http://vaccipedia.jp/api.php?action=feedcontributions&user=Vaccipedia.admin&feedformat=atomVaccipedia | Resources for Vaccines, Tropical medicine and Travel medicine - 利用者の投稿記録 [ja]2024-03-29T12:46:17Z利用者の投稿記録MediaWiki 1.34.0http://vaccipedia.jp/index.php?title=Basics_%26_Definition&diff=3078Basics & Definition2023-12-14T07:02:09Z<p>Vaccipedia.admin: /* Types of variable */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Self-assessment quizzes==<br />
*[https://www.cdc.gov/csels/dsepd/ss1978/index.html CDC Principles of Epidemiology]<br />
*[https://www.med.soton.ac.uk/stats_eLearning/quizzes/index.html Statistics - University of Southampton]<br />
*[https://collegedunia.com/exams/statistics-mcq-mathematics-articleid-4505]<br />
<br />
==Types of variable==<br />
{{#mermaid:<br />
flowchart TB<br />
a[Variable]<br />
b[*Quantitative<br>*Numerical]<br />
c[*Categorical<br>*Nominal]<br />
d[Continuous]<br />
e[Discrete<br>Integer]<br />
f[Binary<br>Dichotomous]<br />
g[Non-ordinal<br>Non-ordered]<br />
h[Ordinal<br>Ordered]<br />
a --- b & c<br />
b --- d & e<br />
c --- f & g & h<br />
}}<br />
* *Quantitative/numerical variable is also called as '''covariate''' when it is an explanatory (independent) variable<br />
* *Categorical/nominal variable is also called as '''factor''' when it is an explanatory (independent) variable<br />
<br />
==Ratio, Rate, Proportion==<br />
Every fraction is ratio.<br />
<br />
[https://sphweb.bumc.bu.edu/otlt/MPH-Modules/PH717-QuantCore/PH717_BasicQuantitativeConcepts/PH717_BasicQuantitativeConcepts4.html Refer to this page too]<br />
<br />
{{#mermaid:<br />
flowchart TB<br />
a[Ratio<br> = all fractions] -- ratio of part to whole ---b[Proportion]<br />
a -- ratio of quantity in time-scale ---c[Rate]<br />
}}<br />
<br />
==Probability, Likelihood==<br />
<br />
--> ''see'' [[Data distribution#Probability, Likelihood|'Probability, Likelihood' in 'Data distribution']]<br />
<br />
==Origin of terminology==<br />
===Why is it called "''Z''"?===<br />
<br />
===Why is it called "''Student's t''"?===<br />
William Gosset was a mathematician around the 19th to 20th century as well as he worked for the famous brewery Guinness. [https://www.geo.fu-berlin.de/en/v/soga/Basics-of-statistics/Continous-Random-Variables/Students-t-Distribution/index.html He found a new statistical distribution but Guinness did not allow their employees to publish any papers related to their business confidential affairs. Thus Gosset published his achievement under a nickname of ''Student''].<br />
<br />
[https://www.jstor.org/stable/2683058 ''t'' itself was later named through correspondences between Gosset and a statistician R.A. Fisher]. The first description of ''t'' is appeared on [https://digital.library.adelaide.edu.au/dspace/bitstream/2440/15183/1/36.pdf the article by Fisher in 1924].<br />
<br />
===Why is it called "''regression''"?===<br />
In the 19th century, Sir Francis Galton investigated association between parents' heights and their offspring's heights. He found association between them had some characteristics that the higher the parents were the higher the offspring are but the offspring tended to shorter than their parents, and vise versa. [https://www.biostat.jhsph.edu/courses/bio653/misc/JMPer%20Cable%20Summer%2098%20Why%20is%20it%20called%20Regression.htm He described the association as 'offspring's heights to ''regress'' (go back) towards mediocrity (average)'].<br />
<br />
Since then [https://www.sciencedirect.com/science/article/abs/pii/S0039368120302090 ''regression to the mean''] has expanded to the regression model which provides the estimates of association between one dependent variable and one or more independent variables by a line.<br />
<br />
===Why is it called "''logistic''"?===<br />
The true reason remains unclear.<br />
<br />
The French mathematician who created this term Pierre-Fran&ccedil;ois Verhulst first described this word "''logistique''" (Fr.) in his literature in 1845, [https://eudml.org/doc/182533 "Recherches mathématiques sur la loi d'accroissement de la population," in NOUVEAUX MÉMOIRES DE L'ACADÉMIE ROYALE DES SCIENCES ET BELLES-LETTRES DE BRUXELLES, vol. 18, p 3].<br />
<br />
In a figure Verhulst described an usual exponential curve as "''logarithmique''", and created a new word "''logistique''" to describe a distinct curve he created by his formula which is now known as a logistic regression formula, but he didn't note through what derivation he created the word.<br />
<br />
Description of [https://en.wikipedia.org/wiki/Logistic_function#History Logistic function in Wikipedia is here].<br />
<br />
At least, it seems to have nothing to do with a general term "logistics".<br />
<br />
===Why is it called "''bootstrapping''"?===<br />
''Bootstrap'' is a piece of cloth or leather at the back or the side of a boot that is used to help you pull it on. A broader meaning is also added the word as an approach to creating something with the minimum amount of possible resources.<br />
<br />
There is also an idiom or a template expression of [https://en.wiktionary.org/wiki/pull_oneself_up_by_one%27s_bootstraps ''pull oneself up by one's bootstraps''], which means to improve one's situation on one's own efforts without any other's help.<br />
<br />
The method of bootstrapping is to derive new samples from the original observations with replacement, not from other data source, i.e., pulling samples up from themselves, which implies ''pull oneself up by one's bootstraps''.</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Basics_%26_Definition&diff=3077Basics & Definition2023-12-14T06:59:30Z<p>Vaccipedia.admin: /* Types of variable */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Self-assessment quizzes==<br />
*[https://www.cdc.gov/csels/dsepd/ss1978/index.html CDC Principles of Epidemiology]<br />
*[https://www.med.soton.ac.uk/stats_eLearning/quizzes/index.html Statistics - University of Southampton]<br />
*[https://collegedunia.com/exams/statistics-mcq-mathematics-articleid-4505]<br />
<br />
==Types of variable==<br />
{{#mermaid:<br />
flowchart TB<br />
a[Variable]<br />
b[Quantitative<br>Numerical]<br />
bb[Covariate<br>*only as explanatory]<br />
c[Categorical<br>Nominal]<br />
cc[Factor<br>*only as explanatory]<br />
d[Continuous]<br />
e[Discrete<br>Integer]<br />
f[Binary<br>Dichotomous]<br />
g[Non-ordinal<br>Non-ordered]<br />
h[Ordinal<br>Ordered]<br />
a --- b & c<br />
b --- bb --- d & e<br />
c --- cc --- f & g & h<br />
}}<br />
<br />
==Ratio, Rate, Proportion==<br />
Every fraction is ratio.<br />
<br />
[https://sphweb.bumc.bu.edu/otlt/MPH-Modules/PH717-QuantCore/PH717_BasicQuantitativeConcepts/PH717_BasicQuantitativeConcepts4.html Refer to this page too]<br />
<br />
{{#mermaid:<br />
flowchart TB<br />
a[Ratio<br> = all fractions] -- ratio of part to whole ---b[Proportion]<br />
a -- ratio of quantity in time-scale ---c[Rate]<br />
}}<br />
<br />
==Probability, Likelihood==<br />
<br />
--> ''see'' [[Data distribution#Probability, Likelihood|'Probability, Likelihood' in 'Data distribution']]<br />
<br />
==Origin of terminology==<br />
===Why is it called "''Z''"?===<br />
<br />
===Why is it called "''Student's t''"?===<br />
William Gosset was a mathematician around the 19th to 20th century as well as he worked for the famous brewery Guinness. [https://www.geo.fu-berlin.de/en/v/soga/Basics-of-statistics/Continous-Random-Variables/Students-t-Distribution/index.html He found a new statistical distribution but Guinness did not allow their employees to publish any papers related to their business confidential affairs. Thus Gosset published his achievement under a nickname of ''Student''].<br />
<br />
[https://www.jstor.org/stable/2683058 ''t'' itself was later named through correspondences between Gosset and a statistician R.A. Fisher]. The first description of ''t'' is appeared on [https://digital.library.adelaide.edu.au/dspace/bitstream/2440/15183/1/36.pdf the article by Fisher in 1924].<br />
<br />
===Why is it called "''regression''"?===<br />
In the 19th century, Sir Francis Galton investigated association between parents' heights and their offspring's heights. He found association between them had some characteristics that the higher the parents were the higher the offspring are but the offspring tended to shorter than their parents, and vise versa. [https://www.biostat.jhsph.edu/courses/bio653/misc/JMPer%20Cable%20Summer%2098%20Why%20is%20it%20called%20Regression.htm He described the association as 'offspring's heights to ''regress'' (go back) towards mediocrity (average)'].<br />
<br />
Since then [https://www.sciencedirect.com/science/article/abs/pii/S0039368120302090 ''regression to the mean''] has expanded to the regression model which provides the estimates of association between one dependent variable and one or more independent variables by a line.<br />
<br />
===Why is it called "''logistic''"?===<br />
The true reason remains unclear.<br />
<br />
The French mathematician who created this term Pierre-Fran&ccedil;ois Verhulst first described this word "''logistique''" (Fr.) in his literature in 1845, [https://eudml.org/doc/182533 "Recherches mathématiques sur la loi d'accroissement de la population," in NOUVEAUX MÉMOIRES DE L'ACADÉMIE ROYALE DES SCIENCES ET BELLES-LETTRES DE BRUXELLES, vol. 18, p 3].<br />
<br />
In a figure Verhulst described an usual exponential curve as "''logarithmique''", and created a new word "''logistique''" to describe a distinct curve he created by his formula which is now known as a logistic regression formula, but he didn't note through what derivation he created the word.<br />
<br />
Description of [https://en.wikipedia.org/wiki/Logistic_function#History Logistic function in Wikipedia is here].<br />
<br />
At least, it seems to have nothing to do with a general term "logistics".<br />
<br />
===Why is it called "''bootstrapping''"?===<br />
''Bootstrap'' is a piece of cloth or leather at the back or the side of a boot that is used to help you pull it on. A broader meaning is also added the word as an approach to creating something with the minimum amount of possible resources.<br />
<br />
There is also an idiom or a template expression of [https://en.wiktionary.org/wiki/pull_oneself_up_by_one%27s_bootstraps ''pull oneself up by one's bootstraps''], which means to improve one's situation on one's own efforts without any other's help.<br />
<br />
The method of bootstrapping is to derive new samples from the original observations with replacement, not from other data source, i.e., pulling samples up from themselves, which implies ''pull oneself up by one's bootstraps''.</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Basics_%26_Definition&diff=3076Basics & Definition2023-12-14T06:59:03Z<p>Vaccipedia.admin: /* Types of variable */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Self-assessment quizzes==<br />
*[https://www.cdc.gov/csels/dsepd/ss1978/index.html CDC Principles of Epidemiology]<br />
*[https://www.med.soton.ac.uk/stats_eLearning/quizzes/index.html Statistics - University of Southampton]<br />
*[https://collegedunia.com/exams/statistics-mcq-mathematics-articleid-4505]<br />
<br />
==Types of variable==<br />
{{#mermaid:<br />
flowchart TB<br />
a[Variable]<br />
b[Quantitative<br>Numerical]<br />
bb[Covariate<br>(only as explanatory)]<br />
c[Categorical<br>Nominal]<br />
cc[Factor<br>(only as explanatory)]<br />
d[Continuous]<br />
e[Discrete<br>Integer]<br />
f[Binary<br>Dichotomous]<br />
g[Non-ordinal<br>Non-ordered]<br />
h[Ordinal<br>Ordered]<br />
a --- b & c<br />
b --- bb --- d & e<br />
c --- cc --- f & g & h<br />
}}<br />
<br />
==Ratio, Rate, Proportion==<br />
Every fraction is ratio.<br />
<br />
[https://sphweb.bumc.bu.edu/otlt/MPH-Modules/PH717-QuantCore/PH717_BasicQuantitativeConcepts/PH717_BasicQuantitativeConcepts4.html Refer to this page too]<br />
<br />
{{#mermaid:<br />
flowchart TB<br />
a[Ratio<br> = all fractions] -- ratio of part to whole ---b[Proportion]<br />
a -- ratio of quantity in time-scale ---c[Rate]<br />
}}<br />
<br />
==Probability, Likelihood==<br />
<br />
--> ''see'' [[Data distribution#Probability, Likelihood|'Probability, Likelihood' in 'Data distribution']]<br />
<br />
==Origin of terminology==<br />
===Why is it called "''Z''"?===<br />
<br />
===Why is it called "''Student's t''"?===<br />
William Gosset was a mathematician around the 19th to 20th century as well as he worked for the famous brewery Guinness. [https://www.geo.fu-berlin.de/en/v/soga/Basics-of-statistics/Continous-Random-Variables/Students-t-Distribution/index.html He found a new statistical distribution but Guinness did not allow their employees to publish any papers related to their business confidential affairs. Thus Gosset published his achievement under a nickname of ''Student''].<br />
<br />
[https://www.jstor.org/stable/2683058 ''t'' itself was later named through correspondences between Gosset and a statistician R.A. Fisher]. The first description of ''t'' is appeared on [https://digital.library.adelaide.edu.au/dspace/bitstream/2440/15183/1/36.pdf the article by Fisher in 1924].<br />
<br />
===Why is it called "''regression''"?===<br />
In the 19th century, Sir Francis Galton investigated association between parents' heights and their offspring's heights. He found association between them had some characteristics that the higher the parents were the higher the offspring are but the offspring tended to shorter than their parents, and vise versa. [https://www.biostat.jhsph.edu/courses/bio653/misc/JMPer%20Cable%20Summer%2098%20Why%20is%20it%20called%20Regression.htm He described the association as 'offspring's heights to ''regress'' (go back) towards mediocrity (average)'].<br />
<br />
Since then [https://www.sciencedirect.com/science/article/abs/pii/S0039368120302090 ''regression to the mean''] has expanded to the regression model which provides the estimates of association between one dependent variable and one or more independent variables by a line.<br />
<br />
===Why is it called "''logistic''"?===<br />
The true reason remains unclear.<br />
<br />
The French mathematician who created this term Pierre-Fran&ccedil;ois Verhulst first described this word "''logistique''" (Fr.) in his literature in 1845, [https://eudml.org/doc/182533 "Recherches mathématiques sur la loi d'accroissement de la population," in NOUVEAUX MÉMOIRES DE L'ACADÉMIE ROYALE DES SCIENCES ET BELLES-LETTRES DE BRUXELLES, vol. 18, p 3].<br />
