Performance modeling of ultraviolet Raman lidar systems for daytime profiling of atmospheric water vapor

We describe preliminary results from a comprehensive computer model developed to guide optimization of a Raman lidar system for measuring daytime profiles of atmospheric water vapor, emphasizing an ultraviolet, solar-blind approach

Phenex: Ontological Annotation of Phenotypic Diversity

Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems. Phenex addresses this problem by allowing scientists to employ standard ontologies and syntax to link computable phenotype annotations to evolutionary character matrices, as well as to link taxa and specimens to ontological identifiers. Ontologies have become a foundational technology for establishing shared semantics, and, more generally, for capturing and computing with biological knowledge

A Linear Epitope in the N-Terminal Domain of CCR5 and Its Interaction with Antibody.

The CCR5 receptor plays a role in several key physiological and pathological processes and is an important therapeutic target. Inhibition of the CCR5 axis by passive or active immunisation offers one very selective strategy for intervention. In this study we define a new linear epitope within the extracellular domain of CCR5 recognised by two independently produced monoclonal antibodies. A short peptide encoding the linear epitope can induce antibodies which recognise the intact receptor when administered colinear with a tetanus toxoid helper T cell epitope. The monoclonal antibody RoAb 13 is shown to bind to both cells and peptide with moderate to high affinity (6x10^8 and 1.2x107 M-1 respectively), and binding to the peptide is enhanced by sulfation of tyrosines at positions 10 and 14. RoAb13, which has previously been shown to block HIV infection, also blocks migration of monocytes in response to CCR5 binding chemokines and to inflammatory macrophage conditioned medium. A Fab fragment of RoAb13 has been crystallised and a structure of the antibody is reported to 2.1 angstrom resolution

apex: phylogenetics with multiple genes.

Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The r software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new r package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set

Listening to ironically-enjoyed music: A self-regulatory perspective

This research examines adults’ reported motivations for listening to music that they enjoy ironically. In a pilot (N = 96) and main (N = 175) studies, open-ended responses from adults were analysed using Thematic Analysis. Based on the pilot study, ironically enjoyed music was defined as “Music that is enjoyed because of being bad, despite being bad, or for different reasons than intended.” Although many relevant self-regulatory functions of listening to music in general were also relevant to ironically- enjoyed music, it also emerged that ironic enjoyment of music has characteristics that are unique to it: the additional role of mocking, ridiculing, and laughing at the music, and the social benefit that this provides. Music that was listened to “because of” its negative features had a variety of musical features, and the listening usually served functions unique to ironic enjoyment of music, such as mockery. When music was listened to “despite” negative qualities, the music itself was often described as having attractive rhythm, melody or lyrics, while the irony protected the listener from conflicting values associated with the music, helping the listener communicate to others that they did not identify with the music on a higher level. Unfamiliar music mainly played a social role, whereas familiar music related to nostalgia as well as most other functions

On the influence of the cosmological constant on gravitational lensing in small systems

The cosmological constant Lambda affects gravitational lensing phenomena. The contribution of Lambda to the observable angular positions of multiple images and to their amplification and time delay is here computed through a study in the weak deflection limit of the equations of motion in the Schwarzschild-de Sitter metric. Due to Lambda the unresolved images are slightly demagnified, the radius of the Einstein ring decreases and the time delay increases. The effect is however negligible for near lenses. In the case of null cosmological constant, we provide some updated results on lensing by a Schwarzschild black hole.Comment: 8 pages, 1 figure; v2: extended discussion on the lens equation, references added, results unchanged, in press on PR

The Bioperl toolkit: Perl modules for the life sciences

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort