Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Scaling of pressure spectrum in turbulent boundary layers

Scaling of pressure spectrum in zero-pressure-gradient turbulent boundary layers is discussed. Spatial DNS data of boundary layer at one time instant (Re-theta = 4500) are used for the analysis. It is observed that in the outer regions the pressure spectra tends towards the -7/3 law predicted by Kolmogorov's theory of small-scale turbulence. The slope in the pressure spectra varies from -1 close to the wall to a value close to -7/3 in the outer region. The streamwise velocity spectra also show a -5/3 trend in the outer region of the flow. The exercise carried out to study the amplitude modulation effect of the large scales on the smaller ones in the near-wall region reveals a strong modulation effect for the streamwise velocity, but not for the pressure fluctuations. The skewness of the pressure follows the same trend as the amplitude modulation coefficient, as is the case for the velocity. In the inner region, pressure spectra were seen to collapse better when normalized with the local Reynolds stress (-(u'v') over bar) than when scaled with the local turbulent kinetic energy (q(2) = (u'(2)) over bar + (v'(2)) over bar + (w'(2)) over bar)

Green colored nano-pigments derived from Y2BaCuO5: NIR reflective coatings

A green colored nano-pigment Y2BaCuO5 with impressive near infra-red (NIR) reflectance (61% at 1100 nm) was synthesized by a nano-emulsion method. The developed nano-crystalline powders were characterized by X-ray diffraction (XRD), Transmission electron microscopy (TEM), UV-vis-NIR diffuse reflectance spectroscopy and CIE-L*a*b* 1976 color scales. The XRD and Rietveld analyses of the designed pigment powders reveal the orthorhombic crystal structure for Y2BaCuO5, where yttrium is coordinated by seven oxygen atoms with the local symmetry of a distorted trigonal prism, barium is coordinated by eleven oxygen atoms, and the coordination polyhedron of copper is a distorted square pyramid CuO5]. The UV-vis spectrum of the nano-pigment exhibits an intense d-d transition associated with CuO5 chromophore between 2.1 and 2.5 eV in the visible domain. Therefore, a green color has been displayed by the developed nano-pigment. The potential utility of the nano-pigments as ``Cool Pigments'' was demonstrated by coating on to a building roofing material like cement slab and PVC coatings. (C) 2014 Elsevier Ltd. All rights reserved.

A VARIABLE SWITCHING FREQUENCY PWM TECHNIQUE FOR INVERTER-FED INDUCTION MOTOR TO ACHIEVE SPREAD SPECTRUM

Voltage Source Inverter (VSI) fed induction motors are widely used in variable speed applications. For inverters using fixed switching frequency PWM, the output harmonic spectra are located at a few discrete frequencies. The ac motordrives powered by these inverters cause acoustic noise. This paper proposes a new variable switching frequency pwm technique and compares its performance with constant switching frequency pwm technique. It is shown that the proposed technique leads to spread spectra of voltages and currents. Also this technique ensures that no lower order harmonics are present and the current THD is comparable to that of fixed switching frequency PWM and is even better for higher modulation indices.

Fourier spectrum based extraction of an equivalent trap state density in indium gallium zinc oxide transistors

Segregating the dynamics of gate bias induced threshold voltage shift, and in particular, charge trapping in thin film transistors (TFTs) based on time constants provides insight into the different mechanisms underlying TFTs instability. In this Letter we develop a representation of the time constants and model the magnitude of charge trapped in the form of an equivalent density of created trap states. This representation is extracted from the Fourier spectrum of the dynamics of charge trapping. Using amorphous In-Ga-Zn-O TFTs as an example, the charge trapping was modeled within an energy range of Delta E-t approximate to 0.3 eV and with a density of state distribution as D-t(Et-j) = D-t0 exp(-Delta E-t/kT) with D-t0 = 5.02 x 10(11) cm(-2) eV(-1). Such a model is useful for developing simulation tools for circuit design. (C) 2014 AIP Publishing LLC.

Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency

Information is encoded in neural circuits using both graded and action potentials, converting between them within single neurons and successive processing layers. This conversion is accompanied by information loss and a drop in energy efficiency. We investigate the biophysical causes of this loss of information and efficiency by comparing spiking neuron models, containing stochastic voltage-gated Na+ and K+ channels, with generator potential and graded potential models lacking voltage-gated Na+ channels. We identify three causes of information loss in the generator potential that are the by-product of action potential generation: (1) the voltage-gated Na+ channels necessary for action potential generation increase intrinsic noise and (2) introduce non-linearities, and (3) the finite duration of the action potential creates a `footprint' in the generator potential that obscures incoming signals. These three processes reduce information rates by similar to 50% in generator potentials, to similar to 3 times that of spike trains. Both generator potentials and graded potentials consume almost an order of magnitude less energy per second than spike trains. Because of the lower information rates of generator potentials they are substantially less energy efficient than graded potentials. However, both are an order of magnitude more efficient than spike trains due to the higher energy costs and low information content of spikes, emphasizing that there is a two-fold cost of converting analogue to digital; information loss and cost inflation.

Rainbow Emission from an Atomic Transition in Doped Quantum Dots

Although semiconductor quantum dots are promising materials for displays and lighting due to their tunable emissions, these materials also suffer from the serious disadvantage of self-absorption of emitted light. The reabsorption of emitted light is a serious loss mechanism in practical situations because most phosphors exhibit subunity quantum yields. Manganese-based phosphors that also exhibit high stability and quantum efficiency do not suffer from this problem but in turn lack emission tunability, seriously affecting their practical utility. Here, we present a class of manganese-doped quantum dot materials, where strain is used to tune the wavelength of the dopant emission, extending the otherwise limited emission tunability over the yellow-orange range for manganese ions to almost the entire visible spectrum covering all colors from blue to red. These new materials thus combine the advantages of both quantum dots and conventional doped phosphors, thereby opening new possibilities for a wide range of applications in the future.

Solution Processed Cu2CoSnS4 Thin Films for Photovoltaic Applications

Earth abundant alternative chalcopyrite Cu2CoSnS4 (CCTS) thin films were deposited by a facile sol-gel process onto larger substrates. Temperature dependence of the process control of deposition and desired phase formations was studied in detail. Films were analyzed for complete transformation from amorphous to polycrystalline, with textured structures for stannite phase, as reflected from the X-ray diffraction and with nearly stoichiometric compositions of Cu:Co:Sn:S = 2:0:1:0:1:0:4:0 from EDAX analysis. Morphological investigations revealed that the CCTS films with larger grains, on the order of its thickness, were synthesized at higher temperature of 500 degrees C. The optimal band gap for application in photovoltaics was estimated to be 1.4 eV. Devices with SLG/CCTS/Al geometry were fabricated for real time demonstration of photoconductivity under A.M 1.5 G solar and 1064 rim infrared laser illuminations. A photodetector showed one order current amplification from similar to 1.9 X 10(-6) A in the dark to 2.2 x 10(-5) A and 9.8 X 10(-6) A under A.M 1.5 G illumination and 50 mW cm(-2) IR laser, respectively. Detector sensitivity, responsivity, external quantum efficiency, and gain were estimated as 4.2, 0.12 A/W, 14.74% and 14.77%, respectively, at 50 mW cm(-2) laser illuminations. An ON and OFF ratio of 2.5 proved that CCTS can be considered as a potential absorber in low cost photovoltaics applications.

