http://rivers.icm.edu.pl/api.php?action=feedcontributions&user=Magd&feedformat=atomRiversWiki - User contributions [en]2024-03-29T01:44:45ZUser contributionsMediaWiki 1.27.4http://rivers.icm.edu.pl/index.php?title=Publications&diff=446Publications2010-10-20T07:23:05Z<p>Magd: </p>
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<div># P. Plonski, J.P. Radomski, ''Quick path finding: Quick algorithmic solution for unambiguous labeling of phylogenetic tree nodes'', Comput. Biol. Chem. (2010), in press, [http://dx.doi.org/10.1016/j.compbiolchem.2010.10.002 DOI]<br />
# J.P. Radomski, P.P. Slonimski, ''Alignment Free Characterization of the Influenza A Hemagglutinin Genes by the ISSCOR Method''', Comptes Rendus Biologies (2010), submitted<br />
# P. Plonski, J.P. Radomski, ''DAC – The Use of Neighbor-Joining for Inferring Very Large Phylogenies – Heuristic Method Improvements'', J. Bioinf. Comput. Biol. (2010), submitted<br />
# P. Plonski, J.P. Radomski, ''Phylogenetic Topology, Structure, and Other Features of the Sequences Set – Their Influence on Trees’ Reconstruction'', Comput. Biol. Chem. (2010), submitted<br />
# F. Rakowski, M. Gruziel, L. Bieniasz-Krzywiec, J. P. Radomski, ''Influenza epidemic spread simulation for Poland - a large scale, individual based model study'', Physica A: Statistical Mechanics and its Applications, 389 (2010), 3149-3165, [http://dx.doi.org/10.1016/j.physa.2010.04.029 DOI]<br />
# F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland'', [http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]<br />
# T. Żuk, F. Rakowski, J. P. Radomski, ''Probabilistic model of influenza virus transmissibility at various temperature and humidity conditions '', Comput.Biol.Chem., 33 (2009), 339-343, [http://dx.doi.org/doi:10.1016/j.compbiolchem.2009.07.005 DOI]<br />
# T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Biol.Chem., 33 (2009), 176-180, [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
# J. P. Radomski and P. P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=445Publications2010-10-20T07:00:07Z<p>Magd: </p>
<hr />
<div># P. Plonski, J.P. Radomski, ''Quick path finding: Quick algorithmic solution for unambiguous labeling of phylogenetic tree nodes'', Comput. Biol. Chem. (2010), in press, [http://dx.doi.org/10.1016/j.compbiolchem.2010.10.002 DOI]<br />
# J.P. Radomski, P.P. Slonimski, ''Alignment Free Characterization of the Influenza A Hemagglutinin Genes by the ISSCOR Method''', Comptes Rendus Biologies (2010), submitted<br />
# P. Plonski, J.P. Radomski, ''DAC – The Use of Neighbor-Joining for Inferring Very Large Phylogenies – Heuristic Method Improvements'', J. Bioinf. Comput. Biol. (2010), submitted<br />
# P. Plonski, J.P. Radomski, Phylogenetic Topology, Structure, and Other Features of the Sequences Set – Their Influence on Trees’ Reconstruction, Comput. Biol. Chem. (2010), submitted<br />
# F. Rakowski, M. Gruziel, L. Bieniasz-Krzywiec, J. P. Radomski, ''Influenza epidemic spread simulation for Poland - a large scale, individual based model study'', Physica A: Statistical Mechanics and its Applications, 389 (2010), 3149-3165, [http://dx.doi.org/10.1016/j.physa.2010.04.029 DOI]<br />
# F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland'', [http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]<br />
# T. Żuk, F. Rakowski, J. P. Radomski, ''Probabilistic model of influenza virus transmissibility at various temperature and humidity conditions '', Comput.Biol.Chem., 33 (2009), 339-343, [http://dx.doi.org/doi:10.1016/j.compbiolchem.2009.07.005 DOI]<br />
# T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Biol.Chem., 33 (2009), 176-180, [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
# J. P. Radomski and P. P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=444Publications2010-07-22T07:05:56Z<p>Magd: </p>
<hr />
<div># F. Rakowski, M. Gruziel, L. Bieniasz-Krzywiec, J. P. Radomski, ''Influenza epidemic spread simulation for Poland - a large scale, individual based model study'', Physica A: Statistical Mechanics and its Applications, 389 (2010), 3149-3165, [http://dx.doi.org/10.1016/j.physa.2010.04.029 DOI]<br />
# F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland'', [http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]<br />
# T. Żuk, F. Rakowski, J. P. Radomski, ''Probabilistic model of influenza virus transmissibility at various temperature and humidity conditions '', Comput.Biol.Chem., 33 (2009), 339-343, [http://dx.doi.org/doi:10.1016/j.compbiolchem.2009.07.005 DOI]<br />
# T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Biol.Chem., 33 (2009), 176-180, [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
# J. P. Radomski and P. P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=443Publications2010-07-20T13:59:20Z<p>Magd: </p>
<hr />
<div># F. Rakowski, M. Gruziel, L. Bieniasz-Krzywiec, J. P. Radomski, ''Influenza epidemic spread simulation for Poland - a large scale, individual based model study'', submitted<br />
# F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland'', [http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]<br />
# T. Żuk, F. Rakowski, J. P. Radomski, ''Probabilistic model of influenza virus transmissibility at various temperature and humidity conditions '', Comput.Biol.Chem. 2009 [http://dx.doi.org/doi:10.1016/j.compbiolchem.2009.07.005 DOI]<br />
# T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Biol.Chem. 2009 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
# J. P. Radomski and P. P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=442Publications2010-02-17T18:23:46Z<p>Magd: </p>
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<div>* F. Rakowski, M. Gruziel, L. Bieniasz-Krzywiec, J. P. Radomski, ''Influenza epidemic spread simulation for Poland - a large scale, individual based model study'', submitted<br />
<br />
* F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland'', [http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]<br />
<br />
* T. Żuk, F. Rakowski, J. P. Radomski, ''Probabilistic model of influenza virus transmissibility at various temperature and humidity conditions '', Comput.Biol.Chem. 2009 [http://dx.doi.org/doi:10.1016/j.compbiolchem.2009.07.005 DOI]<br />
<br />
* T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Biol.Chem. 2009 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
<br />
* J. P. Radomski and P. P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=441Publications2010-02-17T08:50:07Z<p>Magd: </p>
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<div>* T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2009 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
<br />
* J. P. Radomski and P. P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]<br />
<br />
* F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland'', [http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]<br />
<br />
* F. Rakowski, M. Gruziel, L. Bieniasz-Krzywiec, J. P. Radomski, ''Influenza epidemic spread simulation for Poland - a large scale, individual based model study'', submitted</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=440Publications2010-02-17T08:47:49Z<p>Magd: </p>
<hr />
<div>* T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2009 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
<br />
* J. P. Radomski and P. P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]<br />
<br />
* F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland'', [http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=439Publications2010-02-17T08:46:48Z<p>Magd: </p>
<hr />
<div>* T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
<!-- http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6X1F-4VHS7R5-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=864d504e8ba99e7653d7027d6a993ef3 DOI]--><br />
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* J. P. Radomski and P. P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]<br />
<br />
* F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland'', <br />
[http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=438Publications2010-02-05T14:07:19Z<p>Magd: </p>
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<div>* T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
<!-- http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6X1F-4VHS7R5-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=864d504e8ba99e7653d7027d6a993ef3 DOI]--><br />
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* Jan P. Radomski and Piotr P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]<br />
<br />
* F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large scale social mobility model - an individual based countrywide simulation study for Poland'', <br />
[http://jasss.soc.surrey.ac.uk/13/1/13.html Journal of Artificial Societies and Social Simulation 13 (1) 13, 2010]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Software&diff=437Software2009-05-19T12:01:37Z<p>Magd: New page: {{Menu Rivers}} <br\> __NOTOC__ For the purpose of simulations of the influenza epidemics in Poland, we developed a software platform <code>pDyn</code>. It allows to perform a stochasti...</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
__NOTOC__<br />
<br />
<br />
For the purpose of simulations of the influenza epidemics in Poland, we developed a software platform <code>pDyn</code>. It allows to perform a stochastic evolution of virus spread within Polish (virtual) society. The software will be described later. We present only selected results of epidemic scenarios, now. <br />
<br />
<br />
The movie of epidemic in Poland for several values of ''f'' and transmission rate <math>\alpha=0.14</math>:<br />
<br />
[http://www.icm.edu.pl/~magd/filmy/epidemic_f0.6.avi '''.avi for ''f'' = 0.6''']<br><br />
[http://www.icm.edu.pl/~magd/filmy/epidemic_f0.8.avi '''.avi for ''f'' = 0.8''']<br><br />
[http://www.icm.edu.pl/~magd/filmy/epidemic_f1.0.avi '''.avi for ''f'' = 1.0''']<br><br />
<br />
The number of infected during each day of epidemic as a function of transmission rate <math>\alpha</math> is presented in Figure A (3-dimensional plots) and as contour plots in Figure B.<br />
<br />
[[Image:infected_3Dplots.png |thumb|left| Figure A]]<br />
[[Image:infected_cplots.png |thumb|left| Figure B]]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=436Research2009-05-19T11:51:26Z<p>Magd: /* Alignment-free genome sequence analysis */</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
__NOTOC__<br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
[[Image:gosp_bw_cap.png |frameless|right|180px]]<br />
<br />
<br><br><br />
<p width="50%"><br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. <br />
Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. <br />
Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | '''More...''']]<br />
</p><br />
</blockquote><br />
<br />
<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
</blockquote>--><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
[[Image:flu_spread_model_zuk_rakowski_radomski_Fig2b.gif |frameless|190px|right]]<br />
<br />
<br><br />
<p width="50%"><br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | '''More..''']]<br />
</p><br />
</blockquote><br />
<br />
=== GENETIC STUDIES ===<br />
<br />
<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
</blockquote>--><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
<!--==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====--><br />
<br />
==== Alignment-free genome sequence analysis ====<br />
<br />
[[Image:occurence_probability.gif |frameless|300px|right]]<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. <br />
<!--[[Genetic:isscor | '''More..''']]--><br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=File:Occurence_probability.gif&diff=435File:Occurence probability.gif2009-05-19T11:50:54Z<p>Magd: </p>
<hr />
<div></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=434Publications2009-05-19T11:47:25Z<p>Magd: </p>
<hr />
<div>* T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
<!-- http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6X1F-4VHS7R5-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=864d504e8ba99e7653d7027d6a993ef3 DOI]--><br />
<br />
* Jan P. Radomski and Piotr P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://dx.doi.org/10.1016/j.crvi.2008.11.008 DOI]<br />
<br />
* F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large scale social mobility model - an individual based countrywide simulation study for Poland'', submitted</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=433Research2009-05-19T11:43:15Z<p>Magd: /* Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings */</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
__NOTOC__<br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
[[Image:gosp_bw_cap.png |frameless|right|180px]]<br />
<br />
<br><br><br />
<p width="50%"><br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. <br />
Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. <br />
Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | '''More...''']]<br />
</p><br />
</blockquote><br />
<br />
<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
</blockquote>--><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
[[Image:flu_spread_model_zuk_rakowski_radomski_Fig2b.gif |frameless|190px|right]]<br />
<br />
<br><br />
<p width="50%"><br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | '''More..''']]<br />
</p><br />
</blockquote><br />
<br />
=== GENETIC STUDIES ===<br />
<br />
<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
</blockquote>--><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
<!--==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====--><br />
<br />
==== Alignment-free genome sequence analysis ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. <br />
<!--[[Genetic:isscor | '''More..''']]--><br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=432Research2009-05-19T11:40:06Z<p>Magd: </p>
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<div>{{Menu Rivers}}<br />
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<br\><br />
__NOTOC__<br />
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=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
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[[Image:gosp_bw_cap.png |frameless|right|180px]]<br />
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<p width="50%"><br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. <br />
Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. <br />
Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | '''More...''']]<br />
</p><br />
</blockquote><br />
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<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
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<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
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The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | '''More..''']]<br />
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=== GENETIC STUDIES ===<br />
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<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
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<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
<!--==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====--><br />
<br />
==== Alignment-free genome sequence analysis ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. <br />
<!--[[Genetic:isscor | '''More..''']]--><br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Archive&diff=431Archive2009-04-21T13:13:10Z<p>Magd: /* Projekt */</p>
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<div>{{Menu Modul socjo}}<br />
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== Projekt ==<br />
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* <big>'''Projekt SSPE-CT-2006-44405 – Badanie i modelowanie odporności wirusów grypy w środowisku, zbiornikach wodnych, w powietrzu, oraz na powierzchniach &#8211; w systemach naturalnych oraz warunkach kontrolowanych laboratoryjnie'''</big><br />
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'''Wprowadzenie''' – Pojawienie się, w znaczącej skali, choroby ptasiej grypy wywoływanej przez wysoko patogenicznego wirusa (H5N1) genotypu A, postawiło wiele pytań i problemów w związku z odpowiedzialnością za politykę ochrony i prewencji, ryzyko gospodarcze i zdrowotne. Wiedza naukowa o ekologii i występowaniu wirusa H5N1 w środowisku naturalnym jest wysoce niedostateczna. W szczególności nie zbadany został strategicznie istotny mechanizm przetrwania wszystkich odmian wirusa HPAIV (Highly Patogenic Avian Influenza Virus), w tym w szczególności szczepu H5N1. Dostępne dane są ograniczone, a często nawet sprzeczne, istnieje bardzo mało informacji dotyczących zachowania się wirusa ptasiej grypy w środowisku, a zatem w akwenach wodnych, w powietrzu oraz w glebie i na powierzchniach gruntowych. Nie istnieją także wypracowane metody oraz standardowe protokoły wykrywania jego obecności w środowisku naturalnym, w odchodach, w glebie, organizmach innych niż ptaki, a także w roślinności. Techniki takie powinny umożliwić szybkie, ilościowe, wystarczająco czułe, a przede wszystkim powtarzalne, oznaczenia obecności i stężenia wirusa w rutynowy sposób, w standardowych warunkach (także, a nawet szczególnie w warunkach polowych, oraz przez niedoświadczony personel). Wyniki badań przeprowadzonych na innych podtypach wirusa grypy nie mogą zostać w prosty sposób zaadaptowane do badań nad wirusem H5N1, choć mogą i powinny służyć za punkt wyjścia przy opracowywaniu matod specyficznych dla serotypu H5N1.<br />
