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PubMed2003

Towards a formalization of disease-specific ontologies for neuroinformatics.

We present issues arising when trying to formalize disease maps, i.e. ontologies to represent the terminological relationships among concepts necessary to construct a knowledge-base of neurological disorders. These disease maps are being created in the context of a large-scale data mediation system being created for the Biomedical Informatics Research Network (BIRN). The BIRN is a multi-university consortium collaborating to establish a large-scale data and computational grid around neuroimaging data, collected across multiple scales. Test bed projects within BIRN involve both animal and human studies of Alzheimer's disease, Parkinson's disease and schizophrenia. Incorporating both the static 'terminological' relationships and dynamic processes, disease maps are being created to encapsulate a comprehensive theory of a disease. Terms within the disease map can also be connected to the relevant terms within other ontologies (e.g. the Unified Medical Language System), in order to allow the disease map management system to derive relationships between a larger set of terms than what is contained within the disease map itself. In this paper, we use the basic structure of a disease map we are developing for Parkinson's disease to illustrate our initial formalization for disease maps.

Electronic Data Processing↗
PubMed2001

Multiple attractors and boundary crises in a tri-trophic food chain.

The asymptotic behaviour of a model of a tri-trophic food chain in the chemostat is analysed in detail. The Monod growth model is used for all trophic levels, yielding a non-linear dynamical system of four ordinary differential equations. Mass conservation makes it possible to reduce the dimension by 1 for the study of the asymptotic dynamic behaviour. The intersections of the orbits with a Poincaré plane, after the transient has died out, yield a two-dimensional Poincaré next-return map. When chaotic behaviour occurs, all image points of this next-return map appear to lie close to a single curve in the intersection plane. This motivated the study of a one-dimensional bi-modal, non-invertible map of which the graph resembles this curve. We will show that the bifurcation structure of the food chain model can be understood in terms of the local and global bifurcations of this one-dimensional map. Homoclinic and heteroclinic connecting orbits and their global bifurcations are discussed also by relating them to their counterparts for a two-dimensional map which is invertible like the next-return map. In the global bifurcations two homoclinic or two heteroclinic orbits collide and disappear. In the food chain model two attractors coexist; a stable limit cycle where the top-predator is absent and an interior attractor. In addition there is a saddle cycle. The stable manifold of this limit cycle forms the basin boundary of the interior attractor. We will show that this boundary has a complicated structure when there are heteroclinic orbits from a saddle equilibrium to this saddle limit cycle. A homoclinic bifurcation to a saddle limit cycle will be associated with a boundary crisis where the chaotic attractor disappears suddenly when a bifurcation parameter is varied. Thus, similar to a tangent local bifurcation for equilibria or limit cycles, this homoclinic global bifurcation marks a region in the parameter space where the top-predator goes extinct. The 'Paradox of Enrichment' says that increasing the concentration of nutrient input can cause destabilization of the otherwise stable interior equilibrium of a bi-trophic food chain. For a tri-trophic food chain enrichment of the environment can even lead to extinction of the highest trophic level.

Animals↗
PubMed2003

Umbilical diagnosis as a non-invasive visual diagnostic aide.

Using Bi-Digital O-Ring Test (Omura, Y. 1977-2002; BDORT), we have researched the abnormal shapes of the umbilicus and the surrounding areas of the umbilicus, and the relationship between diseased internal organs and abnormal shape and direction of the radial sulcus of the umbilicus for several years. In this report we have mapped the organ representation area of the umbilicus and its surrounding areas of a healthy person by using BDORT. Then the abnormal organs around the umbilicus of the patients with certain diseases were mapped by using BDORT. Also Oncogene C-fos Ab2 positive response network (specially relation between the radial sulcus and the disease) of the cancer response (Oncogene C-fos Ab2) positive person were examined all over the body. In many cases, the radial sulcus from the umbilicus and the organ representation area of abnormal organs at the umbilicus of diseased person mapped using BDORT were highly correlated. Abnormality observed in a specific organ with strong resonance by BDORT meridian network was connected to the umbilicus. Mapped chart of the organ representation area surrounding the umbilicus is clinically very useful for non-invasive visual umbilical diagnosis.

Acupuncture Therapy↗
PubMed2002

[A conjecture about Jingluo and suggestions on its research].

The Jingluo is a great hypothesis and theory of Chinese traditional medicine. The physical existence of Jingluo phenomena has been proved by many medical practices, but its real mechanism is still unknown. Here is a conjecture about Jingluo: "The essence of Jingluo is in CNS, the lines of Jingluo on soma is only actually a mapping of some strong connection networks in cortex or white matter of brain". Many new modalities of medical imaging like fMRI, PET, SPECT and Mapping MEG can do a good job on functional brain imaging. If we improve their spatial resolution and develop new methods to indicate brain activities, maybe we can unveil the secret of Jingluo.

