May 23, 2013
07:15 PM
7 views

Molecular visualization tools - Survey and practical tips

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

What would be like to teach a class or describe someone about a protein, without visualizing its structure? Boring is one word that pops in my mind. I vividly remember the professor drawing two blobs touching each other, to describe protein-protein interaction, while explaining it either on the blackboard or on the transparencies of a over-head projector. Those were the days! Tracing back nearly 60 years back, when John Kendrew showed everyone a coiled mess, it has fueled every scientist's imagination to visualize a protein. The coiled mess is aptly titled "Turd of the century"!... Read more »

Craig, P., Michel, L., & Bateman, R. (2013) A survey of educational uses of molecular visualization freeware. Biochemistry and Molecular Biology Education, 41(3), 193-205. DOI: 10.1002/bmb.20693

May 23, 2013
05:00 PM
6 views

The ‘actuator lugs’ on the Newton Running Shoes

by Craig Payne in Running Research Junkie

The ‘actuator lugs’ on the Newton Running Shoes... Read more »

Moran, M., & Greer, B. (2013) Influence of midsole ‘actuator lugs’ on running economy in trained distance runners. Footwear Science, 5(2), 91-99. DOI: 10.1080/19424280.2013.792878

Medicine

May 23, 2013
04:24 PM
13 views

All lobsters are mortal

by Zen Faulkes in NeuroDojo

This appeared earlier today on the Facebook feed I Fucking Love Science:

Argh!

I remember seeing a shark documentary as a kid, hosted by Burgess Meredith, if I remember correctly. It made the same basic claim about great white sharks: too big to have predators, nobody had ever seen them die except by accident or by human hands, blah blah blah, therefore “some have suggested” they are immortal.

That I can remember the end of the show all these years later shows you what a terrific close the “immortal” idea makes. But it only sounds plausible of our disconnect with that natural environment. It plays on our lack of knowledge about the natural world, and that we have a hard time tracking these sorts of things. It’s like asking most city dwellers, “Have you ever seen a baby pigeon?” “No, I haven’t. And you know what, I’ve never seen a dead pigeon, either! Oh my goodness, pigeons must be immortal!”

Sharks and lobsters have a few things in common, too, that makes the “immortality” claim easy to make. They live in the oceans, which means they are hard to track, and few people have first hand experience with them. They are long lived species, and it’s not easy to look at one and know how old it is.

When you add in “they only die from external causes,” you have a huge out. Most animals, including humans, die from external causes, broadly construed. Sure, a predator is an external cause. A bacterial or viral infection is an external cause. What would not count as an “external cause”? The definition is so loose that you can make exceptions for almost every possible counter-example.

And, of course, it links out, not to an actual scientific paper, which would be the sort of action you might expect from a group that proclaims to love science, but to a radio interview.

This is not a slap against the participants in the interview. Jelle Atema is a good scientist with real bona fides. But this radio interview is a long way from the sort of careful science you would need to do to show lobsters are “functionally immortal.”

There is some interesting science to this. Many decapod crustaceans have indeterminate growth (mentioned by Vogt 2008, 2010, who cites others). This means that they keep growing throughout their life, and do not have a set upper limit for size. It’s not just lobsters that do this, as far as I know; crayfish do, too. Lobsters are probably in this meme because they get so much larger than crayfish. It’s easier to people to believe a big animal like a lobster could be so much older than a small animal like a crayfish.

There is about one paper that I have been able to find on lobster longevity by Klapper and colleagues (1998). The introduction says:

Lobsters grow continuously throughout their lifespan, only decreasing growth rates with age. Furthermore, and again in contrast to humans, they are able to regenerate whole limbs even at a high age.

This cites a book chapter by Govind, on... muscle innervation?! The chapter talks a little bit about sarcomeres being added throughout life, but that’s about it. It’s not a chapter on aging and senescence.

More provocatively, the abstract of the Klapper and colleagues says (my emphasis):

Lobsters (Homarus americanus) grow throughout their life and the occurrence of senescence is slow.

