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At least 1,153 records · Page 64Linked to original sources
PubMed1993

Detection and estimation of mRNA levels using a nonlinear model in neurons labeled by in situ hybridization histochemistry.

In situ hybridization histochemistry (ISHH) is an anatomical technique used to monitor gene expression at the cellular level via detection of steady-state levels of mRNA. Previously, densitometric analysis of ISHH-generated autoradiographic material has provided a relatively quantitative measure of the level of a specific mRNA distributed in any given anatomical region. The present study details the development of a parametric modeling technique used to automate the quantitative aspects of ISHH. The ISHH experiments described here utilized a specific DNA probe complementary to mRNA molecules encoding the neuropeptide substance P and related tachykinin peptides. A nonlinear model was used to describe the dark-field intensity pattern of labeled neurons. The model's parameters were then employed in detecting individually hybridized neurons and in estimating levels of preprotachykinin mRNA and associated cellular areas. Total mRNA content was quantified by relating the intensities described by the models to those obtained from 14C autoradiographic standards. Finally, the algorithm's performance was evaluated by comparing these estimates to those obtained from manual grain counts of labeled neurons. Overall, the parametric model presented here facilitates the process of performing quantitative analysis of hybridized neurons based on predetermined and unbiased morphological criteria.

Animals↗
PubMed2005

Real-time interactive viewing of 4D kinematic MR joint studies.

Assessment of soft tissue in normal and abnormal joint motion today gets feasible by acquiring time series of 3D MRI images. However, slice-by-slice viewing of such 4D kinematic images is cumbersome, and does not allow appreciating the movement in a convenient way. Simply presenting slice data in a cine-loop will be compromised by through-plane displacements of anatomy and "jerks" between frames, both of which hamper visual analysis of the movement. To overcome these limitations, we have implemented a demonstrator for viewing 4D kinematic MRI datasets. It allows to view any user defined anatomical structure from any viewing perspective in real-time. Smoothly displaying the movement in a cine-loop is realized by image post processing, fixing any user defined anatomical structure after image acquisition.

Algorithms↗
PubMed2005

Riemannian elasticity: a statistical regularization framework for non-linear registration.

In inter-subject registration, one often lacks a good model of the transformation variability to choose the optimal regularization. Some works attempt to model the variability in a statistical way, but the re-introduction in a registration algorithm is not easy. In this paper, we interpret the elastic energy as the distance of the Green-St Venant strain tensor to the identity, which reflects the deviation of the local deformation from a rigid transformation. By changing the Euclidean metric for a more suitable Riemannian one, we define a consistent statistical framework to quantify the amount of deformation. In particular, the mean and the covariance matrix of the strain tensor can be consistently and efficiently computed from a population of non-linear transformations. These statistics are then used as parameters in a Mahalanobis distance to measure the statistical deviation from the observed variability, giving a new regularization criterion that we called the statistical Riemannian elasticity. This new criterion is able to handle anisotropic deformations and is inverse-consistent. Preliminary results show that it can be quite easily implemented in a non-rigid registration algorithms.

Algorithms↗
PubMed1991

Trans-fissural or trans-sulcal approach versus combined stereotactic-microsurgical approach.

The combined stereotactic-microsurgical approach has been used mainly to allow the removal of small subcortical lesions, determining their location and the route to be followed. In our experience, this approach has been most useful in 5 cases of small paraventricular AVMs and another 6 small deep-seated tumoural lesions. Since the availability of MRI, we have systematically applied Yasargil's proposal to perform dissection of the cisterns or sulci to reach a lesion with minimal or no injury to normal neuroanatomy. Assisted by Computer Aided Design software, we can superimpose the MR images with those provided by conventional or digital angiography (mainly the venous phase). MRI allows us to select a route or pathway through a sulcus, and angiography helps us in locating it on the brain surface. We have applied this technique systematically during the past year, and can report 20 cases (1 AVM, 12 tumoural lesions, 1 abscess and 6 haematomas). This trans-fissural or trans-sulcal approach has allowed us resection with minimal surgical damage, after a prompt and precise location. We think that both methods are not mutually exclusive, although the trans-sulcal approach is more adequate because of less discomfort for the patient, the smaller cerebral parenchyma injury and greater anatomofunctional information for the surgeon.

