Next-generation sequencing reveals large connected networks of intra-host HCV variants

Background: Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.Results: Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient. The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.Conclusions: Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.

Multi-task control strategy for grid-tied inverters based on conservative power theory

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

Single-cell expression profiling reveals a dynamic state of cardiac precursor cells in the early mouse embryo

In the early vertebrate embryo, cardiac progenitor/precursor cells (CPs) give rise to cardiac structures. Better understanding their biological character is critical to understand the heart development and to apply CPs for the clinical arena. However, our knowledge remains incomplete. With the use of single-cell expression profiling, we have now revealed rapid and dynamic changes in gene expression profiles of the embryonic CPs during the early phase after their segregation from the cardiac mesoderm. Progressively, the nascent mesodermal gene Mesp1 terminated, and Nkx2-5+/Tbx5+ population rapidly replaced the Tbx5low+ population as the expression of the cardiac genes Tbx5 and Nkx2-5 increased. At the Early Headfold stage, Tbx5-expressing CPs gradually showed a unique molecular signature with signs of cardiomyocyte differentiation. Lineage-tracing revealed a developmentally distinct characteristic of this population. They underwent progressive differentiation only towards the cardiomyocyte lineage corresponding to the first heart field rather than being maintained as a progenitor pool. More importantly, Tbx5 likely plays an important role in a transcriptional network to regulate the distinct character of the FHF via a positive feedback loop to activate the robust expression of Tbx5 in CPs. These data expands our knowledge on the behavior of CPs during the early phase of cardiac development, subsequently providing a platform for further study.

Ellipsometric Study of Single-Crystal γ-Inse From 1.5 To 9.2 Ev

We report the component E ┴ c of the pseudodielectric-function tensor <ε(E)> = <ε1(E)> + i< ε2(E)> of γ-phase single-crystal InSe, obtained from 1.5 to 9.2 eV by vacuum-ultraviolet spectroscopic ellipsometry with the sample at room temperature. Overlayer artifacts were reduced as far as possible by measuring fresh surfaces prepared by cleavage. Accurate critical-point energies of observed structures were obtained by a combined method of spectral analysis.

Mandibular Angle Fracture Treated With New Three-Dimensional Grid Miniplate

Fractures of the mandibular angle deserve particular attention because they represent the highest percentage of mandibular fractures and have the highest postsurgical complication rate, making them the most challenging and unpredictable mandibular fractures to treat. Despite the evolution in the treatment of maxillofacial trauma and fixation methods, no single treatment modality has been revealed to be ideal for mandibular angle fractures. Several methods of internal fixation have been studied with great variation in complications rates, especially postoperative infections. Recently, new studies have shown reduction of postsurgical complications rates using three-dimensional plates to treat mandibular angle fractures. Nevertheless, only few surgeons have used this type of plate for the treatment of mandibular angle fractures. The aim of this clinical report was to describe a case of a patient with a mandibular angle fracture treated by an intraoral approach and a three-dimensional rectangular grid miniplate with 4 holes, which was stabilized with monocortical screws. The authors show a follow-up of 8 months, without infection and with occlusal stability.

Size-dependent phase transitions in nanostructured zirconia-scandia solid solutions

The dependences of phase stability and solid state phase transitions on the crystallite size in ZrO2-10, 12 and 14 mol% Sc2O3 nanopowders are investigated by X-ray powder diffraction using a synchrotron source (S-XPD). The average crystallite sizes lie within the range of 35 to 100 nm, approximately. At room temperature these solid solutions were previously characterised as mixtures of a cubic phase and one or two rhombohedral phases, beta and gamma, with their fractions depending on composition and average crystallite sizes. In this study, it is shown that at high temperatures these solid solutions become cubic single-phased. The size-dependent temperatures of the transitions from the rhombohedral phases to the cubic phase at high temperature are determined through the analyses of a number of S-XPD patterns. These transitions were studied on cooling and on heating, exhibiting hysteresis effects whose relevant features are size and composition dependent.

