Enhancing signal-to-noise ratio and resolution in low-field NMR relaxation measurements using post-acquisition digital filters

The traditional way to enhance signal-to-noise ratio (SNR) of nuclear magnetic resonance (NMR) signals is to increase the number of scans. However, this procedure increases the measuring time that can be prohibitive for some applications. Therefore, we have tested the use of several post-acquisition digital filters to enhance SNR up to one order of magnitude in time domain NMR (TD-NMR) relaxation measurements. The procedures were studied using continuous wave free precession (CWFP-T₁) signals, acquired with very low flip angles that contain six times more noise than the Carr–Purcell–Meiboom–Gill (CPMG) signal of the same sample and experimental time. Linear (LI) and logarithmic (LO) data compression, low-pass infinity impulse response (LP), Savitzky–Golay (SG), and wavelet transform (WA) post-acquisition filters enhanced the SNR of the CWFP-T₁ signals by at least six times. The best filters were LO, SG, and WA that have high enhancement in SNR without significant distortions in the ILT relaxation distribution data. Therefore, it was demonstrated that these post-acquisition digital filters could be a useful way to denoise CWFP-T₁, as well as CPMG noisy signals, and consequently reducing the experimental time. It was also demonstrated that filtered CWFP-T₁ method has the potential to be a rapid and nondestructive method to measure fat content in beef and certainly in other meat samples.     

Heisenberg-limited Measurements and Sub-Planck Structures in Phase Space

It is shown how sub-Planck phase-space structures can be used to achieve Heisenberg-limited sensitivity in weak force measurements. Nonclassical states of harmonic oscillators, such as superpositions of coherent states, are shown to be useful for the measurement of weak forces that cause translations or rotations in phase space, which is done by entangling the quantum oscillator with a two-level system. This method is closely related to the Loschmidt echo techniques employed in nuclear magnetic resonance experiments. Implementations of this strategy in cavity QED and ion traps are described.     

Affine Arithmetic: Concepts and Applications

Affine arithmetic is a model for self-validated numerical computation that keeps track of first-order correlations between computed and input quantities. We explain the main concepts in affine arithmetic and how it handles the dependency problem in standard interval arithmetic. We also describe some of its applications.     

A modular integer GCD algorithm

This paper describes the first algorithm to compute the greatest common divisor (GCD) of two n-bit integers using a modular representation for intermediate values U, V and also for the result. It is based on a reduction step, similar to one used in the accelerated algorithm [T. Jebelean, A generalization of the binary GCD algorithm, in: ISSAC '93: International Symposium on Symbolic and Algebraic Computation, Kiev, Ukraine, 1993, pp. 111–116; K. Weber, The accelerated integer GCD algorithm, ACM Trans. Math. Softw. 21 (1995) 111–122] when U and V are close to the same size, that replaces U by (U−bV)/p, where p is one of the prime moduli and b is the unique integer in the interval (−p/2,p/2) such that . When the algorithm is executed on a bit common CRCW PRAM with O(nlognlogloglogn) processors, it takes O(n) time in the worst case. A heuristic model of the average case yields O(n/logn) time on the same number of processors.     

First-principles studies of kinetics in epitaxial growth of III–V semiconductors

We demonstrate how first-principles calculations using density-functional theory (DFT) can be applied to gain insight into the molecular processes that rule the physics of materials processing. Specifically, we study the molecular beam epitaxy (MBE) of arsenic compound semiconductors. For homoepitaxy of GaAs on GaAs (001), a growth model is presented that builds on results of DFT calculations for molecular processes on the β2-reconstructed GaAs (001) surface, including adsorption, desorption, surface diffusion, and nucleation. Kinetic Monte Carlo simulations on the basis of the calculated energetics enable us to model MBE growth of GaAs from beams of Ga and As₂ in atomistic detail. The simulations show that island nucleation is controlled by the reaction of As₂ molecules with Ga adatoms on the surface. The analysis reveals that the scaling laws of standard nucleation theory for the island density as a function of growth temperature are not applicable to GaAs epitaxy. We also discuss heteroepitaxy of InAs on GaAs (001), and report first-principles DFT calculations for In diffusion on the strained GaAs substrate. In particular, we address the effect of heteroepitaxial strain on the growth kinetics of coherently strained InAs islands. The strain field around an island is found to cause a slowing down of material transport from the substrate towards the island, and thus helps to achieve more homogeneous island sizes. Received: 2 May 2001 / Accepted: 23 July 2001 / Published online: 3 April 2002     

Memory effects in gas chromatographic detection with a microwave-induced plasma

Capillary gas chromatography coupled to microwave-inducedplasma detection furnishes sensitivity adequate for trace analysis when the signal is monitored at a carbon emission line. Work performed with one of these systems at high electronic gain for the carbon signal has revealed solvent band widths in excess of four minutes; these impeded quantification of peaks eluting after the solvent. This report discusses two phenomena which could be related to the unexpected intensity of this solvent response: photomultiplier tube saturation and carbon deposits in the quartz plasma discharge tube.     

