NGC1052 - A study of the pc-scale twin jet

We present results of a VLBA multi-frequency study of the pc-scale twin jet in NGC1052. We observed this object at epoch 1998.99 with the VLBA at 5, 8.4, 22 and 43 GHz both in total and linearly polarized intensity. The spectral analysis confirms the necessity of a free-free absorbing medium, obscuring the innermost part of both jets. At 5 GHz we found a compact linearly polarized emission region at the base of the eastern jet with a degree of polarization of 1.5%. At higher frequencies there is no evidence for polarization in our data. A core shift analysis constrains the position of the central engine to ~0.03 pc. The shift rates of the apparent core position with frequency confirm the strong influence of free-free absorption in conjunction with steep pressure gradients at the bases of both jets.Comment: Proceedings of the conference "SRT: the impact of large antennas on Radio Astronomy and Space Science", Cagliari, Italy, 7-10 November 2001, in press; 6 pages, 5 figures, needs srt_style.st

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence

NestedMICA is a new, scalable, pattern-discovery system for finding transcription factor binding sites and similar motifs in biological sequences. Like several previous methods, NestedMICA tackles this problem by optimizing a probabilistic mixture model to fit a set of sequences. However, the use of a newly developed inference strategy called Nested Sampling means NestedMICA is able to find optimal solutions without the need for a problematic initialization or seeding step. We investigate the performance of NestedMICA in a range scenario, on synthetic data and a well-characterized set of muscle regulatory regions, and compare it with the popular MEME program. We show that the new method is significantly more sensitive than MEME: in one case, it successfully extracted a target motif from background sequence four times longer than could be handled by the existing program. It also performs robustly on synthetic sequences containing multiple significant motifs. When tested on a real set of regulatory sequences, NestedMICA produced motifs which were good predictors for all five abundant classes of annotated binding sites

Dalliance: interactive genome viewing on the web

Summary: Dalliance is a new genome viewer which offers a high level of interactivity while running within a web browser. All data is fetched using the established distributed annotation system (DAS) protocol, making it easy to customize the browser and add extra data

Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster

A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs) that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes

A nano-indentation study of the contact resistance and resistivity of a bi-layered Au/multi-walled carbon nanotube composite

A bi-layer metal-carbon nanotube composite has been developed as a potential low-force electrical contact surface, for application in micro-electromechanical systems switching devices. The samples consist of a vertically aligned forest of multi-walled carbon nanotube (MWCNT), sputter coated with a layer of Au. The effect of varying the components and composition are investigated by means of a modified nano-indenter. By measuring the contact resistance of the composites under various loading conditions, the electrical properties and performance can be evaluated. The composites are shown to have homogenous properties, with each of the layers influencing the total electrical characteristics of the samples. The internal structure of the sample, the MWCNT height and penetration of gold into the forest is shown to directly influence the performance and characteristics of the samples. By analyzing the samples as bulk, the effective resistivities of the composites are also determined to have values from 303 n? m down to 54 n? m, depending on the composition of the sample

A functional methylome map of ulcerative colitis

The etiology of inflammatory bowel diseases is only partially explained by the current genetic risk map. It is hypothesized that environmental factors modulate the epigenetic landscape and thus contribute to disease susceptibility, manifestation, and progression. To test this, we analyzed DNA methylation (DNAm), a fundamental mechanism of epigenetic long-term modulation of gene expression. We report a three-layer epigenome-wide association study (EWAS) using intestinal biopsies from 10 monozygotic twin pairs (n = 20 individuals) discordant for manifestation of ulcerative colitis (UC). Genome-wide expression scans were generated using Affymetrix UG 133 Plus 2.0 arrays (layer 1). Genome-wide DNAm scans were carried out using Illumina 27k Infinium Bead Arrays to identify methylation variable positions (MVPs, layer 2), and MeDIP-chip on Nimblegen custom 385k Tiling Arrays to identify differentially methylated regions (DMRs, layer 3). Identified MVPs and DMRs were validated in two independent patient populations by quantitative real-time PCR and bisulfite-pyrosequencing (n = 185). The EWAS identified 61 disease-associated loci harboring differential DNAm in cis of a differentially expressed transcript. All constitute novel candidate risk loci for UC not previously identified by GWAS. Among them are several that have been functionally implicated in inflammatory processes, e.g., complement factor CFI, the serine protease inhibitor SPINK4, and the adhesion molecule THY1 (also known as CD90). Our study design excludes nondisease inflammation as a cause of the identified changes in DNAm. This study represents the first replicated EWAS of UC integrated with transcriptional signatures in the affected tissue and demonstrates the power of EWAS to uncover unexplained disease risk and molecular events of disease manifestation

Large deviations for polling systems

Related INRIA Research report available at : http://hal.inria.fr/docs/00/07/27/62/PDF/RR-3892.pdfInternational audienceWe aim at presenting in short the technical report, which states a sample path large deviation principle for a resealed process n-1 Qnt, where Qt represents the joint number of clients at time t in a single server 1-limited polling system with Markovian routing. The main goal is to identify the rate function. A so-called empirical generator is introduced, which consists of Q t and of two empirical measures associated with S t the position of the server at time t. The analysis relies on a suitable change of measure and on a representation of fluid limits for polling systems. Finally, the rate function is solution of a meaningful convex program

ARK: Autonomous mobile robot in an industrial environment

This paper describes research on the ARK (Autonomous Mobile Robot in a Known Environment) project. The technical objective of the project is to build a robot that can navigate in a complex industrial environment using maps with permanent structures. The environment is not altered in any way by adding easily identifiable beacons and the robot relies on naturally occurring objects to use as visual landmarks for navigation. The robot is equipped with various sensors that can detect unmapped obstacles, landmarks and objects. In this paper we describe the robot's industrial environment, it's architecture, a novel combined range and vision sensor and our recent results in controlling the robot in the real-time detection of objects using their color and in the processing of the robot's range and vision sensor data for navigation