A Virtual Personal Assistant for Researchers and Writers

In my never ending quest to be more organized and keep track of little snippets of information that might be useful, well…sometime…I came across a couple of helpful tools worthy of sharing.

First is Zotero. Great application, and easy enough even for determinedly non-techie types to learn. I was attracted to try Zotero by its pedigree—the project is produced by Center for History and New Media at George Mason University, and is funded by the Andrew W. Mellon Foundation, the Institute of Museum and Library Services, and the Alfred P. Sloan Foundation. They provide Zotero as a free program, which is installed onto Firefox. When you see a page you want to save while you are browsing, you can hit the friendly little Z icon. A screen will pop-up in the lower part of your open Firefox page, and you can take a snapshot of the page or just save the link. There are a number of very easy to follow screencast tutorials that illustrate different aspects of saving or searching, but much of Zotero is self-explanatory.

For me (and other OCD researchers, I suspect), one of the best parts of the Zotero program is that it automatically captures citation information from the web pages or papers. This tool is invaluable and would have saved me countless hours and angst when I was trying to verify all of my references for my book, Conducting Clinical Research, just prior to going to press.

Other great features of Zotero are that:
-You can save pretty much any type of article or file—newspaper clippings, images, pdfs, web pages, and word files. You can then link these to files or pdfs and tag them. Zotero’s search feature has jogged my memory accurately, thus far. I don’t know if that will change as I add a zillion more references, or if the program will choke; I suspect it is tougher than I am.

-You can make linked or standalone notes. I like to jot down “factoids” but sometimes have trouble remembering which articles they were associated with. Now I can more easily link the two together in an easily searchable database.

-You can readily mark up or annotate your pdfs for later reference.

-Rumor has it that you can integrate Zotero with word processing programs. I haven’t tried yet. Nor have I tried accessing my files in cyberspace.

-You can also work with Zotero off-line.

-Zotero is open-source, a goal worthy of support.

What’s not to like? Not much, so far.

-I don’t like the way it identifies folders, as you can’t tell what is in them readily.
-When it takes a snapshot of a page, I wish it would discard a lot of the images or advertising on a web page and save space, but it hasn’t learned that skill yet. Zotero stored my files in a peculiar path, which made backing up my files like a scavenger hunt at first.

I’m sure there are other features I’ll learn to love. If a little elf came with Zotero and would go back through all the other folders on my hard drive’s files and import them into Zotero, along with suitable tags, I would commit to Zotero for life.

Zotero is a great little program that should save considerable time and angst by helping to collect, manage, and accurately cite references in writing any type of article. It really is almost like having a personal research assistant, only a lot less expensive. Let me know what you think!

Comic Relief from Swine Flu

Funny Swine flu song from Putnam Pig! Welcome relief. . .but time to go back to work updating the Medpedia site. Care to join me in that task? Medpedia is an exciting new project, but the wiki will work better with input and discussion from others. Come and join the fun.

Swine Flu on Medpedia

After a hiatus from writing while working and traveling, I’m settling back in, prompted by the H1N1 (swine) flu outbreak. I’m honored to have been asked to work with Medpedia on providing information on this topic. I adapted some from CDC, WHO, CIDRAP, and others. Please check the Medpedia.com/Influenza A H1N1 site, which I will update regularly, trying to provide news and perspective on recommendations in a common sense way. Other physicians will also hopefully contribute to this great new medical wiki project. Please also e-mail me with questions you would like answered or leave a comment. Thanks!

FDA Approves a New Drug for the Annoyingly Cheerful

In one of the best satires I've seen since "That Was the Week That Was," the Women's Bioethics Blog called my attention to the FDA's approval of Pfizer's new drug, Despondex, to cure the Pollyannas among us.



I wonder how sales will compare to Viagra? Stay tuned...

Medpedia-A Valuable Health Wiki is Born

Eye on FDA, one of my favorite sources, brought Medpedia's launch to my attention today. Medpedia is a authoritative medical wiki powered by a collaboration between the medical schools of Harvard, Stanford, Michigan, and the University of California Berkely School of Public Health.

As a wiki, Medpedia will likely be fluid, uptodate, and interactive. It promises to provide a wealth of useful information about health and medically related topics. Check it out!

