index [link.springer.com]978-1-59745-520-6/1.pdf · mri, 229 reconstruction, 211 ... 159, see...
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Index
11×N
mapping, 28129X1/SVJ
mouse strain, 222
22D, 214
anisotropic series, 221grid, 313image, 202series, 221
2DG, 201autoradiography, 197
33D, 214
atlas, 220, 224atlas server, 212, 228coordinate system, 226data sets, 220atlas server, 228fMRI, 198motion, 221MRI, 229reconstruction, 211storage format, 228time series, See 4Dviewer, 211volume, 221, 225
3D–3D alignment, 221
44D, 214
55-HT, 145, 147, See serotonin
Aabducent nerve, 74A-beta, 374
Abstract Schema Language, 330ABXD5F2
mouse strain, 222Access, 172, See MS Accessaccuracy, 178ACeDB, 58acetylcholine, See ACh
signaling, 355acetylsalicylic acid, 49, See aspirinACh, 325, See acetylcholineaction potentials, 127activation
time-dependent, 137, 145time-independent, 137voltage-dependent, 145
activation functiontime-dependent, 143voltage-dependent, 137, 143
activation variable, 178Active Data Objects, 31activity profile, 177activity-dependent facilitation, 148activity-dependent Hebbian model, 324AD, 315, 322, 323, 329, 366, See Alzheimer’s
Diseaseadaptive parameter, 309ADO, See Active Data Objectsafferent
damage to pathways, 329synaptic transmission, 325
afferent/efferentneurons, 41
affirmers lexical, 17affirming/negating, 5, 10Affymetrix, 290, 294, 350AFNI, 240, 241, 242, 253, See Analysis
of Functional NeuroImagesAFP, 214AFS, See Andrews File Systemage, 54Agilent, 351, 359agonal state, 347
383
384 Index
agonists, 49AIR, 192, 240, 241, 252, See Automated Image
RegistrationAIR5, 187aldehyde, 207Align Warp module, 191allele frequency disease, 339alleles, 296, 341
disease-related, 342Allen Brain Atlas, 79, 281alpha relaxation state, 328alpha-amino-3-hydroxy-5-methyl-4-
isoxazolepropionic acid, SeeAMPA
ALS, See amyotrophic lateral sclerosisAltaVista, 68alternate average creation, 185Alzforum, 366, 371, See Alzheimer’s Research
ForumAntibody Database, 379
AlzGene, 370, 372Alzheimer Research Forum, See ARFAlzheimer’s Disease, 7, 307, 357, See ADambiguity discrimination, 11amino acid-altering polymorphism, 342ammon horn, 69, 74AMPA, 12, 319amygdala, 74amygdaloid nuclear complex, 74amyloid precursor protein, 368amyotrophic lateral sclerosis, 365Analysis of Functional NeuroImages, 237ANALYZE75, 185anatomic variance, 184Andrews File System, 241Angleman Syndrome, 345ANN, 159, See artificial neural networkantagonist, 49anterior–posterior
olfactory bulb, 197antibody, 372anticholinergic, 49anti-inflammatory drugs, 49antonym, 49API, 70, See Application Programming InterfaceAplysia, 129, 139, 140, 145–147apolipoprotein, 370APP, See amyloid precursor proteinArabidopsis, 289archipallium, 308
archival tables, 14area V1, 282ARF, 377Aricept, 322artificial intelligence, 7artificial neural network, 157artificial neuron, 309artificial scotoma, 319ASCII, 128, 130aspirin, 49aspx, 70associative memory models, 305atherosclerosis, 357atlas
brain, 183digital, 184digital-canonical, 70minimum deformation, See MDAmouse brain, 184construction, 184
attributes, 45–46attribute–value, 50auto-launch, 92automated, 25
nonlinear registration, 223Automated Image Registration, 237automatic deposition, 8autoradiographic, 276autoradiographic mapping, 267autoradiography, 197, 268, 277–278autosomal dominant, 339average
intensity-based, 183activation frequency, 112
axial resistance, 117axon, 111, 207axonal
branches, 98arborizations, 58
Azores, 348
Bbackpropagation, 306BAMM, See Brain Activation and Morphological
MappingBAMMfx, 237BAMS, 81basal
forebrain, 322ganglia, 317
Index 385
basic statistics, 294BatchFtp, 242BaxGrid, 237BBTsyntax, 58behavioral traits, 301Benjamini-Hochberg correction, 356benzaldehyde, 43beta amyloid, 355BIC toolkit, 192bimodal, 139, 144BIMS, See Brain Information Management
Systemsbinary, 51
branch tree, 58BIND, 360biochemical, 104bioinformatics, 287, 337Bioinformatics Research Network, 23biological mechanisms, 306biological pathway, 361
schizophrenia, 357biomarker, 378
for neuropsychiatric disease, 357bipolar
disorder, 308, 340, 345, 357neurons, 80
BIRN, 28, 31, 214–215, See BioinformaticsResearch Network
BIRN-CC, 31BLAST, 6Blue Brain project, 308Boltzman, 130, 132Bonfire, 33–34Boolean, 30, 47–48, 50, 310BPEL, See Business Process Execution
LanguageBPEL4WS, See BPELbrain, 7
atlas, 60, 183comprehensive, 73macaque, 84mouse, 84probabilistic, 183
hierarchy, 71cortex, 196dynamics, 305functions, hierarchical approach to modeling, 315hemispheres, 268images, 235mammalian, 195
map, 271primate, 73, 80mouse, 212
mapping, 195parcellation, 281pH, 347region, 48, 54, 276regions, rat, 59slices, 268spatial normalization, 211structure, 69structures in, 39tissue, 197
Brain Activation and MorphologicalMapping, 237
Brain Information Management Systems, 69Brain Surface Extractor, 192Brain Voyager, 237BrainInfo, 67–70, 73–74, 79–80, 84brain-mapping, 184BrainMaps, 79BrainML, 25, 56, 91, 101, 251BrainML/XML, 28BrainPharm, 7BrainPy, 248brainstem, 217BrainSuite, 2, 185, 188, 237BrainVISA/Anatomis, 237BrainVoyager, 241, 250
