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At least 19 recordsLinked to original sources

[Dietary preferences of domestic ruminants (cattle, sheep, goats) grazing on natural Sahelian and Sudano-Sahelian ranges. III. Epidermal characteristics of the principal plant species consumed on the pastures: compilation of a reference atlas with a view toward study of dietary preferences].

Microscopic analysis of vegetal fragments contained in the faeces and in the alimentary bolus is a method for studying the animals' diet on pastures. This work is conducted within the scope of a ruminant diet enquiry over Sahelian and Sudano-Sahelian pastures in Senegal. The author describes the epidermal characteristics of the main grazed plants (28 species) so as to constitute a reference atlas. An example of the identification key is exposed for 19 dicotyledons from their epidermal characteristics. This key will have to be completed and will help to recognize the plant debris contained in the faeces and in the alimentary bolus.

Animal Feed↗

scATAnno: Automated Cell Type Annotation for Single-cell ATAC-seq Data.

Recent advances in single-cell epigenomic techniques have increased the demand for single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) analysis. One key analytical task is to determine cell type identity based on epigenetic data. Here, we introduce scATAnno, a Python package designed to automatically annotate scATAC-seq data using large-scale scATAC-seq reference atlases. This workflow generates reference atlases from publicly available datasets, enabling accurate cell type annotation by integrating query data with reference atlases without the use of single-cell RNA sequencing (scRNA-seq) data. To enhance annotation accuracy, we incorporated k-nearest neighbors (KNN)-based and weighted distance-based uncertainty scores to effectively detect cell populations within the query data that are distinct from all cell types in the reference data. We compared and benchmarked scATAnno against five other published cell annotation approaches, demonstrating its superior performance across multiple datasets and metrics. We further showcased the utility of scATAnno across multiple datasets, including peripheral blood mononuclear cells (PBMCs), triple-negative breast cancer (TNBC), and basal cell carcinoma (BCC), and demonstrated that scATAnno accurately annotates cell types across diverse biological conditions. Overall, scATAnno is a useful tool for scATAC-seq reference atlas construction and cell type annotation and can facilitate the interpretation of new scATAC-seq datasets in complex biological systems. scATAnno is publicly available at https://scatanno-main.readthedocs.io/.

Single-Cell Analysis↗

The EULAR-OMERACT rheumatoid arthritis MRI reference image atlas: the wrist joint.

This paper presents the wrist joint MR images of the EULAR-OMERACT rheumatoid arthritis MRI reference image atlas. Reference images for scoring synovitis, bone oedema, and bone erosions according to the OMERACT RA MRI scoring (RAMRIS) system are provided. All grades (0-3) of synovitis are illustrated in each of the three wrist joint areas defined in the scoring system--that is, the distal radioulnar joint, the radiocarpal joint, and the intercarpal-carpometacarpal joints. For reasons of feasibility, examples of bone abnormalities are limited to five selected bones: the radius, scaphoid, lunate, capitate, and a metacarpal base. In these bones, grades 0-3 of bone oedema are illustrated, and for bone erosion, grades 0-3 and examples of higher grades are presented. The presented reference images can be used to guide scoring of wrist joints according to the OMERACT RA MRI scoring system.

Arthritis, Rheumatoid↗

The EULAR-OMERACT rheumatoid arthritis MRI reference image atlas: the metacarpophalangeal joints.

This paper presents the metacarpophalangeal (MCP) joint magnetic resonance images of the EULAR-OMERACT rheumatoid arthritis MRI reference image atlas. The illustrations include synovitis in the MCP joints (OMERACT RA magnetic resonance imaging scoring system (RAMRIS), grades 0-3), bone oedema in the metacarpal head and the phalangeal base (grades 0-3), and bone erosion in the metacarpal head and the phalangeal base (grades 0-3, and examples of higher grades). The presented reference images can be used to guide scoring of MCP joints according to the OMERACT RA MRI scoring system.

Arthritis, Rheumatoid↗

An introduction to the EULAR-OMERACT rheumatoid arthritis MRI reference image atlas.

This article gives a short overview of the development and characteristics of the OMERACT rheumatoid arthritis MRI scoring system (RAMRIS), followed by an introduction to the use of the EULAR-OMERACT rheumatoid arthritis MRI reference image atlas. With this atlas, MRIs of wrist and metacarpophalangeal joints of patients with rheumatoid arthritis can be scored for synovitis, bone oedema, and bone erosion, guided by standard reference images.

