Saturday, October 31, 2009


Good morning, P.M.!   I'm tired.  I'm tired of waking up at 4am almost every day after waking up at least three times during the night to oblige my full bladder and/or angry bowels.  It's like house training a puppy who doesn't have circadian rhythms.

My renowned GI, who supposedly got back into town last week, did not manage to communicate with me.  I'm about ready to give up on solving the mystery -- which is to say, the Diet and Doctor Experiment -- and just accept that I have a new pace with a heightened baseline level of pain.  P.M. and The Compulsion, however, who are rapt and scrupulous scientists, are not pleased with this option.  They prefer to encourage this moribund progression wherein I slowly lose sight of my sanity in the face of being overwhelmed with both task and absence of physical momentum to achieve said task, while continuing to conduct the Diet and Doctor Experiment.  

November is a horrendously packed month, and has the potential to be the greatest I've seen in quite some time.  It does require, however, that I be -- to a degree convincing to my boss, coworkers and family -- mentally and physically functional.  I'm so tired.  Let's go read some journal articles and finish those graduate school applications...

Tuesday, October 27, 2009

On the Evolution of Eating Animals

Everyone writes about vegetarianism and veganism in terms of either animal rights/worker rights/environmental sustainability or health/nutrition.  And never the twain shall meet.

I caught a post by Natalie Portman on HuffPost this morning about Jonathan Safran Foer's new book Eating Animals.  It may be the first time I've appreciated Natalie Portman since Leon: The Professional... or, perhaps, I'm just appreciative of the HuffPost editors.  In any case, I was frustrated, yet again, by the book's lack of discussion of the evolution of human health alongside the evolution of the animal farming industry.

Why doesn't anyone talk about how the need for meat in the human diet has changed with our changing physicality/intellect and industry/economy when the context of one is so important to understanding the other?

Closer, but no cigar.

I'm too burnt into the ground to explore this tonight.  When this rush-week is over and I've done my presentation, compiled necessary data for November's grant, finished my post-doc's manuscript, submitted my grad school applications, gotten an inkling of sleep between aberrant episodes of Residual Weekly Throughput and relieving the ever-full bladder... I'll do this subject follow-up-justice.

Curtailing Monday

It appears that I have lied again.  The Weekly Throughput has arrived... on Tuesday?  I attribute the 48h delay to PPR/food, and the significant decline of accompanying pain to the 6oz of prune juice which I have endowed my guts every day for the last week.

I supposed it is only fitting, since today is the 27th.

Monday, October 26, 2009

Slaking the Compulsion

The Compulsion and P.M. aside, I actually slept in until 830am on Sunday.  Granted, there were about four half-consciously bumbled trips to relieve my ever-shrinking bladder, but otherwise an impressively sound sleep.

The Compulsion wins when I am unable to turn off the barage of "what ifs".  If I didn't have a car, I would have had to walk to the transit station at 6am in the pouring rain and black freezing cold while having an attack... and I would not have survived.  If H.B. wasn't also currently stay-at-home-boyfriend, I would not be able to solicit his chauffeuring services on days when I don't think I'll make the bus ride home without an incident... and I would not survive.  The Compulsion doesn't like to let me enjoy these small pleasures, these cosetting habits of which I take advantage, because it thinks that without them I would be lost.  Thanks ever so much, Conscience, for reminding me in such anxious terms that I depend on certain luxuries in order to function.

This weekend is the first that I can report, aside from the bloated pains of having anything in my gut at all, there was no major attack. ....?!! That's right.  The oxycodone bottle sat neglected on the nightstand.  For the first time in 3 months.  Another luxury on which I depended this weekend, without which I would not have been able to put together my journal club presentation, or edit my post-doc's manuscript, or write an already belated letter to my aunt, or put together Halloween gifts for the lab. 

You know something, though?  This weekend was lovely because The Compulsion and P.M. did not win.  It's just not healthy to assess everything you do in life based on how easy you have it while you're doing it.  I've earned my life.  What luxuries it has, I've proven myself capable of functioning without before.  Just because I'm living easy now doesn't mean I've forgotten how to work around obstacles when things are not so pleasant.  In fact -- and hilariously -- I touted that strength in my Statement of Purpose.  Never convinced that I have enough time (when I always make sure I do); never convinced that I'm not taking the easy way out (which usually results in my burning the candle at both ends).  I blame P.M. for revitalizing The Compulsion, but I blame myself for letting it rule over rationale.

There is always time.  There is always warrant for method.

Friday, October 23, 2009

SBFTs and Poor, Confused Gastroenterologists

I'm having fun.  And more importantly, I think the hospital is having fun.

The results of my SBFT are as follows:  Dr. P sees strictures in the small bowel, but they aren't very tight, so he's not concerned that surgery is imminent, but he is concerned if I are still on 40mg/d prednisone... (which I am) 

The problems with this response are as follows:  1) Dr. P is the on-call doctor who is the surrogate for Dr. W who is my not-on-call surrogate for Dr. S who remains incommunicado until next week.  So basically, I have access to nobody who has a "complete" understanding of my history.  I may not be a doctor, but I was close enough to becoming one  four months ago that I can tell you that medical history is kind of important when interpreting the results of any medical test.  Sorry, that's just how it works.  2) Since Dr. P followed up his interpretation of my SBFT with the questions, "are you still on prednisone?" and "what are your current symptoms?", I have deduced that being on-call he did not feel compelled to look at my history before telling me what my SBFT meant.  Therefore, I can more accurately tell me what my test means than he can.  'Ya ready?

