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PubMed2000

Modeling dynamic PET-SPECT studies in the wavelet domain.

This work develops a theoretical framework and corresponding algorithms for the modeling of dynamic PET-SPECT studies both in time and space. The problem of estimating the spatial dimension is solved by applying the wavelet transform to each scan of the dynamic sequence and then performing the kinetic modeling and statistical analysis in the wavelet domain. On reconstruction through the inverse wavelet transform, one obtains parametric images that are consistent estimates of the spatial patterns of the kinetic parameter of interest. The theoretical setup allows the use of linear techniques currently used in PET-SPECT for kinetic analysis. The method is applied to artificial and real data sets. The application to dynamic PET-SPECT studies was performed both for validation purposes, when the spatial patterns are known, and for illustration of the advantages offered by the technique in case of tracers with an unknown pattern of distribution.

Benzamides↗

PubMed1999

Molecular aspects and natural source of procalcitonin.

The search for sensitive and specific markers of systemic infection has shown that procalcitonin levels are increased in sepsis, and, consequently, this plasma protein has come into the focus of clinical research. Human procalcitonin is encoded by the Calc-l gene, which gives rise to two alternatively spliced transcripts. Despite systemic investigation of the Calc-l gene and mechanisms of the tissue-specific regulation and alternative splicing, little is known about the biology of procalcitonin and the cells which express this protein during inflammation. Here we focus on the molecular and biochemical properties of the molecule and summarize the known biological functions of procalcitonin. We report on the structure of the Calc-l gene, the amino acid conservation of procalcitonin in different species, and the consensus sequences of the protein with regard to sites relevant for posttranslational modification, spatial distribution, and homologies to other cytokines. We discuss aspects of intracellular location of procalcitonin and demonstrate that it has the characteristics of a secreted protein.

Alternative Splicing↗

PubMed2003

Optimal transsaccadic integration explains distorted spatial perception.

We scan our surroundings with quick eye movements called saccades, and from the resulting sequence of images we build a unified percept by a process known as transsaccadic integration. This integration is often said to be flawed, because around the time of saccades, our perception is distorted and we show saccadic suppression of displacement (SSD): we fail to notice if objects change location during the eye movement. Here we show that transsaccadic integration works by optimal inference. We simulated a visuomotor system with realistic saccades, retinal acuity, motion detectors and eye-position sense, and programmed it to make optimal use of these imperfect data when interpreting scenes. This optimized model showed human-like SSD and distortions of spatial perception. It made new predictions, including tight correlations between perception and motor action (for example, more SSD in people with less-precise eye control) and a graded contraction of perceived jumps; we verified these predictions experimentally. Our results suggest that the brain constructs its evolving picture of the world by optimally integrating each new piece of sensory or motor information.

Humans↗

PubMed1998

Release from masking due to spatial separation of sources in the identification of nonspeech auditory patterns.

A nonspeech pattern identification task was used to study the role of spatial separation of sources on auditory masking in multisource listening environments. The six frequency patterns forming the signal set were comprised of sequences of eight 60-ms tone bursts. Bursts of masking sounds were played synchronously with the signals. The main variables in the study were (1) the difference in spatial separation in the horizontal plane between signals and maskers and (2) the nature of the masking produced by the maskers. Spatial separation of signal and masker ranged from 0-180 degrees. The maskers were of two types: (1) a sequence of eight 60-ms bursts of Gaussian noise intended to produce predominantly peripherally based "energetic masking" and (2) a sequence of eight 60-ms bursts of eight-tone complexes intended to produce primarily centrally based "informational masking." The results indicated that identification performance improved with increasing separation of signal and masker. The amount of improvement depended upon the type of masker and the center frequency of the signal patterns. Much larger improvements were found for spatial separation of the signal and informational masker than for the signal and energetic masker. This was particularly apparent when the acoustical advantage of the signal-to-noise ratio in the more favorable of the two ears (the ear nearest the signal) was taken into account. The results were interpreted as evidence for an important role of binaural hearing in reducing sound source or message uncertainty and may contribute toward solving the "cocktail party problem."

Adult↗

PubMed2004

Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold.

EcoRII is a type IIE restriction endonuclease that interacts with two copies of the DNA recognition sequence 5'CCWGG, one being the actual target of cleavage, the other serving as the allosteric effector. The mode of enzyme activation by effector binding is unknown. To investigate the molecular basis of activation and cleavage mechanisms by EcoRII, the crystal structure of EcoRII mutant R88A has been solved at 2.1A resolution. The EcoRII monomer has two domains linked through a hinge loop. The N-terminal effector-binding domain has a novel DNA recognition fold with a prominent cleft. The C-terminal catalytic domain has a restriction endonuclease-like fold. Structure-based sequence alignment identified the putative catalytic site of EcoRII that is spatially blocked by the N-terminal domain. The structure together with the earlier characterized EcoRII enzyme activity enhancement in the absence of its N-terminal domain reveal an autoinhibition/activation mechanism of enzyme activity mediated by a novel effector-binding fold. This is the first case of autoinhibition, a mechanism described for many transcription factors and signal transducing proteins, of a restriction endonuclease.

