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Functional MRI of the Spinal CordEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Evidence to date shows that fMRI of the spinal cord (spinal fMRI) can reliably demonstrate regions involved with sensation of tactile, thermal, and painful stimuli, and with motor tasks. The spin-echo-based spinal fMRI method with “signal enhancement by extravascular protons” contrast has been developed more extensively than the BOLD (blood oxygen level dependent)-based method. Results have demonstrated good localization to areas of activity within the spinal cord cross-section and to the spinal cord segmental level, in both the cervical and lumbar spinal cord, with a range of thermal stimuli as well as tactile...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Integration of Measures of Functional and Structural MRIEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent years have seen a renewed interest in brain anatomy in the neuroimaging community. Developments in techniques for structural MR acquisition and analysis have opened new opportunities for structural mapping of the living human brain. For example, high-resolution MR imaging can be used for “in vivo histology”, techniques such as voxel-based morphometry can be used to localise structural variation across populations, diffusion imaging provides information on system-level anatomical connectivity. fMRI studies are increasingly making use of the information provided by such structural mapping techniques in ord...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Application of fMRI to Monitor Motor RehabilitationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motor deficits contribute to disability in a number of neurological conditions. A wide range of emerging restorative therapies has the potential to reduce this by favorably modifying function. In many medical contexts, a study of target organ function improves efficacy of a therapeutic intervention. However, the optimal methods to prescribe a restorative therapy in the setting of central nervous system (CNS) disease are not clear. Brain mapping studies have the potential to provide useful insights in this regard. Examples of restorative therapies are provided, and human trials are summarized whereby brain mapping data have...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Pharmacological Applications of fMRIEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Modern drug development presents new challenges by the unmet medical needs of chronic neurological and psychiatric disease. Imaging provides a potentially powerful tool for more efficiently translating pre-clinical and clinical studies and enhancing confidence in progression through early phase clinical development. Pharmacological MRI (phMRI) refers specifically to the applications of fMRI methods for direct or indirect measures of drug action. phMRI can be coupled to advanced structural methods to relate pharmacological effects and functional anatomy. Current and potential applications of phMRI to target stratification, ...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI in NeurosurgeryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Functional magnetic resonance imaging has evolved from a basic research application to a useful clinical tool that also has found its place in modern neurosurgery. The localization of functional important brain areas as language and sensorimotor cortex has been the focus of numerous investigations and can now be implemented in neurosurgical planning. Since the neurosurgeon must have detailed knowledge about the individual anatomy and related neurological function to resect a brain tumor with the highest safety, the need for individualized maps of brain function is essential. Advanced fMRI techniques and modern imaging meth...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI in Neurodegenerative Diseases: From Scientific Insights to Clinical ApplicationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
fMRI is a technology with great promise as a tool to probe abnormalities of brain activity in neurodegenerative diseases. The detection of functional brain abnormalities may be useful, in the appropriate clinical context, for early diagnosis, differential diagnosis, or prognostication. Prediction of response to treatment or therapeutic monitoring may also be possible with fMRI. In addition, fMRI has the potential to provide a variety of scientific insights that may have clinical relevance, including compensatory hyperactivation of brain circuits or genetic modulation of functional brain activity.
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI in EpilepsyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This chapter provides an overview of the application of functional MRI applied to the field of Epilepsy and is divided into two sections, covering cognitive mapping and imaging of paroxysmal activity, respectively. In addition to a review of the most scientifically and clinically relevant findings, technical and methodological background information is provided to help the reader better understand the data acquisition process. We show how both approaches may play a role in the pre-surgical evaluation of patients with drug-resistant focal epilepsy and provide opportunities for new insights into the neuropathological process...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI in Psychiatric DisordersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Functional neuroimaging has become an important tool for clinical research, with the potentiality to provide information on psychiatric disease pathology and treatment response. We review functional magnetic resonance imaging (fMRI) research findings for six psychiatric disorders: schizophrenia, major depressive disorder, bipolar disorder, obsessive-compulsive disorder, posttraumatic stress disorder, and Alzheimer’s disease. Brain functional abnormalities and possible underlying mechanisms for disease symptoms are discussed, with a focus on future clinical implications for fMRI in psychiatric disease.
