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PubMed1993

A genetic linkage map of the chromosome 4 short arm.

We have generated an 18-interval contiguous genetic linkage map of human chromosome 4 spanning the entire short arm and proximal long arm. Fifty-seven polymorphisms, representing 42 loci, were analyzed in the Venezuelan reference pedigree. The markers included seven genes (ADRA2C, ALB, GABRB1, GC, HOX7, IDUA, QDPR), one pseudogene (RAF1P1), and 34 anonymous DNA loci. Four loci were represented by microsatellite polymorphisms and one (GC) was expressed as a protein polymorphism. The remainder were genotyped based on restriction fragment length polymorphism. The sex-averaged map covered 123 cM. Significant differences in sex-specific rates of recombination were observed only in the pericentromeric and proximal long arm regions, but these contributed to different overall map lengths of 115 cM in males and 138 cM in females. This map provides 19 reference points along chromosome 4 that will be particularly useful in anchoring and seeding physical mapping studies and in aiding in disease studies.

Base Sequence↗

PubMed2001

Representation of the visual field in the lateral intraparietal area of macaque monkeys: a quantitative receptive field analysis.

The representation of the visual field in the primate lateral intraparietal area (LIP) was examined, using a rapid, computer-driven receptive field (RF) mapping procedure. RF characteristics of single LIP neurons could thus be measured repeatedly under different behavioral conditions. Here we report data obtained using a standard ocular fixation task during which the animals were required to monitor small changes in color of the fixated target. In a first step, statistical analyses were conducted in order to establish the experimental limits of the mapping procedure on 171 LIP neurons recorded from three hemispheres of two macaque monkeys. The characteristics of the receptive fields of LIP neurons were analyzed at the single cell and at the population level. Although for many neurons the assumption of a simple two-dimensional gaussian profile with a central area of maximal excitability at the center and progressively decreasing response strength at the periphery can represent relatively accurately the spatial structure of the RF, about 19% of the cells had a markedly asymmetrical shape. At the population level, we observed, in agreement with prior studies, a systematic relation between RF size and eccentricity. However, we also found a more accentuated overrepresentation of the central visual field than had been previously reported and no marked differences between the upper and lower visual representation of space. This observation correlates with an extension of the definition of LIP from the posterior third of the lateral intraparietal sulcus to most of the middle and posterior thirds. Detailed histological analyses of the recorded hemispheres suggest that there exists, in this newly defined unitary functional cortical area, a coarse but systematic topographical organization in area LIP that supports the distinction between its dorsal and ventral regions, LIPd and LIPv, respectively. Paralleling the physiological data, the central visual field is mostly represented in the middle dorsal region and the visual periphery more ventral and posterior. An anteroposterior gradient from the lower to the upper visual field representations can also be identified. In conclusion, this study provides the basis for a reliable mapping method in awake monkeys and a reference for the organization of the properties of the visual space representation in an area LIP extended with respect to the previously described LIP and showing a relative emphasis of central visual field.

Animals↗

PubMed2003

Linkage map of Cucumis melo including phenotypic traits and sequence-characterized genes.

A new linkage map of Cucumis melo, derived from the F2 progeny of a cross between PI 414723 and C. melo 'TopMark' is presented. The map spans a total of 1421 cM and includes 179 points consisting of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSRs), simple sequence repeats (SSRs), and restriction fragment length polymorphism (RFLP) markers. The map also includes an aphid resistance trait (Vat) and the sex type gene, andromonoecious (a), the two of which are important in resistance breeding and the control of hybrid seed production, as well as a seed-color gene, Wt-2. Most RFLPs represent sequence-characterized cDNA probes from C. melo and Cucumis sativus. These include resistance gene homologues and genes involved in various aspects of plant development and metabolism. A sub-set of our SSR and RFLP markers were also mapped, as part of this study, on additional mapping populations that were published for this species. This provides important reference points ("anchors"), enabling us to identify several linkage groups with respect to other melon maps.

Chromosome Mapping↗

PubMed2005

[Novel splice-site mutation in the pre-mRNA splicing gene PRPF31 in a Chinese family with autosomal dominant retinitis pigmentosa].