Allosteric Regulation↗

PubMed2003

Single excitation multiple image RARE (SEMI-RARE): ultra-fast imaging of static and flowing systems.

This paper describes the development and application of a new rapid, full k-space acquisition imaging pulse sequence based on the rapid acquisition with relaxation enhancement (RARE) methodology. We have termed this pulse sequence single excitation multiple image RARE (SEMI-RARE). We demonstrate the application of SEMI-RARE to the visualisation of a static liquid phantom and it is shown that up to 120 images can be acquired from a single excitation. By exploiting the inherent relaxation and diffusion contrast within the series of images, the SEMI-RARE provides an ultra-fast method for characterising the spatial distribution of chemical species and phases within complex systems. The pulse sequence is then applied to the study of single- and two-phase flow in a single narrow tube of inner diameter 2.9mm. In particular, it is shown that 8 two-dimensional slice-selective images for two-phase bubble-train flow in a single tube can be acquired from a single excitation at effective echo-times of 37, 109, 181, 253, 325, 397, 469, and 541ms. The visualisation enables the determination of gas/liquid bubble sizes and velocities during two-phase flow. We also report the first direct evidence, obtained from magnetic resonance measurements, of liquid re-circulation zones associated with bubble-train flow. The robustness of the SEMI-RARE technique makes it an attractive fast imaging technique for the study of multi-phase flow phenomena, which are often characterised by large variations in magnetic susceptibility, and are of widespread interest in chemical engineering.

Journal Article↗

PubMed2000

Dynamic three-dimensional magnetic resonance abdominal angiography and perfusion: implementation and preliminary experience.

Implementation of and preliminary experience with an ultra-fast partial-Fourier radiofrequency (RF) spoiled gradient-echo sequence for gadolinium-enhanced imaging are presented. Three-dimensional angiograms can be acquired in less than 6 seconds. Repetition of the acquisition allows the three-dimensional visualization of several distinct vascular phases. Feasibility is demonstrated in three healthy volunteers. The trade-offs among spatial resolution, temporal resolution, and spatial coverage as well as the technical aspects of gadolinium-enhanced pulse sequences are discussed.

Abdomen↗

PubMed2000

Temperature monitoring of internal body heating induced by decoupling pulses in animal (13)C-MRS experiments.

A temperature monitoring method to promote safety with regard to tissue heating induced by RF irradiation during MRI procedures, especially carbon-13 magnetic resonance spectroscopy ((13)C-MRS), is proposed. The method is based on the temperature dependence of the water proton chemical shift (-0.01 ppm/ degrees C) combined with phase mapping. Using this method, temperature changes were measured in rats (n = 4) employing practical (1)H-decoupled (13)C-MRS pulse sequences for 1D projections (TR = 1000 ms, acquisition time = 15 ms, matrix = 256, spatial resolution = 0.2 mm) and 2D images (TR = 1500 ms, acquisition time = 840 ms, matrix = 128x32, spatial resolution = 0.8x1.5 mm). Measurement error was 0.18 degrees C (SD) for 1D acquisition and 0.39 degrees C (SD) for 2D acquisition, demonstrating the feasibility of this temperature mapping method. Further studies should be conducted in human subjects to monitor patient safety and to optimize the pulse sequences employed. Magn Reson Med 43:796-803, 2000.

Animals↗

PubMed2000

Characterization of a zebrafish (Danio rerio) desmin cDNA: an early molecular marker of myogenesis.

