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anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

05.02.2026	current
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	+	</style><div id="homecolumns"></html>
	+
	+
	+	~~NOTOC~~
	+
	+
	+
	+	====== Home ======
	+
	+
	+	<columns 100% 62% 2% 35% ->
	+
	+
	+	<html><h2 style="font-size: 24px; font-weight: bold;">Welcome to the MPKB</h2></html>
	+
	+	The Marshall Protocol or MP is a therapy for chronic inflammatory diseases devised by Trevor Marshall, PhD. The MP is based on an explanation for how an infectious cascade of pathogens slow the immune response and allow for subsequent infections to proliferate, thereby causing the symptoms and markers of disease.
	+
	+	<html><h2 style="font-size: 24px; font-weight: bold;">Search</h2></html>
	+
	+	<phpinc=homesearch.php>
	+
	+	\\
	+
	+
	+
	+	<html>
	+	<div class="homelinks">
	+	<h2 class="homelinksheader">For Patients</h2></html>
	+	\\
	+	* Why microbes may cause chronic inflammatory diseases
	+	* [[home:patients:pathogenesis_overview\|Introduction to the Marshall Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:pathogenesis:microbiota\|Microbes in the human body]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:pathogenesis:evidence_bacteria\|The available evidence]]
	+	* What is the Marshall Protocol? – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:patients:protocol_overview\|Introduction]]
	+	* [[home:patients:mp_duration\|Length]] – may take several years depending on how sick a patient is
	+	* [[home:patients:cost_of_mp\|Cost]] – insurance often pays for certain basic expenses; drugs can be [[home:mp:olmesartan:buying\|ordered online]] at a discount
	+	* [[home:patients:assessing_literature:palliative\|Palliative vs. curative treatments]] – many widely used treatments and supplements such as vitamin D compromise the immune response to microbes and are therefore contraindicated
	+	* Considering the Marshall Protocol
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:tests:vitdinterpretation\|Vitamin D Metabolite Calculator]] – get automated feedback on vitamin D blood tests
	+	* [[home:patients:patient_interviews\|Patient interviews]]
	+	* Starting the treatment – [[home:starting\|Overview]] \| [[home:starting:prempchecklist\|Checklist]]
	+	* Physicians – [[home:starting:physician:finding\|Finding a physician]] \| [[home:starting:physician\|Working with a physician]]
	+	* The Protocol – [[home:mp\|In-depth overview of the Protocol]] \| [[home:translations\|Translations of this and other articles]]
	+	* [[home:mp:immunopathology\|Immunopathology]] – temporary increase in disease symptoms experienced by MP patients that is the result of microbial death; appears to be necessary for recovery
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:lifestyle:light\|Light restriction]] – patients who are photosensitive on the MP become less symptomatic when they limit skin exposure to light when [[home:lifestyle:light:outdoor\|outdoors]], and skin and [[home:lifestyle:light:eye_protection\|eye exposure]] when [[home:lifestyle:light:indoor\|indoors]]
	+	* [[home:food\|Food & drink]] – patients limit vitamin D
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* Learn more
	+	* [[home:index\|Site map]] contains a list of all articles in the KB
	+	* [[home:patients:glossary\|Glossary of terms]]
	+
	+	<html>
	+	</div>
	+
	+
	+	<div class="homelinks">
	+	<h2 class="homelinksheader">For Physicians</h2></html>
	+
	+	* [[home:physicians\|Resources for physicians]]
	+	* [[home:pathogenesis\|The Marshall Pathogenesis]]
	+	* [[home:protocol:immunopathology\|About immunopathology a.k.a. the Jarisch-Herxheimer reaction]]
	+	* Safety of the Protocol – [[home:protocol:olmesartan:safety\|olmesartan (Benicar)]], [[home:protocol:mp_antibiotics:antibiotics_concerns\|antibiotics]]
	+	* [[home:mp\|Summary of MP]], [[https://autoimmunityResearch.org/phase1.pdf\|Guidelines]]
	+	* [[home:physicians:concerns\|Physicians' concerns]]
	+	* [[home:physicians:emergency\|Notice for emergency]]
	+	<html>
	+	</div>
	+	</html>
	+
	+	<newcolumn top>
	+
	+
	+	<newcolumn top>
	+	<html><div class="highlightedh2" style="color: #f8f8f8 !important;">News and highlights</div></html>
	+
	+	<phpinc=twit.php>
	+
	+	\\
	+
	+	<html><div class="highlightedh2" style="color: #f8f8f8 !important; margin-top: 0px !important;">Publications/presentations</div></html>
	+	\|[[home:publications:proal_molecular_2011\|Immunostimulation in the era of the human metagenome]] - paper in //Molecular and clinical immunology// that reviews a case series of Marshall Protocol patients and discusses how immunostimulatory approaches may require rethinking medicine \|
	+	\|[[home:publications:proal_metagenomics_2010\|Autoimmune disease and the human metagenome]] - book chapter in Springer's //Metagenomics of the human body// that discusses how the process of <html>successive infection may be responsible for autoimmune disease</html> \|
	+	\|[[home:publications:marshall_autoimmunity_2010\|Olmesartan overcomes antibiotic resistance, inducing recovery from advanced autoimmune disease]] – presentation by Trevor Marshall, PhD at International Congress on <html>Autoimmunity</html> \|
	+	\|[[home:publications:blaney_autoimmunity_2010\|Olmesartan medoxomil and treatment of autoimmune disease]] – presentation by Greg Blaney, MD \\ \\ → [[home:publications\|Complete list]]\|
	+
	+
	+	=== About the MPKB Project ===
	+	The MPKB currently contains about 400 pages and draws from the best possible evidence to support its mission. As of May 2011, about 85% of those articles are complete with the remainder scheduled to be completed.
	+	* [[home:index#site_map\|Site Map]] (formerly on the home page)
	+	* [[home:index#incomplete_articles\|Incomplete articles]]
	+	* [[home:patients:tipsformpkb\|Tips for using this resource]]
	+
	+
	+	=== About Autoimmunity Research Foundation ===
	+
	+	[[https://autoimmunityresearch.org\|Autoimmunity Research Foundation]] is a California-based 501(c)3 (tax deductible) non-profit formed to educate the public about the nature of, and study a treatment for, chronic inflammatory disease.
	+	* [[home:arf:timeline\|History and timeline of the Autoimmunity Research Foundation]]
	+
	+	</columns>
	+

Home

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

05.02.2026	current
Line 1:	Line 1:
	+	<html><style type="text/css">
	+	.breadcrumbs {display: none;}
	+	.gsc-completion-container {
	+	font-family: helvetica, sans-serif !important;
	+	font-size: 18px !important;
	+	border: 1px solid #666666;
	+	margin-left: 0;
	+	margin-right: 0;
	+	/* The top, left, and width are set in JavaScript. */
	+	-moz-box-shadow: 5px 5px 5px #999;
	+	-webkit-box-shadow: 5px 5px 5px #999;
	+	box-shadow: 5px 5px 5px #999;
	+	background-color: #fafafa; /* Needed for IEs */
	+	}
	+
	+	.gsc-completion-container > tbody {
	+	position: relative; /* This protects the inner element from being blurred */
	+	background-color: #DDD; }
	+
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	+	td#csc-completion-selected { background: #FEFAF4 !important; }
	+
	+
	+
	+
	+	</style></html>
	+
	+	~~NOTOC~~
	+
	+
	+	====== Home ======
	+	<WRAP homepage>
	+
	+
	+
	+	<columns 100% 62% 2% 35% ->
	+
	+
	+	<WRAP h2 welcome>Welcome to the MPKB</WRAP>
	+
	+
	+	The <html>Marshall Protocol</html> is a therapy for chronic inflammatory diseases created by Trevor Marshall, PhD. It is based on an explanation for how an infectious cascade of pathogens slow the immune response, allowing subsequent infections to proliferate, thereby causing the symptoms and markers of disease.
	+
	+	<WRAP h2>Search</WRAP><phpinc=homesearch.html>
	+	<WRAP tabber><WRAP tabbertab><html><h3>For Patients</h3></html>
	+	* Why microbes may cause chronic inflammatory diseases
	+	* [[home:patients:pathogenesis_overview\|Introduction to the Marshall Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:familial_aggregation\|Familial aggregation]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:pathogenesis:microbiota\|Microbes in the human body]]
	+	* [[home:pathogenesis:evidence_bacteria\|Evidence that chronic disease is caused by pathogens]]
	+	* <html><b>What is the Marshall Protocol?</b></html> – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:patients:protocol_overview\|Introduction]]
	+	* [[home:patients:mp_duration\|Length]] – may take several years depending on how sick a patient is
	+	* [[home:patients:cost_of_mp\|Cost]] – insurance often pays for certain basic expenses; drugs can be [[home:mp:olmesartan:buying\|ordered online]] at a discount
	+	* [[home:patients:assessing_literature:palliative\|Palliative vs. curative treatments]] – many widely used treatments and supplements such as vitamin D compromise the immune response to microbes and are therefore contraindicated
	+	* <html><b>Considering the Marshall Protocol</b></html>
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:tests:vitdinterpretation\|Vitamin D Metabolite Calculator]] – get automated feedback on vitamin D blood tests
	+	* [[home:patients:patient_interviews\|Patient interviews]]
	+	* Starting the treatment – [[home:starting\|Overview]] \| [[home:starting:prempchecklist\|Checklist]]
	+	* Physicians – [[home:starting:physician:finding\|Finding a physician]] \| [[home:starting:physician\|Working with a physician]]
	+	* The Protocol – [[home:mp\|In-depth overview of the Protocol]] \| [[home:translations\|Translations of this and other articles]]
	+	* [[home:mp:immunopathology\|Immunopathology]] – temporary increase in disease symptoms experienced by MP patients that is the result of microbial death; appears to be necessary for recovery
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:lifestyle:light\|Light restriction]] – patients who are photosensitive on the MP become less symptomatic when they limit skin exposure to light when [[home:lifestyle:light:outdoor\|outdoors]], and skin and [[home:lifestyle:light:eye_protection\|eye exposure]] when [[home:lifestyle:light:indoor\|indoors]]
	+	* [[home:food\|Food & drink]] – patients limit vitamin D
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* Learn more
	+	* [[home:index\|Site map]] – contains a list of all articles in the KB
	+	* [[home:publications\|Publications and presentations]]
	+	* [[home:patients:glossary\|Glossary of terms]]
	+	</WRAP>
	+	<WRAP tabbertab><html><h3>For Physicians</h3></html>
	+	* <html><b>The Marshall Pathogenesis</b></html> – an explanation for how microbes may cause chronic inflammatory diseases
	+	* [[home:pathogenesis\|Science behind Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:pathogenesis:evidence_bacteria\|Evidence that chronic disease is caused by pathogens]]
	+	* [[home:pathogenesis:vitamind\|Science behind vitamin D]] \| [[home:pathogenesis:vitamind:metabolism\|Metabolism of vitamin D and the Vitamin D Receptor]]
	+	* <html><b>What is the Marshall Protocol?</b></html> – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:mp\|Marshall Protocol]] – one-page summary of the MP geared towards physicians
	+	* [[home:physicians:concerns\|Physicians' concerns]] – olmesartan, antibiotics, light, vitamin D, <html>immunopathology</html>, clinical evidence
	+	* [[home:protocol:olmesartan\|Olmesartan (Benicar)]] – [[home:protocol:olmesartan:safety\|Safety of olmesartan]] \| [[home:protocol:olmesartan:kidney_disease\|Olmesartan and kidney disease]]
	+	* Antibiotics – [[home:protocol:mp_antibiotics:dosing\|Pulsed low-dose antibiotics]] \| [[home:protocol:mp_antibiotics:antibiotics_concerns\|Safety]]
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:protocol:immunopathology\|Immunopathology]] – also known as the Jarisch-Herxheimer reaction
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* [[home:physicians:emergency\|Notice for emergency]]
	+	* Alternative models for chronic disease
	+	* [[home:alternate:autoimmunity\|Autoimmune theory of disease]]
	+	* [[home:alternate:genetic_predisposition\|Genetic predisposition to disease]]
	+	* [[home:alternate:psychosomatic\|Psychosomatic explanations for disease]]
	+	* Learn more
	+	* [[home:physicians\|Resources for physicians]]
	+	* [[home:publications\|Publications and presentations]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:patients:glossary\|Glossary of terms]]
	+	* [[home:index\|Site map]] – contains a list of all articles in the KB
	+
	+
	+
	+	</WRAP></WRAP><newcolumn top>
	+
	+	<newcolumn top>
	+	<html><div class="highlightedh2">News and highlights </div></html><phpinc=twit.html>
	+
	+
	+	<html><div class="highlightedh2" style="margin-top: 18px !important;">Publications and presentations</div></html>
	+	\|[[home:publications:proal_molecular_2011\|Immunostimulation in the era of the human metagenome]] - paper in //Molecular and clinical immunology// that reviews a case series of <html>Marshall Protocol</html> patients and discusses how immunostimulatory approaches may require rethinking medicine \|
	+	\|[[home:publications:proal_metagenomics_2010\|Autoimmune disease and the human metagenome]] - book chapter in Springer's //Metagenomics of the human body// that discusses how the process of <html>successive infection may be responsible for autoimmune disease</html> \|
	+	\|[[home:publications:marshall_autoimmunity_2010\|Olmesartan overcomes antibiotic resistance, inducing recovery from advanced autoimmune disease]] – presentation by Trevor Marshall, PhD at International Congress on <html>Autoimmunity</html> \|
	+	\|[[home:publications:blaney_autoimmunity_2010\|Olmesartan medoxomil and treatment of autoimmune disease]] – presentation by Greg Blaney, MD \\ \\ → [[home:publications\|Complete list]]\|
	+
	+
	+	<WRAP h4>About the MPKB Project</WRAP>
	+
	+	The MPKB currently contains about 400 pages and draws from the best possible evidence to support its mission. As of May 2011, about 85% of those articles are complete with the remainder scheduled to be completed.
	+	* [[home:index#site_map\|Site Map]] (formerly on the home page)
	+	* [[home:index#incomplete_articles\|Incomplete articles]]
	+	* [[home:patients:tipsformpkb\|Tips for using this resource]]
	+
	+	<WRAP h4>About Autoimmunity Research Foundation</WRAP>
	+
	+	[[https://autoimmunityresearch.org\|Autoimmunity Research Foundation]] is a California-based 501(c)3 (tax deductible) non-profit formed to educate the public about the nature of, and study a treatment for, chronic inflammatory disease.
	+	* [[home:arf:timeline\|History and timeline of the Autoimmunity Research Foundation]]
	+
	+	</columns>
	+	</WRAP>
	+

Home

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

05.02.2026	current
Line 1:	Line 1:
	+	<html><style type="text/css">
	+	.breadcrumbs {display: none;}
	+	.gsc-completion-container {
	+	font-family: helvetica, sans-serif !important;
	+	font-size: 18px !important;
	+	border: 1px solid #666666;
	+	margin-left: 0;
	+	margin-right: 0;
	+	/* The top, left, and width are set in JavaScript. */
	+	-moz-box-shadow: 5px 5px 5px #999;
	+	-webkit-box-shadow: 5px 5px 5px #999;
	+	box-shadow: 5px 5px 5px #999;
	+	background-color: #fafafa; /* Needed for IEs */
	+	}
	+
	+	.gsc-completion-container > tbody {
	+	position: relative; /* This protects the inner element from being blurred */
	+	background-color: #DDD; }
	+
	+	.gsc-completion-container > tbody > tr > td { padding: 5px; }
	+	td#csc-completion-selected { background: #FEFAF4 !important; }
	+
	+	</style></html>
	+
	+	~~NOTOC~~
	+
	+
	+	====== Home ======
	+	<WRAP homepage>
	+
	+
	+	<WRAP leftdivhome><WRAP h2 welcome>Welcome to the MPKB</WRAP>
	+
	+	The <html>Marshall Protocol</html> is a therapy for chronic inflammatory diseases created by Trevor Marshall, PhD. It is based on an explanation for how an infectious cascade of pathogens slow the immune response, allowing subsequent infections to proliferate, thereby causing the symptoms and markers of disease.
	+
	+	<WRAP h2>Search</WRAP><phpinc=homesearch.html>
	+	<WRAP tabber><WRAP tabbertab><html><h3>For Patients</h3></html>
	+	* Why microbes may cause chronic inflammatory diseases
	+	* [[home:patients:pathogenesis_overview\|Introduction to the Marshall Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:familial_aggregation\|Familial aggregation]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:pathogenesis:microbiota\|Microbes in the human body]]
	+	* [[home:pathogenesis:evidence_bacteria\|Evidence that chronic disease is caused by pathogens]]
	+	* <html><b>What is the Marshall Protocol?</b></html> – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:patients:protocol_overview\|Introduction]]
	+	* [[home:patients:mp_duration\|Length]] – may take several years depending on how sick a patient is
	+	* [[home:patients:cost_of_mp\|Cost]] – insurance often pays for certain basic expenses; drugs can be [[home:mp:olmesartan:buying\|ordered online]] at a discount
	+	* [[home:patients:assessing_literature:palliative\|Palliative vs. curative treatments]] – many widely used treatments and supplements such as vitamin D compromise the immune response to microbes and are therefore contraindicated
	+	* <html><b>Considering the Marshall Protocol</b></html>
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:tests:vitdinterpretation\|Vitamin D Metabolite Calculator]] – get automated feedback on vitamin D blood tests
	+	* [[home:patients:patient_interviews\|Patient interviews]]
	+	* Starting the treatment – [[home:starting\|Overview]] \| [[home:starting:prempchecklist\|Checklist]]
	+	* Physicians – [[home:starting:physician:finding\|Finding a physician]] \| [[home:starting:physician\|Working with a physician]]
	+	* The Protocol – [[home:mp\|In-depth overview of the Protocol]] \| [[home:translations\|Translations of this and other articles]]
	+	* [[home:mp:immunopathology\|Immunopathology]] – temporary increase in disease symptoms experienced by MP patients that is the result of microbial death; appears to be necessary for recovery
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:lifestyle:light\|Light restriction]] – patients who are photosensitive on the MP become less symptomatic when they limit skin exposure to light when [[home:lifestyle:light:outdoor\|outdoors]], and skin and [[home:lifestyle:light:eye_protection\|eye exposure]] when [[home:lifestyle:light:indoor\|indoors]]
	+	* [[home:food\|Food & drink]] – patients limit vitamin D
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* Learn more
	+	* [[home:index\|Site map]] – contains a list of all articles in the KB
	+	* [[home:publications\|Publications and presentations]]
	+	* [[home:patients:glossary\|Glossary of terms]]
	+	</WRAP>
	+	<WRAP tabbertab><html><h3>For Physicians</h3></html>
	+	* <html><b>The Marshall Pathogenesis</b></html> – an explanation for how microbes may cause chronic inflammatory diseases
	+	* [[home:pathogenesis\|Science behind Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:pathogenesis:evidence_bacteria\|Evidence that chronic disease is caused by pathogens]]
	+	* [[home:pathogenesis:vitamind\|Science behind vitamin D]] \| [[home:pathogenesis:vitamind:metabolism\|Metabolism of vitamin D and the Vitamin D Receptor]]
	+	* <html><b>What is the Marshall Protocol?</b></html> – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:mp\|Marshall Protocol]] – one-page summary of the MP geared towards physicians
	+	* [[home:physicians:concerns\|Physicians' concerns]] – olmesartan, antibiotics, light, vitamin D, <html>immunopathology</html>, clinical evidence
	+	* [[home:protocol:olmesartan\|Olmesartan (Benicar)]] – [[home:protocol:olmesartan:safety\|Safety of olmesartan]] \| [[home:protocol:olmesartan:kidney_disease\|Olmesartan and kidney disease]]
	+	* Antibiotics – [[home:protocol:mp_antibiotics:dosing\|Pulsed low-dose antibiotics]] \| [[home:protocol:mp_antibiotics:antibiotics_concerns\|Safety]]
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:protocol:immunopathology\|Immunopathology]] – also known as the Jarisch-Herxheimer reaction
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* [[home:physicians:emergency\|Notice for emergency]]
	+	* Alternative models for chronic disease
	+	* [[home:alternate:autoimmunity\|Autoimmune theory of disease]]
	+	* [[home:alternate:genetic_predisposition\|Genetic predisposition to disease]]
	+	* [[home:alternate:psychosomatic\|Psychosomatic explanations for disease]]
	+	* Learn more
	+	* [[home:physicians\|Resources for physicians]]
	+	* [[home:publications\|Publications and presentations]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:patients:glossary\|Glossary of terms]]
	+	* [[home:index\|Site map]] – contains a list of all articles in the KB
	+
	+	</WRAP></WRAP></WRAP>
	+
	+	<WRAP rightdivhome>
	+	<html><div class="highlightedh2">News and highlights </div></html><phpinc=twit.html>
	+
	+
	+	<html><div class="highlightedh2 pubs">Publications and presentations</div></html>
	+	\|[[home:publications:proal_molecular_2011\|Immunostimulation in the era of the human metagenome]] - paper in //Molecular and clinical immunology// that reviews a case series of <html>Marshall Protocol</html> patients and discusses how immunostimulatory approaches may require rethinking medicine \|
	+	\|[[home:publications:proal_metagenomics_2010\|Autoimmune disease and the human metagenome]] - book chapter in Springer's //Metagenomics of the human body// that discusses how the process of <html>successive infection may be responsible for autoimmune disease</html> \|
	+	\|[[home:publications:marshall_autoimmunity_2010\|Olmesartan overcomes antibiotic resistance, inducing recovery from advanced autoimmune disease]] – presentation by Trevor Marshall, PhD at International Congress on <html>Autoimmunity</html> \|
	+	\|[[home:publications:blaney_autoimmunity_2010\|Olmesartan medoxomil and treatment of autoimmune disease]] – presentation by Greg Blaney, MD \\ \\ → [[home:publications\|Complete list]]\|
	+
	+
	+	<WRAP h4>About the MPKB Project</WRAP>
	+
	+	The MPKB currently contains about 400 pages and draws from the best possible evidence to support its mission. As of May 2011, about 85% of those articles are complete with the remainder scheduled to be completed.
	+	* [[home:index#site_map\|Site Map]] (formerly on the home page)
	+	* [[home:index#incomplete_articles\|Incomplete articles]]
	+	* [[home:patients:tipsformpkb\|Tips for using this resource]]
	+
	+	<WRAP h4>About Autoimmunity Research Foundation</WRAP>
	+
	+	[[https://autoimmunityresearch.org\|Autoimmunity Research Foundation]] is a California-based 501(c)3 (tax deductible) non-profit formed to educate the public about the nature of, and study a treatment for, chronic inflammatory disease.
	+	* [[home:arf:timeline\|History and timeline of the Autoimmunity Research Foundation]]
	+
	+	</WRAP>
	+	</WRAP>
	+

