We review recent developments in brain mapping and computational anatomy that have greatly expanded our ability to analyze brain structure and function. The enormous diversity of brain maps and imaging methods has spurred the development of population-based digital brain atlases. These atlases store information on how the brain varies across age and gender, across time, in health and disease, and in large human populations. We describe how brain atlases, and the computational tools that align new datasets with them, facilitate comparison of brain data across experiments, laboratories, and from different imaging devices. The major methods are presented for the construction of probabilistic atlases, which store information on anatomic and functional variability in a population. Algorithms are reviewed that create composite brain maps and atlases based on multiple subjects. We show that group patterns of cortical organization, asymmetry, and disease-specific trends can be resolved that may not be apparent in individual brain maps. Finally, we describe the creation of four-dimensional (4D) maps that store information on the dynamics of brain change in development and disease. Digital atlases that correlate these maps show considerable promise in identifying general patterns of structural and functional variation in human populations, and how these features depend on demographic, genetic, cognitive, and clinical parameters. (+info)
Examining geographic patterns of mortality: the atlas of mortality in small areas in Spain (1987-1995).
BACKGROUND: Small-area mortality atlases have been demonstrated to be a useful tool for both showing general geographical patterns in mortality data and identifying specific high-risk locations. In Spain no study has so far systematically examined geographic patterns of small-area mortality for the main causes of death. This paper presents the main features, contents and potential uses of the Spanish Atlas of Mortality in small areas (1987-1995). METHODS: Population data for 2,218 small areas were drawn from the 1991 Census. Aggregated mortality data for 14 specific causes of death for the period 1987-1995 were obtained for each small area. Empirical Bayes-model-based estimates of age-adjusted relative risk were displayed in small-area maps for each cause/gender/age group (0-64 or 65 and over) combination using the same range of values (i.e. septiles) and colour schemes. RESULTS: The 'Spanish Atlas of Mortality' includes multiple choropleth (area-shaded) small-area maps and graphs to answer different questions about the data. The atlas is divided into three main sections. Section 1 includes the methods and comments on the main maps. Section 2 presents a two-page layout for each leading cause of death by gender including 1) a large map with relative risk estimates, 2) a map that indicates high- and low-risk small areas, 3) a graph with median and interquartile range of relative risk estimates for 17 large regions of Spain, and 4) relative-risk maps for two age groups. Section 3 provides specific information on the geographical units of analysis, statistical methods and other supplemental maps. CONCLUSION: The 'Spanish Atlas of Mortality' is a useful tool for examining geographical patterns of mortality risk and identifying specific high-risk areas. Mortality patterns displayed in the atlas may have important implications for research and social/health policy planning purposes. (+info)
Getting the most out of your practice--the Practice Health Atlas and business modelling opportunities.
BACKGROUND: The Practice Health Atlas (PHA) is a decision support tool for general practice, designed by the Adelaide Western Division of General Practice (AWDGP). OBJECTIVE: This article describes the features of the PHA and its potential role in enhancing health care. DISCUSSION: In developing the PHA, the AWDGP utilises a range of software tools and consults with a practice to understand its clinical data management approach. The PHA comprises three sections: epidemiology, business and clinical modelling systems, access to services. The objectives include developing a professional culture around quality health data and synthesis of aggregated de-identified general practice data at both practice and divisional level (and beyond) to assist with local health needs assessment, planning, and funding. Evaluation occurs through group feedback sessions and from the general practitioners and staff. It has demonstrated its potential to fulfill the objectives in outcome areas such as data quality and management, team based care, pro-active practice population health care, and business systems development, thereby contributing to improved patient health outcomes. (+info)
Assessment of image-based technology: impact of referral cutoff on accuracy and reliability of remote retinopathy of prematurity diagnosis.
Telemedicine has potential to improve the delivery, quality, and accessibility of ophthalmic care for infants with Retinopathy of Prematurity (ROP). Using a telemedicine screening strategy, three potential diagnostic cutoffs may be used to define disease that warrants ophthalmologic referral: presence of any ROP, presence of moderate ("type-2 prethreshold") ROP, or presence of severe ROP requiring treatment. This study examines the relationship between accuracy and reliability of diagnosis by three masked ophthalmologist graders at each of these diagnostic cutoffs. The sensitivity, specificity, inter-grader reliability, and intra-grader reliability showed significant variation depending on the diagnostic cutoff, with best results at cutoffs of type-2 prethreshold ROP or treatment-requiring ROP. Before the large-scale adoption of telemedicine for image-based screening of diseases such as ROP, standards defining clinically-relevant referral cutoffs must be established, and diagnostic accuracy and reliability at these cutoffs must be characterized. (+info)
Simulating deformations of MR brain images for validation of atlas-based segmentation and registration algorithms.
