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PubMed1994

Subregional mapping of the human lymphocyte-specific protein tyrosine kinase gene (LCK) to 1p35-->p34.3 and its position relative to the 1p marker D1S57.

The LCK gene encodes a lymphocyte-specific member of the Src family of protein tyrosine kinases. This gene was previously assigned to human chromosome region 1p35-->p32 by isotopic in situ hybridization. We report here its more refined localization to bands 1p35-->p34.3 by fluorescence in situ hybridization on R-banded metaphase chromosomes and its mapping relative to the reference marker pYNZ2 (D1S57).

Base Sequence↗
PubMedDate not supplied

Topographic mapping of brain electromagnetic signals: a review of current technology.

Topographic mapping of brain electromagnetic signals has become increasingly popular in recent years both as a clinical tool and as an area of research in its own right. The capabilities of existing computerized systems for displaying such maps and for performing localization of current sources in the brain have continued to expand. In this paper we review some of the methodological and technological issues concerning topographic mapping. These include issues of choice of interpolation algorithm, what to map, head geometry, EEG reference location, and scaling. We also discuss characteristics of clinical databases for patient comparison and the usefulness of quantitative EEG (which includes mapping) for the diagnosis of nervous system disorders. Finally, we compare five representative systems in terms of their topographic mapping capabilities. The overall conclusion is that future developments must make use of integrated data from other neuroimaging technologies such as MRI, PET, and SPECT, and determination of the normal limits of topographic parameters must be more carefully examined.

Brain Mapping↗
PubMed1988

Clinical utility of topographic EEG brain mapping.

Topographic EEG brain mapping was performed on 100 patients referred for both EEG and neuroimaging procedures. Topographic maps were abnormal in 78% of patients with stroke, 50% with head trauma and 100% of those with space occupying lesions (tumor, abscess or intracerebral hematoma). Of the patients with abnormal EEG maps 30% had either sole or better localization with mapping than routine EEG or neuroimaging procedures. In no cases were there false localizing abnormalities by EEG mapping. Topographic mapping appears to provide better detection of low amplitude slow activity not easily discernible by routine EEG. It also provides faithful correspondence with localization of many lesions on neuroimaging procedures, and at times distinguishes abnormalities not immediately definable by CT/MRI. Topographic EEG mapping is a valuable adjunct to routine EEG.

Adolescent↗
PubMed1994

A genetic and physical map of bovine chromosome 11.

A genetic map of bovine Chromosome (Chr) 11 (BTA11, synteny group U16) has been constructed from 330 animals belonging to 21 families, which constitute the international bovine reference panel (IBRP). This map is based on 13 polymorphic microsatellite markers, two of which were chosen in previously published maps. Three markers have been isolated from cosmids. Two of the three cosmids have been physically localized by fluorescence in situ hybridization (FISH), to anchor the genetic map on the chromosome. In addition, a biallelic polymorphism in the beta-lactoglobulin gene (LGB) has been genetically positioned relative to the microsatellite markers. The most probable order of the markers is: cen-INRA044-BM716-INRA177-(TGLA327, INRA198, INRA131)-INRA111-INRABERN169-(INRA115, INRA032)-INRA108-INRABERN162-INRA195-LGB. The total linkage group spans 126 cM, which probably corresponds to most of the chromosome length. The average intermarker distance is about 10.5 cM, allowing the potential detection of a genetic linkage with any Economic Trait Loci (ETL) of this chromosome. Seven of these markers have been previously published by Vaiman and coworkers (1994), two will be published as part of a set of markers (Eggen et al. in preparation), two are described in this paper, and two (BM716, TGLA327) were chosen from the published maps of BTA11 in order to integrate our data with existing maps. All these markers were assigned to synteny group U16 by use of a previously characterized panel of hamster/bovine somatic hybrid cell lines (Guérin et al. 1994).(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

Topography of auditory evoked long-latency potentials in normal children, with particular reference to the N1 component.

Topographic maps of late auditory evoked potentials were obtained with the Brain Atlas III system in 34 healthy, normal hearing children aged 8-16 years. The stimulus was a 100 msec, 500 Hz tone burst, presented separately to the left and right ears, at 75 dB HL. The resulting auditory evoked potentials showed a prominent N1, after about 100 msec, and a topographic map with a corresponding fronto-lateral focus designated as the focus of N1 (FN1). Foci with varying positions and amplitudes were identified in 33 of 34 subjects after left ear stimulation and in 29 of 32 subjects after right ear stimulation. The topography showed a high degree of stability in most subjects, with the position of the negative "peak" of FN1 in front of the interaural line and with a dominance contralateral to the ear stimulated. There was a significant decrease in the latency of N1 with increasing age. FN1 tended to change position with age and some differences from adults were also observed. In conclusion, a distinct topographic pattern of the N1 component of the late auditory evoked potentials was seen in the majority of children. It remains to be established to what extent this method may be clinically useful for disclosing functional disturbances in the central auditory pathways.

