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Planning and spatial working memory following frontal lobe lesions in man.

Twenty-six patients with unilateral or bilateral frontal lobe excisions were compared with age and IQ matched controls on a computerized battery of tests of spatial working memory and planning. A computerized test of spatial short term memory capacity revealed no significant impairment in the patients' ability to execute a given sequence of visuo-spatial moves. In contrast, a paradigm designed to assess spatial working memory capacity, revealed significant impairments in the patient group in both possible types of search errors. Furthermore, additional analysis showed that the frontal lobe patients were less efficient than controls in their usage of a strategy for improving performance on this test. Higher level planning was also investigated using a test based on the "Tower of London" problem [SHALLICE, T. Phil. Trans. R. Soc. Lond. B. 298, 199-209, 1982]. Patients with frontal lobe damage required more moves to complete the problems and a yoked motor control condition revealed that movement times were significantly increased in this group. Taking both of these factors into consideration, initial thinking (planning) time was unimpaired in the patient group although the thinking time subsequent to the first move was significantly prolonged. These data are compared to previous findings from patients with idiopathic Parkinson's disease and are discussed in terms of an impairment of higher cognitive functioning following frontal lobe damage.

Attention↗

Effect of artifacts due to flowing blood on the reproducibility of phase-contrast measurements of myocardial motion.

The reproducibility of myocardial motion trajectories calculated from cine phase-contrast (PC) velocity data is reduced by artifacts due to the inconsistent motion of intracardiac blood. Spatial presaturation reduces these artifacts but requires a longer sequence TR, with a potentially negative effect on trajectory accuracy and reproducibility. We investigated the effect of spatial presaturation on trajectory reproducibility. A mid-ventricular transaxial slice was imaged in five normal volunteers. The same slice was imaged three times each with sequences using spatial presaturation or not. Because the most serious artifacts originate in the heart chambers and propagate in the phase-encoded direction, myocardial regions that were in line with the heart chambers (in the phase-encode direction) had the highest artifact level in the scans without spatial presaturation. The reproducibility of trajectories for regions placed in these areas (the anterior wall, septum and posterior wall in the transaxial scans with phase encoding in the anterior-posterior direction) improved by a factor of two when presaturation was used (P < .001). In areas that were not in line with the heart chambers (eg, the anterior aspect of the lateral wall in the transaxial scans), the effect of presaturation was not significant. These results correlate well with the measured reduction in artifact level. The reproducibility of myocardial motion trajectories over large areas of the heart is improved to approximately 1 mm when presaturation is used. Therefore, use of presaturation is recommended for myocardial motion studies using cine PC velocity data.

Adult↗

RF safety of wires in interventional MRI: using a safety index.

With the rapid growth of interventional MRI, radiofrequency (RF) heating at the tips of guidewires, catheters, and other wire-shaped devices has become an important safety issue. Previous studies have identified some of the variables that affect the relative magnitude of this heating but none could predict the absolute amount of heating to formulate safety margins. This study presents the first theoretical model of wire tip heating that can accurately predict its absolute value, assuming a straight wire, a homogeneous RF coil, and a wire that does not extend out of the tissue. The local specific absorption rate (SAR) amplification from induced currents on insulated and bare wires was calculated using the method of moments. This SAR gain was combined with a semianalytic solution to the bioheat transfer equation to generate a safety index. The safety index ( degrees C/(W/kg)) is a measure of the in vivo temperature change that can occur with the wire in place, normalized to the SAR of the pulse sequence. This index can be used to set limits on the spatial peak SAR of pulse sequences that are used with the interventional wire. For the case of a straight resonant wire in a tissue with very low perfusion, only about 100 mW/kg/ degrees C spatial peak SAR may be used at 1.5 T. But for < or =10-cm wires with an insulation thickness > or =30% of the wire radius that are placed in well-perfused tissues, normal operating conditions of 4 W/kg spatial peak SAR are possible at 1.5 T. Further model development to include the influence of inhomogeneous RF, curved wires, and wires that extend out of the sample are required to generate safety indices that are applicable to common clinical situations. We propose a simple way to ensure safety when using an interventional wire: set a limit on the SAR of allowable pulse sequences that is a factor of a safety index below the tolerable temperature increase.

