Depth-dependent local structures in thin films unraveled by grazing-incidence X-ray absorption spectroscopy

A method of using X-ray absorption spectroscopy together with resolved grazing-incidence geometry for depth profiling of atomic, electronic or chemical local structures in thin films is presented. The quantitative deconvolution of thickness-dependent spectral features is performed by fully considering both scattering and absorption formalisms. Surface oxidation and local structural depth profiles in nanometric FePt films are determined, exemplifying the application of the method.

Gradient-dependent density functionals of the Perdew-Burke-Ernzerhof type for atoms, molecules, and solids

One of the standard generalized-gradient approximations (GGAs) in use in modern electronic-structure theory [Perdew-Burke-Ernzerhof (PBE) GGA] and a recently proposed modification designed specifically for solids (PBEsol) are identified as particular members of a family of functionals taking their parameters from different properties of homogeneous or inhomogeneous electron liquids. Three further members of this family are constructed and tested, together with the original PBE and PBEsol, for atoms, molecules, and solids. We find that PBE, in spite of its popularity in solid-state physics and quantum chemistry, is not always the best performing member of the family and that PBEsol, in spite of having been constructed specifically for solids, is not the best for solids. The performance of GGAs for finite systems is found to sensitively depend on the choice of constraints stemming from infinite systems. Guidelines both for users and for developers of density functionals emerge from this work.

Observation of charge-dependent azimuthal correlations and possible local strong parity violation in heavy-ion collisions

Parity (P)-odd domains, corresponding to nontrivial topological solutions of the QCD vacuum, might be created during relativistic heavy-ion collisions. These domains are predicted to lead to charge separation of quarks along the orbital momentum of the system created in noncentral collisions. To study this effect, we investigate a three-particle mixed-harmonics azimuthal correlator which is a P-even observable, but directly sensitive to the charge-separation effect. We report measurements of this observable using the STAR detector in Au + Au and Cu + Cu collisions at root s(NN) = 200 and 62 GeV. The results are presented as a function of collision centrality, particle separation in rapidity, and particle transverse momentum. A signal consistent with several of the theoretical expectations is detected in all four data sets. We compare our results to the predictions of existing event generators and discuss in detail possible contributions from other effects that are not related to P violation.

Instability of the time dependent Horava-Witten model

We consider scalar perturbations in the time dependent Horava-Witten model in order to probe its stability. We show that during the nonsingular epoque the model evolves without instabilities until it encounters the curvature singularity where a big crunch is supposed to occur. We compute the frequencies of the scalar field oscillation during the stable period and show how the oscillations can be used to prove the presence of such a singularity.

Decoherence-free evolution of time-dependent superposition states of two-level systems and thermal effects

In this paper we detail some results advanced in a recent letter [Prado et al., Phys. Rev. Lett. 102, 073008 (2009).] showing how to engineer reservoirs for two-level systems at absolute zero by means of a time-dependent master equation leading to a nonstationary superposition equilibrium state. We also present a general recipe showing how to build nonadiabatic coherent evolutions of a fermionic system interacting with a bosonic mode and investigate the influence of thermal reservoirs at finite temperature on the fidelity of the protected superposition state. Our analytical results are supported by numerical analysis of the full Hamiltonian model.

Equivalence between Redfield- and master-equation approaches for a time-dependent quantum system and coherence control

We present a derivation of the Redfield formalism for treating the dissipative dynamics of a time-dependent quantum system coupled to a classical environment. We compare such a formalism with the master equation approach where the environments are treated quantum mechanically. Focusing on a time-dependent spin-1/2 system we demonstrate the equivalence between both approaches by showing that they lead to the same Bloch equations and, as a consequence, to the same characteristic times T(1) and T(2) (associated with the longitudinal and transverse relaxations, respectively). These characteristic times are shown to be related to the operator-sum representation and the equivalent phenomenological-operator approach. Finally, we present a protocol to circumvent the decoherence processes due to the loss of energy (and thus, associated with T(1)). To this end, we simply associate the time dependence of the quantum system to an easily achieved modulated frequency. A possible implementation of the protocol is also proposed in the context of nuclear magnetic resonance.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni

Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

Physical signatures of discontinuities of the time-dependent exchange-correlation potential

The exact exchange-correlation (XC) potential in time-dependent density-functional theory (TDDFT) is known to develop steps and discontinuities upon change of the particle number in spatially confined regions or isolated subsystems. We demonstrate that the self-interaction corrected adiabatic local-density approximation for the XC potential has this property, using the example of electron loss of a model quantum well system. We then study the influence of the XC potential discontinuity in a real-time simulation of a dissociation process of an asymmetric double quantum well system, and show that it dramatically affects the population of the resulting isolated single quantum wells. This indicates the importance of a proper account of the discontinuities in TDDFT descriptions of ionization, dissociation or charge transfer processes.

Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale

This paper describes a new and simple method to determine the molecular weight of proteins in dilute solution, with an error smaller than similar to 10%, by using the experimental data of a single small-angle X-ray scattering (SAXS) curve measured on a relative scale. This procedure does not require the measurement of SAXS intensity on an absolute scale and does not involve a comparison with another SAXS curve determined from a known standard protein. The proposed procedure can be applied to monodisperse systems of proteins in dilute solution, either in monomeric or multimeric state, and it has been successfully tested on SAXS data experimentally determined for proteins with known molecular weights. It is shown here that the molecular weights determined by this procedure deviate from the known values by less than 10% in each case and the average error for the test set of 21 proteins was 5.3%. Importantly, this method allows for an unambiguous determination of the multimeric state of proteins with known molecular weights.

Polarity-Dependent Transcranial Direct Current Stimulation Effects on Central Auditory Processing

Given the polarity dependent effects of transcranial direct current stimulation (tDCS) in facilitating or inhibiting neuronal processing, and tDCS effects on pitch perception, we tested the effects of tDCS on temporal aspects of auditory processing. We aimed to change baseline activity of the auditory cortex using tDCS as to modulate temporal aspects of auditory processing in healthy subjects without hearing impairment. Eleven subjects received 2mA bilateral anodal, cathodal and sham tDCS over auditory cortex in a randomized and counterbalanced order. Subjects were evaluated by the Random Gap Detection Test (RGDT), a test measuring temporal processing abilities in the auditory domain, before and during the stimulation. Statistical analysis revealed a significant interaction effect of time vs. tDCS condition for 4000 Hz and for clicks. Post-hoc tests showed significant differences according to stimulation polarity on RGDT performance: anodal improved 22.5% and cathodal decreased 54.5% subjects' performance, as compared to baseline. For clicks, anodal also increased performance in 29.4% when compared to baseline. tDCS presented polarity-dependent effects on the activity of the auditory cortex, which results in a positive or negative impact in a temporal resolution task performance. These results encourage further studies exploring tDCS in central auditory processing disorders.

Characterization of dynamic solid phase DNA extraction from blood with magnetically controlled silica beads

A novel solid phase extraction technique is described where DNA is bound and eluted from magnetic silica beads in a manner where efficiency is dependent on the magnetic manipulation of the beads and not on the flow of solution through a packed bed. The utility of this technique in the isolation of reasonably pure, PCR-amplifiable DNA from complex samples is shown by isolating DNA from whole human blood, and subsequently amplifying a fragment of the beta-globin gene. By effectively controlling the movement of the solid phase in the presence of a static sample, the issues associated with reproducibly packing a solid phase in a microchannel and maintaining consistent flow rates are eliminated. The technique described here is rapid, simple, and efficient, allowing for recovery of more than 60% of DNA from 0.6 mu L of blood at a concentration which is suitable for PCR amplification. In addition, the technique presented here requires inexpensive, common laboratory equipment, making it easily adopted for both clinical point-of-care applications and on-site forensic sample analysis.

Heparin affects the interaction of kininogen on endothelial cells

In the plasma kallikrein-kinin system, it has been shown that when plasma prekallikrein (PM) and high molecular weight kininogen (HK) assemble on endothelial cells, plasma kallikrein (huPK) becomes available to cleave HK, releasing bradykinin, a potent mediator of the inflammatory response. Because the formation of soluble glycosaminoglycans occurs concomitantly during the inflammatory processes, the effect of these polysaccharides on the interaction of HK on the cell surface or extracellular matrix (ECM) of two endothelial cell lines (ECV304 and RAEC) was investigated. In the presence of Zn(+2), HK binding to the surface or ECM of RAEC was abolished by heparin; reduced by heparan sulfate, keratan sulfate, chondroitin 4-sulfate or dermatan sulfate; and not affected by chondroitin 6-sulfate. By contrast, only heparin reduced HK binding to the ECV304 cell surface or ECM. Using heparin-correlated molecules such as low molecular weight dextran sulfate, low molecular weight heparin and N-desulfated heparin, we suggest that these effects were mainly dependent on the charge density and on the N-sulfated glucosamine present in heparin. Surprisingly, PM binding to cell- or ECM-bound-HK and PM activation was not modified by heparin. However, the hydrolysis of HK by huPK, releasing BK in the fluid phase, was augmented by this glycosaminoglycan in the presence of Zn(2+). Thus, a functional dichotomy exists in which soluble glycosaminoglycans may possibly either increase or decrease the formation of BK. In conclusion, glycosaminoglycans that accumulated in inflammatory fluids or used as a therapeutic drug (e.g., heparin) could act as pro- or anti-inflammatory mediators depending on different factors within the cell environment. (C) 2011 Elsevier Masson SAS. All rights reserved.

