SEARCH · PubMed Health

Results for “spatial sequencing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources

PubMed2006

Multiecho sequence for velocity imaging in inhomogeneous rf fields.

The unambiguous determination of velocities with spatial resolution in a multiecho PFG NMR sequence strongly depends on the homogeneity of the B1 field. This affects, in particular, the use of surface coils that bear considerable potential for on-line flow monitoring where a fast-imaging sequence can become vital. However, even with most rf coils dedicated for imaging applications, B1 inhomogeneities are sufficiently large to generate severe problems in performing velocity-imaging experiments. In this paper, the use of a combination of different phase cycles in Carr-Purcell sequences is discussed. The suggested phase cycling scheme tolerates large flip angle imperfections arising in inhomogeneous B1 fields, and thus allows acquisition of a maximum number of echoes within a pulse train. The performance of the velocity-imaging sequence is proven by using phantom samples developing known laminar flow patterns.

Journal Article↗

PubMed2006

Beyond spatial memory: the anterior thalamus and memory for the temporal order of a sequence of odor cues.

Influential recent proposals state that the anterior thalamic (AT) nuclei constitute key components of an "extended hippocampal system." This idea is, however, based on lesion studies that used spatial memory tasks and there has been no evidence that AT lesions cause deficits in any hippocampal-dependent nonspatial tasks. The present study investigated the role of the AT nuclei in nonspatial memory for a sequence of events based on the temporal order of a list of odors, because this task has recently been shown to depend on the integrity of the hippocampal formation. After preoperative training, rats with excitotoxic lesions of the AT nuclei showed a severe and selective postoperative impairment when required to remember the order of pseudorandom sequences of six odors. The rats with AT lesions were able instead to learn two new tasks that required recognition memory and the identification of the prior occurrence of events independent of their order. These results strongly matched those described after hippocampal lesions and provide the first unequivocal evidence of a detrimental effect of an AT lesion on a nonspatial hippocampal-dependent memory task.

Animals↗

PubMed2006

Brief communication: identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA.

We present a method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1-2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1-2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1-2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5a1a, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen.

Bone and Bones↗

PubMed1981

Enhanced graphic matrix analysis of nucleic acid and protein sequences.

The enhanced graphic matrix procedure analyzes nucleic acid and amino acid sequences for features of possible biological interest and reveals the spatial patterns of such features. When a sequence is compared to itself the technique shows regions of self-complementarity, direct repeats, and palindromic subsequences. Comparison of two different sequences, exemplified by immunoglobulin kappa light chain genes, by using colored graphic matrices showed domains of similarity, regions of divergence, and features explainable by transpositions. Analysis of mouse constant domain immunoglobulin sequences revealed self-complementary regions that can be used to fold the molecule into a structure consistent with electron microscopic observations. Computer translation of nucleic acid sequences into all possible amino acid sequences followed by graphic matrix analysis provides a way to detect the most likely protein encoding regions and can predict the correct reading frames in sequences in which splicing patterns are not defined. Application of this technique to regions of simian virus 40 and polyoma virus demonstrates the frames of translation and shows the agreement of sequences determined in separate laboratories with different virus isolates. The graphic matrix technique can also be used to assemble fragmentary sequences during determination, to display local variations in base composition, to detect distant evolutionary relationships, and to display intragenic variation in rates of evolution.

Amino Acid Sequence↗

PubMed2000

Body surface mapping of counterclockwise and clockwise typical atrial flutter: a comparative analysis with endocardial activation sequence mapping.

