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  • January 13, 2014
  • 03:36 PM

Cristiano Ronaldo - How many times did he undergo an MRI exam?

by Know Your Images in Know Your Images

Cristiano Ronaldo was announced today Ballon d'Or and it made me remember something I read some time ago about football players and their injuries. Most of football players injuries are assessed with medical imaging. Medical Imaging provides information about the extent of the injury (e.g. involvement of tendons) and also information about the recovery. The most important exams are: MRI and Ultrasound. Some clubs even have their own ultrasound machine. However, it is still recognized among experts that medical imaging for sports injuries needs further research, because at times it still does not have high sensitivity. So how many times did Cristiano Ronaldo undergo an MRI exam?Ate least three that I could find:November 2013 August 2010October 2009More information here and there:Woods C, Hawkins RD, Maltby S, Hulse M, Thomas A, Hodson A, & Football Association Medical Research Programme (2004). The Football Association Medical Research Programme: an audit of injuries in professional football--analysis of hamstring injuries. British journal of sports medicine, 38 (1), 36-41 PMID: 14751943... Read more »

Woods C, Hawkins RD, Maltby S, Hulse M, Thomas A, Hodson A, & Football Association Medical Research Programme. (2004) The Football Association Medical Research Programme: an audit of injuries in professional football--analysis of hamstring injuries. British journal of sports medicine, 38(1), 36-41. PMID: 14751943  

  • January 13, 2014
  • 01:04 PM

Scientist Proposes ‘Comminution’ as Alternative to Fracking

by dailyfusion in The Daily Fusion

Instead of pumping deep underground enormous amounts of water to fracture shale, Northwestern University professor Zdeněk P. Bažant proposes exploring an alternative to fracking: using the kinetic energy of high-rate shearing generated by an underground explosion to reduce the rock to small fragments, so as to release the gas trapped in its pores.... Read more »

  • January 9, 2014
  • 05:00 PM

Best practices addendum: find and follow the conventions of your programming community

by Juan Nunez-Iglesias in I Love Symposia!

I suggest one more piece of advice for the list of Wilson et al's Best Practices for Scientific Computing, in PLOS Biol.... Read more »

Greg Wilson, DA Aruliah, C Titus Brown, Neil P Chue Hong, Matt Davis, Richard T Guy, Steven HD Haddock, Kathryn D Huff, Ian M Mitchell, Mark D Plumbley.... (2014) Best Practices for Scientific Computing. PLoS Biol, 12(1). DOI: 10.1371/journal.pbio.1001745  

  • January 8, 2014
  • 02:21 PM

High-Temperature Optical Gas Sensing to Increase Power Plant Efficiency

by dailyfusion in The Daily Fusion

The sensors team at DOE’s National Energy Technology Laboratory (NETL) is working on sensor technologies to enable embedded gas sensing at high temperature. The team’s goal is to develop novel materials with large optical responses and high-temperature stability for integration with optical sensor platforms.... Read more »

  • January 8, 2014
  • 09:54 AM

Google Biases Your Search for Scientific Information

by Nura Rutten in United Academics

Top-ranked sites on Google have different thematic emphasis than lower-ranked sites when searching for scientific information.... Read more »

