WorldWideScience

Sample records for integrated biomedical platform

  1. Wafer-scale integrated micro-supercapacitors on an ultrathin and highly flexible biomedical platform.

    Science.gov (United States)

    Maeng, Jimin; Meng, Chuizhou; Irazoqui, Pedro P

    2015-02-01

    We present wafer-scale integrated micro-supercapacitors on an ultrathin and highly flexible parylene platform, as progress toward sustainably powering biomedical microsystems suitable for implantable and wearable applications. All-solid-state, low-profile (supercapacitors are formed on an ultrathin (~20 μm) freestanding parylene film by a wafer-scale parylene packaging process in combination with a polyaniline (PANI) nanowire growth technique assisted by surface plasma treatment. These micro-supercapacitors are highly flexible and shown to be resilient toward flexural stress. Further, direct integration of micro-supercapacitors into a radio frequency (RF) rectifying circuit is achieved on a single parylene platform, yielding a complete RF energy harvesting microsystem. The system discharging rate is shown to improve by ~17 times in the presence of the integrated micro-supercapacitors. This result suggests that the integrated micro-supercapacitor technology described herein is a promising strategy for sustainably powering biomedical microsystems dedicated to implantable and wearable applications.

  2. An integrated biomedical knowledge extraction and analysis platform: using federated search and document clustering technology.

    Science.gov (United States)

    Taylor, Donald P

    2007-01-01

    High content screening (HCS) requires time-consuming and often complex iterative information retrieval and assessment approaches to optimally conduct drug discovery programs and biomedical research. Pre- and post-HCS experimentation both require the retrieval of information from public as well as proprietary literature in addition to structured information assets such as compound libraries and projects databases. Unfortunately, this information is typically scattered across a plethora of proprietary bioinformatics tools and databases and public domain sources. Consequently, single search requests must be presented to each information repository, forcing the results to be manually integrated for a meaningful result set. Furthermore, these bioinformatics tools and data repositories are becoming increasingly complex to use; typically they fail to allow for more natural query interfaces. Vivisimo has developed an enterprise software platform to bridge disparate silos of information. The platform automatically categorizes search results into descriptive folders without the use of taxonomies to drive the categorization. A new approach to information retrieval for HCS experimentation is proposed.

  3. Requirements for data integration platforms in biomedical research networks: a reference model.

    Science.gov (United States)

    Ganzinger, Matthias; Knaup, Petra

    2015-01-01

    Biomedical research networks need to integrate research data among their members and with external partners. To support such data sharing activities, an adequate information technology infrastructure is necessary. To facilitate the establishment of such an infrastructure, we developed a reference model for the requirements. The reference model consists of five reference goals and 15 reference requirements. Using the Unified Modeling Language, the goals and requirements are set into relation to each other. In addition, all goals and requirements are described textually in tables. This reference model can be used by research networks as a basis for a resource efficient acquisition of their project specific requirements. Furthermore, a concrete instance of the reference model is described for a research network on liver cancer. The reference model is transferred into a requirements model of the specific network. Based on this concrete requirements model, a service-oriented information technology architecture is derived and also described in this paper.

  4. Magnetic microfluidic platform for biomedical applications using magnetic nanoparticles

    KAUST Repository

    Stipsitz, Martin

    2015-05-01

    Microfluidic platforms are well-suited for biomedical analysis and usually consist of a set of units which guarantee the manipulation, detection and recognition of bioanalyte in a reliable and flexible manner. Additionally, the use of magnetic fields for perfoming the aforementioned tasks has been steadily gainining interest. This is due to the fact that magnetic fields can be well tuned and applied either externally or from a directly integrated solution in the diagnostic system. In combination with these applied magnetic fields, magnetic nanoparticles are used. In this paper, we present some of our most recent results in research towards a) microfluidic diagnostics using MR sensors and magnetic particles and b) single cell analysis using magnetic particles. We have successfully manipulated magnetically labeled bacteria and measured their response with integrated GMR sensors and we have also managed to separate magnetically labeled jurkat cells for single cell analysis. © 2015 Trans Tech Publications, Switzerland.

  5. Magnetic microfluidic platform for biomedical applications using magnetic nanoparticles

    KAUST Repository

    Stipsitz, Martin; Kokkinis, Georgios; Gooneratne, Chinthaka Pasan; Kosel, Jü rgen; Cardoso, Susana; Cardoso, Filipe; Giouroudi, Ioanna

    2015-01-01

    Microfluidic platforms are well-suited for biomedical analysis and usually consist of a set of units which guarantee the manipulation, detection and recognition of bioanalyte in a reliable and flexible manner. Additionally, the use of magnetic fields for perfoming the aforementioned tasks has been steadily gainining interest. This is due to the fact that magnetic fields can be well tuned and applied either externally or from a directly integrated solution in the diagnostic system. In combination with these applied magnetic fields, magnetic nanoparticles are used. In this paper, we present some of our most recent results in research towards a) microfluidic diagnostics using MR sensors and magnetic particles and b) single cell analysis using magnetic particles. We have successfully manipulated magnetically labeled bacteria and measured their response with integrated GMR sensors and we have also managed to separate magnetically labeled jurkat cells for single cell analysis. © 2015 Trans Tech Publications, Switzerland.

  6. Biomedical sensor technologies on the platform of mobile phones

    Science.gov (United States)

    Liu, Lin; Liu, Jing

    2011-06-01

    Biomedical sensors have been widely used in various areas of biomedical practices, which play an important role in disease detection, diagnosis, monitoring, treatment, health management, and so on. However, most of them and their related platforms are generally not easily accessible or just too expensive or complicated to be kept at home. As an alternative, new technologies enabled from the mobile phones are gradually changing such situations. As can be freely available to almost everyone, mobile phone offers a unique way to improve the conventional medical care through combining with various biomedical sensors. Moreover, the established systems will be both convenient and low cost. In this paper, we present an overview on the state-of-art biomedical sensors, giving a brief introduction of the fundamental principles and showing several new examples or concepts in the area. The focus was particularly put on interpreting the technical strategies to innovate the biomedical sensor technologies based on the platform of mobile phones. Some challenging issues, including feasibility, usability, security, and effectiveness, were discussed. With the help of electrical and mechanical technologies, it is expected that a full combination between the biomedical sensors and mobile phones will bring a bright future for the coming pervasive medical care.

  7. Designing Polymeric Microfluidic Platforms for Biomedical Applications

    DEFF Research Database (Denmark)

    Vedarethinam, Indumathi

    Micro- and Nanotechnology have the potential to offer a smart solution for diagnostics and academia research with rapid, low cost, robust analysis systems to facilitate biological analyses. New, high throughput microfluidic platforms have the potential to surpass in performance the conventional...... analyses systems in use today. The overall goal of this PhD project is to address two different areas using microfluidics : i) Chromosome analysis by metaphase FISH such a platform, if successful, can immediately substitute the routine, labor-intensive, glass slide-based FISH analyses in Clinical...... Cytogenetics laboratories. During the course of this project, initially the suitability of the polymeric chip substrate was tested and a microfluidic device was developed for performing interphase FISH analysis. With this device, the key factors involved in chromosome spreading crucial to FISH analysis were...

  8. Spintronic microfluidic platform for biomedical and environmental applications

    Science.gov (United States)

    Cardoso, F. A.; Martins, V. C.; Fonseca, L. P.; Germano, J.; Sousa, L. A.; Piedade, M. S.; Freitas, P. P.

    2010-09-01

    Faster, more sensitive and easy to operate biosensing devices still are a need at important areas such as biomedical diagnostics, food control and environmental monitoring. Recently, spintronic-devices have emerged as a promising alternative to the existent technologies [1-3]. A number of advantages, namely high sensitivity, easy integration, miniaturization, scalability, robustness and low cost make these devices potentially capable of responding to the existent technological need. In parallel, the field of microfluidics has shown great advances [4]. Microfluidic systems allow the analysis of small sample volumes (from micro- down to pico-liters), often by automate sample processing with the ability to integrate several steps into a single device (analyte amplification, concentration, separation and/or labeling), all in a reduced assay time (minutes to hours) and affordable cost. The merging of these two technologies, magnetoresistive biochips and microfluidics, will enable the development of highly competitive devices. This work reports the integration of a magnetoresistive biochip with a microfluidic system inside a portable and autonomous electronic platform aiming for a fully integrated device. A microfluidic structure fabricated in polydimethylsiloxane with dimensions of W: 0.5mm, H: 0.1mm, L: 10mm, associated to a mechanical system to align and seal the channel by pressure is presented (Fig. 1) [5]. The goal is to perform sample loading and transportation over the chip and simultaneously control the stringency and uniformity of the wash-out process. The biochip output is acquired by an electronic microsystem incorporating the circuitry to control, address and read-out the 30 spin-valve sensors sequentially (Fig. 1) [2]. This platform is being applied to the detection of water-borne microbial pathogens (e.g. Salmonella and Escherichia coli) and genetic diseases diagnosis (e.g. cystic fibrosis) through DNA hybridization assays. Open chamber measurements were

  9. Integrated Biomaterials for Biomedical Technology

    CERN Document Server

    Ramalingam, Murugan; Ramakrishna, Seeram; Kobayashi, Hisatoshi

    2012-01-01

    This cutting edge book provides all the important aspects dealing with the basic science involved in materials in biomedical technology, especially structure and properties, techniques and technological innovations in material processing and characterizations, as well as the applications. The volume consists of 12 chapters written by acknowledged experts of the biomaterials field and covers a wide range of topics and applications.

  10. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  11. sCLIP-an integrated platform to study RNA-protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs.

    Science.gov (United States)

    Kargapolova, Yulia; Levin, Michal; Lackner, Karl; Danckwardt, Sven

    2017-06-02

    RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing. sCLIP exploits linear amplification of the immunoprecipitated RNA improving the complexity of the sequencing-library despite significantly reducing the amount of input material and omitting several purification steps. Additionally, it permits a radiolabel-free visualization of immunoprecipitated RNA. In a proof of concept, we identify that CSTF2tau binds many previously not recognized RNAs including histone, snoRNA and snRNAs. CSTF2tau-binding is associated with internal oligoadenylation resulting in shortened snRNA isoforms subjected to rapid degradation. We provide evidence for a new mechanism whereby CSTF2tau controls the abundance of snRNAs resulting in alternative splicing of several RNAs including ANK2 with critical roles in tumorigenesis and cardiac function. Combined with a bioinformatic pipeline sCLIP thus uncovers new functions for established RBPs and fosters the illumination of RBP-protein interaction landscapes in health and disease. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Integrating biomedical and herbal medicine in Ghana

    DEFF Research Database (Denmark)

    Boateng, Millicent Addai; Danso-Appiah, Anthony; Turkson, Bernard Kofi

    2016-01-01

    Background: Over the past decade there has been growing interest in the use of herbal medicine both in developed and developing countries. Given the high proportion of patients using herbal medicine in Ghana, some health facilities have initiated implementation of herbal medicine as a component...... of their healthcare delivery. However, the extent to which herbal medicine has been integrated in Ghanaian health facilities, how integration is implemented and perceived by different stakeholders has not been documented. The study sought to explore these critical issues at the Kumasi South Hospital (KSH) and outline...... the definition, process and goals of integration were lacking, with respondents sharing different views about the purpose and value of integration of herbal medicine within public health facilities. Key informants were supportive of the initiative. Whilst biomedical health workers perceived the system...

  13. KaBOB: ontology-based semantic integration of biomedical databases.

    Science.gov (United States)

    Livingston, Kevin M; Bada, Michael; Baumgartner, William A; Hunter, Lawrence E

    2015-04-23

    The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources. We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license. KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for

  14. Quantum photonics hybrid integration platform

    Energy Technology Data Exchange (ETDEWEB)

    Murray, E.; Floether, F. F. [Cambridge Research Laboratory, Toshiba Research Europe Limited, 208 Science Park, Milton Road, Cambridge CB4 0GZ (United Kingdom); Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Ellis, D. J. P.; Meany, T.; Bennett, A. J., E-mail: anthony.bennet@crl.toshiba.co.uk; Shields, A. J. [Cambridge Research Laboratory, Toshiba Research Europe Limited, 208 Science Park, Milton Road, Cambridge CB4 0GZ (United Kingdom); Lee, J. P. [Cambridge Research Laboratory, Toshiba Research Europe Limited, 208 Science Park, Milton Road, Cambridge CB4 0GZ (United Kingdom); Engineering Department, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA (United Kingdom); Griffiths, J. P.; Jones, G. A. C.; Farrer, I.; Ritchie, D. A. [Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom)

    2015-10-26

    Fundamental to integrated photonic quantum computing is an on-chip method for routing and modulating quantum light emission. We demonstrate a hybrid integration platform consisting of arbitrarily designed waveguide circuits and single-photon sources. InAs quantum dots (QD) embedded in GaAs are bonded to a SiON waveguide chip such that the QD emission is coupled to the waveguide mode. The waveguides are SiON core embedded in a SiO{sub 2} cladding. A tuneable Mach Zehnder interferometer (MZI) modulates the emission between two output ports and can act as a path-encoded qubit preparation device. The single-photon nature of the emission was verified using the on-chip MZI as a beamsplitter in a Hanbury Brown and Twiss measurement.

  15. Observation Platform for Dynamic Biomedical and Biotechnology Experiments using the ISS Light Microscopy Module, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed "Observation platform for dynamic biomedical and biotechnology experiments using the ISS Light Microscopy Module" consists of a platen sized to fit the...

  16. Biomedical engineering: A platform for research and innovation in ultrasound

    Science.gov (United States)

    Holland, Christy K.

    2004-05-01

    An undergraduate or graduate degree in biomedical engineering prepares students to solve problems at the interface between engineering and medicine. Biomedical engineering encompasses evolving areas such as advanced medical imaging for diagnosis and treatment of disease, tissue engineering for designing and manufacturing biological implants for damaged or diseased tissues and organs, and bioinformatics for determining which genes play a major role in health and disease. Biomedical engineering academic programs produce graduates with the ability to pursue successful careers in the biomedical device industry or to obtain advanced degrees leading to careers in biomedical engineering research, medicine, law or business. Biomedical engineering majors take courses in biology, anatomy, physics, chemistry, engineering, mathematics and medical product design and value life-long learning. Students learn to work effectively in interdisciplinary teams comprised of individuals with diverse social, cultural and technical backgrounds. Biomedical engineering is becoming increasingly important in imaging and image-guided research. Some examples of innovative ultrasound technology under development are ultrasound devices to accelerate the dissolution of blood clots, advanced surgical instruments with ultrasound guidance and ultrasound contrast agents for targeted drug delivery. Biomedical engineering is a great career choice for technically minded individuals who endeavor to work on applied problems that are medically relevant.

  17. Design of e-Science platform for biomedical imaging research cross multiple academic institutions and hospitals

    Science.gov (United States)

    Zhang, Jianguo; Zhang, Kai; Yang, Yuanyuan; Ling, Tonghui; Wang, Tusheng; Wang, Mingqing; Hu, Haibo; Xu, Xuemin

    2012-02-01

    More and more image informatics researchers and engineers are considering to re-construct imaging and informatics infrastructure or to build new framework to enable multiple disciplines of medical researchers, clinical physicians and biomedical engineers working together in a secured, efficient, and transparent cooperative environment. In this presentation, we show an outline and our preliminary design work of building an e-Science platform for biomedical imaging and informatics research and application in Shanghai. We will present our consideration and strategy on designing this platform, and preliminary results. We also will discuss some challenges and solutions in building this platform.

  18. e-Science platform for translational biomedical imaging research: running, statistics, and analysis

    Science.gov (United States)

    Wang, Tusheng; Yang, Yuanyuan; Zhang, Kai; Wang, Mingqing; Zhao, Jun; Xu, Lisa; Zhang, Jianguo

    2015-03-01

    In order to enable multiple disciplines of medical researchers, clinical physicians and biomedical engineers working together in a secured, efficient, and transparent cooperative environment, we had designed an e-Science platform for biomedical imaging research and application cross multiple academic institutions and hospitals in Shanghai and presented this work in SPIE Medical Imaging conference held in San Diego in 2012. In past the two-years, we implemented a biomedical image chain including communication, storage, cooperation and computing based on this e-Science platform. In this presentation, we presented the operating status of this system in supporting biomedical imaging research, analyzed and discussed results of this system in supporting multi-disciplines collaboration cross-multiple institutions.

  19. qPortal: A platform for data-driven biomedical research.

    Science.gov (United States)

    Mohr, Christopher; Friedrich, Andreas; Wojnar, David; Kenar, Erhan; Polatkan, Aydin Can; Codrea, Marius Cosmin; Czemmel, Stefan; Kohlbacher, Oliver; Nahnsen, Sven

    2018-01-01

    Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis. We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data. The backend leverages a variety of concepts and technologies, such as relational databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. Users are empowered to conduct their experiments from the experimental design to the visualization of their results through the platform. Here, we illustrate the feature-rich portal by simulating a biomedical study based on publically available data. We demonstrate the software's strength in supporting the entire project life cycle. The software supports the project design and registration, empowers users to do all-digital project management and finally provides means to perform analysis. We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology. Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy). qPortal, a one-stop-shop solution for biomedical projects offers up-to-date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query metadata for statistics and future re-analysis on

  20. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

    Science.gov (United States)

    Afgan, Enis; Baker, Dannon; Batut, Bérénice; van den Beek, Marius; Bouvier, Dave; Cech, Martin; Chilton, John; Clements, Dave; Coraor, Nate; Grüning, Björn A; Guerler, Aysam; Hillman-Jackson, Jennifer; Hiltemann, Saskia; Jalili, Vahid; Rasche, Helena; Soranzo, Nicola; Goecks, Jeremy; Taylor, James; Nekrutenko, Anton; Blankenberg, Daniel

    2018-05-22

    Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

  1. SCALEUS: Semantic Web Services Integration for Biomedical Applications.

    Science.gov (United States)

    Sernadela, Pedro; González-Castro, Lorena; Oliveira, José Luís

    2017-04-01

    In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web. Despite the evident benefits of this technology, its adoption introduced new challenges related with the migration process, from existent systems to the semantic level. To facilitate this transition, we have developed Scaleus, a semantic web migration tool that can be deployed on top of traditional systems in order to bring knowledge, inference rules, and query federation to the existent data. Targeted at the biomedical domain, this web-based platform offers, in a single package, straightforward data integration and semantic web services that help developers and researchers in the creation process of new semantically enhanced information systems. SCALEUS is available as open source at http://bioinformatics-ua.github.io/scaleus/ .

  2. Optical microassembly platform for constructing reconfigurable microenvironment for biomedical studies

    DEFF Research Database (Denmark)

    Rodrigo, Peter John; Kelemen, Lóránd; Palima, Darwin

    2009-01-01

    Cellular development is highly influenced by the surrounding microenvironment. We propose user-reconfigurable microenvironments and bio-compatible scaffolds as an approach for understanding cellular development processes. We demonstrate a model platform for constructing versatile microenvironment...

  3. Biomedical data integration in computational drug design and bioinformatics.

    Science.gov (United States)

    Seoane, Jose A; Aguiar-Pulido, Vanessa; Munteanu, Cristian R; Rivero, Daniel; Rabunal, Juan R; Dorado, Julian; Pazos, Alejandro

    2013-03-01

    In recent years, in the post genomic era, more and more data is being generated by biological high throughput technologies, such as proteomics and transcriptomics. This omics data can be very useful, but the real challenge is to analyze all this data, as a whole, after integrating it. Biomedical data integration enables making queries to different, heterogeneous and distributed biomedical data sources. Data integration solutions can be very useful not only in the context of drug design, but also in biomedical information retrieval, clinical diagnosis, system biology, etc. In this review, we analyze the most common approaches to biomedical data integration, such as federated databases, data warehousing, multi-agent systems and semantic technology, as well as the solutions developed using these approaches in the past few years.

  4. Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.

    Science.gov (United States)

    Müller, H-M; Van Auken, K M; Li, Y; Sternberg, P W

    2018-03-09

    The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. In addition, TPC allows users to create a customized corpus by uploading and processing documents of their choosing. TPC is UIMA compliant, to facilitate compatibility with external processing modules, and takes advantage of Lucene indexing and search technology for efficient handling of millions of full text documents. Like Textpresso, TPC searches can be performed using keywords and/or categories (semantically related groups of terms), but to provide better context for interpreting and validating queries, search results may now be viewed as highlighted passages in the context of full text. To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements

  5. Emerging heterogeneous integrated photonic platforms on silicon

    Directory of Open Access Journals (Sweden)

    Fathpour Sasan

    2015-05-01

    Full Text Available Silicon photonics has been established as a mature and promising technology for optoelectronic integrated circuits, mostly based on the silicon-on-insulator (SOI waveguide platform. However, not all optical functionalities can be satisfactorily achieved merely based on silicon, in general, and on the SOI platform, in particular. Long-known shortcomings of silicon-based integrated photonics are optical absorption (in the telecommunication wavelengths and feasibility of electrically-injected lasers (at least at room temperature. More recently, high two-photon and free-carrier absorptions required at high optical intensities for third-order optical nonlinear effects, inherent lack of second-order optical nonlinearity, low extinction ratio of modulators based on the free-carrier plasma effect, and the loss of the buried oxide layer of the SOI waveguides at mid-infrared wavelengths have been recognized as other shortcomings. Accordingly, several novel waveguide platforms have been developing to address these shortcomings of the SOI platform. Most of these emerging platforms are based on heterogeneous integration of other material systems on silicon substrates, and in some cases silicon is integrated on other substrates. Germanium and its binary alloys with silicon, III–V compound semiconductors, silicon nitride, tantalum pentoxide and other high-index dielectric or glass materials, as well as lithium niobate are some of the materials heterogeneously integrated on silicon substrates. The materials are typically integrated by a variety of epitaxial growth, bonding, ion implantation and slicing, etch back, spin-on-glass or other techniques. These wide range of efforts are reviewed here holistically to stress that there is no pure silicon or even group IV photonics per se. Rather, the future of the field of integrated photonics appears to be one of heterogenization, where a variety of different materials and waveguide platforms will be used for

  6. Biomedical Platforms Based on Composite Nanomaterials and Cellular Toxicity

    Science.gov (United States)

    Bellucci, Stefano; Bergamaschi, A.; Bottini, M.; Magrini, A.; Mustelin, T.

    2007-03-01

    Carbon nanotubes possess unique chemical, physical, optical, and magnetic properties, which make them suitable for many uses in industrial products and in the field of nanotechnology, including nanomedicine. We describe fluorescent nanocomposites for use in biosensors or nanoelectronics. Then we describe recent results on the issue of cytotoxicity of carbon nanotubes obtained in our labs. Silica nanoparticles have been widely used for biosensing and catalytic applications due to their large surface area-to-volume ratio, straightforward manufacture, and the compatibility of silica chemistry with covalent coupling of biomolecules. Carbon nanotubes-composite materials, such as those based on Carbon nanotubes bound to nanoparticles, are suitable, in order to tailor Carbon nanotubes properties for specific applications. We present a tunable synthesis of Multi Wall Carbon nanotubes-Silica nanoparticles. The control of the nanotube morphology and the bead size, coupled with the versatility of silica chemistry, makes these structures an excellent platform for the development of biosensors (optical, magnetic and catalytic applications). We describe the construction and characterization of supramolecular nanostructures consisting of ruthenium-complex luminophores, directly grafted onto short oxidized single-walled carbon nanotubes or physically entrapped in silica nanobeads, which had been covalently linked to short oxidized single-walled carbon nanotubes or hydrophobically adsorbed onto full-length multi-walled carbon nanotubes. These structures have been evaluated as potential electron-acceptor complexes for use in the fabrication of photovoltaic devices, and for their properties as fluorescent nanocomposites for use in biosensors or nanoelectronics. Finally, we compare the toxicity of pristine and oxidized Multi Walled Carbon nanotubes on human T cells - which would be among the first exposed cell types upon intravenous administration of Carbon nanotubes in therapeutic

  7. BioAnnote: a software platform for annotating biomedical documents with application in medical learning environments.

    Science.gov (United States)

    López-Fernández, H; Reboiro-Jato, M; Glez-Peña, D; Aparicio, F; Gachet, D; Buenaga, M; Fdez-Riverola, F

    2013-07-01

    Automatic term annotation from biomedical documents and external information linking are becoming a necessary prerequisite in modern computer-aided medical learning systems. In this context, this paper presents BioAnnote, a flexible and extensible open-source platform for automatically annotating biomedical resources. Apart from other valuable features, the software platform includes (i) a rich client enabling users to annotate multiple documents in a user friendly environment, (ii) an extensible and embeddable annotation meta-server allowing for the annotation of documents with local or remote vocabularies and (iii) a simple client/server protocol which facilitates the use of our meta-server from any other third-party application. In addition, BioAnnote implements a powerful scripting engine able to perform advanced batch annotations. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  8. The community FabLab platform: applications and implications in biomedical engineering.