neuroimaging package, 241branch point, 136, 147BRENDA, 6bridge
table, in databases, 50Bruker
spectrometer, 197BSE, 188burst, 174
duration, 168, 176period, 168, 176spiking, 320
burster, 110conditional, 146
bursting, 174activity, 147discharge frequency, 172neuron, 139
Business Process Execution Language, 243BXA1
mouse strain, 222
386 Index
BXD, 289–291, 293, 298, 300BXD1, 291BXD100, 291
CC++, 64, 170, 238C57BL
mouse strain, 290C57BL/6J
mouse strain, 212–215, 291Ca1
pyramidal cell, 92CA1, 69, 80CA2, 69, 80Ca2+, 139, 144, 147
intracellular concentration of, Seeion channel, 12
Ca2+-dependent K+ current, 146CA3, 69, 80, 121
cell model simulation, 108hippocampal, 121, 326pyramidal, 10pyramidal cell, 122cells, 10
Caenorhabditis elegans, 58calcium
intracellular concentration, 110imaging, 196
cAMPaccumulation of, 147regulation of, 139bimodal regulation of, 144
cancer, 288candidate gene, 337, 342caption, 45Caret
brain mapping program, 198cartesian coordinates, 116CAS, See Chemical Abstracts ServicesCaspase, 355Castor, 64Catacomb, 63, 101Catalyzer, 60catfish, 43CCDB, 49, See Cell Centered DatabaseCDM, See Common Data ModelCelera, 291cell
morphology, 59processing, 24
signalling, 24population, 276
Cell Centred Database, 31CellML, 91CellPropDB, 3–5, 7, 10, 15, 25cellular composition, 347central pattern generator, See CPGcerebellar
cortex, 31Purkinje neuron, See Purkinje
cerebellum, 10–11, 13, 17, 217, 290, 317cerebral cortex, 198cerebral palsy, 315c-fos, 208CGH, 359, See comparative genome
hybridizationCGI-PERL, 11channels, 40, 48Chemical Abstract Services, 202Chiron, 248, 254chlorpromazine
dopamine antagonist, 49Choice_Set_Values, 44Choice_Sets, 44cholinergic, 322
innervation, 325chromosomal
aberrations, 337regions, 341
circuit diagram, 137C-language, 160
vector-oriented, 160class
child, 47parent, 47
Class_Hierarchy, 47classes, 46Classes/Attributes, 51classes/tables, 38
bridge, 41many-to-many, 41
clinical trial, 378cluster map, 293, See QTL cluster mapcluster tree, 299clustering, 157CNFT, See continuum neural field theoryCNS, 230CoCoDat, 268, 269CoCoMac, 81, 267–269, 276, 283Cognex, 322
Index 387
cognition, 24cognitive computational neuroscience, 305cognitive deficits
VCFS, 345cognitive impairment, See Alzheimer’s DiseaseCollation of Receptor Data, See CoReDatcolumn/row, 164combinatorial methods, 338Common Data Model, 26community-building, 374comparative genome hybridization, 361compare correlates, 293, 301complex trait, 296
analysis, See trait analysismodulation, 287
computationallinguistics, 7model, 155, 330
in psychiatry, 305psychiatry, 315simulation, 168speed, 178
Computer Science and Artificial IntelligenceLaboratory, 380
concordance table, 51Condor, 216, 253conductance, 132, 174
cyclic nucleotide gated, 139ion, 134voltage-dependent, 132–133, 136
confocal imaging, 64connectionism, 306connectionist
mode, 309model, 310networks, 310
connexins, 316context, 5, 7–8
statistical, 68contextual, 16continuum neural field theory, 306control current, 132control population, 342controlled vocabulary, 37copy number, 341copy number analysis, 349CORBA, 245, 253CoReDat, 267–269, 276, 283coronally sliced, 217correlation matrix, 293–294, 301
cortexglobal model, 306
corticalareas, 319lesions, 317map reorganization, 318neurons, 319reorganization, 305sublayer, 275volume, 324
cortical columns, 328cortico-basal-ganglia-thalamic-cortical loop, 317cPath, 360CPG, 129, 140, 147–148CPU, 245
Linux, 252cranial nerve, 74craniofacial abnormalities
VCFS, 345cryosection, 268CSAIL, See Computer Science and Artificial
Intelligence LaboratoryCsm, 145curator, 70, 74, 367current, See ionic, reverse potential
external, 132hyperpolarization, Seeintrinsic, See ion channelvoltage-dependent, 137, 146
cvapp, 58cyclic AMP, See cAMPcyclic attractor, 312, 317cyclic nucleotide-gated conductance, 146Cygwin, 104Cygwin-X, 123cytoarchitectonics, 268, 274cytogenetic locui, 355Cytoscape, 348, 358, 360
web link, 357
DDAG, See Directed Acyclic Graphdata
analysis, 267binding, 57complexity, 38conversion, 243copy number, 341definition language triggers, 44derivation, 246diversity, 38
388 Index
elements, 38extraction, 176format conversion, 235genotyping, 351repository, 27, 212haplotype, 341heterogeneity, 23integration, 27–28, 155interoperability, See interoperabilitylineage, 246mediation, 28mediator, 27mining, 155–156model, 38, 271organization, 43pedigree, 246presentation, 44provenance, 251repositories, 27temporal dependencies, 244
Data Source Server, 28–29database, 24, 37, 159, 172
architecture, 4, 37, 271construction, 177construction and analysis, 176data-mining, 156design, 38electrophysiology, 54external, 27federation, 27genetics, 370integration,
centralized, 27mediated, 27
interface, 201mediators, 23neuronal, 40programmer/manager, 70relational, 37schema, 249simulation, 174–175single neuron, 177spatial, 67, 70symbolic, 70text-based, 267transaction, 235transcriptome, 290
