Hamilton's Turns for the Lorentz Group

Hamilton in the course of his studies on quaternions came up with an elegant geometric picture for the group SU(2). In this picture the group elements are represented by ``turns'', which are equivalence classes of directed great circle arcs on the unit sphere $S^2$, in such a manner that the rule for composition of group elements takes the form of the familiar parallelogram law for the Euclidean translation group. It is only recently that this construction has been generalized to the simplest noncompact group $SU(1,1) = Sp(2, R) = SL(2,R)$, the double cover of SO(2,1). The present work develops a theory of turns for $SL(2,C)$, the double and universal cover of SO(3,1) and $SO(3,C)$, rendering a geometric representation in the spirit of Hamilton available for all low dimensional semisimple Lie groups of interest in physics. The geometric construction is illustrated through application to polar decomposition, and to the composition of Lorentz boosts and the resulting Wigner or Thomas rotation.Comment: 13 pages, Late

Characterization of a Quantum Light Source Based on Spontaneous Parametric Down-Conversion

We have built a quantum light source capable of producing different types of quantum states. The quantum light source is based on entangled state preparation in the process of spontaneous parametric down-conversion. The single-photon detection rate of eight-hundred thousand per second demonstrates that we have created a bright state-of-the-art quantum light source. As a part of the characterization we measured two-photon quantum interference in a Hong-Ou-Mandel interferometer.Comment: 33 page

BamView: visualizing and interpretation of next-generation sequencing read alignments.

So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence. It is a desktop application for browsing the aligned or mapped reads [Ruffalo, M, LaFramboise, T, Koyutürk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27:2790-6] at different levels of magnification, from nucleotide level, where the base qualities can be seen, to genome or chromosome level where overall coverage is shown. To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data. Multiple read alignment files can be overlaid to compare results from different experiments, and filters can be applied to facilitate the interpretation of the aligned reads. As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of the reference genome. Single nucleotide polymorphism (SNP) density and candidate SNP sites can be highlighted and investigated, and read-pair information can be used to discover large structural insertions and deletions. The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user

CLASSICAL CEPHEID LIGHT CURVES REVISITED

Fourier decompositions are made of the B, V, R, and I classical Cepheid observations of Moffett and Barnes. The Fourier diagrams for V agree very well with the corresponding plots of Simon and Lee. The B, R, and I diagrams resemble the plots for V, but with small, systematic shifts in the phases ϕ21 and ϕ31. The 2.5-day star, DT Cyg, is confirmed as a likely overtone pulsator by its anomalous position in the Fourier plots. Finally, we study the Fourier phase quantity ϕ41 and introduce phase-phase diagrams to look at the Hertzsprung progression. Discontinuities in these diagrams support the idea that the long-period and short-period Cepheids may reach their limit cycles in different ways

Circlator: automated circularization of genome assemblies using long sequencing reads

The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. Here we present Circlator, the first tool to automate assembly circularization and produce accurate linear representations of circular sequences. Using Pacific Biosciences and Oxford Nanopore data, Circlator correctly circularized 26 of 27 circularizable sequences, comprising 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of Plasmodium falciparum and a human mitochondrion. Circlator is available at http://sanger-pathogens.github.io/circlator/

Galactic cosmic rays in the heliosphere

Simon R Thomas, Mathew J Owens and Mike Lockwood discuss how neutron monitor counts can help map space weather. This won the 2014 Rishbeth Prize for the best student talk at the Hot Spring MIST Meeting in Bath, April 2014

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

AimMeiofaunal communities that inhabit the marine benthos offer unique opportunities to simultaneously study the macroecology of numerous phyla that exhibit different life-history strategies. Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy. LocationUK and mainland European coast. MethodsNext-generation sequencing techniques (NGS; Roche 454 FLX platform) using 18S nuclear small subunit ribosomal DNA (rDNA) gene. Pyrosequences were analysed using AmpliconNoise followed by chimera removal using Perseus. ResultsRarefaction curves revealed that sampling saturation was only reached at 15% of sites, highlighting that the bulk of meiofaunal diversity is yet to be discovered. Overall, 1353 OTUs were recovered and assigned to 23 different phyla. The majority of sampled sites had c. 60-70 unique operational taxonomic units (OTUs) per site, indicating high levels of beta diversity. The environmental parameters that best explained community structure were seawater temperature, geographical distance and sediment size, but most of the variability (R-2=70%-80%) remains unexplained. Main conclusionsHigh percentages of endemic OTUs suggest that meiobenthic community composition is partly niche-driven, as observed in larger organisms, but also shares macroecological features of microorganisms by showing high levels of cosmopolitanism (albeit on a much smaller scale). Meiobenthic communities exhibited patterns of isolation by distance as well as associations between niche, latitude and temperature, indicating that meiobenthic communities result from a combination of niche assembly and dispersal processes. Conversely, isolation-by-distance patterns were not identified in the featured protists, suggesting that animals and protists adhere to radically different macroecological processes, linked to life-history strategies.Natural Environment Research Council (NERC) [NE/E001505/1, NE/F001266/1, MGF-167]; Portuguese Foundation for Science and Technology (FCT) [SFRH/BD/27413/2006, SFRH/BPD/80447/2014]; EPSRC [EP/H003851/1]; BBSRC CASE studentship; Unilever; Biotechnology and Biological Sciences Research Council [987347]; Engineering and Physical Sciences Research Council [EP/H003851/1]; Natural Environment Research Council [NE/F001290/1, NE/F001266/1, NE/E001505/1, NBAF010002]info:eu-repo/semantics/publishedVersio