Electric Wiring↗

High resolution MRI of small joints: impact of spatial resolution on diagnostic performance and SNR.

This study focuses on the spatial resolution required for cartilage imaging. The purposes of this study were (I) to analyze the diagnostic performance in diagnosing artificially produced cartilage lesions in a small joint model using an optimized fat saturated three-dimensional gradient-echo sequence, (II) to relate the lesion size and depth as diagnosed in the magnetic resonance images with the corresponding pathologic findings and (III) to assess signal-to-noise (SNR) ratios for each of the protocols. Twenty-five artificial cartilage lesions were created in the knee joints of 10 rabbits. These specimens and seven specimens without lesions were imaged at 1.5 T using a three-dimensional gradient-echo sequence with varying slice thickness, field of view and matrix. A total of 404 corresponding images were selected, 50% with and 50% without cartilage lesions. Six radiologists scored all images according to five levels of confidence and receiver operating characteristic (ROC) analysis was performed. Lesion size and depth were compared to the corresponding pathological specimen sections. Additionally SNR ratios were calculated. ROC analysis of pooled data from all readers showed the highest area under the ROC curve for the sequence with the highest spatial resolution, while the diagnostic performance was significantly lower in the other sequences (p <0.01). Assessment of the lesion size and depth was correct in 45% and 40% respectively with the highest resolution and in 29% and 23% with the lowest resolution. SNR ratios decreased with increasing spatial resolution. In conclusion this study shows that increasing spatial resolution improves diagnostic performance in cartilage lesions, though SNR decreases substantially. Assessment of correct lesion size and depth still is limited.

Animals↗

The promoter of a gene encoding a novel Dictyostelium spore coat protein.

The cAMP-inducible prespore gene, PL3, encodes a protein which is a novel component of the spore coat. Unlike the well-characterized spore coat proteins (SP60, SP70, and SP96) which are found in the outer layer of the coat, the PL3 gene product is localized to a subregion of the coat beneath the outer proteinaceous layer. Moreover, a substantial portion of the PL3 protein is tightly associated with the spore coat and not released under the conditions that led to the identification of the other coat proteins. The promoter for this novel spore coat gene is described. Unlike the other coat-protein gene promoters, it lacks the extensive CA-type elements. It contains two short CA boxes and five prominent G-rich regions. Sequential deletions from the 5' end of the promoter which remove both CA boxes as well as two of the G-rich regions reduce the level of expression but do not alter the spatial regulation of expression. Despite the sequence differences, the PL3 promoter still confers correct spatial, temporal, and cell type-specific regulation on a reporter gene. Escherichia coli beta-galactosidase enzyme activity expressed under the control of this PL3 promoter first appears in randomly isolated cells at the loose mound stage. Because of the sensitivity of the assay, beta-galactosidase activity is detectable prior to the appearance of the PL3 protein on Western blots and by immunofluorescence. Later the number of cells staining for beta-galactosidase activity and the intensity of staining increases. During tipped mound, slug, and culminant stages, cells expressing beta-galactosidase under the control of the PL3 promoter are localized to prespore regions and are spatially coincident with cells expressing the PL3 protein.

Animals↗

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

BACKGROUND: Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. RESULTS: We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. CONCLUSION: The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

Algorithms↗

Multidimensional sequence learning in patients with focal basal ganglia lesions.

Parkinson's patients have been found to be impaired in learning movement sequences. In the current study, patients with unilateral basal ganglia lesions due to stroke were tested on a serial reaction time task in which responses were based on the spatial location of each stimulus. The spatial locations either followed a fixed sequence or were selected at random, with learning operationalized as the difference in reaction time between these two conditions. In addition, three response-to-stimulus intervals were used, and these either followed a fixed sequence or were randomized. Compared to control participants, the patients showed normal learning of the spatial and temporal sequences, as well as normal cross-dimensional learning. This was true for performance with either the contralesional or ipsilesional hand. Sequence learning was not correlated with maximum tapping rate, a simple measure of motor impairment. These results raise questions concerning the use of Parkinson's disease as a model for studying basal ganglia dysfunction.

