Category Archives: Research

Standards and Services and PRISMA, Oh My! Systematic Reviews at MLAnet16, Day One

First posted at the MLAnet16 blog: http://www.mlanet.org/blog/standards-and-services-and-prisma,-oh-my!-systematic-reviews-at-mlanet16,-day-one


Toronto Scenery

Wow, wow, wow! What an AMAZING day! I’m at the Medical Library Association Annual Meeting, and trying to get to as many of the systematic review events as I can. Today is the first full day of the conference, and it was a jackpot — PRISMA for searches, a session on EBM/EBHC training, and a session on systematic review services. Lots of posters, too, but I haven’t had a chance to go look at those yet.

I tweeted a screenshot of the special session on systematic reviews this afternoon.

Dean Giustini asked me what’s new, so let me get right to that.

PRISMA

I saw an event in the program, something about PRISMA standards, so I thought I’d poke my head in. When I poked my head back out later, I could not stop talking about it. The gist of it is that PRISMA, whom most medical librarians and journal editors know of as providing standards and guidelines for how systematic review data should be reported, are branching out. Me, I’ve been watching with excitement the various PRISMA extensions that have been being added recently. Thsee include standards for reporting protocols, meta-analyses, patient data, abstracts, and more. Well, it turns out there is a pretty substantial team working on developing PRISMA guidelines for reporting search strategies. This is pretty exciting for me! And somehow, I had missed it until today. The group today was opening the results from the original team to a broader audience and asking for reactions. They had come up with 123 guidelines, which they narrowed down to 53, and then we broke into four subgroups (search strategy, grey literature, documenting results, database characteristics) brainstorming about how to narrow down even further, into truly actionable points. I tell you, this is a group to watch.

Some of my favorite lines:

“I did this review according to PRISMA standards.” “You can’t. PRISMA is a ‘reporting’ standard, not a ‘doing.'” (Margaret Foster)

“The faculty are asking individual students to do something that is essentially a team sport.” (Ana Patricia Ayala)

“Cochrane says, ‘You will not limit by language.’ PRISMA says, ‘You will report any limits.'” (Margaret Sampson)

Here is just one of the flip boards from the conversation to whet the appetite of the systematic review methods nerds.

Priorities for Systematic Review Search Strategy Reporting

SYSTEMATIC REVIEW SERVICES

Later in the day, there was a complete session devoted to systematic review services in medical libraries. Yes, this is the same one from the tweet earlier in this post. I was dashing in late from the poster session, so I missed the beginning of the presentation on training needs by Catherine Boden and Hellsten. I was disappointed, because they were citing many wonderful articles I wanted to look into later. I’m sure glad the slides are in the online MLA system, because I’ll have to go find them! Being late also means I didn’t get any photos from their talk. The most provocative concept I pulled from their talk was the idea that systematic reviews are actually “a constellation of related methods rather than a single methodology.” So elegantly put, and so true. It’s a helpful way to reframe how we think about what we do, and is supported by the same drive that is motivating the various PRISMA extensions mentioned above.

MLAnet16 Systematic Review Services

Sarah Vistinini presented for her team on scoping reviews, their similarities to and differences from systematic reviews, and the value of being included in the ENTIRE process (which she cleverly described as giving a “better appreciation of all the moving parts.”). Sarah showed some very cool evidence mapping (see pic above), dot prioritization, and more. There were glowing recommendations of the 2005 Arksey and O’Malley article on scoping review methodologies and a wonderful link to all the references: bit.ly/visin-2016.