Luminescence studies and EPR investigation of derived Eu doped ZnO

ZnO:Eu (0.1 mol%) nanopowders have been synthesized by auto ignition based low temperature solution combustion method. Powder X-ray diffraction (PXRD) patterns confirm the nanosized particles which exhibit hexagonal wurtzite structure. The crystallite size estimated from Scherrer's formula was found to be in the range 35-39 nm. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) studies reveal particles are agglomerated with quasi-hexagonal morphology. A blue shift of absorption edge with increase in band gap is observed for Eu doped ZnO samples. Upon 254 nm excitation, ZnO:Eu nanopowders show peaks in regions blue (420-484 nm), green (528 nm) and red (600 nm) which corresponds to both Eu2+ and Eu3+ ions. The electron paramagnetic resonance (EPR) spectrum exhibits a broad resonance signal at g= 4.195 which is attributed to Eu2+ ions. Further, EPR and thermo-luminescence (TL) studies reveal presence of native defects in this phosphor. Using TL glow peaks the trap parameters have been evaluated and discussed. (C) 2014 Elsevier B.V. All rights reserved.

CuIn1-xAlxSe2 Solar Cells Fabricated on the Flexible Substrates by CoSputtering and Modified Selenization

CuIn1-xAlxSe2 (CIAS) thin films were grown on the flexible stainless steel substrates, by de co-sputtering from the elemental cathodes. CuInAl alloyed precursor films were selenized both by noble gas assisted Se vapor transport and vacuum evaporation of Se. X-ray diffraction, scanning electron microscopy and UV-visible absorption spectroscopy were used to characterize the selenized films The composition (x=Al/Al+In) with 0 <= x <= 0.65 was varied by substituting Al with indium in CuInSe2. Lattice parameters, average crystallite sizes and compact density of the films compared to CuInSe2, decreased and (112) peak shifted to higher Bragg's angle, with Al incorporation. Cells were fabricated with the device structure SS/Mo/CIAS/CdS/iZno-AZO/Al. Best cell showed the efficiency of 6.8%, with x=0.13, Eg=1.17 eV, fill factor 45.04, short circuit current density J 30 mA/cm(2).

Effect of thermal annealing on dual photoluminescence emission characteristics of chemically synthesized uncapped Mn2+ doped ZnS quantum dots

Dual photoluminescence (PL) emission characteristics of Mn2+ doped ZnS (ZnS:Mn) quantum dots (QDs) have drawn a lot of attention recently. However, here we report the effect of thermal annealing on the PL emission characteristics of uncapped ZnS:Mn QDs of average sizes similar to 2-3 nm, synthesized by simple chemical precipitation method by using de-ionized (DI) water at room temperature. As-synthesized samples show dual PL emissions, having one UV PL band centred at similar to 400 nm and the other in the visible region similar to 610 nm. But when the samples are isochronally annealed for 2 h at 100-600 degrees C temperature range in air, similar to 90% quenching of Mn2+ related visible PL emission intensity takes place at the annealing temperature of 600 degrees C. X-ray diffraction data show that the as-synthesized cubic ZnS has been converted to wurtzite ZnO at 600 degrees C annealing temperature. The nanostructural properties of the samples are also determined by transmission electron micrograph, electron probe micro-analyser and UV-vis spectrophotometry. The photocatalytic property of the annealed ZnS:Mn sample has been demonstrated and photo-degradation efficiency of the as-synthesized and 600 degrees C annealed ZnS:Mn sample has been found out to be similar to 35% and similar to 61%, respectively, for the degradation of methylene blue dye under visible light irradiation. The synthesized QDs may find significant applications in future optoelectronic devices. (C) 2014 Elsevier B.V. All rights reserved.

