AMIN domains have a predicted role in localization of diverse periplasmic protein complexes

We describe AMIN (Amidase N-terminal domain), a novel protein domain found specifically in bacterial periplasmic proteins. AMIN domains are widely distributed among peptidoglycan hydrolases and transporter protein families. Based on experimental data, contextual information and phyletic profiles, we suggest that AMIN domains mediate the targeting of periplasmic or extracellular proteins to specific regions of the bacterial envelope.

Automatic and objective assessment of alternating tapping performance in Parkinson’s disease

This paper presents the development and evaluation of a method for enabling quantitative and automatic scoring of alternating tapping performance of patients with Parkinson’s disease (PD). Ten healthy elderly subjects and 95 patients in different clinical stages of PD have utilized a touch-pad handheld computer to perform alternate tapping tests in their home environments. First, a neurologist used a web-based system to visually assess impairments in four tapping dimensions (‘speed’, ‘accuracy’, ‘fatigue’ and ‘arrhythmia’) and a global tapping severity (GTS). Second, tapping signals were processed with time series analysis and statistical methods to derive 24 quantitative parameters. Third, principal component analysis was used to reduce the dimensions of these parameters and to obtain scores for the four dimensions. Finally, a logistic regression classifier was trained using a 10-fold stratified cross-validation to map the reduced parameters to the corresponding visually assessed GTS scores. Results showed that the computed scores correlated well to visually assessed scores and were significantly different across Unified Parkinson’s Disease Rating Scale scores of upper limb motor performance. In addition, they had good internal consistency, had good ability to discriminate between healthy elderly and patients in different disease stages, had good sensitivity to treatment interventions and could reflect the natural disease progression over time. In conclusion, the automatic method can be useful to objectively assess the tapping performance of PD patients and can be included in telemedicine tools for remote monitoring of tapping.

Comparison of the Polar S810i monitor and the ECG for the analysis of heart rate variability in the time and frequency domains

The aim of the present study was to compare heart rate variability (HRV) at rest and during exercise using a temporal series obtained with the Polar S810i monitor and a signal from a LYNX® signal conditioner (BIO EMG 1000 model) with a channel configured for the acquisition of ECG signals. Fifteen healthy subjects aged 20.9 ± 1.4 years were analyzed. The subjects remained at rest for 20 min and performed exercise for another 20 min with the workload selected to achieve 60% of submaximal heart rate. RR series were obtained for each individual with a Polar S810i instrument and with an ECG analyzed with a biological signal conditioner. The HRV indices (rMSSD, pNN50, LFnu, HFnu, and LF/HF) were calculated after signal processing and analysis. The unpaired Student t-test and intraclass correlation coefficient were used for data analysis. No statistically significant differences were observed when comparing the values analyzed by means of the two devices for HRV at rest and during exercise. The intraclass correlation coefficient demonstrated satisfactory correlation between the values obtained by the devices at rest (pNN50 = 0.994; rMSSD = 0.995; LFnu = 0.978; HFnu = 0.978; LF/HF = 0.982) and during exercise (pNN50 = 0.869; rMSSD = 0.929; LFnu = 0.973; HFnu = 0.973; LF/HF = 0.942). The calculation of HRV values by means of temporal series obtained from the Polar S810i instrument appears to be as reliable as those obtained by processing the ECG signal captured with a signal conditioner.

Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda)

The binding selectivity of the M(phen)(edda) (M = Cu, Co, Ni, Zn; phen = 1,10-phenanthroline, edda = ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(11) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N4O2 octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling. (C) 2008 Elsevier B.V. All rights reserved.