OBJECTIVES: This study was directed at developing spatial 62-lead electrocardiogram (ECG) criteria for classification of counterclockwise (CCW) and clockwise (CW) typical atrial flutter (Fl) in patients with and without structural heart disease. BACKGROUND: Electrocardiographic classification of CCW and CW typical atrial Fl is frequently hampered by inaccurate and inconclusive scalar waveform analysis of the 12-lead ECG. METHODS: Electrocardiogram signals from 62 torso sites and multisite endocardial recordings were obtained during CCW typical atrial Fl (12 patients), CW typical Fl (3 patients), both forms of typical Fl (4 patients) and CCW typical and atypical atrial Fl (1 patient). All the Fl wave episodes were divided into two or three successive time periods showing stable potential distributions from which integral maps were computed. RESULTS: The initial, intermediate and terminal CCW Fl wave map patterns coincided with: 1) caudocranial activation of the right atrial septum and proximal-to-distal coronary sinus activation, 2) craniocaudal activation of the right atrial free wall, and 3) activation of the lateral part of the subeustachian isthmus, respectively. The initial, intermediate and terminal CW Fl wave map patterns corresponded with : 1) craniocaudal right atrial septal activation, 2) activation of the subeustachian isthmus and proximal-to-distal coronary sinus activation, and 3) caudocranial right atrial free wall activation, respectively. A reference set of typical CCW and CW mean integral maps of the three successive Fl wave periods was computed after establishing a high degree of quantitative interpatient integral map pattern correspondence irrespective of the presence or absence of organic heart disease. CONCLUSIONS: The 62-lead ECG of CCW and CW typical atrial Fl in man is characterized by a stereotypical spatial voltage distribution that can be directly related to the underlying activation sequence and is highly specific to the direction of Fl wave rotation. The mean CCW and CW Fl wave integral maps present a unique reference set for improved clinical detection and classification of typical atrial Fl.

Aged↗

PubMed2002

Experimental and computational studies of determinants of membrane-protein folding.

Recent experiments and analysis have demonstrated the important roles of hydrogen bonding and polar-polar interactions in driving transmembrane helix-helix association. Further details of the energetics of helix-helix association and interhelical packing geometry are being mapped out. Many sequence motifs and a few spatial motifs promoting helical associations have also been identified.

Amino Acid Motifs↗

PubMed2006

High-resolution 3D MR spectroscopic imaging of the prostate at 3 T with the MLEV-PRESS sequence.

A 3 T MLEV-point-resolved spectroscopy (PRESS) sequence employing optimized spectral-spatial and very selective outer-voxel suppression pulses was tested in 25 prostate cancer patients. At an echo time of 85 ms, the MLEV-PRESS sequence resulted in maximally upright inner resonances and minimal outer resonances of the citrate doublet of doublets. Magnetic resonance spectroscopic imaging (MRSI) exams performed at both 3 and 1.5 T for 10 patients demonstrated a 2.08+/-0.36-fold increase in signal-to-noise ratio (SNR) at 3 T as compared with 1.5 T for the center citrate resonances. This permitted the acquisition of MRSI data with a nominal spatial resolution of 0.16 cm3 at 3 T with similar SNR as the 0.34-cm3 data acquired at 1.5 T. Due to the twofold increase in spectral resolution at 3 T and the improved magnetic field homogeneity provided by susceptibility-matched endorectal coils, the choline resonance was better resolved from polyamine and creatine resonances as compared with 1.5 T spectra. In prostate cancer patients, the elevation of choline and the reduction of polyamines were more clearly observed at 3 T, as compared with 1.5 T MRSI. The increased SNR and corresponding spatial resolution obtainable at 3 T reduced partial volume effects and allowed improved detection of the presence and extent of abnormal metabolite levels in prostate cancer patients, as compared with 1.5 T MRSI.

Aged↗

PubMed2006

[Imaging of cartilage].

The motivation for cartilage repair is the preservation of adequate joint motion. Repairing joint surface congruity and providing balanced load bearing are crucial for this. MRI can contribute to this goal by describing number, depth, size, and distribution of cartilage lesions throughout the different joint compartments. Essential to such a contribution are adequate spatial resolution at a reasonable SNR together with good contrast between both cartilage and the subchondral bone as well as the joint space. For TSE sequences, this is achieved using TEs between 30 and 50 ms. Diagnostic accuracy is optimal when a lesion is depicted in more than one plane. Short TE, high bandwidth, and the appropriate orientation of the frequency encoding direction contribute to minimizing metal artifacts. Besides internal alterations of the cartilage's matrix, moderately T2-weighted TSE sequences sensitively depict bone marrow edema such as signal alterations and joint effusion, both contributing to highlight even subtle cartilage lesions. T1-weighted FS/WE 3D GE sequences profit from their high spatial resolution to appreciate gradual erosion of the cartilage. In OD the interface to the surrounding bone, the integrity of the overlying cartilage, and associated cysts are used to determine stability. The presence of two or more findings increases diagnostic accuracy. Prognosis is associated with the size of the affected area.

Cartilage↗

PubMed1987

Temporal and spatial characteristics in repetitive movement.

