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At least 631 records · Page 35Linked to original sources
PubMed1990

Spatially-localized NMR spectroscopy employing an inhomogeneous surface-spoiling magnetic field gradient. 2. Surface coil experiments with multicompartment phantom and rat in vivo.

The use of inhomogeneous surface-spoiling magnetic field gradients for elimination of signal from surface lying regions of a sample was theoretically examined in the companion article (W. Chen and J.J.H. Ackerman, NMR Biomed. 3, 147-157 (1990)). Using the spoiling gradient coil design described therein, this article presents experimental verification of the feasibility of such an approach to enhanced spatial localization. Single coil mode 31P NMR surface coil interrogation of both a two compartment phantom and rat in vivo are shown to provide excellent suppression of surface lying regions with minimal degradation of signal from the deep lying region of interest. Both pulse-and-collect and spin echo sequences were highly efficient in concert with spoiling gradient periods of 0.5-2 ms and driving currents of 0.5-2 A. The use of a current-generated surface spoiling gradient offers a robust means to remove surface tissue signal contributions and can be implemented with a wide range of localizing pulse sequences and imaging protocols.

Animals↗
PubMed1984

Perceptual organization as nested control.

It is argued here that perceptual organization is the structuring of environmental stimuli into nested structures of control. This view is derived from our proposal that the perceptual system forces any stimulus set to have the algebraic structure G of a machine, and that G is given a specific factorization sequence, G = G1 X G2 X ... X Gn, induced by dynamical systems criteria which the organism imposes on the environment. An investigation into these factorization sequences reveals that any such sequence is split into two subsequences, one structuring the way in which the stimulus set can change under external action, and the other describing the way in which the set is perceived as internally generated. An examination of the nested control structure of the latter yields a theory of grouping. The external and internal sequences are shown to be strongly related to each other in that the symmetry axes of the internal sequence are eigenspaces of the most stable subgroup factors of the external sequence. It is claimed that cartesian reference frames are subsequences of the full sequences. Using these principles, a unified theory is offered of several apparently quite separate perceptual areas; e.g. Marr-Nishihara shape perception, gestalt grouping, the orientation-and-form problem, and motion perception. The final claim is that planning hierarchies have the same dynamically-structured algebraic sequences and therefore that the study of perceptual organization should, in a very deep sense, be formally equivalent to the study of planning.

Cognition↗
PubMed1996

CT and MRI in iatrogenic and sporadic Creutzfeldt-Jakob disease: as far as imaging perceives.

Creutzfeldt-Jakob Disease (CJD), an invariably fatal dementing illness, affects patients in middle and old age (sporadic form). However, the association of CJD with certain treatments (iatrogenic form) has been described in younger patients. The clinical onset of the two forms seems to differ; in the iatrogenic form a high frequency of the ataxic CJD variant has been reported. Nowadays, a definitive diagnosis of CJD is exclusively histological. We present five cases of CJD, one sporadic and the others iatrogenic, following dura mater grafts and analyse their CT and MRI features. CT typically demonstrates brain atrophy, generally progressive, but in sporadic CJD midfield MRI also showed abnormal signal, with predominant deep grey matter involvement. The use of narrow windows with proton-density sequences may reveal subtle cortical signal abnormalities not clearly visible with conventional windows. The early demonstration of these changes, in the appropriate clinical context, may suggest CJD and this supports the use of mid- or high magnetic fields in the diagnosis of CJD and other forms of dementia. In our cases of iatrogenic CJD, low-field MRI did not reveal more than the progressive atrophy displayed by CT, and raises the question on the one hand of possible differences, based on imaging, from the sporadic form, and on the other of the lack of sensitivity of low-field magnets to signal changes in CJD.

Adolescent↗
PubMed1999

A stress protein is induced in the deep-sea barophilic hyperthermophile Thermococcus barophilus when grown under atmospheric pressure.

