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At least 415 records · Page 23Linked to original sources
PubMed1986

An atlas of the brain of the horseshoe crab Limulus polyphemus.

An atlas of the brain of the horseshoe crab Limulus polyphemus is developed. All of the neuronal groups are identified and named, and regions of neuropil are segregated and named where possible. The nomenclature incorporates functionally neutral earlier names and assigns geographical names to newly distinguished structures. The atlas provides a basis for correlating the results of neuroanatomical, neurophysiological, and neurochemical studies, which yield information about individual neurons or groups of neurons in this species.

Animals↗
PubMed2001

The vascular anatomy of the developing zebrafish: an atlas of embryonic and early larval development.

We have used confocal microangiography to examine and describe the vascular anatomy of the developing zebrafish, Danio rerio. This method and the profound optical clarity of zebrafish embryos make it possible to view the entire developing vasculature with unprecedented resolution. A staged series of three-dimensional images of the vascular system were collected beginning shortly after the onset of circulation at 1 day postfertilization through early- to midlarval stages at approximately 7 days postfertilization. Blood vessels in every region of the animal were imaged at each stage, and detailed "wiring patterns" were derived describing the interconnections between every major vessel. We present an overview of these data here in this paper and in an accompanying Web site "The interactive atlas of zebrafish vascular anatomy" online at (http://eclipse.nichd.nih.gov/nichd/lmg/redirect.html). We find a highly dynamic but also highly stereotypic pattern of vascular connections, with different sets of primitive embryonic vessels severing connections and rewiring in new configurations according to a reproducible plan. We also find that despite variation in the details of the vascular anatomy, the basic vascular plan of the developing zebrafish shows strong similarity to that of other vertebrates. This atlas will provide an invaluable foundation for future genetic and experimental studies of vascular development in the zebrafish.

Angiography↗
PubMed2000

A DNA structural atlas for Escherichia coli.

We have performed a computational analysis of DNA structural features in 18 fully sequenced prokaryotic genomes using models for DNA curvature, DNA flexibility, and DNA stability. The structural values that are computed for the Escherichia coli chromosome are significantly different from (and generally more extreme than) that expected from the nucleotide composition. To aid this analysis, we have constructed tools that plot structural measures for all positions in a long DNA sequence (e.g. an entire chromosome) in the form of color-coded wheels (http://www.cbs.dtu. dk/services/GenomeAtlas/). We find that these "structural atlases" are useful for the discovery of interesting features that may then be investigated in more depth using statistical methods. From investigation of the E. coli structural atlas, we discovered a genome-wide trend, where an extended region encompassing the terminus displays a high of level curvature, a low level of flexibility, and a low degree of helix stability. The same situation is found in the distantly related Gram-positive bacterium Bacillus subtilis, suggesting that the phenomenon is biologically relevant. Based on a search for long DNA segments where all the independent structural measures agree, we have found a set of 20 regions with identical and very extreme structural properties. Due to their strong inherent curvature, we suggest that these may function as topological domain boundaries by efficiently organizing plectonemically supercoiled DNA. Interestingly, we find that in practically all the investigated eubacterial and archaeal genomes, there is a trend for promoter DNA being more curved, less flexible, and less stable than DNA in coding regions and in intergenic DNA without promoters. This trend is present regardless of the absolute levels of the structural parameters, and we suggest that this may be related to the requirement for helix unwinding during initiation of transcription, or perhaps to the previously observed location of promoters at the apex of plectonemically supercoiled DNA. We have also analyzed the structural similarities between groups of genes by clustering all RNA and protein-encoding genes in E. coli, based on the average structural parameters. We find that most ribosomal genes (protein-encoding as well as rRNA genes) cluster together, and we suggest that DNA structure may play a role in the transcription of these highly expressed genes.

Bacterial Proteins↗
PubMed1996

High-resolution random mesh algorithms for creating a probabilistic 3D surface atlas of the human brain.