  • January 8, 2014
  • 05:01 AM

Autism, gastrointestinal disorders and comorbidity clusters

by Paul Whiteley in Questioning Answers

I start this post with a few important observations. Please feel free to disagree with me (as long as you can provide peer-reviewed evidence for your alternate viewpoint).Bunting @ Wikipedia (1) Comorbidity can, and quite frequently does, surround a diagnosis of autism.(2) Gastrointestinal (GI) issues form an important part of that comorbidity spectrum.(3) The relationship between autism and comorbidity is, at present, poorly understood insofar as which influences the appearance of which and how the two are related.So, with those statements in mind, I offer some discussion today on two potentially very important papers which variably reference the above points.The first paper is from Brittany Peters and colleagues* (with many, many thanks to Natasa for the paper) which suggests that there indeed may be an important relationship between GI issues and rigid-compulsive behaviours noted in cases of autism. The second paper is from Finale Doshi-Velez and colleagues** (again, with thanks to Natasa) who looked at 'comorbidity clusters' when it comes to the autism spectrum.Both these papers come from groups who have some 'research form' in their respective areas. For the Peters paper it comes in the guise of the valuable research contribution from Gorrindo and colleagues*** which basically said that yes, parents might know when their children with autism present with bowel issues: "parents were sensitive to the existence, although not necessarily the nature, of GID [gastrointestinal dysfunction]". For the Doshi-Velez paper I'll link back to the paper by Kohane and colleagues**** (covered in this post) and their notion of 'significantly over-represented' when it comes to the comorbidity burden with autism in mind.The more recent papers make for interesting reading. Starting with the Peters paper:The authors start with a hypothesis: "a possible association between rigid-compulsive behaviors and GI symptoms" based on their clinical experience of the autism spectrum conditions.They tested their hypothesis on data from participants (N=5076) in the Autism Treatment Network (ATN) and various measures collected from the ATN database. Alongside including diagnostic data, the database also contains data from a GI symptom questionnaire; both of which were used to collect information for their study analysis.Results: Nearly half of the total cohort (43.5%) "had at least one GI symptom". In light of other quite recent reports (see here and here) this finding is not totally unexpected.Based on data from children (aged 2-17 years) - nearly 3000 of which were in the 'no GI symptoms' group (n=2957) and 806 in the 'constipation plus diarrhea or underwear staining' - several other details emerged from the data. The latter GI symptoms group were "more likely to have a parental report of repetitive behavior.... or compulsive behavior... and OCD [obsessive compulsive disorder] diagnosis". Ritualistic behaviours were also picked up more frequently in the GI group by clinician report (ADOS) over the no GI symptoms group.A few other research nuggets: children in GI symptoms group were "more likely to have a family history of anxiety or OCD" and also more likely to have received "treatment with an atypical antipsychotic".The authors conclude that, allowing for potential issues with the use of the ATN database and missing values, "all five primary measures of rigid-compulsive behavior were significantly associated with constipation and diarrhea or underwear staining". And then we have the Doshi-Velez paper:This was a study looking at "patterns of co-occurence of medical comorbidities in ASDs".Electronic medical records or rather electronic health records (EHR) were the source material for the paper and in particular, the ICD-9 codes relevant to particular conditions derived from the i2b2 National Center for Biomedical Computing (N=13,740). This sounds to me like a similar job to that of SHRINE (used in the previous Kohane paper)."Key patterns" identified from this rather large participant group were then tested on a smaller, independent cohort comprising 496 participants from Wake Forest University Health Sciences.With the application of some technical and statistical wizardry, various subgroups were identified within the cases examined based on the clustering of comorbidity alongside the diagnosis of autism.Results: "Four subgroups were identified" based on medical comorbidity and the paper offers quite a bit of detail about the hows and whens certain comorbidity tend to present.Group 1. That old comorbidity nemesis seizures (I assume to indicate some kind of epilepsy) was the focus for the first group with a prevalence of 77% within this group. Group 2. Then came in "multisystem disorders" to form group 2 which included GI disorders (distinct from just functional GI issues). That being said "early ear infections" seemed to stand head and shoulders above other comorbidities for this group particularly with preschool presentation. Group 3. Next for comorbidity was group 3 "characterised by psychiatric disorders" (33%). This group "had the highest rate of individuals with Asperger syndrome and the lowest rate of intellectual disability" and included some familiar conditions including anxiety (see here). That being said (again!), "Hyperkinetic syndrome of childhood" also prominently featured in the group 3 comorbidity profile. Group 4. Finally, there was a 'not' resolved group. Not much more to say there really.Buried in the text is the quite alarming suggestion that: "All of these subgroups had higher levels of cardiac disorders" which, similar to the example of schizophrenia (see here), implies that health screening should be high on any physician's list when someone presents with autism save any charges of health inequality being levelled.The authors conclude that the identification of these comorbidity subgroups centred on the autism spectrum may very well indicate "distinct etiologies with different genetic and environmental contributions". I'm minded to say that we have another possible piece of evidence pertinent to the plural concept of 'the autisms'.Combined, both these papers offer some really quite important information about the autisms and their very complicated presentation including comorbidity. I would hasten to point out that there is still quite a bit of 'fuzziness' about these results as for example, seen in a quote from the Doshi-Velelz paper: "The 3 subgroups from our original clustering analysis consisted of <10% [less than 10%] of the overall sample". In short, it's complicated. But don't let that take anything away from these results...Oh and since we're on the topic of 'the autisms'... Read more »

