Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework

Mitochondrial DNA (mtDNA) analysis is usually a last resort in routine forensic DNA casework. However, it has become a powerful tool for the analysis of highly degraded samples or samples containing too little or no nuclear DNA, such as old bones and hair shafts. The gold standard methodology still constitutes the direct sequencing of polymerase chain reaction (PCR) products or cloned amplicons from the HVS-1 and HVS-2 (hypervariable segment) control region segments. Identifications using mtDNA are time consuming, expensive and can be very complex, depending on the amount and nature of the material being tested. The main goal of this work is to develop a less labour-intensive and less expensive screening method for mtDNA analysis, in order to aid in the exclusion of non-matching samples and as a presumptive test prior to final confirmatory DNA sequencing. We have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) [1] to be typed using SNaPShotTM (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between the SNP typing and DNA sequencing when results were compared, with the exception of allelic dropouts observed in a few haplotypes. Haplotype diversity simulations were performed using 172 mtDNA sequences representative of the Brazilian population and a score of 0.9794 was obtained when the 14 SNPs were used, showing that the theoretical prediction approach for the selection of highly discriminatory SNPs suggested by Salas and Amigo (2010) [1] was confirmed in the population studied. As the main goal of the work is to develop a screening assay to skip the sequencing of all samples in a particular case, a pair-wise comparison of the sequences was done using the selected SNPs. When both HVS-1/HVS-2 SNPs were used for simulations, at least two differences were observed in 93.2% of the comparisons performed. The assay was validated with casework samples. Results show that the method is straightforward and can be used for exclusionary purposes, saving time and laboratory resources. The assay confirms the theoretic prediction suggested by Salas and Amigo (2010) [1]. All forensic advantages, such as high sensitivity and power of discrimination, as also the disadvantages, such as the occurrence of allele dropouts, are discussed throughout the article. © 2013 Elsevier B.V.

Synthesis and characterization of lead zirconate titanate (PZT) obtained by two chemical methods

Lead zirconate titanate (PZT) was synthesized at the ratio of Zr/Ti=52/48 using two synthesis methods: the polymeric precursor method (PPM) and the microwave-assisted hydrothermal method (MAHM). The synthesized materials were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), particle size distribution by sedimentation, hysteresis measurements and photoluminescence (PL). The results showed that PZT powders are composed of tetragonal and rhombohedral phases. Different particle sizes and morphologies were obtained depending upon the synthesis method. From the hysteresis loop verified that PZT powders synthesized by the PPM have a typical loop of ferroelectric material and are more influenced by spatial charges while particles synthesized by the MAHM have a hysteresis loop similar to paraelectric material and are less influenced by spatial charges. Both samples showed PL behavior in the green region (525 nm) whereas the sample synthesized by the PPM showed higher intensity in spectra. © 2013 Elsevier Ltd and Techna Group S.r.l.

All-loop infrared-divergent behavior of most-subleading-color gauge-theory amplitudes

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Entanglement universality of two-qubit X-states

We demonstrate that for every two-qubit state there is a X-counterpart, i.e., a corresponding two-qubit X-state of same spectrum and entanglement, as measured by concurrence, negativity or relative entropy of entanglement. By parametrizing the set of two-qubit X-states and a family of unitary transformations that preserve the sparse structure of a two-qubit X-state density matrix, we obtain the parametric form of a unitary transformation that converts arbitrary two-qubit states into their X-counterparts. Moreover, we provide a semi-analytic prescription on how to set the parameters of this unitary transformation in order to preserve concurrence or negativity. We also explicitly construct a set of X-state density matrices, parametrized by their purity and concurrence, whose elements are in one-to-one correspondence with the points of the concurrence versus purity (CP) diagram for generic two-qubit states. (C) 2014 Elsevier Inc. All rights reserved.

