Bugs & Genes, Mice & Poop, Worms & Shrooms: 24 Take-Aways from the Microbiome Symposium

Loving the Microbiome Symposium

This time of year seems to be nonstop conferences, symposiums, presentations, meetings, and chats. I’ve been trying to catch up with the Storify collections for all of the ones I’ve been attending or lurking in recently. The Microbiome Symposium was a HUGE one!

In case you didn’t know, I’m fascinated by the microbiome, and have been for years. I’ve been tracking research about it, playing with personal microbiome testing services, finagled my way into being the liaison librarian to the Host-Microbiome Initiative here on campus, and doing my level best to make myself a useful collaborator with them. This all gained me access to the day-long Microbiome Symposium sponsored by Cayman Chemistry, where a few of us live-tweeted. I want to take just a brief moment to talk about some of the highlights. But in case you don’t have time, here is the number one most important critical thing to remember (the rest are in no particular order):

NUMBER ONE: Eat fiber. Lots of fiber. Many kinds.

2. What we don’t know about the microbiome is how all the species interact.

3. Microbes are sort of little factories that make all sorts of chemicals, drugs and poisons (which aren’t regulated by the FDA).

4. Liver and bile are way more important than we expected. To the gut. Yeah, really.

5. Nutrients from food are not one-size-fits-all. What you get out of your food is tailored by your microbiome.

6. The reverse is also true! What you eat tailors your microbiome!

7. What we don’t know about the microbiome is how it interacts with the rest of what our body does, say, for example, exercise.

8. We might be able to predict different diseases by watching changes to our microbiome, like cancer and diabetes.

9. If we can spot predictive changes early enough, we might be able to head them off by changing diet.

10. Most of the bacteria that show colon cancer seem to come via the mouth. So brush your teeth!

11. Don’t eat fiber? Changes your microbiome. Degrades mucosa. Erodes protection from mucus, first line defense. Triggers inflammation. OOPS!

12. It’s complicated.

13. Complexity is important. Eat the rainbow.

14. Fiber is IMPORTANT. Especially eating a diversity of fiber. Try counting how many different plants are in your meals.

15. A diet poor in what make the bacteria happy (fiber, a.k.a. microbiota-accessible carbohydrates, a.k.a. MACs) has immediate impacts on them, long term impacts on us.

16. Diet is a tool to engineer (program) our bodies to meet our goals. What are your goals? Optimize yourself, your health, and your mood, with food!

17. Break the chain, it stays broken. (Once you kill off the diversity of bacteria in your body through poor diet, they don’t tend to come back.)

18. How do you get a diversity of bugs in your gut again? Fecal transplants.

19. Avoid antibiotics whenever possible. but especially early in life.

20. Bugs I want to remember: FLVR = Faecalibacterium prausnitzii, Lachnospira multipara, Veillonella parvula, Rothia mucilaginosa.

21. High fiber diets help protect against allergies, and allergens, and asthma.

22. High fiber diets help protect against different types of gut pain.

23. About probiotics: Dead bacteria don’t work. They have to be live, the kind you keep in the fridge.

24. This isn’t regulated territory yet, the FDA has little sway. Be cautious about product claims.

Now, those were the official take aways, but there were some deeply intrigued nuggets in the hallways conversations and posters as well. There was a lot of unofficial buzz around fungus, and worms (helminth therapy). Things to watch for in the future. Here’s the Storify, if you want to dig into this more deeply.

And in the meantime, I found ANOTHER Storify from a symposium that focused on microbiomics, so here’s that (from Cell Symposia as #CSMicrobiome) as a bonus.

“Nothing in this world is indifferent to us:” Technology and Ethics through the Words of the Pope

20-09-2015 Incontro Giovani

With the visit of Pope Francis to the United States, I thought it might be interesting and pertinent to explore emerging technologies in the context of the official teachings of the Roman Catholic Church. I self-describe my religion on Facebook as Zen Pagan Catholic (which makes for some interesting conversations from time to time), and primarily practice as a Catholic, but I have a deep fondness for many other faiths as well (Quaker! Judaism! More!) and like to look at ideas and concepts in a broad ethical framework. This is just a small ‘deep dive’ into an area where a global leader in ethics touches on the impacts and ethics surrounding emerging and existing technologies. There are many such, and many ways to explore this.

I thought the image opening this post was a real treasure illustrating how current technologies, services, and memes (selfies? Instagram?) are being adopted by or associated with even institutions as ancient as the Catholic Church. This image, and most of the images used in this post, are from the Flickr stream of the Vatican itself. That says something right there about the adoption and use of social media and new communication technologies by the Vatican and the Papacy.

Earlier this year, Pope Francis released his encyclical Laudato Si’, subtitled “On Care for our Common Home.” It made a lot of buzz, and you’ve probably already heard about it. I immediately started scanning the Italian version, and as soon as I could find the English translation on the Vatican website, I downloaded the PDF. Very quickly I realized that throughout the document there are an enormous number of mentions of technology, its strengths and weaknesses. I was, shall we say, surprised? I wanted to blog about it then, but I think this is actually a better time.

Pope Francis begins Laudato Si’ with establishing the context for it in earlier works of church doctrine, specifically referencing a presentation to the FAO by Pope Paul VI back in 1970 and another from the the Greek Orthodox Patriarch Bartholomew in 2012. Back in 1970, Pope Paul had adopted use of television and the existing technology structure of the times for carrying the message. I was surprised again to learn how many videos are in Youtube of his travels that year: departing from Rome, Hong Kong, Philippines, Syndney (Australia), and more. So, this image from the Vatican of Pope Francis in front of film cameras might be very similar to views that would have existed of Pope Paul VI.

24-09-2015 Visita al Congresso degli Stati Uniti d'America

Pope Francis cites one specific portion of Pope Paul’s words on the risks and importance of technology, but there are some great nuggets in the rest of the speech as well.


“But the carrying out of these technical possibilities at an accelerated pace is not accomplished without dangerous repercussions on the balance of our natural surroundings. The progressive deterioration of that which has generally come to be called the environment, risks provoking a veritable ecological catastrophe. Already we see the pollution of the air we breathe, the water we drink. We see the pollution of rivers, lakes, even oceans – to the point of inspiring fear of a true «biological death» in the near future, if energetic measures are not immediately and courageously taken and rigorously put into practice. It is a formidable prospect which you must diligently explore in order to save from destruction the fruit of millions of years of natural and human selection. In brief, everything is bound up together.”

“Will the prodigious progressive mastery of plant, animal and human life and the discovery of even the secrets of matter lead to anti-matter and to the explosion of death? In this decisive moment of its history, humanity hesitates, uncertain before fear and hope. Who still does not see this? The most extraordinary scientific progress, the most astounding technical feats and the most amazing economic growth, unless accompanied by authentic moral and social progress, will in the long run go against man.”

“We must repeat this today: the Church, on her part, in every domain of human action encourages scientific and technical progress, but always claiming respect for the inviolable rights of the human person whose primary guarantors are the public authorities.”

“One of the best assured invariable principles of your action is that the finest technical achievements and the greatest economic progress cannot effect by themselves the development of a people. However necessary they may be, planning and money are not enough. Their indispensable contribution, like that of the technology which they sponsor, would be sterile were it not made fruitful by men’s confidence and their progressive conviction that they can little by little get away from their miserable condition through work made possible with means at their disposal.”

The words and thoughts are so powerful and so relevant today, that I find it almost hard to believe they were spoken roughly 45 years ago. The really critical part is “unless accompanied by authentic moral and social progress.” I don’t care what religion you are, or aren’t, that much should seem like common sense: that technological discovery unbounded by ethics is a risk to all. Isn’t that the story behind an overwhelming number of science fiction stories and novels? Take a technology, just one, and see how it could go wrong. Then try taking two, or three. And then just imagine everything we are discovering now, all of it. It is frankly astonishing that we persist, and it speaks well of us that we do. That we haven’t destroyed ourselves yet, despite so many close calls, is hopeful. How long can we ride this rollercoaster and keep from flinging ourselves off?

That’s the introduction. Now, what does Pope Francis say to expand on these earlier thoughts from Pope Paul VI? He mentions technology at least 95 times in the encyclical. NINETY-FIVE TIMES in six chapters, with the preponderance of them in Chapter Three: “The Human Roots of the Ecological Crisis”, for which the first section is titled, “Technology: Creativity and Power.” Whoa. Frankly, technology, while a significant presence in the document, is only a small part of it. Here is a visualization of the major themes in Laudato Si’. You can find “technology” at the tip of the far left lobe of the leaf.

Laudato Si 2

When he does mention technology, sometimes it is to point out technologies of concern, or philosophies of concern, and other times it is to point out technologies that are desperately needed, or which need to be more widely available. This document is the opposite of a Luddite point of view, instead carefully and judiciously framing the conversation around technology in the context of where is it helpful for the world and humanity, as compared to when is it simply being developed out of curiosity, laziness, or for its own sake. Obviously, Pope Francis argues clearly and strongly for a sane, humane philosophy of technological development and access, within the overarching vision of stewardship and responsibility. Because the document as a whole focuses on ecology, it is often assumed that this is all that’s in it. Pope Francis takes it farther, talking about technology in the service of equity and social justice, medicine, transportation, artistry, welfare, and others, attempting to show through that diversity how a single challenge connects throughout the entirety of human life and how we touch and connect throughout the entirety of the context in which we exist, the world.