  • January 7, 2014
  • 11:44 AM

Researchers Coordinate Wind Power Generation to Minimize Disruptions

by dailyfusion in The Daily Fusion

Researchers from North Carolina State University and Johns Hopkins University have devised a technique to coordinate wind power generation and energy storage in order to minimize the potential for power disruptions.... Read more »

  • January 6, 2014
  • 06:38 PM

A Missing Genetic Link in Human Evolution

by Perikis Livas in Tracing Knowledge

Humans have multiple copies of a gene known as SRGAP2, which is thought to be involved in brain development. Chimps and orangutans have only one copy.

By: Emily Singer

Further reading... Read more »

Charrier C, Joshi K, Coutinho-Budd J, Kim JE, Lambert N, de Marchena J, Jin WL, Vanderhaeghen P, Ghosh A, Sassa T.... (2012) Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Cell, 149(4), 923-35. PMID: 22559944  

Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner PA, & Eichler EE. (2007) Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nature genetics, 39(11), 1361-8. PMID: 17922013  

Marques-Bonet T, & Eichler EE. (2009) The evolution of human segmental duplications and the core duplicon hypothesis. Cold Spring Harbor symposia on quantitative biology, 355-62. PMID: 19717539  

  • January 6, 2014
  • 05:00 PM

Synthetic Biology: Engineering Life To Examine It

by Jalees Rehman in The Next Regeneration

Two scientific papers that were published in the journal Nature in the year 2000 marked the beginning of engineering biological circuits in cells. The paper "Construction of a genetic toggle switch in Escherichia coli" by Timothy Gardner, Charles Cantor and James Collins created a genetic toggle switch by simultaneously introducing an artificial DNA plasmid into a bacterial cell. This DNA plasmid contained two promoters (DNA sequences which regulate the expression of genes) and two repressors (genes that encode for proteins which suppress the expression of genes) as well as a gene encoding for green fluorescent protein that served as a read-out for the system. ... Read more »

Daniel R, Rubens JR, Sarpeshkar R, & Lu TK. (2013) Synthetic analog computation in living cells. Nature, 497(7451), 619-23. PMID: 23676681  

  • January 4, 2014
  • 02:07 PM

Science Is Interpretation

by Neuroskeptic in Neuroskeptic_Discover

You don’t need new data to produce new science. A re-analysis or re-interpretation can be just as important and original as a new set of results. I say this because there’s an interesting discussion going on over at PubPeer. In brief, British physicists Julian Stirling and colleagues have released a draft paper using reanalysis to […]The post Science Is Interpretation appeared first on Neuroskeptic.... Read more »

Julian Stirling, Ioannis Lekkas, Adam Sweetman, Predrag Djuranovic, Quanmin Guo, Josef Granwehr, Raphaël Lévy, & Philip Moriarty. (2013) Critical assessment of the evidence for striped nanoparticles. arXiv. arXiv: 1312.6812v1

  • January 3, 2014
  • 09:03 AM

HZB Scientists Upgrade Chalcopyrite Solar Cells

by dailyfusion in The Daily Fusion

A team of scientists at the Helmholtz-Zentrum Berlin for Materials and Energy have developed a way to produce chalcopyrite solar cells without cadmium-based buffer layer. A single layer takes on the job of what used to be two layers, doing away with the wet chemical process. Despite a much simplified production method, efficiencies of greater than 18 percent are well within reach.... Read more »

Klenk, R., Steigert, A., Rissom, T., Greiner, D., Kaufmann, C. A., Unold, T. and Lux-Steiner, M. Ch. (2013) Junction formation by Zn(O,S) sputtering yields CIGSe-based cells with efficiencies exceeding 18%. Progress in Photovoltaics: Research and Applications. DOI: 10.1002/pip.2445  

