Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Optical mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 559 records · Page 31Linked to original sources
PubMed2005

The mitochondrial origin of postischemic arrhythmias.

Recovery of the mitochondrial inner membrane potential (DeltaPsi(m)) is a key determinant of postischemic functional recovery of the heart. Mitochondrial ROS-induced ROS release causes the collapse of DeltaPsi(m) and the destabilization of the action potential (AP) through a mechanism involving a mitochondrial inner membrane anion channel (IMAC) modulated by the mitochondrial benzodiazepine receptor (mBzR). Here, we test the hypothesis that this mechanism contributes to spatiotemporal heterogeneity of DeltaPsi(m) during ischemia-reperfusion (IR), thereby promoting abnormal electrical activation and arrhythmias in the whole heart. High-resolution optical AP mapping was performed in perfused guinea pig hearts subjected to 30 minutes of global ischemia followed by reperfusion. Typical electrophysiological responses, including progressive AP shortening followed by membrane inexcitablity in ischemia and ventricular fibrillation upon reperfusion, were observed in control hearts. These responses were reduced or eliminated by treatment with the mBzR antagonist 4'-chlorodiazepam (4'-Cl-DZP), which blocks depolarization of DeltaPsi(m). When applied throughout the IR protocol, 4'-Cl-DZP blunted AP shortening and prevented reperfusion arrhythmias. Inhibition of ventricular fibrillation was also achieved by bolus infusion of 4'-Cl-DZP just before reperfusion. Conversely, treatment with an agonist of the mBzR that promotes DeltaPsi(m) depolarization exacerbated IR-induced electrophysiological changes and failed to prevent arrhythmias. The effects of these compounds were consistent with their actions on IMAC and DeltaPsi(m). These findings directly link instability of DeltaPsi(m) to the heterogeneous electrophysiological substrate of the postischemic heart and highlight the mitochondrial membrane as a new therapeutic target for arrhythmia prevention in ischemic heart disease.

Action Potentials↗
PubMed2003

A study and optimization of lumbar spine X-ray imaging systems.

A Monte Carlo program has been developed that incorporates a voxel phantom of an adult patient in a model of the complete X-ray imaging system, including the anti-scatter grid and screen-film receptor. This allows the realistic estimation of patient dose and the corresponding image (optical density map) for a wide range of equipment configurations. This paper focuses on the application of the program to lumbar spine anteroposterior and lateral screen-film examinations. The program has been applied to study the variation of physical image quality measures and effective dose for changing system parameters such as tube voltage, grid design and screen-film system speed. These variations form the basis for optimization of these system parameters. In our approach to optimization, the best systems are those that can match (or come close to) the calculated image quality measure of systems preferred in a recent European clinical trial, but with lower patient dose. The largest dose savings found were 21% for a 400 speed class system with a grid having a strip density of 40 cm(-1) and a grid ratio of 16. A further dose saving of 13% was possible when a 600 speed class system was employed. The best systems found from the optimization correspond to those recommended by the European Commission guidelines on image quality criteria for diagnostic radiographic images.

Adult↗
PubMed2003

Phase retrieval in digital speckle pattern interferometry by use of a smoothed space-frequency distribution.

We evaluate the use of a smoothed space-frequency distribution (SSFD) to retrieve optical phase maps in digital speckle pattern interferometry (DSPI). The performance of this method is tested by use of computer-simulated DSPI fringes. Phase gradients are found along a pixel path from a single DSPI image, and the phase map is finally determined by integration. This technique does not need the application of a phase unwrapping algorithm or the introduction of carrier fringes in the interferometer. It is shown that a Wigner-Ville distribution with a smoothing Gaussian kernel gives more-accurate results than methods based on the continuous wavelet transform. We also discuss the influence of filtering on smoothing of the DSPI fringes and some additional limitations that emerge when this technique is applied. The performance of the SSFD method for processing experimental data is then illustrated.

Journal Article↗
PubMed2006

Simultaneous absorption, scattering, and luminescence mappings for the characterization of optical coatings and surfaces.

An experimental setup, based on the laser-induced deflection technique, is developed to measure simultaneously the 244 nm laser absorption, scattering, and luminescence on optical components. The different techniques and methods that have been specifically developed to obtain both high resolution (micronic) and sensitivity (a few 10(-7) of the incident power for the absorption, 10(-8) for scattering and fluorescence) are presented. Different applications are then explored: the study of losses in deep UV multilayer coatings (HfO2/SiO2 mirrors) and the analysis of contamination defects on bare substrate and structural defects in optical coatings.

