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Results for “spatial sequencing”

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At least 55 records · Page 3Linked to original sources
PubMed2002

[Combination of low and high resolution T1-weighted sequences for improved evaluation of morphologic criteria in dynamic contrast enhanced MRI of the breast].

PURPOSE: Presentation of a new protocol for simultaneous acquisition of both low and high resolution T 1 -weighted images of breast lesions for dynamic contrast-enhanced MR mammography. Demonstration of possible diagnostic improvement with representative measurements in patients with suspected breast cancer by adding morphologic parameters from high resolution sequences to the analysis of the signal-time curve. MATERIALS AND METHODS: Dynamic MR imaging was performed with a 1.5 T system (Magnetom SONATA, Siemens Medical Systems, Germany) and the manufacturer's double-breast coil. Coronal T 1 -weighted 3D FLASH sequences (spatial resolution 1.25 x 1.25 mm 2; slice thickness 1.7 mm) were acquired once before and five times after administration of contrast medium (Gd-DTPA, 0.15 mmol/kg) injection. In addition, a high resolution T 1 -weighted 3D-FLASH sequence (spatial resolution, 0.63 x 0.63 mm 2) was obtained before administration of contrast medium and after the third post-contrast low-resolution sequence. Except for the acquisition matrix, all imaging parameters were identical for both 3D pulse sequences. To assure comparison of the measured signal intensities for both T 1 -weighted sequences, calibrating phantom measurements were performed using a dilution series of Gd-DTPA. RESULTS: Phantom measurements demonstrated similar signal intensities and enhancement pattern for both sequences. A combined protocol consisting of both pulse sequences can be employed and does not interfere with the signal-time curve analysis. By measuring one high resolution sequence 3:18 minutes after administration of contrast medium, morphologic features can be evaluated without interference from barely enhancing surrounding tissue. The overall study time is not increased. The improved spatial resolution slightly increases the severity of motion artifacts. CONCLUSION: The new protocol is a clever way to improve the measurement of morphologic features without relevant loss of dynamic information. It is superior to converting the entire investigation to high resolution sequences and does not add any costs by not extending or duplicating the investigation. How much the new protocol can improve the specificity or sensitivity of MR-mammography is currently investigated on a larger patient group.

Breast↗
PubMed1991

DNA and RNA within the nucleus: how much sequence-specific spatial organization?

Spatial organization of various nuclear components is often proposed as a means by which nuclei more efficiently carry out their various tasks. Such functional compartmentalization may involve a sequence-specific packaging and placement of DNA and RNA. Here we review recent insights, allowed primarily by advances in fluorescent in situ hybridization methodology, into the organization of nucleic acids within individual nuclei.

Cell Cycle↗
PubMed1992

The design of pulse sequences employing spatial presaturation for the suppression of flow artifacts.

The use of spatial presaturation to suppress the signal, and therefore also the artifacts, from flowing blood has become an important tool in the arsenal of techniques to suppress pulsatile flow artifacts in magnetic resonance images. However, a detailed theoretical analysis of the behavior of these flow artifact suppression pulses and of the important aspects of implementing suppression pulses in combination with particular imaging sequences has yet to be presented. In this paper we present a general theoretical framework to describe the flow artifact suppression technique. This analysis addresses the following four major issues: (1) the spin washout characteristics of the imaging sequence, (2) the interference between the flow signal suppression pulses and the imaging sequence, (3) the flow velocity range for a single application of the suppression pulse, and (4) the total flow velocity range for a suppression pulse repeated with a constant time interval between applications of the pulse. The predictions of our theoretical model are confirmed by experimental measurements made with stationary and flow phantoms. The results of this investigation provide guidelines for the design of flow artifact suppression pulse sequences and, in addition, should aid in the future development and refinement of the spatial presaturation technique as applied to flow signal suppression.

Artifacts↗
PubMed1991

Food caching in captive coyotes: stereotypy of action sequence and spatial distribution of cache sites.

This paper describes some aspects of the food caching behaviour of four captive coyotes. Detailed observations of the actions used by coyotes to cache food revealed them to be strikingly similar to those previously described for timber wolves. The similarities included the identity of the movements used, their temporal sequencing, and their susceptibility to interruption. This suggests that there exists a stereotypy across canids in the action sequences used in caching. Second, an examination of the distribution of cache sites revealed that each coyote scattered cache sites widely within a wooded region of their enclosure and preferentially in terrains close to exposed tree roots.

Animals↗
PubMed1995

Sequence and spatial requirements for regulated muscle-specific processing of the sarco/endoplasmic reticulum Ca(2+)-ATPase 2 gene transcript.