My interpretation is as follows:  I think that I was correct in predicting stricture(s) of the small bowel based on the observations that the location is new, and that the pain has been persistent despite the prednisone, which, were this a normal inflammation would have slaked the flare and turned it to scar tissue.  I think that the very slow evolution of nausea/emesis/bloating since April of this year to incredible new pain/back-up supports the idea that a stricture has been developing.
"Patients may not know that they have an intestinal stricture. The stricture may not cause symptoms if it is not causing significant blockage (obstruction) of the bowel. If a stricture is narrow enough to hinder the smooth passage of the bowel contents, however, it may cause abdominal pain, cramps, and bloating (distention). If the stricture causes an even more complete obstruction of the bowel, patients may experience more severe pain, nausea, vomiting, and an inability to pass stools." (1
I think that Dr. P's suggestion that I begin tapering off of prednisone is excellent, considering how long I've been on it and how little it's done to help the problem.  Finally, I think that Dr. P's suggestion that I go back on "soft foods and liquid diet and see if that improves things" is bullshit.  Had he looked at my recent history, he would have seen that I just started reintroducing solid foods, and he would have made the connection that it was probably not a good idea to tell me to take a step backward without suggesting how to help me move forward.  Am I wrong? 

Disclaimer: I know that being a doctor is hard.  I know that insurance companies and Big Pharma have infiltrated the world of medicine in the most destructive and back-breaking ways.  I know that 90% of a doctor's non-patient time is spent dealing with the utter nonsense draped before them by the two monsters that dictate the way they practice medicine.  However, I have absolutely no tolerance for the inability to take ten minutes to figure out what is going on with the patient before making a diagnosis.  The Bernstein paper I cited the other day says something about SBFT's being so ancient that very few are read properly unless they are read in a radiology center with a SBFT specialist.  This observation in concert with Dr. P's seemingly confused and half-assed diagnosis... has me concerned.  But I'm having fun.  Truly.

In other news, this is Lamar.  Due to the extrusive nature of the PPR-face this year, he is part of my Halloween costume.  What.

Tofu, Squash and the Microbial Squadron

In the quest to ween off of the short-term friendly diet base of breads and rice, I am finding two things:
1) My allergies dictate that a myriad of exceptions from the rules be formulated, and
2) These diets -- particularly the ones that are based on moving away from modern food-preservation and agricultural technology -- are far too nit-picky for my stress level.  That is fantastic for people who can and/or need to be that scrupulous with what they put into their bodies (often Coeliacs and Rheumatoid Arthritics, both malabsorption-centric), but not for me.
Current quests: 
1) to replace most rice noodles with various stringed squashes, and
2) replace most breads with tofu.
Current obstacles:
1) If my SBFT results come back rampant with strictures, I will not be able to eat stringed squash, and
2) tofu is "illegal" on the SCD diet (my guiding reference).
Current absurdities:
1)   Spaghetti squash is high in complex carbohydrates.  Why is it on the SCD diet if this is so?  Because these complex carbohydrates are not starches (2), the favorite sustenance of the microbial squadron.  Therefore, spaghetti squash is excellent for the SCD diet, but not so excellent for me... in terms of making it through my system, rice noodles are better.  Sacrifice the carbohydrate eradication or risk intestinal rupture?  This is going to involve a very slow process of replacing carbs with fiber one food at a time; elsewise, my poor brain will not be able to suppress the hormonal onslaught of PPR-bred anxiety.
2) The reason that tofu is illegal on the SCD diet is because of the ambivalence of its carbohydrate content.  Apparently, no one has bothered to figure out what carbohydrate prevalence results from the fermentation and processing of the genetically manipulated soy beans that beget tofu.  My condition at the moment is more defined by "solid substance sensitivity" than by my concern for entirely starving out the microbial forces in my gut (see above).  Therefore, the carbohydrate content of tofu being so minimal as compared to its protein and fiber content -- even as its carbohydrate chain specificities are unknown -- I will allow it.  I simply can't afford to eliminate everything by-the-molecule, only to reduce.  Baby steps.
Additionally, screw complete elimination of rice because if I cannot eat sushi once in a while life is just not worth the hassle.

Tuesday, October 20, 2009

Statement of Purpose

Today, following a morning of writhing on the bathroom floor and an afternoon of walking around PSU's farmer's market in the South Park Blocks, I finalized my SOP.  The following are a compilation of my recommendations for aggressively tackling this process.

1) Choose your layout strategically.  I had two separate drafts in front of me this evening.  The first was a statement by chronology, the second, a statement by subject.  Print out a draft, cut up the paragraphs, have a seat on the living room floor and rearrange your topics until they become more adhesive.  In my case, things were made much stronger by topical layout.

2) Show your SOP to your letter of recommendation writers. Your letters should fill in the blanks that your SOP doesn't expatiate.  My boss, for instance, included an anecdote about my being singled out by the benefactor of one of my undergraduate research grants at the reception following my presentation (which I did not know she was attending!), and that this woman is now a friend of mine.

3)  Keep the intro short and powerful.  Honestly, three sentences introducing your unique passion, your resolve and perhaps a plug for the program are all you need to be epic, here.

4) Every paragraph should relate back to your research interests, experience and future.  Don't talk about what a passionate, hard worker you are; show how you are and what you've done.

5)  Read out loud.  Seriously.  All of the errors that your eyes didn't catch will be like fresh wounds to your ears.

After five drafts, I am finally proud of my self-representation.  I struggled more with this essay than any other I have written in my life. 