<br />
== Uczestnicy Konsorcjum ==<br />
<br />
W projekcie Resistance of Influenza Viruses in Environmental Reservoirs and Systems (RIVERS) uczestniczy dziewięć instytucji, w tym trzy z kontynentu azjatyckiego:<br />
<br />
# '''Institut Pasteur de Paris''' (koordynator projektu) – 25-28 rue du Docteur Roux, 75015, Paris, France<br />
# '''Cantacuzino National Institute of Research and Development Microbiology and Immunology''' – Splaiul Independentei 103, district 5, Bucuresti, 1-525 050096, Romania<br />
# '''The Stephan Angeloff Institute of Microbiology''' – Acad. G. Bonchev Str. 26, Sofia, 1113, Bulgaria<br />
# '''Institut Pasteur du Cambodge''' – 5, Monivong Boulevard, Phnom Penh, 983, Cambodia <br />
# '''Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences''' – Pasteur Institute of Shanghai – 225 South Chong Qing Rd., #2, Shanghai, 200025, China<br />
# '''Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)''' – 42 rue Scheiffer, 75116 Paris, France<br />
# '''Institut Pasteur de Lille''' – 1 rue du Professeur Calmette, 59019, Lille, France<br />
# '''Interdyscyplinarne Centrum Modelowania Matematycznego i Komputerowego Uniwersytetu Warszawskiego''' – Pawińskiego 5A, Blok D, Warszawa PL-02-106, Poland<br />
# '''Wuhan Institute of Virology, Chinese Academy of Sciences''' – Xiaohongshan 44, Wuhan, 430071, China<br />
<br />
Działają one na rzecz opracowania metod wykrywania i identyfikacji wirusa ptasiej grypy serotypu A(H5N1) w celu zapobiegania i ewentualnej kontroli wybuchów epidemii ptasiej grypy. Wśród zadań postawionych w projekcie należy wyszczególnić: [1] – mikrobiologiczne zbadanie podstaw przeżywalności wirusa ptasiej grypy, [2] – zbadanie wpływu związków chemicznych i warunków fizycznych na przetrwanie wirusa, [3] – wyznaczenie roli zbiorników środowiskowych, [4] – opracowanie standardowych metod wykrywania oraz pomiarów koncentracji wirusa w środowiskach wodnych, materiałach spożywczych, wodach ściekowych, itp., [5] – przygotowanie adekwatnej bazy danych wraz z odpowiednimi narzędziami do ich analizy, a jeśli to możliwe, także zbudowania odpowiednich modeli symulacyjnych, w celu opracowania schematów działań opartych na danych obserwacyjnych, które służyłyby zapobieganiu i kontroli rozprzestrzeniania się wirusa ptasiej grypy wśród ludzi i zwierząt. Szczególnie w trakcie ponownego przywracania hodowli, po wypadkach jej całkowitego zniszczenia w trybie prewencyjnym.<br />
<br />
== Cele Projektu ==<br />
<br />
Zasadniczym celem projektu RIVERS (Resistance of Influenza Viruses in Environmental Reservoirs and Systems) typu STREP (Specific Targeted REsearch or innovation Project), w ramach szóstego programu ramowego Unii Europejskiej, jest wypracowanie metod prewencyjnych i kontrolnych w stosunku do rozprzestrzeniania się wirusa ptasiej grypy A(H5N1). W ramach celu ogólnego można wyszczególnić następujące grupy:<br />
* zebranie danych dotyczących przetrwania wirusa ptasiej grypy w środowiskach naturalnych<br />
* uzyskanie podstaw naukowych wiedzy o przetrwaniu wirusa ptasiej grypy w warunkach eksperymentalnych<br />
* znalezienie zależności wpływu różnorodnych czynników chemicznych i/lub fizycznych na przetrwanie wirusa ptasiej grypy<br />
* znalezienie zależności wpływu różnych technologii stosowanych w przemyśle spożywczym na przetrwanie wirusa, oraz ewentualne opracowanie technologii zapobiegających<br />
* w sytuacji gdy dostępne będą stosowne dane o zachowaniu wirusa A(H5N1), próba opracowania modeli analitycznych, a zwłaszcza modeli symulacyjnych, opisujących zdolności przetrwania i dynamikę rozwoju populacji wirusa ptasiej grypy w różnych środowiskach, oraz w warunkach kontrolowanych laboratoryjnie, dla istotnych gatunków zwierząt – tak hodowlanych jak i swobodnie migrujących, w określonych biotypach środowiska naturalnego.<br />
<br />
<br />
== Pakiety zadań projektu ==<br />
<br />
Pakiety (WP – WorkPackages) projektu RIVERS zgrupowane są w cztery programy (WPG – WorkProgrammes) według struktury i zawartości merytorycznej podanej jak następuje:<br />
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'''WPG I''' – Przetrwanie wirusa ptasiej grypy w środowiskach i zbiornikach wodnych<br />
* WP0: Podstawy molekularne dla przetrwania i mutacji wirusa, w szczególności badania tzw. „bio-equivalence” w odniesieniu do możliwości stosowania metod wypracowanych dla identyfikacji i wykrywalności wirusa grypy typu A(H1N1) dla analogicznych sytuacji w odniesieniu do wirusa A(H5N1).<br />
* WP1: Koncentracja, identyfikacja i szacowanie ilościowe występowania wirusa grypy w zbiornikach wodnych, w terenach podmokłych i w faunie wodnej.<br />
* WP2: Obserwacja wirusa ptasiej grypy w środowisku naturalnym<br />
* WP3: Obserwacja koncentracji i przetrwania wirusa ptasiej grypy w warunkach eksperymentalnych <br />
* WP4: Wpływ związków występujących w wodzie na przetrwanie wirusa AIV.<br />
'''WPG II''' – Przetrwanie wirusa ptasiej grypy w powietrzu i na powierzchniach<br />
* WP5: Wpływ czynników atmosferycznych na przetrwanie wirusa<br />
* WP6: Żywotność wirusa w otoczeniu gospodarstw wiejskich.<br />
* WP7: Wpływ związków w występujących powietrzu i na powierzchniach gruntowych na przetrwanie wirusa<br />
* WP8: Określenie wpływu wybranych parametrów procesu produkcji spożywczej na przetrwanie wirusa.<br />
<br />
'''WPG III''' – Modelowanie teoretyczne wraz z wnioskami i rekomendacjami<br />
* WP9: Modelowanie dynamiki populacji wirusa grypy w naturalnych zbiornikach wodnych, w powietrzu oraz na powierzchniach, ze szczególnym uwzględnieniem gleby, akwenów wodnych i habitatów naturalnych.<br />
<br />
'''WPG IV''' – Wykorzystanie i rozpowszechnienie wyników. Zarządzanie projektem.<br />
* WP10: Wnioski i rekomendacje dla zapobieganiu, kontroli i zarządzania kryzysowego w razie wybuchów epidemii ptasiej grypy wśród ptactwa dzikiego i hodowlanego, potencjalnie prowadzących do powstania warunków dla pandemii porównywalnej z wysoce śmiertelnym epizodem tzw. grypy hiszpanki w latach 1918-1919.<br />
* WP11: Zarządzanie projektem.<br />
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== Planowane wyniki projektu ==<br />
<br />
'''Zakładane wyniki projektu i ich ewentualny wpływ na rozwój badań'''<br />
Projekt RIVERS skierowany jest na zagadnienia związane z infekcyjnością, w powiązaniu epidemiologią i kontrolą, a szczególnie z warunkami i czasem przetrwania wirusa ptasiej grypy w środowisku, na fermach hodowlanych, w akwenach wodnych, w powietrzu oraz zanieczyszczonych powierzchniach – zarówno w warunkach naturalnych, jak i kontrolowanych laboratoryjnie. Przeżywalność wirusa będzie badana w związku z jego podatnością na działanie czynników chemicznych, fizycznych – np. temperatury czy promieniowania ultrafioletowego, oraz ich wpływu na genotypową i fenotypową zmienność populacji, w określonych warunkach możliwych do wystąpienia w habitatach o największym prawdopodobieństwie wybuchu epidemii. Stężenia wirusa w określonych sytuacjach i środowiskach, uzyskane w pierwszych stadiach projektu, stanowić będą podstawę do: [a] tworzenia bazy danych zawierającej informacje o infekcyjnych i przetrwalnościowych własności wirusa ptasiej grypy, [b] budowania modeli cząstkowych, zarówno analitycznych – o ile statystyczna istotność danych na to pozwoli – oraz symulacyjnych w oparciu o hipotezy robocze, weryfikowalne następnie w pętli sprzężenia zwrotnego w oparciu o nowe dane eksperymentalne. Następnie wysiłek zostanie rozszerzony w kierunku standaryzowanych protokołów szybkiego wykrywania wirusa H5N1, w oparciu o konieczne do wypracowania metody i techniki detekcji. Informacja pozyskana w wyniku prac konsorcjum RIVERS pozwolić powinna na lepsze określenie stosownych wytycznych UE, oraz innych organizacji międzynarodowych w odniesieniu do metod detekcji, dezaktywacji, dezynfekcji, kontroli i zapobiegania powstawaniu ognisk występowania wirusa ptasiej grypy.<br />
