Below are the 20 most recent journal entries recorded in djohn89's LiveJournal:

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Saturday, May 31st, 2008
9:06 am	Intro to my journal This blog about my research in MRI, obesity, and being a graduate student. This entry has been dated in the future to make it visible to all visitors. (In fact it's dated when I plan to finish my PhD.) I hope it doesn't show up on Friends pages all the time. I warn you now: I often review dull papers and write about obscure topics. I don't have time for flashy graphics. Current Mood: anxious (5 Comments |Comment on this)
Saturday, March 11th, 2006
9:19 pm	Ice cream solves all problems Or this entry could be called "How I learned to stop worrying and start enjoying my research." Hey arasus, is this random enough for you? I spent hours searching for the perfect container -- my Holy Grail -- the box or cylinder I needed to make progress in my research. My requirements were simple; it had to be translucent, transparent, lightweight, MRI-compatible, water-tight, cheap and inert to MgCl2(aq). My plan was simple; I wanted to put 18 plastic vials (50 ml each) of various % fat/water emulsions into a big container of water. They couldn't be allowed to move around very much because that would screw up the MRI, and the MRI would only fit objects with a diameter under 250 mm. I was aiming for about 3 L of total volume. Finding such a container proved to be a real challenge when the chemistry dept glassware store was utterly unhelpful. I had to search five stores to find a container with all of those properties AND be the right size. The biggest show-stopper was the size of the cap/neck -- if the diameter was too small then there was no way to put my plastic vials inside. Most pouring bottles (lotions, cleaning supplies, vinegar, soda, alcohol) had too narrow of a cap because they were only intended to dispense their contents and be discarded. Canning supplies were always far too small. Bulk food stores tend to sell things in bags, so I was mostly searching regular grocery stores. The top candidates with good caps included windshield washer fluid bottles, pickle jars, tupperware storage containers, traditional flour jars, and ice cream containers. I got really sick of measuring these containers, especially when the curvature of the vessel ruined the chances of actually using it. The salespeople must have thought it was really weird to see a guy walking around with a ruler and holding containers up to a cardboard cut-out hexagon (of the minimum size of the base to fit all the plastic vials). I must have carefully measured at least 15 distinct containers. I finally found an acceptable ice cream tub and bought it. Yes, that's right -- 5 quarts (4.7 L) of Fudge Royale ice cream solved my problems. Mmmm... ice cream and obesity research is clearly a match made in heaven. Current Mood: creative (Comment on this)
Wednesday, February 8th, 2006
11:08 pm	Rats are good at "recycling" You haven't had the full grad student experience until, in desperation, you do this: you find black tape, black paper and a black trash bag for a backdrop. Then you use your lab's dilapidated 8 year old digital camera to take pictures of two rodents who are scrambling around, licking each other's rears, and copiously defecating. They also fight over their synthetic "rat bone," which is a composite of blue food coloring and rat chow. Finally you photoshop the images and put them into your conference powerpoint slides. That is the grad school experience. Current Mood: crushed (Comment on this)
Thursday, February 2nd, 2006
10:08 am	insane link between obesity and viruses Adipogenic potential of multiple human adenoviruses in vivo and in vitro in animals Leah D. Whigham,1 Barbara A. Israel,2 and Richard L. Atkinson1 http://ajpregu.physiology.org/cgi/content/full/290/1/R190 ABSTRACT Human adenovirus-36 (Ad-36) increases adiposity in chickens, mice, and nonhuman primates and is associated with human obesity. Ad-36 paradoxically reduces serum cholesterol and triglycerides in animal models. Ad-36 increases adipocyte differentiation and triglyceride accumulation in 3T3-L1 cells in vitro. This study evaluated whether three other human adenoviruses increase adiposity in chickens and in 3T3-L1 cells in vitro. We inoculated chickens with human Ad-2, Ad-31, Ad-37, or media at age 3 wk. Food intake and weights were recorded for 3.5 wk, and then chickens were killed and visceral fat, body composition, serum lipids, and viral antibody status were determined. Visceral fat and total body fat were significantly elevated (P < 0.001) in the Ad-37 group compared with all other groups. Final body weights were higher in chickens inoculated with Ad-37 compared with Ad-2, but not significantly higher than in control or Ad-31 groups. Food intake did not differ among groups. Serum cholesterol was elevated in Ad-37 chickens compared with control (P < 0.01) but was not affected by other viruses. Triglycerides were reduced in Ad-37 chickens (P < 0.0001) but were not affected by other viruses. In 3T3-L1 cells in vitro, Ad-31, Ad-36, and Ad-37, but not Ad-2, increased adipocyte differentiation and triglycerides accumulation. In summary, Ad-37 is another human adenovirus that increases adiposity and reduces serum triglycerides in an animal model. However, the response of serum cholesterol is opposite that of Ad-36. Evaluation of other human adenoviruses to determine their effects on adiposity and serum lipids is warranted, but in vitro assays may not be definitive for this purpose. Current Mood: confused (1 Comment |Comment on this)
Friday, December 30th, 2005
12:16 pm	No rest for the weary You'd be wrong to think that just because campus is closed this week that all grad students would get a break. No, we're actually pretty busy right now. Some of the first year grad students do go home, but a lot of us are too far from home to afford the plane flight, and all of us need to catch up on research and/or lab work. I've been meaning to review a paper, and another student pointed out that you can publish in Medical Image Analysis with next to zero innovation. So here we go, a completely unoriginal paper: Integrating segmentation methods from the Insight Toolkit into a visualization application Ken Martin, Luis Ibáñez, Lisa Avila, Sébastien Barré, Jon H. Kaspersen Medical Image Analysis. 9(6): 579-593. December, 2005 Abstract The Insight Toolkit (ITK) initiative from the National Library of Medicine has provided a suite of state-of-the-art segmentation and registration algorithms ideally suited to volume visualization and analysis. A volume visualization application that effectively utilizes these algorithms provides many benefits: it allows access to ITK functionality for non-programmers, it creates a vehicle for sharing and comparing segmentation techniques, and it serves as a visual debugger for algorithm developers. This paper describes the integration of image processing functionalities provided by the ITK into VolView, a visualization application for high performance volume rendering. A free version of this visualization application is publicly available and is available in the online version of this paper. The process for developing ITK plugins for VolView according to the publicly available API is described in detail, and an application of ITK VolView plugins to the segmentation of Abdominal Aortic Aneurysms (AAAs) is presented. The source code of the ITK plugins is also publicly available and it is included in the online version. Observations This was unoriginal because the authors just wrote a GUI for the functions in ITK. Admittedly ITK is pretty hard to use unless you know a lot of C++ STL, and even then you end up writing a new program for each thing you want to do. Their GUI does have value, but it is something more like what a company should be doing. Their abdominal aortic aneurysm segmentation was pretty simple when you consider they simply used the ITK built-in level sets and region growing filters. But this is exactly what ITK is meant to do, and it's certainly not a novel application. My conclusion: yes, you can publish in Medical Image Analysis with virtually no innovation. Perfect! Current Mood: busy (Comment on this)
Monday, November 21st, 2005
3:21 pm	NSAIDs for arasus So we talked about NSAIDs and other fun drugs once, and I'm writing this mostly to clear things up for myself. Nonsteroidal Anti-Inflammatory Drugs (NSAID) by chemical structure (blatently stolen text) Carboxylic Acid Groups Salicylates (Acetylsalicylate (Aspirin ), Choline salicylate, Diflunisal, Magnesium choline salicylate, Magnesium salicylate, Salsalate) Acetic Acids (Bendazac, Diclofenac, Etodolac, Indomethacin, Ketorolac, Nabumetone, Sulindac, Tolmetin) Propionic acids (Carprofen, Fenoprofen, Flurbiprofen, Ibuprofen (Advil ), Ketoprofen, Loxoprofen, Naproxen, Naproxen sodium, Oxaprozin, Vedaprofen) Anthranilic acids (Meclofenamic acid, Meclofenamate sodium, Tolfenamic acid) Phenylacetic acids Aminonicotinic acids (Flunixin) Indole Analogs (Indomethacin, Nabumetone, Ketorolac, Etodolac,) Enolic Acid Groups (which doesn't have carboxylic group but acid due to the enolic hydroxy substituent) Pyrazolones (Phenylbutazone, Oxyphenbutazone, Dipyrone, Ramifenazone) Oxicams (Meloxicam, Piroxicam, Tenoxicam) Sudafed (Pseudoephedrine hydrochloride) is not an NSAID   It is not far from Methamphetamine which is just missing a methyl group Current Mood: ignorant (Comment on this)
Monday, October 31st, 2005
2:43 pm	exercise reduces visc adipose tissue Title: Greater beneficial effects of visceral fat reduction compared with subcutaneous fat reduction on parameters of the metabolic syndrome: a study of weight reduction programmes in subjects with visceral and subcutaneous obesity. Author: Park, H S; Lee, K Appears In: Diabetic medicine : a journal of the British Diabetic Association. vol. 22, no. 3 (2005 Mar): 266-72. Journal Info: Abbreviation: Diabet Med. Journal Subset: IM.. Country of Publication: England. Abstract: AIMS: To evaluate the effect of weight reduction on parameters of the metabolic syndrome in obese patients according to their pattern of abdominal fat distribution. METHODS: A longitudinal intervention study, consisting of a 12-week weight reduction programme, including lifestyle modification and adjuvant appetite suppressant, in 38 subjects with visceral obesity and 47 subjects with subcutaneous obesity. Visceral, subcutaneous and total adipose tissue areas were determined by CT scan at the level of L4-L5. Parameters for components of the metabolic syndrome were measured before and after weight reduction. RESULTS: Reductions in body weight, BMI and subcutaneous adipose tissue area were greater in the subcutaneous than in the visceral obesity group. In contrast, changes in fasting plasma glucose, insulin, and HOMA score were higher in the visceral than in the subcutaneous obesity group. Changes in visceral adipose tissue area were significantly related to changes in fasting plasma glucose, triglycerides and HOMA score. CONCLUSIONS: Visceral fat reduction induced greater beneficial effects on parameters of the metabolic syndrome than subcutaneous fat reduction. Evaluation of changes in abdominal fat distribution is necessary when obese subjects enter a weight reduction programme. Commentary: This is a great paper.  If you skip to table 4, it shows a lot of correlation coeffients, and it's particularly interesting that insulin resistance (HOMA score) decreases when visceral fat decreases.  On the downside, the method they used to measure body fat mass was bioimpedence.  Also a negative -- they only did a single CT slice, which is known to mask variations in the fat distribution.  Think of the difference in shape of a small soccer ball and a football when they both have a similar cross section.  But the paper really redeems itself with this section: Free fatty acid (FFA) flux into the liver is increased in visceral obesity, leading to insulin resistance and increased production of very low density lipoprotein [25,26]. In our study, loss of visceral adipose tissue during weight reduction may have decreased FFA flux into the liver, leading to lower fasting plasma glucose, triglycerides and HOMA score. We found no significant correlation between changes in VAT or VSR and changes in blood pressure or HDL-cholesterol. It is not clear why these components of the metabolic syndrome were not changed by loss of visceral fat. This finding, however, agrees with previous studies showing no relation between changes in visceral fat mass and changes in blood pressure [27] or HDL-cholesterol [28]. Factor analysis also revealed that blood pressure is not closely linked with the other components of the metabolic syndrome [29,30]. In support of this notion, modification of diet alone was found to decrease blood pressure [31,32], whereas exercise, even without any change in body weight, increased HDL-cholesterol [33,34]. This is great!  If we're ever going to figure out the metabolic syndrome, we're going to have to eliminate some of the red herrings like blood pressure.  Also they showed that their caloric intake reduction drug wasn't helpful.  It was exercise that really helped these people.  Bottom line: Over and over again, exercise with a reasonable diet is the answer to obesity.  It's going to take years to convince all the clinicians of this. Current Mood: excited (Comment on this)
Thursday, October 6th, 2005
9:06 am	Dielectric constant for fat measurement D. Laaksonen, J. Nuutinen, T. Lahtinen, A. Rissanen, and L. K. Niskanen, "Changes in abdominal subcutaneous fat water content with rapid weight loss and long-term weight maintenance in abdominally obese men and women," International journal of obesity and related metabolic disorders : journal of the International Association for the Study of Obesity, vol. 27, no. 6, pp. 677-683, 2003. The amount of water in tissues varies with vascularization, and one theory is that obesity is correlated with decreased blood flow to adipose tissue, which makes it less responsive to hormonal signals (ie insulin).  