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A Novel Interpretation of Structural Dot Plots of Genomes Derived from the Analysis of Two Strains of Neisseria meningitidis

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Genomics, Proteomics & Bioinformatics 2010年第3期8卷 159-169页

作者： Wilfred R. Cuff Venkata R.S.K. Duvvuri Binhua Liang Bhargavi Duvvuri Gillian E. Wu Jianhong Wu Raymond S.W. Tsang Public Health Agency of Canada Canadian Science Centre for Human and Animal Health Winnipeg Canada center for disease modelling York Institute for Health Research York University Toronto Canada Department of Biology York University Toronto Canada Department of Medical Microbiology University of Manitoba Winnipeg Canada School of Kinesiology and Health Sciences York University Toronto Canada Department of Mathematics and Statistics York University Toronto Canada.

Neisseria meningitidis is the agent of invasive meningococcal disease, including cerebral meningitis and septicemia. Because the diseases caused by different clonal groups （sequence types） have their own epidemiological characteristics, it is important to understand the differences among the genomes of the N. meningitidis clonal groups. To this end, a novel interpretation of a structural dot plot of genomes was devised and applied; exact nu- cleotide matches between the genomes ofN. meningitidis serogroup A strain Z2491 and serogroup B strain MC58 were identified, leading to the specification of various structural regions. Known and putative virulence genes for each N. meningitidis strain were then classified into these regions. We found that virulence genes of MC58 tend more to the translocated regions （chromosomal segments in new sequence contexts） than do those of Z2491, notably tending towards the interface between one of the translocated regions and the collinear region. Within the col- linear region, virulence genes tend to occur within 16 kb of gaps in the exact matches. Verification of these tendencies using genes clustered in the cps locus was sufficiently supportive to suggest that these tendencies can be used to focus the search for and understanding of virulence genes and mechanisms of pathogenicity in these two organisms.

关键词： structural dot plots virulence genes translocation match regions MUMmer Neisseria meningitidis

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Challenges and Limitations in Speech Recognition Technology:A Critical Review of Speech Signal Processing Algorithms,Tools and Systems

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Computer Modeling in Engineering & Sciences 2023年第5期135卷 1053-1089页

作者： Sneha Basak Himanshi Agrawal Shreya Jena Shilpa Gite Mrinal Bachute Biswajeet Pradhan Mazen Assiri Computer Science and Information Technology Department Symbiosis Institute of TechnologySymbiosis International(Deemed University)Pune412115India Symbiosis Centre for Applied Artificial Intelligence Symbiosis International(Deemed University)Pune412115India Centre for Advanced modelling and Geospatial Information Systems(CAMGIS) School of Civil and Environmental EngineeringFaculty of Engineering and Information TechnologyUniversity of Technology SydneyNew South Wales2007Australia center of Excellence for Climate Change Research King Abdulaziz UniversityJeddah21589Saudi Arabia Earth Observation Centre Institute of Climate ChangeUniversity Kebangsaan MalaysiaBangiSelangor43600Malaysia

Speech recognition systems have become a unique human-computer interaction(HCI)*** is one of the most naturally developed human abilities;speech signal processing opens up a transparent and hand-free computation *** paper aims to present a retrospective yet modern approach to the world of speech recognition *** development journey of ASR(Automatic Speech Recognition)has seen quite a few milestones and breakthrough technologies that have been highlighted in this paper.A step-by-step rundown of the fundamental stages in developing speech recognition systems has been presented,along with a brief discussion of various modern-day developments and applications in this *** review paper aims to summarize and provide a beginning point for those starting in the vast field of speech signal *** speech recognition has a vast potential in various industries like telecommunication,emotion recognition,healthcare,etc.,this review would be helpful to researchers who aim at exploring more applications that society can quickly adopt in future years of evolution.

