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Results for “spatial sequencing”

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At least 667 records · Page 37Linked to original sources

PubMed2006

Localized in vivo isotropic-anisotropic correlation 1H NMR spectroscopy using ultraslow magic angle spinning.

In a previous work (1), the susceptibility broadening in the (1)H NMR metabolite spectrum obtained in a live mouse was separated from the isotropic information, which significantly increased the spectral resolution. This was achieved using ultraslow magic angle spinning (MAS) of the animal combined with a modified phase-corrected magic angle turning (PHORMAT) pulse sequence. However, PHORMAT cannot be used for spatially selective spectroscopy. This article introduces a modified sequence called localized magic angle turning (LOCMAT) that makes this possible. Proton LOCMAT spectra were obtained from the liver and heart of a live mouse while the animal was spun at a speed of 4 Hz in a 2 Tesla field. It was found that even in this relatively low field, LOCMAT provided isotropic line widths that were a factor of 4-10 times smaller than those obtained in a stationary animal. Furthermore, the susceptibility broadening of the heart metabolites showed unusual features that are not observed in dead animals. The limitations of LOCMAT and possible ways to improve the technique are discussed. It is concluded that in vivo LOCMAT can significantly enhance the utility of NMR spectroscopy for biomedical research.

Animals↗

PubMed2002

Archaeology and cognitive evolution.

Archaeology can provide two bodies of information relevant to the understanding of the evolution of human cognition--the timing of developments, and the evolutionary context of these developments. The challenge is methodological. Archaeology must document attributes that have direct implications for underlying cognitive mechanisms. One example of such a cognitive archaeology is found in spatial cognition. The archaeological record documents an evolutionary sequence that begins with ape-equivalent spatial abilities 2.5 million years ago and ends with the appearance of modern abilities in the still remote past of 400,000 years ago. The timing of these developments reveals two major episodes in the evolution in spatial ability, one, 1.5 million years ago and the other, one million years later. The two episodes of development in spatial cognition had very different evolutionary contexts. The first was associated with the shift to an open country adaptive niche that occurred early in the time range of Homo erectus. The second was associated with no clear adaptive shift, though it does appear to have coincided with the invasion of more hostile environments and the appearance of systematic hunting of large mammals. Neither, however, occurred in a context of modern hunting and gathering.

Animals↗

PubMed1999

Temporal sequence compression by an integrate-and-fire model of hippocampal area CA3.

Cells in the rat hippocampus fire as a function of the animal's location in space. Thus, a rat moving through the world produces a statistically reproducible sequence of "place cell" firings. With this perspective, spatial navigation can be viewed as a sequence learning problem for the hippocampus. That is, learning entails associating the relationships among a sequence of places that are represented by a sequence of place cell firing. Recent experiments by McNaughton and colleagues suggest the hippocampus can recall a sequence of place cell firings at a faster rate than it was experienced. This speedup, which occurs during slow-wave sleep, is called temporal compression. Here, we show that a simplified model of hippocampal area CA3, based on integrate-and-fire cells and unsupervised Hebbian learning, reproduces this temporal compression. The amount of compression is proportional to the activity level during recall and to the relative timespan of associativity during learning. Compression seems to arise from an alteration of network dynamics between learning and recall. During learning, the dynamics are paced by external input and slowed by a low overall level of activity. During recall, however, external input is absent, and the dynamics are controlled by intrinsic network properties. Raising the activity level by lowering inhibition increases the rate at which the network can transition between previously learned states and thereby produces temporal compression. The tendency for speeding up future activations, however, is limited by the temporal range of associations that were present during learning.

Animals↗

PubMed2001

MR angiography using spin-lock flow tagging.