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI in Cerebrovascular DisordersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Stroke is a major cause of long-term disability worldwide. One of the key factors underpinning recovery of function is reorganization of surviving neural networks. Noninvasive techniques such as fMRI allow this reorganization to be studied in humans. However, the design of experiments involving patients with impairment requires careful consideration and is often constrained. Difficulty with some tasks can lead to a number of performance confounds, and so tasks and task parameters that avoid or minimize this should be selected. Furthermore, when studying patients with cerebrovascular disease, it is important to consider the...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Application of fMRI to Multiple Sclerosis and Other White Matter DisordersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The variable effectiveness of reparative and recovery mechanisms following tissue damage is among the factors that might contribute to explain, at least partially, the paucity of the correlation between clinical and magnetic resonance imaging (MRI) findings in patients with white matter disorders. Among the mechanisms of recovery, brain plasticity is likely to be one of the most important with several possible different substrates (including increased axonal expression of sodium channels, synaptic changes, increased recruitment of parallel existing pathways or “latent” connections, and reorganization of distant...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI of the Central Auditory SystemEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Over the years, blood oxygen level-dependent (BOLD) fMRI has made important contributions to the understanding of central auditory processing in humans. Although there are significant technical challenges to overcome in the case of auditory fMRI, the unique methodological advantage of fMRI as an indicator of population neural activity lies in its spatial precision. It can be used to examine the neural basis of auditory representation at a number of spatial scales, from the micro-anatomical scale of population assemblies to the macro-anatomical scale of cortico-cortical circuits. The spatial resolution of fMRI is maximised ...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Functional Imaging of the Human Visual SystemEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The human visual system consists of a large, yet unknown number of cortical areas. We summarize the efforts made to identify these areas, using the macaque visual cortex as a guide. So far, retinotopic mapping has identified several regions and study of functional properties such as motion and shape has revealed further expanses of visual cortex. Macaques and humans share early areas (V1, V2, and V3) and a motion-sensitive middle temporal (MT/V5) region, but the intervening cortex has considerably developed in humans with the appearance of new areas. The kinetic occipital region is located in this part of cortex between V3...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI of the Sensorimotor SystemEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The extensive application of fMRI to the assessment of the human sensorimotor system has disclosed a complexity that is largely beyond our original understanding. From the available data, it is accepted that this system consists of a large, and somewhat yet unknown, number of cortical and subcortical areas, with a precise location and a specialized function. In particular, a large number of regions in the frontal and parietal lobes contribute to different aspects of motor act performance. It is also evident that the properties and potentialities of this network still need to be fully elucidated by further research. Definin...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI of PaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The field of pain research has progressed immensely due to the advancement of brain imaging techniques. The initial goal of this research was to expand our understanding of the cerebral mechanisms underlying the perception of pain; more recently the research objectives have shifted toward chronic pain – understanding its origins, developing methods for its diagnosis, and exploring potential avenues for its treatment. While several different neuroimaging approaches have certain advantages for the study of pain, fMRI has ultimately become the most widely utilized imaging technique over the past decade because of its no...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI of EmotionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent brain imaging work has expanded our understanding of the mechanisms of perceptual, cognitive, and motor functions in human subjects, but research into the cerebral control of emotional and motivational function is at a much earlier stage. Important concepts and theories of emotion are briefly introduced, as are research designs and multimodal approaches to answering the central questions in the field. We provide a detailed inspection of the methodological and technical challenges in assessing the cerebral correlates of emotional activation, perception, learning, memory, and emotional regulation behavior in healthy h...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI of MemoryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Numerous fMRI studies have investigated the network of brain regions critical for memory. Whereas neuropsychological techniques can delineate the brain regions that are necessary for intact memory function, neuroimaging techniques can be used to investigate which regions are recruited during healthy memory formation, storage, and retrieval. For example, fMRI studies have shown that lateral prefrontal cortex (PFC) supports some components of working memory function. However, working memory is not localized to a single brain region but is likely a property of the functional interaction between the PFC and posterior brain reg...