Friday, June 29, 2018

Springer Flyer for Intermediate Physics for Medicine and Biology

Springer is the publisher of Intermediate Physics for Medicine and Biology, and they have their own webpage for our textbook. They do a decent job promoting the book, although they’ve never asked me to do a book signing and I haven’t seen Russ Hobbie on Oprah. They have a “Bookmetrix” page with some data about downloads.

Data for the number of downloads per year, for Intermediate Physics for Medicine and Biology.
The number of downloads per year for
Intermediate Physics for Medicine and Biology
(June 22, 2018).

The year was less than half over when I obtained this data. If downloads continue at their current rate, 2018 will be a record year. Thank you to all our wonderful readers!

The Springer IPMB website has a link where you can “Download Product Flyer.” I downloaded it, and it is a nice summary of the book. But I thought I could make it better. Below is my annotated version of Springer’s IPMB flyer (or click on the link for a pdf copy, or download it from Russ and my book website). Enjoy!

The annotated version of Springer's flyer about Intermediate Physics for Medicine and Biology

Friday, June 22, 2018

Frequency Locking of Meandering Spiral Waves in Cardiac Tissue

In Chapter 10 of Intermediate Physics for Medicine and Biology, Russ Hobbie and I discuss spiral waves of electrical activity in the heart.
The study of spiral waves in the heart is currently an active field .... They can lead to ventricular tachycardia, they can meander, much as a tornado does, and their breakup into a pattern resembling turbulence is a possible mechanism for the development of ventricular fibrillation.
Twenty years ago, I published a paper about meandering in Physical Review E.
Roth, B. J., 1998, Frequency locking of meandering spiral waves in cardiac tissue. Phys. Rev. E, 57:R3735-3738.
The influence of anisotropy on spiral waves meandering in a sheet of cardiac tissue is studied numerically. The FitzHugh-Nagumo model represents the tissue excitability, and the bidomain model characterizes the passive electrical properties. The anisotropy ratios in the intracellular and extracellular spaces are unequal. This condition does not induce meandering or destabilize spiral waves; however, it imposes fourfold symmetry onto the meander path and causes frequency locking of the rotation and meander frequencies when the meander path has nearly fourfold symmetry.
A meandering spiral wave
A spiral wave meandering in a sheet of cardiac tissue.
Above is a picture of a meandering spiral wave. Color indicates the transmembrane potential: purple is resting tissue and yellow is depolarized. The thin red band indicates where the transmembrane potential is half way between rest and depolarized. The red region, however, can be in one of two states. The outer red band (next to the deeper purple) is where the transmembrane potential is increasing (depolarizing) during the action potential upstroke, and the inner red band (next to the royal blue) is where the transmembrane potential is decreasing (repolarizing) during the refractory period. The point where the two red bands meet near the center of the tissue is called the phase singularity. There, you can’t tell if the transmembrane potential is increasing or decreasing (to learn more about phase singularities, try Homework Problem 44 in Chapter 10 of IPMB). The spiral wave rotates about the phase singularity, in this case counterclockwise.

One interesting feature about a rotating spiral wave is that its phase singularity sometimes moves around: it meanders. In the above picture, the meander path is white. Often this path looks like it was drawn while playing Spirograph. The motion consists of two parts, each with its own frequency: one corresponds to the rotation of the spiral wave and another creates the petals of the flower-like meander. All this was known long before I entered the field (see, for instance, Art Winfree’s lovely paper: “Varieties of spiral wave behavior: An experimentalist's approach to the theory of excitable media,” Chaos, Volume 1, Pages 303–334, 1991).

What I found in my 1998 paper was that the bidomain nature of cardiac tissue can entrain the two frequencies (force them to be the same, or lock them in to some simple integer ratio). In the bidomain model the intracellular and extracellular spaces are both anisotropic (the electrical resistance depends on direction), but the amount of anisotropy is different in the two spaces. The intracellular space is highly anisotropic and the extracellular space is less so. This property of unequal anisotropy ratios causes the two frequencies to adjust so that the meander path has four-fold symmetry.

My 2004 paper “Art Winfree and the Bidomain Model of Cardiac Tissue” tells the rest of the story (I quote from my original submission, available on ResearchGate, and not the inferior version ultimately published in the Journal of Theoretical Biology).
Most of the mail I get each day is junk, but occasionally, something arrives that has a major impact on my research. One day in June, 2001, I opened my mail to find a letter and preprint from a Canadian mathematician I had never heard of, named Victor LeBlanc. To my astonishment, Victor’s preprint contained analytical proofs specifying what conditions result in locking of the meander pattern to the underlying symmetry of the tissue, and what conditions lead to drift [another type of spiral wave meander]. These conclusions, which I had painstakingly deduced after countless hours of computer simulations, he could prove with paper and pencil. Plus, his analysis predicted many other cases of locking and drifting that I had not examined. I am not enough of a mathematician to understand the proofs, but I could appreciate the results well enough. I contacted Victor, and we tested his predictions using my computer program. The analytical and computational results were consistent in every case we tested. Ironically, Victor predicted that the meander path should have a two-fold symmetry, not the four-fold symmetry that originally motivated my study, and he was correct.... My last email correspondence with Art [Winfree], just a few months before he died, was about a joint paper Victor and I published, describing these results.
I will close with a photo that appeared in the 1997 Annual Report of the Whitaker Foundation, which funded my work on spiral wave meandering. Enjoy!