A method for MR angiography using an RF labeling technique is suggested. The method utilizes a slice-selective spin-lock pulse sequence for tagging the spins of inflowing blood. The pulse sequence begins with a spatially selective 90 degrees (x) RF pulse, followed by a nonselective composite locking pulse of 135 degrees (y) - n[360 degrees (y)]-135 degrees (y) and by a 90 degrees (-x) pulse. A spoiler gradient is then applied. A rapid imaging stage, which yields a T(1)rho-weighted signal from the tagged spins, completes the sequence. Untagged spins are thoroughly dephased and consequently suppressed in the image. Thus, contrast is obtained without an injection of a contrast material or image subtraction. Furthermore, the flow of the tagged bolus can be visualized. The sequence was implemented on phantoms and on human volunteers using a 1.5T scanner. The results indicate the feasibility of the suggested sequence.

Coronary Circulation↗

PubMed1995

Sex differences in learning and memory in mice: effects of sequence of testing and cholinergic blockade.

Sexual dimorphism in spatial and cued navigation using the Morris water maze was examined in C57BL/6 mice both with and without administration of scopolamine, a cholinergic blocker. In Exp. 1, female and male mice learned to perform first a spatial, then a cued, navigation task. Both performed a spatial task similarly; males, however, performed a cued task better than females. In Exp. 2, the sequence of navigation testing was reversed. Both performed similarly on a cued task; however, males performed a spatial task better than females. In both experiments, females were more sensitive than males to the effects of scopolamine. No significant confounding sex differences were found in either spontaneous activity or passive avoidance retention. These data indicate that sex differences in spatial and cued tasks are dependent on the sequence of task presentation and implicate a role for the cholinergic system in these differences.

Animals↗

PubMed2002

Standardized MR protocol for the evaluation of MRA sequences and/or contrast agents effects in high-degree arterial stenosis analysis.

PURPOSE: To investigate the relative role of high resolution (spatial or temporal) magnetic resonance angiography (MRA) sequence and of contrast agent properties in the evaluation of high-degree arterial stenosis. METHODS: We qualitatively and quantitatively studied both 50 and 95% (300 microm diameter) stenosis of a 6 mm arterial phantom with two contrast agents (CA), Gd-DOTA (r(1)=2.9 mM(-1) s(-1)) versus P760 (r(1)=25 mM(-1) s(-1)) at several CA concentrations, including arterial peak concentration after injection of either a single or double dose of CA, using either a high temporal (booster) or high spatial (HR) resolution 3D MRA sequences. Experimental data were then compared to theoretical data. RESULTS: With the 3D HR sequence, both visual and quantitative analysis were significantly better compared to the 3D booster sequence, at each phantom diameter. Quantitative analysis was significantly improved by injection of a double versus a single dose of each CA (Gd-DOTA or P760), primarily in high degree stenosis. CONCLUSION: Combined MRA spatial resolution and high CA efficiency are mandatory to correctly evaluate high degree stenosis.

Arterial Occlusive Diseases↗

PubMed2002

Time-resolved, undersampled projection reconstruction imaging for high-resolution CE-MRA of the distal runoff vessels.

Imaging of the blood vessels below the knee using contrast-enhanced (CE) MRI is challenging due to the need to coordinate image acquisition and arrival of the contrast in the targeted vessels. Time-resolved acquisitions have been successful in consistently capturing images of the arterial phase of the bolus of contrast agent in the distal extremities. Although time-resolved exams are robust in this respect, higher spatial resolution for the depiction of tight stenoses and the small vessels in the lower leg is desirable. A modification to a high-spatial-resolution T(1)-weighted pulse sequence (projection reconstruction-time resolved imaging of contrast kinetics (PR-TRICKS)) that improves the through-plane spatial resolution by a factor of 2 and maintains a high frame rate is presented. The undersampled PR-TRICKS pulse sequence has been modified to double the spatial resolution in the slice direction by acquiring high-spatial-frequency slice data only after first pass of the bolus of contrast agent. The acquisition reported in the present work (PR-hyperTRICKS) has been used to image healthy volunteers and patients with known vascular disease. The temporal resolution was found to be beneficial in capturing arterial phase images in the presence of asymmetric filling of vessels.

Contrast Media↗

PubMed2026

Spatially guided in vivo single-cell functional genomics of postnatal heart.

