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Results for “spatial sequencing”

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At least 1,729 records · Page 96Linked to original sources

PubMed1978

Opponent hues in visual masking.

Temporal interactions among opponent and non-opponent hues were investigated in a visual masking paradigm in which both backward and forward temporal sequences were employed. Subjective confidence ratings rather than identification thresholds alone served as response indicators for masking sequences. Results indicate that in the backward sequence (test stimulus followed by masking stimulus) a greater masking effect occurred when the stimuli were of non-opponent hue pairs (red-yellow, red-blue, green-yellow, green-blue) than when compared with opponent hue pairs (red-green, yellow-blue). For the forward sequence (test stimulus preceded by masking stimulus) the masking effect was reduced when compared with the backward sequence. These findings appear to reflect the presumed temporal and spatial antagonistic qualities of opponent hue processes as postulated in the Hering model of color vision.

Color↗

PubMed2000

[Role of MRI in the diagnosis of breast diseases].

UNLABELLED: ADVANTAGES AND LIMITATIONS: Magnetic resonance imaging of the breast is probably the most sensitive method for detecting or ruling out breast disease. It is however not as specific as expected. TECHNIQUE: All examinations are performed with and without gadolinium intravenous administration, excepted in the case of silicone implant reconstruction mammoplasty. Dynamic contrast-enhanced MRI sequences are necessary with a permanent balance between temporal resolution, spatial resolution, and signal. MRI of the breast is not indicated as a routine examination in a screening program, neither to improve the specificity of infra-clinic lesions, nor in simply dense breasts without any known risk factor or in circumscribed masses. INDICATIONS: MRI is best used to improved the sensitivity of mammography and sonography in selected patients. The selected indications are: evaluation of the volume and extension of breast lesions evaluation of the therapeutic response after chemotherapy, and detection or exclusion of the local recurrence in patients with breast conservation therapy. PERSPECTIVES: The future indications and perspectives of MRI include interventional breast radiology (MRI-guided core biopsy), and thermocoagulation therapy. It may be interesting for the evaluation of patients with contrast enhanced MRI lesions with normal mammography and sonography, and also in woman with a genetically defined high breast cancer risk.

Biopsy↗

PubMedDate not supplied

Short echo time MR spectroscopic imaging for neonatal pediatric imaging.

A short echo time (30 milliseconds) MR spectroscopic imaging pulse sequence was implemented for applications of neonatal brain imaging. Multiple spatial saturation bands were used to eliminate strong signals originating from the subcutaneous lipids to enable volumetric region coverage. Metabolite signal intensity-to-noise ratio < or =40 was acquired in 9 minutes of scan time over an 8 x 8 x 8 spatial matrix with 1 cm(3) isoresolution.

Brain Chemistry↗

PubMed1989

[Morphologic mechanisms of blood flow regulation in the hemomicrocirculatory system of the human heart during ontogenesis].

Hearts of 220 human corpses, who had not any cardiovascular system disease during their life, have been distributed into age groups, beginning from fetuses up to old age. By means of injection, silver nitrate impregnation and scanning electron microscopy methods, applied to corrosive preparations, morphological mechanisms of the blood stream regulation in the hemomicrocirculatory bed of the human heart have been revealed in ontogenesis. The first group of the regulation mechanisms includes proper mechanisms inherent in the links of the microbed: spatial orientation of microvessels, precapillary sphincters, anastomoses between these vessels, sequence in arrangement of the endothelial cell nuclei, length, diameter and number of links in the microcirculatory bed. The second group embraces those mechanisms, that depend on structure of the myocardial wall, influencing the microcirculatory bed.

Aging↗

PubMed1994

[Study of femoro-tibial cartilage diseases with MRI].

