Difference between revisions of "Burkholderia pseudomallei: Dose Response Models"

From QMRAwiki
Jump to: navigation, search
Line 1: Line 1:
 
{{Buttons - Burkholderia Pseudomallei: Dose Response Models}}
 
{{Buttons - Burkholderia Pseudomallei: Dose Response Models}}
 
==<center>'''''Burkholderia pseudomallei'''''</center>==
 
  
 
<center><big>'''Author: Mark H. Weir'''</big></center>
 
<center><big>'''Author: Mark H. Weir'''</big></center>
Line 7: Line 5:
  
  
==='''Overview: ''Burkholderia and meliodosis''===
+
='''Overview: ''Burkholderia and meliodosis''=
  
 
Melioidosis, which typically infects horses, mules and donkeys but can also present a potentially life threatening disease in humans as well, is caused by the bacterium ''Bukholderia pseudomallei ''(''B. pseudomallei''). The bacterium is present in numerous tropical regions such as Central and South America and Southeast Asia. ''Burkholderia mallei ''(''B. mallei'') is a close relative of ''B. pseudomallei'' both of which have been categorized as a B level bioterror agent by the CDC. No dose response models are available for ''B. mallei''.
 
Melioidosis, which typically infects horses, mules and donkeys but can also present a potentially life threatening disease in humans as well, is caused by the bacterium ''Bukholderia pseudomallei ''(''B. pseudomallei''). The bacterium is present in numerous tropical regions such as Central and South America and Southeast Asia. ''Burkholderia mallei ''(''B. mallei'') is a close relative of ''B. pseudomallei'' both of which have been categorized as a B level bioterror agent by the CDC. No dose response models are available for ''B. mallei''.
 
----
 
 
==='''Summary Data'''===
 
 
Brett, P.J. and Woods, D.E.(2000) Pathogenesis of and Immunity to Melioidosis ''Acta Tropica'' '''74''': 201-210
 
 
Miller, W.R., Pannel, I., Cravitz, I., Tanner, W.A., Rosebury, T. (1947) Studies on Certain Biological Characteristics of ''Melleomyces mallei'' and ''Malleomyces pseudomallei'' II. Virulence and Infectivity for Animals ''Journal of Bacteriology'' '''55''': 127-135
 
 
 
{{DRSummaryTableStart|agent=''Burkholderia pseudomallei''}}
 
{{DRSummaryTablePreferredModel|expID=18|refer = Brett and Woods 2000|reference=Brett, P.J. and Woods, D.E.(2000) [http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=271036&_user=1111158&_pii=S0001706X99000716&_check=y&_origin=&_coverDate=05-Feb-2000&view=c&wchp=dGLzVBA-zSkWA&md5=1de3999eee66ca154743edbc00367cc3/1-s2.0-S0001706X99000716-main.pdf Pathogenesis of and Immunity to Melioidosis] ''Acta Tropica'' '''74''': 201-210|host= mouse |agentStrain= KHW |route= intranasal |nDoses= 5 |doseUnits= CFU |response= Infection  |bestFitModel=exponential|parameters=k =  1.00E-04 |N50= 6.92E+03 }}
 
{{DRSummaryNonpreferredModel|expID= 17 |refer = Brett and Woods 2000|reference=Brett, P.J. and Woods, D.E.(2000) [http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=271036&_user=1111158&_pii=S0001706X99000716&_check=y&_origin=&_coverDate=05-Feb-2000&view=c&wchp=dGLzVBA-zSkWA&md5=1de3999eee66ca154743edbc00367cc3/1-s2.0-S0001706X99000716-main.pdf Pathogenesis of and Immunity to Melioidosis] ''Acta Tropica'' '''74''': 201-210 |host= mouse |agentStrain= KHW |route= intranasal |nDoses= 5 |doseUnits= CFU |response= Infection  |bestFitModel=exponential|parameters=k =  1.04E-02 |N50= 6.63E+01 }}
 
{{DRSummaryTableNonpreferredModel|expID= 21 |refer = Miller 1947|reference=Miller, W.R., Pannel, I., Cravitz, I., Tanner, W.A., Rosebury, T. (1947) Studies on Certain Biological Characteristics of ''Melleomyces mallei'' and ''Malleomyces pseudomallei'' II. Virulence and Infectivity for Animals ''Journal of Bacteriology'' '''55''': 127-135|host= guinea pig |agentStrain= W294 |route= intraperitoneal |nDoses= 6 |doseUnits= CFU |response= death |bestFitModel=beta-Poisson|parameters=&alpha; =  2.67E-01 , N<sub>50</sub> =  2.55E+02 |N50= 2.55E+02 }}
 
{{DRSummaryTableEnd}}
 
 
=== '''<sup>*</sup> Recommended Model''' ===
 
 
Since intranasal exposure is closer to inhalation which is the likeliest exposure route for humans, especially compared to intraperitoneal, the data sets and resulting models from the Brett and Woods (2000) article is preferred.  Also given the improved fit between the two data sets experiment 18 is chosen as the recommended model.
 
 
a:[[File:Exponential and betapoisson model.jpg|thumb|none|550px]]
 
 
----
 
 
===Optimization Output for experiment 18===
 
 
{{DRExperimentDataTable5|title=C57BL/6 Mice KHW Strain Data|refer = Brett and Woods 2000|reference=Brett, P.J. and Woods, D.E.(2000) [http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=271036&_user=1111158&_pii=S0001706X99000716&_check=y&_origin=&_coverDate=05-Feb-2000&view=c&wchp=dGLzVBA-zSkWA&md5=1de3999eee66ca154743edbc00367cc3/1-s2.0-S0001706X99000716-main.pdf Pathogenesis of and Immunity to Melioidosis] ''Acta Tropica'' '''74''': 201-210|pos=Infected|neg=Non-infected |d1=150|p1=0|n1=6|t1=6|d2=450|p2=1|n2=5|t2=6|d3=1350|p3=1|n3=5|t3=6|d4=4050|p4=3|n4=3|t4=6|d5=12200|p5=3|n5=3|t5=6}}
 
 
 
{{DRFit|filename=ADDFILENAMEHERE.xls|tablenum=ADDTABLENUMBERHERE|title=Goodness of fit and model selection|devE=3.36|devB=1.19|delta=2.17|DFE=4|DFB=3|X2bPbetter=3.84|pbPbetter=0.141|X2GOFe=9.49|pGOFe=0.499|X2GOFb=7.81|pGOFb=0.755|interpretation=Exponential is preferred to beta-Poisson; cannot reject good fit for exponential.}}
 
 
 
{{DRConfidenceExponential|filename=ADDFILENAMEHERE.xls|tablenum=ADDTABLENUMBERHERE|title=Optimized parameters for the exponential model, from 10000 bootstrap iterations|MLEk=1E-04|p5k=2.87E-05|p25k=4.15E-05|p50k=4.99E-05|p950k=1.89E-04|p975k=2.13E-04|p995k=2.70E-04|N50type=ID50/LD50/ETC|MLEN=6.92E+03|p5N=2.57E+03|p25N=3.26E+03|p50N=3.68E+03|p950N=1.39E+04|p975N=1.67E+04|p995N=2.41E+04}}
 
 
 
 
[[File:ExpHisto ID18.png|thumb|left|500px|'''Parameter histogram for exponential model (uncertainty of the parameter)''']][[File:ExpModel ID18.png|thumb|none|500px|'''Exponential model plot, with confidence bounds around optimized model''']]<br>
 
 
 
===Optimization Output for experiment 17===
 
 
{{DRExperimentDataTable5|title=BALB/c Mice KHW Strain Data|refer = Brett and Woods 2000|reference=Brett, P.J. and Woods, D.E.(2000) [http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=271036&_user=1111158&_pii=S0001706X99000716&_check=y&_origin=&_coverDate=05-Feb-2000&view=c&wchp=dGLzVBA-zSkWA&md5=1de3999eee66ca154743edbc00367cc3/1-s2.0-S0001706X99000716-main.pdf Pathogenesis of and Immunity to Melioidosis] ''Acta Tropica'' '''74''': 201-210 |pos=Infected|neg=Non-infected |d1=5|p1=0|n1=6|t1=6|d2=15|p2=0|n2=6|t2=6|d3=45|p3=3|n3=1|t3=4|d4=135|p4=4|n4=2|t4=6|d5=405|p5=6|n5=0|t5=6}}
 
 
 