databasing, 155receptor distributions, 267simulation-centric, 158
DBA/2Jmouse strain, 290–291
dbCollator, 277DBMS, 26, 28, 44–46dbSNP, 291Decentralized Information Group, 380decision tree, 13decrease-conductance, 143–144
general equation, 142delusion, 339dendrite, 111, 319–320
compartment, 112dendritic
arborizations, 58compartments, 4location, 161morphology, 103
density mechanisms, 96densocellular, 72dentate gyrus, 11, 72, 325depolarization, 142
slow, 146deviation, 178DICOM, 251differential equation
second-order, 139Diffusion Constant, 192digital atlas, 184dimensional stacking, 177
model neuron database, 173Directed Acyclic Graph, 249disease, 337, See infectiousdisease susceptibility, 287disease-induced, 184dissected tissue, 290DNA
alterations, 337damage, 365
Document Object Model, 57DOM, See Document Object Modeldomain, 70domain-dependent, 16dopamine, 49, 292, 317
receptors, 355dorsal, 200dorsal root ganglion, 321dorsolateral prefontal cortex, 361Douglas syntax, 58down-regulate, 145Drosophila, 289
Index 389
drug, 50anti-inflammatory, 49non-steroidal, 49
dsArchweb link, 46
DSS, 29–31, See Data Source ServersDTSearch, 8duty cycle, 171dyslexia, 314
EEAV, 37, 41, 43, 51
triple, 41EAV triplets, 45EAV/CR, 25–26, 28–29, 41–42, 45–46EAV_Flag, 46Edge Constant, 192EEG, 316, 328e-forum, 373electrical
coupling, 132non-synaptic communication, 316
electroencephalogram, See EEGelectrophysiology, 157
button, dialog box, 108database, 54
Em, 117enhancing
score, 11Ensembl, 294
Genome Browser, 296enthorinal, 325Entities/Objects, 42entity, 271
neuroanatomic, 34, 71, 73, 81, 271, 345entity–attribute–value, 41, See EAV, EAV/CRentorhinal cortex, 322Entrez, 41
Gene, 293Nucleotide, 293
environmental risk factors, 288epidemiologic, 378epilepsy, 305, 315epileptic-like discharge, 316episodic memory, 314epistasis, 339EPSP, 142equilibrium potential, 137, 143equivalent electrical circuit, 137erosion size, 192
ESRI GIS, 70EUCOURSE
web link, 105Eutectic, 58excitatory, 311
neuron, 320synaptically activated channel, 111stellate, 320
executive functionsdisturbances in, 322
expert-mediated, 5expression, 288Extended Markup Language Document Object
Model, 31Extensible Markup Language, See XML
Ffalse-negatives, 9false-positive, 68familial AD mutations, 372family-based association, 340FAQ, 302fast indexing, 16FE, See forward Eulerfeedback
loop, 145negative, 146positive, 146
feedback connections, 316feedforward, 306Fiswidgets, 236–238, 240–242, 245
workflow editor, 239flow diagram, 8fMRI, 195, 197, 201–202, 206–208, 235FMRIB, 237forebrain, 80formalin-fixed, 72FormatConvert, 242forward Euler, 135frequency
average activation, 112frontal cortex, 322frontal lobe, 80frontotemporal dementia, 368FScell, 112, 117FSecell, 112FSL, 241FTDP-17, 368, 372functional genomics, 337, 348functional magnetic resonance imaging, 200
390 Index
functionstime-dependent, 142voltage-dependent, 142
GGABA, 319, 356
neurons, 361receptor, 320, 356signalling, 355synthesis, 361
GABAergic, 360signalling, 361
galactose metabolism, 357, 359gamma
bursts, 326rhythm, 326
GenBank, 25gene, 50, 337
amplification, 345effects, 341expression, 291, 338, 357
P-values, 357screens, 341traits, 293
ontology, 287pleiotropy, 288variants, 50, 287
Gene Expression/Genotyping, 359Gene Ontology, 39, 348, 378GeneChip, 356GeneNetwork, See GNGEneral NEural SImulation System, See
GENESISGENESIS, 101, 103, 111, 115, 121, 123, 148,
170, 319, 326, 330Reference Manual, 105scripting, 115simulator, 63software, 58syntax, 105web link, 104
GeneSpring GT, 351, 353–354, 356GeneSpring Network, 361genetic, 337
analysis, 338association, 342complexity, 288correlations, 290, 297covariance, 288disease, 338
makeup, 291manipulation, Seemarkers, 349reference population, 287screen, 349variation, 291
GenMAPP, 360genome
linkage analysis, 337, 343projects, 156
Genome Scan Meta-Analysis, 344schzophrenia, 344
genomics, 24genotype, 291
phenotype relations, 289genotyping, 342Gensat, 281gif, 70Globus, 242
Toolkit, 245glomerular layer, 199, 207glomerulus, 200glutamate, 356
receptors, 12glutamine, 338GN, 287–289, 293, 298, 302GNU, 104GO, See Gene Ontologygoodness-of-fit, 176gradient-echo imaging, 197grammatical analysis, 310graphemes, 309graphical interface, 106gray scale intensities, 251Grid
architectures, 244environment, 252
GRID, 215, 216Grid Services Flow Language, 249GRID-based, 214GridFTP, 242Growth Factor Receptor Bound Protein, 359GRP, 290, 291 See genetic reference populationGSFL, See Grid Services Flow LanguageGUI, 112, 128, 133, 241, 248gyri tracts, 72Gyrus F1, 74
Hhallucination, 339haplotype, 341, 351, 353, 361
Index 391
Hardy–Weinberg Equilibrium, 351HBP, See Human Brain ProjectHD, 338, 357, See Huntington’s DiseaseHDF5, 242hearing defects
VCFS, 345Hebbian
model, 324–325hematopoietic stem cells, 290hemorrhagic stroke, 315heptanal, 203heterosynaptic plasticity, 139HH, 128, 135, 137, 148HHRR, 354hierarchies, 17
of modules, 330hierarchy, 5, 7, 9, 80