Magnetic resonance imaging provides excellent tissue contrast resolution and can therefore be used to visualize joint cartilage. The goal of this study was to evaluate the value of magnetic resonance imaging for the diagnosis of femorotibial cartilage lesions. Spin-echo magnetic resonance imaging was performed in 37 patients. As compared with arthroscopy, the accuracy, sensitivity, and specificity of magnetic resonance imaging were 72.5%, 47%, and 95.5%, respectively. Only advanced cartilage lesions with exposure of subchondral bone were clearly seen on magnetic resonance sections. Limiting factors included insufficient spatial resolution and the chemical shift phenomenon. Spin-echo sequences used in everyday practice are not appropriate for detecting small cartilage lesions. Controlled studies are needed to determine whether gradient echo sequences are more satisfactory.

Adult↗

PubMed1995

Photolabile oligoDNA probes of internal Escherichia coli ribosomal structure.

We are examining the spatial arrangement of ribosomal components in the vicinity of rRNA sequences of particular significance for ribosome structure and function through the use of radioactive, photolabile derivatives of oligoDNAs complementary to such sequences. The oligoDNA probes bind to their target sequences in intact ribosomal subunits, and, on photolysis, incorporate into neighboring ribosomal components. Labeled ribosomal proteins are subsequently identified by SDS-PAGE, RP-HPLC and immunoprecipitation. Labeled rRNA is identified at the nucleotide level by RNase H cleavage and primer extension. The results obtained provide a description of the neighborhood surrounding a particular rRNA sequence and impose important constraints on the evolving three-dimensional models of both the 30S and 50S subunits, since they typically oblige several ribosomal components to fall within defined distances of the targeted rRNA. Our results will be discussed in terms of these models, emphasizing their consistency or inconsistency.

Base Sequence↗

PubMed1998

Minimal sizes of deletions detected by comparative genomic hybridization.

Comparative genomic hybridization (CGH) has been used widely for the molecular cytogenetic analysis of tumors. Until now, the spatial resolution of this technique for diagnosing deletions of chromosomal sequences has not been assessed in detail. In the present study, we performed CGH analyses on five DNA samples derived from B-cell leukemias with 11q deletions, the sizes of which ranged from 3 Mbp to 14-18 Mbp. CGH experiments were evaluated by two established commercial analysis systems. Deletions down to a size of 10-12 Mbp were diagnosed based on a diagnostic threshold value of 0.8, if the vast majority of cells carried the deletion. For cases with smaller deletions, the ratio profiles were shifted toward underrepresentation at the respective chromosomal bands; however, the diagnostic threshold value was not reached. In all five cases, there was complete agreement between the two image analysis systems.

Chromosome Deletion↗

PubMed1997

Anatomical and microstructural factors affecting the electrical activity of the heart. Experimental findings and mathematical simulations.

We developed an experimental preparation in which we record 1500 intramural electrograms from the ventricular walls of an isolated dog heart. The heart is plunged into an electrolytic tank shaped as a human thorax. The tank carries 1300 electrodes uniformly distributed in the conducting volume and on its surface. We obtain 2800 electric signals which enable us to define the spread of excitation and the sequence of repolarization in the heart, and to map the spatial distribution of potentials and currents in the heart, in the chest and on the body surface during a heart beat. Experimental results and mathematical simulations show that excitation, repolarization, the spatial distribution of heart potentials and the shape of the electrocardiograms are dominated by a small number of anatomical factors, namely: the geometry of the ventricles, the epi-endocardial rotation of myocardial fibers orientation in the ventricular walls, the obliqueness of the fibers relative to the epicardial surface and structure of the conduction system.

Animals↗

PubMed1998

Spatio-temporal influences at the neural level of object recognition.

In late 1988, Miyashita published work reporting recordings of single cells in the inferotemporal cortex of the macaque monkey (Miyashita 1988 Nature 335 817-20). He described the responses of neurons to a sequence of random fractal pattern images, and how many of the neurons tested were seen to respond strongly to a subset of the images on the basis of sequence presentation order, i.e. appearance in time, rather than their spatial similarity. In this work, I describe a local Hebb-like learning rule which in conjunction with a simple feedforward neural architecture is capable of replicating the type of temporal-order association apparent in the cells from which he made recordings. The paper also advances reasons for requiring such learning by describing its possible role in establishing transformation invariant representations of objects.

