Local Installation Research Articles

544. Prepubic Approach for Urethral Recurrence After Radical Cystectomy - Novel Approach

Background: The incidence of urethral recurrence after radical cystoprostatectomy for bladder cancer varies from 4 to18%. Complete urethrectomy is the treatment of choice for urethral recurrence, having been shown to be superior to transurethral resection and local BCG installation. The perineal approach is the traditional method for excision of urethral recurrence after cystoprostatectomy. The aim of this work is to discuss the feasibility, implications and possible technical difficulties of applying the prepubic approach for excision of urethral recurrence.

Bi-objective optimization of a water network via benchmarking

This paper presents an approach to water system retrofitting by estimating both the economic and environmental impacts of a water network structure, using bi-objective optimization. The environmental impact is evaluated via benchmarking. By using benchmarking, the decision maker can have an insight, not only into the environmental impacts of certain designs belonging to Pareto optimal solutions, but also into the competitiveness of the design within a particular production sector. The economic criterion used is the total cost of the water network involving the freshwater cost, wastewater treatment cost, and the annual investment costs of storage tank, piping, and local treatment unit installation. A mixed-integer nonlinear programming (MINLP) model is used for water re-use and regeneration re-use within batch and semi-continuous processes. The Pareto fronts are generated using the classic and adaptive weighted-sum methods. The proposed approach was applied to an industrial case study within a brewery. The results obtained show that the benchmark could not be reached by process integration within the packaging area, therefore investment is needed regarding new technologies that lower freshwater consumption. Within the production area, however, the freshwater consumption could be reduced below the benchmark by water re-use and regeneration re-use, meaning that the brewery could achieve better performance than its competitors.

Management of osteomyelitis with topical negative pressure wound therapy with local installation of antibiotics

Management of osteomyelitis with topical negative pressure wound therapy with local installation of antibiotics

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts

Summary: SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats.Availability and implementation: SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie.Contact: mryan@insilico.us.comSupplementary Information: Supplementary data are available at Bioinformatics online.

Customizable web service interface for light scattering simulation programs

Investigation of light scattering by simulations became increasingly important in recent years. Applications range from plasmonics to optical particle characterization. While there are hundreds of programs available, using them can be very time consuming: installation, configuration and operation often are laborious. As a result potential users of such software might be discouraged by the complexity of the necessary tasks. Not only ‘casual users’ – scientists who need light scattering simulation results for their daily work but who are not specialized on the topic – could benefit from tools to execute the calculations online via an easy to use web-interface accessed by a browser. In this case no local installation of the software is necessary, a user friendly interface helps learning and understanding the use of programs, while calculations can be done from anywhere and any time as long as a user is connected to the internet.This paper describes a newly developed interface that can be used for these purposes. It is made freely available to everyone and can be adapted to a variety of existing light scattering programs.

Availability of Services in the Era of Cloud Computing

One of the most important areas for consumers is security, performance and availability when it comes to cloud computing. Availability refers to the uptime of a system, a network of systems, hardware and software that collectively provide a service during its usage. Traditionally the availability of these has been limited to local installations of hardware and software resources which businesses and consumers deployed and maintained. With the advent of cloud services there is a considerable shift of these resources into the cloud. While cloud computing presents some cost effective benefits for the consumers and businesses, it is also extremely important for the cloud service providers to offer environments that are highly scalable and high in availability. This will in many ways dictate the credibility of these cloud services. Regardless of the size of an organization prolonged downtime of the service might be disastrous to its business, customer loyalty and brand value. This paper discusses the state of availability of services in the cloud.

Problems and Solutions of Solar Energy Development and Utilization in Coral Reefs

To develop and take advantage of solar energy resources in coral reefs, the paper discussed the problems about local solar resources, typhoon, corrosion, geology, transportations and installation. The analysis indicates that the typhoon-prone, serious corrosion and bad geology will cause many difficulties to installation and use of solar power equipments. Authors believe that, installing and using small solar power equipment in coral reefs is feasible, but the suitable measure of anti-typhoon, anti-corrosion, transportation, installation and maintenance must be accepted, which needs a great deal of budget support.