Kate Krause presented for a team primarily from the Texas Medical Center Library about their efforts to launch a new systematic review service, and the resulting “opportunities” (wink, wink, nudge, nudge, we all know what THAT means). The moderator described their presentation as a “collective therapy session,” which generated considerable amusement among the audience. The most important parts of her talk were, of course, the solutions! They require systematic review requests to come through an online request form, which gives them solid statistics and allows them to manage workflow better. They are using a memorandum of understanding (MOU) with faculty to facilitate a discussion of the duties, timeline, and expectations. They are providing different levels of service, with some interesting requirements for the highest level of service (like, if I understood correctly, mandatory five face-to-face meetings with the project lead). One curious nugget for which they are seeking the citation was heard at a prior MLA meeting — the more face-to-face meetings you have with a systematic review researcher, the more likely they are to actually publish on the project. They have a wonderful-sounding information packet given to new SR researchers, but I didn’t catch everything in it. I did catch bits (Cochrane timeline? list of other review types?) that make me want to know more!

MLAnet16 Systematic Review Services

Lynn Kysh and Robert E. Johnson presented a talk with the awesome title: “Blinded Ambition, misperceptions & misconceptions of systematic reviews.” They discussed some of the challenges to co-authorship and publication being assumed as an automatic good for librarians working on systematic review teams. Lynn described constraints to completing publication, and described times when librarians there removed their name from articles being submitted for publication because of methodological concerns. Very very interesting content. Well, and then there were the forest plot kittenz.

Last but not least, Maylene Kefeng Qiu represented a team that did the bulk of the work for a rapid review in … three weeks. Intense! Much of the challenge centered around timing, expertise available, staffing, workflow, and management coordination. The librarians on this team actually did the critical appraisal of the articles before giving the final dataset to the faculty member writing the review. My favorite line from her talk was, “Stick to your inclusion/exclusion criteria.” Their slide deck had so many wonderful images illustrating parallels and differences between systematic reviews and rapid reviews. I hope it’s ok if I share just one.

MLAnet16 Systematic Review Services

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.”

Researchpalooza 2015!

Researchpalooza 2015Researchpalooza 2015 at a Glance

Researchpalooza! A place for the bold! The bright! The blue!

Researchpalooza is a big festival for people all around the University of Michigan campuses who are engaged with, supportive of, or otherwise a part of life sciences research. From the service side to the production side, people come out, play games and eat ice cream, and talk about the services they provide and the discoveries they’ve supported. They talk about resources, people, and places. They make new connections and foster new collaborations. People discover opportunities they weren’t aware of, get excited, and share their own passions. Basically, this is a pretty awesome event. I took a lot of pictures, and collected pictures and tweets into a portrait of the event. You can explore below, or go directly to the Researchpalooza 2015 Storify and find more.

UofM Student Research on 3D Everything (Except Printing)

#mlibres Students on #3d

Last week there was another of the wonderful Emergent Research Series of lectures sponsored by the University of Michigan Libraries Research Unit (2014 archive, 2013 archive).

Main topics covered were spatial tracking, 3d virtual reality, optical motion capture, holography, optical tracking, acoustic motion tracking. During the Q&A, a major diversion (at least for me) was “Sim-sickness”, in which 3d immersive virtual reality (think of Oculus Rift & Google Cardboard) make folk nauseous, some to the point of actually tossing their cookies. There are videos in Youtube. I don’t need to find them for you. Fun topics mentioned included virtual augmented reality, Hololens, holography for teaching anatomy, biomechanics, cultural preservation, robotics, aerospace engineering, body slicing with the Kinect, body tracking, and DIY arduino acoustic sensors and automated echolocation. There were lots of tips and tricks, what works and what doesn’t. Many interesting links in the Storify below.

What Patients Think about Clinical Trial Engagement (#patientchat)

At the Doctor's Office

I had really wanted to participate in this Twitter chat today (#patientchat), on how patients find clinical trials, decide to engage with them, what resources they use, their expectations, and their concerns. I missed the chat, but it is archived in Symplur, so I was able to scroll through, search, dig, prowl around, and find my favorite bits. Since I went through all of that, I thought I’d share it. I’d recommend reading more deeply in the transcript for anyone in clinical trial research or recruitment, patients with basically any kind of diagnosis (as Mighty Casey eloquently said), people interested in translational medicine (where patients play a crucial role), as well as clinicians. Evidently, patients consider clinical trial recommendation from the primary care clinicians to be an obligation, not an optional part of providing care. Who knew? I bet we could automate relevant clinical trial notifications in EHR and as part of clinic visit prep. Why not? Explore below and see what other surprises and creative nuggets appear.