partitive, 80hindbrain, 80hippocampal, 121
networks, 326hippocampus, 74, 83, 290, 306, 316, 325histological
delineation, 282markers, 283mask, 268
histostained tissue sections, 204HMA, See Human Mapping AssayHodgkin and Huxley, 130, See Hodgkin-HuxleyHodgkin–Huxley, 112, 122, 131, 134, 136, See HHhodological, 81homogeneity
population, 349homology, 282homonyms, 38homosynaptic plasticity, 137, 144Hopfield
autoassociative memory, 324networks, 312
Hopfield network, 312HTML, 54, 57, 70, 105, 247, 249, 302HTTP, 31, 58, 214–215HTTPS, 227Human Brain
Atlas of, 79Human Brain Project, 23, 42human genome
annotation, 347Human Mapping Assay, 350human-readable, 73
human-recognizable, 73label, 74
Huntingtin, 338Huntington, 365
disease, 338HyperCard
Apple/MacIntosh, 81Hyperdoc, 106hyperpolarization current, 92hypertext, 81Hypertext Markup Language, See HTMLhypothalamus, 79
paraventricular nucleus of, 79hypothesis testing, 287hypothetical neuron
equivalent electrical circuit, 139
II/O, 148IATR, See Internet Analysis Tools RegistryIBM, 308Iclamp, 110image
alignment, 220analysis, 306-based query, 211brain, 24histological, 212human-recognizable, 73magnetic resonance microsopy, 183processing, 235radiological, 212registration, 211
Image Queryweb service, 226
imagingfunctional magnetic resonance, See fMRImodality, 211neuroanatomical, 183
impaled recording electrodes, 196inbred strains, 287increase-conductance, 143, 144index
hierarchical, 80string-based, 68
indexing, 3citation, 68neuroanatomical database, 211word, See
inductive database, 155infectious disease, 289
392 Index
inferior temporal cortex, 321informatics, 287information
extraction, 3, 5, 7, 16processing, 309source map, 30
informativeness, 342Ingenuity, 348inheritance modes, 339inhibitory, 311, 320
neuron, 320postsynaptic potentials, See IPSPsynaptically activated channels, 111
input/output, 131, See I/Ointegrate-and-fire
cell, 129, 132integrator Servers, See ISIntegrin signalling, 355Intel Xeon, 70intensity-rescaling, 190interface, 8
constraints, 37graphical, See graphical, interface
intermarker D score, 344Internet Analysis Tools Registry, 250interneurons, 10interoperability, 4, 25, 91, 148, 235InterPro, 348intersection
XML schema approach, 55inter-spike interval, 176intracellular ion pool, 132intracellular pool, 146
multiple, 146ion
channel, 4, 167, 173, 316current, 174pool, 144, 146
intracellular, 136ionic
channel, 320conductances, See channelscurrent, 14, 134
reversal potential, 132IPSP, 142IS, 28, 30ischemic stroke, 315ISM, See information source mapisodisomy, 345isolate, 340
JJ2EE, 213, 216, 224, 227Java, 57, 62, 64, 212–223, 240–241
applet, 70virtual machine, See JVM
Java 2 Enterprise Edition, See J2EEJava Beans, 216Java Message Service, 245, See JMSJava Remote Method Invocation (RMI), 245JAXB, 64Jftp, 242JMS, 245jpeg, See jpgjpg, 70jsp, 70JVM, 129, 133
KK
channels, 122KB, 379, See knowledgebaseKDD, 156, See knowledge discovery and data
miningKEGG, 348, 360keywords, 5, 10
score, 13Kinetikit, 110–111knockout, 287knowledge
base, See KBdiscovery, 155domain, 71management, 365repository, 73
knowledge base, See knowledgebaseknowledge discovery and data mining, 155knowledgebase, 3, 5, 8, 11, 14, 16knowledge-base, See knowledgebaseKnowMe, 34Kohonen network, 313
Llaboratory data management system, 60LabSWAN, 378language skills
degradation of, 322lateral inhibition, 321lateralization, 308late-response, 196
Index 393
layer, 72III, 320IV, 320V, 320
LD, 344, See linkage disequilibriumleak conductance, 134learning
algorithm, 309supervised, 3, 8, 14unsupervised, 3, 11
left–right hemisphere, 308lesions, 317, 318leukocyte, 347, 349, 354lexical, 5
affirmers, 18constraints, 16negators, 18
ligand, 267, 269ligand-binding, 268likelihood ratio statistic, See LRSlimbic, 308, 322limits of detection, 343linguistics, 16linkage, 338, 340linkage calculations, 344linkage disequilibrium, 340Linux, 104, 123, 192, 217LISP, 41list association, 41Load Simulation, 135local voltage, 176locus ceruleus/coeruleus, 74LOD, 350, See limitsof detection
score, 358logical
neuron model, 310typing, 242
long-term potentiation, 320LONI, 79, 185, 190, 192, 224, 237, 251–253, 282
Debabler, 187Pipeline, 189
lower bound, 48LRS, See likelihood ratio stastisticsLTP, See long-term potentiationLycos, 68lymphoblast, 347
MMac, 192Mac OS, 223
Mac OS/X, See OS Xmacaque, 79, 282
atlas, 69machine learning, 159, 306MacOS, 217MacroVoxel, 228Madeira, 348MAGE XML, 64magnetic
field strength, 197resonance imaging, See MRIresonance microscopy image, 183
Magneto and Electroencephalogram, 237major depressive disorder, 345Mann–Whitney
testing, 356map
locus, 287odor, See odor mapsserver, 70
mapping, 267markers, 340Marquardt–Levenberg, 223MAS5, 290mask values, 251MathML, 56, 62MATLAB, 172, 240–241Mauthner, 230maximal conductance, 168MBL, See Mouse Brain LibraryMDA, 184, 185, 186, 187, 191, See minimim
deformation atlasMDT, 190, 191, 192, See minimum deformation
targetMDT2, 191mean, 157mean-square-root