Converged properties of clean metal surfaces by all-electron first-principles calculations

All-electron full-potential linearized augmented plane-wave calculations of the surface energy, work function, and interlayer spacings of close-packed metal surfaces are presented, in particular, for the free-electron-like metal surfaces, Mg(0 0 0 1) and Al(1 1 1), and for the transition metal surfaces, Ti(0 0 0 1), Cu(1 1 1), Pd(1 1 1), and Pt(1 1 1). We investigate the convergence of the surface energy as a function of the number of layers in the slab, using the Cu(1 1 1) surface as an example. The results show that the surface energy, as obtained using total energies of the slab and bulk from separate calculations, converges well with respect to the number of layers in the slab. Obviously, it is necessary that bulk and surface calculations are performed with the same high accuracy. Furthermore, we discuss the performance of the local-density and generalized gradient approximations for the exchange-correlation functional in describing the various surface properties.     

Determination of ionizable groups of proteins by potentiometric titration in concentrated solutions of guanidine hydrochloride

A linearization method based on modified Gran functions, and a general nonlinear regression program were used to study potentiometric titration curves of denatured ovalbumin and lysozyme in 6 mol L^–1 guanidine hydrochloride medium with the aim of determining the ionizable species. With both numerical techniques it was possible to determine the sum of the carboxylic groups, the imidazol, the α-amine, and the sum of ɛ-amine, phenolic and sulfhydryl groups, if the protein is completely denatured, and assumes a randomly coiled conformation. A total of 87.8 ± 2.5 and 20.7 ± 0.6 groups per mol were determined in the ovalbumin and lysozyme, respectively. These values are very close to the 88 and 21 groups expected by aminoacid composition of both proteins, indicating that all ionizable groups were exposed to the solvent. For ovalbumin the distribution of groups was very similar to that expected by the aminoacid composition, but for lysozyme some anomalies were observed, suggesting the existence of interactions between ionizable groups, altering the dissociation constants. Received: 9 December 1996 / Revised: 27 February 1997 / Accepted: 4 March 1997     

Lipase from a Brazilian StrainPenicillium citrinum Cultured in a Simple and Inexpensive Medium st]Heat-Denaturation, Kinetics, and pH Stability

This work is a study of lipase production by a Brazilian strain ofPenicillium citrinum using an inexpensive and simple medium without organic nitrogen sources and of some important industrial properties, including thermostability in relation to ionic strength. The maximal lipase activity (1585 U/L) was obtained whenPenicillium citrinum was cultured on 0.75% ammonium sulfate complemented with minerals salts instead of yeast extract. Although this activity was about 55% lower than that produced in medium with yeast extract (2850 U/L), the specific activity (7.8 U/mg proteins) was higher than that obtained with the yeast extract (4.9 U/mg proteins). The morphology of fungus changed totally, with yeast extract there are smooth, solid, and spherical pellets whereas on ammonium sulfate there are small “hairy” pellets uniformly suspended in the medium. The effect of ferrous (Fe⁺⁺) ions was carried out using medium MA with and without Fe⁺⁺ ions. Lipase production byPenicillium citrinum in medium MA requires Fe⁺⁺ ions, the absence of which caused a decreased of about 50% in the specific activity (3.5 U/mg proteins). The utilization of commercial, locally available oils as carbon sources, such as soybean oil (236 U/L) and corn oil (74 U/L) resulted in lower activity compared to olive oil, showing that lipase production byPenicillium citrinum is specifically induced by olive oil. Potassium concentration in the medium can effects the production of lipase (1 mM (1585 U/L), 10 mM (1290 U/L), and 30 mM (1238 U/L), 50 mM (195 U/L), and 100 mM (2 U/L). The crude culture filtered was susceptable to thermal deactivation. It was stable at pH 6.0, but was not stable at the optimum pH (8.0-8.5) at 50 mM. At the low ionic concentration (1-25 mM) this lipase was stable at low pH (3.5-4.0). The activation energy was 22.4 ±2.2 Kcal. mol 1.     

Phase separation of p53 precedes aggregation and is affected by oncogenic mutations and ligands

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF). The mechanism of the formation of the aggregates in the nucleus remains uncertain. The present study demonstrated that the DNA-binding domain of p53 (p53C) underwent phase separation (PS) on the pathway to aggregation under various conditions. p53C phase separated in the presence of the crowding agent polyethylene glycol (PEG). Similarly, mutant p53C (M237I and R249S) underwent PS; however, the process evolved to a solid-like phase transition faster than that in the case of wild-type p53C. The data obtained by microscopy of live cells indicated that transfection of mutant full-length p53 into the cells tended to result in PS and phase transition (PT) in the nuclear compartments, which are likely the cause of the GoF effects. Fluorescence recovery after photobleaching (FRAP) experiments revealed liquid characteristics of the condensates in the nucleus. Mutant p53 tended to undergo gel- and solid-like phase transitions in the nucleus and in nuclear bodies demonstrated by slow and incomplete recovery of fluorescence after photobleaching. Polyanions, such as heparin and RNA, were able to modulate PS and PT in vitro. Heparin apparently stabilized the condensates in a gel-like state, and RNA apparently induced a solid-like state of the protein even in the absence of PEG. Conditions that destabilize p53C into a molten globule conformation also produced liquid droplets in the absence of crowding. The disordered transactivation domain (TAD) modulated both phase separation and amyloid aggregation. In summary, our data provide mechanistic insight into the formation of p53 condensates and conditions that may result in the formation of aggregated structures, such as mutant amyloid oligomers, in cancer. The pathway of mutant p53 from liquid droplets to gel-like and solid-like (amyloid) species may be a suitable target for anticancer therapy.

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF).