Ignacio Arganda, a young researcher from San Sebastián de los Reyes (Madrid) working for the Massachusetts Institute of Technology (MIT) is one of the driving forces behind Fiji, an open source platform that allows for application sharing as a way of improving biomedical-image processing. Arganda explains to SINC that Fiji, which has enjoyed the voluntary collaboration of some 20 developers from all over the world, has become a de facto standard that assists laboratories and microscope companies in their development of more precise products.
Ignacio Arganda is a postdoctoral researcher at the Laboratory of Computational Neuroscience of the Massachusetts Institute of Technology (MIT). Along with a group of researchers he implemented Fiji, a platform that allows for applications to be shared in order to improve and advance in the processing and analysis of biomedical imaging. “All of this in open source,” outlines Arganda.
The platform was built from a previous one, ImageJ, which was well known in the industry at the time. ImageJ was not an open source platform but it was publicly accessible. According to Arganda, it had the advantage that any person working in medical imaging could easily create small software applications to resolve their particular problems and then incorporate it into the platform by means of a plug-in (an application which is linked to another providing a new or specific function).
Nonetheless, the researcher adds that this platform became too chaotic with applications of all kinds, some of which were not related to biomedical-imaging. It also began being used to handle astronomical images, in video tracking, etc. “There was a significant lack of control and structure,” he says.
Therefore, “in a spontaneous manner and without any help” this group of researchers decided to create the new open source platform that could put order to that already in place, reusing what was of interest and useful in their work.
"We created a webpage organised like Wikipedia where people could contribute and use their knowledge to help others. To our surprise, it became very popular," he ensures. According to Ignacio Aranda, Fiji currently has 127,000 unique visits (20,000 each month).
(Source: eurekalert.org)
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Filed under Fiji biomedical imaging medical imaging electron microscopy neuroscience science
Mathematical models developed by scientists at the University of Bristol are providing new insights into why the placebo effect exists and when it should occur. Their research is published in the journal of Evolution and Human Behaviour.
A placebo – such as a sugar pill – is a treatment which is not effective through its direct action on the body but works because of its effect on the patient’s beliefs. But if individuals are capable of recovering without external aid, why do they rely on an external cue? In other words, why have individuals not evolved the ability to get better immediately on their own?
Members of the Modelling Animal Decisions group in the University of Bristol’s School of Biological Sciences built mathematical models of the placebo effect which examine the trade-off between the costs and benefits of an immune response when faced with a health problem.
The work is based on an idea proposed by the theoretical psychologist Professor Nicholas Humphrey. He proposed that, as it can be beneficial to hold the immune system back from full operation due to uncertainties about the state of the world (such as the possibility of starvation), cues which indicate a change can therefore lead to an altered level of immune response.
The models take this argument even further and demonstrate that the placebo effect is modulated by the patient’s expectations. Previous studies measuring brain activity using functional magnetic resonance imaging (fMRI) provide experimental evidence which support the models, by showing correlations between the placebo effect and regions of the brain associated with expectation.
The models show why changes to the perceived cost of getting well, the value of being well or external environmental factors can induce the placebo effect.
Dr Pete Trimmer, lead author of the work, said: “The placebo effect comes down to expectations about when to take action. Waiting for a useless pill before taking action is not optimal. But the general responsiveness to cues is adaptive, so it is logical for evolved organisms to display the placebo effect.”
The models indicate that under stress it can be better for the immune system to work less effectively. However, the most important finding of the research is that the particular type of belief in the treatment can lead to positive or negative effects. The belief that a treatment will cure, without any need for the immune system to do anything, could have deleterious effects on the patient’s health.
Now that a theoretical approach has laid the foundations of understanding the placebo effect, future empirical work may provide insights as to how the placebo effect can be invoked and controlled in a clinical environment. The Bristol study clearly shows that the focus of future placebo studies should be shifted to the type of belief patients have about their treatment rather than just whether a treatment is helpful or harmful. A better understanding of the placebo effect may change the code of practice for health practitioners and save human lives.
Source: University of Bristol
Filed under mathematical model neuroscience placebo placebo effect psychology science expectations
The MIT and University of Pennsylvania team decided that mimicking animal behaviour in robotics was not enough — by mimicking the genetic materials that allow those behaviours, they could make a giant leap towards feasible biorobots. It is the first time skeletal muscle has ever been manipulated to react to light, with past studies focusing only on cardiac muscle cells.
"With bio-inspired designs, biology is a metaphor, and robotics is the tool to make it happen," said MIT engineering professor Harry Asada, who has co-authored a paper on the study, due to appear in the journal Lab on a Chip. “With bio-integrated designs, biology provides the materials, not just the metaphor. This is a new direction we’re pushing in biorobotics.”
Filed under biorobotics engineering neuroscience robotics science technology muscle cells
On the surface, ants and the Internet don’t seem to have much in common. But two Stanford researchers have discovered that a species of harvester ants determine how many foragers to send out of the nest in much the same way that Internet protocols discover how much bandwidth is available for the transfer of data. The researchers are calling it the “anternet.”
Filed under technology internet foraging neuroscience ants biology science
Columbia University Medical Center (CUMC) researchers have identified a potential medical treatment for the cognitive effects of stress-related disorders, including post-traumatic stress disorder (PTSD). The study, conducted in a PTSD mouse model, shows that an experimental drug called S107, one of a new class of small-molecule compounds called Rycals, prevented learning and memory deficits associated with stress-related disorders. The findings were published in the online edition of Cell.