  • December 19, 2013
  • 12:34 PM

When Roughly Is Good Enough: Approximate Computing Saves Energy

by dailyfusion in The Daily Fusion

Scientists are creating a new type of computers capable of “approximate computing”—performing calculations that are good enough for certain tasks that don’t require perfect accuracy—potentially doubling efficiency and reducing energy consumption.... Read more »

Swagath Venkataramani, Vinay K. Chippa, Srimat T. Chakradhar, Kaushik Roy, & Anand Raghunatha. (2013) Quality programmable vector processors for approximate computing. Proceedings of the 46th Annual IEEE/ACM International Symposium on Microarchitecture, 1-12. info:/10.1145/2540708.2540710

  • December 17, 2013
  • 11:34 AM

Do you know this song?

by Henkjan Honing in Music Matters

A challenging Citizen-Science Name-That-Tune game to study what makes a melody stick in our minds...... Read more »

J.A. Burgoyne et al. (2013) Hooked: A game for discovering what makes music catchy. Proceedings ISMIR. info:/

  • December 16, 2013
  • 11:15 PM

Lower bounds by negative adversary method

by Artem Kaznatcheev in Evolutionary Games Group

Are some questions harder than others? Last week I quantified hardness of answering a question with a quantum computer as the quantum query complexity. I promised that this model would allow us to develop techniques for proving lower bounds. In fact, in this model there are two popular tools: the polynomial method, and the (negative) […]... Read more »

Peter Hoyer, Troy Lee, & Robert Spalek. (2007) Negative weights make adversaries stronger. STOC. arXiv: quant-ph/0611054v2

  • December 16, 2013
  • 05:38 PM

New Method Predicts Power Grid Outages

by dailyfusion in The Daily Fusion

A method of assessing the stability of large-scale power grids in real time could bring the world closer to its goal of producing and utilizing a smart grid.... Read more »

  • December 16, 2013
  • 10:31 AM

New Geothermal Plant Design Uses Carbon Dioxide to Boost Output Tenfold

by dailyfusion in The Daily Fusion

Researchers are developing a new geothermal plant design that will lock away unwanted carbon dioxide (CO2) underground and use it as a tool to boost electric power generation by at least 10 times compared to conventional geothermal power.... Read more »

  • December 12, 2013
  • 07:09 PM

How You can Learn the Programming Basics in an Hour (Code Week 2013)

by Geoffrey Hannigan in Prophage

This probably would have best been posted a few days ago, but this week is computer science education week, or "code week" (coding just means writing computer programs). From December 9th to the 15th, over a million people all over the US are promoting computer science for students ranging from elementary school to college, as well as those of us finished with school. This is not only really cool because it is generating enthusiasm for computer science education, but it is also providing a lot of real educational resources (like online tutorials) for people of all ages to learn how to code (how cool is that?!).... Read more »

Libeskind-Hadas R, & Bush E. (2013) A first course in computing with applications to biology. Briefings in bioinformatics, 14(5), 610-7. PMID: 23449003  

  • December 11, 2013
  • 08:36 AM

New project to remove conflict among galaxy simulations

by Usman Paracha in SayPeople

Main Point:

In a new project dubbed AGORA, researchers are working to remove the discrepancies among different computer models of galaxy formation by comparing different codes against each other.

Published in:


Study Further:

The project AGORA is the short form for Assembling Galaxies of Resolved Anatomy. “We investigate galaxy formation with high-resolution numerical simulations and compare the results across different platforms, and with observation,” Project AGORA website noted.

Nine codes, nine galaxy formation scenarios: this is the sort of problem that AGORA is devoting itself to resolving by comparing different supercomputer simulations. (Credit: Simulations performed by Samuel Leitner (ART-II), Ji-hoon Kim (ENZO), Oliver Hahn (GADGET-2- CFS), Keita Todoroki (GADGET-3), Alexander Hobbs (GADGET-3-CFS and GADGET-3-AFS), Sijing Shen (GASOLINE), Michael Kuhlen (PKDGRAV-2), and Romain Teyssier (RAMSES))
Nine codes, nine galaxy formation scenarios: this is the sort of problem that AGORA is devoting itself to resolving by comparing different supercomputer simulations.
(Credit: Simulations performed by Samuel Leitner (ART-II), Ji-hoon Kim (ENZO), Oliver Hahn (GADGET-2- CFS), Keita Todoroki (GADGET-3), Alexander Hobbs (GADGET-3-CFS and GADGET-3-AFS), Sijing Shen (GASOLINE), Michael Kuhlen (PKDGRAV-2), and Romain Teyssier (RAMSES))