There are two probes stuck into the patient at 1 cm deep to measure the impedance of the skin, and then they are put deeper (3 cm) to measure the impedance of the adipose tissue.  Consider the fat as a capacitor and blood vessels as a resistor in parallel.  By putting low current through at 300 MHz, the capacitance can be determined (presumably from the time constant, tau = R*C).  The hypothesis is that the resistance decreases with weight loss because there is more vascularization in the tissue. I think this is a rather poor measurement: subcutaneous fat is not the important fat depot, and these measurements are approximate at best due to changes in extracellular fluid volume.  Dietary sodium will change the water retention of cells, not to mention that the interstitial tissue was completely uncharacterized in this paper.  To sum it up: yes, you can make this measurement, and yes, you can show that it doesn't change much if you don't lose weight.  But it's a poor metric (clinically) and it's a poor measurement (numerically).  I wouldn't recommend buying one of those cheap "Body Fat Analyzer" machines because that measurement is even worse. Current Mood: uncomfortable with probes (Comment on this)
Wednesday, October 5th, 2005
9:52 am	Magnetic Resonance Spectroscopy for whole body fat composition B. Kunnecke, P. Verry, et al. "Quantitative body composition analysis in awake mice and rats by magnetic resonance relaxometry," Obesity Research, vol. 12, no. 10, pp. 1604-1615, 2004. Magnetic Resonance Spectroscopy can be used for whole body fat composition.  It's dead simple if you understand some MRI: this is just a T2-weighted multiecho experiment.  They put 700 mice into little plastic jars (with air holes) and put them each into the MRI and treated the jar as one voxel.  Basically the hydrogen signal from fat vs. water was differentiated by the slight difference in T2 (60 vs 50 ms, resp. according to my MRI textbook).  They made the measurements quantative by using meat phantoms: chicken breasts (low fat, high muscle) and bacon (high fat, low muscle).  Just imagine that big heap of uncooked bacon shoved in a plastic jar in the scanner. In summary: yes, you can make this measurement cheaply (quickly, < 2 min/mouse when MRI time usually costs $300/hour) but it doesn't tell you where the fat is coming from, and you can't tell how much other lipid signals are getting in (from bone, liver, etc).  So it gives a better measurement than bioelectrical impedance, but  I still don't like it.  The impressive part of this study is its sheer scale: 700 mice and 400 rats. I love Obesity Research; it is my favorite journal ever. Current Mood: blank (Comment on this)
Wednesday, September 14th, 2005
4:35 pm	Can't sleep because classes will eat me After taking 19-21 credit hours per semester for every undergrad semester, doing one semester with 3 grad classes and 3 undergrad, and taking classes out of order, I never had a problem with coursework. But now I think I might have finally overloaded my schedule. I'm taking EBME 431, EBME 403, and NTRN 452, and I'm TA for EBME 320/410. I also need to write a conference paper for SPIE Medical Imaging 2006. Of course I have my lab job doing computer admin stuff. I wouldn't really recommend anyone else to try this schedule, but I really need these classes for my research. NTRN 452 is already helping me to understand the diets that the rodents go on, and EBME 431 is great for learning MRI. I was told that I have to take EBME 403 because everyone has to take it, and I'm not so enthusiastic about it. Current Mood: determined (5 Comments |Comment on this)
Friday, August 19th, 2005
1:55 pm	IACUC fun I'm trying to obtain access to the animal housing facility (Wearn, aka the ARC). I must first be appended to an IACUC approved protocol. Running an animal study isn't so easy; see the rules summarized in the Ten Commandments. Specifically #4 (Mice may not re-enter Wearn after leaving) and #2 (None may enter the facility after contact with mice from outside Wearn that same day) are very strict. #4 implies that longitudinal studies (repeatedly imaging the animal over time) are impossible, and #2 implies that I'd just as well go home after I leave Wearn to do anything else useful (handle animals in other studies). All of these rules make sense, but together they make my research nearly impossible to conduct. I'm not sure how I will ever get any of the fun stuff done. I'm sure it's just as bad at other universities. The only real solution is to have animal housing inside the imaging facility (or vice versa). In the meantime I'll be filling out lots. of. paperwork. Current Mood: confused (Comment on this)
Monday, August 1st, 2005