    Science.gov (United States)

    Stephenson, Makeda K; Dow, Douglas E

    2014-01-01

    Skill development in science, technology, engineering and math (STEM) education present one of the most formidable challenges of modern society. The Community FabLab platform presents a viable solution. Each FabLab contains a suite of modern computer numerical control (CNC) equipment, electronics and computing hardware and design, programming, computer aided design (CAD) and computer aided machining (CAM) software. FabLabs are community and educational resources and open to the public. Development of STEM based workforce skills such as digital fabrication and advanced manufacturing can be enhanced using this platform. Particularly notable is the potential of the FabLab platform in STEM education. The active learning environment engages and supports a diversity of learners, while the iterative learning that is supported by the FabLab rapid prototyping platform facilitates depth of understanding, creativity, innovation and mastery. The product and project based learning that occurs in FabLabs develops in the student a personal sense of accomplishment, self-awareness, command of the material and technology. This helps build the interest and confidence necessary to excel in STEM and throughout life. Finally the introduction and use of relevant technologies at every stage of the education process ensures technical familiarity and a broad knowledge base needed for work in STEM based fields. Biomedical engineering education strives to cultivate broad technical adeptness, creativity, interdisciplinary thought, and an ability to form deep conceptual understanding of complex systems. The FabLab platform is well designed to enhance biomedical engineering education.

  9. 2009 Integrated Biorefinery Platform Review Report

    Energy Technology Data Exchange (ETDEWEB)

    Ferrell, John [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States)

    2009-12-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program‘s Integrated Biorefinery (IBR) platform review meeting, held on February 18–19, 2009, at the Westin National Harbor, National Harbor, Maryland.

  10. Integrated Spintronic Platforms for Biomolecular Recognition Detection

    Science.gov (United States)

    Martins, V. C.; Cardoso, F. A.; Loureiro, J.; Mercier, M.; Germano, J.; Cardoso, S.; Ferreira, R.; Fonseca, L. P.; Sousa, L.; Piedade, M. S.; Freitas, P. P.

    2008-06-01

    This paper covers recent developments in magnetoresistive based biochip platforms fabricated at INESC-MN, and their application to the detection and quantification of pathogenic waterborn microorganisms in water samples for human consumption. Such platforms are intended to give response to the increasing concern related to microbial contaminated water sources. The presented results concern the development of biological active DNA chips and protein chips and the demonstration of the detection capability of the present platforms. Two platforms are described, one including spintronic sensors only (spin-valve based or magnetic tunnel junction based), and the other, a fully scalable platform where each probe site consists of a MTJ in series with a thin film diode (TFD). Two microfluidic systems are described, for cell separation and concentration, and finally, the read out and control integrated electronics are described, allowing the realization of bioassays with a portable point of care unit. The present platforms already allow the detection of complementary biomolecular target recognition with 1 pM concentration.

  11. Hybrid Integrated Platforms for Silicon Photonics

    Science.gov (United States)

    Liang, Di; Roelkens, Gunther; Baets, Roel; Bowers, John E.

    2010-01-01

    A review of recent progress in hybrid integrated platforms for silicon photonics is presented. Integration of III-V semiconductors onto silicon-on-insulator substrates based on two different bonding techniques is compared, one comprising only inorganic materials, the other technique using an organic bonding agent. Issues such as bonding process and mechanism, bonding strength, uniformity, wafer surface requirement, and stress distribution are studied in detail. The application in silicon photonics to realize high-performance active and passive photonic devices on low-cost silicon wafers is discussed. Hybrid integration is believed to be a promising technology in a variety of applications of silicon photonics.

  12. Hybrid Integrated Platforms for Silicon Photonics

    Directory of Open Access Journals (Sweden)

    John E. Bowers

    2010-03-01

    Full Text Available A review of recent progress in hybrid integrated platforms for silicon photonics is presented. Integration of III-V semiconductors onto silicon-on-insulator substrates based on two different bonding techniques is compared, one comprising only inorganic materials, the other technique using an organic bonding agent. Issues such as bonding process and mechanism, bonding strength, uniformity, wafer surface requirement, and stress distribution are studied in detail. The application in silicon photonics to realize high-performance active and passive photonic devices on low-cost silicon wafers is discussed. Hybrid integration is believed to be a promising technology in a variety of applications of silicon photonics.

  13. Strict integrity control of biomedical images

    Science.gov (United States)

    Coatrieux, Gouenou; Maitre, Henri; Sankur, Bulent

    2001-08-01

    The control of the integrity and authentication of medical images is becoming ever more important within the Medical Information Systems (MIS). The intra- and interhospital exchange of images, such as in the PACS (Picture Archiving and Communication Systems), and the ease of copying, manipulation and distribution of images have brought forth the security aspects. In this paper we focus on the role of watermarking for MIS security and address the problem of integrity control of medical images. We discuss alternative schemes to extract verification signatures and compare their tamper detection performance.

  14. Hybrid Photonic Integration on a Polymer Platform

    Directory of Open Access Journals (Sweden)

    Ziyang Zhang

    2015-09-01

    Full Text Available To fulfill the functionality demands from the fast developing optical networks, a hybrid integration approach allows for combining the advantages of various material platforms. We have established a polymer-based hybrid integration platform (polyboard, which provides flexible optical input/ouptut interfaces (I/Os that allow robust coupling of indium phosphide (InP-based active components, passive insertion of thin-film-based optical elements, and on-chip attachment of optical fibers. This work reviews the recent progress of our polyboard platform. On the fundamental level, multi-core waveguides and polymer/silicon nitride heterogeneous waveguides have been fabricated, broadening device design possibilities and enabling 3D photonic integration. Furthermore, 40-channel optical line terminals and compact, bi-directional optical network units have been developed as highly functional, low-cost devices for the wavelength division multiplexed passive optical network. On a larger scale, thermo-optic elements, thin-film elements and an InP gain chip have been integrated on the polyboard to realize a colorless, dual-polarization optical 90° hybrid as the frontend of a coherent receiver. For high-end applications, a wavelength tunable 100Gbaud transmitter module has been demonstrated, manifesting the joint contribution from the polyboard technology, high speed polymer electro-optic modulator, InP driver electronics and ceramic electronic interconnects.

  15. Graphene-Plasmonic Hybrid Platform for Label-Free SERS Biomedical Detection

    Science.gov (United States)

    Wang, Pu

    reliable SERS quantification approach using the hybrid platform was proposed. The SERS mapping based approach not only leverages the ultra-sensitivity but also minimizes the spot-to-spot variations. Feasibility of biomedical diagnosis with the hybrid platform was exploited by colon cancer cell sensing and time-dependent SERS of amyloid beta protein monomer. The capabilities of the platform are demonstrated by colon cancer cell detection in simulated body fluid background with cell concentration down to 50 cells /mL. Sensitivity of 95% was evidenced by Principle Components Analysis (PCA). Besides, a noticeable evolution profile of the Abeta SERS peaks was observed and attributed to the Abeta configurational change. Taken together, the results suggested the graphene-plasmonic hybrid platform can potentially deliver a biomedical detection and diagnostic imaging platform with superior sensitivity and resolution.

  16. A Versatile Integrated Ambient Ionization Source Platform

    Science.gov (United States)

    Ai, Wanpeng; Nie, Honggang; Song, Shiyao; Liu, Xiaoyun; Bai, Yu; Liu, Huwei

    2018-04-01

    The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique. All individual and combined ionization modes can be easily attained by modulating parameters. In particular, the FAPA/DART&DESI mode can realize the detection of polar and nonpolar compounds at the same time with two different ionization mechanisms: proton transfer and charge transfer. The introduction of LD contributes to the mass spectrometry imaging and the surface-assisted laser desorption (SALDI) under ambient condition. Compared with other individual or multi-mode ion source, the iAmIS platform provides the flexibility of choosing different ionization modes, broadens the scope of the analyte detection, and facilitates the analysis of complex samples. [Figure not available: see fulltext.

  17. An integrated platform for biomolecule interaction analysis

    Science.gov (United States)

    Jan, Chia-Ming; Tsai, Pei-I.; Chou, Shin-Ting; Lee, Shu-Sheng; Lee, Chih-Kung

    2013-02-01

    We developed a new metrology platform which can detect real-time changes in both a phase-interrogation mode and intensity mode of a SPR (surface plasmon resonance). We integrated a SPR and ellipsometer to a biosensor chip platform to create a new biomolecular interaction measurement mechanism. We adopted a conductive ITO (indium-tinoxide) film to the bio-sensor platform chip to expand the dynamic range and improve measurement accuracy. The thickness of the conductive film and the suitable voltage constants were found to enhance performance. A circularly polarized ellipsometry configuration was incorporated into the newly developed platform to measure the label-free interactions of recombinant human C-reactive protein (CRP) with immobilized biomolecule target monoclonal human CRP antibody at various concentrations. CRP was chosen as it is a cardiovascular risk biomarker and is an acute phase reactant as well as a specific prognostic indicator for inflammation. We found that the sensitivity of a phaseinterrogation SPR is predominantly dependent on the optimization of the sample incidence angle. The effect of the ITO layer effective index under DC and AC effects as well as an optimal modulation were experimentally performed and discussed. Our experimental results showed that the modulated dynamic range for phase detection was 10E-2 RIU based on a current effect and 10E-4 RIU based on a potential effect of which a 0.55 (°/RIU) measurement was found by angular-interrogation. The performance of our newly developed metrology platform was characterized to have a higher sensitivity and less dynamic range when compared to a traditional full-field measurement system.

  18. Offshore platform integration and floatover technology

    CERN Document Server

    Liu, Gengshen

    2017-01-01

    This book discusses offshore platform integration technology, focusing on the floatover methodology and its applications. It also addresses topics related to safety and cost-effectiveness, as well as ensuring the success of a project through careful planning and established detailed operation procedure/working manuals, which are rarely found in the published literature. Unlike other publications in this area, the book not only includes details of technology development, but also presents real project cases in the discussion to make it more comprehensible. Each topic is illustrated with carefully created sketches to show the complex operation procedures. .

  19. Integration of Fractal Biosensor in a Digital Microfluidic Platform

    KAUST Repository

    Mashraei, Yousof

    2016-06-08

    The digital microfluidic (DMF) platform introduces many applications in biomedical assays. If it is to be commercially available to the public, it needs to have the essential features of smart sensing and a compact size. In this work, we report on a fractal electrode biosensor that is used for both droplet actuation and sensing C-reactive protein (CRP) concentration levels to assess cardiac disease risk. Our proposed electrode is the first two-terminal electrode design to be integrated into DMF platforms. A simulation of the electrical field distribution shows reduced peak intensities and uniform distribution of the field. When compared to a V-notch square electrode, the fractal electrode shows a superior performance in both aspects, i.e. field uniformity and intensity. These improvements are translated into a successful and responsive actuation of a water droplet with 100V. Likewise, the effective dielectric strength is improved by a 33% increase in the fractal electrode breakdown voltage. Additionally, the capability of the fractal electrode to work as a capacitive biosensor is evaluated with CRP quantification test. Selected fractal electrodes undergo a surface treatment to immobilize anti-CRP antibodies on their surface. The measurement shows a response to the added CRP in capacitance within three minutes. When the untreated electrodes were used for quantification, there was no significant change in capacitance, and this suggested that immobilization was necessary. The electrodes configuration in the fabricated DMF platform allows the fractal electrodes to be selectively used as biosensors, which means the device could be integrated into point-of-care applications.

  20. Integrative structure modeling with the Integrative Modeling Platform.

    Science.gov (United States)

    Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano; Pellarin, Riccardo; Greenberg, Charles H; Saltzberg, Daniel; Sali, Andrej

    2018-01-01

    Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use. © 2017 The Protein Society.

  1. Fully Integrated Biochip Platforms for Advanced Healthcare

    Directory of Open Access Journals (Sweden)

    Giovanni De Micheli

    2012-08-01

    Full Text Available Recent advances in microelectronics and biosensors are enabling developments of innovative biochips for advanced healthcare by providing fully integrated platforms for continuous monitoring of a large set of human disease biomarkers. Continuous monitoring of several human metabolites can be addressed by using fully integrated and minimally invasive devices located in the sub-cutis, typically in the peritoneal region. This extends the techniques of continuous monitoring of glucose currently being pursued with diabetic patients. However, several issues have to be considered in order to succeed in developing fully integrated and minimally invasive implantable devices. These innovative devices require a high-degree of integration, minimal invasive surgery, long-term biocompatibility, security and privacy in data transmission, high reliability, high reproducibility, high specificity, low detection limit and high sensitivity. Recent advances in the field have already proposed possible solutions for several of these issues. The aim of the present paper is to present a broad spectrum of recent results and to propose future directions of development in order to obtain fully implantable systems for the continuous monitoring of the human metabolism in advanced healthcare applications.

  2. Fully integrated biochip platforms for advanced healthcare.

    Science.gov (United States)

    Carrara, Sandro; Ghoreishizadeh, Sara; Olivo, Jacopo; Taurino, Irene; Baj-Rossi, Camilla; Cavallini, Andrea; de Beeck, Maaike Op; Dehollain, Catherine; Burleson, Wayne; Moussy, Francis Gabriel; Guiseppi-Elie, Anthony; De Micheli, Giovanni

    2012-01-01

    Recent advances in microelectronics and biosensors are enabling developments of innovative biochips for advanced healthcare by providing fully integrated platforms for continuous monitoring of a large set of human disease biomarkers. Continuous monitoring of several human metabolites can be addressed by using fully integrated and minimally invasive devices located in the sub-cutis, typically in the peritoneal region. This extends the techniques of continuous monitoring of glucose currently being pursued with diabetic patients. However, several issues have to be considered in order to succeed in developing fully integrated and minimally invasive implantable devices. These innovative devices require a high-degree of integration, minimal invasive surgery, long-term biocompatibility, security and privacy in data transmission, high reliability, high reproducibility, high specificity, low detection limit and high sensitivity. Recent advances in the field have already proposed possible solutions for several of these issues. The aim of the present paper is to present a broad spectrum of recent results and to propose future directions of development in order to obtain fully implantable systems for the continuous monitoring of the human metabolism in advanced healthcare applications.

  3. Integrated platform and API for electrophysiological data.

    Science.gov (United States)

    Sobolev, Andrey; Stoewer, Adrian; Leonhardt, Aljoscha; Rautenberg, Philipp L; Kellner, Christian J; Garbers, Christian; Wachtler, Thomas

    2014-01-01

    Recent advancements in technology and methodology have led to growing amounts of increasingly complex neuroscience data recorded from various species, modalities, and levels of study. The rapid data growth has made efficient data access and flexible, machine-readable data annotation a crucial requisite for neuroscientists. Clear and consistent annotation and organization of data is not only an important ingredient for reproducibility of results and re-use of data, but also essential for collaborative research and data sharing. In particular, efficient data management and interoperability requires a unified approach that integrates data and metadata and provides a common way of accessing this information. In this paper we describe GNData, a data management platform for neurophysiological data. GNData provides a storage system based on a data representation that is suitable to organize data and metadata from any electrophysiological experiment, with a functionality exposed via a common application programming interface (API). Data representation and API structure are compatible with existing approaches for data and metadata representation in neurophysiology. The API implementation is based on the Representational State Transfer (REST) pattern, which enables data access integration in software applications and facilitates the development of tools that communicate with the service. Client libraries that interact with the API provide direct data access from computing environments like Matlab or Python, enabling integration of data management into the scientist's experimental or analysis routines.

  4. A theoretical-experimental methodology for assessing the sensitivity of biomedical spectral imaging platforms, assays, and analysis methods.

    Science.gov (United States)

    Leavesley, Silas J; Sweat, Brenner; Abbott, Caitlyn; Favreau, Peter; Rich, Thomas C

    2018-01-01

    Spectral imaging technologies have been used for many years by the remote sensing community. More recently, these approaches have been applied to biomedical problems, where they have shown great promise. However, biomedical spectral imaging has been complicated by the high variance of biological data and the reduced ability to construct test scenarios with fixed ground truths. Hence, it has been difficult to objectively assess and compare biomedical spectral imaging assays and technologies. Here, we present a standardized methodology that allows assessment of the performance of biomedical spectral imaging equipment, assays, and analysis algorithms. This methodology incorporates real experimental data and a theoretical sensitivity analysis, preserving the variability present in biomedical image data. We demonstrate that this approach can be applied in several ways: to compare the effectiveness of spectral analysis algorithms, to compare the response of different imaging platforms, and to assess the level of target signature required to achieve a desired performance. Results indicate that it is possible to compare even very different hardware platforms using this methodology. Future applications could include a range of optimization tasks, such as maximizing detection sensitivity or acquisition speed, providing high utility for investigators ranging from design engineers to biomedical scientists. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Mediator infrastructure for information integration and semantic data integration environment for biomedical research.

    Science.gov (United States)

    Grethe, Jeffrey S; Ross, Edward; Little, David; Sanders, Brian; Gupta, Amarnath; Astakhov, Vadim

    2009-01-01

    This paper presents current progress in the development of semantic data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net) project. BIRN is sponsored by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). A goal is the development of a cyberinfrastructure for biomedical research that supports advance data acquisition, data storage, data management, data integration, data mining, data visualization, and other computing and information processing services over the Internet. Each participating institution maintains storage of their experimental or computationally derived data. Mediator-based data integration system performs semantic integration over the databases to enable researchers to perform analyses based on larger and broader datasets than would be available from any single institution's data. This paper describes recent revision of the system architecture, implementation, and capabilities of the semantically based data integration environment for BIRN.

  6. A Semantic Web management model for integrative biomedical informatics.

    Directory of Open Access Journals (Sweden)

    Helena F Deus

    2008-08-01

    Full Text Available Data, data everywhere. The diversity and magnitude of the data generated in the Life Sciences defies automated articulation among complementary efforts. The additional need in this field for managing property and access permissions compounds the difficulty very significantly. This is particularly the case when the integration involves multiple domains and disciplines, even more so when it includes clinical and high throughput molecular data.The emergence of Semantic Web technologies brings the promise of meaningful interoperation between data and analysis resources. In this report we identify a core model for biomedical Knowledge Engineering applications and demonstrate how this new technology can be used to weave a management model where multiple intertwined data structures can be hosted and managed by multiple authorities in a distributed management infrastructure. Specifically, the demonstration is performed by linking data sources associated with the Lung Cancer SPORE awarded to The University of Texas MD Anderson Cancer Center at Houston and the Southwestern Medical Center at Dallas. A software prototype, available with open source at www.s3db.org, was developed and its proposed design has been made publicly available as an open source instrument for shared, distributed data management.The Semantic Web technologies have the potential to addresses the need for distributed and evolvable representations that are critical for systems Biology and translational biomedical research. As this technology is incorporated into application development we can expect that both general purpose productivity software and domain specific software installed on our personal computers will become increasingly integrated with the relevant remote resources. In this scenario, the acquisition of a new dataset should automatically trigger the delegation of its analysis.

  7. Snap: an integrated SNP annotation platform

    DEFF Research Database (Denmark)

    Li, Shengting; Ma, Lijia; Li, Heng

    2007-01-01

    Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...

  8. MIMI: multimodality, multiresource, information integration environment for biomedical core facilities.

    Science.gov (United States)

    Szymanski, Jacek; Wilson, David L; Zhang, Guo-Qiang

    2009-10-01

    The rapid expansion of biomedical research has brought substantial scientific and administrative data management challenges to modern core facilities. Scientifically, a core facility must be able to manage experimental workflow and the corresponding set of large and complex scientific data. It must also disseminate experimental data to relevant researchers in a secure and expedient manner that facilitates collaboration and provides support for data interpretation and analysis. Administratively, a core facility must be able to manage the scheduling of its equipment and to maintain a flexible and effective billing system to track material, resource, and personnel costs and charge for services to sustain its operation. It must also have the ability to regularly monitor the usage and performance of its equipment and to provide summary statistics on resources spent on different categories of research. To address these informatics challenges, we introduce a comprehensive system called MIMI (multimodality, multiresource, information integration environment) that integrates the administrative and scientific support of a core facility into a single web-based environment. We report the design, development, and deployment experience of a baseline MIMI system at an imaging core facility and discuss the general applicability of such a system in other types of core facilities. These initial results suggest that MIMI will be a unique, cost-effective approach to addressing the informatics infrastructure needs of core facilities and similar research laboratories.

  9. Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

    Science.gov (United States)

    Himmelstein, Daniel Scott; Lizee, Antoine; Hessler, Christine; Brueggeman, Leo; Chen, Sabrina L; Hadley, Dexter; Green, Ari; Khankhanian, Pouya; Baranzini, Sergio E

    2017-09-22

    The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data were integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms. Next, we identified network patterns that distinguish treatments from non-treatments. Then, we predicted the probability of treatment for 209,168 compound-disease pairs (het.io/repurpose). Our predictions validated on two external sets of treatment and provided pharmacological insights on epilepsy, suggesting they will help prioritize drug repurposing candidates. This study was entirely open and received realtime feedback from 40 community members.

  10. Miniaturization for Point-of-Care Analysis: Platform Technology for Almost Every Biomedical Assay.

    Science.gov (United States)

    Schumacher, Soeren; Sartorius, Dorian; Ehrentreich-Förster, Eva; Bier, Frank F

    2012-10-01

    Platform technologies for the changing need of diagnostics are one of the main challenges in medical device technology. From one point-of-view the demand for new and more versatile diagnostic is increasing due to a deeper knowledge of biomarkers and their combination with diseases. From another point-of-view a decentralization of diagnostics will occur since decisions can be made faster resulting in higher success of therapy. Hence, new types of technologies have to be established which enables a multiparameter analysis at the point-of-care. Within this review-like article a system called Fraunhofer ivD-platform is introduced. It consists of a credit-card sized cartridge with integrated reagents, sensors and pumps and a read-out/processing unit. Within the cartridge the assay runs fully automated within 15-20 minutes. Due to the open design of the platform different analyses such as antibody, serological or DNA-assays can be performed. Specific examples of these three different assay types are given to show the broad applicability of the system.

  11. Carboxylated SiO2-coated α-Fe nanoparticles: towards a versatile platform for biomedical applications.

    Science.gov (United States)

    Kohara, Kaori; Yamamoto, Shinpei; Seinberg, Liis; Murakami, Tatsuya; Tsujimoto, Masahiko; Ogawa, Tetsuya; Kurata, Hiroki; Kageyama, Hiroshi; Takano, Mikio

    2013-03-28

    Carboxylated SiO2-coated α-Fe nanoparticles have been successfully prepared via CaH2-mediated reduction of SiO2-coated Fe3O4 nanoparticles followed by surface carboxylation. These α-Fe-based nanoparticles, which are characterized by ease of coating with additional functional groups, a large magnetization of 154 emu per g-Fe, enhanced corrosion resistivity, excellent aqueous dispersibility, and low cytotoxicity, have potential to be a versatile platform in biomedical applications.

  12. The ImageJ ecosystem: An open platform for biomedical image analysis.

    Science.gov (United States)

    Schindelin, Johannes; Rueden, Curtis T; Hiner, Mark C; Eliceiri, Kevin W

    2015-01-01

    Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. © 2015 Wiley Periodicals, Inc.

  13. KinomeXplorer: an integrated platform for kinome biology studies

    DEFF Research Database (Denmark)

    Horn, Heiko; Schoof, Erwin; Kim, Jinho

    2014-01-01

    A letter to the editor is presented related to the KinomeXplorer, an integrated platform providing workflows to efficiently analyze phosphorylation dependent interaction networks or kinase signaling networks....

  14. Structural Integrity Management for Fixed Offshore Platforms in Malaysia

    OpenAIRE

    Narayanan Sambu Potty; Mohammad Kabir B. Mohd Akram

    2009-01-01

    Structural Integrity Management (SIM) is important for the protection of offshore crew, environment, business assets and company and industry reputation. API RP 2A contained guidelines for assessment of existing platforms mostly for the Gulf of Mexico (GOM). ISO 19902 SIM framework also does not specifically cater for Malaysia. There are about 200 platforms in Malaysia with 90 exceeding their design life. The Petronas Carigali Sdn Bhd (PCSB) uses the Asset Integrity Management ...

  15. PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

    Directory of Open Access Journals (Sweden)

    Chuong Cheng-Ming

    2006-10-01

    Full Text Available Abstract Background Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. Results PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. Conclusion We have developed citations' prioritisation algorithm based on journal impact factor, forward referencing volume, referencing dynamics, and author's contribution level. It can be applied either to the primary set of PubMed search results or to the subsets of these results identified through key terms from controlled biomedical vocabularies and ontologies. NCI (National Cancer Institute thesaurus and MGD (Mouse Genome Database mammalian gene orthology have been implemented for key terms analytics. PubFocus provides a scalable platform for the integration of multiple available ontology databases. PubFocus analytics can be adapted for input sources of biomedical citations other than PubMed.

  16. Portable blood extraction device integrated with biomedical monitoring system

    Science.gov (United States)

    Khumpuang, S.; Horade, M.; Fujioka, K.; Sugiyama, S.

    2006-01-01

    Painless and portable blood extraction device has been immersed in the world of miniaturization on bio-medical research particularly in manufacturing point-of-care systems. The fabrication of a blood extraction device integrated with an electrolyte-monitoring system is reported in this paper. The device has advantages in precise controlled dosage of blood extracted including the slightly damaged blood vessels and nervous system. The in-house blood diagnostic will become simple for the patients. Main components of the portable system are; the blood extraction device and electrolyte-monitoring system. The monitoring system consists of ISFET (Ion Selective Field Effect Transistor) for measuring the concentration level of minerals in blood. In this work, we measured the level of 3 ions; Na+, K+ and Cl-. The mentioned ions are frequently required the measurement since their concentration levels in the blood can indicate whether the kidney, pancreas, liver or heart is being malfunction. The fabrication of the whole system and experimentation on each ISM (Ion Sensitive Membrane) will be provided. Taking the advantages of LIGA technology, the 100 hollow microneedles fabricated by Synchrotron Radiation deep X-ray lithography through PCT (Plane-pattern to Cross-section Transfer) technique have been consisted in 5x5 mm2 area. The microneedle is 300 μm in base-diameter, 500 μm-pitch, 800 μm-height and 50 μm hole-diameter. The total size of the blood extraction device is 2x2x2 cm 3. The package is made from a plastic socket including slots for inserting microneedle array and ISFET connecting to an electrical circuit for the monitoring. Through the dimensional design for simply handling and selection of disposable material, the patients can self-evaluate the critical level of the body minerals in anywhere and anytime.