Home

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

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	+	<html></p><style type="text/css">.breadcrumbs, .addthis_default_style {display:none;}</style><div id="homecolumns"></html>

	+
	+	~~NOTOC~~
	+
	+	====== Home ======
	+
	+	<columns 100% 34% 30% 35% ->
	+	===== For Patients =====
	+
	+	The Marshall Protocol (MP) is a treatment for chronic inflammatory diseases.
	+
	+	* [[home:patients\|Resources for patients]]
	+	* [[home:patients:pathogenesis_overview\|Marshall's theory of chronic inflammatory disease]]
	+	* [[home:patients:protocol_overview\|Introduction to the treatment]] – [[home:patients:mp_duration\|Length]], [[home:patients:cost_of_mp\|Cost]], [[home:patients:patient_interviews\|Patient Interviews]], [[home:patients:glossary\|Glossary]]
	+	* Suitability of the MP – [[home:starting:therapeutic_probe\|Therapeutic probe]], [[home:tests:vitdinterpretation\|Vitamin D Metabolite Calculator]]
	+	* [[home:starting\|Getting Started]] – [[home:starting:prempchecklist\|Checklist]], [[home:starting:physician:finding\|Finding a physician]], [[home:starting:physician\|Working with a physician]]
	+	* Doing the MP – [[home:lifestyle:light\|Light restriction?]], [[home:food\|Food & drink]], [[home:mp:immunopathology\|Immunopathology]], [[home:mp:managing_immunopathology\|Managing immunopathology]], [[https://autoimmunityResearch.org/phase1.pdf\|Guidelines]], [[home:othertreatments\|Non-MP treatments]]
	+
	+	<newcolumn top>
	+	===== For Physicians =====
	+
	+	The MP is based on the hypothesis that chronic inflammatory diseases are the result of infection by [[home:pathogenesis:microbiota\|communities of microbes]], which downregulate innate immune function.
	+	* [[home:physicians\|Resources for physicians]]
	+	* [[home:pathogenesis\|The Marshall Pathogenesis]]
	+	* [[home:protocol:immunopathology\|About immunopathology a.k.a. the Jarisch-Herxheimer reaction]]
	+	* Safety of the Protocol – [[home:protocol:olmesartan:safety\|olmesartan (Benicar)]], [[home:protocol:mp_antibiotics:antibiotics_concerns\|antibiotics]]
	+	* [[home:mp\|Summary of MP]], [[https://autoimmunityResearch.org/phase1.pdf\|Guidelines]]
	+	* [[home:physicians:concerns\|Physicians' concerns]]
	+	* [[home:physicians:emergency\|Notice for emergency]]
	+
	+
	+	<newcolumn top>
	+
	+
	+
	+	===== Publications/Presentations =====
	+
	+
	+	* Book chapter by Amy Proal //et al.// – [[home:publications:proal_metagenomics_2010\|Autoimmune disease and the human metagenome]]
	+	* Presentation by Trevor Marshall, PhD – [[home:publications:marshall_autoimmunity_2010\|Olmesartan overcomes antibiotic resistance, inducing recovery from advanced autoimmune disease]]
	+	* Presentation by Greg Blaney, MD – [[home:publications:blaney_autoimmunity_2010\|Olmesartan medoxomil and treatment of autoimmune disease]]
	+	* [[home:publications\|Complete list]]
	+
	+
	+	===== News =====
	+
	+
	+	* //Feb. 2011// – paper describing the Marshall Protocol written by ARF researchers [[home:publications:proal_molecular_2011\|now available]]
	+
	+	* //March 2011// - [[home:translations:german\|Deutsche übersetzung]]
	+
	+	</columns>
	+	<html>
	+	</div>
	+	</html>
	+
	+	==== About Autoimmunity Research Foundation and the MPKB Project ====
	+
	+	[[https://autoimmunityresearch.org\|Autoimmunity Research Foundation]] is a California-based 501(c)3 (tax deductible) non-profit formed to educate the public about the nature of, and study a treatment for, chronic inflammatory disease. The MPKB currently contains about 400 pages and draws from the best possible evidence to support its mission. As of October 2010, about 80% of those articles are complete with the remainder scheduled to be completed in the next year.
	+
	+	* [[home:index#site_map\|Site Map]] (formerly on the home page)
	+	* [[home:index#incomplete_articles\|Incomplete articles]]
	+	* [[home:patients:tipsformpkb\|Tips for using this resource]]
	+	* [[home:arf:timeline\|History and timeline of the Autoimmunity Research Foundation]]

anonymous@undisclosed.example.com (Anonymous) — Tue, 03 Jan 2012 04:20:27 +0000

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		+	<phpinc=x.html>

anonymous@undisclosed.example.com (Anonymous) — Tue, 03 Jan 2012 04:20:27 +0000

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	+	<phpinc=x.html>

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

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	+	</script>
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	+	<style type="text/css">
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	+	html {
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	+
	+	<div id="wheel">Please be patient …</div>
	+	</html>
	+
	+
	+
	+

anonymous@undisclosed.example.com (Anonymous) — Tue, 03 Jan 2012 04:20:28 +0000

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Customizations

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

Intracellular microbes in opthalmic disease: a reappraisal

anonymous@undisclosed.example.com (Anonymous) — Wed, 14 Sep 2022 05:14:49 +0000

11.09.2011		current
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	====== Intracellular microbes in opthalmic disease: a reappraisal ======		====== Intracellular microbes in opthalmic disease: a reappraisal ======

-	Over the past century, Koch's presumptions about how microbes would necessarily cause disease have sidetracked a lot of fruitful scientific inquiries.	+	Abstract
-		+
-	Only 5% of the human body's microbes can be grown outside the confines of the body. Like other fields of study opthalmologyres has yet to fully come to grips with the magnitude of this false negative.	+
-		+
-	given microbiologists a distorted view of the human microbiome.	+
-	* molecular tools microbes are not where they should be	+
-	* culture-based methods offer a distorted view	+
-	* microbes are likely culprits in eye diseases	+
-	* microbiology a victim of its own success	+
-	* beyond usual suspects	+
-		+
-	The notion of microbes in the eyes would seem like new work but it is not. Scientists in the 70s and 80s identified a variety of microbes. This work faced opposition that is no longer relevant.	+
-		+
-	This paper examines how this early work is informative.	+
-		+
-	Timeline/table of important studies	+


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	===== Introduction =====		===== Introduction =====

-	In 2010, Washington University ophthalmologist Van Gelder concluded it is "highly doubtful" that all the major pathogens associated with ocular diseases have been identified.(({{pubmed>long:21036206}})) XX - DISCONNECT Ioannidis's 2008 //Science// analysis that it is often decades between discovery and translation into common practice.(({{pubmed>long:18772421}})) As we will show, the advent of metagenomic tools may pave the way for reconsidering earlier studies of difficult-to-culture microbes. Such tools have shown that, like the brain, the eyes are not nearly as sterile or "immunologically privileged" as once supposed.	+	In 2010, Washington University ophthalmologist Van Gelder concluded it is "highly doubtful" that all the major pathogens associated with ocular diseases have been identified.(({{pmid>long:21036206}})) As we will show, the advent of metagenomic tools may pave the way for reconsidering earlier studies of difficult-to-culture microbes. Such tools have shown that, like the brain, the eyes are not nearly as sterile or "immunologically privileged" as once supposed.

	Over the past decades, high throughput sequencing tools have revolutionized the way we search for, classify, and characterize microbes. Also, they have changed our understanding of microbial persistence in the human body, with unexpected or novel microbes recurrently showing up in these studies. Microbes are now known to inhabit tissues and blood, and hundreds of species are known to exist in tissues previously believed to be sterile.		Over the past decades, high throughput sequencing tools have revolutionized the way we search for, classify, and characterize microbes. Also, they have changed our understanding of microbial persistence in the human body, with unexpected or novel microbes recurrently showing up in these studies. Microbes are now known to inhabit tissues and blood, and hundreds of species are known to exist in tissues previously believed to be sterile.

-	Between 1970 and through 2004 and as described in dozens of papers, Columbia University-based opthalmologist Emil Wirostko and collaborators found a number of microbes in the eyes of patients with inflammatory diseases. While some of these findings were duplicated,(({{pubmed>long:1426393}})) they were still largely ignored, if not dismissed. This publication looks at the reasons why Wirostko's work was rejected at the time, and explains why, when viewed in the context of the human microbiome, this body of work should be <del>reinterpreted</del> XX taken more seriously.	+	Between 1970 and through 2004 and as described in dozens of papers, Columbia University-based opthalmologist Emil Wirostko and collaborators found a number of microbes in the eyes of patients with inflammatory diseases. While some of these findings were duplicated,(({{pmid>long:1426393}})) they were still largely ignored, if not dismissed. This publication looks at the reasons why Wirostko's work was rejected at the time, and explains why, when viewed in the context of the human microbiome, this body of work should be reexamined.


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	Wirostko used a transmission electron microscope to document, within the immune cells, a range of intracellular forms, most of which lacked cell walls. The group called these forms "mycoplasma-like organisms" (MLOs). Such cells were collected from the vitreous and orbital tissues of the eyes, and occurred in a variety of chronic inflammatory conditions: uveitis, vitritis, ocular disease in juvenile rheumatoid arthritis, Crohn’s disease, and sarcoidosis.		Wirostko used a transmission electron microscope to document, within the immune cells, a range of intracellular forms, most of which lacked cell walls. The group called these forms "mycoplasma-like organisms" (MLOs). Such cells were collected from the vitreous and orbital tissues of the eyes, and occurred in a variety of chronic inflammatory conditions: uveitis, vitritis, ocular disease in juvenile rheumatoid arthritis, Crohn’s disease, and sarcoidosis.

-	For example, in 1989, Wirostko, Johnson, and Wirostko published a series of images of parasitized monocyctes collected from a patient with sarcoidosis associated uveitis.(({{pubmed>long:2801045}})) In another study, cell wall deficient microbes were observed in 2 to 10% of leukocytes invading the aqueous humor.(({{pubmed>long:3140479}})) XX Wrong cite!	+	For example, in 1989, Wirostko, Johnson, and Wirostko published a series of images of parasitized monocyctes collected from a patient with sarcoidosis associated uveitis.(({{pmid>long:2801045}})) In another study, cell wall deficient microbes were observed in 2 to 10% of leukocytes invading the aqueous humor.(cite?)

-	Many of the infected immune cells appeared to have dozens, if not hundreds, of microbe-like tubulo-spherical inclusions. MLOs varied in diameter between 0.005 and 1.0 microns and filaments between 0.005 and 0.01 microns.(({{pubmed>long:3140479}})) In some monocytes, the cells were almost completely replaced by MLOs.(({{pubmed>long:3395980}})) The long entities, in particular, fail to fit with anything known to be a structure in the cell. XX How do we know this is what we're seeing?	+	Many of the infected immune cells appeared to have dozens, if not hundreds, of microbe-like tubulo-spherical inclusions. MLOs varied in diameter between 0.005 and 1.0 microns and filaments between 0.005 and 0.01 microns.(({{pmid>long:3140479}})) In some monocytes, the cells were almost completely replaced by MLOs.(({{pmid>long:3395980}})) The long entities, in particular, fail to fit with anything known to be a structure in the cell.(is this true?)

-	The bodies found by Wirostko are structurally very similar to MLOs found in plants.(({{pubmed>long:7892050}})) In both humans and plants, these MLOs replace the cytoplasm and destroy the organelles. They also produce distinct nuclear alterations, which we will discuss later. MLO may destroy the host cell, or they may continue to exist within a dysfunctional or proliferating cell.	+	The bodies found by Wirostko are structurally very similar to MLOs found in plants.(({{pmid>long:7892050}})) In both humans and plants, these MLOs replace the cytoplasm and destroy the organelles. They also produce distinct nuclear alterations, which we will discuss later. MLO may destroy the host cell, or they may continue to exist within a dysfunctional or proliferating cell.

-	In addition to their ultrastructural studies of MLOs, Wirostko's team also showed in several studies that these microbes can be passed to laboratory animals to induce similar symptoms and indistinguishable ultrastructural features compared to human MLOs.(({{pubmed>long:2801045}})) Inoculation into mouse eyelids produced intraocular, orbital, and lethal systemic chronic progressive inflammatory disease at all disease sites. Such mice exhibited "sarcoid-like" granuloma.	+	In addition to their ultrastructural studies of MLOs, Wirostko's team also showed in several studies that these microbes can be passed to laboratory animals to induce similar symptoms and indistinguishable ultrastructural features compared to human MLOs.(({{pmid>long:2801045}})) Inoculation into mouse eyelids produced intraocular, orbital, and lethal systemic chronic progressive inflammatory disease at all disease sites. Such mice exhibited "sarcoid-like" granuloma.

	Wirostko's provocative research into the presence and behavior of fastidious microbes failed to receive widespread interest perhaps because it contradicted several long-held assumptions about microbes and disease, particularly Koch's postulates. First, despite decades of effort, no culture system exists for these organisms. Second, Wirostko was never able to show that these microbes acted independently to cause disease as has been the case with certain other pathogens. Finally, the MLOs were found in areas of the body believed to be free of microbes, even in disease.		Wirostko's provocative research into the presence and behavior of fastidious microbes failed to receive widespread interest perhaps because it contradicted several long-held assumptions about microbes and disease, particularly Koch's postulates. First, despite decades of effort, no culture system exists for these organisms. Second, Wirostko was never able to show that these microbes acted independently to cause disease as has been the case with certain other pathogens. Finally, the MLOs were found in areas of the body believed to be free of microbes, even in disease.
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	The notion that microbes always grow in culture undeniably served microbiology in its formative stages as researchers like Koch (//Mycobacterium tuberculosis//), Fehleisen and Pasteur (//Streptococcus//), Schaudinn and Hoffmann (//Treponema pallidum//), and Hayflick (//Mycoplasma pneumoniae//) succeeded in culturing a range of microbes. However, the field may have been a victim of its early successes.		The notion that microbes always grow in culture undeniably served microbiology in its formative stages as researchers like Koch (//Mycobacterium tuberculosis//), Fehleisen and Pasteur (//Streptococcus//), Schaudinn and Hoffmann (//Treponema pallidum//), and Hayflick (//Mycoplasma pneumoniae//) succeeded in culturing a range of microbes. However, the field may have been a victim of its early successes.

-	Wirostko's electron micrographs clearly show colonies of small cell wall-less bacteria resembling mycoplasma, but these microbes could not be cultured. At a 1972 London symposium on mycoplasma, the luminary Dr. Leonard Hayflick detailed how it took nearly a year of effort before he could isolate and cultivate //Mycoplasma pneumoniae//.((Hayflick, L. (1972). Mycoplasma as pathogens. Pathogenic mycoplasmas. A Ciba Foundation Symposium. Ciba Foundation for the Promotion of International Cooperation. Amsterdam; New York, Associated Scientific Publishers: 17-37.)) According to him, only by fulfilling Koch's postulates could he conclude that what we now know as primary atypical pneumonia is definitely caused by //M. pneumoniae//. For Hayflick, this experience offered an invaluable lesson as it illustrated that sufficiently diligent researchers can culture any bacteria which causes a given illness. Hayflick went on to chastise his "neophyte" colleagues who made suggestions to the contrary: "I am, therefore, earnest in my plea that the laws governing scientific proof [i.e. Koch's postulates], based on evidence under controlled conditions, be applied equally and particularly to the class //Mollicutes//." Eighteen years later, an anonymous 1990 //Lancet// comment critical of Emil Wirostko's work echoed Hayflick's objection: "The case for uncultured organisms even existing let alone remaining uncultured has not been proven and repetitive uncontrolled observations do not serve the scientific community well and may mislead the unwary."(({{pubmed>long:1970375}}))	+	Wirostko's electron micrographs clearly show colonies of small cell wall-less bacteria resembling mycoplasma, but these microbes could not be cultured. At a 1972 London symposium on mycoplasma, the luminary Dr. Leonard Hayflick detailed how it took nearly a year of effort before he could isolate and cultivate //Mycoplasma pneumoniae//.((Hayflick, L. (1972). Mycoplasma as pathogens. Pathogenic mycoplasmas. A Ciba Foundation Symposium. Ciba Foundation for the Promotion of International Cooperation. Amsterdam; New York, Associated Scientific Publishers: 17-37.)) According to him, only by fulfilling Koch's postulates could he conclude that what we now know as primary atypical pneumonia is definitely caused by //M. pneumoniae//. For Hayflick, this experience offered an invaluable lesson as it illustrated that sufficiently diligent researchers can culture any bacteria which causes a given illness. Hayflick went on to chastise his "neophyte" colleagues who made suggestions to the contrary: "I am, therefore, earnest in my plea that the laws governing scientific proof [i.e. Koch's postulates], based on evidence under controlled conditions, be applied equally and particularly to the class //Mollicutes//." Eighteen years later, an anonymous 1990 //Lancet// comment critical of Emil Wirostko's work echoed Hayflick's objection: "The case for uncultured organisms even existing let alone remaining uncultured has not been proven and repetitive uncontrolled observations do not serve the scientific community well and may mislead the unwary."(({{pmid>long:1970375}}))

-	A number of researchers studying fastidious microbes in other sites of the body including the kidneys, heart, gut, and blood also identified organisms that could not be grown easily in a laboratory setting, or at all.((Mattman)) (({{pubmed>long:9105757}})) Perhaps the study of microbes would have continued to be sidelined in this fashion were it not for a fundamental shift in microbiology that succeeded the sequencing of the human genome.	+	A number of researchers studying fastidious microbes in other sites of the body including the kidneys, heart, gut, and blood also identified organisms that could not be grown easily or at all in laboratory conditions. Such discrepancies include pH, temperature, nutrient conditions as well as the presence of other microbes.((Mattman, L. (2000). Cell Wall Deficient Forms: Stealth Pathogens. Boca Raton, FL, CRC Press.)) (({{pmid>long:9105757}})) Perhaps the study of microbes would have continued to be sidelined in this fashion were it not for a fundamental shift in microbiology that succeeded the sequencing of the human genome.
-		+
-	XX - INCLUDE SOME REASONS WHY CULTURE IS NOT SO EASY. TEMPERATURE, GROWTH MEDIA.	+

	In Wirostko's time, there was a limited notion of the 100 trillion microbes the comprise the human microbiome, but that changed some ten years ago with the advent of high throughput genomic technologies. About a decade ago, tools originally used to sequence the human genome were first trained on the the body's microbial inhabitants, allowing them to be identified, characterized, and understood based on their DNA. As this search coalesced into the NIH-funded initiative known as the Human Microbiome Project, scientists have pointed to a growing number of microbes that defy culture-based techniques or previous assumptions about infection.		In Wirostko's time, there was a limited notion of the 100 trillion microbes the comprise the human microbiome, but that changed some ten years ago with the advent of high throughput genomic technologies. About a decade ago, tools originally used to sequence the human genome were first trained on the the body's microbial inhabitants, allowing them to be identified, characterized, and understood based on their DNA. As this search coalesced into the NIH-funded initiative known as the Human Microbiome Project, scientists have pointed to a growing number of microbes that defy culture-based techniques or previous assumptions about infection.

