Antiretroviral drug resistance mutations in naïve and experienced patients in Shiraz, Iran, 2014

Resistance to antiretroviral agents is a significant concern in the clinical management of HIV-infected individuals, particularly in areas of the world where treatment options are limited. In this study, we aimed to identify HIV drug-resistance-associated mutations in 40 drug-naïve patients and 62 patients under antiretroviral therapy (ART) referred to the Shiraz HIV/AIDS Research Center – the first such data available for the south of Iran. HIV reverse transcriptase and protease genes were amplified and sequenced to determine subtypes and antiretroviral- resistance-associated mutations (RAMs). Subtype CRF35-AD recombinant was the most prevalent in all patients (98 of 102, 96 % ), followed by subtype A1, and subtype B (one each, 2 % ). Among the 40 ART-naïve patients, two mutations associated with nucleoside reverse transcriptase inhibitor (NRTI) resistance (two with Y115F and T215I) and three associated with non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance (two with G190S and Y181C, four with V179T) were found. Among ART-experienced patients, four mutations associated with resistance to NRTI, four with NNRTI, and five with protease inhibitors (PI) were found. Twenty patients with high levels of resistance were already on second-line therapy. We document for the first time in this region of Iran high levels of ART resistance to multiple drugs. Our findings call for more vigilant systematic ART resistance surveillance, increased resistance testing, careful management of patients with existing regimens, and strong advocacy for expansion of available drugs in Iran. © 2016, Springer-Verlag Wien

Seismic Emissions from a Highly Impulsive M6.7 Solar Flare

On 10 March 2001 the active region NOAA 9368 produced an unusually impulsive solar flare in close proximity to the solar limb. This flare has previously been studied in great detail, with observations classifying it as a type 1 white-light flare with a very hard spectrum in hard X-rays. The flare was also associated with a type II radio burst and coronal mass ejection. The flare emission characteristics appeared to closely correspond with previous instances of seismic emission from acoustically active flares. Using standard local helioseismic methods, we identified the seismic signatures produced by the flare that, to date, is the least energetic (in soft X-rays) of the flares known to have generated a detectable acoustic transient. Holographic analysis of the flare shows a compact acoustic source strongly correlated with the impulsive hard X-ray, visible continuum, and radio emission. Time-distance diagrams of the seismic waves emanating from the flare region also show faint signatures, mainly in the eastern sector of the active region. The strong spatial coincidence between the seismic source and the impulsive visible continuum emission reinforces the theory that a substantial component of the seismic emission seen is a result of sudden heating of the low photosphere associated with the observed visible continuum emission. Furthermore, the low-altitude magnetic loop structure inferred from potential--field extrapolations in the flaring region suggests that there is a significant inverse correlation between the seismicity of a flare and the height of the magnetic loops that conduct the particle beams from the corona.Comment: 16 pages, 7 figures, Solar Physics Topical Issue: SOHO 19/GONG 2007 "Seismology of Magnetic Activity", Accepte

The carrier-multipath observable: a new carrier-phase multipath mitigation technique

Modeling and mitigating carrier-phase multi- path errors continue to be a significant challenge for high- accuracy positioning using global navigation satellite sys- tems. The multipath error is dependent on the operational environment and therefore cannot be mitigated by differ- encing techniques. The effect of multipath is accentuated when observables based on linear combinations of mea- surements from two or more frequencies are formulated. We develop a new carrier-phase multipath error observable that isolates the inter-frequency carrier-phase multipath error for linear combinations of observables, such as wide- lane (WL). Real-time kinematic positioning results from varying baseline lengths show that a significant reduction in between 14 and 47 % in the time to initial ambiguity resolution are achieved by correcting the WL observable using the new carrier-phase multipath error observable

Entropy of English text: Experiments with humans and a machine learning system based on rough sets

The goal of this paper is to show the dependency of the entropy of English text on the subject of the experiment, the type of English text, and the methodology used to estimate the entropy. Claude Shannon first described the technique for estimating the entropy of English text by a human subject guessing the next letter after viewing a string of characters taken from actual text. We show how this result is affected by using different humans in the experiment (Shannon used only his wife) and by using different types of text material (Shannon used only a single book). We also show how the results are affected when we replace the human subjects with a machine learning system based on rough sets. Automating the play of the guessing game with this system, called LERS, gives rise to a lossless data compression scheme. (C) Elsevier Science Inc. 1998

Micro-tearing modes in spherical and conventional tokamaks

The onset and characteristics of Micro-Tearing Modes (MTM) in the core of spherical (NSTX) and conventional tokamaks (ASDEX Upgrade and JET) are studied through local linear gyrokinetic simulations with gyro [J. Candy and E. Belli, General Atomics Report GA-A26818 In all these plasmas, finite collisionality is needed for MTMs to become unstable and the electron temperature gradient is found to be the fundamental drive. However, a significant difference is observed in the dependence of linear growth rate of MTMs on electron temperature gradient. While it varies weakly and non-monotonically in JET and ASDEX Upgrade plasmas, in NSTX it increases with the electron temperature gradient

Detectable contributions of colloids to soil P and C content in arid and hyperarid region of the Atacama (Chile)

Atacama Desert is mainly known as the driest place on Earth where life has been developed under arid to hyper arid conditions since Oligocene-Miocene. Therefore, soils of Atacama contain fingerprints of past and present life which might be used as an analog to study the evolution of life under equivalent arid conditions, like Mars. In this study, we quantify the colloidal phosphorus and carbon distribution in the first 10 cm of soil profile along an altitudinal transect. Samples were taken along a transect in the region of Quebrada Aroma spanning from the arid Percordillera of the Andes (2720 m a.s.l.) towards the hyper arid core of the desert (1340 m a.s.l.). Water dispersible colloids (WDC) were separated and measured using the field-flow-field fractionation (FFF) method and subsequently their Corg and P content were characterized and quantified by detectors (DLS, ICP-MS, UV, OCD, fluorescence). Data was compared to total C, P and (available) Olsen-P also measured in the samples. The Olsen-P (available-P) varied within the Aroma transect from ca. 2 to 8 mg P kg-1, but was not related to either altitude or depth in the upper soil (0-10 cm). Colloidal P contents ranged from <0.1 to 4 mg P kg-1 soil, with increasing trend from low to higher elevations. Thereby, suggesting an increasing proportion of the available P potential being present in the WDC fraction. The Colloidal Corg content of the Aroma transect did range from 65 to 90 (for sites 2020 to 1340m) and 110 mg Corg kg-1 soil WDC (2720 m). Colloidal Corg content as a function of the altitude showed a similar trend to the Corg content of the soils: the highest colloidal Corg content was found at 2720 m. The proportion of soil Corg within the colloidal fraction was up to 6% of the bulk soil organic matter (OM) content, as the OM content was intensively enriched in the colloidal fraction. Further quantification of phosphorus and carbon content in WDC in deeper part of soil is required to obtain a more comprehensive view of role of colloidal inputs and dynamics in the Atacama Desert

Spin Fidelity for Three-qubit Greenberger-Horne-Zeilinger and W States Under Lorentz Transformations

Constructing the reduced density matrix for a system of three massive spin$-\frac{1}{2}$ particles described by a wave packet with Gaussian momentum distribution and a spin part in the form of GHZ or W state, the fidelity for the spin part of the system is investigated from the viewpoint of moving observers in the jargon of special relativity. Using a numerical approach, it turns out that by increasing the boost speed, the spin fidelity decreases and reaches to a non-zero asymptotic value that depends on the momentum distribution and the amount of momentum entanglement.Comment: 12pages, 2 figure

Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?

We have characterized the conformational ensembles of polyglutamine peptides of various lengths (ranging from to ), both with and without the presence of a C-terminal polyproline hexapeptide. For this, we used state-of-the-art molecular dynamics simulations combined with a novel statistical analysis to characterize the various properties of the backbone dihedral angles and secondary structural motifs of the glutamine residues. For (i.e., just above the pathological length for Huntington's disease), the equilibrium conformations of the monomer consist primarily of disordered, compact structures with non-negligible -helical and turn content. We also observed a relatively small population of extended structures suitable for forming aggregates including - and -strands, and - and -hairpins. Most importantly, for we find that there exists a long-range correlation (ranging for at least residues) among the backbone dihedral angles of the Q residues. For polyglutamine peptides below the pathological length, the population of the extended strands and hairpins is considerably smaller, and the correlations are short-range (at most residues apart). Adding a C-terminal hexaproline to suppresses both the population of these rare motifs and the long-range correlation of the dihedral angles. We argue that the long-range correlation of the polyglutamine homopeptide, along with the presence of these rare motifs, could be responsible for its aggregation phenomena

Calmodulin-Binding Proteins in Muscle: A Minireview on Nuclear Receptor Interacting Protein, Neurogranin, and Growth-Associated Protein 43

Calmodulin (CaM) is an important Ca2+-sensing protein with numerous downstream targets that are either CaM-dependant or CaM-regulated. In muscle, CaM-dependent proteins, which are critical regulators of dynamic Ca2+ handling and contractility, include calcineurin (CaN), CaM-dependant kinase II (CaMKII), ryanodine receptor (RyR), and dihydropyridine receptor (DHPR).CaM-regulated targets include genes associated with oxidative metabolism, muscle plasticity, and repair. Despite its importance in muscle, the regulation of CaM—particularly its availability to bind to and activate downstream targets—is an emerging area of research. In this minireview, we discuss recent studies revealing the importance of small IQ motif proteins that bind to CaM to either facilitate (nuclear receptor interacting protein; NRIP) its activation of downstream targets, or sequester (neurogranin, Ng; and growth-associated protein 43, GAP43) CaM away from their downstream targets. Specifically, we discuss recent studies that have begun uncovering the physiological roles of NRIP, Ng, and GAP43 in skeletal and cardiac muscle, thereby highlighting the importance of endogenously expressed CaM-binding proteins and their regulation of CaM in muscle.Brock University Library Open Access Publishing Fun