OneZoom: A Fractal Explorer for the Tree of Life
Our knowledge of the tree of life—a phylogenetic tree summarizing the evolutionary relationships among all life on Earth—is expanding rapidly. “Mega-trees” with millions of tips (species) are expected to appear imminently (for example, see http://www.opentree.wikispaces.com). Unfortunately, there has so far been no practical and intuitive way to explore even the much smaller trees with thousands of tips that are now being routinely produced. Without a way to view megatrees, these wondrous objects, representing the culmination of decades of scientific effort, cannot be fully appreciated. The field really needs a solution to this problem to enable scientists to communicate important evolutionary concepts and data effectively, both to each other and to the general public.
Just like Google Earth changed the way people look at geography, a sophisticated tree of life browser could really change the way we look at the life around us … Our advances in understanding evolution are moving really fast now, but the tools for looking at these big trees are lagging behind. (Westneat, February 2009)
Displaying large trees is a hard problem that has so far resisted solution. We are still waiting for the equivalent of a Google Maps. (Page, June 2012)
In this manuscript, we introduce a new approach that solves the problem. Trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps.
Filed under tree of life evolution phylogeny species data neuroscience science
Computational Medicine Begins to Enhance the Way Doctors Detect and Treat Disease
Computational medicine, a fast-growing method of using computer models and sophisticated software to figure out how disease develops–and how to thwart it–has begun to leap off the drawing board and land in the hands of doctors who treat patients for heart ailments, cancer and other illnesses. Using digital tools, researchers have begun to use experimental and clinical data to build models that can unravel complex medical mysteries.
These are some of the conclusions of a new review of the field published in the Oct. 31 issue of the journal Science Translational Medicine. The article, “Computational Medicine: Translating Models to Clinical Care,” was written by four Johns Hopkins professors affiliated with the university’s Institute for Computational Medicine.
In recent years, “The field has exploded. There is a whole new community of people being trained in mathematics, computer science and engineering, and they are being cross-trained in biology,” said institute director Raimond Winslow. “This allows them to bring a whole new perspective to medical diagnosis and treatment. Engineers traditionally construct models of the systems they are designing. In our case, we’re building computational models of what we trying to study, which is disease.”
Filed under medicine computational models diseases science
A daily multivitamin supplement may improve brain efficiency in older women, according to new research from Swinburne University of Technology.
Centre for Human Psychopharmacology researcher at Swinburne, Dr Helen Macpherson’s four month study of the commercial product Swisse Women’s Ultivite 50+ found some evidence that multivitamin supplements may influence cognitive function by altering electrical activity in the brain.
"The main finding of the study was that 16 weeks supplementation with the Swisse Women’s 50+ multivitamin modulated brain activity," Dr Macpherson said.
"This is an important result as it shows there are direct effects of multivitamins on the brain.
"Previous research has used measures of behaviour to determine whether multivitamins can affect brain function, but this is the first trial to directly measure brain activity."
The study was conducted over 16 weeks with 56 women aged between 64 and 79 who were concerned about their memory or experiencing memory difficulties. They were randomly assigned to take the multivitamin supplement or a placebo daily.
Volunteers underwent a recording of their brain electrical activity whilst performing a spatial working memory task.
The research was published in Physiology and Behavior.
A previous paper published in Psychopharmacology reported that multivitamin supplementation improved behavioural performance on a similar task, in the same group of participants.
The study concluded that 16 weeks of supplementation with a combined multivitamin, mineral and herbal formula may benefit memory, by enabling the brain to work in a more efficient way.
"When considered with our other findings of benefits to memory performance, there is increasing evidence that multivitamins may be useful to combat cognitive decline in the elderly," Dr Macpherson said.
(Source: swinburne.edu.au)
Filed under brain cognitive decline memory brain function multivitamin neuroscience psychology science
In a column appearing in the current issue of the journal Nature, McLean Hospital biostatistician Nicholas Lange, ScD, cautions against heralding the use of brain imaging scans to diagnose autism and urges greater focus on conducting large, long-term multicenter studies to identify the biological basis of the disorder.
"Several studies in the past two years have claimed that brain scans can diagnose autism, but this assertion is deeply flawed," said Lange, an associate professor of Psychiatry and Biostatistics at Harvard Medical School. "To diagnose autism reliably, we need to better understand what goes awry in people with the disorder. Until its solid biological basis is found, any attempt to use brain imaging to diagnose autism will be futile."
While cautioning against current use of brain imaging as a diagnostic tool, he is a strong proponent of using this technology to help scientists better understand autism. Through the use of various brain imaging techniques, including functional magnetic resonance imaging (MRI), positron emission tomography (PET), and volumetric MRI, Lange points out that researchers have made important discoveries related to early brain enlargement in the disorder, how those with autism focus during social interaction and the role of serotonin in someone with autism.
"Brain scans have led to these extremely valuable advances, and, with each discovery, we are getting closer to solving the autism pathology puzzle," said Lange. "What individuals with autism and their parents urgently need is for us to carry out large-scale studies that lead us to find reliable, sensitive and specific biological markers of autism with high predictive value that allow clinicians to identify interventions that will improve the lives of people with the disorder."
Autism and autism spectrum disorder (ASD) are terms regularly used to describe a group of complex disorders of brain development. This spectrum characterized, in varying degrees, by difficulties in social interaction, verbal and nonverbal communication, and repetitive behaviors, whose criteria have been revised in the newly proposed Diagnostic and Statistical Manual of Mental Disorders (DSM-5). The prevalence of ASD in the United States has increased 78 percent in the last decade, with the Centers for Disease Control estimating that one in 88 children has ASD.
(Source: eurekalert.org)
Filed under brain brain scans neuroimaging autism ASD neuroscience psychology science
Simulations improve predictability of aneurysm development
Using new computer models of blood flow in the vicinity of cerebral aneurysms (dilated sections of blood vessels in the brain), it is now possible to calculate every detail of the patient-specific situation. This has resulted in powerful new techniques for predicting a further weakening or even rupture of the blood vessel’s wall, and for effective intervention. Julia Mikhal was awarded a PhD on this topic by the University of Twente.
Read more
Filed under brain aneurysm blood flow haemorrhages computer models neuroscience science
Bacteria yield clues about why proteins go bad in ALS and Alzheimer’s
Scientists are unsure why proteins form improperly and cluster together in bunches, a hallmark of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), Alzheimer’s and Mad Cow Disease. In the Nov. 1 issue of the journal Molecular Cell, Yale scientists shed light on protein aggregate formation by studying the process in bacteria.
“The question we are all asking is what happens when protein synthesis goes wrong?” said Jesse Rinehart, assistant professor of cellular and molecular physiology at Yale’s West Campus and co-senior author of the paper.
Proteins are created from instructions encoded in DNA and assembled in ribosomes within the cells. However, sometimes they are not assembled correctly, and these misfolded proteins tend to aggregate, a process typified by the plaques that form in the brains of Alzheimer’s patients.
The Yale team — led by Rinehart and Dieter Söll, Sterling Professor of Molecular Biophysics and Biochemistry and professor of chemistry — showed that the antibiotic streptomycin can trigger protein aggregations in the bacterium E. coli. Using large-scale proteomics and genetic screens, they analyzed the aggregates and searched for bacterial proteins that make E. coli cells resistant to antibiotics and other threats. The researchers discovered how one of these proteins protecting the bacteria from hydrogen peroxide also suppressed the aggregation of proteins triggered by streptomycin.
Filed under brain alzheimer alzheimer's disease ALS proteins E.coli neurodegenerative diseases neuroscience science
Making a Game Out of Improving the ‘Sticky’ Brain
UCSF neuroscientists have found that by training on attention tests, people young and old can improve brain performance and multitasking skills.