End-to-side loop neurorrhaphy: axonal comparative stereological study

Accidents or diseases can affect the peripheral part of the nervous system, which raises clinical and surgical therapies, among others. In this context, the technique of end-to-side neurorrhaphy is a treatment option, yet its modification loop needs some additional efficacy studies. The purpose of this study was to compare, among rats, stereological results (axons volume density) after end-to-side neurorrhaphy and after end-to-side loop neurorrhaphy. Thirty Wistar rats were used, divided into six groups (five animals per group), consisting of two control groups (for the fibular and tibial nerves), two study groups for the fibular nerve (one with an end-to-side neurorrhaphy, and the other with an end-to-side loop neurorrhaphy) and two study groups for the tibial nerve (with an endto- side neurorrhaphy and the other one with an end-to-side loop neurorrhaphy). After 180 days, all groups were sacrificed for axonal stereological analysis (volume density) in distal nerve stumps. There was significant maintenance of neuronal-axonal density in the distal stumps to neurorrhaphy (p< 0.005) compared with the normal stumps. The end-to-side loop neurorrhaphy is a therapeutic option as suture technique after complete nerve section, in order to restore most of the axonal functional integrity.

Yang-Lee zeros of the two- and three-state Potts model defined on π3 Feynman diagrams

We present both analytical and numerical results on the position of partition function zeros on the complex magnetic field plane of the q=2 state (Ising) and the q=3 state Potts model defined on phi(3) Feynman diagrams (thin random graphs). Our analytic results are based on the ideas of destructive interference of coexisting phases and low temperature expansions. For the case of the Ising model, an argument based on a symmetry of the saddle point equations leads us to a nonperturbative proof that the Yang-Lee zeros are located on the unit circle, although no circle theorem is known in this case of random graphs. For the q=3 state Potts model, our perturbative results indicate that the Yang-Lee zeros lie outside the unit circle. Both analytic results are confirmed by finite lattice numerical calculations.

A two-layer approximation to the Brazil Current-Intermediate Western Boundary Current System between 20 degrees S and 28 degrees S

It has been shown that the vertical structure of the Brazil Current (BC)-Intermediate Western Boundary Current (IWBC) System is dominated by the first baroclinic mode at 22 degrees S-23 degrees S. In this work, we employed the Miami Isopycnic Coordinate Ocean Model to investigate whether the rich mesoscale activity of this current system, between 20 degrees S and 28 degrees S, is reproduced by a two-layer approximation of its vertical structure. The model results showed cyclonic and anticyclonic meanders propagating southwestward along the current axis, resembling the dynamical pattern of Rossby waves superposed on a mean flow. Analysis of the upper layer zonal velocity component, using a space-time diagram, revealed a dominant wavelength of about 450 km and phase velocity of about 0.20 ms(-1) southwestward. The results also showed that the eddy-like structures slowly grew in amplitude as they moved downstream. Despite the simplified design of the numerical experiments conducted here, these results compared favorably with observations and seem to indicate that weakly unstable long baroclinic waves are responsible for most of the variability observed in the BC-IWBC system. (C) 2009 Elsevier Ltd. All rights reserved.

Temperature Effect on the Two-Photon Absorption Spectrum of All-trans-beta-carotene

In this report, we investigate the influence of temperature on the two-photon absorption (2PA) spectrum of all-trans-beta-carotene using the femtosecond white-light-continuum Z-scan technique. We observed that the 2PA cross-section decreases quadratically with the temperature. Such effect was modeled using a three-energy-level diagram within the sum-over-essential states approach, assuming temperature dependencies to the transition dipole moment and refractive index of the solvent. The results show that the transition dipole moments from ground to excited state and between the excited states, which governed the two-photon matrix element, have distinct behaviors with the temperature. The first one presents a quadratic dependence, while the second exhibits a linear dependence. Such effects were attributed mainly to the trans -> cis thermal interconversion process, which decreases the effective conjugation length, contributing to diminishing the transition dipole moments and, consequently, the 2PA cross-section.