But there is no citation for the “slow senescence” claim. And there is no original empirical data supporting that in the Klapper paper (e.g., longevity and activity and health and mortality data). The paper shows that adult lobsters still make an enzyme called telomerase, but it does not show that lobsters are long lived because of it.

How old does this “functionally immortal” lobster get? Well, if lobsters really were “functionally immortal,” why would you note expect them to live for centuries? Bodnar (2009) has a table that puts the oldest lobster on record in the 50-100 range. Bodnar cites Finch (1990), which again does not seem to have much more than a table with an estimated maximum lifespan, connected to another reference I haven’t. Nobody seems to define what “slow senescence” is, or how it has been measured in lobsters.

Regardless, a “functionally immortal” animal that has a shorter recorded maximum lifespan than a human? Colour me unimpressed.

For such a bold claim, it has been disappointingly hard to track down the real science. It’s also disappointing to see such a credulous claim come from a source that contends it fucking loves science. I think it is fair to call this one:

Sadly, I suspect this myth might have a longer lifespan than many lobsters.

Reference

Bodnar AG. 2009. Marine invertebrates as models for aging research. Experimental Gerontology 44(8): 477-484. DOI: 10.1016/j.exger.2009.05.001

Govind CK. 1995. Muscles and their innervation. In: Factor, J.R. (Ed.), Biology of the Lobster Homarus americanus, pp. 291–312, Academic Press, San Diego, CA.

Klapper W, Kühne K, Singh KK, Heidorn K, Parwaresch R, Krupp G. 1998. Longevity of lobsters is linked to ubiquitous telomerase expression. FEBS Letters 439(1-2): 143-146. DOI: 10.1016/S0014-5793(98)01357-X

Vogt G. 2008. How to minimize formation and growth of tumours: Potential benefits of decapod crustaceans for cancer research. International Journal of Cancer 123: 2727-2734. DOI: 10.1002/ijc.23947

Vogt G. 2008. The marbled crayfish: a new model organism for research on development, epigenetics and evolutionary biology. Journal of Zoology 276: 1-13. DOI: 10.1111/j.1469-7998.2008.00473.x

Vogt G. 2010. Suitability of the clonal marbled crayfish for biogerontological research: A review and perspective, with remarks on some further crustaceans. Biogerontology 11: 643-669. DOI: 10.1007/s10522-010-9291-6... Read more »

Bodnar A.G. (2009) Marine invertebrates as models for aging research. Experimental Gerontology, 44(8), 477-484. DOI: 10.1016/j.exger.2009.05.001

Klapper Wolfram, Kühne Karen, Singh Kumud K, Heidorn Klaus, Parwaresch Reza, & Krupp Guido. (1998) Longevity of lobsters is linked to ubiquitous telomerase expression. FEBS Letters, 439(1-2), 143-146. DOI: 10.1016/S0014-5793(98)01357-X

Biology

May 23, 2013
03:37 PM
10 views

Researchers Turn a Smartphone into a Biosensor

by Jason Carr in Wired Cosmos

University of Illinois at Urbana-Champaign researchers have developed a cradle and app for the iPhone that uses the phone’s built-in camera and processing power as a biosensor to detect toxins, proteins, bacteria, viruses and other molecules. Having such sensitive biosensing capabilities in the field could enable on-the-spot tracking of groundwater contamination, combine the phone’s GPS … Read More →... Read more »

Gallegos, D., Long, K., Yu, H., Clark, P., Lin, Y., George, S., Nath, P., & Cunningham, B. (2013) Label-free biodetection using a smartphone. Lab on a Chip, 13(11), 2124. DOI: 10.1039/C3LC40991K

May 23, 2013
01:01 PM
16 views

Bach to the blues, our emotions match music to colors

by Perikis Livas in Tracing Knowledge

Whether we’re listening to Bach or the blues, our brains are wired to make music-color connections depending on how the melodies make us feel, according to new research from the University of California, Berkeley. For instance, Mozart’s jaunty Flute Concerto No. 1 in G major is more apt to be associated with bright yellow and orange, whereas his dour Requiem in D minor is more likely to be linked to dark, bluish gray.... Read more »