A picture of a spiral wave and Brad Roth from the 1997 Whitaker Foundation Annual Report.
A picture of a spiral wave and me from the 1997 Whitaker Foundation Annual Report.
Cover of the 1997 Whitaker Foundation Annual Report.
Cover of the 1997 Whitaker Foundation Annual Report.

Friday, June 15, 2018

Search Engine Optimization and Intermediate Physics for Medicine and Biology

Lately I’ve become fascinated by search engine optimization. My goal is to increase the visibility—and more specifically, the number of pageviews—of this blog. The gurus claim my pagerank will increase if I focus on well-chosen keywords or keyword phrases, so I selected the phrase Intermediate Physics for Medicine and Biology. I’m supposed to use my keyword phrase, Intermediate Physics for Medicine and Biology, often in each post, especially in the first paragraph. I’ve gotten into the habit of using the acronym IPMB for Intermediate Physics for Medicine and Biology, but now I realize this is killing my ranking! I'm a fan of good writing, and this repetition of Intermediate Physics for Medicine and Biology is annoying. So, dear readers, I will avoid repeating the phrase Intermediate Physics for Medicine and Biology too often.

Google helps you refine your selection of keywords. I typed Intermediate Physics for Medicine and Biology into the search bar and looked at the bottom of the page to see popular alternative keyword suggestions.

Google's alternative keywords when searchng for "Intermediate Physics for Medicine and Biology." The first suggestion adds the words "pdf free download"!
Popular alternative keywords related to the phrase Intermediate Physics for Medicine and Biology.

Oh my; people are being naughty. I don’t condone illegal downloading, but it’s nice to know somebody wants to read Intermediate Physics for Medicine and Biology.

Many searches are looking for Intermediate Physics for Medicine and Biology's solution manual. Russ Hobbie and I provide the solution manual only to instructors, and we try to keep it off the internet. I hope we have succeeded, but I’m not sure. It’s like trying to stop the tide from coming in. Instructors should forget about Google and just send Russ or me an email. We may require you to jump through hoops to prove you aren’t an imposter, but ultimately we’ll send you the solution manual.

What other strategies have I adopted for search engine optimization? I’ve started using the “description” box in the Blogger software (thank you Mr. Google for letting me use this wonderful software for free!). I’m using “alt text” for images, which helps readers interpret an image if they can’t see it (my real reason for using “alt text,” however, is to up my ranking). They say to compose identifying anchor text for your links, instead of writing “click here.” I now give descriptive names to picture files rather than calling them “picture1.jpg.” I also heard that putting your keyword phrase in bold, italics, and underlining helps: Intermediate Physics for Medicine and Biology. I even read that you should use your keyword phrase as a heading.

Intermediate Physics for Medicine and Biology

Search engines value hyperlinks, so I’m trying to increase the number of links to External links are best, but I can’t control them. I can control internal links from one blog post to another, which led to my April 13 creation of the Blog to IPMB Mapping, a shameless orgy of internal linking.

Blogger’s analytics software lets me monitor pageviews. I’ve become addicted to checking these statistics. A few weeks ago a burst of views originated from inside Russia. Someone there read almost every post in one night, binging on Intermediate Physics for Medicine and Biology. My most viewed post is an article about Frank Netter, Medical Illustrator. I don’t know why it’s so popular, but I suspect Google ranking has something to do with it.

Experts recommend repeating your keyword phrase near the end of the post, so I’ll leave you with these final words: Intermediate Physics for Medicine and Biology.

Friday, June 8, 2018

The Radium Girls

The Radium Girls: The Dark Story of America's Shining Women, by Kate Moore, superimposed on the cover of Intermediate Physics for Medicine and Biology
The Radium Girls:
The Dark Story of
America's Shining Women,
by Kate Moore.
I recently finished Kate Moore's The Radium Girls: The Dark Story of America’s Shining Women. I chose to read this book because of its relation to topics about radiation risk in Intermediate Physics for Medicine and Biology, but I soon discovered that it isn’t about medical physics. Rather, it focuses on the young women who suffered from occupational radiation exposure. After reviewing previous books about the radium girls, Moore writes:
As a storyteller and a non-academic, I was struck by the fact that the books focused on the legal and scientific aspects of the women’s story, and not on the compelling lives of the girls themselves. In fact, I soon discovered that no book existed that put the radium girls center stage and told the story from their perspective. The individual women who had fought and died for justice had been eclipsed by their historic achievements; they were now known only by the anonymous moniker of “the Radium Girls.” Their unique experiences—their losses and their loves; their triumphs and their terrors—had been forgotten, if ever charted in the first place.

I became determined to correct that omission.
The job of a radium girl was to paint luminous dials on clocks and instruments, so you could see them in the dark. They used a radioluminescent paint containing radioactive radium mixed with a scintillator such as zinc-sulfide. Most worked for either the United States Radium Corporation in Orange, New Jersey, or the Radium Dial Company in Ottawa, Illinois. Their supervisors taught them to make a fine point on their paint brush by putting it in their mouth, a process called lip-pointing. Each time they lip-pointed, they ingested a bit of radium.

Radium girls lip-pointing in a dial factory: "Lip, Dip, Paint."
Radium girls lip-pointing in a dial factory: “Lip, Dip, Paint.” From Wikipedia.
Moore examines the individual lives of these girls—many in their 20s, some in their teens—and explains their physical symptoms and health problems in excruciating detail. Don’t read the book if you’re squeamish; for instance, one of the first symptoms was a tooth ache, but when a dentist extracted the tooth a chunk of the jaw would come out too. Radium—an alpha emitter in the same column of the periodic table as calcium—is taken up by bones. With a half-life of 1600 years, it irradiates the bones throughout the girl’s life.

The heroes of this story are women like Grace Fryer and Catherine Donohue, who demanded justice for themselves and other victims. The villains are the leaders of the corporations. I had some sympathy for these companies at first, because the dangers from radiation were not well understood in the 1920s, so how could they know? But as time went by and the hazards became obvious, the executives denied the facts and covered up the risks. By the book’s end, these men personify evil.

Sometimes I get frustrated when people believe conspiracy theories and fairy tales about the danger from low levels of radiation, but The Radium Girls helps me understand why it happens. When people in authority ignore the risk to others for their own profit and then lie about it, they undermine trust, until no one believes even the most solid science.

If you are driving through Illinois on I-80, stop in Ottawa and see the statue of a dial painter. Moore describes its creation:
For a long time—too long—the legacy of the radium girls was recorded only in the law books and in scientific files. But in 2006, an eighth-grade Illinois student called Madeline Piller read a book on the dial-painters by Dr. Ross Mullner. “No monuments,” he wrote, “have ever been erected in their memory.”

Madeline was determined to change that. “They deserve to be remembered,” she said. “Their courage brought forth federal health standards. I want people to know [there] is a memorial to these brave women.”

When she began to champion her cause, she found that Ottawa, at last, was ready to honor its native heroines and their comrades-in-arms. The town held fish-fry fund-raisers and staged plays to secure the $80,000 needed. “The mayor was supportive,” said Len Grossman. “It was a complete turnaround. That was wonderful to see.”

On September 2, 2011, the bronze statue for the dial-painters was unveiled by the governor in Ottawa, Illinois. It is a statue of a young woman from the 1920’s, with a paintbrush in one hand and a tulip in the other, standing on a clock face. Her skirt swishes, as though at any moment she might step down from her time-ticking pedestal and come to life.
The blog Backyard Tourist has excellent photos of the statue.

The Radium Girls doesn’t explain much of the physics behind radiation exposure, but it does remind us why we study medical physics. For a history lesson, a case study in occupational safety, an inspirational story, and a great read, I recommend The Radium Girls.

The Radium Girls discusses radiation risks that are covered in Section 16.12 of Intermediate Physics for Medicine and BIology
The Radium Girls discusses radiation risk, a topic covered in Section 16.12 of
Intermediate Physics for Medicine and Biology.

A YouTube video of Kate Moore talking about her book The Radium Girls.

Friday, June 1, 2018

Sepulveda, Roth and Wikswo (1989): How to Write a Scientific Paper

In 1989, Nestor Sepulveda, John Wikswo and I published “Current Injection into a Two-Dimensional Anisotropic Bidomain” (Biophysical Journal, 55:987–999). Of my papers, this is one of my favorites.

When I teach my graduate Bioelectric Phenomena class here at Oakland University, we study the Sepulveda et al. (1989) article. The primary goal of the class is to introduce students to bioelectricity, but a secondary goal is to analyze how to write scientific papers. When we get to our paper, I let students learn the scientific content from the publication itself. Instead, I use class time to analyze scientific writing. The paper lends itself to this task: It is written well enough to serve as an example of technical writing, but it is written poorly enough to illustrate how writing can be improved. Critically tearing apart the writing of someone else’s paper in front of students would be rude, but because this writing is partly mine I don’t feel guilty.