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI of Language SystemsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Language refers to the uniquely human capacity for communication through productive combination of symbolic representations. Functional neuroimaging studies have in recent decades greatly expanded our knowledge of the brain systems supporting language, producing a dramatic reawakening of interest in this topic and a call to revise and extend the nineteenth century neuroanatomical model formulated by Broca, Wernicke, and others. This chapter presents some theoretical issues regarding functional imaging of language systems, a model of the functional neuroanatomy of language based on recent empirical results in several select...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Imaging Brain Attention Systems: Control and Selection in VisionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Selective attention is an essential cognitive ability that permits us to effectively process and act upon relevant information while ignoring distracting events. The human capacity to focus attention is at the core of mental functioning. Elucidating the neural bases of human selective attention remains a key challenge for neuroscience and represents an essential aim in translational efforts to ameliorate attentional deficits in a wide variety of neurological and psychiatric disorders. In this chapter, we discuss how functional imaging methods have helped us to understand fundamental aspects of attention: How attention is c...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

fMRI: Applications in Cognitive NeuroscienceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Neuroimaging has, in many respects, revolutionized the study of cognitive neuroscience, the discipline that attempts to determine the neural mechanisms underlying cognitive processes. Early studies of brain–behavior relationships relied on a precise neurological exam as the basis for hypothesizing the site of brain damage that was responsible for a given behavioral syndrome. The advent of structural brain imaging, first with computerized tomography and later with magnetic resonance imaging, paved the way for more precise anatomical localization of the cognitive deficits that manifest after brain injury. In recent yea...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Brain Atlases: Their Development and Role in Functional InferenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe how brain atlases, and the computational tools that align new datasets with them, facilitate comparison of brain data across experiments, laboratories, and from different imaging devices. The major philosophies are presented that underlie the construction of probabilistic atlases, which store information on anatomic and functional variability in a population. Algorithms that create composite brain maps and atlases based on multiple subjects are examined. We show that group patterns of cortical organization, asymmetry, and disease-specific trends can be resolved that may not be apparent in individual brain maps....
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Dynamic Causal Modelling of Brain ResponsesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This chapter is about modelling-distributed brain responses and, in particular, the functional integration among neuronal systems. Inferences about the functional organisation of the brain rest on models of how measurements of evoked responses are caused. These models can be quite diverse, ranging from conceptual models of functional anatomy to mathematical models of neuronal and haemodynamics. The aim of this chapter is to introduce dynamic causal models. These models can be regarded as generalisations of the simple models employed in conventional analyses of regionally specific brain responses. In what follows, we will s...
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Experimental DesignEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This chapter addresses issues particular to the optimal design of fMRI experiments. It describes procedures for isolating the psychological process of interest and gives an overview of block, event-related, and participant-response dependent designs. An additional focus is placed on data analysis with emphasis on optimizing and isolating the neuroimaging signal in activated brain regions. Finally, the chapter addresses a number of practical matters including optimal sample sizes and trial durations that confront all researchers when designing their experiments.
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Preparing fMRI Data for Statistical AnalysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This chapter describes the procedures applied to fMRI data prior to their statistical analysis. This usually begins with converting the data from original MR format to a form that can be used by the analysis software. The data are then motion corrected. If an anatomical scan is collected for the subject, then it would be co-registered with the fMRI, and may serve to estimate the warps needed to spatially normalise the fMRI to some standard space. The final pre-processing step is usually to smooth the data.
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Statistical Analysis of fMRI DataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
fMRI is a powerful tool used in the study of brain function. It can non-invasively detect signal changes in areas of the brain where neuronal activity is varying. This chapter is a comprehensive description of the various steps in the statistical analysis of fMRI data. This will cover topics such as the general linear model (including orthogonality, haemodynamic variability, noise modelling, and the use of contrasts), multi-subject statistics, and statistical thresholding (including random field theory and permutation methods).
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Selection of Optimal Pulse Sequences for fMRIEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this chapter, we discuss technical considerations regarding pulse sequence selection and sequence parameter selection that can affect fMRI studies. The major focus is on optimizing MRI data acquisitions for blood oxygen level-dependent signal detection. Specific recommendations are made for generic 1.5-T and 3.0-T MRI scanners.