Astrocytoma↗
PubMed1992

A prediction of the three-dimensional structure of maize NADP(+)-dependent malate dehydrogenase which explains aspects of light-dependent regulation unique to plant enzymes.

A model has been built for the plant NADP-malate dehydrogenase from Zea mays, a key enzyme in photosynthesis, which undergoes light-dependent regulation. The model was based on sequence and presumed structural homology to the known three-dimensional structure of mammalian porcine cytosolic NAD-malate dehydrogenase. A cystine-loop present in an extended C-terminal region of plant NADP-malate dehydrogenases was modelled using molecular mechanics and computer graphical methods, based on the assumption that a disulphide bridge exists in the inactive form of the enzyme between Cys351 and Cys363. The predicted conformation of the intact C-terminal cystine-loop suggests that the extended polypeptide will bind in the active centre and inhibit enzyme activity. Another ionizable cysteine residue in the active site is predicted to control the charge of the catalytic His215 and might be responsible for the uniquely tight binding of the positively charged nicotinamide ring of NADP+ in this and other C4 and C3 plant NADP-malate dehydrogenases.

Amino Acid Sequence↗
PubMed1995

The atom assignment problem in automated de novo drug design. 2. A method for molecular graph and fragment perception.

If atom assignment onto 3D molecular graphs is to be optimized, an efficient scheme for placement must be developed. The strategy adopted in this paper is to analyze the molecular graphs in terms of cyclical and non-cyclical nodes; the latter are further divided into terminal and non-terminal nodes. Molecular fragments, from a fragments database, are described in a similar way. A canonical numbering scheme for the fragments and the local subgraph of the molecular graph enables fragments to be placed efficiently onto the molecular graph. Further optimization is achieved by placing similar fragments into bins using a hashing scheme based on the canonical numbering. The graph perception algorithm is illustrated in detail.

Algorithms↗
PubMed1991

Modeling and conformation analysis of beta-cyclodextrin complexes.

A series of beta-cyclodextrin complexes containing various guest molecules was studied using computer-aided molecular modeling and conformation analysis techniques. The geometry of each complex was studied using crystallographic data. The positions of the glycosidic O4 atoms indicate that the beta-cyclodextrin molecules are elliptically distorted. This distortion can be related to the van der Waals volume of the guest molecules. This correlation is different for aromatic and non-aromatic guest compounds. Rigid body docking experiments demonstrated that in crystal structures the guest molecule occupies a position in the cavity of nearly minimum interaction energy when there are no other molecules having interactions with the guest molecule. From the crystallographic data several rules could be deduced which seem to determine the conformation of beta-cyclodextrin molecules in complexes. A procedure was developed to construct beta-cyclodextrin molecules that are able to encompass guest molecules having a given van der Waals volume.

Carbohydrate Conformation↗
PubMed1992

Molecular characterization of genetic mutations in human lactate dehydrogenase (LDH) B (H) variant.

We have previously detected a single base substitution of G by A at the Arg codon CGC in exon 4 of the mutant lactate dehydrogenase (LDH) gene, an unstable LDH-B variant (case 1). Here, we use the polymerase chain reaction (PCR) to amplify genomic DNA of two cases (the original case 1 and a new patient, case 2). We were able to confirm that case 1 is homozygous for the mutation, causing a replacement of the conserved Arg by His at residue 173. The resulting LDH-B variant subunit is unstable in vivo. Whereas the mutation in exon 4 was not observed in case 2, a different single base substitution of A by C was detected at the Ser codon AGT in exon 3. This mutation causes a replacement of the conserved Ser by Arg at residue 131. Genomic analysis of the family of case 2 by mismatched PCR showed that the missense mutation was consistent with their biochemical phenotypes. The replacement results in a conformational change of the residues near the Ser, probably because the side chain of Arg is much more bulky than that of Ser. The change may affect the arrangement of the cofactor binding site and result in the loss of enzyme activity. The experimental observations are consistent with computer graphics analyses.