Anyone who tries to perform two tasks at once is likely to do worse on both. Why that is so at the neurological level has largely been terra incognita. But research now is starting to reveal the impact of multitasking on short-term memory and attention.
Adam Gazzaley, MD, PhD, associate professor of neurology, physiology and psychiatry, and researchers at the UCSF Neuroscience Imaging Center use EEG, MRI and other non-invasive tools to study cognitive processes while people try their best on drills that test short-term memory.
Filed under brain cognitive processes memory STM research neuroscience psychology science
UC Santa Barbara has reported an important discovery in the interdisciplinary study of split-brain research. The findings uncover dynamic changes in brain coordination patterns between left and right hemispheres.
Split-brain research has been conducted for decades, and scientists have long ago shown that language processing is largely located in the left side of the brain. When words appear only in the left visual field –– an area processed by the right side of the brain –– the right brain must transfer that information to the left brain, in order to interpret it. The new study at UCSB shows that healthy test subjects respond less accurately when information is shown only to the right brain.
While hemispheric specialization is considered accurate, the new study sheds light on the highly complex interplay –– with neurons firing back and forth between distinct areas in each half of the brain. The findings rely on extremely sensitive neuroscience equipment and analysis techniques from network science, a fast-growing field that draws on insights from sociology, mathematics, and physics to understand complex systems composed of many interacting parts. These tools can be applied to systems as diverse as earthquakes and brains.
Fifty years ago, UC Santa Barbara neuroscientist Michael S. Gazzaniga moved the field forward when he was a graduate student at the California Institute of Technology and first author of a groundbreaking report on split-brain patients. The study, which became world-renowned, was published in the Proceedings of the National Academy of Sciences (PNAS) in August 1962. This week, in the very same journal, Gazzaniga and his team announced major new findings in split-brain research. The report is an example of the interdisciplinary science for which UCSB is well known.
"The occasion of this paper is on the 50th anniversary of the first report on human split-brain research reported in PNAS," said Gazzaniga. "That study showed how surgically dividing the two hemispheres of the human brain –– in an attempt to control epilepsy –– allowed for studying how each isolated half-brain was specialized for cognitive function.
"In the present study, new techniques –– not present 50 years ago –– begin to allow for an understanding of how the normal, undivided brain integrates the special functions of each half brain. It is a new beginning and very exciting," said Gazzaniga, professor of psychology in UCSB’s Department of Psychological and Brain Sciences, and director of UCSB’s SAGE Center for the Study of Mind.
(Source: ia.ucsb.edu)
Filed under brain brain research split-brain neural oscillations neuroscience psychology science
Brain’s Code for Visual Working Memory Deciphered in Monkeys
The brain holds in mind what has just been seen by synchronizing brain waves in a working memory circuit, an animal study supported by the National Institutes of Health suggests. The more in-sync such electrical signals of neurons were in two key hubs of the circuit, the more those cells held the short-term memory of a just-seen object.
Charles Gray, Ph.D., of Montana State University, Bozeman, a grantee of NIH’s National Institute of Mental Health (NIMH), and colleagues, report their findings Nov. 1, 2012, online, in the journal Science Express.
“This work demonstrates, for the first time, that there is information about short term memories reflected in in-sync brainwaves,” explained Gray.
“The Holy Grail of neuroscience has been to understand how and where information is encoded in the brain. This study provides more evidence that large scale electrical oscillations across distant brain regions may carry information for visual memories,” said NIMH director Thomas R. Insel, M.D.
Prior to the study, scientists had observed synchronous patterns of electrical activity between the two circuit hubs after a monkey saw an object, but weren’t sure if the signals actually represent such short-term visual memories in the brain. Rather, it was thought that such neural oscillations might play the role of a traffic cop, directing information along brain highways.
Filed under brain brainwaves working memory visual memories STM neuroscience psychology science