Arthritis, Rheumatoid↗

A probabilistic atlas and reference system for the human brain: International Consortium for Brain Mapping (ICBM).

Motivated by the vast amount of information that is rapidly accumulating about the human brain in digital form, we embarked upon a program in 1992 to develop a four-dimensional probabilistic atlas and reference system for the human brain. Through an International Consortium for Brain Mapping (ICBM) a dataset is being collected that includes 7000 subjects between the ages of eighteen and ninety years and including 342 mono- and dizygotic twins. Data on each subject includes detailed demographic, clinical, behavioural and imaging information. DNA has been collected for genotyping from 5800 subjects. A component of the programme uses post-mortem tissue to determine the probabilistic distribution of microscopic cyto- and chemoarchitectural regions in the human brain. This, combined with macroscopic information about structure and function derived from subjects in vivo, provides the first large scale opportunity to gain meaningful insights into the concordance or discordance in micro- and macroscopic structure and function. The philosophy, strategy, algorithm development, data acquisition techniques and validation methods are described in this report along with database structures. Examples of results are described for the normal adult human brain as well as examples in patients with Alzheimer's disease and multiple sclerosis. The ability to quantify the variance of the human brain as a function of age in a large population of subjects for whom data is also available about their genetic composition and behaviour will allow for the first assessment of cerebral genotype-phenotype-behavioural correlations in humans to take place in a population this large. This approach and its application should provide new insights and opportunities for investigators interested in basic neuroscience, clinical diagnostics and the evaluation of neuropsychiatric disorders in patients.

Adult↗

A general strategy for generating expert-guided, simplified views of ontologies.

Annotation of biomedical entities with widely used, well-structured ontologies and ontology-aware tools ensures data and analyses are Findable, Accessible, Interoperable, and Reusable (FAIR). Standardized terms with synonyms support lexical search, while ontology structure enables biologically meaningful grouping of annotations, such as by location and type. However, ontologies serving diverse communities are often more complex than needed for specific applications, creating barriers to adoption by researchers and resource developers. For example, cell atlases often attempt simplifications by manually building term hierarchies linking to cell type and anatomy ontologies, but these may include relationship types unsuitable for grouping annotations. We present tools for validating human expert curated term hierarchies, developed in two human reference atlas projects, against ontology structures. The tools provide tabular statistics plus graphical views of matching and non-matching terms and relationships to support discussion and conflict resolution. The HuBMAP Human Reference Atlas (HRA) effort is used to validate the approach and tools, and the Human Developmental Cell Atlas is featured as a use case.

Journal Article↗

The development of the EULAR-OMERACT rheumatoid arthritis MRI reference image atlas.

Based on a previously developed rheumatoid arthritis MRI scoring system (OMERACT 2002 RAMRIS), the development team agreed which joints, MRI features, MRI sequences, and image planes would best illustrate the scoring system in an atlas. After collecting representative examples for all grades for each abnormality (synovitis, bone oedema, and bone erosion), the team met for a three day period to review the images and choose by consensus the most illustrative set for each feature, site, and grade. A predefined subset of images (for example, for erosion--all coronal slices through the bone) was extracted. These images were then re-read by the group at a different time point to confirm the scores originally assigned. Finally, all selected images were photographed and formatted by one centre and distributed to all readers for final approval.

Arthritis, Rheumatoid↗

A computerized brain atlas: construction, anatomical content, and some applications.

An adjustable computerized atlas of the human brain has been developed, which can be adapted to fit individual anatomy. It is primarily intended for positron emission tomography (PET) but may also be used for single photon emission CT, transmission CT, magnetic resonance imaging, and neuroimaging-based procedures, such as stereotactic surgery and radiotherapy. The atlas is based on anatomical information obtained from brains fixed in situ soon after death. All structures have been drawn in on digitized photos of slices from one cryosectioned brain. The definition and classification of the anatomical structures and divisions are in agreement with the standard textbooks of anatomy, and the nomenclature is that of the Nomina Anatomica of 1965. The boundaries of the cortical cytoarchitectonic areas (Brodmann areas) have been determined using information from several sources, since three-dimensional literature data on their distribution are incomplete, scarce, and partly contradictory. However, no analysis of the cytoarchitectonics of the atlas brain itself has been undertaken. At present the data base contains three-dimensional representations of the brain surface, the ventricular system, the cortical gyri and sulci, as well as the Brodmann cytoarchitectonic areas. The major basal ganglia, the brain stem nuclei, the lobuli of the vermis, and the cerebellar hemispheres are also included. The computerized atlas can be used to improve the quantification and evaluation of PET data in several ways. For instance, it can serve as a guide in selecting regions of interest. It may also facilitate comparisons of data from different individuals or groups of individuals, by applying the inverse atlas transformation to PET data volume, thus relating the PET information to the anatomy of the reference atlas rather than to the patient's anatomy. Reformatted PET data from individuals can thus be averaged, and averages from different categories or different functional states of patients can be compared.

