Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA)

The thrombin binding aptamer (TBA) is a promising nucleic acid-based anticoagulant. We studied the effects of chemical modifications, such as dendrimer Trebler and NHS carboxy group, on TBA with respect to its structures and thrombin binding affinity. The two dendrimer modifications were incorporated into the TBA at the 5′ end and the NHS carboxy group was added into the thymine residues in the thrombin binding site of the TBA G-quadruplex (at T4, T13 and both T4/T13) using solid phase oligonucleotide synthesis. Circular dichroism (CD) spectroscopy confirmed that all of these modified TBA variants fold into a stable G-quadruplex. The binding affinity of TBA variants with thrombin was measured by surface plasmon resonance (SPR). The binding patterns and equilibrium dissociation constants (K_D) of the modified TBAs are very similar to that of the native TBA. Molecular dynamics simulations studies indicate that the additional interactions or stability enhancement introduced by the modifications are minimized either by the disruption of TBA–thrombin interactions or destabilization elsewhere in the aptamer, providing a rational explanation for our experimental data. Overall, this study identifies potential positions on the TBA that can be modified without adversely affecting its structure and thrombin binding preference, which could be useful in the design and development of more functional TBA analogues.     

An adaptive heuristic algorithm for VLSI test vectors selection

The increasing complexity of today’s system-on-a-chip designs is putting more pressure on the already stressed design verification process. The verification plan must cover several individual cores as well as the overall chip design. Conditions to be verified are identified by the system’s architects, the designers, and the verification team. Testing for these conditions is a must for the design to tape out, especially for high priority conditions. A significant bottleneck in the verification process of such designs is that not enough time is usually given to the final coverage phase, which makes computing cycles very precious. Thus, intelligent selection of test vectors that achieve the best coverage using the minimum number of computing cycles is crucial for on time tape out. This paper presents a novel heuristic algorithm for test vectors selection. The algorithm attempts to achieve the best coverage level while minimizing the required number of computing cycles.     

Algèbres et cogèbres de Gerstenhaber et cohomologie de Chevalley-Harrison

The fundamental example of Gerstenhaber algebra is the space Tpoly(Rd) of polyvector fields on Rd, equipped with the wedge product and the Schouten bracket. In this paper, we explicitely describe what is the enveloping G_∞ algebra of a Gerstenhaber algebra G. This structure gives us a definition of the Chevalley-Harrison cohomology operator for G. We finally show the nontriviality of a Chevalley-Harrison cohomology group for a natural Gerstenhaber subalgebra in Tpoly(Rd).     

Photocatalytic self-assembled solid porphyrin microcrystals from water-soluble porphyrins: Synthesis,characterization and application

In this article, we report on the formation of a photocatalytic porphyrin crystalline structure using two oppositely charged commercially available low cost porphyrins, [meso-tetra(N-methy-4-pyridyl)porphyrin tetratosylate (TMPyP) and zinc-tetrakis(4-sulfonatophenyl)porphyrin (Zn-TPPS)], by self-assembly at room temperature without acidification. Using optical microscopy, the crystals were determined to have a length of 30–55 μm and width of 2–50 μm, depending on the molar ratio of the porphyrins in the starting solution. The porphyrin crystals were characterized by means of powder X-ray diffraction and UV–Vis, fluorescence, and optical microscopic techniques. The UV–Vis absorbance spectrum of the crystalline structure is different than those of the monomer solutions, involving a broadened Soret band that is split into two blue-shifted and red-shifted peaks and broadened red-shifted Q-bands. The crystals exhibit a different emission spectrum from those of the porphyrin solutions in that they are red-shifted, split, and show a dramatic decrease in intensities. A hypothetical model for the crystal structure of the porphyrin crystals is developed. Illumination of the crystals in a 2,4,6-trinitrotoluene solution with a tungsten lamp results in TNT reduction to 1,3,5-trinitrobenzene and 4-amino-2,6-dinitrotoluene.     