Animals↗

PubMed1998

Functional magnetic resonance imaging of motor, sensory, and posterior parietal cortical areas during performance of sequential typing movements.

We investigated the activation of sensory and motor areas involved in the production of typing movements using functional magnetic resonance imaging (fMRI). Eleven experienced typists performed tasks, in which the spatial and temporal requirements as well as the number of digits involved were varied. These included a simple uni-digit repetitive task, a uni-digit sequential task, a dual-digit sequential task, a multi-digit sequential task, and typing text from memory. We found that the production of simple repetitive keypresses with the index finger primarily involved the activation of contralateral primary motor cortex (M1), although a small activation of the supplementary motor area (SMA) and other regions was sometimes observed as well. The sequencing of keypresses involved bilateral M1 and a stronger activation of the SMA and to a lesser extent the premotor area, cingulate gyrus, caudate, and lentiform nuclei. However, the activation of these areas did not exclusively depend on the complexity of the movements, since they were often activated during more simple movements, such as alternating two keypresses repeatedly. Somatosensory and parietal regions were also found to be activated during typing sequences. The activation of parietal areas did not exclusively depend on the spatial requirements of the task, since similar activation was observed during movements within intra-personal space (finger-thumb opposition) and may instead be related to the temporal requirements of the task. Our findings suggest that the assembly of well-learned, goal-directed finger movement sequences involves the SMA and other secondary motor areas as well as somatosensory and parietal areas.

Adult↗

PubMed1991

Effects of acute aspartame and acute alcohol ingestion upon the cognitive performance of pilots.

Anecdotal evidence has associated the artificial sweetener aspartame with a number of symptoms of central nervous system (CNS) dysfunction. There are, however, little scientific data concerning the effect of aspartame upon complex mental operations such as those necessary for flying an aircraft. Thirteen pilots were tested in a double-blind study using the SPARTANS cognitive test battery of aviation-relevant information-processing tasks. These tasks relate to perceptual-motor abilities, spatial abilities, working memory, attentional performance, risk taking, processing flexibility, planning and sequencing ability. Subjects were tested over five sessions consisting of pretest and posttest controls and three randomly ordered treatment sessions. The treatment conditions involved an aspartame dose of 50 mg/kg body weight, a placebo condition, and an ethyl alcohol (0.1% BAL) condition as the positive control. No detectable performance decrements were associated with the aspartame condition, although decrements in psychomotor and spatial abilities were detected in the ethanol condition. Results were found to be consistent with prior flight-simulator studies of alcohol, but do not appear to support the concerns expressed in anecdotal testimony regarding the deleterious effects of aspartame upon cognitive performance.

Aerospace Medicine↗

PubMed2005

Spatial epidemiology and natural population structure of Campylobacter jejuni colonizing a farmland ecosystem.

Recent progress in determining the population structure of Campylobacter jejuni, and discerning associations between genotypes and specific niches, has emphasized the shortfall in our understanding of the ecology and epidemiology of this bacterium. We examined the natural structure of the C. jejuni community associated with cattle farmland in the UK by structured spatiotemporal sampling of habitats, including livestock and wild animal faeces, environmental water and soil, over a 10-week period within a 100 km2 area. A total of 172 isolates were characterized using multilocus sequence typing into 65 sequence types (STs). Isolates from cattle faeces were significantly over-represented in the ST-61 complex, whereas isolates from wildlife faeces and water were more likely to belong to the ST-45 complex and a number of unusual STs, many of which were first encountered during this study. Sampling within a narrow spatiotemporal window permitted the application of novel statistical methods exploring the relationship between the genetic relatedness and spatial separation of isolates. This approach showed that isolates from the same sampling squares and squares separated by <1.0 km were genetically more similar than isolates separated by greater distances. Our study demonstrates the potential of multilocus sequence typing combined with spatial modelling in exploring natural transmission pathways for C. jejuni.

Agriculture↗

PubMed1996

Accurate velocity mapping with FAcE.