Yasmin Anwar. (2013) Bach to the blues, our emotions match music to colors. UC Berkeley News Center. info:/

May 23, 2013
01:00 PM
8 views

Microbial Misadventures: Exploits in Botulism & Pruno In Our Prison Population

by Rebecca Kreston in BODY HORRORS

Drinking pruno is a risky endeavor, both in terms of its offense to culinary sensibilities and to one's health. However, turned stomachs are not the only hazard here; you may add a desire to avoid botulism to your list of reasons to shy away from you'r mates latest batch of prison hooch. The soil-dwelling bacterium Clostridium botulinum can contaminate fruits and veggies, and, in warm, oxygen-deprived conditions, produces the neuroparalytic toxin botulinum. Even more wholesome DIY endeavors, such as canning fruits and crafting jams, can create an excellent staging ground for growing one's own C. botulinum.... Read more »

Centers for Disease Control and Prevention (CDC). (2013) Notes from the field: botulism from drinking prison-made illicit alcohol - Arizona, 2012. MMWR. Morbidity and mortality weekly report, 62(5), 88. PMID: 23388552

May 23, 2013
12:44 PM
7 views

If you chew that mRNA, you must make a new one!

by Gal Haimovich in Green Fluorescent Blog

Gene expression is very complex. My paper, which was published in Cell today, just shows that it is more complicated than previously realized. Traditionally, eukaryotic gene expression is divided into five steps: Transcription (mRNA synthesis): this step is subdivided into … Continue reading →... Read more »

Haimovich, G., Medina, D., Causse, S., Garber, M., Millán-Zambrano, G., Barkai, O., Chávez, S., Pérez-Ortín, J., Darzacq, X., & Choder, M. (2013) Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis. Cell, 153(5), 1000-1011. DOI: 10.1016/j.cell.2013.05.012

Haimovich G, Choder M, Singer RH, & Trcek T. (2013) The fate of the messenger is pre-determined: A new model for regulation of gene expression. Biochimica et biophysica acta, 1829(6-7), 643-53. PMID: 23337853

May 23, 2013
12:00 PM
9 views

Very beautiful findings related to Down syndrome

by Usman Paracha in SayPeople

Main Point:

Researchers, in 2011, reported that the parents, siblings and even the people with Down syndrome reported positive experiences about their life and relations.

Published in:

American Journal of Medical Genetics

Study Further:

Down syndrome refers to the condition in which the extra genetic material in the body causes the slow development of the child, mentally and physically. It affects 1 in every 800 babies born in United States.

Researchers, in three different studies, surveyed 4,924 parents, siblings and the people with Down syndrome.

In first study, researchers worked on the surveys from 2,044 parents or guardians (with estimated response rate of 29%) and found that 99% of the parents love their child with Down syndrome. More interestingly, 79% of the people felt more positive feelings about life because of their child. Only 5% felt embarrassed by their child and 4% felt regret for their child.

In second study, researchers worked on the surveys from 822 brothers and sisters (with estimated response rate of 19%) and found that among the children with age 12 and older 94% of the brothers and sisters felt proud about their sibling with Down syndrome. More interestingly, 88% of them reported that they were better people because of their sibling with Down syndrome. Only 7% felt embarrassed by their sibling and 4% reported that they would trade their sibling for another.

Among the children in the age range of 9-11, 97% of the children reported that they love their sibling and 90% felt that their friend felt comfortable with their sibling.

In third study, researchers worked on the surveys from 284 people with Down syndrome (with estimated response rate of 17%). Those people had an average age of 23 and 83% of them were living with one or both parents/guardians. Researchers found that 99% of the people reported that they were happy with their lives, 97% liked who they were, 96% liked their look, 86% reported that they could make friends easily and only 4% reported sadness about their life.

According to researchers, the finding would have some selection bias but it is representing a positive experience related to Down syndrome. These researches also showed that the expecting parents must not be worried about their children as the positive experiences always enhance with the coming child.

