Are Individualistic Orientations Collectively Valuable in Group Negotiations?

This experiment examines how members' individualistic or cooperative motivational orientations affect the processes and outcomes of negotiating groups. A total of 228 students participated in a three-person negotiation simulation where motivational orientations were induced through written instructions and members were aware of each other's orientations. Results showed that groups with only cooperative members were more satisfied with their negotiations than were groups with other member compositions. Conversely, groups with only individualistic members achieved higher joint gains than did groups with other member compositions. Process analyses indicated that individualistic groups increased their integrative activities and decreased their distributive activities toward the end of their negotiations. Our results challenge the dominant view that individualistic orientations are detrimental for group processes and outcomes

On the Whitehead spectrum of the circle

The seminal work of Waldhausen, Farrell and Jones, Igusa, and Weiss and Williams shows that the homotopy groups in low degrees of the space of homeomorphisms of a closed Riemannian manifold of negative sectional curvature can be expressed as a functor of the fundamental group of the manifold. To determine this functor, however, it remains to determine the homotopy groups of the topological Whitehead spectrum of the circle. The cyclotomic trace of B okstedt, Hsiang, and Madsen and a theorem of Dundas, in turn, lead to an expression for these homotopy groups in terms of the equivariant homotopy groups of the homotopy fiber of the map from the topological Hochschild T-spectrum of the sphere spectrum to that of the ring of integers induced by the Hurewicz map. We evaluate the latter homotopy groups, and hence, the homotopy groups of the topological Whitehead spectrum of the circle in low degrees. The result extends earlier work by Anderson and Hsiang and by Igusa and complements recent work by Grunewald, Klein, and Macko.Comment: 52 page

PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology

PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith–Waterman and ParAlign. The ParAlign algorithm is similar to Smith–Waterman in sensitivity, while as quick as BLAST for protein searches. A form of parallel computing technology known as multimedia technology that is available in modern processors, but rarely used by other bioinformatics software, has been exploited to achieve the high speed. The software is also designed to run efficiently on computer clusters using the message-passing interface standard. A public search service powered by a large computer cluster has been set-up and is freely available at , where the major public databases can be searched. The software can also be downloaded free of charge for academic use

The ‘dance’ of life: visualizing metamorphosis during pupation in the blow fly Calliphora vicina by X-ray video imaging and micro-computed tomography

© 2017 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. The attached file is the published version of the article

A Quick Guide for Developing Effective Bioinformatics Programming Skills

Bioinformatics programming skills are becoming a necessity across many facets of biology and medicine, owed in part to the continuing explosion of biological dat

When counting cattle is not enough: multiple perspectives in agricultural and veterinary research

A traditional approach in agricultural and veterinary research is focussing on the biological perspective where large cattle-databases are used to analyse the dairy herd. This approach has yielded valuable insights. However, recent research indicates that this knowledge-base can be further increased by examining agricultural and veterinary challenges from other perspectives. In this paper we suggest three perspectives that may supplement the biological perspective in agricultural and veterinary research; the economic-, the managerial-, and the social perspective. We review recent studies applying or combining these perspectives and discuss how multiple perspectives may improve our understanding and ability to handle cattle-health challenges

Accelerated Profile HMM Searches

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches

SHRiMP: Accurate Mapping of Short Color-space Reads

The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp

Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats

3-methyladenine DNA glycosylases initiate repair of cytotoxic and promutagenic alkylated bases in DNA. We demonstrate by comparative modelling that Bacillus cereus AlkD belongs to a new, fifth, structural superfamily of DNA glycosylases with an alpha–alpha superhelix fold comprising six HEAT-like repeats. The structure reveals a wide, positively charged groove, including a putative base recognition pocket. This groove appears to be suitable for the accommodation of double-stranded DNA with a flipped-out alkylated base. Site-specific mutagenesis within the recognition pocket identified several residues essential for enzyme activity. The results suggest that the aromatic side chain of a tryptophan residue recognizes electron-deficient alkylated bases through stacking interactions, while an interacting aspartate–arginine pair is essential for removal of the damaged base. A structural model of AlkD bound to DNA with a flipped-out purine moiety gives insight into the catalytic machinery for this new class of DNA glycosylases