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PubMedDate not supplied

Towards a microMRI atlas of mouse development.

This study investigates the potential of microscopic Magnetic Resonance Imaging to obtain information for 3D digital atlases of mouse development using fixed samples. Fixed samples allow direct comparison with already published atlases and provide a testing ground for future in vivo efforts. 3D MR images of mouse embryos (dpc 6.5-16) illustrate that the necessary contrast and level of detail is available with this technique. Diffusion weighted imaging, diffusion tensor imaging, and multi-valued data sets are presented as examples of uniquely MR methods of obtaining anatomical information. MRI is performed non-invasively on the intact sample, leaving open the possibility of other manipulations (e.g. classical histology, immunohistochemistry, in situ hybridization, and in vitro growth for unfixed samples) after conducting the MRI experiment.

Animals↗
PubMed2003

Automatic brain tumor segmentation by subject specific modification of atlas priors.

RATIONALE AND OBJECTIVES: Manual segmentation of brain tumors from magnetic resonance images is a challenging and time-consuming task. An automated system has been developed for brain tumor segmentation that will provide objective, reproducible segmentations that are close to the manual results. Additionally, the method segments white matter, grey matter, cerebrospinal fluid, and edema. The segmentation of pathology and healthy structures is crucial for surgical planning and intervention. MATERIALS AND METHODS: The method performs the segmentation of a registered set of magnetic resonance images using an expectation-maximization scheme. The segmentation is guided by a spatial probabilistic atlas that contains expert prior knowledge about brain structures. This atlas is modified with the subject-specific brain tumor prior that is computed based on contrast enhancement. RESULTS: Five cases with different types of tumors are selected for evaluation. The results obtained from the automatic segmentation program are compared with results from manual and semi-automated methods. The automated method yields results that have surface distances at roughly 1-4 mm compared with the manual results. CONCLUSION: The automated method can be applied to different types of tumors. Although its performance is below that of the semi-automated method, it has the advantage of requiring no user supervision.

Automation↗
PubMed2001

Tethering of the vertebral artery in the congenital arcuate foramen of the atlas vertebra: a possible cause of vertebral artery dissection in children.

Twelve children with vertebrobasilar artery stroke are reported (seven males, five females; aged 6 months to 15 years). Patient 1 showed an arcuate foramen in the posterior arch of the atlas, an anatomical variant occurring in 3 to 15% of the population. It was hypothesized that the presence of the arcuate foramen might cause tethering of the vertebral artery and lead to its dissection by repetitive trauma. Lateral plain films of the cervical spine in cases of posterior circulation stroke were taken. Eight of 11 patients showed aberrant arcuate foramina. Of the remaining three patients, one had normal cervical spine X-rays, one had an absent right posterior arch of the atlas following previous surgery for a cervical meningocele, and one patient had incomplete ossification of the vertebrae. Seven of the nine patients with arcuate foramina had vertebral angiograms. In all cases this showed the vertebral artery passing through the arcuate foramen before entering the brain and an appearance consistent with arterial dissection and occlusion at the same site below the foramen. Most documented cases of posterior circulation stroke in children follow trauma, which may be minimal or repetitive, with thrombotic occlusion of the artery at C1-C2 level. The association with an arcuate foramen and its possible causative role in the genesis of posterior circulation stroke in children has not been previously recognized. There may be a causal association between the presence of an arcuate foramen, tethering of the vertebral artery in the foramen, and dissection from repetitive trauma with movement of the neck.

Adolescent↗
PubMed2026

Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.

RNA splicing shapes neuronal identity and disease risk, yet current maps lack the developmental resolution and depth to resolve this complexity. Here, we integrate deep long-read RNA sequencing and proteomics in induced pluripotent stem cell-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half previously unknown) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences. Population genetics demonstrates that variants affecting novel exons and splice sites are under negative selection, underscoring the potential significance of these isoforms. During neuronal maturation, we observe that autism risk genes undergo dynamic isoform switching, including microexon inclusion and intron retention, that remodel key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between alternative transcript processing events, including transcription start sites, exon splicing, and polyadenylation. Finally, our atlas enables variant reinterpretation in autism, highlighting the value of an isoform-centric view for interpreting pathogenic variation in neurodevelopment.

Humans↗
PubMed2026

A single-nucleus transcriptomic atlas of human inner ear development.

Hearing and balance rely on coordinated activity of multiple inner ear cell types, yet the mechanisms governing their development and specification in humans remain unclear. Consequently, this limits our understanding of how disease genes affect cell type formation and function, limiting the development of targeted treatments, including gene therapies. Here we present the Human Inner Ear Development snRNA-seq Atlas (HIEDRA), a single-nucleus transcriptomic atlas of the human inner ear spanning the first and second trimesters. HIEDRA maps sensory and nonsensory epithelia, neurons and mesenchyme-associated populations, including undercharacterized secretory cells required for ion homeostasis. We identify selective vulnerability in sensory and secretory lineages to disease-associated genes, infer regulatory networks and show that Hedgehog signaling suppression is required for secretory cell specification. We validate this mechanism in human inner ear organoids, expanding the model to include all major cell types. Altogether, these findings provide insights into human inner ear cell type specification, improve in vitro models and establish HIEDRA as a resource for investigating human inner ear development.

Journal Article↗
PubMed2002

FDG-PET images quantified by probabilistic atlas of brain and surgical prognosis of temporal lobe epilepsy.

PURPOSE: This study evaluated the relation between hypometabolism, diagnosed by fluorodeoxyglucose positron emission tomography (FDG-PET), and the surgical outcome of a large and homogeneous series of cases of mesial temporal lobe epilepsy (mTLE), by using a probabilistic atlas of the human brain (statistical probabilistic anatomical maps: SPAM). METHODS: Ninety-five surgically proven intractable mTLE patients and 22 age-matched controls were spatially normalized to the average brain PET template of international consortium of brain mapping (ICBM). The diagnosis of mTLE was confirmed by the presence of hippocampal sclerosis on magnetic resonance imaging (MRI) and video-EEG monitoring. Counts from normalized PET images were multiplied by the probability from 98 volumes of interest (VOIs) of SPAM. Asymmetric indexes (AIs) reflecting the severity of hypometabolism were calculated by counts of selected 12 VOIs from SPAM images in both temporal lobes. Extent of hypometabolism was determined by the number of voxels showing decreased metabolism in each VOI segmented by SPAM. RESULTS: Of the 95 patients studied, 76 (80%) were seizure free, and 19 (20%) had postoperative seizures for the > or =2-year follow-up period. No significant association between the severity of hypometabolism in each VOI of the temporal lobe and surgical outcome was identified (p > 0.05). The number of voxels showing decreased hypometabolism was not significantly different between the good- and poor-outcome groups (p > 0.05). CONCLUSIONS: Our results demonstrated that focal severity and extent of hypometabolism quantified by a probabilistic atlas of brain were not related to the surgical outcome in mTLE patients who had hippocampal sclerosis on MRI. We should develop a more localized and specified anatomic map for mTLE for further results.

Adult↗
PubMedDate not supplied

A precise, three-dimensional atlas of myocardial perfusion correlated with coronary arteriographic anatomy.

To map precise myocardial perfusion anatomy, we correlated detailed coronary arteriographic anatomy for every coronary artery and all secondary branches in the heart that had flow-limiting stenosis with corresponding specific, circumscribed, myocardial perfusion defects by positron emission tomography. Eight hundred ninety-five patients with abnormal coronary arteriograms showing any visible coronary artery narrowing of greater than 10% diameter stenosis underwent positron emission tomography perfusion imaging at rest and after dipyridamole stress; the data obtained were processed automatically into 3-dimensional topographic displays of relative radionuclide uptake in anterior, septal, left lateral, and inferior quadrant views, without attenuation artifacts, depth-dependent resolution, or spatial distortion of polar displays. The selection criterion for detailed anatomic analysis was the presence of a discrete, localized, moderate to severe, dipyridamole-induced perfusion defect, defined by automated algorithms as 1 quadrant view outside 2 SDs of healthy control subjects with which a specific stenotic coronary artery and/or its secondary branches could be correlated unequivocally on the coronary arteriogram for mapping precise perfusion anatomy, not for determining sensitivity or specificity. Because the anatomy of myocardial perfusion is inherently not statistical data, the results are presented as a summary atlas and series of individual cases that illustrate myocardial perfusion anatomy. Because the patterns of myocardial perfusion anatomy were derived from a large number of subjects, the atlas provides generalized information, not previously published, that correlates detailed arteriographic anatomy with perfusion anatomy including secondary diagonal, marginal, and posterior descending branches of the coronary arteries.