Amino Acid Sequence↗
PubMed1977

Uptake of horseradish peroxidase by geniculo-cortical axons in the golden hamster: analysis by computer reconstruction.

Micro-injections of horseradish peroxidase (HRP) were made into the visual cortex of the golden hamster. The "projection lines" of labelled neurons in the dorsal lateral geniculate nucleus (LGNd) were three-dimensionally reconstructed, using a computer graphics technique. The lines run rostrally and medially from their origins at the lateral surface of the nucleus. Using an anatomically determined retinotopic map of the LGNd, the positions of all labelled cells near the lateral surface were converted into equivalent visual field co-ordinates and displayed on a physiologically determined retinotopic map of the primary visual cortex. Comparison between the scatter of these equivalent retinotopic loci and an actual reconstruction of the injection site revealed that: 1. there was general agreement between the independent retinotopic maps of LGNd and visual cortex; 2. there was greater retinotopic scatter of labelled LGNd cells than could be accounted for by the area of tissue injury in the cortex; 3. the retinotopic scatter matched more closely the total visible halo of HRP staining in the grey matter; 4. HRP can be taken up from a cytoarchitectonic field into which it diffuses after injection into a neighbouring area; 5. HRP is probably not taken up by undamaged axons in the white matter. These results are compared with those obtained in other animals and other systems. No general rules emerge, but the possibility of uptake from wide areas of diffusion must be considered when interpreting results of HRP injection.

Animals↗
PubMed1984

The spatial structure of the axially bound methionine in solution conformations of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c551 by 1H NMR.

A generally applicable method for the determination of the spatial structure of the heme iron-bound methionine in c-type ferrocytochromes at atomic resolution is presented. It relies primarily on measurements of nuclear Overhauser effects between the individual hydrogen atoms of the axial methionine, and between individual hydrogens of the methionine and the heme group. Four different methionine conformers, corresponding to the four possible stereospecific assignments for the methionine methylene proton resonances, are generated by a structural interpretation of the nuclear Overhauser effects with the use of an interactive computer graphics technique. A unique structure and unique stereospecific resonance assignments are then obtained by discriminating between these four conformers on the basis of van der Waals' constraints and heme ring current effects on the chemical shifts. The use of the method is illustrated with studies of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c 551. Comparison with the crystal structures shows close coincidence between the methionine conformations in solution and in single crystals of these proteins.

Animals↗
PubMedDate not supplied

3-D vision technology applied to advanced minimally invasive surgery systems.

Current-generation vision for laparoscopic surgery involves flat two-dimensional display on a video monitor; this approach makes it difficult to accurately place the tip of a surgical instrument in the three-dimensional real space of the patient. The surgeon must rely on motion parallax, monocular cues, and other indirect evidence of depth to judge accurately the correct spatial relationship of objects in the field of view. Stereoscopic video can return accuracy to the surgeon. Critical elements in creating stereovision are the biophysical laws governing field of view, focal point, depth of field, accommodation, and convergence. In addition, engineering constraints must be followed, such as fitting a 10-mm port, which are compatible with current systems and economic feasibility. There are two methods for 3-D vision under development which are variations on the same theme of modifying standard laparoscopes by using lenses, mirrors and prisms, and optical shuttering. One method uses two video cameras to simultaneous capture two separate images from a paired optical system. Each image is alternately transmitted to the video monitor (field sequential video) and viewed with electronic or polarizing glasses for a 3-D image. Another method uses a standard laparoscope, optically splits this one image into alternating right/left images, and reconstructs the image as above. A major challenge for both systems is that the distance between the optical elements in the laparoscope is not greater than 10 mm apart and fixed, whereas the human interpupillary distance is greater than 650 mm and can accommodate.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Graphics↗
PubMed1992

Interstitial cells associated with the deep muscular plexus of the guinea-pig small intestine, with special reference to the interstitial cells of Cajal.

