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PubMedDate not supplied

Magnetic resonance imaging of the normal feline abdomen: an anatomic reference.

Magnetic resonance images of two adult domestic short-haired cats were obtained with a whole body scanner. Images of the abdomen were compared with cross-sectional anatomy cadaver specimens from the same two cats. Anatomic structures were first identified on the cadaver specimens with the aid of anatomy texts and references and were then identified and labeled on the magnetic resonance images. Results from this project provide an atlas of normal cross-sectional MRI anatomy of the feline abdomen.

Abdomen↗
PubMed2005

High abundance protein profiling of cystic fibrosis lung epithelial cells.

Protein profiles of cultured cystic fibrosis (CF) lung epithelial cells were analyzed by two-dimensional gel electrophoresis and mass spectrometry (MS). The analysis gave rise to a protein map over the pI range of 4-7, and a molecular weight range of ca. 100-10 kDa. The map contains 194 identified proteins, which were detectable by silver stain. All silver stained features were identified by matrix-assisted laser desorption/ionization-time of flight MS of tryptic peptides. Some proteins were found to be represented by multiple features on the 2-D gel. Among the high abundance proteins identified were sets of proteins associated with inflammation, including the classical NFkappaB, p65 (RelA) and NFkappaB, p65 (RelB). We suggest that this composite atlas of the high abundance CF lung epithelial proteome will serve as a reference database for future studies of candidate CF drugs, validating different approaches to CFTR gene therapy, and analogous investigations of other types of human lung disorders.

Cell Culture Techniques↗
PubMed2026

A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.

Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities with adult glioma, it comprises distinct disease entities. In this study, we longitudinally profile a molecularly diverse cohort of 16 pHGG patients through single-nucleus RNA and ATAC sequencing, whole-genome sequencing, and CODEX spatial proteomics to capture the evolution of neoplastic and microenvironmental features during disease progression and treatment. We define a set of core pHGG neoplastic cell states and observe differential tumor-myeloid interactions between malignant cell phenotypes. We find that essential neuromodulators and the interferon response are upregulated post-therapy, implicating them as malignant cell-intrinsic targets. We observe an increase in oligodendrocytes upon progression and that they coordinate spatial motifs with proneural tumor cells. This multiomic atlas of longitudinal pHGG captures features of therapy response and provides a scalable reference for the study of pediatric brain tumors.

Humans↗
PubMed1998

A web-accessible digital atlas of the distribution of nitric oxide synthase in the mouse brain.

We have produced a digital atlas of the distribution of nitric oxide synthase (NOS) in the mouse brain as a reference source for our studies on the roles of nitric oxide in brain development and plasticity. NOS was labeled using nicotinamide adenine dinucleotide phosphate diaphorase (NADPHd) histochemistry. In addition, choline acetyltransferase (ChAT) immunocytochemistry was used to identify cholinergic cells because many of the NADPHd positive cells were thought to colocalize acetylcholine. Some sections were also labeled with antibodies to either the neuronal (nNOS) or endothelial (eNOS) isoforms of NOS. Series of sections from 11 C57/BL6 mice were collected and labeled for NADPHd and/or ChAT. We collected two types of data from this material: color digital photographs illustrating the density of cell and fiber labeling, and computer/microscope plots of the locations of all the labeled cells in selected sections. The data can be viewed as either a series of single-section maps produced by combining the plots with the digital images, or as 3-D views derived from the cell plots. The atlas of labeled cell maps, together with selected color photographs and 3-D views, is available for viewing via the World Wide Web (http:@nadph.anatomy.lsumc.edu). Examination of the atlas data has revealed several points about the distribution of NOS throughout the mouse brain. Firstly, different populations of NADPHd-positive neurons can be distinguished by different patterns of staining. In some brain areas neurons are intensely stained by the NADPHd technique where label fills the cell bodies and much of the dendritic trees. In other brain regions labeling is much lighter, is principally confined to the cytoplasm of the cell soma, and extends only a short distance within proximal dendrites. Intense labeling is typical of neurons in the caudate/putamen and mesopontine tegmental nuclei. Most of the labeled neurons in the cortex also stain this way. Lighter, "granular" label is found in many other nuclei, including the medial septum, hippocampus, and cerebellum. In addition to staining pattern, we have also noted that different subpopulations of NOS-neurons can be distinguished on the basis of colocalization with ChAT. Substantial overlap of the distributions of these two substances was observed although very little colocalization was found in most cholinergic cell groups except the mesopontine tegmental nuclei. Other points of interest arising from this project include the apparent lack of NADPHd labeling in the CA1 pyramidal cells of the hippocampus or the Purkinje neurons in the cerebellum. This observation is especially relevant given that synaptic plasticity in these regions is reported to be nitric-oxide dependent.