Source:

Boston Children’s Hospital

References:

Skotko, B., Levine, S., & Goldstein, R. (2011). Having a son or daughter with Down syndrome: Perspectives from mothers and fathers American Journal of Medical Genetics Part A, 155 (10), 2335-2347 DOI: 10.1002/ajmg.a.34293

Skotko, B., Levine, S., & Goldstein, R. (2011). Having a brother or sister with Down syndrome: Perspectives from siblings American Journal of Medical Genetics Part A, 155 (10), 2348-2359 DOI: 10.1002/ajmg.a.34228

Skotko, B., Levine, S., & Goldstein, R. (2011). Self-perceptions from people with Down syndrome American Journal of Medical Genetics Part A, 155 (10), 2360-2369 DOI: 10.1002/ajmg.a.34235... Read more »

Skotko, B., Levine, S., & Goldstein, R. (2011) Having a son or daughter with Down syndrome: Perspectives from mothers and fathers. American Journal of Medical Genetics Part A, 155(10), 2335-2347. DOI: 10.1002/ajmg.a.34293

Skotko, B., Levine, S., & Goldstein, R. (2011) Having a brother or sister with Down syndrome: Perspectives from siblings. American Journal of Medical Genetics Part A, 155(10), 2348-2359. DOI: 10.1002/ajmg.a.34228

Skotko, B., Levine, S., & Goldstein, R. (2011) Self-perceptions from people with Down syndrome. American Journal of Medical Genetics Part A, 155(10), 2360-2369. DOI: 10.1002/ajmg.a.34235

Psychology

May 23, 2013
11:58 AM
11 views

New Method for Clean and Safe Hydrogen Production Proposed

by dailyfusion in The Daily Fusion

Duke University engineers have developed a new safer method for catalytic hydrogen production. According to the authors of the study, it does not require high temperatures and produces smaller amounts of toxic chemicals than other industrial hydrogen production technologies.... Read more »

Shodiya, T., Schmidt, O., Peng, W., & Hotz, N. (2013) Novel nano-scale Au/α-Fe2O3 catalyst for the preferential oxidation of CO in biofuel reformate gas. Journal of Catalysis, 63-69. DOI: 10.1016/j.jcat.2012.12.027

May 23, 2013
09:21 AM
15 views

Should you worry about vitamin D deficiency? Maybe. Or maybe not.