Aged↗

Radial GRASE: implementation and applications.

RAD-GRASE is an MRI sequence that combines radial (RAD) k-space scanning with the gradient and spin-echo (GRASE) technique. RAD-GRASE has the advantages of all radial data acquisition methods in that it can reduce motion sensitivity and correct motion-induced data errors, which can be exploited to achieve high-resolution diffusion-weighted imaging (DWI). One can obtain different types of image contrast, including DWI, T(1), T(2), and T(2)*, in RAD-GRASE by controlling the magnetization preparation and sequence timing. Moreover, because there is oversampling of the low spatial frequencies inherent to radial sequences, partial data reconstruction can be used to achieve multiple forms of image contrast from a single acquired data set, and to generate parametric image maps of equilibrium magnetization, T(2), and T(2) (dagger). The RAD-GRASE technique can also be used to achieve fat-suppressed and/or separated fat and water images by choosing the appropriate timing parameters.

Abdomen↗

Sequence homology between encephalomyocarditis virus protein VPI and histidyl-tRNA synthetase supports a hypothesis of molecular mimicry in polymyositis.

The amino acid sequence of histidyl-tRNA synthetase, the Jo-I antigen of polymyositis, has been compared with that of the polyprotein of encephalomyocarditis virus (EMCV), an agent shown recently to produce polymyositis symptoms in mice. It is shown that there is significant sequence homology between a region of the synthetase formerly identified by us as a possible epitope and a region on the coat protein VPI of EMCV. The viral protein also shows significant sequence homology with several muscle proteins. Identification of the likely spatial location of the VPI sequence on the shell of the virus by comparison with two other picornaviruses whose three dimensional structures have been determined, reveals it to be homologous with known immunogenic sites on these viruses. Independent structural localisation of the possible epitope by comparison with two aminoacyl-tRNA synthetases, whose three dimensional structures are known, also reveals that the sequence in question is likely to be favourably placed on histidyl-tRNA synthetase to crossreact with appropriate antibodies. These findings provide more definitive evidence in support of our previous suggestion that molecular mimicry could explain the origin of serum antibodies to aminoacyl-tRNA synthetases in polymyositis and suggests a likely viral etiology for the disease.

Amino Acid Sequence↗

Action of a transposable element in coding sequence fusions.

The original Casadaban technique for isolating fused cistrons encoding hybrid beta-galactosidase proteins used a Mucts62 prophage to align the upstream coding sequence and lacZ prior to selection. Kinetic analysis of araB-lacZ fusion colony emergence indicated that the required DNA rearrangements were regulated and responsive to conditions on selection plates. This has been cited as an example of "directed mutation." Here we show genetically that the MuA and integration host factor (IHF) transposition functions are involved in the formation of hybrid araB-lacZ cistrons and propose a molecular model for how fusions can form from the initial strand-transfer complex. These results confirm earlier indications of direct Mu involvement in the fusion process. The proposed model explains how rearranged Mu sequences come to be found as interdomain linkers in certain hybrid cistrons and indicates that the fusion process involves a spatially and temporally coordinated sequence of biochemical reactions.

Base Sequence↗

A new approach for studying gene regulation by distant DNA elements in transgenic mice.

