#immune dysfunction

Deep Learning for In-silico Drug Discovery and Drug Repurposing: Artificial Intelligence to search for molecules boosting response rates in Cancer Immunotherapy: Insilico Medicine @John Hopkins University

Deep Learning for In-silico Drug Discovery and Drug Repurposing: Artificial Intelligence to search for molecules boosting response rates in Cancer Immunotherapy: Insilico Medicine @John Hopkins University

Reporter: Aviva Lev-Ari, PhD, RN

Insilico Medicine –>>> transcriptome-based pathway perturbation analysis

Insilico Medicine, Inc. is a bioinformatics company located at the Emerging Technology…

Here is the original article:

            June 21st, 1999

            For most of this decade, I suffered horribly from the profoundly devastating effects of Chronic Fatigue (Immune Dysfunction) Syndrome {CFS}.  It is a disease that, by the accounts of many sufferers I’ve known, pummels you into utter exhaustion, and keeps beating you from there. CFS gave me six plus years of hell and hopelessness that pains me to put into words.  My earliest knowledge of CFS involved a symptomatically diverse flu-like illness that is the direct result of a severely malfunctioning immune system.  Personally, I had low and unpredictable energy, heavy legs, a sore throat, muscle aches, anxiety, depression, and severe sleep difficulties.  I was “sick all over”; essentially, a vital young man shot down in his physical prime. 

            Apparently, I had an alien illness.  The many doctors, all with outmoded information, had no answers or insight.  So I had no hope.  Neither did millions of others like me, who sucked daily on a fragment of their lives.  Repeatedly I heard the cautions, that I may have to live “as is”; as damaged goods, in other words.  But not me; not this fighter.  I kept my eyes and ears open and continued doing research.  I wasn’t looking for the best coping method.  I demanded a cure.

            In 1995 I found a naturopath.  His recommendations gave me much of my health back, and gave me hope.  Since I began seeing him, I have been able to cope.  I discovered a world of natural medicine that alleviated many of my worst symptoms and helped control most of the others.  But I suffered still.  I was energy depleted, and therefore still not a full-functioning being.

            Until a few weeks ago, I woke up every day mindful of the (natural) medicine I couldn’t live without: first, the ever-requisite multi-vitamin.  Then the bovine tissue extract for my hypothyroidism.  Often, a probiotic formula to replenish the good bacteria in my gut.  Sometimes a citrus extract to flush out the candidiasis (yeast).  Different things for my adrenal gland problems.  There were others too.  At times, I’d add one thing, and subtract another, depending on my immediate needs.

            About six months ago, I began listening to a radio doctor named Gabe Mirkin.  His is a straightforward, unpolluted and holistic point of view that is squarely directed on getting results.  He talks a lot about an infection called mycoplasma, a tiny and menacing bacteria --a micro-organism-- that slowly invades tissue and penetrates deep inside white blood cells, eventually reaching all tissues and organs of the body, causing complex symptoms.  Mycoplasma has been implicated as a cofactor in many of today’s most threatening illnesses, including AIDS, rheumatoid arthritis, respiratory infection, and CFS.

            Many of his callers describe problems that Dr. Mirkin reasons are associated with mycoplasma or a related infection, which Dr. Mirkin claims can only be cured with long-term antibiotics.  Dr. Mirkin asks them about their symptoms.  For example: Do they have chronic joint pain, a sore throat, low energy?  Do they feel burning upon urination?  Do they have an uncontrollable need to urinate in the middle of the night?  Having listened long enough, and having noticed how often the callers’ symptoms paralleled mine, I did some research.  I saw that mycoplasma can break down a weak immune system, leading to chronic illness.  The data pointed overwhelmingly in favour of my having the infection.  So I implored my doctor to put me on antibiotics.  Dr. Mirkin says, and my research affirms, that there is no reliable diagnostic test for mycoplasma.  Antibiotics are taken on speculation.  Heeding this, I didn’t bother to solicit a doctor’s opinion.  Though I’d long been suspicious of drugs, I’d heard enough to convince me it would be worth it.

