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At least 685 records · Page 38Linked to original sources
PubMedDate not supplied

Classical polymorphisms in Berbers from Moyen Atlas (Morocco): genetics, geography, and historical evidence in the Mediterranean peoples.

BACKGROUND: Mediterranean population relationships have recently been reviewed through the analysis of classical and DNA markers. The differentiation between Berbers and Arabic-speakers to the south, and the genetic impact of the seven centuries of Muslim domination in the Iberian Peninsula have been among the most interesting questions posed in these studies. AIM: The present study seeks to assess the degree of genetic affinity between the two main population groups of Morocco: Berbers and Arabic-speakers. Data from the Berber study population were also compared with published information on 20 circum-Mediterranean groups. SUBJECTS AND METHODS: A Berber sample of 140 individuals from Moyen Atlas (Morocco) has been characterized using 15 classical markers (ABO, Duffy, MNSs, Rh, ACPl, AKl, ESD, GLOI, 6-PGD, PGMl, GC, HP, PI, PLG and TF). RESULTS: Allele frequencies in the Berbers fit well into the general southern Mediterranean ranges, albeit with some peculiarities, such as the high FY*A, ACPl*C, and PI*S values. The general pattern of relationships among Mediterranean peoples tested by genetic variance analysis was compatible with a north-south geographical differentiation. Spatial auto-correlation analysis in the different geographical regions of the Mediterranean reveals that the highest degree of association between allele frequencies and geographical distances corresponds to the western (41% of significant correlograms) and northern Mediterranean populations (33%). When only southern Mediterranean groups were considered, the degree of geographical structure considerably decreases (11% of significant correlograms). CONCLUSIONS: The different loci studied revealed close similarity between the Berbers and other north African groups, mainly with Moroccan Arabic-speakers, which is in accord with the hypothesis that the current Moroccan population has a strong Berber background. Differences in the spatial pattern of allele frequencies also are compatible with specific population histories in distinct Mediterranean areas, rather than general population movements across the whole region.

Alleles↗
PubMedDate not supplied

An early hand-wrist atlas and its implications for secular change in bone age.

A little-known 'Skiagraphic Atlas' documenting radiographic changes in the bones of the hand and wrist was published by Poland in 1898. Nineteen skiagrams of British children, 1-17 years of age, were included. Tanner-Whitehouse-2 bone ages were assessed for 15 individuals in this series and differences from chronological ages were calculated. Mean differences for 20-bone, RUS and carpal bone ages are significantly larger than zero. Hence, these children were relatively advanced compared to present children. Comparisons of Poland's expected ages for onset and fusion of secondary ossification centres in the hand and wrist with more recent reference data indicated a secular increase in the rates of skeletal maturation of approximately 0.22-0.66 year/decade, with relatively greater change in expected ages of fusion.

Adolescent↗
PubMed2026

CMAtlas: a comprehensive DNA methylation atlas for exploring epigenetic alterations in 34 human cancer types.

MOTIVATION: Aberrant DNA methylation is a fundamental epigenetic hallmark of cancer. However, existing resources often lack technological diversity and comprehensive cancer coverage. Furthermore, most platforms fail to achieve deep multi-omics integration and tend to ignore cancer-type-specific methylation features, limiting their utility in precision oncology and drug discovery. RESULTS: We developed Cancer Methylation Atlas (CMAtlas), a comprehensive platform integrating 13 753 samples across 34 cancer types. By applying technology-tailored pipelines to data from various profiling technologies, we identified 830 725 tumor-specific differentially methylated elements (DMEs) and 1 480 098 differentially methylated regions (DMRs), alongside 1 154 256 cancer-type-specific DMEs and 329 154 DMRs. The platform demonstrates high cross-platform consistency and strong concordance between tumor tissues and cell lines, ensuring the robustness of our findings. All DMEs and DMRs are annotated with multi-omics data (RNA expression, somatic mutations, and chromatin accessibility) and clinical relevance (survival associations and cell-free DNA profiling). We further demonstrate the utility of CMAtlas by identifying prognostic aberrant methylation in colorectal cancer driver genes. AVAILABILITY AND IMPLEMENTATION: CMAtlas is freely accessible at {{https://cmatlas.renlab.cn/}}. The platform offers an intuitive web interface supporting gene-centric and cancer-centric queries, alongside customizable analysis modules designed to facilitate user-specific research needs.