Ann McKee on Boxing, Football, and the Brain (Leiter Lecture) [#mlanet15]

Part 4 of a series of blogposts I wrote for the recent Annual Meeting of the Medical Library Association.


Was it just yesterday? I was sitting in the Leiter Lecture listening to the incredible Dr. Ann McKee present about past, present, and future trends in concussion research. I had been reading about her work in the indie-published award-winning book from 2014, Conquering Concussion, and was very interested in learning more. By the end of the talk, I wasn’t the only person who had tweeted out that I had tears in my eyes.

The story she told that touched me the most was of the athlete who had been diagnosed with ALS, but who phoned her, suspecting that what he really had was, “what you’re studying, Doc.” That would be Chronic Traumatic Encephalopathy (CTE). Basically, CTE is what happens when you bounce someone’s brain around on a regular basis, and they never really have a chance to heal. Some folk with that history develop CTE, some don’t, and Dr. McKee would really like to know why. To do this research, people or families donate their brains after they die. This athlete had met with her a few times, and there was a relationship, a sense of trust between them. Then the call came (I’m paraphrasing here, working from memory), “Hey, Doc, we’re having a big party! All my family and friends, a big blast. I’ve decided to go off respiratory support, and my docs don’t think I’ll make it through the weekend.” He died the next day. Someone went to pick up his brain, and when they ran the tests, he was right — he did have CTE.

I shared that story later that day in the airport waiting room with a man whose wife and son both had a history of severe concussions. I also shared that Dr. McKee’s insights on a possible genetic connection (for why some folk never develop CTE) and what people can do NOW to help prevent the long term:

* EXERCISE
* Diet (rich in antioxidants)
* Sleep
* Avoid conditions or triggers that cause inflammation in your body

Dr. McKee is also working on finding biomarkers so CTE can be diagnosed before people die, and needs donations of NORMAL brains to be able to identify the differences. A friend of mine asked me on Twitter what qualifies as ‘normal,’ and for this, let’s just say it would be someone who doesn’t have a history of multiple concussions, or subconcussions. There was a lot more, but I’ll limit myself to sharing the Concussion Checklist she recommended, and the Storify, if you want more. There are several interviews with her and other articles about her, if you want to dig in a little more deeply.

Molecular Biology & Genomics SIG Meeting #mlanet15

Part 1 of a series of blogposts I wrote for the recent Annual Meeting of the Medical Library Association.


MolBio & Genomics SIG #mlanet15

I’m trying to track what’s going on with emerging technologies, new tools, new-to-me tools, and so forth. I’m not an official member of the MolBioGen SIG, but I wish I was (especially since personal genomics is one of my hobbies). I learned so much at their meeting Monday morning. The best part was the Round Table, where they each talked about who they are, what they do, what’s new at their place. Now, this was exciting! They talked about many tools they seemed to all know and take for granted, and I’ll share some of those later. They also had so many exciting and creative ideas for how to engage their target audiences, types of classes that are most effective, crowdsourcing instruction from within the audience, strategic partnerships that make a difference, strategies for point-of-care genomics, and so much more.

Here are the tools that I found most interesting.

PhenoTips
PhenoTips

Reactome
Reactome

Online Bioinformatics Resource Collection
Bioinformatics MOOCs Example

Galaxy Project
Galaxy

Open Helix
OpenHelix
(Note: These folk are in the Exhibit Hall, if you haven’t seen them yet.)

BioStars
BioStars

GenePool
GenePool

Data Carpentry
Data Carpentry

Project Hydra
Hydra

Fedora
Fedora

NCBI: Gene Expression Omnibus (GEO)
GEO (Gene Expression Omnibus)

Complete Genome: Public Genome Data
Complete Genomics Public Data

NYU Data Catalog
NYU Data Catalog

Want more? Check out the Storify!