            On May 10th, I began taking doxycycline, the recommended drug.  One week later, I felt pretty good, so I stopped taking melatonin --a natural hormone that I was depending on for sleep; and then I stopped my thyroid medicine.  Still okay.  I passed through the Herxheimer reaction, a temporary re-surfacing of symptoms, if you will.  It was mild for me.  My mental sharpness has returned.  My 7-year long sore throat is loosening steadily.  My legs feel lighter.  Best of all, I am sleeping like a baby, like I haven’t slept in years.  The recovery feels like one step back for every two steps forward.  I feel good most parts of most days, and I’m slowly getting better.  All this in only six weeks.  So a lot of hope has returned, and a full recovery seems imminent.  Meanwhile I cross my fingers and hope.

            The experts don’t yet know if mycoplasma alone is responsible for the onset of CFS, but they don’t think it’s that simple.  A recent study found that 52% of CFS patients have some kind of mycoplasma infection (as compared to 15% of healthy people).  Therefore, it is likely that mycoplasma will exacerbate an already weak immune system; so mycoplasma, when it exists in the CFS (or pre-CFS) patient, is very likely a co-factor in the onset of CFS.  My question is: can mycoplasma in a healthy person cause the immune system to weaken enough to make the onset of CFS innevitable?  More research is currently being done.

            Why is all of this so important?  Because, as Dr. Majid Ali states in The Canary and Chronic Fatigue --the book I long considered my CFS “bible”-- CFS will be the most predominant chronic health disorder of the 21st century.  In fact, it’s already ruined thousands of lives.  Should we worry?  Well, consider this: It’s been said that the level of functioning of the average CFS patient is roughly equivalent to that of an AIDS patient with 2 months left to live.  Except CFS doesn’t kill you; it leaves you to live in misery.  Given these parameters, it must be considered momentous to have discovered, finally, what reasons to be the essential root of CFS.  For me, it’s everything.

             July 13th, 1999

            Last week, I slept a lot.  I was exhausted.  It was a particular type of exhaustion; I’d experienced it before.  It was my body healing.  This time it was doxycycline evidently giving my system one final cleansing.  My wife Kim was worried.  She always worries when I need to sleep a lot.  I reassured her.  This time, I was sure; CFS had finally run its course in me.  I’d finally beat it.

            My energy the last couple of days has been quite good.  I’ve felt symptom free.  So I have asked myself, does this mean CFS is gone, once and for all?  I certainly hope so; but I’ve grown accustomed to viewing occasions like this with guarded optimism.  I fight the unbridled optimism daily.  A relapse hurts less that way.

            If my recovery is not yet complete, then I hope it will continue until it is.  I want badly to feel the infinite thrill of having unearthed a treasure that’s been searched for long and hard.  Yet I see all too clearly the reality of my situation.  The truth is that I’m just beginning a momentous struggle to discover things that once seemed forever lost; I’m just starting to make things happen, things that I yearn to have made happen a long time ago: the career, the home, the family … fulfillment.  It will be terribly difficult of course, but I’m ready.  And I’ll only get more ready.  I feel well equipped to do battle: I’m only 32; I have my writing skills, I have a wonderful wife, and I have peace of mind.  Now I must move forward ... one day at a time.

             January 11th, 2000

            In August I went off doxycycline.  My late summer allergies were acting up, and the medication was causing them to run amok.  I was taking my probiotics regularly (to replenish the good bacteria that the antibiotics had depleted).  A couple of weeks went by and I felt pretty good –though I didn’t yet know what pretty good really felt like– and I started thinking that maybe, somehow, I was cured, like by magic.  I thought there was a possibility that I wouldn’t need the doxycycline any more.

            In early October, the symptoms began to re-appear.  It wasn’t long before I was back on doxycycline.  This time I promised myself that I would stay on it until the mycoplasma was gone.  I wanted to squash it.

