A protocol for enumeration of aquatic viruses by epifluorescence microscopy using Anodisc™ 13 membranes

<p>Abstract</p> <p>Background</p> <p>Epifluorescence microscopy is a common method used to enumerate virus-like particles (VLP) from environmental samples and relies on the use of filter membranes with pore sizes < 0.02 μm; the most commonly used protocols employ 25 mm Anodisc™ membranes with a built-in support ring. Other filters with small pore sizes exist, including the 13 mm Anodisc™ membranes without a support ring. However, the use of these membranes for viral enumeration has not been previously reported.</p> <p>Results</p> <p>Here we describe a modified protocol for 13 mm Anodisc membranes that uses a custom filter holder that can be readily constructed in individual investigators' laboratories from commercially available Swinnex^®filter holders. We compared VLP concentrations obtained from phage lysates and seawater samples using both Anodisc membranes, as well as Nuclepore™ small pore-size membranes (0.015 or 0.030 μm). The 13 mm Anodisc membranes gave comparable estimates of VLP abundance to those obtained with the 25 mm Anodisc membranes when similar staining methods were employed. Both Nuclepore membranes typically gave an order of magnitude lower VLP abundance values for environmental samples.</p> <p>Conclusions</p> <p>The 13 mm Anodisc membranes are less costly and require smaller sample volumes than their 25 mm counterpart making them ideal for large-scale studies and sample replication. This method increases the options of reliable approaches available for quantifying VLP from environmental samples.</p

Dissipation from a heavy quark moving through N=4 super-Yang-Mills plasma

Using AdS/CFT, we compute the Fourier space profile of generated by a heavy quark moving through a thermal plasma of strongly coupled N=4 super-Yang-Mills theory. We find evidence of a wake whose description includes gauge fields with large momenta. We comment on the possible relevance of our results to relativistic heavy ion collisions.Comment: 17 pages, 2 figures. v2: reference added, other minor improvements. v3: improved the phrasing describing directional structure

4CeeD: Real-Time Data Acquisition and Analysis Framework for Material-related Cyber-Physical Environments

In this paper, we propose a data acquisition and analysis framework for materials-to-devices processes, named 4CeeD, that focuses on the immense potential of capturing, accurately curating, correlating, and coordinating materials-to-devices digital data in a real-time and trusted manner before fully archiving and publishing them for wide access and sharing. In particular, 4CeeD consists of: (i) a curation service for collecting data from experimental instruments, curating, and wrapping of data with extensive metadata in real-time and in a trusted manner, (ii) a cloudlet for caching collected data from curation service and coordinating data transfer with the back-end, and (iii) a cloud-based coordination service for storing data, extracting meta-data, analyzing and finding correlations among the data. Our evaluation results show that our proposed approach is able to help researchers significantly save time and cost spent on experiments, and is efficient in dealing with high-volume and fast-changing workload of heterogeneous types of experimental data.National Science Foundation/NSF ACI 1443013Ope

Extending African Knowledge Infrastructures: Sharing, Creating, Maintaining

World Bank, Knowledge for Development ProgramPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61201/1/Jackson et al, Extending African Knowledge Infrastructures (March 2008).pd

Implementing health research through academic and clinical partnerships : a realistic evaluation of the Collaborations for Leadership in Applied Health Research and Care (CLAHRC)

Background: The English National Health Service has made a major investment in nine partnerships between higher education institutions and local health services called Collaborations for Leadership in Applied Health Research and Care (CLAHRC). They have been funded to increase capacity and capability to produce and implement research through sustained interactions between academics and health services. CLAHRCs provide a natural ‘test bed’ for exploring questions about research implementation within a partnership model of delivery. This protocol describes an externally funded evaluation that focuses on implementation mechanisms and processes within three CLAHRCs. It seeks to uncover what works, for whom, how, and in what circumstances. Design and methods: This study is a longitudinal three-phase, multi-method realistic evaluation, which deliberately aims to explore the boundaries around knowledge use in context. The evaluation funder wishes to see it conducted for the process of learning, not for judging performance. The study is underpinned by a conceptual framework that combines the Promoting Action on Research Implementation in Health Services and Knowledge to Action frameworks to reflect the complexities of implementation. Three participating CLARHCS will provide indepth comparative case studies of research implementation using multiple data collection methods including interviews, observation, documents, and publicly available data to test and refine hypotheses over four rounds of data collection. We will test the wider applicability of emerging findings with a wider community using an interpretative forum. Discussion: The idea that collaboration between academics and services might lead to more applicable health research that is actually used in practice is theoretically and intuitively appealing; however the evidence for it is limited. Our evaluation is designed to capture the processes and impacts of collaborative approaches for implementing research, and therefore should contribute to the evidence base about an increasingly popular (e.g., Mode two, integrated knowledge transfer, interactive research), but poorly understood approach to knowledge translation. Additionally we hope to develop approaches for evaluating implementation processes and impacts particularly with respect to integrated stakeholder involvement

UNC-108/RAB-2 and its effector RIC-19 are involved in dense core vesicle maturation in Caenorhabditis elegans

Uncoordinated movement in Rab2 mutants is caused by impaired retention of cargo on dense core vesicles, not by defective synaptic vesicle release. (Also see the companion article by Edwards et al. in this issue.

Breakdown in the Smart City: Exploring Workarounds with Urban-sensing Practices and Technologies

Smart cities are now an established area of technological development and theoretical inquiry. Research on smart cities spans from investigations into its technological infrastructures and design scenarios, to critiques of its proposals for citizenship and sustainability. This article builds on this growing field, while at the same time accounting for expanded urban-sensing practices that take hold through citizen-sensing technologies. Detailing practice-based and participatory research that developed urban-sensing technologies for use in Southeast London, this article considers how the smart city as a large-scale and monolithic version of urban systems breaks down in practice to reveal much different concretizations of sensors, cities, and people. By working through the specific instances where sensor technologies required inventive workarounds to be setup and continue to operate, as well as moments of breakdown and maintenance where sensors required fixes or adjustments, this article argues that urban sensing can produce much different encounters with urban technologies through lived experiences. Rather than propose a “grassroots” approach to the smart city, however, this article instead suggests that the smart city as a figure for urban development be contested and even surpassed by attending to workarounds that account more fully for digital urban practices and technologies as they are formed and situated within urban projects and community initiatives

A meta-analysis of N-acetylcysteine in contrast-induced nephrotoxicity: unsupervised clustering to resolve heterogeneity

<p>Abstract</p> <p>Background</p> <p>Meta-analyses of N-acetylcysteine (NAC) for preventing contrast-induced nephrotoxicity (CIN) have led to disparate conclusions. Here we examine and attempt to resolve the heterogeneity evident among these trials.</p> <p>Methods</p> <p>Two reviewers independently extracted and graded the data. Limiting studies to randomized, controlled trials with adequate outcome data yielded 22 reports with 2746 patients.</p> <p>Results</p> <p>Significant heterogeneity was detected among these trials (<it>I</it>²= 37%; <it>p </it>= 0.04). Meta-regression analysis failed to identify significant sources of heterogeneity. A modified L'Abbé plot that substituted groupwise changes in serum creatinine for nephrotoxicity rates, followed by model-based, unsupervised clustering resolved trials into two distinct, significantly different (<it>p </it>< 0.0001) and homogeneous populations (<it>I</it>²= 0 and <it>p </it>> 0.5, for both). Cluster 1 studies (<it>n </it>= 18; 2445 patients) showed no benefit (relative risk (RR) = 0.87; 95% confidence interval (CI) 0.68–1.12, <it>p </it>= 0.28), while cluster 2 studies (<it>n </it>= 4; 301 patients) indicated that NAC was highly beneficial (RR = 0.15; 95% CI 0.07–0.33, <it>p </it>< 0.0001). Benefit in cluster 2 was unexpectedly associated with NAC-induced decreases in creatinine from baseline (<it>p </it>= 0.07). Cluster 2 studies were relatively early, small and of lower quality compared with cluster 1 studies (<it>p </it>= 0.01 for the three factors combined). Dialysis use across all studies (five control, eight treatment; <it>p </it>= 0.42) did not suggest that NAC is beneficial.</p> <p>Conclusion</p> <p>This meta-analysis does not support the efficacy of NAC to prevent CIN.</p