  17. The fully integrated biomedical engineering programme at Eindhoven University of Technology

    NARCIS (Netherlands)

    Slaaf, D.W.; Genderen, van M.H.P.

    2009-01-01

    The development of a fully integrated biomedical engineering programme (life sciences included from the start) is described. Details are provided about background, implementation, and didactic concept: design centred learning combined with courses. The curriculum has developed into a

  18. Development of integrated platform for computational material design

    Energy Technology Data Exchange (ETDEWEB)

    Kiyoshi, Matsubara; Kumi, Itai; Nobutaka, Nishikawa; Akifumi, Kato [Center for Computational Science and Engineering, Fuji Research Institute Corporation (Japan); Hideaki, Koike [Advance Soft Corporation (Japan)

    2003-07-01

    The goal of our project is to design and develop a problem-solving environment (PSE) that will help computational scientists and engineers develop large complicated application software and simulate complex phenomena by using networking and parallel computing. The integrated platform, which is designed for PSE in the Japanese national project of Frontier Simulation Software for Industrial Science, is defined by supporting the entire range of problem solving activity from program formulation and data setup to numerical simulation, data management, and visualization. A special feature of our integrated platform is based on a new architecture called TASK FLOW. It integrates the computational resources such as hardware and software on the network and supports complex and large-scale simulation. This concept is applied to computational material design and the project 'comprehensive research for modeling, analysis, control, and design of large-scale complex system considering properties of human being'. Moreover this system will provide the best solution for developing large and complicated software and simulating complex and large-scaled phenomena in computational science and engineering. A prototype has already been developed and the validation and verification of an integrated platform will be scheduled by using the prototype in 2003. In the validation and verification, fluid-structure coupling analysis system for designing an industrial machine will be developed on the integrated platform. As other examples of validation and verification, integrated platform for quantum chemistry and bio-mechanical system are planned.

  19. Development of integrated platform for computational material design

    International Nuclear Information System (INIS)

    Kiyoshi, Matsubara; Kumi, Itai; Nobutaka, Nishikawa; Akifumi, Kato; Hideaki, Koike

    2003-01-01

    The goal of our project is to design and develop a problem-solving environment (PSE) that will help computational scientists and engineers develop large complicated application software and simulate complex phenomena by using networking and parallel computing. The integrated platform, which is designed for PSE in the Japanese national project of Frontier Simulation Software for Industrial Science, is defined by supporting the entire range of problem solving activity from program formulation and data setup to numerical simulation, data management, and visualization. A special feature of our integrated platform is based on a new architecture called TASK FLOW. It integrates the computational resources such as hardware and software on the network and supports complex and large-scale simulation. This concept is applied to computational material design and the project 'comprehensive research for modeling, analysis, control, and design of large-scale complex system considering properties of human being'. Moreover this system will provide the best solution for developing large and complicated software and simulating complex and large-scaled phenomena in computational science and engineering. A prototype has already been developed and the validation and verification of an integrated platform will be scheduled by using the prototype in 2003. In the validation and verification, fluid-structure coupling analysis system for designing an industrial machine will be developed on the integrated platform. As other examples of validation and verification, integrated platform for quantum chemistry and bio-mechanical system are planned

  20. A service integration platform for collaborative networks

    NARCIS (Netherlands)

    Osorio, A. L.; Afsarmanesh, H.; Camarinha-Matos, L.M.

    2011-01-01

    Integrated manufacturing constitutes a complex system made of heterogeneous information and control subsystems. Those subsystems are not designed to the cooperation. Typically each subsystem automates specific processes, and establishes closed application domains, therefore it is very difficult to

  1. The BioIntelligence Framework: a new computational platform for biomedical knowledge computing.

    Science.gov (United States)

    Farley, Toni; Kiefer, Jeff; Lee, Preston; Von Hoff, Daniel; Trent, Jeffrey M; Colbourn, Charles; Mousses, Spyro

    2013-01-01

    Breakthroughs in molecular profiling technologies are enabling a new data-intensive approach to biomedical research, with the potential to revolutionize how we study, manage, and treat complex diseases. The next great challenge for clinical applications of these innovations will be to create scalable computational solutions for intelligently linking complex biomedical patient data to clinically actionable knowledge. Traditional database management systems (DBMS) are not well suited to representing complex syntactic and semantic relationships in unstructured biomedical information, introducing barriers to realizing such solutions. We propose a scalable computational framework for addressing this need, which leverages a hypergraph-based data model and query language that may be better suited for representing complex multi-lateral, multi-scalar, and multi-dimensional relationships. We also discuss how this framework can be used to create rapid learning knowledge base systems to intelligently capture and relate complex patient data to biomedical knowledge in order to automate the recovery of clinically actionable information.

  2. Cardiomyocytes from human pluripotent stem cells: From laboratory curiosity to industrial biomedical platform.

    Science.gov (United States)

    Denning, Chris; Borgdorff, Viola; Crutchley, James; Firth, Karl S A; George, Vinoj; Kalra, Spandan; Kondrashov, Alexander; Hoang, Minh Duc; Mosqueira, Diogo; Patel, Asha; Prodanov, Ljupcho; Rajamohan, Divya; Skarnes, William C; Smith, James G W; Young, Lorraine E

    2016-07-01

    Cardiomyocytes from human pluripotent stem cells (hPSCs-CMs) could revolutionise biomedicine. Global burden of heart failure will soon reach USD $90bn, while unexpected cardiotoxicity underlies 28% of drug withdrawals. Advances in hPSC isolation, Cas9/CRISPR genome engineering and hPSC-CM differentiation have improved patient care, progressed drugs to clinic and opened a new era in safety pharmacology. Nevertheless, predictive cardiotoxicity using hPSC-CMs contrasts from failure to almost total success. Since this likely relates to cell immaturity, efforts are underway to use biochemical and biophysical cues to improve many of the ~30 structural and functional properties of hPSC-CMs towards those seen in adult CMs. Other developments needed for widespread hPSC-CM utility include subtype specification, cost reduction of large scale differentiation and elimination of the phenotyping bottleneck. This review will consider these factors in the evolution of hPSC-CM technologies, as well as their integration into high content industrial platforms that assess structure, mitochondrial function, electrophysiology, calcium transients and contractility. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Study on integrated design and analysis platform of NPP

    International Nuclear Information System (INIS)

    Lu Dongsen; Gao Zuying; Zhou Zhiwei

    2001-01-01

    Many calculation software have been developed to nuclear system's design and safety analysis, such as structure design software, fuel design and manage software, thermal hydraulic analysis software, severe accident simulation software, etc. This study integrates those software to a platform, develops visual modeling tool for Retran, NGFM90. And in this platform, a distribution calculation method is also provided for couple calculation between different software. The study will improve the design and analysis of NPP

  4. Distributed System for Spaceflight Biomedical Support

    Data.gov (United States)

    National Aeronautics and Space Administration — Our project investigated whether a software platform could integrate as wide a variety of devices and data types as needed for spaceflight biomedical support. The...

  5. Booly: a new data integration platform

    Directory of Open Access Journals (Sweden)

    Karten Harvey J

    2010-10-01

    Full Text Available Abstract Background Data integration is an escalating problem in bioinformatics. We have developed a web tool and warehousing system, Booly, that features a simple yet flexible data model coupled with the ability to perform powerful comparative analysis, including the use of Boolean logic to merge datasets together, and an integrated aliasing system to decipher differing names of the same gene or protein. Furthermore, Booly features a collaborative sharing system and a public repository so that users can retrieve new datasets while contributors can easily disseminate new content. Results We illustrate the uses of Booly with several examples including: the versatile creation of homebrew datasets, the integration of heterogeneous data to identify genes useful for comparing avian and mammalian brain architecture, and generation of a list of Food and Drug Administration (FDA approved drugs with possible alternative disease targets. Conclusions The Booly paradigm for data storage and analysis should facilitate integration between disparate biological and medical fields and result in novel discoveries that can then be validated experimentally. Booly can be accessed at http://booly.ucsd.edu.

  6. CILogon: An Integrated Identity and Access Management Platform for Science

    Science.gov (United States)

    Basney, J.

    2016-12-01

    When scientists work together, they use web sites and other software to share their ideas and data. To ensure the integrity of their work, these systems require the scientists to log in and verify that they are part of the team working on a particular science problem. Too often, the identity and access verification process is a stumbling block for the scientists. Scientific research projects are forced to invest time and effort into developing and supporting Identity and Access Management (IAM) services, distracting them from the core goals of their research collaboration. CILogon provides an IAM platform that enables scientists to work together to meet their IAM needs more effectively so they can allocate more time and effort to their core mission of scientific research. The CILogon platform enables federated identity management and collaborative organization management. Federated identity management enables researchers to use their home organization identities to access cyberinfrastructure, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to collaboration platforms (e.g., wikis, mailing lists, and domain applications). CILogon's IAM platform serves the unique needs of research collaborations, namely the need to dynamically form collaboration groups across organizations and countries, sharing access to data, instruments, compute clusters, and other resources to enable scientific discovery. CILogon provides a software-as-a-service platform to ease integration with cyberinfrastructure, while making all software components publicly available under open source licenses to enable re-use. Figure 1 illustrates the components and interfaces of this platform. CILogon has been operational since 2010 and has been used by over 7,000 researchers from more than 170 identity providers to access cyberinfrastructure including Globus, LIGO, Open Science Grid

  7. Cell-phone-based platform for biomedical device development and education applications.

    Directory of Open Access Journals (Sweden)

    Zachary J Smith

    Full Text Available In this paper we report the development of two attachments to a commercial cell phone that transform the phone's integrated lens and image sensor into a 350x microscope and visible-light spectrometer. The microscope is capable of transmission and polarized microscopy modes and is shown to have 1.5 micron resolution and a usable field-of-view of 150 x 50 with no image processing, and approximately 350 x 350 when post-processing is applied. The spectrometer has a 300 nm bandwidth with a limiting spectral resolution of close to 5 nm. We show applications of the devices to medically relevant problems. In the case of the microscope, we image both stained and unstained blood-smears showing the ability to acquire images of similar quality to commercial microscope platforms, thus allowing diagnosis of clinical pathologies. With the spectrometer we demonstrate acquisition of a white-light transmission spectrum through diffuse tissue as well as the acquisition of a fluorescence spectrum. We also envision the devices to have immediate relevance in the educational field.

  8. Cell-phone-based platform for biomedical device development and education applications.

    Science.gov (United States)

    Smith, Zachary J; Chu, Kaiqin; Espenson, Alyssa R; Rahimzadeh, Mehdi; Gryshuk, Amy; Molinaro, Marco; Dwyre, Denis M; Lane, Stephen; Matthews, Dennis; Wachsmann-Hogiu, Sebastian

    2011-03-02

    In this paper we report the development of two attachments to a commercial cell phone that transform the phone's integrated lens and image sensor into a 350x microscope and visible-light spectrometer. The microscope is capable of transmission and polarized microscopy modes and is shown to have 1.5 micron resolution and a usable field-of-view of 150 x 50 with no image processing, and approximately 350 x 350 when post-processing is applied. The spectrometer has a 300 nm bandwidth with a limiting spectral resolution of close to 5 nm. We show applications of the devices to medically relevant problems. In the case of the microscope, we image both stained and unstained blood-smears showing the ability to acquire images of similar quality to commercial microscope platforms, thus allowing diagnosis of clinical pathologies. With the spectrometer we demonstrate acquisition of a white-light transmission spectrum through diffuse tissue as well as the acquisition of a fluorescence spectrum. We also envision the devices to have immediate relevance in the educational field.

  9. MIMI: Multimodality, Multiresource, Information Integration Environment for Biomedical Core Facilities

    OpenAIRE

    Szymanski, Jacek; Wilson, David L.; Zhang, Guo-Qiang

    2007-01-01

    The rapid expansion of biomedical research has brought substantial scientific and administrative data management challenges to modern core facilities. Scientifically, a core facility must be able to manage experimental workflow and the corresponding set of large and complex scientific data. It must also disseminate experimental data to relevant researchers in a secure and expedient manner that facilitates collaboration and provides support for data interpretation and analysis. Administrativel...

  10. Surface-Enhanced Raman Spectroscopy Integrated Centrifugal Microfluidics Platform

    DEFF Research Database (Denmark)

    Durucan, Onur

    This PhD thesis demonstrates (i) centrifugal microfluidics disc platform integrated with Au capped nanopillar (NP) substrates for surface-enhanced Raman spectroscopy (SERS) based sensing, and (ii) novel sample analysis concepts achieved by synergistical combination of sensing techniques and minia......This PhD thesis demonstrates (i) centrifugal microfluidics disc platform integrated with Au capped nanopillar (NP) substrates for surface-enhanced Raman spectroscopy (SERS) based sensing, and (ii) novel sample analysis concepts achieved by synergistical combination of sensing techniques...... dense array of NP structures. Furthermore, the wicking assisted nanofiltration procedure was accomplished in centrifugal microfluidics platform and as a result additional sample purification was achieved through the centrifugation process. In this way, the Au coated NP substrate was utilized...

  11. Multiscale integration of -omic, imaging, and clinical data in biomedical informatics.

    Science.gov (United States)

    Phan, John H; Quo, Chang F; Cheng, Chihwen; Wang, May Dongmei

    2012-01-01

    This paper reviews challenges and opportunities in multiscale data integration for biomedical informatics. Biomedical data can come from different biological origins, data acquisition technologies, and clinical applications. Integrating such data across multiple scales (e.g., molecular, cellular/tissue, and patient) can lead to more informed decisions for personalized, predictive, and preventive medicine. However, data heterogeneity, community standards in data acquisition, and computational complexity are big challenges for such decision making. This review describes genomic and proteomic (i.e., molecular), histopathological imaging (i.e., cellular/tissue), and clinical (i.e., patient) data; it includes case studies for single-scale (e.g., combining genomic or histopathological image data), multiscale (e.g., combining histopathological image and clinical data), and multiscale and multiplatform (e.g., the Human Protein Atlas and The Cancer Genome Atlas) data integration. Numerous opportunities exist in biomedical informatics research focusing on integration of multiscale and multiplatform data.

  12. Fundamentals of power integrity for computer platforms and systems

    CERN Document Server

    DiBene, Joseph T

    2014-01-01

    An all-encompassing text that focuses on the fundamentals of power integrity Power integrity is the study of power distribution from the source to the load and the system level issues that can occur across it. For computer systems, these issues can range from inside the silicon to across the board and may egress into other parts of the platform, including thermal, EMI, and mechanical. With a focus on computer systems and silicon level power delivery, this book sheds light on the fundamentals of power integrity, utilizing the author's extensive background in the power integrity industry and un

  13. Biomass Program 2007 Peer Review - Integrated Biorefinery Platform Summary

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2009-10-27

    This document discloses the comments provided by a review panel at the U.S. Department of Energy Office of the Biomass Program Peer Review held on November 15-16, 2007 in Baltimore, MD and the Integrated Biorefinery Platform Review held on August 13-15, 2007 in Golden, Colorado.

  14. Integration of the TNXYZ computer program inside the platform Salome

    International Nuclear Information System (INIS)

    Chaparro V, F. J.

    2014-01-01

    The present work shows the procedure carried out to integrate the code TNXYZ as a calculation tool at the graphical simulation platform Salome. The TNXYZ code propose a numerical solution of the neutron transport equation, in several groups of energy, steady-state and three-dimensional geometry. In order to discretized the variables of the transport equation, the code uses the method of discrete ordinates for the angular variable, and a nodal method for the spatial dependence. The Salome platform is a graphical environment designed for building, editing and simulating mechanical models mainly focused on the industry and unlike other software, in order to form a complete scheme of pre and post processing of information, to integrate and control an external source code. Before the integration the in the Salome platform TNXYZ code was upgraded. TNXYZ was programmed in the 90s using Fortran 77 compiler; for this reason the code was adapted to the characteristics of the current Fortran compilers; in addition, with the intention of extracting partial results over the process sequence, the original structure of the program underwent a modularization process, i.e. the main program was divided into sections where the code performs major operations. This procedure is controlled by the information module (YACS) on Salome platform, and it could be useful for a subsequent coupling with thermal-hydraulics codes. Finally, with the help of the Monte Carlo code Serpent several study cases were defined in order to check the process of integration; the verification process consisted in performing a comparison of the results obtained with the code executed as stand-alone and after modernized, integrated and controlled by the Salome platform. (Author)

  15. Harvest: an open platform for developing web-based biomedical data discovery and reporting applications.

    Science.gov (United States)

    Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

    2014-01-01

    Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu.

  16. An integrated biotechnology platform for developing sustainable chemical processes.

    Science.gov (United States)

    Barton, Nelson R; Burgard, Anthony P; Burk, Mark J; Crater, Jason S; Osterhout, Robin E; Pharkya, Priti; Steer, Brian A; Sun, Jun; Trawick, John D; Van Dien, Stephen J; Yang, Tae Hoon; Yim, Harry

    2015-03-01

    Genomatica has established an integrated computational/experimental metabolic engineering platform to design, create, and optimize novel high performance organisms and bioprocesses. Here we present our platform and its use to develop E. coli strains for production of the industrial chemical 1,4-butanediol (BDO) from sugars. A series of examples are given to demonstrate how a rational approach to strain engineering, including carefully designed diagnostic experiments, provided critical insights about pathway bottlenecks, byproducts, expression balancing, and commercial robustness, leading to a superior BDO production strain and process.

  17. G-DOC Plus - an integrative bioinformatics platform for precision medicine.

    Science.gov (United States)

    Bhuvaneshwar, Krithika; Belouali, Anas; Singh, Varun; Johnson, Robert M; Song, Lei; Alaoui, Adil; Harris, Michael A; Clarke, Robert; Weiner, Louis M; Gusev, Yuriy; Madhavan, Subha

    2016-04-30

    G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. G-DOC Plus currently holds data from over 10,000 patients selected from private and public resources including Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT), caArray studies of lung and colon cancer, ImmPort and the 1000 genomes data sets. The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer and non-cancer studies for hypothesis generation and validation; biomarker discovery and multi-omics analysis, to explore somatic mutations and cancer MRI images; as well as for training and graduate education in bioinformatics, data and computational sciences. Several of these use cases are described in this paper to demonstrate its multifaceted usability. G-DOC Plus can be used to support a variety of user groups in multiple domains to enable hypothesis generation for precision medicine research. The long-term vision of G-DOC Plus is to extend this translational bioinformatics platform to stay current with emerging omics technologies and analysis methods to continue supporting novel hypothesis generation, analysis and validation for integrative biomedical research. By integrating several aspects of the disease and exposing various data elements, such as outpatient lab workup, pathology, radiology, current treatments, molecular signatures and expected outcomes over a web interface, G-DOC Plus will continue to strengthen precision medicine research. G-DOC Plus is available

  18. Multi-function microfluidic platform for sensor integration

    DEFF Research Database (Denmark)

    Fernandes, Ana C.; Semenova, Daria; Panjan, Peter

    2018-01-01

    The limited availability of metabolite-specific sensors for continuous sampling and monitoring is one of the main bottlenecks contributing to failures in bioprocess development. Furthermore, only a limited number of approaches exist to connect currently available measurement systems with high...... throughput reactor units. This is especially relevant in the biocatalyst screening and characterization stage of process development. In this work, a strategy for sensor integration in microfluidic platforms is demonstrated, to address the need for rapid, cost-effective and high-throughput screening...... of the sample solution up to 10 times. In order to highlight the features of the proposed platform, inline monitoring of glucose levels is presented and discussed. Glucose was chosen due to its importance in biotechnology as a relevant substrate. The platform demonstrated continuous measurement of substrate...

  19. Integrated Confocal and Scanning Probe Microscopy for Biomedical Research

    Directory of Open Access Journals (Sweden)

    B.J. Haupt

    2006-01-01

    Full Text Available Atomic force microscopy (AFM continues to be developed, not only in design, but also in application. The new focus of using AFM is changing from pure material to biomedical studies. More frequently, it is being used in combination with other optical imaging methods, such as confocal laser scanning microscopy (CLSM and fluorescent imaging, to provide a more comprehensive understanding of biological systems. To date, AFM has been used increasingly as a precise micromanipulator, probing and altering the mechanobiological characteristics of living cells and tissues, in order to examine specific, receptor-ligand interactions, material properties, and cell behavior. In this review, we discuss the development of this new hybrid AFM, current research, and potential applications in diagnosis and the detection of disease.

  20. Wolfram technologies as an integrated scalable platform for interactive learning

    Science.gov (United States)

    Kaurov, Vitaliy

    2012-02-01

    We rely on technology profoundly with the prospect of even greater integration in the future. Well known challenges in education are a technology-inadequate curriculum and many software platforms that are difficult to scale or interconnect. We'll review an integrated technology, much of it free, that addresses these issues for individuals and small schools as well as for universities. Topics include: Mathematica, a programming environment that offers a diverse range of functionality; natural language programming for getting started quickly and accessing data from Wolfram|Alpha; quick and easy construction of interactive courseware and scientific applications; partnering with publishers to create interactive e-textbooks; course assistant apps for mobile platforms; the computable document format (CDF); teacher-student and student-student collaboration on interactive projects and web publishing at the Wolfram Demonstrations site.

  1. From NHS Choices to the integrated customer service platform.

    Science.gov (United States)

    Gann, Bob; Grant, Maria J

    2013-03-01

    In 2013 the NHS Commissioning Board launches its new integrated customer service platform. The new service utilises the full range of channels (web, telephone, apps etc) to provide access to information to support transparency, participation and transactions. Digital health services have proven benefits in informed choice, shared decision making and patient participation. © 2013 The authors. Health Information and Libraries Journal © 2013 Health Libraries Group.

  2. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  3. Genomics Portals: integrative web-platform for mining genomics data

    Directory of Open Access Journals (Sweden)

    Ghosh Krishnendu

    2010-01-01

    Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  4. Multi-function microfluidic platform for sensor integration.

    Science.gov (United States)

    Fernandes, Ana C; Semenova, Daria; Panjan, Peter; Sesay, Adama M; Gernaey, Krist V; Krühne, Ulrich

    2018-03-06

    The limited availability of metabolite-specific sensors for continuous sampling and monitoring is one of the main bottlenecks contributing to failures in bioprocess development. Furthermore, only a limited number of approaches exist to connect currently available measurement systems with high throughput reactor units. This is especially relevant in the biocatalyst screening and characterization stage of process development. In this work, a strategy for sensor integration in microfluidic platforms is demonstrated, to address the need for rapid, cost-effective and high-throughput screening in bioprocesses. This platform is compatible with different sensor formats by enabling their replacement and was built in order to be highly flexible and thus suitable for a wide range of applications. Moreover, this re-usable platform can easily be connected to analytical equipment, such as HPLC, laboratory scale reactors or other microfluidic chips through the use of standardized fittings. In addition, the developed platform includes a two-sensor system interspersed with a mixing channel, which allows the detection of samples that might be outside the first sensor's range of detection, through dilution of the sample solution up to 10 times. In order to highlight the features of the proposed platform, inline monitoring of glucose levels is presented and discussed. Glucose was chosen due to its importance in biotechnology as a relevant substrate. The platform demonstrated continuous measurement of substrate solutions for up to 12 h. Furthermore, the influence of the fluid velocity on substrate diffusion was observed, indicating the need for in-flow calibration to achieve a good quantitative output. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Harvest: a web-based biomedical data discovery and reporting application development platform.

    Science.gov (United States)

    Italia, Michael J; Pennington, Jeffrey W; Ruth, Byron; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; Miller, Jeffrey; White, Peter S

    2013-01-01

    Biomedical researchers share a common challenge of making complex data understandable and accessible. This need is increasingly acute as investigators seek opportunities for discovery amidst an exponential growth in the volume and complexity of laboratory and clinical data. To address this need, we developed Harvest, an open source framework that provides a set of modular components to aid the rapid development and deployment of custom data discovery software applications. Harvest incorporates visual representations of multidimensional data types in an intuitive, web-based interface that promotes a real-time, iterative approach to exploring complex clinical and experimental data. The Harvest architecture capitalizes on standards-based, open source technologies to address multiple functional needs critical to a research and development environment, including domain-specific data modeling, abstraction of complex data models, and a customizable web client.

  6. Integrated Care Model Developed by the Rwanda Biomedical ...

    African Journals Online (AJOL)

    : Integrated Care Model, psychological Interventions, genocide, ... ate a resurgence of memories from the genocide itself. ... interventions to be available throughout the commemo- .... allows easier accessibility with a strong professionally net-.

  7. Integration of DYN3D inside the NURESIM platform

    International Nuclear Information System (INIS)

    Gomez T, A. M.; Sanchez E, V. H.; Kliem, S.; Gommlich, A.; Rohde, U.