OBJECTIVE: To identify mutations in a four-generation Chinese family with retinitis pigmentosa and to investigate its clinical phenotype. METHODS: Ophthalmic and electrophysiological examinations of patients with RP were performed. A genome-wide scan and linkage analysis were conducted in this family. Direct genomic sequencing was used to evaluate the candidate gene. A restriction assay was used to confirm the mutation status in this family, and to exclude it as a polymorphism in a reference population. RESULTS: The mutation gene was mapped close to RP11 in chromosomal region 19q13.4 by linkage analysis. A novel single heterozygous base substitution (G > C) was detected at the beginning of intron 8 in the PRPF31 gene whereby the consensus GT dinucleotide of the intron 8 splice donor site was changed to CT. The mutation was co-segregated completely with the disease phenotype, but was absent in the unaffected relatives and in 100 reference subjects, thus supporting its pathogenic nature in this family. The clinical findings of RP patients were consistent with a relatively severe and diffuse type of RP. CONCLUSION: A novel splice site mutation (IVS8 + 1G > C) in the PRPF31 gene caused retinitis pigmentosa in the four-generation Chinese RP family studied.

Asian People↗

PubMed2000

Ruggedness study of HPLC peptide mapping for the identity of a drug compound: a chemometrics approach.

A statistically more reliable approach than the traditional visual inspection of peptide maps to identify a drug compound is to generate a set of reference standards from a designed experiment that incorporates many possible factors that affect variation of peptide mapping. In fact, the experiment can be done for a ruggedness study as part of a high-performance liquid chromatography (HPLC) method validation. Once the ruggedness is proved with the study, those articles in the experiment may form a set of reference standards, and future articles can be compared to the set later to prove identity. A quantitative analysis of the ruggedness study can be done using a chemometrics approach, principal component analysis (PCA). The analysis is used to reduce the many channels of peptide maps to a few manageable dimensions. The scores projected onto the reduced dimensions are used to test factor effects of the ruggedness study. As a by-product, the analysis provides visual inspection of the set of articles in the experiment for any outliers and anomalies.

Antibodies, Monoclonal↗

PubMed1997

High-resolution recombinational map of mouse chromosome 16.

Five intersubspecific backcrosses and an intercross were used to establish a sex-averaged recombinational map spanning 56 cM across most of mouse Chromosome 16 (Chr 16). A total of 123 markers were ordered using an interval mapping approach to identify 425 recombination sites in a collection of 1154 meioses from 1155 progeny generated in the six crosses. The markers include the 10 "classic" Chr 16 reference markers, 26 additional genes or transcripts including two phenotypic markers (Pit1dw and Kcnj6wv), and 87 simple sequence length polymorphisms (SSLPs). One set of monozygotic twins was detected among the 304 meioses mapped to highest resolution. The reference markers and SSLPs allow the map to be well integrated with existing maps of Chr 16. The average distance between crossover sites is less than 500 kb for most chromosomes, making this collection of recombinant chromosomes useful as a binning and ordering resource for YAC-based physical map assembly on Chr 16.

Animals↗

PubMed1998

Application of Kohonen neural networks for the non-morphological distinction between glomerular and tubular renal disease.

BACKGROUND: A Kohonen topological map is an artificial intelligence system of the connectionist school (neural networks). The map learns the typical features of the subclasses in the learning set by means of a shortest Euclidean distance algorithm, after which self-adaptation of the neurons occurs. By its ability of self-organization and generalization, a Kohonen map is useful for pattern recognition, and its application in the medical field as an aid for decision making seems promising. This study describes the use of a Kohonen topological mapping system in the classification of renal diseases as being glomerular or tubular on basis of clinical characteristics and laboratory results. METHODS: Forty-one parameters from 75 patients were retrospectively retrieved and used to train four different Kohonen maps of 10 x 10 neurons. For reference diagnostic classification, we referred to the results of the light-microscopic examination. The classification of the patients by the four different Kohonen networks was compared to the classification by a rule-based system and by three nephrologists. We also developed a 'hybrid' decision system that makes a classification on basis of the opinion of the four networks and that of the rule-based system. RESULTS: The results show that a Kohonen map is capable of classifying the patients as having glomerular or tubular disease with a higher sensitivity and predictive value than the nephrologists and the rule-based system, and that the best classification was performed by the hybrid system: sensitivity and predictive value for the diagnosis 'glomerular' respectively 100 and 88% for the network with the most adequate results, 90 and 83% for the nephrologists, 90 and 95% for the rule-based system, and 95 and 96% for the hybrid system; sensitivity and predictive value for the diagnosis 'tubular' respectively 50 and 100% for the neural networks, 31 and 45% for the nephrologists, 81 and 68% for the rule-based system, and 87 and 82% for the hybrid system). CONCLUSION: We conclude that a Kohonen map is capable of classifying the patients as having glomerular or tubular disease with a high sensitivity and predictive value. The rule-based system performs worse than the neural networks. The most adequate results were obtained with the hybrid system.

Adult↗

PubMed2006

Stepwise approach to substrate modification of ventricular tachycardia after myocardial infarction.

BACKGROUND: Recently, substrate mapping (SM) has been described to facilitate catheter ablation of stable and unstable ventricular tachycardia (VT) after myocardial infarction. However, SM is time consuming with potential disadvantages of multiple ablation lines such as impairment of ventricular function or proarrhythmia. The aim of the present study was to delineate a stepwise approach to SM to shorten procedure time and limit the possibility of complications. METHODS: SM was performed in 14 infarct survivors referred for VT ablation using an electroanatomical mapping system (CARTO) to define infarct regions. A new stepwise approach for SM was designed as follows. The initial ablation site was identified by pace- and entrainment mapping in case of stable VT and by pace mapping only in case of unstable VT. Based on the CARTO voltage mapping, linear ablation was done from this site to the center of the scar and perpendicular to the boundary of the scar or to the mitral annulus. Additional lines were performed only when VT remained inducible. A maximum of 3 ablation lines were created during one procedure. RESULTS: A total of 57 VTs (21 stable, 36 unstable) were induced during the procedures. VT was no longer inducible after the first linear ablation in 2 patients, after the second linear ablation in 6 patients and after the third linear ablation in 3 patients. Either VT or ventricular fibrillation was still inducible at the end of the procedure in 3 patients. Procedure time averaged (291 +/- 85) minutes, fluoroscopy time (10 +/- 7) minutes. VT recurred in 3 patients. Following a second procedure in 2 patients, there were no further VT recurrences. Overall, there was a significant reduction in VT episodes 3 months after [median: 0, interquartile ranges (IQR): 0 - 1] compared with 3 months before ablation (median: 25, IQR: 16 - 105, P < 0.01). CONCLUSIONS: This stepwise approach to SM is effective in facilitating ablation of stable and unstable VT. It reduces procedure and fluoroscopy time, and may help to improve the risk-benefit ratio of VT ablation.

Aged↗

PubMed2005

Parametric mapping of binding in human brain of D2 receptor ligands of different affinities.

UNLABELLED: (11)C-Raclopride has been widely used for PET studies of dopamine D(2/3) receptors in human brain. The long half-life of (18)F may impart advantages to the novel moderate-affinity benzamide (18)F-desmethoxyfallypride and its high-affinity congener (18)F-fallypride for competition studies and for detection of extrastriatal binding. However, the in vivo kinetics of these compounds and the quantification approaches for parametric mapping of their specific bindings have not been systematically compared. METHODS: Dynamic emission recordings of the 3 tracers were obtained in groups of healthy subjects. A conventional model, graphical analysis using metabolite-corrected arterial inputs, and models with reference tissue inputs were used to calculate voxelwise parametric maps of the equilibrium distribution volume (V(d)) and the binding potential (BP) of the 3 radioligands in brain. To test for bias, voxelwise kinetic results were compared with those obtained by volume-of-interest (VOI) analysis. RESULTS: The V(d) and BP estimates obtained by VOI analysis did not differ from the mean of voxelwise estimates in the same striatal volumes. In striatum, the mean (18)F-desmethoxyfallypride BP ranged from 1.9 to 2.5, whereas the mean (11)C-raclopride BP ranged from 3 to 4, depending on the method used for calculation. In contrast, the mean BP of (18)F-fallypride ranged from 16 to 27 in striatum and could also be readily quantified in the thalamus. CONCLUSION: Reference tissue methods for the voxelwise calculation of binding parameters are suitable for parametric mapping of the 3 dopamine D(2/3) receptor ligands.