Terbium(III) and dysprosium(III) 8-connected 3D networks containing 2,5-thiophenedicarboxylate anion: Crystal structures and photoluminescence studies

Two novel coordination polymers with the formula {[Ln(2)(2,5-tdc)(3)(dmso)(2)].H2O}(n) (Ln = Tb(III) for (1) and Dy(III) for (2)), (2,5-tdc(2-) = 2,5-thiophenedicarboxylate and dmso = dimethylsulfoxide) have been synthesized by the diffusion method and characterized by thermal analysis, vibrational spectroscopy and single crystal X-ray diffraction analysis. Structure analysis reveals that 2,5-tdc(2-) play a versatile role toward different lanthanide ions to form three-dimensional metal-organic frameworks (MOFs) in which the lanthanides ions are heptacoordinated. Photophysical properties were studied using excitation and emission spectra, where the photoluminescence data show the high emission intensity of the characteristic transitions D-5(4 ->) F-7(J) (J= 6, 5, 4 and 3) for (1) and (F9/2 -> HJ)-F-4-H-6 (J = 15/2, 13/2 and 11/2) for (2), indicating that 2,5-tdc(2-) is a good sensitizer. (C) 2012 Elsevier Ltd. All rights reserved.

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.

A scheme for synchronizing clocks connected by a packet communication network

Consider a communication system in which a transmitter equipment sends fixed-size packets of data at a uniform rate to a receiver equipment. Consider also that these equipments are connected by a packet-switched network, which introduces a random delay to each packet. Here we propose an adaptive clock recovery scheme able of synchronizing the frequencies and the phases of these devices, within specified limits of precision. This scheme for achieving frequency and phase synchronization is based on measurements of the packet arrival times at the receiver, which are used to control the dynamics of a digital phase-locked loop. The scheme performance is evaluated via numerical simulations performed by using realistic parameter values. (C) 2011 Elsevier By. All rights reserved.

Signatures of quantum phase transitions in parallel quantum dots: Crossover from local moment to underscreened spin-1 Kondo physics

We study a strongly interacting "quantum dot 1" and a weakly interacting "dot 2" connected in parallel to metallic leads. Gate voltages can drive the system between Kondo-quenched and non-Kondo free-moment phases separated by Kosterlitz-Thouless quantum phase transitions. Away from the immediate vicinity of the quantum phase transitions, the physical properties retain signatures of first-order transitions found previously to arise when dot 2 is strictly noninteracting. As interactions in dot 2 become stronger relative to the dot-lead coupling, the free moment in the non-Kondo phase evolves smoothly from an isolated spin-one-half in dot 1 to a many-body doublet arising from the incomplete Kondo compensation by the leads of a combined dot spin-one. These limits, which feature very different spin correlations between dot and lead electrons, can be distinguished by weak-bias conductance measurements performed at finite temperatures.

Analysis of carvedilol enantiomers in human plasma using chiral stationary phase column and liquid chromatography with tandem mass spectrometry

Carvedilol is an antihypertensive drug available as a racemic mixture. (-)-(S)-carvedilol is responsible for the nonselective beta-blocker activity but both enantiomers present similar activity on a1-adrenergic receptor. To our knowledge, this is the first study of carvedilol enantiomers in human plasma using a chiral stationary phase column and liquid chromatography with tandem mass spectrometry. The method involves plasma extraction with diisopropyl ether using metoprolol as internal standard and direct separation of the carvedilol enantiomers on a Chirobiotic T (R) (Teicoplanin) column. Protonated ions [M + H]+ and their respective ion products were monitored at transitions of 407 > 100 for the carvedilol enantiomers and 268 > 116 for the internal standard. The quantification limit was 0.2 ng ml-1 for both enantiomers in plasma. The method was applied to study enantioselectivity in the pharmacokinetics of carvedilol administered as a single dose of 25 mg to a hypertensive patient. The results showed a higher plasma concentration of (+)-(R)-carvedilol (AUC08 205.52 vs. 82.61 (ng h) ml-1), with an enantiomer ratio of 2.48. Chirality, 2012. (C) 2012 Wiley Periodicals, Inc.