Monday, October 19, 2009

On MRIs, Small Bowel Follow-Throughs and CT Scans

Dr. W is apparently my surrogate GI until Dr. S is back in town.  He is concerned about my symptoms (the Weekly Throughput and ossified left intestine), suspects an obstruction (stricture, fibrosis, or scarring) and wants to do a small bowel follow through.

At this point, I realize that without these magnificent instruments of medical speculation, I really have no freaking idea whether the left side distension/rigidity is my sigmoid colon or duodenojejunal flexure (the former being almost directly anterior to the latter).  I also have no freaking idea what's going on in my Prednisone-resistant mid-lower small intestine.  What I do know from historical diagnosis is that I have ileal obstruction (on the right side) which has been fairly reticent during this flare; not particularly helpful in addressing the small bowel pain and left side distension/rigidity.

In the last two months, I've been recommended an MRI, a CT scan, and now a small bowel follow through (SBFT).  The first two were suggested by Dr. S, the last by his surrogate.  The reason endo/colonoscopies are not on this list is because they have shown zero new information about my new symptoms as they have developed over the last eleven years.  Endo/colonoscopies don't span a great breadth of the intestinal tract (endo goes down to the duodenum, colono goes up to the top left juncture of the descending colon).

For those who are equally confused as to why their GIs can't make up their minds about which procedure is best for diagnosing which kinds of Crohn's or IBD symptoms, below is a compilation of my findings.  The general concensus seems to be that SBFT are more accurate in identifying strictures, and MRI and CT are better at identifying fistulas, abscesses and active inflammation in deep tissue.

In a study comparing MRI and SBFT (Bernstein et al 2005):
"SBFT revealed additional information in four [patients], including a stricture (none found on MRI, n=1), jejunal site of obstruction versus unclear site on MRI (n-1), and ileosigmoid fistulas (n=2)."
"For tight strictures, SBFT gave information on number but did not delineate findings between the strictures, or on extramural disease.  Obstruction and stricture detection was comparable but characterization was more detailed with MRI."
In a study comparing MRI, CT and SBFT imaging of the small bowel (Lee et al 2009):
"The mean number of bowel segments other than the terminal ileum with active inflammation per patient was slightly higher as detected by using CT enterography and MR enterography than it was as detected by using SBFT.  However, these differences were not significant.  The level of agreement between the readers was excellent for CT enterography, MR enterography and SBFT."
"The low level of agreement observed for SBFT may reflect inherent disadvantages of this technique, including incomplete evaluation of bowel segments located deep in the pelvic cavity owing to overlapped bowel loops and suboptimal evaluation of the small bowel distal to the tight stricture (10, 12, 32)." (Note: The paper doesn't specify how the SBFT were conducted, but I know that during this procedure they have the option of pushing your guts to one side or another to get a better image if they want to, so in my opinion this observation is inaccuate)
"CT and MR enterography were more capable than was SBFT of depicting extraenteric complications of CD, including fistulas, sinus tracts, and abscesses.  Although our findings are consistent with findings in most previous studies (4, 10, 12, 33), conflicting results have been reported for the detection of enteric fistulas and sinus tracts (4, 10, 33).  Bernstein et al (10) compared MR enterography and SBFT in 30 patients with CD and found that SBFT allowed identification of two ileocolic fistulas that were missed using MR enterographic images."
In a study looking at the accuracy of CT enterography preoperative diagnosis in the small bowel (Vogel et al 2007):
"For the 36 patients, the presence or absence of stricture or fistula was correctly identified by CTE in 36 (100 percent) and 34 (96 percent), respectively." (Note: Since "preoperative diagnosis" can be assumed to refer to the presence of a stricture, I think it is implied, here, that the CT scan is an accurate way to identify small bowel obstruction.)
"SBFT is accurate in the prediciton of fistula, stricture and mucosal abnormalities with specificity and sensitivity reported in the 85 to 95 percent range (MacKalski & Bernstein 2006)."
"In the 18 patients with one or more strictures, CTE was correct for stricture number in 12 (67 percent)."
A review of Crohn's disease imaging advancements (Grand 2009):
"The small bowel series and barium enema are essentially historic examinations for the detection and evaluation of inflammatory bowel disease.  These studies, while effective at detecting mucosal abnormalities, are poorly tolerated by sick patients, provide assessment only of the bowel lumen (particularly the mucosa) and are physician dependent, limiting their reproducibility.  A properly performed and interpreted SBFT or BE is unfortunately a lost art..." (Note: Again, SBFT seems accurate for identifying fibrosis, but not deep tissue inflammation in active Crohn's)
"The ability to assess disease activity is probably the most important advantage of MRe over CTe.  Clinically, it is often difficult to distinguish between active and chronic changes of inflammatory bowel disease in symptomatic patients.  This distinction has become increasingly important with the advent of new, boilogic therapies for active inflammatory disease which, while extremely effective, are expensive and may also be potentially toxic.  Although beneficial for patients with active inflammatory disease, these agents do not benefit patients whose symptoms are secondary to a fibrotic stricture.  Rather, these latter patients will require surgery for symptomatic relief" (Note: Since I am currently on biologic therapy, it's pretty important that I be able to figure out whether the last three Remicade infusions were not even necessary.  If I end up needing surgery for a stricture as Dr. W suspects... I'm going to be pissed that Dr. S put me on the PPR combo so hastily.)
"Because negative contrast is used for CTe, small abscesses may be difficult to distinguish from loops of bowel and regular CT or MRe should be employed if abscess is suspected or in the immediate post-operative state." (Note: In agreement with Lee et al paper)

Sunday, October 18, 2009

Of Milestones, Aliens and Confused Symptoms

Well, two hours ago I had hoped to announce this weekend as the first during this flare which has not involved a major Throughput episode.