Animals↗
PubMed2006

Visualization, reconstruction, and integration of neuronal structures in digital brain atlases.

Brain atlases are used in neuroanatomy to define the spatial layout of neuronal structures. Their digital variant can serve as a database and common reference frame for integrating data from different biological experiments. This article presents an overview of methods for three-dimensional visualization of neuroanatomical image data, reconstructing neuronal structures from image data, creating digital brain atlases, and registering data in an atlas. This enables analysis of spatial relations between individual structures imaged in different experiments as well as between these structures and the atlas.

Animals↗
PubMed1996

Skeletal maturation of wrist and hand ossification centers in normal Spanish boys and girls: a study using the Greulich-Pyle method.

The skeletal maturation of the upper limb distal segment was studied in 239 Spanish boys and girls between birth and 14 years of age. The atlas of Greulich and Pyle, offering standards of skeletal development of white North American children, was used as reference. The results obtained show firstly that in absolute terms, the ossification process is earlier in girls than in boys. This difference is maximum between 5 and 11 years of age. The boys show a delay of around 3 months with respect to their North American opposites. The girls, in contrast, show a better fit to the corresponding (female) standard of the atlas. In general, the highest agreement between bone age and chronologic age is for the ossification centers of the distal epiphysis of the ulna and radius and for those of the metacarpal bones. At the level of the carpus, individual analysis of the ossification centers shows that the capitate and hamate bones in the girls evolve most in accord with chronologic age. At the other extreme, and in both sexes, the ossification centers of the trapezium and trapezoid bones are statistically furthest from chronologic age.

Adolescent↗
PubMed1986

Some observations on the posterior and lateral bridge of the atlas.

Six hundred and seventy-two atlas vertebrae of 6 population groups were examined for the presence of a posterior and/or lateral bridge. Of these, 174 (25.9%) presented with partial posterior bridge formation and 53 (7.9%) with a complete bridge. Twenty-six (3.8%) showed some form of lateral bridging. Although controversy exists as to the origin of atlas bridging, the findings of the present study show that aging could be a factor predisposing to complete bridge formation. The clinical significance of bridge formation is discussed with reference to their possible effect on normal vertebral artery function, particularly in rotation.

Cervical Atlas↗
PubMed2005

The organization of the brainstem and spinal cord of the mouse: relationships between monoaminergic, cholinergic, and spinal projection systems.

Information regarding the organization of the CNS in terms of neurotransmitter systems and spinal connections in the mouse is sparse, especially at the level of the brainstem. An overview is presented of monoaminergic and cholinergic systems in the brainstem and spinal cord that were visualized immunohistochemically in inbred C57BL/6 and outbred CD-1 mice. This information is complemented with data on spinal cord-projecting systems that were characterized using retrograde tracing, spinal hemisections, and double labeling techniques. Attention is given to differences in these systems related to spinal levels. The data are discussed with reference to studies in the rat, and to standardized information as provided in the atlas of the mouse brain. Although the overall organization of these systems in the mouse is largely similar to those in the rat, species differences are present in relative location, size and/or connectivity of cell groups. For example, catecholaminergic neurons in the (ventro)lateral pons (A5 and A7 cell groups) in the mouse project to the spinal cord mainly via contralateral, and not ipsilateral, pathways. The data further supplement information as provided in standardized brainstem sections of the C57BL/6 mouse [Paxinos, G., Franklin, K.B.J., 2001. The mouse brain in stereotaxic coordinates. Academic Press, San Diego], especially with respect to the size and/or location of the catecholaminergic retrorubral field (A8 group), A5, A1, and C1 cell groups, and the serotonergic B4 group, reticulotegmental nucleus (B9 group), lateral paragigantocellular nucleus and raphe magnus nucleus (B3 group). Altogether this study provides a comprehensive overview of the spatial relationships of neurochemically and anatomically defined neuronal systems in the mouse brainstem and spinal cord.