<br />
In a figure Verhulst described an usual exponential curve as "''logarithmique''", and created a new word "''logistique''" to describe a distinct curve he created by his formula which is now known as a logistic regression formula, but he didn't note through what derivation he created the word.<br />
<br />
Description of [https://en.wikipedia.org/wiki/Logistic_function#History Logistic function in Wikipedia is here].<br />
<br />
At least, it seems to have nothing to do with a general term "logistics".<br />
<br />
===Why is it called "''bootstrapping''"?===<br />
''Bootstrap'' is a piece of cloth or leather at the back or the side of a boot that is used to help you pull it on. A broader meaning is also added the word as an approach to creating something with the minimum amount of possible resources.<br />
<br />
There is also an idiom or a template expression of [https://en.wiktionary.org/wiki/pull_oneself_up_by_one%27s_bootstraps ''pull oneself up by one's bootstraps''], which means to improve one's situation on one's own efforts without any other's help.<br />
<br />
The method of bootstrapping is to derive new samples from the original observations with replacement, not from other data source, i.e., pulling samples up from themselves, which implies ''pull oneself up by one's bootstraps''.</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Basics_%26_Definition&diff=3075Basics & Definition2023-12-14T06:55:17Z<p>Vaccipedia.admin: /* Types of variable */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Self-assessment quizzes==<br />
*[https://www.cdc.gov/csels/dsepd/ss1978/index.html CDC Principles of Epidemiology]<br />
*[https://www.med.soton.ac.uk/stats_eLearning/quizzes/index.html Statistics - University of Southampton]<br />
*[https://collegedunia.com/exams/statistics-mcq-mathematics-articleid-4505]<br />
<br />
==Types of variable==<br />
{{#mermaid:<br />
flowchart TB<br />
a[Variable]<br />
b[Quantitative<br>Numerical]<br />
bb[=Covariate]<br />
c[Categorical<br>Nominal]<br />
cc[=Factor]<br />
d[Continuous]<br />
e[Discrete<br>Integer]<br />
f[Binary<br>Dichotomous]<br />
g[Non-ordinal<br>Non-ordered]<br />
h[Ordinal<br>Ordered]<br />
a --- b & c<br />
b --- bb --- d & e<br />
c --- cc --- f & g & h<br />
}}<br />
<br />
==Ratio, Rate, Proportion==<br />
Every fraction is ratio.<br />
<br />
[https://sphweb.bumc.bu.edu/otlt/MPH-Modules/PH717-QuantCore/PH717_BasicQuantitativeConcepts/PH717_BasicQuantitativeConcepts4.html Refer to this page too]<br />
<br />
{{#mermaid:<br />
flowchart TB<br />
a[Ratio<br> = all fractions] -- ratio of part to whole ---b[Proportion]<br />
a -- ratio of quantity in time-scale ---c[Rate]<br />
}}<br />
<br />
==Probability, Likelihood==<br />
<br />
--> ''see'' [[Data distribution#Probability, Likelihood|'Probability, Likelihood' in 'Data distribution']]<br />
<br />
==Origin of terminology==<br />
===Why is it called "''Z''"?===<br />
<br />
===Why is it called "''Student's t''"?===<br />
William Gosset was a mathematician around the 19th to 20th century as well as he worked for the famous brewery Guinness. [https://www.geo.fu-berlin.de/en/v/soga/Basics-of-statistics/Continous-Random-Variables/Students-t-Distribution/index.html He found a new statistical distribution but Guinness did not allow their employees to publish any papers related to their business confidential affairs. Thus Gosset published his achievement under a nickname of ''Student''].<br />
<br />
[https://www.jstor.org/stable/2683058 ''t'' itself was later named through correspondences between Gosset and a statistician R.A. Fisher]. The first description of ''t'' is appeared on [https://digital.library.adelaide.edu.au/dspace/bitstream/2440/15183/1/36.pdf the article by Fisher in 1924].<br />
<br />
===Why is it called "''regression''"?===<br />
In the 19th century, Sir Francis Galton investigated association between parents' heights and their offspring's heights. He found association between them had some characteristics that the higher the parents were the higher the offspring are but the offspring tended to shorter than their parents, and vise versa. [https://www.biostat.jhsph.edu/courses/bio653/misc/JMPer%20Cable%20Summer%2098%20Why%20is%20it%20called%20Regression.htm He described the association as 'offspring's heights to ''regress'' (go back) towards mediocrity (average)'].<br />
<br />
Since then [https://www.sciencedirect.com/science/article/abs/pii/S0039368120302090 ''regression to the mean''] has expanded to the regression model which provides the estimates of association between one dependent variable and one or more independent variables by a line.<br />
<br />
===Why is it called "''logistic''"?===<br />
The true reason remains unclear.<br />
<br />
The French mathematician who created this term Pierre-Fran&ccedil;ois Verhulst first described this word "''logistique''" (Fr.) in his literature in 1845, [https://eudml.org/doc/182533 "Recherches mathématiques sur la loi d'accroissement de la population," in NOUVEAUX MÉMOIRES DE L'ACADÉMIE ROYALE DES SCIENCES ET BELLES-LETTRES DE BRUXELLES, vol. 18, p 3].<br />
<br />
In a figure Verhulst described an usual exponential curve as "''logarithmique''", and created a new word "''logistique''" to describe a distinct curve he created by his formula which is now known as a logistic regression formula, but he didn't note through what derivation he created the word.<br />
<br />
Description of [https://en.wikipedia.org/wiki/Logistic_function#History Logistic function in Wikipedia is here].<br />
<br />
At least, it seems to have nothing to do with a general term "logistics".<br />
<br />
===Why is it called "''bootstrapping''"?===<br />
''Bootstrap'' is a piece of cloth or leather at the back or the side of a boot that is used to help you pull it on. A broader meaning is also added the word as an approach to creating something with the minimum amount of possible resources.<br />
<br />
There is also an idiom or a template expression of [https://en.wiktionary.org/wiki/pull_oneself_up_by_one%27s_bootstraps ''pull oneself up by one's bootstraps''], which means to improve one's situation on one's own efforts without any other's help.<br />
<br />
The method of bootstrapping is to derive new samples from the original observations with replacement, not from other data source, i.e., pulling samples up from themselves, which implies ''pull oneself up by one's bootstraps''.</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3074Missing data and imputation2023-12-10T08:18:31Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
<hr />
<div>{{Floating Menu}}<br />
<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Missing depends on/<br>Missing occurs because of<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones. Demographic variables are also collected.<br />
|-<br />
!style="width:7em"|missing (unobserved) value itself<br />
!style="width:7em"|other observed variable(s)<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|<big>YES</big><br />
|style="text-align:center"|&mdash;<br />
|<br />
*Some participants '''intentionally denied to report higher body weights they didn't like''' and only reported lower body weights they accepted<br />
*Researchers have no information why they denied to report body weights in several weeks<br />
**Missing occurred '''because of the missing values themselves'''<br />
**Researchers cannot explain/predict the missing mechanism from other observed (reported) body weights or other variables<br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|<big>NO</big><br />
|style="text-align:center"|<big>YES</big><br />
|<br />
*'''15% of female participants denied to report''' their body weights after participation '''regardless of measured body weights''', but only 1% of male denied to report<br />
*Researchers can identify that female participants more likely denied to report body weights than male<br />
**Missing occurred NOT because of body weights themselves but '''because of another variable ''sex'''''<br />
**Missing mechanism is at random, i.e., free from missing values only inside each participant, but NOT at random, i.e., NOT free from variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|<big>NO</big><br />
|style="text-align:center"|<big>NO</big><br />
|<br />
*A participant '''moved to outside cohort area''' because of family affair and was lost to follow up<br />
*A participant '''failed to report body weights because of malfunction of the app'''<br />
**Missing occurred NOT because of body weights themselves NOR other variables<br />
**Missing mechanism is completely at random, i.e., completely free from both of missing (unobserved) values and observed values in body weight or in other variables<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3073Missing data and imputation2023-12-10T08:17:36Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
<hr />
<div>{{Floating Menu}}<br />
<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Missing depends on/<br>Missing occurs because of<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones. Demographic variables are also collected.<br />
|-<br />
!style="width:7em"|missing (unobserved) value itself<br />
!style="width:7em"|other observed variable(s)<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|<big>YES</big><br />
|style="text-align:center"|&mdash;<br />
|<br />
*Some participants '''intentionally denied to report higher body weights they didn't like''' and only reported lower body weights they accepted<br />
*Researchers have no information why they denied to report body weights in several weeks<br />
**Missing occurred '''because of the missing values themselves'''<br />
**Researchers cannot explain/predict the missing mechanism from other observed (reported) body weights or other variables<br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|<big>NO</big><br />
|style="text-align:center"|<big>YES</big><br />
|<br />
*'''15% of female participants denied to report''' their body weights after participation '''regardless of measured body weights''', but only 1% of male denied to report<br />
*Researchers can identify that female participants more likely denied to report body weights than male<br />
**Missing occurred NOT because of body weights themselves but '''because of another variable ''sex'''''<br />
**Missing mechanism is at random, i.e., free from missing values only inside each participant but NOT at random, i.e., NOT free from variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|<big>NO</big><br />
|style="text-align:center"|<big>NO</big><br />
|<br />
*A participant '''moved to outside cohort area''' because of family affair and was lost to follow up<br />
*A participant '''failed to report body weights because of malfunction of the app'''<br />
**Missing occurred NOT because of body weights themselves NOR other variables<br />
**Missing mechanism is completely at random, i.e., completely free from both of missing (unobserved) values and observed values in body weight or in other variables<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3072Missing data and imputation2023-12-10T08:16:19Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Missing depends on/<br>Missing occurs because of<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones. Demographic variables are also collected.<br />
|-<br />
!style="width:7em"|missing (unobserved) value itself<br />
!style="width:7em"|other observed variable(s)<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|YES<br />
|style="text-align:center"|&mdash;<br />
|<br />
*Some participants '''intentionally denied to report higher body weights they didn't like''' and only reported lower body weights they accepted<br />
*Researchers have no information why they denied to report body weights in several weeks<br />
**Missing occurred '''because of the missing values themselves'''<br />
**Researchers cannot explain/predict the missing mechanism from other observed (reported) body weights or other variables<br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|YES<br />
|<br />
*'''15% of female participants denied to report''' their body weights after participation '''regardless of measured body weights''', but only 1% of male denied to report<br />
*Researchers can identify that female participants more likely denied to report body weights than male<br />
**Missing occurred NOT because of body weights themselves but '''because of another variable ''sex'''''<br />
**Missing mechanism is at random, i.e., free from missing values only inside each participant but NOT at random, i.e., NOT free from variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|NO<br />
|<br />
*A participant '''moved to outside cohort area''' because of family affair and was lost to follow up<br />
*A participant '''failed to report body weights because of malfunction of the app'''<br />
**Missing occurred NOT because of body weights themselves NOR other variables<br />
**Missing mechanism is completely at random, i.e., completely free from both of missing (unobserved) values and observed values in body weight or in other variables<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3071Missing data and imputation2023-12-10T08:15:41Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Missing depends on/<br>Missing occurs because of<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones. Demographic variables are also collected.<br />
|-<br />
!style="width:7em"|missing value itself<br />
!style="width:7em"|other observed variable(s)<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|YES<br />
|style="text-align:center"|&mdash;<br />
|<br />
*Some participants '''intentionally denied to report higher body weights they didn't like''' and only reported lower body weights they accepted<br />
*Researchers have no information why they denied to report body weights in several weeks<br />
**Missing occurred '''because of the missing values themselves'''<br />
**Researchers cannot explain/predict the missing mechanism from other observed (reported) body weights or other variables<br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|YES<br />
|<br />
*'''15% of female participants denied to report''' their body weights after participation '''regardless of measured body weights''', but only 1% of male denied to report<br />