At least, that’s the way I’m reading the document. I’ve selected just a few examples (24), a few snippets, phrases and sentences that seem illustrative to me. There is much that was relevant to the questions and concerns raised, written in beautiful language, that is perhaps not explicitly focused on technology. Much of what he says on other topics echoes strongly the debates in healthcare from the empowered patient movement, the flipped clinic conversations, and other initiatives designed on making healthcare more responsive and patient-centric. Where he talks about economics and lifestyle choices, it echoes the need for patient choice, and placing clinical guidelines and recommendations within the context of the patient’s goals and priorities for their own life. Pope Francis places a strong emphasis on collaborative and shared decisionmaking. I have made a conscious effort to not select the non-technological quotes for this post, but I sincerely hope that these few tidbits below might inspire you to look more deeply into this exceptionally lovely, deeply thoughtful, and eloquent essay.

Festival of families in Philadelphia Festival of families in Philadelphia



“I urgently appeal, then, for a new dialogue about how we are shaping the future of our planet. … Obstructionist attitudes, even on the part of believers, can range from denial of the problem to indifference, nonchalant resignation or blind confidence in technical solutions. We require a new and universal solidarity. … All of us can cooperate as instruments of God for the care of creation, each according to his or her own culture, experience, involvements and talents.”


“Technology, which, linked to business interests, is presented as the only way of solving these problems, in fact proves incapable of seeing the mysterious network of relations between things and so sometimes solves one problem only to create others.”


“[T]heir disappearance will have to be compensated for by yet other techniques which may well prove harmful.”


“We must be grateful for the praiseworthy efforts being made by scientists and engineers dedicated to finding solutions to man-made problems. But a sober look at our world shows that the degree of human intervention, often in the service of business interests and consumerism, is actually making our earth less rich and beautiful, ever more limited and grey, even as technological advances and consumer goods continue to abound limitlessly. We seem to think that we can substitute an irreplaceable and irretrievable beauty with something which we have created ourselves.”


“The social dimensions of global change include the effects of technological innovations on employment, social exclusion, an inequitable distribution and consumption of energy and other services, social breakdown, increased violence and a rise in new forms of social aggression, drug trafficking, growing drug use by young people, and the loss of identity.”


“Furthermore, when media and the digital world become omnipresent, their influence can stop people from learning how to live wisely, to think deeply and to love generously. In this context, the great sages of the past run the risk of going unheard amid the noise and distractions of an information overload. Efforts need to be made to help these media become sources of new cultural progress for humanity and not a threat to our deepest riches.”


“Today’s media do enable us to communicate and to share our knowledge and affections. Yet at times they also shield us from direct contact with the pain, the fears and the joys of others and the complexity of their personal experiences.”


“It is remarkable how weak international political responses have been. The failure of global summits on the environment make it plain that our politics are subject to technology and finance. There are too many special interests, and economic interests easily end up trumping the common good and manipulating information so that their own plans will not be affected. … The alliance between the economy and technology ends up sidelining anything unrelated to its immediate interests.”


“In some countries, there are positive examples of environmental improvement: rivers, polluted for decades, have been cleaned up; native woodlands have been restored; landscapes have been beautified thanks to environmental renewal projects; beautiful buildings have been erected; advances have been made in the production of non-polluting energy and in the improvement of public transportation.”


“Finally, we need to acknowledge that different approaches and lines of thought have emerged regarding this situation and its possible solutions. At one extreme, we find those who doggedly uphold the myth of progress and tell us that ecological problems will solve themselves simply with the application of new technology and without any need for ethical considerations or deep change. At the other extreme are those who view men and women and all their interventions as no more than a threat, jeopardizing the global ecosystem, and consequently the presence of human beings on the planet should be reduced and all forms of intervention prohibited. Viable future scenarios will have to be generated between these extremes, since there is no one path to a solution.”


“The basic problem goes even deeper: it is the way that humanity has taken up technology and its development according to an undifferentiated and one-dimensional paradigm.”


“We have to accept that technological products are not neutral, for they create a framework which ends up conditioning lifestyles and shaping social possibilities along the lines dictated by the interests of certain powerful groups. Decisions which may seem purely instrumental are in reality decisions about the kind of society we want to build.”


“A science which would offer solutions to the great issues would necessarily have to take into account the data generated by other fields of knowledge, including philosophy and social ethics; but this is a difficult habit to acquire today. Nor are there genuine ethical horizons to which one can appeal. Life gradually becomes a surrender to situations conditioned by technology, itself viewed as the principal key to the meaning of existence.”


“Yet we can once more broaden our vision. We have the freedom needed to limit and direct technology; we can put it at the service of another type of progress, one which is healthier, more human, more social, more integral. Liberation from the dominant technocratic paradigm does in fact happen sometimes, for example, when cooperatives of small producers adopt less polluting means of production, and opt for a non-consumerist model of life, recreation and community. Or when technology is directed primarily to resolving people’s concrete problems, truly helping them live with more dignity and less suffering. Or indeed when the desire to create and contemplate beauty manages to overcome reductionism through a kind of salvation which occurs in beauty and in those who behold it. An authentic humanity, calling for a new synthesis, seems to dwell in the midst of our technological culture, almost unnoticed, like a mist seeping gently beneath a closed door. Will the promise last, in spite of everything, with all that is authentic rising up in stubborn resistance?”


“There is also the fact that people no longer seem to believe in a happy future; they no longer have blind trust in a better tomorrow based on the present state of the world and our technical abilities. … This is not to reject the possibilities which technology continues to offer us. But humanity has changed profoundly, and the accumulation of constant novelties exalts a superficiality which pulls us in one direction. It becomes difficult to pause and recover depth in life.”


“We were created with a vocation to work. The goal should not be that technological progress increasingly replace human work, for this would be detrimental to humanity. Work is a necessity, part of the meaning of life on this earth, a path to growth, human development and personal fulfillment.”


“It is difficult to make a general judgement about genetic modification (GM), whether vegetable or animal, medical or agricultural, since these vary greatly among themselves and call for specific considerations. The risks involved are not always due to the techniques used, but rather to their improper or excessive application.”


“Ecology, then, also involves protecting the cultural treasures of humanity in the broadest sense. More specifically, it calls for greater attention to local cultures when studying environmental problems, favouring a dialogue between scientific-technical language and the language of the people. Culture is more than what we have inherited from the past; it is also, and above all, a living, dynamic and participatory present reality, which cannot be excluded as we rethink the relationship between human beings and the environment.”


“Attempts to resolve all problems through uniform regulations or technical interventions can lead to overlooking the complexities of local problems which demand the active participation of all members of the community.”


“Merely technical solutions run the risk of addressing symptoms and not the more serious underlying problems. There is a need to respect the rights of peoples and cultures, and to appreciate that the development of a social group presupposes an historical process which takes place within a cultural context and demands the constant and active involvement of local people from within their proper culture. Nor can the notion of the quality of life be imposed from without, for quality of life must be understood within the world of symbols and customs proper to each human group.”


“Taking advantage of abundant solar energy will require the establishment of mechanisms and subsidies which allow developing countries access to technology transfer, technical assistance and financial resources, but in a way which respects their concrete situations, since ‘the compatibility of [infrastructures] with the context for which they have been designed is not always adequately assessed’.”


“This does not mean being opposed to any technological innovations which can bring about an improvement in the quality of life. But it does mean that profit cannot be the sole criterion to be taken into account, and that, when significant new information comes to light, a reassessment should be made, with the involvement of all interested parties. The outcome may be a decision not to proceed with a given project, to modify it or to consider alternative proposals.”


“Compulsive consumerism is one example of how the techno-economic paradigm affects individuals.”


“By learning to see and appreciate beauty, we learn to reject self-interested pragmatism. If someone has not learned to stop and admire something beautiful, we should not be surprised if he or she treats everything as an object to be used and abused without scruple. If we want to bring about deep change, we need to realize that certain mindsets really do influence our behaviour. Our efforts at education will be inadequate and ineffectual unless we strive to promote a new way of thinking about human beings, life, society and our relationship with nature. Otherwise, the paradigm of consumerism will continue to advance, with the help of the media and the highly effective workings of the market.”

“Most of us will experience a significant diagnostic error in our lifetime”

Today was the webcast for the official release of “Improving Diagnosis in Health Care: Resources to Facilitate Communication Between Patients and Clinicians September 22, 2015.” A distillation of the 8 recommendations includes a focus on improving diagnosis through:

1. Teamwork
2. Education
3. Technology
4. Workflow
5. Culture
6. Reporting
7. Payments
8. Research

There were an incredible number of excellent and insightful statements. I’m hoping later for a full transcript of the remarks! Meanwhile, here is a Storify of reactions to the webcast as it occurred, with what people watching captured as most important.

And the video shown at the end of the webcast.

Improving Diagnosis in Healthcare: https://www.youtube.com/watch?v=fStBWT6fa3E

Health Professions Education Day & Taubman Library Grand Opening

I just wanted to say how button-busting proud I am of last week’s Health Professions Education Day and the Grand (re)-Opening of our library. There was an enormous amount of content related to both, so I made them into two separate Storify. The #HPEDay collection includes a rich overview of the innovative and collaborative approach to health education across all seven of the University of Michigan schools and colleges (dentistry, kinesiology, medicine, nursing, pharmacy, public health, and social work), with rich visionary insights into professional ethics and leadership. Profound, and worth a slow deep exploration. The Taubman Health Sciences Library re-opening collection includes many images from tours of the new building which was designed to support these visions. Enjoy!