Acetylcholine↗
PubMed1999

[Anterior screw fixation combined with posterior interlaminar fusion for fracture of axis: report of two cases].

Two cases of axis fracture are reported. Traffic accidents were the cause of injury in both cases. The odontoid process was dislocated anterolaterally with fracture of the lateral mass of the axis in both cases. In Case 1 good alignment of the atlas and axis could not be maintained even with a Halo-vest. The case 2 patient with spinal cord compression caused by dislocation of the axis was referred to our hospital 8 weeks after the accident. Both cases were surgically treated in a similar fashion. Because of the lateral mass fracture and lateral displacement of the atlas relative to the axis, posterior screw fixation with interlaminar fixation (Magerl) was thought to carry a risk of causing damage to the vertebral artery. Because of this, anterior screw fixation combined with posterior wiring was conducted. First, the odontoid process was fixed anteriorly by a screw because it was able to be placed back in good alignment while the patient was in the supine position. Then, the posterior C1-2 interlaminar wiring with iliac bone graft was added. Rigid fixation was obtained without any complication. Various kinds of fixation, such as posterior interlaminar wiring, odontoid screw fixation and Magerl's fixation, have been reported for the treatment of unstable axis fracture. Among them Magerl's method has been regarded as the most stable. When it is not applicable, combination of the first two methods can be an alternative way of treatment for this odontoid process fracture.

Accidents, Traffic↗
PubMed1997

Multiarchitectonic and stereotactic atlas of the human thalamus.

To improve anatomical definition and stereotactic precision of thalamic targets in neurosurgical treatments of chronic functional disorders, a new atlas of the human thalamus has been developed. This atlas is based on multiarchitectonic parcellation in sections parallel or perpendicular to the standard intercommissural reference plane. The calcium-binding proteins parvalbumin (PV), calbindin D-28K (CB), and calretinin (CR) were used as neurochemical markers to further characterize thalamic nuclei and delimit subterritories of functional significance for stereotactic explorations. Their overall distribution reveals a subcompartmentalization of thalamic nuclei into several groups. Predominant PV immunostaining characterizes primary somatosensory, visual and auditory nuclei, the ventral lateral posterior nucleus, reticular nucleus (R), and to a lesser degree also, lateral part of the centre median nucleus, and anterior, lateral, and inferior divisions of the pulvinar complex. In contrast, CB immunoreactivity is prevalent in medial thalamic nuclei (intralaminar and midline), the posterior complex, ventral posterior inferior nucleus, the ventral lateral anterior nucleus, ventral anterior, and ventral medial nuclei. The complementary distributions of PV and CB appear to correlate with distinct lemniscal and spinothalamic somatosensory pathways and to cerebellar and pallidal motor territories, respectively. Calretinin, while overlapping with CB in medial thalamic territories, is also expressed in R and limbic associated anterior group nuclei that contain little or no CB. Preliminary analysis indicates that interindividual nuclear variations cannot easily be taken into account by standardization procedures. Nevertheless, some corrections in antero-posterior coordinates in relation to different intercommissural distances are proposed.

Adult↗
PubMed1984

A Golgi analysis of the primate globus pallidus. III. Spatial organization of the striato-pallidal complex.