-	Drawing from data gathered from high throughput technologies, Relman estimated in 2007 that 90% of microbes in the human body had not yet been cultivated.(({{pubmed>long:17943117}})) Early work on the eyes is in line with this estimate. In 2011, Shestopalov //et al.// used deep sequencing of the 16S rRNA gene amplicon libraries generated from total conjunctival swab DNA to examine the conjunctival rDNA from four subjects.(({{pubmed>long:21571682}})) The team found a striking degree of species variability between individuals: the conjuctiva for each individual had a different predominant genera. Even different swab pressures in at the same site in the same individual revealed significant changes in relative abundances of many microbial genera. All together, Shestopalov identified a total of five phyla and 59 distinct genera. Most striking of all though, 31% of all DNA reads belonged to unclassified or novel bacteria, and 42 out of 59 the classified bacterial genera had not been previously reported in healthy eyes. Thus far, [[http://microbiota.org/cgi-bin/ocular/index.cgi\|Shestopalov and the Ocular Microbiome Project]] have demonstrated that as many as 300 different bacterial phylotypes are present on the human conjunctiva, which is four times more than previously identified in culture. XX - BELOW?	+	Drawing from data gathered from high throughput technologies, Relman estimated in 2007 that 90% of microbes in the human body had not yet been cultivated.(({{pmid>long:17943117}}))

	===== Objection #2: "Eyes are largely sterile" =====		===== Objection #2: "Eyes are largely sterile" =====

-	In 2006, the ophthalmologist Jerry Niederkorn characterized a broad number of chronic diseases including idiopathic uveitis and sympathetic ophthalmia as being caused by the "loss of immune privilege" at the brain, the pregnant uterus, and the eye.(({{pubmed>long:16550198}})) This begs the question: what is responsible for the loss of immune privilege?	+	In 2006, the ophthalmologist Jerry Niederkorn characterized a broad number of chronic diseases including idiopathic uveitis and sympathetic ophthalmia as being caused by the "loss of immune privilege" at the brain, the pregnant uterus, and the eye.(({{pmid>long:16550198}})) This begs the question: what is responsible for the loss of immune privilege?

-	The assumption that the vitreous and the retina are protected from both immune cells and microbes has scarcely changed since Ehrlich XX ???.(({{pubmed>long:7775114}})) (({{pubmed>long:18268029}})) The 1994 textbook //Duane's Clinical opthalmology// writes: "It should be noted that the intraocular contents are expected to be sterile at all times."((Tasman, W. (1994). //Duane's clinical opthalmology//. Philadelphia, Pa., Lippincott.))((There is a [[http://www.worldcat.org/title/duanes-foundations-of-clinical-ophthalmology/oclc/468864805&referer=brief_results\|more recent edition]]. If we like this quote, I can get it through interlibrary loan.))	+	The assumption that the vitreous and the retina are protected from both immune cells and microbes has
		+	scarcely changed since the time of Ehrlich.(({{pmid>long:7775114}})) (({{pmid>long:18268029}})) The 1994 textbook //Duane's Clinical opthalmology// writes: "It should be noted that the intraocular contents are expected to be sterile at all times."((Tasman, W. (1994). //Duane's clinical opthalmology//. Philadelphia, Pa., Lippincott.))(There is a [[https://www.worldcat.org/title/duanes-foundations-of-clinical-ophthalmology/oclc/468864805&referer=brief_results\|more recent edition]]. If we like this quote but not the year in which it was made, I'm sure I could find a better one.)

-	However, today we realize each of the body's "privileged" sites is susceptible to infection in previously unanticipated ways. For example, microbes can cross the blood-brain barrier transcellularly, paracellularly and/or in infected phagocytes.(({{pubmed>long:18604221}})) Kim writes that a range of bacteria and bacterial toxins routinely establish intimate interactions with endothelial cells, triggering inflammatory responses and coagulation processes and modifying endothelial cell plasma membranes and junctions to adhere to their surfaces and then invade, cross and even disrupt the endothelial barrier.(({{pubmed>long:20040916}}))	+	Now because of metagenomics, such statements have been completely undermined. Early work on the eyes is in line with this estimate. In 2011, Shestopalov //et al.// used deep sequencing of the 16S rRNA gene amplicon libraries generated from total conjunctival swab DNA to examine the conjunctival rDNA from four subjects.(({{pmid>long:21571682}})) The team found a striking degree of species variability between individuals: the conjuctiva for each individual had a different predominant genera. Even different swab pressures in at the same site in the same individual revealed significant changes in relative abundances of many microbial genera. All together, Shestopalov identified a total of five phyla and 59 distinct genera. Most striking of all though, 31% of all DNA reads belonged to unclassified or novel bacteria, and 42 out of 59 the classified bacterial genera had not been previously reported in healthy eyes. Thus far, [[https://microbiota.org/cgi-bin/ocular/index.cgi\|Shestopalov and the Ocular Microbiome Project]] have demonstrated that as many as 300 different bacterial phylotypes are present on the human conjunctiva, which is four times more than previously identified in culture.

-	A brief examination of the body's other "sterile" compartments is instructive. Alzheimer's disease has been presumed by many to be the result of a lifelong accumulation of amyloid-beta proteins.(({{pubmed>long:1763432}})) However, a 2008 //Lancet// paper showed that an experimental vaccine succeeded in reducing production of amyloids (and the deposition of amyloids in the brain) but without slowing neurological decline.(({{pubmed>long:18640458}})) This suggested that while amyloid deposits were associated with the disease, they did not cause it. In a seminal 2010 study, a team of Harvard researchers showed that amyloid beta can act as an antimicrobial peptide, having antimicrobial activity against eight common microorganisms, including //Streptococcus//, //Staphylococcus aureus//, and //Listeria//.(({{pubmed>long:20209079}})) As a result, study author Rudolph E. Tanzi concluded that amyloid-beta is "the brain's protector."	+	However, today we realize each of the body's "privileged" sites is susceptible to infection in previously unanticipated ways. For example, microbes can cross the blood-brain barrier transcellularly, paracellularly and/or in infected phagocytes.(({{pmid>long:18604221}})) Kim writes that a range of bacteria and bacterial toxins routinely establish intimate interactions with endothelial cells, triggering inflammatory responses and coagulation processes and modifying endothelial cell plasma membranes and junctions to adhere to their surfaces and then invade, cross and even disrupt the endothelial barrier.(({{pmid>long:20040916}}))

-	Several teams have found the intracellular bacterium //Chlamydia pneumoniae// in the brains of Alzheimer's disease patients.(({{pubmed>long:20182626}})) (({{pubmed>long:9749980}})) In humans, //C. pneumoniae// has been shown to reach the central nervous system via infected mononuclear cells following the breach of blood-brain barrier(({{pubmed>long:12584732}})) (({{pubmed>long:10024578}})) and to induce Alzheimer's-like amyloid deposits in mouse brain upon injection.(({{pubmed>long:15013562}})) (({{pubmed>long:17581756}})) Miklossy's 2011 review found that antibodies to several types of spirochetes including //Treponema// and //Borrelia burgdorferi// were consistently detected in patients with Alzheimer's.(({{pubmed>long:21816039}}))	+	A brief examination of the body's other "sterile" compartments is instructive. Alzheimer's disease has been presumed by many to be the result of a lifelong accumulation of amyloid-beta proteins.(({{pmid>long:1763432}})) However, a 2008 //Lancet// paper showed that an experimental vaccine succeeded in reducing production of amyloids (and the deposition of amyloids in the brain) but without slowing neurological decline.(({{pmid>long:18640458}})) This suggested that while amyloid deposits were associated with the disease, they did not cause it. In a seminal 2010 study, a team of Harvard researchers showed that amyloid beta can act as an antimicrobial peptide, having antimicrobial activity against eight common microorganisms, including //Streptococcus//, //Staphylococcus aureus//, and //Listeria//.(({{pmid>long:20209079}})) As a result, study author Rudolph E. Tanzi concluded that amyloid-beta is "the brain's protector."

-	While Hayflick complained in 1971 of getting six to eight queries a year from "impressionable" physicians asking him to isolate microbes in cases of spontaneous abortion, we now know that microbes seem to play an important factor in whether a woman will carry a pregnancy to term. Using real-time PCR to quantify bacterial count in pregnant women's amniotic fluid, DiGiulio //et al.// showed in 2008 dose-response association between bacterial rDNA abundance and gestational age at delivery.(({{pubmed>long:18725970}})) The positive predictive value of PCR for preterm delivery was 100 percent.	+	Several teams have found the intracellular bacterium //Chlamydia pneumoniae// in the brains of Alzheimer's disease patients.(({{pmid>long:20182626}})) (({{pmid>long:9749980}})) In humans, //C. pneumoniae// has been shown to reach the central nervous system via infected mononuclear cells following the breach of blood-brain barrier(({{pmid>long:12584732}})) (({{pmid>long:10024578}})) and to induce Alzheimer's-like amyloid deposits in mouse brain upon injection.(({{pmid>long:15013562}})) (({{pmid>long:17581756}})) Miklossy's 2011 review found that antibodies to several types of spirochetes including //Treponema// and //Borrelia burgdorferi// were consistently detected in patients with Alzheimer's.(({{pmid>long:21816039}}))

-	In the last several years, opthalmologists have also generated increasing evidence that microbes play key roles in the diseases they study. //Bacillus cereus// produces a toxin which disrupts the function of retinal pigment epithelium (RPE) cells, the primary cells of the blood-retina barrier.(({{pubmed>long:18268029}})) (({{pubmed>long:19264886}})) Kountouras has presented evidence that //Helicobacter pylori// contributes to glaucoma, showing a high prevalence of //H. pylori// infection in Greek patients with primary open-angle glaucoma as well as exfoliative glaucoma.(({{pubmed>long:11237916}})) Kountaros further showed a beneficial effect of //H. pylori// eradication on glaucoma progression.(({{pubmed>long:12038941}})) Even so, there are also indications there is much more to learn.	+	While Hayflick complained in 1971 of getting six to eight queries a year from "impressionable" physicians asking him to isolate microbes in cases of spontaneous abortion, we now know that microbes seem to play an important factor in whether a woman will carry a pregnancy to term. Using real-time PCR to quantify bacterial count in pregnant women's amniotic fluid, DiGiulio //et al.// showed in 2008 dose-response association between bacterial rDNA abundance and gestational age at delivery.(({{pmid>long:18725970}})) The positive predictive value of PCR for preterm delivery was 100 percent.

-	Shestopalov's 2011 identification of unclassified or novel bacteria from the conjuctival microbiome(({{pubmed>long:21571682}})) raises the question: exactly how many microbes have gone undetected by PCR? Given that PCR remains the mainstay of pathogen detection in ocular diseases within the clinical setting,(({{pubmed>long:19169309}})) it is worth wondering how many microbes have gone undetected for failure to select a proper primer if such a choice is even possible.	+	In the last several years, opthalmologists have also generated increasing evidence that microbes play key roles in the diseases they study. //Bacillus cereus// produces a toxin which disrupts the function of retinal pigment epithelium (RPE) cells, the primary cells of the blood-retina barrier.(({{pmid>long:18268029}})) (({{pmid>long:19264886}})) Kountouras has presented evidence that //Helicobacter pylori// contributes to glaucoma, showing a high prevalence of //H. pylori// infection in Greek patients with primary open-angle glaucoma as well as exfoliative glaucoma.(({{pmid>long:11237916}})) Kountaros further showed a beneficial effect of //H. pylori// eradication on glaucoma progression.(({{pmid>long:12038941}})) Even so, there are also indications there is much more to learn.

-	Even the most commonly used DNA and RNA amplification techniques like PCR typically offer an incomplete picture of the human microbiome. De Groot-Mijnes //et al.//'s used real-time PCR to test for the presence of microbes in patients suspected of infectious uveitis.(({{pubmed>long:20691420}})) Though the team found microbes in only six of 139 patients, this work is hardly complete. The study used primers for only three bacteria and six viruses.	+	Shestopalov's 2011 identification of unclassified or novel bacteria from the conjuctival microbiome(({{pmid>long:21571682}})) raises the question: exactly how many microbes have gone undetected by PCR? Given that PCR remains the mainstay of pathogen detection in ocular diseases within the clinical setting,(({{pmid>long:19169309}})) it is worth wondering how many microbes have gone undetected for failure to select a proper primer if such a choice is even possible.

-	Hong //et al.// observe that "even with unlimited sampling and sequencing effort, a single combination of PCR primers/DNA extraction technique enables theoretical recovery of only half of the richness recoverable with three such combinations."(({{pubmed>long:19693101}})) Yeung concludes that PCR's high specificity can lead to false-negative results when primers are chosen for a polymorphic region of the pathogen’s DNA where sequence variations exist between strains.(({{pubmed>long:19169309}})) Often the genetic composition of microbes change so rapidly that one does not know which target gene to use a primer. Conversely, deep sequencing tools are more precise, but they are not as sensitive, requiring hundreds of copies of DNA or RNA to make a positive match.	+	Even the most commonly used DNA and RNA amplification techniques like PCR typically offer an incomplete picture of the human microbiome. De Groot-Mijnes //et al.//'s used real-time PCR to test for the presence of microbes in patients suspected of infectious uveitis.(({{pmid>long:20691420}})) Though the team found microbes in only six of 139 patients, this work is hardly complete. The study used primers for only three bacteria and six viruses.
		+
		+	Hong //et al.// observe that "even with unlimited sampling and sequencing effort, a single combination of PCR primers/DNA extraction technique enables theoretical recovery of only half of the richness recoverable with three such combinations."(({{pmid>long:19693101}})) Yeung concludes that PCR's high specificity can lead to false-negative results when primers are chosen for a polymorphic region of the pathogen’s DNA where sequence variations exist between strains.(({{pmid>long:19169309}})) Often the genetic composition of microbes change so rapidly that one does not know which target gene to use a primer. Conversely, deep sequencing tools are more precise, but they are not as sensitive, requiring hundreds of copies of DNA or RNA to make a positive match.

	===== Objection #3: Single species act independently =====		===== Objection #3: Single species act independently =====

-	While Koch's postulates are no longer invoked with quite the "great solemnity" described by Hanson,(({{pubmed>long:3286904}})) there should be no doubt they persist. The most enduring of Koch's postulates may be the one that still remains largely fixed in the minds of researchers: a given microorganism that causes disease must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms. Even today, the failure to meet Koch's first postulate is consistently cited to partially or completely discount results. Mombaerts criticized Wirostko's conclusion that MLOs have a role in causing orbital pseudotumors stating: "Unless further studies establish the presence of MLOs in all orbital pseudotumors, including the histopathologically classical type, MLOs should not be regarded as the responsible agents for orbital pseudotumor."(({{pubmed>long:8874418}})) On the other hand, the eminent British ophthalmologist Wallace Foulds was able to confirm the presence of MLOs in biopsies of two patients with retinal pigment epitheliopathy, but not others.(({{pubmed>long:1426393}}))	+	While Koch's postulates are no longer invoked with quite the "great solemnity" described by Hanson,(({{pmid>long:3286904}})) there should be no doubt they persist. The most enduring of Koch's postulates may be the one that still remains largely fixed in the minds of researchers: a given microorganism that causes disease must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms. Even today, the failure to meet Koch's first postulate is consistently cited to partially or completely discount results. Mombaerts criticized Wirostko's conclusion that MLOs have a role in causing orbital pseudotumors stating: "Unless further studies establish the presence of MLOs in all orbital pseudotumors, including the histopathologically classical type, MLOs should not be regarded as the responsible agents for orbital pseudotumor."(({{pmid>long:8874418}})) On the other hand, the eminent British ophthalmologist Wallace Foulds was able to confirm the presence of MLOs in biopsies of two patients with retinal pigment epitheliopathy, but not others.(({{pmid>long:1426393}}))

-	Mombaerts' criticism ignores the possibility that various species and forms interact with each other to cause disease. Recent work using culture-independent tools have revealed that the collection of microbes which comprise the human superorganism XX - DEFINE? change frequently, exist even in healthy tissue, and work in concert with other microbes.	+	Mombaerts' criticism ignores the possibility that various species and forms interact with each other to cause disease. Recent work using culture-independent tools have revealed that the collection of microbes which comprise the human microbiome change frequently, exist even in healthy tissue, and work in concert with other microbes.

-	One significant liability of this postulate is the sheer scope of horizontal gene transfer (HGT), the process by which microbes exchange genetic material. According to Gorgarten, HGT occurs more frequently "than most biologists could even imagine a decade ago." As a result, the process has turned the idea that we can classify organisms in a simple "tree of life" on its head. Some have argued convincingly that due to the frequency with which microbes exchange genetic material and change through evolutionary adaptation, there may be no such thing as a species.(({{pubmed>long:17020593}}))	+	One significant liability of this postulate is the sheer scope of horizontal gene transfer (HGT), the process by which microbes exchange genetic material. According to Gorgarten, HGT occurs more frequently "than most biologists could even imagine a decade ago." As a result, the process has turned the idea that we can classify organisms in a simple "tree of life" on its head. Some have argued convincingly that due to the frequency with which microbes exchange genetic material and change through evolutionary adaptation, there may be no such thing as a species.(({{pmid>long:17020593}}))

-	Another problem with this postulate is that it implicitly assumes that healthy tissue is free of pathogens. While it is accepted practice to assign one group of patients participating in a controlled trial to be the "healthy control group," subclinical infection among such patients is not the exception but the rule. Shestopalov's metagenomic study of the conjuctiva of "healthy" patients found 24 genera that include many species of common ocular pathogens (XX - or microbes, or what is the line?). In fact, only four genera, //Chrysobacterium, Enterobacter, Flavimonas// and //Nocardia// harboring well-known ocular pathogen strains, remained undetected in this survey. Similarly, Graham //et al.// used PCR to measure the flora of the eye in both healthy patients and those with dry eye. The team identified a range of atypical microbes including //Rhodococcus erythropolis, Erwinia sp.,// and //Klebsiella oxytoca// – the last of which is reputed to be associated an "especially poor visual prognosis."(({{pubmed>long:15488221}})) These microbes were identified in cases of overt inflammation and, most provocatively, on the normal ocular surface.(({{pubmed>long:18055811}})) XX - IN WHAT PROPORTIONS?	+	Another problem with this postulate is that it implicitly assumes that healthy tissue is free of pathogens. While it is accepted practice to assign one group of patients participating in a controlled trial to be the "healthy control group," subclinical infection "showing minimal signs of infection,"(({{pmid>long:18055811}})) among such patients is not the exception but the rule. Shestopalov's metagenomic study of the conjuctiva of "healthy" patients found 24 genera that include many species of common ocular pathogens. In fact, only four genera, //Chrysobacterium, Enterobacter, Flavimonas// and //Nocardia// remained undetected in this survey. Similarly, Graham //et al.// used PCR to measure the flora of the eye in both healthy patients and those with dry eye. The team identified a range of atypical microbes including //Rhodococcus erythropolis, Erwinia sp.,// and //Klebsiella oxytoca// – the last of which is reputed to be associated an "especially poor visual prognosis."(({{pmid>long:15488221}})) These microbes were identified in cases of overt inflammation and, most provocatively, on the normal ocular surface.(({{pmid>long:18055811}})) Thus, microbes may contribute to vision conditions such as dry eye which occur in relatively healthy eyes. Even commensal ocular microbes degrade the body's antimicrobials, as Berry showed by observing the mucinolytic activity of such microbes.(({{pmid>long:12446377}}))

-	Even commensal ocular microbes degrade the body's antimicrobials, as Berry showed by observing the mucinolytic activity of such microbes.(({{pubmed>long:12446377}})) Researchers are apt to make a clear distinction between health and disease, but results like these begin to suggest the dichotomy is forced. Instead, it may be more accurate to think of the states of health and disease as poles along a spectrum. Thus, it would be overly simplistic to say there is such a thing as a truly healthy control subject.	+	Researchers are apt to make a clear distinction between health and disease, but results like these begin to suggest the dichotomy is forced. Instead, it may be more accurate to think of the states of health and disease as poles along a spectrum. Thus, it would be overly simplistic to say there is such a thing as a truly healthy control subject.