            Before Christmas I processed a short but nasty flu bug.  As it left me, I felt great, better than I had in years.  I felt so good that it was playing on my mind.  I needed to be certain that I was actually well, and not just between stages of recovery.  I began to test myself.  I worked out hard and took long walks.  And I got less sleep than I should have.  But I was still okay.  Sleep-deprived, but functioning well.  And I continued to be okay, right through the holidays and despite all the sugar I consumed.  I felt good up until I caught this current case of the flu.  But this flu is hitting millions, and I have only a slight case of it.

            Unless something extraterrestrial has happened to me, I am recovered.  Like never before, I am quick-witted, fast with my reflexes, long on concentration, full of vigor, and ready to handle buggers.  (Buggers are folks who dare to stand in the way of my success.)

Here is the text for a speech I delivered in 1998 about my case of Chronic Fatigue Syndrome.  I’m recovered now but oh, how I still remember the bad bad days.       

There is no glory in convalescing all day long in a near-comatose stupor, for week upon week and month upon month.  And God-damn it, I want glory.

 Here's an article I wrote 10 years ago, about my health struggles.  I've never put it out there so maybe it's about time.

                      June 21st, 1999

            For most of this decade, I suffered horribly from the profoundly devastating effects of Chronic Fatigue (Immune Dysfunction) Syndrome {CFS}.  It is a disease that, by the accounts of many sufferers I’ve known, pummels you into utter exhaustion, and keeps beating you from there. CFS gave me six plus years of hell and hopelessness that pains me to put into words.  My earliest knowledge of CFS involved a symptomatically diverse flu-like illness that is the direct result of a severely dysfunctioning immune system.  Personally, I had low and unpredictable energy, heavy legs, a sore throat, muscle aches, anxiety, depression, and severe sleep difficulties.  I was “sick all over”; essentially, a vital young man shot down in his physical prime. 

            Apparently, I had an alien illness.  The many doctors, all with outmoded information, had no answers or insight.  So I had no hope.  Neither did millions of others like me, who sucked daily on a fragment of their lives.  Repeatedly I heard the cautions, that I may have to live “as is”; as damaged goods, in other words.  But not me; not this fighter.  I kept my eyes and ears open and continued doing research.  I wasn’t looking for the best coping method.  I demanded a cure.

This paragraph is above the "Read More" break.

This paragraph is behind the "Read More" break.

            In 1995 I found a naturopath.  His recommendations gave me much of my health back, and gave me hope.  Since I began seeing him, I have been able to cope.  I discovered a world of natural medicine that alleviated many of my worst symptoms and helped control most of the others.  But I suffered still.  I was energy depleted, and therefore still not a full-functioning being.

            Until a few weeks ago, I woke up every day mindful of the (natural) medicine I couldn’t live without: first, the ever-requisite multi-vitamin.  Then the bovine tissue extract for my hypothyroidism.  Often, a probiotic formula to replenish the good bacteria in my gut.  Sometimes a citrus extract to flush out the candidiasis (yeast).  Different things for my adrenal gland problems.  There were others too.  At times, I’d add one thing, and subtract another, depending on my immediate needs.

            About six months ago, I began listening to a radio doctor named Gabe Mirkin.  His is a straightforward, unpolluted and holistic point of view that is squarely directed on getting results.

He talks a lot about an infection called mycoplasma, a tiny and menacing bacteria --a micro-organism-- that slowly invades tissue and penetrates deep inside white blood cells, eventually reaching all tissues and organs of the body, causing complex symptoms.  Mycoplasma has been implicated as a cofactor in many of today’s most threatening illnesses, including AIDS, rheumatoid arthritis, respiratory infection, and CFS.

            Many of his callers describe problems that Dr. Mirkin reasons are associated with mycoplasma or a related infection, which Dr. Mirkin claims can only be cured with long-term antibiotics.  Dr. Mirkin asks them about their symptoms.  For example: Do they have chronic joint pain, a sore throat, low energy?  Do they feel burning upon urintation?  Do they have an uncontrollable need to urinate in the middle of the night?  Having listened long enough, and having noticed how often the callers’ symptoms paralleled mine, I did some research.  I saw that mycoplasma can break down a weak immune system, leading to chronic illness.  The data pointed overwhelmingly in favour of my having the infection.  So I implored my doctor to put me on antibiotics.  Dr. Mirkin says, and my research affirms, that there is no reliable diagnostic test for mycoplasma.  Antibiotics are taken on speculation.  Heeding this, I didn’t bother to solicit a doctor’s opinion.  Though I’d long been suspicious of drugs, I’d heard enough to convince me it would be worth it.