Striking variations exist, across individuals, in the internal and external geometry of the brain. Such normal variations in the size, orientation, topology, and geometric complexity of cortical and subcortical structures have complicated the problem of quantifying deviations from normal anatomy and of developing standardized neuroanatomical atlases. This paper describes the design, implementation, and results of a technique for creating a three-dimensional (3D) probabilistic surface atlas of the human brain. We have developed, implemented, and tested a new 3D statistical method for assessing structural variations in a data-base of anatomic images. The algorithm enables the internal surface anatomy of new subjects to be analyzed at an extremely local level. The goal was to quantify subtle and distributed patterns of deviation from normal anatomy by automatically generating detailed probability maps of the anatomy of new subjects. Connected systems of parametric meshes were used to model the internal course of the following structures in both hemispheres: the parieto-occipital sulcus, the anterior and posterior rami of the calcarine sulcus, the cingulate and marginal sulci, and the supracallosal sulcus. These sulci penetrate sufficiently deeply into the brain to introduce an obvious topological decomposition of its volume architecture. A family of surface maps was constructed, encoding statistical properties of local anatomical variation within individual sulci. A probability space of random transformations, based on the theory of Gaussian random fields, was developed to reflect the observed variability in stereotaxic space of the connected system of anatomic surfaces. A complete system of probability density functions was computed, yielding confidence limits on surface variation. The ultimate goal of brain mapping is to provide a framework for integrating functional and anatomical data across many subjects and modalities. This task requires precise quantitative knowledge of the variations in geometry and location of intracerebral structures and critical functional interfaces. The surface mapping and probabilistic techniques presented here provide a basis for the generation of anatomical templates and expert diagnostic systems which retain quantitative information on intersubject variations in brain architecture.

Algorithms↗
PubMed1999

Three-dimensional MRI atlas of the human cerebellum in proportional stereotaxic space.

We have prepared an atlas of the human cerebellum using high-resolution magnetic resonance-derived images warped into the proportional stereotaxic space of Talairach and Tournoux. Software that permits simultaneous visualization of the three cardinal planes facilitated the identification of the cerebellar fissures and lobules. A revised version of the Larsell nomenclature facilitated a simple description of the cerebellum. This atlas derived from a single individual was instrumental in addressing longstanding debates about the gross morphologic organization of the cerebellum. It may serve as the template for more precise identification of cerebellar topography in functional imaging studies in normals, for investigating clinical-pathologic correlations in patients, and for the development of future probabilistic maps of the human cerebellum.

Cerebellum↗
PubMed2003

An algorithm for rapid calculation of a probabilistic functional atlas of subcortical structures from electrophysiological data collected during functional neurosurgery procedures.

The paper introduces an optimal algorithm for rapid calculation of a probabilistic functional atlas (PFA) of subcortical structures from data collected during functional neurosurgery procedures. The PFA is calculated based on combined intraoperative electrophysiology, pre- and intraoperative neuroimaging, and postoperative neurological verification. The algorithm converts the coordinates of the neurologically most effective contacts into probabilistic functional maps taking into account the geometry of a stimulating electrode. The PFA calculation comprises the reconstruction of the contact coordinates from two orthogonal projections, normalizing (warping) the contacts modeled as cylinders, voxelizing the contact models, calculating the atlas, and computing probability. In addition, an analytical representation of the PFA is formulated based on Gaussian modeling. The initial PFA has been calculated from the data collected during the treatment of 274 Parkinson's disease patients, most of them operated bilaterally (487 operated hemispheres). It contains the most popular stereotactic targets, the subthalamic nucleus, globus pallidus internus, and ventral intermedius nucleus. The key application of the algorithm is targeting in stereotactic and functional neurosurgery, and it also can be employed in human and animal brain research.

Algorithms↗
PubMed2005

Incorporating statistical measures of anatomical variability in atlas-to-subject registration for conformal brain radiotherapy.

Deforming a digital atlas towards a patient image allows the simultaneous segmentation of several structures. Such an intersubject registration is difficult as the deformations to recover are highly inhomogeneous. A priori information about the local amount of deformation to expect is precious, since it allows to optimally balance the quality of the matching versus the regularity of the deformation. However, intersubject variability makes it hard to heuristically estimate the degree of deformation. Indeed, the sizes and shapes of various structures differ greatly and their relative positions vary in a rather complex manner. In this article, we perform a statistical study of the deformations yielded by the registration of an image database with an anatomical atlas, and we propose methods to re-inject this information into the registration. We show that this provides more accurate segmentations of brain structures.

