Local Factors Determine Plant Community Structure on Closely Neighbored Islands

Despite the recent popularity of the metacommunity concept, ecologists have not evaluated the applicability of different metacommunity frameworks to insular organisms. We surveyed 50 closely spaced islands in the Thousand-Island Lake of China to examine the role of local (environmental) and regional (dispersal) factors in structuring woody plant assemblages (tree and shrub species) on these islands. By partitioning the variation in plant community structure into local and regional causes, we showed that local environmental conditions, specifically island morphometric characteristics, accounted for the majority of the variation in plant community structure among the studied islands. Spatial variables, representing the potential importance of species dispersal, explained little variation. We conclude that one metacommunity framework–species sorting–best characterizes these plant communities. This result reinforces the idea that the traditional approach of emphasizing the local perspective when studying ecological communities continues to hold its value

Assessing the recovery of an Antarctic predator from historical exploitation

The recovery of whale populations from centuries of exploitation will have important management and ecological implications due to greater exposure to anthropogenic activities and increasing prey consumption. Here, a Bayesian population model integrates catch data, estimates of abundance, and information on genetics and biology to assess the recovery of western South Atlantic (WSA) humpback whales (Megaptera novaeangliae). Modelling scenarios evaluated the sensitivity of model outputs resulting from the use of different data, different model assumptions and uncertainty in catch allocation and in accounting for whales killed but not landed. A long period of exploitation drove WSA humpback whales to the brink of extinction. They declined from nearly 27 000 (95% PI = 22 800–33 000) individuals in 1830 to only 450 (95% PI = 200–1400) whales in the mid-1950s. Protection led to a strong recovery and the current population is estimated to be at 93% (95% PI = 73–100%) of its pre-exploitation size. The recovery of WSA humpback whales may result in large removals of their primary prey, the Antarctic krill (Euphausia superba), and has the potential to modify the community structure in their feeding grounds. Continued monitoring is needed to understand how these whales will respond to modern threats and to climate-driven changes to their habitats

Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling

Toll-like receptor (TLR) signaling is a key innate immunity response to pathogens. Recruitment of signaling adapters such as MAL (TIRAP) and MyD88 to the TLRs requires Toll/interleukin-1 receptor (TIR)-domain interactions, which remain structurally elusive. Here we show that MAL TIR domains spontaneously and reversibly form filaments in vitro. They also form cofilaments with TLR4 TIR domains and induce formation of MyD88 assemblies. A 7-Å-resolution cryo-EM structure reveals a stable MAL protofilament consisting of two parallel strands of TIR-domain subunits in a BB-loop-mediated head-to-tail arrangement. Interface residues that are important for the interaction are conserved among different TIR domains. Although large filaments of TLR4, MAL or MyD88 are unlikely to form during cellular signaling, structure-guided mutagenesis, combined with in vivo interaction assays, demonstrated that the MAL interactions defined within the filament represent a template for a conserved mode of TIR-domain interaction involved in both TLR and interleukin-1 receptor signaling

The CCP4 suite: integrative software for macromolecular crystallography

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world

The safety of occam

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The relationship between water, sanitation and schistosomiasis : a systematic review and meta-analysis

BACKGROUND: Access to "safe" water and "adequate" sanitation are emphasized as important measures for schistosomiasis control. Indeed, the schistosomes' lifecycles suggest that their transmission may be reduced through safe water and adequate sanitation. However, the evidence has not previously been compiled in a systematic review. METHODOLOGY: We carried out a systematic review and meta-analysis of studies reporting schistosome infection rates in people who do or do not have access to safe water and adequate sanitation. PubMed, Web of Science, Embase, and the Cochrane Library were searched from inception to 31 December 2013, without restrictions on year of publication or language. Studies' titles and abstracts were screened by two independent assessors. Papers deemed of interest were read in full and appropriate studies included in the meta-analysis. Publication bias was assessed through the visual inspection of funnel plots and through Egger's test. Heterogeneity of datasets within the meta-analysis was quantified using Higgins' I2. PRINCIPAL FINDINGS: Safe water supplies were associated with significantly lower odds of schistosomiasis (odds ratio (OR) = 0.53, 95% confidence interval (CI): 0.47-0.61). Adequate sanitation was associated with lower odds of Schistosoma mansoni, (OR = 0.59, 95% CI: 0.47-0.73) and Schistosoma haematobium (OR = 0.69, 95% CI: 0.57-0.84). Included studies were mainly cross-sectional and quality was largely poor. CONCLUSIONS/SIGNIFICANCE: Our systematic review and meta-analysis suggests that increasing access to safe water and adequate sanitation are important measures to reduce the odds of schistosome infection. However, most of the studies were observational and quality was poor. Hence, there is a pressing need for adequately powered cluster randomized trials comparing schistosome infection risk with access to safe water and adequate sanitation, more studies which rigorously define water and sanitation, and new research on the relationships between water, sanitation, hygiene, human behavior, and schistosome transmissio

Comparing design techniques for modelling fault tolerant systems

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Engineering safety-related parallel systems

A growing number of safety-related applications are dependent on software for their control. High performance and redundancy requirements in modern control systems can be satisfied by parallel processing. This paper considers the requirements for the software engineering of safe parallel systems and the specific problems that need to be addressed: safe state analysis and temporal analysis. The benefits to be gained from utilizing commercial CASE tools and extending them to facilitate the required analysis are detailed

Parallel processing: a safer option for real-time control software

Software is increasingly being used to control applications demanding high performance and high reliability. Modern parallel processing technologies can offer systems designers many advances towards satisfying these requirements. This paper considers whether the current software safety standards, and the methods they advocate, are sufficiently mature to reach this objective. A particular example of a parallel development method derived from formal mathematics is explored. The aim is to identify both a pragmatic and intuitive development method suitable to control systems applications. This method should permit a fair degree of automation of a control system's behaviour analysis necessary to establish a safe parallel implementation