            On May 10th, I began taking doxycycline, the recommended drug.  One week later, I felt pretty good, so I stopped taking melatonin --a natural hormone that I was depending on for sleep; and then I stopped my thyroid medicine.  Still okay.  I passed through the Herxheimer reaction, a temporary re-surfacing of symptoms, if you will.  It was mild for me.  My mental sharpness has returned.  My 7-year long sore throat is loosening steadily.  My legs feel lighter.  Best of all, I am sleeping like a baby, like I haven’t slept in years.  The recovery feels like one step back for every two steps forward.  I feel good most parts of most days, and I’m slowly getting better.  All this in only six weeks.  So a lot of hope has returned, and a full recovery seems imminent.  Meanwhile I cross my fingers and hope.

            The experts don’t yet know if mycoplasma alone is responsible for the onset of CFS, but they don’t think it’s that simple.  A recent study found that 52% of CFS patients have some kind of mycoplasma infection (as compared to 15% of healthy people).  Therefore, it is likely that mycoplasma will exacerbate an already weak immune system; so mycoplasma, when it exists in the CFS (or pre-CFS) patient, is very likely a co-factor in the onset of CFS.  My question is: can mycoplasma in a healthy person cause the immune system to weaken enough to make the onset of CFS innevitable?  More research is currently being done.

            Why is all of this so important?  Because, as Dr. Majid Ali states in The Canary and Chronic Fatigue --the book I long considered my CFS “bible”-- CFS will be the most predominant chronic health disorder of the 21st century.  In fact, it’s already ruined thousands of lives.  Should we worry?  Well, consider this: It’s been said that the level of functioning of the average CFS patient is roughly equivalent to that of an AIDS patient with 2 months left to live.  Except CFS doesn’t kill you; it leaves you to live in misery.  Given these parameters, it must be considered momentous to have discovered, finally, what reasons to be the essential root of CFS.  For me, it’s everything.

              July 13th, 1999

            Last week, I slept a lot.  I was exhausted.  It was a particular type of exhaustion; I’d experienced it before.  It was my body healing.  This time it was doxycycline evidently giving my system one final cleansing.  My wife Kim was worried.  She always worries when I need to sleep a lot.  I reassured her.  This time, I was sure; CFS had finally run its course in me.  I’d finally beat it.

            My energy the last couple of days has been quite good.  I’ve felt symptom free.  So I have asked myself, does this mean CFS is gone, once and for all?  I certainly hope so; but I’ve grown accustomed to viewing occasions like this with guarded optimism.  I fight the unbridled optimism daily.  A relapse hurts less that way.

            If my recovery is not yet complete, then I hope it will continue until it is.  I want badly to feel the infinite thrill of having unearthed a treasure that’s be searched for long and hard.  Yet I see all too clearly the reality of my situation.  The truth is that I’m just beginning a momentous struggle to discover things that once seemed forever lost; I’m just starting to make things happen, things that I yearn to have made happen a long time ago: the career, the home, the family, fulfillment.  It will be terribly difficult of course, but I’m ready.  And I’ll only get more ready.  I feel well equipped to do battle: I’m only 32; I have my writing skills, I have a wonderful wife, and I have peace of mind.  Now I must move forward ... one day at a time.

              January 11th, 2000

            In August I went off doxycycline.  My late summer allergies were acting up , and the medication was causing them to run amok.  I was taking my probiotics regularly (to replenish the good bacteria that the antibiotics had depleted).  A couple of weeks went by and I felt pretty good –though I didn’t yet know what pretty good really felt like– and I started thinking that maybe, somehow, I was cured, like by magic.  I thought there was a possibility that I wouldn’t need the doxycycline any more.