An atlas of transverse sections of the globus pallidus and striatum was established in macaque with reference to ventricular coordinates. The three-dimensional geometry of the striato-pallidal complex was investigated by means of sagittal and horizontal reconstructions. Both a personal case studied with autoradiography and data from literature were used to analyze the distribution of cortical axons into the striatum. One may distinguish two striatal territories: one, somatotopically arranged, sensorimotor territory extending over the major part of the putamen; and the other, an associative territory, comprising the caudate nucleus and antero-medial and postero-inferior parts of the putamen. The striato-pallido-nigral bundle was studied using Golgi, Perls, and Fink-Heimer techniques. The bundle is described in four parts: prepallidal (subdivided into caudato-pallidal and putamino-pallidal subparts), transpallidal, pallido-nigral, and nigral. The tracing of the limit between the caudate (associative) and putaminal (essentially sensorimotor) territories shows that the two components are of roughly the same size in the pallidum. The data were compared with geometry and orientation of the dendritic arborizations of large pallidal neurons analyzed in Yelnik et al. ('84). Each pallidal dendritic disc is able to receive axons from a wide region of the striatum. This leads to a convergence on pallidal neurons of striatal axons from different striatal somatotopic strips and from the sensorimotor and associative territories. This is an indication that the globus pallidus may have an integrative role.

Animals↗
PubMed2003

Computer-assisted diagnosis system in digestive endoscopy.

The purpose of this paper is to present an intelligent atlas of indexed endoscopic lesions that could be used in computer-assisted diagnosis as reference data. The development of such a system requires a mix of medical and engineering skills for analyzing and reproducing the cognitive processes that underlie the medical decision-making process. The analysis of both endoscopists experience and endoscopic terminologies developed by professional associations shows that diagnostic reasoning in digestive endoscopy uses a scene-object approach. The objects correspond to the endoscopic findings and the medical context of examination and the scene to the endoscopic diagnosis. According to expert assessment, the classes of endoscopic findings and diagnoses, their primitive characteristics (or indices), and their relationships have been listed. Each class describes an endoscopic finding or diagnosis in an intensive way. The retrieval method is based on a similarity metric that estimates the membership value of the case under investigation and the prototype of the class. A simulation test with randomized objects demonstrates a good classification of endoscopic findings. The correct class is the unique response in 68% of the tested objects, the first of multiple responses in 28%. Four descriptors are shown to be of major importance in the classification algorithm: anatomic location, shape, color, and relief. At the present time, the application database contains approximately 150 endoscopic images and is accessible via Internet. Experiments are in progress with endoscopists for the validation of the system and for the understanding of the similarity between images. The next step will integrate the system in a learning tool for junior endoscopists.

Algorithms↗
PubMed2005

Mindboggle: automated brain labeling with multiple atlases.

BACKGROUND: To make inferences about brain structures or activity across multiple individuals, one first needs to determine the structural correspondences across their image data. We have recently developed Mindboggle as a fully automated, feature-matching approach to assign anatomical labels to cortical structures and activity in human brain MRI data. Label assignment is based on structural correspondences between labeled atlases and unlabeled image data, where an atlas consists of a set of labels manually assigned to a single brain image. In the present work, we study the influence of using variable numbers of individual atlases to nonlinearly label human brain image data. METHODS: Each brain image voxel of each of 20 human subjects is assigned a label by each of the remaining 19 atlases using Mindboggle. The most common label is selected and is given a confidence rating based on the number of atlases that assigned that label. The automatically assigned labels for each subject brain are compared with the manual labels for that subject (its atlas). Unlike recent approaches that transform subject data to a labeled, probabilistic atlas space (constructed from a database of atlases), Mindboggle labels a subject by each atlas in a database independently. RESULTS: When Mindboggle labels a human subject's brain image with at least four atlases, the resulting label agreement with coregistered manual labels is significantly higher than when only a single atlas is used. Different numbers of atlases provide significantly higher label agreements for individual brain regions. CONCLUSION: Increasing the number of reference brains used to automatically label a human subject brain improves labeling accuracy with respect to manually assigned labels. Mindboggle software can provide confidence measures for labels based on probabilistic assignment of labels and could be applied to large databases of brain images.

Journal Article↗
PubMed2003

Automatic construction of 3-D statistical deformation models of the brain using nonrigid registration.

