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How do we visualize the world around us? To answer this question, researchers are using virtual reality to gain insight into how we perceive our surroundings. At the University of Reading, Dr. Andrew Glennerster and his international team are utilizing this technology to study how people generate a three-dimensional representation of the world around them. His recently published PLoS ONE article, A Demonstration of ‘Broken’ Visual Space, tests the theory on whether there is a one-to-one match between reference points in our internal representation of the world and those in our actual surroundings. In this author spotlight, Dr. Glennerster answers questions about his background, his research and his PLoS ONE manuscript.

Let’s start off with your background.  How did you become interested in studying human vision and what role does virtual reality play in assisting your research?

I originally studied medicine at Cambridge. It was an exciting time for vision research there, and in my 3rd year I was taught by lots of the big names in vision like Horace Barlow and John Robson. I found it fascinating and went back to studying vision after I had finished my clinical training.

I have set up a virtual reality lab because it allows us to study people’s 3D vision as they move around.  It is a much more difficult technical challenge than studying 3D vision from binocular stereopsis, like in a 3D movie, but moving around is the main way that animals see in 3D.  To study this process systematically, you need virtual reality.

In your paper, you mention that most theories on three-dimensional vision suggest that the way we represent space in our visual systems assumes that we generate a one-to-one model of space in our brains. Why did your team test this theory and what did you find?

We tested this theory because, for a long time, it has been the dominant one in the literature. It is very easy to believe people have something like a ‘model of the world’ in their heads, but by itself that is not a good argument. We need to move away from accounts that are easy to imagine yet hard to explain at a neural level and toward ones that are based on operations we know the brain can carry out even if they are more conceptually challenging. We do not yet have a well worked out alternative to the one-to-one, ‘reconstruction’  model, but there are some promising beginnings.

When a three-dimensional illusion is depicted in a two-dimensional picture, certain paradoxes occur that wouldn’t be possible to replicate in real life. Given this, how does the Penrose staircase illusion, included in Figure 1 of your paper, compare to your experiment? Where there any similarities?

The similarity between the Penrose staircase and people’s representation of space is that if you tried to build a real 3D model of either you would fail. You cannot make sense of people’s responses in this experiment using a real 3D model. People believe they are in a stable room during the whole experiment. Anyone who suggests that a stable perception comes from the observer having an unchanging 3D ‘model’ of the environment in their head has a difficult time explaining these data. If you try to pick coordinates in some perceptual space for each of the objects in the experiment then you get tangled up in just the same way that you do with the Penrose staircase: you cannot say whether one object is in front of or behind another one. The solution is to give up trying to assign coordinates to each of the objects.

How does your research help further our understanding of human perception? Does it have real world applications?

There is an increasing focus within visual neuroscience on the issue of stability: what is it in the brain that remains constant as we move our eyes around and, even more problematically, as we walk around?

What’s next? Where do you hope to go from here?

This paper attacks the current dominant model, but the next, more positive, stage is to build coherent alternative models. I believe that working with colleagues in computer vision is a good way to do this as robots have to deal with images arriving in real time and react accordingly. Currently in computer vision, new types of representation are being developed that are not at all like a reconstruction. These can act as an inspiration for testable models of human vision. Equally, if neuroscientists produce good evidence about how the brain represents a scene, it could influence the way that mobile robots are programmed.

To learn more about University of Reading’s Virtual Reality Research Group and Dr. Andrew Glennerster’s work, click here. To find more PLoS ONE research on human vision and virtual reality click here.

Filed under:Aggregators, Author Spotlight, Interviews, Media, Topic Focus | Tagged: 2D, 3D, Andrew Glennerster, human vision, illusion, three dimensional, University of Reading, Virtual Reality

Depiction of the SpikerBox (a) and iPhone running custom open-source iOS software (b) used for electrophysiology experiments in the classroom.

Pictured above is the SpikerBox, a low cost, open-source BioAmplifier developed by a team of scientist/engineers in their quest to bring neuroscience education to the K-12 curricula. The SpikerBox can be built by students and teachers in the classroom and enables a variety of experiments that, in the authors’ words, “provides a great way to learn about how the brain works by letting you hear and even see the electrical impulses of neurons!”

In their manuscript, “The SpikerBox: A Low Cost, Open-Source BioAmplifier for Increasing Public Participation in Neuroscience Inquiry” published last week in PLoS ONE, authors Timothy C. Marzullo and Gregory J. Gage describe the design of the SpikerBox and detail experiments employing the device in a classroom setting. They also provide learning materials and supplemental resources, including an assembly guide and student questions, for use in a lesson plan. Marzullo and Gage’s work is an excellent example of bringing together open-source hardware and open-access publication to support science education.

From the abstract:

Although people are generally interested in how the brain functions, neuroscience education for the public is hampered by a lack of low cost and engaging teaching materials. To address this, we developed an open-source tool, the SpikerBox, which is appropriate for use in middle/high school educational programs and by amateurs. This device can be used in easy experiments in which students insert sewing pins into the leg of a cockroach, or other invertebrate, to amplify and listen to the electrical activity of neurons. With the cockroach leg preparation, students can hear and see (using a smartphone oscilloscope app we have developed) the dramatic changes in activity caused by touching the mechanosensitive barbs. Students can also experiment with other manipulations such as temperature, drugs, and microstimulation that affect the neural activity. We include teaching guides and other resources in the supplemental materials. These hands-on lessons with the SpikerBox have proven to be effective in teaching basic neuroscience.

Filed under:Aggregators, Featured Image, Topic Focus, Worth A Thousand Words | Tagged: bioamplifier, Education, Neuroscience, Spikerbox

Increasing your vegetable and fruit intake could improve your appearance, according to a new study. Scientists from the University of St Andrews in Scotland observed 35 participants who increased their fruit and vegetable intake over a 6 week period. They noticed significant changes in the skin’s yellow and red coloring, due to the absorption of carotenoids. To measure the impact of this change, undergraduate students then viewed images of those individuals with increased pigmentation and reported the subject’s appearance as more attractive and healthy. You can read more about this article at NPR, The Huffington Post and ABC News.

Fossil remains found in China’s Yunnan Province provide evidence of a prehistoric human species researchers are calling the “Red Deer Cave people”, as they were thought to feed on an extinct species of native deer. According to radiocarbon dating, this population lived just 14,500 to 11,500 years ago, and that these remains possess both modern (H. sapiens) and archaic (putative plesiomorphic) traits making the findings rather unusual. National Geographic, The Guardian and The History Channel covered this study.

In January of 2011, Daryl Bem of Cornell University published a study in the Journal of Personality and Social Psychology suggesting the existence of precognition, or the ability to predict future events. Dr. Bem invited other scientists in the field to replicate the study, to encourage scientific credibility. A team of researchers, led by Dr. Stuart Ritchie independently replicated the study three times, and were unable to replicate the results. The Chicago Tribune The Guardian and MSNBC covered this story.

No other animal can bite as powerfully as the crocodile, according to a new study covered by National Geographic, The New York Times and The Huffington Post. For the first time, scientists from the University of Florida used a transducer, a device that converts pressure into an electrical signal, to record bite forces and tooth pressures in all 23 existing crocodilian species. They found that the Crocodylus porosus, or the saltwater crocodile, bites with 3,689 pounds of force, the highest recorded of any living creature.

For more in-depth coverage on news and blog articles about PLoS ONE papers, please visit our Media Tracking Project.

Filed under:Aggregators, Images, Media | Tagged: appearance, crocodile bite, Daryl Bem, fruit, media roudup, PLoS ONE News, Red Deer Cave People, vegetable

The American Heart Association Council on Functional Genomics and Translational Biology recently released their list of “Top Advances in Functional Genomics and Translational Biology for 2011” and we are pleased to announce that PLoS ONE article “A mighty small heart: the cardiac proteome of adult Drosophila melanogaster”(1) is one of 10 featured publications!  All 10 articles were summarized in a paper published in Circulation: Cardiovascular Genetics, published by the American Heart Association(2).  The finalists were selected from hundreds of papers in the literature, with input from the Early Career Committee of the Council on Functional Genomics and Translational Biology.

In this article, Cammarato and colleagues describe the full complement of proteins that exist in the adult Drosophila heart.  The insect heart, also referred to as the dorsal vessel, is a simple pulsing tube that maintains the flow of haemolymph (ie. bug blood) through its open circulatory system (lower image and inset, shown with nearby abdominal muscle).  The haemolymph is not restricted to vessels — there are no veins and arteries — but instead bathes the tissues in one big internal cavity.  Unlike our circulatory systems, the insect system has no role in delivering oxygen to tissues and cells, so the haemolymph contains no red blood cells.  Similarly to our system, it does carry various immune cells and nutrients necessary for the health and function of the animal.  Despite any differences, we have long known that many of the genes involved in making a fly heart are the same as those needed to make a mammalian heart.