Farewell to Pharmalot...and Ed Silverman's Return

I was delighted to discover that Ed Silverman, of Pharmalot fame, will be blogging again. He can now be found occasionally on the InVivo blog.

It was nice, albeit sad, to see his farewell from Pharmalot.



While I wish I had discovered his blog earlier, I enjoyed reading it very much--his writing was often pointed, provocative, and perceptive...and always thought-provoking.

I wish Ed the best, and hope we'll hear from him regularly from his new home.

Algeferin Conquers Antibiotic Resistant Bacteria: Too Good to be True?

An intriguing report from Science News touts the discovery of algeferin, a chemical from sponges. Algerferin said to be able to reprogram antibiotic resistant bacteria to make them susceptible to antibiotics again. Preliminary tests against "superbugs" (such as MRSA) and biofilms are said to be very promising.

The potential for treating biofilms, clusters of bacteria that cause serious nosocomial (hospital acquired) infections by adhering to foreign devices, such as IV catheters, is quite intriguing, as such infections are particularly difficult to treat. Especially notable was the statement that biofilms "dissolved when treated with fragments of the algeferin molecule. And new biofilms did not form."

Thus far, algeferin has been tested against a variety of resistant organisms, including MRSA and Pseudomonas. That the chemical can restore bacterial susceptibility to antibiotics would be terrific, if it holds up. We are running out of effective antibiotics, which are often irresponsibly squandered (from bacterial resistance partly due to inappropriate use of these drugs for viral illness and in “animal growth” feed, for example). Resistant bacteria are also spread throughout hospitals and nursing homes by ineffective or sometimes irrational infection control policies, as well as by carelessness and increasingly harried staff.

The promise of algeferin is quite exciting...but based on the history of antibiotic development, misuse, and resistance, I have little doubt the bacteria will outsmart algeferin--or its prescribers-- too.

Nigerian Suit Against Pfizer Revived in U.S.

There is more to the Nigerian Trovan trial debate than has been mentioned in the Washington Post and similar articles. First, it is important to note that some illnesses are more common in developing countries—e.g., the “meningitis belt” in Africa, and thus studies need to be conducted in these settings, rather than in the U.S.

For example, in the 1996 meningococcal meningitis outbreak in Nigeria, ~12,000 children died over 6 months. (Three or four cases in a U.S. community would be considered an “outbreak.”) Pfizer’s study compared Ceftriaxone, given by intramuscular injections, to Trovafloxacin, given orally. Pfizer has been criticized regarding their informed consent documentation and IRB approval–not without justification, from the second-hand reports I’ve read, but…

What is rarely mentioned is that the survival rate was reportedly 94.4% Trovan vs. 93.8 Ceftriaxone. Nor is it widely known that Trovan was also being studied for meningitis in the US by well-respected pediatric infectious diseases specialists. The outcome in the US was clinical success in 79% of the Trovan patients vs. 81% in the Ceftriaxone group, and the longer-term sequelae showed no difference between the groups. (The Pediatric Infectious Disease Journal:Volume 21(1) January 2002, pp 14-22)

Nor is the value of developing oral treatments for infections generally discussed. Doctors Without Borders was treating other meningitis with intramuscular injections of Chloramphenicol—a wonderful drug that is now rarely used because it kills ~1/30,000 patients who receive it.

Multiple IM injections are painful, require sterile technique and more skilled health care workers than do oral medications. Supplies for injected drugs are more difficult and expensive to handle and administer, particularly in poorer, tropical countries.

Pfizer may not have not conducted this trial perfectly or with adequate informed consent—I don’t know, as I wasn’t there. But I do know the horror of watching young people die from meningococcal disease, and I do understand the rationale and goal of developing an oral drug for a devastating disease that episodically kills thousands of children. While I am often critical of this company, they deserve a fair trial.

Politics, One: Women, Zero

Last week, I was very buoyed by President Obama’s eloquent speeches and talk of rising above politics, particularly with his repealing the Global Gag rule. Today, I am sorely disappointed by Obama’s selling out to Republican conservatives, removing a provision in the proposed Economic Stimulus package that would have provided family planning coverage through Medicaid to more low-income women. This pandering to the right is at the expense of women’s health care needs and economic well-being.