Desmin is a muscle-specific protein and a constitutive subunit of the intermediate filaments (IF) in skeletal, cardiac and smooth muscles. It is an early marker of skeletal muscle myogenesis. We have characterized a clone of desmin cDNA from an embryonic zebrafish (Danio rerio) cDNA library. The full-length cDNA comprised 1798 nucleotides, encoding a protein of 473 amino acids. The predicted amino acid sequence of the zebrafish desmin shares a high degree of similarity to other vertebrate desmins, but also contains a sequence at the carboxyl terminal of the tail domain that is unique to the zebrafish. It carries many features which are distinctive of IF subunit proteins. These include the T/SSYRRXF/Y motif in the head domain, and the intermediate filament signature consensus, [I/V]-X-[T/A/C/I]-Y-[R/K/H]-X-[L/M]-L-[D/E], located in the carboxyl terminus of the central helical rod. Unlike other 3' UTR sequences, the 3' UTR of the zebrafish cDNA sequence has two CAYUG elements flanking a single polyadenylation site. The temporal and spatial expression patterns of desmin mRNA during early zebrafish development were studied. The onset of desmin expression occurred at the 1-3 somite stage (11 hpf). It increased throughout somitogenesis, with maximum expression at the Prim-6 stage (25 hpf), and decreasing expression towards the protruding-mouth stage (72 hpf). Desmin mRNA was initially localised exclusively to the somites, but was subsequently also detected in other musculature in the developing heart and fins. The onset of expression and the spatial localization of desmin mRNA in the zebrafish coincides with that reported for MyoD and myogenin.

Amino Acid Sequence↗

PubMed2000

High-resolution CMR(O2) mapping in rat cortex: a multiparametric approach to calibration of BOLD image contrast at 7 Tesla.

The blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) method, which is sensitive to vascular paramagnetic deoxyhemoglobin, is dependent on regional values of cerebral metabolic rate of oxygen utilization (CMR(O2)), blood flow (CBF), and volume (CBV). Induced changes in deoxyhemoglobin function as an endogenous contrast agent, which in turn affects the transverse relaxation rates of tissue water that can be measured by gradient-echo and spin-echo sequences in BOLD fMRI. The purpose here was to define the quantitative relation between BOLD signal change and underlying physiologic parameters. To this end, magnetic resonance imaging and spectroscopy methods were used to measure CBF, CMR(O2), CBV, and relaxation rates (with gradient-echo and spin-echo sequences) at 7 Tesla in rat sensorimotor cortex, where cerebral activity was altered pharmacologically within the autoregulatory range. The changes in tissue transverse relaxation rates were negatively and linearly correlated with changes in CBF, CMR(O2), and CBV. The multiparametric measurements revealed that CBF and CMR(O2) are the dominant physiologic parameters that modulate the BOLD fMRI signal, where the ratios of (deltaCMR(O2)/CMR(O2)/(deltaCBF/ CBF) and (deltaCBV/CBV)/(deltaCBF/CBF) were 0.86 +/- 0.02 and 0.03 +/- 0.02, respectively. The calibrated BOLD signals (spatial resolution of 48 microL) from gradient-echo and spin-echo sequences were used to predict changes in CMR(O2) using measured changes in CBF, CBV, and transverse relaxation rates. The excellent agreement between measured and predicted values for changes in CMR(O2) provides experimental support of the current theory of the BOLD phenomenon. In gradient-echo sequences, BOLD contrast is affected by reversible processes such as static inhomogeneities and slow diffusion, whereas in spin-echo sequences these effects are refocused and are mainly altered by extravascular spin diffusion. This study provides steps by which multiparametric MRI measurements can be used to obtain high-spatial resolution CMR(O2) maps.

Animals↗

PubMedDate not supplied

Is monocular perception of depth through the rigid endoscope a disadvantage compared to binocular vision through the operating microscope in paranasal sinus surgery?

Vision through the endoscope is strictly monocular. Perception of depth (stereopsis) during ethmoid surgery through the operating microscope would be expected to be superior due to binocular view. To investigate whether monocularity of the endoscope is a disadvantage in paranasal sinus surgery, we compared stereoacuity in a model of the nasal cavity using a headlamp, an operating microscope, and a 0 degree-Hopkins-endoscope. Twenty volunteers were asked to touch defined points in a spatial model of the nasal cavity. Due to the configuration of the model, which allowed binocular vision of all contact points with headlamp, performance was significantly better than with optical instruments. Manipulations were performed faster with the endoscope than with the microscope. Under microscopic guidance more faults in point sequence were made than with the endoscope. Various monocular phenomena obviously allow sufficient spatial orientation through the endoscope, so that monocularity of the endoscope appears not to be a disadvantage for quick and safe manipulations during functional endoscopic sinus surgery.

Depth Perception↗

PubMed1993

Role of the left and right supplementary motor areas in memory-guided saccade sequences.

Six right-handed patients with a lesion affecting the left (3 patients) or right (3 patients) supplementary motor area were studied using single and sequential memory-guided saccade paradigms. Accuracy of single saccades was preserved in both groups, compared to control subjects, and the chronology of saccade sequences was disturbed in the group with the left lesion but not in the group with the right lesion. The results suggest that neither side of the supplementary motor area is involved in spatial memory, and that the left supplementary motor area plays a greater role in motor sequencing than does the right supplementary motor area.