The whole-cell protein inventory of the deep-sea barophilic hyperthermophile Thermococcus barophilus was examined by one-dimensional SDS gradient gel electrophoresis when grown under different pressure conditions at 85 degrees C (Topt). One protein (P60) with a molecular mass of approximately 60 kDa was prominent at low pressures (0.3 MPa hydrostatic pressure and 0.1 MPa atmospheric pressure) but not at deep-sea pressures (10, 30, and 40 MPa). About 17 amino acids were sequenced from the N-terminal end of the protein. Sequence homology analysis in the GenBank database showed that P60 most closely resembled heat-shock proteins in some sulfur-metabolizing Archaea. A high degree of amino acid identity (81%-93%) to thermosome subunits in Thermococcales strains was found. Another protein (P35) with molecular mass of approximately 35.5 kDa was induced at 40 MPa hydrostatic pressure but not under low-pressure conditions. No amino acid sequence homology was found for this protein when the 40 amino acids from the N-terminal end were compared with homologous regions of proteins from databases. A PTk diagram was generated for T. barophilus. The results suggest that Phabitat is about 35 MPa, which corresponds to the in situ pressure where the strain was obtained.

Amino Acid Sequence↗
PubMed1987

Structure of the complex of yeast adenylate kinase with the inhibitor P1,P5-di(adenosine-5'-)pentaphosphate at 2.6 A resolution.

Adenylate kinase from yeast cytosol was crystallized as a 1:1 complex with the inhibitor P1,P5-di(adenosine-5'-)pentaphosphate. The crystalline structure was solved by multiple isomorphous replacement at a resolution of 3 A (1 A = 0.1 nm) and subsequent structural refinement at 2.6 A resolution. The yeast enzyme belongs to the group of large variants among the adenylate kinases, whereas the structurally known porcine cytosolic enzyme is a small variant. A comparison showed that the additional 31-residue segment of the large variants covers the active center. This had not been expected, because small and large variants show similar enzyme kinetics. Apart from this insertion, the chain folds of both adenylate kinases are the same. The yeast enzyme with bound inhibitor, however, assumes a much more closed form. In relation to the porcine enzyme without substrate, a segment of 28 residues containing two helices is rotated by about 30 degrees, closing the deep cleft at the active center. This corresponds to the expected induced fit. Sequence comparisons with other adenylate kinases suggest that one of the adenosine moieties of the inhibitor does not bind at a native nucleotide-binding site of the enzyme.

Adenine Nucleotides↗
PubMed1989

Periplasmic binding protein structure and function. Refined X-ray structures of the leucine/isoleucine/valine-binding protein and its complex with leucine.

The three-dimensional structure of the native unliganded form of the Leu/Ile/Val-binding protein (Mr = 36,700), an essential component of the high-affinity active transport system for the branched aliphatic amino acids in Escherichia coli, has been determined and further refined to a crystallographic R-factor of 0.17 at 2.4 A resolution. The entire structure consists of 2710 non-hydrogen atoms from the complete sequence of 344 residues and 121 ordered water molecules. Bond lengths and angle distances in the refined model have root-mean-square deviations from ideal values of 0.05 A and 0.10 A, respectively. The overall shape of the protein is a prolate ellipsoid with dimensions of 35 A x 40 A x 70 A. The protein consists of two distinct globular domains linked by three short peptide segments which, though widely separated in the sequence, are proximal in the tertiary structure and form the base of the deep cleft between the two domains. Although each domain is built from polypeptide segments located in both the amino (N) and the carboxy (C) terminal halves, both domains exhibit very similar supersecondary structures, consisting of a central beta-sheet of seven strands flanked on either side by two or three helices. The two domains are far apart from each other, leaving the cleft wide open by about 18 A. The cleft has a depth of about 15 A and a base of about 14 A x 16 A. Refining independently the structure of native Leu/Ile/Val-binding protein crystals soaked in a solution containing L-leucine at 2.8 A resolution (R-factor = 0.15), we have been able to locate and characterize an initial, major portion of the substrate-binding site of the Leu/Ile/Val-binding protein. The binding of the L-leucine substrate does not alter the native crystal structure, and the L-leucine is lodged in a crevice on the wall of the N-domain, which is in the inter-domain cleft. The L-leucine is held in place primarily by hydrogen-bonding of its alpha-ammonium and alpha-carboxylate groups with main-chain peptide units and hydroxyl side-chain groups; there are no salt-linkages. The charges on the leucine zwitterion are stabilized by hydrogen-bond dipoles. The side-chain of the L-leucine substrate lies in a depression lined with non-polar residues, including Leu77, which confers specificity to the site by stacking with the side-chain of the leucine substrate.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2006

The complete mitochondrial genome of the black coral Chrysopathes formosa (Cnidaria:Anthozoa:Antipatharia) supports classification of antipatharians within the subclass Hexacorallia.

