June 13, 2006
Oh my god, that's me!
I was just picking up some lunch at the campus Union. Orientation is going on now for entering freshman, so it was more crowded than a usual Summer day. I happened to walk past the hall where they hold most of the orientation events and was a bit shocked to see myself up on the big screen at the far end of the hall. "Oh my god, that's me!"
A while back I was involved in the student health clinic's advisory committee. One of the directors asked if I would participate in a video the clinic was producing to show at orientation and highlight all of the services the clinic provides. They wanted to include some interviews with current students. I'd really come to appreciate the clinic's dedication to students and student involvement, so I happily said "yes" and showed up for the interview and just winged it.
Of course, I saw the video right after it was produced. It looked quite good. But I had one of those "that's what I look like?!" reactions to my portion of it. I was nervous during the interview and I tried to give thoughtful answers. What that came out looking like was that I was half asleep and a bit slow. Like I said, that was all a while ago, maybe two years, so I'd forgotten about it. Well, the video is still in rotation and "half asleep and a bit slow" looks even worse on a gigantic theatre screen.
Oh well, no Hollywood career for me...
May 17, 2006
Back to work...
After a lovely ten days in France, and a rewarding and energizing commencement ceremony, it's now time to get my writing done. It's been an amazing but crazy two weeks. The conference and vacation in France was amazing. Then, two days after my return I participated in the School of Public Health's commencement ceremony. They only have commencement once a year, so they allow students who will be finishing in the Summer to participate early. Most of my family were able to be there to see me hooded by my adviser. The celebration was very energizing and it was very rewarding to be able thank so many who have supported me. It does seem a little silly to have the ceremony before my actually graduation, but I feel focused now on the last remaining pieces.
I'll be posting some travel pictures of Normandy and Brittany in a few days.
January 17, 2006
Winter break pix
A few quick pix from Winter Break. We had a really nice Christmas spent visiting family and friends on the East Coast. Amidst our traveling, Ben and I made a quick trip into New York City. We did some tourist-y sight-seeing, like visiting the Christmas tree at Rockefeller Center.
Neither of us had been to an opera before and we thought seeing a performance at the Metropolitan Opera House would be a great New York experience. As fate would have it, our first taste of opera would be a light operetta -- something to get our feet wet, so to speak. The Metropolitan Opera was performing Johann Strauss' Die Fledermaus. A comedic story of drink, dance, frolic, and pranks.
Lincoln Center was beautiful. They had their own Christmas tree -- this one decorated with the shapes of various musical instruments.
The inside of the Opera House was very beautiful as well. There's a grant atrium decorated with crystal chandeliers and plush red fabrics. Here's the view from our seats. You can see there is a railing in front of each row of seats. Embedded in the railings are small display screens that show English subtitles for the performances (you are given the option of disabling the subtitles). Die Fledermaus was performed with the traditional German songs, but with English dialogue. I was at first surprised when the subtitles displayed during the dialogue as well as the songs, but that turned out to be useful since some of the singers/actors had thick accents.
Saving the best for last, we were delighted to be able to visit my sister and her husband and their new baby, Henry.
January 11, 2006
A little winter exercise...
I'm a little sore this morning. Got back on the bike for the first time since before winter break. But I wasn't riding, I was spinning. And I wasn't alone. It was me and Ben and 198 riders from the 2003 Tour de France.
Ben and I got a new bike trainer just before Christmas, since the old one bit the dust. At some point over the summer its fluid must have leaked out because when we set it up this winter there was no resistance--we were just spinning a hollow tube. The new one is much better and it is designed to handle the wider real wheel we have on our tandem. (The old one Ben had to jury-rig with some stiff wire.)
Spinning on a tandem works out pretty well. We can both exercise at the same time, like when we get home from work, or one of us can exercise alone. Ben did some solo spinning over the weekend when I was away, so I'm sure he's not as sore as I am this morning.
But what really makes spinning fun--or at least more enjoyable--is keeping your mind engaged during the workout. We're not interested in training videos, and most of what's on television won't cut it either. Last year we started buying DVDs of old cycling races and those are perfect. The races keep us engaged and motivated and set the right pace.
This year for Christmas, Ben gave me the awesome 12-hour 6-disc set of the 2003 Tour de France. (By the way, the DVD producer, World Cycling Productions, has its home right here in St. Paul, Minnesota.) We popped it in for the first time last night. Ah, it's a classic, right? The chases, the crashes, the suspense. It was great to see big Jan Ulrich in the Team Bianchi colors, now-defunct teams like ONCE, and Tyler Hamilton riding for the Danish CSC team. We just finished the Prologue--bad luck for David Millar whose chain slipped off and cost him the win--and the 1st stage that saw a horrific crash in sight of the finish line, one that broke Hamilton's collar bone and portended a wild and woolly Tour.
