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PubMed1996

Temporal resolution improvement in dynamic imaging.

In some dynamic imaging applications, only a fraction, 1/n, of the field of view (FOV) may show considerable change during the motion cycle. A method is presented that improves the temporal resolution for a dynamic region by a factor, n, while maintaining spatial resolution at a cost of square root of n in signal-to-noise ratio (SNR). Temporal resolution is improved, or alternatively, total imaging time is reduced by reducing the number of phase encodes acquired for each temporal frame by 1/n. To eliminate aliasing, a representation of the signal from the static outer portion of the FOV is constructed using all the raw data. The k-space data derived from this representation is subtracted from the original data sets, and the differences correspond to the dynamic portion of the FOV. Improved resolution results are presented in phantom studies, and in vivo phase contrast quantitative flow imaging.

Algorithms↗

PubMed1997

High resolution electron paramagnetic resonance imaging of biological samples with a single line paramagnetic label.

The application of electron paramagnetic resonance imaging (EPRI) to obtain information from biological samples has been limited by the lack of ideal single line radical labels. The commonly used nitroxides exhibit multiple lines causing either hyperfine-based limitations in the maximum obtainable image resolution or hyperfine-based artifacts in the reconstructed image. The use of a novel single-line triarylmethyl paramagnetic label that enables marked enhancement in image quality and resolution is reported. This label exhibits a single line EPR spectrum that is sharp (linewidth approximately 60 mG in the absence of oxygen) and relatively stable in tissues. The potential of this label in enabling high resolution EPR imaging of biological samples was demonstrated in a series of phantoms and isolated biological organs such as the rat kidney. The images demonstrate that resolutions better than 100 microns could be obtained at L-band on samples of up to 20 mm in size.

Animals↗

PubMed1997

Limitations of temporal resolution in functional MRI.

In fMRI, images can be collected in a very short time; therefore, high temporal resolution is possible in principle. However, the temporal resolution is limited by a blurred intrinsic hemodynamic response and a finite signal-to-noise ratio. To determine the upper limit of temporal resolution in a single area during repeated tasks, motor cortex activity was investigated during visually instructed finger movements. Without averaging, a sequence of four single-finger movements with an execution time of approximately 2 s can be resolved when the delay time between consecutive sequences is at least 3 s. The hemodynamic response time is constant for each subject, but not among different subjects. The temporal resolution can be better when the signal from spatially distinct regions is examined. For a series of experiments involving a visually instructed delayed cued finger movement task with a well-defined, independently determined, variable delay time, time courses in the motor area are distinct from each other in two experiments if the difference in delay time is as little as 2 s. The activation in the visual area due to the presentation of the task serves here as an internal time reference. By comparing a set of fMRI time courses in multiple distinct areas, serial neural processing may be investigated.

Brain↗

PubMed2006

Three-dimensional reconstruction of limited-view projections for contrast-enhanced magnetic resonance angiography at high temporal and spatial resolution.

The feasibility of reconstructing three-dimensional (3D) MRI data sets from limited-view projections is investigated in phantom and in vivo animal studies to improve the temporal resolution of magnetic resonance angiography without sacrificing spatial resolution. Thirty-two pairs of orthogonal biplane projections are acquired in an interleaved manner during the first pass of a contrast agent. The full data set is reconstructed as a priori 3D information. Each pair of projections is then reconstructed into an individual 3D data set based on a correlation analysis with the a priori data set. In this way, time-resolved 3D data sets at 1- to 2-s time intervals are reconstructed with submillimeter spatial resolution. Artifacts are limited if the image is simply structured or sparse and if SNR is sufficient in the projection images. With this technique, both high temporal and spatial resolution can be achieved simultaneously.

Animals↗

PubMed2006

Electron paramagnetic resonance imaging of tumor hypoxia: enhanced spatial and temporal resolution for in vivo pO2 determination.

