Novel methodology for 3D reconstruction of carotid arteries and plaque characterization based upon magnetic resonance imaging carotid angiography data

In this study, we present a novel methodology that allows reliable segmentation of the magnetic resonance images (MRIs) for accurate fully automated three-dimensional (3D) reconstruction of the carotid arteries and semiautomated characterization of plaque type. Our approach uses active contours to detect the luminal borders in the time-of-flight images and the outer vessel wall borders in the T(1)-weighted images. The methodology incorporates the connecting components theory for the automated identification of the bifurcation region and a knowledge-based algorithm for the accurate characterization of the plaque components. The proposed segmentation method was validated in randomly selected MRI frames analyzed offline by two expert observers. The interobserver variability of the method for the lumen and outer vessel wall was -1.60%±6.70% and 0.56%±6.28%, respectively, while the Williams Index for all metrics was close to unity. The methodology implemented to identify the composition of the plaque was also validated in 591 images acquired from 24 patients. The obtained Cohen's k was 0.68 (0.60-0.76) for lipid plaques, while the time needed to process an MRI sequence for 3D reconstruction was only 30 s. The obtained results indicate that the proposed methodology allows reliable and automated detection of the luminal and vessel wall borders and fast and accurate characterization of plaque type in carotid MRI sequences. These features render the currently presented methodology a useful tool in the clinical and research arena.     

Emerging nanocomposite biomaterials as biomedical adsorbents: an overview

Abstract

Biomedicine and pharmacy identify highly important scientific fields within the present time. However, increased advancements in these sciences have influenced the identification of increased levels in environmental degradation through pollution. Pharmaceutical production has influenced increased scientific and public concern regarding the increasing rate of pollution attributed to high levels of toxicological properties within the products. Pharmaceutical compounds are not fully removed through the integration of wastewater treatment plants (WWTP). This renders pharmaceutical compounds, municipal effluents together with hospitals as the major culprits in the development of the majority of the sources that enhance environmental degradation. A wide range of the compounds have been the identified within WWTP effluents, surface water together with ground and drinking water on a global scale. All above has influenced the research development in technological field developing new ways for efficient removal of pharmaceuticals from wastewater produced from the pharmaceuticals or biomedical industries. This situation may be altered through the utilization of adsorbents. Therefore more studies have been published investigating the use of nanocomposite biomaterials for removing the pharmaceutical compounds existing in biomedical effluents.     

Contact metric manifolds

In this paper we study contact metric manifoldsM ²ⁿ⁺¹(, , ,g) with characteristic vector field belonging to thek-nullity distribution. Moreover we prove that there exist i) nonK-contact, contact metric manifolds of dimension greater than 3 with Ricci operator commuting with and ii) 3-dimensional contact metric manifolds with non-zero constant -sectional curvature.     

Encapsulation and controlled release from core–shell nanoparticles fabricated by plasma polymerization

Core–shell nanostructures have been synthesized by plasma deposition in radio-frequency plasma reactor. Silica and KCl nanoparticles were encapsulated by deposition of isopropanol-based films of amorphous hydrogenated carbon. Through control of the deposition time, under constant deposition rate of 1 nm/min, particles are encapsulated in a layer of plasma polymer with thickness between 15 and 100 nm. Films are robust, chemically inert, thermally stable up to 250°C. The permeability of the shells is determined by depositing films of various thickness onto KCl nanoparticles and monitoring the dissolution of the core in aqueous solution. The dissolution profile is characterized by an initial rapid release, followed by a slow release that lasts up to 30 days for the thickest films. The profile is analyzed by Fickian diffusion through a spherical matrix. We find that this model captures very accurately the entire release profile except for the first 12 hours during which, the dissolution rate is higher than that predicted by the model. The overall diffusion coefficient for the dissolution of KCl is 3 × 10⁻²¹ m²/s.     

Energetic determinants of oligomeric state specificity in coiled coils

The coiled coil is one of the simplest and best-studied protein structural motifs, consisting of two to five helices wound around each other. Empirical rules have been established on the tendency of different core sequences to form a certain oligomeric state but the physical forces behind this specificity are unclear. In this work, we model four sequences onto the structures of dimeric, trimeric, tetrameric, and pentameric coiled coils. We first examine the ability of an effective energy function (EEF1.1) to discriminate the correct oligomeric state for a given sequence. We find that inclusion of the translational, rotational, and side-chain conformational entropy is necessary for discriminating the native structures from their misassembled counterparts. The decomposition of the effective energy into residue contributions yields theoretical values for the oligomeric propensity of different residue types at different heptad positions. We find that certain calculated residue propensities are general and consistent with existing rules. For example, leucine at d favors dimers, leucine at a favors tetramers or pentamers, and isoleucine at a favors trimers. Other residue propensities are sequence context dependent. For example, glutamine at d favors trimers in one context and pentamers in another. Charged residues at e and g positions usually destabilize higher oligomers due to higher desolvation. Nonpolar residues at these positions confer pentamer specificity when combined with certain residues at positions a and d. Specifically, the pair Leua-Alag' or the inverse was found to stabilize the pentamer. The small energy gap between the native and misfolded counterparts explains why a few mutations at the core sites are sufficient to induce a change in the oligomeric state of these peptides. A large number of possible experiments are suggested by these results.     