    2010-10-01

    The NURISP project (Nuclear Reactor Integrated Simulation Project) is focused on the further development of the European Nuclear Reactor Simulation (NURESIM) platform for advanced numerical reactor design and safety analysis tools. NURESIM is based on an open source platform - called SALOME - that offers flexible and powerful capabilities for pre- and post processing as well as for coupling of multi-physics and multi-scale solutions. The developments within the NURISP project are concentrated in the areas of reactors, physics, thermal hydraulics, multi-physics, and sensitivity and uncertainty methodologies. The aim is to develop experimentally validated advanced simulation tools including capabilities for uncertainty and sensitivity quantification. A unique feature of NURESIM is the flexibility in selecting the solvers for the area of interest and the interpolation and mapping schemes according to the problem under consideration. The Sub Project 3 (S P3) of NURISP is focused on the development of multi-physics methodologies at different scales and covering different physical fields (neutronics, thermal hydraulics and pin mechanics). One of the objectives of S P3 is the development of multi-physics methodologies beyond the state-of-the-art for improved prediction of local safety margins and design at pin-by-pin scale. The Karlsruhe Institute of Technology and the Research Center Dresden-Rossendorf are involved in the integration of the reactor dynamics code DYN3D into the SALOME platform for coupling with a thermal hydraulic sub-channel code (FLICA4) at fuel assembly and pin level. In this paper, the main capabilities of the SALOME platform, the steps for the integration process of DYN3D as well as selected preliminary results obtained for the DYN3D/FLICA4 coupling are presented and discussed. Finally the next steps for the validation of the coupling scheme at fuel assembly and pin basis are given. (Author)

  8. Observation Platform for Dynamic Biomedical and Biotechnology Experiments Using the International Space Station (ISS) Light Microscopy Module (LMM)

    Science.gov (United States)

    Kurk, Michael A. (Andy)

    2015-01-01

    Techshot, Inc., has developed an observation platform for the LMM on the ISS that will enable biomedical and biotechnology experiments. The LMM Dynamic Stage consists of an electronics module and the first two of a planned suite of experiment modules. Specimens and reagent solutions can be injected into a small, hollow microscope slide-the heart of the innovation-via a combination of small reservoirs, pumps, and valves. A life science experiment module allows investigators to load up to two different fluids for on-orbit, real-time image cytometry. Fluids can be changed to initiate a process, fix biological samples, or retrieve suspended cells. A colloid science experiment module conducts microparticle and nanoparticle tests for investigation of colloid self-assembly phenomena. This module includes a hollow glass slide and heating elements for the creation of a thermal gradient from one end of the slide to the other. The electronics module supports both experiment modules and contains a unique illuminator/condenser for bright and dark field and phase contrast illumination, power supplies for two piezoelectric pumps, and controller boards for pumps and valves. This observation platform safely contains internal fluids and will greatly accelerate the research and development (R&D) cycle of numerous experiments, products, and services aboard the ISS.

  9. Biomedical instruments versus toys:a preliminary comparison of force platforms and the nintendo wii balance board - biomed 2011.

    Science.gov (United States)

    Pagnacco, Guido; Oggero, Elena; Wright, Cameron H G

    2011-01-01

    Biomedical sciences rely heavily on devices to acquire and analyze the physiological data needed to understand and model the biological processes of humans and animals. Therefore, the results of the investigations, clinical or academic, depend heavily on the instrumentation used. Unfortunately, all too often the users do not understand their instruments and end up compromising the results of their investigations by choosing an inadequate instrument or by not using it appropriately. One field where this is particularly apparent is posturography: the misconceptions about instruments are so widespread and deep that just recently there have been articles published in scientific journals suggesting the use of a “toy”, the Nintendo Wii Balance Board, instead of instrument grade force platform to acquire posturographic data. Characterizing the tools used for research becomes the first and probably the most important step in producing sound research and clinical results, and in the case of posturographic force platforms and the Nintendo Wii Balance Board a simple experimental setup can be used to find their characteristics. Furthermore, based on the preliminary results of this investigation, a mathematical formula can be used to predict the behavior of a posturographic tool, once its noise characteristics and “dead weight” response are known.

  10. Efficient Sensor Integration on Platforms (NeXOS)

    Science.gov (United States)

    Memè, S.; Delory, E.; Del Rio, J.; Jirka, S.; Toma, D. M.; Martinez, E.; Frommhold, L.; Barrera, C.; Pearlman, J.

    2016-12-01

    In-situ ocean observing platforms provide power and information transmission capability to sensors. Ocean observing platforms can be mobile, such as ships, autonomous underwater vehicles, drifters and profilers, or fixed, such as buoys, moorings and cabled observatories. The process of integrating sensors on platforms can imply substantial engineering time and resources. Constraints range from stringent mechanical constraints to proprietary communication and control firmware. In NeXOS, the implementation of a PUCK plug and play capability is being done with applications to multiple sensors and platforms. This is complemented with a sensor web enablement that addresses the flow of information from sensor to user. Open standards are being tested in order to assess their costs and benefits in existing and future observing systems. Part of the testing implied open-source coding and hardware prototyping of specific control devices in particular for closed commercial platforms where firmware upgrading is not straightforward or possible without prior agreements or service fees. Some platform manufacturers such as European companies ALSEAMAR[1] and NKE Instruments [2] are currently upgrading their control and communication firmware as part of their activities in NeXOS. The sensor development companies Sensorlab[3] SMID[4] and TRIOS [5]upgraded their firmware with this plug and play functionality. Other industrial players in Europe and the US have been sent NeXOS sensors emulators to test the new protocol on their platforms. We are currently demonstrating that with little effort, it is also possible to have such middleware implemented on very low-cost compact computers such as the open Raspberry Pi[6], and have a full end-to-end interoperable communication path from sensor to user with sensor plug and play capability. The result is an increase in sensor integration cost-efficiency and the demonstration will be used to highlight the benefit to users and ocean observatory

  11. Should biomedical research be like Airbnb?

    Directory of Open Access Journals (Sweden)

    Vivien R Bonazzi

    2017-04-01

    Full Text Available The thesis presented here is that biomedical research is based on the trusted exchange of services. That exchange would be conducted more efficiently if the trusted software platforms to exchange those services, if they exist, were more integrated. While simpler and narrower in scope than the services governing biomedical research, comparison to existing internet-based platforms, like Airbnb, can be informative. We illustrate how the analogy to internet-based platforms works and does not work and introduce The Commons, under active development at the National Institutes of Health (NIH and elsewhere, as an example of the move towards platforms for research.

  12. Should biomedical research be like Airbnb?

    Science.gov (United States)

    Bonazzi, Vivien R; Bourne, Philip E

    2017-04-01

    The thesis presented here is that biomedical research is based on the trusted exchange of services. That exchange would be conducted more efficiently if the trusted software platforms to exchange those services, if they exist, were more integrated. While simpler and narrower in scope than the services governing biomedical research, comparison to existing internet-based platforms, like Airbnb, can be informative. We illustrate how the analogy to internet-based platforms works and does not work and introduce The Commons, under active development at the National Institutes of Health (NIH) and elsewhere, as an example of the move towards platforms for research.

  13. The fully integrated biomedical engineering programme at Eindhoven University of Technology.

    Science.gov (United States)

    Slaaf, D W; van Genderen, M H P

    2009-05-01

    The development of a fully integrated biomedical engineering programme (life sciences included from the start) is described. Details are provided about background, implementation, and didactic concept: design centred learning combined with courses. The curriculum has developed into a bachelor-master's programme with two different master's degrees: Master's Degree in Biomedical Engineering and Master's Degree in Medical Engineering. Recently, the programme has adopted semester programming, has included a major and minor in the bachelor's degree phase, and a true bachelor's degree final project. Details about the programme and data about where graduates find jobs are provided in this paper.

  14. Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts

    Science.gov (United States)

    Fiszman, Marcelo; Rindflesch, Thomas C.; Kilicoglu, Halil

    2003-01-01

    Semantic processing provides the potential for producing high quality results in natural language processing (NLP) applications in the biomedical domain. In this paper, we address a specific semantic phenomenon, the hypernymic proposition, and concentrate on integrating the interpretation of such predications into a more general semantic processor in order to improve overall accuracy. A preliminary evaluation assesses the contribution of hypernymic propositions in providing more specific semantic predications and thus improving effectiveness in retrieving treatment propositions in MEDLINE abstracts. Finally, we discuss the generalization of this methodology to additional semantic propositions as well as other types of biomedical texts. PMID:14728170

  15. Ethics and integrative medicine: moving beyond the biomedical model.

    Science.gov (United States)

    Guinn, D E

    2001-01-01

    For the most part, those who have written on the ethics of complementary and alternative medicine (CAM) and integrative medicine have attempted simply to apply traditional bioethics (in the form of principles of autonomy, beneficence, nonmaleficence, and justice) to this new area of healthcare. In this article I argue that adopting the practices of CAM requires a new ethical understanding that incorporates the values implicit in those practices. The characteristics of CAM and conventional medicine can be translated into the language of healthcare values in a variety of ways. I suggest that they support 5 core values: integrated humanity, ecological integrity, naturalism, relationalism, and spiritualism. Characteristics of both CAM and conventional medicine are present in value. What is now thought of as principlism is, in this understanding, simply a subset within these values.

  16. REopt: A Platform for Energy System Integration and Optimization: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Simpkins, T.; Cutler, D.; Anderson, K.; Olis, D.; Elgqvist, E.; Callahan, M.; Walker, A.

    2014-08-01

    REopt is NREL's energy planning platform offering concurrent, multi-technology integration and optimization capabilities to help clients meet their cost savings and energy performance goals. The REopt platform provides techno-economic decision-support analysis throughout the energy planning process, from agency-level screening and macro planning to project development to energy asset operation. REopt employs an integrated approach to optimizing a site?s energy costs by considering electricity and thermal consumption, resource availability, complex tariff structures including time-of-use, demand and sell-back rates, incentives, net-metering, and interconnection limits. Formulated as a mixed integer linear program, REopt recommends an optimally-sized mix of conventional and renewable energy, and energy storage technologies; estimates the net present value associated with implementing those technologies; and provides the cost-optimal dispatch strategy for operating them at maximum economic efficiency. The REopt platform can be customized to address a variety of energy optimization scenarios including policy, microgrid, and operational energy applications. This paper presents the REopt techno-economic model along with two examples of recently completed analysis projects.

  17. A game-based platform for crowd-sourcing biomedical image diagnosis and standardized remote training and education of diagnosticians

    Science.gov (United States)

    Feng, Steve; Woo, Minjae; Chandramouli, Krithika; Ozcan, Aydogan

    2015-03-01

    Over the past decade, crowd-sourcing complex image analysis tasks to a human crowd has emerged as an alternative to energy-inefficient and difficult-to-implement computational approaches. Following this trend, we have developed a mathematical framework for statistically combining human crowd-sourcing of biomedical image analysis and diagnosis through games. Using a web-based smart game (BioGames), we demonstrated this platform's effectiveness for telediagnosis of malaria from microscopic images of individual red blood cells (RBCs). After public release in early 2012 (http://biogames.ee.ucla.edu), more than 3000 gamers (experts and non-experts) used this BioGames platform to diagnose over 2800 distinct RBC images, marking them as positive (infected) or negative (non-infected). Furthermore, we asked expert diagnosticians to tag the same set of cells with labels of positive, negative, or questionable (insufficient information for a reliable diagnosis) and statistically combined their decisions to generate a gold standard malaria image library. Our framework utilized minimally trained gamers' diagnoses to generate a set of statistical labels with an accuracy that is within 98% of our gold standard image library, demonstrating the "wisdom of the crowd". Using the same image library, we have recently launched a web-based malaria training and educational game allowing diagnosticians to compare their performance with their peers. After diagnosing a set of ~500 cells per game, diagnosticians can compare their quantified scores against a leaderboard and view their misdiagnosed cells. Using this platform, we aim to expand our gold standard library with new RBC images and provide a quantified digital tool for measuring and improving diagnostician training globally.

  18. A game-based crowdsourcing platform for rapidly training middle and high school students to perform biomedical image analysis

    Science.gov (United States)

    Feng, Steve; Woo, Min-jae; Kim, Hannah; Kim, Eunso; Ki, Sojung; Shao, Lei; Ozcan, Aydogan

    2016-03-01

    We developed an easy-to-use and widely accessible crowd-sourcing tool for rapidly training humans to perform biomedical image diagnostic tasks and demonstrated this platform's ability on middle and high school students in South Korea to diagnose malaria infected red-blood-cells (RBCs) using Giemsa-stained thin blood smears imaged under light microscopes. We previously used the same platform (i.e., BioGames) to crowd-source diagnostics of individual RBC images, marking them as malaria positive (infected), negative (uninfected), or questionable (insufficient information for a reliable diagnosis). Using a custom-developed statistical framework, we combined the diagnoses from both expert diagnosticians and the minimally trained human crowd to generate a gold standard library of malaria-infection labels for RBCs. Using this library of labels, we developed a web-based training and educational toolset that provides a quantified score for diagnosticians/users to compare their performance against their peers and view misdiagnosed cells. We have since demonstrated the ability of this platform to quickly train humans without prior training to reach high diagnostic accuracy as compared to expert diagnosticians. Our initial trial group of 55 middle and high school students has collectively played more than 170 hours, each demonstrating significant improvements after only 3 hours of training games, with diagnostic scores that match expert diagnosticians'. Next, through a national-scale educational outreach program in South Korea we recruited >1660 students who demonstrated a similar performance level after 5 hours of training. We plan to further demonstrate this tool's effectiveness for other diagnostic tasks involving image labeling and aim to provide an easily-accessible and quickly adaptable framework for online training of new diagnosticians.

  19. Photonic integration and photonics-electronics convergence on silicon platform

    CERN Document Server

    Liu, Jifeng; Baba, Toshihiko; Vivien, Laurent; Xu, Dan-Xia

    2015-01-01

    Silicon photonics technology, which has the DNA of silicon electronics technology, promises to provide a compact photonic integration platform with high integration density, mass-producibility, and excellent cost performance. This technology has been used to develop and to integrate various photonic functions on silicon substrate. Moreover, photonics-electronics convergence based on silicon substrate is now being pursued. Thanks to these features, silicon photonics will have the potential to be a superior technology used in the construction of energy-efficient cost-effective apparatuses for various applications, such as communications, information processing, and sensing. Considering the material characteristics of silicon and difficulties in microfabrication technology, however, silicon by itself is not necessarily an ideal material. For example, silicon is not suitable for light emitting devices because it is an indirect transition material. The resolution and dynamic range of silicon-based interference de...

  20. Biomedical text mining for research rigor and integrity: tasks, challenges, directions.

    Science.gov (United States)

    Kilicoglu, Halil

    2017-06-13

    An estimated quarter of a trillion US dollars is invested in the biomedical research enterprise annually. There is growing alarm that a significant portion of this investment is wasted because of problems in reproducibility of research findings and in the rigor and integrity of research conduct and reporting. Recent years have seen a flurry of activities focusing on standardization and guideline development to enhance the reproducibility and rigor of biomedical research. Research activity is primarily communicated via textual artifacts, ranging from grant applications to journal publications. These artifacts can be both the source and the manifestation of practices leading to research waste. For example, an article may describe a poorly designed experiment, or the authors may reach conclusions not supported by the evidence presented. In this article, we pose the question of whether biomedical text mining techniques can assist the stakeholders in the biomedical research enterprise in doing their part toward enhancing research integrity and rigor. In particular, we identify four key areas in which text mining techniques can make a significant contribution: plagiarism/fraud detection, ensuring adherence to reporting guidelines, managing information overload and accurate citation/enhanced bibliometrics. We review the existing methods and tools for specific tasks, if they exist, or discuss relevant research that can provide guidance for future work. With the exponential increase in biomedical research output and the ability of text mining approaches to perform automatic tasks at large scale, we propose that such approaches can support tools that promote responsible research practices, providing significant benefits for the biomedical research enterprise. Published by Oxford University Press 2017. This work is written by a US Government employee and is in the public domain in the US.

  1. Chiral DOTA chelators as an improved platform for biomedical imaging and therapy applications.

    Science.gov (United States)

    Dai, Lixiong; Jones, Chloe M; Chan, Wesley Ting Kwok; Pham, Tiffany A; Ling, Xiaoxi; Gale, Eric M; Rotile, Nicholas J; Tai, William Chi-Shing; Anderson, Carolyn J; Caravan, Peter; Law, Ga-Lai

    2018-02-27

    Despite established clinical utilisation, there is an increasing need for safer, more inert gadolinium-based contrast agents, and for chelators that react rapidly with radiometals. Here we report the syntheses of a series of chiral DOTA chelators and their corresponding metal complexes and reveal properties that transcend the parent DOTA compound. We incorporated symmetrical chiral substituents around the tetraaza ring, imparting enhanced rigidity to the DOTA cavity, enabling control over the range of stereoisomers of the lanthanide complexes. The Gd chiral DOTA complexes are shown to be orders of magnitude more inert to Gd release than [GdDOTA] - . These compounds also exhibit very-fast water exchange rates in an optimal range for high field imaging. Radiolabeling studies with (Cu-64/Lu-177) also demonstrate faster labelling properties. These chiral DOTA chelators are alternative general platforms for the development of stable, high relaxivity contrast agents, and for radiometal complexes used for imaging and/or therapy.

  2. Integration of the program TNXYZ in the platform SALOME

    International Nuclear Information System (INIS)

    Chaparro V, F. J.; Silva A, L.; Del Valle G, E.; Gomez T, A. M.; Vargas E, S.

    2013-10-01

    This work presents the procedure realized to integrate the code TNXYZ like a processing tool to the graphic simulation platform SALOME. The code TNXYZ solves the neutron transport equation in stationary state, for several energy groups, quantizing the angular variable by the discrete ordinates method and the space variable by nodal methods. The platform SALOME is a graphic surrounding designed for the construction, edition and simulation of mechanical models focused to the industry and contrary to other software, it allows to integrate external source codes to the surrounding, to form a complete scheme of execution, supervision, pre and post information processing. The code TNXYZ was programmed in the 90s in a Fortran compiler, but to be used at the present time the code should be actualized to the current compiler characteristics; also, in the original scheme was carried out a modularization process, that is to say, the main program was divided in sections where the code carries out important operations, with the intention of flexibility the data extraction process along its processing sequence and that can be useful in a later development of coupling. Finally, to verify the integration a fuel assembly BWR was modeled, as well as a control cell. The cross sections were obtained with the Monte Carlo Serpent code. Some results obtained with Serpent were used to verify and to begin with the validation of the code, being obtained an acceptable comparison in the infinite multiplication factor. The validation process should extend and one has planned to present in a future work. This work is part of the development of the research group formed between the Escuela Superior de Fisica y Matematicas del Instituto Politecnico Nacional (IPN) and the Instituto Nacional de Investigaciones Nucleares (ININ) in which a simulation Mexican platform of nuclear reactors is developed. (Author)

  3. Voltage margin control for offshore multi-use platform integration

    DEFF Research Database (Denmark)

    Mier, V.; Casielles, P.G.; Koto, J.

    This paper discusses a multiterminal direct current (MTDC) connection proposed for integration of offshore multi-use platforms into continental grids. Voltage source converters (VSC) were selected for their suitability for multiterminal dc systems and for their flexibility in control. A five...... terminal VSC-MTDC which includes offshore generation, storage, loads and ac connection, was modeled and simulated in DigSILENT Power Factory software. Voltage margin method has been used for reliable operation of the MTDC system without the need of fast communication. Simulation results show......, sell or store energy attending to the price in the electricity market....

  4. Integration of fractal biosensor in a digital microfluidic platform

    KAUST Repository

    Mashraei, Yousof

    2015-11-01

    Fractal capacitive electrodes have been successfully integrated into a digital microfluidic open-platform. These electrodes perform actuation and withstand voltages up to 300V without insulation-layer breakdown. They were used to quantify the concentration levels of C-reactive protein (CRP) to determine the risk of cardiovascular disease. The capacitance increased sevenfold and stabilized in less than 5 minutes. The sensor shows a decreasing trend of capacitance readouts with the increase of concentrations. The same immunoassay was tested with untreated electrodes and showed no significant response, which suggests that immobilization was necessary. This configuration allows the electrodes to be used as biosensors.

  5. Integration of a Copper-Containing Biohybrid (CuHARS with Cellulose for Subsequent Degradation and Biomedical Control

    Directory of Open Access Journals (Sweden)

    Anik Karan

    2018-04-01

    Full Text Available We previously described the novel synthesis of a copper high-aspect ratio structure (CuHARS biohybrid material using cystine. While extremely stable in water, CuHARS is completely (but slowly degradable in cellular media. Here, integration of the CuHARS into cellulose matrices was carried out to provide added control for CuHARS degradation. Synthesized CuHARS was concentrated by centrifugation and then dried. The weighed mass was re-suspended in water. CuHARS was stable in water for months without degradation. In contrast, 25 μg/mL of the CuHARS in complete cell culture media was completely degraded (slowly in 18 days under physiological conditions. Stable integration of CuHARS into cellulose matrices was achieved through assembly by mixing cellulose micro- and nano-fibers and CuHARS in an aqueous (pulp mixture phase, followed by drying. Additional materials were integrated to make the hybrids magnetically susceptible. The cellulose-CuHARS composite films could be transferred, weighed, and cut into usable pieces; they maintained their form after rehydration in water for at least 7 days and were compatible with cell culture studies using brain tumor (glioma cells. These studies demonstrate utility of a CuHARS-cellulose biohybrid for applied applications including: (1 a platform for biomedical tracking and (2 integration into a 2D/3D matrix using natural products (cellulose.

  6. Integrative set enrichment testing for multiple omics platforms

    Directory of Open Access Journals (Sweden)

    Poisson Laila M

    2011-11-01

    Full Text Available Abstract Background Enrichment testing assesses the overall evidence of differential expression behavior of the elements within a defined set. When we have measured many molecular aspects, e.g. gene expression, metabolites, proteins, it is desirable to assess their differential tendencies jointly across platforms using an integrated set enrichment test. In this work we explore the properties of several methods for performing a combined enrichment test using gene expression and metabolomics as the motivating platforms. Results Using two simulation models we explored the properties of several enrichment methods including two novel methods: the logistic regression 2-degree of freedom Wald test and the 2-dimensional permutation p-value for the sum-of-squared statistics test. In relation to their univariate counterparts we find that the joint tests can improve our ability to detect results that are marginal univariately. We also find that joint tests improve the ranking of associated pathways compared to their univariate counterparts. However, there is a risk of Type I error inflation with some methods and self-contained methods lose specificity when the sets are not representative of underlying association. Conclusions In this work we show that consideration of data from multiple platforms, in conjunction with summarization via a priori pathway information, leads to increased power in detection of genomic associations with phenotypes.

  7. Dendritic silica particles with center-radial pore channels: promising platforms for catalysis and biomedical applications.

    Science.gov (United States)

    Du, Xin; Qiao, Shi Zhang

    2015-01-27

    Dendritic silica micro-/nanoparticles with center-radial pore structures, a kind of newly created porous material, have attracted considerable attention owing to their unique open three-dimensional dendritic superstructures with large pore channels and highly accessible internal surface areas compared with conventional mesoporous silica nanoparticles (MSNs). They are very promising platforms for a variety of applications in catalysis and nanomedicine. In this review, their unique structural characteristics and properties are first analyzed, then novel and interesting synthesis methods associated with the possible formation mechanisms are summarized to provide material scientists some inspiration for the preparation of this kind of dendritic particles. Subsequently, a few examples of interesting applications are presented, mainly in catalysis, biomedicine, and other important fields such as for sacrificial templates and functional coatings. The review is concluded with an outlook on the prospects and challenges in terms of their controlled synthesis and potential applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Hybrid Integrated Silicon Microfluidic Platform for Fluorescence Based Biodetection

    Directory of Open Access Journals (Sweden)

    André Darveau

    2007-09-01

    Full Text Available The desideratum to develop a fully integrated Lab-on-a-chip device capable ofrapid specimen detection for high throughput in-situ biomedical diagnoses and Point-of-Care testing applications has called for the integration of some of the novel technologiessuch as the microfluidics, microphotonics, immunoproteomics and Micro ElectroMechanical Systems (MEMS. In the present work, a silicon based microfluidic device hasbeen developed for carrying out fluorescence based immunoassay. By hybrid attachment ofthe microfluidic device with a Spectrometer-on-chip, the feasibility of synthesizing anintegrated Lab-on-a-chip type device for fluorescence based biosensing has beendemonstrated. Biodetection using the microfluidic device has been carried out usingantigen sheep IgG and Alexafluor-647 tagged antibody particles and the experimentalresults prove that silicon is a compatible material for the present application given thevarious advantages it offers such as cost-effectiveness, ease of bulk microfabrication,superior surface affinity to biomolecules, ease of disposability of the device etc., and is thussuitable for fabricating Lab-on-a-chip type devices.

  9. Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform

    Directory of Open Access Journals (Sweden)

    List Markus

    2017-06-01

    Full Text Available Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows. To address this challenge, several Docker containers need to be instantiated and properly integrated, which complicates the software deployment process unnecessarily. Here, we demonstrate how an extension to Docker, Docker compose, can be used to mitigate these problems by providing a unified setup routine that deploys several tools in an integrated fashion. We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable in just two lines of codes.

  10. Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

    Science.gov (United States)

    List, Markus

    2017-06-10

    Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows. To address this challenge, several Docker containers need to be instantiated and properly integrated, which complicates the software deployment process unnecessarily. Here, we demonstrate how an extension to Docker, Docker compose, can be used to mitigate these problems by providing a unified setup routine that deploys several tools in an integrated fashion. We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable in just two lines of codes.