The time-domain (TD) mode of electron paramagnetic resonance (EPR) data collection offers a means of estimating the concentration of a paramagnetic probe and the oxygen-dependent linewidth (LW) to generate pO2 maps with minimal errors. A methodology for noninvasive pO2 imaging based on the application of TD-EPR using oxygen-induced LW broadening of a triarylmethyl (TAM)-based radical is presented. The decay of pixel intensities in an image is used to estimate T2*, which is inversely proportional to pO2. Factors affecting T2* in each pixel are critically analyzed to extract the contribution of dissolved oxygen to EPR line-broadening. Suitable experimental and image-processing parameters were obtained to produce pO2 maps with minimal artifacts. Image artifacts were also minimized with the use of a novel data collection strategy using multiple gradients. Results from a phantom and in vivo imaging of tumor-bearing mice validated this novel method of noninvasive oximetry. The current imaging protocols achieve a spatial resolution of approximately 1.0 mm and a temporal resolution of approximately 9 s for 2D pO2 mapping, with a reliable oxygen resolution of approximately 1 mmHg (0.12% oxygen in gas phase). This work demonstrates that in vivo oximetry can be performed with good sensitivity, accuracy, and high spatial and temporal resolution.

Algorithms↗

PubMed2006

Comparison of errors associated with single- and multi-bolus injection protocols in low-temporal-resolution dynamic contrast-enhanced tracer kinetic analysis.

Accurate sampling of the arterial input function (AIF) in low-temporal-resolution quantitative dynamic contrast-enhanced MRI (DCE-MRI) studies is crucial for accurate and reproducible parameter estimation. However, when conventional AIFs are sampled at low temporal resolution, they introduce an unpredictable degree of error. An alternative double contrast agent (CA) bolus injection protocol designed to compensate for temporal mis-sampling of the AIF and tissue uptake curve was simulated in addition to a commonly used single CA bolus injection protocol. A range of tissue uptake curves for each AIF form were generated using a distributed parameter model, and Monte Carlo simulation studies were performed over a range of offset times (to mimic temporal mis-sampling), temporal resolutions and SNR in order to compare the performance of both AIF forms in compartmental modeling. Insufficient data sampling of the single bolus AIF at temporal resolutions in excess of 9 s leads to large errors, which can be reduced by employing an additional, appropriately administered, second CA bolus injection.

Algorithms↗

PubMedDate not supplied

Predicting BOLD signal changes as a function of blood volume fraction and resolution.

The appropriate choice of resolution in fMRI remains an open question. To address this issue, we simulate the signal change between activated and resting states as a function of blood volume fraction (lambda). From these results, the relative contrast-to-noise ratio (CNR) from the resting to the activated state can be calculated as a function of resolution. We consider different vessel orientations and note that, in most cases, the most efficient scanning procedure is for low resolution imaging. To overcome this limitation, a T(1) enhancing contrast agent is proposed to increase the signal from the blood and, hence, the intravascular contribution to the BOLD effect. We show that this effect dramatically increases both the signal changes and the efficiency of high-resolution imaging and should lead to much better visualization and localization of parenchymal changes.

Blood Volume↗

PubMed2002

High-resolution magic angle spinning MRS of breast cancer tissue.

High-resolution magic angle spinning (HR MAS) may develop into a new diagnostic tool for studying intact tissue samples, and several types of cancer have been investigated with promising results. In this study HR MAS spectra of breast cancer tissue from 10 patients have been compared to conventional high-resolution spectra of perchloric acid extracts of the same tissue type. The HR MAS spectra show resolution comparable to spectra of extracts, and two-dimensional techniques lead to identification of a majority of the constituents. More than 30 different metabolites have been detected and assigned. To our knowledge this is the most detailed assignment of biochemical components in intact human breast tissue. The spectra of intact breast cancer tissue differ from perchloric acid extracts by the presence of lipids and fewer signals in the low field region. HR MAS analysis of intact breast tissue specimens is a rapid method, providing spectra with resolution where relative quantification of the majority of the detected metabolites is possible.

Adult↗

PubMed2005

Anatomical and functional brain imaging using high-resolution echo-planar spectroscopic imaging at 1.5 Tesla.