Dependence of brittle-to-ductile transition on crystallographic direction in diamond turning of single-crystal silicon

The objective of this paper is to show the dependence relationship between the crystallographic orientations upon brittle-to-ductile transition during diamond turning of monocrystalline silicon. Cutting tests were performed using a -5 degrees rake angle round nose diamond tool at different machining scales. At the micrometre level, the feedrate was kept constant at 2.5 micrometres per revolution (mu m/r), and the depth of cut was varied from 1 to 5 mu m. At the submicrometre level, the depth of cut was kept constant at 500 nm and the feedrate varied from 5 to 10 mu m/r. At the micrometre level, the uncut shoulder generated with an interrupted cutting test procedure provided a quantitative measurement of the ductile-to-brittle transition. Results show that the critical chip thickness in silicon for ductile material removal reaches a maximum of 285 nm in the [100] direction and a minimum of 115 nm in the [110] direction, when the depth of cut was 5 mu m. It was found that when a submicrometre depth of cut was applied, microcracks were revealed in the [110] direction, which is the softer direction in silicon. Micro Raman spectroscopy was used to estimate surface residual stress after machining. Compressive residual stress in the range 142 MPa and smooth damage free surface finish was probed in the [100] direction for a depth of cut of 5 mu m, whereas residual stresses in the range 350 MPa and brittle damage was probed in the [110] direction for a depth of cut of 500 nm.

Spectrum of cognitive impairment in neurocysticercosis Differences according to disease phase

Objectives: Cognitive decline related to neurocysticercosis (NC) remains poorly characterized and underdiagnosed. In a cross-sectional study with a prospective phase, we evaluated cognitive decline in patients with strictly calcified form (C-NC), the epidemiologically largest subgroup of NC, and investigated whether there is a spectrum of cognitive abnormalities in the disease. Methods: Forty treatment-naive patients with C-NC aged 37.6 +/- 11.3 years and fulfilling criteria for definitive C-NC were submitted to a comprehensive cognitive and functional evaluation and were compared with 40 patients with active NC (A-NC) and 40 healthy controls (HC) matched for age and education. Patients with dementia were reassessed after 24 months. Results: Patients with C-NC presented 9.4 +/- 3.1 altered test scores out of the 30 from the cognitive battery when compared to HC. No patient with C-NC had dementia and 10 patients (25%) presented cognitive impairment-no dementia (CIND). The A-NC group had 5 patients (12.5%) with dementia and 11 patients (27.5%) with CIND. On follow-up, 3 out of 5 patients with A-NC with dementia previously still presented cystic lesions with scolex on MRI and still had dementia. One patient died and the remaining patient no longer fulfilled criteria for either dementia or CIND, presenting exclusively calcified lesions on neuroimaging. Conclusions: Independently of its phase, NC leads to a spectrum of cognitive abnormalities, ranging from impairment in a single domain, to CIND and, occasionally, to dementia. These findings are more conspicuous during active vesicular phase and less prominent in calcified stages. Neurology (R) 2012; 78: 861-866

A Phase I clinical trial of lodenafil carbonate, a new phosphodiesterase Type 5 (PDE5) inhibitor, in healthy male volunteers

Lodenafil carbonate is a new phosphodiesterase Type 5 (PDE5) inhibitor used in treatment of erectile dysfunction. Objective: The present study was conducted to evaluate the safety, tolerability, and pharmacokinetics of lodenafil carbonate after administering ascending (1 - 100 mg) single oral doses to healthy male volunteers (n = 33). Methods: The study was an open-label, dose-escalation, Phase I clinical trial involving the administration of single oral doses of lodenafil carbonate. Lodenafil carbonate was administered sequentially, escalating in single doses of 1 mg - 100 mg with a washout period of at least 1 week between each dose. The progression to the next dose was allowed after clinical and laboratory exams, Ambulatory Monitoring of Arterial Pressure (AMAP) without relevant clinical modifications and adverse events without clinical relevancy. Blood samples were collected at pre-dose, 0.25, 0.5, 0.75, 1, 1.25, 1.5, 1.75, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 10, 12, 14, 16, 20 and 24 h post-dosing. Plasma samples for measurement of lodenafil carbonate and lodenafil were analyzed by liquid chromatography coupled to tandem mass spectrometry. Results: No serious adverse events were observed, and none of the subjects discontinued the study due to intolerance. The AMAP measurements, clinical and laboratory exams and ECG revealed no significant changes even at higher doses. Lodenafil carbonate was not detected in any samples, indicating that it acts as a prodrug. The mean lodenafil pharmacokinetic parameters for t(max) and t(1/2) were 1.6 (+/- 0.4) h and 3.3 (+/- 1.1) h, respectively. This study demonstrated that lodenafil carbonate was well tolerated and showed a good safety profile in healthy male volunteers.