MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant.

The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-Dependent RNA Polymerase 2 (RDR2) for their biogenesis. By analyzing an rdr2 loss-of-function mutant using two different parallel sequencing technologies, MPSS and 454, we characterized the complement of miRNAs expressed in Arabidopsis inflorescence to considerable depth. Nearly all known miRNAs were enriched in this mutant and we identified 13 new miRNAs, all of which were relatively low abundance and constitute new families. Trans-acting siRNAs (ta-siRNAs) were even more highly enriched. Computational and gel blot analyses suggested that the minimal number of miRNAs in Arabidopsis is approximately 155. The size profile of small RNAs in rdr2 reflected enrichment of 21-nt miRNAs and other classes of siRNAs like ta-siRNAs, and a significant reduction in 24-nt heterochromatic siRNAs. Other classes of small RNAs were found to be RDR2-independent, particularly those derived from long inverted repeats and a subset of tandem repeats. The small RNA populations in other Arabidopsis small RNA biogenesis mutants were also examined; a dcl2/3/4 triple mutant showed a similar pattern to rdr2, whereas dcl1-7 and rdr6 showed reductions in miRNAs and ta-siRNAs consistent with their activities in the biogenesis of these types of small RNAs. Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs.

Role of RNA polymerase IV in plant small RNA metabolism.

In addition to the three RNA polymerases (RNAP I-III) shared by all eukaryotic organisms, plant genomes encode a fourth RNAP (RNAP IV) that appears to be specialized in the production of siRNAs. Available data support a model in which dsRNAs are generated by RNAP IV and RNA-dependent RNAP 2 (RDR2) and processed by DICER (DCL) enzymes into 21- to 24-nt siRNAs, which are associated with different ARGONAUTE (AGO) proteins for transcriptional or posttranscriptional gene silencing. However, it is not yet clear what fraction of genomic siRNA production is RNAP IV-dependent, and to what extent these siRNAs are preferentially processed by certain DCL(s) or associated with specific AGOs for distinct downstream functions. To address these questions on a genome-wide scale, we sequenced approximately 335,000 siRNAs from wild-type and RNAP IV mutant Arabidopsis plants by using 454 technology. The results show that RNAP IV is required for the production of >90% of all siRNAs, which are faithfully produced from a discrete set of genomic loci. Comparisons of these siRNAs with those accumulated in rdr2 and dcl2 dcl3 dcl4 and those associated with AGO1 and AGO4 provide important information regarding the processing, channeling, and functions of plant siRNAs. We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors.

FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition

The nuclear RNA binding protein, FCA, promotes Arabidopsis reproductive development. FCA contains a WW protein interaction domain that is essential for FCA function. We have identified FY as a protein partner for this domain. FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. We propose that FCA controls 3' end formation of specific transcripts and that in higher eukaryotes, proteins homologous to FY may have evolved as sites of association for regulators of RNA 3' end processing.

Parameter extraction and calorimetric validation for a silicon carbide jfet pspice model

This paper focuses on the PSpice model of SiC-JFET element inside a SiCED cascode device. The device model parameters are extracted from the I-V and C-V characterization curves. In order to validate the model, an inductive test rig circuit is designed and tested. The switching loss is estimated both using oscilloscope and calorimeter. These results are found to be in good agreement with the simulated results.

Treatment of Phaeodactylum tricornutum cells with papain facilitates lipid extraction.

Triacylglycerols (TAGs) from microalgae have the potential to be used for biodiesel, but several technical and economic hurdles have to be overcome. A major challenge is efficient extraction of intracellular TAGs from algae. Here we investigate the use of enzymes to deconstruct algal cell walls/membranes. We describe a rapid and simple assay that can assess the efficacy of different enzyme treatments on TAG-containing algae. By this means crude papain and bromelain were found to be effective in releasing TAGs from the diatom Phaeodactylum tricornutum, most likely because of their cysteine protease activity. Pre-treating algal biomass with crude papain enabled complete extraction of TAGs using heptane/isopropyl alcohol. Heptane as a single solvent was also effective, although complete recovery of TAG was not obtained. Economic implications of these findings are discussed, with the aim to reduce the complexity of, and energy needed in, TAG extraction.

