News and Highlights

As open science neuroinformatics databases the Brede Database and Brede Wiki seek to make distribution and federation of their content as easy and transparent as possible. The databases rely on simple formats and allow other online tools to reuse their content. This paper describes the possible interconnections on different levels between the Brede tools and other databases.

In Frontiers in Neuroinformatics, researchers present a Matlab package that makes it easy to apply population decoding analyses to neural activity. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact.

Frontiers announces the launch of a new journal, Frontiers in Bioengineering and Biotechnology. A broad scope journal covering all specialties, Frontiers in Bioengineering and Biotechnology will provide a single open-access platform for diverse and emerging bioengineering and biotechnology research to be disseminated and discussed.

In Nature, researchers define the various functions of sleep, from how we learn to the regulation of metabolism and immunity. New ways to treat troubled sleeping are being developed, and better sleep practice can help people with mood disorders.

In Frontiers of Neuroinformatics, members of the INCF US Node, explore the use of ontologies to create formal descriptions of structural phenotypes across scales that are machine processable and amenable to logical inference.

In Frontiers of Computational Neuroscience, researchers suggest a new biophysical motivated derivation of a single compartment model that integrates the non-linear effects of shunting inhibition, where an inhibitory input on the route of an excitatory input to the soma cancels or “shunts” the excitatory potential.

In Frontiers of Computational Neuroscience, researchers discuss how a better understanding of astrocyte-neuron coupling may lead to providing building blocks for studying the regulatory capability of astrocytic networks on a larger scale, through nine papers which cover a range of issues from computational models of astrocyte-neuron interactions to the role of astrocytes in neurological disorders.

To facilitate the quantification of neuronal cell patterns, researchers have developed RipleyGUI, a MATLAB-based software that can be used to detect patterns in the 3D distribution of cells. 

In Science, researchers report a link between cognitive challenges, adult brain neurogenesis, and the development of individuality. This relationship supports the idea that a key function of adult neurogenesis is to shape neuronal connectivity in the brain according to individual needs.

In Nature, researchers discuss how inflammation-activated signalling pathways in the brain's hypothalamus control the production of ageing-related hormones. This finding provides a link between inflammation, stress responses and systemic ageing.

To celebrate the European Month of the Brain, researchers funded by the European Research Council (ERC) will participate in two key events organised by the European Commission in Brussels on 14 May, and in Dublin on 27 and 28 of May 2013. On this occasion, the ERC has issued a new publication entitled 'ERC projects to unlock mysteries of the human brain'.

In PNAS, researchers describe a strategy designed to identify RNAs that are actively transported to synapses during learning. Their approach is based on the characterization of RNA transport complexes carried by molecular motor kinesin.

This Newsletter features: Launch of Victoria Node, INCF Short courses for 2013, HBP wins top European science funding, Profiles in Neuroinformatics: A new INCF blog feature and Publications in Brief.

 INCF welcomed its 17th Node last February, when two Victorian supercomputing facilities joined INCF: MASSIVE and VLSCI. The INCF National Node of Victoria, Australia is born. 

From next month, Nature and the Nature research journals will introduce editorial measures to address the problem of irreproducibility by improving the consistency and quality of reporting in life-sciences articles.

For the third year, INCF will participate as a mentoring organization in the Google Summer of Code program with more than ten project proposals. Student application ends on May 3rd. Apply today!

In PNAS, researchers discuss how by viral expression of neural fate determinants, it is possible to directly reprogram mouse and human fibroblasts into functional neurons, also known as induced neurons. The resulting cells can be used for obtaining patient- and disease-specific neurons to be used for disease modeling and for development of cell therapy.

In early April EUDAT was glad to welcome a new Associated Partner: the International Neuroinformatics Coordinating Facility (INCF). The INCF's involvement in the development of EUDAT services will focus mainly on testing and using the services that are relevant for the Neuroinformatics community.

In Nature Neuroscience Reviews, researchers discuss the inter-individual differences in the thickness or volume of a brain region, which often co-vary with inter-individual differences in other brain regions. They discuss this phenomenon of structural co-variance, its underlying mechanisms and its potential value in the understanding of various brain disorders.