by EE Giorgi in CHIMERAS

Since my last blog post, where I shared my thoughts on BRCA1, BRCA2, and preventive mastectomies, I've been asked what else can a woman do to reduce her risk of breast cancer. I've heard a big deal about vitamin D, so I did a bit of research on the matter. As a disclaimer, I should tell you up front that, though many correlations between vitamin D deficiency and cancer risk have been found, just as many have been refuted or found inconclusive. You can read more about it on the wikipedia page.What is vitamin D? The name "vitamin D" includes a group of steroid-like molecules (they are similar to steroids, but not quite steroids) that help our intestine absorb calcium and phosphates. Since calcium is essential in bone development, vitamin D deficiency has been most commonly associated to osteoporosis and other bone-related diseases. There aren't many foods rich in vitamin D, however, vitamin D can be endogenously synthesized when the skin is exposed to sunlight. Unfortunately, modern lifestyle keeps us cooped up many hours in office cubicles, or in the house during chores, or in malls. When we're out enjoying the sunshine we cover up with hats and super-protective sunscreens because we've been told that the sun is bad for the skin and can cause malignancies. As a consequence, vitamin D deficiency is increasing world-wide. There is a foundation for all the studies that have analyzed correlations between several diseases, including cancers, and vitamin D: (i) several ecological studies have found a trend for an increase in incidence of certain cancers at higher latitudes, suggesting that longer exposures to the sun may have a protective effect. (ii) The vitamin D receptor (VDR) is expressed in many cells of the immune system, and mouse models have shown that vitamin D deficiency can promote certain auto-immune diseases. In a recent review, Sundaram and Coleman examine the link between vitamin D and influenza [Adv. Nutr. 2012 3: 517-525]. (iii) "VDR regulates a wide range of cellular mechanisms central to cancer development, such as apoptosis (cell death), cell proliferation (uncontrolled cell growth), differentiation, angiogenesis, and metastasis [1]". In line with this observation, Pereira, Larriba, and Munoz published a review on the evidence that vitamin D plays a protective role in colon cancer [Endocr. Relat. Cancer 2012 19: R51-R71].In [1], Crew discusses the use of vitamin D supplementation as part of breast cancer prevention. She presents many interesting findings, for example:"Colon, breast, and lung cancer have all demonstrated downregulation of expression of VDR when compared to normal cells and well-differentiated tumors have shown comparably more VDR expression as measured by immunohistochemistry when compared to their poorly differentiated counterparts. Higher tumor VDR expression has also been correlated with better prognosis in cancer patients [1]."Crew looks at different types of studies: some suggest beneficial effects from using vitamin D (calcitriol) in combination with other anti-cancer treatments; some found an inverse association with mammography density, a biomarker for breast cancer (supposedly high density increases the risk of cancer); some found an inverse association between better breast cancer prognosis and vitamin D deficiency. However, many of these studies have limitations. For example, some only assess the levels of vitamin D through dietary intake, which is not a good measure of the circulating levels because it doesn't account for vitamin D synthesized through sun exposure. Some were confounded by obesity since fat is known to sequestrate vitamin D and also raise breast cancer risk. In light of all these considerations, Crew concludes:"Even with substantial literature on vitamin D and breast cancer, future studies need to focus on gaining a better understanding of the biologic effects of vitamin D in breast tissue. Despite compelling data from experimental and observational studies, there is still insufficient data from clinical trials to make recommendations for vitamin D supplementation for breast cancer prevention or treatment [1]."As I often do in my posts, rather than giving you answers, I make an effort to provide you with pointers and food for thought: in the end you have to make your own decisions about your health and the wellbeing of your family. As a personal note, I'll add that on my last blood report my vitamin D circulating levels were undetectable. I had no symptoms whatsoever, but I am now taking a vitamin D supplement. I'm also much less paranoid about smothering my kiddos with sunscreen when they play outside (which has made them much happier, two birds with one stone). [1] Crew, K. (2013). Vitamin D: Are We Ready to Supplement for Breast Cancer Prevention and Treatment? ISRN Oncology, 2013, 1-22 DOI: 10.1155/2013/483687... Read more »

Crew, K. (2013) Vitamin D: Are We Ready to Supplement for Breast Cancer Prevention and Treatment?. ISRN Oncology, 1-22. DOI: 10.1155/2013/483687

May 23, 2013
09:14 AM
22 views

New Reliable Blood Test Can Detect Depression

by Pieter Carriere in United Academics

Depression or Major Depressive Disorder (MDD) has multiple genetic and environmental causes. Genetic factors are hard to find and the discovered factors usually are also associated with other mood disorders. Furthermore, twin studies reveal that genetics can predict 37% of the depressions, which is a much lower heritability than in bipolar disorder, a comparable mood disorder (reviewed in Belmaker et al., 2008). ... Read more »

Papakostas, G., Shelton, R., Kinrys, G., Henry, M., Bakow, B., Lipkin, S., Pi, B., Thurmond, L., & Bilello, J. (2011) Assessment of a multi-assay, serum-based biological diagnostic test for major depressive disorder: a Pilot and Replication Study. Molecular Psychiatry, 18(3), 332-339. DOI: 10.1038/mp.2011.166

Pariante, C., & Lightman, S. (2008) The HPA axis in major depression: classical theories and new developments. Trends in Neurosciences, 31(9), 464-468. DOI: 10.1016/j.tins.2008.06.006

Raison, C. (2012) A Randomized Controlled Trial of the Tumor Necrosis Factor Antagonist Infliximab for Treatment-Resistant DepressionThe Role of Baseline Inflammatory BiomarkersInfliximab for Treatment-Resistant Depression. Archives of General Psychiatry, 1. DOI: 10.1001/2013.jamapsychiatry.4

