Post List

  • February 1, 2011
  • 02:20 PM
  • 1,268 views

modENCODE: the data bonanza ensues

by Mary in OpenHelix

Another of the “big data” projects that is underway is the ENCODE project, or Encyclopedia of DNA Elements, to provide comprehensive annotation of genomic elements.  Some people are aware of this and are using the data already. If you aren’t, you should check out the online tutorial, freely available because it is sponsored by the UCSC ENCODE Data Coordination Center (DCC) team, for an overview of the organization and availability of the ENCODE mammal data that you can find in........ Read more »

Celniker, S., Dillon, L., Gerstein, M., Gunsalus, K., Henikoff, S., Karpen, G., Kellis, M., Lai, E., Lieb, J., MacAlpine, D.... (2009) Unlocking the secrets of the genome. Nature, 459(7249), 927-930. DOI: 10.1038/459927a  

Gerstein, M., Lu, Z., Van Nostrand, E., Cheng, C., Arshinoff, B., Liu, T., Yip, K., Robilotto, R., Rechtsteiner, A., Ikegami, K.... (2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science, 330(6012), 1775-1787. DOI: 10.1126/science.1196914  

The modENCODE Consortium., Roy, S., Ernst, J., Kharchenko, P., Kheradpour, P., Negre, N., Eaton, M., Landolin, J., Bristow, C., Ma, L.... (2010) Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science, 330(6012), 1787-1797. DOI: 10.1126/science.1198374  

  • February 1, 2011
  • 02:00 PM
  • 1,261 views

The trouble with encryption

by sciencebase in Sciencebase Science Blog

Lots of us encrypt files using the likes of AxCrypt and TrueCrypt. If there’s a risk of losing a device carrying sensitive information such as contacts, email, bank statements, invoices etc, then it is worth using such a tool. The ease with which a file, folder or even complete hard drive or USB device can [...]The trouble with encryption is a post from: Sciencebase Science Blog
... Read more »

George R.S. Weir, & Michael Morran. (2010) Hiding the hidden message: approaches to textual steganography. Int. J. Electronic Security and Digital Forensics, 3(3), 223-233. info:/

  • February 1, 2011
  • 12:37 PM
  • 1,257 views

Oxytocin, ethnocentrism and "hormonal determinism"

by Daniel in Ego sum Daniel

There is an inordinate readiness, both within scientific circles and in popular scientific understanding, to ascribe direct causation to the actions of hormones, especially when it comes to moods and behaviors. For example, consider how you’d usually interpret the common expression “being hormonal”. I consider the thought that hormones somehow “control” our moods and behaviors a falsehood; a popular misunderstanding or oversimplification that hinders the understanding of what’s actu........ Read more »

De Dreu, C., Greer, L., Van Kleef, G., Shalvi, S., & Handgraaf, M. (2011) Oxytocin promotes human ethnocentrism. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1015316108  

De Dreu, C., Greer, L., Handgraaf, M., Shalvi, S., Van Kleef, G., Baas, M., Ten Velden, F., Van Dijk, E., & Feith, S. (2010) The Neuropeptide Oxytocin Regulates Parochial Altruism in Intergroup Conflict Among Humans. Science, 328(5984), 1408-1411. DOI: 10.1126/science.1189047  

  • February 1, 2011
  • 12:21 PM
  • 1,055 views

Real-time Q&As are intense

by Bradley Voytek in Oscillatory Thoughts

Sorry for the self-promotional nature of this post, but I wanted to talk about a novel, interesting experience.A little over a week ago, my research examining how people with prefrontal stroke compensate for brain damage was profiled in a piece in the Washington Post. As with all my research, I did a lay post explaining that work here before.The whole media experience happened very quickly, but was pretty cool. You'll notice that the Washington Post article is actually focused on Rep. Gabrielle ........ Read more »

Voytek B, Davis M, Yago E, Barceló F, Vogel EK, & Knight RT. (2010) Dynamic neuroplasticity after human prefrontal cortex damage. Neuron, 68(3), 401-8. PMID: 21040843  

  • February 1, 2011
  • 12:17 PM
  • 1,481 views

Stress and Neurodegeneration

by Brian Mossop in The Decision Tree

I have a new feature at Scientific American, describing recent research that shows how stress is linked to neurodegenerative diseases like Alzheimer’s and Parkinson’s. In the past, we have feared Alzheimer’s, because people rarely get better once they find out they have the disease. We watch in horror, as our aging relatives slowly become different [...]... Read more »

  • February 1, 2011
  • 12:02 PM
  • 1,618 views

ppGpp mediates cross-talk between the stringent and acid stress responses

by Vasili Hauryliuk in stringent response

We know that stringent response alarmone ppGpp can do about anything, interacting with RNA Polymerase, translational GTPases, polynucleotide phosphorylase, DnaG primase, IMP dehydrogenase and adenylosuccinate synthetase to name a few. In general the result is: production of ribosomes and tRNAs is halted, cell cycle is arrested, and amino acids produced.Well, now one more target was discovered, lysine decarboxylase Ldc1/CadA. Lysine decarboxylase is induced upon acid stress conditions and protect........ Read more »

  • February 1, 2011
  • 11:18 AM
  • 1,776 views

A welding robot for all those hard to reach places

by FrauTech in Design. Build. Play.