In Nature Neuroscience Reviews, researchers review our current understanding of the role of astrocytes (formation, maturation, function and elimination of synapses and support the formation of appropriate neural circuits) and highlight unanswered questions for future research.

Researchers discuss in Nature how hippocampal place cells encode information about an animal’s spatial world and how these same neurons envisage a future journey moments before a rat sets off.

Researchers discuss the birth and development of the field of Neuroinformatics in this paper published at the Official Journal of the American Academy of Neurology, and acknowledge the coordinative role of INCF.  

The twelfth annual Wiley Prize in Biomedical Sciences has been awarded to Dr. Michael Young, Dr. Jeffrey Hall, and Dr. Michael Rosbash for the discovery of the molecular mechanisms governing circadian rhythms.

In Nature, scientists at Stanford University have made a whole mouse brain, and part of a human brain, transparent so that networks of neurons that receive and send information can be highlighted in stunning color and viewed in all their three-dimensional complexity without slicing up the organ, and preserve the biochemistry of the brain as well. 

Researchers at the University of Calgary's Hotchkiss Brain Institute have discovered that stress circuits in the brain undergo profound learning early in life. Using a number of cutting edge approaches, including optogenetics, Jaideep Bains, PhD, and colleagues have shown stress circuits are capable of self-tuning following a single stress. These findings demonstrate that the brain uses stress experience during early life to prepare and optimize for subsequent challenges.

Nature Publishing Group NPG  announces the Spring 2014 launch of Scientific Data. Open for submissions this autumn, Scientific Data is a new open-access, online-only platform for the publication of descriptions of scientifically valuable datasets. Scientific Data will initially focus on experimental datasets from the life, biomedical and environmental science communities with future plans to expand to other fields in the natural sciences.

This year's "Brain Prize" by the Grete Lundbeck European Brain Research Prize Foundation will be awarded to six leading scientists for their joint development of "optogenetics". Bernstein network member Ernst Bamberg (BFNT Göttingen and Max Planck Institute of Biophysics, Frankfurt), Peter Hegemann, Georg Nagel (both Germany), Gero Miesenböck (Austria), Ed Boyden and Karl Deisseroth (both USA) are this year's awardees.

In Frontiers of Neural Circuits, using computational tools, researchers explore the impact of local synaptic inhibition on the plasticity of excitatory synapses in dendrites and characterized the dependence of excitatory synaptic plasticity on dendritic morphology, loci and strength, as well as on the spatial distribution of inhibitory synapses and on the level of excitatory activity.

President Obama unveiled the “BRAIN” Initiative—a bold new research effort to revolutionize our understanding of the human mind and uncover new ways to treat, prevent, and cure brain disorders like Alzheimer’s, schizophrenia, autism, epilepsy, and traumatic brain injury. The BRAIN Initiative calls for historic investments in research and development to fuel the innovation, job creation, and economic growth that together create a thriving middle class.

In Frontiers of Neuroanatomy, members of the US Node hypothesize and detail 7 functional circuits corresponding to psychological perspectives on the brain: consolidated long-term declarative memory, short-term declarative memory, working memory/information processing, behavioral memory selection, behavioral memory output, cognitive control, and cortical information flow regulation.

In Frontiers of Neural Circuits, members of the INCF Japan and Germany Node discuss how in motor cortex, a precise spatio-temporal pattern of activation is involved for the control of reach-to-grasp movements and provide some new insight about the functional organization of motor cortex during reaching and object manipulation.

The primary goal of this proposal is to highlight and detail ITKv4’s segmentation and registration methodology and its application to a variety of neuroinformatics problems. By using ITKv4 as a core platform and disseminating the analysis pipelines, the papers selected by this proposal will promote reproducible practices and act as a guide for other researchers who wish to use ITKv4 in their own research.