Fractal Dimension of Microbead Assemblies Used for Protein Detection

We use fractal analysis to calculate the protein concentration in a rotating magnetic assembly of microbeads of size 1 μm, which has optimized parameters of sedimentation, binding sites and magnetic volume. We utilize the original Forrest–Witten method, but due to the relatively small number of bead particles, which is of the order of 500, we use a large number of origins and also a large number of algorithm iterations. We find a value of the fractal dimension in the range 1.70–1.90, as a function of the thrombin concentration, which plays the role of binding the microbeads together. This is in good agreement with previous results from magnetorotation studies. The calculation of the fractal dimension using multiple points of reference can be used for any assembly with a relatively small number of particles.     

The Weighted Weak Type Inequality for the Strong Maximal Function

We prove the natural Fefferman-Stein weak type inequality for the strong maximal function in the plane, under the assumption that the weight satisfies a strong Muckenhoupt condition. This complements the corresponding strong type result due to Jawerth. It also extends the weighted weak type inequality for strong A₁ weights due to Bagby and Kurtz.     

Slow dissociation of a charged ligand: analysis of the primary quinone Q(A) site of photosynthetic bacterial reaction centers

Reaction centers (RCs) are integral membrane proteins that undergo a series of electron transfer reactions during the process of photosynthesis. In the Q(A) site of RCs from Rhodobacter sphaeroides, ubiquinone-10 is reduced, by a single electron transfer, to its semiquinone. The neutral quinone and anionic semiquinone have similar affinities, which is required for correct in situ reaction thermodynamics. A previous study showed that despite similar affinities, anionic quinones associate and dissociate from the Q(A) site at rates ≈10(4) times slower than neutral quinones indicating that anionic quinones encounter larger binding barriers (Madeo, J.; Gunner, M. R. Modeling binding kinetics at the Q(A) site in bacterial reaction centers. Biochemistry 2005, 44, 10994-11004). The present study investigates these barriers computationally, using steered molecular dynamics (SMD) to model the unbinding of neutral ground state ubiquinone (UQ) and its reduced anionic semiquinone (SQ(-)) from the Q(A) site. In agreement with experiment, the SMD unbinding barrier for SQ(-) is larger than for UQ. Multi Conformational Continuum Electrostatics (MCCE), used here to calculate the binding energy, shows that SQ(-) and UQ have comparable affinities. In the Q(A) site, there are stronger binding interactions for SQ(-) compared to UQ, especially electrostatic attraction to a bound non-heme Fe(2+). These interactions compensate for the higher SQ(-) desolvation penalty, allowing both redox states to have similar affinities. These additional interactions also increase the dissociation barrier for SQ(-) relative to UQ. Thus, the slower SQ(-) dissociation rate is a direct physical consequence of the additional binding interactions required to achieve a Q(A) site affinity similar to that of UQ. By a similar mechanism, the slower association rate is caused by stronger interactions between SQ(-) and the polar solvent. Thus, stronger interactions for both the unbound and bound states of charged and highly polar ligands can slow their binding kinetics without a conformational gate. Implications of this for other systems are discussed.     

Thermodynamics of buried water clusters at a protein-ligand binding interface

The structure of the complex of cyclophilin A (CypA) with cyclosporin A (CsA, 1) shows a cluster of four water molecules buried at the binding interface, which is rearranged when CsA is replaced by (5-hydroxynorvaline)-2-cyclosporin (2). The thermodynamic contributions of each bound water molecule in the two complexes are explored with the inhomogeneous fluid solvation theory and molecular dynamics simulations. Water (WTR) 133 in complex 1 contributes little to the binding affinity, while WTR6 and 7 in complex 2 play an essential role in mediating protein-ligand binding with a hydrogen bond network. The calculations reveal that the rearrangement of the water molecules contributes favorably to the binding affinity, even though one of them is displaced going from ligand 1 to 2. Another favorable contribution comes from the larger protein-ligand interactions of ligand 2. However, these favorable contributions are not sufficient to overcome the unfavorable desolvation free energy change and the conformational entropy of the hydroxylpropyl group of ligand 2 in the complex, leading to a lower binding affinity of ligand 2. These physical insights may be useful in the development of improved scoring functions for binding affinity prediction.