Source: Springer protocols feed by Neuroscience - May 1, 2009 Category: Neuroscience Source Type: info

Complexity Untangled: Large-Scale Realistic Computational Models in EpilepsyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the epilepsy field, the creation of large-scale data-driven models that incorporate decades worth of experimental data has led to substantial innovations over current methodologies. Such models and sophisticated visualization software that makes the models truly come to life have brought computational neuroscience closer to reality for all epilepsy researchers. In this chapter, we discuss detailed, data-driven models that have resulted in significant, testable, theoretical advances that have contributed to our knowledge of how large-scale biological neuronal networks interact to promote hyperexcitability and hypersynchr...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Organotypic Hippocampal Slice Cultures as a Model of Limbic EpileptogenesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Organotypic hippocampal slice cultures experience trauma, deafferentation due to cell loss or transection of afferent pathways, and neuronal circuitry rearrangements much like the events that can lead to acquired temporal lobe epilepsy. Organotypic hippocampal slice cultures can be maintained for months in vitro and exhibit a latent period followed by onset of electrographic seizures involving the dentate granule cells, which is a hallmark of epileptogenesis and acquired epilepsy in humans and in vivo animal models. The advantages of organotypic hippocampal slice cultures over in vivo models are that slice cultures exhibit...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Seizure Analysis and Detection In VivoEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Understanding seizure generation, the transition from interictal to ictal states, and its underlying mechanisms requires continuous electrophysiologic monitoring. Though the duration of monitoring may vary from brief experiments over minutes to months of continuous recording, all recording of this nature requires a similar set of hardware and software tools. This chapter reviews the basic setup and requirements for successful continuous EEG monitoring in vivo and provides a set of computational “tools” that our group has found useful for continuous EEG monitoring in the laboratory. These include methods for sei...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Viral Vector Gene Therapy for EpilepsyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Theoretically, gene therapy offers an attractive alternative for the treatment of focal epilepsies, and recently, studies have established the basic viability of anti-seizure gene therapy by employing a number of diverse approaches. Using recombinant adeno-associated virus (AAV) vectors, significant seizure suppression has been obtained in vivo by interrupting NMDA receptor function or by altering GABA receptor composition. Similarly, engineering cells to release GABA or adenosine has been shown to exert significant anti-seizure actions. In addition, studies have reported seizure suppression using in vivo, viral vector-med...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Neural Stem Cells in Experimental Mesial Temporal Lobe EpilepsyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Neurogenesis persists in the adult mammalian hippocampal dentate gyrus and is influenced by epileptogenic insults. Studies of rodent mesial temporal lobe epilepsy (mTLE) models indicate that status epilepticus acutely increases dentate granule cell (DGC) neurogenesis, but in chronic stages neurogenesis may decrease. The functional implications of altered neurogenesis in either stage of mTLE are poorly understood. Accumulating evidence suggests, however, that altered neurogenesis contributes to several well-characterized cellular abnormalities seen in human and experimental mTLE. These abnormalities include mossy fiber spro...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

The Nematode, Caenorhabditis elegans, as an Emerging Model for Investigating EpilepsyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Acquiring a holistic understanding of epilepsy, an intricate and often multifactorial disorder, is certain to necessitate considerable effort from a diverse and global assortment of scientists and clinicians. For most of its history, a combination of basic research with rodent models and clinical research with patients has dominated the approach of the epilepsy research community. These complementary approaches will undoubtedly remain as the ultimate direction in which research should move before new treatments for epilepsy are established, as mammalian nervous systems are exemplified by a degree of complexity, which sets ...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

The Genetics and Molecular Biology of Seizure Susceptibility in DrosophilaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There has been an increased interest recently in various Drosophila models of human disease. The goals are to uncover the fundamental biological principles underlying causes and cures of human pathology utilizing the power of Drosophila genetics. A particularly exciting prospect is that new therapeutics could be forthcoming through identification of disease-causing genes followed by targeted drug development or by the development of platforms for high-throughput drug screening. This chapter reviews a model of human epilepsy based on a set of seizure-sensitive Drosophila mutants that exhibit features resembling some human e...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

The Albino Xenopus laevis Tadpole as a Novel Model of Developmental SeizuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Here we describe a novel model system based on the transparent albino Xenopus laevis tadpole which is particularly well suited for the study of seizures and their sequelae within the intact developing brain. This system allows in vivo imaging of neuronal circuit activity with single-cell resolution, as well as acute and long-term imaging of neuronal growth and synapse formation, within the intact unanesthetized brain. Mounting evidence supports a strong role for neuronal transmission in regulating major aspects of brain circuit formation, including synaptogenesis, synapse strengthening and elimination, as well as axonal an...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Zebrafish as a Simple Vertebrate Organism for Epilepsy ResearchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