deviation, 176mechanoreceptors, 319medial dorsal nucleus, 72mediator, 67Medical Subject Headings, See MeSHmedium spiny neuron, 12MEG/EEG, See magneto and
electroencephalogrammelanophores, 43membrane, 7
capacitance, 134, 174conductances, 132, 144–146current, 168
394 Index
membrane potential, 177of neurons, 196simulation, 110soma, 116
memory, 306decline, 324loss, 365
Mendelian genetics, 288–289Mercator, 208MERLIN, 351, 353MeSH, 17Message Passing Interface, 240metabolic-vascular state, 197metadata, 12, 16, 23, 25–26, 30–31, 37, 42–44, 45,
47, 60, 156, See meta-datameta-data, 250, 253
fields, 251meta-database, 30meta-language, 164metaphysical, 72metathesaurus
UMLS, 84MGH, 376MIAME, 64microarray, 290, 294
data sets, 288Microbrightfield, 58microdletions, 345microsatellite, 291, 341, 349, 350Microsoft Access, 45, 81Microsoft IIS, 201Microsoft Visual C++,
See C++microstructure of cognition, 306midbrain, 80middleware, 246MINC, 187, 189, 251, 253mind objects, 315minimum deformation atlas, 183minimum deformation target, 183, 187misfolded proteins, 365mitochondria, 355MLP, 312model, See Poirazi
compartmentalized cell, 121computational, 129connectionist, 310hierarchical, 81multicompartment, 147networks, 177
neuralspiking, 314
neural systems, 176neuron,
high-dimensional, 178neurons, 177psychiatric, 72single neurons, 103systemic, 81
ModelDB, 91, 100, 129, 148modeling
neuronal, See neuronal, modelingModelView, 91, 93, 96, 100MODm, 144–145modulation, 144modulatory
function, 145relationships, 132synapse, 138, 144–145transmitter, 144–145
moduleAlign Warp, 191Crop, 190Soft Mean
molecular layer, 72mollusc, 129Mollweide, 208monozygotic twins, 339mood instability
VCFS, See velocardiofacial syndromemood swings, 308MorphML, 53, 56, 58, 100–101
schema, 59viewer, 60
morphology, 53, 184dendritic, 103
mossy fibers, 10motor
cortex, 317function
disturbances in, 322mouse brain, 212mouse brain atlas, 281Mouse Brain Library, 79, 217
Project, 214Mouse Pheromone Database, 291movement disorders, 195MPI, See Message Passing InterfaceMRI, 183–184, 188, 197, 201, 235MRM, 186–187, 191
Index 395
mRNA, 341expression, 290transcripts, 342
MS Access, 25, 269MS Access XP® „ 271MS Excel, 25MS Windows, 70, 92, 104MS-SQL, 70Mulit-layer perceptron feedforward network, 311multi-compartmental models, 310multifactorial analysis, 269Multilayer Perceptron, 311Multiple Interval Mapping, 299multiple mapping, 293Multiple QTL Mapping, 300multi-point downstream linkage analysis, 351Multipoint Engine for Rapid Likelihood Inference,
See MERLINmultivariate analysis, 269mutant
mice, 183mutation, 368
disease-causing, 339myeloarchitectonics, 268MySql, 25MySQL, 269MySQL® 4,1,10, 271MySWAN, 378
NNa
channel, 118, 122nanoAmps, 110narrow distribution, 176N-ary, 43NAS, See Network Attached StorageNational Alliance for Research on Schizophrenia
and Depression, See NARSADNational Center for Biotechnology Information, See
NCBINational Library of, 39National Library of Medicine, 15, 84, 201natural language processing, 35Nature
journal, 371NCBI, 41, 348NDG, See Neuroscience Database Gatewaynegating
contextually, 12score, 11
negatorslexical, 17
neocortex, 306, 308, 316neostriatum, 12nerve bundle, 207nerve cell, See neuronnervous system, 23NetCDF, 189NetOStat, 223–226, 229
Brain Atlas Navigator, 226Netscape, 244network
graph, 293Hopfield, 312nodes, 309non-rhythmic, 174rhythmic, 174simulations, 161
Network Attached Storage, 242network databases, 170
model, 170Network File System, See NFSNeuoinformatics Information Framework, 23neural
activities, 198cell assemblies, 308circuits, 128, 196function, 127information processing, 310model, 309, 326network, 305, 311, 128, 140, 147,
155, 167networks, 24, 127, 130, 316plasticity, 306processes, 305query system, See NQSsimulation, 103, 157–158, 314system, 127
complex, 177function, 167
systems, 24Neural Simulation Language, 330neuregulin1, See NRG1neuroanatomical, 288
informatics, 211neuroanatomist, 79neuroanatomy, 59, 67, 71–72
hierarchy, 80database
indexing, 211
396 Index
microscopic, 72texts and atlases, 69
Neurobase, 377neuroConstruct, 63neurodegenerative, 7neurodegenerative disorders, 365, 371neurodynamic, 315neurodynamics, 315neurogenetics, 287neuroimaging, 185, 235, 246, 249
Informatics, See NIfTIsize and complexity of, data, 243
Neuroimaging Informatics Technology Initiative,See NIfTI
neuroinformatics, 3, 53–54, 67, 83, 129, 148, 211,235, 305
Neurokit, 107, 111neurological, 7
diseases, 195terminology, 72
Neurolucida, 58NeuroML, 53, 55–56, 101
Development Kit, 56, 60, 62neuromodulation
acetylcholine, 326neuromorphic devices, 306neuron, 7, 14, 17, 30, 40, 48, 130
activation, 309activity
bursting, 168afferent, Seeafferent/efferent, 41biophysical and biochemical properties, 128bipolar, 80computational element, 136electrical coupling between, 147excitability, 162HH-type, 132, 136large-scale networks, 55medium spiny, 34, Seepyramidal, 80reticular, 4thalamic reticulartonically spiking, 176tracing system (software), 58two-compartment, 111two-state, 312