Spin dislocation between the slice selection, phase encoding, and frequency encoding is a source of image distortions. Two strategies can be pursued to improve the appearance of moving spins in an image. Either the sequence is made equally sensitive to velocity-dependent dislocation artifacts for all spatial directions or the sensitivity is reduced with a shorter echo time. The first approach increases the dislocation for the phase-encoding direction and is therefore not useful if velocity maps with minimal distortion are the goal. FAcE (FID acquired echoes) is a sequence with separate sampling of the left and right k-space half-planes that allows for very short echo times. It was applied for velocity mapping of flow in the slice select direction. Special attention was paid to a compact design of the velocity-encoding select gradient to achieve short echo times even with high velocity sensitivity. Artifacts introduced by in-plane motion were studied for FAcE and conventional gradient-echo sequences, both in phantom experiments and simulation. FAcE allows for very short echo times with inherent motion compensation of the frequency-encoding gradient. Thus, both motion-related dislocation artifacts and signal voids due to coherence loss in regions with irregular flow are minimal.

Artifacts↗

PubMed2002

[MRI of intraosseous fistulous systems and sequesters in chronic osteomyelitis with standard spin echo sequences, highly selective chemical-shift imaging, diffusion weighted imaging, and magnetization-transfer].

PURPOSE: To study and test the impact of modern MRI techniques in diagnostic imaging in the evaluation of intra-osseous fistulous systems and sequesters. MATERIALS AND METHODS: In a prospective study, nine patients with chronic osteomyelitis of the legs were examined by MRI. Patients with clinical signs of osteomyelitis requiring surgery were included in the study. T1-weighted spin echo (SE) sequences, proton density (PD) and T2-weighted fast spin echo (FSE) sequences, water- and fat-selective FSE sequences, and diffusion weighted (DW) PSIF sequences were used preoperatively. Furthermore, magnetizing transfer (MT) with gradient echo (GRE) sequences was evaluated. RESULTS: Water selective sequences revealed the highest sensitivity for the detection of fistulas (100%), providing the best delineation of the extent of the entire fistulous systems. Fat-selective sequences (sensitivity 55.6%) and T1-weighted sequences (sensitivity 77.8%) displayed fistulas as hypointense bands, which, however, cannot be well differentiated from cortical bone in the transcortical areas. PD and T2-weighted images were found to have a poor sensitivity (55.6% and 66.7%) for fistulas in any location. The sensitivity of water-selective sequences to demonstrate intraosseous sequesters was 100%. The sensitivity was low for the other sequences. In 4 of 5 patients with surgically proven infection, DW and MT revealed an abnormal spatial distribution, with high diffusion in the central parts of the fistulas and high MT effect peripherally surrounding a weak MT effect centrally. CONCLUSION: Water-selective sequences are superior when demonstrating fistulous systems and intraosseous sequesters. The combined use of MT and DW sequences seems to allow a differentiation between solid granulation tissue and liquid pus.

Adult↗

PubMed2003

A PRESTO-SENSE sequence with alternating partial-Fourier encoding for rapid susceptibility-weighted 3D MRI time series.

A 3D sequence for dynamic susceptibility imaging is proposed which combines echo-shifting principles (such as PRESTO), sensitivity encoding (SENSE), and partial-Fourier acquisition. The method uses a moderate SENSE factor of 2 and takes advantage of an alternating partial k-space acquisition in the "slow" phase encode direction allowing an iterative reconstruction using high-resolution phase estimates. Offering an isotropic spatial resolution of 4 x 4 x 4 mm(3), the novel sequence covers the whole brain including parts of the cerebellum in 0.5 sec. Its temporal signal stability is comparable to that of a full-Fourier, full-FOV EPI sequence having the same dynamic scan time but much less brain coverage. Initial functional MRI experiments showed consistent activation in the motor cortex with an average signal change slightly less than that of EPI.

Algorithms↗

PubMed2026

Genome-informed qPCR tracking revealed preferential persistence of Bacillus subtilis BS9 in the broiler chicken gastrointestinal tract.