Adult↗

PubMed1997

Detailed analysis of a 17q21 microdissection library by sequence bioinformatics and isolation of region-specific clones.

A region-specific microdissection library originating from human chromosome 17q21, was constructed using the MboI linker-adaptor microcloning technique. DNA sequencing of 241 microclones resulted in the identification of 74 novel coding sequences, paralogs of known genes, and known, but previously unmapped, genes or expressed sequence tags that were "virtually" mapped to chromosome 17q21. By pooling the microclones as multiplexed hybridization probes, and by virtue of their origin on 17q21, we were able to identify approximately 150 P1 clones from the human Reference Library Data Base P1 Library that potentially map to chromosome 17q21. Verification of the 17q21 location of 16 P1 clones was accomplished by PCR analysis with STS primer pairs to known 17q21 genes or by FISH. Our results demonstrate the substantial advantage of combining the sequence analysis of microclones with multiplex hybridization strategies for gene discovery and mapping specific gene rich regions of the genome.

Base Sequence↗

PubMed1990

In vivo induction of "focal" triggered ventricular arrhythmias and responses to overdrive pacing in the canine heart.

Delayed afterdepolarizations and triggered activity were evoked in focal areas of myocardium in vivo by local exposure of endocardium to ouabain by means of a catheter electrode system capable of recording monophasic action potentials (MAPs) and delivering ouabain to the recording site. MAPs were recorded from the septum and the posterior wall of the left ventricle with silver-silver chloride electrode catheters. Ouabain (10(-5) M) was infused through the MAP recording catheter onto the endocardial surface of the septum. After infusion of 10 micrograms/kg ouabain, the amplitude of MAPs recorded from the septum (the site of ouabain infusion) decreased from 37.4 +/- 11.8 to 32.0 +/- 10.1 mV (p less than 0.01), MAP duration at 50% repolarization shortened from 160 +/- 29 to 148 +/- 34 msec (p less than 0.01), and MAP duration at 90% repolarization shortened from 198 +/- 38 to 189 +/- 46 msec (p less than 0.01). MAPs recorded from the posterior wall (the reference site) were unchanged. Delayed afterdepolarizations were recorded at the site of ouabain infusion, but not at the reference site, when the heart was paced at cycle lengths of 200-600 msec. Additional infusion of ouabain induced sustained monomorphic ventricular tachycardia (VT) (mean cycle length, 369 +/- 12 msec) in all 15 dogs studied. The mean concentration of ouabain required to induce VT was 20.9 +/- 10.0 micrograms/kg. Paced QRS complexes when stimulated at the site of ouabain infusion had the same morphology as those of spontaneous VT. Local perfusion of verapamil, 0.015-0.034 mg/kg, through the MAP recording catheter onto the site of ouabain infusion completely eliminated VT and premature ventricular contractions. After perfusion of verapamil, delayed afterdepolarizations could no longer be induced by pacing. These observations indicate that induced VT originated from the site of ouabain infusion, and the presence of delayed afterdepolarizations before development of VT strongly suggests that the induced VT was due to triggered activity. Using this model, we examined the responses to rapid ventricular pacing of "focal" triggered VT. The first beat of the reinitiated tachycardia displayed the same morphology as the spontaneous VT. Local perfusion of verapamil, 0.015-0.034 mg/kg, through the MAP recording catheter onto the site of ouabain infusion completely eliminated VT and premature ventricular contractions. After perfusion of verapamil, delayed afterdepolarizations could no longer be induced by pacing. These observations indicate that induced VT originated from the site of ouabain infusion, and the presence of delayed afterdepolarizations before development of VT strongly suggests that the induced VT was due to triggered activity.(ABSTRACT TRUNCATED AT 400 WORDS)

Action Potentials↗

PubMed1979

Use of two-dimensional electrophoresis to identify and map new mouse genes.