Journal Article↗
PubMed2006

Nomarski imaging interferometry to measure the displacement field of micro-electro-mechanical systems.

We propose to use a Nomarski imaging interferometer to measure the out- of-plane displacement field of micro-electro-mechanical systems. It is shown that the measured optical phase arises from both height and slope gradients. By using four integrating buckets, a more efficient approach to unwrap the measured phase is presented, thus making the method well suited for highly curved objects. Slope and height effects are then decoupled by expanding the displacement field on a functions basis, and the inverse transformation is applied to get a displacement field from a measured optical phase map change with a mechanical loading. A measurement reproducibility of approximately 10 pm is achieved, and typical results are shown on a microcantilever under thermal actuation, thereby proving the ability of such a setup to provide a reliable full-field kinematic measurement without surface modification.

Journal Article↗
PubMed2001

Optical dipole model for photodetection in the near field.

Near-field photodetection optical microscopy (NPOM) is a scanning probe technique that has been developed to perform nanometer-scale optical intensity mapping and spectroscopy. In NPOM a nanometer-scale photodiode detector absorbs power directly as it is scanned in the near field of an illuminated sample surface. A model of photodetection in the near and intermediate fields is presented. A brief review of far-field absorption is given for comparison. Far-field absorption measurements measure the imaginary part of the polarizability to first order. In contrast, photodetection in the near field measures the real part of the polarizability. Other aspects of near-field photodetection are also examined, including contrast mechanisms and lateral resolution. NPOM measurements performed on isolated 300-nm spheres show good agreement with the theory.

Journal Article↗
PubMed2026

PSIP1::TBL1X: a recurrent gene fusion in pancreatic neuroendocrine tumors.

Effective treatment of metastatic neuroendocrine tumors (NETs) is limited by a lack of targeted therapies and clinically useful predictive biomarkers. We applied complementary genomic profiling technologies, including optical genome mapping (OGM) and whole exome sequencing (WES), to 70 liver metastases of NETs from multiple anatomical primary sites to identify actionable genomic alterations. We detected recurrent fusions involving TBL1X (PSIP1::TBL1X) and BEND2 (CHD7::BEND2 and NEO1::BEND2) by OGM in pancreatic neuroendocrine tumors (pNETs). The expression of the PSIP1::TBL1X fusion was confirmed by PacBio Iso-Seq long-read transcriptome sequencing and nested rtPCR, and fusion protein expression was established by western blotting. Expression of the PSIP1::TBL1X fusion was also assayed in a separate cohort of 31 specimens from 28 pNET cases by rtPCR. Across both cohorts, PSIP1::TBL1X was identified in 11% of pNET patients with available metastatic tissue, but was not detected in primary tumor specimens. All PSIP1::TBL1X fusion isoforms were found to retain early exons of PSIP1 and the complete coding sequence of TBL1X. Consistent with prior reports, BEND2 fusions were associated with high-grade tumors and may represent a clinically useful biomarker for aggressive disease. Notably, TBL1X and BEND2 fusions did not co-occur with ATRX/DAXX mutations, defining a distinct molecular subgroup of pNETs. This study highlights the importance of structural variant profiling in molecular profiling studies and supports a revised view of the role of gene fusions in neuroendocrine malignancies.

Humans↗
PubMed2003

A tissue level tolerance criterion for living brain developed with an in vitro model of traumatic mechanical loading.

Traumatic brain injury (TBI) is caused by brain deformations resulting in the pathophysiological activation of cellular cascades which produce delayed cell damage and death. Understanding the consequences of mechanical injuries on living brain tissue continues to be a significant challenge. We have developed a reproducible tissue culture model of TBI which employs organotypic brain slice cultures to study the relationship between mechanical stimuli and the resultant biological response of living brain tissue. The device allows for the independent control of tissue strain (up to 100%) and strain rate (up to 150 s-1) so that tolerance criteria at the tissue level can be developed for the interpretation of computational simulations. The application of texture correlation image analysis algorithms to high speed video of the dynamic deformation allows for the direct calculation of substrate strain and strain rate which was found to be equi-biaxial and independent of radial position. Precisely controlled, mechanical injuries were applied to organotypic hippocampal slice cultures, and resultant cell death was quantified. Cell death was found to be dependent on both strain magnitude and rate and required several days to develop. An immunohistological examination of injured cultures with antibodies to amyloid precursor protein revealed the presence of traumatic axonal injury, suggesting that the model closely replicates in vivo TBI but with advantages gained in vitro. We anticipate that a combined in vitro approach with optical strain mapping will provide a more detailed understanding of the dependence of brain cell injury and death on strain and strain rate.

Journal Article↗
PubMed1979

[Topography of the tecto-tectal component of the main ipsilateral visual pathway of the frog (Rana esculenta L.)].

The detailed topography of the tecto-tectal component of the Frog's ipsilateral visual pathway is electrophysiologically obtained by mapping the optic lobes. This linkage transfers the visual information explored along a transversal tectal row on to an homologous line oriented at 130 degrees on the opposite tectum. The ipsilateral projection of the temporo-nasal axis of the retina, but not of the antero-posterior axis of the visual field, is reversed compared to its contralateral projection. Finally, the majority of the homologous tectal points are asymmetrical with respect to the animal's sagittal axis.

Animals↗
PubMed2002

Biaxial strain distributions in explanted porcine bioprosthetic valves.

BACKGROUND AND AIMS OF THE STUDY: Testing whole explanted porcine bioprosthetic valves provides information on changes the valves undergo over time in vivo, and may help elucidate a possible mechanism for bioprosthetic valve failure. The study aim was to measure the static pressure/strain response of whole explanted porcine bioprostheses. METHODS: Three bioprosthetic valves were explanted prophylactically prior to structural failure. Loading curves (pressure versus strain curves) were generated for these valves using a whole-valve optical strain mapping system. Maximum strain, stiffness, and the occurrence of 'negative compliance' (inverse relationship between cusp strain and applied pressure) were obtained from these curves. RESULTS: All three cusps had very low extensibility (3-10% in the radial direction; 2-4% in the circumferential direction). The non-coronary (NC) cusp was less extensible than the right (RC) or left coronary (LC) cusps in two of the valves. In one valve, the smallest strains were in the RC cusp, where large amounts of calcification were noted. Negative strains were present primarily in one valve. CONCLUSION: The extensibilities of the three explanted valves were lower than those seen in fresh valves, due to either glutaraldehyde fixation and/or extension of the fibrosal corrugations. Furthermore, the uniqueness of the mechanical properties of the NC cusp previously seen in fresh porcine valves remained through glutaraldehyde fixation and stenting. It is concluded that cusp anisotropy and heterogeneity, as well as the occurrence of negative strains seen in fresh porcine valves, are preserved during the fabrication of porcine bioprostheses.

Aged↗
PubMed1988

The rib cage and abdominal components of respiratory system compliance in tetraplegic patients.

The specific compliance of the chest wall and lungs combined was measured in eight patients with stable tetraplegia. Expiration was impeded with a series of spring-loaded resistances, and end-expiratory pressures plotted against changes in chest wall volume at end-expiration. An optical contour mapping system was used to partition changes in chest wall volume into rib cage and abdominal components. These measurements suggest that the compliance of the whole system is reduced by one third in patients with stable tetraplegia, compared with normal subjects. This may be because of abnormal stiffening of the rib cage.

Abdominal Muscles↗
PubMedDate not supplied

The individuality of chest wall motion in tetraplegia.

We have studied the motion of the chest wall in eight supine tetraplegic subjects using optical contour mapping. Measurements were obtained during quiet breathing, exaggerated breathing, during the course of a deep inspiration and during static inspiratory efforts. The pattern of motion showed a high degree of individual variability which did not appear to be related to the age of the patient, the duration of injury or the presence of intercostal muscle spasticity. By contrast, it did appear to be related to the presence of bony rib cage stiffness, and possibly the action of the neck accessory muscles. The pattern of rib cage motion in tetraplegia is more complex than conventionally thought.

Abdominal Muscles↗
PubMed2001

Validation of diffusion tensor magnetic resonance axonal fiber imaging with registered manganese-enhanced optic tracts.