DelPhi: a comprehensive suite for DelPhi software and associated resources

BackgroundAccurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.ResultsHere we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding investigation. Non-experienced researchers can download examples containing all necessary data to carry out DelPhi runs on a set of selected examples illustrating various DelPhi features and demonstrating DelPhi’s accuracy against analytical solutions.ConclusionsDelPhi suite offers not only the DelPhi executable and sources files, examples and parameter files, but also provides links to third party developed resources either utilizing DelPhi or providing plugins for DelPhi. In addition, the users and developers are offered a forum to share ideas, resolve issues, report bugs and seek help with respect to the DelPhi package. The resource is available free of charge for academic users from URL: http://compbio.clemson.edu/DelPhi.php.

MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis

First released in 2009, MetaboAnalyst (www.metaboanalyst.ca) was a relatively simple web server designed to facilitate metabolomic data processing and statistical analysis. With continuing advances in metabolomics along with constant user feedback, it became clear that a substantial upgrade to the original server was necessary. MetaboAnalyst 2.0, which is the successor to MetaboAnalyst, represents just such an upgrade. MetaboAnalyst 2.0 now contains dozens of new features and functions including new procedures for data filtering, data editing and data normalization. It also supports multi-group data analysis, two-factor analysis as well as time-series data analysis. These new functions have also been supplemented with: (i) a quality-control module that allows users to evaluate their data quality before conducting any analysis, (ii) a functional enrichment analysis module that allows users to identify biologically meaningful patterns using metabolite set enrichment analysis and (iii) a metabolic pathway analysis module that allows users to perform pathway analysis and visualization for 15 different model organisms. In developing MetaboAnalyst 2.0 we have also substantially improved its graphical presentation tools. All images are now generated using anti-aliasing and are available over a range of resolutions, sizes and formats (PNG, TIFF, PDF, PostScript, or SVG). To improve its performance, MetaboAnalyst 2.0 is now hosted on a much more powerful server with substantially modified code to take advantage the server’s multi-core CPUs for computationally intensive tasks. MetaboAnalyst 2.0 also maintains a collection of 50 or more FAQs and more than a dozen tutorials compiled from user queries and requests. A downloadable version of MetaboAnalyst 2.0, along detailed instructions for local installation is now available as well.

Allergen specific IgG augments Th2 mediated inflammation in the lungs through FcγRIII signaling and upregulation of IL-33 (125.1)

Abstract Asthma is a chronic inflammatory disease of the lungs marked by mast cell activation, eosinophilia, and airway remodeling. It has been seen that primary sensitization to inhaled allergens leads to increased production of allergen specific IgE and IgG1. Several studies have shown a critical role for IgE in allergic lung disease, but it is unclear how IgG1 might contribute to the initiation and perpetuation of this disease. Previous work in our lab identified a key role for FcγRIII on dendritic cells (DC) in the development of optimal Th2-dependent airway inflammation. As FcγRIII is efficiently engaged by IgG1-immune complexes, we hypothesized that sensitized individuals could form allergen-specific immune complexes upon secondary exposure which could contribute to the augmented Th2 responses found in allergic asthma. We used two different models of immune complex mediated Th2 inflammation through either immune complex formation in vivo or local installation of preformed immune complexes. Both models showed that this process was mediated through FcγRIII. Utilizing both in vitro and in vivo approaches, we then identified IL-33 as a gene downstream of FcγRIII signaling on DCs. Notably, immune complex mediated Th2 inflammation in the lungs was decreased in ST2-/- mice with a specific loss of eosinophilia suggesting a critical role for IL-33. Our findings that previous sensitization can direct the response of DCs could provide a new paradigm for the development of Th2 inflammation.