<br />
Oprócz zadań w obrębie Programu Tematycznego III ('''WPG III'''), którego Interdyscyplinarne Centrum Modelowania Matematycznego i Komputerowego jest koordynatorem, oraz zadań wynikających z kierowania Pakietem Tematycznym 9 ('''WP9'''), ICM uczestniczy we wszystkich fazach planowania eksperymentów, asymilacji, weryfikacji i walidacji danych w Pakietach '''WP0-WP5''' i '''WP8''', oraz konsultuje analogiczne zadania w Pakietach '''WP6-WP7'''.<br />
<br />
Wykorzystując dane uzyskane sukcesywnie w trakcie realizacji Programów Tematycznych '''WPG I''' i '''WPG II''' przewiduje się zbudowanie analitycznych i symulacyjnych modeli opisujących przeżywalność wirusa w naturalnych zbiornikach wodnych, w powietrzu i na powierzchniach gruntownych. Zbiorniki wodne jako nieredukowalny element cyklu występowania wirusa pełnią szczególnie ważną rolę. <br />
Pakiet zadań '''WP9''' zakłada także możliwość powiązania rezultatów prac z projektu RIVERS, oraz rezultatów innych badań w projektach ze zgłoszenia SSP-5B Influenza, realizowanymi w szczególności w obrębie zadań Task 3 i Task 4 w SSP-5B-INFLUENZA, dotyczącymi ekologii nosicieli wirusa oraz globalnego mechanizmu występowania wirusa w przyrodzie. <br />
<br />
Projekt RIVERS koncentruje się na zagadnieniach środowiskowych, przy czym centralne rolę w rozprzestrzeniania się wirusa grypy stanowi jego infekcyjności w odniesieniu do ptaków wodnych, które uważa się za pierwotnego nosiciela wirusa grypy. Chociaż istnieje pewien zbiór danych dotyczących infekcji wirusa wśród dzikiego ptactwa, niewiele wiadomo o ekologii wirusa AIV. Zarówno dane zawierające informacje o okresach zainfekowania dzikiego ptactwa wirusem AIV, jak i dane dotyczące cyrkulacji wirusa w środowiskach naturalnych i hodowlanych są niekompletne, a mechanizm przetrwania wirusa nie został wyjaśniony. Jednym z możliwych celów pakietu '''WP9''' jest opracowanie przypuszczalnych modeli opisujących występowanie i dynamikę populacji wirusa w trakcie rocznego cyklu. O ile znajdzie to potwierdzenie w danych gromadzonych w obrębie zadań WP0-WP8, oraz biorąc pod uwagę założenia powstałe z uwzględnieniem aktualnego stanu wiedzy dotyczącej rozprzestrzeniania się i występowania wirusa AIV w przyrodzie można będzie zapewne wstępnie zaproponować szereg schematów koncepcyjnych ewentualnej cyrkulacji wirusa H5N1 w rocznym cyklu rozwojowym.<br />
<br />
== Symulacje w modelu dynamiki społecznej ==<br />
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''' Wielkoskalowy model symulacyjny dynamiki zachowań różnych subtypów wirusa grypy w wielomilionowych populacjach nosicieli '''<br />
Z uwagi na niemal całkowity brak danych dotyczących przetrwalności oraz sposobów dezaktywacji wirusa ptasiej grypy A(H5N1) w środowiskach naturalnych, ze szczególnym uwzględnieniem akwenów wodnych, warunków sprzyjających przetrwaniu wirusa H5N1 w powietrzu, na powierzchniach czy w glebie – w początkowym etapie prac projektu RIVERS, zadania związane z budową modeli symulacyjnych koncentrować się będą na stworzeniu stochastycznej symulacji Monte Carlo. Model bazować będzie na metodologii, indywidualnych, heterogenicznych agentów software’owych, wyposażonych w atrybuty zarówno nosicieli (ludzkich), jak i ich immunologicznej historii przebytych infekcji z uwzględnieniem zakażenia szybko-zmiennymi serotypami HA1, HA3 oraz HB. Symulacje osiągnąć mają przede wszystkim zebranie statystycznie istotnych informacji o przebiegu epidemii, a zatem jej wybuchu, rozwoju i wygasania ognisk infekcji grypy wirusa A z uwzględnieniem genetycznej konkurencji serotypów H1N1, H3N2, oraz wirusa typu B. Model przewiduje asymilacje danych o gęstości populacji, rozmieszczeniu dużych zakładów pracy, szkół, oraz lokalizacji innych obiektów o wysokim współczynniku potencjalnych kontaktów osobników zakażonych i zdrowych, a także opartych o rozkłady gęstości informacji o częstotliwości i kierunkach podróży – zarówno jako typowych dojazdów do pracy/szkół etc, jak i z wykorzystaniem transportu na większych odległościach. Planowane jest przeprowadzenie symulacji w czasie quasi rzeczywistym, oraz z udziałem skalowalnej reprezentacji i rozmieszczenia skupisk ludności z uwzględnieniem ich georeferencji. Prawdopodobnie dla oddania zjawisk w 38-miomilionowej populacji modelowanej, wystarczające będzie używanie każdorazowo ok. 12–15 milionów osobników (agentów symulacji). Walidacja modelu powinna zatem, w pierwszej kolejności, umożliwić weryfikację zasadności i stosowalności przyjętego rodzaju skalowania. Następnie przewidziana jest analiza wrażliwości użytego modelu symulacyjnego w odniesieniu do parametrów wewnętrznych oraz walidacja w oparciu dostępne dane epidemiologiczne dla przemienności i fluktuacji występowania w populacji nosicieli subtypów wirusa H1N1, H3N2 oraz B. Bardzo istotnym elementem, w znaczny sposób decydującym o stopniu, w jakim powyższy model symulacyjny może być uznany za mimetyczny, czyli dobrze korespondujący z danymi obserwacyjnymi, jest jakościowe podobieństwo rezultatów analizy filogenetycznej odpowiadających sobie zespołów danych w obu przypadkach. Planowane jest w/z tym podjęcie prób przejścia z opisu jakościowego, do opisu chociażby pół-ilościowego, a zatem także do próby wypracowania kryteriów określenia stochastycznej istotności zmian obserwowanych w wyniku mutacyjnego dryfu kodu genetycznego poszczególnych serotypów wirusa grypy, oraz współbieżnych z nimi rezultatów modelowych. Jedną z możliwości jest zastosowanie metod nie wymagających uliniowania sekwencji podczas analizy, użyteczne np. przy filogenetycznych porównaniach całkowitych genomów, jednak ich stosowalność w przypadku analizy wirusów grypy wymagać będzie odrębnego potraktowania i weryfikacji.<br />
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== Rekomendacje i Popularyzacja ==<br />
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'''Rekomendacje''' – ICM jest w projekcie RIVERS koordynatorem Programu Tematycznego III (WPG III), w ramach którego koordynuje prace nad wypracowaniem rekomendacji dla zapobiegania, kontroli i zarządzania kryzysowego w razie wybuchów epidemii ptasiej grypy wśród ptactwa dzikiego i hodowlanego, oraz innych działań, w oparciu o pozyskane dane eksperymentalne, wyniki modeli cząstkowych oraz modelu dynamiki zachowań wirusa A(H5N1) w różnych środowiskach.<br />
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'''Popularyzacja''' – udostępnianie i rozpowszechnianie wyników projektu odbywać się będzie przede wszystkim poprzez publikacje naukowe, a także w postaci raportów dla komitetu SPP-5B-INFLUENZA przy komisarzu UE. Zasadnicze informacje o przebiegu prac znajdą się na oficjalnej stronie konsorcjum [http://www.rivers.eu RIVERS]. Dodatkowo, dedykowany serwer zlokalizowany w ICM, obok pełnienia funkcji bezpiecznego repozytorium danych dla sieci intranet wewnątrz konsorcjum, służy jako platforma udostępniania i wizualizacji wyników symulacji, ze szczególnym uwzględnieniem rezultatów tematu: „Wielkoskalowy model symulacyjny dynamiki zachowań różnych subtypów wirusa grypy w wielomilionowych populacjach nosicieli”, który z uwagi na wykorzystywanie wyłącznie publicznie dostępnych danych populacyjnych i genetycznych, oraz epidemiologiczny charakter oczekiwanych wyników jest szczególnie predestynowany do szerokiego upowszechnienia. ICM, równolegle do zadań realizowanych w ramach umowy konsorcyjnej, popularyzować będzie także wyniki polskie. Zadania popularyzacyjne będzie częściowo finansowane ze środków własnych centrum. Względy aktualności informacji, polityki upowszechniania wiedzy w ICM, etc., wymagają utrzymania i stałej aktualizacji stron WWW projektu. Poza obsługą techniczną potrzebna będzie także stała praca edytorska, redakcyjna i dokonywanie przekładów. W ramach wkładu własnego ICM zapewni obsługę techniczną serwera WWW, oraz aktualizację bieżącą stron WWW.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=430Publications2009-04-20T17:18:14Z<p>Magd: </p>
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<div>* T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
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* Jan P. Radomski and Piotr P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies, 332 (2009), 336-350 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6X1F-4VHS7R5-1&_user=3934946&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000054122&_version=1&_urlVersion=0&_userid=3934946&md5=9843980cd20c7da16db446af9b7f8439 DOI]<br />