*Researchers can identify that female participants more likely denied to report body weights than male<br />
**Missing occurred NOT because of body weights themselves but '''because of another variable ''sex'''''<br />
**Missing mechanism is at random, i.e., free from missing values only inside each participant but NOT at random, i.e., NOT free from variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|NO<br />
|<br />
*A participant '''moved to outside cohort area''' because of family affair and was lost to follow up<br />
*A participant '''failed to report body weights because of malfunction of the app'''<br />
**Missing occurred NOT because of body weights themselves NOR other variables<br />
**Missing mechanism is completely at random, i.e., completely free from both of missing (unobserved) values and observed values in body weight or in other variables<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3070Missing data and imputation2023-12-10T07:13:13Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Missing depends on/<br>Missing occurs because of<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones. Demographic variables are also collected.<br />
|-<br />
!style="width:7em"|missing value itself<br />
!style="width:7em"|other observed variable(s)<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|YES<br />
|style="text-align:center"|&mdash;<br />
|<br />
*Some participants '''intentionally denied to report higher body weights they didn't like''' and only reported lower body weights they accepted<br />
*Researchers have no information why they denied to report body weights in several weeks<br />
**Missing occurred '''because of the values themselves'''<br />
**Researchers cannot explain/predict the missing mechanism from other observed (reported) body weights or other variables<br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|YES<br />
|<br />
*'''15% of female participants denied to report''' their body weights after participation '''regardless of measured body weights''', but only 1% of male denied to report<br />
*Researchers can identify that female participants more likely denied to report body weights than male<br />
**Missing occurred NOT because of body weights themselves but '''because of another variable ''sex'''''<br />
**Missing mechanism is at random, i.e., free from missing values only inside each participant but NOT at random, i.e., NOT free from variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|NO<br />
|<br />
*A participant '''moved to outside cohort area''' because of family affair and was lost to follow up<br />
*A participant '''failed to report body weights because of malfunction of the app'''<br />
**Missing occurred NOT because of body weights themselves NOR other variables<br />
**Missing mechanism is completely at random, i.e., completely free from both of missing (unobserved) values and observed values in body weight or in other variables<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3069Missing data and imputation2023-12-10T07:12:15Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Missing depends on/<br>Missing occurs because of<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones. Demographic variables are also collected.<br />
|-<br />
!style="width:7em"|missing value itself<br />
!style="width:7em"|other observed variable(s)<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|YES<br />
|style="text-align:center"|&mdash;<br />
|<br />
*Some participants '''intentionally denied to report higher body weights they didn't like''' and only reported lower body weights they accepted<br />
*Researchers have no information why they denied to report body weights in several weeks<br />
**Missing occurred '''because of the values themselves'''<br />
**Researchers cannot explain/predict the missing mechanism from other observed (reported) body weights or other variables<br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|YES<br />
|<br />
*'''15% of female participants denied to report''' their body weights after participation '''regardless of measured body weights''', but only 1% of male denied to report<br />
*Researchers can identify that female participants more likely denied to report body weights than male<br />
**Missing occurred not because of body weights themselves but '''because of another variable ''sex'''''<br />
**Missing mechanism is at random, i.e., free from missing values only inside each participant but NOT at random, i.e., NOT free from variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|NO<br />
|<br />
*A participant '''moved to outside cohort area''' because of family affair and was lost to follow up<br />
*A participant '''failed to report body weights because of malfunction of the app'''<br />
**Missing occurred not because of body weights themselves nor other variables<br />
**Missing mechanism is completely at random, i.e., completely free from both of missing (unobserved) values and observed values in body weight or in other variables<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3068Missing data and imputation2023-12-10T07:08:44Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Missing depends on/<br>Missing occurs because of<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones for 52 weeks in total. Demographic variables are also collected.<br />
|-<br />
!style="width:7em"|missing value itself<br />
!style="width:7em"|other observed variable(s)<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|YES<br />
|style="text-align:center"|&mdash;<br />
|<br />
*Some participants intentionally denied to report higher body weights they didn't like and only reported lower body weights they accepted<br />
*Researchers have no information why they denied to report body weights in several weeks<br />
**Missing occurred because of the values themselves<br />
**Researchers cannot explain/predict the missing mechanism from other observed (reported) body weights or other variables<br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|YES<br />
|<br />
*15% of female participants denied to report their body weights after participation regardless of measured body weights, but only 1% of male denied to report<br />
*Researchers can identify that female participants more likely denied to report body weights than male<br />
**Missing occurred not because of body weights themselves but because of another variable ''sex''<br />
**Missing mechanism is at random, i.e., free from missing values, but it's applicable only inside each participant<br />
**Missing mechanism is NOT at random, i.e., NOT free from variable ''sex''; missing occurred depending on the values in the variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|NO<br />
|<br />
*A participant moved to outside cohort area because of family affair and was lost to follow up after the 10th week<br />
*A participant failed to report body weights because of malfunction of the app between the 15th and 17th weeks<br />
**Missing occurred not because of body weights themselves nor other variables<br />
**Missing mechanism is completely at random, i.e., completely free from both of missing (unobserved) values and observed values in body weight or in other variables<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3067Missing data and imputation2023-12-10T06:54:00Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Missing depends on/<br>Missing occurs because of<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones for 52 weeks in total<br />
|-<br />
!style="width:7em"|missing value itself<br />
!style="width:7em"|other observed variable(s)<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|YES<br />
|style="text-align:center"|&mdash;<br />
|<br />
*Some participants '''intentionally deny to report higher body weights they don't like''' and only report lower body weights they like<br />
**Data of those participants are missed '''because of the values in the variable ''body weight'' themselves'''<br />
**Researchers cannot explain/predict the missing mechanism by <br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|YES<br />
|<br />
*15% of female participants denied to report their body weights after the agreement regardless of measured body weights, but only 1% of male denied to report:<br />
**Unobserved (missing, unrepoted) values in the variable ''body weight'' themselves did not affect the missing, but another variable ''sex'' can explain the reason of missing<br />
**Missing mechanism is at random, i.e., free from unobserved (missing) values only inside each participant<br />
**Missing mechanism is NOT at random, i.e., NOT free from another variable ''sex''; missing occurred depending on the values in the variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|NO<br />
|<br />
*A participant moved to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up after the 10th week<br />
*A participant fails to report body weights because of malfunction of the app between the 15th and 17th weeks<br />
**The reasons (mechanisms) of missing have nothing to do with other observed (certainly reported) values, values in other variables, nor unobserved (missing) values themselves<br />
**Missing mechanism is completely at random, i.e., completely free from either of observed values or unobserved (missing) values<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3066Missing data and imputation2023-12-10T06:49:45Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em" rowspan="2"|<br />
!style="witdh:4em" rowspan="2"|Abbr.<br />
!colspan="2"|Does missing depend on...<br />
!rowspan="2"|[Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones for 52 weeks in total<br />
|-<br />
!style="width:5em"|missing value itself?<br />
!style="width:5em"|other observed variable(s)?<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|style="text-align:center"|YES<br />
|<br />
|<br />
*Some participants '''intentionally deny to report higher body weights they don't like''' and only report lower body weights they like<br />
**Data of those participants are missed '''because of the values in the variable ''body weight'' themselves'''<br />
**Researchers cannot explain/predict the missing mechanism by <br />
|-<br />
!Missing at randam<br />
!MAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|YES<br />
|<br />
*15% of female participants denied to report their body weights after the agreement regardless of measured body weights, but only 1% of male denied to report:<br />
**Unobserved (missing, unrepoted) values in the variable ''body weight'' themselves did not affect the missing, but another variable ''sex'' can explain the reason of missing<br />
**Missing mechanism is at random, i.e., free from unobserved (missing) values only inside each participant<br />
**Missing mechanism is NOT at random, i.e., NOT free from another variable ''sex''; missing occurred depending on the values in the variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|style="text-align:center"|NO<br />
|style="text-align:center"|NO<br />
|<br />
*A participant moved to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up after the 10th week<br />
*A participant fails to report body weights because of malfunction of the app between the 15th and 17th weeks<br />
**The reasons (mechanisms) of missing have nothing to do with other observed (certainly reported) values, values in other variables, nor unobserved (missing) values themselves<br />
**Missing mechanism is completely at random, i.e., completely free from either of observed values or unobserved (missing) values<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3065Missing data and imputation2023-12-10T06:39:52Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:7em"|<br />
!style="witdh:4em"|Abbr.<br />
!style="width:15em"|Description<br />
![Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones for 52 weeks in total<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|<br />
*Missing depends on observed data<br />
|<br />
*Some participants '''intentionally deny to report higher body weights they don't like''' and only report lower body weights they like<br />
**Data of those participants are missed '''because of the values in the variable ''body weight'' themselves'''<br />
**Researchers cannot explain/predict the missing mechanism by <br />
|-<br />
!Missing at randam<br />
!MAR<br />
|<br />
*Missing does not depend on '''unobserved (missing) values''' themselves, but may depend on '''(other) observed values'''<br />
|<br />
*15% of female participants denied to report their body weights after the agreement regardless of measured body weights, but only 1% of male denied to report:<br />
**Unobserved (missing, unrepoted) values in the variable ''body weight'' themselves did not affect the missing, but another variable ''sex'' can explain the reason of missing<br />
**Missing mechanism is at random, i.e., free from unobserved (missing) values only inside each participant<br />
**Missing mechanism is NOT at random, i.e., NOT free from another variable ''sex''; missing occurred depending on the values in the variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|<br />
*Missing does NOT depend on '''(other) observed values''' NOR on '''unobserved (missing) values''' themselves<br />
|<br />
*A participant moved to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up after the 10th week<br />
*A participant fails to report body weights because of malfunction of the app between the 15th and 17th weeks<br />
**The reasons (mechanisms) of missing have nothing to do with other observed (certainly reported) values, values in other variables, nor unobserved (missing) values themselves<br />
**Missing mechanism is completely at random, i.e., completely free from either of observed values or unobserved (missing) values<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3064Missing data and imputation2023-12-10T06:39:35Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!style="width:8em"|<br />
!style="witdh:4em"|Abbr.<br />
!style="width:15em"|Description<br />
![Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones for 52 weeks in total<br />
|-<br />
!Missing not at random<br />
!MNAR<br />
|<br />
*Missing depends on observed data<br />
|<br />
*Some participants '''intentionally deny to report higher body weights they don't like''' and only report lower body weights they like<br />