Cytosol polypeptides from mouse liver have been examined using two-dimensional electrophoresis. About 250 spots were readily discernible. When cytosols from strains BALB/cBy and C57BL/6By were compared eight genetically determined differences were observed. Other strain pairs show comparable numbers of differences. These eight phenotypes were scored in seven recombinant inbred lines derived from the two parental strains, and their strain distribution patterns were compared with previously determined patterns for other genetic markers that differ between the two progenitor strains. Using this information, tentative chromosomes assignments for the genes controlling five of the variant phenotypes have been made, and two of the assignments have been confirmed using congenic resistant strains. These eight genes will be useful reference markers in future crosses designed to map new genes.

Animals↗

PubMed1995

Comparison of elevation, curvature, and power descriptors for corneal topographic mapping.

Corneal topography systems sample thousands of surface points and from these data different descriptors are derived to create maps of the cornea. Without visualizing and comparing the maps, it is difficult to appreciate the implications of each descriptor for mapping. We created and compared several maps of an ellipsotoric cornea based on the following surface descriptors: relative elevation, dioptric curvature, and refractive power. Each map presented a different picture of the same cornea. Only elevation maps show true topography but must be calculated relative to an appropriate reference surface to reveal important features. Axial and to a greater degree instantaneous curvature maps bring out optically significant shape asymmetries but misrepresent refractive power away from the apex. Ray tracing maps display optical properties that are not apparent from the elevation or curvature maps, including spherical aberration. Oblique astigmatism can be described using a pair of maps for the sagittal and tangential powers at each surface point. A knowledge of these principles is necessary to interpret color maps of the corneal surface correctly.

Cornea↗

PubMed2005

[Regional modulation of primary motor cortex after peripheral nerve injury: a functional magnetic resonance imaging study].

OBJECTIVE: To map dynamic changes of primary motor cortex after total brachial plexus traction injury by using functional magnetic resonance imaging, and to explore underlying probable mechanisms. METHODS: Five patients with total traumatic root avulsions of the brachial plexus underwent varied kinds of nerve transfer to restore partially shoulder or elbow function. Four of them (cases 1, 3, 4, 5) accepted the first fMRI examination prior to surgery treatment, and four of them (cases 2, 3, 4, 5) accepted second or third or fourth fMRI follow-up re-examinations after surgery treatment. Maps of neuronal activation within the motor cortex were generated for both hands in each patient by using BOLD-fMRI and the cluster size and position were recorded. The motor tasks consisted of simple hand grasping of both hands respectively. Patients with paralytic hand were asked to complete task under "virtual" condition. The cluster size and intensity as well as location of motor activation within the primary motor cortex of the affected hand generated were compared with those of unaffected hand generated as reference in single subject, and the resultant maps of follow-up re-examinations were also compared with those of the prior examinations. RESULTS: All patients' unaffected hand movement generated strong signal change within the contralateral primary motor cortex. In contrast, the clusters generated by affected hand showed very small and lower intensity than usual (2 cases) or could not be induced (2 case) in the first examination that prior to surgery treatment and seemed larger gradually in the following re-examination with time increasing. CONCLUSION: Peripheral nerve injury can produced significant changes in the motor cortex of human brain. fMRI is a valuable tool to evaluate neural plasticity in motor cortex after peripheral nerve injury.

Adolescent↗

PubMed2025

CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov-Arnold network.