Adult↗

PubMed2026

Spatial mapping of RNA turnover kinetics in the mouse brain.

Gene regulation requires coordinated control of RNA synthesis and degradation, yet measuring RNA turnover across intact tissues remains challenging. Here we present spatial NT-seq, a method that combines transgenesis-free metabolic RNA labeling with in situ chemical recoding on spatial transcriptomics platforms to co-map newly synthesized and pre-existing RNAs. Applying spatial NT-seq to the mouse brain reveals pronounced regional heterogeneity in RNA turnover and identifies the dentate gyrus as a spatial hotspot marked by coordinated upregulation of basal RNA synthesis and decay. Moreover, spatial NT-seq uncovers rapid, brain region-specific transcriptional and post-transcriptional responses to electroconvulsive stimulation, a clinically relevant treatment for refractory depression. Finally, we leverage computational modeling to identify sequence features and post-transcriptional regulators that shape transcriptome-wide mRNA stability across spatial and cellular contexts in the mouse brain. Together, this integrated 'in vivo timescope' framework provides a spatially resolved view of RNA turnover kinetics and reveals the regulatory architecture of RNA stability in vivo.

Journal Article↗

PubMed1994

spalt encodes an evolutionarily conserved zinc finger protein of novel structure which provides homeotic gene function in the head and tail region of the Drosophila embryo.

The region specific homeotic gene spalt (sal) of Drosophila melanogaster promotes the specification of terminal pattern elements as opposed to segments in the trunk. Our results show that the previously reported sal transcription unit was misidentified. Based on P-element mediated germ line transformation and DNA sequence analysis of sal mutant alleles, we identified the transcription unit that carries sal function. sal is located close to the misidentified transcription unit, and it is expressed in similar temporal and spatial patterns during embryogenesis. The sal gene encodes a zinc finger protein of novel structure composed of three widely spaced 'double zinc finger' motifs of internally conserved sequences and a single zinc finger motif of different sequence. Antibodies produced against the sal protein show that sal is first expressed at the blastoderm stage and later in restricted areas of the embryonic nervous system as well as in the developing trachea. The antibodies detect sal homologous proteins in corresponding spatial and temporal patterns in the embryos of related insect species. Sequence analysis of the sal gene of Drosophila virilis, a species which is phylogenetically separated by approximately 60 million years, suggests that the sal function is conserved during evolution, consistent with its proposed role in head formation during arthropod evolution.

Amino Acid Sequence↗

PubMed1994

Alignment of (dA).(dT) homopolymer tracts in gene flanking sequences suggests nucleosomal periodicity in D. discoideum DNA.

It has been shown that the frequency versus size distribution of A and T overlapping and non-overlapping homopolymer tracts of N > 5 in D. discoideum gene flanking and intron regions are significantly greater than in coding regions(1). In the present report, we demonstrate, that a spatial periodicity exists in long A and T tracts (N > 10) in long flanking sequences by scored alignments of those tracts (N > 10) with the nucleosomal repeat. A tract spacing was found at 185-190 bp that corresponds to a maximum alignment score. This is exactly the average spacing of D. discoideum nucleosomes determined experimentally. A majority of A and T tracts in flanking sequences are often spaced by short DNA stretches and the total length of adjacent A and T tracts plus the interrupting short DNA stretch corresponds closely to the average experimentally measured nucleosomal linker DNA size in D. discoideum-42 bp. These data suggest a model which has A and T runs of N > 10 bp in flanking DNA of D. discoideum organized in a regular phase with nonhomopolymer sequences along the DNA. This model has functional implications for A and T tracts, suggesting that they are found in nucleosomal linker DNA regions of chromatin during some necessary portion(s) of the life of the cell.

Animals↗

PubMed1982

Complete nucleotide sequences of the coat protein messenger RNAs of brome mosaic virus and cowpea chlorotic mottle virus.

The nucleotide sequences of the subgenomic coat protein messengers (RNA4's) of two related bromoviruses, brome mosaic virus (BMV) and cowpea chlorotic mottle virus (CCMV), have been determined by direct RNA and CDNA sequencing without cloning. BMV RNA4 is 876 b long including a 5' noncoding region of nine nucleotides and a 3' noncoding region of 300 nucleotides. CCMV RNA 4 is 824 b long, including a 5' noncoding region of 10 nucleotides and a 3' noncoding region of 244 nucleotides. The encoded coat proteins are similar in length (188 amino acids for BMV and 189 amino acids for CCMV) and display about 70% homology in their amino acid sequences. Length difference between the two RNAs is due mostly to a single deletion, in CCMV with respect to BMV, of about 57 b immediately following the coding region. Allowing for this deletion the RNAs are indicate that mutations leading to divergence were constrained in the coding region primarily by the requirement of maintaining a favorable coat protein structure and in the 3' noncoding region primarily by the requirement of maintaining a favorable RNA spatial configuration.