Simulated deformations and images can act as the gold standard for evaluating various template-based image segmentation and registration algorithms. Traditional deformable simulation methods, such as the use of analytic deformation fields or the displacement of landmarks followed by some form of interpolation, are often unable to construct rich (complex) and/or realistic deformations of anatomical organs. This paper presents new methods aiming to automatically simulate realistic inter- and intra-individual deformations. The paper first describes a statistical approach to capturing inter-individual variability of high-deformation fields from a number of examples (training samples). In this approach, Wavelet-Packet Transform (WPT) of the training deformations and their Jacobians, in conjunction with a Markov random field (MRF) spatial regularization, are used to capture both coarse and fine characteristics of the training deformations in a statistical fashion. Simulated deformations can then be constructed by randomly sampling the resultant statistical distribution in an unconstrained or a landmark-constrained fashion. The paper also describes a model for generating tissue atrophy or growth in order to simulate intra-individual brain deformations. Several sets of simulated deformation fields and respective images are generated, which can be used in the future for systematic and extensive validation studies of automated atlas-based segmentation and deformable registration methods. The code and simulated data are available through our Web site. (+info)
Investments in cancer genomics: who benefits and who decides.
The Cancer Genome Atlas--formerly the Human Cancer Genome Project--provides an opportunity for considering how social concerns about resource allocation are interrelated with practical decisions about specific research strategies--part of a continuing convergence between scientific and public evaluations of priorities for biomedical research funding. For example, the manner, order, and extent that The Cancer Genome Atlas selects tumor types and populations to be sampled will determine who benefits most from its findings. Those choices will be determined on the basis of both scientific and social values. By soliciting public involvement and conducting rigorous policy analysis in the design of large scientific projects such as The Cancer Genome Atlas, cancer researchers can help democratize the allocation of scientific resources and foster public confidence in biomedical research. (+info)
Prediction of highly expressed genes in microbes based on chromatin accessibility.
BACKGROUND: It is well known that gene expression is dependent on chromatin structure in eukaryotes and it is likely that chromatin can play a role in bacterial gene expression as well. Here, we use a nucleosomal position preference measure of anisotropic DNA flexibility to predict highly expressed genes in microbial genomes. We compare these predictions with those based on codon adaptation index (CAI) values, and also with experimental data for 6 different microbial genomes, with a particular interest in experimental data from Escherichia coli. Moreover, position preference is examined further in 328 sequenced microbial genomes. RESULTS: We find that absolute gene expression levels are correlated with the position preference in many microbial genomes. It is postulated that in these regions, the DNA may be more accessible to the transcriptional machinery. Moreover, ribosomal proteins and ribosomal RNA are encoded by DNA having significantly lower position preference values than other genes in fast-replicating microbes. CONCLUSION: This insight into DNA structure-dependent gene expression in microbes may be exploited for predicting the expression of non-translated genes such as non-coding RNAs that may not be predicted by any of the conventional codon usage bias approaches. (+info)
www.derm101.com: a growing online resource for learning dermatology and dermatopathology.
The internet is increasingly being used to distribute knowledge in medicine in novel and unconventional ways. In this article, we give a brief introduction into the website www.derm101.com, which was founded by A. B. Ackerman for the purpose of teaching dermatology and dermatopathology. A clinical atlas, online books such as the 3rd edition of his volume "Histologic diagnosis of inflammatory skin diseases", works on clues and differential diagnoses in dermatopathology, a resource on therapeutic strategies in dermatology, a video lecture library on controversial issues in dermatology, the quarterly online journal Dermatopathology: Practical and Conceptual and much more can be found on derm101.com. The site is enriched with new contents biweekly and offers several interactive teaching devices. Currently, www.derm101.com is the most comprehensive online library of dermatology resources. (+info)