Local installation methods for low head pico-hydropower in the Lao PDR

Low head pico-hydropower is commonly used in the remote mountainous provinces of the Lao PDR due to the widespread lack of access to grid electricity, favourable hydropower conditions and availability of cheap pico-hydro turbines. Manufacturers of pico-hydro turbines tend to recommend a standing method of installation using a pre-fabricated draft channel and draft tube. This method is the most efficient and delivers the most consistent power to the turbine shaft, but is only practical given the right topography at the installation site. Throughout the Lao PDR, local adaptations have arisen in installation methods at sites where the recommended installation method is impractical. This paper examines the main types of installation methods and local adaptations that were observed during field surveys in the rural parts of the Lao PDR. The requirements, performance and merits of each type of installation are then evaluated.

Computation of Turbulent Flows in Natural Gas Pipes with Different Rectifiers

With the development of natural gas industry, improving the accuracy of the flowmeter systems is becoming the common concerned problem both corporations and customers. Many experiments demonstrate that the different flow field structures in pipes with diverse baffle installations have great influence on the measure accuracy of flowmeters. In order to measure the flux in pipes more accurate, the flowmeters must be installed downstream the baffles far away so that the irregular flows induced by baffles have less influence on the flowmeters. However, the installation lengths downstream baffles for flowmeters in ISO are are usually much longer than the allowable lengths for the local flowmeters. To decrease the installation lengths and loss measure accuracy of flowmeters as little as possible, it is necessary to study the flows in pipes with baffles. CFD is a good tool for the study. Here, the flows in a diffusive pipe with various rectifiers are computed as examples. The lengths of the irregular flows induced by the diffuser and rectifier are shown. By analyzing and comparison the numerical results, the installation lengths for flowmeters and the rectification of the different rectifiers are confirmed. The study conclusions will be very useful for guiding the local flowmeter selection and installation in the future.

GSV: a web-based genome synteny viewer for customized data.

BackgroundThe analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis.ResultsWe have developed the web-based Genome Synteny Viewer (GSV) that allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation.ConclusionsGSV provides a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. A web server hosting GSV is provided at http://cas-bioinfo.cas.unt.edu/gsv, and the software is also freely available for local installations.

The Application of Wind and Solar Power Generation System in the Ocean Marginal Oil Field Development

Facing the growing energy needs, ocean marginal fields more and more attention. But the supply is one of the constraints of ocean marginal oil field development. Therefore research and development in power supply system of local installation, low cost, easy maintenance and management, resource conservation, environmental-friendly is critical. This paper investigates the application of wind and solar energy development, as against the existing marginal oil field development project, through designing wind and solar power generation system to discuss the development of marginal oil fields in the feasibility of the application to make constructive comments.

Conserved Interaction between Transferrin and Transferrin-binding Proteins from Porcine Pathogens

Gram-negative porcine pathogens from the Pasteurellaceae family possess a surface receptor complex capable of acquiring iron from porcine transferrin (pTf). This receptor consists of transferrin-binding protein A (TbpA), a transmembrane iron transporter, and TbpB, a surface-exposed lipoprotein. Questions remain as to how the receptor complex engages pTf in such a way that iron is positioned for release, and whether divergent strains present distinct recognition sites on Tf. In this study, the TbpB-pTf interface was mapped using a combination of mass shift analysis and molecular docking simulations, localizing binding uniquely to the pTf C lobe for multiple divergent strains of Actinobacillus plueropneumoniae and suis. The interface was further characterized and validated with site-directed mutagenesis. Although targeting a common lobe, variants differ in preference for the two sublobes comprising the iron coordination site. Sublobes C1 and C2 participate in high affinity binding, but sublobe C1 contributes in a minor fashion to the overall affinity. Further, the TbpB-pTf complex does not release iron independent of other mediators, based on competitive iron binding studies. Together, our findings support a model whereby TbpB efficiently captures and presents iron-loaded pTf to other elements of the uptake pathway, even under low iron conditions.

Online design of Matlab/Simulink block schemes

The paper presents a new online tool that enables to build a Matlab/Simulink block scheme in the Internet environment. The block scheme can be designed in similar manner as it is offered by local installation of Simulink. The application was created by widely used technologies as XHTML, CSS, JavaScript, PHP together with AJAX approach. The created application can be used as a supporting tool in virtual and remote laboratories.

