tag:www.urmc.rochester.edu,2006-03-10:/rcbu/2011-11-28T15:45:11.781-05:00tag:www.urmc.rochester.edu,2006-03-10:/rcbu/221167802011-11-25T00:00:00Z

Conformational changes are important in RNA for binding and catalysis and understanding these changes is important for understanding how RNA functions. Computational techniques using all-atom molecular models can be used to characterize conformational changes in RNA. These techniques are applied to an RNA conformational change involving a single base pair within a nine base pair RNA duplex. The Adenine-Adenine (AA) non-canonical pair in the sequence 5'GGUGAAGGCU3' paired with 3'PCCGAAGCCG5', where P is Purine, undergoes conformational exchange between two conformations on the timescale of tens of microseconds, as demonstrated in a previous NMR solution structure [Chen, G., et al., Biochemistry, 2006. 45: 6889-903]. The more populated, major, conformation was estimated to be 0.5 to 1.3 kcal/mol more stable at 30 °C than the less populated, minor, conformation. Both conformations are trans-Hoogsteen/sugar edge pairs, where the interacting edges on the adenines change with the conformational change. Targeted Molecular Dynamics (TMD) and Nudged Elastic Band (NEB) were used to model the pathway between the major and minor conformations using the AMBER software package. The adenines were predicted to change conformation via intermediates in which they are stacked as opposed to hydrogen-bonded. The predicted pathways can be described by an improper dihedral angle reaction coordinate. Umbrella sampling along the reaction coordinate was performed to model the free energy profile for the conformational change using a total of 1800 ns of sampling. Although the barrier height between the major and minor conformations was reasonable, the free energy difference between the major and minor conformations was the opposite of that expected based on the NMR experiments. Variations in the force field applied did not improve the misrepresentation of the free energies of the major and minor conformations. As an alternative, the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approximation was applied to predict free energy differences between the two conformations using a total of 800 ns of sampling. MM-PBSA also incorrectly predicted the major conformation to be higher in free energy than the minor conformation.

KP Van NostrandSD Kennedy/people/?u=20103149DH TurnerDH Mathewstag:www.urmc.rochester.edu,2006-03-10:/rcbu/220880212011-11-17T00:00:00Z

Particle displacements can be much greater near bubbles than they would be in a homogeneous liquid or tissue when exposed to an acoustic wave. In a plane wave, shear and bulk strains are of the same order of magnitude. In contrast, for a bubble oscillating close to its resonance frequency, the shear strain in the medium near the bubble is roughly four orders of magnitude greater than the bulk strain. This can lead to shear strains of a few percent even with acoustic excitation pressures far below the pressure thresholds required to cause inertial cavitation. High shear strains near oscillating bubbles could potentially be the cause of bioeffects. After acoustic exposures at audio frequencies, hemorrhages in tissues as diverse as lung, liver, and kidney have been observed at shear strains on the order of 1%.

E CarstensenSM Gracewskihttp://www.me.rochester.edu/Faculty/grace.htmlD Dalecki/bme/people/faculty/bio/?id=242tag:www.urmc.rochester.edu,2006-03-10:/rcbu/220880082011-11-17T00:00:00Z

Motivated by various clinical applications of ultrasound contrast agents within blood vessels, the natural frequencies of two bubbles in a compliant tube are studied analytically, numerically, and experimentally. A lumped parameter model for a five degree of freedom system was developed, accounting for the compliance of the tube and coupled response of the two bubbles. The results were compared to those produced by two different simulation methods: (1) an axisymmetric coupled boundary element and finite element code previously used to investigate the response of a single bubble in a compliant tube and (2) finite element models developed in comsol Multiphysics. For the simplified case of two bubbles in a rigid tube, the lumped parameter model predicts two frequencies for in- and out-of-phase oscillations, in good agreement with both numerical simulation and experimental results. For two bubbles in a compliant tube, the lumped parameter model predicts four nonzero frequencies, each asymptotically converging to expected values in the rigid and compliant limits of the tube material.

NW JangA ZakrzewskiC RossiD Dalecki/bme/people/faculty/bio/?id=242S Gracewskihttp://www.me.rochester.edu/Faculty/grace.htmltag:www.urmc.rochester.edu,2006-03-10:/rcbu/220376482011-11-01T00:00:00Z

This paper describes methods that provide pre-requisite information for computing circumferential stress in modulus elastograms recovered from vascular tissue-information that could help cardiologists detect life-threatening plaques and predict their propensity to rupture. The modulus recovery process is an ill-posed problem; therefore, additional information is needed to provide useful elastograms. In this work, prior geometrical information was used to impose hard or soft constraints on the reconstruction process. We conducted simulation and phantom studies to evaluate and compare modulus elastograms computed with soft and hard constraints versus those computed without any prior information. The results revealed that (1) the contrast-to-noise ratio of modulus elastograms achieved using the soft prior and hard prior reconstruction methods exceeded those computed without any prior information; (2) the soft prior and hard prior reconstruction methods could tolerate up to 8% measurement noise, and (3) the performance of soft and hard prior modulus elastograms degraded when incomplete spatial priors were employed. This work demonstrates that including spatial priors in the reconstruction process should improve the performance of model-based elastography, and the soft prior approach should enhance the robustness of the reconstruction process to errors in the geometrical information.