Anatomy, Artistic↗

Bregma, lambda and the interaural midpoint in stereotaxic surgery with rats of different sex, strain and weight.

Craniometric and stereotaxic data from rats of different sex, strain and weight were compared. It was found that stereotaxic atlases can be used with rats of different sex and strain provided that the weights of the rats conform to those used in the reference atlas. If rats of different weights are used, greater accuracy can be achieved if bregma is used as the reference point for work with rostral structures and the interaural line for work with caudal structures.

Animals↗

A computerized adjustable brain atlas.

A computerized brain atlas, adjustable to the patients anatomy, has been developed. It is primarily intended for use in positron emission tomography, but may also be employed in other fields utilizing neuro imaging, such as stereotactic surgery, transmission computerized tomography (CT) and magnetic resonance imaging (MRI). The atlas is based on anatomical information obtained from a digitized cryosectioned brain. It can be adjusted to fit a wide range of images from individual brains with normal anatomy. The corresponding transformation is chosen so that the modified atlas agrees with a set of CT or NMR images of the patient. The computerized atlas can be used to improve the quantification and evaluation of PET data by: Aiding and improving the selection of regions of interests. Facilitating comparisons of functional image data from different individuals or groups of individuals. Facilitating the comparison of different examinations of the same patient, thus reducing the need of reproducible fixation systems. Providing external a priori anatomical information to be used in the image reconstruction. Improving the attenuation and scatter corrections. Aiding in selecting a suitable patient orientation during the PET study. By applying the inverse atlas transformation to PET data set it is possible to relate the PET information to the anatomy of the reference atlas. Thus reformatted PET data from different patients can be averaged, and averages from different categories of patients can be compared. This procedure will facilitate the identification of statistically significant differences in the PET information from different groups of patients.

Brain↗

Applications of a computerized adjustable brain atlas in positron emission tomography.

A computerized brain atlas, adjustable to the patient's anatomy, has been developed. It is primarily intended for use in positron emission tomography (PET), but may also be employed in other fields utilizing neuro-imaging, such as stereotactic surgery. The atlas is based on anatomic information obtained from digitized cryosectioned cadaver brains. It can be adjusted to fit a wide range of individual brains with reasonable accuracy. The corresponding transformation is chosen so that the modified atlas agrees with a set of CT or MR images of the patient. The computerized atlas can be used to facilitate and improve the quantification and evaluation of PET data by: enabling the merging and comparison of results from different individuals or groups of individuals; serving as a vehicle in the comparison of different examinations of the same patient, thus reducing the need of reproducible fixation systems; supplying external information to be used in the image reconstruction, such as proper three-dimensional regions of interest; improving the attenuation and scatter corrections; helping to select suitable patient orientation during the PET study. By applying the inverse atlas transformation to the PET data volume it is possible to relate the PET information to the anatomy of the reference atlas. Reformatted PET data from different patients can thus be averaged, and averages from different categories of patients can be compared. The method will facilitate the identification of statistically significant differences in the PET information from different groups of patients.

Brain↗

Evaluation of the possibility to assess bone age on the basis of DXA derived hand scans-preliminary results.

