Filtering and scalability in the ECO distributed event model

Event-based communication is useful in many application domains, ranging from small, centralised applications to large, distributed systems. Many different event models have been developed to address the requirements of different application domains. One such model is the ECO model which was designed to support distributed virtual world applications. Like many other event models, ECO has event filtering capabilities meant to improve scalability by decreasing network traffic in a distributed implementation. Our recent work in event-based systems has included building a fully distributed version of the ECO model, including event filtering capabilities. This paper describes the results of our evaluation of filters as a means of achieving increased scalability in the ECO model. The evaluation is empirical and real data gathered from an actual event-based system is used

African freshwater fisheries: what needs to be managed?

The management of African freshwater fisheries in Southern African Development Coordination (SADC) countries is discussed. Changes in catch and fishing effort in the SADC freshwater fisheries in the past 50 years, the main causes behind the patterns of change in fishing effort, the effects of fishing effort and environment on the regeneration of fish stocks, as well as existing and proposed fisheries management regulations are investigated

Partitioning of trace elements in a entrained flow IGCC plant: Influence of selected operational conditions

The partitioning of trace elements and the influence of the feed conditions (50:50 coal/pet-coke feed blend and limestone addition) was investigated in this study. To this end feed fuel, fly ash and slag samples were collected under different operational conditions at the 335 MW Puertollano IGCC power plant (Spain) and subsequently analysed. The partitioning of elements in this IGCC plant may be summarised as follows: (a) high volatile elements (70–>99% in gas phase): Hg, Br, I, Cl and S; (b) moderately volatile elements (up to 40% in gas phase and 60% in fly ash): As, Sb, Se, B, F, Cd, Tl, Zn and Sn; (c) elements with high condensation potential: (>90% in fly ash): Pb, Ge, Ga and Bi; (d) elements enriched similarly in fly ash and slag 30–60% in fly ash: Cu, W, (P), Mo, Ni and Na; and (e) low volatile elements (>70% in slag): Cs, Rb, Co, K, Cr, V, Nb, Be, Hf, Ta, Fe, U, Ti, Al, Si, Y, Sr, Th, Zr, Mg, Ba, Mn, REEs, Ca and Li. The volatility of As, Sb, and Tl and the slagging of S, B, Cl, Cd and low volatile elements are highly influenced by the fuel geochemistry and limestone dosages, respectively

Subcellular distribution of nuclear import-defective isoforms of the promyelocytic leukemia protein

<p>Abstract</p> <p>Background</p> <p>The promyelocytic leukemia (PML) protein participates in a number of cellular processes, including transcription regulation, apoptosis, differentiation, virus defense and genome maintenance. This protein is structurally organized into a tripartite motif (TRIM) at its N-terminus, a nuclear localization signal (NLS) at its central region and a C-terminus that varies between alternatively spliced isoforms. Most PML splice variants target the nucleus where they define sub-nuclear compartments termed PML nuclear bodies (PML NBs). However, PML variants that lack the NLS are also expressed, suggesting the existence of PML isoforms with cytoplasmic functions. In the present study we expressed PML isoforms with a mutated NLS in U2OS cells to identify potential cytoplasmic compartments targeted by this protein.</p> <p>Results</p> <p>Expression of NLS mutated PML isoforms in U2OS cells revealed that PML I targets early endosomes, PML II targets the inner nuclear membrane (partially due to an extra NLS at its C-terminus), and PML III, IV and V target late endosomes/lysosomes. Clustering of PML at all of these subcellular locations depended on a functional TRIM domain.</p> <p>Conclusions</p> <p>This study demonstrates the capacity of PML to form macromolecular protein assemblies at several different subcellular sites. Further, it emphasizes a role of the variable C-terminus in subcellular target selection and a general role of the N-terminal TRIM domain in promoting protein clustering.</p

What Google Maps can do for biomedical data dissemination: examples and a design study

BACKGROUND: Biologists often need to assess whether unfamiliar datasets warrant the time investment required for more detailed exploration. Basing such assessments on brief descriptions provided by data publishers is unwieldy for large datasets that contain insights dependent on specific scientific questions. Alternatively, using complex software systems for a preliminary analysis may be deemed as too time consuming in itself, especially for unfamiliar data types and formats. This may lead to wasted analysis time and discarding of potentially useful data. RESULTS: We present an exploration of design opportunities that the Google Maps interface offers to biomedical data visualization. In particular, we focus on synergies between visualization techniques and Google Maps that facilitate the development of biological visualizations which have both low-overhead and sufficient expressivity to support the exploration of data at multiple scales. The methods we explore rely on displaying pre-rendered visualizations of biological data in browsers, with sparse yet powerful interactions, by using the Google Maps API. We structure our discussion around five visualizations: a gene co-regulation visualization, a heatmap viewer, a genome browser, a protein interaction network, and a planar visualization of white matter in the brain. Feedback from collaborative work with domain experts suggests that our Google Maps visualizations offer multiple, scale-dependent perspectives and can be particularly helpful for unfamiliar datasets due to their accessibility. We also find that users, particularly those less experienced with computer use, are attracted by the familiarity of the Google Maps API. Our five implementations introduce design elements that can benefit visualization developers. CONCLUSIONS: We describe a low-overhead approach that lets biologists access readily analyzed views of unfamiliar scientific datasets. We rely on pre-computed visualizations prepared by data experts, accompanied by sparse and intuitive interactions, and distributed via the familiar Google Maps framework. Our contributions are an evaluation demonstrating the validity and opportunities of this approach, a set of design guidelines benefiting those wanting to create such visualizations, and five concrete example visualizations