  11. An Approach to Integrating Health Disparities within Undergraduate Biomedical Engineering Education.

    Science.gov (United States)

    Vazquez, Maribel; Marte, Otto; Barba, Joseph; Hubbard, Karen

    2017-11-01

    Health disparities are preventable differences in the incidence, prevalence and burden of disease among communities targeted by gender, geographic location, ethnicity and/or socio-economic status. While biomedical research has identified partial origin(s) of divergent burden and impact of disease, the innovation needed to eradicate health disparities in the United States requires unique engagement from biomedical engineers. Increasing awareness of the prevalence and consequences of health disparities is particularly attractive to today's undergraduates, who have undauntedly challenged paradigms believed to foster inequality. Here, the Department of Biomedical Engineering at The City College of New York (CCNY) has leveraged its historical mission of access-and-excellence to integrate the study of health disparities into undergraduate BME curricula. This article describes our novel approach in a multiyear study that: (i) Integrated health disparities modules at all levels of the required undergraduate BME curriculum; (ii) Developed opportunities to include impacts of health disparities into undergraduate BME research projects and mentored High School summer STEM training; and (iii) Established health disparities-based challenges as BME capstone design and/or independent entrepreneurship projects. Results illustrate the rising awareness of health disparities among the youngest BMEs-to-be, as well as abundant undergraduate desire to integrate health disparities within BME education and training.

  12. An ultra-efficient nonlinear planar integrated platform for optical signal processing and generation

    DEFF Research Database (Denmark)

    Pu, Minhao; Ottaviano, Luisa; Semenova, Elizaveta

    2017-01-01

    This paper will discuss the recently developed integrated platform: AlGaAs-oninsulator and its broad range of nonlinear applications. Recent demonstrations of broadband optical signal processing and efficient frequency comb generations in this platform will be reviewed.......This paper will discuss the recently developed integrated platform: AlGaAs-oninsulator and its broad range of nonlinear applications. Recent demonstrations of broadband optical signal processing and efficient frequency comb generations in this platform will be reviewed....

  13. Integration of Multi-Modal Biomedical Data to Predict Cancer Grade and Patient Survival.

    Science.gov (United States)

    Phan, John H; Hoffman, Ryan; Kothari, Sonal; Wu, Po-Yen; Wang, May D

    2016-02-01

    The Big Data era in Biomedical research has resulted in large-cohort data repositories such as The Cancer Genome Atlas (TCGA). These repositories routinely contain hundreds of matched patient samples for genomic, proteomic, imaging, and clinical data modalities, enabling holistic and multi-modal integrative analysis of human disease. Using TCGA renal and ovarian cancer data, we conducted a novel investigation of multi-modal data integration by combining histopathological image and RNA-seq data. We compared the performances of two integrative prediction methods: majority vote and stacked generalization. Results indicate that integration of multiple data modalities improves prediction of cancer grade and outcome. Specifically, stacked generalization, a method that integrates multiple data modalities to produce a single prediction result, outperforms both single-data-modality prediction and majority vote. Moreover, stacked generalization reveals the contribution of each data modality (and specific features within each data modality) to the final prediction result and may provide biological insights to explain prediction performance.

  14. Survey of biomedical and environental data bases, models, and integrated computer systems at Argonne National Laboratory

    International Nuclear Information System (INIS)

    Murarka, I.P.; Bodeau, D.J.; Scott, J.M.; Huebner, R.H.

    1978-08-01

    This document contains an inventory (index) of information resources pertaining to biomedical and environmental projects at Argonne National Laboratory--the information resources include a data base, model, or integrated computer system. Entries are categorized as models, numeric data bases, bibliographic data bases, or integrated hardware/software systems. Descriptions of the Information Coordination Focal Point (ICFP) program, the system for compiling this inventory, and the plans for continuing and expanding it are given, and suggestions for utilizing the services of the ICFP are outlined

  15. Survey of biomedical and environental data bases, models, and integrated computer systems at Argonne National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Murarka, I.P.; Bodeau, D.J.; Scott, J.M.; Huebner, R.H.

    1978-08-01

    This document contains an inventory (index) of information resources pertaining to biomedical and environmental projects at Argonne National Laboratory--the information resources include a data base, model, or integrated computer system. Entries are categorized as models, numeric data bases, bibliographic data bases, or integrated hardware/software systems. Descriptions of the Information Coordination Focal Point (ICFP) program, the system for compiling this inventory, and the plans for continuing and expanding it are given, and suggestions for utilizing the services of the ICFP are outlined.

  16. Plasmonic nanofocusing of light in an integrated silicon photonics platform.

    Science.gov (United States)

    Desiatov, Boris; Goykhman, Ilya; Levy, Uriel

    2011-07-04

    The capability to focus electromagnetic energy at the nanoscale plays an important role in nanoscinece and nanotechnology. It allows enhancing light matter interactions at the nanoscale with applications related to nonlinear optics, light emission and light detection. It may also be used for enhancing resolution in microscopy, lithography and optical storage systems. Hereby we propose and experimentally demonstrate the nanoscale focusing of surface plasmons by constructing an integrated plasmonic/photonic on chip nanofocusing device in silicon platform. The device was tested directly by measuring the optical intensity along it using a near-field microscope. We found an order of magnitude enhancement of the intensity at the tip's apex. The spot size is estimated to be 50 nm. The demonstrated device may be used as a building block for "lab on a chip" systems and for enhancing light matter interactions at the apex of the tip.

  17. Technology for 3D System Integration for Flexible Wireless Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Wen-Cheng Kuo

    2018-05-01

    Full Text Available This paper presents a new 3D bottom-up packing technology for integrating a chip, an induction coil, and interconnections for flexible wireless biomedical applications. Parylene was used as a flexible substrate for the bottom-up embedding of the chip, insulation layer, interconnection, and inductors to form a flexible wireless biomedical microsystem. The system can be implanted on or inside the human body. A 50-μm gold foil deposited through laser micromachining by using a picosecond laser was used as an inductor to yield a higher quality factor than that yielded by thickness-increasing methods such as the fold-and-bond method or thick-metal electroplating method at the operation frequency of 1 MHz. For system integration, parylene was used as a flexible substrate, and the contact pads and connections between the coil and chip were generated using gold deposition. The advantage of the proposed process can integrate the chip and coil vertically to generate a single biocompatible system in order to reduce required area. The proposed system entails the use of 3D integrated circuit packaging concepts to integrate the chip and coil. The results validated the feasibility of this technology.

  18. InP-based generic foundry platform for photonic integrated circuits

    NARCIS (Netherlands)

    Augustin, L.M.; Lemos Alvares Dos Santos, R.M.; den Haan, E.; Kleijn, S.E.F.; Thijs, P.J.A.; Latkowski, S.; Zhao, D.; Yao, W.; Bolk, J.; Ambrosius, H.P.M.M.; Mingaleev, S.; Richter, A.; Bakker, A.; Korthorst, T.

    2017-01-01

    The standardization of photonic integration processes for InP has led to versatile and easily accessible generic integration platforms. The generic integration platforms enable the realization of a broad range of applications and lead to a dramatic cost reduction in the development costs of photonic

  19. Integrating biomedical and herbal medicine in Ghana - experiences from the Kumasi South Hospital: a qualitative study.

    Science.gov (United States)

    Boateng, Millicent Addai; Danso-Appiah, Anthony; Turkson, Bernard Kofi; Tersbøl, Britt Pinkowski

    2016-07-07

    Over the past decade there has been growing interest in the use of herbal medicine both in developed and developing countries. Given the high proportion of patients using herbal medicine in Ghana, some health facilities have initiated implementation of herbal medicine as a component of their healthcare delivery. However, the extent to which herbal medicine has been integrated in Ghanaian health facilities, how integration is implemented and perceived by different stakeholders has not been documented. The study sought to explore these critical issues at the Kumasi South Hospital (KSH) and outline the challenges and motivations of the integration process. Qualitative phenomenological exploratory study design involving fieldwork observations, focus group discussion, in-depth interviews and key informants' interviews was employed to collect data. Policies and protocols outlining the definition, process and goals of integration were lacking, with respondents sharing different views about the purpose and value of integration of herbal medicine within public health facilities. Key informants were supportive of the initiative. Whilst biomedical health workers perceived the system to be parallel than integrated, health personnel providing herbal medicine perceived the system as integrated. Most patients were not aware of the herbal clinic in the hospital but those who had utilized services of the herbal clinic viewed the clinic as part of the hospital. The lack of a regulatory policy and protocol for the integration seemed to have led to the different perception of the integration. Policy and protocol to guide the integration are key recommendations.

  20. A wireless sensor tag platform for container security and integrity

    Science.gov (United States)

    Amaya, Ivan A.; Cree, Johnathan V.; Mauss, Fredrick J.

    2011-04-01

    Cargo containers onboard ships are widely used in the global supply chain. The need for container security is evidenced by the Container Security Initiative launched by the U.S. Bureau of Customs and Border Protection (CBP). One method of monitoring cargo containers is using low power wireless sensor tags. The wireless sensor tags are used to set up a network that is comprised of tags internal to the container and a central device. The sensor network reports alarms and other anomalies to a central device, which then relays the message to an outside network upon arrival at the destination port. This allows the port authorities to have knowledge of potential security or integrity issues before physically examining the container. Challenges of using wireless sensor tag networks for container security include battery life, size, environmental conditions, information security, and cost among others. PNNL developed an active wireless sensor tag platform capable of reporting data wirelessly to a central node as well as logging data to nonvolatile memory. The tags, operate at 2.4 GHz over an IEEE 802.15.4 protocol, and were designed to be distributed throughout the inside of a shipping container in the upper support frame. The tags are mounted in a housing that allows for simple and efficient installation or removal prior to, during, or after shipment. The distributed tags monitor the entire container volume. The sensor tag platform utilizes low power electronics and provides an extensible sensor interface for incorporating a wide range of sensors including chemical, biological, and environmental sensors.

  1. VOLTTRON Lite: Integration Platform for the Transactional Network

    Energy Technology Data Exchange (ETDEWEB)

    Haack, Jereme N.; Katipamula, Srinivas; Akyol, Bora A.; Lutes, Robert G.

    2013-10-31

    In FY13, Pacific Northwest National Laboratory (PNNL) with funding from the Department of Energy’s (DOE’s) Building Technologies Office (BTO) designed, prototyped and tested a transactional network platform. The platform is intended to support energy, operational and financial transactions between any networked entities (equipment, organizations, buildings, grid, etc.). Initially, in FY13, the concept demonstrated transactions between packaged rooftop units (RTUs) and the electric grid using applications or “agents” that reside on the platform, on the equipment, on local building controller or in the Cloud. This document describes the core of the transactional network platform, the Volttron Lite™ software and associated services hosted on the platform. Future enhancements are also discussed. The appendix of the document provides examples of how to use the various services hosted on the platform.

  2. a Workflow for UAV's Integration Into a Geodesign Platform

    Science.gov (United States)

    Anca, P.; Calugaru, A.; Alixandroae, I.; Nazarie, R.

    2016-06-01

    This paper presents a workflow for the development of various Geodesign scenarios. The subject is important in the context of identifying patterns and designing solutions for a Smart City with optimized public transportation, efficient buildings, efficient utilities, recreational facilities a.s.o.. The workflow describes the procedures starting with acquiring data in the field, data processing, orthophoto generation, DTM generation, integration into a GIS platform and analyzing for a better support for Geodesign. Esri's City Engine is used mostly for 3D modeling capabilities that enable the user to obtain 3D realistic models. The workflow uses as inputs information extracted from images acquired using UAVs technologies, namely eBee, existing 2D GIS geodatabases, and a set of CGA rules. The method that we used further, is called procedural modeling, and uses rules in order to extrude buildings, the street network, parcel zoning and side details, based on the initial attributes from the geodatabase. The resulted products are various scenarios for redesigning, for analyzing new exploitation sites. Finally, these scenarios can be published as interactive web scenes for internal, groups or pubic consultation. In this way, problems like the impact of new constructions being build, re-arranging green spaces or changing routes for public transportation, etc. are revealed through impact and visibility analysis or shadowing analysis and are brought to the citizen's attention. This leads to better decisions.

  3. An integrated platform for assessing biologics (Conference Presentation)

    Science.gov (United States)

    Schein, Perry; O'Dell, Dakota; Erickson, David

    2016-04-01

    Protein therapeutics are a rapidly growing portion of the pharmaceuticals market and have many significant advantages over traditional small molecule drugs. As this market expands, however, critical regulatory and quality control issues remain, most notably the problem of protein aggregation. Individual target proteins often aggregate into larger masses which trigger an immune response in the body, which can reduce the efficacy of the drug for its intended purpose, or cause serious anaphylactic side-effects. Although detecting and minimizing aggregate formation is critical to ensure an effective product, aggregation dynamics are often highly complicated and there is little hope of reliable prediction and prevention from first principles. This problem is compounded for aggregates in the subvisible range of 100 nm to 10 micrometers where traditional techniques for detecting aggregates have significant limitations. Here, we present an integrated optofluidic platform for detecting nanoscale protein aggregates and characterizing interactions between these aggregates and a reference surface. By delivering light to a solution of proteins with an optical waveguide, scattered light from individual protein aggregates can be detected and analyzed to determine the force profile between each particle and the waveguide surface. Unlike existing methods which only determine size or charge, our label-free screening technique can directly measure the surface interaction forces between single aggregates and the glass substrate. This direct measurement capability may allow for better empirical predictions of the stability of protein aggregates during drug manufacturing and storage.

  4. A service platform architecture design towards a light integration of heterogeneous systems in the wellbeing domain.

    Science.gov (United States)

    Yang, Yaojin; Ahtinen, Aino; Lahteenmaki, Jaakko; Nyman, Petri; Paajanen, Henrik; Peltoniemi, Teijo; Quiroz, Carlos

    2007-01-01

    System integration is one of the major challenges for building wellbeing or healthcare related information systems. In this paper, we are going to share our experiences on how to design a service platform called Nuadu service platform, for providing integrated services in occupational health promotion and health risk management through two heterogeneous systems. Our design aims for a light integration covering the layers, from data through service up to presentation, while maintaining the integrity of the underlying systems.

  5. Future of Hydroinformatics: Towards Open, Integrated and Interactive Online Platforms

    Science.gov (United States)

    Demir, I.; Krajewski, W. F.

    2012-12-01

    Hydroinformatics is a domain of science and technology dealing with the management of information in the field of hydrology (IWA, 2011). There is the need for innovative solutions to the challenges towards open information, integration, and communication in the Internet. This presentation provides an overview of the trends and challenges in the future of hydroinformatics, and demonstrates an information system, Iowa Flood Information System (IFIS), developed within the light of these challenges. The IFIS is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, flood-related data, information and interactive visualizations for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and rainfall conditions are available in the IFIS by streaming data from automated IFC bridge sensors, USGS stream gauges, NEXRAD radars, and NWS forecasts. 2D and 3D interactive visualizations in the IFIS make the data more understandable to general public. Users are able to filter data sources for their communities and selected rivers. The data and information on IFIS is also accessible through web services and mobile applications. The IFIS is optimized for various browsers and screen sizes to provide access through multiple platforms including tablets and mobile devices. The IFIS includes a rainfall-runoff forecast model to provide a five-day flood risk estimate for more

  6. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

    Directory of Open Access Journals (Sweden)

    Sai Lakshmi Subramanian

    2015-08-01

    Full Text Available The large diversity and volume of extracellular RNA (exRNA data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b retrieval of a data slice from the exRNA Atlas for integrative analysis and (c interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.

  7. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

    Science.gov (United States)

    Subramanian, Sai Lakshmi; Kitchen, Robert R; Alexander, Roger; Carter, Bob S; Cheung, Kei-Hoi; Laurent, Louise C; Pico, Alexander; Roberts, Lewis R; Roth, Matthew E; Rozowsky, Joel S; Su, Andrew I; Gerstein, Mark B; Milosavljevic, Aleksandar

    2015-01-01

    The large diversity and volume of extracellular RNA (exRNA) data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a) selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b) retrieval of a data slice from the exRNA Atlas for integrative analysis and (c) interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.

  8. An integrative clinical database and diagnostics platform for biomarker identification and analysis in ion mobility spectra of human exhaled air

    DEFF Research Database (Denmark)

    Schneider, Till; Hauschild, Anne-Christin; Baumbach, Jörg Ingo

    2013-01-01

    data integration and semi-automated data analysis, in particular with regard to the rapid data accumulation, emerging from the high-throughput nature of the MCC/IMS technology. Here, we present a comprehensive database application and analysis platform, which combines metabolic maps with heterogeneous...... biomedical data in a well-structured manner. The design of the database is based on a hybrid of the entity-attribute-value (EAV) model and the EAV-CR, which incorporates the concepts of classes and relationships. Additionally it offers an intuitive user interface that provides easy and quick access...... to have a clear understanding of the detailed composition of human breath. Therefore, in addition to the clinical studies, there is a need for a flexible and comprehensive centralized data repository, which is capable of gathering all kinds of related information. Moreover, there is a demand for automated...

  9. 2011 Biomass Program Platform Peer Review. Integrated Biorefineries

    Energy Technology Data Exchange (ETDEWEB)

    Rossmeissl, Neil [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States)

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s IBR Platform Review meeting.

  10. Towards Digital Integration: Platform Thinking in the Fashion Business

    DEFF Research Database (Denmark)

    Schou, Finn

    2005-01-01

    ¬quately to changing demands in their business activities. However many companies find it dif¬ficult to achieve the full poten¬tial of these technologies as practical advices that can help companies and the management in their decision-making, selecting and implementing new technology are rare (Boer and Krabbendam......, 1998). The intention of this paper is, through illustrative case studies from France and Denmark within the highly competitive business of optical frame design (fashion) to present a model for strategy as well as a practical model for improvement of time to market of styling objects by use of digital...... platforms. Aspects are: 1) selection of platform from a strategic point of view, 2) selection of 2D and 3D CAD from a practical point of view and 3) creation and implementation of digital platforms. Finally, briefly aspects of teaching of platform theory at the department of Architecture & Industrial design...

  11. A perspective for biomedical data integration: Design of databases for flow cytometry

    Directory of Open Access Journals (Sweden)

    Lakoumentas John

    2008-02-01

    Full Text Available Abstract Background The integration of biomedical information is essential for tackling medical problems. We describe a data model in the domain of flow cytometry (FC allowing for massive management, analysis and integration with other laboratory and clinical information. The paper is concerned with the proper translation of the Flow Cytometry Standard (FCS into a relational database schema, in a way that facilitates end users at either doing research on FC or studying specific cases of patients undergone FC analysis Results The proposed database schema provides integration of data originating from diverse acquisition settings, organized in a way that allows syntactically simple queries that provide results significantly faster than the conventional implementations of the FCS standard. The proposed schema can potentially achieve up to 8 orders of magnitude reduction in query complexity and up to 2 orders of magnitude reduction in response time for data originating from flow cytometers that record 256 colours. This is mainly achieved by managing to maintain an almost constant number of data-mining procedures regardless of the size and complexity of the stored information. Conclusion It is evident that using single-file data storage standards for the design of databases without any structural transformations significantly limits the flexibility of databases. Analysis of the requirements of a specific domain for integration and massive data processing can provide the necessary schema modifications that will unlock the additional functionality of a relational database.

  12. Platforms.

    Science.gov (United States)

    Josko, Deborah

    2014-01-01

    The advent of DNA sequencing technologies and the various applications that can be performed will have a dramatic effect on medicine and healthcare in the near future. There are several DNA sequencing platforms available on the market for research and clinical use. Based on the medical laboratory scientist or researcher's needs and taking into consideration laboratory space and budget, one can chose which platform will be beneficial to their institution and their patient population. Although some of the instrument costs seem high, diagnosing a patient quickly and accurately will save hospitals money with fewer hospital stays and targeted treatment based on an individual's genetic make-up. By determining the type of disease an individual has, based on the mutations present or having the ability to prescribe the appropriate antimicrobials based on the knowledge of the organism's resistance patterns, the clinician will be better able to treat and diagnose a patient which ultimately will improve patient outcomes and prognosis.

  13. Wireless, smartphone controlled potentiostat integrated with lab-on-disc platform

    DEFF Research Database (Denmark)

    Cheng, Chung-Hsiang; Zor, Kinga; Wang, Jen-Hung

    A smartphone controlled wireless data transmitting and inductive powering Power Lab-on-disc (PLoD) platform is developed based on 2.4 GHz Bluetooth and 205 kHz Qi techniques, respectively. A potentiostat is integrated on the PLoD platform, and amperometric measurements are performed. The wireless...

  14. Biomedical photonics handbook biomedical diagnostics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

    Shaped by Quantum Theory, Technology, and the Genomics RevolutionThe integration of photonics, electronics, biomaterials, and nanotechnology holds great promise for the future of medicine. This topic has recently experienced an explosive growth due to the noninvasive or minimally invasive nature and the cost-effectiveness of photonic modalities in medical diagnostics and therapy. The second edition of the Biomedical Photonics Handbook presents fundamental developments as well as important applications of biomedical photonics of interest to scientists, engineers, manufacturers, teachers, studen

  15. Multi-platform Integrated Positioning and Attitude Determination using GNSS

    NARCIS (Netherlands)

    Buist, P.J.

    2013-01-01

    There is trend in spacecraft engineering toward distributed systems where a number of smaller spacecraft work as a larger satellite. However, in order to make the small satellites work together as a single large platform, the precise relative positions (baseline) and orientations (attitude) of the

  16. Platform Innovations and System Integration for Unmanned Air, Land and Sea Vehicles Symposium. Technical Evaluation Report

    National Research Council Canada - National Science Library

    Decuypere, Roland; Selegan, David

    2007-01-01

    ...) of the Research and Technology Organization (RTO) of NATO organized a joint symposium on Platform Innovations and System Integration for Unmanned Air, Land and Sea Vehicles which met from 14-18 May 2007 in Florence Italy...

  17. Integrated vehicle-based safety systems (IVBSS) : light vehicle platform field operational test data analysis plan.

    Science.gov (United States)

    2009-12-22

    This document presents the University of Michigan Transportation Research Institutes plan to : perform analysis of data collected from the light vehicle platform field operational test of the : Integrated Vehicle-Based Safety Systems (IVBSS) progr...

  18. Integrated vehicle-based safety systems (IVBSS) : heavy truck platform field operational test data analysis plan.

    Science.gov (United States)

    2009-11-23

    This document presents the University of Michigan Transportation Research Institutes plan to perform : analysis of data collected from the heavy truck platform field operational test of the Integrated Vehicle- : Based Safety Systems (IVBSS) progra...

  19. Understanding the Pathological Basis of Neurological Diseases Through Diagnostic Platforms Based on Innovations in Biomedical Engineering: New Concepts and Theranostics Perspectives

    Directory of Open Access Journals (Sweden)

    Laura Ganau

    2018-02-01

    Full Text Available The pace of advancement of genomics and proteomics together with the recent understanding of the molecular basis behind rare diseases could lead in the near future to significant advances in the diagnosing and treating of many pathological conditions. Innovative diagnostic platforms based on biomedical engineering (microdialysis and proteomics, biochip analysis, non-invasive impedance spectroscopy, etc. are introduced at a rapid speed in clinical practice: this article primarily aims to highlight how such platforms will advance our understanding of the pathological basis of neurological diseases. An overview of the clinical challenges and regulatory hurdles facing the introduction of such platforms in clinical practice, as well as their potential impact on patient management, will complement the discussion on foreseeable theranostic perspectives. Indeed, the techniques outlined in this article are revolutionizing how we (1 identify biomarkers that better define the diagnostic criteria of any given disease, (2 develop research models, and (3 exploit the externalities coming from innovative pharmacological protocols (i.e., those based on monoclonal antibodies, nanodrugs, etc. meant to tackle the molecular cascade so far identified.

  20. Third-party Reverse logistics platform and method Based on Bilateral Resource Integration

    Directory of Open Access Journals (Sweden)

    Zheng Hong Zhen

    2016-01-01

    Full Text Available Dispersion of reverse logistics resources makes it difficult to create relationships between demanders and providers, thereby the personalized demand for the construction of enterprise reverse logistics cannot be satisfied and the service quality cannot be guaranteed. Aiming at these problems, this paper presents a platform and method of enterprise reverse logistics based on bilateral resource integration (RLBRI. The method creates a third-party reverse logistics platform to accumulate a mass of reverse logistics demanders and providers together. And the platform integrates bilateral resources and acts as an intermediary to establish relationships between two sides. Through the platform, a complete and high-quality business chain for enterprise reverse logistics will be built efficiently. Finally put forward an effective strategy of non-defective reverse logistics depends on the integrity checking service provided by third-party logistics. By using this strategy it can short the distance of non-defective reverse transportation. Computational tests validate the strategy.