I had hoped to attribute this feat of baby-step recovery to my self-inflicted intervention with protein and soluble fiber, in concert with my third Remicade infusion.

I had hoped to say that the tide had begun to turn!

Now that Sunday's Weekly Throughput has occurred, I must report that, although sustained, its might was 2/3 that of its usual caliber.  Hazzah!  Hazzah?

Yeah.  It seems that the tide has just become indolent.

Evidently, I woke up in the middle of the night last night with a tightness in my abdomen, flailed until I woke up H.B. who, in turn, woke me up enough to tell him of the accompanying nightmare in which I was Jesse Ventura in Predator and had just had my guts blown out of me by a laser grenade, and proceeded to koala the poor boy until once again losing consciousness.  So, when the tightness in my left small intestine returned this afternoon, the half-aware nostalgia was bemusing.  Today was the first showing of this symptom which I attributed to Backup until the Weekly Throughput occurred.  Now that it's over, the tightness remains.  Noted.

Conclusions:  The attenuation of pain during the Weekly Throughput, although gradual and minuscule, is continuing.  This week I introduced tiny portions of cooked root vegetables and mushrooms, Tofutti BTCC, and low-sugar pomegranate juice.  Seeing as the flare has not responded in escalated rancorous retaliation, I am comfortable  suggesting that it matters slightly less what exactly I'm putting into my system, and more that I'm putting things into my system at all.  This has been my perspective from early on.  Apparently I have a message from another GI -- who Dr. S's nurse was kind enough to recruit in lieu of my latest symptom update -- to retrieve tomorrow morning; and, apparently, he has a suggestion for me...

Friday, October 16, 2009


My poster is going to the Society for Neuroscience meeting in Chicago without me!

If you're going to be there, and if you are not presenting your own poster between 1-2pm on Tuesday (as are my favorite college professor and boss, about which I am really bummed cause they wont meet each other)... check me out.  I'm #CC-67.

Thursday, October 15, 2009

On the Evolution of Diet

My experience has always been that during the ebb of a Crohn's flare, carbohydrates pass with the least residual damage.  In the long term, however, carbohydrates are increasingly the spotlighted culprit of havoc-wreaking; and not solely by way of Klebsiella.

I've flirted with the Paleolithic (or, SCD) diet before; before diving headlong into this most recent flare (2.5 mos, and counting), I was balancing quite nicely in a Me Friendly version of the Paleo diet.  Because I had only been doing so for several days before The Fall, and because my gastrointestinal condition had been sloughing downhill for almost a year, I wasn't able to give the diet a legitimate chance.

Now that I'm working on climbing out of this crevice, however, I'm trying to shift my current selection of solid foods away from Carbo Loaded and into Paleocentric orbit.  My Me Friendly version of this was additionally limiting the red meats (fats), nuts (fats and allergies) and very fibrous vegetables (obstruction).

What I aim to do nearly without:
dairy (no brainer)
sugar (no brainer)
salt (no brainer)
grains (categorically similar to dairy in terms of damage, but I don't seem to have a gluten problem so we'll keep those with low glycemic indices)
legumes (see above; I could never entirely eliminate legumes...)
red meat (fats)
nuts (fats and allergies)
berries (seeds)... These last three are part of the "Do Consume" stipulation of the Paleo/SCD diets; alas, knowing that they destroy me I cannot invite mucosal carnage.

What I aim to tolerate:
poultry and fish
fruit (without pulp or small seeds)
root vegetables (non-stringy)
fermented foods (this should be interesting)
other foods with low glycemic indices

I'm typically quite skeptical of the hardcore diet reversions that try to re-plant us in the days before preservatives and cooking.  Most of the diets that come recommended with Crohn's are pre-processing, or Paleolithic era (Dr. Balzer summarizes this nicely).  Atkin's, Raw Food, SCD-- they're all based on caveman diets.  And that's fine, except that we haven't been Cro-Magnon for 20,000 years.  Very, very few proponents of these diets take into consideration the evolution that has occurred in the human gut during the gap between then and now (not to mention the inherent shift in caloric intake).  I'm truly at a loss as to why. 

It's sort of like how Western culture touts that if we all ate three rice-based meals a day -- heavy on the salts and carbs, mind you -- we'd all sport Asian slender, low cholesterol and have beautiful creamy skin.  This false-cause fallacy forgets that one can train the body to produce the proper enzymes to accommodate such an adjustment, but it's not all about enzymes... there are genes involved (Ley et al 2008; Bengmark 1998).  The anthropologists argue that we currently evolve too rapidly for these genetic influences to accommodate (Kligler & Lee 2004); my position continues to be that epigenetics and post-translational modifications negate that stance.  The microbes that inhabit our gut and help us process food have co-evolved with us, any may respond to a dynamic change in diet either positively or negatively depending on your physiology and genetic predisposition.

My bias is moderation.  Unless you have a predictable or distinguishable allergy, it is usually not helpful to eliminate something from your diet entirely.  Gluten, yes.  Dairy, okay.  Carbohydrates, not so much.  Fruit, definitely not so much.  I can't do a hardcore Paleolithic or SCD diet because I have never been able to limit my diet that strictly for an extended time without invoking a flare -- which is something else the caveman diet prognosticators tend to neglect; the importance of variety.  Variety is why people on the Homeopathic route take Probiotics. 