The Religious Coalition for Reproductive Choice's president, Rev. Carlton Veazey, notes that a woman living in poverty is four times as likely to have an unintended pregnancy and five times as likely to have an unintended birth as a higher-income counterpart. Allowing more access to family planning services and contraceptives enables a woman to better choose when and how many children she might be able to support and nurture, and allows her to time pregnancies to enable her to become more educated or further advance herself. Denying these services is perpetuating the old efforts to keep the women barefoot and pregnant—and is in stark contrast to what is in the best interests of the women. Nor does it illustrate the promise of rational, evidence based decision-making.

The decision to cut family planning is short-sighted in other ways, too. Economically, a 2007 Congressional Budget Office report estimated that this Medicaid provision would save the government $200 million over five years by decreasing costs related to pregnancies and post-natal care.

Additionally, didn’t Obama say his goal was to reduce unwanted pregnancies and the need for abortions? This is an odd way of going about it.

With the tanking economy and sky-rocketing unemployment, women are facing loss of jobs, healthcare, or their housing. They should not have the added burden of facing unintended pregnancies through misogynist policies.

It is ironic that women’s needs got short shrift in an obvious attempt to curry favor and win Republican support for the economic package—even though those votes were not necessary for passage. How successful was this strategy? It garnered zero votes.

So, once again, the score is Politics, One: Women, Zero.

A Refreshing News Model-Rachel Maddow

I don’t watch much TV…but while surfing around before the election, I stumbled upon the Rachel Maddow show, and was immediately enthralled. I have continued to watch her show regularly and remain quite impressed. While the presentation is, on occasion, a bit too light for my taste, I love her wry and perceptive take on the news. This past week had two outstanding shows you can view via podcasts, or by getting transcripts.

First, there was Mon 12/15’s clips on the NSA’s warrantless wiretapping and the first interview granted by whistleblower Thomas Tamm. Her subsequent commentary on Bush’s reign was insightful and right-on target. She continued the week with commentaries on absurd aspects of the financial bailouts, environmental and foreign policies, among others. Monday’s show brought us a scathing analysis of the application and oversight of the $700 billion TARP loans, the double standards in access to financial help, and the lack of transparency:

“That‘s it actually. That‘s the whole two pages. That is the full application process for a piece of the $700 billion worth of our money that the government is doling out.

Have you ever applied for a loan for anything? House, car, small business, anything? Have you ever applied for public assistance, unemployment, food stamps welfare? If you haven‘t, I can tell you this, the application asks for more of a commitment than name, address, how much do you want, anything else we should know, love, Bilbo Baggins.

For regular humans—that‘s not what getting a loan is like. It‘s certainly not what getting welfare is like, which is why I‘m going to try to turn myself into a bank holding company. Then maybe we all should.”

The final event prompting this post was her frank admission and obvious remorse on Monday, when she confessed to having made an error in making a background check on her guest, economist Laura Tyson. When David Sirota called her attention to an overlooked conflict-of-interest that might well have tainted Tyson’s comments, Dr. Maddow promptly issued an apology, castigating herself in the process.

I had been immediately impressed by Rachel Maddow’s credentials—she is certainly no bimbo, unlike many of the young “reporters” who uncritically read scripts on some of the major news streams. Her bio notes that she holds a degree in public policy from Stanford University. At graduation she was awarded the John Gardner Public Service and Leadership Development Fellowship. She was then awarded a Rhodes Scholarship in 1995, and used it to study at Oxford University, where she received her doctorate. She has a long-standing passion for social justice issues, having previously focused on prison reform, HIV/AIDS, and Health Care Reform.

It has been a joy to watch a bright, highly-educated young woman anchoring a prominent show. This week’s candid admission of error greatly raised my esteem for Dr. Maddow, as it reflected an unusual level of integrity and humility. Rachel has earned a loyal follower here.

Thanksgiving continued...

On the related note…of charity and end-of-year gift giving:

Despite the hard times, many have a desire to continue their charitable efforts. In addition to the Neglected Tropical Diseases initiative, there are some other ways of stretching your charitable dollars.