If you have specific questions, feel free to post them below, and perhaps they can trigger additional blogposts that go into more detail about specifics.

[Updated Sept22 to correct list of participating schools & colleges.]

“Send Silence Packing” at University of Michigan

Send Silence Packing #SendSilencePacking

Yesterday, I was walking towards the Diag at the heart of the University of Michigan’s Ann Arbor campus. I noticed some chalk drawings on the sidewalk, and took pictures. I noticed some carving on a treetrunk and took pictures.

And then I noticed all the backpacks. Everywhere. And all the students standing, bending, crouching to look at the backpacks more closely. I stopped. I bent over. I read the stories. Each backpack represents one person who died of suicide. Most of the backpacks have their story attached to it, with farewells from grieving loved ones. Some are the actual backpack the person used in their own student experience.

I walked around the collection of backpacks slowly. I snapped photos. I finished looking at one section of the backpacks and thought, WOW. Then I started walking again. And then I stopped again. Because it wasn’t just one section. The backpacks were everywhere. I kept looking, and watching, and taking pics, but did not even try to get pictures of ALL of the backpacks.

As I finally straightened up and was about to leave, I heard a woman’s voice behind me, saying "Hurry up. I don’t want to see this. I know, it’s probably a fact of life, but … " It was a woman who is probably my age, certainly past student age, but dressed like a student in tight leggings and a tshirt, with the arms of a light sweater tied around her shoulders. She and her companion sped up, almost sprinting past the display, her dyed-blonde ponytail bouncing in the sunlight of the beautiful day.

Read more from the Michigan Daily:

From the Arxiv (What Caught My Eye Last Week)

Quantifying the impact of weak, strong, and super ties in scientific careers
Alexander Michael Petersen
PDF: http://arxiv.org/pdf/1509.01804v1.pdf
Soundbite: “We find that super ties contribute to above-average productivity and a 17% citation increase per publication, thus identifying these partnerships – the analog of life partners – as a major factor in science career development.”

Do we need another coffee house? The amenity space and the evolution of neighborhoods
César A. Hidalgo, Elisa E. Castañer
PDF: http://arxiv.org/pdf/1509.02868v1.pdf
Soundbite: “Neighborhoods populated by amenities, such as restaurants, cafes, and libraries, are considered to be a key property of desirable cities. … Finally, we use the Amenity Space to build a recommender system that identifies the amenities that are missing in a neighborhood given its current pattern of specialization.”

Liberating language research from dogmas of the 20th century
Ramon Ferrer-i-Cancho, Carlos Gómez-Rodríguez
PDF: http://arxiv.org/pdf/1509.03295v1.pdf
Soundbite: ” Those tenets can be summarized as a belief in the existence of word order constraints that cannot be explained by evolutionary processes or requirements of performance or learning, and instead require either (a) heavy assumptions that compromise the parsimony of linguistic theory as a whole or (b) explanations based on internal constraints of obscure nature.”
Interesting: “We submitted our commentary to PNAS but it was rejected. We hope that the availability of our submission helps to liberate language research from dogmas of the 20th century”

Estimating Reproducibility in Genome-Wide Association Studies
Wei Jiang, Jing-Hao Xue, Weichuan Yu
PDF: http://arxiv.org/pdf/1508.06715v1.pdf
Soundbite: “This can be used to generate a list of potentially true associations in the irreproducible findings for further scrutiny.”

Nucleosome positioning: resources and tools online
Vladimir B. Teif
PDF: http://arxiv.org/pdf/1508.06916v4.pdf
About: Gene Regulation Info
Includes: Nucleosome positioning datasets sorted by cell type

Combining exome and gene expression datasets in one graphical model of disease to empower the discovery of disease mechanisms
Aziz M. Mezlini, Fabio Fuligni, Adam Shlien, Anna Goldenberg
PDF: http://arxiv.org/pdf/1508.07527v1.pdf
Soundbite: “It is not unusual to observe a significant gene expression change in thousands of genes, the majority being a downstream, rather than the driver, effect (e.g. inflammation, drug response, etc) Additionally, and more importantly, there is a large heterogeneity in gene expression in cancer: many patients within the same subtype will appear to have an abberant expression. These variations are of unknown cause.”

Using Genetic Distance to Infer the Accuracy of Genomic Prediction
Marco Scutari, Ian Mackay, David Balding
PDF: http://arxiv.org/pdf/1509.00415v2.pdf
Soundbite: ” In human genetics, decay curves could be used study to what extent predictions are accurate and thus to improve the performance of medical diagnostics for the general population. In plant and animal breeding, on the other hand, it is common to incorporate distantly related individuals in selection programs to maintain a sufficient level of genetic variability.”