Enhancement of Nematic Order and Global Phase Diagram of a Lattice Model for Coupled Nematic Systems

We use an infinite-range Maier-Saupe model, with two sets of local quadrupolar variables and restricted orientations, to investigate the global phase diagram of a coupled system of two nematic subsystems. The free energy and the equations of state are exactly calculated by standard techniques of statistical mechanics. The nematic-isotropic transition temperature of system A increases with both the interaction energy among mesogens of system B, and the two-subsystem coupling J. This enhancement of the nematic phase is manifested in a global phase diagram in terms of the interaction parameters and the temperature T. We make some comments on the connections of these results with experimental findings for a system of diluted ferroelectric nanoparticles embedded in a nematic liquid-crystalline environment.

Manipulation effects of prior exercise intensity feedback by the Borg scale during open-loop cycling

Objective To verify the effects of exercise intensity deception by the Borg scale on the ratings of perceived exertion (RPE), heart rate (HR) and performance responses during a constant power output open-loop exercise. Methods Eight healthy men underwent a maximal incremental test on a cycle ergometer to identify the peak power output (PPO) and heart rate deflection point (HRDP). Subsequently, they performed a constant power output trial to exhaustion set at the HRDP intensity, in deception (DEC) and informed (INF) conditions: DEC-subjects were told that they would be cycling at an intensity corresponding to two categories below the RPE quantified at the HRDP; INF-subjects were told that they would cycle at the exact intensity corresponding to the RPE quantified at the HRDP. Results The PPO and power output at the HRDP obtained in maximal incremental tests were 247.5 +/- 32.1 W and 208.1 +/- 27.1 W, respectively. No significant difference in the time to exhaustion was found between DEC (525 +/- 244 s) or INF (499 +/- 224 s) trials. The slope and the first and second measurements of the RPE and HR parameters showed no significant difference between trials. Conclusions Psychophysiological variables such as RPE and HR as well as performance were not affected when exercise intensity was deceptively manipulated via RPE scores. This may suggest that unaltered RPE during exercise is a regulator of performance in this open-loop exercise.

Experimental and Theoretical Study on the One- and Two-Photon Absorption Properties of Novel Organic Molecules Based on Phenylacetylene and Azoaromatic Moieties

This Article reports a combined experimental and theoretical analysis on the one and two-photon absorption properties of a novel class of organic molecules with a pi-conjugated backbone based on phenylacetylene (JCM874, FD43, and FD48) and azoaromatic (YB3p2S) moieties. Linear optical properties show that the phenylacetylene-based compounds exhibit strong molar absorptivity in the UV and high fluorescence quantum yield with lifetimes of approximately 2.0 ns, while the azoaromatic-compound has a strong absorption in the visible region with very low fluorescence quantum yield. The two-photon absorption was investigated employing nonlinear optical techniques and quantum chemical calculations based on the response functions formalism within the density functional theory framework. The experimental data revealed well-defined 2PA spectra with reasonable cross-section values in the visible and IR. Along the nonlinear spectra we observed two 2PA allowed bands, as well as the resonance enhancement effect due to the presence of one intermediate one-photon allowed state. Quantum chemical calculations revealed that the 2PA allowed bands correspond to transitions to states that are also one-photon allowed, indicating the relaxation of the electric-dipole selection rules. Moreover, using the theoretical results, we were able to interpret the experimental trends of the 2PA spectra. Finally, using a few-energy-level diagram, within the sum-over-essential states approach, we observed strong qualitative and quantitative correlation between experimental and theoretical results.

Alzheimer random walk model: Two previously overlooked diffusion regimes

A non-Markovian one-dimensional random walk model is studied with emphasis on the phase-diagram, showing all the diffusion regimes, along with the exactly determined critical lines. The model, known as the Alzheimer walk, is endowed with memory-controlled diffusion, responsible for the model's long-range correlations, and is characterized by a rich variety of diffusive regimes. The importance of this model is that superdiffusion arises due not to memory per se, but rather also due to loss of memory. The recently reported numerically and analytically estimated values for the Hurst exponent are hereby reviewed. We report the finding of two, previously overlooked, phases, namely, evanescent log-periodic diffusion and log-periodic diffusion with escape, both with Hurst exponent H = 1/2. In the former, the log-periodicity gets damped, whereas in the latter the first moment diverges. These phases further enrich the already intricate phase diagram. The results are discussed in the context of phase transitions, aging phenomena, and symmetry breaking.