-	Finally, given that, as we discussed before, about nine of ten human microbes have not yet been been proven to grow independently, it seems sensible to discount the possibility that each pathogen must cause disease independently. The best known example of how microbes work together is a collective called a biofilm. Biofilms are densely packed communities of microbial cells that grow inside or outside cells and surround themselves with secreted polymers. A given biofilm is truly an ecosystem and may have over 500 different species. The bacteria that become part of a biofilm engage in quorum sensing, a type of decision-making process in which behavior is coordinated through a "chemical vocabulary."(({{pubmed>long:18004304}})) The structural and physiological complexity of biofilms has led to the idea that they are coordinated and cooperative groups, analogous to multicellular organisms.(({{pubmed>long:19067751}})) Biofilm have been implicated in a range of diseases: chronic wounds, atherosclerosis, chronic sinusitis, periodontal disease, osteomyelitis, urinary tract infections, and otitis media. Only several years ago researchers realized that biofilms cause most infections associated with contact lens use. In 2006, Bausch & Lomb withdrew its ReNu with MoistureLoc contact lens solution because it was associated with a high proportion of corneal (XX - BIOFILM?) infections.(({{pubmed>long:17999966}}))	+	Finally, given that, as we discussed before, about nine of ten human microbes have not yet been been proven to grow independently, it seems sensible to discount the possibility that each pathogen must cause disease independently. The best known example of how microbes work together is a collective called a biofilm. Biofilms are densely packed communities of microbial cells that grow inside or outside cells and surround themselves with secreted polymers. A given biofilm is truly an ecosystem and may have over 500 different species. The bacteria that become part of a biofilm engage in quorum sensing, a type of decision-making process in which behavior is coordinated through a "chemical vocabulary."(({{pmid>long:18004304}})) The structural and physiological complexity of biofilms has led to the idea that they are coordinated and cooperative groups, analogous to multicellular organisms.(({{pmid>long:19067751}})) Biofilm have been implicated in a range of diseases: chronic wounds, atherosclerosis, chronic sinusitis, periodontal disease, osteomyelitis, urinary tract infections, and otitis media. Only several years ago researchers realized that biofilms cause most infections associated with contact lens use. In 2006, Bausch & Lomb withdrew its ReNu with MoistureLoc contact lens solution because it led to the formation of contact lens-associated fungal biofilm, causing a high proportion of corneal infections.(({{pmid>long:17999966}}))

-	We have previously defined successive infection as the process by which an infectious cascade of pathogens slow the immune response and allow for subsequent infections to proliferate.((Proal, A. D., P. J. Albert, et al. (2010). Autoimmune disease and the human metagenome. Metagenomics of the Human Body. K. E. Nelson, Springer: 231-275.)) In successive infection, the host microbiome shifts further and further away from a natural homeostatic state. Human genes are up- or downregulated by acquired components of the microbiota, and infected cells progressively struggle to correctly produce human metabolites in the presence of the numerous proteins, enzymes and metabolites generated by the pathogenic genomes. As a result of this cascade, each infectious disease state becomes the sum of a person's dynamic and diverse mix of microbes. While Graham showed that pathogens routinely exist in healthy ocular tissue, "showing minimal signs of infection,"(({{pubmed>long:18055811}})) most study designs fail to account for the existence of subclinical infections, much less their ability to disrupt the immune response in this fashion.	+	We have previously defined successive infection as the process by which an infectious cascade of pathogens alter expression of key antimicrobials such as those transcribed by the VDR to slow the immune response and allow for subsequent infections to proliferate.((Proal, A. D., P. J. Albert, et al. (2010). Autoimmune disease and the human metagenome. Metagenomics of the Human Body. K. E. Nelson, Springer: 231-275.)) In successive infection, the host microbiome shifts further and further away from a natural homeostatic state. Human genes are up- or downregulated by acquired components of the microbiota, and infected cells progressively struggle to correctly produce human metabolites in the presence of the numerous proteins, enzymes and metabolites generated by the pathogenic genomes. As a result of this cascade, each infectious disease state becomes the sum of a person's dynamic and diverse mix of microbes.

-	In the arms race of host–microbe co-evolution, successful microbial pathogens have evolved a number of ingenious ways to evade or subvert the human host's immune responses.(({{pubmed>long:21350579}})) One of these is through altering transcription and translation of te nuclear receptors, particularly the vitamin D receptor (VDR). When active, the VDR affects transcription of at least 913 genes and impacts processes ranging from calcium metabolism to several families of key endogenous antimicrobials including beta-defensins, cathelicidin, and TLR2. Perversion of VDR function would clearly ease pressure on microbes, especially intracellular communities, thus making it an ideal target. For example, //Borrelia burgdorferi// reduces VDR expression in monocytes (phagocytes) by 50 times, and lysates ("dead" //Borrelia//) reduced it by 8 times(({{pubmed>long:19461888}})) while another intracellular microbe //Mycobacterium tuberculosis// was shown to downregulate the VDR 3.3-fold (({{pubmed>long:12890386}})) Equivalent actions have been documented in Epstein-Barr virus, cytomegalovirus, HIV, and //Aspergillus fumigatus//. Disrupting immune function through such initial insults to homeostasis could readily allow additional microbes to proliferate with greater ease.	+	In the arms race of host–microbe co-evolution, successful microbial pathogens have evolved a number of ingenious ways to evade or subvert the human host's immune responses.(({{pmid>long:21350579}})) One of these is through altering transcription and translation of the nuclear receptors, particularly the vitamin D receptor (VDR). When active, the VDR affects transcription of at least 913 genes and impacts processes ranging from calcium metabolism to several families of key endogenous antimicrobials including beta-defensins, cathelicidin, and TLR2. In addition to the endogenous antimicrobials, a robust VDR transcribes a number of proteins responsible for vision: Epidermal retinal dehydrogenase, retinal outer segment membrane protein, retinal pigment epithelium-specific protein, retinal short chain dehydrogenase reductase; retinal outer segment membrane protein 1; retinal degeneration slow protein; arrestin 3, retinal; and retinaldehyde binding protein 1.(({{pmid>long:16002434}})) Disruption of the VDR activity by intracellular pathogens provides a plausible mechanism for degradation of the eye whether it is through vision loss or inflammatory disease.

-	For example, German researchers found in subjects ages three to 90 that the range of aerobic bacteria colonizing a clinically healthy conjunctiva diversifies and increases with age.(({{pubmed>long:7869685}})) Another example of successive infection is human immunodeficiency virus (HIV), a pathogen associated with a variety of opthalmic manifestations including uveitis. A patient with HIV can thrive for decades, however when the infection is left untreated by antiretroviral therapy, the microbe begins to profoundly inhibit the immune response. In HIV-mediated immunosuppression, the body enters a state of immunosuppression in which otherwise easily dispatched microbes become fatal.(({{pubmed>long:15488221}})) Even the transmission of HIV is substantially increased by the presence of an existing infection. A 2011 study found that women with bacterial vaginosis, an infection of the vaginal canal, [[http://technorati.com/women/article/common-infection-increases-risk-of-transmitting/\|were three times as likely]] to transmit HIV to their male sexual partners.	+	Perversion of VDR function would clearly ease pressure on microbes, especially intracellular communities, thus making it an ideal target. For example, //Borrelia burgdorferi// reduces VDR expression in monocytes (phagocytes) by 50 times, and lysates ("dead" //Borrelia//) reduced it by 8 times(({{pmid>long:19461888}})) while another intracellular microbe //Mycobacterium tuberculosis// was shown to downregulate the VDR 3.3-fold (({{pmid>long:12890386}})) Equivalent actions have been documented in Epstein-Barr virus, cytomegalovirus, HIV, and //Aspergillus fumigatus//. Disrupting immune function through such initial insults to homeostasis could readily allow additional microbes to proliferate with greater ease.

-	We have discussed before how Wirostko inoculated eyelids of mice with MLO taken from inflamed ocular tissues from humans. For the first two months, no ocular inflammation was noted. But from the third month onward, these mice were significantly more likely to develop ocular diseases such as cataracts but also diseases in vital organs such as the heart,(({{pubmed>long:3377965}})) lungs,(({{pubmed>long:3219289}})) liver,(({{pubmed>long:2206991}})) and gastrointestinal tract.(({{pubmed>long:8398804}})) The onset of such comorbidities in an animal model adds to the evidence both that these conditions are caused by microbes and that such microbes may be capable of spreading throughout the body in a manner consistent with successive infection. Indeed, this process may explain why in the middle Norway eye-screening study, the prevalence of exfoliative glaucoma in both members of married couples is significantly higher than expected.(({{pubmed>long:10463402}}))	+	For example, German researchers found in subjects ages three to 90 that the range of aerobic bacteria colonizing a clinically healthy conjunctiva diversifies and increases with age.(({{pmid>long:7869685}})) Human immunodeficiency virus (HIV) is a pathogen associated with a variety of opthalmic manifestations including uveitis. A patient with HIV can thrive for decades, however when the infection is left untreated by antiretroviral therapy, the microbe begins to profoundly inhibit the immune response. In HIV-mediated immunosuppression, the body enters a state of immunosuppression in which otherwise easily dispatched microbes become fatal.(({{pmid>long:15488221}})) Even the transmission of HIV is substantially increased by the presence of an existing infection. A 2011 study found that women with bacterial vaginosis, an infection of the vaginal canal, [[https://technorati.com/women/article/common-infection-increases-risk-of-transmitting/\|were three times as likely]] to transmit HIV to their male sexual partners.
-		+
-	XX - retinal gene expression	+	We have discussed before how Wirostko inoculated eyelids of mice with MLO taken from inflamed ocular tissues from humans. For the first two months, no ocular inflammation was noted. But from the third month onward, these mice were significantly more likely to develop ocular diseases such as cataracts but also diseases in vital organs such as the heart,(({{pmid>long:3377965}})) lungs,(({{pmid>long:3219289}})) liver,(({{pmid>long:2206991}})) and gastrointestinal tract.(({{pmid>long:8398804}})) The onset of such comorbidities in an animal model adds to the evidence both that these conditions are caused by microbes and that such microbes may be capable of spreading throughout the body in a manner consistent with successive infection. Indeed, this process may explain why in the middle Norway eye-screening study, the prevalence of exfoliative glaucoma in both members of married couples is significantly higher than expected.(({{pmid>long:10463402}})) XX - no don't put that here.
		+

	===== Intracellular microbes =====		===== Intracellular microbes =====

-	Even while some conclude that inflammatory diseases like uveitis tend to recur "for no apparent reason,"(([[http://www.ingentaconnect.com/content/ben/cir/2011/00000007/00000003/art00012\|Intraocular Immune Mechanisms in Uveitis]])) researchers diminish the role of understudied bacteria in disease – particularly cell wall less and intracellular bacteria. The 2008 textbook //Review of Medical Microbiology and Immunology// writes, "Characteristic of medically important bacteria's outer surface is a rigid cell wall containing peptidoglycan." Another recent textbook //Review of Medical Microbiology and Immunology// states that "the cell wall is the outermost component common to all bacteria except //Mycoplasma// species." Though it is certainly true that //Mycoplasma// lack a cell wall, it is incorrect to claim that the balance of bacteria, or even "medically important" bacteria, always have a cell wall.	+	Even while some conclude that inflammatory diseases like uveitis tend to recur "for no apparent reason,"(([[https://www.ingentaconnect.com/content/ben/cir/2011/00000007/00000003/art00012\|Intraocular Immune Mechanisms in Uveitis]])) researchers diminish the role of understudied bacteria in disease – particularly cell wall less and intracellular bacteria. The 2008 textbook //Review of Medical Microbiology and Immunology// writes, "Characteristic of medically important bacteria's outer surface is a rigid cell wall containing peptidoglycan." Another recent textbook //Review of Medical Microbiology and Immunology// states that "the cell wall is the outermost component common to all bacteria except //Mycoplasma// species." Though it is certainly true that //Mycoplasma// lack a cell wall, it is incorrect to claim that the balance of bacteria, or even "medically important" bacteria, always have a cell wall.

-	Wirostko's finding of dozens, if not hundreds, of cell wall-less intracellular microbes inside a given cell at the site of ocular disease has important implications. These cells in which inclusions were present also had profound alterations of the cell nuclei. Changes included chromatin lysis with clumping, irregular frayed nuclear contours, and/or enlarged "halo-like" paranuclear spaces. Immune cells lacking the abnormal intracytoplasmic bodies displayed a normal ultrastructural appearance.(({{pubmed>long:2801045}})) In 2009, Kountouras wrote that the influx of activated monocytes infected with //Chlamydia pneumoniae// through the BBB could have dire consequences in the brain leading to the development of degenerative diseases, including Alzherimer's disease and possibly glaucoma.(({{pubmed>long:19854735}}))	+	Wirostko's finding of dozens, if not hundreds, of cell wall-less intracellular microbes inside a given cell at the site of ocular disease has important implications. These cells in which inclusions were present also had profound alterations of the cell nuclei. Changes included chromatin lysis with clumping, irregular frayed nuclear contours, and/or enlarged "halo-like" paranuclear spaces. Immune cells lacking the abnormal intracytoplasmic bodies displayed a normal ultrastructural appearance.(({{pmid>long:2801045}})) In 2009, Kountouras wrote that the influx of activated monocytes infected with //Chlamydia pneumoniae// through the BBB could have dire consequences in the brain leading to the development of degenerative diseases, including Alzherimer's disease and possibly glaucoma.(({{pmid>long:19854735}}))

-	Generally speaking, while a pathogen living in a biofilm outside a cell (for example, a biofilm on a hip joint) can elicit an immune reaction, a pathogen living inside a nucleated cell, especially an immune cell, can persist for longer periods of time,(({{pubmed>long:232125}})) resulting in cell proliferation, destruction, or dysfunction(({{pubmed>long:8140710}})) – in essence, changing the way the body works. In particular, an intraphagocytic pathogen can change the way that the immune system works. Kozarov //et al.// conclude, "the key step [towards systemic infection] is the persistence of intracellular bacteria in phagocytes."(({{pubmed>long:16513386}})) Early intraphagocytic infection is a likely culprit in a cascade of events that makes the body increasingly hospitable for microbes.	+	Generally speaking, while a pathogen living in a biofilm outside a cell (for example, a biofilm on a hip joint) can elicit an immune reaction, a pathogen living inside a nucleated cell, especially an immune cell, can persist for longer periods of time,(({{pmid>long:232125}})) resulting in cell proliferation, destruction, or dysfunction(({{pmid>long:8140710}})) – in essence, changing expression of our genes. In particular, an intraphagocytic pathogen can change the way that the immune system works. Kozarov //et al.// conclude, "the key step [towards systemic infection] is the persistence of intracellular bacteria in phagocytes."(({{pmid>long:16513386}})) Early intraphagocytic infection is a likely culprit in a cascade of events that makes the body increasingly hospitable for microbes.

-	We have discussed how the chronic eye diseases have long been assigned a reputation for being caused by a hyperactive immune response. Interestingly, even in the autoimmune diseases – long reputed to be driven by an overactive immune response – the innate immune response is attenuated. Kanchwala showed that patients with sarcoidosis expressed the antimicrobial peptide cathelicidin less than healthy subjects, and that sicker sarcoidosis patients expressed it least of all.((Kanchwala, A., B. Barna, et al. (2009). [[http://meeting.chestpubs.org/cgi/content/abstract/136/4/127S-a\|Deficiencies of cathelicidin and vitamin D accompany disease severity in sarcoidosis]].)) Wiken demonstrated that there was a reduced TLR2 mRNA expression in patients with Lofgren's syndrome (a type of acute sarcoidosis).(({{pubmed>long:20813038}})) Finally, Wang showed that Crohn's patients a decline in expression of key antimicrobial peptides including cathelicidin and Beta-defensin-2.(({{pubmed>long:19948723}}))	+	We have discussed how the chronic eye diseases have long been assigned a reputation for being caused by a hyperactive immune response. Interestingly, even in the autoimmune diseases – long reputed to be driven by an overactive adaptive immune response – the innate immune response is attenuated. Kanchwala showed that patients with sarcoidosis expressed the antimicrobial peptide cathelicidin less than healthy subjects, and that sicker sarcoidosis patients expressed it least of all.((Kanchwala, A., B. Barna, et al. (2009). [[https://meeting.chestpubs.org/cgi/content/abstract/136/4/127S-a\|Deficiencies of cathelicidin and vitamin D accompany disease severity in sarcoidosis]].)) Wiken demonstrated that there was a reduced TLR2 mRNA expression in patients with Lofgren's syndrome (a type of acute sarcoidosis).(({{pmid>long:20813038}})) Finally, Wang showed that Crohn's patients a decline in expression of key antimicrobial peptides including cathelicidin and Beta-defensin-2.(({{pmid>long:19948723}}))

-	In addition to the endogenous antimicrobials we discussed before, a robust VDR transcribes a number of proteins responsible for vision: Epidermal retinal dehydrogenase, retinal outer segment membrane protein, retinal pigment epithelium-specific protein, retinal short chain dehydrogenase reductase; retinal outer segment membrane protein 1; retinal degeneration slow protein; arrestin 3, retinal; and retinaldehyde binding protein 1.(({{pubmed>long:16002434}})) Disruption of the VDR provides a plausible mechanism for degradation of the eye whether it is through vision loss or inflammatory disease.


	===== Clinical applications =====		===== Clinical applications =====

-	Researchers concluding that microbes play a minimal role in idiopathic ocular diseases advocate measures that "re-establish immune privilege." For them, advances will come in fine-tuning methods for undermining an immune response that causes chronic inflammatory disease.(({{pubmed>long:16550198}})) There are currently a variety of widely used treatments that exemplify this approach including the glucocorticoids, the first-line therapy for the treatment of uveitis((Intraocular immune mechanisms in uveitis)).	+	Researchers concluding that microbes play a minimal role in idiopathic ocular diseases advocate measures that "re-establish immune privilege." For them, advances will come in fine-tuning methods for undermining an immune response that causes chronic inflammatory disease.(({{pmid>long:16550198}})) There are currently a variety of widely used treatments that exemplify this approach including the glucocorticoids, the first-line therapy for the treatment of uveitis((Intraocular immune mechanisms in uveitis)).

-	However, the continued definition of certain chronic inflammatory ocular diseases as "noninfectious" seems tenuous at best. It may not be coincidental that as McCluskey writes, "Infection can closely mimic the ocular signs of endogenous inflammation",(({{pubmed>long:15589311}})) In O'Connor's words, "inflammation is a clear potential link between infectious agents and chronic diseases."(({{pubmed>long:16836820}})) Metagenomic tools give us the ability to characterize how infection drives inflammation.	+	However, the continued definition of certain chronic inflammatory ocular diseases as "noninfectious" seems tenuous at best. It may not be coincidental that as McCluskey writes, "Infection can closely mimic the ocular signs of endogenous inflammation",(({{pmid>long:15589311}})) In O'Connor's words, "inflammation is a clear potential link between infectious agents and chronic diseases."(({{pmid>long:16836820}})) Metagenomic sequencing tools give us the ability to characterize how infection drives inflammation.

