Measurement of storage time, estimation of ion number and study of absorption line profile in a Paul trap

Europium (Eu⁺) ions were confined in a Paul trap and detected by non-destructive method. Storage time of Eu⁺ ions achieved in vacuum was improved by orders of magnitude employing buffer gas cooling. The experimentally detected signal was fitted to the ion response signal and the total number of ions trapped was estimated. It is found that the peak signal amplitude as well as the product of FWHM and the peak signal amplitude is proportional to the total number of trapped ions. The trapped ion secular frequency was swept at different rates and its effect on the absorption line profile was studied both experimentally and theoretically.     

Chemical basis of DNA sugar-phosphate cleavage by low-energy electrons

DNA damage by low-energy electrons (LEE) was examined using a novel system in which thin solid films of oligonucleotide tetramers (CGTA and GCAT) were irradiated with monoenergetic electrons (10 eV) under ultrahigh vacuum. The products of irradiation were examined by HPLC. These analyses permitted the quantitation of 16 nonmodified nucleobase, nucleoside, and nucleotide fragments of each tetramer resulting from the cleavage of phosphodiester and N-glycosidic bonds. The distribution of nonmodified products suggests a mechanism of damage involving initial electron attachment to nucleobase moieties, followed by electron transfer to the sugar-phosphate backbone, and subsequent dissociation of the phosphodiester bond. Moreover, virtually all the nonmodified fragments contained a terminal phosphate group at the site of cleavage. These results demonstrate that the phosphodiester bond breaks by a distinct pathway in which the negative charge localizes on the phosphodiester bond giving rise to nonmodified fragments with an intact phosphate group. Conversely, the radical must localize on the sugar moiety to give as yet unidentified modifications. In summary, the reaction of LEE with simple tetramers involved dissociative electron attachment leading to phosphodiester bond cleavage and the formation of nonmodified fragments.     

Modeling the frequency dependence (5-120 MHz) of ultrasound backscattering by red cell aggregates in shear flow at a normal hematocrit

The frequency dependence of the ultrasound signal backscattered by blood in shear flow was studied using a simulation model. The ultrasound backscattered signal was computed with a linear model that considers the characteristics of the ultrasound system and tissue acoustic properties. The tissue scattering properties were related to the position and shape of the red blood cells (RBCs). A 2D microrheological model simulated the RBC dynamics in a Couette shear flow system. This iterative model, described earlier [Biophys. J. 82, 1696-1710 (2002)], integrates the hydrodynamic effect of the flow, as well as adhesive and repulsive forces between RBCs. RBC aggregation was simulated at 40% hematocrit and shear rates of 0.05-2 s(-1). The RBC aggregate sizes ranged, on average, from 3.3 RBCs at 2 s(-1) to 33.5 cells at 0.05 s(-1). The ultrasound backscattered power was studied at frequencies between 5-120 MHz and insonification angles between 0-180 degrees. At frequencies below approximately 30 MHz, the ultrasound backscattered power increased as the shear rate was decreased and the size of the aggregates was raised. A totally different scattering behavior was noted above 30 MHz. Typical spectral slopes of the backscattered power (log-log scale) between 5-25 MHz equaled 3.8, whereas slopes down to 0.6 were measured at 0.05 s(-1), between 40-60 MHz. The ultrasound backscattered power was shown to be angle dependent at low frequencies (5-25 MHz). The anisotropy persisted at high frequencies (>25 MHz) for small aggregates (at 2 s(-1)). In conclusion, this study sheds some light on the blood backscattering behavior with an emphasis on the non-Rayleigh regime. Additional experimental studies may be necessary to validate the simulation results, and to fully understand the relation between the ultrasound backscattered power, level of RBC aggregation, shear rate, frequency, and insonification angle.     

High-frequency ultrasound backscattering by blood: analytical and semianalytical models of the erythrocyte cross section

This paper proposes analytical and semianalytical models of the ultrasonic backscattering cross section (BCS) of various geometrical shapes mimicking a red blood cell (RBC) for frequencies varying from 0 to 90 MHz. By assuming the first-order Born approximation and by modeling the shape of a RBC by a realistic biconcave volume, different scattering behaviors were identified for increasing frequencies. For frequencies below 18 MHz, a RBC can be considered a Rayleigh scatterer. For frequencies less than 39 MHz, the general concept of acoustic inertia tensor is introduced to describe the variation of the BCS with the frequency and the incidence direction. For frequencies below 90 MHz, ultrasound backscattering by a RBC is equivalent to backscattering by a cylinder of height 2 microm and diameter 7.8 microm. These results lay the basis of ultrasonic characterization of RBC aggregation by proposing a method that distinguishes the contribution of the individual RBC acoustical characteristics from collective effects, on the global blood backscattering coefficient. A new method of data reduction that models the frequency dependence of the ultrasonic BCS of micron-sized weak scatterers is also proposed. Applications of this method are in tissue characterization as well as in hematology.     

Correction: Dermatan sulfate in tunicate phylogeny: Order-specific sulfation pattern and the effect of [→4IdoA(2-Sulfate)β-1→3GalNAc(4-Sulfate)β-1→] motifs in dermatan sulfate on heparin cofactor II activity

After the publication of the work entitled "Dermatan sulfate in tunicate phylogeny: Order-specific sulfation pattern and the effect of [→4IdoA(2-Sulfate)β-1→3GalNAc(4-Sulfate)β-1→] motifs in dermatan sulfate on heparin cofactor II activity", by Kozlowski et al., BMC Biochemistry 2011, 12:29, we found that the legends to Figures 2 to 5 contain serious mistakes that compromise the comprehension of the work. This correction article contains the correct text of the legends to Figures 2 to 5.     

Enumeration of polyominoes inscribed in a rectangle

We develop a number of formulas and generating functions for the enumeration of general polyominoes inscribed in a rectangle of given size according to their area. These formulae are then used for the enumeration of lattice trees inscribed in a rectangle with minimum area plus one.