The NYTimes Giving section and the related Ensuring That Gifts Go Where They’re Needed have tips in an article with a global perspective, as well as local needs. While not the most highly ranked, I still like Heifer's animal kits and Grameen because they are programs intended to be self-sustaining for the beneficiary. Another favorite is Kiva, which provides microcredit loans worldwide. For immediate direct help to others, my top picks include Feeding America (formerly America’s Second Harvest), Mazon, and the longstanding International Rescue Committee, which focuses on refugees.

For further information, check out Charity Navigator, which has extensive listings and ratings of charities. Another terrific source of info is Daniel Borochoff’s
American Institute of Philanthropy, with recommendations for a myriad of diverse interests.

With that, I’ll close with a reminder from one of my favorite books—remember,
"It Could Always be Worse."

Wishing you Happy Holidays and a better New Year.

Thanksgiving...

Ironically, Dr. Hotez’ new book, “Forgotten People, Forgotten Diseases” was part of my Thanksgiving fare this year, and served as an excellent reminder of all we do have to be thankful for in our economically more developed countries. Even now, with the rapid decline in our own country’s economic health and a pall on Christmas cheer, his book serves up a valuable dose of perspective.

Dr. Hotez skillfully introduces readers to an array of “neglected tropical diseases” which devastate the world’s poorest populations—2.7 billion of whom live on less than $2 per day. Because of their poverty, these people lack a voice and are largely ignored. Some of the diseases that affect them, such as worms, schistosomiasis, or filarial (elephantiasis) cause debilitating illnesses, are less dramatic and attention fetching than malaria and HIV/AIDS. Dr. Hotez calls much needed attention to a dozen of these diseases.

One of the striking things about this book is how clearly and simply Dr. Hotez explains these diseases and their impact. He also excels at helping readers to understand non-obvious links between poverty, parasitic infections, and HIV/AIDS. This book is therefore surprisingly appropriate for high-school to post-graduate levels of readers. It is an excellent primer, with numerous references for more detailed exploration. For example, Dr. Hotez explains how schistosomiasis, a water-transmitted worm, increases a person’s susceptibility to HIV infection. Anemia from the parasites can impair learning and subsequent income-earning ability. This book is an excellent primer, with numerous references for more detailed exploration.

Each chapter provides an overview of the organism, the illness it causes, and the social and economic impact of each of these illnesses. The accompanying photographs make a striking impression, and they, as well as the other helpful illustrations, have great visual impact.

I had the pleasure of hearing Dr. Hotez and a number of his colleagues speak two years ago at the Global Network for Neglected Tropical Diseases conference. One of the major conference themes, which was new to me although I am an infectious diseases physician, is that 7 major neglected tropical diseases could be eradicated for less than 50 cents per person/per year. Since learning that, I have incorporated some of this material about NTDs into my talks, and the slides for these are available at my site's links.

This book is clearly written and inspirational, and is a call to action. What are we waiting for?

OLPC's XO Makes History

Uruguay has just become the first country to begin widespread deployment of the revolutionary XO laptop to all of it's children. An inspiring personal story and moving pictures about the historical moment is recounted by Ivan Krstic, OLPC's brilliant director of security architecture, who was shipped off to Uruguay along with the first laptops, as a just in case trouble shooter. My congratulations to all at OLPC!

I hope other countries will join this move, as the laptop is incredible. Shame on Intel and Microsoft for trying to sabotage this nonprofit's venture!

I had the opportunity to try exploring the OLPC XO a bit last week and was extraordinarily impressed by some of it's features. The design is incredible--intelligent, attractive (an eye-catching kid magnet!) and extremely durable. Makes me ask why my other laptops don't have some of these features. The machine appears to be almost indestructible under normal use conditions--dust, dirt, pet hair, and liquid spills won't harm it. The carrying handle is an incredible plus I would love to have on my slick laptop. The ability to view the screen in bright sunlight is impressive. The machine will clearly be able to be repaired by most older kids and adults with 1 (supplied) screwdriver.

Yes, the XO software is slower than what I normally use. And yes, there are occasional software glitches, as with any new product. The difference, however, is that this is all open source and thus can be accessed and fixed by mere mortals. And soon there will be a large community of interested individuals who can readily support and teach each other.