I also have a resistance to thoroughly processed foods heavy on the preservatives, sugars and salts; this resistance escalates to phobia when I am on PPR.  The Ley group argues that the evolution of agriculture and cooking didn't have an appreciable effect on our Gut Flora -- that the preparation of otherwise inedible grains which are the primary sustenance of our microbiotic friends did not significantly encourage their co-evolution.  Others suggest that these new tools were the paradigm shift that brought about an exponential predisposition to gastrointestinal disorders.  My bias aside, there is more sufficient evidence for the latter case from genetic, microbiological, anthropological and other fields (Cordain et al 2005; Wrangham et al 1999). 

So we'll see how this unfolds.

Wednesday, October 14, 2009

Of Sushi, Star Trek and Klebsiella

Enough of these Crohn's disease-linked genes!  I found this phenomenal post the other day from Dr. Ayers at the College of Idaho on a link between a particular flora and Crohn's diseaseKlebsiella pneumoniae is a bacteria that colonizes in the healthy mouth, lungs and intestines.  Dr. Ayers writes about the excess of this bacteria in the intestines of Crohn's disease patients.  Its role in Crohn's patients, he suggests, may be related to its ability to produce hydrogen gas, on which the notorious H. pylori feeds.  Here is the bridge:  carbohydrates feed Klebsiella, which produces the hydrogen gas that feeds H. pylori, which then destroys the mucosal and epithelial lining of the stomach and upper intestines...

Intrigued, I of course had to hunt down the primary literature of these claims (tsk tsk, Professor Ayers!).  Below is a compilation of my favorite excerpts; this is a beautifully put together review paper by Rashid et al 2009.
"Klebsiella microbes have been isolated from the large bowel biopsy specimens in more than 25% of patients with CD or UC [42], and relapses in patients with CD were found to be associated with Klebsiella intestinal infections [43]. In a study using immunohistochemistry, however, it has been observed that the majority of patients with IBD had negative staining
specimens for E. coli, L. monocytogenes and K. pneumoniae taken from the bowel mucosa [44]. These latter findings indicate that it is the microbial bulk in the intestinal lumen rather than at the sites of the pathological lesions, which is important in evoking both local mucosal and general antibacterial immune responses.
"Elevated levels of antiKlebsiella antibodies have been reported in patients with CD from six different centres in the UK (Table 2). Significantly elevated levels of antibodies against K. pneumoniae and Y. enterocolitica microbial agents were observed in patients with CD and UC when compared with healthy controls [48]. Similar findings were later shown by other groups from Scotland, where IgA antibody levels against K. pneumoniae were found to be elevated in patients with AS and IBD [49,50].
 "Klebsiella microbes possess a powerful debranching enzyme, pullulanase, which is a molecular complex consisting of 17 components and some of these exhibit molecular mimicry with several collagens. pulA cross-reacts with collagens I, III and IV [46]... Significantly elevated levels of antibodies against Klebsiella microbes as well as autoantibodies to collagens I, III and IV were observed in patients with AS and CD [55].
"The hypothesis proposed is that exposure to the cross-reactive antigens of pulA found in Klebsiella pullulanase leads to the production of autoantibodies that can have a pathological effect on the collagens found in the intestinal mucosa and eventually lead to the characteristic lesions of established CD (Fig. 2).
"In a study carried out by a group from Los Angeles, it was observed that the mean number of faecal Klebsiella microorganisms in individuals taking high-carbohydrate/ low-protein diet was 40 times higher than in those individuals receiving low-carbohydrate/high-protein diet [69]. In a comparative study, it has been observed that the mean number of Klebsiella was 10 times higher for simple sugars per gram of substrate compared with the value obtained after incubation with 11 different amino acids [70].
"A clear link is observed between increased intake of starch and the bulk of intestinal microflora, among which Klebsiella microbes constitute an important part. High dietary starch intake leads to increased growth of these microbes in the bowel."
 But what about the provision of hydrogen gas to H. pylori by an intestinal Klebsiella bloom?

Crohn's patients have a heightened immuno-sensitivity to Klebsiella microflora (Rashid et al 2009).
Klebsiella yields a high molar ratio of hydrogen per starch (Chen et al 2005).
Hydrogen gas feeds H. pylori (Olson et al 2004).
Klebsiella feeds on starches, mono- and disaccharides (Rashid et al 2009).
Ergo: starve out the Klebsiella with a low starch/carbohydrate diet, and in doing so, starve out the H. pylori.  Lowering your H. pylori levels, if this particular bacterium is a prominent contributor to your Crohn's, IBS or Colitis, may substantially alleviate a great deal of epithelial destruction, and suppress the inflammatory response.  I like it.  Go, science!


In other, more important news, last night was homemade sushi and Star Trek night.  Tuna, crab, Tofutti BTCC, avocado, Insurrection.  There are just too few relaxing evenings that even come close to challenging that.

Sunday, October 11, 2009

Food of the Day: Pumpkin Cheesecake

"To live in a creative way requires extreme and sensitive perception of the orders and structures of relationship to individuals, society and nature.  In this case, creativity can flower.  It is only when creativity is made subservient to external goals, which are implied by the seeking of rewards, that the whole activity begins to whither and degenerate" -- David Bohm & F. David Peat; Science, Order and Creativity
Yesterday's adventure to the South Park Blocks Farmers Market with my parents resulted in the acquisition of some very tasty treats.  Among them; chanterelles, orange anise sugared buns and a particularly eminent Sun Spot pumpkin.  A little inspiration from Mom lead to the conclusion that since everything I eat, no matter how mild, seems to feed this flare, there is no reason to so conservatively restrict myself.   Why not use the tools at hand to do some more creatively aggressive tracing of causal relationships?