The classical method of skeletal age assessment is based on the recognition of changes in the radiographic appearance of the maturity indicators in hand-wrist radiographs by comparison with a reference atlas. The purpose of this study was the evaluation of the possibility to assess bone age using a less invasive method such as dual-energy X-ray absorptiometry (DXA). Bone ages of 50 children free of any chronic diseases (5-18 years old) and ten with multihormonal pituitary deficiency (MPD) (8-20 years old) were assessed using an Expert-XL densitometer. Hand scans and classical hand-wrist radiographs were evaluated by two independent observers for bone age by visual comparison with reference standards of skeletal development published in the atlas. The precision errors of duplicate bone age ratings were low both for radiographs (<1%) and DXA hand scans (<0.9%). A high degree of agreement between bone age ratings done by two observers was assessed by intraclass correlation coefficients. The same bone age based on radiographs and DXA hand scans was assessed in 44 of 60 cases (73.3%); in 16 cases the differences between bone age were no higher than 0.5 year. No significant difference between mean bone age based on radiographs and DXA hand scans was observed ( P>0.05). Moreover, there was a very strong correlation between bone age results ( r=0.998; r(2)=0.996; P<0.0001), indicating agreement of bone age assessments based on DXA and radiographic images. Remarkable differences (up to 3 years) between bone age and chronological age were observed in healthy subjects, probably reflecting the effect of the secular trend towards earlier maturation or alterations in pubertal development. The study indicates that evaluation of skeletal maturity using DXA images is less invasive (up to 8 micro Sv) than radiography, giving results comparable to the classical method.

Absorptiometry, Photon↗

Volume rendering of visible human data for an anatomical virtual environment.

In this work, we utilize the axial anatomical human male sections from the National Library of Medicine's Visible Human Project to generate three-dimensional (3-D) volume representations of the human male subject. The two-dimensional (2-D) projection images were produced by combining ray tracing techniques with automated image segmentation routines. The resultant images provide accurate and realistic volumetric representations of the Visible Human data set which is ultimately needed in medical virtual environment simulation. Ray tracing techniques provide methods by which 2-D volume views of a 3-D voxel array can be produced. The cross-sectional images can be scanned at different angles to produce rotated views of the voxel array. By combining volume views at incremental angles over 360 degrees a full volumetric representation of the voxel array, in this case the human male data set, can be computer generated and displayed without the speed and memory limitations of trying to display the entire data array. Additional texture and feature information can be obtained from the data by applying optical property equations to the ray scans. The imaging effects that can be added to volume renderings using these equations include shading, shadowing, and transparency. The automated segmentation routines provide a means to distinguish between various anatomical structures of the body. These routines can be used to differentiate between skin, fat, muscle, cartilage, blood vessels, and bone. By combining automated segmentation routines with the ray-tracing techniques, 2-D volume views of various anatomical structures and features can be isolated from the full data set. Examples of these segmentation abilities are demonstrated for the human male data set which include volume views of the skeletal systems, the musculoskeletal system, and part of the vascular system. The methods described above allow us to generate lifelike images, NURBS surface models, and realistic texture maps of specific anatomical structures. We have the capability to generate images that are both accurate and lifelike, much like photographic anatomical atlases. We can also generate images, models, and textures that have the clarity of medical artwork/illustrations, by highlighting the coloring of the ray traced structures with conventional colors instead of the natural color of the specimen. We are currently in the process of generating a comprehensive reference atlas of volume rendered images of the human body, soon to be published by Mosby-Year Book. The segmentation techniques needed to create this atlas also offer the accuracy and realism needed to create surface models and texture maps for a virtual environment for surgery simulation.

Anatomy, Cross-Sectional↗

Epigenetic Liquid Biopsy Enables Universal Mutation-Agnostic Molecular Surveillance for High-Risk Neuroblastoma.

PURPOSE: Liquid biopsy monitoring in pediatric solid tumors is limited by low mutational burden and lack of trackable genomic drivers. We sought to develop a mutation-agnostic, methylation-based liquid biopsy framework enabling universal molecular surveillance of high-risk neuroblastoma. EXPERIMENTAL DESIGN: Using whole-genome Oxford Nanopore Technologies sequencing of high-risk neuroblastoma tumors, we compared tumor-derived methylation profiles with a comprehensive atlas of normal human cell types and identified 72 neuroblastoma-specific differentially methylated regions (meNBL) that were reliably detectable in cell-free DNA (cfDNA). Marker robustness and specificity were validated using independent neuroblastoma methylation datasets and assessed against methylation profiles from other cancer types. We established neuroblastoma as a distinct methylation entity within the reference atlas by integrating a panel of 25 meNBLs, enabling quantitative estimation of tumor-derived cfDNA. Assay performance was evaluated across diagnostic, remission, relapse, and healthy control samples and compared with mutation-based and copy number-based approaches. RESULTS: Neuroblastoma-derived cfDNA was consistently detected at diagnosis and relapse but was absent in healthy controls and during confirmed remission. Methylation-based deconvolution demonstrated high specificity, with no detectable background signal in controls, and improved performance relative to copy number-based tumor fraction estimation. Longitudinal profiling enabled early molecular detection of relapse and reliable disease monitoring. CONCLUSIONS: We establish a robust, mutation-independent methylation-based liquid biopsy strategy for neuroblastoma that enables accurate, quantitative disease monitoring across all high-risk patients, including those lacking trackable genomic alterations. This approach supports the clinical translation of methylation-based cfDNA deconvolution as a broadly applicable platform for pediatric precision oncology.