{{DRFit|filename=ADDFILENAMEHERE.xls|tablenum=ADDTABLENUMBERHERE|title=Goodness of fit and model selection|devE=5.25|devB=5.25|delta=-0.000362|DFE=4|DFB=3|X2bPbetter=3.84|pbPbetter=1|X2GOFe=9.49|pGOFe=0.263|X2GOFb=7.81|pGOFb=0.154|interpretation=Exponential is preferred to beta-Poisson; cannot reject good fit for exponential.}}
 
 
 
{{DRConfidenceExponential|filename=ADDFILENAMEHERE.xls|tablenum=ADDTABLENUMBERHERE|title=Optimized parameters for the exponential model, from 10000 bootstrap iterations|MLEk=1.04E-02|p5k=4.94E-03|p25k=5.96E-03|p50k=6.60E-03|p950k=1.92E-02|p975k=2.45E-02|p995k=2.45E-02|N50type=ID50/LD50/ETC|MLEN=6.63E+01|p5N=2.82E+01|p25N=2.82E+01|p50N=3.61E+01|p950N=1.05E+02|p975N=1.16E+02|p995N=1.40E+02}}
 
 
 
[[File:ExpHisto ID17.png|thumb|left|500px|'''Parameter histogram for exponential model (uncertainty of the parameter)''']][[File:ExpModel ID17.png|thumb|none|500px|'''Exponential model plot, with confidence bounds around optimized model''']]<br>
 
 
 
===Optimization Output for experiment 21===
 
 
{{DRExperimentDataTable6|title=Guinea Pigs W294 Strain Data|refer = Miller 1947|reference=Miller, W.R., Pannel, I., Cravitz, I., Tanner, W.A., Rosebury, T. (1947) Studies on Certain Biological Characteristics of ''Melleomyces mallei'' and ''Malleomyces pseudomallei'' II. Virulence and Infectivity for Animals ''Journal of Bacteriology'' '''55''': 127-135
 
|pos=Dead|neg=Survived|d1=44|p1=1|n1=4|t1=5|d2=440|p2=3|n2=2|t2=5|d3=4400|p3=4|n3=1|t3=5|d4=44000|p4=5|n4=0|t4=5|d5=440000|p5=5|n5=0|t5=5|d6=4.4E+06|p6=4|n6=1|t6=5}}
 
 
 
{{DRFit|filename=ADDFILENAMEHERE.xls|tablenum=ADDTABLENUMBERHERE|title=Goodness of fit and model selection|devE=70.3|devB=4.14|delta=66.1|DFE=5|DFB=4|X2bPbetter=3.84|pbPbetter=4.44e-16|X2GOFe=11.1|pGOFe=8.93e-14|X2GOFb=9.49|pGOFb=0.387|interpretation=Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.}}
 
 
 
{{DRConfidenceBetaPoisson|filename=ADDFILENAMEHERE.xls|tablenum=ADDTABLENUMBERHERE|title=Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations|MLEa=2.67E-01|p5a=3.36E-02|p25a=8.80E-02|p50a=1.16E-01|p950a=1.05E+01|p975a=3.45E+02|p995a=3.55E+03|MLEN=2.55E+02|p5N=4.80E-07|p25N=2.49E+00|p50N=1.48E+01|p950N=1.35E+03|p975N=1.80E+03|p995N=3.22E+03}}
 
 
 
[[File:BPscatter ID21.png|thumb|left|500px|'''Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.''']][[File:BPmodel ID21.png|thumb|none|500px|'''beta Poisson model plot, with confidence bounds around optimized model''']]<br>
 
 
 
=== References ===
 
<references />
 
 
[[Category:Completed Dose Response Models: Bacteria]][[Category:Dose Response Model]][[Category:Burkholderia]]
 

Revision as of 01:53, 22 August 2012

Template:Buttons - Burkholderia Pseudomallei: Dose Response Models

Author: Mark H. Weir
If you want to download this chapter in pdf format, please click here


Overview: Burkholderia and meliodosis

Melioidosis, which typically infects horses, mules and donkeys but can also present a potentially life threatening disease in humans as well, is caused by the bacterium Bukholderia pseudomallei (B. pseudomallei). The bacterium is present in numerous tropical regions such as Central and South America and Southeast Asia. Burkholderia mallei (B. mallei) is a close relative of B. pseudomallei both of which have been categorized as a B level bioterror agent by the CDC. No dose response models are available for B. mallei.