            In early October, the symptoms began to re-appear.  It wasn’t long before I was back on doxycycline.  This time I promised myself that I would stay on it until the mycoplasma was gone.  I wanted to squash it.

            Before Christmas I processed a short but nasty flu bug.  As it left me, I felt great, better than I had in years.  I felt so good that it was playing on my mind.  I needed to be certain that I was actually well, and not just between stages of recovery.  I began to test myself.  I worked out hard and took long walks.  And I got less sleep than I should have.  But I was still okay.  Sleep-deprived, but functioning well.  And I continued to be okay, right through the holidays and despite all the sugar I consumed.  I felt good up until I caught this current case of the flu.  But this flu is hitting millions, and I have only a slight case of it.

            Unless something extraterrestrial has happened to me, I am recovered.  Like never before, I am quick-witted, fast with my reflexes, long on concentration, full of vigor, and ready to handle buggers.  (Buggers are folks who dare to stand in the way of my success.)

            I don’t even question the possibility of my wellness any more.  I am well.  I might even get more well.  I am still on doxycycline, but only because I need to be sure.  Now I am moving on.  I’m not questioning the possibility of my success.  It’ll come.  All I ever needed was my health.  The rest I can handle.

              In 1995 I found a naturopath.  His recommendations gave me much of my health back, and gave me hope.  Since I began seeing him, I have been able to cope.  I discovered a world of natural medicine that alleviated many of my worst symptoms and helped control most of the others.  But I suffered still.  I was energy depleted, and therefore still not a full-functioning being.

            Until a few weeks ago, I woke up every day mindful of the (natural) medicine I couldn’t live without: first, the ever-requisite multi-vitamin.  Then the bovine tissue extract for my hypothyroidism.  Often, a probiotic formula to replenish the good bacteria in my gut.  Sometimes a citrus extract to flush out the candidiasis (yeast).  Different things for my adrenal gland problems.  There were others too.  At times, I’d add one thing, and subtract another, depending on my immediate needs.

            About six months ago, I began listening to a radio doctor named Gabe Mirkin.  His is a straightforward, unpolluted and holistic point of view that is squarely directed on getting results.

He talks a lot about an infection called mycoplasma, a tiny and menacing bacteria --a micro-organism-- that slowly invades tissue and penetrates deep inside white blood cells, eventually reaching all tissues and organs of the body, causing complex symptoms.  Mycoplasma has been implicated as a cofactor in many of today’s most threatening illnesses, including AIDS, rheumatoid arthritis, respiratory infection, and CFS.

            Many of his callers describe problems that Dr. Mirkin reasons are associated with mycoplasma or a related infection, which Dr. Mirkin claims can only be cured with long-term antibiotics.  Dr. Mirkin asks them about their symptoms.  For example: Do they have chronic joint pain, a sore throat, low energy?  Do they feel burning upon urintation?  Do they have an uncontrollable need to urinate in the middle of the night?  Having listened long enough, and having noticed how often the callers’ symptoms paralleled mine, I did some research.  I saw that mycoplasma can break down a weak immune system, leading to chronic illness.  The data pointed overwhelmingly in favour of my having the infection.  So I implored my doctor to put me on antibiotics.  Dr. Mirkin says, and my research affirms, that there is no reliable diagnostic test for mycoplasma.  Antibiotics are taken on speculation.  Heeding this, I didn’t bother to solicit a doctor’s opinion.  Though I’d long been suspicious of drugs, I’d heard enough to convince me it would be worth it.

            On May 10th, I began taking doxycycline, the recommended drug.  One week later, I felt pretty good, so I stopped taking melatonin --a natural hormone that I was depending on for sleep; and then I stopped my thyroid medicine.  Still okay.  I passed through the Herxheimer reaction, a temporary re-surfacing of symptoms, if you will.  It was mild for me.  My mental sharpness has returned.  My 7-year long sore throat is loosening steadily.  My legs feel lighter.  Best of all, I am sleeping like a baby, like I haven’t slept in years.  The recovery feels like one step back for every two steps forward.  I feel good most parts of most days, and I’m slowly getting better.  All this in only six weeks.  So a lot of hope has returned, and a full recovery seems imminent.  Meanwhile I cross my fingers and hope.