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* F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large scale social mobility model - an individual based countrywide simulation study for Poland'', submitted</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Epidemics:poland&diff=429Epidemics:poland2009-03-25T14:10:06Z<p>Magd: </p>
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<div>{{Menu Research}}<br />
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<!--Incidence of influenza and influenza-like illness in Poland can be found at [http://www.pzh.gov.pl/oldpage/epimeld/grypa/aindex.htm National Institute of Public Health] pages. In the last week of October 2008, there were 4305 instances of influenza-like cases, which yielded the daily infectivity rate of 1.25 per 100 thousands of individuals. The accessible data archives start in 2000, giving weekly reports on influenza incidence in each voivodeship.<br />
--><br />
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The movie of epidemic in Poland for several values of ''f'' and transmission rate <math>\alpha=0.14</math>:<br />
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[http://www.icm.edu.pl/~magd/filmy/epidemic_f0.6.avi '''.avi for ''f'' = 0.6''']<br><br />
[http://www.icm.edu.pl/~magd/filmy/epidemic_f0.8.avi '''.avi for ''f'' = 0.8''']<br><br />
[http://www.icm.edu.pl/~magd/filmy/epidemic_f1.0.avi '''.avi for ''f'' = 1.0''']<br><br />
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The number of infected during each day of epidemic as a function of transmission rate <math>\alpha</math> is presented in Figure A (3-dimensional plots) and as contour plots in Figure B.<br />
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[[Image:infected_3Dplots.png |thumb|left| Figure A]]<br />
[[Image:infected_cplots.png |thumb|left| Figure B]]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=File:Infected_cplots.png&diff=428File:Infected cplots.png2009-03-25T13:58:23Z<p>Magd: </p>
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<div></div>Magdhttp://rivers.icm.edu.pl/index.php?title=File:Infected_3Dplots.png&diff=427File:Infected 3Dplots.png2009-03-25T13:57:31Z<p>Magd: </p>
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<div></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=426Research2009-03-25T10:03:50Z<p>Magd: /* GENETIC STUDIES */</p>
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<div>{{Menu Rivers}}<br />
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__NOTOC__<br />
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=== EPIDEMIC SIMULATIONS ===<br />
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<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
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Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | '''More...''']]<br />
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<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
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<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
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The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | '''More..''']]<br />
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=== GENETIC STUDIES ===<br />
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<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
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<!--==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====--><br />
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==== Alignment-free genome sequence analysis ====<br />
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Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. <br />
<!--[[Genetic:isscor | '''More..''']]--><br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=People&diff=425People2009-03-22T11:17:23Z<p>Magd: New page: {{Menu Rivers}} '''Coordinator:''' Jan Radomski '''Group:''' Franciszek Rakowski<br> Tomasz Żuk<br> Piotr Płoński<br> '''Current and previous co-workers:''' Michał Krych<br> Ł...</p>
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<div>{{Menu Rivers}}<br />
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'''Coordinator:'''<br />
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Jan Radomski<br />
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'''Group:'''<br />
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Franciszek Rakowski<br><br />
Tomasz Żuk<br><br />
Piotr Płoński<br><br />
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'''Current and previous co-workers:'''<br />
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Michał Krych<br><br />
Łukasz Bieniasz-Krzywiec<br><br />
Tomasz Badowski<br><br />
Kamil Walas<br><br />
Magdalena Gruziel<br></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=424Research2009-03-21T12:10:40Z<p>Magd: </p>
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<div>{{Menu Rivers}}<br />
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__NOTOC__<br />
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=== EPIDEMIC SIMULATIONS ===<br />
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<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | '''More...''']]<br />
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<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
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<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | '''More..''']]<br />
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=== GENETIC STUDIES ===<br />
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<!--<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
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<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
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Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. [[Genetic:isscor | '''More..''']]<br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Genetic:isscor&diff=423Genetic:isscor2009-03-18T16:01:52Z<p>Magd: New page: {{Menu Research}}</p>
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<div>{{Menu Research}}<br />
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The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future.<br />
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The model described in the [[ epidemics:guineapigs:data |'''Data''']], [[ epidemics:guineapigs:model | '''Model''']], [[ epidemics:guineapigs:results | '''Results''']] tabs has been published:<br />
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[http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Virtual_society&diff=421Virtual society2009-03-18T15:57:34Z<p>Magd: </p>
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Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age (and, say, luck) should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model.<br />
This virtual society was based on accessible [[Virtual_society:data | '''data''']].<br />
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Depending on the [[Virtual_society:data | '''data''']] available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of [[Virtual_society:model | '''methods''']]. <br />
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The outcome, that is the virtual society we obtained, is presented in the [[Virtual_society:results | '''Results''']] tag of the menu.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Epidemics:virus_evolution&diff=420Epidemics:virus evolution2009-03-18T15:56:32Z<p>Magd: </p>
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== Review of the models ==<br />
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=== Ferguson's, evolutionary<ref name="ferguson2003">FERGUSON N M, Galvani A P, and Bush R M, Ecological and immunological determinants of influenza evolution, Nature, 422 (2003), pp. 428-433</ref> ===<br />
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== References ==<br />
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<references/></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Epidemics:guineapigs&diff=419Epidemics:guineapigs2009-03-18T15:56:03Z<p>Magd: </p>
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The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future.<br />
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The model described in the Data, Model, Results tabs has been published:<br />
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[http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Epidemics:poland&diff=418Epidemics:poland2009-03-18T15:55:37Z<p>Magd: </p>
