Accelerating Multiple Sequence Alignment with the Cell BE Processor

The Cell Broadband Engine (BE) Architecture is a new heterogeneous multi-core architecture targeted at compute-intensive workloads. The architecture of the Cell BE has several features that are unique in high-performance general-purpose processors, most notably the extensive support for vectorization, scratch pad memories and explicit programming of direct memory accesses (DMAs) and mailbox communication. While these features strongly increase programming complexity, it is generally claimed that significant speedups can be obtained by using Cell BE processors. This paper presents our experiences with using the Cell BE architecture to accelerate Clustal W, a bio-informatics program for multiple sequence alignment. We report on how we apply the unique features of the Cell BE to Clustal W and how important each is in obtaining high performance. By making extensive use of vectorization and by parallelizing the application across all cores, we demonstrate a speedup of 24.4 times when using 16 synergistic processor units on a QS21 Cell Blade compared to single-thread execution on the power processing unit. As the Cell BE exploits a large number of slim cores, our highly optimized implementation is just 3.8 times faster than a 3-thread version running on an Intel Core2 Duo, as the latter processor exploits a small number of fat cores.

An exploration of the attitudes and strategic responses of soleproprietor micro-enterprises in adopting information and communication technology

This article analyses longitudinal case-based research exploring the attitudes and strategic responses of micro-enterprise owners in adopting information and communication technology (ICT). In so doing, it contributes to the limited literature on micro-enterprise ICT adoption, with a particular focus on sole proprietors. It provides a basis for widening the theoretical base of the literature pertaining to ICT adoption on two levels. First, a framework is developed which integrates the findings to illustrate the relationships between attitudes towards ICT adoption, endogenous and exogenous influencers of these attitudes and subsequent strategic response in ICT adoption. Second, building upon this framework the article reveals the unique challenges, opportunities and implications of ICT adoption for sole-proprietor micro-enterprises. © The Author(s) 2012

Visualising Textual Knowledge about Risks to Aid Risk Communication

This paper demonstrates a potential application for latent semantic analysis and similar techniques in visualising the differences between two levels of knowledge about a risk issue. The HIV/AIDS risk issue will be examined and the semantic clusters of key words in a technical corpora derived from specific literature about HIV/AIDS will be compared with the semantic clusters of those in more general corpora. It is hoped that these comparisons will create a fast and efficient complementary approach to the articulation of mental models of risk issues that could be used to target possible inconsistencies between expert and lay mental models.

A defeasible reasoning model of inductive concept learning from examples and communication

This paper introduces a logical model of inductive generalization, and specifically of the machine learning task of inductive concept learning (ICL). We argue that some inductive processes, like ICL, can be seen as a form of defeasible reasoning. We define a consequence relation characterizing which hypotheses can be induced from given sets of examples, and study its properties, showing they correspond to a rather well-behaved non-monotonic logic. We will also show that with the addition of a preference relation on inductive theories we can characterize the inductive bias of ICL algorithms. The second part of the paper shows how this logical characterization of inductive generalization can be integrated with another form of non-monotonic reasoning (argumentation), to define a model of multiagent ICL. This integration allows two or more agents to learn, in a consistent way, both from induction and from arguments used in the communication between them. We show that the inductive theories achieved by multiagent induction plus argumentation are sound, i.e. they are precisely the same as the inductive theories built by a single agent with all data. © 2012 Elsevier B.V.

Identifying functional stakeholder clusters to maximise communication for the ecosystem approach to fisheries management

Interaction with ecological models can improve stakeholder participation in fisheries management. Problems exist in efficiently communicating outputs to stakeholders and an objective method of structuring stakeholder differences is lacking. This paper aims to inform the design of a multi-user communication interface for fisheries management by identifying functional stakeholder groups. Intuitive categorisation of stakeholders, derived from survey responses, is contrasted with an Evidence-Based method derived from analysis of stakeholder literature. Intuitive categorisation relies on interpretation and professional judgement when categorising stakeholders among conventional stakeholder groups. Evidence-Based categorisation quantitatively characterises each stakeholder with a vector of four management objective interest-strength values (Yield, Employment, Profit and Ecosystem Preservation). Survey respondents agreed little in forming intuitive groups and the groups were poorly defined and heterogeneous in interests. In contrast the Evidence-Based clusters were well defined and largely homogeneous, so more useful for identifying functional relations with model outputs. The categorisations lead to two different clusterings of stakeholders and suggest unhelpful stereotyping of stakeholders may occur with the Intuitive categorisation method. Stakeholder clusters based on literature-evidence show a high degree of common interests among clusters and is encouraging for those seeking to maximise dialogue and consensus forming. © 2013 Elsevier Ltd.

