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At least 433 records · Page 24Linked to original sources
PubMed1997

Construction of a standard reference for PET studies of methionine accumulation using a computerised brain atlas.

Positron emission tomography (PET) is valuable for assessing the biochemistry and physiology of the human brain. A computerised brain atlas has been developed which allows demonstration of anatomical regions of PET images and manipulation of these images into a standardised anatomical space. Once the images are in this standardised three-dimensional space it is possible to make comparisons between individuals and groups of individuals. We describe the use of this atlas in the generation of a set of mean reference images using methionine PET images of normal volunteers.

Adult↗
PubMed2004

A case of progressive myelopathy with atlas hypoplasia in an infant: controversy in the surgical strategy.

CASE REPORT: The authors report a case of isolated atlas hypoplasia in an 18-month-old infant who experienced delayed motor development confined to the lower extremities, in the absence of other clinical features. Nonetheless, MRI revealed the upper cervical cord to be highly compressed with a high signal intensity lesion apparent at the craniovertebral junction. The patient underwent atlas laminectomy in addition to occipital decompression, resulting in a good neurological recovery. DISCUSSION: We speculate on the significance of this unique clinical presentation and discuss surgical strategies for this condition.

Cranial Fossa, Posterior↗
PubMed2001

Integration of microstructural and functional aspects of human somatosensory areas 3a, 3b, and 1 on the basis of a computerized brain atlas.

In this study we analyzed structural and functional aspects of the human primary somatosensory areas 3a, 3b, and 1 on the basis of a computerized brain atlas. The approach overcomes many of the problems associated with subjective architectonic parcellations of the cortex and with 'classical" brain maps published in a "rigid" print format. Magnetic resonance (MR) scans were obtained from ten postmortem brains. The brains were serially sectioned at 20 microm, and sections were stained for cell bodies. Areas 3a, 3b, and 1 were delineated statistically on the basis of differences in the laminar densities of neuronal cell bodies. The borders of the areas were topographically variable across different brains and did not match macroanatomical landmarks of the postcentral gyrus. After correction of the sections for deformations due to histological processing, each brain's 3-D reconstructed histological volume and the volume representations of areas 3a, 3b, and 1 were adapted to the reference brain of a computerized atlas and superimposed in 3-D space. For each area, a population map was generated that described, for each voxel, how many brains had a representation of that area. Despite considerable interindividual variability, representations of areas 3a, 3b, and 1 in > or = 50% of the brains were found in the fundus of the central sulcus, in the rostral bank, and on the crown of the postcentral gyrus, respectively. For each area, a volume of interest (VOI) was defined that encompassed that area's representation in > or = 50% of the brains. Despite close spatial relationship in the postcentral gyrus, the three VOIs overlapped by < 1% of their volumes. Changes in regional cerebral blood flow (rCBF) were measured with positron emission tomography when six right-handed subjects discriminated differences in the speed of a rotating brush stimulating the palmar surface of the right hand. With co-registered MR images, the rCBF data were adapted to the same reference brain and superimposed with the microstructural VOIs. Discrimination of moving stimuli, contrasted to rest, increased the rCBF in the VOIs of areas 3b and 1, but not in area 3a. This approach opens up the possibility of (1) defining VOIs of cortical areas which are not based on macroanatomical landmarks but instead on observer-independent cytoarchitectonic mapping of postmortem brains and of (2) determining in these VOIs changes in rCBF data obtained from functional imaging experiments.

Adult↗
PubMed1996

Evaluation of the CLINITEK ATLAS for routine macroscopic urinalysis.

OBJECTIVES: To evaluate the performance of a new, benchtop, fully automated urine analyzer the CLINITEK ATLAS and compare it with the URICHEM 1000 CHEMSTRIP UA analyzer. Macroscopic analysis included measurement of 8 urine analyte chemistries and specific gravity by the refractive index method (SgRl). METHODS: The analytical performance studies conducted were calibration stability, precision (within-run and day-to-day), comparison of results of 437 fresh patient urine specimens, analysis of time performance, and problem logging over a 16-day evaluation period. RESULTS: Satisfactory calibration reproducibility, within-run (n = 10), and day-to-day (n = 16) precision was found because results fell within the +/- one color-block by the proposed National Committee for Clinical Laboratory Standards (NCCLS) criteria. Patient results (n = 437) from the 2 analyzers giving the same color-block agreement was found to be for pH, 52%; glucose, 92%; ketones, 86%; protein, 79%; bilirubin, 97%; leukocytes, 72%; blood, 80%; and nitrite, 98%. The concordance defined by the NCCLS criteria as the agreement of results +/- one color-block between the 2 analyzers was found to be for pH, 96%; glucose, 99%; ketones, 100%; protein, 95%; bilirubin, 100%; leukocytes, 97%; and blood 86%. The SgRl determined on ATLAS was correlated with the RD-10 Rapid Density analyzer with the following results: slope = 0.97, intercept = 0.033, r = 0.94, Syx = 0.003, for a range of values from 1.002 to 1.070. CONCLUSION: Our preliminary data indicate that the analytical performance, and automatable features for complete walk-away function of this analyzer can significantly increase the overall testing efficiency in the urinalysis laboratory.