Central Nervous System↗
PubMed1999

Evolutionarily conserved pathways of energetic connectivity in protein families.

For mapping energetic interactions in proteins, a technique was developed that uses evolutionary data for a protein family to measure statistical interactions between amino acid positions. For the PDZ domain family, this analysis predicted a set of energetically coupled positions for a binding site residue that includes unexpected long-range interactions. Mutational studies confirm these predictions, demonstrating that the statistical energy function is a good indicator of thermodynamic coupling in proteins. Sets of interacting residues form connected pathways through the protein fold that may be the basis for efficient energy conduction within proteins.

Amino Acid Sequence↗
PubMed2002

Hopping diffusion of two coupled particles in the random trap model.

We show that the hopping dynamics of two strongly connected particles can be mapped exactly to single particle dynamics. In this way we are able to calculate the exact asymptotic diffusion coefficient of two connected particles on a linear chain in the random trap model. In particular we calculate the diffusion coefficient for exponentially distributed site energies and show that there exists a critical temperature below which a subdiffusive behavior appears. It turns out that this critical temperature is twice higher than the critical temperature in the single particle case [S. Havlin, B. L. Trus, and G. H. Weiss, J. Phys. A: Math. Gen. 19, L817 (1986)].

Journal Article↗
PubMed2003

Advances in B-cell epitope analysis of autoantigens in connective tissue diseases.

The characterization of autoantibody specificities in rheumatic diseases is important in both diagnostic and basic research areas. Identification of the epitopes recognized by autoantibodies and their clinical and biological significance is not a trivial task. Epitopes may range in complexity from simple linear sequences of amino acids to complex quaternary structures. In addition to this structural complexity the frequency with which an autoantigen and its epitopes are recognized in a patient population may be useful in diagnosis, defining disease subgroups, and may offer information on disease prognosis. In this review recent advances in the epitope mapping of autoantigens in connective tissue diseases are discussed, with particular emphasis placed on the methodologies used to identify epitopes and the classification of the structural features of epitopes. To illustrate the identification of epitope structure, clinically relevant autoantigens, including CENP-A, PM/Scl-100, fibrillarin, filaggrin, Ro-52, and dsDNA, are discussed as examples of each type of epitope.

Amino Acid Sequence↗
PubMed2004

The HBP1 transcriptional repressor and the p38 MAP kinase: unlikely partners in G1 regulation and tumor suppression.

Mechanisms that inhibit cell cycle progression and establish growth arrest are fundamental to tumor suppression and to normal cell differentiation. A complete understanding of these mechanisms should provide new diagnostic and therapeutic targets for future clinical applications related to cancer-specific pathways. This review will focus on the HMG-box protein 1 (HBP1) transcriptional repressor and its roles in cell cycle progression and tumor suppression. The work of several labs now suggests a new pathway for inhibiting G1 progression with exciting possible implications for tumor suppression. Our recent work suggests that the two previously unassociated proteins-the HBP1 transcription factor and the p38 MAP kinase pathway-may now participate together in a G1 regulatory network. Several recent papers collectively highlight an unexpected role and connection of the p38 MAP kinase-signaling pathway in cell cycle control, senescence, and tumor suppression. Together, these initially divergent observations may provide clues into a new tumor suppressive network and spur further investigations that may contribute to new diagnostic and therapeutic targets for cancer.

Amino Acid Sequence↗
PubMed1983

Topographic organization of certain tectal afferent and efferent connections can develop normally in the absence of retinal input.

To test the hypothesis that the topographic organization of the connections of the optic tectum is determined during development by the "retinotopically" ordered input that it receives from the eye, we have mapped certain of the connections of the tectum in chicken embryos and chicks in which both eye rudiments were removed before the outgrowth of optic fibers. Because several of the connections of the tectum are normally organized retinotopically, we should expect, if this hypothesis were correct, that some or all of these connectional patterns would be significantly altered in such "eyeless" chickens. In fact, we have found that the connections formed between the optic tectum and two of the isthmic nuclei, with which it is reciprocally connected, show the same topographic organization in "eyeless" animals as in control chickens raised under the same conditions. This clearly indicates that the topographic organization of the chicken optic tectum is independently specified and is not contingent upon the input that it receives from the retina.

Afferent Pathways↗
PubMed1997

Assignment of the gene for human tetranectin (TNA) to chromosome 3p22-->p21.3 by somatic cell hybrid mapping.