Enhanced efficiency of envelope-tracking based broadband inverse class-E power amplifier

In this paper, the envelope-tracking technique is exploited to boost average efficiency of the newly introduced broadband Inverse Class-E power amplifier. A 2.26 GHz - 20.5 dBm - 3 V power amplifier was designed, constructed, and measured. For a multi-carrier input signal with 10 dB peak-to-average ratio, the average PAE was increased from 5.7% to 54.5%. © 2008 IEEE.

Assessing family members' satisfaction with information sharing and communication during Hospital care at the end of life

Context: Despite the fact that most deaths occur in hospital, problems remain with how patients and families experience care at the end of life when a death occurs in a hospital. Objectives: (1) assess family member satisfaction with information sharing and communication, and (2) examine how satisfaction with information sharing and communication is associated with patient factors. Methods: Using a cross-sectional survey, data were collected from family members of adult patients who died in an acute care organization. Correlation and factor analysis were conducted, and internal consistency assessed using Cronbach's alpha. Linear regression was performed to determine the relationship among patient variables and satisfaction on the Information Sharing and Communication (ISC) scale. Results: There were 529 questionnaires available for analysis. Following correlation analysis and the dropping of redundant and conceptually irrelevant items, seven items remained for factor analysis. One factor was identified, described as information sharing and communication, that explained 76.3% of the variance. The questionnaire demonstrated good content and reliability (Cronbach's alpha 0.96). Overall, family members were satisfied with information sharing and communication (mean total satisfaction score 3.9, SD 1.1). The ISC total score was significantly associated with patient gender, the number of days in hospital before death, and the hospital program where the patient died. Conclusions: The ISC scale demonstrated good content validity and reliability. The ISC scale offers acute care organizations a means to assess the quality of information sharing and communication that transpires in care at the end of life. © Copyright 2013, Mary Ann Liebert, Inc.

HIV-1 Nef limits communication between linker of activated T cells and SLP-76 to reduce formation of SLP-76-signaling microclusters following TCR stimulation

Signal initiation by engagement of the TCR triggers actin rearrangements, receptor clustering, and dynamic organization of signaling complexes to elicit and sustain downstream signaling. Nef, a pathogenicity factor of HIV, disrupts early TCR signaling in target T cells. To define the mechanism underlying this Nef-mediated signal disruption, we employed quantitative single-cell microscopy following surface-mediated TCR stimulation that allows for dynamic visualization of distinct signaling complexes as microclusters (MCs). Despite marked inhibition of actin remodeling and cell spreading, the induction of MCs containing TCR-CD3 or ZAP70 was not affected significantly by Nef. However, Nef potently inhibited the subsequent formation of MCs positive for the signaling adaptor Src homology-2 domain-containing leukocyte protein of 76 kDa (SLP-76) to reduce MC density in Nef-expressing and HIV-1-infected T cells. Further analyses suggested that Nef prevents formation of SLP-76 MCs at the level of the upstream adaptor protein, linker of activated T cells (LAT), that couples ZAP70 to SLP-76. Nef did not disrupt pre-existing MCs positive for LAT. However, the presence of the viral protein prevented de novo recruitment of active LAT into MCs due to retargeting of LAT to an intracellular compartment. These modulations in MC formation and composition depended on Nef's ability to simultaneously disrupt both actin remodeling and subcellular localization of TCR-proximal machinery. Nef thus employs a dual mechanism to disturb early TCR signaling by limiting the communication between LAT and SLP-76 and preventing the dynamic formation of SLP-76-signaling MCs.

Effect of environmental multipath on line of sight body to body communication at 2.45 GHz

Body to body links are the most scenario dependent form of body centric communications with performance highly dependent on the users' movements, relative positioning and the local operating environment. This paper focuses on line of sight cases which although they should be the most dependent, still have considerable variability depending on local propagation conditions. The results presented in the paper also raise important questions about the statistical characterisation of such links and the effect of different approaches to local mean averaging on fading characteristics. © 2012 IEEE.