Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Maps as Topic”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,621 records · Page 90Linked to original sources
PubMed1979

The cytoarchitecture of the interfascicular nucleus and ventral tegmental area of Tsai in the rat.

The cytoarchitecture of the ventral tegmental area of Tsai (VTA) has been studied in detail in the rat with the acid of both conventional techniques and glyoxylic acid-fluorescence histochemistry. Three main dopamine containing cells groups can be distinguished: nucleus paranigralis, nucleus parabrachialis pigmentosus, nucleus linearis raphe caudalis. Nucleus parabrachialis pigmentosus lies dorsally, and nucleus paranigaralis ventrally in the VTA, while nucleus linearis continues posteriorly and medially from VTA and extends dorsally in the midline up towards the dorsal raphe nucleus. Fluorescent neurons in these three groups correspond to the A10 group. In addition to these previously described findings, the present study shows evidence for further small but cytoarchitecturally distinct dopaminergic group called the interfascicular necleus. This lies anteriorly and ventrally in the ventral tegmentum in the midline, dorsal to the rostral portion of the interpeduncular nucleus and interpeduncular fossa. The significance of these cytoarchitectural findings is discussed in relation to the known connections of the region.

Animals↗
PubMed1979

Projections from the subiculum to the deep layers of the ipsilateral presubicular and entorhinal cortices in the guinea pig.

Projections from the subiculum to retrohippocampal areas were studied by reduced silver impregnation of anterograde degeneration and by autoradiographic tracing of transported proteins following injections of radioactive amino acids. The subiculum was found to project to the presubiculum and to the medial and lateral parts of the entorhinal area. The projections are exclusively ipsilateral, and arranged in a dorso-ventral topographical order with the terminations confined to the deep cortical layers. The projections form part of multisynaptic chains within the hippocampal region and must also be implicated in output routes for hippocampal activity additional to the fimbria-fornix system.

Afferent Pathways↗
PubMed1995

Molecular compartmentation expressed in cerebellar cultures in the absence of neuronal activity and neuron-glia interactions.

The purpose of the study was to determine if zebrin compartmentation developed in permanently isolated cerebellar cultures, in the presence of agents that block neuronal activity and in the absence of myelination and astrocytic ensheathment of Purkinje cells. Parasagittally oriented organotypic cultures derived from newborn mice and carefully undercut at explantation to exclude extracerebellar afferents were subjected to three conditions: 1) Some were maintained in standard nutrient medium; 2) some were chronically exposed to tetrodotoxin and elevated levels of magnesium to block neuronal activity; and 3) some were exposed to cytosine arabinoside for the first 5 days in vitro (DIV) to destroy granule cells and oligodendrocytes and functionally compromise astrocytes, so that the astrocytic survivors did not ensheath Purkinje cells. Cultures fixed as whole-mount preparations were reacted with antibody to zebrin II. Cultures that were cryostat sectioned were dually reacted with antibody to zebrin II and calbindin. Groups of zebrin+ and zebrin- Purkinje cells were evident after 14 DIV in all of the experimental conditions, indicating that zebrin compartmentation developed 1) in isolated cerebellar explants, 2) in the absence of neuronal activity, and 3) in the absence of neuron-glia interactions such as myelination and glial ensheathment of Purkinje cell somata and dendrites. These results are consistent with the concept that expression of the zebrin+ and zebrin- phenotypes is an intrinsic property of Purkinje cells. The fact that zebrin expression seems to depend on an intrinsic program of differentiation in Purkinje cells suggests some role for zebrin compartmentation in cerebellar function.

Animals↗
PubMed2003

More "mapping" in brain mapping: statistical comparison of effects.