I can't wait to get back on the bike and see what happens next...
Category "PhD Process"
Category "Public Health"
Category "Science and Policy"
December 2, 2005
Outbreaks, Dissertation work, and Sprouts
An e-mail newsletter in my Inbox today contained links to two stories. The first story described a recent study by the Center for Science in the Public Interest concluding that produce contributed to more illnesses than poultry, eggs, and other animal products. CSPI studied reports of food-related outbreaks and noted the implicated foods that were the source of the disease-causing organisms.
This report comes at a very influential time in the food safety arena and it raises exactly the questions I am tackling in my dissertation work. There's a great interest in these types of attribution studies that seek to learn where foodborne illness cases are coming from. What types of foods are contributing most to the burden of disease?
But what we really want to know isn't just "what" but also "how" and "where." How are these foods becoming contaminated? Where in the food production, transportation, and preparation steps is this contamination occurring?
In outbreak investigations, the point of contamination can sometimes be difficult to discern. Produce may have been contaminated in preparation, often cross-contaminated from other foods in the kitchen. But there are increasing numbers of multi-state outbreaks where cases crop up in multiple places at about the same time. In these instances, it seems most likely that the implicated food was contaminated on the farm or during processing or shipping. This is where our ability to conduct trace-back investigations is key to solving the mystery of exactly where and how, and, hopefully, preventing similar contamination in the future. CSPI is lobbying for better record-keeping and ID tagging of foods to help in these efforts.
Another difficulty is lack of data. This study looked at outbreaks that had both an identified pathogen -- the bacteria, virus, toxin, or parasite was recovered -- and an identified source -- there was conclusive evidence that pointed to a food. But what about the unknown and unidentified? What about the people who become ill and never see a doctor and don't get tested? We don't have great data on the food side, either -- especially produce where no routine testing is done.
My work is to identify the first two of Sec. Donald Rumsfeld's information trilogy -- the known knowns, the known unknowns, and the unknown unknowns -- and give an account of where our knowledge lies in attributing Salmonella cases to foods at the point of production. [Secretary Rumsfeld got a lot of ribbing after that news briefing, but I've found his words very useful in my work and explaining my work to others!]
The other story in that e-mail relates more to a personal joke than the actual news item. The story is about a recent Salmonella outbreak in Ontario from mung bean sprouts. There have been several Salmonella outbreaks from various types of sprouts in the past decade or so. One of the difficulties in preventing these outbreaks is that Salmonella can contaminate the sprout seed itself, as well as during the growing phase.
The joke here is that I'd heard extensive accounts of these sprout-associated outbreaks from one of my major professors, Dr. Craig Hedberg. We'd worked closely on several food safety projects when I first arrived at the U of M. One time when we were on our way to a meeting off campus, we stopped for lunch at a little sandwich shop. I ordered the veggie special but told them to "hold the sprouts." Craig's eyebrow shot up, he gave a wry smile and said, "Don't do that on my account." I gave a snort and replied that if not on his account -- foodborne disease expert, veteran outbreak investigator -- than whose? And I'm not the only one. Our entire department, it seems, is sprout averse from Craig's stories. So, you see why I smiled when I saw that headline today. Craig is now over in Paris for a year, working with French officials on improving their foodborne disease surveillance. I have to wonder if he's sitting in a little French café at this moment, regaling his company with similar stories.
Category "Around town"
November 9, 2005
Wednesday squirrel blogging
You've heard of Friday cat blogging. Well, after a long day of cleaning up statistical programming code, I thought I'd take a break and do a bit of frivolous blogging.
This is a picture I took last month -- the result of me trying to take a quick snap of a new visitor to our backyard. Saint Paul is the only place I've lived where I've seen white squirrels. I don't know if they are true albinos or just white, but there are at least two areas where you see them. One is in the Como area and by the U of M's St. Paul Campus, the other is in Highland and Macalester-Groveland area. (As an aside, there are more St. Paul neighborhood maps here.)
In addition to the pleasure of spotting one in my neighborhood, the squirrels are kind of interesting from a genetic standpoint. There must be a high enough prevalence of the "white" gene circulating around in the squirrel populations in these neighborhoods to keep that trait from dying out. I wonder if there are any other traits conferred along with the whiteness.
Anyway, right after I took this picture, a black squirrel and grey squirrel swooped in and shooed the white squirrel away. It's too bad I couldn't get a picture of all three. I hope it comes back to visit!