Adult↗
PubMed2002

Clinical field-testing of ATLAS prosthetic system for trans-tibial amputees.

The ATLAS prosthetic system was tested on 81 trans-tibial amputees in two tropical areas and followed for about two years. At the conclusion 19% (15/81) had given up its use; mostly because of unsatisfactory socket fit, but in 7% (6/81) system related failures were the cause of non-compliance; mostly because of a shrieking noise from the shin-foot piece during use. System related failures were encountered in 62% (41/66) of users; the most serious threat to patient safety was fractures of the shank in 39% (26/66) and badly worn feet in 12% (8/66). With a failure rate of about 41% after one and a half years the ATLAS system is considered unacceptable for general use in trans-tibial amputees.

Adolescent↗
PubMed2001

The Edinburgh Mouse Atlas: using the CD.

This paper provides a simple introduction to the reconstructions and data-handling tools stored on the Edinburgh Mouse Atlas CD, together with some of the ways in which the viewers and software can be used to understand mouse development and analyse data. The key aspect of the Mouse Atlas is that the underlying models are a complete representation of the histology, which has not been constrained to a particular interpretation. This means, for example, that the current anatomy domains can be further subdivided as required to any resolution up to the resolution of the models (2-7 microm). In the CD of the early embryos described here, virtually all tissues that can be usefully distinguished either by the histology or morphologically have been delineated.

Animals↗
PubMed2026

ECLIPSE: exploring the dark proteome of ESKAPE pathogens through the sequence similarity network of the Protein Universe Atlas.

MOTIVATION: The accelerating crisis of antimicrobial resistance among the critical so-called ESKAPE pathogens demands the urgent identification of novel molecular targets. However, a substantial fraction of ESKAPE proteomes remains functionally uncharacterized, with many genes annotated as encoding hypothetical proteins. These protein sequences often lack significant similarity to known protein families when conventional homology-based annotation methods are used and thus remain "dark". This limits our ability to explore their roles in pathogenicity, and it is thus crucial to bridge this substantial gap in pathogen biology by developing new strategies to illuminate these "dark" regions of the ESKAPE pan-proteome. RESULTS: We introduce ECLIPSE (ESKAPE Connectome Linkage and Inference for Proteome Sequence Exploration), a network-based computational framework that systematically identifies and prioritizes functionally dark protein families in ESKAPE pan-proteomes. ECLIPSE embeds target ESKAPE pathogen proteomes within the global sequence similarity network of the Protein Universe Atlas. It detects connected components composed entirely of unannotated proteins, called the "dark proteome." As a case study, we applied ECLIPSE to a pan-proteome of 3 460 657 protein sequences from 635 strains of Pseudomonas aeruginosa (PA). ECLIPSE identified 120 985 proteins (4%) residing in completely dark connected components. Furthermore, we have performed a taxonomic diversity analysis using normalized Shannon indices to characterize each dark component by its enrichment in ESKAPE pathogens. The analysis utilized the evenness (E) value (see Methods 2.1), which distinguishes Pseudomonas-specific (target-specific) from ESKAPE-enriched dark components. We then developed the Dark Proteome Prioritization Score (DPPS), a composite multidimensional scoring framework (see Methods 2.5). It ranks these dark components by biological relevance across four orthogonal axes: (i) functional darkness, (ii) P. aeruginosa proportion in the Atlas, (iii) AMR-clade taxonomic restriction, and (iv) conservation across the 635 P. aeruginosa strains. This framework outputs a robust four-tier scoring system; the prioritized Tier I components were validated by weight sensitivity analysis and remained stable across 500 Monte Carlo weight perturbations. Structural characterization of one of the top-ranked ESKAPE-enriched dark components revealed that it belongs to the beta-barrel fold DUF1302 (PF06980) family, for which no experimentally solved three-dimensional structure exists in the PDB. The genomic context analysis indicates that it is co-localized with a LuxR-type transcriptional regulator. Collectively, ECLIPSE identifies evolutionarily conserved, structurally defined, and functionally dark proteins enriched across ESKAPE pathogens; these dark proteins can further be utilized as alternative antimicrobial targets for experimental characterization. AVAILABILITY AND IMPLEMENTATION: The source code and dataset are available for free at: Github: https://github.com/surabhilata/ECLIPSE.git, Zenodo: DOI: 10.5281/zenodo.21064323.

