A guideline for the distance measurement plans of site-directed spin labels for structural prediction of nucleic acids.

CONTEXT AND RESULTS: Site-directed spin labeling (SDSL) combined with electron paramagnetic resonance spectroscopy methods has been successfully used to predict the structures of nucleic acids. These methods measure the distances between spin labels yielding distance equations that are solved using numerical algorithms to provide one or several structural predictions. In this work, the minimum number of SDSL distance measurements and distance measurement types required to predict a unique nucleic acid structure were investigated. Our results indicate that at least six distance measurements should be obtained given that the distance measurements do not connect one SDSL on one arm with more than three SDSLs on the other arm. Moreover, there may be a preference for 1-to-1 SLs distance measurements rather than 1-to-many SLs as the latter was linked to undefined structures discussed in this study. METHODS: Pairs of double-helical arms of nucleic acid were simulated using the finite element software Pro/ENGINEER (PTC Inc., Boston, MA). In each simulation, a specific SDSL distance measurement plan was adopted and the resulting structure was tested for movability. Immovable structures indicate that this plan will potentially result in a unique structural prediction of the nucleic acid. All the possible plans for SDSL distance measurements were investigated either by direct measurement or by extrapolation.

Multiplexing potential of NIR resonant and non-resonant Raman reporters for bio-imaging applications.

Multiplexed imaging, which allows for the interrogation of multiple molecular features simultaneously, is vital for addressing numerous challenges across biomedicine. Optically unique surface-enhanced Raman scattering (SERS) nanoparticles (NPs) have the potential to serve as a vehicle to achieve highly multiplexed imaging in a single acquisition, which is non-destructive, quantitative, and simple to execute. When using laser excitation at 785 nm, which allows for a lower background from biological tissues, near infrared (NIR) dyes can be used as Raman reporters to provide high Raman signal intensity due to the resonance effect. This class of imaging agents are known as surface-enhanced resonance Raman scattering (SERRS) NPs. Investigators have predominantly utilized two classes of Raman reporters in their nanoparticle constructs for use in biomedical applications: NIR-resonant and non-resonant Raman reporters. Herein, we investigate the multiplexing potential of five non-resonant SERS: BPE, 44DP, PTT, PODT, and BMMBP, and five NIR resonant SERRS NP flavors with heptamethine cyanine dyes: DTTC, IR-770, IR-780, IR-792, and IR-797, which have been extensively used for biomedical imaging applications. Although SERRS NPs display high Raman intensities, due to their resonance properties, we observed that non-resonant SERS NP concentrations can be quantitated by the intensity of their unique emissions with higher accuracy. Spectral unmixing of five-plex mixtures revealed that the studied non-resonant SERS NPs maintain their detection limits more robustly as compared to the NIR resonant SERRS NP flavors when introducing more components into a mixture.

Hemodynamic Performance of Dysfunctional Prosthetic Heart Valve with the Concomitant Presence of Subaortic Stenosis: In Silico Study.

The prosthetic heart valve is vulnerable to dysfunction after surgery, thus a frequent assessment is required. Doppler electrocardiography and its quantitative parameters are commonly used to assess the performance of the prosthetic heart valves and provide detailed information on the interaction between the heart chambers and related prosthetic valves, allowing early detection of complications. However, in the case of the presence of subaortic stenosis, the accuracy of Doppler has not been fully investigated in previous studies and guidelines. Therefore, it is important to evaluate the accuracy of the parameters in such cases to get early detection, and a proper treatment plan for the patient, at the right time. In the current study, a CFD simulation was performed for the blood flow through a Bileaflet Mechanical Heart Valve (BMHV) with concomitant obstruction in the Left Ventricle Outflow Tract (LVOT). The current study explores the impact of the presence of the subaortic on flow patterns. It also investigates the accuracy of (BMHV) evaluation using Doppler parameters, as proposed in the American Society of Echocardiography (ASE) guidelines.

Nuclear magnetic resonance analysis of a chemically cross-linked ferrous-methylthymol blue-polyvinyl alcohol radiochromic gel dosimeter.

