Tuesday, May 31, 2016

A Useful Bookmark: The PLoS WHO Global Foodborne Diseases Collection

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Friday, May 27, 2016

Around town: Shatner and early grammar woes

William_Shatner_Star_Trek_first_episode_1966(Or why you should hire an editor.)

Local institution the University of British Columbia (UBC) is celebrating its 100th anniversary this school year. This weekend, as part of its centenary celebrations, UBC is running a daylong event: UBC100: What’s Next? A day of exploring the future, a series of talks on upcoming issues in science, community and technology. To round off the day in style, actor, musician, author and horse breeder William Shatner will share his perspective in a talk called The Curious Life, and will take questions from the audience.

My Around Town series, as I’ve explained previously, is a collection of posts highlighting great local science events. I usually pull together interesting news from conferences happening in Vancouver or explore the topics of the conferences in a more general way. With Captain Kirk himself in town, there are so many potential topics for an Around Town blog post here: NASAStar Trek…space…technology…horse breeding?

Should I focus on the amazing science portrayed through the decades and presented seamlessly by Shatner and fellow actors in one of the most iconic science fiction series of all time? From phasers to automatic doors, ion drives and warp speed to tricorders and teleportation, there’s so much to cover that has or is making its way from fiction into our modern life. As a series, Star Trek presented future science in a highly believable and engaging way, inspiring kids and adults alike to think creatively about technological development. The science of Star Trek is an obvious choice.

Or is it?

Alfabeto_klinzhai_del_klingonMaybe I should instead focus on the social impact of Star Trek—that first televised interracial kiss, for example? Or discuss the unluckiness of the red jersey? Or TribblesKlingon?

What about life on other planets?

Again, no, though it may be highly illogical. Much has been written by writers more fanatical than myself, so instead I will focus on something a little more mundane but still highly relevant.

How about grammar?

To boldly go: a.k.a. splitting the infinitive.

With every opening credits sequence enunciated in Mr. Shatner’s sweet (and Canadian) tones, the adults around me would smugly comment, “He’s splitting an infinitive” and then tut-tut knowingly.

For most of my adult life, “to boldly go” has neatly encapsulated what can go wrong with text and how little the average user understands grammar. Although there are indeed basics that are easy to follow, without which the text screams out from the page like a siren, making educated readers shudder inwardly, there is still a lot of grammar that makes no sense to writers. Splitting an infinitive is one, though in that lovely confusing world of modern and dynamic grammar, maybe it isn’t. Infinitive splitting may simply be the triumph of personal style and influence over common usage. And this is the conundrum: as a writer, should I be worrying about content or syntax? Should I focus on mechanics or creativity?

In answer, let me quote you some William Shatner: “I’ve discovered that the more freedom I have to be creative, the more creative I become.” Maybe hand over some of the worry to an editor, who will not only run the red pen through the text but also understand the art and craft of grammar. Doubly lucky if the editor also “speaks science.”

Language use is evolving, though maybe not at the warp speeds of science and technology, and it’s probably safe to say that split infinitives won’t be a major part of UBC’s exploration day. Although “to boldly go” might only be mentioned in a Star Trek context, don’t forget its grammatical importance. Hire an editor so you too can explore strange new worlds words.

Make it so!


UBC100: What’s Next? A day of exploring the future
Chan Centre, UBC, May 28, 2016


[Editor’s note: I, too, grew up surrounded by grammar-sensitive adults (which is probably why I became one!). I remember my dad reprimanding CBC every time he heard a split infinitive on the radio. When I learned that the split infinitive rule is in fact a holdover from Latin and doesn’t really make sense as a rule in English, I felt a total thrill of rebellion. (For my cautious self, the rebellion felt so liberating because I wasn’t breaking a rule…there was really no rule to break to begin with.) Most style guides, including The Chicago Manual of Style, say it’s okay to split infinitives. It’s also worth noting that many, Chicago included, use the famed “to boldly go” as an example to highlight their point. —Roma]


The post Around town: Shatner and early grammar woes appeared first on Talk Science to Me.

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The Residual Proteome: ECM Proteins in Decellularized Organ Scaffolds

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Wednesday, May 25, 2016

Data Acquisition Revamp for Large-Scale PRM Proteomics

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Tuesday, May 24, 2016

Science communication along the garden path

Friday, May 20, 2016

Biomarker Discovery: Low-Abundance Protein Enrichment via Gel Filtration

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Analyzing gel results. Image: SINITAR/Shutterstock.comRising interest in less-invasive sampling using blood, urine or other easily accessible biological fluids for biomarker discovery is expanding analytical methods for many –omics technologies. Chen et al. (2015) explored a new sample-preparation workflow for mass spectrometry–based proteomic analysis of human serum, seeking to facilitate enrichment of low-abundance, low–molecular weight (LMW) proteins.1

Although blood is a good starting material for biomarker discovery, high-abundance proteins (HAPs) such as albumin threaten to mask changes in LMW compounds below 30 kDa. The most valuable biomarkers are often low-abundance LMW proteins, which show variation in terms of quantity, post-translational modification and isoform expression according to disease. Quantitative proteomic analysis using liquid chromatography–mass spectrometry (LC-MS) characterization is thus a valuable tool in biomarker discovery, since it is sensitive enough for both detection and quantitation. However, the necessary removal of HAPs during sample preparation often results in loss of LMW proteins in addition to incomplete removal, masking their quantitative evaluation.

Chen et al. propose a gel filtration enrichment step during sample preparation that passively sieves out the HAPs using a four-layer tracking tricine sodium dodecyl polyacrylamide gel electrophoresis (SDS-PAGE) technique. The technique uses the following four layers:

  1. A standard stacking layer (5%)
  2. A funnel layer (8%–10%) that prevents more abundant proteins from clogging up the interface
  3. A blocking layer (16%–20%) that retains the high–molecular weight proteins
  4. A separating gel (10%–12%) that presents the LMW proteins as separate bands for in-gel trypsin digestion

The researchers obtained serum samples from six healthy volunteers (three male, three female), pooling the volumes to minimize variation. They then took aliquots of the pooled sample and prepared them according to the following workflows:

  • Denaturing glycine SDS-PAGE
  • Optimized differential solubilization (ODS) and PAGE
  • Gel filtration enrichment: four-layer stacking tricine SDS-PAGE

Once the researchers separated the proteins, they digested the proteins using trypsin prior to LC–tandem mass spectrometry evaluation (LC-MS/MS) using an LTQ Obitrap Velos mass spectrometer (Thermo Scientific).

The team also used a commercial bead enrichment kit to separate proteins prior to trypsin digestion and LC-MS/MS. They conducted recovery assessment for this method in addition to gel filtration enrichment and ODS using a stable isotope labeling in culture absolute quantitation (SILAC-AQUA) approach to label recombinant proteins, which they then spiked into the human serum before processing according to the workflows described above.

On direct examination of the gels, Chen et al. found that the gel filtration enrichment showed better resolution of LMWs than ODS or glycine SDS-PAGE, with no loss of protein bands. The team found that the gel filtration enrichment resulted in a clear demarcation between blocking and separating gel interfaces. Furthermore, band density varied according to sample load, although volumes above 10 µL resulted in saturation with merging into the separation layer. Compared to the glycine and ODS methods, gel filtration enrichment was more consistent and highly efficient, resulting in more proteins, as shown by band intensity.

The team confirmed this using LC-MS/MS, where final analysis yielded more protein identifications from the gel filtration enrichment (1,576) than from the other two workflows (ODS = 1,022; glycine = 1,186) in 10 µL of serum. Of the 1,576 proteins identified, 559 were LMW below 30 kDa. Gel filtration enrichment also gave good recoveries from spiked samples as assessed by SILAC-AQUA. Compared to ODS (18.7%) and the commercial kit (9.6%), gel filtration enrichment resulted in recoveries of 33.1%. 

Chen et al. conclude that quantitative LC-MS/MS shows that gel filtration results in good enrichment without protein bias. Furthermore, the workflow efficiently captures the LMW proteins of interest for biomarker discovery without excessive losses during preparation. Removal of HAPs removes interference with quantitative proteomic evaluation, thus increasing the value of this method for biomarker characterization.


1. Chen L., et al. (2015) “Development of gel-filter method for high enrichment of low-molecular weight proteins from serum,” PLoS ONE 10(2): e0115862. doi: 10.1371/journal.pone.0115862

Post Author: Amanda Maxwell. Mixed media artist; blogger and social media communicator; clinical scientist and writer. A digital space explorer, engaging readers by translating complex theories and subjects creatively into everyday language.

The post Biomarker Discovery: Low-Abundance Protein Enrichment via Gel Filtration appeared first on Accelerating Proteomics.