INCF Short Courses for 2013 are: Introduction to Neuroinformatics (Stockholm, Sweden), Imaging the brain at different scales: How to integrate multi-scale structural information? (Antwerp, Belgium), Neuroinformatics, Neurogenomics and Brain Disease (Fraueninsel -Bavaria-, Germany), and
Achieving Excellence in Neuroinformatics in Latin America (Havana, Cuba).

The Brain Prize - Denmark's 1 million euro brain research prize - is awarded to six leading scientists for the development of ‘optogenetics’, a revolutionary technique that advances our understanding of the brain and its disorders.

The mechanisms of perception, cognition, and action remain mysterious because they emerge from the real-time interactions of large sets of neurons in densely interconnected, widespread neural circuits. In Science, researchers propose building technologies to enable comprehensive mapping of neural circuit activity to understand brain function and disease. 

In PNAS, researchers Investigate the distribution of spatial patterns, since recent functional magnetic resonance imaging studies have shown that the brain is remarkably active even in the absence of overt behavior, and this activity occurs in spatial patterns that are reproducible across subjects and follow the brain’s established functional subdivision. 

In PNAS, researchers discuss how neurons in mammals do not undergo replicative aging, and, in absence of pathologic conditions, their lifespan is limited only by the maximum lifespan of the organism.

Brain Awareness Week (BAW) is the global campaign to increase public awareness of the progress and benefits of brain research.Every March, BAW unites the efforts of partner organizations worldwide in a celebration of the brain for people of all ages. Events are limited only by the organizers’ imaginations and include open days at neuroscience labs; exhibitions about the brain; lectures on brain-related topics; displays at libraries and community centers; classroom workshops; and more.

Launched the research topic Python in Neuroscience II in Frontiers in Brain Imaging Methods. Article submissions now open! Deadline for full article submission: 15 Jul 2013 Extended deadline for full article submission: 15 Aug 2013

Members of the Bernstein Center have developed a neuroinformatics platform with a brain simulator that incorporates a range of neuronal models and dynamics at its core. This integrated framework allows the model-based simulation, analysis and inference of neurophysiological mechanisms over several brain scales that underlie the generation of macroscopic neuroimaging signals. 

A study published in Nature Neuroscience finds that microglia are quite distinct from blood-borne macrophages and derive from an erythromyeloid precursor cell of the embryonic hematopoiesis.

Frontiers is joining forces with Nature Publishing Group (NPG) in a strategic alliance to support and develop open access publishing.

Frontiers in Neuroinformatics special topic “Recent advances and the future generation of neuroinformatics infrastructure” call for papers. Deadline for Abstract Submission: 31 Jul 2013. Deadline for Article Submission: 31 Oct 2013.

In Nature Reviews Neuroscience, researchers discuss the neural mechanisms underlying the perception of duration and present recent theoretical developments and empirical findings indicating that 'climbing' neural activity has a central role in time perception.

In Nature Reviews Neuroscience, INCF members describe a possible taxonomical solution for classifying GABAergic interneurons of the cerebral cortex based on a novel, web-based interactive system that allows experts to classify neurons with pre-determined criteria.

In Frontiers of Computational Neuroscience, researchers describe a model for cortical development, synchrony and synaptic self-organization, that solves long-standing difficulties of earlier models.

In Frontiers of Neuroinformatics, researchers describe the NEuronMOrphological analysis tool NEMO.  Morphometric analysis of neurons and brain tissue is relevant to the study of neuron circuitry development during the first phases of brain growth or for probing the link between microstructural morphology and degenerative diseases.

In Nature, researchers discuss the complexity of bilingual acquisition in bilingual infants, how perceptually available cues like prosody can bootstrap grammatical structure and how and why infants acquire grammar so early and effortlessly.

In Frontiers in Systems Neuroscience, members of the INCF Japan and German Node discuss the cross-frequency interaction of the eye-movement related local field potential (LFP) signals in V1 of freely viewing monkeys.

Professor, researcher, neuroscientist and author, David Willshaw talks to INCF about his research, projects and achievements.

In PLoS One, INCF researchers replicate normal and pathological patterns of visual scanning, line bisection, and the differences between hemianopia and hemineglect. This model will help explain why compensatory processes that counter the effects of hemianopia are ineffective in hemineglect.