Understanding how spatial organization and cell-cell interactions shape gene regulatory programs is central to decoding tissue development and function. The transition at birth, marked by increased circulatory demands and rapid tissue growth, requires precise spatiotemporal coordination of cardiac maturation. In this study, we generated a high-resolution spatial and temporal atlas of the postnatal mouse heart by integrating single-nucleus RNA sequencing with image-based spatial transcriptomics. This framework revealed dynamic cellular interactions, niche-specific signaling and transcriptional programs guiding cardiomyocyte maturation. To functionally test prioritized regulators in vivo and at scale, we developed PIP-seq (probe-based indel-detectable Perturb-seq), a high-throughput platform that detects single guide RNA identity, infers gene editing and profiles transcription from fixed nuclei. Applying PIP-seq to the developing postnatal heart, we identified 21 previously uncharacterized regulators of cardiomyocyte maturation, including genes essential for sarcomere assembly, metabolic reprogramming and electrophysiological transitions. Together, our findings define how microenvironmental signals and intrinsic gene programs cooperate to guide heart maturation and establish a broadly applicable framework for functional genomics in complex tissues.

Animals↗

PubMed2001

The use of SPAMM to assess spatial distortion due to static field inhomogeneity in dental MRI.

In planning placement of dental implants using MRI, a SPAMM (spatial modulation of magnetization) magnetization preparation sequence was incorporated into a spin-echo imaging sequence. A phantom was imaged with a ferromagnetic object attached. Spatial distortion due to deviations in Larmor frequency was detected by a deviation of SPAMM lines. Both SPAMM line deviation and interline spacing were found to agree with a deltaB0 map generated from phase images. Imaging of a volunteer with and without typically used metallic implants positioned in a template showed SPAMM line deviations to correlate with expected deviations in vivo. SPAMM lines showed possible distortion due to chemical shift in the bone marrow and the presence of titanium implants to be insignificant. SPAMM may thus be used to provide a qualitative estimate of the accuracy of the MRI image when planning dental implants.

Calibration↗

PubMed2001

Error threshold for spatially resolved evolution in the quasispecies model.

The error threshold for quasispecies in 1, 2, 3, and infinity dimensions is investigated by stochastic simulation and analytically. The results show a monotonic decrease in the maximal sustainable error probability with decreasing diffusion coefficient, independently of the spatial dimension. It is thereby established that physical interactions between sequences are necessary in order for spatial effects to enhance the stabilization of biological information. The analytically tractable behavior in an infinity-dimensional (simplex) space provides a good guide to the spatial dependence of the error threshold in lower dimensional Euclidean space.

Evolution, Molecular↗

PubMed1993

[Dynamic MR imaging of the pituitary gland by the fast spin echo (RARE) sequence].

The Fast Spin Echo (RARE: Rapid Acquisition with Relaxation enhancement) sequence for the dynamic MRI of the pituitary gland was performed in 18 patients suspected of the intracranial lesions. The SNR of the plain image of 5 pituitary glands was measured on the FSE 400 and 200/17/8/2 (TR/effective TE/echo train length/excitation) and the spin echo 100/11/2 (TR/TE/excitation) sequence. The FSE (TR = 400) provided the highest SNR than others, The FSE sequence was able to acquire increased spatial resolution and reduced acquisition time, and was the significant sequence for the dynamic MRI of the pituitary gland.

Adolescent↗

PubMed1994

Assignment of human satellite 1 DNA as revealed by fluorescent in situ hybridization with oligonucleotides.

We have used a fluorescent in situ hybridization procedure to detect human satellite 1 DNA, the simple sequence family that constitutes the non-male-specific fraction of classical satellite 1 DNA. Satellite 1 appears to be located on pericentromeric regions of chromosomes 3, 4 and 13, and on satellites of each acrocentric chromosome. These results suggest a possible relationship between quinacrine fluorescence of heterochromatin and DNA composition. Furthermore, by means of multicolour in situ hybridization, we have spatially resolved satellite 1 sequences and centromeric alpha-satellite within heterochromatic blocks.