Proteome↗
PubMed2004

CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.

UNLABELLED: Currently, new bacterial genomes are being published on a monthly basis. With the growing amount of genome sequence data, there is a demand for a flexible and easy-to-maintain structure for storing sequence data and results from bioinformatic analysis. More than 150 sequenced bacterial genomes are now available, and comparisons of properties for taxonomically similar organisms are not readily available to many biologists. In addition to the most basic information, such as AT content, chromosome length, tRNA count and rRNA count, a large number of more complex calculations are needed to perform detailed comparative genomics. DNA structural calculations like curvature and stacking energy, DNA compositions like base skews, oligo skews and repeats at the local and global level are just a few of the analysis that are presented on the CBS Genome Atlas Web page. Complex analysis, changing methods and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues. AVAILABILITY: A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/. SUPPLEMENTARY INFORMATION: This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase.

Algorithms↗
PubMed2001

Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated.

The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) is an Internet database aimed at genes involved in cancer, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It presents information in concise and updated reviews (cards) or longer texts (deep insights), a (new) case report section, a huge portal towards genetics and/or cancer databases, and teaching items in genetics for students in medicine and the sciences. This database is made for and by clinicians and researchers in the above-mentioned fields, who are encouraged to contribute. It deals with cancer research, genomics and cytogenomics. It is at the crossroads of research, post-university teaching and telemedicine. The Atlas is available at no cost.

Chromosome Aberrations↗
PubMed2003

Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003.

The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) contains concise and updated cards on genes involved in cancer, cytogenetics and clinical entities in oncology, and cancer-prone diseases, a portal towards genetics/cancer, and teaching materials in genetics. This database is made for and by researchers and clinicians, who are encouraged to contribute. The Atlas is part of the genome project and it participates in research on cancer epidemiology.

Cytogenetic Analysis↗
PubMed2006

Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community.

The nuclear receptor signaling (NRS) field has generated a substantial body of information on nuclear receptors, their ligands and coregulators, with the ultimate goal of constructing coherent models of the biological and clinical significance of these molecules. As a component of the Nuclear Receptor Signaling Atlas (NURSA)--the development of a functional atlas of nuclear receptor biology--the NURSA Bioinformatics Resource is developing a strategy to organize and integrate legacy and future information on these molecules in a single web-based resource (www.nursa.org). This entails parallel efforts of (i) developing an appropriate software framework for handling datasets from NURSA laboratories and (ii) designing strategies for the curation and presentation of public data relevant to NRS. To illustrate our approach, we have described here in detail the development of a web-based interface for the NURSA quantitative PCR nuclear receptor expression dataset, incorporating bioinformatics analysis which provides novel perspectives on functional relationships between these molecules. We anticipate that the free and open access of the community to a platform for data mining and hypothesis generation strategies will be a significant contribution to the progress of research in this field.

Animals↗
PubMed2005

Induced radioactivity in the forward shielding and semiconductor tracker of the ATLAS detector.