Unusual eigenvalue spectrum and relaxation in the Levy-Ornstein-Uhlenbeck process

We consider the rates of relaxation of a particle in a harmonic well, subject to Levy noise characterized by its Levy index mu. Using the propagator for this Levy-Ornstein-Uhlenbeck process (LOUP), we show that the eigenvalue spectrum of the associated Fokker-Planck operator has the form (n + m mu)nu where nu is the force constant characterizing the well, and n, m is an element of N. If mu is irrational, the eigenvalues are all nondegenerate, but rational mu can lead to degeneracy. The maximum degeneracy is shown to be 2. The left eigenfunctions of the fractional Fokker-Planck operator are very simple while the right eigenfunctions may be obtained from the lowest eigenfunction by a combination of two different step-up operators. Further, we find that the acceptable eigenfunctions should have the asymptotic behavior vertical bar x vertical bar(-n1-n2 mu) as vertical bar x vertical bar -> infinity, with n(1) and n(2) being positive integers, though this condition alone is not enough to identify them uniquely. We also assert that the rates of relaxation of LOUP are determined by the eigenvalues of the associated fractional Fokker-Planck operator and do not depend on the initial state if the moments of the initial distribution are all finite. If the initial distribution has fat tails, for which the higher moments diverge, one can have nonspectral relaxation, as pointed out by Toenjes et al. Phys. Rev. Lett. 110, 150602 (2013)].

Self-Assembled, Aligned ZnO Nanorod Buffer Layers for High-Current-Density, Inverted Organic Photovoltaics

Two different soft-chemical, self-assembly-based solution approaches are employed to grow zinc oxide (ZnO) nanorods with controlled texture. The methods used involve seeding and growth on a substrate. Nanorods with various aspect ratios (1-5) and diameters (15-65 nm) are grown. Obtaining highly oriented rods is determined by the way the substrate is mounted within the chemical bath. Furthermore, a preheat and centrifugation step is essential for the optimization of the growth solution. In the best samples, we obtain ZnO nanorods that are almost entirely oriented in the (002) direction; this is desirable since electron mobility of ZnO is highest along this crystallographic axis. When used as the buffer layer of inverted organic photovoltaics (I-OPVs), these one-dimensional (1D) nanostructures offer: (a) direct paths for charge transport and (b) high interfacial area for electron collection. The morphological, structural, and optical properties of ZnO nanorods are studied using scanning electron microscopy, X-ray diffraction, and ultraviolet-visible light (UV-vis) absorption spectroscopy. Furthermore, the surface chemical features of ZnO films are studied using X-ray photoelectron spectroscopy and contact angle measurements. Using as-grown ZnO, inverted OPVs are fabricated and characterized. For improving device performance, the ZnO nanorods are subjected to UV-ozone irradiation. UV-ozone treated ZnO nanorods show: (i) improvement in optical transmission, (ii) increased wetting of active organic components, and (iii) increased concentration of Zn-O surface bonds. These observations correlate well with improved device performance. The devices fabricated using these optimized buffer layers have an efficiency of similar to 3.2% and a fill factor of 0.50; this is comparable to the best I-OPVs reported that use a P3HT-PCBM active layer.

Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry

Graphene Oxide-MnFe2O4 Magnetic Nanohybrids for Efficient Removal of Lead and Arsenic from Water

We show that the hybrids of single-layer graphene oxide with manganese ferrite magnetic nanoparticles have the best adsorption properties for efficient removal of Pb(II), As(III), and As(V) from contaminated water. The nanohybrids prepared by coprecipitation technique were characterized using atomic force and scanning electron microscopies, Fourier transformed infrared spectroscopy, Raman spectroscopy, X-ray diffraction, and surface area measurements. Magnetic character of the nanohybrids was ascertained by a vibrating sample magnetometer. Batch experiments were carried out to quantify the adsorption kinetics and adsorption capacities of the nanohybrids and compared with the bare nanoparticles of MnFe2O4. The adsorption data from our experiments fit the Langmuir isotherm, yielding the maximum adsorption capacity higher than the reported values so far. Temperature-dependent adsorption studies have been done to estimate the free energy and enthalpy of adsorption. Reusability, ease of magnetic separation, high removal efficiency, high surface area, and fast kinetics make these nanohybrids very attractive candidates for low-cost adsorbents for the effective coremoval of heavy metals from contaminated water.