3:49 pm	the funding process sucks Small Business Technology Transfer (STTR) Programs: up to $800k to commercialize your research. Sounds nice enough. Here are the forms to fill out. They take "40 hours" to fill out, which does not include time to develop your actual ideas, but rather just time spent generating mindless forms and formatting things. I spent almost two weeks on these forms, but it was my first time. Be prepared to have fun if you get audited! Current Mood: tired (Comment on this)
Tuesday, July 12th, 2005
2:10 pm	Voronoi diagrams are cool Don't take my word for it, try it here Voronoi Diagram and Delaunay Triangulation. This seems like a really cool way to segment images! (Comment on this)
Friday, July 1st, 2005
10:01 am	What part of SATA RAID 5 don't you understand? Having passed the qualifying exam, I have to move on to other projects. I have to price and implement a new Windows 2003 file server and domain controller for the lab. Everyone wants regular backups and high uptime. Of course, I thought that RAID would be an integral part of the solution. Even Dell sells SATA RAID controllers, and I would have a better job if we bought a prepackaged solution. Personally I want one of these. But no, I don't think it will happen because lab politics are in the way. We'll probably just get two computers with lots of independent 250 GiB drives in them, not even in a RAID, just running off of the on-board controllers. A nightly rsync script will copy files between the computers. I hate to think about the gnashing of teeth when the first hard drive fails. The fourth floor rennovations finished, so we moved back to the fourth floor. I'm in a cubicle now. I have rationalized this as motivation to graduate. More importantly I should really be doing more research, especially the type that would get funded. We acquired some good T1/T2 maps the other day, and I'm hopeful for writing a paper about it. Current Mood: disappointed (1 Comment |Comment on this)
Thursday, May 19th, 2005
1:19 pm	Date: Thu, 19 May 2005 10:36:32 -0400 Subject: FW: Qualifying exam results will be postponed MEMO To: All BME students taking the 2005 PhD qualifying exam cc: BME Faculty The grading and review of the qualifying exam results will be completed on June 6. This is one week later than originally intended, but my decision to postpone the review is based on the need for faculty to have adequate time to grade it fairly. I know that this prolongs your uncertainty of the results, and I apologize for the added delay. This probably means they changed the exam too much and everybody failed. (2 Comments |Comment on this)
Monday, May 9th, 2005
9:27 am	jerkmeter: an instrument for measuring jerk It is well known that the first derivative of position (symbol x) with respect to time is velocity (symbol v) and the second is acceleration (symbol a).  It is a little less well known that the third derivative, i.e. the rate of change of acceleration, is technically known as jerk (symbol j).  In the case of the Hubble space telescope, the engineers are said to have even gone as far as specifying limits on the magnitude of the fourth derivative.  There is no universally accepted name for the fourth derivative, i.e. the rate of change of jerk, The term jounce has been used but it has the drawback of using the same initial letter as jerk so it is not clear which symbol to use.  Another less serious suggestion is snap (symbol s), crackle (symbol c) and pop (symbol p) for the 4th, 5th and 6th derivatives respectively. So how do you get a jerkmeter? Sadly they are absent from eBay. Probably the best option is to buy/build an accelerometer and take the time derivative. I needed to design a pedometer (counts steps and estimates speed by the time interval between steps assuming a constant stride), so I planned to measure jerk (because you accelerate your foot up when you start a step and accelerate it down when you step). Mechanical pedometer are less reliable but cheaper to design (a step completes a circuit which increments a counter, and a spring reopens the switch in the circuit). All of this is being caused by studying for the qualifying exam. (Comment on this)
Thursday, April 7th, 2005