The radioactivity induced in the forward shielding, copper collimator and semiconductor tracker modules of the ATLAS detector has been studied. The ATLAS detector is a long-term experiment which, during operation, will require to have service and access to all of its parts and components. The radioactivity induced in the forward shielding was calculated by Monte Carlo methods based on GEANT3 software tool. The results show that the equivalent dose rates on the outer surface of the forward shielding are very low (at most 0.038 microSv h(-1)). On the other hand, the equivalent dose rates are significantly higher on the inner surface of the forward shielding (up to 661 microSv h(-1)) and, especially, at the copper collimator close to the beampipe (up to 60 mSv h(-1)). The radioactivity induced in the semiconductor tracker modules was studied experimentally. The module was activated by neutrons in a training nuclear reactor and the delayed gamma ray spectra were measured. From these measurements, the equivalent dose rate on the surface of the semiconductor tracker module was estimated to be < 100 microSv h(-1) after 100 d of Large Hadron Collider (LHC) operation and 10 d of cooling.

Construction Materials↗
PubMed2025

A single-cell transcriptomic atlas of the pigtail macaque placenta in late gestation.

The placenta is a complex organ with multiple immune and non-immune cell types that promote fetal tolerance and facilitate the transfer of nutrients and oxygen. The nonhuman primate (NHP) is a key experimental model for studying human pregnancy complications, in part due to similarities in placental structure, which makes it essential to understand how single-cell populations compare across the human and NHP maternal-fetal interface. We constructed a single-cell RNA-Seq (scRNA-Seq) atlas of the placenta from the pigtail macaque ( Macaca nemestrina ) in the third trimester, comprising three different tissues at the maternal-fetal interface: the chorionic villi (placental disc), chorioamniotic membranes, and the maternal decidua. Each tissue was separately dissociated into single cells and processed through the 10X Genomics and Seurat pipeline, followed by aggregation, unsupervised clustering, and cluster annotation. Next, we determined the maternal-fetal origins of cell populations and analyzed single-cell RNA trajectory, Gene Ontology enrichment, and cell-cell communication. Single-cell populations in the pigtail macaque were strikingly similar in their identity and frequency to those found in the human placenta, including cells from trophoblast, stromal cell, immune, and macrophage lineages. An advantage of our approach was the deep sequencing of three tissues at the maternal-fetal interface, which yielded a rich diversity of common and rare single-cell populations. The third-trimester pigtail macaque single-cell atlas enables the identification of cellular subclusters analogous to those in humans and provides a powerful resource for understanding experimental perturbations on the NHP placenta.

Journal Article↗
PubMed1997

Surface-based labeling of cortical anatomy using a deformable atlas.

We describe a computerized method to automatically find and label the cortical surface in three-dimensional (3-D) magnetic resonance (MR) brain images. The approach we take is to model a prelabeled brain atlas as a physical object and give it elastic properties, allowing it to warp itself onto regions in a preprocessed image. Preprocessing consists of boundary-finding and a morphological procedure which automatically extracts the brain and sulci from an MR image and provides a smoothed representation of the brain surface to which the deformable model can rapidly converge. Our deformable models are energy-minimizing elastic surfaces that can accurately locate image features. The models are parameterized with 3-D bicubic B-spline surfaces. We design the energy function such that cortical fissure (sulci) points on the model are attracted to fissure points on the image and the remaining model points are attracted to the brain surface. A conjugate gradient method minimizes the energy function, allowing the model to automatically converge to the smoothed brain surface. Finally, labels are propagated from the deformed atlas onto the high-resolution brain surface.

Algorithms↗
PubMed2005

Tailored reversible watermarking schemes for authentication of electronic clinical atlas.

It is accepted that digital watermarking is quite relevant in medical imaging. However, due to the special nature of clinical practice, it is often required that watermarking not introduce irreversible distortions to medical images. The electronic clinical atlas has such a need of "lossless" watermarking. We present two tailored reversible watermarking schemes for the clinical atlas by exploiting its inherent characteristics. We have implemented the schemes and our experimental results look very promising.

Algorithms↗