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Wednesday, May 18, 2016

daily snapshot: May 18, 2016 at 10:33AM

wordless wednesday: yesterday's#gouache
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Tuesday, May 17, 2016

Halley’s comet, impending doom and communicating science

http://ift.tt/1ODuHr4's_Comet_-_May_29_1910.jpgOn May 18, 1910, Halley’s comet made its closest recorded contact (0.15 astronomical units,* or approximately 23 million kilometres) with our planet, and the Earth passed through its tail. The event was full of scientific excitement and wonder, since photographic plates and spectroscopy were newly available to researchers. With these new tools, astronomers and the public got a better view of the comet itself and also a first inkling of what it contained.

Exciting times for science!

However, as the comet approached, the spectroscopy results revealed that among other gases, the comet’s tail showed strong band signatures for the toxic gas cyanogen. First synthesized in 1815, cyanogen is toxic, since it reduces rapidly to form cyanide and thus poisons the essential cytochrome c oxidase system to mess with mitochondrial function (not good).

http://ift.tt/1so4Zg7Although many chose to report the existence of the gas in the comet tail scientifically and without alarm (because there was no reason for alarm), some did not let science get in the way of a good story and launched into the general doom-mongering that often accompanies the appearance of celestial bodies.

According to astronomer Camille Flammarion, cyanogen gas would extinguish life on Earth as the planet passed through the comet’s tail. Despite reassurances from more responsible experts who no doubt pointed out the space/vacuum/distance/protective effect of atmospheric abundancy factors, some news outlets, including the New York Times, chose to report this alarming speculation.

Stardust was okay, but the public was not happy with the thought of being bathed in cyanogen; in the panic, sales of gas masks and comet pills increased.

May 19 dawned; Earth passed safely through the comet tail. Mark Twain, the only “casualty,” had died a month earlier (just sayin’).

  1. Clickbait and misreporting science are not new phenomena.
  2. Communicating science should be done accurately and responsibly to avoid unnecessary panic or profiteering.
  3. Caveat lector!


For more information on spotting clickbait, check out these blog posts:


* One astronomical unit (AU) is equivalent to the mean distance between the Sun and the Earth, according to this blog post from the Jet Propulsion Laboratory at the California Institute of Technology.

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daily snapshot: May 17, 2016 at 10:51AM

Today's adventure: me and the bike via TransLink into Vancouver. Lessons learned so far = not all bus drivers are helpful; replace the bike rack; use the stairs if the lift is out; go the long way round (don't change at Commercial). Stay tuned :)
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Friday, May 13, 2016

daily snapshot: May 13, 2016 at 10:32PM

Frustration: my #opus Athabasca studio easel still in pieces in its box on the floor
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Around town, a.k.a. back to school

By User Ancheta Wis on en.wikipedia [Public domain], via Wikimedia Commons One of the reasons for highlighting upcoming science conferences in Vancouver in my Around Town series is that it gives me a push to find out more on a subject I may have little exposure to. It’s also a great inspiration for a regular series of blog posts!

Last month, press releases ahead of one of these conferences, the 68th American Academy of Neurology Annual Meeting, caught my eye. As is common in the promotion of meetings for large organizations, the preceding month saw a few press releases announcing some of the research coming to the Vancouver Convention Centre. The first reported a preliminary study on the effect of daylight saving time (DST) on incidence of ischemic stroke, and the second investigated engagement in various mentally stimulating activities in older age and the effect on development of thinking and memory problems.

When I blog about upcoming events, I usually write about something that fascinates me from the program, or brush up on terminology, or even wax lyrical about proteins. Press releases are a handy inspiration. All of this takes careful research, and it’s equally true for the press releases.

2016-03-29 18.20.22At around the same time as I was exploring the American Academy of Neurology conference, Talk Science Mastermind Eve and I took part in a workshop for health sciences students at Kwantlen University, where we explained a little about the science communications work Talk Science to Me does and about science writing in general. A few of the questions from the students focused on how we find subjects to write about and how we work out whether they are valid.

So, here’s a brief summary of the workflow I go through when choosing a topic.

Summaries first

In the first study I read about, Finnish researchers found an association between the incidence of stroke in the first two days following the switch to DST. In the second, a team from the Mayo Clinic found that a group of seniors 70 years or older regularly taking part in late-life mentally stimulating activities were less likely to develop mild cognitive impairment over four years.

Why did the press releases catch my eye?

Apart from the fact that they turned up in my feed reader’s daily aggregation, the topics seemed highly relevant to me in the moment. Number one: for the first time ever, I think, I missed the dreaded Spring Forward by virtue of travel and location, being in the United Kingdom for the North American transition, then missing European DST a couple of weeks later when I flew back home. And number two: my reason for travel was to visit my parents, both in the older age group.

How did I decide if the topics were appropriate for the Talk Science blog?