Black corals comprise a globally distributed shallow- and deep-water taxon whose phylogenetic position within the Anthozoa has been debated. We sequenced the complete mitochondrial genome of the antipatharian Chrysopathes formosa to further evaluate its phylogenetic relationships. The circular mitochondrial genome (18,398 bp) consists of 13 energy pathway protein-coding genes and two ribosomal RNAs, but only two transfer RNA genes (trnM and trnW), as well as a group I intron within the nad5 gene that contains the only copies of nad1 and nad3. No novel genes were found in the antipatharian mitochondrial genome. Gene order and genome content are most similar to those of the sea anemone Metridium senile (subclass Hexacorallia), with differences being the relative location of three contiguous genes (cox2-nad4-nad6) and absence (from the antipatharian) of a group I intron within the cox1 gene. Phylogenetic analyses of multiple protein-coding genes support classifying the Antipatharia within the subclass Hexacorallia and not the subclass Ceriantipatharia; however, the sister-taxon relationships of black corals within Hexacorallia remain inconclusive.

Animals↗
PubMed2003

Magnetic resonance: new approaches to imaging of the musculoskeletal system.

Recent technical advances in magnetic resonance imaging are reviewed. Purpose designed musculoskeletal magnetic resonance (MR) systems are now available. A great deal of pulse sequence development has been carried out with ultrashort TE (UTE) imaging, blood oxygenation level detection (BOLD) studies, diffusion weighted and other sequences. Image processing and measurement techniques have improved. In hyaline articular cartilage the deep layer can now be identified. Contrast agents are now being used to study the reduction in proteoglycans in cartilage. Enhancement is seen in tendons, ligaments and menisci and can be used to study perfusion. Signal is detected from cortical bone and periosteum and this can be used to monitor perfusion in serial studies. Muscle metabolism can also be studied. Contrast transport into intervertebral discs can be observed as well as effects attributable to iron deposition.

Humans↗
PubMed2003

An improved method for plant BAC library construction.

Large genomic DNA insert-containing libraries are required as critical tools for physical mapping, positional cloning, and genome sequencing of complex genomes. The bacterial artificial chromosome (BAC) cloning system has become a dominant system over others to clone large genomic DNA inserts. As the costs of positional cloning, physical mapping, and genome sequencing continuously decrease, there is an increasing demand for high-quality deep-coverage large insert BAC libraries. In our laboratory, we have constructed many high-quality deep-coverage large insert BAC libraries including arabidopsis, manocot and dicot crop plants, and plant pathogens. Here, we present the protocol used in our laboratory to construct BAC libraries.

Chromosome Mapping↗
PubMed2000

Properties of the bimodal fluorescent protein produced by Photobacterium phosphoreum.

A fluorescent protein isolated from the deep-sea luminous bacterium Photobacterium phosphoreum strain bmFP has been purified, cloned and sequenced. The protein is 96.5% identical in amino acid sequence to FP390, the weakly fluorescent flavoprotein encoded by the luxF gene characteristic of Photobacterium species. Similar to FP390, bmFP is a dimer of two homologous subunits binding four FMN-myristate chromophores but has the distinctive feature of emitting a bimodal fluorescence with maxima at about 488 and 517 nm, hence the name bmFP. For both bands of this fluorescence, the excitation spectrum exhibits a peak at 336 nm, not corresponding to its flavin-like absorption spectrum. Heating of bmFP in urea resulted in a decrease in the intensity of the 488 nm band along with the appearance of a new fluorescence peaking at 423 nm, partially reversible upon the removal of the urea. Upon complete denaturation, either by heat or guanidium chloride at 65 degrees C, fluorescence characteristic of both free flavin and this 423 nm species appears. It is speculated that chromophores in different states of protonation, associated with a single protein, are responsible for the unusual spectral properties of bmFP.

Amino Acid Sequence↗
PubMed2004

Intraoperative stereoscopic QuickTime Virtual Reality.