Noninvasive mapping of white matter tracts using diffusion tensor magnetic resonance imaging (DTMRI) is potentially useful in revealing anatomical connectivity in the human brain. However, a gold standard for validating DTMRI in defining axonal fiber orientation is still lacking. This study presents the first validation of the principal eigenvector of the diffusion tensor in defining axonal fiber orientation by superimposing DTMRI with manganese-enhanced MRI of optic tracts. A rat model was developed in which optic tracts were enhanced by manganese ions. Manganese ion (Mn(2+)) is a potent T1-shortening agent and can be uptaken and transported actively along the axon. Based on this property, we obtained enhanced optic tracts with a T1-weighted spin-echo sequence 10 h after intravitreal injection of Mn(2+). The images were compared with DTMRI acquired with exact spatial registration. Deviation angles between tangential vectors of the enhanced tracts and the principal eigenvectors of the diffusion tensor were then computed pixel by pixel. We found that under signal-to-noise (SNR) of 30, the variance of deviation angles was (13.27 degrees). In addition, the dependence of this variance on SNR obeys stochastic behavior if SNR is greater than 10. Based on this relation, we estimated that an rms deviation of less than 10 degrees could be achieved with DTMRI when SNR is 40 or greater. In conclusion, our method bypasses technical difficulties in conventional histological approach and provides an in vivo gold standard for validating DTMRI in mapping white matter tracts.

Animals↗
PubMed2004

Optical coherence tomography can measure axonal loss in patients with ethambutol-induced optic neuropathy.

PURPOSE: To map and identify the pattern, in vivo, of axonal degeneration in ethambutol-induced optic neuropathy using optical coherence tomography (OCT). Ethambutol is an antimycobacterial agent often used to treat tuberculosis. A serious complication of ethambutol is an optic neuropathy that impairs visual acuity, contrast sensitivity, and color vision. However, early on, when the toxic optic neuropathy is mild and partly reversible, the funduscopic findings are often subtle and easy to miss. METHODS: Three subjects with a history of ethambutol (EMB)-induced optic neuropathy of short-, intermediate-, and long-term visual deficits were administered a full neuro-ophthalmologic examination including visual acuity, color vision, contrast sensitivity, and fundus examination. In addition, OCT (OCT 3000, Humphrey-Zeiss, Dublin, CA) was performed on both eyes of each subject using the retinal nerve fiber layer (RNFL) analysis protocol. OCT interpolates data from 100 points around the optic nerve to effectively map out the RNFL. RESULTS: The results were compared to the calculated average RNFL of normal eyes accumulated from four prior studies using OCT, n=661. In all subjects with history of EMB-induced optic neuropathy, there was a mean loss of 72% nerve fiber layer thickness in the temporal quadrant (patient A, with eventual recovery of visual acuity and fields, 58% loss; patient B, with intermediate visual deficits, 68% loss; patient C, with chronic visual deficits, 90% loss), with an average mean optic nerve thickness of 26+/-16 microm. There was a combined mean loss of 46% of fibers from the superior, inferior, and nasal quadrants in the (six) eyes of all three subjects (mean average thickness of 55+/-29 microm). In both sets (four) of eyes of the subjects with persistent visual deficits (patients B and C), there was an average loss of 79% of nerve fiber thickness in the temporal quadrant. CONCLUSIONS: The OCT results in these patients with EMB-induced optic neuropathy show considerable loss especially of the temporal fibers. This is consistent with prior histopathological studies that show predominant loss of parvo-cellular axons (or small-caliber axons) within the papillo-macular bundle in toxic or hereditary optic neuropathies. OCT can be a valuable tool in the quantitative analysis of optic neuropathies. Additionally, in terms of management of EMB-induced optic neuropathy, it is important to properly manage ethambutol dosing in patients with renal impairment and to achieve proper transition to a maintenance dose once an appropriate loading dose has been reached.

Aged↗
PubMed1998

Detection of optic disc changes with Glaucoma-Scope probability maps.

PURPOSE: To test whether a statistical method using a probability map could detect true changes in optic disc topography. METHODS: The average of three Glaucoma-Scope images (Ophthalmic Imaging Systems were used for analysis at each of two sessions. A Glaucoma-Scope probability map was constructed for each eye using statistical methods. The proportion of topographic locations with p values less than 0.05 on a modified two-sample t test (p-proportion) and the difference in the mean position of the disc (MPD) from two imaging sessions were calculated. Two pairs of stereoscopic disc photographs for 43 eyes with longitudinal follow-up were evaluated for change by four experienced glaucoma specialists masked to patient clinical information. Clinical change was considered to have occurred when the assessments of at least three of the four specialists were agreed on. The cutoff values for p-proportion and change in MPD that provided 95% specificity were calculated using a separate sample of 69 subjects who had serial images taken at two separate sessions on the same day, and thus showed no clinical change in the optic disc. RESULTS: The cutoff values of 95% specificity for the p-proportion and the change in MPD were 18% and 25.1 microns, respectively. Of 43 eyes with longitudinal follow-up, 14 showed definite clinical change. Sensitivity of the p-proportion and change in MPD for detecting this change was 100% and 85.7%, respectively. For all 43 patients with longitudinal follow-up, the percent change in intraocular pressure (IOP) correlated strongly with both the p-proportion and the change in MPD. CONCLUSION: Using data obtained with the Glaucoma-Scope, a statistical method based on probability mapping can be used to detect true changes in disc topography. The p-proportion was more sensitive than change in MPD in detecting clinical change in the study eyes. This statistical methodology may also be applicable for interpretation of data obtained with other optic disc analyzers.