High-resolution echo-planar spectroscopic imaging (EPSI) of water resonance (i.e. without water suppression) is proposed for anatomic and functional imaging of the human brain at 1.5 T. Water spectra with a resolution of 2.6 Hz and a bandwidth of 333 Hz were obtained in small voxels (1.7 x 1.7 x 3 mm3) across a single slice. Although water spectra appeared Lorentzian in most of the voxels in the brain, non-Lorentzian broadening of the water resonance was observed in voxels containing blood vessels. In functional experiments with a motor task, robust activation in motor cortices was observed in high-resolution T2* maps generated from the EPSI data. Shift of the water resonance frequency occurred during neuronal activation in motor cortices. The activation areas appeared to be more localized after excluding the voxels in which the lineshape of the water resonance had elevated T2* and became more non-Lorentzian during the motor task. These preliminary results suggest that high-resolution EPSI is a promising tool to study susceptibility-related effects, such as BOLD contrast, for improved anatomical and functional imaging of the brain.

Adult↗

PubMed2005

Stem cell implantation in ischemic mouse heart: a high-resolution magnetic resonance imaging investigation.

Advances in the biology of stem cells have evoked great interest in cell replacement therapies for the regeneration of heart tissue after myocardial infarction. However, results from human trials are controversial, since the destination of the injected cells, their engraftment and their long-term fate have remained unclear. Here we investigate whether transplanted cells can be identified in the intact and lesioned murine myocardium employing high-resolution MRI. Cardiac progenitor cells, expressing the enhanced green fluorescent protein (EGFP), were labeled with ultra-small paramagnetic iron-oxide (USPIO) nanoparticles and transplanted into the intact or injured myocardium of mice. Their precise location was determined with high-resolution MRI and compared with histological tissue sections, stained with Prussian blue for iron content. These experiments showed that iron nanoparticle-loaded cells could be identified at high resolution in the mouse heart. However, ischemic myocardium (after cryoinjury or left coronary artery ligation) was characterized by a signal attenuation similar to that induced by USPIO-labeled cells in T2*-weighted MR images, making detection of labeled stem cells in this area by T2*-sensitive contrast rather difficult. In animals with myocardial injury only, the signal attenuated areas were of the same size in proton density- and T2*-weighted MR images. In injured animals also receiving labeled cells the lesioned area appeared larger in T2*--than in proton density-weighted MR images. This sequence-dependent lesion size change is due to the increased signal loss caused by the iron oxide nanoparticles, most sensitively detectable in the T2*-sensitive images. Thus, using the novel combination of these two parameter weightings, USPIO-labeled cells can be detected at high resolution in ischemic myocardium.

Animals↗

PubMed2005

Echo train shifted multi-echo FLASH for functional MRI of the human brain at ultra-high spatial resolution.

This paper describes the development of a novel technique for functional MRI of the human brain at 0.135 microL resolution for a whole brain section. In comparison with conventional studies at 3 mm isotropic resolution or 27 microL voxel size, the method yields an improvement by a factor of 200. To achieve optimum image quality, the approach is based on a multi-echo fast low-angle shot (FLASH) sequence with unipolar traversals of k-space in the frequency-encoding dimension and echo train shifting to avoid amplitude discontinuities in the phase-encoding dimension. These strategies ensure a smooth point-spread function and eliminate image ghosting artifacts without the need for any phase correction or other post-processing. Signal-to-noise losses due to the considerably reduced voxel sizes are compensated for by single slice acquisitions, optimized bandwidths and an experimental four-channel shoulder coil matched to the posterior portion of the head. Multi-echo FLASH studies of the human brain (2.9 T, seven echoes, 200 Hz/pixel bandwidth, effective echo time 36 ms, acquisition time 6 s) at 300 microm resolution (no interpolation) and 1.5 mm slice thickness revealed robust activations in primary visual areas in response to binocular stimulation. The new method holds promise for refined studies of the columnar organization of specific brain systems and for functional assessments of the gray matter at laminar resolution.

Animals↗

PubMed1990

Relationship of hope, coping styles, concurrent losses, and setting to grief resolution in the elderly widow(er).

