthorized tampering with outsourced data can result in significant losses for both data owner and *** integrity therefore becomes an important factor in outsourced data *** this paper,we address this problem and propose a scheme for verifying the integrity of outsourced *** first propose a new authenticated data structure for authenticating membership queries in sets based on accumulators,and then show how to apply it to the problem of verifying the integrity of outsourced *** also prove that our scheme is secure under the q-strong DiffieHellman *** importantly,our scheme has the constant cost communication,meanwhile keeping other complexity measures *** to previous schemes based on accumulators,our scheme reduces update cost and so improves previous schemes based on *** addition,the experimental comparison shows that our scheme outperforms the previous schemes.

关键词： outsourced data authenticated datastructure data integrity constant complexity

Design of Fe–Mn–Ag Alloys as Potential Candidates for Biodegradable Metals

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Acta Metallurgica Sinica(English Letters) 2018年第6期31卷 584-590页

作者： Ruo-yu Liu Ran-gan He Li-Qun Xu Sheng-Feng Guo Faculty of Materials and Energy Southwest University

In this work,a series of biodegradable pure iron,Fe–30Mn and Fe–30Mn–Ag alloys were developed by using a rapid solidification technology.A fine a-Fe dendrite was formed in pure iron,resulting in a high compressive yield strength of above 300 *** Fe–30Mn alloy doped with only 1%Ag exhibited a significant increase in the degradation rate in simulated body fluid due to the precipitation of Ag-rich particles in alloy matrix and the induction of the microgalvanic *** addition,the novel Fe–30Mn–Ag alloy also exhibited a good magnetic compatibility and offered a closely approaching requirement for biodegradable medical applications.

关键词： Biodegradable metals Fe-based alloys Corrosion rate Magnetic compatibility

Behaviours of existing shield tunnels due to tunnelling underneath considering asymmetric ground settlements

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Underground Space 2022年第5期7卷 882-897页

作者： Xiaolu gan Jianlin yu Xiaonan Gong Nianwu Liu Dongzhu Zheng Research Centre of Coastal and Urban Geotechnical Engineering Zhejiang UniversityHangzhou 310058China Engineering Research Centre of Urban Underground Development Zhejiang UniversityHangzhou 310058China School of Civil Engineering and Architecture Zhejiang Sci-Tech UniversityHangzhou 310018China Department of Civil Engineering Ghent UniversityGhent 9052Belgium

New tunnelling underneath could influence existing shield tunnels in underground *** evaluation of the influences of tunnelling-induced ground movements on existing tunnels has been a major concern during urban *** paper presents a two-stage analytical method that considers the asymmetric ground settlement for investigating the longitudinal tunnel responses to new *** improved semi-analytical solution considering the horizontal movement of the new tunnel is established for evaluating the tunnelling-induced asymmetric greenfield *** proposed method is verified with field measurement data from a case study.A parametric analysis is conducted to study the influences of the input parameters on the tunnel *** indicate that the horizontal movement of the new tunnel due to bias loading or asymmetric construction may lead to asymmetric responses of the existing *** increasing tunnel horizontal movement,the asymmetry of the tunnel responses becomes more *** increase in the pillar depth and decreases in the tunnel horizontal movement and skew angle lower the internal forces induced by new tunnelling.

关键词： Analytical method Tunnelling undercrossing Asymmetric ground movement Longitudinal tunnel behaviours Tunnel horizontal movement

Effect of Ag on the Microstructure,Mechanical and Bio-corrosion Properties of Fe–30Mn Alloy

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Acta Metallurgica Sinica(English Letters) 2019年第11期32卷 1337-1345页

作者： Ruo-yu Liu Ran-gan He Yan-Xia Chen Sheng-Feng Guo School of Materials and Energy Southwest University

In the current work, biodegradable Fe–30 Mn– X Ag( X = 1, 2, 5, 10 wt%) alloys were prepared by the rapid solidifi cation with copper-mold-casting technology. Phase analysis demonstrates that Fe–30 Mn– X Ag alloys consist of austenite γ phase with a fcc structure and martensite ε phase with a hcp structure. The yield strength of the samples increases with increasing Ag contents. Compared with Fe–30 Mn alloy, the degradation rates of Fe–30 Mn– X Ag in Hank’s solution are signifi cantly improved. Cytotoxicity evaluation reveals that the Fe–30 Mn–1 Ag and Fe–30 Mn–2 Ag alloys perform less toxicity on the Human Umbilical Vein Endothelial Cells(HUVEC), while Fe–30 Mn–5 Ag and Fe–30 Mn–10 Ag alloys perform no toxicity on it. The contact angles of deionized water on the Fe–30 Mn– X Ag alloy surface were ranged from 55° to 69°, which is benefi cial to the adhesion and growth of the cells. Besides, the addition of Ag leads to a much lower M/H slope, particularly for the Fe–30 Mn–5 Ag alloy exhibiting a non-magnetic property as SS316 L. Therefore, the present Fe–30 Mn– X Ag alloys would be potential candidates for degradable metals.

关键词： Biodegradable metals Fe-based alloy Corrosion behavior Biocompatibility

Helical Conformation Tunability via Hydrogen Bonding in Supramolecular Frameworks

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CCS Chemistry 2022年第4期4卷 1405-1413页

作者： Zhijie Xue Fuwei gan hong Liu Chengshuo Shen Huibin Qiu Bo Yang Ping yu School of Physical Science and Technology ShanghaiTech University201210 Shanghai School of Chemistry and Chemical Engineering State Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University200240 Shanghai

Hydrogen-bonded molecules and their dynamics are significantly important in chemistry and biology due to their widespread *** their natural abundance and diversity,applications of molecules with dynamic conformations in artificial networks allow information storage and molecular motor design on the nanometer ***,we report hydrogen-bonded molecular networks with tunable helical conformation on metal *** dynamics of helical conformation in two-dimensional hydrogenbond networks are triggered and resolved by scanning probe microscopy at the single-molecule *** combinationwith theoretical calculations,the surfacespecific hydrogen bonds are identified as the origin of the dynamic helical *** results provide a distinctive access to molecular architecture with tunable helical conformation driven by hydrogenbond interaction on surfaces.

关键词： scanning probe microscope dynamic conformation hydrogen bond molecular frameworks DFT calculation