Bilirubin↗
PubMed1980

Reconstruction of an arbitrary cross section from the serial drawings of a stereotaxic brain atlas.

A method is described for the reconstruction of arbitrary cross section from the serial line drawings of a stereotaxic brain atlas. Mathematically, the problem reduces to the intersection of a plane with a line pattern lying in another plane. However, the calculation yields a cloud of points, often confusing and unusable for the surgeon. Because it is impossible to link correctly all the calculated points in all cases [1,2], we propose a method where the number of points is drastically reduced: only regions of interest are depicted, i.e., the area where the electrode point is situated and the neighbouring regions. Instead of points, symbols are displayed, each symbol representing a different region. The efficiency of the method is shown using an atlas simulation of four intersecting spheres in the three dimensional space, Although the procedure is useful for all stereotaxic brain atlasses, a practical example is given where the poor quality of the reconstructed images does not allow good interpretation.

Analog-Digital Conversion↗
PubMed1989

Digital rat brain: a computerized atlas.

Digital brain mapping provides the techniques required for 3 dimensional (3D) reconstruction and display. This paper describes work which extends the data published in the Paxinos and Watson (1982) atlas of the rat brain to a computerized form. The product of these experiments is a 3D digital neuroanatomic atlas. The data were transformed from 2D outlines to 3D volumes each associated with a specific neuroanatomic structure. The system which manages this transformation also provides tools to manipulate the composition, orientation and appearance of the displays interactively.

Animals↗
PubMedDate not supplied

A digital three-dimensional atlas of structure/function relationships.

The techniques and issues relevant to the development of a digital three-dimensional atlas of brain structure and function are discussed. The goals were to develop the appropriate methods for an interactive and quantitative stereotactic atlas to describe both anatomy and physiology. The work presented here used serial sections from unstained, thionein-stained and 2-deoxyglucose autoradiographic data sets.

Animals↗
PubMed1996

An analysis of alternative classification schemes for medical atlas mapping.

Most national disease atlases adopt a classification scheme based on either the percentile distribution of rates or on the national mean. Although these schemes have a direct interpretation, they are based on the univariate statistical distribution of rates and not on their spatial distribution, and distort the underlying spatial autocorrelation in the data. If the purpose of the maps is to represent spatial patterns, alternative classification schemes might be more appropriate. This research proposes an alternative classification method that maximises spatial similarity among contiguous units in the same class interval. The method has been illustrated using selected data from the German Cancer Atlas published in 1984.

Colonic Neoplasms↗
PubMed2026

An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

The immunoregulatory architecture of human oral tissues remains poorly defined. We present an integrated single-cell and spatial proteotranscriptomic atlas profiling >250,000 single-cell transcriptomes and >4 million spatially resolved cells across 13 niches. Using our AI-enabled AstroSuite, we defined neighborhoods and interaction modules, revealing peri-epithelial fibroblast-centered hubs enriched in effector cytokines. We harmonized fibroblast subtypes (universal, immune, peri-epithelial, peri-vascular, peri-neural, antigen-presenting cell [APC]-like, stress responsive, and myofibroblasts) with stress-responsive subtypes partitioning between mucosae and glands (type I and II). Spatial multiomics mapped ligand-receptor programs and identified mucosal stress-responsive fibroblasts as putative immunoregulatory hubs. Niche-aware integration of healthy and diseased datasets revealed fibroblast rewiring into inflammatory and reparative niches. Disease neighborhoods exhibited expansion of major histocompatibility complex (MHC)-I+, MHC-II+, and programmed cell death ligand 1 (PD-L1)+ fibroblasts and predicted spatial engagement with T cells at tertiary lymphoid structures. Together, this atlas identifies fibroblasts as central regulators of structural immunity and provides a scalable framework to target stromal-immune interactions across barrier organs.

Journal Article↗
PubMed2006

Multi-modal image set registration and atlas formation.