Adult↗
PubMedDate not supplied

Photogrammetric analysis of the three-dimensional geometry of normal and glaucomatous optic cups.

Using photogrammetrically generated maps and measurements, the geometric configuration of the optic cups from a group of normal, hypertensive, and glaucomatous eyes were analyzed in detail. Six distinct three-dimensional shapes were found to characterize the range of normal cups. These forms closely resemble a cone, a cylinder, a hemisphere, a cone-cylinder, a cone-hemisphere, and a cylinder-hemisphere. A composite picture of glaucomatous change was produced by collating the data obtained from different nerve heads which were thought to represent serial stages of disease. Among the many topographic features identified by this analysis is the early deepening of the optic cup which seems to take place only in disc in which the lamina was not visible before glaucoma began. In cups in which this process has occurred and in those in which the lamina was already exposed during the physiologic state, no further increase in the maximum value of this dimension appears to take place until late in the course of the disease. On the surface of the disc, the pattern of erosion is more vertical than horizontal in direction, creating a vertically oriented ellipse of the cup orifice. Its enlargement occurs in a concentric fashion and usually leads to the disappearance of the superior or inferior disc margins or both before losing the rest of the rim. In spite of the precision with which the optic cup morphology was mapped and measured, the end result still lacks the specificity which could be achieved by actually following the same optic discs while they are undergoing progressive atrophy. Such a study is now underway.

Glaucoma↗
PubMed1989

Neural maps of interaural time and intensity differences in the optic tectum of the barn owl.

This report describes the binaural basis of the auditory space map in the optic tectum of the barn owl (Tyto alba). Single units were recorded extracellularly in ketamine-anesthetized birds. Unit tuning for interaural differences in timing and intensity of wideband noise was measured using digitally synthesized sound presented through earphones. Spatial receptive fields of the same units were measured with a free field sound source. Auditory units in the optic tectum are sharply tuned for both the azimuth and the elevation of a free field sound source. To determine the binaural cues that could be responsible for this spatial tuning, we measured in the ear canals the amplitude and phase spectra produced by a free field noise source and calculated from these measurements the interaural differences in time and intensity associated with each of 178 locations throughout the frontal hemisphere. For all frequencies, interaural time differences (ITDs) varied systematically and most strongly with source azimuth. The pattern of variation of interaural intensity differences (IIDs) depended on frequency. For low frequencies (below 4 kHz) IID varied primarily with source azimuth, whereas for high frequencies (above 5 kHz) IID varied primarily with source elevation. Tectal units were tuned for interaural differences in both time and intensity of dichotic stimuli. Changing either parameter away from the best value for the unit decreased the unit's response. The tuning of units to either parameter was sharp: the width of ITD tuning curves, measured at 50% of the maximum response with IID held constant (50% tuning width), ranged from 18 to 82 microsecs. The 50% tuning widths of IID tuning curves, measured with ITD held constant, ranged from 8 to 37 dB. For most units, tuning for ITD was largely independent of IID, and vice versa. A few units exhibited systematic shifts of the best ITD with changes in IID (or shifts of the best IID with changes in ITD); for these units, a change in the value of one parameter to favor one ear shifted the best value of the other parameter in favor of the same ear, i.e., in the direction opposite to that expected from "time-intensity trading." Overall sound intensity had little or no effect on ITD tuning, but did increase the best IIDs of units tuned to nonzero IIDs. The tuning of units for ITD and IID changed systematically along different dimensions of the optic tectum to create coextensive, independent neurophysiological maps of ITD and IID.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2005

Decomposition of the optical transfer function: wavefront coding imaging systems.

We describe the mapping of the optical transfer function (OTF) of an incoherent imaging system into a geometrical representation. We show that for defocused traditional and wavefront-coded systems the OTF can be represented as a generalized Cornu spiral. This representation provides a physical insight into the way in which wavefront coding can increase the depth of field of an imaging system and permits analytical quantification of salient OTF parameters, such as the depth of focus, the location of nulls, and amplitude and phase modulation of the wavefront-coding OTF.

Algorithms↗