Multidimensional scaling analysis of virus diseases

Abstract Background and Objective Viruses are infectious agents that replicate inside organisms and reveal a plethora of distinct characteristics. Viral infections spread in many ways, but often have devastating consequences and represent a huge danger for public health. It is important to design statistical and computational techniques capable of handling the available data and highlighting the most important features. Methods This paper reviews the quantitative and qualitative behaviour of 22 infectious diseases caused by viruses. The information is compared and visualized by means of the multidimensional scaling technique. Results The results are robust to uncertainties in the data and revealed to be consistent with clinical practice. Conclusions The paper shows that the proposed methodology may represent a solid mathematical tool to tackle a larger number of virus and additional information about these infectious agents.

[1]  Elmar Heinzle,et al.  Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry combined with multidimensional scaling, binary hierarchical cluster tree and selected diagnostic masses improves species identification of Neolithic keratin sequences from furs of the Tyrolean Iceman Oetzi. , 2012, Rapid communications in mass spectrometry : RCM.

[2]  John J. Treanor,et al.  167 – Influenza (Including Avian Influenza and Swine Influenza) , 2015 .

[3]  Marion Koopmans,et al.  Global prevalence of norovirus in cases of gastroenteritis: a systematic review and meta-analysis. , 2014, The Lancet. Infectious diseases.

[4]  A. Gershon,et al.  Rubella Virus (German Measles) , 2015 .

[5]  K. Mølbak,et al.  Varicella in Europe-A review of the epidemiology and experience with vaccination. , 2015, Vaccine.

[6]  Kamaljit Singh,et al.  165 – Rabies (Rhabdoviruses) , 2015 .

[7]  E. Tramont,et al.  The human immunodeficiency virus. , 1991, Dermatologic clinics.

[8]  O Matouch,et al.  [Survival of rabies virus under external conditions]. , 1987, Veterinarni medicina.

[9]  S. Perlman,et al.  Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) , 2014, Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases.

[10]  William B. Karesh,et al.  Stability of Middle East Respiratory Syndrome Coronavirus in Milk , 2014, Emerging infectious diseases.

[11]  A. Lopes,et al.  Dynamic analysis of earthquake phenomena by means of pseudo phase plane , 2013 .

[12]  C. Thèves,et al.  The rediscovery of smallpox. , 2014, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[13]  Mudassar Imran,et al.  Estimating the basic reproduction number for single-strain dengue fever epidemics , 2014, Infectious Diseases of Poverty.

[14]  J. E. Bennett,et al.  Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases , 2014 .

[15]  S. Clarke,et al.  Bioterrorism: an overview , 2002, British journal of biomedical science.

[16]  Didier Raoult,et al.  Chikungunya outbreaks--the globalization of vectorborne diseases. , 2007, The New England journal of medicine.

[17]  Ross Ah,et al.  Modification of Chicken Pox in Family Contacts by Administration of Gamma Globulin , 1962 .

[18]  Frankie K. W. Chan,et al.  Efficient Weighted Multidimensional Scaling for Wireless Sensor Network Localization , 2009, IEEE Transactions on Signal Processing.

[19]  T. Caliński,et al.  A dendrite method for cluster analysis , 1974 .

[20]  Mark Fenton,et al.  Multidimensional scaling and tourism research , 1988 .

[21]  Alan Trounson,et al.  The persistence of memory , 2010, Nature Medicine.

[22]  Peter M Strebel,et al.  Measles - The epidemiology of elimination. , 2014, Vaccine.

[23]  David B. Stephenson,et al.  Statistical methods for interpreting Monte Carlo ensemble forecasts , 2000 .

[24]  Cecile Viboud,et al.  Global Seasonality of Rotavirus Disease , 2013, The Pediatric infectious disease journal.

[25]  Cherie Drenzek,et al.  Epidemiology of Human Rabies in the United States, 1980 to 1996 , 1998, Annals of Internal Medicine.

[26]  A L Baughman,et al.  Measles herd immunity. The association of attack rates with immunization rates in preschool children. , 1992, JAMA.

[27]  Forrest W. Young,et al.  Introduction to Multidimensional Scaling: Theory, Methods, and Applications , 1981 .

[28]  Rense Corten,et al.  Visualization of Social Networks in Stata Using Multidimensional Scaling , 2011 .

[29]  A. Osterhaus,et al.  H5N1 influenza in Hong Kong: virus characterizations. , 2002, Vaccine.

[30]  J. Leduc,et al.  Emerging and Re-emerging Infectious Disease Threats , 2015 .

[31]  Mick Roberts,et al.  Modelling the epidemiology of hepatitis B in New Zealand. , 2011, Journal of theoretical biology.

[32]  G. Dusheiko,et al.  Hepatitis B virus and hepatitis delta virus. , 1992, Molecular and cell biology of human diseases series.

[33]  Joseph L. Zinnes,et al.  Theory and Methods of Scaling. , 1958 .

[34]  J. Gower.  Generalized procrustes analysis , 1975 .