NEURON, 91–92, 101, 148, 155, 157–160, 164,170, 330
software, 58
neuron databasesmodel, 170
neuronalactivity
odor-stimulated, 196compartment, 8, 10compartments, 14death, 322membrane properties, 4model, 55modelingmorphology, See morphologynetwork, 155, 167pathways, 49, 81signals, 195
neuronal excitability, 134NeuroNames, 33, 67, 69–72, 74, 79–80, 82, 84,
212, 224, 251NeuronDB, 3–5, 7, 10, 15, 25, 48, 49neuropharmacological, 288neurophysiology, 155, 329neuropil, 33neuropsychiatric
diseases, 356disorders, 345
neuropsychological syndromes, 305neuropsychopharmacology, 314neuroscience, 267, 305, 315, 330
ontologies, 67Society For, 71XML in, 55
NeuroscienceJournal of, 3, 8, 14
Neuroscience Database Gateway, 267Neuroscience Information Framework, 71neurosimulator, 130, 148neurosimulators, 128NeuroSys, 25, 27, 60NeuroTerrain, 212, 224–225
Atlas Server, 228mouse atlas, 229
NeuroText, 3, 5, 7– 8, 10–11, 13, 15–16, 19web link, 3
neurotransmitter-receptor transcripts, 356neurotransmitters, 4, 10, 14neurotransmitters/neuromodulators, 48Nevin, 58nextToken, 57NFS, 214, 241NIF, See Neuroscience Information Framework
Index 397
NIH, 379NIH Blueprint for Neuroscience
Research, 71NIMH, 307Nissl-stained, 72, 212, 230, 282
atlas, 223NLP, 7, 18, See Natural Language ProcessingNMDA, 319
channel, 320receptor, 320–321, 374
NMOD, 158nodes, 306nodulation, 138nomenclature, 70Nomina Anatomica, 72non-declarative memory, 327nonparametric linkage, 343
analysis, 351nonspecific hybridization, 294nonspiking neurons, 307non-steroidal drugs, 49noradrenaline, 38norepinephrine, 38normal
genetic pathwaysdisruption, 183
maps, 320probability plot, 294
normalizedcorrelation, 205fluorescence, 294
NPAIRS, 237NPL Z score, 353, See nonparametric linkage Z
scoreNQS, 155, 157–161, 163–164NTDB, 6NT-SDK, 229numerical
classification, 157simulation, 178
OOB, 198, 207–208, See Olfactory Bulbobesity, 289object, 271
class, 55objects/entities, 50octanal, 203odds ratio test, 14
ODE, 148, See ordinary differentialequation
odor, 43map, 195, 198, 200–202, 204–205mapping, 197–198stimuli, 196, 202, 207
OdorDB, 201OdorMapBuilder, 198, 200, 206–207OdorMapComparer, 195, 202–203, 206OdorMapDB, 195, 201–202, 206olfaction, 24olfactory
bulb, 195, See OBreceptor, 207
interactions with odor, 202signals, 208
olivary nucleus, 39OME, See open microscopy environmentOMIM, 292, 293ontological, 23ontology, 27, 29, 33, 50, 67–68, 157, 287
neuroanatomical, 72neuroscientific, 68XTM databases, 82
Ontology Server, See OSOpen Microscopy Environment, 242open reading frames, 347OpenGL, 185Openmicroscopy, 64OpenPBS
workflow, 216optimization algorithm
stacking order, 177Oracle, 25, 27, 44ORDB, 201ordinary differential equation, 136ORF, See open reading framesorthographical representations, 314OS, 28, 30–31OS X, 92overtransmission, 340oxidative phosphorylation, 355
Ppair-scan, 297pair-scan mapping, 296paleomammalian, 308PANTHER, 292Parallel Distributed Processing,
See PDP
398 Index
parameterchange
minimization, 178combination, 174–175space, 174
parametric linkage, 343paranoid delusions, 322paraventricular nucleus, 75–76, 79Parkinson, 365Parkinson’s, 7Parkinson’s disease, 315, 329, 345, 373Parkinsonism, 315, 368parsing
contextual, 3fine-grained, 11lexical, 3semantic, 3syntactic, 6
partitive, See partitive, hierarchyparvalbumin, 361pathogenesis
Alzheimer’s Disease, 323pathogenic event, 378pathologic change, 378pathophysiologic, 378Pathway Assist
commercial software, 348pattern recognition, 306PDGene, 376PDNN, 299, See position-dependent nearest
neighborPDP, 306PDP++, 330per burst
interval, 176peripheral
leukocytes, 347, 356nervous system, 196receptor, 207
PERL, 8, 64Perlegen/NIEHS
resequencing project, 291perturbation, 378pFam, 348pH, 347phantom limb, 320, 321phase relations, 310phenothiazine
chlorpromazine, 49phenotype, 288, 291, 299–300, 337, 342
phonemes, 309–310phonological, 314phonology, 314phosphorylation, 357
regularion pathway, 359photomicrographs, 184PHP, 57, 64physiological traits, 301physiopathology, 24PIC, See Portuguese Island Collectionpipeline, 211, 214, 228, 235, See LONI
image_processing, 214NeuroTerrain, 213
piriform, 110pivoting, 43plasticity
function, 140heterosynaptic, 145homosynaptic, 142, 145
plateau potentials, 148pleiotropic, 299plexiform layer, 199PNAS
journal, 371point attractor, 312point processes, 96Poirazi model, 93polygenic
disease, 288traits, 289
polymorphism, 50, 356amino acid-altering, 342
population isolate, See isolatePortuguese Island Collection, 354position-dependent nearest neighbor, See PDNNposterior parietal cortex, 321PostgreSQL, 25, 213, 215post-processing, 10, 11postscript, 249postsynaptic
cell, 139, 145potentials, 143
multicomponent, 142receptor, 161
potassium channel, 110, 112, 118gene, 292
POW, 370PowerBuilder, 45PowerPoint, 302Prader-WIlli Syndrome, 345
Index 399
precision, 8prefrontal cortex, 317presenilin-1, 368, 372presenilin-2, 368, 372presynaptic
activity, 138, 142cell, 161
spikes, 142primates, 281probabilistic brain atlas, 183probe, 294process
non-linear, 167process management, 248processing
natural language, 3projection pathways, 196Protégé, 27protein interactions, 55proteomics, 24protocols
standardized, 24prototype
library, 118provenance, 253pruning, 323PSD95, 374PSM, 140PSP, 142, 143, See postsynaptic potential
time-dependent, 143voltage-dependnet, 143
psychological, 315psychology, 315psychotic features, 322PubMed, 3, 15, 17, 25, 74, 290, 357, 367, 375, 379pull-down, 45purine metabolism, 357, 359Purkinje, 10, 13, 17, 110
dendrites, 33neurons, 33
putamen, 317P-value, 298pyramidal neurons, 80, 316Python, 64, 237
QQC, 219, 220QIS, 28, 30–31QTL, 287–288
cluster map, 293, 299
quasi-stable statesattractor networks, 315
querylanguage, 158translation, 28web-service, 214
Query Integration System, 29Query Integrator System,
See QIS
Rradial separation, 204radioactively labeled, 268radioactivity, 268random number variable, 137, 143rate-constant equation
HH-type, 132RDBMS, 28, 212, 215–216, 227RDF, 16, SeeReactome, 360readcell, 116reading, 306recall, 8receptor, 4, 10, 14, 40, 43, 48, 278
binding, 276ligands, 268table, 279
recessive allelesdisease-causing, 345
recombinant inbred, See RIrecombination events, 342recording-site, 54red/green/blue, 201reference atlas, 211regulators
intracellular, 139regulatory agents
intracellular, 137, 142relational database, 267relational database management system, See
RDBMSrelationship
binary, 41many-to-many, 40
resequencing project, 291Resource Description Framework, See RDF,
See RDFresting conductance, 142resting potential, 171
400 Index
retrieval, 68information, 74precision, 68
reversal potential, 132RGB, 203, See red/green/bluerheumatoid arthritis, 357rhythmic network, 176RI, 297–298, See recombinant inbredribosomal, 355rigidity, 316RMA, 356, See robust multichip analysis or robust
multiarray averagingRMI, See remote method invocationRobust Multiarray Averaging, See RMArobust multichip analysis, 290rodents, 281Roget’s Thesaurus, 10, 18RPPL, 248Ruby scripts, 216rule-based systems, 310Run Pipeline in Parallel, See RPPLrun simulation, 135
SSAMBA, 214Sao Miguel Azores, 348SAX, 31, See Simple Application Programming for
XMLXML parser, 63
SBML, 56scalability, 246Scalable Vector Graphics, 31schema, 40, 44
complex-database, 39continually evolving, 38global, 28mixed, 45RDF, 378simplification, 40SWAN, 379
schematic, 139schizophrenia, 289, 316, 337–339, 345–346, 349,
356–357, 361Schizophrenia Research Forum, 376Science
journal, 371SCIL, 216scotoma, See artificial scotomascreen-scraping, 25scrolling lists, 14
SDP, See strain distribution patternsecond messenger, 132, 138, 145
pool, 144second messengers, 144secondary database, 176secondary dendrites, 230sectioning, 184segmentation, 185
errors, 219layer, 223
Selbst-Erhaltungs-Therapie, See Self-MaintenanceTherapy
self organized mapping networks, 318Self-Maintenance therapy, 327self-organizing, 309
networks, 321Self-Organizing Mapping, See SOMsemantic, 5
-based indexes, 68data models, 23data-types, 251inverse/reciprocal, 49metadata annotations, 23phrases, 11reciprocal, 49relationship, 11Web, 35web services, 26relationships, 8
Semantic Web Applications in Neuromedicine, SeeSWAN
Semantic Web in Life Sciences, 377senile plaque, 325SenseLab, 4, 7, 14–15, 42, 46, 48–49,
92, 158sensitivity, 8, 9, 10sensory perceptions
abnormal, 195sentence processing, 306sequence, 24, 50serotonin, 139, See 5-HT
signalling, 355shared cluster, 175short oligomer microarrays, 290sigmoidal, 310signal
analysis, 306encoding, 195neuronal, See neuronal signals
Index 401
silentdischarge frequency, 172neuron model, 175
Simple Application Programming Interface, 57Simple Application Programming Interface for
XML, 31simple interval mapping, 295Simple Object Access Protocol, See SOAPSimToolDB, 158simulation, 118–119, 155, 159, 168
full network, 178large networks, 104program, 174time, 174
simulator for neural networks and action potentials,See SNNAP
singlehidden layer, 311neuron excitability, 161spikes, 309
single-chromosome Map Viewer, 296single-nucleotide polymorphism, See SNPsingle-point
downstream linkage analysis, 351slower synaptic learning, 318SMART ATLAS, 224smell
perception of, 196SNNAP, 127–128, 130, 133, 135–136, 143,
147–148Tutorial Manual, 129, 133web link, 129
SNP, 291, 338, 341, 351, 353, See single nucleotidepolymorphism
database, 291genotype, 349genotyping, 349haplotype, 342haplotyping, 349LOD scores, 357–358
SOAP, 26sodium
channel, 112Soft Mean module, 190SOM, 313, 318soma, 111–112, 117, 319somatosensory cortex, 318–319, 320spatial
correlation, 205coefficient, 203
discretization, 94distributed markers, 268frequency, 220indexer, 211normalization, 183–184, 212, 220
species, 54specificity, 10speech perception, 306spike, 112, 174
activity, 145–146, 161, Seecount, 176duration, 142frequency, 171, 310
histogram, 173generator, 112, 118per burst, 171propagation, 136
spiketrain, 115spiking