The authors of the PLoS ONE study carry out a comprehensive survey of proteins that make up the adult Drosophila heart.  Importantly, they compared their results to those found by researchers that have examined adult mouse hearts, and the similarities they identified are astonishing.  Essentially, the authors have paved the way for new studies that will use Drosophila in research of heart disease and its treatment.

For decades, research in Drosophila has provided insight into various complex biomedical problems, and now we can turn to this model to fight the number one cause of death worldwide (3).  We offer our heartfelt congratulations to Cammarato and colleagues, and we ask that you forgive the pun.

1. Cammarato A, Ahrens CH, Alayari NN, Qeli E, Rucker J, et al. (2011) PLoS ONE 6(4): e18497. doi:10.1371/journal.pone.0018497
2. Circulation: Cardiovascular Genetics. 2012; 5: 143-145 doi: 10.1161/​CIRCGENETICS.111.962621
3. http://www.who.int/mediacentre/factsheets/fs310/en/index.html

Images by André Karwath, used under CC-BY-SA license http://commons.wikimedia.org/wiki/File:Drosophila_melanogaster_-_side_(aka).jpg and from http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0018497

Filed under:Aggregators, Awards, General, Images, Topic Focus | Tagged: 2011, Awards, cardiac proteome, Drosophila, fly heart, genes, Top Advances in Functional Genomics and Translational Biology

Tibetans and Incas are so well adapted to their high altitude homes that the low oxygen levels don’t even faze them, but for those of us living near sea level, traveling up to the mountains can put a lot of stress on our bodies.  Even so, we can still do some of our own short-term biological adjustments, and a new study published today in PLoS ONE identifies some of the specific genetic changes that are involved in this high altitude acclimation.

The research team, composed of 26 scientists from institutions in China and Denmark, studied four climbers of Himalayan peak Mount Xixiabangama, which rises 8,012 meters, or 26,286 feet, above sea level. (For comparison, Mount Everest is 8,848 meters tall.)  They collected blood samples before, during, and after the trip, which took almost 30 days, and then determined how the climbers’ gene expression – which genes were “on” or “off” – changed over time.

Changing gene expression is one of the fastest ways to adjust to a new environment or situation. The DNA itself can’t change to accommodate rapidly developing needs, but gene expression is can change quickly and plays a large role in determining how a cell behaves. By looking at the climbers’ gene expression, the researchers aimed to find out which genes were most important for the physiological changes that helped the climbers temporarily adjust to life at high altitude.

The results showed a complex network of expression changes, particularly for genes involved in red blood cells and inflammation, which makes sense given the unique rigors of high altitude climbing. As a climber myself (though not nearly to the same extent as those in this study), I’m now left with the question of how my own gene expression may change while I’m on the wall.

Citation: Chen F, Zhang W, Liang Y, Huang J, Li K, et al. (2012) Transcriptome and Network Changes in Climbers at Extreme Altitudes. PLoS ONE 7(2): e31645. doi:10.1371/journal.pone.0031645

Image source: Rupert Taylor-Price on Flickr

Filed under:Aggregators | Tagged: Climbing, Editor's choice, Gene expression, genetics, Network analysis, Transcriptome

Egg sac of the spider Meta menardi.

Spiderman, watch out! There’s a new, super-strength spider silk in town! Researchers from Politecnico di Torino in Italy performed stress tests on the stalks of silk egg sacs produced by the cave spider, Meta menardi (pictured above), and suggest that it could be the most stretchable spider silk ever tested.

The scientists,  led by Dr. Nicola Pugno, collected 15 egg sacs from different caves in Piedmont (a north-western region of Italy), and used a tensile testing machine to pull on the stalk of the sac until the fibers broke. They recorded that silk strands produced by these spiders can stretch up to 7.5 times their original length, which could bode well for future understanding of nano-materials.

The researchers claim that such results may be linked to the fact that these egg sacs were collected from nature, and thus more reflective of actual stresses, as opposed to silk that may have been produced in a lab.

Read the full article here.

Filed under:Aggregators, Images, Media | Tagged: egg sacs, image, spider silk, Worth a Thousand Words

This month in PLoS ONE: synchronized eating, depression’s link to working overtime (surprise!), a step towards understanding Alzheimer’s, the oldest living thing on earth and a species of very small chameleons.