Humans↗

Automatic matching of homologous histological sections.

The role of neuroanatomical atlases is undergoing a significant redefinition as digital atlases become available. These have the potential to serve as more than passive guides and to hold the role of directing segmentation and multimodal fusion of experimental data. Key elements needed to support these new tasks are registration algorithms. For images derived from histological procedures, the need is for techniques to map the two-dimensional (2-D) images of the sectional material into the reference atlas which may be a full three-dimensional (3-D) data set or one consisting of a series of 2-D images. A variety of 2-D-2-D registration methods are available to align experimental images with the atlas once the corresponding plane of section through the atlas has been identified. Methods to automate the identification of the homologous plane, however, have not been previously reported. In this paper we use the external section contour to drive the identification and registration procedure. For this purpose, we model the contours by B-splines because of their attractive properties the most important of which are: 1) smoothness and continuity; 2) local controllability which implies that local changes in shape are confined to the B-spline parameters local to that change; 3) shape invariance under affine transformation, which means that the affine transformed curve is still a B-spline whose control points are related to the object control points through the transformation. In this paper we present a fast algorithm for estimating the control points of the B-spline which is robust to nonuniform sampling, noise, and local deformations. Curve matching is achieved by using a similarity measure that depends directly on the parameters of the B-spline. Performance tests are reported using histological material from rat brains.

Animals↗

Growth patterns of Labrador Inuit youth: II. Skeletal age.

Few studies have been conducted on skeletal maturity of circumpolar populations despite its importance as background knowledge to orthopedic and orthodontic procedures or for other medical problems involving endocrine disturbances. The purpose of this study was to compare skeletal age with chronological age of Labrador Inuit youth aged between 5-18 years and to compare these results with data from a national survey of United States youth. The sample included 32% (n = 100) of the Inuit youth living in Nain, Labrador, Canada (Male = 41, female = 59). Hand wrist radiographs, collected during a field study in 1991, were used to estimate bone age using the Greulich and Pyle bone specific method. The mean relative Inuit skeletal ages increased almost consistently with chronological age but showed considerable individual variation as shown by the 95% confidence intervals. The pattern of growth of skeletal vs chronological age was similar to the National Center for Health Statistics data but the tempo was slower. The Z-scores for mean male relative bone ages ranged from -0.7 to -1.9 and for females from -0.6 to -1.4. The results indicated that Inuit males started to reach adult skeletal maturity levels by the chronological age of 17 years 9 months, and Inuit females by 15 years 8 months. Generally, Inuit skeletal ages were delayed by 10-24 months behind the reference atlas skeletal ages and 9-22 months behind the Inuit chronological ages.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

Contouring the middle and inner ear on radiotherapy planning scans.

The purpose of this study was to establish guidelines that help radiation oncologists contour the inner and middle ear on treatment planning scans. The radiotherapy computed tomography (CT) scans of 15 previously treated patients were reviewed for the ability to identify 3 separate auditory structures. The middle ear, the cochlea, and the vestibular apparatus were identified and contoured on each scan using anatomic landmarks. The volume and maximum axial dimension of each contour were calculated. The middle ear, cochlea, and vestibular apparatus were identified on all scans. The middle ear was defined by the tympanic membrane laterally and by the interface between air and the temporal bone in all other directions. The plane of the internal auditory canal through the temporal bone was the landmark distinguishing the vestibular apparatus from the cochlea. The mean volume of the middle ear, vestibular apparatus, and cochlea were 0.58 cm3, 0.44 cm3, and 0.14 cm3, respectively. The maximum axial dimension across the contour averaged 1.57 cm for the middle ear, 1.10 cm for the vestibular apparatus, and 0.69 cm for the cochlea. A reference atlas was constructed that shows the contour of each structure on 5 consecutive CT images. Accurate identification of the middle ear and inner ear structures on radiotherapy planning scans is possible and is necessary if critical auditory organs are to be spared during radiotherapy of targets that are located near the base of the skull. The information generated in this study will help radiation oncologists contour auditory structures accurately.

Ear, Inner↗