Amino Acid Sequence↗

PubMed2005

Using BAC clones to characterize unbalanced chromosome abnormalities in interphase cells.

Carriers of balanced translocations usually carry alterations in gene sequences, which lead to dysfunction during early and late embryogenesis. Related spatial rearrangement causes either cumulative delay in cell cycles and/or anomalies in transcription and translation. This has also an important impact at the time of genomic activation, the longest cell cycle of preimplantation development. Carrier patients may be affected either with primary infertility or by repeated miscarriages [Hum. Reprod. 12 (1997) 2019.]. Assuming that a fraction of the germ cells is karyotypically normal, these patients would greatly benefit from efficient procedures for generation and use of breakpoint-specific DNA hybridisation probes in preconception and preimplantation genetic diagnosis (PGD) after polar body or blastomere biopsy of the embryos. The objective of this research was to design an approach of patient-specific probes for preimplantation diagnosis of chromosome translocations and which could be used eventually to select chromosomally normal embryos from balanced or unbalanced interphase cells prior to their transfer to the mother's womb. This approach was used for a couple, where the female partner was a carrier of a balanced translocation 46,XX,t(4;12)(p16.1;q24.31). First, BAC/PAC clones were chosen from specific chromosome bands from the genome sequence that hybridise adjacent to the chromosomal breakpoints or span them. Then, the probes and hybridisation conditions were optimised using unrelated normal amniocytes, lymphoblastoid cells and lymphocytes from the carrier to increase hybridisation signal intensity and decrease background. Finally, the probes were tested on target cells before they were used for mimicking preconception or preimplantation genetic diagnosis. Three slides were analysed blindly from a normal karyotype, an unbalanced and a balanced translocation. A total of 78 cells were analysed of which in the slide A 19/22 (86%) were found to be unbalanced, in slide B 25/31 (81%) were normal and in slide C 21/25 (84%) were balanced. Thus, it was demonstrated that cells with known structural abnormalities could be detected, based on hybridisation of breakpoint spanning bacterial artificial chromosome (BAC) DNA probes in interphase cells.

Adult↗

PubMed1995

[Temporal and spatial pattern analysis of pharyngeal swallowing in patients with abnormal sensation in the throat].

There are many patients who complain of abnormal sensations, such as an obstructive sensation, foreign body sensation, difficulty in swallowing, etc., in the throat, which do not have an obvious cause. The causes of such unpleasant symptoms have not been adequately investigated. As one of the potential factors in volved in abnormal sensations in the throat, we considered the existence of subclinical dysphagia. We then performed videofluoroscopic analysis in patients with an abnormal sensation in the throat to examine whether or not there were functional disorders in swallowing. Videofluoroscopy was performed in 42 subjects, 30 patients with abnormal sensation in the throat and 12 volunteers without swallowing problems. We devised a temporal and spatial analysis system of swallowing using personal computer technology. Videofluoroscopic swallowing sequences during spoon feeding (3-5ml) and drinking from a cup (15-20ml) of liquid barium, were analyzed. The results suggest that two temporal measurements of swallow from videofluoroscopic studies are appropriate for parameter of subclinical dysphagia: the time it takes the bolus to move through pharynx from the point at which the bolus head passes the tongue base until the bolus head extends caudally beyond the piriform sinus while feeding from a spoon (S2), and the time it takes the bolus to move through the upper esophagus from the point at which the bolus head passes the bottom of the piriform sinus until the bolus tail passes the same point while drinking from a cup (C1). Then, we selected C1 and S2 for variables and detect the patients who have subclinical dysphagia with cluster analysis. Forty-two subjects were divided into two groups: those composed of 14 patients (cluster 1), and those composed of 16 patients and 12 controls (cluster 2). We thought 14 patients in cluster 1 would have subclinical dysphagia for the cause of abnormal sensation in the throat. Temporal and spatial analysis revealed three forms of pharyngeal swallow in cluster 1. In 6 patients, the bolus stall in the valleculae prior to the onset of the pharyngeal swallow. In other 6 patients, the bolus stall in the piriform sinus before swallowing reflex. In the other 2 patients, the bolus moved smoothly but slowly without delay in pharynx. Our results indicate that a delayed swallowing reflex is the main functional finding in videofluoroscopy in patients with subclinical dysphagia contributing to an abnormal sensatin in the throat.

Adult↗