Your choice of dining companion may have a greater influence on your meal consumption than you first expect. Researchers found that 70 pairs of female diners tended to mimic each other in eating behavior, taking bites simultaneously and consuming similar amounts of food. This study was covered by Scientific American, MSNBC and CNN

It seems logical to connect working long hours with feeling down but now you can point to new scientific evidence of this correlation. In this five year study of more than 2,000 British civil servants, men and women who routinely worked 11 hours or more per day more than doubled their risk of developing depression, compared with co-workers who put in eight hour days. This study was covered by ABC, NPR, LA Times and others.

The implications are profound for new research supporting the concept that Alzheimer’s spreads through the brain like an infection. Originating in the entorhinal cortex, abnormal tau proteins seem to progress from neuron to neuron across synapses, creating tangles of protein fibers in areas needed for memory creation and storage. Covered by NPR, The New York Times and Reuters, this research could be used to help diagnose Alzheimer’s in earlier stages and improve treatment.

The oldest living thing on earth may be a giant patch of seagrass found in the Mediterranean. Beds of this clonal organism, Posidonia oceania, are likely at least 100,000 years old, almost 60,000 years older than the previously thought oldest living organism (a Tasmanian plant), but may be under threat from rising ocean temperatures. This study was covered by the Huffington Post, BBC and Voice of America.

Tiniest but not least, a newly discovered dwarf chameleon species represents “an extreme case of island dwarfism” in Madagascar. Reaching only about 16mm fully grown, these chameleons are among the smallest vertebrates in the world. Their discovery was covered by Wired, Discovery and by Slate on Youtube.

For more in-depth coverage on news and blog articles about PLoS ONE papers, please visit our Media Tracking Project.

Image Credit: Frank Glaw

Filed under:Media | Tagged: Alzheimer's, depression, dining companions, Madagascar, seagrass, tiny chameleons, work

Forget the elephant in the room. Try the elephant on the farm, raiding crops for a tasty treat while risking the wrath of frustrated farmers.

This tug-of-war for territory and resources is just one manifestation of the growing tensions between economic development and environmental conservation, and today we have two papers, from two continents, that provide new information about how we might be able to strike the right balance between sometimes conflicting development goals.

The first study compares the behavior of Asian elephants in fragmented versus non-fragmented forests in Borneo. Using a satellite tracking program to monitor five female elephants, the researchers found that the home range, or the area covered by a wild animal over the course of a year, for elephants in non-fragmented forest was approximately 250 to 400 square kilometers. When the forest was fragmented, though – primarily by human developments such as roads, farms, and villages – the home range nearly doubled, to about 600 square kilometers.

The authors, led by Raymond Alfred of Sabah University of Malaysia, suggest that the significant increase in the home range could reflect increased difficulty in satisfying food and water needs in a highly fragmented environment. Their results could possibly help alleviate some of this elephant stress by providing guidelines for determining how much space is needed for long-term elephant preserves.

Using such guidelines could also help control elephant crop raiding, which has become a major problem in both Asia and Africa. As people move into  elephant habitat, elephants have begun sampling their crops to enrich their diet – leading farmers to sometimes kill the thieves, which is particularly concerning given the conservation listings for both Asian (endangered) and African (vulnerable) elephants.

There has been some work to develop methods to protect both the elephants and the crops, including installing “beehive fences” as deterrents (see this paper for more information about the surprising relationship between elephants and bees), but today’s paper, led by Patrick Chiyo of University of Notre Dame, takes a different angle, looking at what can cause an elephant to initiate crop-raiding behavior.

Crop raiding is known to be more common among male than female elephants, so the team investigated the raiding behavior of male African elephants in Amboseli National Park in Kenya. Out of about 365 male elephants, they identified 43 individual crop raiders, and estimated that there could be an additional 40 perpetrators who remained undetected. In other words, about 20% of the male elephants may be raiders. Males at their reproductive peak were nearly twice as likely to raid, and the authors suggest that his behavior could be due to increased energetic needs for mating, or increased risk-taking behavior associated with their age.

Furthermore, the elephants were more likely to raid if their elephant “friends” were raiders as well. It’s not all about peer pressure though – the effect gets stronger the older the raider friends are, suggesting that the elephants are actually learning from their older, wiser companions. This implied intelligence should come as no surprise, given all the evidence for elephant smarts (see, for example, this study on elephant learning) – and it makes me think that, conservation concerns aside, elephants might have something to teach us about respecting our elders.