Tetranectin is a plasminogen-binding protein that is induced during the mineralization phase of osteogenesis. By screening a human chromosome 3 somatic cell hybrid mapping panel, we have localized the human tetranectin gene (TNA) to 3p22-->p21.3, which is distinct from the loci of two human connective tissue disorders that map to the short arm of chromosome 3, MFS2 and LRS1.

Base Sequence↗
PubMed1999

High-resolution landmark framework for the sequence-ready mapping of Xq23-q26.1.

We have established a landmark framework map over 20-25 Mb of the long arm of the human X chromosome using yeast artificial chromosome (YAC) clones. The map has approximately one landmark per 45 kb of DNA and stretches from DXS7531 in proximal Xq23 to DXS895 in proximal Xq26, connecting to published framework maps on its proximal and distal sides. There are three gaps in the framework map resulting from the failure to obtain clone coverage from the YAC resources available. Estimates of the maximum sizes of these gaps have been obtained. The four YAC contigs have been positioned and oriented using somatic-cell hybrids and fluorescence in situ hybridization, and the largest is estimated to cover approximately 15 Mb of DNA. The framework map is being used to assemble a sequence-ready map in large-insert bacterial clones, as part of an international effort to complete the sequence of the X chromosome. PAC and BAC contigs currently cover 18 Mb of the region, and from these, 12 Mb of finished sequence is available.

Blotting, Southern↗
PubMed2005

Retinotectal mapping: new insights from molecular genetics.

The sensory and motor components of nervous systems are connected topographically and contain neural maps of the external world. The paradigm for such maps is the precisely ordered wiring of the output cells of the eye to their synaptic targets in the tectum of the midbrain. The retinotectal map is organized in development through the graded activity of Eph receptor tyrosine kinases and their ephrin ligands. These signaling proteins are arrayed in complementary expression gradients along the orthogonal axes of the retina and tectum, and provide both input and recipient cells with Cartesian coordinates that specify their location. Molecular genetic studies in the mouse indicate that these coordinates are interpreted in the context of neuronal competition for termination sites in the tectum. They further suggest that order in the retinotectal map is determined by ratiometric rather than absolute difference comparisons in Eph signaling along the temporal-nasal and dorsal-ventral axes of the eye.

Animals↗
PubMed2006

Neural connections of the posteromedial cortex in the macaque.

The posterior cingulate and the medial parietal cortices constitute an ensemble known as the posteromedial cortex (PMC), which consists of Brodmann areas 23, 29, 30, 31, and 7m. To understand the neural relationship of the PMC with the rest of the brain, we injected its component areas with four different anterograde and retrograde tracers in the cynomolgus monkey and found that all PMC areas are interconnected with each other and with the anterior cingulate, the mid-dorsolateral prefrontal, the lateral parietal cortices, and area TPO, as well as the thalamus, where projections from some of the PMC areas traverse in an uninterrupted bar-like manner, the dorsum of this structure from the posteriormost nuclei to its rostralmost tip. All PMC regions also receive projections from the claustrum and the basal forebrain and project to the caudate, the basis pontis, and the zona incerta. Moreover, the posterior cingulate areas are interconnected with the parahippocampal regions, whereas the medial parietal cortex projects only sparsely to the presubiculum. Although local interconnections and shared remote connections of all PMC components suggest a functional relationship among them, the distinct connections of each area with different neural structures suggests that distinct functional modules may be operating within the PMC. Our study provides a large-scale map of the PMC connections with the rest of the brain, which may serve as a useful tool for future studies of this cortical region and may contribute to elucidating its intriguing pattern of activity seen in recent functional imaging studies.

Animals↗
PubMed1997

Ornithine decarboxylase overexpression in mouse 10T1/2 fibroblasts: cellular transformation and invasion.