The question addressed is whether temporal or spatial characteristics of a movement sequence are represented in a motor program. Subjects executed one to five straight-line strokes as fast as possible on a digitizing tablet. The duration and length of each stroke were computed and intercorrelated. Nineteen out of 20 possible correlations were significant for length per stroke data while only one of the 20 correlations was significant for duration. Further, performance data on the five stroke patterns were sorted to examine whether the first stroke determined the overall temporal/spatial pattern of the subsequent strokes executed. It was found that only sorting by length of the first stroke produced different subsets of movement patterns. These results are argued to be in support of the hypothesis that the spatial microstructure is controlled in a prepared movement sequence.

Female↗

PubMed2002

[2D-SPLASH spectroscopy to determine the fat/water ratio in the muscle of the rotator cuff].

AIM: The degree of fatty infiltration of the rotator cuff is an important factor for the prognosis of an operative reconstruction afterrotator cuff tear. The aim of this work was to develop a method using a clinical MR scanner that allows the quantification of the fat/water ratio with the necessary spatial resolution. METHOD: A SPLASH sequence consisting of 19 complex 2D-FLASH images was implemented on a clinical 1.5 T MR scanner. The echo time was gradually increased from 5.0 ms to 50.0 ms. A spatial in plane resolution of 1.17 mm, a spectral resolution of 0.33 ppm and a spectral width of 6.25 ppm were achieved in a total acquisition time of about 3 min. The quantitative evaluation of the spectra in arbitrarily shaped regions of interest (ROIs) was obtained using a home-built reconstruction program and the time domain fit program AMARES. RESULTS: Phantom studies show a linear relation of the concentration determined by SPLASH spectroscopy (r = 0.997). Because of the high spatial resolution and the possibility to evaluate arbitrarily shaped ROIs, the determination of the fat/water ratio in single muscles in the shoulder has been possible. CONCLUSIONS: By the use of the 2D-SPLASH sequence the degree of fatty infiltration in the rotator cuff can now be determined quantitatively for the first time.

Adipose Tissue↗

PubMed2026

ARCADIA reveals spatially dependent transcriptional programs through integration of scRNA-seq and spatial proteomics.

MOTIVATION: Cellular states are strongly influenced by spatial context, but single-cell RNA sequencing (scRNA-seq) loses information about local tissue organization, while spatial proteomic assays capture limited marker panels that constrain transcriptomic inference. Integrating these modalities can elucidate how spatial niches shape transcriptional programs, yet existing approaches depend on either feature-level correspondence such as gene-protein linkage or cell-level barcode pairing, which is often unavailable. RESULTS: We present ARCADIA (ARchetype-based Clustering and Alignment with Dual Integrative Autoencoders), a generative framework for cross-modal integration that operates without cell barcode pairing and does not assume direct feature-to-feature correspondence. ARCADIA identifies modality-specific archetypes, that is, convex combinations of cells representing extreme phenotypic states, and aligns these anchors across modalities by minimizing the discrepancy between their cell-type composition profiles. The aligned archetypes define a shared coordinate system that anchors dual variational autoencoders (VAEs) trained with cross-modal geometric regularization, preserving archetype structure and spatial neighborhood information while enabling bidirectional translation between modalities. On semi-synthetic CITE-seq data, ARCADIA outperforms existing weak-linkage methods. Applied to independent human tonsil scRNA-seq and CODEX data, ARCADIA reconstructs known tissue architecture and reveals spatially dependent transcriptional programs linking B-cell maturation and T-cell activation or exhaustion to microenvironmental niches. AVAILABILITY AND IMPLEMENTATION: Source code is accessible at https://github.com/azizilab/ARCADIA_public. Reproducibility scripts and data are available at https://github.com/azizilab/arcadia_reproducibility.

Proteomics↗

PubMedDate not supplied

T2-weighted MR imaging of focal hepatic lesions: comparison of various RARE and fat-suppressed spin-echo sequences.