Humans↗
PubMed2026

Atlas-level single-cell integration and clustering-free differential expression analysis with GEDI 2.0.

MOTIVATION: GEDI is a generative framework for multi-sample, multi-condition single-cell analysis that performs batch correction, latent representation learning, and clustering-free differential expression within a unified model. However, the original implementation suffered from prohibitive memory use and runtime, preventing its application to modern atlas-scale datasets. RESULTS: We present GEDI 2.0, a complete high-performance reimplementation featuring a standalone C++ computational core with pre-allocated workspaces, strict sparse-matrix preservation, optimized BLAS routines, and multi-threaded block-coordinate descent. Across extensive benchmarks spanning up to 500 000 cells and 10 000 features, GEDI 2.0 achieves 40%-63.6% mean reduction in peak memory, 2.98× mean single-threaded speedups, and up to 11.5× acceleration with parallel execution, while maintaining full numerical equivalence to the original method. These improvements enable GEDI 2.0 to analyze million-cell datasets, a scale not achievable with the legacy implementation. GEDI 2.0 provides R and Python interfaces and seamless interoperability with common single-cell workflows. AVAILABILITY AND IMPLEMENTATION: Source code, documentation, reproducible codebase, and tutorials are available at https://github.com/csglab/gedi2.

Single-Cell Analysis↗
PubMed2001

Cortical change in Alzheimer's disease detected with a disease-specific population-based brain atlas.

We report the first detailed population-based maps of cortical gray matter loss in Alzheimer's disease (AD), revealing prominent features of early structural change. New computational approaches were used to: (i) distinguish variations in gray matter distribution from variations in gyral patterns; (ii) encode these variations in a brain atlas (n = 46); (iii) create detailed maps localizing gray matter differences across groups. High resolution 3D magnetic resonance imaging (MRI) volumes were acquired from 26 subjects with mild to moderate AD (age 75.8+/-1.7 years, MMSE score 20.0+/-0.9) and 20 normal elderly controls (72.4+/-1.3 years) matched for age, sex, handedness and educational level. Image data were aligned into a standardized coordinate space specifically developed for an elderly population. Eighty-four anatomical models per brain, based on parametric surface meshes, were created for all 46 subjects. Structures modeled included: cortical surfaces, all major superficial and deep cortical sulci, callosal and hippocampal surfaces, 14 ventricular regions and 36 gyral boundaries. An elastic warping approach, driven by anatomical features, was then used to measure gyral pattern variations. Measures of gray matter distribution were made in corresponding regions of cortex across all 46 subjects. Statistical variations in cortical patterning, asymmetry, gray matter distribution and average gray matter loss were then encoded locally across the cortex. Maps of group differences were generated. Average maps revealed complex profiles of gray matter loss in disease. Greatest deficits (20-30% loss, P<0.001-0.0001) were mapped in the temporo-parietal cortices. The sensorimotor and occipital cortices were comparatively spared (0-5% loss, P>0.05). Gray matter loss was greater in the left hemisphere, with different patterns in the heteromodal and idiotypic cortex. Gyral pattern variability also differed in cortical regions appearing at different embryonic phases. 3D mapping revealed profiles of structural deficits consistent with the cognitive, metabolic and histological changes in early AD. These deficits can therefore be (i) charted in a living population and (ii) compared across individuals and groups, facilitating longitudinal, genetic and interventional studies of dementia.

Aged↗
PubMed2005

Motor control in basal ganglia circuits using fMRI and brain atlas approaches.

In this study, we examined how the motor, premotor and associative basal ganglia territories process movement parameters such as the complexity and the frequency of movement. Twelve right-handed volunteers were studied using EPI BOLD contrast (3 T) while performing audio-paced finger tapping tasks designed to differentiate basal ganglia territories. Tasks varied movement complexity (repetitive index tapping, simple sequence of finger movements and complex sequence of 10 moves) and frequency (from 0.5 to 3 Hz). Activation maps were coregistered onto a 3-D brain atlas derived from post-mortem brains. Three main patterns of activation were observed. In the posterior putamen and the sensorimotor cortex, signal increased with movement frequency but not with movement complexity. In premotor areas, the anterior putamen and the ventral posterolateral thalamus, signal increased regularly with increasing movement frequency and complexity. In rostral frontal areas, the caudate nucleus, the subthalamic nucleus and the ventral anterior/ventrolateral thalamus, signal increased mainly during the complex task and the high frequency task (3 Hz). These data show the different roles of motor, premotor and associative basal ganglia circuits in the processing of motor-related operations and suggest that activation can be precisely located within the entire circuitry of the basal ganglia.