This study aimed to develop a strain-specific quantitative PCR (qPCR) assay for Bacillus subtilis BS9 and characterize its persistence and spatial distribution in the broiler chicken gastrointestinal tract. Whole-genome sequencing and comparative genomic analysis identified a unique 110-bp sequence within a strain-specific genomic island, which was used to design a highly specific qPCR assay with excellent efficiency and sensitivity. In a 14-day in vivo trial, broiler chicks receiving daily oral doses of BS9 were analyzed using both culture-based methods and the newly developed qPCR. The assay was applied qualitatively, presence or absence, to detect BS9 in intestinal samples. BS9 was detected exclusively in the duodenum, jejunum, and cecum, with no presence in the gizzard or ileum. These findings demonstrate that BS9 exhibits region-specific persistence in the gut, likely reflecting adaptation to distinct physiological niches, which may contribute to its probiotic mechanisms.IMPORTANCEThis work provides the first detailed account of B. subtilis BS9's spatial persistence in poultry, revealing preferential adherence to specific intestinal regions. The strain-specific qPCR assay developed here offers a precise, culture-independent tool for tracking BS9 in complex gut environments. These insights into the genetic basis and tissue tropism of BS9 persistence advance our understanding of probiotic-host interactions and establish a framework for characterizing novel probiotic strains.

Bacillus subtilis↗

PubMedDate not supplied

Both upstream and intragenic sequences of the human neurofilament light gene direct expression of lacZ in neurons of transgenic mouse embryos.

Initial expression of the neurofilament light gene coincides with the appearance of postmitotic neurons. To investigate the molecular mechanisms involved in neuron-specific gene expression during embryogenesis, we generated transgenic mice carrying various regions of the human neurofilament light gene (hNF-L) fused to the lacZ reporter gene. We found that 2.3 or 0.3 kb of the hNF-L promoter region directs expression of lacZ in neurons of transgenic embryos. Addition of 1.8 kb hNF-L intragenic sequences (IS) enlarges the neuronal pattern of transgene expression. The 2.3-kb hNF-L promote lacZ-IS construct contains all regulatory elements essential for both spatial and temporal expression of the hNF-L gene during embryogenesis and in the adult. The use of a heterologous promoter demonstrated that the 1.8-kb hNF-L intragenic sequences are sufficient to direct the expression of lacZ in a NF-L-specific manner both temporally and spatially during development and in the adult. We conclude that these hNF-L intragenic sequences contain cis-acting DNA regulatory elements that specify neuronal expression. Taken together, these results show that the neurofilament light gene contains separate upstream and intragenic elements, each of which directs lacZ expression in embryonic neurons.

Animals↗

PubMed1996

Mapping of a regulatory important site for protein kinase C phosphorylation in the N-terminal domain of annexin II.

Annexin II is a Ca(2+)-regulated membrane- and cytoskeleton-binding protein implicated in membrane transport events along the Ca(2+)-regulated secretory and the early endocytic pathway. Biochemical properties of this annexin and its intracellular distribution are regulated by complex formation with p11 (S100A10), a member of the S100 protein family. The annexin II-p11 interaction is mediated through the unique N-terminal domain of annexin II and is inhibited by protein kinase C phosphorylation of a serine residue in annexin II. To map this regulatory serine phosphorylation site we developed a baculovirus-mediated expression system for wild-type annexin II and for a series of annexin II mutants which contained substitutions in one or more serine residues present in the N-terminal domain. The different mutant derivatives were purified and shown to display the same biochemical properties as recombinant wild-type annexin II and the authentic protein purified from porcine intestine. However, significant differences in phosphate incorporation were observed when the individual serine mutants were subjected to phosphorylation by protein kinase C. A comparison of the phosphorylation patterns obtained identified Ser-II as the protein kinase C site responsible for regulating the annexin II-p11 interaction. Ser-II lies within the sequence mediating p11 binding, i.e. amino-acid residues 1 to 14 of annexin II, and phosphorylation at this site most likely leads to a direct spatial interference with p11 binding.

Amino Acid Sequence↗