Acoustic Stimulation↗
PubMed1993

A primary genetic linkage map of 14 polymorphic loci for the short arm of human chromosome 8.

A genetic linkage map of markers for the short arm of human chromosome 8 has been constructed with 14 polymorphic DNA markers on the basis of genotypes obtained in 40 CEPH reference families. This unbroken map spans 45 cM in males and 79 cM in females. The 14 markers include three genes, MSR, LPL, and NEFL, and one anonymous DNA segment that were previously assigned to chromosome 8. The other 10 marker had been isolated from a chromosome 8-specific cosmid library and physically localized to chromosomal bands by fluorescence in situ hybridization. The order of loci determined by genetic linkage was consistent with their physical locations. This map will facilitate efficient linkage studies of human genetic diseases that may be segregating on chromosome 8p and will provide anchor points for development of high-resolution maps for this chromosomal region.

Chromosome Mapping↗
PubMed1992

The mouse genome: an overview.

A genetic map with one molecularly marked locus per cM will be available for the mouse in the near future. A map of this density should provide molecular reference points that connect genetic and physical maps, identify sites to initiate positional cloning studies for the molecular characterization of mutant loci, and define homologous regions of mouse and human genomes.

Animals↗
PubMedDate not supplied

Mean arterial pressure readings: variations with positions and transducer level.

The purpose of this study was to examine the relationship between mean arterial pressure (MAP) readings, measured at two reference points, the right atrium (RA) and the catheter site (CS), and in two body positions, supine and semi-Fowler's. Four MAP readings were taken on 29 CCU patients, 17 males and 12 females, with ages ranging from 33 to 93 (mean = 57.8; SD = 14.3). MAPs were obtained in the semi-Fowler's position-RA reference point (mean = 82.6), semi-Fowler's-CS reference point (mean = 90.3), supine-RA reference point (means = 82.2), and supine-CS reference point (mean = 84.03). All r values for pairs of readings were greater than .90 (p less than .001); therefore the readings are extremely comparable. However, when the comparability of readings is taken into account with MANOVA, the Hotelling's T2 is 58.06; the associated F is 17.97 (df = 3,26) with p less than .001. Therefore, in stable patients, MAP readings are comparable, but use of RA as the reference point for either position is the most preferable. A patient would not have to be lowered to the supine position for each MAP reading. However, in patients who are not stable, the significant differences among MAPs must be considered. The same position and the RA is preferable for all MAPs on these patients.

Adult↗
PubMed1993

Chromosomal distribution of 320 genes from a brain cDNA library.

We have determined the chromosomal assignment of 320 brain expressed genes by studying the segregation of polymerase chain reaction (PCR) products in human rodent somatic cell hybrids and by genetically mapping polymorphic cDNAs using the CEPH (Centre d'Etude du Polymophisme Humaine) reference pedigrees and database. These mapped genes can function as markers on the physical map of the human genome, as well as serve as candidate disease gene loci. Distribution of these genes to the human chromosomes correlates well with the GC content of the chromosomes. However, the distribution of these genes does not correlate well with the cytogenetic length of each chromosome.

Animals↗
PubMed1993

New markers, D16FC1 and Tp12, differentiate between rat chromosomes 16 and 17.

Problems in differentiating rat chromosomes 16 and 17 cytogenetically can be resolved with unique probes mapped to these chromosomes. Using somatic cell hybridization and nonisotopic in situ hybridization, probes D16FC1 and Tp12 were localized to 16p16-->p15 and 17q12.1-->q12.2, respectively. The locations of these probes can serve as reference points to facilitate mapping of future probes to rat chromosomes 16 and 17.

Animals↗
PubMed1994

Genetic linkage analysis of the Ak1, Col5a1, Epb7.2, Fpgs, Grp78, Pbx3, and Notch1 genes in the region of mouse chromosome 2 homologous to human chromosome 9q.

The genes for adenylate kinase-1 (AK1), folyl polyglutamate synthetase (FPGS), the collagen pro alpha 1(V) chain (COL5A1), erythrocyte protein band 7.2b (EPB72), and a proto-oncogene homeobox (PBX3) all map to the distal portion of human chromosome 9q (HSA9q) but have not previously been mapped by linking analysis in the mouse. In this study, we have used two interspecific backcrosses to map the mouse homologues of each of these genes to mouse chromosome 2 (MMU2). The Ak1, Col5a1, Epb7.2, Fpgs, and Pbx3 genes were mapped with respect to the genes for Grp78, Rxra, Notch1 (the mouse homologue of TAN1), Spna2, Abl, and Hc (the mouse homologue of C5), all of which have previously been mapped by linkage analysis on MMU2 and have human homologues that map to HSA9q. Two of the reference loci for MMU2, D2Mit1 and Acra, were also mapped in the same cross to facilitate comparisons with existing maps. The consensus gene order deduced by combining data from both crosses is D2Mit1-(Dbh,Notch1)-(Col5a1,Rxra)-Spna2-Ab l-(Ak1,Fpgs)- (Grp78,Pbx3)-(Epb7.2,Hc,Gsn)-Acra. These loci therefore form part of the conserved synteny between HSA9q and MMU2.