The term "mapping" in the context of brain imaging conveys to most the concept of localization; that is, a brain map is meant to reveal a relationship between some condition or parameter and specific sites within the brain. However, in reality, conventional voxel-based maps of brain function, or for that matter of brain structure, are generally constructed using analyses that yield no basis for inferences regarding the spatial nonuniformity of the effects. In the normal analysis path for functional images, for example, there is nowhere a statistical comparison of the observed effect in any voxel relative to that in any other voxel. Under these circumstances, strictly speaking, the presence of significant activation serves as a legitimate basis only for inferences about the brain as a unit. In their discussion of results, investigators rarely are content to confirm the brain's role, and instead generally prefer to interpret the spatial patterns they have observed. Since "pattern" implies nonuniform effects over the map, this is equivalent to interpreting results without bothering to test their significance, a practice most of the experimentally-trained would eschew in other contexts. In this review, we appeal to investigators to adopt a new standard of data presentation that facilitates comparison of effects across the map. Evidence for sufficient effect size difference between the effects in structures of interest should be a prerequisite to the interpretation of spatial patterns of activation.

Brain Mapping↗
PubMed2005

Automated analysis of meta-analysis networks.

The high information content in large data sets from voxel-based meta-analyses is complex, making it hard to readily resolve details. Using the meta-analysis network as a standardized data structure, network analysis algorithms can examine complex interrelationships and resolve hidden details. Two new network analysis algorithms have been adapted for use with meta-analysis networks. The first, called replicator dynamics network analysis (RDNA), analyzes co-occurrence of activations, whereas the second, called fractional similarity network analysis (FSNA), uses binary pattern matching to form similarity subnets. These two network analysis methods were evaluated using data from activation likelihood estimation (ALE)-based meta-analysis of the Stroop paradigm. Two versions of these data were evaluated, one using a more strict ALE threshold (P < 0.01) with a 13-node meta-analysis network, and the other a more lax threshold (P < 0.05) with a 22-node network. Java-based applications were developed for both RDNA and FSNA. The RDNA algorithm was modified to provide multiple subnets or maximal cliques for meta-analysis networks. Three different similarity measures were evaluated with FSNA to form subsets of nodes and experiments. RDNA provides a means to gauge importance of metanalysis subnets and complements FSNA, which provides a more comprehensive assessment of node similarity subsets, experiment similarity subsets, and overall node-to-factors similarity. The need to use both presence and absence of activations was an important finding in similarity analyses. FSNA revealed details from the pooled Stroop meta-analysis that would otherwise require separate highly filtered meta-analyses. These new analysis tools demonstrate how network analysis strategies can simplify greatly and enhance voxel-based meta-analyses.

Brain Mapping↗
PubMed2005

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.

With the human Plasma Proteome Project (PPP) pilot phase completed, the largest and most ambitious proteomics experiment to date has reached its first milestone. The correspondingly impressive amount of data that came from this pilot project emphasized the need for a centralized dissemination mechanism and led to the development of a detailed, PPP specific data gathering infrastructure at the University of Michigan, Ann Arbor as well as the protein identifications database project at the European Bioinformatics Institute as a general proteomics data repository. One issue that crept up while discussing which data to store for the PPP concerns whether the raw, binary data coming from the mass spectrometers should be stored, or rather the more compact and already significantly processed peak lists. As this debate is not restricted to the PPP but relates to the proteomics community in general, we will attempt to detail the relative merits and caveats associated with centralized storage and dissemination of raw data and/or peak lists, building on the extensive experience gained during the PPP pilot phase. Finally, some suggestions are made for both immediate and future storage of MS data in public repositories.

Computational Biology↗
PubMed2003

CAPRI: a Critical Assessment of PRedicted Interactions.

CAPRI is a communitywide experiment to assess the capacity of protein-docking methods to predict protein-protein interactions. Nineteen groups participated in rounds 1 and 2 of CAPRI and submitted blind structure predictions for seven protein-protein complexes based on the known structure of the component proteins. The predictions were compared to the unpublished X-ray structures of the complexes. We describe here the motivations for launching CAPRI, the rules that we applied to select targets and run the experiment, and some conclusions that can already be drawn. The results stress the need for new scoring functions and for methods handling the conformation changes that were observed in some of the target systems. CAPRI has already been a powerful drive for the community of computational biologists who development docking algorithms. We hope that this issue of Proteins will also be of interest to the community of structural biologists, which we call upon to provide new targets for future rounds of CAPRI, and to all molecular biologists who view protein-protein recognition as an essential process.