-	In the 80s and 90s, the human microbiome was scarcely a concept. At the time of his work, Wirostko did not have the tools to characterize microbes absent ambiguity and consequently had to rely on direct direction via TEM. For Wirostko's critics, ultrastructural studies were not sufficient to conclude conclusively what types of microbes were observed underneath his electron microscope. It is possible that these "mycoplasma-like" organisms were another kind (or other kinds) of microbe entirely. While ophthalmology has long been "comfortable with the limits of Koch’s postulates,"(({{pubmed>long:12854031}})) the identification of these organisms in opthalmic disease should not be discounted just because they fail to conform to a centuries-old notion of illness. According to Van Gelder, the importance of testing intraocular fluids will increase as the next wave of technologies advancing microbiology becomes available including panmicrobial and panviral gene chips, and deep sequencing for pathogens, and characterization of short RNAs as signatures for infectious agents.(({{pubmed>long:12854031}}))	+	In the 80s and 90s, the human microbiome was scarcely a concept. At the time of his work, Wirostko did not have the tools to characterize microbes absent ambiguity and consequently had to rely on direct direction via TEM. For Wirostko's critics, ultrastructural studies were not sufficient to conclude conclusively what types of microbes were observed underneath his electron microscope. It is possible that these "mycoplasma-like" organisms were another kind (or other kinds) of microbe entirely. While ophthalmology has long been "comfortable with the limits of Koch’s postulates,"(({{pmid>long:12854031}})) the identification of these organisms in opthalmic disease should not be discounted just because they fail to conform to a centuries-old notion of illness. According to Van Gelder, the importance of testing intraocular fluids will increase as the next wave of technologies advancing microbiology becomes available including panmicrobial and panviral gene chips, and deep sequencing for pathogens, and characterization of short RNAs as signatures for infectious agents.(({{pmid>long:12854031}}))

-	Such tools will be especially welcome in the study of how therapies for the ocular diseases upset the ocular metagenome. Of these, it is particularly important to know how antibiotics affect microbes in ocular diseases. The immunosuppressive properties of antibiotics have been long known. Labro asserts that when it comes to treating inflammatory diseases, immunosuppression is "recognized as the basis for antibiotic action."(({{pubmed>long:11023961}})) Such immunosuppression might reduce inflammation in the near term but allow microbes to spread unchecked by the immune response. One important avenue for exploration is the use of antibiotics in pulsed lower dosing to limit the effect these drugs have on immune function and host surveillance.	+	Such tools will be especially welcome in the study of how therapies for the ocular diseases further dysregulate the ocular metagenome. Of these, it is particularly important to know how antibiotics affect microbes in ocular diseases. The immunosuppressive properties of antibiotics have been long known. Labro asserts that when it comes to treating inflammatory diseases, immunosuppression is "recognized as the basis for antibiotic action."(({{pmid>long:11023961}})) Such immunosuppression might reduce inflammation in the near term but allow microbes to spread unchecked by the immune system. One important avenue for exploration is the use of antibiotics in pulsed lower dosing to limit the effect these drugs have on immune function and host surveillance.

		+	===== Discussion =====


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	* chlamydia harvard		* chlamydia harvard
-	* H. pylori (({{pubmed>long:19854738}})) and http://bjo.bmj.com/content/93/11/1413.long	+	* H. pylori (({{pmid>long:19854738}})) and https://bjo.bmj.com/content/93/11/1413.long
	* endotoxin		* endotoxin
	* more than the usual suspects?		* more than the usual suspects?
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	Look at scanned PDF "Intraocular immune mechanisms in uveitis"		Look at scanned PDF "Intraocular immune mechanisms in uveitis"
		+
		+	Over the past century, Koch's presumptions about how microbes would necessarily cause disease have sidetracked a lot of fruitful scientific inquiries.
		+
		+	Only 5% of the human body's microbes can be grown outside the confines of the body. Like other fields of study opthalmologyres has yet to fully come to grips with the magnitude of this false negative.
		+
		+	given microbiologists a distorted view of the human microbiome.
		+	* molecular tools microbes are not where they should be
		+	* culture-based methods offer a distorted view
		+	* microbes are likely culprits in eye diseases
		+	* microbiology a victim of its own success
		+	* beyond usual suspects
		+
		+	The notion of microbes in the eyes would seem like new work but it is not. Scientists in the 70s and 80s identified a variety of microbes. This work faced opposition that is no longer relevant.
		+
		+	This paper examines how this early work is informative.
		+
		+	Timeline/table of important studies
		+

	===== References =====		===== References =====

Framework for managing the stages of recovery

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

11.04.2010		current
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	====== Framework for managing the stages of recovery ======		====== Framework for managing the stages of recovery ======
-	* __Draft #8:__ in work here: http://mpkb.org/home/devel/framework	+	* __Draft #8:__ in work here: https://mpkb.org/home/devel/framework
	* Added indexing to paragraphs to facilitate text flow while providing locations to link into comments.		* Added indexing to paragraphs to facilitate text flow while providing locations to link into comments.
-	* Note: I'd like to add some text about how the “bigger hammer mentality must die”… hammer (bug-killing) v.s. sustainable pace (reserves left for healing)… – Paul has promised to add words here: Pulsed low-dose antibiotics.	+	* Note: I'd like to add some text about how the “bigger hammer mentality must die”… hammer (bug-killing) v.s. sustainable pace (reserves left for healing)… – Paul has promised to add words here: [[home:protocol:mp_antibiotics:dosing]].
	* This document does not stand alone (at this time.) The links to other KB articles are essential for the practitioner to develop a deeper understanding of the science and the clinical application.		* This document does not stand alone (at this time.) The links to other KB articles are essential for the practitioner to develop a deeper understanding of the science and the clinical application.

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	<sup>103.a. </sup>		<sup>103.a. </sup>
-	Stage 3 starts with the introduction of [[home:mp:mpmeds:olmesartan\|olmesartan (Benicar)]], which acts on multiple receptors to provide both //stimulation of the immune response// and //palliation of symptoms//.	+	Stage 3 starts with the introduction of [[home:mp:olmesartan\|olmesartan (Benicar)]], which acts on multiple receptors to provide both //stimulation of the immune response// and //palliation of symptoms//.

	<sup>103.b. </sup>		<sup>103.b. </sup>
Line 75:		Line 75:

	<sup>103.i. </sup>		<sup>103.i. </sup>
-	The antibiotic [[home:mp:mpmeds:minocycline\|minocycline]] is the first antibiotic introduced once the need for additional immune stimulation is evident. Minocycline's effectiveness is based on both immune stimulatory and palliative actions.	+	The antibiotic [[home:mp:minocycline\|minocycline]] is the first antibiotic introduced once the need for additional immune stimulation is evident. Minocycline's effectiveness is based on both immune stimulatory and palliative actions.

	<sup>103.j. </sup>		<sup>103.j. </sup>
Line 81:		Line 81:

	<sup>103.k. </sup>		<sup>103.k. </sup>
-	Only when symptoms levels are negligible at the maximum dose of minocycline taken every 48 hours should the innate immune response be further stimulated by adding other short-acting antibiotics ([[home:mp:mpmeds:bactrimds\|Bactrim DS (co-trimoxazole)]], [[home:mp:mpmeds:clindamycin\|clindamycin]], [[home:mp:mpmeds:demeclocycline\|demeclocycline (Declomycin)]]).	+	Only when symptoms levels are negligible at the maximum dose of minocycline taken every 48 hours should the innate immune response be further stimulated by adding other short-acting antibiotics ([[home:mp:bactrimds\|Bactrim DS (co-trimoxazole)]], [[home:mp:clindamycin\|clindamycin]], [[home:mp:demeclocycline\|demeclocycline (Declomycin)]]).

Marshall Protocol Legacy Link Index

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

Logos

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Jul 2022 12:06:16 +0000

05.15.2010		current
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	==== White Background ====		==== White Background ====

-	* [[http://mpkb.org/_detail/home/admin/mpkb-logo-small-whitebg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]	+	* [[https://mpkb.org/_detail/home/admin/mpkb-logo-small-whitebg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]
-	* [[http://mpkb.org/_detail/home/admin/mpkb-logo-large-whitebg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]	+	* [[https://mpkb.org/_detail/home/admin/mpkb-logo-large-whitebg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]
-	* [[http://mpkb.org/_detail/home/admin/mpkb-logo-large-whitebg.eps?id=home%3Aadmin%3Alogo\|EPS]]	+	* [[https://mpkb.org/_detail/home/admin/mpkb-logo-large-whitebg.eps?id=home%3Aadmin%3Alogo\|EPS]]


Line 17:		Line 17:
	==== White Background ====		==== White Background ====

-	* [[http://mpkb.org/_detail/home/admin/arf-logo-small-whitebg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-small-whitebg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]
-	* [[http://mpkb.org/_detail/home/admin/arf-logo-large-whitebg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-large-whitebg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]
-	* [[http://mpkb.org/_detail/home/admin/arf-logo-large-whitebg.eps?id=home%3Aadmin%3Alogo\|EPS]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-large-whitebg.eps?id=home%3Aadmin%3Alogo\|EPS]]


	==== Black Background ====		==== Black Background ====

-	* [[http://mpkb.org/_detail/home/admin/arf-logo-small-blackbg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-small-blackbg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]
-	* [[http://mpkb.org/_detail/home/admin/arf-logo-large-blackbg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-large-blackbg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]
-	* [[http://mpkb.org/_detail/home/admin/arf-logo-large-blackbg.eps?id=home%3Aadmin%3Alogo\|EPS]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-large-blackbg.eps?id=home%3Aadmin%3Alogo\|EPS]]

Paul's Notes

anonymous@undisclosed.example.com (Anonymous) — Wed, 14 Sep 2022 05:14:49 +0000

anonymous@undisclosed.example.com (Anonymous) — Tue, 03 Jan 2012 04:20:35 +0000

05.02.2026		current
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		+	{{quiz>home:quizsource}}

Quiz title

anonymous@undisclosed.example.com (Anonymous) — Tue, 03 Jan 2012 04:20:35 +0000

10.02.2010		current

Markers for Study Design

anonymous@undisclosed.example.com (Anonymous) — Wed, 14 Sep 2022 05:14:49 +0000

07.20.2011		current
Line 7:		Line 7:
	===== Direct detection of bacteria =====		===== Direct detection of bacteria =====

-	* [[http://gtresearchnews.gatech.edu/maltodextrin-probes/\|Detecting Disease: New Contrast Agents Detect Bacterial Infections with High Sensitivity and Specificity]]	+	* [[https://gtresearchnews.gatech.edu/maltodextrin-probes/\|Detecting Disease: New Contrast Agents Detect Bacterial Infections with High Sensitivity and Specificity]]
-	* [[http://dl.dropbox.com/u/2014679/nmat3074.pdf\|full text]]	+	* [[https://dl.dropbox.com/u/2014679/nmat3074.pdf\|full text]]

	* Now, this seems to be an interesting test. Inge		* Now, this seems to be an interesting test. Inge
Line 36:		Line 36:

	===== Endotoxins =====		===== Endotoxins =====
-	* [[http://www.sciencedaily.com/releases/2011/05/110519141615.htm\|Liquid Crystal Droplets Discovered to Be Exquisitely Sensitive to an Important Bacterial Lipid]]	+	* [[https://www.sciencedaily.com/releases/2011/05/110519141615.htm\|Liquid Crystal Droplets Discovered to Be Exquisitely Sensitive to an Important Bacterial Lipid]]
-	* [[http://dl.dropbox.com/u/2014679/Science-2011-Lin-1297-300.pdf\|Full text]]	+	* [[https://dl.dropbox.com/u/2014679/Science-2011-Lin-1297-300.pdf\|Full text]]


Line 92:		Line 92:

	I've also read about tests which measure lipopolysaccharide binding protein (LBP). For example:		I've also read about tests which measure lipopolysaccharide binding protein (LBP). For example:
-	http://www.cellsciences.com/content/p-detail.asp?rowid=4392&buy=4392	+	https://www.cellsciences.com/content/p-detail.asp?rowid=4392&buy=4392

	If we want to demonstrate that our therapy increases serum bioavailability of endotoxins (which suggests bacteria die-off) what marker and/or assay, would you recommend?		If we want to demonstrate that our therapy increases serum bioavailability of endotoxins (which suggests bacteria die-off) what marker and/or assay, would you recommend?
Line 153:		Line 153:
	===== Antimicrobial peptides =====		===== Antimicrobial peptides =====

-	[{{ :home:alternate:sarcoidosiscathelicidin.001.png?370\|If anything, patients with autoimmune disease are //immunocompromised//. A study of the prevalence of the key antimicrobial peptide showed that patients with sarcoidosis expressed it less than healthy subjects, and that sicker sarcoidosis patients expressed it least of all. Source: [[http://dl.dropbox.com/u/2014679/CathelicidinDeficiencies.pdf\|Kanchwala et al.]]}}]	+	[{{ :home:alternate:sarcoidosiscathelicidin.001.png?370\|If anything, patients with autoimmune disease are //immunocompromised//. A study of the prevalence of the key antimicrobial peptide showed that patients with sarcoidosis expressed it less than healthy subjects, and that sicker sarcoidosis patients expressed it least of all. Source: [[https://dl.dropbox.com/u/2014679/CathelicidinDeficiencies.pdf\|Kanchwala et al.]]}}]

-	* Kanchwala //et al.// showed that patients with sarcoidosis expressed the antimicrobial peptide cathelicidin less than healthy subjects, and that sicker sarcoidosis patients expressed it least of all.((Kanchwala, A., B. Barna, et al. (2009). [[http://dl.dropbox.com/u/2014679/CathelicidinDeficiencies.pdf\|Deficiencies of cathelicidin and vitamin D accompany disease severity in sarcoidosis]].)) Wiken //et al.// showed that there was a reduced TLR2 mRNA expression in patients with Lofgren's syndrome (a type of acute sarcoidosis).((Wiken M. //et al.// [[http://respiratory-research.com/content/11/1/121/citation\|No evidence of altered alveolar macrophage polarization, but reduced expression of TLR2, in bronchoalveolar lavage cells in sarcoidosis]] //Respiratory Research// 2010, 11:121.)) Note that TLR2 (which the Marshall Pathogenesis theorizes is downregulated in autoimmune disease states) is expressed by the VDR.	+	* Kanchwala //et al.// showed that patients with sarcoidosis expressed the antimicrobial peptide cathelicidin less than healthy subjects, and that sicker sarcoidosis patients expressed it least of all.((Kanchwala, A., B. Barna, et al. (2009). [[https://dl.dropbox.com/u/2014679/CathelicidinDeficiencies.pdf\|Deficiencies of cathelicidin and vitamin D accompany disease severity in sarcoidosis]].)) Wiken //et al.// showed that there was a reduced TLR2 mRNA expression in patients with Lofgren's syndrome (a type of acute sarcoidosis).((Wiken M. //et al.// [[https://respiratory-research.com/content/11/1/121/citation\|No evidence of altered alveolar macrophage polarization, but reduced expression of TLR2, in bronchoalveolar lavage cells in sarcoidosis]] //Respiratory Research// 2010, 11:121.)) Note that TLR2 (which the Marshall Pathogenesis theorizes is downregulated in autoimmune disease states) is expressed by the VDR.
-	* Wang //et al.// have demonstrated in Crohn's patients a decline in expression of key antimicrobial peptides including cathelicidin and Beta-defensin-2.(({{pubmed>long:19948723}})) Consistent with the Marshall Pathogenesis, the group points to the Vitamin D Receptor as being important in Crohn's patients.	+	* Wang //et al.// have demonstrated in Crohn's patients a decline in expression of key antimicrobial peptides including cathelicidin and Beta-defensin-2.(({{pmid>long:19948723}})) Consistent with the Marshall Pathogenesis, the group points to the Vitamin D Receptor as being important in Crohn's patients.
-	* [[http://dl.dropbox.com/u/2014679/j.1440-1843.2011.01924.x.pdf\|Vitamin D, innate immunity and outcomes in community acquired pneumonia]]	+	* [[https://dl.dropbox.com/u/2014679/j.1440-1843.2011.01924.x.pdf\|Vitamin D, innate immunity and outcomes in community acquired pneumonia]]


Line 264:		Line 264:
	Interesting TED lecture on bacterial communication via specialized chemicals - both species specific and generic.		Interesting TED lecture on bacterial communication via specialized chemicals - both species specific and generic.

-	http://www.ted.com/index.php/talks/bonnie_bassler_on_how_bacteria_communicate.html	+	https://www.ted.com/index.php/talks/bonnie_bassler_on_how_bacteria_communicate.html

	So...if a biofilm can excrete a chemical marker, whose concentration "tells" the collection of bacteria when to become mobile and "invade", it's a small stretch to include excreted markers that encourage conversion to invasive CWD forms, or cysts (Borrelia), or migration to low O2 regions, or migration to heart/lung/CNS tissue, etc..		So...if a biofilm can excrete a chemical marker, whose concentration "tells" the collection of bacteria when to become mobile and "invade", it's a small stretch to include excreted markers that encourage conversion to invasive CWD forms, or cysts (Borrelia), or migration to low O2 regions, or migration to heart/lung/CNS tissue, etc..
Line 277:		Line 277:
	==== Interleukin-6 ====		==== Interleukin-6 ====

-	[[http://www.sabiosciences.com/ELISA.php?bhn_mid=2200941&bhn_rid=531708925&cmpid=EL091118\|Multi-Analyte ELISArray™ Kits]]	+	[[https://www.sabiosciences.com/ELISA.php?bhn_mid=2200941&bhn_rid=531708925&cmpid=EL091118\|Multi-Analyte ELISArray™ Kits]]


	<blockquote>		<blockquote>
-	Full text [[http://dl.dropbox.com/u/2014679/sdarticlera.pdf\|here]]	+	Full text [[https://dl.dropbox.com/u/2014679/sdarticlera.pdf\|here]]

	Clin Biochem. 2010 Nov;43(16-17):1309-14. Epub 2010 Jul 23.		Clin Biochem. 2010 Nov;43(16-17):1309-14. Epub 2010 Jul 23.
Line 305:		Line 305:
	PMID: 20655893</blockquote>		PMID: 20655893</blockquote>

		+	===== Antigens in blood using amplification, arrays =====
		+	<blockquote>Despite the great strides medicine has made in the past century, diagnosing infectious disease remains a difficult – and often impossible – task. One major barrier in diagnosis is knowing what to look for. Which of the millions of potentially antigenic products that a pathogen makes can actually be found in bodily fluids and used as indicators of infection? After all, not every protein or polysaccharide belonging to a pathogen can make it into a handy sample of urine or blood, so which CAN we use?