The authors prospectively compared four T2-weighted magnetic resonance (MR) sequences, including high-resolution 512 x 512 (matrix size) RARE (rapid acquisition with relaxation enhancement), 256 x 256 RARE, 128 x 256 breath-hold RARE, and 192 x 256 fat-suppressed spin-echo (T2FS) sequences, in the evaluation of 16 patients with focal hepatic masses. MR images were evaluated by quantitative lesion-liver signal difference-to-noise ratios (SDNRs) and subjective evaluation of image artifact and image quality. No significant differences were observed between RARE sequences in SDNR values. The T2FS sequence had a significantly higher SDNR than the 512 x 512 RARE sequence (24.6 +/- 15.0 vs 14.5 +/- 9.7) (P = .008). Image quality was rated highest for the 512 x 512 RARE and T2FS sequences (P = .006). The inherent advantage of high spatial resolution suggests that the 512 x 512 RARE sequence may be of value in detecting hepatic lesions.

Artifacts↗

PubMed1995

[Equipment and transducer-independent 3D ultrasound in the maxillofacial area].

AIM: The use of a new 3D ultrasound system should reduce the drawbacks of former 3D workstations (long image generation time, limited use due to the need for special 3D transducers), so that it is now applicable in daily clinical routine. METHOD: An ultrasound 3D workstation was used based on a pentium PC platform, employing a magnetoelectronic position detection system for spatial reconstruction of conventional 2D B-scan image sequences. RESULTS: Better assessment of topographico-anatomical spatial relationships was achieved when presenting pathological findings, especially in assessing lymph nodes and salivary stones. Pathological processes in the maxillofacial area occurring during a period of five months were visualised. CONCLUSION: The method of 3D reconstruction of standard two-dimensional electronic scans, as presented here, is the first method of its kind enabling applicability in daily clinical routine thanks to rapid imaging. The images can be produced with any ultrasound unit or transducer. First clinical results in maxillofacial surgery clearly show improved diagnostic possibilities although there still room for an improvement of the image quality. The possibility of semi-automatic exact volumetry appears meaningful especially in the investigation of lymph nodes. Integration of colour duplex sonography will further enhance the diagnostic value of this method.

Humans↗

PubMed1996

DTEF-1, a novel member of the transcription enhancer factor-1 (TEF-1) multigene family.

M-CAT motifs mediate muscle-specific transcriptional activity via interaction with binding factors that are antigenically and biochemically related to vertebrate transcription enhancer factor-1 (TEF-1), a member of the TEA/ATTS domain family of transcription factors. M-CAT binding activities present in cardiac and skeletal muscle tissues cannot be fully accounted for by existing cloned isoforms of TEF-1. TEF-1-related cDNAs isolated from heart libraries indicate that at least three classes of TEF-1-related cDNAs are expressed in these and other tissues. One class are homologues of the human TEF-1 originally cloned from HeLa cells (Xiao, J. H., Davidson, I., Matthes, H., Garnier, J. M., and Chambon, P. (1991) Cell 65, 551-568). A second class represents homologues of the avian TEF-1-related gene previously isolated (Stewart, A. F., Larkin, S. B., Farrance, I. K., Mar, J. H., Hall, D. E., and Ordahl, C. P. (1994) J. Biol. Chem. 269, 3147-3150). The third class consists of a novel, divergent TEF-1 cDNA, named DTEF-1, and its preliminary characterization is described here. Two isoforms of DTEF-1 (DTEF-1A and DTEF-1B) were isolated as 1.9-kilobase pair clones with putative open reading frames of 433 and 432 amino acids whose differences are attributable to alternative splicing at the C terminus of the TEA DNA binding domain. Cardiac muscle contains high levels of DTEF-1 transcripts, but unexpectedly low levels are detected in skeletal muscle. DTEF-1 transcripts are present at intermediate levels in gizzard and lung, and at low levels in kidney. DTEF-1A is a sequence-specific M-CAT-binding factor. The distinct spatial pattern of expression, and unusual amino acid sequence in its DNA binding domain, may indicate a particular role for DTEF-1 in cell-specific gene regulation. Recent work also suggests that at least one more TEF-1-related gene exists in vertebrates. We propose a naming system for the four TEF-1 gene family members identified to date that preserves existing nomenclature and provides a means for extending that nomenclature as additional family members may be identified.

Amino Acid Sequence↗

PubMedDate not supplied

Morphometric analysis of sonographic images by spatial geometric modeling.

