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The Allen Institute for Brain Science is a Seattle-based independent, nonprofit medical research organization dedicated to accelerating the understanding of how the human brain works. The Allen Institute promotes the advance of brain research by providing free data and tools to scientists worldwide with the aim of catalyzing discovery in disparate research programs and disease areas.Started with $100 million in seed money from philanthropist Paul Allen in 2003, the Institute tackles projects at the leading edge of science—far-reaching projects at the intersection of biology and technology. The resulting data create free, publicly available resources that fuel discovery for countless researchers. Wikipedia.


Tononi G.,University of Wisconsin - Madison | Koch C.,Allen Institute for Brain Science
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2015

The science of consciousness has made great strides by focusing on the behavioural and neuronal correlates of experience. However, while such correlates are important for progress to occur, they are not enough if we are to understand even basic facts, for example, why the cerebral cortex gives rise to consciousness but the cerebellum does not, though it has even more neurons and appears to be just as complicated. Moreover, correlates are of little help in many instances where we would like to know if consciousness is present: patients with a few remaining islands of functioning cortex, preterm infants, non-mammalian species and machines that are rapidly outperforming people at driving, recognizing faces and objects, and answering difficult questions. To address these issues, we need not only more data but also a theory of consciousness—one that says what experience is and what type of physical systems can have it. Integrated information theory (IIT) does so by starting from experience itself via five phenomenological axioms: intrinsic existence, composition, information, integration and exclusion. From these it derives five postulates about the properties required of physical mechanisms to support consciousness. The theory provides a principled account of both the quantity and the quality of an individual experience (a quale), and a calculus to evaluate whether or not a particular physical system is conscious and of what. Moreover,IIT can explain a range of clinical and laboratory findings, makes a number of testable predictions and extrapolates to a number of problematic conditions. The theory holds that consciousness is a fundamental property possessed by physical systems having specific causal properties. It predicts that consciousness is graded, is common among biological organisms and can occur in some very simple systems. Conversely, it predicts that feed-forward networks, even complex ones, are not conscious, nor are aggregates such as groups of individuals or heaps of sand. Also, in sharp contrast to widespread functionalist beliefs, IIT implies that digital computers, even if their behaviour were to be functionally equivalent to ours, and even if they were to run faithful simulations of the human brain, would experience next to nothing. © 2015 The Authors. Source


Strange B.A.,Center for Biomedical Technology | Strange B.A.,Alzheimerfs Disease Research Center | Witter M.P.,Norwegian University of Science and Technology | Lein E.S.,Allen Institute for Brain Science | Moser E.I.,Norwegian University of Science and Technology
Nature Reviews Neuroscience | Year: 2014

The precise functional role of the hippocampus remains a topic of much debate. The dominant view is that the dorsal (or posterior) hippocampus is implicated in memory and spatial navigation and the ventral (or anterior) hippocampus mediates anxiety-related behaviours. However, this 'dichotomy view' may need revision. Gene expression studies demonstrate multiple functional domains along the hippocampal long axis, which often exhibit sharply demarcated borders. By contrast, anatomical studies and electrophysiological recordings in rodents suggest that the long axis is organized along a gradient. Together, these observations suggest a model in which functional long-axis gradients are superimposed on discrete functional domains. This model provides a potential framework to explain and test the multiple functions ascribed to the hippocampus. © 2014 Macmillan Publishers Limited. All rights reserved. Source


Mudrik L.,California Institute of Technology | Faivre N.,California Institute of Technology | Koch C.,California Institute of Technology | Koch C.,Allen Institute for Brain Science
Trends in Cognitive Sciences | Year: 2014

Information integration and consciousness are closely related, if not interdependent. But, what exactly is the nature of their relation? Which forms of integration require consciousness? Here, we examine the recent experimental literature with respect to perceptual and cognitive integration of spatiotemporal, multisensory, semantic, and novel information. We suggest that, whereas some integrative processes can occur without awareness, their scope is limited to smaller integration windows, to simpler associations, or to ones that were previously acquired consciously. This challenges previous claims that consciousness of some content is necessary for its integration; yet it also suggests that consciousness holds an enabling role in establishing integrative mechanisms that can later operate unconsciously, and in allowing wider-range integration, over bigger semantic, spatiotemporal, and sensory integration windows. © 2014 Elsevier Ltd. Source


Hunnicutt B.J.,Allen Institute for Brain Science
Nature neuroscience | Year: 2014

The thalamus relays sensori-motor information to the cortex and is an integral part of cortical executive functions. The precise distribution of thalamic projections to the cortex is poorly characterized, particularly in mouse. We employed a systematic, high-throughput viral approach to visualize thalamocortical axons with high sensitivity. We then developed algorithms to directly compare injection and projection information across animals. By tiling the mouse thalamus with 254 overlapping injections, we constructed a comprehensive map of thalamocortical projections. We determined the projection origins of specific cortical subregions and verified that the characterized projections formed functional synapses using optogenetic approaches. As an important application, we determined the optimal stereotaxic coordinates for targeting specific cortical subregions and expanded these analyses to localize cortical layer-preferential projections. This data set will serve as a foundation for functional investigations of thalamocortical circuits. Our approach and algorithms also provide an example for analyzing the projection patterns of other brain regions. Source


Ding S.-L.,Allen Institute for Brain Science | Van Hoesen G.W.,University of Iowa
Journal of Comparative Neurology | Year: 2015

The hippocampal formation (HF) is one of the hottest regions in neuroscience because it is critical to learning, memory, and cognition, while being vulnerable to many neurological and mental disorders. With increasing high-resolution imaging techniques, many scientists have started to use distinct landmarks along the anterior-posterior axis of HF to allow segmentation into individual subfields in order to identify specific functions in both normal and diseased conditions. These studies urgently call for more reliable and accurate segmentation of the HF subfields DG, CA3, CA2, CA1, prosubiculum, subiculum, presubiculum, and parasubiculum. Unfortunately, very limited data are available on detailed parcellation of the HF subfields, especially in the complex, curved hippocampal head region. In this study we revealed detailed organization and parcellation of all subfields of the hippocampal head and body regions on the base of a combined analysis of multiple cyto- and chemoarchitectural stains and dense sequential section sampling. We also correlated these subfields to macro-anatomical landmarks, which are visible on magnetic resonance imaging (MRI) scans. Furthermore, we created three versions of the detailed anatomic atlas for the hippocampal head region to account for brains with four, three, or two hippocampal digitations. These results will provide a fundamental basis for understanding the organization, parcellation, and anterior-posterior difference of human HF, facilitating accurate segmentation and measurement of HF subfields in the human brain on MRI scans. J. Comp. Neurol. 523:2233-2253, 2015. © 2015 Wiley Periodicals, Inc. Source

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