Many of the challenges in ship building or ship maintenance stem from environmental concerns: from the seemingly minor in not wanting ship material or ship waste to enter to the ocean to the obvious preventing future spills or catastrophic failures like the Exxon Valdez. One of the solutions to making liquid-cargo ships more resistant to failure is a double hull design.When major disasters like mining disasters or situations like the gulf oil spill occur one question people often ask is why we s........ Read more »

Lee, D., Ku, N., Kim, T., Kim, J., Lee, K., & Son, Y. (2011) Development and application of an intelligent welding robot system for shipbuilding. Robotics and Computer-Integrated Manufacturing, 27(2), 377-388. DOI: 10.1016/j.rcim.2010.08.006  

  • February 1, 2011
  • 10:50 AM
  • 1,230 views

Footsteps of a Dinosaur Deity

by Brian Switek in Dinosaur Tracking

In 1999, construction workers creating a highway from Tibet’s Bangda Airport to Changdu County uncovered a set of enormous tracks. They had been left more than 160 million years ago by a large sauropod dinosaur, but the local Tibetan people had other interpretations. Some believed that the tracks had been left by the “Deity of [...]... Read more »

Xing, Li-da; Harris, Jerald; Currie, Philip. (2011) First record of dinosaur trackway from Tibet, China. Geological Bulletin of China, 30(1), 173-178. info:/

  • February 1, 2011
  • 08:34 AM
  • 1,499 views

Self-Help for Seabirds: How to manage your time and outcompete your neighbors for maximum survival

by Hannah Waters in Sleeping with the Fishes

Last night was my first night in NYC and, as such, it was my first experience with modern-day human foraging: the Trader Joes in Chelsea at 7:30 pm.  Despite the many shelves previously stuffed with various types of bagged lettuce, there was NO LETTUCE LEFT.  No granola bars.  The customers were nasty, ramming their carts into me to get to the dried cranberries.  While sometimes I’ve been to groceries that have been out of a particular item I wanted, I have never thought to myself, &#........ Read more »

Masello, J., Mundry, R., Poisbleau, M., Demongin, L., Voigt, C., Wikelski, M., & Quillfeldt, P. (2010) Diving seabirds share foraging space and time within and among species. Ecosphere, 1(6). DOI: 10.1890/ES10-00103.1  

  • February 1, 2011
  • 08:33 AM
  • 1,327 views

The Size-Weight Illusion is Functional, and It's About Throwing

by Andrew Wilson in Notes from Two Scientific Psychologists

My colleagues, Geoff Bingham and Qin Zhu, have recently published some fascinating data which has emerged from their work on the uniquely human skill, long-distance throwing. This is a novel and rich perception-action task which Bingham and Zhu (and recently, me) have been investigating for some time, with many interesting results. I'll get onto blogging about this project once I've caught up with the coordination studies and have had some time to get my head around the data I'm helping generate........ Read more »

  • February 1, 2011
  • 08:00 AM
  • 2,004 views

Ghrelin Growls at Glucose Tolerance

by Arya M. Sharma in Dr. Sharma's Obesity Notes

Regular readers of these pages probably recall that the hormone ghrelin, released largely from the stomach, is a key regulator of hunger and energy metabolism.
A recent study by Jenny Tong and colleagues from the University of Cincinnati, published in DIABETES, now shows that ghrelin also plays an important role in suppressing the insulin response to [...]... Read more »

  • February 1, 2011
  • 06:37 AM
  • 722 views

A wonderful confirmation

by Marco Frasca in The Gauge Connection

Contributions to proceedings to Ghent conference “The many faces of QCD” are starting to appear on arxiv and today appeared one of the most striking one I have heard of at that conference: Orlando Oliveira, Pedro Bicudo and Paulo Silva published their paper (see here). This paper represents a true cornerstone for people doing computations [...]... Read more »

  • February 1, 2011
  • 06:19 AM
  • 1,630 views

The hot and cold of butterfly dancing

by GrrlScientist in Maniraptora

Hypothesis: environmental temperatures experienced by developing larvae and/or pupae of the butterfly, Bicyclus anynana, controls expression of behaviour and morphology... Read more »

  • February 1, 2011
  • 06:10 AM
  • 1,877 views

Guest post: One cartwheel to rule them all (and in 9-fold symmetry bind them!)