Category "Cool web stuff"
Category "PhD Process"
October 28, 2005
Mind maps and Gantt Charts
|A simple example of a FreeMind mind map|
My thesis project is shifting into high gear now--hurray! But all the ideas that keep popping up, and all the leads I want to chase down, are in serious danger of being lost. I need a place to collect all the various aspects of my work, but in a way that the information is readily accessible, easy to organize, and will give me the ability to see the whole project at once, but also to focus in on a particular point.
The answer to all of this, I believe, is FreeMind. FreeMind is free (open source) concept mapping software that allows you to construct mind maps -- diagrams that depict the aspects of a topic as nodes, and the interrelatedness of the nodes with branches (called "edges") and arrows. Mind maps have a central topic node, with all other nodes radiating out from it. (Note: FreeMind isn't strictly in the Tony Buzan sense of Mind Maps®, but the concept is similar.)
My husband has been using FreeMind for quite a while now and finds it very useful. He uses it to plan projects, to plan meetings, and even to take meeting notes. And we've used it quite a bit at home for planning trips--especially camping trips where there's a lot of gear to keep track of. But I've not really thought about using for my work until now.
FreeMind has recently launched a new version with lots of great features. You have more choices and control over how things look, can add internal and external (web page) links for easy jumping, add notes to any node, and there lots of choices for exporting and publishing your map. There are several HTML and XHTML options, including one with clickable links. I like the "export as Adobe PDF" option for sharing with my committee members. Printing out these maps can be unwieldy, though. I had to print one out recently and wound up printing it on multiple pages in Adobe Acrobat, then cutting and taping the pieces together.
But printing isn't really the point of it all for me anyway. The beauty of FreeMind is that you aren't constrained by a page style, or an outline format, or margins. I can open it up and just start adding things without immediately trying forcing things into a hierarchy. Then when I'm ready to group items, FreeMind makes it easy.
As an aside, when I was talking with my advisor about mind maps, he asked if they were similar to Gantt charts. That was a term I didn't know, so I did a little research. It turns out that I had seen many Gantt charts before without knowing what they were. Gantt charts are used primarily in creating project timelines, something else that might be useful to keep me on track and finishing on time. Perhaps I can use it to create a reverse calendar for my dissertation. If you're interested, there is also a free open source Gantt chart software called GanttProject. Check out their demo--it's pretty good.
Category "PhD Process"
Category "Scientific interpretation"
August 26, 2005
Daily affirmation: "Matrix algebra is my friend!"
Non-negative definite matrices are also called "positive semi-definite" matrices...
I've been reading a bit about matrix algebra lately. Notice I said reading and not learning. There's a lot in mathematics that I just don't grok. I definitely feel like a non-native speaker. I wonder if people who are really good in mathematics have trouble understanding other things - things that I may be fairly good at - and if they feel as completely disoriented as I do when I'm trying to understand terms like determinant, orthogonal, and classical adjoint.
The reason for this self-flagellation is not so much directly related to my dissertation, but to improve myself as a methodologist. You see, matrix algebra is the foundation for regression analysis. Regression is used a lot in epidemiology to predict associations between exposures and outcomes or diseases. My problem is that I have a growing concern that methods like regression are misused - that they are applied in the wrong instances and leave the epidemiologist with a false confidence in the results.
So, I'm going back and reviewing regression from scratch. I'm reading a new book by David Freedman, a well-known statistics professor at UC Berkeley, and someone whom I've heard to be critical of how certain statistical tools are used in practice. I was heartened to read in the book's preface:
Much of the discussion [in this book] is organized around published studies... Some may find the tone of the discussion too skeptical. If you are among them, I would make an unusual request: suspend belief until you finish reading the book. (Suspension of disbelief is all too easily obtained, but that is a topic for another day.) [Emphasis added]
I'm looking forward to reading what he has to say. For now, it's back to
If G is non-negative definite rather than positive definite, that is, x'Gx = 0 for some x ≠ 0, then G is not invertible...
July 19, 2005
The joys of a tandem
The '05 Cannondale (we have an '03). Isn't it beautiful?
My husband and I were out for a long ride on Saturday. It had been awhile since we had been able to get out on our tandem, and I was looking forward to working off some nervous jitters before a big conference presentation I had on Sunday. It was super hot and even though we had water with us, it still feels like I drank a gallon and a half when we got back home.
After recovering, I was able to reflect on the joys of riding on a tandem:
· Conversing is easy -- the other person is only a few inches away.
· The more powerful rider never gets too far ahead; the less powerful one never falls too far behind.
· Wow appeal! I love people's positive reaction to the relatively rare sight of a tandem. And kids love us! (Minor adoration is still adoration...)
· Steady on up the hills. Hills are tough, but with two people cranking you get a pretty steady momentum up the hill. Even if one person momentarily falters, that steady momentum keeps you on track and helps you recover.
· Speed demon down the hills. Thanks to the laws of physics, our doubled mass on a single machine means increased velocity down those hills. We can really get flying!
Other things I've learned:
› You really have to communicate with your partner. Shifting your weight, coasting, getting out of the saddle - all those things you do on your solo bike without thinking need to be communicated so the other can prepare.
› You know someone is a tandem rider when they use the term solo bike. I'd never heard of this term until I became a tandem owner. Now I use it all the time.
› The person in front is called the captain; the person in back is called the stoker.
› I'm the stoker because I'm much less experienced than my husband. If I had a dollar for every time someone quipped to me, "So, do you sit back there and relax while he does all the work?", I'd be able to afford our dream tandem. Okay, that's an exaggeration. But my husband and I weigh about the same, so if I don't work, we don't go anywhere -- period.
› Tandems, like solo bikes, come in different styles for different uses. When we were first thinking about getting a tandem, we rented one at a state park we were visiting and took it for a spin. I think it was a Schwinn cruiser -- big tires, big saddles, upright position, and heavy frame. By the end of two hours I was beat and thinking a tandem wasn't a great idea. When we got home, we test-drove some light-weight road tandems -- huge difference!
› If you're interested in learning more, one of the best books we've found is The Tandem Book by Angel Rodriguez and Carla Black.
June 17, 2005
Hennepin Canal Trail, Central Illinois
My husband and I have had great success in finding ways to do some exploring on our bicycle as we travel to visit family and friends. This past weekend we were in Davenport, Iowa, for a lovely family visit and also happened to discover a great piece of history.
The Hennepin Canal was designed to link barge traffic between the Illinois River and the Rock River which flows into the Mississippi at Rock Island, Illinois. But by the time construction was completed in 1907, seventeen years after building began and thirty-six years after Congress authorized survey funding, the Canal had "missed the boat" in terms of commerce innovation since by then the rail system was well established and a cheaper way to ship goods. By the 1930s, the Canal was mainly used by recreational boats.
Luckily for us, one person's expensive commercial disappointment is another person's fabulously beautiful and serene biking, hiking, and horseback-riding trail. The entire 155 miles from Bureau Junction/Hennepin in the East to Colona in the West is now the Hennepin Canal Parkway State Park.
We biked from the western end at Colona to Geneseo and back, about 24 miles round trip. For much of the way you are riding on the old towpath right next to the canal. It reminded us both of an old European tree-lined boulevard. I'd only seen canals in BBC television mysteries like Inspector Morse, never in person, so it was a totally new experience for me. We saw lots of birds and sunbathing turtles, plus a few people fishing and some scouts out for a hike. But for the most part we were quite alone. Many of the original locks are still there and some have been refurbished. Here's an old lift bridge the trail crosses over near one of the locks.
The biking was good and quite easy since it's very level. One thing we found odd was the recommendation to use mountain bikes instead of road bikes on the trail because of the surface. But the surface was quite good for our part -- a tar base layer with small rocks a crushed rocks on top. The was a short dirt section of 100 yards or so through a wildlife preservation area, but the dirt was very firm so no problem there. There were nice toilet facilities at major access points along the way and information for finding food and other services in the larger towns we passed.
Check out this best website for the trail to see more pictures, maps, elevation charts, and more.
Category "Hiking n' Camping"
May 15, 2005
California central coast trip
Our vacation along California's Route 1 highway was a beautiful tour of sea, sand, coastal wildlife, and very twisty roads. By camping our way up the coast from San Luis Obispo to San Francisco, we had access to some of California's best beaches and parks on the cheap. This is definitely a "must see" experience!
This was the view from our solo camp site at Monta�a de Oro State Park, near San Luis Obispo. By far the best view we've experienced in our long years of camping.
Dining with a view... We've got this sunset all to ourselves. Interested? You can reserve it online (it's the Deer Flats site)
MdO also had amazing tide pools, easily accessible from their coastal trail.
Our drive up the coast was gorgeous... and hair-raising. Hwy 1 up to Big Sur gives new meaning to those yellow "caution: winding roads" road signs.
Monterey Bay is a spectacular and special place. We saw lots of marine life on our whale watch tour, including a huge pack of Risso's dolphins.
Lots of wildlife, big and small. This voracious snail was part of a large group that emerged after a long rain to snack on the lovely garden in the Mission San Luis Obispo de Toloso.