Or, in other words, am I falling for clickbait? Old age, Alzheimer’s disease, DST, stroke, debility…these are all newsworthy subjects, so how do I know that I’m not falling under the spell?

First, what are my trusted sources saying about the subject? My handy feed reader turned up nothing critical of the reports. Now this in itself is not perfect, but it has in the past been a good indicator of questionable veracity. There are many gifted scientific writers out there to learn from, and they are much sharper at digging into the data than I am. No early alarm bells rang for either of these press releases. Note, though, that if I were writing a feature piece for a bigger organization, independent fact-checking would be required; phoning an expert on the subject for comment is a good first step here. At Talk Science, we have a number of experts we can turn to for this kind of verification.

I also turned to two other critical resources, Health News Review and the United Kingdom’s National Health Services Behind the Headlines blog, to see if there was any discussion. I found none. Both are pretty sharp at picking up and dissecting bogus hype.

Critical reading

Then I reread the press releases, in addition to looking at the two conference abstracts supplied and noting that neither had been through journal peer review for publication. In terms of study numbers, looking for sufficient sample size for veracity, data for the first study on stroke and DST came from ten years’ worth of health records. This encompassed over 11,000 individuals for the control group and more than 3,000 patients. The second study followed almost 2,000 seniors over four years.

One of the key areas for clickbait generation is the confusion between association and causation. For example, while rising costs for a bag of potato chips are statistically associated with an increase in reported deaths for wheelchair users (r = 0.971706), they are unlikely to be a root cause even if the data suggest otherwise. In both the neurology studies, neither the research team nor the press release stated absolute causation for the observed results, stating only that x was associated with y.

The DST/stroke study press release quoted one of the study authors as saying, “Further studies must now be done to better understand the relationship between these transitions and stroke risk…”

Janina Krell-Roesch, co-author of the mental activity and cognitive decline study, described the study as showing only an association, not cause and effect; however, she also suggested in the press release that “…as people age, they may want to consider participating in activities like these because they may keep a mind healthier, longer.”

I am the first to admit that my critical thinking skills and grasp of study design/statistical analysis are rusty. Applying my own critical eye in addition to scoping out other informed reactions is a part of my process for avoiding clickbait. While none of the steps described above is by itself foolproof, the results obtained are usually enough for me to decide whether or not to mention studies on the Talk Science blog.

In conclusion: nothing sensational here, but interesting studies that I felt were worth sharing.

If you have any more tips on checking out possible science stories, please leave a comment below.

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Wednesday, May 11, 2016

daily snapshot: May 11, 2016 at 10:37AM

wordless wednesday: inspirational view from my desk #studiodog #studio #writerslife
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Tuesday, May 10, 2016

daily snapshot: May 10, 2016 at 07:49PM

Me and my shadow
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daily snapshot: May 10, 2016 at 01:44PM

Tuesday texture
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Sunday, May 08, 2016

joy of colour

oilbars in action

Saturday, May 07, 2016

daily snapshot: May 07, 2016 at 12:18PM

white pants + peri-menopause + period = Diva Cup #forthewin #divacup #iwouldnotwearanythingelse
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Friday, May 06, 2016

i thought of you today

i thought of you today.

with every pass of the ultrasound probe, running over tender ribs to scan through the gaps between the bones i remember the full weight behind every single kick.
a lifetime has passed; the bruising has not.

lying sideways on the couch, i feel pain; my ribs creak and ache under the ultrasonographer's probing.

flattened into the carpet, absorbing kick after kick.

deep breath in, and i fill my lungs to provide contrast; she probes some more, refreshing old wounds.

unable to breathe, silenced - winded by your first punch. felled. exposed. inert.

breathe, she instructs.
breathe, i told myself as you crawled into bed beside me, seeking reassurance in my arms.
just breathe.

Note: this happened a long time ago, in another lifetime; sometimes the memory triggers then fades again. However, it really troubled me recently that the women in the trial kept in contact, until I remembered my own story; I too sought to normalize the situation; never reporting the assault; trying to make things work. Victims seldom follow The Script - I stayed for another four months trying to be a good girlfriend. The only correct way to respond is to survive. 

Thursday, May 05, 2016

daily snapshot: May 05, 2016 at 11:17AM

spt5may16: all clear
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Tuesday, May 03, 2016

daily snapshot: May 03, 2016 at 08:48AM

Jar #acrylic #acrylicsketch
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Sunday, May 01, 2016

daily snapshot: May 01, 2016 at 10:00AM

On top of the world! Happy birthday @tommybom19
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ebb and flo by pomo mama design click to shop pomo mama design online!