One of the most impressive features is the mesh-networking, which allows the XOs to see others and link to them to work collaboratively on projects. This is ideal for a classroom, but also will be great for families or small group projects.

It is sad, though not surprising, that Intel and Microsoft have tried to undercut the OLPC XO and have thus far done so in Nigeria and Libya (see 11/24 Wall St Journal). The Classmate and Windows, priced temporarily at enticingly low prices, will not be able to be upgraded without considerable investment in support and software. In contrast, all the XO software is open source and can be down-loaded for free--and change as the child's needs do over years. That long-term view is where the real cost-savings are, as there will be no licensing issues or bait and switch tactics with the XO.

My initial motivation for supporting OLPC is that they are a worthy non-profit, with a very valuable project for educating kids in developing countries and reducing the global disparities between the haves and have-nots. Now after seeing the XO, I also see it as a valuable back up for my business/home needs as well. I have been encouraging my friends and colleagues to support the Give One, Get One program or to make charitable donations for children in developing countries. It is an irresistible gift for the holidays. Please help spread the word!

YouTube and Human Rights

“All power tends to corrupt; absolute power corrupts absolutely.”
Lord Acton

There is no question that Google has made my life easier, bringing me access to information from around the world that I would not have had otherwise. Unfortunately, there is a disturbing trend, as Google continues to expand its empire.

First, Google touted itself as “we are not evil.” But then there was its pragmatic support of censorship in some settings, abiding by government restrictions. Google justified this by accurately saying that their presence has benefit in the long-term.

Now, Google, who has since bought YouTube, has blocked the videos and account of Wael Abbas, an anti-torture activist who posted a video of policemen torturing a victim. Strictly speaking, YouTube’s action was correct, according to their terms of service, in that their Community Guideline's terms prohibit the posting of videos which depict pornography, illegal acts, graphic violence, or hate speech. Subsequently, however, they have now further isolated Wael Abbas by disabling his Yahoo account.

I understand YouTube’s not wanting to show graphic violence. Yet surely there is an alternative that would protect viewers from blundering onto a disturbing site, but would support important exposures of human rights violations. There could be a warning “Site contains graphic or disturbing material” notice, that allows news reports of violence. Or perhaps there could be a parallel site, such a Reporters Without Borders, or Project Censored. We need to have a readily available, uncensored forum to expose human rights violations, wherever they occur. Google should work for the forces of good, and make itself part of the solution, rather than gagging human rights activists.

Random Acts of Kindness-Another Bully Bites the Dust

In a heart-warming story, two students in Nova Scotia stood up against bullying.

In response to harassment of a fellow student for the grave sin of wearing a pink shirt, high school seniors David Shepherd and Travis Price encouraged others to wear pink as a sign of solidarity.

Reminds me of "Not in Our Town," a true story of how more than 10,000 people in Billing's Montana stood up to anti-semitism by placing menorahs in their windows.

Perhaps David and Travis could tour the US, with a first stop being in Jena, Louisiana to help the young blacks unjustly imprisoned after a response to a racist hate crime was blamed on them.

I wish them well, and hope they will keep up their good work!

Ouch! and a Clever Concept

I was reading the accounts of BioCryst's initial flu study failure with interest.

The study was a well-designed randomized, double-blind, placebo-controlled clinical trial designed to test whether peramivir, when administered intramuscularly during the acute infection, could reduce the duration of influenza symptoms.

Biocryst used elevated levels of a muscle enzyme, CPK, as a surrogate marker to show whether the patients had received intra-muscular injections, as was intended, as the levels of that enzyme rises with muscle injury. (Unfortunately, it can also rise if someone has severe fever or chills).

Analysis of the study results showed that while a single dose of peramivir did demonstrate improvement compared to placebo, the improvement was not statistically significant. On the other hand, for those patients who showed an elevation in CPK levels compared to their baseline, peramivir showed a dose-related improvement of 64.8 hours at the 300mg dose, and an improvement of 44.6 hours over placebo at the 150mg dose.

The most interesting discussion I read was "Size Does Matter" by Brian Orelli in the Motley Fool. I'm thinking that a 3" needle would be better for many of my patients...but that is another story. I'll be looking forward to seeing the results of further trials.