Nibuya M, Morinobu S, & Duman RS. (1995) Regulation of BDNF and trkB mRNA in rat brain by chronic electroconvulsive seizure and antidepressant drug treatments. The Journal of neuroscience : the official journal of the Society for Neuroscience, 15(11), 7539-47. PMID: 7472505

May 23, 2013
08:28 AM
8 views

It’s great to be a woman scientist; it’s challenging to be a woman scientist

by Stephanie Swift in mmmbitesizescience

I recently volunteered to help organise an event run by the Canadian Science Policy Centre that looked at the status of women in science and technology. To be frank, I was mightily fearful about participating in such an event. I … Continue reading →... Read more »

Wenneras C, & Wold A. (1997) Nepotism and sexism in peer-review. Nature, 387(6631), 341-3. PMID: 9163412

May 23, 2013
08:24 AM
13 views

Fragile mega-galaxy is missing link in history of cosmos

by Perikis Livas in Tracing Knowledge

Two hungry young galaxies that collided 11 billion years ago are rapidly forming a massive galaxy about 10 times the size of the Milky Way, according to UC Irvine-led research published Wednesday in the journal Nature.... Read more »

UC Irvine Media Realease. (2013) Fragile mega-galaxy is missing link in history of cosmos. UC Irvine. info:/

May 23, 2013
07:34 AM
14 views

Smelling Lemons Might Better Treat Autism

by Andrew Porterfield in United Academics

classical music and intense sensory exercises produced improvements in autism symptoms in children after just six months, scientists have found.... Read more »

Woo, C., & Leon, M. (2013) Environmental Enrichment as an Effective Treatment for Autism: A Randomized Controlled Trial. Behavioral Neuroscience. DOI: 10.1037/a0033010

May 23, 2013
04:37 AM
32 views

The mindbus technique for resisting chocolate - should we climb aboard?

by Christian Jarrett in BPS Research Digest

Imagine you are the driver & your chocolate cravings are unruly passengers

If someone gave you a bag of 14 chocolates to carry around for five days, would you be able to resist eating them and any other chocolate? That was challenge faced by 135 undergrads in a new study that compared the effectiveness of two different "mindfulness" resistance techniques.

To help them, Kim Jenkins and Katy Tapper taught 45 of their participants "cognitive diffusion", the essence being that "you are not your thoughts". The students were told to imagine that they are the driver of a mindbus and any difficult thoughts about chocolate are to be seen as awkward passengers. The students chose a specific method for dealing with these difficult thoughts/passengers and practised it for five minutes - either describing them, letting them know who is in charge, making them talk with a different accent, or singing what they are saying.

Another group of students were taught an acceptance technique known as "urge surfing". They were instructed to ride the wave of their chocolate cravings, rather than to sink them or give in to them. A final group of students acted as controls and were taught a relaxation technique.

As well as trying to resist the bag of chocolates, the students in all conditions were asked to avoid eating any other chocolate as far as possible, and to keep a diary of any chocolate they did eat over the five days.

The key finding is that the mindbus group ate fewer chocolates from their bag as compared with students in the control group. By contrast, the urge surfing group ate just as many of their chocolates as the controls. Diary records showed the differences between groups in their other chocolate consumption was not statistically significant, although there was a trend for the mindbus group to eat less (13g vs. 52g in the urge surfing group and 44g in the control condition). Another way of describing the results is to say that 27 per cent of the mindbus group ate some chocolate over the five-day period, compared with 45 per cent of the urge surfers and 45 per cent of controls.

A habits questionnaire suggested the mindbus technique was more effective because it reduced the students' mindless, automatic consumption of chocolate more than the other interventions. Jenkins and Tapper said their results show the mindbus "cognitive diffusion" technique is a "promising brief intervention strategy" for boosting self-control over an extended time period.