This descriptive study was based on Dimond's Bereavement Adaptation Model; investigation was made of the relationship between hope, concurrent losses, coping style, setting (hospital, hospice, nursing home), and grief resolution. Seventy-five elderly persons who had been widowed 12-18 months completed the Herth Hope Scale, the Jalowiec Coping Scale, and the Grief Resolution Index by mail. A significant positive relationship was found between effective grief resolution and a high hope level; 0-1 concurrent losses; the use of confrontive, optimistic, palliative, supportant, and self-reliant coping styles; and the death of the spouse within a hospice setting. The importance of the type of setting, hope level, and specific coping styles on grief resolution in the elderly widow(er) is suggested by the findings.

Adaptation, Psychological↗

PubMed2004

About thiol derivatization and resolution of basic proteins in two-dimensional electrophoresis.

The influence of thiol blocking on the resolution of basic proteins by two-dimensional electrophoresis was investigated. Cysteine blocking greatly increased resolution and decreased streaking, especially in the basic region of the gels. Two strategies for cysteine blocking were found to be efficient: classical alkylation with maleimide derivatives and mixed disulfide exchange with an excess of a low molecular weight disulfide. The effect on resolution was significant enough to allow correct resolution of basic proteins with in-gel rehydration on wide gradients (e.g. 3-10 and 4-12), but anodic cup-loading was still required for basic gradients (e.g. 6-12 or 8-12). These results demonstrate that thiol-related problems are not solely responsible for streaking of basic proteins on two-dimensional gels.

Alkylation↗

PubMed1996

High-resolution X-ray structure of UDP-galactose 4-epimerase complexed with UDP-phenol.

UDP-galactose 4-epimerase from Escherichia coli catalyzes the interconversion of UDP-glucose and UDP-galactose. In recent years, the enzyme has been the subject of intensive investigation due in part to its ability to facilitate nonstereospecific hydride transfer between beta-NADH and a 4-keto hexopyranose intermediate. The first molecular model of the epimerase from E. coli was solved to 2.5 A resolution with crystals grown in the presence of a substrate analogue, UDP-phenol (Bauer AJ, Rayment I, Frey PA, Holden HM, 1992, Proteins Struct Funct Genet 12:372-381). There were concerns at the time that the inhibitor did not adequately mimic the sugar moiety of a true substrate. Here we describe the high-resolution X-ray crystal structure of the ternary complex of UDP-galactose 4-epimerase with NADH and UDP-phenol. The model was refined to 1.8 A resolution with a final overall R-factor of 18.6%. This high-resolution structural analysis demonstrates that the original concerns were unfounded and that, in fact, UDP-phenol and UDP-glucose bind similarly. The carboxamide groups of the dinucleotides, in both subunits, are displaced significantly from the planes of the nicotinamide rings by hydrogen bonding interactions with Ser 124 and Tyr 149. UDP-galactose 4-epimerase belongs to a family of enzymes known as the short-chain dehydrogenases, which contain a characteristic Tyr-Lys couple thought to be important for catalysis. The epimerase/NADH/UDP-phenol model presented here represents a well-defined ternary complex for this family of proteins and, as such, provides important information regarding the possible role of the Tyr-Lys couple in the reaction mechanism.

20-Hydroxysteroid Dehydrogenases↗

PubMed2002

Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models.

Predicting the three-dimensional structure of proteins is still one of the most challenging problems in molecular biology. Despite its difficulty, several investigators have started to produce consistently low-resolution predictions for small proteins. However, in most of these cases, the prediction accuracy is still too low to make them useful. In the present article, we address the problem of obtaining better-quality predictions, starting from low-resolution models. To this end, we have devised a new procedure that uses these models, together with structure comparison methods, to identify the structural family of the target protein. This would allow, in a second step not described in the present work, to refine the predictions using conserved features of the identified family. In our approach, the structure database is investigated using predictions, at different accuracy levels, for a given protein. As query structures, we used both low-resolution versions of the native structures, as well as different sets of low accuracy predictions. In general, we found that for predictions with a resolution of > or =5-7 A, structure comparison methods were able to identify the fold of a protein in the top positions.