OBJECT: The aim of this study was to acquire intraoperative images during neurosurgical procedures for later reconstruction into a stereoscopic image system (QuickTime Virtual Reality [QTVR]) that would improve visualization of complex neurosurgical procedures. METHODS: A robotic microscope and digital cameras were used to acquire left and right image pairs during cranial surgery; a grid system facilitated image acquisition with the microscope. The surgeon determined a field of interest and a target or pivot point for image acquisition. Images were processed with commercially available software and hardware. Two-dimensional (2D) or interlaced left and right 2D images were reconstructed into a standard or stereoscopic QTVR format. Standard QTVR images were produced if stereoscopy was not needed. Intraoperative image sequences of regions of interest were captured in six patients. Relatively wide and deep dissections afford an opportunity for excellent QTVR production. Narrow or restricted surgical corridors can be reconstructed into the stereoscopic QTVR mode by using a keyhole mode of image acquisition. The stereoscopic effect is unimpressive with shallow or cortical surface dissections, which can be reconstructed into standard QTVR images. CONCLUSIONS: The QTVR system depicts multiple views of the same anatomy from different angles. By tilting, panning, or rotating the reconstructed images, the user can view a virtual three-dimensional tour of a neurosurgical dissection, with images acquired intraoperatively. The stereoscopic QTVR format provides depth to the montage. The system recreates the dissection environment almost completely and provides a superior anatomical frame of reference compared with the images captured by still or video photography in the operating room.

Brain↗
PubMedDate not supplied

[Evaluation of the T parameter of TNM classification of tumors of the tonsillar region. Correlation of MR and pathological data].

The purpose of this study was to define MR accuracy in the evaluation of T Stage of tumors in the tonsillar region. Twenty-two patients with a squamous cell carcinoma of the tonsillar region were studied utilizing a superconductive scanner operating at 1.5 T. The study was performed with SE T1 and T2 images before contrast and short SE T1 after Gd-DPTA infusion. MR results were correlated with pathological data on T Stage (TNM classification) and on the relationships between tumors and surrounding structures. A positive correlation between MR and pathological data was obtained in 19/22 cases, with an MR accuracy of 86%. MR did not show the presence of 2 superficial lesions (MR T0, pathological T1), while one lesion was classified T2 with MR, instead of pathology T1. The accuracy of MR was 95% in the evaluation of the relationships between tumors and the base of the tongue and 100% for body of the tongue, retromolar trigone, valleculae, epiglottis, pre-epiglottis, parapharyngeal and masticator space. MR showed high accuracy in the evaluation of T Stage, above all utilizing Gd-DPTA infusion, with short SE T1 sequences. MR did not show the superficial lesions, but in these cases a deep extension of the disease was excluded.

Adult↗
PubMedDate not supplied

Hemangiomas and vascular malformations of the head and neck: MR characterization.

PURPOSE: To characterize the MR appearance of the common hemangioma of infancy as well as low- and high-flow vascular malformations of the head and neck. PATIENTS AND METHODS: Twenty patients with vascular lesions of the head and neck proved either by pathology, angiography, and/or unequivocal clinical diagnosis were included. Vascular lesions included 15 low-flow lesions (four hemangiomas, 10 venous malformations, one lymphatic malformation), and five high-flow lesions (three arteriovenous malformations (AVMs) and two invasive combined malformations). All patients had MR studies (generally 1.5 T using routine T1- and T2-weighted spin-echo sequences). Nine had postgadolinium, gradient recalled-echo, CT, and/or angiographic studies. FINDINGS: Deep hemangiomas and venous malformations demonstrate intermediate signal in T1-weighted images, heterogeneous high signal on T2-weighted images, and prominent enhancement. Involuting hemangiomas show focal areas of high signal intensity on T1-weighted images due to fatty replacement. Venous malformations may demonstrate venous lakes seen as homogeneous regions of high signal intensity on T2-weighted images and phleboliths seen as low signal foci. The one patient with lymphatic malformation showed a large multicystic submandibular mass with large hemorrhage-fluid levels. Features of high-flow lesions (AVMs) include serpiginous signal voids, absence of a dominant mass, and intraosseous extension with decreased marrow signal on T1-weighted images. Invasive combined vascular malformations showed serpiginous flow voids and infiltrative solid masses. Low-flow lesions (hemangiomas, venous, and lymphatic malformations) demonstrate distinct MR findings allowing their differentiation from high-flow lesions (AVMs). Deep hemangiomas and venous malformations appear as solid masses and may look identical. Venous lakes and phleboliths are features of venous malformations which, when present, may help in diagnosis. Combined vascular malformations share features of both low- and high-flow malformations. CONCLUSION: MR is useful in delineating the extent of disease and differentiating low- and high-flow vascular lesions.