  1. Integrated Rapid-Diagnostic-Test Reader Platform on a Cellphone

    Science.gov (United States)

    Mudanyali, Onur; Dimitrov, Stoyan; Sikora, Uzair; Padmanabhan, Swati; Navruz, Isa; Ozcan, Aydogan

    2012-01-01

    We demonstrate a cellphone based Rapid-Diagnostic-Test (RDT) reader platform that can work with various lateral flow immuno-chromatographic assays and similar tests to sense the presence of a target analyte in a sample. This compact and cost-effective digital RDT reader, weighing only ~65 grams, mechanically attaches to the existing camera unit of a cellphone, where various types of RDTs can be inserted to be imaged in reflection or transmission modes under light-emitting-diode (LED) based illumination. Captured raw images of these tests are then digitally processed (within less than 0.2 sec/image) through a smart application running on the cellphone for validation of the RDT as well as for automated reading of its diagnostic result. The same smart application running on the cellphone then transmits the resulting data, together with the RDT images and other related information (e.g., demographic data) to a central server, which presents the diagnostic results on a world-map through geo-tagging. This dynamic spatio-temporal map of various RDT results can then be viewed and shared using internet browsers or through the same cellphone application. We tested this platform using malaria, tuberculosis (TB) as well as HIV RDTs by installing it on both Android based smart-phones as well as an iPhone. Providing real-time spatio-temporal statistics for the prevalence of various infectious diseases, this smart RDT reader platform running on cellphones might assist health-care professionals and policy makers to track emerging epidemics worldwide and help epidemic preparedness. PMID:22596243

  2. Integration of relational and textual biomedical sources. A pilot experiment using a semi-automated method for logical schema acquisition.

    Science.gov (United States)

    García-Remesal, M; Maojo, V; Billhardt, H; Crespo, J

    2010-01-01

    Bringing together structured and text-based sources is an exciting challenge for biomedical informaticians, since most relevant biomedical sources belong to one of these categories. In this paper we evaluate the feasibility of integrating relational and text-based biomedical sources using: i) an original logical schema acquisition method for textual databases developed by the authors, and ii) OntoFusion, a system originally designed by the authors for the integration of relational sources. We conducted an integration experiment involving a test set of seven differently structured sources covering the domain of genetic diseases. We used our logical schema acquisition method to generate schemas for all textual sources. The sources were integrated using the methods and tools provided by OntoFusion. The integration was validated using a test set of 500 queries. A panel of experts answered a questionnaire to evaluate i) the quality of the extracted schemas, ii) the query processing performance of the integrated set of sources, and iii) the relevance of the retrieved results. The results of the survey show that our method extracts coherent and representative logical schemas. Experts' feedback on the performance of the integrated system and the relevance of the retrieved results was also positive. Regarding the validation of the integration, the system successfully provided correct results for all queries in the test set. The results of the experiment suggest that text-based sources including a logical schema can be regarded as equivalent to structured databases. Using our method, previous research and existing tools designed for the integration of structured databases can be reused - possibly subject to minor modifications - to integrate differently structured sources.

  3. Integration of Fractal Biosensor in a Digital Microfluidic Platform

    KAUST Repository

    Mashraei, Yousof; Sivashankar, Shilpa; Buttner, Ulrich; Salama, Khaled N.

    2016-01-01

    fractal electrode biosensor that is used for both droplet actuation and sensing C-reactive protein (CRP) concentration levels to assess cardiac disease risk. Our proposed electrode is the first two-terminal electrode design to be integrated into DMF

  4. An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air

    Directory of Open Access Journals (Sweden)

    Schneider Till

    2013-06-01

    Full Text Available Over the last decade the evaluation of odors and vapors in human breath has gained more and more attention, particularly in the diagnostics of pulmonary diseases. Ion mobility spectrometry coupled with multi-capillary columns (MCC/IMS, is a well known technology for detecting volatile organic compounds (VOCs in air. It is a comparatively inexpensive, non-invasive, high-throughput method, which is able to handle the moisture that comes with human exhaled air, and allows for characterizing of VOCs in very low concentrations. To identify discriminating compounds as biomarkers, it is necessary to have a clear understanding of the detailed composition of human breath. Therefore, in addition to the clinical studies, there is a need for a flexible and comprehensive centralized data repository, which is capable of gathering all kinds of related information. Moreover, there is a demand for automated data integration and semi-automated data analysis, in particular with regard to the rapid data accumulation, emerging from the high-throughput nature of the MCC/IMS technology. Here, we present a comprehensive database application and analysis platform, which combines metabolic maps with heterogeneous biomedical data in a well-structured manner. The design of the database is based on a hybrid of the entity-attribute- value (EAV model and the EAV-CR, which incorporates the concepts of classes and relationships. Additionally it offers an intuitive user interface that provides easy and quick access to the platform’s functionality: automated data integration and integrity validation, versioning and roll-back strategy, data retrieval as well as semi-automatic data mining and machine learning capabilities. The platform will support MCC/IMS-based biomarker identification and validation. The software, schemata, data sets and further information is publicly available at http://imsdb.mpi-inf.mpg.de.

  5. An Integrated Platform for Dynamic Software Updating and its Application in Self-* systems

    DEFF Research Database (Denmark)

    Gregersen, Allan Raundahl; Jørgensen, Bo Nørregaard; Hadaytullah

    2012-01-01

    Practical dynamic updating of modern Java applications requires tool support to become an integral part of the software development and maintenance lifecycle. In this paper we present Javeleon, an easy-to-use tool for dynamic updates of Java applications. To support integration with specific...... frameworks, component systems and application servers, Javeleon currently provides tight integration with the NetBeans Platform, facilitating dynamic updating for applications built on top of the NetBeans Platform in an unconstrained manner. Javeleon supports state-preserving unanticipated runtime evolution...

  6. Vertically integrated monolithic pixel sensors for charged particle tracking and biomedical imaging

    International Nuclear Information System (INIS)

    Ratti, L.; Gaioni, L.; Manghisoni, M.; Re, V.; Traversi, G.

    2011-01-01

    Three-dimensional monolithic pixel sensors have been designed following the same approach that was exploited for the development of the so-called deep N-well (DNW) MAPS in planar CMOS process. The new 3D design relies upon stacking two homogeneous layers fabricated in a 130 nm CMOS technology. One of the two tiers, which are face-to-face bonded, has to be thinned down to about 12μm to expose the through silicon vias connecting the circuits to the back-metal bond pads. As a consequence of the way the two parts of each single chip are designed and fabricated, the prototypes of the 3D monolithic detector will include both samples with a thick substrate underneath the collecting DNW electrode, suitable for charged particle tracking, and samples with a very thin (about 6μm) sensitive volume, which may be used to detect low energy particles in biomedical imaging applications. Device physics simulations have been performed to evaluate the collection properties and detection efficiency of the proposed vertically integrated structures.

  7. Vertically integrated monolithic pixel sensors for charged particle tracking and biomedical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Ratti, L., E-mail: lodovico.ratti@unipv.it [Universita di Pavia, Dipartimento di Elettronica, Via Ferrata 1, I-27100 Pavia (Italy); INFN, Sezione di Pavia, Via Bassi 6, I-27100 Pavia (Italy); Gaioni, L. [INFN, Sezione di Pavia, Via Bassi 6, I-27100 Pavia (Italy); Manghisoni, M.; Re, V.; Traversi, G. [Universita di Bergamo, Dipartimento di Ingegneria Industriale, Via Marconi 5, I-24044 Dalmine (Italy); INFN, Sezione di Pavia, Via Bassi 6, I-27100 Pavia (Italy)

    2011-10-01

    Three-dimensional monolithic pixel sensors have been designed following the same approach that was exploited for the development of the so-called deep N-well (DNW) MAPS in planar CMOS process. The new 3D design relies upon stacking two homogeneous layers fabricated in a 130 nm CMOS technology. One of the two tiers, which are face-to-face bonded, has to be thinned down to about 12{mu}m to expose the through silicon vias connecting the circuits to the back-metal bond pads. As a consequence of the way the two parts of each single chip are designed and fabricated, the prototypes of the 3D monolithic detector will include both samples with a thick substrate underneath the collecting DNW electrode, suitable for charged particle tracking, and samples with a very thin (about 6{mu}m) sensitive volume, which may be used to detect low energy particles in biomedical imaging applications. Device physics simulations have been performed to evaluate the collection properties and detection efficiency of the proposed vertically integrated structures.

  8. Open discovery: An integrated live Linux platform of Bioinformatics tools.

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

    Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

  9. Integrated control platform for converged optical and wireless networks

    DEFF Research Database (Denmark)

    Yan, Ying

    The next generation of broadband access networks is expected to be heterogeneous. Multiple wired and wireless systems can be integrated, in order to simultaneously provide seamless access with an appropriate Quality of Service (QoS). Wireless networks support ubiquitous connectivity yet low data...... rates, whereas optical networks can offer much higher data rates but only provide fixed connection structures. Their complementary characteristics make the integration of the two networks a promising trend for next generation networks. With combined strengths, the converged network will provide both...... the complementary characteristics of the optical networks and the wireless networks, addresses motivations for their interworking, discusses the current progress in hybrid network architectures as well as the functionalities of a control system, and identifies the achieved research contributions in the integrated...

  10. A chip-scale integrated cavity-electro-optomechanics platform

    DEFF Research Database (Denmark)

    Winger, M.; Blasius, T. D.; Mayer Alegre, T. P.

    2011-01-01

    We present an integrated optomechanical and electromechanical nanocavity, in which a common mechanical degree of freedom is coupled to an ultrahigh-Q photonic crystal defect cavity and an electrical circuit. The system allows for wide-range, fast electrical tuning of the optical nanocavity...... resonances, and for electrical control of optical radiation pressure back-action effects such as mechanical amplification (phonon lasing), cooling, and stiffening. These sort of integrated devices offer a new means to efficiently interconvert weak microwave and optical signals, and are expected to pave...

  11. High throughput platforms for structural genomics of integral membrane proteins.

    Science.gov (United States)

    Mancia, Filippo; Love, James

    2011-08-01

    Structural genomics approaches on integral membrane proteins have been postulated for over a decade, yet specific efforts are lagging years behind their soluble counterparts. Indeed, high throughput methodologies for production and characterization of prokaryotic integral membrane proteins are only now emerging, while large-scale efforts for eukaryotic ones are still in their infancy. Presented here is a review of recent literature on actively ongoing structural genomics of membrane protein initiatives, with a focus on those aimed at implementing interesting techniques aimed at increasing our rate of success for this class of macromolecules. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Participatory Planning, Monitoring and Evaluation of Multi-Stakeholder Platforms in Integrated Landscape Initiatives.

    Science.gov (United States)

    Kusters, Koen; Buck, Louise; de Graaf, Maartje; Minang, Peter; van Oosten, Cora; Zagt, Roderick

    2017-03-21

    Integrated landscape initiatives typically aim to strengthen landscape governance by developing and facilitating multi-stakeholder platforms. These are institutional coordination mechanisms that enable discussions, negotiations, and joint planning between stakeholders from various sectors in a given landscape. Multi-stakeholder platforms tend to involve complex processes with diverse actors, whose objectives and focus may be subjected to periodic re-evaluation, revision or reform. In this article we propose a participatory method to aid planning, monitoring, and evaluation of such platforms, and we report on experiences from piloting the method in Ghana and Indonesia. The method is comprised of three components. The first can be used to look ahead, identifying priorities for future multi-stakeholder collaboration in the landscape. It is based on the identification of four aspirations that are common across multi-stakeholder platforms in integrated landscape initiatives. The second can be used to look inward. It focuses on the processes within an existing multi-stakeholder platform in order to identify areas for possible improvement. The third can be used to look back, identifying the main outcomes of an existing platform and comparing them to the original objectives. The three components can be implemented together or separately. They can be used to inform planning and adaptive management of the platform, as well as to demonstrate performance and inform the design of new interventions.

  13. A Platform for Mobile Service Provisioning Based on SOA-Integration

    Science.gov (United States)

    Decker, Michael; Bulander, Rebecca

    A middleware platform designed for the provisioning of data services for mobile computers using wireless data communication (e.g. smartphones or PDAs) has to offer a variety of different features. Some of these features have to be provided by external parties, e.g. billing or content syndication. The integration of all these features while considering mobile-specific challenges is a demanding task. In the article at hand we thus describe a middleware platform for mobile services which follows the idea of a so called Enterprise Service Bus (ESB). We explain the concept of ESB and argue why an ESB is an appropriate fundament for a platform for mobile service provisioning.

  14. A middleware-based platform for the integration of bioinformatic services

    Directory of Open Access Journals (Sweden)

    Guzmán Llambías

    2015-08-01

    Full Text Available Performing Bioinformatic´s experiments involve an intensive access to distributed services and information resources through Internet. Although existing tools facilitate the implementation of workflow-oriented applications, they lack of capabilities to integrate services beyond low-scale applications, particularly integrating services with heterogeneous interaction patterns and in a larger scale. This is particularly required to enable a large-scale distributed processing of biological data generated by massive sequencing technologies. On the other hand, such integration mechanisms are provided by middleware products like Enterprise Service Buses (ESB, which enable to integrate distributed systems following a Service Oriented Architecture. This paper proposes an integration platform, based on enterprise middleware, to integrate Bioinformatics services. It presents a multi-level reference architecture and focuses on ESB-based mechanisms to provide asynchronous communications, event-based interactions and data transformation capabilities. The paper presents a formal specification of the platform using the Event-B model.

  15. Framework programmable platform for the advanced software development workstation. Integration mechanism design document

    Science.gov (United States)

    Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Reddy, Uday; Ackley, Keith; Futrell, Mike

    1991-01-01

    The Framework Programmable Software Development Platform (FPP) is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by this model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated.

  16. Development of mobile platform integrated with existing electronic medical records.

    Science.gov (United States)

    Kim, YoungAh; Kim, Sung Soo; Kang, Simon; Kim, Kyungduk; Kim, Jun

    2014-07-01

    This paper describes a mobile Electronic Medical Record (EMR) platform designed to manage and utilize the existing EMR and mobile application with optimized resources. We structured the mEMR to reuse services of retrieval and storage in mobile app environments that have already proven to have no problem working with EMRs. A new mobile architecture-based mobile solution was developed in four steps: the construction of a server and its architecture; screen layout and storyboard making; screen user interface design and development; and a pilot test and step-by-step deployment. This mobile architecture consists of two parts, the server-side area and the client-side area. In the server-side area, it performs the roles of service management for EMR and documents and for information exchange. Furthermore, it performs menu allocation depending on user permission and automatic clinical document architecture document conversion. Currently, Severance Hospital operates an iOS-compatible mobile solution based on this mobile architecture and provides stable service without additional resources, dealing with dynamic changes of EMR templates. The proposed mobile solution should go hand in hand with the existing EMR system, and it can be a cost-effective solution if a quality EMR system is operated steadily with this solution. Thus, we expect this example to be shared with hospitals that currently plan to deploy mobile solutions.

  17. A chip-scale integrated cavity-electro-optomechanics platform.

    Science.gov (United States)

    Winger, M; Blasius, T D; Mayer Alegre, T P; Safavi-Naeini, A H; Meenehan, S; Cohen, J; Stobbe, S; Painter, O

    2011-12-05

    We present an integrated optomechanical and electromechanical nanocavity, in which a common mechanical degree of freedom is coupled to an ultrahigh-Q photonic crystal defect cavity and an electrical circuit. The system allows for wide-range, fast electrical tuning of the optical nanocavity resonances, and for electrical control of optical radiation pressure back-action effects such as mechanical amplification (phonon lasing), cooling, and stiffening. These sort of integrated devices offer a new means to efficiently interconvert weak microwave and optical signals, and are expected to pave the way for a new class of micro-sensors utilizing optomechanical back-action for thermal noise reduction and low-noise optical read-out.

  18. REopt: A Platform for Energy System Integration and Optimization

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Katherine H. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Cutler, Dylan S. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Olis, Daniel R. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Elgqvist, Emma M. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Li, Xiangkun [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Laws, Nicholas D. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); DiOrio, Nicholas A. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Walker, H. A [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-09-22

    REopt is a techno-economic decision support model used to optimize energy systems for buildings, campuses, communities, and microgrids. The primary application of the model is for optimizing the integration and operation of behind-the-meter energy assets. This report provides an overview of the model, including its capabilities and typical applications; inputs and outputs; economic calculations; technology descriptions; and model parameters, variables, and equations. The model is highly flexible, and is continually evolving to meet the needs of each analysis. Therefore, this report is not an exhaustive description of all capabilities, but rather a summary of the core components of the model.

  19. An Integrated Chip High-Voltage Power Receiver for Wireless Biomedical Implants

    Directory of Open Access Journals (Sweden)

    Vijith Vijayakumaran Nair

    2015-06-01

    Full Text Available In near-field wireless-powered biomedical implants, the receiver voltage largely overrides the compliance of low-voltage power receiver systems. To limit the induced voltage, generally, low-voltage topologies utilize limiter circuits, voltage clippers or shunt regulators, which are power-inefficient methods. In order to overcome the voltage limitation and improve power efficiency, we propose an integrated chip high-voltage power receiver based on the step down approach. The topology accommodates voltages as high as 30 V and comprises a high-voltage semi-active rectifier, a voltage reference generator and a series regulator. Further, a battery management circuit that enables safe and reliable implant battery charging based on analog control is proposed and realized. The power receiver is fabricated in 0.35-μm high-voltage Bipolar-CMOS-DMOStechnology based on the LOCOS0.35-μm CMOS process. Measurement results indicate 83.5% power conversion efficiency for a rectifier at 2.1 mA load current. The low drop-out regulator based on the current buffer compensation and buffer impedance attenuation scheme operates with low quiescent current, reduces the power consumption and provides good stability. The topology also provides good power supply rejection, which is adequate for the design application. Measurement results indicate regulator output of 4 ± 0.03 V for input from 5 to 30 V and 10 ± 0.05 V output for input from 11 to 30 V with load current 0.01–100 mA. The charger circuit manages the charging of the Li-ion battery through all if the typical stages of the Li-ion battery charging profile.

  20. Health-e-Child a grid platform for european paediatrics

    CERN Document Server

    Skaburskas, K; Shade, J; Manset, D; Revillard, J; Rios, A; Anjum, A; Branson, A; Bloodsworth, P; Hauer, T; McClatchey, R; Rogulin, D

    2008-01-01

    The Health-e-Child (HeC) project [1], [2] is an EC Framework Programme 6 Integrated Project that aims to develop a grid-based integrated healthcare platform for paediatrics. Using this platform biomedical informaticians will integrate heterogeneous data and perform epidemiological studies across Europe. The resulting Grid enabled biomedical information platform will be supported by robust search, optimization and matching techniques for information collected in hospitals across Europe. In particular, paediatricians will be provided with decision support, knowledge discovery and disease modelling applications that will access data in hospitals in the UK, Italy and France, integrated via the Grid. For economy of scale, reusability, extensibility, and maintainability, HeC is being developed on top of an EGEE/gLite [3] based infrastructure that provides all the common data and computation management services required by the applications. This paper discusses some of the major challenges in bio-medical data integr...

  1. OTEC platform configuration and integration study. Volume I. Systems engineering and integration. Final report

    Energy Technology Data Exchange (ETDEWEB)

    None

    1978-04-01

    The economic success of an Ocean Thermal Energy Conversion (OTEC) system is highly dependent on a platform which provides adequate support for the power system, accommodates reliably the cold water pipe, and is most cost effective. The results of a study conducted for the Department of Energy to assess six generic types of platforms to determine the most satisfactory platform for severl potential sites are presented. The six platform configurations are ship, circular barge, semi-submersible, Tuned Sphere, submersible, and spar. These represent directional and symmetric types of platforms which operate on the surface, at the interface, and submerged. The five sites for this study were primarily New Orleans, Keahole Point (Hawaii), Brazil, and secondarily Key West and Puerto Rico. Electrical transmission of energy by submarine cable is the planned form of energy transmission for all sites except Brazil, where chemical conversion is to be the method of transmission. This study is devoted to the platform (or ocean systems) of the OTEC plant which is chiefly comprised of the hull and structure, the seawater system, the position control system, and miscellaneous support/assembly systems. The principal elements in the work breakdown structure for the commercial plants are presented. The assessment of the six platform configurations was conducted utilizing a baseline plan (100-MW(e) (Net)) and site (New Orleans) with variations from the baseline to cover the range of interested platforms and sites.

  2. Data exchange between zero dimensional code and physics platform in the CFETR integrated system code

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Guoliang [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026 China (China); Shi, Nan [Institute of Plasma Physics, Chinese Academy of Sciences, No. 350 Shushanhu Road, Hefei (China); Zhou, Yifu; Mao, Shifeng [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026 China (China); Jian, Xiang [State Key Laboratory of Advanced Electromagnetic Engineering and Technology, School of Electrical and Electronics Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Chen, Jiale [Institute of Plasma Physics, Chinese Academy of Sciences, No. 350 Shushanhu Road, Hefei (China); Liu, Li; Chan, Vincent [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026 China (China); Ye, Minyou, E-mail: yemy@ustc.edu.cn [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026 China (China)

    2016-11-01

    Highlights: • The workflow of the zero dimensional code and the multi-dimension physics platform of CFETR integrated system codeis introduced. • The iteration process among the codes in the physics platform. • The data transfer between the zero dimensionalcode and the physical platform, including data iteration and validation, and justification for performance parameters.. - Abstract: The China Fusion Engineering Test Reactor (CFETR) integrated system code contains three parts: a zero dimensional code, a physics platform and an engineering platform. We use the zero dimensional code to identify a set of preliminary physics and engineering parameters for CFETR, which is used as input to initiate multi-dimension studies using the physics and engineering platform for design, verification and validation. Effective data exchange between the zero dimensional code and the physical platform is critical for the optimization of CFETR design. For example, in evaluating the impact of impurity radiation on core performance, an open field line code is used to calculate the impurity transport from the first-wall boundary to the pedestal. The impurity particle in the pedestal are used as boundary conditions in a transport code for calculating impurity transport in the core plasma and the impact of core radiation on core performance. Comparison of the results from the multi-dimensional study to those from the zero dimensional code is used to further refine the controlled radiation model. The data transfer between the zero dimensional code and the physical platform, including data iteration and validation, and justification for performance parameters will be presented in this paper.

  3. Testing an integrated behavioural and biomedical model of disability in N-of-1 studies with chronic pain.

    Science.gov (United States)

    Quinn, Francis; Johnston, Marie; Johnston, Derek W

    2013-01-01

    Previous research has supported an integrated biomedical and behavioural model explaining activity limitations. However, further tests of this model are required at the within-person level, because while it proposes that the constructs are related within individuals, it has primarily been tested between individuals in large group studies. We aimed to test the integrated model at the within-person level. Six correlational N-of-1 studies in participants with arthritis, chronic pain and walking limitations were carried out. Daily measures of theoretical constructs were collected using a hand-held computer (PDA), the activity was assessed by self-report and accelerometer and the data were analysed using time-series analysis. The biomedical model was not supported as pain impairment did not predict activity, so the integrated model was supported partially. Impairment predicted intention to move around, while perceived behavioural control (PBC) and intention predicted activity. PBC did not predict activity limitation in the expected direction. The integrated model of disability was partially supported within individuals, especially the behavioural elements. However, results suggest that different elements of the model may drive activity (limitations) for different individuals. The integrated model provides a useful framework for understanding disability and suggests interventions, and the utility of N-of-1 methodology for testing theory is illustrated.

  4. Aluminum nitride integrated photonics platform for the ultraviolet to visible spectrum.

    Science.gov (United States)

    Lu, Tsung-Ju; Fanto, Michael; Choi, Hyeongrak; Thomas, Paul; Steidle, Jeffrey; Mouradian, Sara; Kong, Wei; Zhu, Di; Moon, Hyowon; Berggren, Karl; Kim, Jeehwan; Soltani, Mohammad; Preble, Stefan; Englund, Dirk

    2018-04-30

    We demonstrate a wide-bandgap semiconductor photonics platform based on nanocrystalline aluminum nitride (AlN) on sapphire. This photonics platform guides light at low loss from the ultraviolet (UV) to the visible spectrum. We measure ring resonators with intrinsic quality factor (Q) exceeding 170,000 at 638 nm and Q >20,000 down to 369.5 nm, which shows a promising path for low-loss integrated photonics in UV and visible spectrum. This platform opens up new possibilities in integrated quantum optics with trapped ions or atom-like color centers in solids, as well as classical applications including nonlinear optics and on-chip UV-spectroscopy.

  5. National Bioenergy Center - Biochemical Platform Integration Project: Quarterly Update, Winter 2010

    Energy Technology Data Exchange (ETDEWEB)

    Schell, D.

    2011-02-01

    Winter 2011 edition of the National Bioenergy Center's Biochemical Platform Integration Project quarterly newsletter. Issue topics: 33rd Symposium on Biotechnology for Fuels and Chemicals program topic areas; results from reactive membrane extraction of inhibitors from dilute-acid pretreated corn stover; list of 2010 task publications.

  6. IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface.

    Science.gov (United States)

    Sun, Yin Xue; Huang, Yan Xin; Li, Feng Li; Wang, Hong Yan; Fan, Cong; Bao, Yong Li; Sun, Lu Guo; Ma, Zhi Qiang; Kong, Jun; Li, Yu Xin

    2012-01-05

    The virtual screening (VS) of lead compounds using molecular docking and pharmacophore detection is now an important tool in drug discovery. VS tasks typically require a combination of several software tools and a molecular graphics system. Thus, the integration of all the requisite tools in a single operating environment could reduce the complexity of running VS experiments. However, only a few freely available integrated software platforms have been developed. A free open-source platform, IVSPlat 1.0, was developed in this study for the management and automation of VS tasks. We integrated several VS-related programs into a molecular graphics system to provide a comprehensive platform for the solution of VS tasks based on molecular docking, pharmacophore detection, and a combination of both methods. This tool can be used to visualize intermediate and final results of the VS execution, while also providing a clustering tool for the analysis of VS results. A case study was conducted to demonstrate the applicability of this platform. IVSPlat 1.0 provides a plug-in-based solution for the management, automation, and visualization of VS tasks. IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at http://kyc.nenu.edu.cn/IVSPlat/.