关键词： Speech recognition automatic speech recognition(ASR) mel-frequency cepstral coefficients(MFCC) hidden Markov model(HMM) artificial neural network(ANN)

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OPTIMAL ERROR ESTIMATES FOR NEDELEC EDGE ELEMENTS FOR TIME-HARMONIC MAXWELL'S EQUATIONS

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Journal of Computational Mathematics 2009年第5期27卷 563-572页

作者： Liuqiang Zhong Shi Shu Gabriel Wittum Jinchao Xu School of Mathematical and Computational Sciences Xiangtan University Xiangtan 411105 China Simulation and modelling Goethe- center for Scientic Computing Goethe-University Kettenhofweg 139 60325 Frankfurt am Main Germany Department of Mathematics Pennsylvania State University University Park PA 16802 USA

In this paper, we obtain optimal error estimates in both L^2-norm and H（curl）-norm for the Nedelec edge finite element approximation of the time-harmonic Maxwell＇s equations on a general Lipschitz domain discretized on quasi-uniform meshes. One key to our proof is to transform the L^2 error estimates into the L^2 estimate of a discrete divergence-free function which belongs to the edge finite element spaces, and then use the approximation of the discrete divergence-free function by the continuous divergence-free function and a duality argument for the continuous divergence-free function. For Nedelec＇s second type elements, we present an optimal convergence estimate which improves the best results available in the literature.

关键词： Edge finite element Time-harmonic Maxwell's equations.

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Pair formation models for sexually transmitted infections:A primer

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Infectious disease modelling 2017年第3期2卷 368-378页

作者： Mirjam Kretzschmar Janneke CMHeijne Julius center for Health Sciences and Primary Care University Medical Center UtrechtThe Netherlands Centre for Infectious disease Control National Institute for Public Health and the Environment(RIVM)BilthovenThe Netherlands

Formodelling sexually transmitted infections,duration of partnerships can strongly influence the transmission dynamics of the *** partnerships are monogamous,pairs of susceptible individuals are protected from becoming infected,while pairs of infected individuals delay onward transmission of the infection as long as they *** addition,for curable infections re-infection froman infected partnermay ***,interventions based on contact tracing rely on the possibility of identifying and treating partners of infected *** reflect these features in a mathematical model,pair formation models were introduced tomathematical epidemiology in the 1980'*** have since been developed into a widely used tool in modelling sexually transmitted infections and the impact of *** we give a basic introduction to the concepts of pair formation models for a susceptibleinfected-susceptible(SIS)*** review some results and applications of pair formation models mainly in the context of chlamydia infection.

关键词： Pair formation Mathematical model Partnership duration Sexually transmitted infections Basic reproduction number

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Impacts of the Leading Modes of Tropical Indian Ocean Sea Surface Temperature Anomaly on Sub-Seasonal Evolution of the Circulation and Rainfall over East Asia during Boreal Spring and Summer

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Journal of Meteorological Research 2017年第1期31卷 171-186页

作者： Senfeng LIU Anmin DUAN State Key Laboratory of Numerical modelling for Atmospheric Sciences and Geophysical Fluid Dynamics Institute of Atmospheric Physics Chinese Academy of Sciences College of Earth Science University of Chinese Academy of Sciences Collaborative Innovation center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science & Technology