Expression of the muscle-specific 2a isoform of the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA2) requires activation of an otherwise inefficient splicing process at the 3'-end of the primary gene transcript. The sequence and topology requirements for this regulated splicing event were studied in the BC3H1 myogenic cell line using a minigene containing the 3'-end of the SERCA2 gene. In undifferentiated BC3H1 cells, the splice process is made inefficient by the presence of a weak muscle-type 5'-donor site (5'D1) and a long terminal intron. Both optimizing the 5'D1 and decreasing the length of the muscle-specific intron, induced muscle-type splicing in undifferentiated myogenic cells. Moreover, the induction of muscle-type transcripts was only observed when two competing processing sites, the polyadenylation site (pAu) used in non-muscle cells and the second neuronal 5'-donor site (5'D2), were weak. Indeed, making 5'D2 consensus induced neuronal-type splicing in undifferentiated myocytes and prevented the appearance of muscle-type transcripts. Similarly, replacing the polyadenylation site (pAu) with a strong site almost completely inhibited muscle-type splicing after myogenic differentiation. We conclude that weak processing sites and a long terminal intron are required for tissue-dependent mRNA processing of the SERCA2 transcript.

Alternative Splicing↗
PubMed2003

Spatial and temporal sequence learning in patients with Parkinson's disease or cerebellar lesions.

The functional role of different subcortical areas in sequence learning is not clear. In the current study, Parkinson's patients, patients with cerebellar damage, and age-matched control participants performed a serial reaction time task in which a spatial sequence and a temporal sequence were presented simultaneously. The responses were based on the spatial sequence, and the temporal sequence was incidental to the task. The two sequences were of the same length, and the phase relationship between them was held constant throughout training. Sequence learning was assessed comparing performance when both sequences were present versus when the dimension of interest was randomized. In addition, sequence integration was assessed by introducing phase-shift blocks. A functional dissociation was found between the two patient groups. Whereas the Parkinson's patients learned the spatial and temporal sequences individually, they did not learn the relationship between the two sequences, suggesting the basal ganglia play a functional role in sequence integration. In contrast, the cerebellar patients did not show any evidence of sequence learning at all, suggesting the cerebellum might play a general role in forming sequential associations.

Aged↗
PubMed1992

An amphioxus homeobox gene: sequence conservation, spatial expression during development and insights into vertebrate evolution.

The embryology of amphioxus has much in common with vertebrate embryology, reflecting a close phylogenetic relationship between the two groups. Amphioxus embryology is simpler in several key respects, however, including a lack of pronounced craniofacial morphogenesis. To gain an insight into the molecular changes that accompanied the evolution of vertebrate embryology, and into the relationship between the amphioxus and vertebrate body plans, we have undertaken the first molecular level investigation of amphioxus embryonic development. We report the cloning, complete DNA sequence determination, sequence analysis and expression analysis of an amphioxus homeobox gene, AmphiHox3, evolutionarily homologous to the third-most 3' paralogous group of mammalian Hox genes. Sequence comparison to a mammalian homologue, mouse Hox-2.7 (HoxB3), reveals several stretches of amino acid conservation within the deduced protein sequences. Whole mount in situ hybridization reveals localized expression of AmphiHox3 in the posterior mesoderm (but not in the somites), and region-specific expression in the dorsal nerve cord, of amphioxus neurulae, later embryos and larvae. The anterior limit to expression in the nerve cord is at the level of the four/five somite boundary at the neurula stage, and stabilises to just anterior to the first nerve cord pigment spot to form. Comparison to the anterior expression boundary of mouse Hox-2.7 (HoxB3) and related genes suggests that the vertebrate brain is homologous to an extensive region of the amphioxus nerve cord that contains the cerebral vesicle (a region at the extreme rostral tip) and extends posterior to somite four.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Dominant negative suppression of arabidopsis photoresponses by mutant phytochrome A sequences identifies spatially discrete regulatory domains in the photoreceptor.

We used the exaggerated short hypocotyl phenotype induced by oat phytochrome A overexpression in transgenic Arabidopsis to monitor the biological activity of mutant phytochrome A derivatives. Three different mutations, which were generated by removing 52 amino acids from the N terminus (delta N52), the entire C-terminal domain (delta C617), or amino acids 617-686 (delta 617-686) of the oat molecule, each caused striking dominant negative interference with the ability of endogenous Arabidopsis phytochrome A to inhibit hypocotyl growth in continuous far-red light ("far-red high irradiance response" conditions). By contrast, in continuous white or red light, delta N52 was as active as the unmutagenized oat phytochrome A protein in suppressing hypocotyl elongation, while delta C617 and delta 617-686 continued to exhibit dominant negative behavior under these conditions. These data suggest that at least three spatially discrete molecular domains coordinate the photoregulatory activities of phytochrome A in Arabidopsis seedlings. The first is the chromophore-bearing N-terminal domain between residues 53 and 616 that is apparently sufficient for the light-induced initiation but not the completion of productive interactions with transduction chain components. The second is the C-terminal domain between residues 617 and 1129 that is apparently necessary for completion of productive interactions under all irradiation conditions. The third is the N-terminal 52 amino acids that are apparently necessary for completion of productive interactions only under far-red high irradiance conditions and are completely dispensable under white and red light regimes.