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Incidence of influenza and influenza-like illness in Poland can be found at [http://www.pzh.gov.pl/oldpage/epimeld/grypa/aindex.htm National Institute of Public Health] pages. In the last week of October 2008, there were 4305 instances of influenza-like cases, which yielded the daily infectivity rate of 1.25 per 100 thousands of individuals. The accessible data archives start in 2000, giving weekly reports on influenza incidence in each voivodeship.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Epidemics:poland&diff=417Epidemics:poland2009-03-18T15:55:23Z<p>Magd: </p>
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Incidence of influenza and influenza-like illness in Poland can be found at [http://www.pzh.gov.pl/oldpage/epimeld/grypa/aindex.htm National Institute of Public Health] pages. In the last week of October 2008, there were 4305 instances of influenza-like cases, which yielded the daily infectivity rate of 1.25 per 100 thousands of individuals. The accessible data archives start in 2000, giving weekly reports on influenza incidence in each voivodeship.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Template:Menu_Research&diff=416Template:Menu Research2009-03-18T15:54:20Z<p>Magd: </p>
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<div>{| class="riversmenu" align="right" width=100% <br />
! colspan="5" align="left" | <big>Research</big><br />
<!--! colspan="2" | [[virtual_society | <big><u>Virtual society</u></big>]] | [[epidemics | Virus spread]] | [[literature | Literature]] | [[archive | Version ]] --><br />
|-<br />
| [[virtual_society | Virtual Society]] || [[ epidemics:poland | Epidemic in Poland ]] || [[ epidemics:guineapigs | Guinea pigs epidemic]] || [[ epidemics:virus_evolution | Multiple strain dynamics ]] || [[ genetic:isscor | Sequence analysis ]]<br />
|}</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Template:Menu_Research&diff=415Template:Menu Research2009-03-18T15:45:51Z<p>Magd: New page: {| class="riversmenu" align="right" width=100% ! colspan="5" align="left" | <big>Research</big> <!--! colspan="2" | <big><u>Virtual society</u></big> | [[epidemics ...</p>
<hr />
<div>{| class="riversmenu" align="right" width=100% <br />
! colspan="5" align="left" | <big>Research</big><br />
<!--! colspan="2" | [[virtual_society | <big><u>Virtual society</u></big>]] | [[epidemics | Virus spread]] | [[literature | Literature]] | [[archive | Version ]] --><br />
|-<br />
| [[virtual_society | '''Virtual Society''']] || [[ epidemics:poland | '''Epidemic in Poland''' ]] || [[ epidemics:guineapigs | ''' Guinea pigs epidemic''']] || [[ epidemics:virus_evolution | '''Multiple strain dynamics''' ]] || [[ genetic:isscor | '''Sequence analysis''' ]]<br />
|}</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Virtual_society&diff=414Virtual society2009-03-18T15:37:20Z<p>Magd: </p>
<hr />
<div>{{Menu Research}}<br />
<!--{{Menu Virtual society}}--><br />
<!--{{stub}}--><br />
<br />
<br/><br/><br />
<br/><br/><br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age (and, say, luck) should be either retired, employed or going to school (kindergarden, primary school, secondary school, college, univerisity). All these basic relations should be reflected in the virtual model.<br />
This virtual society was based on accessible [[Virtual_society:data | data]].<br />
<br />
<br />
Depending on the [[Virtual_society:data | data]] available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of [[Virtual_society:model | methods]]. <br />
<br />
<br />
The outcome, that is the virtual society we obtained, is presented in the [[Virtual_society:results | Results]] tag of the menu.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=413Research2009-03-18T15:25:55Z<p>Magd: /* GENETIC STUDIES */</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
__NOTOC__<br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | '''More...''']]<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | '''More..''']]<br />
</blockquote><br />
<br />
=== GENETIC STUDIES ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. [[Genetic:isscor | '''More..''']]<br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=412Research2009-03-18T15:25:44Z<p>Magd: /* EPIDEMIC SIMULATIONS */</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
__NOTOC__<br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | '''More...''']]<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | '''More..''']]<br />
</blockquote><br />
<br />
=== GENETIC STUDIES ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. [[Genetic:isscor | More..]]<br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=411Research2009-03-18T15:24:42Z<p>Magd: </p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
__NOTOC__<br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | More...]]<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | More..]]<br />
</blockquote><br />
<br />
=== GENETIC STUDIES ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. [[Genetic:isscor | More..]]<br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=410Research2009-03-18T15:24:25Z<p>Magd: /* GENETIC STUDIES */</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | More...]]<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | More..]]<br />
</blockquote><br />
<br />
=== GENETIC STUDIES ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics. [[Genetic:isscor | More..]]<br />
</blockquote></div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=409Research2009-03-18T15:23:09Z<p>Magd: /* Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings */</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | More...]]<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. [[Epidemics:guineapigs | More..]]<br />
</blockquote><br />
<br />
=== GENETIC STUDIES ===<br />
<br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
<br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=408Research2009-03-18T15:22:23Z<p>Magd: /* Agent Based Model of epidemic within the Polish virtual society */</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | More...]]<br />
</blockquote><br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
</blockquote><br />
<br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. <br />
<br />
=== GENETIC STUDIES ===<br />
<br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
<br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=407Research2009-03-18T15:21:59Z<p>Magd: /* A virtual Polish society */</p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
<blockquote style="background: white; border: 1px solid rgb(153, 153, 153); padding: 1em;"><br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. [[Virtual_society | More...]]<br />
</blockquote><br />
<br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
<br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. <br />
<br />
=== GENETIC STUDIES ===<br />
<br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
<br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=406Research2009-03-18T15:14:22Z<p>Magd: </p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
<br />
=== EPIDEMIC SIMULATIONS ===<br />
<br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. <br />
<br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
<br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. <br />
<br />
=== GENETIC STUDIES ===<br />
<br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
<br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=405Research2009-03-18T15:10:33Z<p>Magd: </p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
<br\><br />
<br />
=== Epidemic simulations ===<br />
<br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. <br />
<br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
<br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. <br />
<br />
=== Genetic studies ===<br />
<br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
<br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=404Research2009-03-18T15:10:04Z<p>Magd: </p>
<hr />
<div>{{Menu Rivers}}<br />
<br />
=== Epidemic simulations ===<br />
<br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. <br />
<br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
<br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. <br />
<br />
=== Genetic studies ===<br />
<br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
<br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Rivers&diff=403Rivers2009-03-18T15:08:12Z<p>Magd: </p>
<hr />