Image source: brittanyhock on Flickr

Filed under:Aggregators | Tagged: animal behavior, conservation, development, elephant

Seamounts – submarine ‘mountains’ which can rise from the seafloor to heights of several km – are found in every ocean basin on Earth; there are at least 30,000 large seamounts that are over 1 km high, and hundreds of thousands of smaller knolls.

Seamounts are important features of the deep sea for a number of reasons.  They span a wide depth range, and in many areas provide the only shallow habitat for animals that cannot survive at the depths of the abyssal plains. Most are volcanic in origin, and so are composed of hard rock, enabling animals like corals and sponges to attach. Their shape and form can also enhance localized water movement and create areas of upwelling and eddies which bring in food and trap animals on the seamount. Together these characteristics can result in some seamounts being biological ‘hotspots’ providing feeding habitats and spawning grounds for fish and other larger animals, even including seabirds and marine mammals.  This makes the study of seamount ecology very important for the understanding of ocean ecosystems. However, because seamounts are also sites for commercial fisheries, and potential sources of valuable minerals and heavy metals, there is also an urgent need to ensure sustainable management of human activities.

Despite their biological importance, however, little is known about them. Less than 300 have been surveyed in any detail, and this lack of good information of seamount biodiversity makes it difficult for managers to balance exploitation and conservation.

Introducing CenSeam

The new Census of Marine Life Collection on Seamouts (CenSeam), which launched today in PLoS ONE, aims to improve our knowledge of seamount ecology and answer pressing questions for their management. Running from 2005-2010, it was one of 14 field projects comprising the Census of Marine Life program.

Its principle goal was to create an international network of scientists to examine some of the key research questions surrounding seamounts.  Out of these questions, two overarching themes developed:

1. What factors drive the composition and diversity of communities on seamounts, and how do they differ from non-seamount communities?
2. What are the impacts of human activities on the structure and function of seamount communities?

While CenSeam produced a number of papers, compilations and reviews*, not all of the work was finished by the program’s official end in 2010.  This ongoing work has now become the core of a special PLoS ONE Collection on seamounts, adding to a number of other collections – covering subjects from microbes and chemosynthetic environments to continental margins – conceived under the Census of Marine Life program.

The Collection is being launched with 10 scientific papers, and two more general reviews of CenSeam: one evaluates the organization, administration, and conduct of the project –what worked and what didn’t in setting up a complex international program; and a second overview which looks at some of CenSeam’s primary findings and their implications for setting future science priorities and developing the best ways to manage and conserve seamount environments and resources.

The 10 papers in the Collection vary widely in subject matter, including:

• detailed descriptions of the faunal communities on seamounts (invertebrates and fishes)
• accounts of new species
• studies on biological characteristics and behavior of seamount fauna
• analyses of similarities and differences between seamounts and other environments (e.g., canyons)
• new results from seamounts in regions of the Indian Ocean and near Antarctica that have not been sampled before.

The Collection is available at www.ploscollections.org/CenSeam

Further papers have been submitted, or are currently being prepared, to add to the Collection in coming months.

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* Among these were a book on “Seamounts: Ecology, Fisheries and Conservation”, special issues on seamounts in two journals (‘Oceanography” and “Marine Ecology”), a chapter in a book summarizing the Census of Marine Life, and a review paper in “Annual Review of Marine Sciences”.

This post was written by aimee whitcroft, Web Communications Advisor at NIWA. More information on the CenSeam Collection can be found at http://censeam.niwa.co.nz/.

Filed under:Aggregators | Tagged: Censeam, Census of Marine Life, COML, PLoS ONE, seamounts

I’m trying to submit my manuscript, but when I follow the prompt to check my Artwork Quality results after I build my PDF, I see a “Fail” message. What happened?

First of all, don’t panic! We know you spent a long time putting your manuscript file together. Don’t worry, you won’t lose any of that time.

Next, check to make sure you’ve followed the Figure & Table Guidelines. In short, your figures should be in .TIF or .EPS format, and should be under 10MB each.

If your figures are in the correct format and are less than 10MB each in size, and the figures are visible, clear, and readable in your merged PDF, you can override the error message. For the editorial (pre-publication) process, the most important thing is that the Academic Editor and reviewers can see your figures. Once accepted, our Production team will be able to assist you with making any minor but changes to your figures.

However, please be advised that PLoS ONE does not have an author proofing step: you won’t be able to view the pre-publication formatted proof of the paper after it’s accepted but before it is published, so your paper should be as close to publishable as possible in every other respect.

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