Adolescent↗
PubMed1975

De subitaneis mortibus. XII. Asymmetrical hypertrophy of the heart.

Subjects with asymmetrical hypertrophy of the heart are prone to sudden death. Neither the pathogenesis of the eccentric hypertrophy nor the mechanism of sudden death is fully understood. In this report we describe certain postmortem findings in the hearts of 22 subjects who died suddenly, silently and unexpectedly, and in whom the only significant abnormality at autopsy was asymmetrical hypertrophy of the heart. Deep clefts were present in the septum in seven hearts, the small coronary arteries were abnormally narrowed in ten, the sinus node was sclerosed by fibrosis in 12, there was variable narrowing of the atrioventricular (A-V) node artery in many and the His bundle was too thin in three. There were multiple cysts or channels in the central fibrous body and of the adjacent A-V node and His bundle in four hearts. Most of the hearts displayed a fetal dispersion of the A-V node and His bundle throughout the central fibrous body, but this was particularly conspicuous in 13 hearts. These abnormalities in all parts of the conduction system suggest a variety of possible mechanisms by which the heart could become electrically unstable but do not indicate that one single mechanism is at fault in all. They offer some explanation for the reported high incidence of atrial fibrillation in such patients, and why they fare so badly with this arrhythmia. While the pathogenesis of asymmetrical hypertrophy may in some part be attributable to narrowed small coronary arteries or to an abnormal sequence or speed of septal and ventricular activation or to mechanical deficiency caused by deep septal clefts, none of these features was universally present in our series. Both asymmetrical hypertrophy of the heart and the sudden death which so frequently accompanies it probably develop by a variety of pathogenetic mechanisms.

Adolescent↗
PubMedDate not supplied

Effect of deep digital flexor tendon orientation on magnetic resonance imaging signal intensity in isolated equine limbs-the magic angle effect.

Ten normal equine isolated limbs were imaged using a knee coil in a 1.5 Tesla magnetic field, with short echo time sequences (TE < 15 ms). Magnetic resonance imaging was performed on each isolated limb in different positions, with and without extension of the metacarpophalangeal joint. Deep digital flexor tendon orientation ranged from 20 to 60 degrees in relation to the static magnetic field. Increased intratendinous signal intensity was observed when the angle between the deep digital flexor tendon and the constant magnetic field approached 55 degrees ("magic angle"). The increased signal intensity was independent from extension of the metacarpophalangeal joint. Recognition of the magic angle phenomenon is essential for proper evaluation of magnetic resonance imaging studies of the equine foot.

Animals↗
PubMed1988

Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences.

The 16S rRNAs from the bacterial endosymbionts of six marine invertebrates from diverse environments were isolated and partially sequenced. These symbionts included the trophosome symbiont of Riftia pachyptila, the gill symbionts of Calyptogena magnifica and Bathymodiolus thermophilus (from deep-sea hydrothermal vents), and the gill symbionts of Lucinoma annulata, Lucinoma aequizonata, and Codakia orbicularis (from relatively shallow coastal environments). Only one type of bacterial 16S rRNA was detected in each symbiosis. Using nucleotide sequence comparisons, we showed that each of the bacterial symbionts is distinct from the others and that all fall within a limited domain of the gamma subdivision of the purple bacteria (one of the major eubacterial divisions previously defined by 16S rRNA analysis [C. R. Woese, Microbiol. Rev. 51: 221-271, 1987]). Two host specimens were analyzed in five of the symbioses; in each case, identical bacterial rRNA sequences were obtained from conspecific host specimens. These data indicate that the symbioses examined are species specific and that the symbiont species are unique to and invariant within their respective host species.

Animals↗
PubMed1988

Single-unit analysis of the human ventral thalamic nuclear group: somatosensory responses.