Algorithms↗
PubMed2005

2D/3D deformable registration using a hybrid atlas.

Statistical atlases built by point distribution models (PDMs) using a novel hybrid 3D shape model were used for surface reconstruction. The hybrid shape model removes the need for global scaling in aligning training examples and instance generation, thereby allowing the PDM to capture a wider range of variations. The atlases can be used to reconstruct, or deformably register, the surface model of an object from just two to four 2D x-ray projections of the object. The methods was tested using proximal and distal femurs. Results of simulated projections and fluoroscopic images of cadaver knees show that the new instances can be registered with an accuracy of about 2 mm.

Algorithms↗
PubMed2005

Least biased target selection in probabilistic atlas construction.

Probabilistic atlas has broad applications in medical image segmentation and registration. The most common problem building a probabilistic atlas is picking a target image upon which to map the rest of the training images. Here we present a method to choose a target image that is the closest to the mean geometry of the population under consideration as determined by bending energy. Our approach is based on forming a distance matrix based on bending energies of all pair-wise registrations and performing multidimensional scaling (MDS) on the distance matrix.

Algorithms↗
PubMedDate not supplied

A computerized three-dimensional atlas of the human skull and brain.

PURPOSE: To develop an anatomic atlas of the human head based on a volume model derived from MR and CT. METHODS: Every voxel of this model was labeled by a neuroanatomist concerning its membership to a structural and/or functional region. A computer program was written that, instead of displaying precomputed images, allows the user to choose and compose arbitrary views. RESULTS: The user can subtract parts and ask for annotations just by using the mouse. Conversely, one can compose images by choosing objects from the list of anatomical constituents which is displayed on the screen. A set of dissection tools allows a "look and feel" that comes near to a true dissection. Operations that are not possible in a real dissection, such as reassembly or filling cavities, can be performed. CONCLUSION: The authors have developed a computerized model that can be used for anatomy teaching and also as a reference for radiologists or surgeons. To replace classical atlases, the spatial resolution must be improved and speed must approach real time. Functional imaging data (position emission tomography and single photon emission CT) can be added to the system. The system is mobile and can be situated in classrooms, operating rooms, reading rooms, and libraries.

Brain↗
PubMed1989

The new United States Cancer Atlas.

Published in 1975, the Atlas of Cancer Mortality for U.S. Counties: 1950-1969 proved useful in identifying geographic patterns, especially clusters of high-rate areas, that have stimulated further epidemiologic study of specific cancer sites. These data have been updated to include population and mortality statistics through 1980. Our new atlas presents static maps of area-specific mortality rates for each decade from 1950 to 1980 among white males and females for 33 cancer sites, along with dynamic maps illustrating the trends in these rates over time. Although the geographic distribution of mortality rates has become more uniform for most cancer sites, clusters of high-rate areas have persisted for several common tumors. However, some new patterns have appeared, notably the emergence of several high-rate areas for lung cancer among women. Possible explanations for the geographic peculiarities of cancer are considered, based on the results of correlation and analytic studies prompted by the earlier maps. These successive studies indicate the value of monitoring mortality statistics on a small-area scale as a strategy for generating etiologic clues and targeting epidemiologic research, although one must be mindful of geographic fluctuations in diagnostic and reporting practices, survival rates, and migration patterns.

Chronology as Topic↗
PubMed1995

Computer-assisted multidimensional atlas for functional stereotaxy.

Functional stereotactic operations are currently performed primarily for medically uncontrollable Parkinson's disease and pain. In contrast to the targets in neuro-oncology, those in functional stereotaxy cannot be represented directly by modern imaging methods. The target co-ordinates must therefore be calculated with the aid of special stereotactic atlases. These are publications in which a model brain has been constructed from autopsy examinations on a number of brains, or the data obtained have been compiled in the form of tables and histograms on which the calculation is then based. The target can then be determined based on the classic stereotactic landmarks and reference lines, such as the anterior commissure (AC), the foramen of Monro (FM), the posterior commissure (PC) or the base line FM-PC or AC-PC and the height of thalamus, taking into account the interindividually different anatomical proportions. Since the computational procedures involve repetitious algorithms, it was obvious that such procedures should be run by a computer program. For the most common stereotactic targets, we have developed a computer program for data storage on the one hand and computation and graphic output on the other. The output can be displayed on the monitor and can also be plotted out on paper or overhead transparency. Calibrating between the program and printer renders a 1:1 reproduction, i.e. the graph can be superimposed directly onto original x-rays or images from computed tomography or nuclear magnetic imaging. The graph can be plotted in the three dimensions of the Cartesian co-ordinate system. An additional dimension can be attained by simultaneously including and plotting the data from different atlases and thus from different authors, including one's own data. In addition to the information capacity which this system offers, it also makes possible a considerable reduction in the time for computing the target while at the same time increasing the reliability.

