Millisecond processing beyond chip technology: From electronics to photonics

There is a clear and increasing interest in short time annealing processing far below one second, i.e. the lower limit of Rapid Thermal Processing (RTP) called spike annealing. This was driven by the need of suppressing the so-called Transient Enhanced Diffusion in advanced boronimplanted shallow pn-junctions in silicon technology. Meanwhile the interest in flash lamp annealing (FLA) in the millisecond range spread out into other fields related to silicon technology and beyond. This paper reports on recent experiments regarding shallow junction engineering in germanium, annealing of ITO layers on glass and plastic foil to form an conductive layer as well as investigations which we did during the last years in the field of wide band gap semiconductor materials (SiC, ZnO). A more common feature evolving from our work was related to the modeling of wafer stress during millisecond thermal processing with flash lamps. Finally recent achievements in the field of silicon-based light emission basing on Metal-Oxide-Semiconductor Light Emitting Devices will be reported. © 2007 IEEE.

Advanced thermal processing of semiconductor materials in the msec-range

This paper reviews the advances that flash lamp annealing brings to the processing of the most frequently used semiconductor materials, namely silicon and silicon carbide, thus enabling the fabrication of novel microelectronic structures and materials. The paper describes how such developments can translate into important practical applications leading to a wide range of technological benefits. Opportunities in ultra-shallow junction formation, heteroepitaxial growth of thin films of cubic silicon carbide on silicon, and crystallization of amorphous silicon films, along with the technical reasons for using flash lamp annealing are discussed in the context of state-of-the-art materials processing. © 2005 IEEE.

Bayesian signal processing

The application of Bayes' Theorem to signal processing provides a consistent framework for proceeding from prior knowledge to a posterior inference conditioned on both the prior knowledge and the observed signal data. The first part of the lecture will illustrate how the Bayesian methodology can be applied to a variety of signal processing problems. The second part of the lecture will introduce the concept of Markov Chain Monte-Carlo (MCMC) methods which is an effective approach to overcoming many of the analytical and computational problems inherent in statistical inference. Such techniques are at the centre of the rapidly developing area of Bayesian signal processing which, with the continual increase in available computational power, is likely to provide the underlying framework for most signal processing applications.

RNA processing and Arabidopsis flowering time control.

Plants control their flowering time in order to ensure that they reproduce under favourable conditions. The components involved in this complex process have been identified using a molecular genetic approach in Arabidopsis and classified into genetically separable pathways. The autonomous pathway controls the level of mRNA encoding a floral repressor, FLC, and comprises three RNA-binding proteins, FCA, FPA and FLK. FCA interacts with the 3'-end RNA-processing factor FY to autoregulate its own expression post-transcriptionally and to control FLC. Other components of the autonomous pathway, FVE and FLD, regulate FLC epigenetically. This combination of epigenetic and post-transcriptional control gives precision to the control of FLC expression and flowering time.

Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning.

Small RNAs have several important biological functions. MicroRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) regulate mRNA stability and translation, and siRNAs cause post-transcriptional gene silencing of transposons, viruses and transgenes and are important in both the establishment and maintenance of cytosine DNA methylation. Here, we study the role of the four Arabidopsis thaliana DICER-LIKE genes (DCL1-DCL4) in these processes. Sequencing of small RNAs from a dcl2 dcl3 dcl4 triple mutant showed markedly reduced tasiRNA and siRNA production and indicated that DCL1, in addition to its role as the major enzyme for processing miRNAs, has a previously unknown role in the production of small RNAs from endogenous inverted repeats. DCL2, DCL3 and DCL4 showed functional redundancy in siRNA and tasiRNA production and in the establishment and maintenance of DNA methylation. Our studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs.

An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.

ARGONAUTE4 (AGO4) and RNA polymerase IV (Pol IV) are required for DNA methylation guided by 24 nucleotide small interfering RNAs (siRNAs) in Arabidopsis thaliana. Here we show that AGO4 localizes to nucleolus-associated bodies along with the Pol IV subunit NRPD1b; the small nuclear RNA (snRNA) binding protein SmD3; and two markers of Cajal bodies, trimethylguanosine-capped snRNAs and the U2 snRNA binding protein U2B''. AGO4 interacts with the C-terminal domain of NRPD1b, and AGO4 protein stability depends on upstream factors that synthesize siRNAs. AGO4 is also found, along with the DNA methyltransferase DRM2, throughout the nucleus at presumed DNA methylation target sites. Cajal bodies are conserved sites for the maturation of ribonucleoprotein complexes. Our results suggest a function for Cajal bodies as a center for the assembly of an AGO4/NRPD1b/siRNA complex, facilitating its function in RNA-directed gene silencing at target loci.

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.

Development and evaluation of an alternative method for processing elastic-lidar return signals

A method for interpreting elastic-lidar return signals in heavily-polluted atmospheres is presented. It is based on an equation derived directly from the classic lidar equation, which highlights gradients of the atmospheric backscattering properties along the laser optical path. The method is evaluated by comparing its results with those obtained with the differential absorption technique. The results were obtained from locating and ranging measurements in pollutant plumes and contaminated environments around central México. © World Scientific Publishing Company.

BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net