Computational shelf-life dating : complex systems approaches to food quality and safety

Shelf-life is defined as the time that a product is acceptable and meets the consumers expectations regarding food quality. It is the result of the conjunction of all services in production, distribution, and consumption. Shelf-life dating is one of the most difficult tasks in food engineering. Market pressure has lead to the implementation of shelf-life by sensory analyses, which may not reflect the full quality spectra. Moreover, traditional methods for shelf-life dating and small-scale distribution chain tests cannot reproduce in a laboratory the real conditions of storage, distribution, and consumption on food quality. Today, food engineers are facing the challenges to monitor, diagnose, and control the quality and safety of food products. The advent of nanotechnology, multivariate sensors, information systems, and complex systems will revolutionize the way we manage, distribute, and consume foods. The informed consumer demands foods, under the legal standards, at low cost, high standards of nutritional, sensory, and health benefits. To accommodate the new paradigms, we herein present a critical review of shelf-life dating approaches with special emphasis in computational systems and future trends on complex systems methodologies applied to the prediction of food quality and safety.Fundo Europeu de Desenvolvimento Regional (FEDER) - Programa POS-ConhecimentoFundação para a Ciência e a Tecnologia (FCT) - SFRH/BPD/26133/2005, SFRH/ BPD/20735/200

Functional Connection between Rad51 and PML in Homology-Directed Repair

The promyelocytic leukemia protein (PML) is a tumor suppressor critical for formation of nuclear bodies (NBs) performing important functions in transcription, apoptosis, DNA repair and antiviral responses. Earlier studies demonstrated that simian virus 40 (SV40) initiates replication near PML NBs. Here we show that PML knockdown inhibits viral replication in vivo, thus indicating a positive role of PML early in infection. SV40 large T antigen (LT) induces DNA damage and, consequently, nuclear foci of the key homologous recombination repair protein Rad51 that colocalize with PML. PML depletion abrogates LT-induced Rad51 foci. LT may target PML NBs to gain access to DNA repair factors like Rad51 that are required for viral replication. We have used the SV40 model to gain insight to DNA repair events involving PML. Strikingly, even in normal cells devoid of viral oncoproteins, PML is found to be instrumental for foci of Rad51, Mre11 and BRCA1, as well as homology-directed repair after double-strand break (DSB) induction. Following LT expression or external DNA damage, PML associates with Rad51. PML depletion also causes a loss of RPA foci following γ-irradiation, suggesting that PML is required for processing of DSBs. Immunofluorescent detection of incorporated BrdU without prior denaturation indicates a failure to generate ssDNA foci in PML knockdown cells upon γ-irradiation. Consistent with the lack of RPA and BrdU foci, γ-irradiation fails to induce Chk1 activation, when PML is depleted. Taken together, we have discovered a novel functional connection between PML and the homologous recombination-mediated repair machinery, which might contribute to PML tumor suppressor activity

Nuclear Pore Complex Protein Mediated Nuclear Localization of Dicer Protein in Human Cells

Human DICER1 protein cleaves double-stranded RNA into small sizes, a crucial step in production of single-stranded RNAs which are mediating factors of cytoplasmic RNA interference. Here, we clearly demonstrate that human DICER1 protein localizes not only to the cytoplasm but also to the nucleoplasm. We also find that human DICER1 protein associates with the NUP153 protein, one component of the nuclear pore complex. This association is detected predominantly in the cytoplasm but is also clearly distinguishable at the nuclear periphery. Additional characterization of the NUP153-DICER1 association suggests NUP153 plays a crucial role in the nuclear localization of the DICER1 protein

Replication, Gene Expression and Particle Production by a Consensus Merkel Cell Polyomavirus (MCPyV) Genome

Merkel Cell Polyomavirus (MCPyV) genomes are clonally integrated in tumor tissues of approximately 85% of all Merkel cell carcinoma (MCC) cases, a highly aggressive tumor of the skin which predominantly afflicts elderly and immunosuppressed patients. All integrated viral genomes recovered from MCC tissue or MCC cell lines harbor signature mutations in the early gene transcript encoding for the large T-Antigen (LT-Ag). These mutations selectively abrogate the ability of LT-Ag to support viral replication while still maintaining its Rb-binding activity, suggesting a continuous requirement for LT-Ag mediated cell cycle deregulation during MCC pathogenesis. To gain a better understanding of MCPyV biology, in vitro MCPyV replication systems are required. We have generated a synthetic MCPyV genomic clone (MCVSyn) based on the consensus sequence of MCC-derived sequences deposited in the NCBI database. Here, we demonstrate that transfection of recircularized MCVSyn DNA into some human cell lines recapitulates efficient replication of the viral genome, early and late gene expression together with virus particle formation. However, serial transmission of infectious virus was not observed. This in vitro culturing system allows the study of viral replication and will facilitate the molecular dissection of important aspects of the MCPyV lifecycle