discharge frequency, 172membrane conductances, 174neural models, 314neurons, 314
SPM, 241, 248SQL, 39, 43–44, 81, 82, 160
server, 25squashing functions, 310squid, 110Squid_Na, 130squid-like channels, 112SRB, 214, 227, See Storage Resource BrokerS-shape, 294, See sigmoidalstacking order, 177staining, 184staining-method, 54standard deviation, 157startElement, 63statistical evaluation, 290statistics, 157, 306steady state, 175stereological, 288stimulus
modulatory, 132stimulus current
extrinsic, 134storage
information, 74Storage Request Broker, See SRBStorage Resource Broker, 242strain, 291
402 Index
strain distribution pattern, See SDPstriatum, 290structure
anatomical, 184, 195chemical, 50dendritic, 111genotyping, 351long name, 79pedigree, 351primary, 71superficial, 72
Structured Query Language, See SQLstudy population, 340sub-cellular, 103sub-nuclei, 72sub-ontologies, 84sub-schema, 39sub-structures, 72Sun Grid Engine, 253superior frontal gyrus, 74susceptibility gene, 344SVG, See Scalable Vector GraphicsSWAN, 377–378, 380
schema, 379Sybase, 44SymAtlas, 292symbolic
description, 315information processing, 310
synapse, 161chemical, 132–134, 142database, 292electrical, 134modulatory, 133strength, 174time-dependent, 132voltage-dependent, 132
synapses, 130network, 128
synaptic, 311activation, 143compensation, 323conductances, 143
time-dependent activation, 139connection, 142
exponential growth of, 325connections, 323
per unit cortical volume, 324current, 143deletion, 323
input, 112integration, 92isolation, 177loss, 326plasticity, 128potentials and integration, 137receptors
activation of, 167strength, 139transmission, 128, 142transmissions, 196
synaptic runaway model, 325synaptophysin, 215synchrony, 316SynDB, 292synonym, 5, 10, 42synonyms, 38, 49, 72syntax, 68synuclein, 355systematic reasoning, 310systemic, 81systems
biology, 337, 338genetics, 288theory
non-linear, 168Systems Biology Markup Language, See SBML
TT1, 187
MRI component, 197T1-weighted, See T1T2
MRI component, 197table
bridge, 40column, 161create/alter, 44lookup, 40objects, 41reciprocal attributes, 49
tables/classes, 44tactile, 319tags, 54tal
Fiswidgets application interface, 241tau, 372
gene, 368mutation, 368
taxonomic, 157
Index 403
TCP/IP, 26Telemakus, 370template workflow, 249temporal gradients
memory decline, 324terminological, 67Terms/Synonyms, 50Tesla, 197text
human-readable, 73mining, 3, 348-based databases, 267
TEXTAREA, 48thalamic, 4, 318
interneuron, 319nuclei, 319relay cell model, 319
thalamo-cortical, 318thalamus, 75, 319, 320theta rhythm, 326tiff, 216, 225time constant, 139tonic spikers, 173tonically spiking, 174
neuron, 176Tools/FXParse, 238Topic Maps, 82topographical, 309
map, 313, 318trait
analysis, 287regulation, 299
transcript expression, 287transcriptional
change, 342level, 342profiling, 347
transcriptome database, 290transcripts, 290transgenic, 184, 287transmitter, 132, 136, 144
pool, 146transQTL, See QTLtremor, 316TrialDB
web link, 43trinucleotide repeat, 338triplets, See EAV tripletstriune, 308true-negatives, 14
true-positives, 14t-test, 157tutorial, 103, 106two-state neurons, 312
UUbiquitin, 355UCSC, 294, 348
Genome Browser, 296UMLS, 17, 29, 31, 33–34, 39, 41, 50, 84UniGene, 292, 293uniparental isodisomy, 345unirelational
concepts, hierarchical models, 81Unix, 216, 223, 228, 240UNIX, 104, 107, 123, 192, 228UNIX/Linux, 92upper bound, 48up-regulate, 145URL, 25, 30user, 45
interface, 38, 70
Vvalidation, 8, 13
constraints, 37values, 42VCFS, 359, See velocicardiofacial syndromevelocardiofacial syndrome, 345ventral posterior lateral, See VPLventroposterolateral, See VPLvibration, 319View/Query Designer, 34virtual datasets, 249Virtual Knife, 225, 229Virtual RatBrain Project, 59VisANT, 34Visome, 329visual cortex, 282, 319visualization
dimensional stacking, 173Vm, 117vocabulary
default, 74controlled, 39, 73
VOI, 225voltage
maxima, 174minima, 174
voltage trace, 171, 173
404 Index
per burst, 171voltage-activated
channels, 112voltage-dependent gating, 167volumes of interest, See VOIVoxBo, 237voxel, 251VPL, 79, 319
WW3C, 26, 377WAMBAMM
web link, 105warping algorithm, 204wavelet-based registration, 222Web Service Description Language, See WSDLWeb Services Interoperability Organization, See
WS-IWebGestalt, 299WebQTL, 295, 300
Map Viewer, 296WebStart, 224Wellcome-CTC, 291WFMS, 235–236, 238, 241–242, 245, 248, 252white blood cell, 354Whole Brain Atlas, 79Wikipedia, 379Windows, 123, 217Windows 2000, 185Windows XP, 185
WIRM, 25word morphology, 306word-indexing, See indexingworkbench, 236workflow, 235, 244
for genetic analysis, 351management system, See WFMSneuroimaging, 235verification, 252
working memory, 314wrapper function, 240WS-I, 227
XX Windows, 107XDTM, 243, 252XML, 16, 26, 29–31, 53, 54, 62, 82, 100–101,
238, 251libraries, 57schema, 55
XML Dataset Type and Mapping, See XDTMXML DOM, 31XML Pull Parser, 57XODUS, 106, 121, 123
web link, 104XPP, See XML Pull ParserXTM, 76, 82
ZZ score, 343, 357, 358