For many years, scientists have developed animal models of epilepsy to study specific aspects of the human condition. Rodents are the species of choice in the vast majority of these studies. In a departure from these rodent-centric models, we here describe zebrafish (Danio rerio), a genetically tractable vertebrate that is particularly well suited to epilepsy research. Zebrafish do not possess the complex central nervous system we have come to expect in other animal models and will never be mistaken for miniature versions of the complex mammalian brain. Nonetheless, the nervous system of this “simple” vertebrat...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Modeling Tuberous Sclerosis Complex: Brain Development and HyperexcitabilityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Tuberous sclerosis complex (TSC) is a very important cause of epilepsy particularly in children. Seizures are seen in up to 90% of patients with TSC and often very resistant to standard medical therapies. In addition, patients with TSC also frequently suffer from autism as well as mental retardation and various psychiatric disorders. The causative TSC1 and TSC2 genes were identified in the 1990s. Despite tremendous growth in our knowledge of the TSC genes, encoded proteins, and participation in signaling pathways, we have not yet developed breakthrough therapies that will significantly improve the quality of life of these ...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

BK Potassium Channel Mutations Affecting Neuronal Function and EpilepsyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Many experimental studies of epilepsy are based on rodent models induced by chemical or electrical insult as an instigator of seizures. Although such studies are useful in observing the physiological events that may occur during epileptogenesis, the great complexity of changes that ensue between first seizure and epilepsy makes it difficult to ascribe cause-and-effect to any single protein. In contrast, spontaneous mutations or mutations using gene targeting in mice provide a unique opportunity to evaluate a single protein, at cellular to whole organism level, for its role in epilepsy. Such approaches have uncovered a numb...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Mouse Models of Benign Familial Neonatal Convulsions (BFNC): Mutations in KCNQ (Kv7) GenesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Benign familial neonatal convulsions (BFNC) is caused by mutations in the KCNQ2 (Kv7.2) or KCNQ3 (Kv7.3) genes. These genes encode the KCNQ2 and KCNQ3 subunits that comprise the neuronal M-type potassium channel (M channel). While numerous studies have provided evidence for the inhibitory role of normally functioning M channels in key brain structures related to seizures and epileptogenesis, the BFNC sequelae from mutation to seizure and ultimately to remission is likely very complex. In an effort to determine the role of the KCNQ genes in epilepsy, a number of mouse models with either spontaneous or transgenic muta...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Interneuron Loss as a Cause of Seizures: Lessons from Interneuron-Deficient MiceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Throughout our nervous system, excitation and inhibition are exquisitely balanced to enable a multitude of functions. When this balance is disrupted, neurons experience a surplus or a deficit in excitation, either of which can have devastating consequences. In the cortex, excitation and inhibition are mediated by glutamatergic pyramidal cells and GABAergic interneurons, respectively. The loss of GABAergic inhibition in the epileptic brain places neurons in a hyperexcitable state in which they are vulnerable to the high-frequency firing that defines seizures. The association between seizures and a loss of GABAergic transmis...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

Imaging Seizure Propagation In VitroEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This is perhaps the most beautiful time in human history; it is really pregnant with all kinds of creative possibilities made possible by science and technology. Jonas Salk’s quotation seems particularly pertinent to recent developments in imaging technology, which have provided both beauty and insight in equal measure. We can now manipulate biological systems, both genetically and otherwise, to introduce fluorescent markers, literally adding colour to our preparations. These advances have occurred in parallel with remarkable developments in microscopy technology, with novel means of illumination and light de...
Source: Springer protocols feed by Neuroscience - November 1, 2008 Category: Neuroscience Source Type: info

XML for Data Representation and Model Specification in NeuroscienceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
EXtensible Markup Language (XML) technology provides an ideal representation for the complex structure of models and neuroscience data, as it is an open file format and provides a language-independent method for storing arbitrarily complex structured information. XML is composed of text and tags that explicitly describe the structure and semantics of the content of the document. In this chapter, we describe some of the common uses of XML in neuroscience, with case studies in representing neuroscience data and defining model descriptions based on examples from NeuroML. The specific methods that we discuss include (1) readin...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Model Structure Analysis in NEURON: Toward Interoperability Among Neural SimulatorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
One of the more important recent additions to the NEURON simulation environment is a tool called ModelView, which simplifies the task of understanding exactly what biological attributes are represented in a computational model. Here, we illustrate how ModelView contributes to the understanding of models and discuss its utility as a neuroinformatics tool for analyzing models in online databases and as a means for facilitating interoperability among simulators in computational neuroscience.