Apolipoprotein B (apo-B) plays a crucial role in the assembly of lipoproteins in the liver and the intestine. Here, we review how transgenic mouse expression studies with large genomic clones have been used to define distant cis-acting regulatory DNA sequences that control the expression of the apo-B gene. In early studies, apo-B transgenic mice were generated with approximately 80-kb P1 bacteriophage clones spanning either the human or the mouse apo-B genes. Both the human and mouse clones directed high levels of transgene expression in the liver, but transgene expression was absent in the intestine. The absence of transgene expression in the intestine was surprising because both P1 clones contained more than 11 kb of flanking sequences both 5' and 3' to the gene. Subsequently, we isolated and characterized 145-kb and 207-kb bacterial artificial chromosome (BAC) clones that spanned the human apo-B gene. Each of these BAC's contained extensive 5 and 3' flanking sequences and each directed spatially and physiologically appropriate apo-B gene expression in the intestines of transgenic mice. To define the location of the sequences that control intestinal expression of the apo-B gene, we generated transgenic mice by co-microinjecting the approximately 80-kb P1 bacteriophage clone (which did not confer intestinal expression of apo-B) with either the 5' sequences or the 3' sequences from the 145-kb BAC. Analysis of the apo-B expression pattern in those mice revealed that the DNA sequences controlling intestinal expression were located 5' to the apo-B gene. Next, we used recA-assisted restriction endonuclease (RARE) cleavage to truncate specific segments of the 5' and 3' flanking sequences from the 145-kb BAC. A series of the truncated BAC's containing different lengths of 5' and 3' sequences was used to generate more than 40 additional lines of human apo-B transgenic mice. Analysis of human apo-B gene expression in those mice demonstrated that the sequences controlling the expression of the apo-B gene in the intestine are located more than 50 kb 5' to the apo-B gene. Our studies demonstrate that the RARE cleavage/transgenic expression strategy is a powerful approach for examining gene regulation by distant gene-regulatory elements.

Animals↗

Expression of alpha 2-adrenergic receptor subtypes in the mouse brain: evaluation of spatial and temporal information imparted by 3 kb of 5' regulatory sequence for the alpha 2A AR-receptor gene in transgenic animals.

The present studies characterize the expression of the alpha 2A, alpha 2B and alpha 2C adrenergic receptor subtypes via in situ hybridization analysis of messenger RNA expression in the adult mouse brain, as well as the pattern of expression of alpha 2A adrenergic receptor messenger RNA at embryonic day E9.5, the earliest time for detection of the messenger RNA encoding this receptor subtype. alpha 2A adrenergic receptor messenger RNA is highly expressed in the sixth layer of the cortex and the locus coeruleus, alpha 2B adrenergic receptor messenger RNA predominantly in the thalamus and in the Purkinje layer of the cerebellum, and alpha 2C adrenergic receptor messenger RNA in the putamen caudate region of the mouse brain. Both alpha 2A and alpha 2C adrenergic receptor messenger RNA demonstrate strong expression in the amygdaloid complex, hypothalamus, olfactory system and the hippocampal formation. To develop a molecular understanding of the unique cellular expression of messenger RNA encoding the alpha 2A adrenergic receptor subtype, 2.83 kb of the upstream regulatory sequence for the alpha 2A adrenergic receptor gene was fused to the LacZ gene as a reporter gene and expression of beta-galactosidase activity was assessed in transgenic offspring. Although the spatial expression of the transgene in the adult brain often overlaps that for the endogenous alpha 2A adrenergic receptor, both ectopic expression and the absence of appropriate expression were noted; in contrast five of the six lines show temporal expression characteristic of the endogenous alpha 2A adrenergic receptor gene. The present studies provide the first characterization of messenger RNA localization for the three alpha 2 adrenergic receptor subtypes in the mouse CNS. Because the functional roles of the prazosin-sensitive alpha 2B adrenergic receptor and alpha 2C adrenergic receptor subtypes have been masked in most earlier physiological and pharmacological analyses of alpha 2 adrenergic receptor function, identifying the multiple loci alpha 2 adrenergic receptor subtype expression is an important prelude to understanding the functional roles of these three independent receptor populations in the mouse CNS. The findings in the transgenic animals indicating that approximately 3 kb of regulatory sequence has imparted faithful temporal but not spatial expression for the alpha 2A adrenergic receptor gene suggest that additional regulatory information is necessary for appropriate cell specific expression of messenger RNA for the alpha 2A adrenergic receptor subtype.

Amino Acid Sequence↗

Integrated single-cell and spatial transcriptomic analyses reveal malignant epithelial glycolytic heterogeneity and spatial niche remodeling during colorectal cancer progression.