Rapid membrane protein topology prediction

Summary: State-of-the-art methods for topology of α-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we examine if it is possible to use the consensus of topology prediction methods that are based on single sequences to obtain a similar accuracy as the more accurate multiple sequence-based methods. Here, we show that TOPCONS-single performs better than any of the other topology prediction methods tested here, but ∼6% worse than the best method that is utilizing multiple sequence alignments.Availability and Implementation: TOPCONS-single is available as a web server from http://single.topcons.net/ and is also included for local installation from the web site. In addition, consensus-based topology predictions for the entire international protein index (IPI) is available from the web server and will be updated at regular intervals.Contact: arne@bioinfo.seSupplementary information: Supplementary data are avaliable at Bioinformatics online.

Cost-effectiveness of energy efficiency programmes—evaluating the impacts of a regional programme in France

This paper presents the evaluation of a regional energy efficiency programme implemented in two “departements” of France. Electricite de France (EDF), a French energy company, provides refurbishment advice and financial incentives to end-users in the residential sector as well as specific training courses and certification to local installation contractors and building firms. Refurbishment measures analysed in this paper are efficient space heating equipment (condensing boilers, heat pumps and wood stoves or boilers), solar water heating systems and the installation of double-glazed windows. A billing analysis based on a survey of programme participants’ energy consumption is used to calculate the energy savings attributed to the programme. In order to receive an economic feedback of this demonstration programme, the evaluation of both saved energy and programme costs is of importance. Detailed knowledge of the programme’s cost-effectiveness is essential for EDF to achieve the saving obligations imposed by the French White Certificate scheme at the lowest cost. Results of this evaluation can support the development and implementation of further energy efficiency programmes with similar characteristics in other regions of France. The cost-effectiveness is determined from the perspective of the programme participant and the society as well as the energy company in charge of the programme. All cost and benefit components are calculated in Euro per kilowatt-hour, which allows a direct comparison of levelized costs of conserved energy with the avoidable costs of the energy supply system.

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

The Few, The Proud: The Challenge to Upgrade Infrastructure on Active Military Installations and How One Utility Overcame

Replace, rehabilitate, or simply eliminate? Utilities often struggle to determine the best approach to upgrade existing infrastructure. The approach becomes more complex when the existing infrastructure is located on fully operating Military installations adjacent to wetlands and water bodies. This paper provides an overview of the approach used to improve wastewater assets acquired by the Beaufort-Jasper Water & Sewer Authority (BJWSA) on two local Military installations. Additionally, the paper will provide an overview of why and how the BJWSA acquired aging infrastructure on the Military bases, and the effects the Military's constraints had on selecting the best approaches. As part of a federal utility privatization initiative, the BJWSA competed for and acquired water and wastewater systems located on four Military installations. Consequently, the BJWSA completed an Initial System Modification (ISM) assessment defining projects to be funded by the Utility Privatization (UP) Contract so that the assets are brought up to an acceptable condition. Since being awarded the UP Contract, the BJWSA has implemented a design and construction program for a number of ISM projects that includes strict adherence to each Military installation's security, safety, environmental, and cultural resources protection requirements. Jacobs Engineering Group, Inc. performed pipe rehabilitation services about of 40,000 linear feet (LF) of sewer at the Marine Corps Recruiting Depot at Parris Island (MCRD-PI) and 3,000 LF of sewer at the Naval Hospital. Services included sewer cleaning, smoke testing, CCTV inspection and defect identification, manhole inspection and evaluation. A computerized assessment program was implemented to help manage the data. The sewers at the Naval Hospital have been re-lined using cured-in-place pipe (CIPP) and the sewers at MCRD-PI are slated to be rehabilitated using multiple methods, including CIPP and pipe bursting, beginning in spring, 2011. However, the sewer rehabilitation project represents just one part of an overall ISM program that is anticipated to cost about $14 million and be completed by late 2011. A key point of this paper is that the BJWSA's acquisition of the MCRD-PI Military installation not only improved aging wastewater assets on the bases, but did so without disruption to the day-to-day operations