            The experts don’t yet know if mycoplasma alone is responsible for the onset of CFS, but they don’t think it’s that simple.  A recent study found that 52% of CFS patients have some kind of mycoplasma infection (as compared to 15% of healthy people).  Therefore, it is likely that mycoplasma will exacerbate an already weak immune system; so mycoplasma, when it exists in the CFS (or pre-CFS) patient, is very likely a co-factor in the onset of CFS.  My question is: can mycoplasma in a healthy person cause the immune system to weaken enough to make the onset of CFS innevitable?  More research is currently being done.

            Why is all of this so important?  Because, as Dr. Majid Ali states in The Canary and Chronic Fatigue --the book I long considered my CFS “bible”-- CFS will be the most predominant chronic health disorder of the 21st century.  In fact, it’s already ruined thousands of lives.  Should we worry?  Well, consider this: It’s been said that the level of functioning of the average CFS patient is roughly equivalent to that of an AIDS patient with 2 months left to live.  Except CFS doesn’t kill you; it leaves you to live in misery.  Given these parameters, it must be considered momentous to have discovered, finally, what reasons to be the essential root of CFS.  For me, it’s everything.

            July 13th, 1999

            Last week, I slept a lot.  I was exhausted.  It was a particular type of exhaustion; I’d experienced it before.  It was my body healing.  This time it was doxycycline evidently giving my system one final cleansing.  My wife Kim was worried.  She always worries when I need to sleep a lot.  I reassured her.  This time, I was sure; CFS had finally run its course in me.  I’d finally beat it.

            My energy the last couple of days has been quite good.  I’ve felt symptom free.  So I have asked myself, does this mean CFS is gone, once and for all?  I certainly hope so; but I’ve grown accustomed to viewing occasions like this with guarded optimism.  I fight the unbridled optimism daily.  A relapse hurts less that way.

            If my recovery is not yet complete, then I hope it will continue until it is.  I want badly to feel the infinite thrill of having unearthed a treasure that’s be searched for long and hard.  Yet I see all too clearly the reality of my situation.  The truth is that I’m just beginning a momentous struggle to discover things that once seemed forever lost; I’m just starting to make things happen, things that I yearn to have made happen a long time ago: the career, the home, the family, fulfillment.  It will be terribly difficult of course, but I’m ready.  And I’ll only get more ready.  I feel well equipped to do battle: I’m only 32; I have my writing skills, I have a wonderful wife, and I have peace of mind.  Now I must move forward ... one day at a time.

              January 11th, 2000

            In August I went off doxycycline.  My late summer allergies were acting up , and the medication was causing them to run amok.  I was taking my probiotics regularly (to replenish the good bacteria that the antibiotics had depleted).  A couple of weeks went by and I felt pretty good –though I didn’t yet know what pretty good really felt like– and I started thinking that maybe, somehow, I was cured, like by magic.  I thought there was a possibility that I wouldn’t need the doxycycline any more.

            In early October, the symptoms began to re-appear.  It wasn’t long before I was back on doxycycline.  This time I promised myself that I would stay on it until the mycoplasma was gone.  I wanted to squash it.

            Before Christmas I processed a short but nasty flu bug.  As it left me, I felt great, better than I had in years.  I felt so good that it was playing on my mind.  I needed to be certain that I was actually well, and not just between stages of recovery.  I began to test myself.  I worked out hard and took long walks.  And I got less sleep than I should have.  But I was still okay.  Sleep-deprived, but functioning well.  And I continued to be okay, right through the holidays and despite all the sugar I consumed.  I felt good up until I caught this current case of the flu.  But this flu is hitting millions, and I have only a slight case of it.

            Unless something extraterrestrial has happened to me, I am recovered.  Like never before, I am quick-witted, fast with my reflexes, long on concentration, full of vigor, and ready to handle buggers.  (Buggers are folks who dare to stand in the way of my success.)