Based on his earlier work in heart and muscle disorders, Dr. Marks reasoned that chronic stress could lead to PTSD by destabilizing type 2 ryanodine receptors (RyR2) in the hippocampus, the brain region that plays a central role in learning and memory. RyR2 are channels that regulate the level of calcium in neurons, which is vital to cell survival and function.
“When we examined the hippocampal neurons of the stressed mice, we found that their RyR2 channels had become destabilized and leaky compared with channels from normal non-stressed mice which were not leaky. There was a remodeling of the channels that we had previously seen in heart and skeletal muscles from animal models of chronic diseases including heart failure and muscular dystrophy. We found these same leaky channels in samples from patients with these disorders but not in those from healthy humans,” said Dr. Marks.
Filed under neuroscience brain psychology PTSD stress cognitive function science
USC-led team has designed a low-cost, easily-deployed method for detecting ADHD, Parkinson’s, and Fetal Alcohol Spectrum Disorder
Researchers at the University of Southern California have devised a method for detecting certain neurological disorders through the study of eye movements.
In a study published today in the Journal of Neurology, researchers claim that because Attention Deficit Hyperactivity Disorder (ADHD), Fetal Alcohol Spectrum Disorder (FASD) and Parkinson’s Disease (PD) each involve ocular control and attention dysfunctions, they can be easily identified through an evaluation of how patients move their eyes while they watch television.
“Natural attention and eye movement behavior – like a drop of saliva – contains a biometric signature of an individual and her/his state of brain function or dysfunction,” the article states. “Such individual signatures, and especially potential biomarkers of particular neurological disorders which they may contain, however, have not yet been successfully decoded.”
Typical methods of detection—clinical evaluation, structured behavioral tasks and neuroimaging—are costly, labor-intensive and limited by a patient’s ability to understand and comply with instructions. To solve this problem, doctoral student Po-He Tseng and Professor Laurent Itti of the Department of Computer Science at the USC Viterbi School of Engineering, along with collaborators at Queen’s University in Canada, have devised a new screening method.
Participants in the study were simply instructed to “watch and enjoy” television clips for 20 minutes while their eye movements were recorded. Eye-tracking data was then combined with normative eye-tracking data and a computational model of visual attention to extract 224 quantitative features, allowing the team to use new machine learning techniques to identify critical features that differentiated patients from control subjects.
With eye movement data from 108 subjects, the team was able to identify older adults with Parkinson’s Disease with 89.6% accuracy, and children with either ADHD or FASD with 77.3% accuracy.
Providing new insights into which aspects of attention and gaze control are affected by specific disorders, the team’s method provides considerable promise as an easily-deployed, low-cost, high-throughput screening tool, especially for young children and elderly populations who may be less compliant to traditional tests.
“For the first time, we can actually decode a person’s neurological state from their everyday behavior, without having to subject them to difficult or time-consuming tests,” Itti said.
Source: University of Southern California
Filed under brain disorders eye movements neuroscience psychology science vision diseases
This woman wants to get inside teenagers’ grey matter — by scanning their brains. “Ten years ago, there was virtually nothing out there about adolescents’ brains,” says Sarah-Jayne Blakemore, a cognitive neuroscientist at University College London. “MRI scanning reveals how they change, well into adulthood.”
When Blakemore, 37, began studying teenagers’ brains through behavioural testing and MRI scans eight years ago, she found that the parts of the brain responsible for empathy and social intelligence were soft and constantly morphing. Other studies showed that brains adapt and learn well into adulthood — an important implication for education. "If a child in the UK falls through the net early, the political thinking is that it’s too late to spend public money on them," she says. "That’s not true — funding should be maintained through to their twenties."
To this end, she has helped to set up the Centre for Educational Neuroscience, an inter-institutional project in London which aims to influence educational policy. “We need to instil confidence in teenagers,” she says. As long as they tidy their rooms first.
Source: Wired.co.uk
Filed under neuroscience brain psychology adolescents science
Richard Gershon has a shiny new toolbox for neuroscientists that will revolutionize their clinical research by making it radically faster, cheaper and more accurate. It also will help researchers recruit children and adults for studies because participation will be much less time consuming.
On Sept. 10 and 11, Gershon will introduce the new NIH Toolbox to hundreds of researchers at a special National Institutes of Health (NIH) conference in Bethesda, Maryland. At the end of September, he will give away the tools for free to NIH researchers.
Gershon, an associate professor of medical social sciences at Northwestern University Feinberg School of Medicine, has led an ambitious six-year NIH-funded study reflecting the efforts of 235 scientists around the world that provides the first common measurements for neurological and behavioral health. Currently, one researcher’s test to measure depression, for example, isn’t the same as another’s, so their study results aren’t comparable. Research is built on others’ findings so this hodgepodge mires progress.
Filed under NIH toolbox brain neuroscience psychology research science assessment tools
High quality Denisovan genome sheds light on human evolution: Sequencing our extinct relatives let us know how we differ from chimps.
The discovery that a second branch of the human family shared Asia with our ancestors and the Neanderthals was a real shock, but the Denisovans have continued to surprise many. All we have of them is a bit of a finger and some molars, but those few fragments have yielded a wealth of DNA, and with it the knowledge that the Denisovans interbred with the ancestors of some modern human populations. Now, with the help of a new approach to sequencing ancient DNA, we actually know more about the Denisovans’ genome than we do about Neanderthals’. In the process, we’ve discovered some of the changes that are distinct to modern humans.
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Filed under anthropology evolution genetics genomics neuroscience science DNA
Adding to the mounting evidence that consuming moderate amounts of chocoloate may benefit the heart, comes that of a new study of Swedish men that suggests it may also lower the risk of stroke.
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Filed under brain chocolate neuroscience psychology science stroke flavonoids