Population genomics of intrapatient HIV-1 evolution
Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Göran Bratt, Jan Albert, Richard A. Neher
PDF: http://arxiv.org/pdf/1509.02483v1.pdf
Soundbite: “In most patients, the virus populations was initially homogeneous and diversified over the years, as expected for an infection with a single or small number of similar founder viruses (Keele et al., 2008). In two patients, p3 and p10, the first sample displayed diversity consistent with the transmission of several variants from the same donor.”
Soundbite: “Our reasoning proceeds as follows. Figure 6B indicates that diversity accumulates over a time frame of 2-4 years, i.e., about 1,000 days. Recombination at a rate of 10−5/bp/day hits a genome on average every 100 bps in 1000 days. Mutations further apart than 100bps are hence often separated by recombination and retain little linkage consistent with the observed decay length in Figure 7.”

Inadequate experimental methods and erroneous epilepsy diagnostic criteria result in confounding acquired focal epilepsy with genetic absence epilepsy
Raimondo D’Ambrosio, Clifford L. Eastman, John W. Miller
PDF: http://arxiv.org/pdf/1509.01206v1.pdf
Soundbite: “Because the authors could not induce focal seizures by FPI, they ended up comparing absence epilepsy in their controls with absence epilepsy in FPI rats, and concluded that they look similar. They also used inappropriate epilepsy diagnostic criteria that cannot distinguish between focal non-convulsive seizures and genetic absence epilepsy. Moreover, the authors failed to consider all literature conflicting with their conclusion, and surmised similarities between the absence epilepsy in their rats with the focal seizures we induce by rpFPI.”

Reduction of Alzheimer’s disease beta-amyloid pathology in the absence of gut microbiota
T. Harach, N. Marungruang, N. Dutilleul, V. Cheatham, K. D. Mc Coy, J. J. Neher, M. Jucker, F. Fåk, T., Lasser, T. Bolmont
PDF: http://arxiv.org/pdf/1509.02273v1.pdf
Soundbite: “Our results indicate a microbial involvement in the development of Alzheimer’s disease pathology, and suggest that microbiota may contribute to the development of neurodegenerative diseases.”

Fractal Fluctuations in Human Walking: Comparison of Auditory and Visually Guided Stepping
Philippe Terrier
PDF: http://arxiv.org/pdf/1509.01913v1.pdf
Soundbite: “[B]ecause it can be assumed that AC and VC mobilize the same motor pathways, they can probably be used alternatively in gait rehabilitation. The efficiency of VC to enhance walking abilities in patients with neurological gait disorders needs further studies. However, the high gait variability induced by VC might have detrimental effects, for instance, a lower dynamic balance. This should be taken into account in the development of VC rehabilitation methods.”

The Brain Uses Reliability of Stimulus Information when Making Perceptual Decisions
Sebastian Bitzer, Stefan J. Kiebel
PDF: http://arxiv.org/pdf/1509.01972v1.pdf
Soundbite: “Our analysis suggests that the brain estimates the reliability of the stimulus on a short time scale of at most a few hundred milliseconds.”

Brain Model of Information Based Exchange
James Kozloski
PDF: http://arxiv.org/pdf/1509.02580v1.pdf
Coolness: IBM Neural Tissue Simulator (about NTS | NTS slides | 1st article)

Interplay between the local information based behavioral responses and the epidemic spreading in complex networks
Can Liu, Jia-Rong Xie, Han-Shuang Chen, Hai-Feng Zhang, Ming Tang
PDF: http://arxiv.org/pdf/1509.01321v1.pdf
Soundbite: “The spreading of an infectious disease can trigger human behavior responses to the disease, which in turn plays a crucial role on the spreading of epidemic…. Our finding indicates that, with the increasing of the response rate, the epidemic threshold is enhanced and the prevalence of epidemic is reduced.”

Identification and modeling of discoverers in online social systems
Matus Medo, Manuel S. Mariani, An Zeng, Yi-Cheng Zhang
PDF: http://arxiv.org/pdf/1509.01477v1.pdf
Soundbite: “We develop an analytical time-aware framework which shows that when individuals make choices — which item to buy, for example — in online social systems, a small fraction of them is consistently successful in discovering popular items long before they actually become popular. We argue that these users, whom we refer to as discoverers, are fundamentally different from the previously known opinion leaders, influentials, and innovators.”

Time-aware Analysis and Ranking of Lurkers in Social Networks
Andrea Tagarelli, Roberto Interdonato
PDF: http://arxiv.org/pdf/1509.02030v1.pdf
Soundbite: “Our goal in this work is to push forward research in lurker mining in a twofold manner: (i) to provide an in-depth analysis of temporal aspects that aims to unveil the behavior of lurkers and their relations with other users, and (ii) to enhance existing methods for ranking lurkers by integrating different time-aware properties concerning information-production and information-consumption actions.”

Since Katrina, Part Two: How Has Information Access Changed?

Sign: Closed Due to Hurricane Katrina

I mentioned yesterday that Hurricane Katrina changed my life in many ways. Well, my last name might be Swedish, but I’ve never really self-identified as Swedish. My cultural identity has come more from my mother’s side of the family, the Cajun side.

So when Katrina hit, I was riveted; when New Orleans was so damaged I was bereft. I couldn’t find out how the relatives were from the area (they were fine, but I didn’t know). I watched the newscasts almost constantly, for days, until I would shake while watching, couldn’t take it any longer, and felt ashamed that I couldn’t bear to watch. I did what I could from here. I donated money. I helped advertise and promote other Katrina response and recovery fundraising events. That was how I first became part of the A2B3 group which has been so influential in my keeping current about tech trends and tips around the local community and which has informed so many blogposts here. While I’ve been supporting persons with disabilities for most of my career, somehow I hadn’t completely mentally translated that over to the problems they face as individuals and communities in disaster and crisis response, so this (and 9/11) triggered a richer engagement in disaster and crisis preparation and planning, which is also heavily reflected in this blog. And that led to my interest in the SMEM and SMEMchat communities (SMEM = Social Media Emergency Management).

There was one story in particular which I remember vividly from those days which turned into a personal mission. The way I remember it is a little different from how it really happened, but both make good stories. First, the way I tell the story. Even though this isn’t the way it really happened, it could have been.

There was a library school student who was volunteering in the hurricane shelters. I always imagined this being something that happened in the Superdome. Among the evacuees who were not allowed to leave the shelters was a doctor. He was trying to help the other evacuees, but his phone (with his core clinical references) had died, battery had run out of power, and there was no way to recharge it. There were so many people he could help better if he just had a few key resources, but with the libraries under water, loss of power, and being in the shelter, he was dependent on what he remembered. Now, you have to keep in mind, this was two years before the Kindle e-book readers were available, the phones couldn’t hold much, and the batteries were even worse than they are now. What he needed was print, and how on earth was that going to happen?

The student was smart (after all, she WAS a library school student!), and had initiative, so she went and tracked down a listserv for medical librarians, and sent the doctor’s plea for books out to the list. Medical librarians all over the country grabbed books from their weeding piles, and hopped on Amazon to place special rush orders, and had them shipped to … the Dome, of course, right? Mail was delayed (duh). The books finally arrived the day the Superdome was evacuated, and never made it to the doctor. No one knows what actually happened to all those books.

Heartbreaking. Criminal! There has to be a BETTER WAY!! I’ve spent a lot, and I mean A LOT of time brainstorming better ways. I have a vision, a plan in mind, but that’s an entirely different post.

OK, now, what REALLY happened (yeah, I have a vivid imagination). [PS – I’ve been trying to verify this story for a decade, unsuccessfully, and JUST TODAY found the original email to prove it happened.]

Adelaide M. Fletcher: I am an LSU-SLIS student volunteering at a Red Cross Shelter and today I asked one of the Docs there if he needed any reference books. His face lit up and he told me he could really use the Merck Manual and any of the Washington Manuals for Medicine, Pediatrics or Surgery.

I’m sure the situation is similar for other shelters in the Baton Rouge area (there are several), and I would like to collect any of these books and distribute them if possible. If you have any (slightly out of date is okay) or know any medical librarians who would be willing to donate one, please send them to me and I will deliver them to shelters. I can’t speak for shelters outside of the Baton Rouge area, but if I get too many, I’ll try to pass them on through the Red Cross.[Source: MEDLIB-L September 2, 2005]

Adelaide gave her own personal address. People volunteered to send answers to reference questions and look things up. Concern was expressed that mail would be blocked, but then it was verified that her address was in the unscathed zone. The librarians contacted publishers and vendors suggesting they make donations. The books were presumably shipped there, and it is assumed that Adelaide distributed them across multiple shelters. No one ever mentioned the Superdome. No one verified Adelaide’s identity, they just trusted she was who she said she was. As it turns out, she got her MLIS, ended up working in medical libraries, and spent several years continuing the good work she began with this email, working on library recovery from Katrina. From there, she has done a lot of tech geekery in medical libraries, and from there working on community building projects (especially with tech). I already knew she was my kind of person. :) And this sure sounds like a happy ending to that part of the story.