9:34 am	inevitable I need to return a book to my local library today, and their hours are usually inconvenient. I don't like fines, which are inevitable like taxes, which made me think about death. Here is a recent compilation of life expectancy of Americans by the CDC. Open their 2002 PDF and skip to page 3. Apparently I should expect to live ~56.1 additional years; alternatively, a white male should expect to live to 74.5 years. Having lived to my current age was 98.6% likely. Living to 80 is 45.5% likely. Here is some blatent plagiarism for the ladies: "The increase in life expectancy for females could have been greater were it not for the offsetting effect of increases in mortality from accidents, Alzheimer’s disease, pneumonia, perinatal conditions, and septicemia." And for the gents: "The increase in life expectancy for males could have been greater were it not for the offsetting increases in mortality from accidents, diabetes, septicemia, perinatal conditions, and Alzheimer's disease." I feel good about my research because: "For males, life expectancy increased primarily because of decreases in mortality from heart disease, homicide, cancer, cerebrovascular disease, and HIV disease." I should point out that the statistics do not control for ways that other people might kill me. That is so not fair to my death. I want statistics that remove accidents and murders so that my death is purely a function of my own effort or lack thereof. Current Mood: amused (Comment on this)
Monday, March 28th, 2005
4:25 pm	you can line up any two objects if they are blurred enough Multimodality image registration by maximization of mutual information Maes, F; Collignon, A; Vandermeulen, D; Marchal, G; Suetens, P IEEE transactions on medical imaging. 1997 Apr 16(2): 187-198. Abstract: A new approach to the problem of multimodality medical image registration is proposed, using a basic concept from information theory, mutual information (MI), or relative entropy, as a new matching criterion. The method presented in this paper applies MI to measure the statistical dependence or information redundancy between the image intensities of corresponding voxels in both images, which is assumed to be maximal if the images are geometrically aligned. Maximization of MI is a very general and powerful criterion, because no assumptions are made regarding the nature of this dependence and no limiting constraints are imposed on the image content of the modalities involved. The accuracy of the MI criterion is validated for rigid body registration of computed tomography (CT), magnetic resonance (MR), and photon emission tomography (PET) images by comparison with the stereotactic registration solution, while robustness is evaluated with respect to implementation issues, such as interpolation and optimization, and image content, including partial overlap and image degradation. Our results demonstrate that subvoxel accuracy with respect to the stereotactic reference solution can be achieved completely automatically and without any prior segmentation, feature extraction, or other preprocessing steps which makes this method very well suited for clinical applications. Observations: Maximization of mutual information seems like it might be a good idea because it is really hard to register two mice which vastly different in size. I need to make it non-rigid, which will really cost a lot of computational time. People tend to cut the resolution of the images and blur them a lot to make the computation more tractable. Current Mood: contemplative (Comment on this)
Wednesday, March 16th, 2005
12:40 pm	excellent website for fitness/weight lifting http://www.stumptuous.com/weights.html I ran across this website over spring break when I was trying to remember what my exercise work out sheet meant by a "front" shoulder press. I've been lifting weights for about a month now, and it's been going pretty well. This website is a must-read for anyone new to lifting weights. You could prevent yourself from getting injured at the very least. The diet stuff makes me want to revise some of my research plans. The website is highly amusing, and unlike most fitness-related websites and magazines, the author focuses on dispelling all the lies that advertisers tell people. Especially about toning muscles, buying products to slim down, how to do squats, and how body fat works. It's so refreshing to see someone get their facts straight for a change. I've had conversations with people who just don't know how their bodies work, and it's exceedingly pointless. I've not looked at it, but the author has a livejournal too: http://www.livejournal.com/~krustukles/ Current Mood: enthralled (1 Comment |Comment on this)
Monday, February 28th, 2005
12:13 pm	Awesome SI (metric) table! This graph rocks! http://ts.nist.gov/ts/htdocs/200/202/graphics/SI%20derived%20units.gif It's from this page. http://ts.nist.gov/ts/htdocs/200/202/pub814.htm I keep forgetting what a pascal is. Also, joules are confusing. But it's still better than customary units. I also forget the more esoteric Metric Prefixes occasionally: http://www.essex1.com/people/speer/large.html Like deka-. Who the heck uses a dekaliter (daL) of anything? Also, I love the fact that the mass of the earth is 5983 Yg (yottagrams). I could probably sell yottagrams as Valentine's candy or something. Current Mood: amused (2 Comments |Comment on this)