Base Sequence↗

PubMed1995

CENP-F is a protein of the nuclear matrix that assembles onto kinetochores at late G2 and is rapidly degraded after mitosis.

Centromere protein-F (CENP-F) is mammalian kinetochore protein that was recently identified by an autoimmune serum (Rattner, J. B., A. Rao, M. J. Fritzler, D. W. Valencia, and T. J. Yen. Cell Motil. Cytoskeleton. 26:214-226). We report here the human cDNA sequence of CENP-F, along with its expression and localization patterns at different stages of the HeLa cell cycle. CENP-F is protein of the nuclear matrix that gradually accumulates during the cell cycle until it reaches peak levels in G2 and M phase cells and is rapidly degraded upon completion of mitosis. CENP-F is first detected at the prekinetochore complex during late G2, and is clearly detectable as paired foci that correspond to all the centromeres by prophase. During mitosis, CENP-F is associated with kinetochores from prometaphase until early anaphase and is then detected at the spindle midzone throughout the remainder of anaphase. By telophase, CENP-F is concentrated within the intracellular bridge at either side of the mid-body. The predicted structure of the 367-kD CENP-F protein consists of two 1,600-amino acid-long coil domains that flank a central flexible core. A putative P-loop nucleotide binding site (ADIPTGKT) is located within the globular carboxy terminus. The structural features deduced from our sequence studies and the spatial and temperal distribution of CENP-F revealed in our cytological and biochemical studies suggest that it may play a role in several mitotic events.

Amino Acid Sequence↗

PubMed2000

Profiles of cognitive dysfunction in chronic amphetamine and heroin abusers.

Groups of subjects whose primary drug of abuse was amphetamine or heroin were compared, together with age- and IQ-matched control subjects. The study consisted of a neuropsychological test battery which included both conventional tests and also computerised tests of recognition memory, spatial working memory, planning, sequence generation, visual discrimination learning, and attentional set-shifting. Many of these tests have previously been shown to be sensitive to cortical damage (including selective lesions of the temporal or frontal lobes) and to cognitive deficits in dementia, basal ganglia disease, and neuropsychiatric disorder. Qualitative differences, as well as some commonalities, were found in the profile of cognitive impairment between the two groups. The chronic amphetamine abusers were significantly impaired in performance on the extra-dimensional shift task (a core component of the Wisconsin Card Sort Test) whereas in contrast, the heroin abusers were impaired in learning the normally easier intra-dimensional shift component. Both groups were impaired in some of tests of spatial working memory. However, the amphetamine group, unlike the heroin group, were not deficient in an index of strategic performance on this test. The heroin group failed to show significant improvement between two blocks of a sequence generation task after training and additionally exhibited more perseverative behavior on this task. The two groups were profoundly, but equivalently impaired on a test of pattern recognition memory sensitive to temporal lobe dysfunction. These results indicate that chronic drug use may lead to distinct patterns of cognitive impairment that may be associated with dysfunction of different components of cortico-striatal circuitry.

Adolescent↗

PubMed1998

Increased spatial resolution using a three-dimensional T1-weighted gradient-echo MR sequence results in greater hypointense lesion volumes in multiple sclerosis.

PURPOSE: Our goal was to evaluate whether improved spatial resolution of MR images results in the detection of higher volumes of hypointense lesions in patients with multiple sclerosis (MS). METHODS: A magnetization-prepared rapid acquisition gradient-echo (MP-RAGE) sequence with subsequent reconstruction of axial sections with 5-, 3-, and 1-mm thickness and a dual-echo sequence were obtained in 16 patients with relapsing-remitting or secondary-progressive MS. The volumes of MR imaging abnormalities present on each of these studies were measured using a semiautomated segmentation technique based on local thresholding. The hypointense lesion volumes seen on the three reconstructed MP-RAGE sets of images were compared using the Friedman test and correlated with the hyperintense lesion volume on proton density-weighted images and with scores on the Expanded Disability Status Scale using Spearman's rank correlation coefficient. RESULTS: The median volume of hypointense lesions increased from 1.2 mL (range, 0 to 14.9 mL) on the 5-mm-thick MP-RAGE images to 1.7 mL (range, 0 to 15.8 mL) on the 3-mm-thick images, and to 1.9 mL (range, 0 to 16.2 mL) on the 1-mm-thick images. The hypointense lesion volumes measured on the three MP-RAGE images correlated significantly with the degree of disability, whereas this correlation was not significant with the T2-weighted lesion load. CONCLUSION: Our findings indicate that a significant increase in the volume of potentially disabling MS lesions is observed when obtaining MR images with thin sections.