**Data of those participants are missed '''because of the values in the variable ''body weight'' themselves'''<br />
**Researchers cannot explain/predict the missing mechanism by <br />
|-<br />
!Missing at randam<br />
!MAR<br />
|<br />
*Missing does not depend on '''unobserved (missing) values''' themselves, but may depend on '''(other) observed values'''<br />
|<br />
*15% of female participants denied to report their body weights after the agreement regardless of measured body weights, but only 1% of male denied to report:<br />
**Unobserved (missing, unrepoted) values in the variable ''body weight'' themselves did not affect the missing, but another variable ''sex'' can explain the reason of missing<br />
**Missing mechanism is at random, i.e., free from unobserved (missing) values only inside each participant<br />
**Missing mechanism is NOT at random, i.e., NOT free from another variable ''sex''; missing occurred depending on the values in the variable ''sex''<br />
|-<br />
!Missing completely at random<br />
!MCAR<br />
|<br />
*Missing does NOT depend on '''(other) observed values''' NOR on '''unobserved (missing) values''' themselves<br />
|<br />
*A participant moved to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up after the 10th week<br />
*A participant fails to report body weights because of malfunction of the app between the 15th and 17th weeks<br />
**The reasons (mechanisms) of missing have nothing to do with other observed (certainly reported) values, values in other variables, nor unobserved (missing) values themselves<br />
**Missing mechanism is completely at random, i.e., completely free from either of observed values or unobserved (missing) values<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3063Missing data and imputation2023-12-10T06:37:54Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
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==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!<br />
!Description<br />
![Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones for 52 weeks in total<br />
|-<br />
!Missing not at random<br>MNAR<br />
|<br />
*Missing depends on observed data<br />
|<br />
*Some participants '''intentionally deny to report higher body weights they don't like''' and only report lower body weights they like<br />
**Data of those participants are missed '''because of the values in the variable ''body weight'' themselves'''<br />
**Researchers cannot explain/predict the missing mechanism by <br />
|-<br />
!Missing at randam<br>MAR<br />
|<br />
*Missing does not depend on '''unobserved (missing) values''' themselves, but may depend on '''(other) observed values'''<br />
|<br />
*15% of female participants denied to report their body weights after the agreement regardless of measured body weights, but only 1% of male denied to report:<br />
**Unobserved (missing, unrepoted) values in the variable ''body weight'' themselves did not affect the missing, but another variable ''sex'' can explain the reason of missing<br />
**Missing mechanism is at random, i.e., free from unobserved (missing) values only inside each participant<br />
**Missing mechanism is NOT at random, i.e., NOT free from another variable ''sex''; missing occurred depending on the values in the variable ''sex''<br />
|-<br />
!Missing completely at random<br>MCAR<br />
|<br />
*Missing does NOT depend on '''(other) observed values''' NOR on '''unobserved (missing) values''' themselves<br />
|<br />
*A participant moved to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up after the 10th week<br />
*A participant fails to report body weights because of malfunction of the app between the 15th and 17th weeks<br />
**The reasons (mechanisms) of missing have nothing to do with other observed (certainly reported) values, values in other variables, nor unobserved (missing) values themselves<br />
**Missing mechanism is completely at random, i.e., completely free from either of observed values or unobserved (missing) values<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3062Missing data and imputation2023-12-10T06:29:11Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
<hr />
<div>{{Floating Menu}}<br />
<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!<br />
!Description<br />
![Example]<br>A cohort study in which participants self report their body weight every week via special app installed on their smartphones for 52 weeks in total<br />
|-<br />
!Missing not at random<br>MNAR<br />
|<br />
*Missing depends on observed data<br />
|<br />
*Some participants '''intentionally deny to report higher body weights they don't like''' and only report lower body weights they like<br />
**Data of those participants are missed '''because of the values in the variable ''body weight'' themselves'''<br />
**Researchers cannot explain/predict the missing mechanism by <br />
|-<br />
!Missing at randam<br>MAR<br />
|<br />
*Missing does not depend on '''(other) unobserved data''', but may depend on '''observed data'''<br />
*The cause of missing can be explained by<br />
|<br />
*15% of female participants deny to report their body weights after the agreement regardless of measured body weights, but only 1% of male deny to report:<br />
**Data of female participants are more likely missed not because of data (body weights) themselves but because female are more likely reluctant to report their body weights<br />
**In other words, values in the variable ''body weight'' themselves do not affect the missing but another variable ''sex'' affects the missing of values in the variable ''body weight''<br />
|-<br />
!Missing completely at random<br>MCAR<br />
|<br />
*Missing does NOT depend on '''(other) observed values''' NOR on '''unobserved (missing) values''' themselves<br />
|<br />
*A participant moved to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up after the 10th week<br />
*A participant fails to report body weights because of malfunction of the app between the 15th and 17th weeks<br />
**The reasons (mechanisms) of missing have nothing to do with other observed (certainly reported) values, values in other variables, nor unobserved (missing) values themselves<br />
**Missing mechanism is completely at random, i.e., completely free from either of observed values or unobserved (missing) values<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3061Missing data and imputation2023-12-10T05:54:53Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
<hr />
<div>{{Floating Menu}}<br />
<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!<br />
!Description<br />
![*Example]<br>A cohort study in which participants report their body weight every week to research center for 52 weeks in total<br />
|-<br />
!Missing not at random<br>MNAR<br />
|<br />
*Missing depends on observed data<br />
|<br />
*Some participants '''intentionally deny to report higher body weights they don't like''' and only report lower body weights they like<br />
**Data of those participants are missed '''because of the values in the variable ''body weight'' themselves'''<br />
**Researchers cannot explain/predict the missing mechanism by <br />
|-<br />
!Missing at randam<br>MAR<br />
|<br />
*Missing does not depend on '''unobserved data''', but may depend on '''observed data'''<br />
*The cause of missing can be explained by<br />
|<br />
*15% of female participants deny to report their body weights after the agreement regardless of measured body weights, but only 1% of male deny to report:<br />
**Data of female participants are more likely missed not because of data (body weights) themselves but because female are more likely reluctant to report their body weights<br />
**In other words, values in the variable ''body weight'' themselves do not affect the missing but another variable ''sex'' affects the missing of values in the variable ''body weight''<br />
|-<br />
!Missing completely at random<br>MCAR<br />
|<br />
*Missing does NOT depend on '''observed data''' NOR on '''unobserved data'''<br />
*Missing occurs purely at random independely from any observed and unobserved data<br />
|<br />
*A participant moves to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up at the 10th week:<br />
**Data after the move are missed not because of data (body weights) themselves, nor because of the participant's unobserved (unmeasured) characteristic related to the study<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3060Missing data and imputation2023-12-10T05:24:01Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
<hr />
<div>{{Floating Menu}}<br />
<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!<br />
!Description<br />
![*Example]<br>A cohort study in which participants report their body weight every week to research center for 52 weeks in total<br />
|-<br />
!Missing not at random<br>MNAR<br />
|<br />
*Missing depends on observed data<br />
|<br />
*Some participants '''intentionally deny to report higher body weights they don't like''' and only report lower body weights they like<br />
**Data of those participants are missed '''because of the values in the variable ''body weight'' themselves'''<br />
|-<br />
!Missing at randam<br>MAR<br />
|<br />
*Missing does not depend on '''unobserved data''', but may depend on '''observed data'''<br />
*The cause of missing can be explained by<br />
|<br />
*15% of female participants deny to report their body weights after the agreement regardless of measured body weights, but only 1% of male deny to report:<br />
**Data of female participants are more likely missed not because of data (body weights) themselves but because female are more likely reluctant to report their body weights<br />
**In other words, values in the variable ''body weight'' themselves do not affect the missing but another variable ''sex'' affects the missing of values in the variable ''body weight''<br />
|-<br />
!Missing completely at random<br>MCAR<br />
|<br />
*Missing does NOT depend on '''observed data''' NOR on '''unobserved data'''<br />
*Missing occurs purely at random independely from any observed and unobserved data<br />
|<br />
*A participant moves to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up at the 10th week:<br />
**Data after the move are missed not because of data (body weights) themselves, nor because of the participant's unobserved (unmeasured) characteristic related to the study<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3059Missing data and imputation2023-12-10T05:17:44Z<p>Vaccipedia.admin: /* Three mechanisms (assumptions) of data missing */</p>
<hr />
<div>{{Floating Menu}}<br />
<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!<br />
!Description<br />
![*Example]<br>A cohort study in which participants report their body weight every week to research center for 52 weeks in total<br />
|-<br />
!Missing not at random<br>MNAR<br />
|Missing depends on observed data<br />
|Some participants intentionally deny to report higher body weights they don't like and only report lower body weights they like<br />
*Data of those participants are missed because of the values in the variable ''body weight'' themselves<br />
|-<br />
!Missing at randam<br>MAR<br />
|<br />
*Missing may depend on '''observed data''' but does not depend on ''unobserved data''<br />
*Missing can be explained <br />
|15% of female participants deny to report their body weights after the agreement regardless of measured body weights, but only 1% of male deny to report:<br />
*Data of female participants are more likely missed not because of data (body weights) themselves but because female are more likely reluctant to report their body weights<br />
*In other words, values in the variable ''body weight'' themselves do not affect the missing but another variable ''sex'' affects the missing of values in the variable ''body weight''<br />
|-<br />
!Missing completely at random<br>MCAR<br />
|<br />
*Missing does NOT depend on '''observed data''' NOR on ''unobserved data''<br />
*Missing occurs purely at random independely from any observed and unobserved data<br />
|A participant moves to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up at the 10th week:<br />
*Data after the move are missed not because of data (body weights) themselves, nor because of the participant's unobserved (unmeasured) characteristic related to the study<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Missing_data_and_imputation&diff=3058Missing data and imputation2023-12-10T04:46:58Z<p>Vaccipedia.admin: ページの作成:「{{Floating Menu}} ==Three mechanisms (assumptions) of data missing== {|class="wikitable" style="min-width:400px" |+Mechanisms (assumptions) of data missing |- ! !Descrip…」</p>
<hr />
<div>{{Floating Menu}}<br />
<br />
==Three mechanisms (assumptions) of data missing==<br />
{|class="wikitable" style="min-width:400px"<br />
|+Mechanisms (assumptions) of data missing<br />
|-<br />
!<br />
!Description<br />
![*Example]<br>A cohort study in which participants report their body weight every week to research center<br />
|-<br />
!Missing not at random<br>MNAR<br />
|Missing depends on observed data themselves<br />
|<br />
|-<br />
!Missing at randam<br>MAR<br />
|<br />
*Missing does not depend on observed data but may depend on unobserved data<br />
*Missing can be explained <br />
|Female participants less likely report their body weights than male participants:<br />
*Data of female participants are more likely missed not because of data (body weights) themselves but because female tend to be reluctant to report their body weights<br />
*In other words, the variable of ''body weight'' itself does not affect the missing but another variable ''sex'' affects the missing of values in the variable ''body weight''<br />
|-<br />
!Missing completely at random<br>MCAR<br />
|<br />
*Missing does not depend on observed data nor on unobserved data<br />
*Missing occurs purely at random independely from any observed and unobserved data<br />
|A participant moves to outside cohort area because of family affair which has nothing to do with the study and is lost to follow up:<br />
*Data after the move are missed not because of data (body weights) themselves nor because of the participant's unobserved (unmeasured) characteristic<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=%E3%83%86%E3%83%B3%E3%83%97%E3%83%AC%E3%83%BC%E3%83%88:Submenu_EpiStats&diff=3057テンプレート:Submenu EpiStats2023-12-10T03:48:06Z<p>Vaccipedia.admin: </p>
<hr />
<div>{|class="wikitable alternating" style="width:320px; margin:0;"<br />