Databases, Protein↗

PubMed2004

Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.

The first subatomic resolution structure of a 36 kDa protein [aldose reductase (AR)] is presented. AR was cocrystallized at pH 5.0 with its cofactor NADP+ and inhibitor IDD 594, a therapeutic candidate for the treatment of diabetic complications. X-ray diffraction data were collected up to 0.62 A resolution and treated up to 0.66 A resolution. Anisotropic refinement followed by a blocked matrix inversion produced low standard deviations (<0.005 A). The model was very well ordered overall (CA atoms' mean B factor is 5.5 A2). The model and the electron-density maps revealed fine features, such as H-atoms, bond densities, and significant deviations from standard stereochemistry. Other features, such as networks of hydrogen bonds (H bonds), a large number of multiple conformations, and solvent structure were also better defined. Most of the atoms in the active site region were extremely well ordered (mean B approximately 3 A2), leading to the identification of the protonation states of the residues involved in catalysis. The electrostatic interactions of the inhibitor's charged carboxylate head with the catalytic residues and the charged coenzyme NADP+ explained the inhibitor's noncompetitive character. Furthermore, a short contact involving the IDD 594 bromine atom explained the selectivity profile of the inhibitor, important feature to avoid toxic effects. The presented structure and the details revealed are instrumental for better understanding of the inhibition mechanism of AR by IDD 594, and hence, for the rational drug design of future inhibitors. This work demonstrates the capabilities of subatomic resolution experiments and stimulates further developments of methods allowing the use of the full potential of these experiments.

Acetates↗

PubMed2005

The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.

Docking unbound molecules presents a challenge in the case where no prior biological or bioinformatic knowledge exists. This is mainly due to differences between the structures of the molecules when in a complex and in the free state. Presumably, these differences interfere with the ability of protein-protein docking algorithms, which rely on a dominant shape descriptor, to identify the correct solution and rank it higher than false solutions. In this study we verify the notion that small discords in the molecular fit can be eliminated by using appropriately designed low-resolution shape descriptors, thereby improving the docking results. We exploit the inherent gradual resolution dependency of Fourier transforms and formulate a resolution-dependent shape descriptor by truncating selected Fourier transform terms. Thus, different levels of shape modification are attained, affecting the degree of detail in the depiction of the molecular surface. We applied the modified descriptor to a selection of 23 protein-protein systems, using the unbound structures where possible. The docking results obtained with the new geometric descriptor were considerably superior to former results, improving the ranks of nearly correct solutions for 17 systems. Unification of the results of scans in which different resolutions were employed further improved the ranks of nearly correct solutions to less than 100 for 12 of the 23 systems and less than 300 for 20 systems. The new geometric descriptor can be combined with other descriptors, which typify the electrostatic or hydrophobic character of the molecular surface, and with external experimental or bioinformatic data.

Binding Sites↗

PubMed2006

A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set.

This work presents a novel C(alpha)--C(alpha) distance dependent force field which is successful in selecting native structures from an ensemble of high resolution near-native conformers. An enhanced and diverse protein set, along with an improved decoy generation technique, contributes to the effectiveness of this potential. High quality decoys were generated for 1489 nonhomologous proteins and used to train an optimization based linear programming formulation. The goal in developing a set of high resolution decoys was to develop a simple, distance-dependent force field that yields the native structure as the lowest energy structure and assigns higher energies to decoy structures that are quite similar as well as those that are less similar. The model also includes a set of physical constraints that were based on experimentally observed physical behavior of the amino acids. The force field was tested on two sets of test decoys not in the training set and was found to excel on all the metrics that are widely used to measure the effectiveness of a force field. The high resolution force field was successful in correctly identifying 113 native structures out of 150 test cases and the average rank obtained for this test was 1.87. All the high resolution structures (training and testing) used for this work are available online and can be downloaded from http://titan.princeton.edu/HRDecoys.

Algorithms↗