		+	A study in mBio this week brings us a little closer to identifying those antigens that could be used in diagnostics. Using a technique they call In vivo Microbial Antigen Discovery (InMAD), Nuti et al. were able to amplify the small signals present in an infected mouse’s blood by purifying serum samples and using them to immunize another mouse. Serum from this second mouse contains antibodies for the bacterial components in the blood of the first mouse. They used this serum to probe blots of bacterial lysates and bacterial proteome arrays. The spots on the blot or the array that lit up indicate which antigens the mouse immune system reacts to – precisely the antigens that could be targeted in an assay.
		+	Click on the source link above to read more on mBio's blog, mBiosphere...
		+	</blockquote>
		+
		+	https://www.microbeworld.org/index.php?option=com_jlibrary&view=article&id=7275&utm_source=twitterfeed&utm_medium=twitter&utm_campaign=twitter
	===== Contacts =====		===== Contacts =====

Style Guidelines and Best Practices

anonymous@undisclosed.example.com (Anonymous) — Wed, 14 Sep 2022 05:14:49 +0000

05.02.2026	current
Line 1:	Line 1:
	+	<html><style type="text/css">
	+	.breadcrumbs {display: none;}
	+	.gsc-completion-container {
	+	font-family: helvetica, sans-serif !important;
	+	font-size: 18px !important;
	+	border: 1px solid #666666;
	+	margin-left: 0;
	+	margin-right: 0;
	+	/* The top, left, and width are set in JavaScript. */
	+	-moz-box-shadow: 5px 5px 5px #999;
	+	-webkit-box-shadow: 5px 5px 5px #999;
	+	box-shadow: 5px 5px 5px #999;
	+	background-color: #fafafa; /* Needed for IEs */
	+	}
	+
	+	.gsc-completion-container > tbody {
	+	position: relative; /* This protects the inner element from being blurred */
	+	background-color: #DDD; }
	+
	+	.gsc-completion-container > tbody > tr > td { padding: 5px; }
	+	td#csc-completion-selected { background: #FEFAF4 !important; }
	+
	+
	+
	+
	+	</style></html>
	+
	+	~~NOTOC~~
	+
	+
	+	====== Home ======
	+	<WRAP homepage>
	+
	+
	+
	+	<columns 100% 62% 2% 35% ->
	+
	+
	+	<WRAP h2 welcome>Welcome to the MPKB</WRAP>
	+
	+
	+	The <html>Marshall Protocol</html> is a therapy for chronic inflammatory diseases created by Trevor Marshall, PhD. It is based on an explanation for how an infectious cascade of pathogens slow the immune response, allowing subsequent infections to proliferate, thereby causing the symptoms and markers of disease.
	+
	+	<WRAP h2>Search</WRAP><phpinc=homesearch.html>
	+	<WRAP tabber><WRAP tabbertab><html><h3>For Patients</h3></html>
	+	* Why microbes may cause chronic inflammatory diseases
	+	* [[home:patients:pathogenesis_overview\|Introduction to the Marshall Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:familial_aggregation\|Familial aggregation]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:pathogenesis:microbiota\|Microbes in the human body]]
	+	* [[home:pathogenesis:evidence_bacteria\|Evidence that chronic disease is caused by pathogens]]
	+	* <html><b>What is the Marshall Protocol?</b></html> – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:patients:protocol_overview\|Introduction]]
	+	* [[home:patients:mp_duration\|Length]] – may take several years depending on how sick a patient is
	+	* [[home:patients:cost_of_mp\|Cost]] – insurance often pays for certain basic expenses; drugs can be [[home:mp:olmesartan:buying\|ordered online]] at a discount
	+	* [[home:patients:assessing_literature:palliative\|Palliative vs. curative treatments]] – many widely used treatments and supplements such as vitamin D compromise the immune response to microbes and are therefore contraindicated
	+	* <html><b>Considering the Marshall Protocol</b></html>
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:tests:vitdinterpretation\|Vitamin D Metabolite Calculator]] – get automated feedback on vitamin D blood tests
	+	* [[home:patients:patient_interviews\|Patient interviews]]
	+	* Starting the treatment – [[home:starting\|Overview]] \| [[home:starting:prempchecklist\|Checklist]]
	+	* Physicians – [[home:starting:physician:finding\|Finding a physician]] \| [[home:starting:physician\|Working with a physician]]
	+	* The Protocol – [[home:mp\|In-depth overview of the Protocol]] \| [[home:translations\|Translations of this and other articles]]
	+	* [[home:mp:immunopathology\|Immunopathology]] – temporary increase in disease symptoms experienced by MP patients that is the result of microbial death; appears to be necessary for recovery
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:lifestyle:light\|Light restriction]] – patients who are photosensitive on the MP become less symptomatic when they limit skin exposure to light when [[home:lifestyle:light:outdoor\|outdoors]], and skin and [[home:lifestyle:light:eye_protection\|eye exposure]] when [[home:lifestyle:light:indoor\|indoors]]
	+	* [[home:food\|Food & drink]] – patients limit vitamin D
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* Learn more
	+	* [[home:index\|Site map]] – contains a list of all articles in the KB
	+	* [[home:publications\|Publications and presentations]]
	+	* [[home:patients:glossary\|Glossary of terms]]
	+	</WRAP>
	+	<WRAP tabbertab><html><h3>For Physicians</h3></html>
	+	* <html><b>The Marshall Pathogenesis</b></html> – an explanation for how microbes may cause chronic inflammatory diseases
	+	* [[home:pathogenesis\|Science behind Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:pathogenesis:evidence_bacteria\|Evidence that chronic disease is caused by pathogens]]
	+	* [[home:pathogenesis:vitamind\|Science behind vitamin D]] \| [[home:pathogenesis:vitamind:metabolism\|Metabolism of vitamin D and the Vitamin D Receptor]]
	+	* <html><b>What is the Marshall Protocol?</b></html> – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:mp\|Marshall Protocol]] – one-page summary of the MP geared towards physicians
	+	* [[home:physicians:concerns\|Physicians' concerns]] – olmesartan, antibiotics, light, vitamin D, <html>immunopathology</html>, clinical evidence
	+	* [[home:protocol:olmesartan\|Olmesartan (Benicar)]] – [[home:protocol:olmesartan:safety\|Safety of olmesartan]] \| [[home:protocol:olmesartan:kidney_disease\|Olmesartan and kidney disease]]
	+	* Antibiotics – [[home:protocol:mp_antibiotics:dosing\|Pulsed low-dose antibiotics]] \| [[home:protocol:mp_antibiotics:antibiotics_concerns\|Safety]]
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:protocol:immunopathology\|Immunopathology]] – also known as the Jarisch-Herxheimer reaction
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* [[home:physicians:emergency\|Notice for emergency]]
	+	* Alternative models for chronic disease
	+	* [[home:alternate:autoimmunity\|Autoimmune theory of disease]]
	+	* [[home:alternate:genetic_predisposition\|Genetic predisposition to disease]]
	+	* [[home:alternate:psychosomatic\|Psychosomatic explanations for disease]]
	+	* Learn more
	+	* [[home:physicians\|Resources for physicians]]
	+	* [[home:publications\|Publications and presentations]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:patients:glossary\|Glossary of terms]]
	+	* [[home:index\|Site map]] – contains a list of all articles in the KB
	+
	+
	+
	+	</WRAP></WRAP><newcolumn top>
	+
	+	<newcolumn top>
	+	<html><div class="highlightedh2">News and highlights </div></html><phpinc=twit.html>
	+
	+
	+	<html><div class="highlightedh2" style="margin-top: 18px !important;">Publications and presentations</div></html>
	+	\|[[home:publications:proal_molecular_2011\|Immunostimulation in the era of the human metagenome]] - paper in //Molecular and clinical immunology// that reviews a case series of <html>Marshall Protocol</html> patients and discusses how immunostimulatory approaches may require rethinking medicine \|
	+	\|[[home:publications:proal_metagenomics_2010\|Autoimmune disease and the human metagenome]] - book chapter in Springer's //Metagenomics of the human body// that discusses how the process of <html>successive infection may be responsible for autoimmune disease</html> \|
	+	\|[[home:publications:marshall_autoimmunity_2010\|Olmesartan overcomes antibiotic resistance, inducing recovery from advanced autoimmune disease]] – presentation by Trevor Marshall, PhD at International Congress on <html>Autoimmunity</html> \|
	+	\|[[home:publications:blaney_autoimmunity_2010\|Olmesartan medoxomil and treatment of autoimmune disease]] – presentation by Greg Blaney, MD \\ \\ → [[home:publications\|Complete list]]\|
	+
	+
	+	<WRAP h4>About the MPKB Project</WRAP>
	+
	+	The MPKB currently contains about 400 pages and draws from the best possible evidence to support its mission. As of May 2011, about 85% of those articles are complete with the remainder scheduled to be completed.
	+	* [[home:index#site_map\|Site Map]] (formerly on the home page)
	+	* [[home:index#incomplete_articles\|Incomplete articles]]
	+	* [[home:patients:tipsformpkb\|Tips for using this resource]]
	+
	+	<WRAP h4>About Autoimmunity Research Foundation</WRAP>
	+
	+	[[https://autoimmunityresearch.org\|Autoimmunity Research Foundation]] is a California-based 501(c)3 (tax deductible) non-profit formed to educate the public about the nature of, and study a treatment for, chronic inflammatory disease.
	+	* [[home:arf:timeline\|History and timeline of the Autoimmunity Research Foundation]]
	+
	+	</columns>
	+	</WRAP>
	+

05.02.2026	current
Line 1:	Line 1:
	+	<html><style type="text/css">
	+	.breadcrumbs {display: none;}
	+	.gsc-completion-container {
	+	font-family: helvetica, sans-serif !important;
	+	font-size: 18px !important;
	+	border: 1px solid #666666;
	+	margin-left: 0;
	+	margin-right: 0;
	+	/* The top, left, and width are set in JavaScript. */
	+	-moz-box-shadow: 5px 5px 5px #999;
	+	-webkit-box-shadow: 5px 5px 5px #999;
	+	box-shadow: 5px 5px 5px #999;
	+	background-color: #fafafa; /* Needed for IEs */
	+	}
	+
	+	.gsc-completion-container > tbody {
	+	position: relative; /* This protects the inner element from being blurred */
	+	background-color: #DDD; }
	+
	+	.gsc-completion-container > tbody > tr > td { padding: 5px; }
	+	td#csc-completion-selected { background: #FEFAF4 !important; }
	+
	+	</style></html>
	+
	+	~~NOTOC~~
	+
	+
	+	====== Home ======
	+	<WRAP homepage>
	+
	+
	+	<WRAP leftdivhome><WRAP h2 welcome>Welcome to the MPKB</WRAP>
	+
	+	The <html>Marshall Protocol</html> is a therapy for chronic inflammatory diseases created by Trevor Marshall, PhD. It is based on an explanation for how an infectious cascade of pathogens slow the immune response, allowing subsequent infections to proliferate, thereby causing the symptoms and markers of disease.
	+
	+	<WRAP h2>Search</WRAP><phpinc=homesearch.html>
	+	<WRAP tabber><WRAP tabbertab><html><h3>For Patients</h3></html>
	+	* Why microbes may cause chronic inflammatory diseases
	+	* [[home:patients:pathogenesis_overview\|Introduction to the Marshall Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:familial_aggregation\|Familial aggregation]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:pathogenesis:microbiota\|Microbes in the human body]]
	+	* [[home:pathogenesis:evidence_bacteria\|Evidence that chronic disease is caused by pathogens]]
	+	* <html><b>What is the Marshall Protocol?</b></html> – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:patients:protocol_overview\|Introduction]]
	+	* [[home:patients:mp_duration\|Length]] – may take several years depending on how sick a patient is
	+	* [[home:patients:cost_of_mp\|Cost]] – insurance often pays for certain basic expenses; drugs can be [[home:mp:olmesartan:buying\|ordered online]] at a discount
	+	* [[home:patients:assessing_literature:palliative\|Palliative vs. curative treatments]] – many widely used treatments and supplements such as vitamin D compromise the immune response to microbes and are therefore contraindicated
	+	* <html><b>Considering the Marshall Protocol</b></html>
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:tests:vitdinterpretation\|Vitamin D Metabolite Calculator]] – get automated feedback on vitamin D blood tests
	+	* [[home:patients:patient_interviews\|Patient interviews]]
	+	* Starting the treatment – [[home:starting\|Overview]] \| [[home:starting:prempchecklist\|Checklist]]
	+	* Physicians – [[home:starting:physician:finding\|Finding a physician]] \| [[home:starting:physician\|Working with a physician]]
	+	* The Protocol – [[home:mp\|In-depth overview of the Protocol]] \| [[home:translations\|Translations of this and other articles]]
	+	* [[home:mp:immunopathology\|Immunopathology]] – temporary increase in disease symptoms experienced by MP patients that is the result of microbial death; appears to be necessary for recovery
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:lifestyle:light\|Light restriction]] – patients who are photosensitive on the MP become less symptomatic when they limit skin exposure to light when [[home:lifestyle:light:outdoor\|outdoors]], and skin and [[home:lifestyle:light:eye_protection\|eye exposure]] when [[home:lifestyle:light:indoor\|indoors]]
	+	* [[home:food\|Food & drink]] – patients limit vitamin D
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* Learn more
	+	* [[home:index\|Site map]] – contains a list of all articles in the KB
	+	* [[home:publications\|Publications and presentations]]
	+	* [[home:patients:glossary\|Glossary of terms]]
	+	</WRAP>
	+	<WRAP tabbertab><html><h3>For Physicians</h3></html>
	+	* <html><b>The Marshall Pathogenesis</b></html> – an explanation for how microbes may cause chronic inflammatory diseases
	+	* [[home:pathogenesis\|Science behind Pathogenesis]]
	+	* [[home:pathogenesis:successive_infection\|Successive infection and variability in disease]]
	+	* [[home:pathogenesis:transmission\|Transmission of bacteria and onset of disease]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:pathogenesis:evidence_bacteria\|Evidence that chronic disease is caused by pathogens]]
	+	* [[home:pathogenesis:vitamind\|Science behind vitamin D]] \| [[home:pathogenesis:vitamind:metabolism\|Metabolism of vitamin D and the Vitamin D Receptor]]
	+	* <html><b>What is the Marshall Protocol?</b></html> – The cornerstone of the MP is frequent dosing of olmesartan (brand name Benicar), which stimulates the innate immune response.
	+	* [[home:mp\|Marshall Protocol]] – one-page summary of the MP geared towards physicians
	+	* [[home:physicians:concerns\|Physicians' concerns]] – olmesartan, antibiotics, light, vitamin D, <html>immunopathology</html>, clinical evidence
	+	* [[home:protocol:olmesartan\|Olmesartan (Benicar)]] – [[home:protocol:olmesartan:safety\|Safety of olmesartan]] \| [[home:protocol:olmesartan:kidney_disease\|Olmesartan and kidney disease]]
	+	* Antibiotics – [[home:protocol:mp_antibiotics:dosing\|Pulsed low-dose antibiotics]] \| [[home:protocol:mp_antibiotics:antibiotics_concerns\|Safety]]
	+	* [[home:starting:therapeutic_probe\|Therapeutic probe]] – best method for determining suitability of the Protocol
	+	* [[home:protocol:immunopathology\|Immunopathology]] – also known as the Jarisch-Herxheimer reaction
	+	* [[home:mp:managing_immunopathology\|Managing immunopathology]] – certain strategies are helpful including lowering antibiotics and adjusting olmesartan
	+	* [[home:othertreatments\|Other treatments]] – patients only take other medications that offer needed relief from intolerable symptoms
	+	* [[home:physicians:emergency\|Notice for emergency]]
	+	* Alternative models for chronic disease
	+	* [[home:alternate:autoimmunity\|Autoimmune theory of disease]]
	+	* [[home:alternate:genetic_predisposition\|Genetic predisposition to disease]]
	+	* [[home:alternate:psychosomatic\|Psychosomatic explanations for disease]]
	+	* Learn more
	+	* [[home:physicians\|Resources for physicians]]
	+	* [[home:publications\|Publications and presentations]]
	+	* [[home:diseases\|Diseases]] – articles about microbes' role in a given chronic disease; note: many are works in progress
	+	* [[home:patients:glossary\|Glossary of terms]]
	+	* [[home:index\|Site map]] – contains a list of all articles in the KB
	+
	+	</WRAP></WRAP></WRAP>
	+
	+	<WRAP rightdivhome>
	+	<html><div class="highlightedh2">News and highlights </div></html><phpinc=twit.html>
	+
	+
	+	<html><div class="highlightedh2 pubs">Publications and presentations</div></html>
	+	\|[[home:publications:proal_molecular_2011\|Immunostimulation in the era of the human metagenome]] - paper in //Molecular and clinical immunology// that reviews a case series of <html>Marshall Protocol</html> patients and discusses how immunostimulatory approaches may require rethinking medicine \|
	+	\|[[home:publications:proal_metagenomics_2010\|Autoimmune disease and the human metagenome]] - book chapter in Springer's //Metagenomics of the human body// that discusses how the process of <html>successive infection may be responsible for autoimmune disease</html> \|
	+	\|[[home:publications:marshall_autoimmunity_2010\|Olmesartan overcomes antibiotic resistance, inducing recovery from advanced autoimmune disease]] – presentation by Trevor Marshall, PhD at International Congress on <html>Autoimmunity</html> \|
	+	\|[[home:publications:blaney_autoimmunity_2010\|Olmesartan medoxomil and treatment of autoimmune disease]] – presentation by Greg Blaney, MD \\ \\ → [[home:publications\|Complete list]]\|
	+
	+
	+	<WRAP h4>About the MPKB Project</WRAP>
	+
	+	The MPKB currently contains about 400 pages and draws from the best possible evidence to support its mission. As of May 2011, about 85% of those articles are complete with the remainder scheduled to be completed.
	+	* [[home:index#site_map\|Site Map]] (formerly on the home page)
	+	* [[home:index#incomplete_articles\|Incomplete articles]]
	+	* [[home:patients:tipsformpkb\|Tips for using this resource]]
	+
	+	<WRAP h4>About Autoimmunity Research Foundation</WRAP>
	+
	+	[[https://autoimmunityresearch.org\|Autoimmunity Research Foundation]] is a California-based 501(c)3 (tax deductible) non-profit formed to educate the public about the nature of, and study a treatment for, chronic inflammatory disease.
	+	* [[home:arf:timeline\|History and timeline of the Autoimmunity Research Foundation]]
	+
	+	</WRAP>
	+	</WRAP>
	+

05.02.2026	current
Line 1:	Line 1:
	+	<html></p><style type="text/css">.breadcrumbs, .addthis_default_style {display:none;}</style><div id="homecolumns"></html>

	+
	+	~~NOTOC~~
	+
	+	====== Home ======
	+
	+	<columns 100% 34% 30% 35% ->
	+	===== For Patients =====
	+
	+	The Marshall Protocol (MP) is a treatment for chronic inflammatory diseases.
	+
	+	* [[home:patients\|Resources for patients]]
	+	* [[home:patients:pathogenesis_overview\|Marshall's theory of chronic inflammatory disease]]
	+	* [[home:patients:protocol_overview\|Introduction to the treatment]] – [[home:patients:mp_duration\|Length]], [[home:patients:cost_of_mp\|Cost]], [[home:patients:patient_interviews\|Patient Interviews]], [[home:patients:glossary\|Glossary]]
	+	* Suitability of the MP – [[home:starting:therapeutic_probe\|Therapeutic probe]], [[home:tests:vitdinterpretation\|Vitamin D Metabolite Calculator]]
	+	* [[home:starting\|Getting Started]] – [[home:starting:prempchecklist\|Checklist]], [[home:starting:physician:finding\|Finding a physician]], [[home:starting:physician\|Working with a physician]]
	+	* Doing the MP – [[home:lifestyle:light\|Light restriction?]], [[home:food\|Food & drink]], [[home:mp:immunopathology\|Immunopathology]], [[home:mp:managing_immunopathology\|Managing immunopathology]], [[https://autoimmunityResearch.org/phase1.pdf\|Guidelines]], [[home:othertreatments\|Non-MP treatments]]
	+
	+	<newcolumn top>
	+	===== For Physicians =====
	+
	+	The MP is based on the hypothesis that chronic inflammatory diseases are the result of infection by [[home:pathogenesis:microbiota\|communities of microbes]], which downregulate innate immune function.
	+	* [[home:physicians\|Resources for physicians]]
	+	* [[home:pathogenesis\|The Marshall Pathogenesis]]
	+	* [[home:protocol:immunopathology\|About immunopathology a.k.a. the Jarisch-Herxheimer reaction]]
	+	* Safety of the Protocol – [[home:protocol:olmesartan:safety\|olmesartan (Benicar)]], [[home:protocol:mp_antibiotics:antibiotics_concerns\|antibiotics]]
	+	* [[home:mp\|Summary of MP]], [[https://autoimmunityResearch.org/phase1.pdf\|Guidelines]]
	+	* [[home:physicians:concerns\|Physicians' concerns]]
	+	* [[home:physicians:emergency\|Notice for emergency]]
	+
	+
	+	<newcolumn top>
	+
	+
	+
	+	===== Publications/Presentations =====
	+
	+
	+	* Book chapter by Amy Proal //et al.// – [[home:publications:proal_metagenomics_2010\|Autoimmune disease and the human metagenome]]
	+	* Presentation by Trevor Marshall, PhD – [[home:publications:marshall_autoimmunity_2010\|Olmesartan overcomes antibiotic resistance, inducing recovery from advanced autoimmune disease]]
	+	* Presentation by Greg Blaney, MD – [[home:publications:blaney_autoimmunity_2010\|Olmesartan medoxomil and treatment of autoimmune disease]]
	+	* [[home:publications\|Complete list]]
	+
	+
	+	===== News =====
	+
	+
	+	* //Feb. 2011// – paper describing the Marshall Protocol written by ARF researchers [[home:publications:proal_molecular_2011\|now available]]
	+
	+	* //March 2011// - [[home:translations:german\|Deutsche übersetzung]]
	+
	+	</columns>
	+	<html>
	+	</div>
	+	</html>
	+
	+	==== About Autoimmunity Research Foundation and the MPKB Project ====
	+
	+	[[https://autoimmunityresearch.org\|Autoimmunity Research Foundation]] is a California-based 501(c)3 (tax deductible) non-profit formed to educate the public about the nature of, and study a treatment for, chronic inflammatory disease. The MPKB currently contains about 400 pages and draws from the best possible evidence to support its mission. As of October 2010, about 80% of those articles are complete with the remainder scheduled to be completed in the next year.
	+
	+	* [[home:index#site_map\|Site Map]] (formerly on the home page)
	+	* [[home:index#incomplete_articles\|Incomplete articles]]
	+	* [[home:patients:tipsformpkb\|Tips for using this resource]]
	+	* [[home:arf:timeline\|History and timeline of the Autoimmunity Research Foundation]]