Two structurally discrete GH7-cellobiohydrolases compete for the same cellulosic substrate fiber

Background: Cellulose consisting of arrays of linear beta-1,4 linked glucans, is the most abundant carbon-containing polymer present in biomass. Recalcitrance of crystalline cellulose towards enzymatic degradation is widely reported and is the result of intra-and inter-molecular hydrogen bonds within and among the linear glucans. Cellobiohydrolases are enzymes that attack crystalline cellulose. Here we report on two forms of glycosyl hydrolase family 7 cellobiohydrolases common to all Aspergillii that attack Avicel, cotton cellulose and other forms of crystalline cellulose. Results: Cellobiohydrolases Cbh1 and CelD have similar catalytic domains but only Cbh1 contains a carbohydrate-binding domain (CBD) that binds to cellulose. Structural superpositioning of Cbh1 and CelD on the Talaromyces emersonii Cel7A 3-dimensional structure, identifies the typical tunnel-like catalytic active site while Cbh1 shows an additional loop that partially obstructs the substrate-fitting channel. CelD does not have a CBD and shows a four amino acid residue deletion on the tunnel-obstructing loop providing a continuous opening in the absence of a CBD. Cbh1 and CelD are catalytically functional and while specific activity against Avicel is 7.7 and 0.5 U. mg prot-1, respectively specific activity on pNPC is virtually identical. Cbh1 is slightly more stable to thermal inactivation compared to CelD and is much less sensitive to glucose inhibition suggesting that an open tunnel configuration, or absence of a CBD, alters the way the catalytic domain interacts with the substrate. Cbh1 and CelD enzyme mixtures on crystalline cellulosic substrates show a strong combinatorial effort response for mixtures where Cbh1 is present in 2: 1 or 4: 1 molar excess. When CelD was overrepresented the combinatorial effort could only be partially overcome. CelD appears to bind and hydrolyze only loose cellulosic chains while Cbh1 is capable of opening new cellulosic substrate molecules away from the cellulosic fiber. Conclusion: Cellobiohydrolases both with and without a CBD occur in most fungal genomes where both enzymes are secreted, and likely participate in cellulose degradation. The fact that only Cbh1 binds to the substrate and in combination with CelD exhibits strong synergy only when Cbh1 is present in excess, suggests that Cbh1 unties enough chains from cellulose fibers, thus enabling processive access of CelD.

Stripe-tetragonal phase transition in the two-dimensional Ising model with dipole interactions: Partition function zeros approach

We have performed multicanonical simulations to study the critical behavior of the two-dimensional Ising model with dipole interactions. This study concerns the thermodynamic phase transitions in the range of the interaction delta where the phase characterized by striped configurations of width h = 1 is observed. Controversial results obtained from local update algorithms have been reported for this region, including the claimed existence of a second-order phase transition line that becomes first order above a tricritical point located somewhere between delta = 0.85 and 1. Our analysis relies on the complex partition function zeros obtained with high statistics from multicanonical simulations. Finite size scaling relations for the leading partition function zeros yield critical exponents. that are clearly consistent with a single second-order phase transition line, thus excluding such a tricritical point in that region of the phase diagram. This conclusion is further supported by analysis of the specific heat and susceptibility of the orientational order parameter.

Hero's journey in bifurcation diagram

The hero's journey is a narrative structure identified by several authors in comparative studies on folklore and mythology. This storytelling template presents the stages of inner metamorphosis undergone by the protagonist after being called to an adventure. In a simplified version, this journey is divided into three acts separated by two crucial moments. Here we propose a discrete-time dynamical system for representing the protagonist's evolution. The suffering along the journey is taken as the control parameter of this system. The bifurcation diagram exhibits stationary, periodic and chaotic behaviors. In this diagram, there are transition from fixed point to chaos and transition from limit cycle to fixed point. We found that the values of the control parameter corresponding to these two transitions are in quantitative agreement with the two critical moments of the three-act hero's journey identified in 10 movies appearing in the list of the 200 worldwide highest-grossing films. (C) 2011 Elsevier B.V. All rights reserved.