The serious chocaholics among you may not be so convinced. Although the students were recruited on the basis that they wanted to reduce their chocolate consumption, they appeared to show saintly levels of abstinence. On average, even the control group participants ate just 0.69 chocolates from their bag over the five day period (compared with an average of 0.02 chocolates in the mindbus condition; 0.27 in the urge surfing condition). The controls other chocolate consumption amounted to the equivalent of little more than four individual chocolates over five days. You've got to wonder - how serious were these participants about chocolate and just how tasty were the chocolates in that bag?

Another thing - the researchers included a measure of "behavioural rebound". After the students returned to the lab on day five, they were presented with a bowl of chocolates and invited to eat as many as they liked. The groups didn't differ in the amount of chocolates they consumed, which the researchers interpreted as a good sign - after all, the mindbus group hadn't compensated for their restricted intake during the week. But hang on, they also showed no evidence of greater resistance to the chocolate. Sounds to me like the passengers had taken over the bus.

_________________________________

Jenkins, K., and Tapper, K. (2013). Resisting chocolate temptation using a brief mindfulness strategy. British Journal of Health Psychology DOI: 10.1111/bjhp.12050

Post written by Christian Jarrett (@psych_writer) for the BPS Research Digest.

... Read more »

Jenkins, K., & Tapper, K. (2013) Resisting chocolate temptation using a brief mindfulness strategy. British Journal of Health Psychology. DOI: 10.1111/bjhp.12050

Psychology

May 23, 2013
04:33 AM
16 views

Big data for autism and the promise of newborn bloodspots

by Paul Whiteley in Questioning Answers

An episode of the BBC program Horizon on 'Big Data' recently caught my attention. The content was a fascinating insight into how we are living in a data-rich age and how trawling/mining/dredging such data has the ability to advance medicine, predict crime and even make someone a few quid/dollars/euros on the stock market.Gone (data) fishing @ Wikipedia I'm a big believer in big data. In particular how, with the right sources, technology, techniques and people, big data might be able to open up some real insights into many important areas including mental health research* and very possibly autism research with a specific focus on the science of biomarkers to aid things like early diagnosis. Indeed, I'm not the only one talking about this (see here).I've spoken before on this blog about biomarkers for autism and other conditions - the promises, the problems, the future - and how alongside the various autism research banks (genes, brains, etc.) and systems biology chatter, we are just starting to understand the value of those big data resources such as the archived bloodspot samples which so many neonates provide these days.Indeed with the greatest appreciation for pioneers like Robert Guthrie, I offer a post on an interesting paper by Gerald Mizejewski and colleagues** discussing results suggestive of potential candidate biomarkers for autism based on archived bloodspot samples. I should point out that this is not the first time that Dr Mizejewski has talked about the feasability of biomarkers for autism as per this article*** (open-access) as part of quite a distinguished research career it has to be said (see here) with a specific focus on an interesting molecule called alpha-fetoprotein****.The most recent paper is unfortunately not at the time of writing open-access, so I'll just go through a few summary points about the work:This was a retrospective study based on that tantalising resource of archived bloodspot cards which sit in many a hospital basement. Out of a total case group of 200 families with a child with autism, 40 families with children aged between 3-5 years old were initially contacted for participation. This was eventually whittled down to 16 participants (all diagnosed with autism by the same clinician with the same diagnostic manual) for whom archived neonatal bloodspot cards were available. Two age-matched control specimens located immediately before and after the dried bloodspot card in question in the filing system were also chosen.A small 3mm punch of the Guthrie cards was analysed by immunoassay which in this case, probed for 90 potential biomarkers covering everything from neurotrophins to cytokines, immunoglobulins to more direct inflammatory markers (including C-reactive protein).Some fancy statistical modelling was applied to the obtained results - including Bayesian information criterion (BIC) - which eventually resulted in three models of best-fit based on findings from the bloodspots of those who went to be diagnosed with an autism spectrum disorder (ASD). The 'best model' of five compounds included some familiar names to this blog: glutathione-S-transferase (GST), IL-7, IL-5, TNF-beta and something called Lp(a) (lipoprotein a). Most were increased in quantity in the autism samples aside from GST which was decreased.There is a very nice illustration in the paper (Figure 3) showing how the potential connections between the biomarkers identified and some of the more biomedical themes of autism research might fit. So we have methionine metabolism mentioned (see here and here), oxidative stress (see here), gastrointestinal comorbidity (see here) and immune activation (see here) to name a few. It's all very systems biology.The authors caution that their results are preliminary and that although said biomarkers were modelled as being related to autism they "have not been confirmed to be causative with autism".Before I get too carried away with this research, there are a few issues worth mentioning. Yes, the sample size was small in this preliminary communication and indeed very little information is provided about participants outside of just them fulfilling the DSM-IV criteria for autism in terms of things like comorbidity. Also why out of 200 families such a small number of participants were eventually included for study.Indeed there is also an assumption from this study that a biomarker for autism is present in the neonatal phase which for example, might not take into account the issue of behavioural regression that seems to cover quite a percentage of cases.Whilst the identified best-fit biomarkers are of potentially real interest to autism research as per other similar studies (see here), it is the method and resources used in this paper which is the real 'big data' story allied to all those lovely -omics which reign supreme these days. Parents in many countries will be acquainted with that bloodspot taken during the earliest days of infancy to test for various inborn errors of metabolism such as phenylketonuria (PKU). Many people don't however give a second thought to what happens to those bloodspot cards, and how valuable a resource they might constitute. Although not usually in the business of crystal-ball gazing, I would hazard a guess that we are one day going to hear big news about the big data from those archived bloodspot cards; if not with autism in mind, then something else. ----------* Ayers JW. et al. Seasonality in seeking mental health information on Google. Am JPrev Med. April 2013.** Mizejewski GJ. et al. Newborn screening for autism: in search of candidate biomarkers. Biomark Med. 2013; 7: 247-260.*** Mizejewski GJ. Biomarker testing for suspected autism spectrum disorder in early childhood: is such testing now feasible? Biomark Med. 2012; 6: 503-506.**** Mizejewski GJ. Biological roles of alpha-fetoprotein during pregnancy and perinatal development. Exp Biol... Read more »

