Copper homeostasis in Salmonella is atypical and copper-CueP is a major periplasmic metal complex.

Salmonella enterica sv. typhimurium (S. enterica sv. Typhimurium) has two metal-transporting P(1)-type ATPases whose actions largely overlap with respect to growth in elevated copper. Mutants lacking both ATPases over-accumulate copper relative to wild-type or either single mutant. Such duplication of ATPases is unusual in bacterial copper tolerance. Both ATPases are under the control of MerR family metal-responsive transcriptional activators. Analyses of periplasmic copper complexes identified copper-CueP as one of the predominant metal pools. Expression of cueP was recently shown to be controlled by the same metal-responsive activator as one of the P(1)-type ATPase genes (copA), and copper-CueP is a further atypical feature of copper homeostasis in S. enterica sv. Typhimurium. Elevated copper is detected by a reporter construct driven by the promoter of copA in wild-type S. enterica sv. Typhimurium during infection of macrophages. Double mutants missing both ATPases also show reduced survival inside cultured macrophages. It is hypothesized that elevated copper within macrophages may have selected for specialized copper-resistance systems in pathogenic microorganism such as S. enterica sv. Typhimurium.

Meiosis in flowering plants and other green organisms.

Sexual eukaryotes generate gametes using a specialized cell division called meiosis that serves both to halve the number of chromosomes and to reshuffle genetic variation present in the parent. The nature and mechanism of the meiotic cell division in plants and its effect on genetic variation are reviewed here. As flowers are the site of meiosis and fertilization in angiosperms, meiotic control will be considered within this developmental context. Finally, we review what is known about the control of meiosis in green algae and non-flowering land plants and discuss evolutionary transitions relating to meiosis that have occurred in the lineages giving rise to the angiosperms.

Inference approach to grammar construction

A system of computer assisted grammar construction (CAGC) is presented in this paper. The CAGC system is designed to generate broad-coverage grammars for large natural language corpora by utilizing both an extended inside-outside algorithm and an automatic phrase bracketing (AUTO) system which is designed to provide the extended algorithm with constituent information during learning. This paper demonstrates the capability of the CAGC system to deal with realistic natural language problems and the usefulness of the AUTO system for constraining the inside-outside based grammar re-estimation. Performance results, including coverage, recall and precision, are presented for a grammar constructed for the Wall Street Journal (WSJ) corpus using the Penn Treebank.

Finite volume distance field solution applied to medial axis transform

Accurate and efficient computation of the nearest wall distance d (or level set) is important for many areas of computational science/engineering. Differential equation-based distance/ level set algorithms, such as the hyperbolic-natured Eikonal equation, have demonstrated valuable computational efficiency. Here, in the context, as an 'auxiliary' equation to the main flow equations, the Eikonal equation is solved efficiently with two different finite volume approaches (the cell vertex and cell-centered). Application of the distance solution is studied for various geometries. Moreover, a procedure using the differential field to obtain the medial axis transform (MAT) for different geometries is presented. The latter provides a skeleton representation of geometric models that has many useful analysis properties. As an alternative approach to the pure geometric methods (e.g. the Voronoi approach), the current d-MAT procedure bypasses many difficulties that are usually encountered by pure geometric methods, especially in three dimensional space. It is also shown that the d-MAT approach provides the potential to sculpt/control the MAT form for specialized solution purposes. Copyright © 2010 by the American Institute of Aeronautics and Astronautics, Inc.

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.

In vivo dynamics of the internal fibrous structure in smooth adhesive pads of insects.

Many insects with smooth adhesive pads can rapidly enlarge their contact area by centripetal pulls on the legs, allowing them to cope with sudden mechanical perturbations such as gusts of wind or raindrops. The short time scale of this reaction excludes any neuromuscular control; it is thus more likely to be caused by mechanical properties of the pad's specialized cuticle. This soft cuticle contains numerous branched fibrils oriented almost perpendicularly to the surface. Assuming a fixed volume of the water-filled cuticle, we hypothesized that pulls could decrease the fibril angle, thereby helping the contact area to expand laterally and longitudinally. Three-dimensional fluorescence microscopy on the cuticle of smooth stick insect pads confirmed that pulls significantly reduced the fibril angle. However, the fibril angle variation appeared insufficient to explain the observed increase in contact area. Direct strain measurements in the contact zone demonstrated that pulls not only expand the cuticle laterally, but also add new contact area at the pad's outer edge.

Epigenetic remodeling of meiotic crossover frequency in Arabidopsis thaliana DNA methyltransferase mutants.

Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover (CO). Meiotic CO frequency varies along the physical length of chromosomes and is determined by hierarchical mechanisms, including epigenetic organization, for example methylation of the DNA and histones. Here we investigate the role of DNA methylation in determining patterns of CO frequency along Arabidopsis thaliana chromosomes. In A. thaliana the pericentromeric regions are repetitive, densely DNA methylated, and suppressed for both RNA polymerase-II transcription and CO frequency. DNA hypomethylated methyltransferase1 (met1) mutants show transcriptional reactivation of repetitive sequences in the pericentromeres, which we demonstrate is coupled to extensive remodeling of CO frequency. We observe elevated centromere-proximal COs in met1, coincident with pericentromeric decreases and distal increases. Importantly, total numbers of CO events are similar between wild type and met1, suggesting a role for interference and homeostasis in CO remodeling. To understand recombination distributions at a finer scale we generated CO frequency maps close to the telomere of chromosome 3 in wild type and demonstrate an elevated recombination topology in met1. Using a pollen-typing strategy we have identified an intergenic nucleosome-free CO hotspot 3a, and we demonstrate that it undergoes increased recombination activity in met1. We hypothesize that modulation of 3a activity is caused by CO remodeling driven by elevated centromeric COs. These data demonstrate how regional epigenetic organization can pattern recombination frequency along eukaryotic chromosomes.

Mode division multiplexing over 2km of OM2 fibre using rotationally optimized mode excitation with fibre coupler demultiplexer

A Spatial Light Modulator and a non-specialized multimode coupler are used together to provide sufficient channel isolation and modal bandwidth for 2x12.5Gbps NRZ over 2km of standard graded-index multimode fibre without DSP. © 2012 IEEE.

IPLR: An online resource for Greek word-level and sublexical information

We present a new online psycholinguistic resource for Greek based on analyses of written corpora combined with text processing technologies developed at the Institute for Language & Speech Processing (ILSP), Greece. The "ILSP PsychoLinguistic Resource" (IPLR) is a freely accessible service via a dedicated web page, at http://speech.ilsp.gr/iplr. IPLR provides analyses of user-submitted letter strings (words and nonwords) as well as frequency tables for important units and conditions such as syllables, bigrams, and neighbors, calculated over two word lists based on printed text corpora and their phonetic transcription. Online tools allow retrieval of words matching user-specified orthographic or phonetic patterns. All results and processing code (in the Python programming language) are freely available for noncommercial educational or research use. © 2010 Springer Science+Business Media B.V.

Attenuated Salmonella Typhimurium lacking the pathogenicity island-2 type 3 secretion system grow to high bacterial numbers inside phagocytes in mice.

Intracellular replication within specialized vacuoles and cell-to-cell spread in the tissue are essential for the virulence of Salmonella enterica. By observing infection dynamics at the single-cell level in vivo, we have discovered that the Salmonella pathogenicity island 2 (SPI-2) type 3 secretory system (T3SS) is dispensable for growth to high intracellular densities. This challenges the concept that intracellular replication absolutely requires proteins delivered by SPI-2 T3SS, which has been derived largely by inference from in vitro cell experiments and from unrefined measurement of net growth in mouse organs. Furthermore, we infer from our data that the SPI-2 T3SS mediates exit from infected cells, with consequent formation of new infection foci resulting in bacterial spread in the tissues. This suggests a new role for SPI-2 in vivo as a mediator of bacterial spread in the body. In addition, we demonstrate that very similar net growth rates of attenuated salmonellae in organs can be derived from very different underlying intracellular growth dynamics.

SOI sensing technologies for harsh environment

This paper reviews and addresses certain aspects of Silicon-On-Insulator (SOI) technologies for a harsh environment. The paper first describes the need for specialized sensors in applications such as (i) domestic and other small-scale boilers, (ii) CO2 Capture and Sequestration, (iii) oil & gas storage and transportation, and (iv) automotive. We describe in brief the advantages and special features of SOI technology for sensing applications requiring temperatures in excess of the typical bulk silicon junction temperatures of 150oC. Finally we present the concepts, structures and prototypes of simple and smart micro-hotplate and Infra Red (IR) based emitters for NDIR (Non Dispersive IR) gas sensors in harsh environments. © 2012 IEEE.

Investigation of multilingual deep neural networks for spoken term detection

The development of high-performance speech processing systems for low-resource languages is a challenging area. One approach to address the lack of resources is to make use of data from multiple languages. A popular direction in recent years is to use bottleneck features, or hybrid systems, trained on multilingual data for speech-to-text (STT) systems. This paper presents an investigation into the application of these multilingual approaches to spoken term detection. Experiments were run using the IARPA Babel limited language pack corpora (∼10 hours/language) with 4 languages for initial multilingual system development and an additional held-out target language. STT gains achieved through using multilingual bottleneck features in a Tandem configuration are shown to also apply to keyword search (KWS). Further improvements in both STT and KWS were observed by incorporating language questions into the Tandem GMM-HMM decision trees for the training set languages. Adapted hybrid systems performed slightly worse on average than the adapted Tandem systems. A language independent acoustic model test on the target language showed that retraining or adapting of the acoustic models to the target language is currently minimally needed to achieve reasonable performance. © 2013 IEEE.