The two leading modes of the interannual variability of the tropical Indian Ocean （TIO） sea surface temperature （SST） anomaly are the Indian Ocean basin mode （IOBM） and the Indian Ocean dipole mode （IODM） from March to August. In this paper, the relationship between the TIO SST anomaly and the sub-seasonal evolution of the circula- tion and rainfall over East Asia during boreal spring and summer is investigated by using correlation analysis and composite analysis based on multi-source observation data from 1979 to 2013, together with numerical simulations from an atmospheric general circulation model. The results indicate that the impacts of the IOBM on the circulation and rainfall over East Asia vary remarkably from spring to summer. The anomalous anticyclone over the tropical Northwest Pacific induced by the warm IOBM is closely linked with the Pacific-Japan or East Asia-Pacific telecon- nection pattern, which persists from March to August. In the upper troposphere over East Asia, the warm phase of the IOBM generates a significant anticyclonic response from March to May. In June and July, however, the circulation response is characterized by enhanced subtropical westerly flow. A distinct anomalous cyclone is found in August. Overall, the IOBM can exert significant influence on the western North Pacific subtropical high, the South Asian high, and the East Asian jet, which collectively modulate the precipitation anomaly over East Asia. In contrast, the ef- fects of the IODM on the climate anomaly over East Asia are relatively weak in boreal spring and summer. There- fore, studying the impacts of the TIO SST anomaly on the climate anomaly in East Asia should take full account of the different sub-seasonal response during boreal spring and summer.

关键词： East Asia sub-seasonal evolution Indian Ocean basin mode Indian Ocean dipole mode

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Assessing the effectiveness of the intervention measures of COVID-19 in China based on dynamical method

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Infectious disease modelling 2023年第1期8卷 159-171页

作者： Xiaomeng Wei Mingtao Li Xin Pei Zhiping Liu Juan Zhang Complex Systems Research center Shanxi University030006ShanxiChina Shanxi Key Laboratory of Mathematical Techniques and Big Data Analysis on disease Control and Prevention 030006ShanxiChina School of Mathematical Sciences Shanxi University030006ShanxiChina College of Mathematics Taiyuan University of Technology030024ShanxiChina School of Data Science and Technology North University of China030051ShanxiChina

Normalized interventions were implemented in different cities in China to contain the outbreak of COVID-19 before December ***,the differences in the intensity and timeliness of the implementations lead to differences in final size of the *** the outbreak of COVID-19 in three representative cities Xi'an,Zhengzhou and Yuzhou in January 2022,as examples,we develop a compartmental model to describe the spread of novel coronavirus and implementation of interventions to assess concretely the effectiveness of Chinese interventions and explore their impact on epidemic *** applying reported human confirmed cases to verify the rationality of the model,we apply the model to speculate transmission trend and length of concealed period at the initial spread phase of the epidemic(they are estimated as 10.5,7.8,8.2 days,respectively),to estimate the range of basic reproduction number(2.9,0.7,1.6),and to define two indexes(transmission rate vt and controlled rate vc)to evaluate the overall effect of the *** is shown that for Zhengzhou,vc is always more than v t with regular interventions,and Xi'an take 8 days to achieve vc>v t twice as long as Yuzhou,which can interpret the fact that the epidemic situation in Xi'an was more *** carrying out parameter values,it is concluded that in the early stage,strengthening the precision of close contact tracking and frequency of large-scale nucleic acid testing of non-quarantined population are the most effective on controlling the outbreaks and reducing final ***,if the close contact tracking strategy is sufficiently implemented,at the late stage largescale nucleic acid testing of non-quarantined population is not essential.

关键词： COVID-19 Close contact tracking Large-scale nucleic acid testing Dynamics The basic reproduction number Sensitivity analysis

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A mathematical modeling study of the HIV epidemics at two rural townships in the Liangshan Prefecture of the Sichuan Province of China

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Infectious disease modelling 2016年第1期1卷 3-10页

作者： Zhimin Su Caiting Dong Ping Li Hongxia Deng Yuhan Gong Shiyong Zhong Min Wu Yuhua Ruan Guangming Qin Wen Yang Yiming Shao Michael Li Department of Mathematical and Statistical Sciences University of AlbertaEdmontonAlbertaT6G 2G1Canada Sichuan Provincial center for disease Control and Prevention Chengdu 610041Sichuan ProvinceChina State Key Laboratory of Infectious disease Prevention and Control(SKLID) Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesChinese Center for Disease Control and Prevention(China CDC)Beijing 102206China Guangxi Key Laboratory of AIDS Prevention and Treatment School of Public HealthGuangxi Medical UniversityNanningGuangxi 530021China Butuo Township Hospital Butuo CountySichuan ProvinceChina Liangshan Prefecture center for disease Control and Prevention Sichuan ProvinceChina Butuo center for disease Control and Prevention Butuo CountySichuan ProvinceChina Butuo People’s Hospital Butuo CountySichuan ProvinceChina