Athlete's Remembering Humble Roots

It was refreshing to read Michelle Singletary's column in the Washington Post today.

Several athletes are teaming up with major retailers to produce more reasonably priced branded shoes and clothing--Kevin Durant, of the Seattle SuperSonics, with Nike's sneakers, for example. Others include Sephon Marbury, of the New York Knicks, and Ben Wallace, of the Chicago Bulls, who are teaming up with retailer Steve & Barry's, as is the tennis star Venus Williams.

With luck, these new brands will be affordable for working families and may go a long way to help reduce the enormous and cruel peer pressure adolescents experience.

This is smart marketing--as well as the right thing to do--and looks like a win-win for all.

The Kite Runner Meets the Days of Awe

This past weekend I took a rare, hedonistic adventure, immersing myself in a novel for the first time in eons. The Kite Runner is richly detailed, engrossing, insightful and surprisingly, reminded me that these were the Days of Awe, the time of reflection between Rosh Hashanah, the Jewish New Year, and Yom Kippur, the Day of Atonement.

The themes are universal: regret, repentence, and redemption, though the Afghan/Muslim and Jewish cultures take somewhat disparate routes to get there.

There is ethnic cleansing, be it the Holocaust or the Taliban or myriads of culture wars before. And loss of one’s land and one’s identity, with the struggle to begin again. And then insights from the wise elder, who helps the protagonist understand identical events viewed both from the perspective of childhood and later with the wisdom that comes with age and experience.

And ultimately there is hope—from the courage of an individual, struggling with remorse and his understanding that there is 'a way to be good again.'

Imagine if “For you, a thousand times over” were to become the mantra of our world.

"Animals at Play" Renews the Spirit

For a touching story and photographs, I suggest visiting Dr. Stuart Brown's slide show on PBS' "Speaking of Faith." He expands on the playfulness demonstrated at his National Institute for Play site. Norbert Rosing's images of a wild polar bear and a sled dog are quite striking and the animal's expressions are unmistakable. Treat yourself. Take a minute to visit the site.

Who's Really to Blame-Anna Pou's Story Revisited

Anna Pou has now told her harrowing story of the horrific conditions she and other health care workers struggled in after Hurricane Katrina devastated New Orleans. After a two year ordeal, Dr. Pou was vindicated when a Louisiana grand jury justifiably refused to indict her last month for murder, despite the efforts of grandstanding Attorney General Foti.

For an insight into the previously untold aspects of the story, Newsweek has a compelling recounting.

I am relieved that Dr. Pou, a fine physician, has been exonerated and can go forward with her life and care for her patients, to whom she has been devoted. She had been unfairly subjected for two years to, in her words, “the most effective form of torture—the uncertainty and the waiting and waiting and having everybody take a shot at you.”

Unfortunately, the attention focused on Dr. Pou’s story has distracted from the real issues—the colossal, criminally bungled mismanagement of pre-hurricane flood control, and the post-hurricane relief effort, the abandonment of the hurricane victims, and the pattern of responses of this administration to our country’s most poor, sick, and vulnerable citizens.

The growing gap between the rich and poor were recently highlighted by another story as well. In this case, according to the Kansas City Star, Criste Reimer was blind, had cancer and weighed 75 pounds. Her husband Stanly kissed her and dropped her off a balcony, to her death.

"Mr. Reimer was desperate because he could not pay the bills for his uninsured wife's treatment for neurological problems and uterine cancer. Her medical bills ranged from $700 to $800 per week.”

And this was without the cost of nursing homes or home health aides, which readily cost in the $4000-6000 per month range, and therefore are out of the reach of most of the population.

The heinous crime here was not that Mr. Reimer killed his wife; it is that he was driven to do so out of desperation because of the lack of universal health care. And now, ironically, that sum will be paid by taxpayers to cover his incarceration.

The chilling message sent from the persecution of Dr. Pou and her nurse colleagues is that health care workers should run as fast as they can from future disasters. I doubt that I would have Dr. Pou's courage and selflessness...

In both of these examples, it is perhaps our government that should be on trial for its abysmal failures in planning and response to disasters, both natural and of its own making.