In this paper, we show how the concept of statistical deformation models (SDMs) can be used for the construction of average models of the anatomy and their variability. SDMs are built by performing a statistical analysis of the deformations required to map anatomical features in one subject into the corresponding features in another subject. The concept of SDMs is similar to statistical shape models (SSMs) which capture statistical information about shapes across a population, but offers several advantages over SSMs. First, SDMs can be constructed directly from images such as three-dimensional (3-D) magnetic resonance (MR) or computer tomography volumes without the need for segmentation which is usually a prerequisite for the construction of SSMs. Instead, a nonrigid registration algorithm based on free-form deformations and normalized mutual information is used to compute the deformations required to establish dense correspondences between the reference subject and the subjects in the population class under investigation. Second, SDMs allow the construction of an atlas of the average anatomy as well as its variability across a population of subjects. Finally, SDMs take the 3-D nature of the underlying anatomy into account by analysing dense 3-D deformation fields rather than only information about the surface shape of anatomical structures. We show results for the construction of anatomical models of the brain from the MR images of 25 different subjects. The correspondences obtained by the nonrigid registration are evaluated using anatomical landmark locations and show an average error of 1.40 mm at these anatomical landmark positions. We also demonstrate that SDMs can be constructed so as to minimize the bias toward the chosen reference subject.

Algorithms↗
PubMed2006

Statistical representation of mean diffusivity and fractional anisotropy brain maps of normal subjects.

PURPOSE: To create diffusion tensor atlases from echo planar imaging (EPI) images acquired at 3 T in 10 normal subjects. MATERIALS AND METHODS: Data from 10 right-handed healthy adult volunteers (mean age of 31 +/- 3 years; eight males) were acquired using a 3.0-T scanner. Geometric distortion artifacts correction was accomplished by combining parallel acquisition to reduce the distortion as well as postprocessing by registration to a geometrically accurate T2-weighted fast-spin-echo image. This reduced distortions to within a voxel for most of the internal structures of the brain. The apparent diffusion coefficient (ADC) and fractional anisotropy (FA) atlases were created by warping images using an iterative optical-flow-based local deformation algorithm that used two channels of data: ADC and FA. RESULTS: A three-dimensional distance measure was used to evaluate the accuracy of the registration algorithm with contours defined on two structures: the corpus callosum and cerebellum. The average three-dimensional distance value for the nine subjects (with the 10th as the reference) was 0.2 mm for the corpus callosum and 1.2 mm for the cerebellum. CONCLUSION: A high-resolution, diffusion MR atlas with full brain coverage was developed. Additionally, maps of the SD of the diffusion indices were also generated to provide an estimate of the variance within a normal population. Active shape and texture models were also generated for the corpus callosum as an alternate method of representing the variance in morphology and diffusion indices.

Adult↗
PubMed2001

Atlas of rat fetal skeleton double stained for bone and cartilage.

BACKGROUND: The double staining of fetal skeleton for bone and cartilage is a very useful method to evidence skeletal abnormalities in laboratory animals. However, this method has been rarely used in routine developmental toxicity tests. One reason could be the difficulty of comparing the single skeletal pieces and of having reference points. In this paper the fetal rat skeleton double stained with Alizarin red S and Alcyan Blue is described in detail to produce an atlas for developmental toxicity laboratories.

Alcian Blue↗
PubMed1991

Atlantoaxial malformation in a half-Arabian colt.

A 1-year-old half-Arabian colt was referred for evaluation of a cranial cervical abnormality. Physical examination revealed the left wing of the atlas to be more ventral than the right wing. A head tilt, with the pole deviated to the left, was present because of the malpositioned atlas. Neurologic examination identified symmetrical weakness, ataxia, and proprioceptive deficits in all four limbs. Radiographs of the cranial cervical region revealed fusion of the atlas and axis, and deviation of the atlantoaxial joint to the left of the median plane. Euthanasia was elected. Necropsy confirmed the radiographic findings. The atlas was rotated 20 degrees counterclockwise when viewed from the caudal aspect. Multifocal myelomalacia was present in the first and second cervical spinal cord segments. The malformation was believed to be due to a degenerative process or abnormal embryological development.

Animals↗