Nucleação de vortices e paredes de domínio em nanoestruturas magnéticas

We report a theoretical investigation of the magnetic phases and hysteresis of exchange biased ferromagnetic (F) nanoelements for three di erent systems: exchange biased nanoparticles, exchange biased narrow ferromagnetic stripes and exchange biased thin ferromagnetic lms. In all cases the focus is on the new e ects produced by suitable patterns of the exchange energy coupling the ferromagnetic nanoelement with a large anisotropy antiferromagnetic (AF) substrate. We investigate the hysteresis of iron and permalloy nanoparticles with a square basis, with lateral dimensions between 45 nm and 120 nm and thickness between 12 nm and 21 nm. Interface bias is aimed at producing large domains in thin lms. Our results show that, contrary to intuition, the interface exchange coupling may generate vortex states along the hysteresis loop. Also, the threshold value of the interface eld strength for vortex nucleation is smaller for iron nanoelements. We investigate the nucleation and depinning of an array of domain walls pinned at interface defects of a vicinal stripe/AF bilayer. The interface exchange eld displays a periodic pattern corresponding to the topology of the AF vicinal substrate. The vicinal AF substrate consists of a sequence of terraces, each with spins from one AF subalattice, alternating one another. As a result the interface eld of neighboring terraces point in opposite direction, leading to the nucleation of a sequence of domain walls in the ferromagnetic stripe. We investigated iron an permalloy micrometric stripes, with width ranging from 100 nm and 300 nm and thickness of 5 nm. We focused in domain wall sequences with same chirality and alternate chirality. We have found that for 100nm terraces the same chiraility sequence is more stable, requiring a larger value of the external eld for depinning. The third system consists of an iron lm with a thickness of 5 nm, exchange coupled to an AF substrate with a periodic distribution of islands where the AF spins have the opposite direction of the spins in the background. This corresponds to a two-sublattice noncompensated AF plane (such as the surface of a (100) FeF2 lm), with monolayer-height islands containing spins of one sublattice on a surface containing spins of the opposite sublattice. The interface eld acting in the ferromagnetic spins over the islands points in the opposite direction of that in the spins over the background. This a model system for the investigation of interface roughness e ects. We have studied the coercicivity an exchange bias hysteresis shift as a function of the distance between the islands and the degree of interface roughness. We have found a relevant reduction of coercivity for nearly compensated interfaces. Also the e ective hysteresis shift is not proportional to the liquid moment of the AF plane. We also developed an analytical model which reproduces qualitatively the results of numerical simulations

Gastric motility evaluated by electrogastrography and alternating current biosusceptometry in dogs

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Dynamics in dumbbell domains II. The limiting problem

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A generalized alternating-direction implicit scheme for incompressible magnetohydrodynamic viscous flows at low magnetic Reynolds number

This paper presents numerical simulations of incompressible fluid flows in the presence of a magnetic field at low magnetic Reynolds number. The equations governing the flow are the Navier-Stokes equations of fluid motion coupled with Maxwell's equations of electromagnetics. The study of fluid flows under the influence of a magnetic field and with no free electric charges or electric fields is known as magnetohydrodynamics. The magnetohydrodynamics approximation is considered for the formulation of the non-dimensional problem and for the characterization of similarity parameters. A finite-difference technique is used to discretize the equations. In particular, an extension of the generalized Peaceman and Rachford alternating-direction implicit (ADI) scheme for simulating two-dimensional fluid flows is presented. The discretized conservation equations are solved in stream function-vorticity formulation. We compare the ADI and generalized ADI schemes, and show that the latter is more efficient in simulating low Reynolds number and magnetic Reynolds number problems. Numerical results demonstrating the applicability of this technique are also presented. The simulation of incompressible magneto hydrodynamic fluid flows is illustrated by numerical solution for two-dimensional cases. (c) 2007 Elsevier B.V. All rights reserved.

Shrimp-shape domains in a dissipative kicked rotator

Some dynamical properties for a dissipative kicked rotator are studied. Our results show that when dissipation is taken into account a drastic change happens in the structure of the phase space in the sense that the mixed structure is modified and attracting fixed points and chaotic attractors are observed. A detailed numerical investigation in a two-dimensional parameter space based on the behavior of the Lyapunov exponent is considered. Our results show the existence of infinite self-similar shrimp-shaped structures corresponding to periodic attractors, embedded in a large region corresponding to the chaotic regime. (C) 2011 American Institute of Physics. [doi:10.1063/1.3657917]

Semilinear parabolic problems in thin domains with a highly oscillatory boundary

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A note on the controllability for the wave equation in nonsmooth plane domains

We study exact boundary controllability for a two-dimensional wave equation in a region which is an angular sector of a circle or an angular sector of an annular region. The control, of Neumann type, acts on the curved part of the boundary, while in the straight part we impose homogeneous Dirichlet boundary condition. The initial state has finite energy and the control is square integrable. (c) 2005 Elsevier B.V. All rights reserved.

Dynamics in dumbbell domains I. Continuity of the set of equilibria

We analyze the dynamics of a reaction-diffusion equation with homogeneous Neumann boundary conditions in a dumbbell domain. We provide an appropriate functional setting to treat this problem and, as a first step, we show in this paper the continuity of the set of equilibria and of its linear unstable manifolds. (c) 2006 Elsevier B.V. All rights reserved.