Arabidopsis↗
PubMed2005

Disruption of delayed memory for a sequence of spatial locations following CA1- or CA3-lesions of the dorsal hippocampus.

Axon-sparing neurotoxic lesions of CA1 or CA3 were produced in the dorsal hippocampus to test dissociative lesion effects on spatial working memory for sequential items. Rats were required to remember four different sections sequentially presented on a newly devised maze (i.e., Tulum maze) during a study phase. Each section was cued by a unique object that was specifically associated with each location within the section during the study phase. Following a 15-s delay and during the test phase, rats were required to revisit the location within a section randomly chosen among the previously visited sections in the absence of the cued object. Both CA1 and CA3 lesions similarly disrupted accurate relocation of a previously visited place. However, differential effects of the CA1 and CA3 lesions were observed in serial position curves. CA3-lesions disrupted performance for the first three serial positions, but did not disrupt performance for the last serial position (recency). In contrast, CA1-lesions disrupted performance for all serial positions. The results suggest that temporal separation of spatial memory may depend on the conjoint function of CA1 and CA3 of the hippocampus with a disruption of a spatial pattern completion process following CA3 lesions and a disruption of a temporal pattern separation process following a CA1 lesion.

Animals↗
PubMed2003

The mental representation of ordinal sequences is spatially organized.

In the domain of numbers the existence of spatial components in the representation of numerical magnitude has been convincingly demonstrated by an association between number magnitude and response preference with faster left- than right-hand responses for small numbers and faster right- than left-hand responses for large numbers (Dehaene, S., Bossini, S., & Giraux, P. (1993) The mental representation of parity and number magnitude. Journal of Experimental Psychology: General, 122, 371-396). Because numbers convey not only real or integer meaning but also ordinal meaning, the question of whether non-numerical ordinal information is spatially coded naturally follows. While previous research failed to show an association between ordinal position and spatial response preference, we present two experiments involving months (Experiment 1) and letters (Experiment 2) in which spatial coding is demonstrated. Furthermore, the response-side effect was obtained with two different stimulus-response mappings. The association occurred both when ordinal information was relevant and when it was irrelevant to the task, showing that the spatial component of the ordinal representation can be automatically activated.

Adult↗
PubMed1998

A neuropsychological theory of motor skill learning.

This article describes a neuropsychological theory of motor skill learning that is based on the idea that learning grows directly out of motor control processes. Three motor control processes may be tuned to specific tasks, thereby improving performance: selecting spatial targets for movement, sequencing these targets, and transforming them into muscle commands. These processes operate outside of awareness. A 4th, conscious process can improve performance in either of 2 ways: by selecting more effective goals of what should be changed in the environment or by selecting and sequencing spatial targets. The theory accounts for patterns of impairment of motor skill learning in patient populations and for learning-related changes in activity in functional imaging studies. It also makes a number of predictions about the purely cognitive, including accounts of mental practice, the representation of motor skill, and the interaction of conscious and unconscious processes in motor skill learning.

Amnesia↗
PubMed1991

Histamine-induced calcium oscillations in human vascular smooth muscle: temporal sequence and spatial organization in single cells.

1. Video imaging of single, fura2-loaded vascular smooth muscle cells was used to examine the spatial and temporal alterations in calcium, Ca2+, in response to low levels of vasoconstrictor stimuli. 2. Histamine (0.5 mumol/L) produced repetitive oscillations in Ca2+, which appeared to show some variation in amplitude and frequency between cells. 3. Individual oscillations consisted of an initial increase in Ca2+ in a localized region followed by a wave-like propagation of this region of elevated Ca2+ throughout the rest of the cell cytoplasm. 4. It is suggested that the subcellular spatial organization of Ca2+ that was observed during a Ca2+ oscillation allows a population of cells to operate in unison. Thus, oscillatory fluctuations in Ca2+ may contribute to myogenic tone.

Calcium↗
PubMed1992

Xenopus Hox-2 genes are expressed sequentially after the onset of gastrulation and are differentially inducible by retinoic acid.