[35]  R. Seltser,et al.  A comparison of the clinical features of poliomyelitis in adults and in children. , 1952, The New England journal of medicine.

[36]  P. Rousseeuw.  Silhouettes: a graphical aid to the interpretation and validation of cluster analysis , 1987 .

[37]  J. Dahlberg,et al.  Molecular biology. , 1977, Science.

[38]  T. Endy,et al.  Dengue human infection model performance parameters. , 2014, The Journal of infectious diseases.

[39]  D. Lacher,et al.  Application of multidimensional scaling in numerical taxonomy: analysis of isoenzyme types of Candida species. , 1991, Annals of clinical and laboratory science.

[40]  Ph.D. Joseph Heitman M.D.,et al.  Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases , 2004, Mycopathologia.

[41]  S Reid,et al.  Minimum infective dose of HIV for parenteral dosimetry , 2009, International journal of STD & AIDS.

[42]  Laura Zimmerman,et al.  The epidemiological profile of rubella and congenital rubella syndrome in the United States, 1998-2004: the evidence for absence of endemic transmission. , 2006, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[43]  José António Tenreiro Machado,et al.  Fractional dynamics and MDS visualization of earthquake phenomena , 2013, Comput. Math. Appl..

[44]  Anil K. Jain.  Data clustering: 50 years beyond K-means , 2008, Pattern Recognit. Lett..

[45]  A H ROSS,et al.  Modification of chicken pox in family contacts by administration of gamma globulin. , 1963, The New England journal of medicine.

[46]  T. Geisbert,et al.  Marburg and Ebola Hemorrhagic Fevers (Filoviruses) , 2014, Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases.

[47]  António M. Lopes,et al.  Analysis of temperature time-series: Embedding dynamics into the MDS method , 2014, Commun. Nonlinear Sci. Numer. Simul..

[48]  Clara-Mihaela Ionescu,et al.  The Human Respiratory System: An Analysis of the Interplay between Anatomy, Structure, Breathing and Fractal Dynamics , 2013 .

[49]  Alexander M. Bronstein,et al.  Multigrid multidimensional scaling , 2006, Numer. Linear Algebra Appl..

[50]  Ibrahim Cil,et al.  Consumption universes based supermarket layout through association rule mining and multidimensional scaling , 2012, Expert Syst. Appl..

[51]  G Morin,et al.  Medical Microbiology , 1940, Nature.

[52]  Donald K. Milton,et al.  What was the primary mode of smallpox transmission? Implications for biodefense , 2012, Front. Cell. Inf. Microbio..

[53]  António M. Lopes,et al.  Multidimensional scaling visualization of earthquake phenomena , 2013, Journal of Seismology.

[54]  Kâmil Uğurbil,et al.  Cerebral cortical mechanisms of copying geometrical shapes: a multidimensional scaling analysis of fMRI patterns of activation , 2009, Experimental Brain Research.

[55]  J. Kruskal.  Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis , 1964 .

[56]  L. Jennings,et al.  Aerosol transmission of rhinovirus colds. , 1987, The Journal of infectious diseases.

[57]  Y. Guan,et al.  The aetiology, origins, and diagnosis of severe acute respiratory syndrome , 2004, The Lancet Infectious Diseases.

[58]  Patrick J. F. Groenen,et al.  Modern Multidimensional Scaling: Theory and Applications , 2003 .

[59]  John J. Treanor,et al.  178 – Noroviruses and Sapoviruses (Caliciviruses) , 2015 .

[60]  M W WELLS,et al.  Ventilation in the flow of measles and chickenpox through a community. , 1950, Journal of the American Medical Association.

[61]  R. Baric,et al.  Coronaviruses , 2011, Advances in Experimental Medicine and Biology.

[62]  Desmond G. Higgins,et al.  A Complete Analysis of HA and NA Genes of Influenza A Viruses , 2010, PloS one.

[63]  P. Malani,et al.  Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases , 2010 .

[64]  Craig Packer,et al.  Transmission Dynamics and Prospects for the Elimination of Canine Rabies , 2009, PLoS biology.

[65]  Sharif S. Aly,et al.  Modeling highly pathogenic avian influenza transmission in wild birds and poultry in West Bengal, India , 2013, Scientific Reports.

[66]  G. Grard,et al.  Ebola and Marburg haemorrhagic fever. , 2015, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[67]  R. Whitley,et al.  139 – Chickenpox and Herpes Zoster (Varicella-Zoster Virus) , 2015 .

[68]  D. Palmer,et al.  Human immunodeficiency virus. , 1990, Journal of the American Podiatric Medical Association.

[69]  José António Tenreiro Machado,et al.  Analysis and Visualization of Seismic Data Using Mutual Information , 2013, Entropy.

[70]  John H Connor,et al.  Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection , 2014, BMC Genomics.

[71]  J. Hendley,et al.  Mechanisms of transmission of rhinovirus infections. , 1988, Epidemiologic reviews.

[72]  Hsiu-Hsi Chen,et al.  Stochastic model for hepatitis B virus infection through maternal (vertical) and environmental (horizontal) transmission with applications to basic reproductive number estimation and economic appraisal of preventive strategies , 2014, Stochastic Environmental Research and Risk Assessment.

[73]  David W. Kimberlin,et al.  Poliovirus , 2011, Pediatrics.

[74]  Fionn Murtagh,et al.  A Survey of Recent Advances in Hierarchical Clustering Algorithms , 1983, Comput. J..

[75]  G W Beran,et al.  Virus survival in the environment. , 1991, Revue scientifique et technique.

[76]  P. Kilmarx,et al.  Global epidemiology of HIV , 2009, Current opinion in HIV and AIDS.

[77]  Michael C. Hout,et al.  Multidimensional Scaling , 2003, Encyclopedic Dictionary of Archaeology.

[78]  José António Tenreiro Machado,et al.  Multidimensional Scaling Visualization Using Parametric Similarity Indices , 2015, Entropy.

[79]  J. A. Tenreiro Machado,et al.  Dynamical analysis of compositions , 2011 .

[80]  Cécile Viboud,et al.  Direct and Indirect Effects of Rotavirus Vaccination: Comparing Predictions from Transmission Dynamic Models , 2012, PloS one.

[81]  Sandi Willows-Munro,et al.  Phylogenetic analysis of the polyprotein coding region of an infectious South African bursal disease virus (IBDV) strain. , 2014, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[82]  W. Bellini,et al.  Molecular Epidemiology of Measles Viruses in the United States, 1997–2001 , 2002, Emerging infectious diseases.

[83]  Suresh Mahalingam,et al.  Chikungunya: a re-emerging virus , 2012, The Lancet.

[84]  Christian Drosten,et al.  Middle East Respiratory Syndrome Corona virus, MERS-CoV. Conclusions from the 2nd Scientific Advisory Board Meeting of the WHO Collaborating Center for Mass Gathering Medicine, Riyadh , 2014, International Journal of Infectious Diseases.

[85]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[86]  Jonathan Z Kaye,et al.  Environmental persistence of a highly pathogenic avian influenza (H5N1) virus. , 2010, Environmental science & technology.

[87]  Jacqueline E Tate,et al.  2008 estimate of worldwide rotavirus-associated mortality in children younger than 5 years before the introduction of universal rotavirus vaccination programmes: a systematic review and meta-analysis. , 2011, The Lancet. Infectious diseases.

[88]  Steven Rubin,et al.  Molecular biology, pathogenesis and pathology of mumps virus , 2015, The Journal of pathology.

[89]  Atsushi Kato,et al.  [Mumps virus]. , 2010, Nihon rinsho. Japanese journal of clinical medicine.

[90]  Sangsoo Kim,et al.  A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis , 2010, BMC Bioinformatics.

[91]  C. Bridges,et al.  Transmission of influenza: implications for control in health care settings. , 2003, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[92]  Xiang Ji,et al.  Sensor positioning in wireless ad-hoc sensor networks using multidimensional scaling , 2004, IEEE INFOCOM 2004.

[93]  Scott C Weaver,et al.  Chikungunya: Evolutionary history and recent epidemic spread. , 2015, Antiviral research.

[94]  A. Osterhaus,et al.  Understanding HIV infection for the design of a therapeutic vaccine. Part I: Epidemiology and pathogenesis of HIV infection. , 2015, Annales pharmaceutiques francaises.

[95]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[96]  Harry T. Lawless,et al.  Multidimensional scaling of sorting data applied to cheese perception , 1995 .

[97]  W. El-Sadr,et al.  Ebola: the real lessons from HIV scale-up. , 2015, The Lancet. Infectious diseases.

[98]  C. Althaus.  Estimating the Reproduction Number of Ebola Virus (EBOV) During the 2014 Outbreak in West Africa , 2014, PLoS currents.

[99]  J. Tenreiro Machado,et al.  Analysis of financial data series using fractional Fourier transform and multidimensional scaling , 2011 .

[100]  Jacqueline E Tate,et al.  estimate of worldwide rotavirus-associated mortality in children younger than 5 years before the introduction of universal rotavirus vaccination programmes : a systematic review and meta-analysis , 2011 .

[101]  Donald W. Bouldin,et al.  A Cluster Separation Measure , 1979, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[102]  A. Hajeer,et al.  Severe neurologic syndrome associated with Middle East respiratory syndrome corona virus (MERS-CoV) , 2015, Infection.

[103]  Fernando B. M. Duarte,et al.  Dynamics of the Dow Jones and the NASDAQ stock indexes , 2010 .

[104]  Forrest W. Young.  Multidimensional Scaling: History, Theory, and Applications , 1987 .

[105]  John E. Bennett,et al.  Principles and practice of infectious diseases. Vols 1 and 2. , 1979 .

[106]  Bodo Ahrens,et al.  Distance in spatial interpolation of daily rain gauge data , 2005 .