1. We have studied the functional and somatotopic properties of 531 single mechanoreceptive thalamic neurons in humans undergoing stereotactic surgery for the control of movement disorders and pain. The majority of these somatosensory cells had small receptive fields (RFs) and were activated in a reproducible manner by mechanical stimuli applied to the skin or deep tissues. These neurons, which we termed "lemniscal," could be further classified into those responding to stimulation of cutaneous (76% of lemniscal sensory cells) or deep (24%) structures. 2. The incidence of neurons having cutaneous or mucosal RFs in the perioral region, thumb, and fingers (66%) was much higher than that of neurons having RFs elsewhere on the body. Most of the deep cells were activated by movements of and/or mechanical stimuli delivered to muscles or tendons controlling the elbow, wrist, and fingers. 3. Sequences of cells spanning several millimeters in the parasagittal plane often exhibited overlapping RFs. However, RFs changed markedly for cells separated by the same distances in the mediolateral direction. This suggests that the cutaneous somatotopic representation of each region of the body is organized into relatively thin sheets of cells oriented in the parasagittal plane. 4. By comparing neuronal RFs in different parasagittal planes in thalamus of individual patients we have identified a mediolateral representation of body surface following the sequence from: intraoral structures, face, thumb through fifth finger to palm, with forearm and leg laterally. 5. Along many trajectories in the parasagittal plane the sequence of cells with overlapping RFs was interrupted by another sequence of cells with RFs corresponding to a different body region. The RFs of the intervening sequence characteristically represented body regions known to be located more medially in thalamus (see 3 above). These findings could be explained if the lamellae postulated above were laterally convex. 6. Cells responding to deep stimulation (deep cells) could be further classified into those responding to joint movement (63%), deep pressure (15%), or both (22%). Deep cells were found usually at the anterior-dorsal border and sometimes at the posterior border of the region containing cells responding to cutaneous stimuli. Although there was some overlap in the RFs, deep cells representing wrist were found medial to those representing elbow, and both of these were found medial to cells representing leg.(ABSTRACT TRUNCATED AT 400 WORDS)

Brain Mapping↗
PubMed1998

HiPER1, a phosphatase of the endoplasmic reticulum with a role in chondrocyte maturation.

We have previously identified and partially cloned Band 17, a gene expressed in growth plate chondrocytes transiting from proliferation to hypertrophy. We now rename this gene HiPER1, Histidine Phosphatase of the Endoplasmic Reticulum-1, based on the results reported here. HiPER1 encodes two proteins of 318 (HiPER1(318)) and 449 (HiPER1(449)) amino acids, which are 20-21% identical to a group of yeast acid phosphatases that are in the histidine phosphatase family. HiPER1(449) is significantly more abundant than HiPER1(318), correlating with the abundance of the alternatively spliced messages encoding HiPER449 and HiPER318. Anti-HiPER1 antibodies detect two proteins of 53 and 55 kDa in growth plate chondrocytes that are absent in articular chondrocytes. We confirm that the 53 and 55 kDa proteins are HiPER1(449) by heterologous expression of the HiPER1(449) coding sequence in chick embryo fibroblasts. The 53 and 55 kDa proteins are glycosylated forms of HiPER1(449), as N-glycosidase F digestion reduces these proteins to 48 kDa, the predicted size of HiPER1(449) without the N-terminal signal sequence. Immunocytochemistry demonstrates that HiPER1(449) is found in chondrocytes maturing from proliferation to hypertrophy, but is not detectable in resting zone, deep hypertrophic zone or articular chondrocytes, a distribution that is consistent with the message distribution. HiPER1(449) was predicted to localize to the lumen of endoplasmic reticulum by an N-terminal signal sequence and by the C-terminal sequence Ala-Asp-Glu-Leu, which closely matches the consensus signal for ER retention, Lys-Asp-Glu-Leu. We confirm this prediction by demonstrating colocalization of HiPER1(449) with the ER protein HSP47 using dual-label immunofluorescence. PTHrP, a peptide that prevents hypertrophy in chondrocytes, suppressed HiPER1 and HiPER1(449) expression in vitro, an observation that further supports a role for HiPER1 in chondrocyte maturation. The yeast phosphatase homology, localization to the endoplasmic reticulum and pattern of expression suggest that HiPER1 represents a previously unrecognized intracellular pathway, involved in differentiation of chondrocytes.

Amino Acid Sequence↗