Interstitial cells associated with the deep muscular plexus of the guinea-pig small intestine were studied by electron microscopy, and three-dimensional cell models were reconstructed from serial ultrathin sections with a computer graphic system. Three types of cells were recognized. The first type was similar in shape to smooth muscle cells, but did not contain an organized contractile apparatus. Many large gap junctions comprising about 4% of the cell surface were present; they connected cells of the first type to each other, to the second type of cell and to smooth muscle cells of the outer circular layer. The second type of cell had a well-demarcated cell body with long slender processes and was characterized by a large amount of glycogen comprising about 9% of the cell volume. The third type of cell was similar to fibroblasts, and contained well-developed Golgi apparatus and rough endoplasmic reticulum. Some of these fibroblast-like cells (a possible subtype) formed small gap junctions. All three types of cells showed close relationships with nerve varicosities. This cellular network consisting of gap-junction-rich cells, glycogen-rich cells and smooth muscle cells may be involved in the pacemaking activity of intestinal movement.

Animals↗
PubMed1996

The mu- and delta-opioid pharmacophore conformations of cyclic beta-casomorphin analogues indicate docking of the Phe3 residue to different domains of the opioid receptors.

Cyclic beta-casomorphin analogues with a D-configured amino acid residue in position 2, such as Tyr-c[-Xaa-Phe-Pro-Gly-] and Tyr-c[-Xaa-Phe-D-Pro-Gly-] (Xaa = D-A2bu, D-Orn, D-Lys) were found to bind to the mu-opioid receptor as well as to the delta-opioid receptor, whereas the corresponding L-Xaa2 derivatives are nearly inactive at both. Low-energy conformers of both active and nearly inactive derivatives have been determined in a systematic conformational search or by molecular dynamics simulations using the TRIPOS force field. The obtained conformations were compared with regard to a model for mu-selective opiates developed by Brandt et al. [Drug Des. Discov., 10 (1993) 257]. Superpositions as well as electrostatic, lipophilic and hydrogen bounding similarities with the delta-opioid receptor pharmacophore conformation of t-Hpp-JOM-13 proposed by Mosberg et al. [J. Med. Chem., 37 (1994) 4371, 4384] were used to establish the probable delta-pharmacophoric cyclic beta-casomorphin conformations. These conformations were also compared with a delta-opioid agonist (SNC 80) and the highly potent antagonist naltrindole. These investigations led to a prediction of the mu- and delta-pharmacophore structures for the cyclic beta-casomorphins. Interestingly, for the inactive compounds such conformations could not be detected. The comparison between the mu- and delta-pharmacophore conformations of the cyclic beta-casomorphins demonstrates not only differences in spatial orientation of both aromatic groups, but also in the backbone conformations of the ring part. In particular, the differences on phi2 and psi2 (mu approximately 70 degrees, -80 degrees; delta approximately 165 degrees, 55 degrees) cause a completely different spatial arrangement of the cyclized peptide rings when all compounds are matched with regard to maximal spatial overlap of the tyrosine residue. Assuming that both the mu- and delta-pharmacophore conformations bind with the tyrosine residue in a similar orientation at the same transmembrane domain X of their receptors, the side chain of Phe3 as a second binding site has to dock with different domains.

Computer Graphics↗
PubMed1994

Computer-assisted 3D reconstruction of the terminal branches of the cerebral arteries. I. Anterior cerebral artery.

We present a three-dimensional anatomical computer model of the terminal branches of the anterior cerebral artery, acquired from equidistant serial anatomical slices of three brains. The reconstructions provide a clear picture from all angles of the complicated course of the terminal branches of the cerebral arteries, which can help to identify them on conventional and magnetic resonance angiography. Our rendition of the cerebral arteries can also be matched with CT, MR or PET images to indicate the areas of extension of individual branches, allowing neuromorphological and functional correlations.

Adult↗
PubMed1994

Computer-assisted 3D reconstruction of the terminal branches of the cerebral arteries. II. Middle cerebral artery.

We present a three-dimensional anatomical computer model of the terminal branches of the middle cerebral artery, acquired from equidistant serial anatomical slices of three brains. The reconstructions provide a clear picture from all angles of the complicated course of the terminal branches of the cerebral arteries, which can help to identify them on conventional angiography and magnetic resonance angiography. The arteries can also be matched with CT, MR or PET images to indicate the areas of extension of individual branches, allowing neuromorphological and functional correlations.

Adult↗