<div>{{Menu Rivers}}<br />
__NOTOC__<br />
<br />
== Project summary ==<br />
<br />
'''Resistance of Influenza Viruses in Environmental Reservoirs and Systems (RIVERS) - project No SSPE-CT-2006-44405, maintained within the 6th Framework Programme'''<br />
<br />
The surge of the global avian influenza epizootic caused by the genotype Z highly pathogenic avian influenza virus (HPAIV) has posed numerous questions, in particular to risk managers and policy makers. Scientific knowledge is thin on many aspects of the ecology and environmental properties of HPAIVs, in particular H5N1. Virus survival, a key element in control strategies, is an illustration of this paucity of knowledge. Data from the literature on AIV survival are rather limited, often very old an sometimes not confirmed from one study to another or even contradictory. The results obtained with various sub-types of influenza A viruses cannot be extrapolated to the current A(H5N1) viruses before a careful consideration. Further, few information is provided regarding the survival of influenza viruses in the air and on surfaces.<br />
<br />
Under this project, 9 institutions directly involved in AIV studies, of which 3 from Asian countries, have joined forces in order to investigate the prevention and control of influenza outbreaks in animal population at present and at time of restocking. More precisely, the objectives are:<br />
* to understand the basis of virus survival from a virological point of view,<br />
* to understand the impact of physical and chemical elements on virus survival,<br />
* to evaluate the role of environmental reservoirs,<br />
* to propose general protocols for the concentration and detection of AIVs in waters, including waste waters, and in different matrices including food,<br />
* to provide a database together with analytical tools to allow the generation of evidence based guidelines for the prevention and control of influenza outbreaks in animal and human populations, especially at times of restocking.<br />
<br />
== Participating Institutes ==<br />
<br />
<br />
# '''Institut Pasteur de Paris''' (koordynator projektu) – 25-28 rue du Docteur Roux, 75015, Paris, France<br />
# '''Cantacuzino National Institute of Research and Development Microbiology and Immunology''' – Splaiul Independentei 103, district 5, Bucuresti, 1-525 050096, Romania<br />
# '''The Stephan Angeloff Institute of Microbiology''' – Acad. G. Bonchev Str. 26, Sofia, 1113, Bulgaria<br />
# '''Institut Pasteur du Cambodge''' – 5, Monivong Boulevard, Phnom Penh, 983, Cambodia <br />
# '''Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences''' – Pasteur Institute of Shanghai – 225 South Chong Qing Rd., #2, Shanghai, 200025, China<br />
# '''Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)''' – 42 rue Scheiffer, 75116 Paris, France<br />
# '''Institut Pasteur de Lille''' – 1 rue du Professeur Calmette, 59019, Lille, France<br />
# '''Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw''' – Pawińskiego 5A, Bld. D, Warsaw PL-02-106, Poland<br />
# '''Wuhan Institute of Virology, Chinese Academy of Sciences''' – Xiaohongshan 44, Wuhan, 430071, China<br />
<br />
<!--<br />
== Project objectives ==<br />
--><br />
<br />
== Workpackages ==<br />
<br />
* '''WPG I''': Survival of influenza viruses in waters and aquatic biological systems<br />
* '''WPG II''': Survival of avian influenza viruses in air and surfaces<br />
* '''WPG III''': Modeling and recommendations<br />
* '''WPG IV''': Exploitation and dissemination of the results, Project management<br />
<br />
<!--<br />
== Planned results ==<br />
<br />
== Social dynamics simulations ==<br />
--><br />
<br />
== ICM in RIVERS ==<br />
<br />
ICM coordinates the Work Programme III, in particular the Workpackage 9 - ''Modeling of virus survival and concentration in natural water reservoirs and soiled surfaces''.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Template:Menu_Rivers&diff=402Template:Menu Rivers2009-03-18T15:05:18Z<p>Magd: </p>
<hr />
<div>{| class="riversmenu" align="right" width=100% <br />
! colspan="5" align="left" | <big>Rivers</big><br />
|-<br />
| [[ Research | '''Research''' ]] || [[Software | '''Software''']] || [[Publications | '''Publications''']] || [[People | '''People''' ]] || [[archive | '''Wersja polska''' ]]<br />
|}</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Publications&diff=401Publications2009-03-18T11:28:41Z<p>Magd: New page: * T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008 [http://dx.doi.org/10.1016/j.compbiolchem.20...</p>
<hr />
<div>* T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008 [http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 DOI]<br />
<!-- http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6X1F-4VHS7R5-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=864d504e8ba99e7653d7027d6a993ef3 DOI]--><br />
* Jan P. Radomski and Piotr P. Slonimski, ''ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement – a new method for an alignment-free genome sequence analysis'', Comptes Rendus Biologies 2008 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6X1F-4VHS7R5-1&_user=3934946&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000054122&_version=1&_urlVersion=0&_userid=3934946&md5=9843980cd20c7da16db446af9b7f8439 DOI]<br />
* F. Rakowski, M. Gruziel, M. Krych, J. P. Radomski, ''Large scale social mobility model - an individual based countrywide simulation study for Poland'', submitted</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=400Research2009-03-17T17:19:50Z<p>Magd: </p>
<hr />
<div><!--Menu Rivers}}--><br />
<br />
=== Epidemic simulations ===<br />
<br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
Virtual society exists only in the computer memory. However, in our model, it represents and reproduces the real, Polish, society. Virtual society consists of individual (distinguishable) agents, each assigned to certain, geo-referenced, household. Further, household inhabitants, depending on their age should be either retired, employed or going to school (kindergarten, primary school, secondary school, college, university). All these basic relations should be reflected in the virtual model. This virtual society was based on accessible data. Depending on the data available and on the particular infrastructure element that was to be incorporated into the virtual society, we developed a set of methods. <br />
<br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
<br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future. <br />
<br />
=== Genetic studies ===<br />
<br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
<br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Research&diff=399Research2009-03-17T17:13:22Z<p>Magd: New page: <!--Menu Rivers}}--> === Epidemic simulations === ==== A virtual Polish society ==== ==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish vi...</p>
<hr />
<div><!--Menu Rivers}}--><br />
<br />
=== Epidemic simulations ===<br />
<br />
==== [[ Virtual_society | A virtual Polish society ]] ====<br />
<br />
==== [[Epidemics:poland | Agent Based Model of epidemic within the Polish virtual society ]] ====<br />
<br />
==== [[Epidemics:guineapigs | Agent Based Model of the infection spread within a small population of Guinea pigs, dependent on temperature and humidity conditions of the surroundings ]] ==== <br />
<br />
<br />
<br />
=== Genetic studies ===<br />
<br />
==== [[Epidemics:virus_evolution | Dynamics of influenza virus strains ]] ====<br />
<br />
==== [[Genetic:isscor | Alignment-free genome sequence analysis ]] ====<br />
<br />