Algorithms↗
PubMed1996

A light microscopic atlas of meiosis in Arabidopsis thaliana.

An atlas of meiosis in Arabidopsis thaliana, encompassing all stages from preleptotene to telophase II and early microspore formation, is presented in detail for the first time. The photomicrographs and descriptions are based on staining with the DNA fluorochrome 4',6-diamidino-2-phenylindole (DAPI) combined with a spreading procedure, or haematoxylin-iron alum (HIA) staining. Despite previous reservations about the practicality of cytogenetic meiotic analysis in Arabidopsis due to its small genome size, good-quality and clearly analysable preparations of all meiotic stages were obtained. This atlas of normal, wild-type meiosis is considered an essential prerequisite to informed analyses of meiotic mutants. Furthermore, extended prophase I chromosomes, particularly at the pachytene stage, offer considerable potential for producing a detailed cytogenetic map (karyotype) of Arabidopsis chromosomes with the additional prospect of high-resolution physical mapping based on fluorescence in situ hybridization (FISH) of defined DNA probes to these extended chromosomes.

Anaphase↗
PubMed1992

"Avoidable mortality" as an index of health care outcome: results from the European Community Atlas of "Avoidable Death".

The history of the European Community Atlas of "Avoidable Death" is given. Data from the second Atlas are presented. For all causes of death except asthma there was a decrease in mortality in the period 1980-1984 with respect to 1974-1978. Taking the EC as a whole as the standard (100) population the standardised mortality ratio (SMR) in Ireland in the period 1980-1984 for tuberculosis was 160, for asthma 180 and maternal mortality 58. Ireland had the highest mortality for tuberculosis in both time periods. Asthma mortality increased in all countries except Scotland between 1974-1978 and 1980-1984. Ireland had one of the highest declines in maternal mortality over the two time periods. Within Ireland tuberculosis mortality was highest in the Mid-Western Health Board and lowest in the North-Western Health Board. Asthma mortality was highest in the Western Health Board and lowest in the Mid-Western Health Board. Maternal mortality was highest in the Midland Health board and lowest in the Southern Health Board.

Adolescent↗
PubMed1993

Endemic goiter in Morocco (Skoura-Toundoute areas in the high atlas).

Endemic goiter in Morocco is localized in the Rif and Atlas mountains. In this study, performed in the Skoura-Toundoute areas (high Atlas), we demonstrate that iodine deficiency is the main factor involved in the development of endemic goiter. However it may not constitute the only etiological factor. The median urinary iodine excretion, measured on untimed samples, was low both in goitrous patients, m = 18 micrograms/l (n = 109) and in non goitrous subjects, m = 24 micrograms/l (n = 47). The value found in a nonendemic region (Casablanca) was much higher m = 117 micrograms/l (n = 67). Another approach to evaluate iodine intake per day was the analysis of iodine content of some samples of cereals (barley, wheat and corn), drinking water, sea and rock salt, cow and breast milk. Iodine content is low, specially in the endemic area: barley = 90 micrograms/kg (n = 1); wheat = 227 micrograms/kg (n = 1); corn = 91 micrograms/kg (n = 1); water = 0.92 to 1.30 micrograms/l (n = 3); cow milk = 6 to 33 micrograms/l (n = 10) breast milk = 10 to 55 micrograms/l (n = 14); rock salt = 420 to 660 micrograms/kg (n = 8); sea salt = 90 to 160 micrograms/kg (n = 4). Sodium chloride intake per day, estimated by the measurement of sodium and chloride urinary excretion, is normal both in the Skoura-Toundoute areas (10.7 g and 9.8 g for goitrous and nongoitrous subjects, respectively) and in Casablanca (10.9 g for control persons). Altogether the results demonstrate the importance of introducing the practice of iodinated salt in the prophylaxis of endemic goiter in this area.

Adolescent↗
PubMed2000

Identification of differentially expressed genes in nasopharyngeal carcinoma by means of the Atlas human cancer cDNA expression array.

PURPOSE: To investigate genes of critical areas, including cell cycle/growth control, apoptosis, oncogene/tumor suppressors and growth factor/cytokines, that are differentially expressed in nasopharyngeal carcinoma. METHODS: The Human Cancer cDNA Atlas, which contains 588 genes relating to tumor biology, was used to screen normal nasopharyngeal tissue, nasopharyngeal cancer (NPC). The reverse transcription/polymerase chain reaction was used to confirm the expression pattern of some genes identified by Atlas hybridization. RESULTS: The differentially expressed cell cycle/growth control regulators in NPC showed a stronger tendency toward cell proliferation with the up-regulation of cyclin D1, cyclin D2 etc. The expression pattern of apoptosis-related genes demonstrated the up-regulation of both anti-apoptotic factors such as the BCL-2-related protein A1, TRAF3, the inhibitor of apoptosis protein A1 (IAPI) and apoptotic pathway elements such as Fas/Apo-1, Apo-2 ligand etc. Among oncogenes/tumor suppressors, MDM2, STAT1 and STAT2 were found to be up-regulated in NPC. The expression profile of growth factors/cytokines showed the up-regulation of many growth-enhancing factors such as EGR1, tumor-derived growth factor 1, platelet-derived growth factor A chain etc. as well as Th1-type cytokines e.g. interleukin-1beta and interferons. A smaller number of genes were down-regulated in nasopharyngeal cancer, such as those encoding ERK1, Raf, secreted apoptosis-related protein 1, CD27BP, transforming growth factor beta2, pre-B-cell-stimulating factor homologue etc. CONCLUSION: The consistent tendency toward cell proliferation, the possibility of a stronger antiapoptotic force that operates on the normal apoptotic pathway, or the autocrine or paracrine growth factors may account for the development of NPC. Some genes are reported for the first time to have changed expression in nasopharyngeal carcinoma. The simple, quick, and high-throughput method of profiling gene expression by cDNA array hybridization provides us with a quick overview of key factors that may be involved in NPC, and may identify genes suitable for further study of carcinogenesis mechanism or targets for possible molecular diagnosis or therapy.

Apoptosis↗
PubMed1996

[Product of the month: the Schering Atlas. Sectional anatomy of CT and MRI images].

The Schering Atlas is a teaching file in CT and MRI anatomy designed for physicians and students. It is available on CD-ROM, shows good image quality, and is easy to use in medium-price-range personal computer systems. Because of the amount and quality of image material, the Schering Atlas's price is appropriate for institutions, but not for private users.

Anatomy, Artistic↗
PubMed2005

Molecular mapping of a quantitative trait locus for aluminum tolerance in wheat cultivar Atlas 66.

Genetic improvement of aluminum (Al) tolerance is one of the cost-effective solutions to improve wheat (Triticum aestivum) productivity in acidic soils. The objectives of the present study were to identify quantitative trait loci (QTL) for Al-tolerance and associated PCR-based markers for marker-assisted breeding utilizing cultivar Atlas 66. A population of recombinant inbred lines (RILs) from the cross Atlas 66/Century was screened for Al-tolerance by measuring root-growth rate during Al treatment in hydroponics and root response to hematoxylin stain of Al treatment. After 797 pairs of SSR primers were screened for polymorphisms between the parents, 131 pairs were selected for bulk segregant analysis (BSA). A QTL analysis based on SSR markers revealed one QTL on the distal region of chromosome arm 4DL where a malate transporter gene was mapped. This major QTL accounted for nearly 50% of the phenotypic variation for Al-tolerance. The SSR markers Xgdm125 and Xwmc331 were the flanking markers for the QTL and have the potential to be used for high-throughput, marker-assisted selection in wheat-breeding programs.

Aluminum↗