But, what about the information resources? Those books and resources the doc wanted and couldn’t get his hands on? What he was asking for was basically textbooks.

The Merck Manual is now online free to the public from the publisher. Even if he had no phone or battery or computer, if anyone else did, they could look things up or call someone who could.

Merck Manual: http://www.merckmanuals.com/professional

The Washington Manuals are trickier. The Washington Manual of Medical Therapeutics is available online and also as an app for your phone. There is a “free” version for the phone which evidently is fairly limited, and then tries to sell you the full version for a goodly chunk of change.

Washington Manual of Medical Therapeutics with Unbound MEDLINE/PubMed (Free) https://itunes.apple.com/us/app/washington-manual-medical/id533185430?mt=8
Top in-app purchases:
The Washington Manual of Medical Therapeutics, 34th Edition ($74.99) https://itunes.apple.com/us/app/washington-manual-medical/id853052080?mt=8

There is also a copy in the Internet Archive which has over 10,000 views, although I’m not entirely certain that it is a legal or legitimate copy. Indeed, I suspect it isn’t. If that link goes dead, then you’ll know it wasn’t, eh? The official legal copy is this from Lippincott Williams and Wilkins which is available in print and online combined for the same price as the app.

Washington Manual of Medical Therapeutics https://www.lww.com/Product/9781451188516

Textbooks are absolutely critical in medical response to disaster and crisis. I’m glad to see that the ones he wanted are now more accessible, even if there still are barriers to access. I’m also glad to see that there are many MORE medical textbooks available online and as apps (I just wish there were more free ones for those times we really need them). Here are a few more (iOS) examples.

The 5-Minute Clinical Consult 2016
Anatomy and Physiology Made Incredibly Easy
CDC Health Information for International Travel 2014 – The Yellow Book
Davis’ Drug Guide
Infectious Disease Compendium, A Persiflager’s Guide
Lange CURRENT Practice Guidelines in Primary Care 2014
mobilePDR (Physicians’ Drug Reference)
Mosby’s Dental Drug Reference
Mosby’s Drug Reference
Oxford Handbook of Clinical Medicine
Taber’s Medical Dictionary
Tarascon Primary Care

There are a lot more, too. You could easily spend hundreds or thousands of dollars stuffing medical textbook apps into your phone or tablet. And the money is a barrier to having them widely available at the point of need when the need strikes. And these assume that the person reading them is a healthcare provider or student. Sometimes, in disasters, that isn’t the case. When that happens you need high quality accurate information that is right there. Ideally, it would be either something already installed or available where you can find it, or easy to get. I’ve been thinking Kindle’s have way better battery life than most phones, so when my mom died and I inherited her Kindle, I stuffed the extra one chock full of free info that I thought would be good for situations like Katrina. I also bought a solar charger and back up battery and cables. Yeah, call me paranoid, but I want info ready to hand.

But what about alternatives to textbooks, like, oh, I don’t know, journals and articles? “The percentage of open access (OA) articles published in biomedicine in 2005 was 27%,” said Matsubayashi et al in their article, Status of Open Access in the Biomedical Field in 2005. In 2012, that percentage was over half of all newly published articles, per Laakso & Björk. That was articles. The number of open access journal titles in 2005 was 1,988, according to Heather Morrison, who tracks these things and makes both her findings and her data open access as well. By 2013, there were 8,817.

Here are some more resources that weren’t available ten years ago but which we have now. If you can’t afford the medical textbooks, then first aid manuals are a great idea. And when you are thinking about what info you need to respond to trauma, military medical manuals could be a great boon. And we have them now. Most of them aren’t useful for the public, but look for the ones on survival techniques and medical topics.

Internet Archive: US Military Manual Collection https://archive.org/details/military-manuals?&sort=-downloads&page=2

For the most important and useful titles, people have put them in a variety of places online. This way if one goes down, there is a backup.

Special Forces Medical Handbook (2001): http://www.nh-tems.com/documents/Manuals/SOF_Medical_Handbook.pdf

Medical Field Manual (1942): http://www.ibiblio.org/hyperwar/USA/ref/FM/PDFs/FM8-5.pdf

Army First Aid Manual (2002): http://armypubs.army.mil/doctrine/DR_pubs/dr_a/pdf/fm4_25x11.pdf

The Army has made available free PDFs of a lot more of their medical manuals. A lot. Like over 50 other medical titles, everything from training to prevention to evacuation, with specialty manuals for dental, veterinary, radiology, and how to handle casualties, stress management. and much more.

U.S. Army: Doctrine and Training Publications, 8_Series_Collection (Medical): http://armypubs.army.mil/doctrine/8_Series_Collection_1.html

So, our information environment isn’t quite “there” yet, but you know, it is a lot better than it was ten years ago, and it is headed in the right direction.