In this paper, we review experiments to characterise the developmental expression and the responses to all-trans retinoic acid (RA) of six members of the Hox-2 complex of homeobox-containing genes, during the early development of Xenopus laevis. We showed that the six genes are expressed in a spatial sequence which is colinear with their putative 3' to 5' chromosomal sequence and that five of them are also expressed rapidly after the beginning of gastrulation, in a 3' to 5' colinear temporal sequence. The sixth gene (Xhox2.9) has an exceptional spatial and temporal expression pattern. The six genes all respond to RA by showing altered spatiotemporal expression patterns, and are also RA-inducible, the sequence of the magnitudes of their RA responses being colinear with their 3' to 5' chromosomal sequence, and with their spatial and temporal expression sequences. Our data also reveal that there is a pre-existing anteroposterior polarity in the embryo's competence for a response to RA. These results complement and extend previous findings made using murine and avian embryos and mammalian cell lines. They suggest that an endogenous retinoid could contribute to positional information in the early Xenopus embryo.

Animals↗
PubMed1993

Colinearity in the Xenopus laevis Hox-2 complex.

Here we describe experiments detailing the developmental expression, and the inducibility by all-trans retinoic acid (RA) of six members of the Xenopus Hox-2 complex of homeobox-containing genes. We first report the cloning and characterisation of two novel Xenopus Hox-2 genes (Xhox2.7 and Xhox2.9), and provide evidence that the six genes studied are indeed closely linked in the same chromosomal complex. We next show that all six genes are expressed in a spatial sequence which is colinear with their putative 3' to 5' chromosomal sequence and that five of them are also expressed in a 3' to 5' colinear temporal sequence. The sixth gene (Xhox2.9) has an exceptional spatial and temporal expression pattern. The six genes all respond to RA by showing altered spatiotemporal expression patterns, and are also hyperinduced by RA, with a sequence of magnitudes which is colinear with their 3' to 5' chromosomal sequence and with their spatial and temporal expression sequences. Our data also suggest a pre-existing anteroposterior polarity in the embryo's competence to respond to RA. These results complement and extend previous findings made using murine and avian embryos and mammalian cell lines. They suggest a mechanism whereby an endogenous retinoid could help to provide positional information in the early embryo.

Amino Acid Sequence↗
PubMed2005

The implicit sequence learning deficit in patients with Parkinson's disease: a matter of impaired sequence integration?

Despite the wealth of research investigating the serial reaction time (SRT) learning abilities of people with Parkinson's disease (PD), the role of the basal ganglia in implicit sequence learning remains largely unclear. The present research sought to examine the ability of people with PD to implicitly learn simultaneously operating sequences and integrate patterned information from each sequence dimension. Using a version of the SRT which reduced motor demands, the present experiment investigated the implicit learning of a spatial sequence, a stimulus-response sequence, and an integrated spatial/stimulus-response sequence, all of which are usually confounded in the standard SRT task. Whereas both PD and control groups demonstrated robust learning for the individual spatial and response sequences, only control participants evidenced learning for the integrated sequence. Further, unlike implicit learning for the spatial and object sequences, impaired integrated sequence acquisition was specifically related to the severity of patients' PD symptomatology. The implicit learning deficits of PD patients are discussed with regard to the role played by the basal ganglia in integrative sequence learning in the SRT.

Aged↗
PubMed2002

Reproducibility of left ventricular mass measurement using a half-Fourier black-blood single-shot fast spin-echo sequence within a single breath hold: comparison with a conventional multiple breath-hold segmented gradient echo technique in patients.

PURPOSE: To compare the reproducibility of left ventricular (LV) mass measurements using a black-blood half-Fourier single-shot fast spin-echo (SSFSE) and a segmented gradient echo magnetic resonance (MR) pulse sequence. MATERIAL AND METHODS: Breath-hold SSFSE and segmented gradient echo cardiac MR examinations were performed twice in 32 patients and manual detection of the LV endocardium and epicardium was applied by two blinded reviewers. The SSFSE pulse sequence allowed whole-heart coverage in a single breath hold, while multiple breath holds were required using the segmented gradient echo sequence. Spatial presaturation slabs were used with the SSFSE pulse sequence to reduce the field of view (FOV) and thereby achieve higher spatial resolution. RESULTS: Intraclass correlation coefficients were higher with the SSFSE pulse sequence than with the segmented gradient echo pulse sequence: intraobserver reproducibility reached 0.999 vs. 0.991; interobserver reproducibility: 0.997 vs. 0.981; and interstudy reproducibility: 0.998 vs. 0.936. These higher levels of reproducibility were confirmed on Bland and Altman plots. CONCLUSION: LV mass measurements can be assessed more reproducibly with the single breath-hold SSFSE technique than with the standard multiple breath-hold segmented gradient echo method.

Adult↗