MOTIVATION: The mapping from codon to amino acid is surjective due to codon degeneracy, suggesting that codon space might harbor higher information content. Embeddings from the codon language model have recently demonstrated success in various protein downstream tasks. However, predictive models for residue-level tasks such as phosphorylation sites, arguably the most studied Post-Translational Modification (PTM), and PTM sites prediction in general, have predominantly relied on representations in amino acid space. RESULTS: We introduce a novel approach for predicting phosphorylation sites by utilizing codon-level information through embeddings from the codon adaptation language model (CaLM), trained on protein-coding DNA sequences. Protein sequences are first reverse-translated into reliable coding sequences by mapping UniProt sequences to their corresponding NCBI reference sequences and extracting the exact coding sequences from their GenBank format using a dynamic programming-based global pairwise alignment. The resulting coding sequences are encoded using the CaLM encoder to generate codon-aware embeddings, which are subsequently integrated with amino acid-aware embeddings obtained from a protein language model, through an early fusion strategy. Next, a window-level representation of the site of interest, retaining the full sequence context, is constructed from the fused embeddings. A ConvBiGRU network extracts feature maps that capture spatiotemporal correlations between proximal residues within the window. This is followed by a prediction head based on a Kolmogorov-Arnold network (KAN) using the derivative of gaussian wavelet transform to generate the inference for the site. The overall model, dubbed CaLMPhosKAN, performs better than the existing approaches across multiple datasets. AVAILABILITY AND IMPLEMENTATION: CaLMPhosKAN is publicly available at https://github.com/KCLabMTU/CaLMPhosKAN.

Codon↗

PubMed1990

Chiasma-based genetic maps of chromosome 21.

The available cytogenetic data on meiotic chiasmata have been used to construct sex-specific genetic maps, showing the genetic distances and recombination fractions along the length of 21q. The male maps are based on direct observations of spermatocytes, while the female maps are derivations related to the increased chromosome length in oocytes. The male chiasma data have also been used as a frame of reference for ordering and positioning loci on the physical map with D21S110 as a fixed point.

Chromosome Mapping↗

PubMed1986

Introduction to recombinant DNA.

This paper describes the current state of knowledge of methods for analysing gene structure and localization. Illustrations are given of the preparation of complementary DNA libraries and their screening by positive-negative selection, the use of synthetic oligodeoxynucleotides and the use of antibodies. Analysis of the EGF precursor is used as an example to show its close relationship to plasma membrane receptor and its homology with the LDL receptor. Analysis of cloned genome DNA by use of bacteriophage lambda or cosmids gives useful information about gene regulation and evolution. Mutations by frame shift, point or missence mutations are discussed with reference to the LDL receptor and the apolipoproteins. The techniques of gene mapping by rat-human cell hybridization and hybridization in situ are illustrated, again with reference to genes coding for enzymes of cholesterol metabolism, the apolipoproteins and insulin-like growth factors. Finally the potential of in vitro mutagenesis and the injection of cloned DNA into the fertilized mouse ovum are discussed.

Animals↗

PubMed1998

A multiresolution restoration method for cardiac SPECT imaging.

In this study we present a multiresolution based method for restoring cardiac SPECT projections. Original projections were decomposed into a set of sub-band frequency images by using analyzing functions localized in both the space and frequency domain. This representation allows a simple denoising and restoration procedure by discarding high-frequency channels and performing inversion only in low frequencies. The method was evaluated in bull's eye reconstructions of a realistic cardiac chest phantom with a custom-made liver insert and 99mTc liver-to-heart activity ratios (LHAR) of 0:1, 1.5:1, 2.5:1, and 3.5:1. The cardiac phantom in free air was used as the reference standard. Reconstructions were performed by filtered backprojection using (1) no correction; (2) restoration without attenuation correction; (3) attenuation correction without restoration; and (4) restoration and attenuation correction. The attenuation correction was carried out with the Chang's method for one iteration. Results were compared with those obtained using an optimized prereconstruction Metz filter. Quantitative analysis was performed by calculating the normalized chi-square measure and mean +/- s.d. of bull's eye counts. In reconstructions with high liver activity (LHAR > 2), attenuation correction without restoration severely distorted the polar maps due to the spill-over of liver activity into the inferior myocardial wall. Both restoration methods when combined with an attenuation correction compensated this artifact and yielded uniform polar maps similar to that of the standard reference. There was no visual or quantitative difference between the performance of Metz filtering and multiresolution restoration. However, the main advantage of the multiresolution method is that it states a more concise and straightforward approach to the restoration problem. Multiresolution based methods does not require information about the object image or optimization processes, such as in conventional nuclear medicine restoration filters. In addition, the method is easy to implement using DFT techniques and potentially can be extended to noniterative spatially shift-invariant restorations in SPECT.

Biophysical Phenomena↗