Mizejewski GJ, Lindau-Shepard B, & Pass KA. (2013) Newborn screening for autism: in search of candidate biomarkers. Biomarkers in medicine, 7(2), 247-60. PMID: 23547820

May 23, 2013
02:00 AM
11 views

Quasi-delusions and inequality aversion

by Artem Kaznatcheev in Evolutionary Games Group

Patient M: It’s impossible —- no one could urinate into that bottle -— at least no woman could. I’m furious with her [these are the patient's emphases] and I’m damned if I am going to do it unless she gives me another kind of bottle. It’s just impossible to use that little thing. Analyst: It […]... Read more »

Fehr, E., & Schmidt, K. (1999) A Theory of Fairness, Competition, and Cooperation. The Quarterly Journal of Economics, 114(3), 817-868. DOI: 10.1162/003355399556151

May 23, 2013
01:48 AM
19 views

What if 501(c)4 Organizations Had to Disclose Their Donors?

by Eric Horowitz in peer-reviewed by my neurons

The IRS kerfuffle has increased interest in the tax code by about 5700%, and one outcome is that people are starting to put the various exemption groups under a microscope. Dylan Matthews has thoughtful piece on 501(c)4 organizations, the groups at the center of the scandal. Matthews thinks the real issue is disclosure, and it’s [...]... Read more »

Dowling, C., & Wichowsky, A. (2013) Does It Matter Who's Behind the Curtain? Anonymity in Political Advertising and the Effects of Campaign Finance Disclosure. American Politics Research. DOI: 10.1177/1532673X13480828

May 22, 2013
05:00 PM
22 views

The carbon footprint from running shoes

by Craig Payne in Running Research Junkie

The carbon footprint from running shoes... Read more »

Cheah, L., Ciceri, N., Olivetti, E., Matsumura, S., Forterre, D., Roth, R., & Kirchain, R. (2013) Manufacturing-focused emissions reductions in footwear production. Journal of Cleaner Production, 18-29. DOI: 10.1016/j.jclepro.2012.11.037

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