Approach to local thermodynamic equilibrium and the evolution to a glassy core following neutron/ion radiation impact

Using molecular dynamics simulations and statistical-mechanical metrics, we make quantitative predictions on the local thermodynamic and dynamic states following an ion or neutron impact in three materials – copper, silicon and solid argon. Through a two-energy distribution, we first capture the non-equilibrium temperature evolution and the approach to the local thermal equilibrium in three generic stages. By examining the time-resolved van Hove self-correlator, we then demonstrate that the impact core of all the three materials shows the dynamic characteristics of a jammed or glassy state. We delineate a dynamic atom-hopping mechanism that attests to a rapid defect recovery stage in copper; silicon, on the contrary, accommodates only small displacements which resist recovery. The dissimilitude between copper with a close-packed structure and silicon with an open network structure is further drawn out through an isoconfigurational analysis of displacements, which shows a compact dendritic-like condensation front for the mobile atoms in copper through atom hopping. In contrast, silicon portrays larger-scale spatial oscillations of dynamically separated regions, which appear to be a precursor to dynamic lattice instability and eventual amorphisation.     

Improved LIBS limit of detection of Be, Mg, Si, Mn, Fe and Cu in aluminum alloy samples using a portable Echelle spectrometer with ICCD camera

Laser-induced breakdown spectroscopy (LIBS) is a laser-based technique that can provide non-intrusive, qualitative and quantitative measurement of metals in various environments. LIBS uses the plasma generated by a high-energy laser beam to prepare and excite the sample in one step. In the present work, LIBS has been applied to perform elemental analysis of six trace elements simultaneously in aluminum alloy targets. The plasma is generated by focusing a pulsed Nd:YAG laser on the target in air at atmospheric pressure. LIBS limit of detection (LOD) is affected by many experimental parameters such as interferences, self-absorption, spectral overlap and matrix effect. We aimed to improve the LIBS LOD by optimizing these experimental parameters as possible. In doing so, a portable Echelle spectrometer with intensified CCD camera was used to detect the LIBS plasma emission. This advanced Echelle spectrometer provides a constant spectral resolution (CSR) of 7500 corresponding to 4 pixels FWHM over a wavelength range 200–1000 nm displayable in a single spectrum. Then, the calibration curves for iron, beryllium, magnesium, silicon, manganese and copper as minor elements were achieved with linear regression coefficients between 98–99% on average in aluminum standard sample alloys. New LOD values were achieved in the ppm range with high precision (RSD 3–8%). From the application view point, improving LIBS LOD is very important in the on-line industrial process control to follow-up multi-elements for the correct alloying in metals.     

The Effect of Hemodialysis on Voice: An Acoustic Analysis

Because respiration is part of the well-coordinated process necessary for phonation, this study was conducted with the purpose of analyzing the effect of chronic hemodialysis on voice characteristics of patients with chronic renal failure. A total of 57 patients were recruited for the study, including 31 males and 26 females ranging in age from 16 to 85 years. Patients underwent evaluation of their voice directly before and after hemodialysis using the Kay Elemetric VISI Pitch (Model 330; Kay Elemetric Corporation, Lincoln Park, New Jersey). The vocal acoustic parameters studied include habitual pitch, pitch range, relative average perturbation, shimmer, noise-to-harmonic ratio, voice turbulence index, maximum phonation time, and voice energy. The data were analyzed using the paired t-test for the total sample and the nonparametric test for the female and male subgroups. The total sample analysis showed a statistically significant increase in the habitual pitch after the hemodialyis (p < 0.05), with a borderline increase in the pitch range and maximum phonation time (p < 0.10). In the female group, there was a statistically significant increase in the habitual pitch and a borderline increase in the relative average perturbation. In the male group, there was a significant increase in the habitual pitch with a borderline increase in maximum phonation time. Discussion of the after-mentioned results is presented.