Background:As a response to a severe HIV epidemic in the Liangshan Prefecture,one of the worst in China,population based HIV interventions,including two population-wide HIV screening,have been carried out since 2005 at two townships in a remote mountainous region of *** objective of our mathematical modeling study is to assess the temporal dynamics of the HIV epidemic in the two townships based on the data collected in the study area during the period ***:A mathematical model was set up to describe the population dynamics of HIV transmission in study *** model was calibrated by fitting it to the HIV testing and treatment data from 2005 to *** of the model was done by comparing its predicted value of HIV prevalence in 2010 to the prevalence data obtained in the 2010 population wide HIV *** validated model was used to produce estimation of HIV incidence,prevalence and ***:Our model estimations show that population-based HIV interventions have significantly slowed down the rise of the HIV epidemic in the two *** the five-year period from 2005 to 2010,the year-over-year rate of increase in HIV incidence,prevalence,and death has declined by 91.5%,28.7%,and 52.3%,***:Mathematical models,when integrated with epidemiological and surveillance data,can be an effective tool for predicting the temporal dynamics of HIV and assessing the impacts of HIV interventions.

关键词： HIV epidemiology HIV testing and treatment mathematical modeling

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Obtaining 2D Soil Geotechnical Profiles from Cokriging Interpolation of Sample Data and Electrical Resistivity Tomography (ERT)—Applications in Mass Movements Studies

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International Journal of Geosciences 2024年第7期15卷 525-548页

作者： Cassiano Antonio Bortolozo Noel Howley Andy Legg Tristan Pryer Danielle Silva de Paula Tatiana Sussel Gonçalves Mendes Daniel Metodiev Marcio Roberto Magalhães de Andrade Silvio Jorge Coelho Simões Maiconn Vinicius de Moraes Marcio Augusto Ernesto de Moraes Luana Albertani Pampuch Rodolfo Moreda Mendes Harideva Marturano Egas Institute of Science and Technology So Paulo State University (UNESP) So Jos dos Campos Brazil Cemaden-National center for Monitoring and Early Warning of Natural Disasters General Coordination of Research and Development So Jos dos Campos Brazil Institute for Mathematical Innovation University of Bath Bath UK Department of Mathematical Sciences University of Bath Bath UK

Brazil annually faces significant challenges with mass movements, particularly in areas with poorly constructed housing, inadequate engineering, and lacking sanitation infrastructure. Campos do Jordão, in São Paulo state, is a city currently grappling with these issues. This paper details a study conducted within a pilot area in Campos do Jordão, where geophysical surveys and geotechnical borehole data were integrated. The geophysical surveys provided 2D profiles, and samples were collected to analyse soil moisture and plasticity. These datasets were combined using a Cokriging-based model to produce an accurate representation of the subsurface conditions. The enhanced modelling of subsurface variability facilitates a deeper understanding of soil behavior, which can be used to improve landslide risk assessments. This approach is innovative, particularly within the international context where similar studies often do not address the complexities associated with urban planning deficits such as those observed in some areas of Brazil. These conditions, including the lack of proper sanitation and irregular housing, significantly influence the geological stability of the region, adding layers of complexity to subsurface assessments. Adapting geotechnical evaluation methods to local challenges offers the potential to increase the efficacy and relevance of geological risk management in regions with similar socio-economic and urban characteristics.