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Managing Knowledge in NeuroscienceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Processing text from scientific literature has become a necessity due to the burgeoning amounts of information that are fast becoming available, stemming from advances in electronic information technology. We created a program, NeuroText ( http://senselab.med.yale.edu/textmine/neurotext.pl ), designed specifically to extract information relevant to neuroscience-specific databases, NeuronDB and CellPropDB ( http://senselab.med.yale.edu/senselab/ ), housed at the Yale University School of Medicine. NeuroText extracts relevant information from the Neuroscience literature i...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Data Mining Through Simulation: Introduction to the Neural Query SystemEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Data integration is particularly difficult in neuroscience; we must organize vast amounts of data around only a few fragmentary functional hypotheses. It has often been noted that computer simulation, by providing explicit hypotheses for a particular system and bridging across different levels of organization, can provide an organizational focus, which can be leveraged to form substantive hypotheses. Simulations lend meaning to data and can be updated and adapted as further data come in. The use of simulation in this context suggests the need for simulator adjuncts to manage and evaluate data. We have developed a neural qu...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Brain Spatial Normalization: Indexing Neuroanatomical DatabasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Neuroanatomical informatics, a subspecialty of neuroinformatics, focuses on technological solutions to neuroimage database access. Its current main goal is an image-based query system that is able to retrieve imagery based on anatomical location. Here, we describe a set of tools that collectively form such a solution for sectional material and that are available to investigators to use on their own data sets. The system accepts slide images as input and yields a matrix of transformation parameters that map each point on the input image to a standardized 3D brain atlas. In essence, this spatial normalization makes the atlas...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Alzforum: E-Science for Alzheimer DiseaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Alzheimer Research Forum Web site ( http://www.alzforum.org ) is an independent research project to develop an online community resource to manage scientific knowledge, information, and data about Alzheimer disease (AD). Its goals are to promote rapid communication, research efficiency, and collaborative, multidisciplinary interactions. Introducing new knowledge management approaches to AD research has a potentially large societal value. AD is among the leading causes of disability and death in older people. According to the Alzheimer’s Association, four million Americans currently suff...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Creating Neuroscience OntologiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The insufficiency of terminological standards in neuroscience is increasingly recognized as a serious obstacle to interoperability. Adoption of a controlled vocabulary is a successful solution for small numbers of groups that work closely together but is impractical for large numbers of groups who represent diverse areas of research, index information by various legitimate nomenclatures, or publish in different languages. Interoperability among such disparate databases requires a translation mechanism, or “mediator,” to enable communication and data sharing among databases. Shared ontologies are essential compo...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Interoperability Across Neuroscience DatabasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Data interoperability between well-defined domains is currently performed by leveraging Web services. In the biosciences, more specifically in neuroscience, robust data interoperability is more difficult to achieve due to data heterogeneity, continuous domain changes, and the constant creation of new semantic data models (Nadkarni et al., J Am Med Inform Assoc 6, 478–93, 1999; Miller et al., J Am Med Inform Assoc 8, 34–48, 2001; Gardner et al., J Am Med Inform Assoc 8, 17–33, 2001). Data heterogeneity in neurosciences is primarily due to its multidisciplinary nature. This results in a compelling need to i...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

An Informatics Approach to Systems NeurogeneticsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We outline the theory behind complex trait analysis and systems genetics and describe web-accessible resources including GeneNetwork (GN) that can be used for rapid exploratory analysis and hypothesis testing. GN, in particular, is a tightly integrated suite of bioinformatics tools and data sets, which supports the investigation of complex networks of gene variants, molecules, and cellular processes that modulate complex traits, including behavior and disease susceptibility. Using various statistical tools, users are able to analyze gene expression in various brain regions and tissues, map loci that modulate these traits, ...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Constructing Realistic Neural Simulations with GENESISEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The GEneral NEural SImulation System (GENESIS) is an open source simulation platform for realistic modeling of systems ranging from subcellular components and biochemical reactions to detailed models of single neurons, simulations of large networks of realistic neurons, and systems-level models. The graphical interface XODUS permits the construction of a wide variety of interfaces for the control and visualization of simulations. The object-oriented scripting language allows one to easily construct and modify simulations built from the GENESIS libraries of simulation components. Here, we present procedures for installing G...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info

Brain Atlases and Neuroanatomic ImagingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Quantifying the effect of a genetic manipulation or disease is a complicated process in a population of animals. Probabilistic brain atlases can capture population variability and be used to quantify those variations in anatomy as measured by structural imaging. Minimum deformation atlases (MDAs), a subclass of probabilistic atlases, are intensity-based averages of a collection of scans in a common space unbiased by selection of a single target image. Here, we describe a method for generating an MDA from a set of magnetic resonance microscopy images. First, the images are segmented to remove any non-brain tissue and bias f...
Source: Springer protocols feed by Neuroscience - November 29, 2007 Category: Neuroscience Source Type: info