In this paper, we present a Bayesian framework for both generating inter-subject large deformation transformations between two multi-modal image sets of the brain and for forming multi-class brain atlases. In this framework, the estimated transformations are generated using maximal information about the underlying neuroanatomy present in each of the different modalities. This modality independent registration framework is achieved by jointly estimating the posterior probabilities associated with the multi-modal image sets and the high-dimensional registration transformations mapping these posteriors. To maximally use the information present in all the modalities for registration, Kullback-Leibler divergence between the estimated posteriors is minimized. Registration results for image sets composed of multi-modal MR images of healthy adult human brains are presented. Atlas formation results are presented for a population of five infant human brains.

Algorithms↗
PubMed2003

Geometric atlas: modeling the cortex as an organized surface.

Recent atlases of the cortical surface are based on a modelization of the cerebral cortex as a topological sphere. This captures effectively its organization as a regular bidimensional sheet of layers parallel to the surface and with perpendicular cortical columns. Yet, while in the vertical direction cortices are almost the same throughout phylia, in the sense of its surface the cerebral cortex is one of the most variable and distinctive parts of the nervous system. Indeed, gyri and sulci appear to have a crucial organizing role in an architectonic, connectional, and functional sense. This organization is not explicitly captured by the surface model of the cortex. We propose a geometric model of the cortical anatomy based on flat representations of principal sulci obtained from surface reconstructions of MRI data, and on neuroanatomical and theoretical considerations concerning the folding patterns of the cortex. The cortex is modeled by a sphere where primary sulci are included as axes. The arrangement of the axes is a simplification of the arrangement of principal sulci observed in flat stereographic representations of the whole cortical surface. The position of secondary and tertiary sulci is then defined by a field of orientations parallel and orthogonal to the axes. We consider the use of the geometric model as a synthetic reference cortex for addressing reconstructions of cortical surfaces. We present a method which establishes a bijection between the geometric model and a cortical surface reconstruction by using the axes of the model as boundary conditions for a set of partial differential equations solved over both surfaces. Using the geometric model as atlas provides a natural parameterization of the cortical surface that, unlike angular coordinates, allows for a localization based on the surface distance to its main organizing landmarks and folding patterns.

Algorithms↗
PubMed2006

Expression mapping of tetracycline-responsive prion protein promoter: digital atlasing for generating cell-specific disease models.

We present a digital atlas system that allows mapping of molecular expression patterns at cellular resolution through large series of histological sections. Using this system, we have mapped the distribution of a distinct marker, encoded by the LacZ reporter gene driven by the tetracycline-responsive prion protein promoter in double transgenic mice. The purpose is to evaluate the suitability of this promoter mouse line for targeting genes of interest to specific brain regions, essential for construction of inducible transgenic disease models. Following processing to visualize the promoter expression, sections were counterstained to simultaneously display cytoarchitectonics. High-resolution mosaic images covering entire coronal sections were collected through the mouse brain at intervals of 200 microm. A web-based application provides access to a customized virtual microscopy tool for viewing and navigation within and across the section images. For each section image, the nearest section in a standard atlas is defined, and annotations of key structures and regions inserted. Putative categorization of labeled cells was performed with use of distribution patterns, followed by cell size and shape, as parameters that were compared to legacy data. Among the ensuing results were expression of this promoter in putative glial cells in the cerebellum (and not in Purkinje cells), in putative glial cells in the substantia nigra, in pallidal glial cells or interneurons, and in distinct cell layers and regions of the hippocampus. The study serves as a precursor for a database resource allowing evaluation of the suitability of different promoter mouse lines for generating disease models.

Animals↗
PubMed2026

Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.

The global rise of inflammatory bowel disease (IBD) reflects environmental shifts, yet how these changes are embedded in the gut microbial ecology remains unclear. We construct a microbiome atlas comprising 245,627 profiles. By classifying countries into three epidemiologic stages, we establish a framework. As the IBD burden increases, the gut microbial alpha diversity declines, and community structures form distinct clusters. This transition is characterized by a gradient of core genera. Integrating six shotgun metagenomic cohorts, we identify the depletion of anabolic pathways in IBD patients. Strain-level analysis reveals that epidemiologic staging shapes genetic architecture within species, identifying an IBD-enriched subclade of Eisenbergiella associated with elevated fecal cholic acid. We develop a microbial inflammatory risk score (MIRS), based on 19 genera, that discriminates IBD from controls (area under the curve [AUC] = 0.92). MIRS correlates with IBD prevalence. Our study provides an atlas linking epidemiology to microbiome ecology and strain evolution, offering a foundation for population-level surveillance and interventions in IBD.

Humans↗
PubMed2024

An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing.

