Generating functions for canonical systems of fermions

The method proposed by Pratt to derive recursion relations for systems of degenerate fermions [Phys. Rev. Lett. 84, 4255 (2000), arXiv:nucl-th/9905055] relies on diagrammatic techniques. This efficient formalism assumes no explicit two-body interactions, makes possible the inclusion of conservation laws and requires low computational time. In this brief report, we show that such recursion relations can be obtained from generating functions, without any restriction as concerns the number of conservation laws (e.g. total energy or angular momentum).Comment: submitted to Physical Review

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.

BACKGROUND: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. RESULTS: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. CONCLUSIONS: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data

Pulsed mononode dye laser developed for a geophysical application

Following the extension of the lidar technique in the study of the atmosphere, the necessity of having a high power pulsed laser beam with a narrowed bandwidth and the possibility of selecting a particular wavelength within a certain spectral region arises. With the collaboration of others, a laser cavity using the multiwave Fizeau wedge (MWFW) was developed. Using the classical method of beam amplification with the aid of different stages, a new pulsed dye laser device was designed. The originality resides in the use of reflecting properties of the MFWF. Locally a plan wave coming with a particular angular incidence is reflected with a greater than unity coefficient; this is the consequence of the wedge angle which doubles the participation of every ray in the interferometric process. This dye laser operation and advantages are discussed. The feasibility of different geophysical applications envisageable with this laser is discussed

Productive tensions - engaging geography students in participatory action research with communities

ArticleCopyright © 2013 copyright Taylor & Francis.This study discusses the benefits and challenges of an undergraduate module on participatory geographies, involving students in co-producing research with community partners. The module challenges the knowledge production model predominant in Geography curricula. We argue that it develops students' skills and understanding through engaging them intellectually, socially and emotionally outside the university. As a student, two community partners and a professor, we offer our perspectives on the opportunities and conflicts that arose. We do not gloss over tensions in achieving the module's diverse aims, but suggest that these are productive for teaching, learning, research and the needs of community organizations

Supernova search at intermediate z. I. Spectroscopic analysis

We study 8 supernovae discovered as part of the International Time Programme (ITP) project ``Omega and Lambda from Supernovae and the Physics of Supernova Explosions'' at the European Northern Observatory (ENO). The goal of the project is to increase the sample of intermediate redshift (0.1<z<0.4) SNe Ia for testing properties of SNe Ia along z and for enlarging the sample in the Hubble diagram up to large z.Comment: 2 pages, 2 figures, 1 table, to appear in ``1604-2004: Supernovae as Cosmological Lighthouses'', (extended text upon request

Effect of heat treatment and aging on the mechanical loss and strength of hydroxide catalysis bonds between fused silica samples

Hydroxide catalysis bonds are used in the aLIGO gravitational wave detectors and are an essential technology within the mirror suspensions which allowed for detector sensitivities to be reached that enabled the first direct detections of gravitational waves. Methods aimed at further improving hydroxide catalysis bonds for future upgrades to these detectors, in order to increase detection rates and the number of detectable sources, are explored. Also, the effect on the bonds of an aLIGO suspension construction procedure involving heat, the fibre welding process, is investigated. Here we show that thermal treatments can be beneficial to improving some of the bond properties important to the mirror suspensions in interferometric gravitational wave detectors. It was found that heat treating bonds at 150\,^\circC increases bond strength by a factor of approximately 1.5 and a combination of bond ageing and heat treatment of the optics at 150\,\circC reduces the mechanical loss of a bond from 0.10 to 0.05. It is also shown that current construction procedures do not reduce bond strength

SVAMP: sequence variation analysis, maps and phylogeny.

SUMMARY: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files. Allele frequency map, geographical map of isolates, Tajima's D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time. We demonstrate the utility of SVAMP in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries. We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents. AVAILABILITY AND IMPLEMENTATION: The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online