The quote above from David Bohm and F. David Peat's book is an homage to our conversation in the bustling Market: I have decided that my GI's current adherence to "external goals", aka palliative diagnosis, is impeding on my recovery.  Deferring the goal of quelled symptoms to a more subordinate one, I can explore (carefully) the next steps in terms of testing my tummeh.  This quote -- and this book -- mean many other things to me, but as does most incite from these great physicists, it applies to the manifestation of every infinitely small constituent of existence... especially food.

In other words, my remaining October adventure will be directed at distilling a more comprehensive food-pain pattern.  The more closely I watch the 30hr digestion mark, the more easily I can isolate which episodes are Crohn's, which are IBS, which are from what food and which are/are not clinically improving from the Prednisone-Purinethol-Remicade (PPR).  We'll get into which medication is solving what problem later down the line... right now they are just superfluous variables, and that is bad science.

Therefore (!), avocado, beans, broth and bread; you're lovely, you're truly spectacular foods, but I need to feed my poor immune system some substantial nutrients... 

Tonight I made chicken and chanterelles in a white wine reduction and coconut milk sauce.  Rotini bed not shown.

This Sunday afternoon, however, was devoted to the Dairy-Free Pumpkin Cheesecake Experiment.  Using my Eminent Market pumpkin, I augmented this awesome recipe from Elana's Pantry.  Instead of using whole milk yogurt (which would unequivocally be my undoing), I used a 4oz tub of Tofutti Better Than Cream Cheese (which was proportionally perfect).  I also reduced the amount of Agave nectar, went light on the vanilla extract and added some nutmeg.

Sidenote: Yes, I do have a squash, pumpkin and general October obsession.  You are so lucky that I have refrained from posting about Candycorn and my glow-in-the-dark skeleton oven mit...

Thursday, October 8, 2009

Remicade Round III, and Other Stories

Epic events of the week of October 5th 2009:

1)  My boss brought up that he finally noticed that my face had become a planet.  He had been watching for it, apparently.

2)  I lifted an older woman off of the concrete at the entrance to the Hospital, where she had face-planted after tripping over that obnoxious yellow striped curb.  Approaching the scene, I was about six feet away from her when she fell, headed speedily toward my bus.  Seeing her mid-flight, I surveyed the number of samaritans around that might save weak, immuno-suppressed me from having to be the one to lift her off the ground; a hospital guard, the Veterans' bus driver who delivered her, and three other Veterans were present.  Nonetheless, none of them moved toward her... they just kind of peeked over at her without wanting to get any closer -- yes, the Veterans Hospital GUARD and the Veterans Hospital ESCORT -- and so I was forced to diverge from my path.  Crouching in front of her, I did as I was trained to do as a physical therapy assistant back in yesteryear, blah blah, a crazed and delusional encouter occurred.  I got her to a stable upright position, and glared mercilessly at the guard and escort who had stood by and watched a fellow employee of half their stature do their job for them.  "Is she okay", the guard shimmies toward me with his arms crossed to ascertain the liability of the situation to the hospital.  All she was able to coherently report was that she was fine and that she had fallen over the curb, which is what I relayed to His Daintiness.  Little does he know -- if he didn't deduce from my glare of death -- that he almost got his face punched in.  I may still have the compact build of a gymnast and walk like I'm six feet tall and own the turf beneath my feet, but it just doesn't strike me as logical to let a little girl pick up an older woman twice her build (indeed) when that kind of thing is in your job description for the express purpose of hospital liability.  Hopefully this woman was just crazy, and not carrying any diseases for me to contract.

3)  Monday's Bus Attack was mimicked yesterday.  The pattern of the Weekly Episode has been aggitated: this fourth "weekend" attack which I currently attribute (perhaps erroneously) to the shortening in Bisquik, has officially been three-days prolonged (possibly by the beets, for they were first ingested following Monday's original attack).  We're still looking at three days negative Throughput.  [What this means, I couldn't say.  Neither could my GI, because he is incommunicado.  Neither could his nurse, for she is not allowed to make medical speculations, apparently.]  Fortunately, I got home before the worst set in.  Unfortunately, I had to tank up on oxycodone before heading to my third Remicade infusion, which was delayed by an hour and a half because Wednesday nights are apparently peak traffic time for the Infusion Center.  No Tylenol because the oxycodone was based in Tylenol.  No Benedryl because Benadryl + Percocet = exaggerated sedation and constipation.  No poor reaction because, well, I'm a rock star.

4) Today, I learned to inject rats.  My coworker is on vacation beginning tomorrow, my boss is in New York until Monday, and I -- the Mouse Lady -- have been commissioned to do some palliative sucrose care for some rats who are not recovering ideally from past weeks' surgeries.  Coworker is the Queen of Rat Handling, among other things, and has prepared me well.  The only thing that can stop me from cosseting these sicklings is if my allergy to them activates, which, with the help of Remicade-Prednisone-Purinethol, will not be a problem!  Pretty sweet luck, eh?

5)  My new favorite part of the weekday is Breakfast.  In attempt to develop a habitual food-drug ingestion pattern, I've begun frying an egg with a piece of toast every morning, accompanied by the first of the day's drugs, and a few rounds of board game with H.B. before meandering off to the transit center.  The food is rather crucial to the Prednisone not causing nausea (and thus the additional ingestion of Promethazine).  The board game is essential to getting face time with H.B., which is minimal these days, and for pacing what would otherwise be an unnecessarily rushed morning (id est, I wake up at 530am and leave at 7am instead of 6).  Huge. Fan.