Many readers of Intermediate Physics for Medicine and Biology will eventually write papers of their own, so in this post I share my analysis of scientific writing just as I present it in class. Students read “Current Injection into a Two-Dimensional Anisotropic Bidomain” in advance, and then during class we go through the writing page by page, and often line by line, using a powerpoint presentation that I have placed on the IPMB website. I use the “animation” feature of powerpoint so edits, revisions, and corrections can be considered one at a time. To see for yourself, download the powerpoint and click “slide show.” Then, start using the right arrow to analyze the paper.

The first page of a powerpoint to analyze the scientific writing in the paper Current Injection into a Two-Dimensional Anisotropic Bidomain, by Sepulveda, Roth and Wikswo
A screen shot of the first page of the powerpoint. It looks a mess, but the animation feature lets you consider all these suggestions one by one. You can download it and use it to teach your students.

When using this powerpoint, keep these points in mind:
  • One reason I use Sepulveda et al. (1989) as my example is that it has the classic format of a scientific paper: Introduction, Methods, Results, and Discussion. It also contains an Abstract, References, and other sections of a scientific publication. 
  • Often I highlight a sentence or two of text and ask students to revise and improve it. If you are leading a class using this powerpoint, stop and let the students struggle with the revision. Then compare their revised text to mine. The class should be interactive.
  • I have talked before in this blog about the importance of writing. In the powerpoint, I mention two publications that have helped me become a better writer. First is Strunk and White’s book Elements of Style. The powerpoint illustrates much of their advice—such as their famous admonition to “omit needless words”—with concrete examples. You can read Elements of Style online here. Second is N. David Mermin’s essay “What’s Wrong with These Equations” published in Physics Today (download it here). Mermin explains how to integrate math with prose, and introduces the “Good Samaritan Rule” (remind your reader what an equation is about when you refer to it, rather than just saying “Eq. 4”) and other concepts. 
  • Some of the points raised in my powerpoint are trivial, such as the difference between “there,” “their,” and “they’re.” Others are more substantial, such as sentence construction and clarity. I find it takes most of a 90 minute class to finish the whole thing. 
  • On the sixth page of the powerpoint I have a note reminding me to “Tell Story.” The story is one I wrote about in the original version of my paper “Art Winfree and the Bidomain Model of Cardiac Tissue.” “Nestor Sepulveda, a research assistant professor from Columbia who was working in John [Wikswo]'s lab, had written a finite element computer program that we modified to do bidomain calculations. One of the first simulations he performed was of the transmembrane potential induced in a two-dimensional sheet of cardiac tissue having 'unequal anisotropy ratios' (different degrees of anisotropy in the intracellular and extracellular spaces). Much to our surprise, Nestor found that when he stimulated the tissue through a small cathodal electrode, depolarization (a positive transmembrane potential) appeared under the electrode, but hyperpolarization (a negative transmembrane potential) appeared near the electrode along the fiber direction (Fig. 2). The depolarization was stronger in the direction perpendicular to the fibers, giving those voltage contour lines a shape that John named the ‘dogbone.’ Only Nestor understood the details of his finite element code, and I was a bit worried that his program might contain a bug that caused this weird result. So I quietly returned to my office and developed an entirely different numerical scheme, using Fourier transforms, to do the same calculation. Of course, I got the same result Nestor did (there was no bug). Although I didn’t realize it then, I would spend the next 15 years exploring the implications of Nestor’s result.” During class, I often take off on tangents telling old  “war stories” like this. I can’t help myself.
  • John Wikswo, my coauthor and PhD dissertation advisor, is still active, and he and I continue to collaborate. I learned much about scientific writing from him, but our writing styles are different and he might not agree with all the suggestions in the powerpoint. Tragically, Nestor Sepulveda has passed away; a great loss for bioelectricity research. I miss him.
  • If you are teaching and want to discuss how to write a scientific paper, feel free to use this powerpoint. I encourage you to download it and modify it to suit your needs. Students could even use it for self study, although they would not see some essential hand waving.
Although the powerpoint suggests many changes to the Sepulveda et al. (1989) paper, I nevertheless consider that article to be a success. According to Google Scholar, it has been cited 379 times. I believe it had an impact on the field of pacing and defibrillation of the heart. Overall, I am proud of the writing.

Let me close by emphasizing that writing is an art. Your style might not be the same as mine. Take my suggestions in the powerpoint as just that: suggestions. Yet, whether or not you agree with my suggestions, I believe your students will benefit by going through the process of revising a scientific paper. It’s the next best thing to assigning them to write their own paper. Enjoy!