  7. Integrated nanophotonic frequency shifter on the silicon-organic hybrid (SOH) platform for laser vibrometry

    International Nuclear Information System (INIS)

    Lauermann, M.; Weimann, C.; Palmer, R.; Schindler, P. C.; Koeber, S.; Freude, W.; Koos, C.; Rembe, C.

    2014-01-01

    We demonstrate a waveguide-based frequency shifter on the silicon photonic platform, enabling frequency shifts up to 10 GHz. The device is realized by silicon-organic hybrid (SOH) integration. Temporal shaping of the drive signal allows the suppression of spurious side-modes by more than 23 dB

  8. Towards a fully integrated indium-phosphide membrane on silicon photonics platform

    NARCIS (Netherlands)

    van Engelen, J.P.; Pogoretskiy, V.; Smit, M.K.; van der Tol, J.J.G.M.; Jiao, Y.

    2017-01-01

    Recently a uni-traveling-carrier photodetector with high speed (> 67GHz) and a high-gain optical amplifier (110/cm at 4 kA/cm2) have been demonstrated using the InP membrane-on-Silicon (IMOS) integration technology. Passives in IMOS have shown features comparable to SOI platforms due to the tight

  9. Multi-fields' coordination information integrated platform for nuclear power plant operation preparation

    International Nuclear Information System (INIS)

    Yuan Chang; Li Yong; Ye Zhiqiang

    2011-01-01

    To realize the coordination in multi-fields' work and information sharing, by applying the method of Enterprise Architecture (EA), the business architecture, functional flow and application architecture of Nuclear Power Plant's operation preparation information integrated platform are designed, which can realize the information sharing and coordination of multi fields. (authors)

  10. Integrated nanophotonic frequency shifter on the silicon-organic hybrid (SOH) platform for laser vibrometry

    Energy Technology Data Exchange (ETDEWEB)

    Lauermann, M.; Weimann, C.; Palmer, R.; Schindler, P. C. [Institute of Photonics and Quantum Electronics, Karlsruhe Institute of Technology, 76131 Karlsruhe (Germany); Koeber, S.; Freude, W., E-mail: christian.koos@kit.edu; Koos, C., E-mail: christian.koos@kit.edu [Institute of Photonics and Quantum Electronics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany and Institute of Microstructure Technology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen (Germany); Rembe, C. [Polytec GmbH, 76337 Waldbronn (Germany)

    2014-05-27

    We demonstrate a waveguide-based frequency shifter on the silicon photonic platform, enabling frequency shifts up to 10 GHz. The device is realized by silicon-organic hybrid (SOH) integration. Temporal shaping of the drive signal allows the suppression of spurious side-modes by more than 23 dB.

  11. A hybrid approach to device integration on a genetic analysis platform

    International Nuclear Information System (INIS)

    Brennan, Des; Justice, John; Aherne, Margaret; Galvin, Paul; Jary, Dorothee; Kurg, Ants; Berik, Evgeny; Macek, Milan

    2012-01-01

    Point-of-care (POC) systems require significant component integration to implement biochemical protocols associated with molecular diagnostic assays. Hybrid platforms where discrete components are combined in a single platform are a suitable approach to integration, where combining multiple device fabrication steps on a single substrate is not possible due to incompatible or costly fabrication steps. We integrate three devices each with a specific system functionality: (i) a silicon electro-wetting-on-dielectric (EWOD) device to move and mix sample and reagent droplets in an oil phase, (ii) a polymer microfluidic chip containing channels and reservoirs and (iii) an aqueous phase glass microarray for fluorescence microarray hybridization detection. The EWOD device offers the possibility of fully integrating on-chip sample preparation using nanolitre sample and reagent volumes. A key challenge is sample transfer from the oil phase EWOD device to the aqueous phase microarray for hybridization detection. The EWOD device, waveguide performance and functionality are maintained during the integration process. An on-chip biochemical protocol for arrayed primer extension (APEX) was implemented for single nucleotide polymorphism (SNiP) analysis. The prepared sample is aspirated from the EWOD oil phase to the aqueous phase microarray for hybridization. A bench-top instrumentation system was also developed around the integrated platform to drive the EWOD electrodes, implement APEX sample heating and image the microarray after hybridization. (paper)

  12. Full scale test platform for European TBM systems integration and maintenance

    Energy Technology Data Exchange (ETDEWEB)

    Vála, Ladislav, E-mail: ladislav.vala@cvrez.cz; Reungoat, Mathieu; Vician, Martin

    2016-11-01

    Highlights: • A platform for EU-TBS maintenance and integration tests is described. • Its modular design allows adaptation to non-EU TBSs. • Assembling of the facility will be followed by initial tests in 2016. - Abstract: This article deals with description and current status of a project of a non-nuclear, full size (1:1 scale) test platform dedicated to tests, optimization and validation of integration and maintenance operations for the European TBM systems in the ITER port cell #16. The facility called TBM platform reproduces the ITER port cell #16 and port interspace with all the relevant interfaces and mock-ups of the corresponding main components. Thanks to the modular design of the platform, it is possible to adapt or change completely the interfaces in the future if needed or required according to the updated configuration of TBSs. In the same way, based on customer requirements, it will be possible to adapt the interfaces and piping inside the mock-ups in order to represent also the other, non-EU configurations of TBM systems designed for port cells #02 and #18. Construction of this test platform is realized and funded within the scope of the SUSEN project.

  13. Exploration and implementation of ontology-based cultural relic knowledge map integration platform

    Science.gov (United States)

    Yang, Weiqiang; Dong, Yiqiang

    2018-05-01

    To help designers to better carry out creative design and improve the ability of searching traditional cultural relic information, the ontology-based knowledge map construction method was explored and an integrated platform for cultural relic knowledge map was developed. First of all, the construction method of the ontology of cultural relics was put forward, and the construction of the knowledge map of cultural relics was completed based on the constructed cultural relic otology. Then, a personalized semantic retrieval framework for creative design was proposed. Finally, the integrated platform of the knowledge map of cultural relics was designed and realized. The platform was divided into two parts. One was the foreground display system, which was used for designers to search and browse cultural relics. The other was the background management system, which was for cultural experts to manage cultural relics' knowledge. The research results showed that the platform designed could improve the retrieval ability of cultural relic information. To sum up, the platform can provide a good support for the designer's creative design.

  14. Building integrated pathways to independence for diverse biomedical researchers: Project Pathways, the BUILD program at Xavier University of Louisiana.

    Science.gov (United States)

    Foroozesh, Maryam; Giguette, Marguerite; Morgan, Kathleen; Johanson, Kelly; D'Amour, Gene; Coston, Tiera; Wilkins-Green, Clair

    2017-01-01

    Xavier University of Louisiana is a historically Black and Catholic university that is nationally recognized for its science, technology, engineering and mathematics (STEM) curricula. Approximately 73% of Xavier's students are African American, and about 77% major in the biomedical sciences. Xavier is a national leader in the number of STEM majors who go on to receive M.D. degrees and Ph.D. degrees in science and engineering. Despite Xavier's advances in this area, African Americans still earn about 7.5% of the Bachelor's degrees, less than 8% of the Master's degrees, and less than 5% of the doctoral degrees conferred in STEM disciplines in the United States. Additionally, although many well-prepared, highly-motivated students are attracted by Xavier's reputation in the sciences, many of these students, though bright and capable, come from underperforming public school systems and receive substandard preparation in STEM disciplines. The purpose of this article is to describe how Xavier works to overcome unequal education backgrounds and socioeconomic challenges to develop student talent through expanding biomedical training opportunities and build on an established reputation in science education. The National Institutes of Health (NIH)/National Institute of General Medical Sciences (NIGMS)-funded BUILD (Building Infrastructure Leading to Diversity) Program at Xavier University of Louisiana, Project Pathways , is a highly-innovative program designed to broaden the career interests of students early on, and to engage them in activities that entice them to continue their education towards biomedical research careers. Project strategies involve a transformation of Xavier's academic and non-academic programs through the redesign, supplementation and integration of academic advising, tutoring, career services, personal counseling, undergraduate research training, faculty research mentoring, and development of new biomedical and research skills courses. The Program also

  15. Nucleic Acid-based Detection of Bacterial Pathogens Using Integrated Microfluidic Platform Systems

    Directory of Open Access Journals (Sweden)

    Carl A. Batt

    2009-05-01

    Full Text Available The advent of nucleic acid-based pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques, driving the development of portable, integrated biosensors. The miniaturization and automation of integrated detection systems presents a significant advantage for rapid, portable field-based testing. In this review, we highlight current developments and directions in nucleic acid-based micro total analysis systems for the detection of bacterial pathogens. Recent progress in the miniaturization of microfluidic processing steps for cell capture, DNA extraction and purification, polymerase chain reaction, and product detection are detailed. Discussions include strategies and challenges for implementation of an integrated portable platform.

  16. Integrated Tourism E-Commerce Platform for Scenery Administration Bureau, Travel Agency and Tourist

    Science.gov (United States)

    Liang, Zhixue; Wang, Shui

    Collaboration among multiple travel agencies and with scenery administration bureaus is vital for small or medium sized travel companies to succeed in the fierce competition of the tourism industry; business processes such as regrouping individual travelers between different agencies prove to be difficult and unpleasant user experience; tourists want to be more informed and have more initiative. To address these issues, proposes an integrated tourism e-commerce platform for travel agencies and scenery administration bureaus as well as tourists to interact in a more smooth way; this platform is constructed upon J2EE framework, provides online collaboration & coordination for companies and information services (such as self-navigation using Google Map etc) for tourists. A running implementation of this platform has been put into real business for a small travel company.

  17. Low-loss compact multilayer silicon nitride platform for 3D photonic integrated circuits.

    Science.gov (United States)

    Shang, Kuanping; Pathak, Shibnath; Guan, Binbin; Liu, Guangyao; Yoo, S J B

    2015-08-10

    We design, fabricate, and demonstrate a silicon nitride (Si(3)N(4)) multilayer platform optimized for low-loss and compact multilayer photonic integrated circuits. The designed platform, with 200 nm thick waveguide core and 700 nm interlayer gap, is compatible for active thermal tuning and applicable to realizing compact photonic devices such as arrayed waveguide gratings (AWGs). We achieve ultra-low loss vertical couplers with 0.01 dB coupling loss, multilayer crossing loss of 0.167 dB at 90° crossing angle, 50 μm bending radius, 100 × 2 μm(2) footprint, lateral misalignment tolerance up to 400 nm, and less than -52 dB interlayer crosstalk at 1550 nm wavelength. Based on the designed platform, we demonstrate a 27 × 32 × 2 multilayer star coupler.

  18. Multi-octave spectral beam combiner on ultra-broadband photonic integrated circuit platform.

    Science.gov (United States)

    Stanton, Eric J; Heck, Martijn J R; Bovington, Jock; Spott, Alexander; Bowers, John E

    2015-05-04

    We present the design of a novel platform that is able to combine optical frequency bands spanning 4.2 octaves from ultraviolet to mid-wave infrared into a single, low M2 output waveguide. We present the design and realization of a key component in this platform that combines the wavelength bands of 350 nm - 1500 nm and 1500 nm - 6500 nm with demonstrated efficiency greater than 90% in near-infrared and mid-wave infrared. The multi-octave spectral beam combiner concept is realized using an integrated platform with silicon nitride waveguides and silicon waveguides. Simulated bandwidth is shown to be over four octaves, and measured bandwidth is shown over two octaves, limited by the availability of sources.

  19. Oil and gas platforms with steam bottoming cycles: System integration and thermoenvironomic evaluation

    DEFF Research Database (Denmark)

    Nguyen, Tuong-Van; Tock, Laurence; Breuhaus, Peter

    2014-01-01

    The integration of steam bottoming cycles on oil and gas platforms is currently regarded as the most promising option for improving the performance of these energy-intensive systems. In this paper, a North Sea platform is taken as case study, and a systematic analysis of its energy requirements...... cooling utility, and (iv) the weight limitations on the platform are quantitatively assessed. The results illustrate the benefits of converting the gas turbine process into a combined cycle, since the fuel gas consumption and the total CO2-emissions can be reduced by more than 15 %. Using the cooling...... water from the processing plant reveals to be more profitable than using seawater, as the additional pumping power outweighs the benefit of using a cooling medium at a temperature of about 8 °C lower. This study highlights thereby the importance of analysing energy savings and recovery options...

  20. Radiation-Engineered Functionalized Nanogels as Platform for Biomedical Nanocarriers and Bio-Hybrid, Hierarchically Assembled Nanostructures

    International Nuclear Information System (INIS)

    Dispenza, C.; Sabatino, M.-A.; Alessi, S.; Spadaro, G.

    2011-01-01

    Radiation technologies can be considered as choice methodologies for the creation of new functional materials at the nanoscale, the challenge being now the integration of these and other novel nanomaterials into new materials and products. The possibility of generating nanoscalar PVP-based hydrogels particles, with reactive functional groups for subsequent bioconjugation, using industrial type accelerators has been demonstrated. These functional nanoparticles are under evaluation as nanocarriers for targeted release of drugs, but can also be considered as useful building blocks for the assembly of nanostructured materials with controlled architecture. In particular, molecular recognition strategies can be developed to tailor the structural and functional properties of the composite by attaching complementary sequences of molecules from biological source (peptides or oligonucleotides) that will tie nanoparticles together. Under the present CRP, biodegradable nanoparticles will be developed using xyloglucan, a relatively inexpensive polysaccharide as base material, in alternative to PVP. Chemical modification of xyloglucan will be attempted with the purpose of generating radiation cleavable crosslinked micro/nanoparticles. These micro/nanoparticles will incorporate stabilizers (antioxidants, such as quercetin) or pro-degrading agents (enzymes) and will be either dispersed into a biodegradable film forming polymer or self-assembled to form a supramolecular networked film or scaffold. For the purpose, suitable surface modification will be pursued either to promote compatibilisation with the matrix polymer or to efficiently drive the self-assembly process. UV or quantum beam irradiation will be investigated as trigger for the release of the entrapped actives from micro/nanoparticles. (author)

  1. Radiation-Engineered Functionalized Nanogels as Platform for Biomedical Nanocarriers and Bio-Hybrid, Hierarchically Assembled Nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Dispenza, C.; Sabatino, M. -A.; Alessi, S.; Spadaro, G.

    2011-07-01

    Radiation technologies can be considered as choice methodologies for the creation of new functional materials at the nanoscale, the challenge being now the integration of these and other novel nanomaterials into new materials and products. The possibility of generating nanoscalar PVP-based hydrogels particles, with reactive functional groups for subsequent bioconjugation, using industrial type accelerators has been demonstrated. These functional nanoparticles are under evaluation as nanocarriers for targeted release of drugs, but can also be considered as useful building blocks for the assembly of nanostructured materials with controlled architecture. In particular, molecular recognition strategies can be developed to tailor the structural and functional properties of the composite by attaching complementary sequences of molecules from biological source (peptides or oligonucleotides) that will tie nanoparticles together. Under the present CRP, biodegradable nanoparticles will be developed using xyloglucan, a relatively inexpensive polysaccharide as base material, in alternative to PVP. Chemical modification of xyloglucan will be attempted with the purpose of generating radiation cleavable crosslinked micro/nanoparticles. These micro/nanoparticles will incorporate stabilizers (antioxidants, such as quercetin) or pro-degrading agents (enzymes) and will be either dispersed into a biodegradable film forming polymer or self-assembled to form a supramolecular networked film or scaffold. For the purpose, suitable surface modification will be pursued either to promote compatibilisation with the matrix polymer or to efficiently drive the self-assembly process. UV or quantum beam irradiation will be investigated as trigger for the release of the entrapped actives from micro/nanoparticles. (author)

  2. [Integration of fundamental and applied medical and technical research made at the department of the biomedical systems, Moscow State Institute of Electronic Engineering].

    Science.gov (United States)

    Selishchev, S V

    2004-01-01

    The integration results of fundamental and applied medical-and-technical research made at the chair of biomedical systems, Moscow state institute of electronic engineering (technical university--MSIEE), are described in the paper. The chair is guided in its research activity by the traditions of higher education in Russia in the field of biomedical electronics and biomedical engineering. Its activities are based on the extrapolation of methods of electronic tools, computer technologies, physics, biology and medicine with due respect being paid to the requirements of practical medicine and to topical issues of research and design.

  3. Data integration and knowledge discovery in biomedical databases. Reliable information from unreliable sources

    Directory of Open Access Journals (Sweden)

    A Mitnitski

    2003-01-01

    Full Text Available To better understand information about human health from databases we analyzed three datasets collected for different purposes in Canada: a biomedical database of older adults, a large population survey across all adult ages, and vital statistics. Redundancy in the variables was established, and this led us to derive a generalized (macroscopic state variable, being a fitness/frailty index that reflects both individual and group health status. Evaluation of the relationship between fitness/frailty and the mortality rate revealed that the latter could be expressed in terms of variables generally available from any cross-sectional database. In practical terms, this means that the risk of mortality might readily be assessed from standard biomedical appraisals collected for other purposes.

  4. Integrated method to optimize well connection and platform placement on a multi-reservoir scenario

    Energy Technology Data Exchange (ETDEWEB)

    Sousa, Sergio Henrique Guerra de; Madeira, Marcelo Gomes; Franca, Martha Salles [Halliburton, Rio de Janeiro, RJ (Brazil); Mota, Rosane Oliveira; Silva, Edilon Ribeiro da; King, Vanessa Pereira Spear [Petroleo Brasileiro S.A. (PETROBRAS), Rio de Janeiro, RJ (Brazil)

    2012-07-01

    This paper describes a workflow created to optimize the platform placement and well-platform connections on a multi reservoir scenario using an integrated reservoir simulator paired with an optimization engine. The proposed methodology describes how a new platform, being incorporated into a pre-existing asset, can be better used to develop newly-discovered fields, while helping increase the production of existing fields by sharing their production load. The sharing of production facilities is highly important in Brazilian offshore assets because of their high price (a few billion dollars per facility) and the fact that total production is usually limited to the installed capacity of liquid processing, which is an important constraint on high water-cut well production rates typical to this region. The case study asset used to present the workflow consists of two deep water oil fields, each one developed by its own production platform, and a newly-discovered field with strong aquifer support that will be entirely developed with a new production platform. Because this new field should not include injector wells owing to the strong aquifer presence, the idea is to consider reconnecting existing wells from the two pre-existing fields to better use the production resources. In this scenario, the platform location is an important optimization issue, as a balance between supporting the production of the planned wells on the new field and the production of re-routed wells from the existing fields must be reached to achieve improved overall asset production. If the new platform is too far away from any interconnected production well, pressure-drop issues along the pipeline might actually decrease production from the existing fields rather than augment it. The main contribution of this work is giving the reader insights on how to model and optimize these complex decisions to generate high-quality scenarios. (author)

  5. A service-oriented distributed semantic mediator: integrating multiscale biomedical information.

    Science.gov (United States)

    Mora, Oscar; Engelbrecht, Gerhard; Bisbal, Jesus

    2012-11-01

    Biomedical research continuously generates large amounts of heterogeneous and multimodal data spread over multiple data sources. These data, if appropriately shared and exploited, could dramatically improve the research practice itself, and ultimately the quality of health care delivered. This paper presents DISMED (DIstributed Semantic MEDiator), an open source semantic mediator that provides a unified view of a federated environment of multiscale biomedical data sources. DISMED is a Web-based software application to query and retrieve information distributed over a set of registered data sources, using semantic technologies. It also offers a userfriendly interface specifically designed to simplify the usage of these technologies by non-expert users. Although the architecture of the software mediator is generic and domain independent, in the context of this paper, DISMED has been evaluated for managing biomedical environments and facilitating research with respect to the handling of scientific data distributed in multiple heterogeneous data sources. As part of this contribution, a quantitative evaluation framework has been developed. It consist of a benchmarking scenario and the definition of five realistic use-cases. This framework, created entirely with public datasets, has been used to compare the performance of DISMED against other available mediators. It is also available to the scientific community in order to evaluate progress in the domain of semantic mediation, in a systematic and comparable manner. The results show an average improvement in the execution time by DISMED of 55% compared to the second best alternative in four out of the five use-cases of the experimental evaluation.

  6. Design and Analysis of a Compact Precision Positioning Platform Integrating Strain Gauges and the Piezoactuator

    Directory of Open Access Journals (Sweden)

    Shunguang Wan

    2012-07-01

    Full Text Available Miniaturization precision positioning platforms are needed for in situ nanomechanical test applications. This paper proposes a compact precision positioning platform integrating strain gauges and the piezoactuator. Effects of geometric parameters of two parallel plates on Von Mises stress distribution as well as static and dynamic characteristics of the platform were studied by the finite element method. Results of the calibration experiment indicate that the strain gauge sensor has good linearity and its sensitivity is about 0.0468 mV/μm. A closed-loop control system was established to solve the problem of nonlinearity of the platform. Experimental results demonstrate that for the displacement control process, both the displacement increasing portion and the decreasing portion have good linearity, verifying that the control system is available. The developed platform has a compact structure but can realize displacement measurement with the embedded strain gauges, which is useful for the closed-loop control and structure miniaturization of piezo devices. It has potential applications in nanoindentation and nanoscratch tests, especially in the field of in situ nanomechanical testing which requires compact structures.

  7. The business impact of an integrated continuous biomanufacturing platform for recombinant protein production.

    Science.gov (United States)

    Walther, Jason; Godawat, Rahul; Hwang, Chris; Abe, Yuki; Sinclair, Andrew; Konstantinov, Konstantin

    2015-11-10

    The biotechnology industry primarily uses batch technologies to manufacture recombinant proteins. The natural evolution of other industries has shown that transitioning from batch to continuous processing can yield significant benefits. A quantitative understanding of these benefits is critical to guide the implementation of continuous processing. In this manuscript, we use process economic modeling and Monte Carlo simulations to evaluate an integrated continuous biomanufacturing (ICB) platform and conduct risk-based valuation to generate a probabilistic range of net-present values (NPVs). For a specific ten-year product portfolio, the ICB platform reduces average cost by 55% compared to conventional batch processing, considering both capital and operating expenses. The model predicts that these savings can further increase by an additional 25% in situations with higher-than-expected product demand showing the upward potential of the ICB platform. The ICB platform achieves these savings and corresponding flexibility mainly due to process intensification in both upstream and downstream unit operations. This study demonstrates the promise of continuous bioprocessing while also establishing a novel framework to quantify financial benefits of other platform process technologies. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. SALOME. A software integration platform for multi-physics, pre-processing and visualisation

    International Nuclear Information System (INIS)

    Bergeaud, Vincent; Lefebvre, Vincent

    2010-01-01

    In order to ease the development of applications integrating simulation codes, CAD modelers and post-processing tools. CEA and EDF R and D have invested in the SALOME platform, a tool dedicated to the environment of the scientific codes. The platform comes in the shape of a toolbox which offers functionalities for CAD, meshing, code coupling, visualization, GUI development. These tools can be combined to create integrated applications that make the scientific codes easier to use and well-interfaced with their environment be it other codes, CAD and meshing tools or visualization software. Many projects in CEA and EDF R and D now use SALOME, bringing technical coherence to the software suites of our institutions. (author)

  9. Vertical integration of high-Q silicon nitride microresonators into silicon-on-insulator platform.

    Science.gov (United States)

    Li, Qing; Eftekhar, Ali A; Sodagar, Majid; Xia, Zhixuan; Atabaki, Amir H; Adibi, Ali

    2013-07-29

    We demonstrate a vertical integration of high-Q silicon nitride microresonators into the silicon-on-insulator platform for applications at the telecommunication wavelengths. Low-loss silicon nitride films with a thickness of 400 nm are successfully grown, enabling compact silicon nitride microresonators with ultra-high intrinsic Qs (~ 6 × 10(6) for 60 μm radius and ~ 2 × 10(7) for 240 μm radius). The coupling between the silicon nitride microresonator and the underneath silicon waveguide is based on evanescent coupling with silicon dioxide as buffer. Selective coupling to a desired radial mode of the silicon nitride microresonator is also achievable using a pulley coupling scheme. In this work, a 60-μm-radius silicon nitride microresonator has been successfully integrated into the silicon-on-insulator platform, showing a single-mode operation with an intrinsic Q of 2 × 10(6).

  10. Thermo-economic assessment of the integration of steam cycles on offshore platforms

    DEFF Research Database (Denmark)

    Nguyen, Tuong-Van; Tock, Laurence; Breuhaus, Peter

    2014-01-01

    thermodynamic and economic performance indicators. The results illustrate the benefits of converting the gas turbines into a combined cycle. Using seawater results in smaller power generation and greater CO2-emissions than using process water, as the additional power generation in the combined cycle......The integration of steam bottoming cycles on oil platforms is often seen as a possible route to mitigate the CO2-emissions offshore. In this paper, a North Sea platform and its energy requirements are systematically analysed. The site-scale integration of steam networks is assessed by using...... is compensated by the significant pumping demand. This work emphasises that energy improvement efforts should be analysed at the scale of the overall site and not solely at the level of the combined cycle....

  11. Integration Platform As Central Service Of Data Replication In Distributed Medical System

    Directory of Open Access Journals (Sweden)

    Wiesław Wajs

    2007-01-01

    Full Text Available The paper presents the application of Java Integration Platform (JIP to data replicationin the distributed medical system. After an introductory part on the medical system’s architecture,the focus shifts to a comparison of different approaches that exist with regard totransferring data between the system’s components. A description is given of the historicaldata processing and of the whole area of the JIP application to the medical system.