“The physics of galaxy formation is extremely complicated, and the range of lengths, masses, and timescales that need to be simulated is immense,” stated Piero Madau, professor of astronomy and astrophysics at the University of California, Santa Cruz and co-chair of the AGORA steering committee.

“You incorporate gravity, solve the equations of hydrodynamics, and include prescriptions for gas cooling, star formation, and energy injection from supernovae into the code. After months of number crunching on a powerful supercomputer, you look at the results and wonder if that is what nature is really doing or if some of the outcomes are actually artifacts of the particular numerical implementation you used.”

This project would increase our knowledge about the dark matter and its effects on universe as this object is hard to study physically at this time and such models are the best source to study them.


Project AGORA -

Worldwide collaboration announces project AGORA: Ambitious comparison of high-resolution computer simulations of galaxy formation and evolution - University of California (

Astrophysicists launch ambitious assessment of galaxy formation simulations - University of California (

Ji-hoon Kim, Tom Abel, Oscar Agertz, Greg L. Bryan, Daniel Ceverino, Charlotte Christensen, Charlie Conroy, Avishai Dekel, Nickolay Y. Gnedin, Nathan J. Goldbaum, Javiera Guedes, Oliver Hahn, Alexander Hobbs, Philip F. Hopkins, Cameron B. Hummels, Francesca Iannuzzi, Dusan Keres, Anatoly Klypin, Andrey V. Kravtsov, Mark R. Krumholz, Michael Kuhlen, Samuel N. Leitner, Piero Madau, Lucio Mayer, Christopher E. Moody, Kentaro Nagamine, Michael L. Norman, Jose Oñorbe, Brian W. O'Shea, Annalisa Pillepich, Joel R. Primack, Thomas Quinn, Justin I. Read, Brant E. Robertson, Miguel Rocha, Douglas H. Rudd, Sijing Shen, Britton D. Smith, Alexander S. Szalay, Romain Teyssier, Robert Thompson, Keita Todoroki, Matthew J. Turk, James W. Wadsley, John H. Wise, Adi Zolotov, & for the AGORA Collaboration (2013). The AGORA High-Resolution Galaxy Simulations Comparison Project arXiv arXiv: 1308.2669v4... Read more »

Ji-hoon Kim, Tom Abel, Oscar Agertz, Greg L. Bryan, Daniel Ceverino, Charlotte Christensen, Charlie Conroy, Avishai Dekel, Nickolay Y. Gnedin, Nathan J. Goldbaum.... (2013) The AGORA High-Resolution Galaxy Simulations Comparison Project. arXiv. arXiv: 1308.2669v4

  • December 10, 2013
  • 02:16 PM

Piezoelectric Material Plugs Leaks in Transistors, Saves Energy

by dailyfusion in The Daily Fusion

Tom van Hemert and Ray Hueting of the University of Twente’s MESA Institute for Nanotechnology have found a way to “plug” leakage current in transistors by “squeezing” the transistor with a piezoelectric material.... Read more »

van Hemert T., & Hueting R.J.E. (2013) Piezoelectric Strain Modulation in FETs. IEEE Transactions on Electron Devices, 60(10), 3265-3270. DOI: 10.1109/TED.2013.2274817  

  • December 9, 2013
  • 11:45 PM

Quantum query complexity

by Artem Kaznatcheev in Evolutionary Games Group

You probably noticed a few things about TheEGG: a recent decrease in blog post frequency and an overall focus on the algorithmic lens — especially its view of biology. You might also be surprised by the lack of discussion of quantum information processing: the most successful on-going application of the algorithmic lens. I actually first […]... Read more »

Simon, D.R. (1997) On the power of quantum computation. SIAM Journal on Computing, 1474. DOI: 10.1137/S0097539796298637  

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