|-<br />
|[[Basics & Definition]]<br />
|-<br />
|[[Epidemiology]]<br />
|-<br />
|[[Odds in statistics and Odds in a horse race]]<br />
|-<br />
|[[Collider bias]]<br />
|-<br />
|[[Data distribution]]<br />
|-<br />
|[[Statistical test]]<br />
|-<br />
|[[Regression model]]<br />
|-<br />
|[[Multivariate analysis]]<br />
|-<br />
|[[Marginal effects]]<br />
|-<br />
|[[Prediction and decision]]<br />
|-<br />
|[[Table-related commands in STATA]]<br />
|-<br />
|[[Missing data and imputation]]<br />
|}<br />
</div></div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Neutralizing_antibody_and_its_assay&diff=3056Neutralizing antibody and its assay2023-11-12T04:59:23Z<p>Vaccipedia.admin: </p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
===臨床検査としての抗体===<br />
<br />
==用語==<br />
*中和抗体 neutralizing antibody<br />
*中和抗体価 neutralizing antibody titer<br />
*中和反応 neutralization reaction<br />
*中和試験 neutralization test<br />
*中和アッセイ neutralization assay<br />
<br />
==中和抗体==<br />
===中和抗体は単一の抗体か?複数種の抗体か?===<br />
<br />
==ウイルスの定量:プラーク法==<br />
===1プラークは1ウイルス粒子だけで成り立っているのか?===<br />
<br />
==中和抗体の定量:中和試験==<br />
===幾何平均抗体価 geometric mean titer (GMT)===</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Respiratory_Syncytial_virus&diff=3055Respiratory Syncytial virus2023-11-08T17:54:03Z<p>Vaccipedia.admin: /* Epidemiology in Elderly */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Epidemiology in Children==<br />
<br />
==Epidemiology in Elderly==<br />
*Prospective cohort in Japan<br />
*Followed 1,000 elderly ≥65y/o in community and nursing homes for 52 weeks in years of 2019 to 2020<br />
*RS virus associated acute respiratory disease was detected in 2.4%<br />
*RS virus associated lower respitaroty disease was detected in 0.8%<br />
{{quote|content=<br />
Kurai, D., Natori, M., Yamada, M., Zheng, R., Saito, Y., & Takahashi, H. (2022). Occurrence and disease burden of respiratory syncytial virus and other respiratory pathogens in adults aged ≥65 years in community: A prospective cohort study in Japan. Influenza and Other Respiratory Viruses, 16(2), 298–307. https://doi.org/10.1111/irv.12928<br />
}}<br />
<br />
==Monoclonal antibody for Children==<br />
<br />
==Vaccine for Children (maternal immunization)==<br />
<br />
==Vaccine for Elderly==</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Respiratory_Syncytial_virus&diff=3054Respiratory Syncytial virus2023-11-08T17:20:05Z<p>Vaccipedia.admin: </p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Epidemiology in Children==<br />
<br />
==Epidemiology in Elderly==<br />
<br />
==Monoclonal antibody for Children==<br />
<br />
==Vaccine for Children (maternal immunization)==<br />
<br />
==Vaccine for Elderly==</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Respiratory_Syncytial_virus&diff=3053Respiratory Syncytial virus2023-11-08T17:19:41Z<p>Vaccipedia.admin: ページの作成:「{{Floating_menu}} ==Epidemiology in Children== ==Epidemiology in Elderly== ==Monoclonal antibody for Children== ==Vaccine for Children (maternal immunization)== ==Va…」</p>
<hr />
<div>{{Floating_menu}}<br />
<br />
==Epidemiology in Children==<br />
<br />
==Epidemiology in Elderly==<br />
<br />
==Monoclonal antibody for Children==<br />
<br />
==Vaccine for Children (maternal immunization)==<br />
<br />
==Vaccine for Elderly==</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=%E3%83%86%E3%83%B3%E3%83%97%E3%83%AC%E3%83%BC%E3%83%88:Submenu_Virus&diff=3052テンプレート:Submenu Virus2023-11-08T17:17:10Z<p>Vaccipedia.admin: </p>
<hr />
<div>{|class="wikitable alternating" style="width:320px; margin:0;"<br />
|-<br />
|[[HIV]]<br />
|-<br />
|[[HIV-TB co-infection]]<br />
|-<br />
|[[HIV-STI interaction]]<br />
|-<br />
|[[Viral Hemorrhagic Fever]]<br />
|-<br />
|[[Ebola]]<br />
|-<br />
|[[Crimean-Congo hemorrhagic fever]]<br />
|-<br />
|[[SFTS]]<br />
|-<br />
|[[Rabies]]<br />
|-<br />
|[[Polio]]<br />
|-<br />
|[[Dengue]]<br />
|-<br />
|[[Yellow fever]]<br />
|-<br />
|[[Chikungunya]]<br />
|-<br />
|[[Zika]]<br />
|-<br />
|[[Japanese encephalitis]]<br />
|-<br />
|[[Tick-borne encephalitis]]<br />
|-<br />
|[[Viral hepatitis]]<br />
|-<br />
|[[Measles]]<br />
|-<br />
|[[Smallpox and Monkeypox]]<br />
|-<br />
|[[Respiratory Syncytial virus]]<br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Prediction_and_decision&diff=3051Prediction and decision2023-10-09T11:06:45Z<p>Vaccipedia.admin: /* Skill scores of predictions */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Peirce and the science of the method==<br />
*The historical article which Peirce first proposed 'the science of the method'.<br />
**Peirce's proposal was related to Finley's tornade forecasts which is discussed in the Stephenson's article in the next section.<br />
{{quote|content=<br />
Peirce, C. S. (1884). The Numerical Measure of the Success of Predictions. Science, ns-4(93), 453–454. https://doi.org/10.1126/science.ns-4.93.453.b<br />
}}<br />
<br />
*A review of Peirce's 'the science of the method' and Youden's index which is the identical methodology to the Peirce's method.<br />
{{quote|content=<br />
Baker, S. G., & Kramer, B. S. (2007). Peirce, youden, and receiver operating characteristic curves. American Statistician, 61(4), 343–346. https://doi.org/10.1198/000313007X247643<br />
}}<br />
<br />
<br />
==Skill scores of predictions==<br />
*Investigation of '(forecast) skill scores', which measure accuracy or quality of different forecasting methods, from the view point of meterology.<br />
**Referring to Peirce skill score.<br />
{{quote|content=<br />
Stephenson, D. B. (2000). Use of the “Odds Ratio” for Diagnosing Forecast Skill. Weather and Forecasting, 15(2), 221–232. https://doi.org/10.1175/1520-0434(2000)015<0221:UOTORF>2.0.CO;2<br />
}}<br />
<br />
<br />
*Another review of measures of forecast skills of meterological forecasts<br />
{{quote|content=<br />
山田真吾. (2004). 天気予報の価値をどう測るか. オペレーションズ・リサーチ, 49(5), 268–275. https://orsj.org/wp-content/or-archives50/pdf/bul/Vol.49_05_268.pdf<br />
}}<br />
<br />
==Peirce as a logician==<br />
*Peirce was originally a logician and the article discusses about his 'methodology of science'<br />
{{quote|content=<br />
赤川元昭. (2011). パースと科学の方法. 流通科学大学論集-流通・経営編-, 23(2), 75–90.<br />
}}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Marginal_effects&diff=3050Marginal effects2023-10-09T10:51:15Z<p>Vaccipedia.admin: /* What are marginal effects */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==What are marginal effects==<br />
*Easy explanation of what are marginal effects.<br />
{{quote|content=<br />
Heiss, A. (2022, May 20). Marginalia: A guide to figuring out what the heck marginal effects, marginal slopes, average marginal effects, marginal effects at the mean, and all these other marginal things are. https://doi.org/10.59350/40xaj-4e562<br />
}}<br />
<br />
<br />
*Another instruction of partial effects.<br />
{{quote|content=<br />
Date, S. (n.d.). Understanding Partial Effects, Main Effects, And Interaction Effects In A Regression Model. Time Series Analysis, Regression, and Forecasting With Tutorials in Python. Retrieved October 9, 2023, from https://timeseriesreasoning.com/contents/partial-effect-main-effect-interaction-effect/<br />
}}<br />
<br />
<br />
*On the internet only this page refers to difference between '''marginal effects''' and '''partial effects''' ''without citation'' as follows:<br />
**'''marginal effects''', i.e., the marginal contribution of each variable on the scale of the linear predictor<br />
**'''partial effects''', i.e., the contribution of each variable on the outcome scale, conditional on the other variables involved in the link function transformation of the linear predictor<br />
{{quote|content=<br />
An Introduction to ‘margins.’ (2021, January 21). https://cran.r-project.org/web/packages/margins/vignettes/Introduction.html<br />
}}<br />
<br />
==Marginal effects of ordinary categorical data==<br />
*How to interpret effects in modeling ordinary categorical data<br />
**In this article the authors refer to '''marginal effects''' as same with '''partical effects''' but also mention their possibility of leading misunderstanding<br />
{{quote|content=<br />
Agresti, A., & Tarantola, C. (2018). Simple ways to interpret effects in modeling ordinal categorical data. Statistica Neerlandica, 72(3), 210–223. https://doi.org/10.1111/stan.12130<br />
}}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Marginal_effects&diff=3049Marginal effects2023-10-09T10:50:40Z<p>Vaccipedia.admin: /* What are marginal effects */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==What are marginal effects==<br />
*Easy explanation of what are marginal effects.<br />
{{quote|content=<br />
Heiss, A. (2022, May 20). Marginalia: A guide to figuring out what the heck marginal effects, marginal slopes, average marginal effects, marginal effects at the mean, and all these other marginal things are. https://doi.org/10.59350/40xaj-4e562<br />
}}<br />
<br />
<br />
*Another instruction of partial effects.<br />
{{quote|content=<br />
Date, S. (n.d.). Understanding Partial Effects, Main Effects, And Interaction Effects In A Regression Model. Time Series Analysis, Regression, and Forecasting With Tutorials in Python. Retrieved October 9, 2023, from https://timeseriesreasoning.com/contents/partial-effect-main-effect-interaction-effect/<br />
}}<br />
<br />
<br />
*On the internet only this page refers to difference between '''marginal effects''' and '''partial effects''' ''without citation'' as follows:<br />
**"marginal effects", i.e., the marginal contribution of each variable on the scale of the linear predictor<br />
**p"artial effects", i.e., the contribution of each variable on the outcome scale, conditional on the other variables involved in the link function transformation of the linear predictor<br />
{{quote|content=<br />
An Introduction to ‘margins.’ (2021, January 21). https://cran.r-project.org/web/packages/margins/vignettes/Introduction.html<br />
}}<br />
<br />
==Marginal effects of ordinary categorical data==<br />
*How to interpret effects in modeling ordinary categorical data<br />
**In this article the authors refer to '''marginal effects''' as same with '''partical effects''' but also mention their possibility of leading misunderstanding<br />
{{quote|content=<br />
Agresti, A., & Tarantola, C. (2018). Simple ways to interpret effects in modeling ordinal categorical data. Statistica Neerlandica, 72(3), 210–223. https://doi.org/10.1111/stan.12130<br />
}}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Marginal_effects&diff=3048Marginal effects2023-10-09T10:33:16Z<p>Vaccipedia.admin: /* Marginal effects of ordinary categorical data */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==What are marginal effects==<br />
*Easy explanation of what are marginal effects.<br />
{{quote|content=<br />
Heiss, A. (2022, May 20). Marginalia: A guide to figuring out what the heck marginal effects, marginal slopes, average marginal effects, marginal effects at the mean, and all these other marginal things are. https://doi.org/10.59350/40xaj-4e562<br />
}}<br />
<br />
<br />
*Another instruction of partial effects.<br />
{{quote|content=<br />
Date, S. (n.d.). Understanding Partial Effects, Main Effects, And Interaction Effects In A Regression Model. Time Series Analysis, Regression, and Forecasting With Tutorials in Python. Retrieved October 9, 2023, from https://timeseriesreasoning.com/contents/partial-effect-main-effect-interaction-effect/<br />
}}<br />
<br />
==Marginal effects of ordinary categorical data==<br />
*How to interpret effects in modeling ordinary categorical data<br />
**In this article the authors refer to '''marginal effects''' as same with '''partical effects''' but also mention their possibility of leading misunderstanding<br />
{{quote|content=<br />
Agresti, A., & Tarantola, C. (2018). Simple ways to interpret effects in modeling ordinal categorical data. Statistica Neerlandica, 72(3), 210–223. https://doi.org/10.1111/stan.12130<br />
}}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Marginal_effects&diff=3047Marginal effects2023-10-09T10:17:04Z<p>Vaccipedia.admin: /* What are marginal effects */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==What are marginal effects==<br />
*Easy explanation of what are marginal effects.<br />
{{quote|content=<br />
Heiss, A. (2022, May 20). Marginalia: A guide to figuring out what the heck marginal effects, marginal slopes, average marginal effects, marginal effects at the mean, and all these other marginal things are. https://doi.org/10.59350/40xaj-4e562<br />
}}<br />
<br />
<br />
*Another instruction of partial effects.<br />
{{quote|content=<br />
Date, S. (n.d.). Understanding Partial Effects, Main Effects, And Interaction Effects In A Regression Model. Time Series Analysis, Regression, and Forecasting With Tutorials in Python. Retrieved October 9, 2023, from https://timeseriesreasoning.com/contents/partial-effect-main-effect-interaction-effect/<br />
}}<br />
<br />
==Marginal effects of ordinary categorical data==<br />
*How to interpret effects in modeling ordinary categorical data<br />
{{quote|content=<br />
Agresti, A., & Tarantola, C. (2018). Simple ways to interpret effects in modeling ordinal categorical data. Statistica Neerlandica, 72(3), 210–223. https://doi.org/10.1111/stan.12130<br />
}}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Marginal_effects&diff=3046Marginal effects2023-10-09T10:16:05Z<p>Vaccipedia.admin: ページの作成:「{{Floating_Menu}} ==What are marginal effects== *Easy explanation of what are marginal effects. {{quote|content= Heiss, A. (2022, May 20). Marginalia: A guide to figurin…」</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==What are marginal effects==<br />
*Easy explanation of what are marginal effects.<br />
{{quote|content=<br />
Heiss, A. (2022, May 20). Marginalia: A guide to figuring out what the heck marginal effects, marginal slopes, average marginal effects, marginal effects at the mean, and all these other marginal things are. https://doi.org/10.59350/40xaj-4e562<br />
}}<br />
<br />
*Another instruction of partial effects.<br />
{{quote|content=<br />
Date, S. (n.d.). Understanding Partial Effects, Main Effects, And Interaction Effects In A Regression Model. Time Series Analysis, Regression, and Forecasting With Tutorials in Python. Retrieved October 9, 2023, from https://timeseriesreasoning.com/contents/partial-effect-main-effect-interaction-effect/<br />