Synonymous codons do not occur at equal frequencies. Codon usage and codon bias have been extensively studied. However, the sequential order in which synonymous codons appear within a gene has not been studied until now. Here we describe an in silico method, which is the first attempt to tackle this problem: to what extent this sequential order is unique, and to what extent the succession of synonymous codons is important. This method, which we called Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR), generates, by a Monte Carlo approach, a set of genes which code for the same amino acid sequence, and display the same codon usage, but have random permutations of the synonymous codons, and therefore different sequential codon orders from the original gene. We analyze the complete genome of the bacterium Helicobacter pylori (containing 1574 protein coding genes), and show by various, alignment-free computational methods (e.g., frequency distribution of codon-pairs, as well as that of nucleotide bigrams in codon-pairs), that: (i) not only the succession of adjacent synonymous codons is far from random, but also, which is totally unexpected, the occurrences of non-adjacent synonymous codon-pairs are highly constrained, at strikingly long distances of dozens of nucleotides; (ii) the statistical deviations from the random synonymous codon order are overwhelming; and (iii) the pattern of nucleotide bigrams in codon-pairs can be used in a novel way for characterizing and comparing genes and genomes. Our results demonstrate that the sequential order of synonymous codons within a gene must be under a strong selective pressure, which is superimposed on the classical codon usage. This new dimension can be measured by the ISSCOR method, which is simple, robust, and should be useful for comparative and functional genomics.</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Epidemics:guineapigs&diff=397Epidemics:guineapigs2009-02-11T14:29:04Z<p>Magd: </p>
<hr />
<div>{{Menu epidemics-guineapigs}}<br />
<br />
<br/><br/><br />
<br/><br/><br />
<br />
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility values which seem to be sufficiently accurate to provide partial input for an intended large-scale epidemiological study in the near future.<br />
<br />
<br />
The model described in the Data, Model, Results tabs has been published:<br />
<br />
[http://dx.doi.org/10.1016/j.compbiolchem.2008.12.001 T. Żuk, F. Rakowski, J. P. Radomski, ''A model of influenza virus spread as a function of temperature and humidity'', Comput.Chem.Biol. 2008]</div>Magdhttp://rivers.icm.edu.pl/index.php?title=Epidemics:guineapigs:results&diff=396Epidemics:guineapigs:results2009-02-11T14:20:41Z<p>Magd: </p>
<hr />
<div>{{Menu epidemics-guineapigs}}<br />
<br />
<br/><br/><br />
<br/><br/><br />
<br />
<br />
The obtained classification of experimental points in the parameter space is shown graphically in Figure 2.<br />
<br />
{|border="none", align="center"<br />
|-<br />
| [[Image:flu_spread_model_zuk_rakowski_radomski_Fig2a.gif |400px|left| '''Fig.2a''']] || [[Image:flu_spread_model_zuk_rakowski_radomski_Fig2b.gif |400px|right| '''Fig.2b''' ]]<br />
|- <br />
| colspan="2" | '''Fig. 2: Classification of the parameter sets for (a) 20<math>^\mathrm{o}</math>C and (b) 5<math>^\mathrm{o}</math>C. For both temperatures, each humidity value sets a single compact area in the parameter space. The curved surfaces are boundaries between those areas; the respective humidity values are indicated by the color of the appropriate region of the vertical slice surface. The dark surface on (a) is drawn between the 20% and 65% areas'''<br />
|}<br />
<br />
<br />
The most striking feature is that neither of the parameter sets has been classified to 35% humidity for 20<math>^\mathrm{o}</math>C (the lack of 80% points for 20<math>^\mathrm{o}</math>C is due to lack of the corresponding virus transmission, and of 20% points for 5<math>^\mathrm{o}</math>C, of an appropriate data, respectively). Also the points belonging to 20% humidity lie only in a quite narrow range of high, and rather unexpected, <math>\alpha_2</math> values. We consider the occurrence of late infections in the corresponding experiments, together with the lack of infections on intermediate days, to be a possible cause of this behavior. Indeed, in our model such a situation is most similar to the distributions provided by surprisingly high values of <math>\alpha_2</math>. But this could never be typical because the infection probability is always a decreasing function of time, at least from the 3rd day. However, during Monte Carlo simulations, it is possible sometimes to obtain results that display this feature, even for quite reasonable parameters. Due to the experimental data set limitations, involving a rather small number of animals, it is not easy to determine whether those late infections are simply fluctuations, or rather a symptom of a certain phenomenon the model does not yet take into consideration.<br />
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Another striking feature of the classification for 20<math>^\mathrm{o}</math>C is the fact that the 50% humidity area is placed uppermost, above the areas representing 20% and 65% humidity. This is not consistent with the above-mentioned pattern of transmission dependency on relative humidity that was observed in the experimental results. Indeed, there was a local minimum of transmission observed at this humidity value, and therefore we would rather expect <math>\gamma</math> values in corresponding parameter sets to be smaller, not larger than the rest. This divergence is probably due to the extreme limitation of available data&#8212;as the virus transmission under these conditions was at a low level, only two infection cases occurred. This resulted in a very small, unrealistic standard deviation for the distribution of infection days. Thus, the distance between the simulation results for parameters expected to be relevant and the corresponding experimental result was much greater than it should be and exceeded the distance to the closest improper condition set. On the other hand, a small <math>\sigma</math> value corresponds to the situation that occurs in the model when <math>\gamma</math> is very high&#8212;nearly all pigs become infected on the 1st day. This might be a possible explanation why the parameter sets with high <math>\gamma</math> values have been classified to this humidity level conditions.<br />
<br />
For 5<math>^\mathrm{o}</math>C the least distances (with all experimental points included) appear for the four sets of <math>\alpha_1</math> and <math>\alpha_2</math> values shown in Table 4.<br />
Possible values of <math>\gamma</math> for particular humidity levels at this temperature, provided those values of alphas, are shown in Figure 3. They seem to be consistent with the experimental results of Lowen ''et al.''<ref name="lowen2007">Lowen A C, Mubareka S, Steel J, Palese P, ''Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature'', PLoS Pathogens 3(10), 2007, p151</ref><br />
<br />
<br />
{|align="center" class="rtable" width="50%"<br />
|+ | '''Tab. 4: The four <math>\alpha_1</math> and <math>\alpha_2</math> value sets for which minimal distances at 5<math>^\mathrm{o}</math>C appear, with all humidity values being represented'''<br />
|-<br />
! <math>\alpha_1</math> <br />
| 0.35 || 0.40 || 0.45 || 0.50<br />
|-<br />
! <math>\alpha_2</math><br />
| 0.00 || 0.00 || 0.02 || 0.02<br />
|-<br />
|}<br />
<br />
<br />
{|border="none", align="center"<br />
|-<br />
| [[Image:flu_spread_model_zuk_rakowski_radomski_Fig3a.png |400px|left| '''Fig.3a''']] || [[Image:flu_spread_model_zuk_rakowski_radomski_Fig3b.png |400px|right| '''Fig.3b''' ]]<br />
|- <br />
| colspan="2" | '''Fig. 3: Gamma vs. humidity for 5<math>^\mathrm{o}</math>C and (<math>\alpha_1</math>, <math>\alpha_2</math>) equal (0.35,&nbsp;0) and (0.45,&nbsp;0.02) respectively. Only the points for which the distance is not greater than 0.8 are shown'''<br />
|}<br />
<br />
<br />
For 20<math>^\mathrm{o}</math>C the minimal distances (of about 0.2) to the 65% humidity experimental result occur, with the above alphas, for <math>\gamma</math> values 0.04&#8212;0.045. This is the only conclusion that appears reasonable since the experimental data for other humidity values are probably distorted by statistical fluctuations, arising from the insufficient number of cases. The ''V''-space distances between any point classified to 20% or 50% humidity and the appropriate experimental result are greater than most of the distances between particular experimental results, indicating that the classification for this temperature is not satisfactory. Due to the sparseness of experimental data, it would be interesting to search for another metric that does not rely on the distribution of the days on which infection occurred. Or, possibly, to calibrate our simulation model with a significantly larger experimental data set. Nevertheless, we consider the correlation between experimental and simulation results to be sufficient for the purpose of using transmissibility values obtained from this simple model as one of the inputs for intended large-scale epidemiological studies in the near future.<br />
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== References ==<br />
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<references/></div>Magd