6)  The Pharmacy has me disgruntled.  They did not think that it was necessary to notify me that my GI being incommunicado, they did not successfully get him to renew my Prednisone prescription, which was, consequently, not prepared for me.  At all.  They thought it would be opportune to wait to tell me this until I confronted them.  Fortunately, I had some expired pills from last year's bout, for whatever good they did.  Unfortunately, the pharmacy only gave me three days worth of hold-over pills until such time as they could... do not a damn thing to move the instigation process forward with my GI. 
"Ma'am, I can see there is a record that Dr. S has been notified," says the kind pharmacy technician.
"Yes, I understand that, but he is out of town until the end of October and hasn't responded to the notice.  Since I need this prescription within the next two days, would it be possible to forward the renewal notice to my PC?"
"No, there is a notice for Dr. S so he should respond to it within two days."
"... <dumbfounded pause> Alright, but if he were going to respond, it seems like he would have done so already since I initially called in the renewal ten days ago.  Is there no way to renew the prescription through someone else since it is critical that I pick it up within two days?"
"No, the notice is in the box so he will respond.  If he doesn't respond within two days we will send a notice to someone else," she's quite on-the-ball, this one.

"... Is there a reason we can't just do that now given the time-sensitive nature of the situation?"
There wasn't a reason.  But there was also no going-around said non-existent reason... so I'll be calling again tomorrow.
I don't understand why they don't understand how to pick up a phone, but I know enough about the language and intertwinings of medical services to beat them at their own game of Feigned Idiocy... so I'm on them.

Monday, October 5, 2009

dirge of the adventure food

It waited, today.  It waited all the way through 9 hours of tissue preparation and number crunching until I stepped onto the bus.

I love getting attacks on the bus.  Really, and truly.  It proves a most suspenseful mission to hold in the fetal curling, labor moans and throughput.  Having made it halfway home on the first bus, I retreated into the Fred Meyer across the street and inhabited their fine IBD-friendly establishment for an hour.

As it happened, my bus pass had expired without drawing the attention of any of the bus drivers to whom I'd flashed it over the last five days.  The Indian woman beside me was kind enough to point it out as I clamored like Igor off the bus in front of Freddy's.  I thanked her (I think, but I can't be sure) and proceeded to engage in the activities of the above paragraph.

How fortuitous that I was in a Freddy's, whereupon regaining an erected spine I was able to get an October bus pass and stock up on rice cakes!  And how propitious that H.B. is currently also stay-at-home-boyfriend and was able to come pick me up... for there was no way on this earth that I would have survived another twenty minute bus segment in such a state.  The immediate acquisition of oxycodone was imminent.

In conclusion, Adventure Food of the week was a bust, and I have deemed it a little too soon to be eating even the most benign of cooked veggies.  And am somewhat embittered.  But, for beets?  Totally worth it. 

My GI is out of town until the end of the month, and his nurses know about half (graciously) as much as I do about gastroenterology (which I think is unfair to me), so I am left to speculate this one for myself.  The weekly Throughput appears to prefer the weekends, and to occur in short-lived bouts of unprecedented agony.  The pain continues to focus on my central intestine below the ileum, which, again, is a new location.  New location implies that prednisone should have quelled this fresh inflammation by now.  Seeing as it hasn't, we've either got some seriously increased obstruction from old scar tissue going on or the prednisone is working and IBS is taking the opportunity to mobilize in response to the extreme deficiency of fiber (and variety) in my diet -- the latter, only to mess with me and make me think I'm not recovering when actually I might be.  We will hope for the latter.

Sunday, October 4, 2009

another step backward...

Tonight I made roasted chicken breast with beets (my adventure food of the week!) and onion (which I had to discard).  As soon as I put the dish in the oven, on came an attack quite similar to the one I had last weekend at Family Grill Night... only longer lasting, and more painful.

One major episode a week is fine.

One major episode a week when I'm eating as little as I'm eating while on three different kinds of intense medication is not okay.

What I love about roasting chicken is that it tastes perfect without any additional seasoning, which is great for me; the less rococo the better.  Even the safe seasonings like paprika and turmeric have their short-term risks, sadly.  Fortunately, oxycodone kicked in during the time my supper was roasting, and I was able to enjoy a small portion of it.  I can't explain how incredible roasted beet tasted after so long...

Fear of Sundays

For an animal physiologist -- that is, for someone who understands the importance of rest, recuperation and avoiding burn-out -- I have a very impractical fear of Sundays.

I have this compulsion about reserving free time, which I think stems from the intense anxiety that I nurtured through my undergraduate tenure.  Finding opportunities to recalibrate my blood pressure, gastrointestinal upset, mental condition, chakra, neural discombobulation, etc. was essential... and I always found them.  Always.

The charge of the Compulsion was to plan my schedule grossly overestimating the amount of time I might need to accomplish any given component of the agenda.  In this way, I accounted for Crohn's interference, scientific calamity and whatever other nebulous college surprises and set-backs emerged.  Having overestimated the time consumption of the surprises and set-backs, I was always left with a bit of time in the evenings and on Sundays.

The problem was that when I entered into those glorious and hard-won segments of freedom... I spent them either working ahead on something unnecessarily, or screwing around wasting the time completely in the process of looking for something to work ahead on unnecessarily (this was, of course, only if I was not playing frisbee or on whatever random adventure presented itself... I even learned to crochet a little bit because it got to the point where I couldn't watch an episode of House without getting fidgety...).

Yes, I know.