}}<br />
<br />
==Marginal effects of ordinary categorical data==<br />
*How to interpret effects in modeling ordinary categorical data<br />
{{quote|content=<br />
Agresti, A., & Tarantola, C. (2018). Simple ways to interpret effects in modeling ordinal categorical data. Statistica Neerlandica, 72(3), 210–223. https://doi.org/10.1111/stan.12130<br />
}}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Prediction_and_decision&diff=3045Prediction and decision2023-10-09T09:59:05Z<p>Vaccipedia.admin: </p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Peirce and the science of the method==<br />
*The historical article which Peirce first proposed 'the science of the method'.<br />
**Peirce's proposal was related to Finley's tornade forecasts which is discussed in the Stephenson's article in the next section.<br />
{{quote|content=<br />
Peirce, C. S. (1884). The Numerical Measure of the Success of Predictions. Science, ns-4(93), 453–454. https://doi.org/10.1126/science.ns-4.93.453.b<br />
}}<br />
<br />
*A review of Peirce's 'the science of the method' and Youden's index which is the identical methodology to the Peirce's method.<br />
{{quote|content=<br />
Baker, S. G., & Kramer, B. S. (2007). Peirce, youden, and receiver operating characteristic curves. American Statistician, 61(4), 343–346. https://doi.org/10.1198/000313007X247643<br />
}}<br />
<br />
<br />
==Skill scores of predictions==<br />
*Investigation of '(forecast) skill scores', which measure accuracy or quality of different forecasting methods, from the view point of meterology.<br />
**Referring to Peirce skill score.<br />
{{quote|content=<br />
Stephenson, D. B. (2000). Use of the “Odds Ratio” for Diagnosing Forecast Skill. Weather and Forecasting, 15(2), 221–232. https://doi.org/10.1175/1520-0434(2000)015<0221:UOTORF>2.0.CO;2<br />
}}<br />
<br />
<br />
==Peirce as a logician==<br />
*Peirce was originally a logician and the article discusses about his 'methodology of science'<br />
{{quote|content=<br />
赤川元昭. (2011). パースと科学の方法. 流通科学大学論集-流通・経営編-, 23(2), 75–90.<br />
}}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Prediction_and_decision&diff=3044Prediction and decision2023-10-09T09:58:47Z<p>Vaccipedia.admin: ページの作成:「==Peirce and the science of the method== *The historical article which Peirce first proposed 'the science of the method'. **Peirce's proposal was related to Finley's torn…」</p>
<hr />
<div>==Peirce and the science of the method==<br />
*The historical article which Peirce first proposed 'the science of the method'.<br />
**Peirce's proposal was related to Finley's tornade forecasts which is discussed in the Stephenson's article in the next section.<br />
{{quote|content=<br />
Peirce, C. S. (1884). The Numerical Measure of the Success of Predictions. Science, ns-4(93), 453–454. https://doi.org/10.1126/science.ns-4.93.453.b<br />
}}<br />
<br />
*A review of Peirce's 'the science of the method' and Youden's index which is the identical methodology to the Peirce's method.<br />
{{quote|content=<br />
Baker, S. G., & Kramer, B. S. (2007). Peirce, youden, and receiver operating characteristic curves. American Statistician, 61(4), 343–346. https://doi.org/10.1198/000313007X247643<br />
}}<br />
<br />
<br />
==Skill scores of predictions==<br />
*Investigation of '(forecast) skill scores', which measure accuracy or quality of different forecasting methods, from the view point of meterology.<br />
**Referring to Peirce skill score.<br />
{{quote|content=<br />
Stephenson, D. B. (2000). Use of the “Odds Ratio” for Diagnosing Forecast Skill. Weather and Forecasting, 15(2), 221–232. https://doi.org/10.1175/1520-0434(2000)015<0221:UOTORF>2.0.CO;2<br />
}}<br />
<br />
<br />
==Peirce as a logician==<br />
*Peirce was originally a logician and the article discusses about his 'methodology of science'<br />
{{quote|content=<br />
赤川元昭. (2011). パースと科学の方法. 流通科学大学論集-流通・経営編-, 23(2), 75–90.<br />
}}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=%E3%83%86%E3%83%B3%E3%83%97%E3%83%AC%E3%83%BC%E3%83%88:Submenu_EpiStats&diff=3043テンプレート:Submenu EpiStats2023-10-09T09:31:43Z<p>Vaccipedia.admin: </p>
<hr />
<div>{|class="wikitable alternating" style="width:320px; margin:0;"<br />
|-<br />
|[[Basics & Definition]]<br />
|-<br />
|[[Epidemiology]]<br />
|-<br />
|[[Odds in statistics and Odds in a horse race]]<br />
|-<br />
|[[Collider bias]]<br />
|-<br />
|[[Data distribution]]<br />
|-<br />
|[[Statistical test]]<br />
|-<br />
|[[Regression model]]<br />
|-<br />
|[[Multivariate analysis]]<br />
|-<br />
|[[Marginal effects]]<br />
|-<br />
|[[Prediction and decision]]<br />
|-<br />
|[[Table-related commands in STATA]]<br />
|}<br />
</div></div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=%E3%83%86%E3%83%B3%E3%83%97%E3%83%AC%E3%83%BC%E3%83%88:Submenu_EpiStats&diff=3042テンプレート:Submenu EpiStats2023-10-09T09:25:28Z<p>Vaccipedia.admin: </p>
<hr />
<div>{|class="wikitable alternating" style="width:320px; margin:0;"<br />
|-<br />
|[[Basics & Definition]]<br />
|-<br />
|[[Epidemiology]]<br />
|-<br />
|[[Odds in statistics and Odds in a horse race]]<br />
|-<br />
|[[Collider bias]]<br />
|-<br />
|[[Data distribution]]<br />
|-<br />
|[[Statistical test]]<br />
|-<br />
|[[Regression model]]<br />
|-<br />
|[[Multivariate analysis]]<br />
|-<br />
|[[Marginal effects]]<br />
|-<br />
|[[Decision analysis]]<br />
|-<br />
|[[Table-related commands in STATA]]<br />
|}<br />
</div></div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Pneumococcus&diff=3041Pneumococcus2023-09-29T13:31:10Z<p>Vaccipedia.admin: /* Effectiveness of pneumococcal vaccines */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==epidemiology==<br />
*1.19mi. deaths in 2016<br />
*197.05 mil. episodes in 2016<br />
*the leading cause of lower respiratory infections followed by ''H. influenzae'', influenza /B and RS virus<br />
*50% of pneumococcal deaths in India, Nigeria, DRC and Pakistan<br />
<br />
==serotype==<br />
*all serotypes known more than 90 are pathogenic for human<br />
*differentiation of serotypes is important for epidemiology<br />
<br />
==antimicrobial resitance==<br />
*first reported in late 1960s<br />
<br />
==Vaccine==<br />
*PPSV does not induce T-cell dependent immunity<br />
*PCV induces T-cell dependent immunity<br />
*new product "Pneumosil" from India<br />
**10-valent<br />
**serotypes 1, 5, 6A, 6B, 7F, 9V, 14, 19A, 19F, 23F<br />
*the reason why PCV13 for older population failed to show persistent efficacy against IPD in the U.S. may be contributed by spread of PCV13 for children which has caused serotype substitutions in community<br />
<br />
===History of Pneumococcal vaccines in Japan===<br />
{|class="wikitable"<br />
|+''Table updated on 25th Aug 2023''<br />
|-<br />
!style="width:4em" rowspan="2"|Year<br />
!style="width:12em"|PPSV23<br />
!style="width:12em"|PCV7<br />
!style="width:12em"|PCV13<br />
!style="width:12em"|PCV15<br />
!style="width:12em"|PCV20<br />
|-<br />
!Pneumovax NP||Prevenar||Prevenar13||Vaxneuvance||<br />
|-<br />
!1988<br>昭和63<br />
|'''Approved'''<br>- 2yr≤<br>'''''Covered by Public Health Insurance'''''<br>- Asplenia|| || || || |<br />
|-<br />
!2009<br>平成21<br />
| ||'''Approved'''<br>- 2mo≤ ≤9yr|| || ||<br />
|-<br />
!2010<br>平成22<br />
| ||'''''Routinized'''''<br>- 2mo≤ ≤60mo (<5yr)|| || ||<br />
|-<br />
!2013<br>平成25<br />
| ||'''Terminated''' and switched to PCV13||'''Approved'''<br>- 2mo≤ <6yr<br>'''''Routinized'''''<br>- 2mo≤ ≤60mo (<5yr)|| ||<br />
|-<br />
!2014<br>平成26<br />
|'''''Routinized'''''<br>- at 65yr<br>- 60-64yr with specific chronic conditions|| ||'''Approved'''<br>- 65yr≤ at risk of IPD|| ||<br />
|-<br />
!2020<br>令和2<br />
| || ||'''Approved'''<br>- 6yr≤ at risk of IPD|| ||<br />
|-<br />
!2022<br>令和4<br />
| || || ||'''Approved'''<br>- elderly<br>- adults at risk of IPD||<br />
|-<br />
!2023<br>令和5<br />
| || || ||'''Approved'''<br>- 2mo≤||''Submitted for approval''<br />
|-<br />
! !!PPSV23!!PCV7!!PCV13!!PCV15!!PCV20<br />
|}<br />
<br />
===Efficacy of pneumococcal vaccines===<br />
<br />
===Effectiveness of pneumococcal vaccines===<br />
<br />
===Effectiveness against colonization===<br />
<br />
==Serotype replacement==<br />
<br />
==Overwhelming Post-Splenectomy Infection (OPSI) and pnuemococcus==</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Statistical_test&diff=3040Statistical test2023-09-25T10:48:58Z<p>Vaccipedia.admin: /* Basic concept of statistical tests */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Basic concept of statistical tests==<br />
*First remind that<br />
**Statistical test is to test<br />
<br />
==Comparing Proportions==<br />
{|class="wikitable"<br />
|-<br />
!style="width:80px"|<br />
!style="width:250px"|Independent samples<br>(Unpaired in case of two)<br />
!style="width:250px"|Dependent samples<br>(Paired in case of two)<br />
|-<br />
!2 proportions<br />
|<br />
*'''Z test'''<br />
::<math><br />
\begin{align}<br />
z & = \frac{p_1-p_2}{SE_{pooled(p_1-p_2)}} \\<br />
& = \frac{p_1-p_2}{\sqrt{\frac{\bar{p}(1-\bar{p})}{n_1}+\frac{\bar{p}(1-\bar{p})}{n_2}}}<br />
\end{align}<br />
</math><br />
|<br />
|-<br />
!rowspan="3"|&ge; 3 proportions<br />
|''Enough large sample''<br />
*'''<math>\chi^2</math> test'''<br />
::<math>\chi^2 = \sum \frac{(O - E)^2}{E}</math><br />
::<math>O</math> = observed values<br><math>E</math> = expected values<br />
|rowspan="3" style="vertical-align:top"|<br />
*'''McNemar's <math>\chi^2</math> test'''<br />
::<math><br />
\begin{align}<br />
& McNemar's\ \chi^2 \\<br />
& = \frac{(n_1-n_2)^2}{n_1+n_2}<br />
\end{align}<br />
</math><br />
::<math>n_i</math> = number of observations in discordant pair<br />
|-<br />
|''Testing linear association''<br />
*'''<math>\chi^2</math> trend test'''<br />
::<math><br />
\begin{align}<br />
& \chi^2 trend \\<br />
& = \frac{(\bar{x_1}-\bar{x_2})^2}{s^2(\frac{1}{n_1}+\frac{1}{n_2})} \\<br />
& s = \sqrt{\sum \frac{(x_i-\bar{x_i})^2}{n-1}}<br />
\end{align}<br />
</math><br />
::<math>x_i</math> = weighted values<br />
::<math>n_i</math> = number of observations<br />
|-<br />
|''&ge;1 cell expected value <5''<br />
'''Fisher's exact test'''<br />
*very rare in real researches<br />
|}<br />
<br />
==Comparing Means==<br />
{|class="wikitable"<br />
!rowspan="2" style="width:80px"|<br />
!colspan="2"|Parametric<br>i.e., normally distributed<br />
!colspan="2"|Non-parametric<br>i.e., not normally distributed<br />
|-<br />
!style="width:250px"|Independent samples<br>(Unpaired in case of two)<br />
!style="width:250px"|Dependent samples<br>(Paired in case of two)<br />
!style="width:250px"|Independent samples<br>(Unpaired in case of two)<br />
!style="width:250px"|Dependent samples<br>(Paired in case of two)<br />
|-<br />
!rowspan="3"|2 means<br />
<br />
|''Enough large sample''<br />
*'''Z test'''<br />
::<math><br />
\begin{align}<br />
z & = \frac{\bar{x_1}-\bar{x_2}}{SE_{(\bar{x_1}-\bar{x_2})}} \\<br />
& = \frac{\bar{x_1}-\bar{x_2}}{\sqrt{\frac{s_1^2}{n_1}+\frac{s_2^2}{n_2}}}<br />
\end{align}<br />
</math><br />
<br />
|rowspan="3" style="vertical-align:top"|<br />
*'''Paired Student's t test'''<br />
::''<math>H_0</math> is '''mean of paired differences''' in the population is '''zero'''.''<br />
::<math><br />
\begin{align}<br />
paired\ t & = \frac{\bar{d}}{SE_d} \\<br />
& = \frac{\bar{d}}{\frac{s}{\sqrt{n}}} \\<br />
\end{align}<br />
</math><br />
::where <math>\bar{d}</math> is the mean of differences of paired observations<br />
<br />
|rowspan="3" style="vertical-align:top"|<br />
*'''Wilcoxon rank sum test'''<br>='''Mann-Whitney test'''<br />
::''<math>H_0</math> is '''medians or means of ranks''' in the two population'''s''' are the same''<br />
:#To rank whole combined observations of two groups<br />
:#To separate back the ranks into two groups<br />
:#To look up ''critical range'' relevant to both numbers of observations and whether '''the sum of ranks''' in '''the group of smaller number of observation''' (=statistics) is outside the range or not<br />
::if outside the range, p-value is smaller than designated<br />
<br />
|rowspan="3" style="vertical-align:top"|<br />
*'''Wilcoxon signed rank test'''<br />
::''<math>H_0</math> is '''median of paired differences''' in the population is zero''<br />
:#To calculate differences between pairs and discard 0 differences<br />
:#To rank the absolute values of differences (ignoring 0)<br />
:#To make the sum of ranks of '''positive difference''' and the sum of ranks of '''negative differences''' ('signed rank')<br />
:#To look up '''critical value''' relevant to numbers of pairs with non-0 differences and whether '''the smaller sum of rank''' (=statistics) is smaller than the critical value<br />
::if smaller than the critical value, p-value is smaller than designated<br />
<br />
|-<br />
|''Small sample size <30 in a group''<br />
*'''Student's t test'''<br />
::<math><br />
\begin{align}<br />
t & = \frac{\bar{x_1}-\bar{x_2}}{SE_{(\bar{x_1}-\bar{x_2})}} \\<br />
& = \frac{\bar{x_1}-\bar{x_2}}{\sqrt{\frac{(n_1-1)s_1^2+(n_2-1)s_2^2}{(n_1-1)+(n_2-1)}}\sqrt{\frac{1}{n_1}+\frac{1}{n_2}}}<br />
\end{align}<br />
</math><br />
<br />
|-<br />
|''Large discrepancy in SDs between groups''<br />
*Bootstrap<br />
*Non-parametric<br />
*Fisher-Behrens<br />
*Welch<br />
<br />
|-<br />
!&ge; 3 means<br />
|style="vertical-align:top"|<br />
*'''One-way ANOVA'''<br />
::<math><br />
\begin{align}<br />
F & = \frac{ \sum_{j=1}^k \sum_{j=1}^{n_j} (x_{ij}-\bar{x_j})^2 }{ k-1 } \\<br />
& \div \frac{ \sum_{j=1}^k (\bar{x_j}-\bar{x})^2 }{ n-k }<br />
\end{align}<br />
</math><br />
::<math>n</math> is sample size (whole combined number of observations)<br />
::<math>k</math> is number of groups<br />
<br />
<!--<br />
::The variance of whole combined observations is <br />
::<math>s^2=\frac{\sum_{i=1}^n (x_i-\bar{x})^2}{n-1}</math><br />
::The numarator is ''sum of square''<br />
::<math>\sum_{i=1}^n (x_i-\bar{x})^2</math><br />
::<math>= \sum_{i=1}^n x_i^2 - 2\bar{x} \sum_{i=1}^n x_i + \bar{x}^2 \sum_{i=1}^n 1</math><br />
--><br />
<br />
|style="vertical-align:top"|<br />
*'''Linear regression model'''<br />
*Repeated measures ANOVA<br />
<br />
|style="vertical-align:top"|<br />
*'''Kruskall-Wallis test'''<br />
::''<math>H_0</math> is '''medians or means of ranks''' in the all population'''s''' are the same''<br />
:#To rank whole combined observations of all groups<br />
:#To separate back the ranks into original groups<br />
:#To make sum of ranks in each group<br />
::<math>H = \frac{n-1}{n} \sum_{i=1}^k \frac{n_i(\bar{R}-E_R)}{s^2}</math><br />
::<math>H</math> is Kruskal-Wallis statistics<br />
::<math>n_i</math> is number of observations in group <math>i</math><br />
::<math>\bar{R}</math> is the mean of rank sum in group <math>i</math><br />
::<math>E_R</math> is expected value of the rankings<br />
::<math>s^2</math> is the variance of rank<br />
::To look up ''critical values'' relevant to '''sum of ranks''' in '''the group of smaller number of observation'''<br />
|style="vertical-align:top"|<br />
*<nowiki>*</nowiki>''needs try to transform data into parametric (e.g., logarithmic), or other considerations''<br />
|}<br />
<br />
==Comparing Survival time==<br />
{|class="wikitable"<br />
|-<br />
!style="width:50%"|Life table<br />
!style="width:50%"|Kaplan-Meyer<br />
|-<br />
|colspan="2"|<br />
*'''Log rank test<br>= Mantel-Cox <math>\chi^2</math> test'''<br />
::<math>H_0</math> is event (survival) rates in each interval are all the same in two groups<br />
::<math>Log\ rank\ statistics = \frac{}{}</math><br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Statistical_test&diff=3039Statistical test2023-09-25T07:18:28Z<p>Vaccipedia.admin: /* Comparing Proportions */</p>
<hr />
<div>{{Floating_Menu}}<br />
<br />
==Basic concept of statistical tests==<br />
<br />
<br />
==Comparing Proportions==<br />
{|class="wikitable"<br />
|-<br />
!style="width:80px"|<br />
!style="width:250px"|Independent samples<br>(Unpaired in case of two)<br />
!style="width:250px"|Dependent samples<br>(Paired in case of two)<br />
|-<br />
!2 proportions<br />
|<br />
*'''Z test'''<br />
::<math><br />
\begin{align}<br />
z & = \frac{p_1-p_2}{SE_{pooled(p_1-p_2)}} \\<br />
& = \frac{p_1-p_2}{\sqrt{\frac{\bar{p}(1-\bar{p})}{n_1}+\frac{\bar{p}(1-\bar{p})}{n_2}}}<br />
\end{align}<br />
</math><br />
|<br />
|-<br />
!rowspan="3"|&ge; 3 proportions<br />
|''Enough large sample''<br />
*'''<math>\chi^2</math> test'''<br />
::<math>\chi^2 = \sum \frac{(O - E)^2}{E}</math><br />
::<math>O</math> = observed values<br><math>E</math> = expected values<br />
|rowspan="3" style="vertical-align:top"|<br />
*'''McNemar's <math>\chi^2</math> test'''<br />
::<math><br />
\begin{align}<br />
& McNemar's\ \chi^2 \\<br />
& = \frac{(n_1-n_2)^2}{n_1+n_2}<br />
\end{align}<br />
</math><br />
::<math>n_i</math> = number of observations in discordant pair<br />
|-<br />
|''Testing linear association''<br />
*'''<math>\chi^2</math> trend test'''<br />
::<math><br />
\begin{align}<br />
& \chi^2 trend \\<br />
& = \frac{(\bar{x_1}-\bar{x_2})^2}{s^2(\frac{1}{n_1}+\frac{1}{n_2})} \\<br />
& s = \sqrt{\sum \frac{(x_i-\bar{x_i})^2}{n-1}}<br />
\end{align}<br />
</math><br />
::<math>x_i</math> = weighted values<br />
::<math>n_i</math> = number of observations<br />
|-<br />
|''&ge;1 cell expected value <5''<br />
'''Fisher's exact test'''<br />
*very rare in real researches<br />
|}<br />
<br />
==Comparing Means==<br />
{|class="wikitable"<br />
!rowspan="2" style="width:80px"|<br />
!colspan="2"|Parametric<br>i.e., normally distributed<br />
!colspan="2"|Non-parametric<br>i.e., not normally distributed<br />
|-<br />
!style="width:250px"|Independent samples<br>(Unpaired in case of two)<br />
!style="width:250px"|Dependent samples<br>(Paired in case of two)<br />
!style="width:250px"|Independent samples<br>(Unpaired in case of two)<br />
!style="width:250px"|Dependent samples<br>(Paired in case of two)<br />
|-<br />
!rowspan="3"|2 means<br />
<br />
|''Enough large sample''<br />
*'''Z test'''<br />
::<math><br />
\begin{align}<br />
z & = \frac{\bar{x_1}-\bar{x_2}}{SE_{(\bar{x_1}-\bar{x_2})}} \\<br />
& = \frac{\bar{x_1}-\bar{x_2}}{\sqrt{\frac{s_1^2}{n_1}+\frac{s_2^2}{n_2}}}<br />
\end{align}<br />
</math><br />
<br />
|rowspan="3" style="vertical-align:top"|<br />
*'''Paired Student's t test'''<br />
::''<math>H_0</math> is '''mean of paired differences''' in the population is '''zero'''.''<br />
::<math><br />
\begin{align}<br />
paired\ t & = \frac{\bar{d}}{SE_d} \\<br />
& = \frac{\bar{d}}{\frac{s}{\sqrt{n}}} \\<br />
\end{align}<br />
</math><br />
::where <math>\bar{d}</math> is the mean of differences of paired observations<br />
<br />
|rowspan="3" style="vertical-align:top"|<br />
*'''Wilcoxon rank sum test'''<br>='''Mann-Whitney test'''<br />
::''<math>H_0</math> is '''medians or means of ranks''' in the two population'''s''' are the same''<br />
:#To rank whole combined observations of two groups<br />
:#To separate back the ranks into two groups<br />
:#To look up ''critical range'' relevant to both numbers of observations and whether '''the sum of ranks''' in '''the group of smaller number of observation''' (=statistics) is outside the range or not<br />
::if outside the range, p-value is smaller than designated<br />
<br />
|rowspan="3" style="vertical-align:top"|<br />
*'''Wilcoxon signed rank test'''<br />
::''<math>H_0</math> is '''median of paired differences''' in the population is zero''<br />
:#To calculate differences between pairs and discard 0 differences<br />
:#To rank the absolute values of differences (ignoring 0)<br />
:#To make the sum of ranks of '''positive difference''' and the sum of ranks of '''negative differences''' ('signed rank')<br />
:#To look up '''critical value''' relevant to numbers of pairs with non-0 differences and whether '''the smaller sum of rank''' (=statistics) is smaller than the critical value<br />
::if smaller than the critical value, p-value is smaller than designated<br />
<br />
|-<br />
|''Small sample size <30 in a group''<br />
*'''Student's t test'''<br />
::<math><br />
\begin{align}<br />
t & = \frac{\bar{x_1}-\bar{x_2}}{SE_{(\bar{x_1}-\bar{x_2})}} \\<br />
& = \frac{\bar{x_1}-\bar{x_2}}{\sqrt{\frac{(n_1-1)s_1^2+(n_2-1)s_2^2}{(n_1-1)+(n_2-1)}}\sqrt{\frac{1}{n_1}+\frac{1}{n_2}}}<br />
\end{align}<br />
</math><br />
<br />
|-<br />
|''Large discrepancy in SDs between groups''<br />
*Bootstrap<br />
*Non-parametric<br />
*Fisher-Behrens<br />
*Welch<br />
<br />
|-<br />
!&ge; 3 means<br />
|style="vertical-align:top"|<br />
*'''One-way ANOVA'''<br />
::<math><br />
\begin{align}<br />
F & = \frac{ \sum_{j=1}^k \sum_{j=1}^{n_j} (x_{ij}-\bar{x_j})^2 }{ k-1 } \\<br />
& \div \frac{ \sum_{j=1}^k (\bar{x_j}-\bar{x})^2 }{ n-k }<br />
\end{align}<br />
</math><br />
::<math>n</math> is sample size (whole combined number of observations)<br />
::<math>k</math> is number of groups<br />
<br />
<!--<br />
::The variance of whole combined observations is <br />
::<math>s^2=\frac{\sum_{i=1}^n (x_i-\bar{x})^2}{n-1}</math><br />
::The numarator is ''sum of square''<br />
::<math>\sum_{i=1}^n (x_i-\bar{x})^2</math><br />
::<math>= \sum_{i=1}^n x_i^2 - 2\bar{x} \sum_{i=1}^n x_i + \bar{x}^2 \sum_{i=1}^n 1</math><br />
--><br />
<br />
|style="vertical-align:top"|<br />
*'''Linear regression model'''<br />
*Repeated measures ANOVA<br />
<br />
|style="vertical-align:top"|<br />
*'''Kruskall-Wallis test'''<br />
::''<math>H_0</math> is '''medians or means of ranks''' in the all population'''s''' are the same''<br />
:#To rank whole combined observations of all groups<br />
:#To separate back the ranks into original groups<br />
:#To make sum of ranks in each group<br />
::<math>H = \frac{n-1}{n} \sum_{i=1}^k \frac{n_i(\bar{R}-E_R)}{s^2}</math><br />
::<math>H</math> is Kruskal-Wallis statistics<br />
::<math>n_i</math> is number of observations in group <math>i</math><br />
::<math>\bar{R}</math> is the mean of rank sum in group <math>i</math><br />
::<math>E_R</math> is expected value of the rankings<br />
::<math>s^2</math> is the variance of rank<br />
::To look up ''critical values'' relevant to '''sum of ranks''' in '''the group of smaller number of observation'''<br />
|style="vertical-align:top"|<br />
*<nowiki>*</nowiki>''needs try to transform data into parametric (e.g., logarithmic), or other considerations''<br />
|}<br />
<br />
==Comparing Survival time==<br />
{|class="wikitable"<br />
|-<br />
!style="width:50%"|Life table<br />
!style="width:50%"|Kaplan-Meyer<br />
|-<br />
|colspan="2"|<br />
*'''Log rank test<br>= Mantel-Cox <math>\chi^2</math> test'''<br />
::<math>H_0</math> is event (survival) rates in each interval are all the same in two groups<br />
::<math>Log\ rank\ statistics = \frac{}{}</math><br />
|}</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3038Trichinellosis (Trichinosis)2023-09-23T01:42:26Z<p>Vaccipedia.admin: /* Life cycle and Transmission */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
*Transmission to horse (obligate grazer) is speculated that pasture or hay may be accidentally contaminated by infected carcass (rodents etc.).<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
*The transmission route is speculated that soft-shelled turtles were fed by carrions of pigs dead by diseases and contaminated through the carrions.<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
*Report of trichinellosis outbreak through game bear meat in Japan.<br />
{{quote|content=<br />
海野友梨, 中本有美, & 深谷節子. (2017). 茨城県内で発生した旋毛虫による食中毒事例について. 茨城衛生研究所年報, 55, 37–41. https://www.pref.ibaraki.jp/hokenfukushi/eiken/kikaku/annualreport/documents/32_senmoutyu.pdf<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
===Nurse cell===<br />
*Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE] or the following article<br />
{{quote|content=<br />
Wu, Z., Sofronic-Milosavljevic, L., Nagano, I., & Takahashi, Y. (2008). Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair. Parasites & Vectors, 1(1), 27. https://doi.org/10.1186/1756-3305-1-27<br />
}}<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole<br />
<br />
==Prevention and Control==<br />
{|class="wikitable"<br />
|-<br />
!style="width:50%"|Heat<br />
!style="width:50%"|Freezing<br />
|-<br />
|rowspan="2"|<br />
*Meat core temperature '''≥71&deg;C '''for''' ≥1 min'''<br />
**Color to gray, muscle fibers separated<br />
|<br />
Up to '''15cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥3 weeks'''<br />
|-<br />
|<br />
Up to '''50cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥4 weeks'''<br />
|-<br />
|<br />
|※'''Applicable only to ''T. spiralis'' in pork'''<br />
|}<br />
<br />
※Other species are more resistant to cold temperature<br />
*''T. britovi'' in pork survived for 3 weeks at -20&deg;C<br />
*''T. spiralis'' in horse survived for 4 weeks at -18&deg;C<br />
*Game meat like bear harbors freeze-resistant ''Trichinella''<br />
**5 years in bear meat</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3037Trichinellosis (Trichinosis)2023-09-23T01:41:13Z<p>Vaccipedia.admin: /* Life cycle and Transmission */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
*Transmission to horse (obligate grazer) is speculated that pasture or hay may be accidentally contaminated by infected carcass (rodents etc.).<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
*The transmission route is speculated that soft-shelled turtles were fed by carrions of pigs dead by diseases and contaminated through the carrions.<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
===Nurse cell===<br />
*Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE] or the following article<br />
{{quote|content=<br />
Wu, Z., Sofronic-Milosavljevic, L., Nagano, I., & Takahashi, Y. (2008). Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair. Parasites & Vectors, 1(1), 27. https://doi.org/10.1186/1756-3305-1-27<br />
}}<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole<br />
<br />
==Prevention and Control==<br />
{|class="wikitable"<br />
|-<br />
!style="width:50%"|Heat<br />
!style="width:50%"|Freezing<br />
|-<br />
|rowspan="2"|<br />
*Meat core temperature '''≥71&deg;C '''for''' ≥1 min'''<br />
**Color to gray, muscle fibers separated<br />
|<br />
Up to '''15cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥3 weeks'''<br />
|-<br />
|<br />
Up to '''50cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥4 weeks'''<br />
|-<br />
|<br />
|※'''Applicable only to ''T. spiralis'' in pork'''<br />
|}<br />
<br />
※Other species are more resistant to cold temperature<br />
*''T. britovi'' in pork survived for 3 weeks at -20&deg;C<br />
*''T. spiralis'' in horse survived for 4 weeks at -18&deg;C<br />
*Game meat like bear harbors freeze-resistant ''Trichinella''<br />
**5 years in bear meat</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3036Trichinellosis (Trichinosis)2023-09-23T01:40:55Z<p>Vaccipedia.admin: /* Life cycle and Transmission */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
**Transmission to horse (obligate grazer) is speculated that pasture or hay may be accidentally contaminated by infected carcass (rodents etc.).<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
*The transmission route is speculated that soft-shelled turtles were fed by carrions of pigs dead by diseases and contaminated through the carrions.<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
===Nurse cell===<br />
*Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE] or the following article<br />
{{quote|content=<br />
Wu, Z., Sofronic-Milosavljevic, L., Nagano, I., & Takahashi, Y. (2008). Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair. Parasites & Vectors, 1(1), 27. https://doi.org/10.1186/1756-3305-1-27<br />
}}<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole<br />
<br />
==Prevention and Control==<br />
{|class="wikitable"<br />
|-<br />
!style="width:50%"|Heat<br />
!style="width:50%"|Freezing<br />
|-<br />
|rowspan="2"|<br />
*Meat core temperature '''≥71&deg;C '''for''' ≥1 min'''<br />
**Color to gray, muscle fibers separated<br />
|<br />
Up to '''15cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥3 weeks'''<br />
|-<br />
|<br />
Up to '''50cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥4 weeks'''<br />
|-<br />
|<br />
|※'''Applicable only to ''T. spiralis'' in pork'''<br />
|}<br />
<br />
※Other species are more resistant to cold temperature<br />
*''T. britovi'' in pork survived for 3 weeks at -20&deg;C<br />
*''T. spiralis'' in horse survived for 4 weeks at -18&deg;C<br />
*Game meat like bear harbors freeze-resistant ''Trichinella''<br />