Algorithms↗
PubMed2001

Identification of human liver diacetyl reductases by nano-liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry.

Several forms of diacetyl-reducing enzyme were found to exist in the human liver cytosol. Three (DAR-2, DAR-5, and DAR-7) of them were purified as a single band on SDS-PAGE by a combination of a few kinds of column chromatographies. The in-gel tryptic digests of the purified enzymes were analyzed by nano-liquid chromatography (LC)/Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), which provided peptide masses at a ppm-level accuracy. The enzymes, DAR-2, DAR-5, and DAR-7, were identified as alcohol dehydrogenase beta subunit (ADH2), carbonyl reductase (CBR1), and aldehyde reductase (AKR1A1), respectively, by peptide mass fingerprinting. In addition, an alternating-scan acquisition of nano-LC/FT ICR mass spectra, i.e., switching of normal acquisition conditions and in-source fragmentation conditions scan by scan, provided sets of parent and fragment ion masses of many of the tryptic peptides in a single LC/MS run. The peptide sequence-tag information at the ppm-level accuracy was used to further confirm the protein identities. It was demonstrated that nano-LC/FT ICR MS can be used for rigorous protein identification at a subpicomole level as an alternative technique to nano-LC/MS/MS.

Acetoin Dehydrogenase↗
PubMed1993

Application of cDNA selection techniques to regions of the human MHC.

Identification of transcribed sequences by cDNA selection is a potentially rapid and efficient way of scanning large genomic DNA fragments for the presence of genes. To evaluate this approach further, we have applied it to three yeast artificial chromosomes (YACs) and examined the products obtained from a total of about 1100 kb from two regions of the human major histocompatibility complex (MHC). One YAC was derived from an extensively studied portion of the Class II region of the MHC. The cDNAs recovered from this YAC included representatives of the previously described genes as well as one or more cDNA clones not described in the databases. A second YAC spanned about 330 kb of DNA surrounding the Class I gene HLA-A. In addition to Class I clones, 10 distinct cDNA products were identified from this YAC. A third YAC contained about 700 kb of human DNA, including 260 kb of overlap with the second YAC, and recovered an additional cDNA complementary to YAC B30 H3 DNA. Overall, the method is shown to be able to detect very scarce cDNAs and to detect a large fraction of coding sequences in YAC clones. Advantages and limitations of the approach are discussed.

Chromosome Mapping↗
PubMed1993

Using mitotic recombinant mutant clonal lymphocytes for physical mapping of polymorphic loci on the short arm of human chromosome 6.

Immunoselection has been used to identify human lymphocytes that have undergone spontaneous mutation resulting in the loss of expression of one of the codominant HLA-A alleles. Approximately 35% of such mutations are the consequence of mitotic recombination events. Mitotic recombination is the result of nonsister chromatid exchange that leaves the mutated cell homozygous for all loci distal to the crossover point. The location of the crossover has been regionalized for 99 independently derived mutant lymphocyte clones by identification of their loss or retention of heterozygosity at seven reference polymorphic loci on chromosome 6. If a polymorphic locus of unknown map position is studied in clones from this ordered set of mitotic recombinants, and clones that display loss of heterozygosity and retention of heterozygosity of the locus are observed, then the map position of the locus is between the appropriate reference loci of the ordered set. The newly mapped locus becomes a reference locus in turn. In this way the mitotic recombinant mutant clones can be used to generate an ordered set of crossover points with a theoretical resolution limited only by the number of mutants generated. In this paper such a set of mutants is used to refine or confirm the map position of eight polymorphic loci on chromosome 6.

Chromosome Mapping↗
PubMed1993

Ordered shotgun sequencing, a strategy for integrated mapping and sequencing of YAC clones.