Adolescent↗
PubMed2025

scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants.

Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into plant cellular diversity by enabling high-resolution analyses of gene expression at the single-cell level. However, the complexity of scRNA-seq data, including challenges in batch integration, cell type annotation, and gene regulatory network (GRN) inference, demands advanced computational approaches. To address these challenges, we developed scPlantLLM, a Transformer model trained on millions of plant single-cell data points. Using a sequential pretraining strategy incorporating masked language modeling and cell type annotation tasks, scPlantLLM generates robust and interpretable single-cell data embeddings. When applied to Arabidopsis thaliana datasets, scPlantLLM excels in clustering, cell type annotation, and batch integration, achieving an accuracy of up to 0.91 in zero-shot learning scenarios. Furthermore, the model demonstrates an ability to identify biologically meaningful GRNs and subtle cellular subtypes, showcasing its potential to advance plant biology research. Compared to traditional methods, scPlantLLM outperforms in key metrics such as adjusted rand index (ARI), normalized mutual information (NMI), and silhouette score (SIL), highlighting its superior clustering accuracy and biological relevance. scPlantLLM represents a foundation model for exploring plant single-cell expression atlases, offering unprecedented capabilities to resolve cellular heterogeneity and regulatory dynamics across diverse plant systems. The code used in this study is available at https://github.com/compbioNJU/scPlantLLM.

Single-Cell Analysis↗
PubMed2005

Atlas: a java-based tool for managing genotypes.

With the exponential increase in genotyping capability, it is fundamental to check data consistency and improve genotype management. Atlas is a Java-based application for managing genotypes that also provides a series of tools useful in traceability, parentage testing, and identification, as well as pedigree and marker visualization.

Computational Biology↗
PubMed2000

Atlas of genetics and cytogenetics in oncology and haematology, an interactive database.

The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer ) is a database devoted to chromosome abnormalities in cancer, cancer-prone diseases and genes involved in cancer. Information presented in each page is concise and updated. This database is made for and by: cytogeneticists, molecular biologists, clinicians in oncology and in haematology, and pathologists, who are encouraged to contribute.

Chromosome Aberrations↗
PubMed2026

A transcription factor regulatory atlas for activity inference and perturbation prediction.

Inferring transcription factor (TF) activity from transcriptomes and predicting transcriptome-wide responses to TF perturbations remain challenging, in part because available TF-mRNA resources often face a trade-off between precision and coverage and typically lack signed regulatory information. Here, we present TFActProfiler, a TF-mRNA resource and computational framework that learns signed, quantitative TF-mRNA regulatory coefficients by integrating heterogeneous prior evidence (ChIP-based, motif-based, and curated TF-mRNA annotations) with large-scale bulk and single-cell RNA-seq atlases. TFActProfiler contains 2&#x2009;606&#x2009;176 signed TF-mRNA interactions and improves TF activity inference in TF knockdown benchmarks relative to widely used regulon resources while retaining broad TF and target coverage. In addition, because the same learned regulatory coefficients can be used to model downstream transcriptional effects, TFActProfiler enables prediction of transcriptome-wide gene expression responses to TF knockdown without training on task-matched perturbation data. When perturbation datasets are available, TFActProfiler can be further refined to achieve performance comparable to state-of-the-art machine-learning baselines. By providing a direction-aware representation of TF-mRNA regulation for both activity inference and perturbation-response modeling, TFActProfiler supports systematic dissection of gene regulatory programs across diverse cellular contexts.

Transcription Factors↗
PubMed2003

CASTp: Computed Atlas of Surface Topography of proteins.

Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These include pockets located on protein surfaces and voids buried in the interior of proteins. The measurement includes the area and volume of pocket or void by solvent accessible surface model (Richards' surface) and by molecular surface model (Connolly's surface), all calculated analytically. CASTp can be used to study surface features and functional regions of proteins. CASTp includes a graphical user interface, flexible interactive visualization, as well as on-the-fly calculation for user uploaded structures. CASTp is updated daily and can be accessed at http://cast.engr.uic.edu.

Binding Sites↗
PubMed2004

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.

The Catalytic Site Atlas (CSA) provides catalytic residue annotation for enzymes in the Protein Data Bank. It is available online at http://www.ebi.ac.uk/thornton-srv/databases/CSA. The database consists of two types of annotated site: an original hand-annotated set containing information extracted from the primary literature, using defined criteria to assign catalytic residues, and an additional homologous set, containing annotations inferred by PSI-BLAST and sequence alignment to one of the original set. The CSA can be queried via Swiss-Prot identifier and EC number, as well as by PDB code. CSA Version 1.0 contains 177 original hand- annotated entries and 2608 homologous entries, and covers approximately 30% of all EC numbers found in PDB. The CSA will be updated on a monthly basis to include homologous sites found in new PDBs, and new hand-annotated enzymes as and when their annotation is completed.

Animals↗
PubMed1983

Atlas of computerized blood flow analysis in bone disease.

The role of computerized blood flow analysis in routine bone scanning is reviewed. Cases illustrating the technique include proven diagnoses of toxic synovitis, Legg-Perthes disease, arthritis, avascular necrosis of the hip, fractures, benign and malignant tumors, Paget's disease, cellulitis, osteomyelitis, and shin splints. Several examples also show the use of the technique in monitoring treatment. The use of quantitative data from the blood flow, bone uptake phase, and static images suggests specific diagnostic patterns for each of the diseases presented in this atlas. Thus, this technique enables increased accuracy in the interpretation of the radionuclide bone scan.

Adolescent↗
PubMed1985

Iofetamine HCl I-123 (Iodoamphetamine) brain SPECT atlas.

SPECT brain imaging using Iofetamine HC1 I-123 (IMP) has a great potential in the evaluation of various neurologic disorders. Transverse, coronal, and sagittal sectional IMP images obtained using a single head rotating gamma camera system are correlated with corresponding normal brain slices in this atlas.

Amphetamines↗
PubMed1985

Atlas of hepatic arterial perfusion scintigraphy.

Tc-99m MAA intra-arterial perfusion studies are necessary to determine blood flow distribution for hepatic arterial chemotherapy. In this mini-atlas, examples selected from over 900 cases to illustrate important points to aid in a better understanding and interpretation of these studies with particular emphasis on diagnostic and therapeutic interventions are presented.

Humans↗
PubMed1996

Atlas of iodocholesterol scintigraphy (NP-59) in Cushing's syndrome with CT and MR correlation.

An atlas of I-131 iodocholesterol scintigraphy, each with correlative CT or MRI illustrates the findings in 12 patients with biochemically proven Cushing's syndrome and ultimate surgical cure. Included are patients with both ACTH dependent and independent disease, as well as patients with postoperative functional adrenal remnants. Emphasis will be on the concordance or discordance of the anatomical and functional imaging modalities.

Adosterol↗
PubMed2000

Reproducibility and repeatability of 99Tcm-HMPAO rCBF SPET in normal subjects at rest using brain atlas matching.

The aim of this study was to assess regional cerebral blood flow (rCBF) in normal subjects at rest using 99Tcm-HMPAO single photon emission tomography (SPET). Analysis of reproducibility and repeatability was performed both before and after normalization of flow data. Six healthy volunteers were examined, three times each, according to a routine rCBF protocol. A computerized brain atlas was used to evaluate flow data in eight selected regions. The overall reproducibility of rCBF was evaluated from two scans performed at an average interval of 3 months. Repeatability was evaluated from two scans, 3 h apart and without re-injection of 99Tcm-HMPAO. For the normalized (relative) flow data, the reproducibility was +/- 1.3% and the repeatability +/- 2.2% (i.e. methodological errors dominate). For the non-normalized flow data, the corresponding values were +/- 14.8% and +/- 5.9%. rCBF SPET with 99Tcm-HMPAO is highly reproducible provided that the flow data are normalized. The variation in flow between individuals at one point in time and 3 months later was less than +/- 5% for all brain regions.

Adult↗