Animals↗
PubMed1989

[EEG background activity in patients with dementia of the Alzheimer type--with special reference to analysis by t-statistic significance probability mapping (SPM) in Alzheimer's disease and senile dementia].

EEG power amplitude and power ratio data obtained from 15 (3 men and 12 women) patients with Alzheimer's disease (AD) and 8 (2 men and 6 women) with senile dementia of Alzheimer type (SDAT) were compared with similar data from 40 age- and sex-matched normal controls. Compared with the healthy controls, both patient groups demonstrated increased EEG background slowing, and it indicated more slower in AD than in SDAT. Moreover, both groups showed characteristic findings respectively on EEG topography and t-statistic significance probability mapping (SPM). The differences between AD and their controls indicated high slowing with reductions in alpha 2, beta 1 and beta 2 activity. The SPMs of power ratio in theta and alpha 2 bands showed most prominent significance in the right posterior-temporal region and delta and beta bands did in the frontal region. Severe AD indicated only frontal delta slowing compared to mild AD. The differences between SDAT and their controls indicated only mild slowing in delta and theta bands. The SPM of power amplitude showed occipital slowing, whereas the SPM of power ratio showed the slowing in the frontal region. Judging from both topographic findings, these were considered to denote diffuse slow tendency. In summary, these results presumed that in AD, cortical damages followed by EEG slowing with reductions of alpha 2 and beta bands originated rapidly and thereafter developed subcortical (non-specific area in thalamus) changes with frontal delta activity on SPM. On the other hand, in SDAT, diffuse cortico-subcortical damages with diffuse slowing on EEG topography were caused gradually.

Adult↗
PubMed1989

The importance of alignment in blind subjects' use of tactual maps.

An experiment was conducted to test for the presence of alignment effects (previously found in sighted map users) in blind and visually impaired subjects using tactual maps. The term 'alignment effects' refers to the fact that when points represented as further up on a map do not correspond to points forward from the user in the environment, errors in the directional judgments made by subjects are greatly increased. The results show that alignment effects do exist in blind and visually impaired map users. Blind subjects encoded maps using the 'up equals forward' rule, and demonstrated some similarity to sighted subjects in the types of errors made. There was also some indication of improved performance over repeated trials. Differences between blind and sighted subjects were also found and were tentatively attributed to visual experience with object transformations and/or representational variables. Subject background variables were also investigated and some relationships between background of the subject and performance were drawn.

Adult↗
PubMed1993

The positions of 12 simple sequence repeat markers relative to reference loci on mouse chromosome 16.

The genetic map positions of 12 simple sequence repeat (SSR) markers spanning mouse Chromosome (Chr) 16 were determined relative to reference markers on that chromosome. Interval mapping data were obtained with a panel of DNAs from two intersubspecific backcrosses. All but one of the markers were typed by us of nonradioactive polymerase chain reaction (PCR) products analyzed on agarose gels. The marker order was determined to be Prm-1, D16Mit9, Igl-1, D16Mit29, D16Mit1/D16Mit2, Smst, D16Mit4, D16Mit11, Gap43, D16Mit14, D16Mit30, D16Mit5, Pit-1, D16Mit27, D16H21S16 (formerly D21S16h), D16Mit19, App, D16Mit7, Sod-1. Two of these markers mapped to the known human Chr 21 (HSA21)/Chr 16 conserved linkage group. Nine additional SSR markers could not be typed because they were not polymorphic (four markers), did not amplify MOLD/Rk DNA (three markers), or failed to give PCR products under a range of conditions (two markers). A subset of the most robust SSRs provide a useful marker set for the analysis of previously unmapped crosses.

Animals↗
PubMed2026

nf-core/magmap: Map metatranscriptomes to large collections of genomes.

SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes. AVAILABILITY AND IMPLEMENTATION: The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

Software↗
PubMedDate not supplied

An evaluation of FASTMAP with emphasis on fine-mapping.

We present an evaluation of the FASTMAP method with special reference to the issue of fine-mapping, using both 'real-life' and constructed data, and demonstrate some of the shortcomings of the method. Since the advantages of FASTMAP in terms of savings in computer resources compared to LINK-MAP are enormous, further improvements of the FASTMAP method would be highly desirable.

Chromosome Mapping↗
PubMed1995

Genetic and physical mapping of five novel microsatellite markers on human Xp21.1-p11.22.

Five polymorphic CA-dinucleotide repeats, identified in cosmids from the short arm of the human X chromosome, have been characterized and localized to Xp21.1 (DXS572), Xp11.4 (DXS556, DXS574), and Xp11.22-p11.23 (DXS722, DXS573). Genetic mapping with respect to five reference markers that include the gene for CGD (CYBB in Xp21.1), complemented by physical mapping information, has indicated the order tel-DXS572-CYBB-DXS1110-DXS556-DXS574-D XS7-DXS426-DXS722-DXS573-DXS255-cen.

Animals↗