Sparsity-Inducing Optimization Algorithm for the Extraction of Planar Structures in Noisy Point-Cloud Data

Most of the manual labor needed to create the geometric building information model (BIM) of an existing facility is spent converting raw point cloud data (PCD) to a BIM description. Automating this process would drastically reduce the modeling cost. Surface extraction from PCD is a fundamental step in this process. Compact modeling of redundant points in PCD as a set of planes leads to smaller file size and fast interactive visualization on cheap hardware. Traditional approaches for smooth surface reconstruction do not explicitly model the sparse scene structure or significantly exploit the redundancy. This paper proposes a method based on sparsity-inducing optimization to address the planar surface extraction problem. Through sparse optimization, points in PCD are segmented according to their embedded linear subspaces. Within each segmented part, plane models can be estimated. Experimental results on a typical noisy PCD demonstrate the effectiveness of the algorithm.

Treatment of Phaeodactylum tricornutum cells with papain facilitates lipid extraction

Triacylglycerols (TAGs) from microalgae have the potential to be used for biodiesel, but several technical and economic hurdles have to be overcome. A major challenge is efficient extraction of intracellular TAGs from algae. Here we investigate the use of enzymes to deconstruct algal cell walls/membranes. We describe a rapid and simple assay that can assess the efficacy of different enzyme treatments on TAG-containing algae. By this means crude papain and bromelain were found to be effective in releasing TAGs from the diatom Phaeodactylum tricornutum, most likely because of their cysteine protease activity. Pre-treating algal biomass with crude papain enabled complete extraction of TAGs using heptane/isopropyl alcohol. Heptane as a single solvent was also effective, although complete recovery of TAG was not obtained. Economic implications of these findings are discussed, with the aim to reduce the complexity of, and energy needed in, TAG extraction. © 2012 Elsevier B.V.

Analytical field-effect method for extraction of subgap states in thin-film transistors

We present an analytical field-effect method to extract the density of subgap states (subgap DOS) in amorphous semiconductor thin-film transistors (TFTs), using a closed-form relationship between surface potential and gate voltage. By accounting the interface states in the subthreshold characteristics, the subgap DOS is retrieved, leading to a reasonably accurate description of field-effect mobility and its gate voltage dependence. The method proposed here is very useful not only in extracting device performance but also in physically based compact TFT modeling for circuit simulation. © 2012 IEEE.

Multilinear function factorisation for time series feature extraction

This work applies a variety of multilinear function factorisation techniques to extract appropriate features or attributes from high dimensional multivariate time series for classification. Recently, a great deal of work has centred around designing time series classifiers using more and more complex feature extraction and machine learning schemes. This paper argues that complex learners and domain specific feature extraction schemes of this type are not necessarily needed for time series classification, as excellent classification results can be obtained by simply applying a number of existing matrix factorisation or linear projection techniques, which are simple and computationally inexpensive. We highlight this using a geometric separability measure and classification accuracies obtained though experiments on four different high dimensional multivariate time series datasets. © 2013 IEEE.

A novel method of extraction of blend component structure from SANS measurements of homopolymer bimodal blends

A new method is presented for the extraction of single-chain form factors and interchain interference functions from a range of small-angle neutron scattering (SANS) experiments on bimodal homopolymer blends. The method requires a minimum of three blends, made up of hydrogenated and deuterated components with matched degree of polymerization at two different chain lengths, but with carefully varying deuteration levels. The method is validated through an experimental study on polystyrene homopolymer bimodal blends with M A≈1/2MB. By fitting Debye functions to the structure factors, it is shown that there is good agreement between the molar mass of the components obtained from SANS and from chromatography. The extraction method also enables, for the first time, interchain scattering functions to be produced for scattering between chains of different lengths. © 2014 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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 ΔEt 0.3 eV and with a density of state distribution as Dt(Et-j)=Dt0exp(-ΔEt/ kT)with Dt0 = 5.02 × 1011 cm-2 eV-1. Such a model is useful for developing simulation tools for circuit design. © 2014 AIP Publishing LLC.