Adult↗

PubMed1998

Potato leafroll virus binds to the equatorial domain of the aphid endosymbiotic GroEL homolog.

A GroEL homolog with a molecular mass of 60 kDa, produced by the primary endosymbiotic bacterium (a Buchnera sp.) of Myzus persicae and released into the hemolymph, has previously been shown to be a key protein in the transmission of potato leafroll virus (PLRV). Like other luteoviruses and pea enation mosaic virus, PLRV readily binds to extracellular Buchnera GroEL, and in vivo interference in this interaction coincides with reduced capsid integrity and loss of infectivity. To gain more knowledge of the nature of the association between PLRV and Buchnera GroEL, the groE operon of the primary endosymbiont of M. persicae (MpB groE) and its flanking sequences were characterized and the PLRV-binding domain of Buchnera GroEL was identified by deletion mutant analysis. MpB GroEL has extensive sequence similarity (92%) with Escherichia coli GroEL and other members of the chaperonin-60 family. The genomic organization of the Buchnera groE operon is similar to that of the groE operon of E. coli except that a constitutive promoter sequence could not be identified; only the heat shock promoter was present. By a virus overlay assay of protein blots, it was shown that purified PLRV bound as efficiently to recombinant MpB GroEL (expressed in E. coli) as it did to wild-type MpB GroEL. Mutational analysis of the gene encoding MpB GroEL revealed that the PLRV-binding site was located in the so-called equatorial domain and not in the apical domain which is generally involved in polypeptide binding and folding. Buchnera GroEL mutants lacking the entire equatorial domain or parts of it lost the ability to bind PLRV. The equatorial domain is made up of two regions at the N and C termini that are not contiguous in the amino acid sequence but are in spatial proximity after folding of the GroEL polypeptide. Both the N- and C-terminal regions of the equatorial domain were implicated in virus binding.

Amino Acid Sequence↗

PubMed1986

Effect of sleep on the electrographic manifestations of epilepsy.

Alterations in the level of arousal have profound predictable effects on the electrographic manifestations of epileptogenic abnormalities. The changes produced by sleep are dramatic in patients with generalized epilepsy as compared to patients with partial epilepsy. The epileptiform complexes associated with the generalized epilepsies show changes in spatial distribution, voltage, temporal sequencing, and waveform morphology. The changes are qualitatively similar in the different types of generalized seizure disorders but vary in the degree to which they are expressed in proportion to the "severity" of the seizure disorder. The presence of a generalized epileptogenic abnormality may result in alteration of K-complex waveform morphology. Multifocal spikes occurring in conjunction with bilateral synchronous discharges are frequently represented by a spatial field distribution consistent with a "horizontal dipole," during sleep especially in children.

Adult↗

PubMed2002

Control of saccades in Parkinson's disease.

Parkinson's patients (PD) made pro- and antisaccades: In the no-delay condition, the target appeared concurrent with the GO signal. In the delay condition, the target appeared before the signal for movement. Second, we probed spatial working memory in PD. Subjects looked to the remembered locations of sequential targets. In the no-delay prosaccade condition, PD had faster reaction times, made more express saccades, and exhibited hypometria. In the no-delay antisaccade condition, PD had longer reaction times and made more direction errors. In the delay tasks, PD made more direction errors and had more difficulty withholding a movement. PD made more sequencing errors in the spatial working memory task. These findings are consistent with a basal ganglia pathophysiology influencing eye movement processing in the frontal cortex.

Attention↗