Although I like to think I'm a more healthy mind more recently, I have not been able to overcome the propensity for projects.  As previously posted, almost immediately after finishing the GRE I had a mini-manic episode over having not planned myself any de-briefing projects.  Consequently, here I am on a lazy Sunday fighting the primal urge to work ahead on my Movement Disorders Journal Club presentation... which is at the end of October.

Yes, I know.

The untenable Fear of Sundays expresses itself now in a more projectile fashion: my ever-menacing homunculus toils to convince me that if I indulge in rest now, I may become too fond of it to the point that addiction to slothfulness crashes my graduate school career.

Most of you will be shocked that I spent my day today watching the final episodes of Battlestar Gallactica and a documentary of George Westinghouse, thoroughly cleaning/re-organizing the bathrooms and kitchen, and slothing away on the couch with tea and AC/DC: The Savage Tale of the First Standards War.

No journal club presentation, no work-related science articles, no graduate school applications.  I even made H.B. do the grocery run (let it be known that I ran errands yesterday).  Today is about renewal.

Saturday, October 3, 2009

Food of the Day: Turmeric

In this lonely diet which now consists of rye bread, rice, beans, eggs, avocado, tuna/chicken and bouillon broth... I am cherishing my seasonings.

Today's Food of the Day is Turmeric, which is my favorite thing to do to white rice, and I believe I'm about to put it in my black bean tuna "salad" tonight!  This amazing Indian spice not only dehydrates leeches (sorry -- that one could not be avoided.  see 2:20 for applicable material.), but also sports a flavenoid that has been shown to inhibit several inflammatory responses.

Curcumin is the component of turmeric responsible for its yellow pigment, and for its anti-inflammatory properties; highlighted are Crohn's and IBD:
"The results indicate striking suppression of induced IBD colitis and changes in cytokine profiles, from the pro-inflammatory Th1 to the anti-inflammatory Th2 type. In human IBD, up to now, only one open study has achieved encouraging results. In this study, patients were given curcumin (360 mg/dose) 3 or 4 times/day for three months. Further, curcumin significantly reduced clinical relapse in patients with quiescent IBD. The inhibitory effects of curcumin on major inflammatory mechanisms like COX-2, LOX, TNF-alpha, IFN-gamma, NF-kappaB and its unrivalled safety profile suggest that it has bright prospects in the treatment of IBD. However, randomized controlled clinical investigations in large cohorts of patients are needed to fully evaluate the clinical potential of curcumin."(Hanai & Sugimoto 2009)
Binion et al 2008; Curcumin inhibits VEGF-mediated angiogenesis in human intestinal microvascular endothelial cells through COX-2 and MAPK inhibition
Zhang et al 2006; Curcumin inhibits trinitrobenzene sulphonic acid-induced colitis in rats by activation of peroxisome proliferator-activated receptor gamma
Deguchi et al 2005; Curcumin Prevents the Development of Dextran Sulfate Sodium (DSS)-Induced Experimental Colitis
This article by Laura Owens actually covers a considerable and well-referenced breadth.  Read it.
Did you know turmeric is part of the ginger family?  I didn't.  No wonder I like it so much.  Woody ginger...

Friday, October 2, 2009

Crohn's Genes

On Scottie's  Living with Crohn's Disease blog this morning, I came across the WebMD mention of a study from the September Proceedings of the National Academy of Sciences identifying a strong association between the expression of CD39 (a gene) and Crohn's disease.

There is always a genetic component to the development of disease.  Always.  The dangerous thing about flaunting these correlations, however, is that it isn't always made clear to people what is meant by "genetic link", science writing in mainstream media being what it is.

Contrary to what the populace typically assumes, what is usually meant by "genetic link" is not an inherited  DNA mutation causing a disorder.  Most often, when scientistific media reports "genetic link" they are actually talking about mRNA.  The critical difference here is that mRNA trascribes from DNA, making modifications as dictated by the dynamics of its cellular environment... such as an auto-immune disorder like Crohn's disease.

What I'm getting at here is that when you read about "genetic links" between genes and disease, keep in mind that they're talking about association, not cause.

Good.  Now that we've cleared that up...

The Friedman et al PNAS article (Sept. 2009) found that in people who have Crohn's, a genetic marker for "low CD39 production" was significantly more common than in people who don't have any kind of IBD.  Id est, a deficiency of CD39 mRNA is correlated with having Crohn's.

What I like about this study is that they also did the animals work, creating a knockout mouse model by silencing the expression of CD39.  They found that eliminating the expression of CD39 in the mice made them more susceptible to Dextran sodium sulfate, a chemical that mimics IBD pathophysiology.  It is very rare to see real-time translation between clinical and basic science studies, and I commend the authors for doing so.  I suppose that's why they're on the cover of the September '09 volume.

What I don't like about this study is that it is not open access, so I will have to wait to go back to work on Monday to get some quotes from the actual paper...

Thursday, October 1, 2009

Stripetti Squash Gnocchi

I used the leftover nuked stripetti squash tonight to experiment and make squash gnocchi...

with 3/4 a stripetti squash, three eggs, some flour and nutmeg.  
 which really ended up being more translatable to squash dumplings, as I used more egg and hence more flour than I needed. 
Give me a break -- after spending a significant portion of today with an analytical balance, I was not interested in measuring anything.  Suffice to say, H.B. was not a fan; I, however, loved them.
...with some no-sugar-added apple butter. 

What I learned: Squash is not potato.  It is, in fact, much stickier than potato and negates the use of my extra egg... which negates the use of the extra flour... making the product more dense.  Like gnocchi.  In my defense, this is the first "meal" I've ever concocted that H.B. hasn't liked...