Complete Genome Sequences of Three Propionibacterium acnes Isolates from the Type IA(2) Cluster

Propionibacterium acnes is an anaerobic Gram-positive bacterium that has been linked to a wide range of opportunistic human infections and conditions, most notably acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). We now present the whole-genome sequences of three P. acnes strains from the type IA(2) cluster which were recovered from ophthalmic infections (A. McDowell et al., Microbiology 157:1990-2003, 2011).

A complete lipopolysaccharide inner core oligosaccharide is required for resistance of Burkholderia cenocepacia to antimicrobial peptides and bacterial survival in vivo

Burkholderia cenocepacia is an important opportunistic pathogen of patients with cystic fibrosis. This bacterium is inherently resistant to a wide range of antimicrobial agents, including high concentrations of antimicrobial peptides. We hypothesized that the lipopolysaccharide (LPS) of B. cenocepacia is important for both virulence and resistance to antimicrobial peptides. We identified hldA and hldD genes in B. cenocepacia strain K56-2. These two genes encode enzymes involved in the modification of heptose sugars prior to their incorporation into the LPS core oligosaccharide. We constructed a mutant, SAL1, which was defective in expression of both hldA and hldD, and by performing complementation studies we confirmed that the functions encoded by both of these B. cenocepacia genes were needed for synthesis of a complete LPS core oligosaccharide. The LPS produced by SAL1 consisted of a short lipid A-core oligosaccharide and was devoid of O antigen. SAL1 was sensitive to the antimicrobial peptides polymyxin B, melittin, and human neutrophil peptide 1. In contrast, another B. cenocepacia mutant strain that produced complete lipid A-core oligosaccharide but lacked polymeric O antigen was not sensitive to polymyxin B or melittin. As determined by the rat agar bead model of lung infection, the SAL1 mutant had a survival defect in vivo since it could not be recovered from the lungs of infected rats 14 days postinfection. Together, these data show that the B. cenocepacia LPS inner core oligosaccharide is needed for in vitro resistance to three structurally unrelated antimicrobial peptides and for in vivo survival in a rat model of chronic lung infection.

Core-based Methodology: An Automated Approach for Implementing a Complete System From Algorithms to a Heterogeneous Network Including FPGAs

In this paper, we present a methodology for implementing a complete Digital Signal Processing (DSP) system onto a heterogeneous network including Field Programmable Gate Arrays (FPGAs) automatically. The methodology aims to allow design refinement and real time verification at the system level. The DSP application is constructed in the form of a Data Flow Graph (DFG) which provides an entry point to the methodology. The netlist for parts that are mapped onto the FPGA(s) together with the corresponding software and hardware Application Protocol Interface (API) are also generated. Using a set of case studies, we demonstrate that the design and development time can be significantly reduced using the methodology developed.

Mixing operators on spaces with weak topology

We prove that a continuous linear operator T on a topological vector space X with weak topology is mixing if and only if the dual operator T' has no finite dimensional invariant subspaces. This result implies the characterization of hypercyclic operators on the space $\omega$ due to Herzog and Lemmert and implies the result of Bayart and Matheron, who proved that for any hypercyclic operator T on $\omega$, $T\oplus T$ is also hypercyclic.

A complete analytic theory for structure and dynamics of populations and communities spanning wide ranges in body size

The prediction and management of ecosystem responses to global environmental change would profit from a clearer understanding of the mechanisms determining the structure and dynamics of ecological communities. The analytic theory presented here develops a causally closed picture for the mechanisms controlling community and population size structure, in particular community size spectra, and their dynamic responses to perturbations, with emphasis on marine ecosystems. Important implications are summarised in non-technical form. These include the identification of three different responses of community size spectra to size-specific pressures (of which one is the classical trophic cascade), an explanation for the observed slow recovery of fish communities from exploitation, and clarification of the mechanism controlling predation mortality rates. The theory builds on a community model that describes trophic interactions among size-structured populations and explicitly represents the full life cycles of species. An approximate time-dependent analytic solution of the model is obtained by coarse graining over maturation body sizes to obtain a simple description of the model steady state, linearising near the steady state, and then eliminating intraspecific size structure by means of the quasi-neutral approximation. The result is a convolution equation for trophic interactions among species of different maturation body sizes, which is solved analytically using a novel technique based on a multiscale expansion.

Efficiently exploring architectural design spaces via predictive modeling

Architects use cycle-by-cycle simulation to evaluate design choices and understand tradeoffs and interactions among design parameters. Efficiently exploring exponential-size design spaces with many interacting parameters remains an open problem: the sheer number of experiments renders detailed simulation intractable. We attack this problem via an automated approach that builds accurate, confident predictive design-space models. We simulate sampled points, using the results to teach our models the function describing relationships among design parameters. The models produce highly accurate performance estimates for other points in the space, can be queried to predict performance impacts of architectural changes, and are very fast compared to simulation, enabling efficient discovery of tradeoffs among parameters in different regions. We validate our approach via sensitivity studies on memory hierarchy and CPU design spaces: our models generally predict IPC with only 1-2% error and reduce required simulation by two orders of magnitude. We also show the efficacy of our technique for exploring chip multiprocessor (CMP) design spaces: when trained on a 1% sample drawn from a CMP design space with 250K points and up to 55x performance swings among different system configurations, our models predict performance with only 4-5% error on average. Our approach combines with techniques to reduce time per simulation, achieving net time savings of three-four orders of magnitude. Copyright © 2006 ACM.

Hypercyclic operators on countably dimensional spaces

According to Grivaux, the group GL(X) of invertible linear operators on a separable infinite dimensional Banach space X acts transitively on the set s (X) of countable dense linearly independent subsets of X. As a consequence, each A? s (X) is an orbit of a hypercyclic operator on X. Furthermore, every countably dimensional normed space supports a hypercyclic operator. Recently Albanese extended this result to Fréchet spaces supporting a continuous norm. We show that for a separable infinite dimensional Fréchet space X, GL(X) acts transitively on s (X) if and only if X possesses a continuous norm. We also prove that every countably dimensional metrizable locally convex space supports a hypercyclic operator.

Betwixt spaces: Students’ accounts of turning point experiences in first-year transitions

'Not belonging' is becoming a prevalent theme within accounts of the first-year student experience at university. In this study the notion of not belonging is extended by assuming a more active role for the idea of liminality in a student's transition into the university environments of academic and student life. In doing so, the article suggests that the transition between one place (home) and another (university) can result in an 'in-between-ness' - a betwixt space. Through an interpretative methodology, the study explores how students begin to move from this betwixt space into feeling like fully-fledged members of university life. It is concluded that there is a wide range of turning points associated with the students' betwixt transition, which shapes, alters or indeed accentuates the ways in which they make meaningful connections with university life. Moreover, transitional turning point experiences reveal a cast of characters and symbolic objects; capture contrasting motivations and evolving relationships; display multiple trajectories of interpersonal tensions and conflicts; highlight discontinuities as well as continuities; and together, simultaneously liberate and constrain the students' transition into university life.