Colorectal cancer (CRC) progression is shaped by metabolic reprogramming and complex interactions within the tumor microenvironment. However, the cellular heterogeneity, spatial organization, and clinical relevance of glycolytic activity in CRC remain incompletely understood. In this study, we integrated single-cell RNA sequencing, bulk transcriptomics, and spatial transcriptomics data to systematically characterize glycolytic heterogeneity in CRC. Glycolytic activity was quantified using five independent scoring methods, consistently showing that epithelial cells exhibited the highest glycolytic activity across the two single-cell cohorts. Stratification of CopyKAT-verified aneuploid malignant epithelial cells into high-glycolysis (HG) and low-glycolysis (LG) subgroups by glycolysis scores revealed that HG cells exhibited higher stemness scores and chromosomal copy number variations. Cell-cell communication analysis revealed that, compared with LG cells, HG cells exhibited increased interaction frequency and strength with immune and stromal populations, indicating enhanced malignant epithelial-microenvironment crosstalk. Spatial transcriptomics analyses further revealed that glycolytic activity varied across normal colorectal tissue, primary CRC, and colorectal liver metastases, accompanied by progressive remodeling of epithelial-associated spatial niches and MIF-mediated intercellular communication. Bulk transcriptomic analysis identified a glycolysis-related prognostic signature with robust predictive performance, which served as an independent prognostic factor for overall survival in CRC cohorts. Collectively, these findings indicate that glycolytic heterogeneity is a key feature of CRC malignant epithelial cells and is closely associated with tumor progression, microenvironmental remodeling, and clinical outcomes.

Humans↗

Organization and discrimination of repeating sound sequences by newborn infants.

A study was conducted to determine whether newborn infants organize auditory streams in a manner similar to that of adults. A series of three experiments investigated the ability of 3- to 4-day-old infants to discriminate repeated rising and falling four-tone sequences in two configurations of source timbre and spatial position. It was hypothesized that if the sequences were organized into two auditory streams on the basis of timbre and spatial position, one of the configurations should be discriminable from its reversal while the other should not. The sequences were tested with different pitch and temporal intervals separating the tones. Sequences were discriminated for the first configuration by adults at both fast tempo/small interval and slow tempo/large interval combinations, while only the latter was discriminated by newborns as measured with a non-nutritive high-amplitude sucking paradigm. Neither adults nor infants could discriminate the sequence reversals for the second configuration. The results suggest that newborn infants organize auditory streams on the basis of source timbre and/or spatial position. They also suggest that newborns have limits in temporal and/or pitch resolution when discriminating tone sequences.

Auditory Perception↗

Spurious signals in DQF spectroscopy: two-shot stimulated echoes.

The most widely used technique for double-quantum filtered (DQF) single-voxel spectroscopy (SVS) is based on a symmetric PRESS sequence with two additional spatially unselective pi/2 pulses, one of which is usually frequency selective. The actual filtering, rejecting signals from all uncoupled resonances, can be done by suitable phase cycling of the rf pulses in successive shots, but in practice gradient filtering is always used. Under usual conditions the sequence repetition time is comparable to the spin-lattice relaxation time, and a stimulated echo is formed by five out of the ten rf pulses in two consecutive shots. This echo is not filtered out by the gradients, and additional phase cycling is needed to eliminate it. Its spatial origin is the full transverse slice selected by the last pulse of the PRESS sequence. The SVS shimming procedure may create an important field variation in this slice (outside the volume of interest VOI). Water singlet signals therefore appear in a band of frequencies other than 4.7 ppm, and remain unaffected by water suppression pulses. In practice phase-alternation schemes can reduce these spurious signals by several orders of magnitude, but even then they may mask the weak metabolite signals of interest. We describe a strategy to minimize these spurious signals and propose a 16-step phase cycling scheme that attenuates the stimulated echo in every two-step subcycle.

Algorithms↗

Regulatory elements from the related spec genes of Strongylocentrotus purpuratus yield different spatial patterns with a lacZ reporter gene.

The Spec1 and Spec2 genes of Strongylocentrotus purpuratus are closely associated with the differentiation of aboral ectoderm. To examine cis-regulatory elements involved in the spatial expression of the Spec genes, we fused the Escherichia coli lacZ gene containing a nuclear targeting signal to 5'flanking DNA plus 5' untranslated leader sequences from Spec1, Spec2a, and Spec2c. All three genes contain 700 bp of highly conserved DNA in their upstream regions, but in Spec1 and Spec2c large insertions interrupt the conserved regions. The Spec-lacZ reporter gene plasmids were microinjected into eggs of S. purpuratus, Lytechinus variegatus, and L. pictus, and beta-galactosidase activity was determined in situ by X-gal staining. The Spec2a-lacZ fusion gene, which contained 1516 bp of 5' flanking DNA and 18 bp of 5' untranslated leader sequence, was preferentially expressed in aboral ectoderm cells in all three species. The Spec1-lacZ fusion gene was expressed in a strikingly different fashion--preferentially in primary and secondary mesenchyme cells, occasionally in aboral ectoderm cells, and less often in oral ectoderm and endoderm cells. The staining pattern was the same in either homologous or heterologous embryos. The Spec2c-lacZ fusion gene, like Spec2a-lacZ, was preferentially expressed in aboral ectoderm, but staining of other cell types was frequently observed. To further delineate sequences required for correct spatial expression, we deleted 800 bp of 5' flanking DNA from the Spec2a-lacZ fusion gene, resulting in a delta Spec2a-lacZ fusion gene that contained only the conserved DNA region. This gene fusion showed preferential expression in aboral ectoderm cells. However, the cell type specificity was not as great as with the parental Spec2a-lacZ plasmid. These experiments implied that the conserved DNA region, associated with all Spec genes examined, was insufficient for complete aboral ectoderm specificity, and suggested that a spatial repressor element existed between -1516 and -697 bp in the 5' flanking DNA of Spec2a.

Animals↗

A common prefrontal-parietal network for mnemonic and mathematical recoding strategies within working memory.

Previous studies have indicated that the lateral prefrontal cortex (LPFC) is closely involved in strategic recoding, even when such processes lessen task demands. For example, 2 studies presented, in the spatial and verbal domains, sequences of stimuli for participants to retain during a short interval and then retrieve. Stimuli were either randomly arranged or structured (forming symmetries and regular shapes for the spatial task and mathematical patterns for the verbal task). Although participants performed the structured tasks better by reorganizing or "chunking" them into more efficient forms, LPFC activity was greater for the structured compared with the random sequences. However, although these results demonstrate that LPFC is involved in strategic recoding, regardless of the type of modality, it remains to be seen whether such a result generalizes to different types of strategic recoding processes. To test this, we presented digit sequence trials that separately emphasized mnemonic or mathematical recoding strategies. While participants were able to gain a performance benefit from either type of recoding strategy, increased LPFC activity was observed for both mathematical and mnemonic recoding trials, compared with either unstructured sequences or control conditions matched for mathematical or mnemonic processes. However, mathematically structured trials activated the LPFC significantly more than mnemonic recoding trials. In addition, lateral posterior parietal cortex was consistently coactivated with LPFC for strategic recoding trials, both in the current experiments and in previous related studies. We conclude that a prefrontal-parietal network is involved in strategic recoding in working memory, regardless of the type of recoding process.

Adult↗

Proton spectral editing in the inhomogeneous radiofrequency field of a surface coil using modified stimulated echoes.

It is shown that the modified stimulated echo sequence, [theta](+/- x +/- y)-t1-[theta](+ x)-t2/2-[2 theta](+ x)-t2/2- [theta](+ x)-t1-Acq(+/- x +/- y), denoted as MSTE[2 theta]x according to the exciter phase of the 2 theta pulse, is able to perform proton spectral editing without difference spectra. On the other hand, this sequence appears to be suitable for spatial localization. Sensitivity and spatial selectivity of MSTE and conventional stimulated echo sequence (STE) are briefly compared. MSTE is applied to editing lactate in the rat brain using the locally restricted excitation of a surface coil.

Animals↗