MS RichardsMM Doyleyhttp://www.ece.rochester.edu/html/people/Doyley/Doyley.htmltag:www.urmc.rochester.edu,2006-03-10:/rcbu/219248162011-10-21T00:00:00Z

The successful fabrication of large, three-dimensional (3-D) tissues and organs in vitro requires the rapid development of a vascular network to maintain cell viability and tissue function. In this study, we utilized an application of ultrasound standing wave field (USWF) technology to vascularize 3-D, collagen-based hydrogels in vitro. Acoustic radiation forces associated with USWF were used to noninvasively organize human endothelial cells into distinct, multicellular planar bands within 3-D collagen gels. The formation and maturation of capillary-like endothelial cell sprouts were monitored over time and compared with sham-exposed collagen constructs, which were characterized by a homogeneous cell distribution. USWF-induced cell banding accelerated the formation and elongation of capillary-like sprouts, promoted collagen fiber alignment and resulted in the maturation of endothelial cell sprouts into lumen-containing, anastomosing networks found throughout the entire volume of the collagen gel. USWF-induced endothelial cell networks contained large, arteriole-sized lumen areas that branched into smaller, capillary-sized structures indicating the development of vascular tree-like networks. In contrast, sprout formation was delayed in sham-exposed collagen gels and endothelial cell networks were absent from sham gel centers and failed to develop into the vascular tree-like structures found in USWF-exposed constructs. Our results demonstrate that USWF technology leads to rapid and extensive vascularization of 3-D collagen-based engineered tissue and, therefore, provide a new strategy to vascularize engineered tissues in vitro.

KA GarvinD Dalecki/bme/people/faculty/bio/?id=242DC Hocking/people/?u=22430199tag:www.urmc.rochester.edu,2006-03-10:/rcbu/219625792011-10-21T00:00:00Z

Model-based elastography is an emerging technique with clinical applications in imaging vascular tissues, guiding minimally invasive therapies and diagnosing breast and prostate cancers. Its usage is limited because ultrasound can measure only the axial component of displacement with high precision. The goal of this study was to assess the effect of lateral sampling frequency, lateral beam-width and the number of active transmission elements on the quality of axial and lateral strain elastograms. Elastographic imaging was performed on gelatin-based phantoms with a modified commercial ultrasound scanner. Three groups of radio-frequency (RF) echo frames were reconstructed from fully synthetic aperture data. In the first group, all 128 transmission elements (corresponding to a lateral beamwidth of 0.22 mm at the center of the field of view) were used to reconstruct RF echo frames with A-line densities that varied from 6.4 lines/mm to 51.2 lines/mm. In the second group, the size of the aperture was varied to produce RF echo frames with lateral beamwidths ranging from 0.22 mm to 0.43 mm and a fixed A-line density of 25.6 lines/mm. In the third group, sparse arrays with varying number of active transmission elements (from 2 to 128) were used to reconstruct RF echo frames, whose A-line density and lateral beamwidth were fixed to 25.6 lines/mm and 0.22 mm, respectively. Applying a two-dimensional (2-D) displacement estimator to the pre- and post-deformed RF echo frames produced displacement elastograms. Axial and lateral strain elastograms were computed from displacement elastograms with a least squares strain estimator. The quality of axial and lateral strain elastograms improved with increasing applied strain and A-line density but decreased with increasing lateral beamwidth and deteriorated as the number of active transmission elements in the sparse arrays were reduced. This work demonstrated that the variance incurred when estimating the lateral component of displacement was reduced considerably when elastography was performed with a synthetic aperture ultrasound imaging system. Satisfactory axial and lateral strain elastograms were produced using a sparse array with as few as 16 active transmission elements.

S KorukondaMM Doyleyhttp://www.ece.rochester.edu/html/people/Doyley/Doyley.htmltag:www.urmc.rochester.edu,2006-03-10:/rcbu/219773852011-10-06T00:00:00Z

Pilomatrixomas are uncommon benign skin neoplasms arising from the hair follicle matrix. They occur more commonly in children than adults. Most originate on the head, neck, or upper extremities, less commonly on the trunk or lower extremities, and very infrequently in the breast. We present a rare case of pilomatrixoma of the breast in an adult male. As the patient had a strong family history of breast cancer, a full work-up of the breast mass was performed. Ultimately, an excisional biopsy was carried out for patient reassurance.

CM HubenyJB SykesA O'ConnellVS Dogra/people/?u=23018716tag:www.urmc.rochester.edu,2006-03-10:/rcbu/219494242011-10-06T00:00:00Z

Clinical studies suggest that psychiatric symptoms, particularly depression, anxiety, and trauma, may be associated with inflammation, as indexed by proinflammatory cytokines. Such a link may be especially significant in pregnancy and may shed additional light on the etiology of perinatal mood disorders.

ER BlackmoreJA MoynihanDR RubinowEK Pressman/people/?u=23061316M GilchristTG O'Connortag:www.urmc.rochester.edu,2006-03-10:/rcbu/219666182011-10-03T00:00:00Z

Diagnostic imaging plays an important role in the assessment of patients with mechanical cardiac assist devices. Therefore, it is important for radiologists to be familiar with the basic components, function, and radiographic appearances of these devices in order to appropriately diagnose complications. The purpose of this pictorial essay is to review indications, components, normal imaging appearances, and complications of surgically and percutaneously implanted ventricular assist devices, intra-aortic balloon pumps, and cardiac meshes.

D GinatHT MasseyS BhattVS Dogra/people/?u=23018716