Ordered shotgun sequencing proposes to organize the mapping and sequencing of YACs with a hierarchical strategy that incorporates a feedback loop. Building on current protocols, a YAC is subcloned into plasmids, plasmid insert ends are sequenced, and the sequences are overlapped to create a partial map. Complete sequencing then starts with plasmids whose end-sequence tracts have overlapped, but to a minimal extent. The next plasmids to be sequenced are again selected for least overlap, striking out progressively to span the YAC with minimal directed gap-filling. Simulations support its feasibility and indicate that during the generation of the complete sequence, the approach facilitates the early choice of regions for selective sequencing, for example, for coding units. The sequencing of plasmids would also require less redundancy, and discriminate repetitive sequences more easily, than random sequencing across larger clones. The overall effort scales with YAC size and can be further reduced by additional mapping information.

Chromosome Mapping↗
PubMed1976

Isolation and genetic mapping of Escherichia coli aminopeptidase mutants.

Many mutant strains devoid of aminopeptidase activity have been isolated in Escherichia coli. All of them produce cross-reacting material when tested against specific antiaminopeptidase antibody. The map position of the locus specifying this enzyme has been determined by three conjugations and two P1 mediated transduction experiments. By analogy with Salmonella typhimurium this locus has been called pepN (Miller, 1975). Mutations in pepN are jointly transduced with fabA and pyrD at high frequency. These data and conjugation results suggest a location between 20.5 and 22.5 minutes on E. coli genetic map.

Aminopeptidases↗
PubMed1975

A reliable method of quantifying G-band position in chromosomes.

The locations of chromosomal bands in the muntajac (Muntiacus muntjak, Zimmerman) are shown to be constant, that is the bands occupy the same relative position regardless of the state of contraction of the chormosome. Each band can thus be assigned a precise location. Different banding techniques produce bands at identical locations and thus precisely similar patterns, with one notable exception in which certain bands disappear. It it proposed that this more exact procedure be used to identify chromosomal bands, especially in cases of chromosomal rearrangement. It may be of particular use in computer analyses of karyotypes.

Animals↗
PubMed1986

A description of the amygdalo-hippocampal interconnections in the macaque monkey.

The interconnections between the amygdala and the hippocampal formation were investigated in the macaque monkey using anterograde tracers. The hippocampal inputs to the amygdala arose from the subicular and entorhinal cortices and passed through the angular bundle to terminate principally in the medial basal and lateral basal nuclei, with lighter termination in the lateral nucleus, the periamygdaloid cortex, and the cortical-transition area. The majority of these amygdaloid inputs arose from the rostral hippocampal formation although there was equivocal evidence of an additional projection from the caudal hippocampus to the central nucleus. Projections arose from many of the amygdaloid nuclei to terminate in the molecular layer of the amygdalo-hippocampal area and the adjacent stratum moleculare of the uncal portion of the hippocampus. The accessory basal, lateral basal, and medial basal nuclei also projected to the most rostral portions of the stratum moleculare of fields CA1-3, the heaviest termination occurring in field CA3. Additional projections from the basal nuclei terminated in the prosubiculum, presubiculum, and parasubiculum. The heaviest entorhinal inputs arose from the accessory basal and lateral nuclei and terminated in layers I, II, and III of areas 28b, 28i, and the prorhinal cortex. The major amygdaloid input to the perirhinal cortex arose from the lateral basal nucleus.

Amygdala↗
PubMed1991

Topographic component (parallel factor) analysis of multichannel evoked potentials: practical issues in trilinear spatiotemporal decomposition.

We describe a substantive application of the trilinear topographic components/parallel factors model (TC/PARAFAC, due to Möcks/Harshman) to the decomposition of multichannel evoked potentials (MEP's). We provide practical guidelines and procedures for applying PARAFAC methodology to MEP decomposition. Specifically, we apply techniques of data preprocessing, orthogonality constraints, and validation of solutions in a complete TC analysis, for the first time using actual MEP data. The TC model is shown to be superior to the traditional bilinear principal components model in terms of data reduction, confirming the advantage of the TC model's added assumptions. The model is then shown to provide a unique spatiotemporal decomposition that is reproducible in different subject groups. The components are shown to be consistent with spatial/temporal features evident in the data, except for an artificial component resulting from latency jitter. Subject scores on this component are shown to reflect peak latencies in the data, suggesting a new aspect to statistical analyses based on subject scores. In general, the results support the conclusion that the TC model is a promising alternative to principal components for data reduction and analysis of MEP's.