05.15.2010		current
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	==== White Background ====		==== White Background ====

-	* [[http://mpkb.org/_detail/home/admin/mpkb-logo-small-whitebg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]	+	* [[https://mpkb.org/_detail/home/admin/mpkb-logo-small-whitebg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]
-	* [[http://mpkb.org/_detail/home/admin/mpkb-logo-large-whitebg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]	+	* [[https://mpkb.org/_detail/home/admin/mpkb-logo-large-whitebg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]
-	* [[http://mpkb.org/_detail/home/admin/mpkb-logo-large-whitebg.eps?id=home%3Aadmin%3Alogo\|EPS]]	+	* [[https://mpkb.org/_detail/home/admin/mpkb-logo-large-whitebg.eps?id=home%3Aadmin%3Alogo\|EPS]]


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	==== White Background ====		==== White Background ====

-	* [[http://mpkb.org/_detail/home/admin/arf-logo-small-whitebg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-small-whitebg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]
-	* [[http://mpkb.org/_detail/home/admin/arf-logo-large-whitebg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-large-whitebg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]
-	* [[http://mpkb.org/_detail/home/admin/arf-logo-large-whitebg.eps?id=home%3Aadmin%3Alogo\|EPS]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-large-whitebg.eps?id=home%3Aadmin%3Alogo\|EPS]]


	==== Black Background ====		==== Black Background ====

-	* [[http://mpkb.org/_detail/home/admin/arf-logo-small-blackbg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-small-blackbg.gif?id=home%3Aadmin%3Alogo\|Small GIF]]
-	* [[http://mpkb.org/_detail/home/admin/arf-logo-large-blackbg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-large-blackbg.gif?id=home%3Aadmin%3Alogo\|Large GIF]]
-	* [[http://mpkb.org/_detail/home/admin/arf-logo-large-blackbg.eps?id=home%3Aadmin%3Alogo\|EPS]]	+	* [[https://mpkb.org/_detail/home/admin/arf-logo-large-blackbg.eps?id=home%3Aadmin%3Alogo\|EPS]]

01.03.2012		current
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	^Plugin ^Notes ^Requires ^Dokuwiki Page ^Download Link^		^Plugin ^Notes ^Requires ^Dokuwiki Page ^Download Link^
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-	\|boxes \|in use \|- \|[[http://www.dokuwiki.org/plugin:boxes \|plugin:boxes ]] \|[[http://dokuwiki.jalakai.co.uk/plugin-box.zip\|download]] \|	+	\|boxes \|in use \|- \|[[https://www.dokuwiki.org/plugin:boxes \|plugin:boxes ]] \|[[https://dokuwiki.jalakai.co.uk/plugin-box.zip\|download]] \|
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	===== Plugin customizations =====		===== Plugin customizations =====
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	* lots of files in /conf using the "local..." syntax		* lots of files in /conf using the "local..." syntax
	* /inc/preload.php - removes all but fatal errors		* /inc/preload.php - removes all but fatal errors
		+	* /inc/lang/en/lang.php - changed "login" to "admin login"

09.09.2012		current
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	* Allow users to click to switch stylesheets (Beware, the plugin tplSwitcher generates a file called /conf/local.protected.php that screws up current version of Dokuwiki)		* Allow users to click to switch stylesheets (Beware, the plugin tplSwitcher generates a file called /conf/local.protected.php that screws up current version of Dokuwiki)
	* Allow users to click to increase font size		* Allow users to click to increase font size
-	* [[http://www.sitepoint.com/article/css-simple-style-switcher/\|CSS stylesheet switcher]]	+	* [[https://www.sitepoint.com/article/css-simple-style-switcher/\|CSS stylesheet switcher]]
	- Host autoimmunityresearch.org on the KB using a modified version of this template		- Host autoimmunityresearch.org on the KB using a modified version of this template
	- This error came back: "Warning: array_diff() [function.array-diff]: Argument #1 is not an array in /home/jsmith/domains/mp-dev.com/public_html/mpkb/lib/plugins/tag/helper.php on line 276" Not sure what happened. I might have overwritten your original fix. :( ... Actually, I haven't seen this in a while, so maybe it went away.		- This error came back: "Warning: array_diff() [function.array-diff]: Argument #1 is not an array in /home/jsmith/domains/mp-dev.com/public_html/mpkb/lib/plugins/tag/helper.php on line 276" Not sure what happened. I might have overwritten your original fix. :( ... Actually, I haven't seen this in a while, so maybe it went away.
	- put PMIDs inside thumbinner class		- put PMIDs inside thumbinner class
	- get the filter to work [[home:food:vitamind:dcontentfoods\|here]]		- get the filter to work [[home:food:vitamind:dcontentfoods\|here]]
-	- Use Google Analytics to track outbound links http://davidwalsh.name/mootools-google-analytics-track-outbound-links	+	- Use Google Analytics to track outbound links https://davidwalsh.name/mootools-google-analytics-track-outbound-links
-	- download as PDF plugin? http://www.dokuwiki.org/plugins?plugintag=pdf or this: http://www.dokuwiki.org/tips:pdfexport	+	- download as PDF plugin? https://www.dokuwiki.org/plugins?plugintag=pdf or this: https://www.dokuwiki.org/tips:pdfexport
-	- allow for links to tags without showing the world background image, i.e. [[http://mpkb.org/doku.php/tag:immunosuppressants?do=showtag&tag=immunosuppressants\|immunosuppressants]]	+	- allow for links to tags without showing the world background image, i.e. [[https://mpkb.org/doku.php/tag:immunosuppressants?do=showtag&tag=immunosuppressants\|immunosuppressants]]
	- Dropdown - JQuery conflicts with Dokuwiki; do a workaround? do I even need jquery???		- Dropdown - JQuery conflicts with Dokuwiki; do a workaround? do I even need jquery???
-	* http://stackoverflow.com/questions/134572/jquery-prototype-conflict	+	* https://stackoverflow.com/questions/134572/jquery-prototype-conflict
-	* http://stackoverflow.com/questions/490426/can-dokuwiki-jquery-play-together	+	* https://stackoverflow.com/questions/490426/can-dokuwiki-jquery-play-together


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	<relatedarticle> ... </article>		<relatedarticle> ... </article>
	{{section>:&noheader&firstseconly}}		{{section>:&noheader&firstseconly}}
-	(({{pubmed>long:}}))	+	(({{pmid>long:}}))
	{{backlinks>.}}		{{backlinks>.}}
	{{topic>papers presentations -+}}		{{topic>papers presentations -+}}
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	===== Admin tools =====		===== Admin tools =====

-	* http://loadimpact.com/result/mpkb.mp-dev.com-31153552013631787a0b9a9d35374807	+	* https://loadimpact.com/result/mpkb.mp-dev.com-31153552013631787a0b9a9d35374807

	===== Design =====		===== Design =====

	====Typography====		====Typography====
-	* http://www.smashingmagazine.com/2009/04/03/8-simple-ways-to-improve-typography-in-your-designs/	+	* https://www.smashingmagazine.com/2009/04/03/8-simple-ways-to-improve-typography-in-your-designs/
-	* http://www.typetester.org/	+	* https://www.typetester.org/
-	* http://psd.tutsplus.com/articles/techniques/a-20-minute-intro-to-typography-basics/	+	* https://psd.tutsplus.com/articles/techniques/a-20-minute-intro-to-typography-basics/
-	* http://designm.ag/inspiration/typography/	+	* https://designm.ag/inspiration/typography/
-	* http://workshop.3point7designs.com/style-guide/	+	* https://workshop.3point7designs.com/style-guide/
-	* http://www.webdesignerwall.com/wp-content/uploads/2007/12/typographic-contrast.gif	+	* https://www.webdesignerwall.com/wp-content/uploads/2007/12/typographic-contrast.gif
-	* http://www.smileycat.com/miaow/archives/typography-for-headlines-2.php	+	* https://www.smileycat.com/miaow/archives/typography-for-headlines-2.php
-	* http://typesites.com/typographica/	+	* https://typesites.com/typographica/
-	* http://www.cssaddict.com/blog/websites-with-excellent-css-typography-design/	+	* https://www.cssaddict.com/blog/websites-with-excellent-css-typography-design/
-	* http://www.456bereastreet.com/archive/200608/light_text_on_dark_background_vs_readability/	+	* https://www.456bereastreet.com/archive/200608/light_text_on_dark_background_vs_readability/
-	* http://www.3point7designs.com/blog/2008/06/02/10-examples-of-beautiful-css-typography-and-how-they-did-it/	+	* https://www.3point7designs.com/blog/2008/06/02/10-examples-of-beautiful-css-typography-and-how-they-did-it/


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	====Navigation====		====Navigation====
-	* http://css-tricks.com/examples/SimplejQueryDropdowns/index.html	+	* https://css-tricks.com/examples/SimplejQueryDropdowns/index.html
-	* http://www.sitepoint.com/blogs/2009/03/31/make-a-mega-drop-down-menu-with-jquery/	+	* https://www.sitepoint.com/blogs/2009/03/31/make-a-mega-drop-down-menu-with-jquery/
-	* http://www.smashingmagazine.com/2009/04/06/showcase-of-well-designed-tabbed-navigation/	+	* https://www.smashingmagazine.com/2009/04/06/showcase-of-well-designed-tabbed-navigation/
-	* http://www.smashingmagazine.com/2009/03/24/designing-drop-down-menus-examples-and-best-practices/	+	* https://www.smashingmagazine.com/2009/03/24/designing-drop-down-menus-examples-and-best-practices/
-	* http://www.1stwebdesigner.com/resources/36-eye-catching-jquery-navigation-menus/	+	* https://www.1stwebdesigner.com/resources/36-eye-catching-jquery-navigation-menus/
	====Background====		====Background====
-	* http://vandelaydesign.com/blog/galleries/website-backgrounds/#more-636	+	* https://vandelaydesign.com/blog/galleries/website-backgrounds/#more-636
-	* http://sixrevisions.com/tutorials/photoshop-tutorials/make-high-impact-backgrounds-for-your-designs-with-photoshop/	+	* https://sixrevisions.com/tutorials/photoshop-tutorials/make-high-impact-backgrounds-for-your-designs-with-photoshop/
-	* http://www.smashingmagazine.com/2009/03/31/backgrounds-in-web-design-examples-and-best-practices-2/	+	* https://www.smashingmagazine.com/2009/03/31/backgrounds-in-web-design-examples-and-best-practices-2/
-	* http://www.worldconcern.org/social/index.htm	+	* https://www.worldconcern.org/social/index.htm
	====Foot====		====Foot====
-	* Nice footer: http://sunlightlabs.com/contests/appsforamerica2/	+	* Nice footer: https://sunlightlabs.com/contests/appsforamerica2/
-	* http://www.instantshift.com/2009/04/30/80-perfect-ending-of-modern-website-design-footers/	+	* https://www.instantshift.com/2009/04/30/80-perfect-ending-of-modern-website-design-footers/
-	* http://www.cssbake.com/	+	* https://www.cssbake.com/

	====Technology====		====Technology====
-	* Style changer: http://green-beast.com/experiments/php_style_changer.php?PSC	+	* Style changer: https://green-beast.com/experiments/php_style_changer.php?PSC
	==== Breadcrumbs ====		==== Breadcrumbs ====
-	* http://www.firefly-multimedia.com/chatterbox/?p=26	+	* https://www.firefly-multimedia.com/chatterbox/?p=26

	==== Layout ====		==== Layout ====
-	* http://www.smashingmagazine.com/2009/06/09/smart-fixes-for-fluid-layouts/	+	* https://www.smashingmagazine.com/2009/06/09/smart-fixes-for-fluid-layouts/
	====User interface====		====User interface====
-	* Home page – http://net.tutsplus.com/tutorials/javascript-ajax/create-a-simple-powerful-product-highlighter-with-mootools/	+	* Home page – https://net.tutsplus.com/tutorials/javascript-ajax/create-a-simple-powerful-product-highlighter-with-mootools/
-	* Buttons: http://sixrevisions.com/tutorials/photoshop-tutorials/how-to-create-a-slick-and-clean-button-in-photoshop/	+	* Buttons: https://sixrevisions.com/tutorials/photoshop-tutorials/how-to-create-a-slick-and-clean-button-in-photoshop/
-	* Tooltips: http://developer.yahoo.com/yui/examples/container/tooltip-multi_clean.html	+	* Tooltips: https://developer.yahoo.com/yui/examples/container/tooltip-multi_clean.html
-	* http://vandelaydesign.com/blog/galleries/button-design-showcase/	+	* https://vandelaydesign.com/blog/galleries/button-design-showcase/
-	* http://sixrevisions.com/tutorials/photoshop-tutorials/how-to-create-a-slick-and-clean-button-in-photoshop/	+	* https://sixrevisions.com/tutorials/photoshop-tutorials/how-to-create-a-slick-and-clean-button-in-photoshop/
-	* http://www.emblematiq.com/niceforms/v20/niceforms.html (Nice search button)	+	* https://www.emblematiq.com/niceforms/v20/niceforms.html (Nice search button)
-	* blockquotes: http://www.inquisitr.com/5955/gmail-canned-response-says-a-lot-about-google/	+	* blockquotes: https://www.inquisitr.com/5955/gmail-canned-response-says-a-lot-about-google/
-	* CSS swap hover: http://min.frexy.com/lab/css-swap-hover/sample1.html	+	* CSS swap hover: https://min.frexy.com/lab/css-swap-hover/sample1.html
-	* http://www.smashingmagazine.com/2009/06/04/6-free-psdxhtml-templates/	+	* https://www.smashingmagazine.com/2009/06/04/6-free-psdxhtml-templates/
-	* http://flowplayer.org/tools/demos/index.html	+	* https://flowplayer.org/tools/demos/index.html
-	* http://www.minervity.com/features/inspire_me/52-professional-website-user-interface-photoshop-tutorials/	+	* https://www.minervity.com/features/inspire_me/52-professional-website-user-interface-photoshop-tutorials/
-	* http://web-patterns.net/	+	* https://web-patterns.net/

	====Design and style (general)====		====Design and style (general)====
-	* http://www.smashingmagazine.com/2009/04/02/10-impressive-simple-design-techniques/	+	* https://www.smashingmagazine.com/2009/04/02/10-impressive-simple-design-techniques/
-	* http://www.alistapart.com/articles/taking-the-guesswork-out-of-design/	+	* https://www.alistapart.com/articles/taking-the-guesswork-out-of-design/
-	* http://davidwalsh.name/css-enhancements-user-experience	+	* https://davidwalsh.name/css-enhancements-user-experience
-	* http://sixrevisions.com/tutorials/photoshop-tutorials/how-to-create-a-clean-web-20-style-web-design-in-photoshop/	+	* https://sixrevisions.com/tutorials/photoshop-tutorials/how-to-create-a-clean-web-20-style-web-design-in-photoshop/
-	* http://www.creativepro.com/article/how-choose-colors-everyone-likes	+	* https://www.creativepro.com/article/how-choose-colors-everyone-likes
-	* http://www.ted.com/index.php/talks/joann_kuchera_morin_tours_the_allosphere.html	+	* https://www.ted.com/index.php/talks/joann_kuchera_morin_tours_the_allosphere.html
-	* http://psd.tutsplus.com/tutorials/designing-tutorials/9-essential-principles-for-good-web-design/	+	* https://psd.tutsplus.com/tutorials/designing-tutorials/9-essential-principles-for-good-web-design/
-	* http://psd.tutsplus.com/articles/inspiration/teach-yourself-graphic-design-a-self-study-course-outline/	+	* https://psd.tutsplus.com/articles/inspiration/teach-yourself-graphic-design-a-self-study-course-outline/
-	* http://www.webdesignbooth.com/15-extremely-useful-css-grid-layout-generator-for-web-designers/	+	* https://www.webdesignbooth.com/15-extremely-useful-css-grid-layout-generator-for-web-designers/
-	* http://www.webdesignerdepot.com/2009/06/10-tips-to-create-a-more-usable-web/	+	* https://www.webdesignerdepot.com/2009/06/10-tips-to-create-a-more-usable-web/
-	* http://www.smashingmagazine.com/2009/06/15/take-your-design-to-the-next-level-with-css3/	+	* https://www.smashingmagazine.com/2009/06/15/take-your-design-to-the-next-level-with-css3/
-	* http://ideas.bighugelabs.com	+	* https://ideas.bighugelabs.com
-	* http://www.smashingmagazine.com/2009/06/24/module-tabs-in-web-design-best-practices-and-solutions/	+	* https://www.smashingmagazine.com/2009/06/24/module-tabs-in-web-design-best-practices-and-solutions/

	====Content====		====Content====
-	* http://en.wikipedia.org/wiki/Help:Wikipedia:_The_Missing_Manual	+	* https://en.wikipedia.org/wiki/Help:Wikipedia:_The_Missing_Manual
	==== Image gallery ====		==== Image gallery ====

-	* **http://www.digitalia.be/software/slimbox**	+	* **https://www.digitalia.be/software/slimbox**
-	* http://www.pierrebertet.net/projects/jquery_superbox/	+	* https://www.pierrebertet.net/projects/jquery_superbox/
-	* http://planetozh.com/projects/lightbox-clones/	+	* https://planetozh.com/projects/lightbox-clones/
	====Good-looking sites====		====Good-looking sites====
-	* http://wpwebhost.com/best-wordpress-design-awards-time-to-vote/	+	* https://wpwebhost.com/best-wordpress-design-awards-time-to-vote/
-	* http://biology.plosjournals.org/perlserv/?request=index-html&issn=1545-7885	+	* https://biology.plosjournals.org/perlserv/?request=index-html&issn=1545-7885
-	* http://plugins.movabletype.org/multiblog/	+	* https://plugins.movabletype.org/multiblog/
-	* http://guides.rubyonrails.org/contribute.html	+	* https://guides.rubyonrails.org/contribute.html
-	* http://twitter.threadless.com/	+	* https://twitter.threadless.com/
-	* http://lpi.oregonstate.edu/infocenter/glossary.html	+	* https://lpi.oregonstate.edu/infocenter/glossary.html
-	* http://vandelaydesign.com/blog/galleries/best-educational-websites/	+	* https://vandelaydesign.com/blog/galleries/best-educational-websites/
-	* "First-time? Check here" http://serverfault.com/	+	* "First-time? Check here" https://serverfault.com/
-	* http://sixrevisions.com/design-showcase-inspiration/25-great-examples-of-using-gradient-effects-in-web-designs/	+	* https://sixrevisions.com/design-showcase-inspiration/25-great-examples-of-using-gradient-effects-in-web-designs/
-	* http://dzineblog.com/2009/06/50-beautiful-website-designs-for-your-inspiration.html	+	* https://dzineblog.com/2009/06/50-beautiful-website-designs-for-your-inspiration.html
-	* http://england.shelter.org.uk/get_advice	+	* https://england.shelter.org.uk/get_advice
-	* http://vandelaydesign.com/blog/galleries/best-non-profit-websites/	+	* https://vandelaydesign.com/blog/galleries/best-non-profit-websites/
-	* http://www.dwell.com/articles/interview-evan-kleiman-on-good-food.html	+	* https://www.dwell.com/articles/interview-evan-kleiman-on-good-food.html
-	* http://news.bbc.co.uk/2/hi/entertainment/8102614.stm	+	* https://news.bbc.co.uk/2/hi/entertainment/8102614.stm
-	* http://www.wired.com/wiredscience/	+	* https://www.wired.com/wiredscience/
-	* http://www.scientificamerican.com/biology	+	* https://www.scientificamerican.com/biology
-	* http://creativecommons.org/	+	* https://creativecommons.org/
-	* Dark site: http://probablyinteractive.com/2009/3/29/Amazon%20EC2%20+%20Chef%20=%20Mmmmm.html	+	* Dark site: https://probablyinteractive.com/2009/3/29/Amazon%20EC2%20+%20Chef%20=%20Mmmmm.html
	===== Watch these =====		===== Watch these =====

-	* http://videolectures.net/eccs08_cohen_apcstis/	+	* https://videolectures.net/eccs08_cohen_apcstis/
-	* http://videolectures.net/dnevi_borkakoti_bsbos/	+	* https://videolectures.net/dnevi_borkakoti_bsbos/
-	* http://www.ted.com/index.php/talks/craig_venter_on_dna_and_the_sea.html	+	* https://www.ted.com/index.php/talks/craig_venter_on_dna_and_the_sea.html
-	* http://videolectures.net/google_levinson_hbcd/	+	* https://videolectures.net/google_levinson_hbcd/
-	* http://videolectures.net/google_locksley_hbfi/	+	* https://videolectures.net/google_locksley_hbfi/
-	* http://www.1lec.com/Genetics/Circular%20DNA%20Replication/index.html	+	* https://www.1lec.com/Genetics/Circular%20DNA%20Replication/index.html
	===== Orphans =====		===== Orphans =====


		+	~~ORPHANSWANTED:orphans~~
		+
		+	~~ORPHANSWANTED:wanted!wiki!some~~
		+
		+	?do=backlink

09.01.2010		current
Line 1:		Line 1:
	====== Style Guidelines and Best Practices ======		====== Style Guidelines and Best Practices ======

-	This page endeavors to ask, "How will the MP Knowledge Base be consistently different from the legacy mp.com site?" If you want to see one example of an editorial style guide, take a look at the //[[http://www.economist.com/research/styleguide/\|The Economist]]//'s. (Obviously, ours will necessitate a lot more MP-specific considerations.)	+	This page endeavors to ask, "How will the MP Knowledge Base be consistently different from the legacy mp.com site?" If you want to see one example of an editorial style guide, take a look at the //[[https://www.economist.com/research/styleguide/\|The Economist]]//'s. (Obviously, ours will necessitate a lot more MP-specific considerations.)