BACKGROUND: Ornithine decarboxylase (ODC) plays a pivotal role in the synthesis of polyamines, a group of chemical compounds that are essential for cell growth. Recent reports have shown that ODC overexpression may be involved in malignant transformation of immortalized NIH 3T3 cells. We have demonstrated that ODC-overproducing mouse breast cancer cells are more invasive in vitro than control cells. However, little information is available concerning the relationship between ODC overexpression, tumor invasion, and metastasis and the signal transduction pathways involved in ODC-induced transformation and invasion. PURPOSE: Our purpose was twofold: 1) to determine whether ODC overexpression is directly involved in tumor cell invasion and 2) to determine whether ODC overexpression induces mitogen-activated protein (MAP) kinase activities that are associated with cell growth and transformation. METHODS: We transfected C3H clone 8 mouse 10T1/2 fibroblasts with an expression vector that carries a complementary DNA encoding rat ODC. Neomycin-resistant cells that overproduced ODC (4-6.5 times the control levels) were isolated. The transformed phenotype of these cells was determined by assessing colony formation and anchorage-independent growth in soft agar. The invasiveness of the cells was studied by means of an invasion assay that used Matrigel-coated filters in Boyden chambers. The MAP kinase activity of the cells was assayed by an in-gel kinase assay, using myelin basic protein as the substrate. RESULTS: Overexpression of ODC induced not only cell transformation and anchorage-independent growth in soft agar but also invasiveness through a Matrigel-coated filter. The ODC-overproducing transfectants showed enhanced MAP kinase activity that paralleled the magnitude of cell invasiveness. CONCLUSIONS: ODC plays a pivotal role not only in cell transformation but also in cancer cell invasion. ODC overexpression enhanced MAP kinase activity. IMPLICATIONS: Our results demonstrate a connection between the polyamine/ODC and the MAP kinase signal transduction pathways and suggest that MAP kinase may play a pivotal role in ODC-induced cell transformation and invasion.

Animals↗
PubMed2005

Linkage mapping bovine EST-based SNP.

BACKGROUND: Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. RESULTS: Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM. Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. CONCLUSION: Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and refine assembly of bovine genome sequence. Even after the bovine genome is completely sequenced, the map will continue to be a useful tool to link observable phenotypes and animal genotypes to underlying genes and molecular mechanisms influencing economically important beef and dairy traits.

Alleles↗
PubMed1998

Distribution of response types across entire hemispheres of the mustached bat's auditory cortex.

AILDD1 AC'1 The responses of neurons in the mustached bat's auditory cortex are specialized to extract particular information from biosonar signals. For this study, we mapped response properties across entire hemispheres in several animals. These experiments enabled us to construct a standard map that aided in determining the connections among the areas, as described subsequently. The mapping also yielded quantitative data regarding the relative sizes of areas and the proportion of cortex devoted to different response types. We identified six response types that were distributed in 11 areas. Eight areas, comprising two-thirds of the auditory cortex, contained neurons sensitive to particular components in biosonar signals. Most were facilitated by combinations of frequency modulated and constant frequency biosonar signal components (FMs and CFs, respectively). There were three major types of combination-sensitive neurons: FM-FM, CF/CF, and FM-CF. Each type of combination sensitivity occurred in multiple areas. The largest proportion were FM-FM neurons (approximately 30% of all neurons in auditory cortex), followed by FM1-CF2 (approximately 23%) and CF/CF (approximately 11%). In the other three areas comprising approximately one-third of the auditory cortex, most neurons responded well to frequencies not contained in biosonar signals.

Animals↗
PubMed1987

Computational maps in the brain.

The nervous system performs computations to process information that is biologically important. Some of these computations occur in maps--arrays of neurons in which the tuning of neighboring neurons for a particular parameter value varies systematically. Computational maps transform the representation of information into a place-coded probability distribution that represents the computed values of parameters by sites of maximum relative activity. Numerous computational maps have been discovered, including visual maps of line orientation and direction of motion, auditory maps of amplitude spectrum and time interval, and motor maps of orienting movements. The construction of the auditory map of space is the most thoroughly understood: information about interaural delays and interaural intensity differences is processed in parallel by separate computational maps, and the outputs of these maps feed into a higher order processor that integrates sets of cues corresponding to sound source locations and creates a map of auditory space. Computational maps represent ranges of parameter values that are relevant to the animal, and may differentially magnify the representation of values that are of particular importance. The tuning of individual neurons for values of a mapped parameter is broad relative to the range of the map. Consequently, neurons throughout a large portion of a computational map are activated by any given stimulus, and precise information about the mapped parameter is coded by the locations of peak activity. There are a number of advantages of performing computations in maps. First, information is processed rapidly because the computations are preset and are executed in parallel. Second, maps simplify the schemes of connectivity required for processing and utilizing the information. Third, a common, mapped representation of the results of different kinds of computations allows the nervous system to employ a single strategy for reading the information. Finally, maps enable several classes of neuronal mechanisms to sharpen tuning in a manner not possible for information that is represented in a non-topographic code.

Animals↗
PubMed1998

[Development of an electrode for atrial epicardial mapping].

Procedure of a electrode for atrial epicardial mapping (template electrode) is introduced in this paper. It is easy to made, we can get sharp and clear waveforms and a constant baseline while mapping. If the electrode is connected with computer, it is able to be used for epicardial mapping of atrial arrhythmias, especially atrial fibrillation in real time.

Animals↗