Contuse lesion of the rat spinal cord of moderate intensity leads to a higher time-dependent secondary neurodegeneration than severe one - An open-window for experimental neuroprotective interventions

Secondary neurodegeneration takes place in the surrounding tissue of spinal cord trauma and modifies substantially the prognosis, considering the small diameter of its transversal axis. We analyzed neuronal and glial responses in rat spinal cord after different degree of contusion promoted by the NYU Impactor. Rats were submitted to vertebrae laminectomy and received moderate or severe contusions. Control animals were sham operated. After 7 and 30 days post surgery, stereological analysis of Nissl staining cellular profiles showed a time progression of the lesion volume after moderate injury, but not after severe injury. The number of neurons was not altered cranial to injury. However, same degree of diminution was seen in the caudal cord 30 days after both severe and moderate injuries. Microdensitometric image analysis demonstrated a microglial reaction in the white matter 30 days after a moderate contusion and showed a widespread astroglial reaction in the white and gray matters 7 days after both severities. Astroglial activation lasted close to lesion and in areas related to Wallerian degeneration. Data showed a more protracted secondary degeneration in rat spinal cord after mild contusion, which offered an opportunity for neuroprotective approaches. Temporal and regional glial responses corroborated to diverse glial cell function in lesioned spinal cord. (C) 2007 Elsevier Ltd. All rights reserved.

Age-related difference on weight transfer during unconstrained standing

The ability to transfer weight from one lower limb to the other is essential for the execution of daily life activities and little is known about how weight transfer during unconstrained natural standing is affected by age. This study examined the weight transfer ability of elderly individuals during unconstrained standing (for 30 mill) in comparison to young adults. The subjects (19 healthy elderly adults, range 65-80 years, and 19 healthy young adults, range 18-30 years) stood with each foot on a separate force plate and were allowed to change their posture freely at any time. The limits of stability and base of support width during standing, measures of mobility (using the timed up and go and the preferred walking speed tests), and fear of falling were also measured. In comparison to the young adults, during unconstrained standing the elderly adults produced four times fewer weight transfers of large amplitude (greater than,half of their body weight). The limits of stability and base of support width were significantly smaller for the elderly adults but there were no significant differences in the measures of mobility and in the fear of falling score compared to young adults. The observed significant age-related decrease in the use of weight transfer during unconstrained standing, despite any difference in the measured mobility of the subjects, suggests that this task reveals unnoticed and subtle differences in postural control, which may help to better understand age related impairments in balance that the elderly population experiences. (C) 2010 Elsevier B.V. All rights reserved.

Weight loss associated with exercise training restores ventilatory efficiency in obese children

The purpose of this study was to test the hypothesis that in obese children: 1) Ventilatory efficiency (VentE) is decreased during graded exercise; and 2) Weight loss through diet alone (D) improves VentE, and 3) diet associated with exercise training (DET) leads to greater improvement in VentE than by D. Thirty-eight obese children (10 +/- 0.2 years; BMI > 95(th) percentile) were randomly divided into two Study groups: D (n=17; BMI = 30 +/- 1 kg/m(2)) and DET (n = 21; 28 +/- 1 kg/m(2)). Ten lean children were included in a control group (10 +/- 0.3 years; 17 +/- 0.5 kg/m(2)). All children performed maximal treadmill testing with respiratory gas analysis (breath-by-breath) to determine the ventilatory anaerobic threshold (VAT) and peak oxygen consumption (VO(2) peak). VentE was determined by the VE/VCO(2) method at VAT. Obese children showed lower VO(2) peak and lower VentE than controls (p < 0.05). After interventions, all obese children reduced body weight (p < 0.05). D group did not improve in terms of VO(2) peak or VentE (p > 0.05). In contrast, the DET group showed increased VO(2) peak (p = 0.01) and improved VentE(Delta VE/VCO(2) = -6.1 +/- 0.9; p = 0.01). VentE is decreased in obese children, where weight loss by means of DET, but not D alone, improves VentE and cardiorespiratory fitness during graded exercise.