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	A full list of currently selected tags should referred to before creating a new tag (we want to avoid multiple tags for the same subject). Also, to make tagging really useful, it is better to only use tags for topics with a number of related articles. That is, not creating a tag per article is better.		A full list of currently selected tags should referred to before creating a new tag (we want to avoid multiple tags for the same subject). Also, to make tagging really useful, it is better to only use tags for topics with a number of related articles. That is, not creating a tag per article is better.

-	There is a discussion at dokuwiki about back linking tags [[http://bugs.splitbrain.org/index.php?do=details&task_id=707\|here]]. --- //Joyful 2008/10/11 04:42//	+	There is a discussion at dokuwiki about back linking tags [[https://bugs.splitbrain.org/index.php?do=details&task_id=707\|here]]. --- //Joyful 2008/10/11 04:42//

	===== Repetition of content =====		===== Repetition of content =====
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	* For example: one could review immunopathology in an article in such a way that it makes sense to new patients and another article could be our best description for doctors and researchers.		* For example: one could review immunopathology in an article in such a way that it makes sense to new patients and another article could be our best description for doctors and researchers.
	* Naturally, the shorter more accessible summary of a topic could be the introduction (that is, the first section) for a more technical article. Such a section could be deep-linked from elsewhere.		* Naturally, the shorter more accessible summary of a topic could be the introduction (that is, the first section) for a more technical article. Such a section could be deep-linked from elsewhere.
-	* Sometimes, it may make sense to create lists of links to content. This is something Wikipedia does well. For example: http://en.wikipedia.org/wiki/List_of_countries	+	* Sometimes, it may make sense to create lists of links to content. This is something Wikipedia does well. For example: https://en.wikipedia.org/wiki/List_of_countries
	===== Word choices =====		===== Word choices =====

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	* In discussing the "data" collected, the terms "patient-reported outcomes" and "progress reports" are preferred. For example, "Patient outcomes are documented and studied via online progress reports."		* In discussing the "data" collected, the terms "patient-reported outcomes" and "progress reports" are preferred. For example, "Patient outcomes are documented and studied via online progress reports."
	* Use of acronyms		* Use of acronyms
-	* if you use an acronym in an article, first specify the full term with the acronym in parentheses, adding a link to article if appropriate, i.e. [[http://www.marshallprotocol.com/forum2/10473.html#p125068\|Immunopathology]] (IP).	+	* if you use an acronym in an article, first specify the full term with the acronym in parentheses, adding a link to article if appropriate, i.e. [[https://www.marshallprotocol.com/forum2/10473.html#p125068\|Immunopathology]] (IP).

	* Preferred credential/title format:		* Preferred credential/title format:
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	* "Comprehensive list of..." vs. "All..." vs. "A-Z List of..."? Preferred term (for now) is "A-Z List of..."		* "Comprehensive list of..." vs. "All..." vs. "A-Z List of..."? Preferred term (for now) is "A-Z List of..."
	* example: "A-Z List of Symptoms"		* example: "A-Z List of Symptoms"
-	* To avoid confusion between "l" and "1", capitalize the "L" when abbreviating millilitres (mL), etc. (see [[http://en.wikipedia.org/wiki/Litre#SI_prefixes_applied_to_the_litree\|SI prefixes applied to the litre]]).	+	* To avoid confusion between "l" and "1", capitalize the "L" when abbreviating millilitres (mL), etc. (see [[https://en.wikipedia.org/wiki/Litre#SI_prefixes_applied_to_the_litree\|SI prefixes applied to the litre]]).

	* Avoid writing in first person ("I", "we") and second person ("You").		* Avoid writing in first person ("I", "we") and second person ("You").
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	===== Headers =====		===== Headers =====

-	* Let's emulate [[http://en.wikipedia.org\|Wikipedia]] in the way that they break content every couple paragraphs by headers.	+	* Let's emulate [[https://en.wikipedia.org\|Wikipedia]] in the way that they break content every couple paragraphs by headers.
	* What is the point of headers?		* What is the point of headers?
	* Content needs to be broken up into different sections.		* Content needs to be broken up into different sections.
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	* Headers give the user scanning the article of what the article is about.		* Headers give the user scanning the article of what the article is about.
	* Headers allow us to communicate the hierarchy of a given article. Every article should have //some// sort of hierarchy. If it's doesn't, it might be worth re-thinking the topic.		* Headers allow us to communicate the hierarchy of a given article. Every article should have //some// sort of hierarchy. If it's doesn't, it might be worth re-thinking the topic.
-	* The first letter of a section title is capitalized. Every letter thereafter is not - unless the term is normally capitalized such as a proper name. For examples of proper usage, see [[http://en.wikipedia.org\|Wikipedia]].	+	* The first letter of a section title is capitalized. Every letter thereafter is not - unless the term is normally capitalized such as a proper name. For examples of proper usage, see [[https://en.wikipedia.org\|Wikipedia]].
	* Titles of articles are H1. Main sections of an article are H2. An H3 is used more infrequently. Note that H1, H2 and H3 can be linked to directly via an anchor but that H4 and H5 cannot.		* Titles of articles are H1. Main sections of an article are H2. An H3 is used more infrequently. Note that H1, H2 and H3 can be linked to directly via an anchor but that H4 and H5 cannot.
	* Naturally, headers without content don't show up in the articles themselves.		* Naturally, headers without content don't show up in the articles themselves.
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	* published literature includes articles appearing in PubMed, but can also point to other scholarly and reputable sources such as abstracts, speeches before learned bodies, etc.		* published literature includes articles appearing in PubMed, but can also point to other scholarly and reputable sources such as abstracts, speeches before learned bodies, etc.
	* citing PubMed articles:		* citing PubMed articles:
-	* example: {{pubmed>long:9039911}}	+	* example: {{pmid>long:9039911}}
	* here's the syntax for how to do it (the 9039911 is actually the PubMed Identifier, also known as PMID):		* here's the syntax for how to do it (the 9039911 is actually the PubMed Identifier, also known as PMID):

-	{{pubmed>long:9039911}}	+	{{pmid>long:9039911}}

	* All other citations will be done in the style the journal //Nature// uses.		* All other citations will be done in the style the journal //Nature// uses.
-	* [[http://www.zotero.org/\|Zotero]], a plug-in for Firefox, can automatically format citations in the Nature style.	+	* [[https://www.zotero.org/\|Zotero]], a plug-in for Firefox, can automatically format citations in the Nature style.
	* if you repeat a claim posted on the legacy MP site and it points to a study, make sure the study says what we say it says		* if you repeat a claim posted on the legacy MP site and it points to a study, make sure the study says what we say it says
	* Reliable sources		* Reliable sources
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	* For example: a person the insomnia article might want to know about sleep medications. Or, if an article talks about how to deal with a denied insurance claim, maybe you should refer that user to the article on buying low-cost olmesartan.		* For example: a person the insomnia article might want to know about sleep medications. Or, if an article talks about how to deal with a denied insurance claim, maybe you should refer that user to the article on buying low-cost olmesartan.
	* Direct linking to an article in text is preferred rather than saying "See Also."		* Direct linking to an article in text is preferred rather than saying "See Also."
-	* example (preferred): "West Nile virus is a [[home:diseases:co-infections\|co-infection]]."	+	* example (preferred): "West Nile virus is a [[home:diseases\|co-infection]]."
-	* example (deprecated): "West Nile virus is a co-infection. See also the article on [[home:diseases:co-infections\|co-infections]]."	+	* example (deprecated): "West Nile virus is a co-infection. See also the article on [[home:diseases\|co-infections]]."
-	* Sometimes, it makes sense to link to some of the ARF team's great publications and presentations. See the HIV and AIDS page's section [[home:diseases:hiv_and_aids#relevant_publications_and_presentations\|Relevant publications and presentations]] for an example of that.((As you can see, the formatting is inconsistent and needs work.)) I would also suggest using this space to point to articles on Bacteriality.	+	* Sometimes, it makes sense to link to some of the ARF team's great publications and presentations. See the HIV and AIDS page's section [[home:diseases#relevant_publications_and_presentations\|Relevant publications and presentations]] for an example of that.((As you can see, the formatting is inconsistent and needs work.)) I would also suggest using this space to point to articles on Bacteriality.
	* We need a list of every term that should be linked to when it is used. ((Some terms can display a definition when the mouse 'hovers' over it, others would be more helpful when linked to a longer explanation in another page. //-J// ))		* We need a list of every term that should be linked to when it is used. ((Some terms can display a definition when the mouse 'hovers' over it, others would be more helpful when linked to a longer explanation in another page. //-J// ))
	===== Quoting Individuals =====		===== Quoting Individuals =====
Line 211:		Line 211:
	* Also, be careful not to quote MP patients to excess. For one, they almost always don't fully understand the science.		* Also, be careful not to quote MP patients to excess. For one, they almost always don't fully understand the science.
	* Especially, try to shy away from quoting patients when they are making seemingly extraordinary claim how the MP works. It is always disappointing when a patient says something unequivocally positive about the MP's ability to cure a particular illness and that patient is (apparently) no longer on the treatment.		* Especially, try to shy away from quoting patients when they are making seemingly extraordinary claim how the MP works. It is always disappointing when a patient says something unequivocally positive about the MP's ability to cure a particular illness and that patient is (apparently) no longer on the treatment.
-	* Possible exception: [[http://bacteriality.com/category/interview-patient/\|Bacteriality interviews]]	+	* Possible exception: [[https://bacteriality.com/category/interview-patient/\|Bacteriality interviews]]
	* In cases where the evidence is incomplete, say so explicitly.		* In cases where the evidence is incomplete, say so explicitly.
	* Example: "There is not enough evidence to know why increases in immunopathology seem to be connected to increases in light sensitivity."		* Example: "There is not enough evidence to know why increases in immunopathology seem to be connected to increases in light sensitivity."
Line 218:		Line 218:
	===== Tone =====		===== Tone =====

-	* Ideally contributors to the KB would be mindful of some of the sharper criticisms of ARF such as this [[http://phylogenomics.blogspot.com/2010/08/overselling-microbiome-award-2-marshall.html\|2010 post]] by Jonathan Eisen. There are a number of criticisms of the MP. Some, such as the fact that the MP may be used for a wide range of diseases, is outside our control. Other objections, such as MP advocates' use of unjustifiably certain language, are more within our control. One of the abiding considerations for the KB is, given the available evidence, how much certainty to use in one's language.	+	* Ideally contributors to the KB would be mindful of some of the sharper criticisms of ARF such as this [[https://phylogenomics.blogspot.com/2010/08/overselling-microbiome-award-2-marshall.html\|2010 post]] by Jonathan Eisen. There are a number of criticisms of the MP. Some, such as the fact that the MP may be used for a wide range of diseases, is outside our control. Other objections, such as MP advocates' use of unjustifiably certain language, are more within our control. One of the abiding considerations for the KB is, given the available evidence, how much certainty to use in one's language.
	* To this end, when explaining microbes' role in causing disease, the word "may" often comes in handy. So does saying, "According to the Marshall Pathogenesis...."		* To this end, when explaining microbes' role in causing disease, the word "may" often comes in handy. So does saying, "According to the Marshall Pathogenesis...."
	* Strive for an encyclopedic tone.		* Strive for an encyclopedic tone.

05.10.2010		current
Line 8:		Line 8:
	* Side Topics		* Side Topics

-	Also, we will want to refer to the [[http://www.marshallprotocol.com/view_topic.php?id=2135&forum_id=32&jump_to=43902\|MARSHALL PROTOCOL FAQs Easy Finder & the ABC of MP]] page as we migrate the information.	+	Also, we will want to refer to the [[https://www.marshallprotocol.com/view_topic.php?id=2135&forum_id=32&jump_to=43902\|MARSHALL PROTOCOL FAQs Easy Finder & the ABC of MP]] page as we migrate the information.

	===== Table 1: FAQs =====		===== Table 1: FAQs =====
-	FAQs are listed [[http://www.marshallprotocol.com/forum32/\|here]].	+	FAQs are listed [[https://www.marshallprotocol.com/forum32/\|here]].

	^ Topic(s) ^ID ^		^ Topic(s) ^ID ^
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1080&forum_id=32&jump_to=38646#p38646\|low blood pressure and Benicar]] \|F1 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1080&forum_id=32&jump_to=38646#p38646\|low blood pressure and Benicar]] \|F1 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1080&forum_id=32&jump_to=46837#p46837\|patient reports of low blood pressure]] \|F2 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1080&forum_id=32&jump_to=46837#p46837\|patient reports of low blood pressure]] \|F2 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1080&forum_id=32&jump_to=78974#p78974\|Trevor on low blood pressue]] \|F3 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1080&forum_id=32&jump_to=78974#p78974\|Trevor on low blood pressue]] \|F3 \|
-	\|[[http://www.marshallprotocol.com/forum32/1420.html#p11542\|cardiac symptoms]] \|F4 \|	+	\|[[https://www.marshallprotocol.com/forum32/1420.html#p11542\|cardiac symptoms]] \|F4 \|
-	\|[[http://www.marshallprotocol.com/forum32/1420.html#p55416\|patient experience w/ cardiac IP]] \|F5 \|	+	\|[[https://www.marshallprotocol.com/forum32/1420.html#p55416\|patient experience w/ cardiac IP]] \|F5 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1420&forum_id=32&jump_to=71794#p71794\|patient experience w/ Tachycardia]] \|F6 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1420&forum_id=32&jump_to=71794#p71794\|patient experience w/ Tachycardia]] \|F6 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1420&forum_id=32&jump_to=100007#p100007\|congestive heart failure]] \|F7 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1420&forum_id=32&jump_to=100007#p100007\|congestive heart failure]] \|F7 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1420&forum_id=32&jump_to=119110#p119110\|Atrial fibrillation]] \|F8 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1420&forum_id=32&jump_to=119110#p119110\|Atrial fibrillation]] \|F8 \|
-	\|[[http://www.marshallprotocol.com/forum32/1138.html\|MP and work, letter to employer]] \|F9 \|	+	\|[[https://www.marshallprotocol.com/forum32/1138.html\|MP and work, letter to employer]] \|F9 \|
-	\|[[http://www.marshallprotocol.com/forum32/1263.html\|applicable treatment for my disease?]] \|F10 \|	+	\|[[https://www.marshallprotocol.com/forum32/1263.html\|applicable treatment for my disease?]] \|F10 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=37420#p37420\|MP correct treatment?]] \|F11 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=37420#p37420\|MP correct treatment?]] \|F11 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=48160#p48160\|Blood-brain barrier]] \|F12 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=48160#p48160\|Blood-brain barrier]] \|F12 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=64344#p64344\|OCD, anorexia, autism]] \|F13 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=64344#p64344\|OCD, anorexia, autism]] \|F13 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=91814#p91814\|heart disease]] \|F14 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=91814#p91814\|heart disease]] \|F14 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=28422#p28422\|L-forms isolated in culture]] \|F15 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=28422#p28422\|L-forms isolated in culture]] \|F15 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=36589#p36589\|degree of illness and recovery]] \|F16 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=36589#p36589\|degree of illness and recovery]] \|F16 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=91816#p91816\|rheumatic disease]] \|F17 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1263&forum_id=32&jump_to=91816#p91816\|rheumatic disease]] \|F17 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=41696#p41696\|breathing exercises]] \|F18 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=41696#p41696\|breathing exercises]] \|F18 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=53269#p53269\|improving breathing]] \|F19 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=53269#p53269\|improving breathing]] \|F19 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=72854#p72854\|inhalers and nebulizers]] \|F20 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=72854#p72854\|inhalers and nebulizers]] \|F20 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=82683#p82683\|lung conditions]] \|F21 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=82683#p82683\|lung conditions]] \|F21 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=83450#p83450\|IP and breathing]] \|F22 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=4175&forum_id=23&jump_to=83450#p83450\|IP and breathing]] \|F22 \|
-	\|[[http://www.marshallprotocol.com/forum32/1379.html\|where is Phase 2/3]] \|F23 \|	+	\|[[https://www.marshallprotocol.com/forum32/1379.html\|where is Phase 2/3]] \|F23 \|
-	\|[[http://www.marshallprotocol.com/forum32/2362.html\|pregnancy & conception]] \|F24 \|	+	\|[[https://www.marshallprotocol.com/forum32/2362.html\|pregnancy & conception]] \|F24 \|
-	\|[[http://www.marshallprotocol.com/forum32/1078.html#p42275\|why stop supplements]] \|F25 \|	+	\|[[https://www.marshallprotocol.com/forum32/1078.html#p42275\|why stop supplements]] \|F25 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=43283#p43283\|dietary supplements]] \|F26 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=43283#p43283\|dietary supplements]] \|F26 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=45902#p45902\|Cholestyramine (Questran)]] \|F27 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=45902#p45902\|Cholestyramine (Questran)]] \|F27 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=45960#p45960\|Essential Fatty Acids (EFAs)]] \|F28 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=45960#p45960\|Essential Fatty Acids (EFAs)]] \|F28 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=55298#p55298\|px exp with supp]] \|F29 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=55298#p55298\|px exp with supp]] \|F29 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=55392#p55392\|glucosamine & chrondroitin]] \|F30 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=55392#p55392\|glucosamine & chrondroitin]] \|F30 \|
-	\|[[http://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=62387#p62387\|chelation]] \|F31 \|	+	\|[[https://www.marshallprotocol.com/view_topic.php?id=1078&forum_id=32&jump_to=62387#p62387\|chelation]] \|F31 \|