Brain Mapping↗
PubMed1988

Statistical classification of spikes in benign rolandic epilepsy.

The occurrence of spikes during an electroencephalogram is a basic feature of Benign Rolandic Epilepsy of Childhood (BREC). In this study we addressed the question of whether the interictal spike structure is different between "typical" and "atypical" BREC patients. Atypical BREC patients are characterized by having other neurological abnormalities in addition to the typical BREC symptoms. This question is of interest given the good prognosis associated with the typical form of BREC. We analyzed data from 12 typical and 12 atypical BREC patients using ten variables to describe spike morphology and topography. The non-parametric method of "classification and regression trees" (CART) was used to detect discriminating features and construct a classification rule. In this way the location and amplitude of the spike were found to provide satisfactory discrimination, suggesting that the two groups may be affected by different epileptic processes. The study showed the effectiveness of the CART methodology in dealing with the categorical and non-normal variables that can be obtained from EEG records. It illustrates a simple but logical approach to the analysis of potentially complex topographic data.

Action Potentials↗
PubMed1995

Performances of surface Laplacian estimators: a study of simulated and real scalp potential distributions.

This paper presents a study of the performance of various local and spherical spline methods currently in use for the surface Laplacian (SL) estimate of scalp potential distributions. The SL was estimated from simulated instantaneous event-related scalp potentials generated over a three-shell spherical head model. Laplacian estimators used planar and spherical scalp models. Noise of increasing magnitude and spatial frequency was added to the potential distributions in order to simulate noise presumed to contaminate scalp-recorded event-related potentials. A comparison of noise effects on various Laplacian estimates was made for increasing number of "electrode" positions in variants of the 10-20 system. Furthermore, to evaluate the error due to the use of unrealistic scalp models, the matching between SL estimates of human scalp-recorded movement-related potentials computed on spherical and realistically-shaped MRI-constructed models of the scalp was examined. With all methods the error of the SL estimate increased proportionally with the magnitude and spatial frequency of noise. Increased number of "electrodes" up to 256 significantly reduced the error (p < 0.05). In general, the best SL estimates were computed by second and third order splines including lambda correction, the performances of the second order spline being better with more than 64 "electrodes". Compared with spline Laplacians, the best local methods provided nearly equal estimates with low spatial sampling (19 and 28 "electrodes"), as well as high spatial frequency noise. The error of the SL estimate due to unrealistic scalp model was significant, and it augmented with increased spatial sampling from 64 to 128 electrodes.

Brain↗
PubMed1995

Projection onto centroids difference vectors: a new approach to determine between group topographical differences, applied to P3 amplitude in schizophrenia.

A common problem in electrophysiological research concerns between group analysis of EEG and ERP topography. This paper proposes a new technique for determining whether or not a significant difference exists between multiple scalp site measurements from two groups. The method requires no a priori assumptions about the data and is thus ideal for exploratory data analysis, and it also requires that only one statistical test need be performed (significantly reducing the possibility of type I errors). The Projection onto Centroids Difference Vectors (PCDV) method involves deriving a measure from each individual of whether their measurements across sites are closer overall to the mean measurements of the rest of their experimental group, or to the other group. These measures from each individual are then compared between groups using a Student's t test, which indicates whether one group's data is significantly spatially different from the other. In this study we describe the method in detail and apply it to both stimulated data and to real auditory P3 data in unmedicated, medicated schizophrenics and matched normal controls. The PCDV method was also compared with statistical probability mapping (SPM). The PCDV method revealed the differences between the normal and patient groups more unambiguously than SPM, and the simulated data revealed that it was not liable to type I errors. PCDV provides an appropriate method for testing any between group EEG and ERP topographical differences.

Adult↗