Colorectal cancer (CRC) ranks as the second leading cause of cancer deaths globally. In recent years, short-read single-cell RNA sequencing (scRNA-seq) has been instrumental in deciphering tumor heterogeneities. However, these studies only enable gene-level quantification but neglect alterations in transcript structures arising from alternative end processing or splicing. In this study, we integrated short- and long-read scRNA-seq of CRC samples to build an isoform-resolution CRC transcriptomic atlas. We identified 394 dysregulated transcript structures in tumor epithelial cells, including 299 resulting from various combinations of splicing events. Second, we characterized genes and isoforms associated with epithelial lineages and subpopulations exhibiting distinct prognoses. Among 31,935 isoforms with novel junctions, 330 were supported by The Cancer Genome Atlas RNA-seq and mass spectrometry data. Finally, we built an algorithm that integrated novel peptides derived from open reading frames of recurrent tumor-specific transcripts with mass spectrometry data and identified recurring neoepitopes that may aid the development of cancer vaccines.

Colorectal Neoplasms↗
PubMed2002

[Immediate and long-term results of implantation of the new platinum coronary stent (atlas stent) in patients with coronary artery disease].

BACKGROUND AND OBJECTIVES: We evaluated the technical and clinical results of implantation of the Atlas stent, the hospital stay, and the short and long-term clinical and angiographic outcome. PATIENTS AND METHOD: The study included 169 patients (60.1 10.8 year-old), 60.3% of which had acute coronary syndromes and complex lesions. Immediate success was achieved in 98% of cases. The clinical follow-up in 85.7% of the patients at 14.3 6.8 months, revealed that 89% remained free of adverse events and most (94.4%) were functional class I of the CCS. Angiographic follow-up at 8.4 4.1 months of 40.9% of the cases revealed restenosis in 27.9%. There were 2 cases of subacute thrombosis. CONCLUSIONS: The application of the Atlas stent in patients with a diverse clinical spectrum demonstrated good immediate and long term results, with a rate of restenosis similar to that of other stents available on the market.

Coronary Disease↗
PubMed1998

A stereotaxic atlas of the grey lesser mouse lemur brain (Microcebus murinus).

In response to the growing interest in the prosimian Microcebus murinus for studies on cerebral aging, the stereotaxic atlas of its brain was carried out in view of further anatomical, biochemical, electrophysiological, and behavioral investigations as well as for therapeutic experiments. This primate, which could be a valuable model for neuroscientific studies in various domains, presents numerous physiological advantages (e.g., size, cost, and ability to breed) compared to rodents, which can be used as nonprimate models, and simians. The atlas, valid for adult microcebes of every age and both sexes, consists of 54 frontal plates and 28 sagittal plates. For the establishment of stereotaxic coordinates and for drawings and photographs, 10 adult specimens of Microcebus murinus were used. The brains were frozen, cut into sections of 50 microm thickness, every fourth section being stained with Nissl. First, sections were projected and the outlines of the different structures, nuclei, and fibers were drawn. Then, the accuracy of the analysis was improved by detailed observation directly by microscope and also by computer analysis. Finally, the photographs of the sections were scanned and processed using the software Photoshop and Illustrator. For testing coordinates, several verifications were made. Experiments on lesions and injections of different substances were carried out in specific regions of the brain and brains implanted with needles were fixed in formol and embedded in paraffin wax.

Anatomy, Artistic↗
PubMed1999

Stereotaxic atlas of the pig brain.

A stereotaxic atlas of the pig brain has been established. It consists of 60 frontal and 18 sagittal drawings illustrating Nissl stained sections. A stereotaxic apparatus adapted for the Pig was used to determine the brain coordinates. Radiographic techniques were applied to verify the correct position of the central nervous structures in the apparatus. The zero horizontal plane contains the line joining the recessus preopticus and the posterior commissure (PC) images. These two landmarks were identified by ventriculography. The anterior limit of the PC is used as zero on the stereotaxic atlas. Vertical electrode trajectories implanted at a fixed depth in the brain and at different anterior and lateral levels were used to determine the lateral, vertical and height coordinates in the different planes. Then the brains were perfused and embedded to avoid major displacement of the cerebral structures. Frontal and sagittal serial sections of 100 microns were performed in two different animals. Magnified diagrams of brain sections representing the cellular architecture of the brain structures were produced, some of which are illustrated with photomicrographs. For certain areas, the limits of the nuclei were difficult to determine even when complementary electrophysiological studies were carried out. Each plate is accompanied by a list of abbreviations used to label structures on the plate, together with the terms which they represent. This work should provide a useful anatomical guide for research on the pig brain.

Anatomy, Artistic↗