**5 years in bear meat</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3035Trichinellosis (Trichinosis)2023-09-23T01:14:05Z<p>Vaccipedia.admin: /* Prevention and Control */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
*The transmission route is speculated that soft-shelled turtles were fed by carrions of pigs dead by diseases and contaminated through the carrions.<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
===Nurse cell===<br />
*Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE] or the following article<br />
{{quote|content=<br />
Wu, Z., Sofronic-Milosavljevic, L., Nagano, I., & Takahashi, Y. (2008). Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair. Parasites & Vectors, 1(1), 27. https://doi.org/10.1186/1756-3305-1-27<br />
}}<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole<br />
<br />
==Prevention and Control==<br />
{|class="wikitable"<br />
|-<br />
!style="width:50%"|Heat<br />
!style="width:50%"|Freezing<br />
|-<br />
|rowspan="2"|<br />
*Meat core temperature '''≥71&deg;C '''for''' ≥1 min'''<br />
**Color to gray, muscle fibers separated<br />
|<br />
Up to '''15cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥3 weeks'''<br />
|-<br />
|<br />
Up to '''50cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥4 weeks'''<br />
|-<br />
|<br />
|※'''Applicable only to ''T. spiralis'' in pork'''<br />
|}<br />
<br />
※Other species are more resistant to cold temperature<br />
*''T. britovi'' in pork survived for 3 weeks at -20&deg;C<br />
*''T. spiralis'' in horse survived for 4 weeks at -18&deg;C<br />
*Game meat like bear harbors freeze-resistant ''Trichinella''<br />
**5 years in bear meat</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3034Trichinellosis (Trichinosis)2023-09-23T01:13:52Z<p>Vaccipedia.admin: /* Prevention and Control */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
*The transmission route is speculated that soft-shelled turtles were fed by carrions of pigs dead by diseases and contaminated through the carrions.<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
===Nurse cell===<br />
*Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE] or the following article<br />
{{quote|content=<br />
Wu, Z., Sofronic-Milosavljevic, L., Nagano, I., & Takahashi, Y. (2008). Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair. Parasites & Vectors, 1(1), 27. https://doi.org/10.1186/1756-3305-1-27<br />
}}<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole<br />
<br />
==Prevention and Control==<br />
{|class="wikitable"<br />
|-<br />
!style="width:50%"|Heat<br />
!style="width:50%"|Freezing<br />
|-<br />
|rowspan="2"|<br />
*Meat core temperature '''≥71&deg;C '''for''' ≥1 min'''<br />
**Color to gray, muscle fibers separated<br />
|<br />
Up to '''15cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥3 weeks'''<br />
|-<br />
|<br />
Up to '''50cm thickness''' meat block<br />
*'''≤-15&deg;C '''for''' ≥4 weeks'''<br />
|-<br />
|<br />
|※Applicable only to ''T. spiralis'' in pork<br />
|}<br />
<br />
※Other species are more resistant to cold temperature<br />
*''T. britovi'' in pork survived for 3 weeks at -20&deg;C<br />
*''T. spiralis'' in horse survived for 4 weeks at -18&deg;C<br />
*Game meat like bear harbors freeze-resistant ''Trichinella''<br />
**5 years in bear meat</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3033Trichinellosis (Trichinosis)2023-09-23T01:09:56Z<p>Vaccipedia.admin: /* Treatment */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
*The transmission route is speculated that soft-shelled turtles were fed by carrions of pigs dead by diseases and contaminated through the carrions.<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
===Nurse cell===<br />
*Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE] or the following article<br />
{{quote|content=<br />
Wu, Z., Sofronic-Milosavljevic, L., Nagano, I., & Takahashi, Y. (2008). Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair. Parasites & Vectors, 1(1), 27. https://doi.org/10.1186/1756-3305-1-27<br />
}}<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole<br />
<br />
==Prevention and Control==<br />
{|class="wikitable"<br />
|-<br />
!style="width:50%"|Heat<br />
!style="width:50%"|Freezing<br />
|-<br />
|rowspan="2"|<br />
*Meat core temperature '''≥71&deg;C for ≥1 min'''<br />
**Color to gray, muscle fibers separated<br />
|<br />
Up to '''15cm thickness''' meat block<br />
*'''≤-15&deg;C for ≥3 weeks'''<br />
|-<br />
|<br />
Up to '''50cm thickness''' meat block<br />
*'''≤-15&deg;C for ≥4 weeks'''<br />
|-<br />
|<br />
|※Applicable only to pork with ''T. spiralis''<br />
|}<br />
<br />
※</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3032Trichinellosis (Trichinosis)2023-09-22T06:15:01Z<p>Vaccipedia.admin: /* Life cycle and Transmission */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
*The transmission route is speculated that soft-shelled turtles were fed by carrions of pigs dead by diseases and contaminated through the carrions.<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
===Nurse cell===<br />
*Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE] or the following article<br />
{{quote|content=<br />
Wu, Z., Sofronic-Milosavljevic, L., Nagano, I., & Takahashi, Y. (2008). Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair. Parasites & Vectors, 1(1), 27. https://doi.org/10.1186/1756-3305-1-27<br />
}}<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3031Trichinellosis (Trichinosis)2023-09-22T05:32:47Z<p>Vaccipedia.admin: /* Human disease */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
===Nurse cell===<br />
*Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE] or the following article<br />
{{quote|content=<br />
Wu, Z., Sofronic-Milosavljevic, L., Nagano, I., & Takahashi, Y. (2008). Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair. Parasites & Vectors, 1(1), 27. https://doi.org/10.1186/1756-3305-1-27<br />
}}<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3030Trichinellosis (Trichinosis)2023-09-22T05:16:49Z<p>Vaccipedia.admin: /* Learning resources */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
*[http://www.ichiryusha.com/book/index.php?main_page=product_info&cPath=23&products_id=1154 Illustrated ''Trichinella'' written by Yuzo Takahashi] (not for sale)<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
###Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE]<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole</div>Vaccipedia.adminhttp://vaccipedia.jp/index.php?title=Trichinellosis_(Trichinosis)&diff=3029Trichinellosis (Trichinosis)2023-09-22T05:13:58Z<p>Vaccipedia.admin: /* Human disease */</p>
<hr />
<div>{{TM menu}}<br />
<br />
==Learning resources==<br />
*旋毛虫 in Japanese<br />
<br />
*[https://www.trichinella.org/home THE TRICHINELLA PAGE]<br />
*[https://www.cdc.gov/dpdx/trichinellosis/index.html Trichinellosis - DPDx by US CDC]<br />
<br />
==Pathogen and Taxonomy==<br />
*The genus ''Trichinella'' has '''genetically distinguished''' but '''taxonomically still undetermined''' genotypes other than usual species<br />
*The biggest morphological classification is based on the presence/absence of collagen capsule surrounding the pathogen in cysts in infected muscles<br />
<br />
{|class="wikitable" <br />
|-<br />
!style="width:50%"|Encapsulated<br />
!style="width:50%"|Non-encapsulated<br />
|-style="text-align:center"<br />
|Infect only mammals<br />
|Infect birds and mammals<br />
|-style="vertical-align:top"<br />
|<br />
*''Trichinella spiralis''<br />
*''Trichinella nativa''<br />
*''Trichinella nelsoni''<br />
*''Trichinella britovi''<br />
*''Trichinella murrelli''<br />
*''Trichinella patagoniensis''<br />
*''Trichinella'' genotype T6<br />
*''Trichinella'' genotype T8<br />
*''Trichinella'' genotype T9<br />
|<br />
*''Trichinella pseudospiralis''<br />
*''Trichinella papuae''<br />
*''Trichinella zimbabwensis''<br />
|}<br />
<br />
※Manson's Tropical Infectious Diseases 24th ed. (published in 2023) describes that ''T. spiralis'' has several subspecies but according to [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6333&lvl=3&keep=1&srchmode=1&unlock '''NCBI Taxonomy Browser'''] and the following articles subspecies written in Manson's are classified as species.<br />
<br />
{{quote|content=<br />
Pozio, E., Rosa, G. la, Murrell, K. D., & Lichtenfels, J. R. (1992). Taxonomic Revision of the Genus Trichinella. The Journal of Parasitology, 78(4), 654. https://doi.org/10.2307/3283540<br />
}}<br />
<br />
{{quote|content=<br />
Zarlenga, D., Thompson, P., & Pozio, E. (2020). Trichinella species and genotypes. Research in Veterinary Science, 133, 289–296. https://doi.org/10.1016/j.rvsc.2020.08.012<br />
}}<br />
<br />
==Epidemiology==<br />
*Since ''Trichinella'' infections often cause asymptomatic or mild disease and no serological tests with high performance is available, true epidemiology of human trichinellosis is thought still underestimated.<br />
*Trichinellosis distributes '''worldwide''' from '''arctic region''' through '''the tropics'''.<br />
*Human trichinellosis in developed countries has been dramatically decreased due to improvement of farming and slaughtering of domestic pigs and shrinkage of backyard pig farming in private facilities.<br />
<br />
{{quote|content=<br />
Yayeh, M., Yadesa, G., Erara, M., Fantahun, S., Gebru, A., & Birhan, M. (2020). Epidemiology, diagnosis and public health importance of Trichinellosis. Journal of World’s Poultry Research, 10(3), 131–139. https://doi.org/10.36380/scil.2020.ojafr18<br />
}}<br />
<br />
*Distribution of species (directly linked from [https://www.trichinella.org/home THE TRICHINELLA PAGE])<br />
<br />
https://images.squarespace-cdn.com/content/v1/5adf9528f93fd46f6d3ddb95/1533145049330-8G0LCIZZ85UXA9J9CYP2/geodistribution.gif<br />
<br />
==Life cycle and Transmission==<br />
*Life cycle is maintained amongst host mammals and birds.<br />
**Pigs and rats (domestic cycle) or wild bores, wild bears, polar bears, rats and birds (sylvatic cycle).<br />
**Humans are '''accidental (deadend) hosts''' for ''Trichinella''<br />
**'''Only humans develop clinical symptoms by ''Trichinella'' infection'''<br />
*Refer to [https://www.cdc.gov/dpdx/trichinellosis/index.html DPDx - Trichinellosis]<br />
https://www.cdc.gov/dpdx/trichinellosis/modules/Trichinella_LifeCycle.gif<br />
<br />
*Transmission to human occurs by ingestion of raw or undercooked meat including '''pigs''', '''wild bores''', '''horse''', '''dog''', '''bear''', '''polar bear''', '''badger''' and '''soft-shelled turtle (スッポン)'''.<br />
<br />
{{quote|content=<br />
Rostami, A., Gamble, H. R., Dupouy-Camet, J., Khazan, H., & Bruschi, F. (2017). Meat sources of infection for outbreaks of human trichinellosis. Food Microbiology, 64, 65–71. https://doi.org/10.1016/j.fm.2016.12.012<br />
}}<br />
<br />
*'''The world-first report''' of trichinellosis originated from '''soft-shelled turtle''' was published in Japan in 2009 (but only in Japanese and neglected from English literature).<br />
<br />
{{quote|content=<br />
前田卓哉, 藤井毅, 岩本愛吉, 長野功, 呉志良, & 高橋優三. (2009). スッポンを感染源とする旋毛虫症例. 病原微生物検出情報, 30(10), 272–273. https://idsc.niid.go.jp/iasr/30/356/kj3563.html<br />
}}<br />
<br />
==Human disease==<br />
*Humans are '''accidental (deadend) hosts'''.<br />
#Ingestion of larvae-infected meat<br />
#'''Enteric phase'''<br />
##In 2-7 days incubation, larvae penetrate duodenal and jejunal mucosa<br />
##Nausea, vomitting, abdominal colic, fever<br />
###Maculopapular skin rash and pneumonitis may accompany<br />
#'''Migration (invasion) phase'''<br />
##Larvae invade blood vessels and migrate toward striated muscle cells in '''diaphragm''', '''masseters''', '''intercostals''', '''laryngeal''', '''tongue''' and '''ocular muscles'''<br />
##Severe myalgia, difficulty of mastication, difficulty of breathing, dysphagia, periorbital edema, paralysis of extremities, high fever, petechiae in nails and conjunctivae<br />
##Eosinophilia arises but subsides in a week<br />
###In some case myocardial complication, neurological complication occurs<br />
#'''Encystment phase'''<br />
##Weeks after infection, larvae encyst in striated muscles they arrived<br />
##Cachexia, edema, extreme dehydration<br />
##In 6 months calcification of cysts takes place<br />
##Inside calcified cysts, '''<nowiki>'</nowiki>nurse cells<nowiki>'</nowiki>''' which is transformed from normal striated muscle cells by larvae secretion encapsulate and nourish larvae<br />
###Refer to [https://www.trichinella.org/the-nurse-cell Nurse cell formation in THE TRICHINELLA PAGE]<br />
##'''Encapsulated larvae can survive months to decades in human striated muscles'''<br />
*The larger number of larvae infect, the more severe symptoms are<br />
**<10 larvae: asymptomatic to mild<br />
**50-500 larvae: moderate<br />
**<1000 larvae: severe to fatal<br />
<br />
==Diagnosis==<br />
{|class="wikitable" style="width:800px"<br />
|+Case definitions by ECDC<br />
|-<br />
!style="width:33%"|Clinical<br />
!style="width:33%"|Laboratory<br />
!style="width:33%"|Epidemiological<br />
|-style="vertical-align:top"<br />
|At least 3 of<br />
*Fever<br />
*Myalgia<br />
*Gastrointestinal symptoms<br />
*Facial edema<br />
*Eosinophillia<br />
*Subconjunctival, sublingual and retinal hemorrhage<br />
|At least 1 of<br />
*''Trichinella'' larvae in muscle biopsy specimen<br />
*''Trichinella''-specific antibody by ELISA or Western blot<br />
|At least 1 of<br />
*Ingestion of laboratory-confirmed contaminated meat<br />
*Ingestion of potentially contaminated meat from laboratory-confirmed infected animal<br />
*Epidemiological link to laboratory-confirmed human case with the common source<br />
|}<br />
{{quote|content=<br />
Gottstein, B., Pozio, E., & Nöckler, K. (2009). Epidemiology, Diagnosis, Treatment, and Control of Trichinellosis. Clinical Microbiology Reviews, 22(1), 127–145. https://doi.org/10.1128/CMR.00026-08<br />
}}<br />
<br />
<br />
*'''Trichinoscopy'''<br />
**Encystment phase begins 1 week after infection at the shortest<br />
**Muscle biopsy specimen is thin-sliced and pressed between two slides without any stain and cysts are observed<br />
*ELISA for antibody detection is common<br />
*Multiplex PCR is also used<br />
<br />
===Differential diagnoses===<br />
*Trichinellosis is a great mimicker<br />
**Typhoid, encephalitis, myositis, tetanus, Katayama syndrome, hookworm infection, strongyloidiasis, periarthritis nodosa, rheumatoid arthritis<br />
<br />
==Treatment==<br />
*Albendazole and mebendazole</div>Vaccipedia.admin