A methodology able to derive spatial geometric models from input sequences of sonographic slices is proposed. The developed modeling procedure can be utilized to perform computer-assisted anatomic 3D analysis both on all echo space and selected subregions. The modeling procedure is mainly composed of three sequential phases: a) automatic acquisition and preprocessing of time sequences of 2D echotomograms; b) 3D reconstruction of images and computing of discrete distance maps of selected echoes according to predefined projective laws; and c) generation of a spatial geometric model of the examined object starting from the previously computed maps.

Algorithms↗

PubMed1994

Endpoint bias in large Tn10-catalyzed inversions in Salmonella typhimurium.

A genetic strategy identified Salmonella typhimurium strains carrying large (> 40 kb) Tn 10-catalyzed inversions; the inverted segments were characterized by XbaI digestion and pulsed field gel electrophoresis. Two size classes of large inversions were found. More than half of the inversions extended 40-80 kb either clockwise or counterclockwise of the original Tn10 site. The remaining inversions extended up to 1620 kb (33% of the genome), but the distal endpoints of these inversions were not randomly scattered throughout the chromosome. Rather, each Tn10 repeatedly yielded similar (though not identical) inversions. The biased endpoint selection may reflect the limited search for target DNA sequences by the Tn10 transposase, and the spatial proximity of the donor and target regions in the folded S. typhimurium nucleoid. Using this interpretation, the data suggest that DNA sequences 40-80 kb clockwise and counterclockwise of the insertion site are in spatial proximity with the insertion, perhaps reflecting the organization of DNA into approximately 120-kb nucleoid domains. In addition, the data predict the spatial proximity of several distant DNA regions, including DNA sequences equidistant from the origin of DNA replication.

Base Sequence↗

PubMed1998

Sequence-specific binding of human immunodeficiency virus type 1 nucleocapsid protein to short oligonucleotides.

We have analyzed the binding of recombinant human immunodeficiency virus type 1 nucleocapsid protein (NC) to very short oligonucleotides by using surface plasmon resonance (SPR) technology. Our experiments, which were conducted at a moderate salt concentration (0.15 M NaCl), showed that NC binds more stably to runs of d(G) than to other DNA homopolymers. However, it exhibits far more stable binding with the alternating base sequence d(TG)n than with any homopolymeric oligodeoxyribonucleotide; thus, it shows a strong sequence preference under our experimental conditions. We found that the minimum length of an alternating d(TG) sequence required for stable binding was five nucleotides. Stable binding to the tetranucleotide d(TG)2 was observed only under conditions where two tetranucleotide molecules were held in close spatial proximity. The stable, sequence-specific binding to d(TG)n required that both zinc fingers be present, each in its proper position in the NC protein, and was quite salt resistant, indicating a large hydrophobic contribution to the binding. Limited tests with RNA oligonucleotides indicated that the preferential sequence-specific binding observed with DNA also occurs with RNA. Evidence was also obtained that NC can bind to nucleic acid molecules in at least two distinct modes. The biological significance of the specific binding we have detected is not known; it may reflect the specificity with which the parent Gag polyprotein packages genomic RNA or may relate to the functions of NC after cleavage of the polyprotein, including its role as a nucleic acid chaperone.

Capsid↗

PubMed2000

Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes.

The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous advances in elucidating the function of the encoded protein and the physiological basis of cystic fibrosis. However, numerous areas of cystic fibrosis biology require additional investigation, some of which would be facilitated by information about the long-range sequence context of the CFTR gene. For example, the latter might provide clues about the sequence elements responsible for the temporal and spatial regulation of CFTR expression. We thus sought to establish the sequence of the chromosomal segments encompassing the human CFTR and mouse Cftr genes, with the hope of identifying conserved regions of biologic interest by sequence comparison. Bacterial clone-based physical maps of the relevant human and mouse genomic regions were constructed, and minimally overlapping sets of clones were selected and sequenced, eventually yielding approximately 1.6 Mb and approximately 358 kb of contiguous human and mouse sequence, respectively. These efforts have produced the complete sequence of the approximately 189-kb and approximately 152-kb segments containing the human CFTR and mouse Cftr genes, respectively, as well as significant amounts of flanking DNA. Analyses of the resulting data provide insights about the organization of the CFTR/Cftr genes and potential sequence elements regulating their expression. Furthermore, the generated sequence reveals the precise architecture of genes residing near CFTR/Cftr, including one known gene (WNT2/Wnt2) and two previously unknown genes that immediately flank CFTR/Cftr.

Animals↗