A new formulation of hydrogel dosimeter consisting of ferrous-methylthymol blue (MTB)-polyvinyl alcohol (PVA) cross-linked chemically with glutaraldehyde (GTA) was studied and evaluated by nuclear magnetic resonance analysis by means of the R2 spin-spin relaxation rate. Previous optical studies of this transparent solid chemically cross-linked gel showed important dosimetric features in terms of sensitivity, auto-oxidation rate, and diffusion. This study shows that the MTB-PVA-GTA dosimeter has a reproducible linear dose response up to 40 Gy. For the optimum formulation of 0.1 mM MTB, 2.5% PVA, and 26.6 mM GTA, the measured R2 sensitivity was higher than that of traditional natural matrix-containing gels (MTB-gelatin) and all other reported PVA gel-based radiochromic dosimeters with MTB, xylenol orange (XO), or GTA (MTB-PVA, XO-PVA, XO-PVA-GTA). Additionally, the auto-oxidation rate was approximately ten times lower than that of the Fricke-MTB-gelatin system, which is consistent with the spectrophotometry results. The results of the independent experimental spectrophotometry and nuclear magnetic resonance analyses indicate that the transparent cross-linked dosimeter has good and consistent dosimetric features.

3-D spatial compounding using a row-column array.

2-D spatial compounding has long been investigated to reduce speckle in ultrasound images. To further reduce speckle, several 3-D spatial compounding studies using 1-D and 1.5 D arrays with mechanical translation and position tracking have been reported. However, the fixed elevational focus and mechanical translation can degrade image quality in elevation. Using 2-D arrays, a better elevational resolution can be achieved with electronic focusing. Furthermore, 2-D arrays can generate greater number of independent images than 1-D arrays and the need for mechanical scanning is eliminated. In this paper, we present our 3-D spatial compounding images of two gel-based contrast phantoms and one resolution phantom. These images were acquired using a prototype 4 cm x 4 cm ultrasonic row-column prototype 2-D array operating at 5 MHz. Compounding nine decorrelated volumes showed a speckle signal-to-noise ratio (SNR) improvement of 2.68. The average improvement of the lesion contrast-to-noise ratio (CNR) was 2.45. However, using a smaller aperture to generate these volumes worsened the lateral resolution as predicted by theory.

A dual-layer transducer array for 3-D rectilinear imaging.

Very large element counts (16,000-65,000) are required for 2-D arrays for 3-D rectilinear imaging. The difficulties in fabricating and interconnecting 2-D arrays with a large number of elements (>5,000) have limited the development of suitable transducers for 3-D rectilinear imaging. In this paper, we propose an alternative solution to this problem by using a dual-layer transducer array design. This design consists of 2 perpendicular 1-D arrays for clinical 3-D imaging of targets near the transducer. These targets include the breast, carotid artery, and musculoskeletal system. This transducer design reduces the fabrication complexity and the channel count, making 3-D rectilinear imaging more realizable. With this design, an effective N x N 2-D array can be developed using only N transmitters and N receivers. This benefit becomes very significant when N becomes greater than 128, for example. To demonstrate feasibility, we constructed a 4 x 4 cm prototype dual-layer array. The transmit array uses diced PZT-5H elements, and the receive array is a single sheet of undiced P[VDF-TrFE] copolymer. The receive elements are defined by the copper traces on the flexible interconnect circuit. The measured -6 dB fractional bandwidth was 80% with a center frequency of 4.8 MHz. At 5 MHz, the nearest neighbor crosstalk of the PZT array and PVDF array was -30.4 +/- 3.1 dB and -28.8 +/- 3.7 dB, respectively. This dual-layer transducer was interfaced with an Ultrasonix Sonix RP system, and a synthetic aperture 3-D data set was acquired. We then performed offline 3-D beamforming to obtain volumes of nylon wire targets. The theoretical lateral beamwidth was 0.52 mm compared with measured beamwidths of 0.65 mm and 0.67 mm in azimuth and elevation, respectively. Then, 3-D images of an 8 mm diameter anechoic cyst phantom were also acquired.

3D strain imaging using a rectilinear 2D array.

Under mechanical compression, tissue movements are inherently three-dimensional. 2-D strain imaging can suffer from decorrelation noise caused by out-of-plane tissue movement in elevation. With 3-D strain imaging, all tissue movements can be estimated and compensated, hence minimizing out-of-plane decorrelation noise. Promising 3-D strain imaging results have been shown using 1-D arrays with mechanical translation in elevation. However, the relatively large slice thickness and mechanical translation can degrade image quality. Using 2-D arrays, an improved elevational resolution can be achieved with electronic focusing. Furthermore, scanning with 2-D arrays is also done electronically, which eliminates the need for mechanical translation. In this paper, we demonstrate the feasibility of 3-D strain imaging using a 4 cm x 4 cm ultrasonic sparse rectilinear 2-D array operating at 5MHz. The signal processing combinations of 2-D or 3-D beamforming followed by 2-D or 3-D strain imaging are studied and compared to each other to evaluate the performance of our 3-D strain imaging system. 3-D beamforming followed by 3-D strain imaging showed best performance in all experiments.