In Frontiers of Neuroinformatics, US researchers discuss the extent to which homotypic forces might influence real dendritic morphologies, and speculate about the influence of other environmental cues on neuronal shape and circuitry.

Nature Neuroscience dedicates its latest issue to memory, comprising Commentaries, Reviews and Perspectives discussing some of the most exciting recent developments and emerging ideas in our understanding of the neurobiology of learning and memory.

In Frontiers of Computational Neuroscience, researchers discuss how protein amyloid-beta concentration perturbs pre-synaptic release in hippocampal neurons through a computational model. The results suggest that the increased protein significantly contribute to abnormal hippocampal function during Alzheimer´s Disease.

The Human Brain Project  (HBP), a Swiss based effort that comprises 87 organisations in 23 different countries (of which 16 are European) including universities, research organisations and industry, has been awarded one of European Commission FET Flagship projects. The new project will federate European efforts to address one of the greatest challenges of modern science: understanding the human brain.

In Nature Neuroscience Reviews, researchers discuss several animal models for Traumatic Brain Injury (TBI), to better understand the underlying pathophysiology and to explore potential treatments.

Dr Upinder Bhalla, member of the INCF India Node, National Centre for Biological Sciences Bangalore, India, talks to INCF about his life as neuroinformatics researcher, projects and interests.

In Nature, Chris A. Mattmann explains "to get the best out of big data, funding agencies should develop shared tools for optimizing discovery and train a new breed of researchers"

Frontiers of Neuromorphic Engineering has accepted a paper by members of the INCF German Node, in which they present a highly configurable neuromorphic computing substrate and use it for emulating several types of neural networks and describe the successful emulation of six different neural networks which cover a broad spectrum of both structure and functionality.

In Trends of Cognitive Sciences, researchers discuss how the scientific community often maintains an overly simplistic linear view without considering the perspective of the neurons. In order to understand the brain, only the neurons’ perspective matters, thus change in the neuroscientists’ perspective is needed. 

In Neuroinformatics, US researchers present a a graphics processing unit accelerated motion correction algorithm and modular system for real-time fMRI, a motion correction algorithm that provides an estimate of motion with essentially no processing delay as well as a modular rt-fMRI system design.

Under the direction of Abigail Morrison, neuroscientists, physicians, computer scientists, mathematicians and physicists can work intensively together in order to optimize the use of computer simulations of the brain for supercomputers.

In Nature Neuroscience, researchers explain how using simultaneous quadruple-octuple in vitro and dual in vivo whole-cell recordings, they found two previously unknown interneuronal circuits that link cortical layer 1–3 (L1–3) interneurons and L5 pyramidal neurons in the rat neocortex.

In Frontiers of Computational Neuroscience, members of the INCF Germany Node  discuss how movement representation facilitates learning significantly and leads to better generalization to new task settings without re-learning.

Are you producing valuable data? Are you producing reusable data? INCF and One Mind for Research have launched the Data Share Award, offering $10,000 in prize money and hosting, to encourage individuals, research groups, and organizations to make their datasets open and freely accessible to all through the INCF Dataspace.

Members of the INCF UK Node have recently published in Frontiers of Psychiatry Higher how late-life depression is associated with overall increased functional connectivity strength and changes in the average distance between connected nodes.

F1000Research is a far-reaching alternative Open Access publishing program in biology and medicine, that challenges traditional scholarly publishing models by defining new standards for its speed, peer review, data publication and for publishing good science.

In Frontiers of Neuroinformatics, members of the INCF Germany Node develop a scalable, low-cost and open source solution for continuous integration (CI), a technique that ensures the quality of changes to the code base during the development procedure, rather than relying on a pre-release integration phase.

In Frontiers of Neuroinformatics, members of the INCF Germany and Netherlands Nodes discuss the features of the CoCoMac 2.0 database, which contains the results of several hundred published axonal tract-tracing studies in the macaque monkey brain, and how they compare to six connectome related projects.