关键词： Mass Movements Geophysics ERT Geotechnical Surveys Campos do Jordão Cokriging

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Diagnosis of Moist Vorticity and Moist Divergence for a Heavy Precipitation Event in Southwestern China

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Advances in Atmospheric Sciences 2017年第1期34卷 88-100页

作者： Gang LI Daoyong YANG Xiaohua JIANG Jing PAN Yanke TAN Xichang Satellite Launch center Xichang 615000China State key Laboratory at Numerical modelling for Atmospheric Sciences and Geophysical Fluid Dynamics Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China College of Meteorology and Oceanography PLA University of Science and TechnologyNanjing 211101China

A regional heavy precipitation event that occurred over Sichuan Province on 8-9 September 2015 is analyzed based on hourly observed precipitation data obtained from weather stations and NCEP FNL data. Two moist dynamic parameters, i.e., moist vorticity （mζ and moist divergence （mδ）, are used to diagnose this heavy precipitation event. Results show that the topography over southwestern China has a significant impact on the ability of these two parameters to diagnose precipitation. When the impact of topography is weak （i.e., low altitude）, rn（ cannot exactly depict the location of precipitation in the initial stage of the event. Then, as the precipitation develops, its ability to depict the location improves significantly. In particular, m（ coincides best with the location of precipitation during the peak stage of the event. Besides, the evolution of the m（ center shows high consistency with the evolution of the precipitation center. For mδ, although some false-alarm regions are apparent, it reflects the location of precipitation almost entirely during the precipitation event. However, the mδ center shows inconsistency with the precipitation center. These results suggest that both m（ and mδ have a significant ability to predict the location of precipitation. Moreover, m（ has a stronger ability than mδ in terms of predicting the variability of the precipitation center. However, when the impact of topography is strong （i.e., high altitude）, both of these two moist dynamic parameters are unable to depict the location and center of precipitation during the entire precipitation event, suggesting their weak ability to predict precipitation over complex topography.

关键词： moist vorticity moist divergence heavy precipitation southwestern China

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Analysis about the Behavior and Modeling of pH-Sensitive Hydrogels with Different Ratios of Chitosan and Polyvinylpyrrolidone

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Journal of Materials Science and Chemical Engineering 2019年第8期7卷 64-76页

作者： Daniela Ribeiro Gabriel Yuto Silvia Lenyra Meirelles Campos Titotto center of Engineering Modelling and Applied Social Sciences Federal University of ABC Santo André Brazil

Smart material can be defined as a material that can dock or convert energy between physical domains or as a material that can generate a response, in their characteristics, properties or geometries, when submitted to an external stimulus, for example, to heat, water presence, light, etc. In this paper, the second definition will be approached. Hydrogels are crosslinked materials that can absorb a big amount of water. They generally can be considered as smart materials once they exhibit sensibility to external stimuli like to pH variation, as will be approached in this paper. Thus, chitosan/polyvinylpyrrolidone hydrogels of three different ratios between these two polymers (1:1, 7:3 and 3:7) were synthesized and putted in aqueous solution with different pHs. The pH was adjusted adding drops of NaOH and HCl, slowly. After the collection of results and in order to understand the phenomena in a visual way, models of the molecules were also elaborated using the Avogadro software. Therefore, it was possible to realize that the greater the ratio of chitosan in the hydrogel, the greater its sensitivity to pH. Such characteristic is associated with the amino (-NH2) groups in it structure, which are capable of protonating and deprotonating (depending of the pH), generating charges under the chemical structure of the material, which will expand its volume in order to minimize the repulsion between charges. In addition, it was also noted that the hydrogel expansion is inversely proportional to the pH increase. By practical tests, it was possible to conclude that chitosan/PVP hydrogel with ratio 7:3 is the most interesting once it presented a greater quantity of chitosan in its composition, what implied in more rigidity than the others and greater ease of handling, resulting in more reliable results. This hydrogel also showed higher sensitivity to pH.

关键词： Chitosan Hydrogel Smart Material pH Sensitivity Polyvinylpyrrolidone Modeling

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