by Wellcome Trust in Wellcome Trust Blog

Centrioles play a key part in cell division – faults can lead to cancer – yet we know little about how they themselves duplicate. Dr John Vakonakis, a Wellcome Trust Research Development Fellow at the University of Oxford, explains how new research is providing some clues. Every day in our lives millions of cells inside [...]... Read more »

Kitagawa D, Vakonakis I, Olieric N, Hilbert M, Keller D, Olieric V, Bortfeld M, Erat MC, Flückiger I, Gönczy P.... (2011) Structural Basis of the 9-Fold Symmetry of Centrioles. Cell. PMID: 21277013  

  • February 1, 2011
  • 06:06 AM
  • 1,167 views

Can fluorescent-‘labelled’ viruses illuminate their mechanisms of pathogenesis?

by Connor Bamford in The Rule of 6ix

Have you ever wanted to visualise viral infection? Ever wanted to observe how they enter and spread throughout their host organism? Ever wanted to know how exactly they caused disease – at the cellular and whole-organism level? Well, this may be entirely possible using fluorescent-labeled recombinant viruses infecting a relevant model system. So how does [...]... Read more »

Lemon, K., de Vries, R., Mesman, A., McQuaid, S., van Amerongen, G., Yüksel, S., Ludlow, M., Rennick, L., Kuiken, T., Rima, B.... (2011) Early Target Cells of Measles Virus after Aerosol Infection of Non-Human Primates. PLoS Pathogens, 7(1). DOI: 10.1371/journal.ppat.1001263  

Coombes, J., & Robey, E. (2010) Dynamic imaging of host–pathogen interactions in vivo. Nature Reviews Immunology, 10(5), 353-364. DOI: 10.1038/nri2746  

  • February 1, 2011
  • 06:06 AM
  • 3,333 views

Can fluorescent-‘labelled’ viruses illuminate their mechanisms of pathogenesis?

by Connor Bamford in The Rule of 6ix

Have you ever wanted to visualise viral infection? Ever wanted to observe how they enter and spread throughout their host organism? Ever wanted to know how exactly they caused disease - at the cellular and whole-organism level? Well, this may be entirely possible using fluorescent-labeled recombinant viruses infecting a relevant model system.[caption id="" align="aligncenter" width="504" caption="GFP-virus infected cells"][/caption]So how does it work?Lemon et al recently report the continued in........ Read more »

Lemon, K., de Vries, R., Mesman, A., McQuaid, S., van Amerongen, G., Yüksel, S., Ludlow, M., Rennick, L., Kuiken, T., Rima, B.... (2011) Early Target Cells of Measles Virus after Aerosol Infection of Non-Human Primates. PLoS Pathogens, 7(1). DOI: 10.1371/journal.ppat.1001263  

Coombes, J., & Robey, E. (2010) Dynamic imaging of host–pathogen interactions in vivo. Nature Reviews Immunology, 10(5), 353-364. DOI: 10.1038/nri2746  

  • February 1, 2011
  • 05:35 AM
  • 2,365 views

The hot and cold of butterfly dancing

by GrrlScientist in GrrlScientist

Hypothesis: environmental temperatures experienced by developing larvae and/or pupae of the butterfly, Bicyclus anynana, controls expression of behaviour and morphology ... Read more »

  • February 1, 2011
  • 05:30 AM
  • 758 views

When the real world is more rational than the model

by Becky in It Takes 30

Those of you who stop by regularly have probably noticed that I rarely write about papers that I don’t think are particularly good.  This may be partly a lingering result of early training (“If you can’t say anything nice, don’t say anything at all”), but is mostly because better papers are more interesting to write [...]... Read more »

Cornforth DM, Reluga TC, Shim E, Bauch CT, Galvani AP, Meyers LA. (2011) Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks. PLoS Computational Biology, 7(1). info:/doi:10.1371/journal.pcbi.1001062

  • February 1, 2011
  • 04:00 AM
  • 1,197 views

How to navigate a Viking longboat with a king, some bees and a DC-8

by Alun in AlunSalt

Jo Marchant has reported on a new paper, On the trail of Vikings with polarized skylight: experimental study of the atmospheric optical prerequisites allowing polarimetric navigation by Viking seafarers, for Nature news. She also adds more on her own blog including the link to the paper that you can access for free. The research is [...]... Read more »

  • February 1, 2011
  • 02:00 AM
  • 814 views

100 cities ranked according to greenhouse gas emissions

by SAGE Insight in SAGE Insight

Cities and greenhouse gas emissions: moving forwardFrom Environment and Urbanization  This study examines greenhouse gas emissions for over 100 cities in 33 countries and suggests 28 policy tools that city governments can use to take action on climate change. It looks at who produces the most, and urges a new look at cities and climate change. [...]... Read more »

Daniel Hoornweg,, Lorraine Sugar and, & Claudia Lorena Trejos Gomez. (2011) Cities and greenhouse gas emissions: moving forward . Environment and Urbanization . info:/10.1177/0956247810392270

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