  12. On challenges and opportunities of designing integrated IT platforms for supporting knowledge works in organizations

    OpenAIRE

    Laha, Arijit

    2009-01-01

    Designing and implementing comprehensive IT-based support environments for KM in organizations is fraught with many problems. Solving them requires intimate knowledge about the information usage in knowledge works and the scopes of technology intervention. In this paper, the Task-oriented Organizational Knowledge Management or TOKM, a design theory for building integrated IT platforms for supporting organizational KM, is proposed. TOKM brings together two apparently mutually exclusive practic...

  13. Power System and Energy Storage Models for Laser Integration on Naval Platforms

    Science.gov (United States)

    2015-09-30

    Power System and Energy Storage Models for Laser Integration on Naval Platforms A.L. Gattozzi, J.D. Herbst, R.E. Hebner Center for... Electromechanics , University of Texas Austin, Texas a.gattozzi@cem.utexas.edu J.A. Blau, K.R. Cohn, W.B. Colson, J.E. Sylvester, M.A. Woehrman Physics...emerging technologies present significant challenges to the electric power distribution and thermal management systems, particularly for

  14. An Integrated System for Disabled People Developed with the Agent Platform PANGEA

    Directory of Open Access Journals (Sweden)

    Carolina ZATO

    2013-11-01

    Full Text Available New trends in multi-agent systems call for self-adaptation and high dynamics, hence the new model of open MAS or virtual organization of agents. However, as existing agent platforms are not yet equipped to support this behavior, it is necessary to create new systems and mechanisms to facilitate the development of these new architectures. This article presents PANGEA, an agent platform to develop open multi-agent systems, specifically those including organizational aspects such as virtual agent organizations. The platform allows the integral management of organizations and offers tools to the end user. Additionally, it includes a communication protocol based on the IRC standard, which facilitates implementation and remains robust even with a large number of connections. The introduction of a CommunicationAgent and a Sniffer make it possible to offer Web Services for the distributed control of interaction. In order to test PANGEA, an integral system was developed to help the disabled, gathering a set of easily deployable and integrated services under a single architecture.

  15. The Role of Semantics in Open-World, Integrative, Collaborative Science Data Platforms

    Science.gov (United States)

    Fox, Peter; Chen, Yanning; Wang, Han; West, Patrick; Erickson, John; Ma, Marshall

    2014-05-01

    As collaborative science spreads into more and more Earth and space science fields, both participants and funders are expressing stronger needs for highly functional data and information capabilities. Characteristics include a) easy to use, b) highly integrated, c) leverage investments, d) accommodate rapid technical change, and e) do not incur undue expense or time to build or maintain - these are not a small set of requirements. Based on our accumulated experience over the last ~ decade and several key technical approaches, we adapt, extend, and integrate several open source applications and frameworks to handle major portions of functionality for these platforms. This includes: an object-type repository, collaboration tools, identity management, all within a portal managing diverse content and applications. In this contribution, we present our methods and results of information models, adaptation, integration and evolution of a networked data science architecture based on several open source technologies (Drupal, VIVO, the Comprehensive Knowledge Archive Network; CKAN, and the Global Handle System; GHS). In particular we present the Deep Carbon Observatory - a platform for international science collaboration. We present and discuss key functional and non-functional attributes, and discuss the general applicability of the platform.

  16. Integrating cell on chip—Novel waveguide platform employing ultra-long optical paths

    Directory of Open Access Journals (Sweden)

    Lena Simone Fohrmann

    2017-09-01

    Full Text Available Optical waveguides are the most fundamental building blocks of integrated optical circuits. They are extremely well understood, yet there is still room for surprises. Here, we introduce a novel 2D waveguide platform which affords a strong interaction of the evanescent tail of a guided optical wave with an external medium while only employing a very small geometrical footprint. The key feature of the platform is its ability to integrate the ultra-long path lengths by combining low propagation losses in a silicon slab with multiple reflections of the guided wave from photonic crystal (PhC mirrors. With a reflectivity of 99.1% of our tailored PhC-mirrors, we achieve interaction paths of 25 cm within an area of less than 10 mm2. This corresponds to 0.17 dB/cm effective propagation which is much lower than the state-of-the-art loss of approximately 1 dB/cm of single mode silicon channel waveguides. In contrast to conventional waveguides, our 2D-approach leads to a decay of the guided wave power only inversely proportional to the optical path length. This entirely different characteristic is the major advantage of the 2D integrating cell waveguide platform over the conventional channel waveguide concepts that obey the Beer-Lambert law.

  17. Integrating cell on chip—Novel waveguide platform employing ultra-long optical paths

    Science.gov (United States)

    Fohrmann, Lena Simone; Sommer, Gerrit; Pitruzzello, Giampaolo; Krauss, Thomas F.; Petrov, Alexander Yu.; Eich, Manfred

    2017-09-01

    Optical waveguides are the most fundamental building blocks of integrated optical circuits. They are extremely well understood, yet there is still room for surprises. Here, we introduce a novel 2D waveguide platform which affords a strong interaction of the evanescent tail of a guided optical wave with an external medium while only employing a very small geometrical footprint. The key feature of the platform is its ability to integrate the ultra-long path lengths by combining low propagation losses in a silicon slab with multiple reflections of the guided wave from photonic crystal (PhC) mirrors. With a reflectivity of 99.1% of our tailored PhC-mirrors, we achieve interaction paths of 25 cm within an area of less than 10 mm2. This corresponds to 0.17 dB/cm effective propagation which is much lower than the state-of-the-art loss of approximately 1 dB/cm of single mode silicon channel waveguides. In contrast to conventional waveguides, our 2D-approach leads to a decay of the guided wave power only inversely proportional to the optical path length. This entirely different characteristic is the major advantage of the 2D integrating cell waveguide platform over the conventional channel waveguide concepts that obey the Beer-Lambert law.

  18. SERVIR-Africa: Developing an Integrated Platform for Floods Disaster Management in Africa

    Science.gov (United States)

    Macharia, Daniel; Korme, Tesfaye; Policelli, Fritz; Irwin, Dan; Adler, Bob; Hong, Yang

    2010-01-01

    SERVIR-Africa is an ambitious regional visualization and monitoring system that integrates remotely sensed data with predictive models and field-based data to monitor ecological processes and respond to natural disasters. It aims addressing societal benefits including floods and turning data into actionable information for decision-makers. Floods are exogenous disasters that affect many parts of Africa, probably second only to drought in terms of social-economic losses. This paper looks at SERVIR-Africa's approach to floods disaster management through establishment of an integrated platform, floods prediction models, post-event flood mapping and monitoring as well as flood maps dissemination in support of flood disaster management.

  19. The waste management program VUB-AZ: An integrated solution for nuclear biomedical waste management

    International Nuclear Information System (INIS)

    Covens, P.; Sonck, M.; Eggermont, G.; Meert, D.

    2001-01-01

    Due to escalating costs and the lack of acceptance of near-surface disposal facilities, the University of Brussels (VUB) and its Academic hospital (AZ) have developed an on-site waste storage program in collaboration with Canberra Europe. This programme is based on selective collection, measurement before decay, storage for decay of short-lived radionuclides, measurement after decay and eventual clearance as non-nuclear waste. It has proved its effectiveness over the past 5 years. Effective characterisation for on-site storage for decay of short-lived radionuclides makes selective collection of waste streams mandatory and requires motivated and trained laboratory staff. Dynamic optimisation of this selective collection increases the efficiency of the storage for decay programme. The accurate qualitative and quantitative measurement of nuclear biomedical waste before decay has several advantages such as verification of correct selective collection, optimisation of the decay period and possibility of clearance below the minimal detectable activity. In the research phase of the program several measurement techniques were investigated. The following measurement concept was selected. Closed PE drums containing low density solid waste materials contaminated with small amounts of β/γ-or pure β-emitting radionuclides are assessed for specific activity by the Canberra measurement unit for nuclear biomedical waste, based on a HPGe-detector. Liquid waste containing (β/γ-emitters are characterised by the same technique while for pure β-emitting liquid waste a Packard liquid scintillation counter is used. Measurement results are obtained by using the gamma-spectroscopy software Genie-2000. A user-friendly interface, based on Procount-2000 and optimised by Canberra for the characterisation of nuclear biomedical waste, has increased the sample throughput of the measurement concept. The MDA (minimal detectable activity) of different radionuclides obtained by the measurement

  20. Design of the Hospital Integrated Information Management System Based on Cloud Platform.

    Science.gov (United States)

    Aijing, L; Jin, Y

    2015-12-01

    At present, the outdated information management style cannot meet the needs of hospital management, and has become the bottleneck of hospital's management and development. In order to improve the integrated management of information, hospitals have increased their investment in integrated information management systems. On account of the lack of reasonable and scientific design, some hospital integrated information management systems have common problems, such as unfriendly interface, poor portability and maintainability, low security and efficiency, lack of interactivity and information sharing. To solve the problem, this paper carries out the research and design of a hospital information management system based on cloud platform, which can realize the optimized integration of hospital information resources and save money.

  1. Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach.

    Science.gov (United States)

    Liang, Muxuan; Li, Zhizhong; Chen, Ting; Zeng, Jianyang

    2015-01-01

    Identification of cancer subtypes plays an important role in revealing useful insights into disease pathogenesis and advancing personalized therapy. The recent development of high-throughput sequencing technologies has enabled the rapid collection of multi-platform genomic data (e.g., gene expression, miRNA expression, and DNA methylation) for the same set of tumor samples. Although numerous integrative clustering approaches have been developed to analyze cancer data, few of them are particularly designed to exploit both deep intrinsic statistical properties of each input modality and complex cross-modality correlations among multi-platform input data. In this paper, we propose a new machine learning model, called multimodal deep belief network (DBN), to cluster cancer patients from multi-platform observation data. In our integrative clustering framework, relationships among inherent features of each single modality are first encoded into multiple layers of hidden variables, and then a joint latent model is employed to fuse common features derived from multiple input modalities. A practical learning algorithm, called contrastive divergence (CD), is applied to infer the parameters of our multimodal DBN model in an unsupervised manner. Tests on two available cancer datasets show that our integrative data analysis approach can effectively extract a unified representation of latent features to capture both intra- and cross-modality correlations, and identify meaningful disease subtypes from multi-platform cancer data. In addition, our approach can identify key genes and miRNAs that may play distinct roles in the pathogenesis of different cancer subtypes. Among those key miRNAs, we found that the expression level of miR-29a is highly correlated with survival time in ovarian cancer patients. These results indicate that our multimodal DBN based data analysis approach may have practical applications in cancer pathogenesis studies and provide useful guidelines for

  2. Integrating Contemplative Tools into Biomedical Science Education and Research Training Programs

    Directory of Open Access Journals (Sweden)

    Rodney R. Dietert

    2014-01-01

    Full Text Available Academic preparation of science researchers and/or human or veterinary medicine clinicians through the science, technology, engineering, and mathematics (STEM curriculum has usually focused on the students (1 acquiring increased disciplinary expertise, (2 learning needed methodologies and protocols, and (3 expanding their capacity for intense, persistent focus. Such educational training is effective until roadblocks or problems arise via this highly-learned approach. Then, the health science trainee may have few tools available for effective problem solving. Training to achieve flexibility, adaptability, and broadened perspectives using contemplative practices has been rare among biomedical education programs. To address this gap, a Cornell University-based program involving formal biomedical science coursework, and health science workshops has been developed to offer science students, researchers and health professionals a broader array of personal, contemplation-based, problem-solving tools. This STEM educational initiative includes first-person exercises designed to broaden perceptional awareness, decrease emotional drama, and mobilize whole-body strategies for creative problem solving. Self-calibration and journaling are used for students to evaluate the personal utility of each exercise. The educational goals are to increase student self-awareness and self-regulation and to provide trainees with value-added tools for career-long problem solving. Basic elements of this educational initiative are discussed using the framework of the Tree of Contemplative Practices.

  3. A Ubiquitous Sensor Network Platform for Integrating Smart Devices into the Semantic Sensor Web

    Science.gov (United States)

    de Vera, David Díaz Pardo; Izquierdo, Álvaro Sigüenza; Vercher, Jesús Bernat; Gómez, Luis Alfonso Hernández

    2014-01-01

    Ongoing Sensor Web developments make a growing amount of heterogeneous sensor data available to smart devices. This is generating an increasing demand for homogeneous mechanisms to access, publish and share real-world information. This paper discusses, first, an architectural solution based on Next Generation Networks: a pilot Telco Ubiquitous Sensor Network (USN) Platform that embeds several OGC® Sensor Web services. This platform has already been deployed in large scale projects. Second, the USN-Platform is extended to explore a first approach to Semantic Sensor Web principles and technologies, so that smart devices can access Sensor Web data, allowing them also to share richer (semantically interpreted) information. An experimental scenario is presented: a smart car that consumes and produces real-world information which is integrated into the Semantic Sensor Web through a Telco USN-Platform. Performance tests revealed that observation publishing times with our experimental system were well within limits compatible with the adequate operation of smart safety assistance systems in vehicles. On the other hand, response times for complex queries on large repositories may be inappropriate for rapid reaction needs. PMID:24945678

  4. Design Considerations for Integration of Terahertz Time-Domain Spectroscopy in Microfluidic Platforms

    Directory of Open Access Journals (Sweden)

    Rasha Al-Hujazy

    2018-03-01

    Full Text Available Microfluidic platforms have received much attention in recent years. In particular, there is interest in combining spectroscopy with microfluidic platforms. This work investigates the integration of microfluidic platforms and terahertz time-domain spectroscopy (THz-TDS systems. A semiclassical computational model is used to simulate the emission of THz radiation from a GaAs photoconductive THz emitter. This model incorporates white noise with increasing noise amplitude (corresponding to decreasing dynamic range values. White noise is selected over other noise due to its contributions in THz-TDS systems. The results from this semiclassical computational model, in combination with defined sample thicknesses, can provide the maximum measurable absorption coefficient for a microfluidic-based THz-TDS system. The maximum measurable frequencies for such systems can be extracted through the relationship between the maximum measurable absorption coefficient and the absorption coefficient for representative biofluids. The sample thickness of the microfluidic platform and the dynamic range of the THz-TDS system play a role in defining the maximum measurable frequency for microfluidic-based THz-TDS systems. The results of this work serve as a design tool for the development of such systems.

  5. OpenDrop: An Integrated Do-It-Yourself Platform for Personal Use of Biochips

    Directory of Open Access Journals (Sweden)

    Mirela Alistar

    2017-05-01

    Full Text Available Biochips, or digital labs-on-chip, are developed with the purpose of being used by laboratory technicians or biologists in laboratories or clinics. In this article, we expand this vision with the goal of enabling everyone, regardless of their expertise, to use biochips for their own personal purposes. We developed OpenDrop, an integrated electromicrofluidic platform that allows users to develop and program their own bio-applications. We address the main challenges that users may encounter: accessibility, bio-protocol design and interaction with microfluidics. OpenDrop consists of a do-it-yourself biochip, an automated software tool with visual interface and a detailed technique for at-home operations of microfluidics. We report on two years of use of OpenDrop, released as an open-source platform. Our platform attracted a highly diverse user base with participants originating from maker communities, academia and industry. Our findings show that 47% of attempts to replicate OpenDrop were successful, the main challenge remaining the assembly of the device. In terms of usability, the users managed to operate their platforms at home and are working on designing their own bio-applications. Our work provides a step towards a future in which everyone will be able to create microfluidic devices for their personal applications, thereby democratizing parts of health care.

  6. Information Integration Platform for Patient-Centric Healthcare Services: Design, Prototype and Dependability Aspects

    Directory of Open Access Journals (Sweden)

    Yohanes Baptista Dafferianto Trinugroho

    2014-03-01

    Full Text Available Technology innovations have pushed today’s healthcare sector to an unprecedented new level. Various portable and wearable medical and fitness devices are being sold in the consumer market to provide the self-empowerment of a healthier lifestyle to society. Many vendors provide additional cloud-based services for devices they manufacture, enabling the users to visualize, store and share the gathered information through the Internet. However, most of these services are integrated with the devices in a closed “silo” manner, where the devices can only be used with the provided services. To tackle this issue, an information integration platform (IIP has been developed to support communications between devices and Internet-based services in an event-driven fashion by adopting service-oriented architecture (SOA principles and a publish/subscribe messaging pattern. It follows the “Internet of Things” (IoT idea of connecting everyday objects to various networks and to enable the dissemination of the gathered information to the global information space through the Internet. A patient-centric healthcare service environment is chosen as the target scenario for the deployment of the platform, as this is a domain where IoT can have a direct positive impact on quality of life enhancement. This paper describes the developed platform, with emphasis on dependability aspects, including availability, scalability and security.

  7. A review on microscale polymerase chain reaction based methods in molecular diagnosis, and future prospects for the fabrication of fully integrated portable biomedical devices.

    Science.gov (United States)

    Lee, Nae Yoon

    2018-05-08

    Since the advent of microfabrication technology and soft lithography, the lab-on-a-chip concept has emerged as a state-of-the-art miniaturized tool for conducting the multiple functions associated with micro total analyses of nucleic acids, in series, in a seamless manner with a miniscule volume of sample. The enhanced surface-to-volume ratio inside a microchannel enables fast reactions owing to increased heat dissipation, allowing rapid amplification. For this reason, PCR has been one of the first applications to be miniaturized in a portable format. However, the nature of the basic working principle for microscale PCR, such as the complicated temperature controls and use of a thermal cycler, has hindered its total integration with other components into a micro total analyses systems (μTAS). This review (with 179 references) surveys the diverse forms of PCR microdevices constructed on the basis of different working principles and evaluates their performances. The first two main sections cover the state-of-the-art in chamber-type PCR microdevices and in continuous-flow PCR microdevices. Methods are then discussed that lead to microdevices with upstream sample purification and downstream detection schemes, with a particular focus on rapid on-site detection of foodborne pathogens. Next, the potential for miniaturizing and automating heaters and pumps is examined. The review concludes with sections on aspects of complete functional integration in conjunction with nanomaterial based sensing, a discussion on future prospects, and with conclusions. Graphical abstract In recent years, thermocycler-based PCR systems have been miniaturized to palm-sized, disposable polymer platforms. In addition, operational accessories such as heaters and mechanical pumps have been simplified to realize semi-automatted stand-alone portable biomedical diagnostic microdevices that are directly applicable in the field. This review summarizes the progress made and the current state of this

  8. Paper-based electrochemical sensing platform with integral battery and electrochromic read-out.

    Science.gov (United States)

    Liu, Hong; Crooks, Richard M

    2012-03-06

    We report a battery-powered, microelectrochemical sensing platform that reports its output using an electrochromic display. The platform is fabricated based on paper fluidics and uses a Prussian blue spot electrodeposited on an indium-doped tin oxide thin film as the electrochromic indicator. The integrated metal/air battery powers both the electrochemical sensor and the electrochromic read-out, which are in electrical contact via a paper reservoir. The sample activates the battery and the presence of analyte in the sample initiates the color change of the Prussian blue spot. The entire system is assembled on the lab bench, without the need for cleanroom facilities. The applicability of the device to point-of-care sensing is demonstrated by qualitative detection of 0.1 mM glucose and H(2)O(2) in artificial urine samples.

  9. Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes.

    Science.gov (United States)

    Margaria, Tiziana; Kubczak, Christian; Steffen, Bernhard

    2008-04-25

    With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution. As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.

  10. Supporting Building Portfolio Investment and Policy Decision Making through an Integrated Building Utility Data Platform

    Energy Technology Data Exchange (ETDEWEB)

    Aziz, Azizan [Carnegie Mellon Univ., Pittsburgh, PA (United States); Lasternas, Bertrand [Carnegie Mellon Univ., Pittsburgh, PA (United States); Alschuler, Elena [US DOE; View Inc; Loftness, Vivian [Carnegie Mellon Univ., Pittsburgh, PA (United States); Wang, Haopeng [Carnegie Mellon Univ., Pittsburgh, PA (United States); Mo, Yunjeong [Carnegie Mellon Univ., Pittsburgh, PA (United States); Wang, Ting [Carnegie Mellon Univ., Pittsburgh, PA (United States); Zhang, Chenlu [Carnegie Mellon Univ., Pittsburgh, PA (United States); Sharma, Shilpi [Carnegie Mellon; Stevens, Ivana [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    2016-03-18

    The American Recovery and Reinvestment Act stimulus funding of 2009 for smart grid projects resulted in the tripling of smart meters deployment. In 2012, the Green Button initiative provided utility customers with access to their real-time1 energy usage. The availability of finely granular data provides an enormous potential for energy data analytics and energy benchmarking. The sheer volume of time-series utility data from a large number of buildings also poses challenges in data collection, quality control, and database management for rigorous and meaningful analyses. In this paper, we will describe a building portfolio-level data analytics tool for operational optimization, business investment and policy assessment using 15-minute to monthly intervals utility data. The analytics tool is developed on top of the U.S. Department of Energy’s Standard Energy Efficiency Data (SEED) platform, an open source software application that manages energy performance data of large groups of buildings. To support the significantly large volume of granular interval data, we integrated a parallel time-series database to the existing relational database. The time-series database improves on the current utility data input, focusing on real-time data collection, storage, analytics and data quality control. The fully integrated data platform supports APIs for utility apps development by third party software developers. These apps will provide actionable intelligence for building owners and facilities managers. Unlike a commercial system, this platform is an open source platform funded by the U.S. Government, accessible to the public, researchers and other developers, to support initiatives in reducing building energy consumption.

  11. An intermittent rocking platform for integrated expansion and differentiation of human pluripotent stem cells to cardiomyocytes in suspended microcarrier cultures

    Directory of Open Access Journals (Sweden)

    Sherwin Ting

    2014-09-01

    In conclusion, we have developed a simple robust and scalable platform that integrates both hESC expansion and CM differentiation in one unit process which is capable of meeting the need for large amounts of CMs.

  12. Work station learning activities: a flexible and scalable instrument for integrating across basic subjects in biomedical education.

    Science.gov (United States)

    González-Soltero, Rocío; Learte, Ana Isabel R; Sánchez, Ana Mª; Gal, Beatriz

    2017-11-29

    Establishing innovative teaching programs in biomedical education involves dealing with several national and supra-national (i.e. European) regulations as well as with new pedagogical and demographic demands. We aimed to develop and validate a suitable instrument to integrate activities across preclinical years in all Health Science Degrees while meeting requirements of national quality agencies. The new approach was conceived at two different levels: first, we identified potentially integrative units from different fields according to national learning goals established for each preclinical year (national quality agency regulations). Secondly, we implemented a new instrument that combines active methodologies in Work Station Learning Activities (WSLA), using clinical scenarios as a guiding common thread to instruct students from an integrated perspective. We evaluated students' perception through a Likert-type survey of a total of 118 students enrolled in the first year of the Bachelor's Degree in Medicine. Our model of integrated activities through WSLA is feasible, scalable and manageable with large groups of students and a minimum number of instructors, two major limitations in many medical schools. Students' perception of WSLA was positive in overall terms. Seventy nine percent of participants stated that WSLA sessions were more useful than non-integrated activities. Eighty three percent confirmed that the WSLA methodology was effective at integrating concepts covered by different subjects. The WSLA approach is a flexible and scalable instrument for moving towards integrated curricula, and it can be successfully adapted to teach basic subjects in preclinical years of Health Science degrees. WSLA can be applied to large groups of students in a variety of contexts or environments using clinical cases as connecting threads.

  13. Integrated Microfluidic Lectin Barcode Platform for High-Performance Focused Glycomic Profiling

    Science.gov (United States)

    Shang, Yuqin; Zeng, Yun; Zeng, Yong

    2016-02-01

    Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges in analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and speed of lectin microarray. Moreover, we established an on-chip lectin assay which employs a very simple blocking method to effectively suppress the undesired background due to lectin binding of antibodies. Using this technology, we demonstrated focused differential profiling of tissue-specific glycosylation changes of a biomarker, CA125 protein purified from ovarian cancer cell line and different tissues from ovarian cancer patients in a fast, reproducible, and high-throughput fashion. Highly sensitive CA125 detection was also demonstrated with a detection limit much lower than the clinical cutoff value for cancer diagnosis. This microfluidic platform holds the potential to integrate with sample preparation functions to construct a fully integrated “sample-to-answer” microsystem for focused differential glycomic analysis. Thus, our technology should present a powerful tool in support of rapid advance in glycobiology and glyco-biomarker development.

  14. "Exploring knowledge-user experiences in integrated knowledge translation: a biomedical investigation of the causes and consequences of food allergy".

    Science.gov (United States)

    Dixon, Jenna; Elliott, Susan J; Clarke, Ann E

    2016-01-01

    Food allergy is a serious public health problem in Canada and other high-income countries, as it is potentially life threatening and severely impacts the quality of life for individuals and their families. Yet, many questions still remain as to its origins and determinants, and the best practices for treatment. Formed to tackle these very questions, the GET-FACTS research study centers on a novel concept in biomedical research: in order to make this science useful, knowledge creation must include meaningful interactions with knowledge-users. With this, knowledge-users are present at every stage of the research and are crucial, central and equal contributors. This study reflects on the early part of that journey from the perspective of the knowledge-users. We conducted interviews with all non-scientist members of the GET-FACTS steering committee, representing Canadian organizations that deal with patient advocacy and policy with regards to food allergy. Steering committee members had a clear sense that scientists and knowledge-users are equally responsible for putting knowledge into action and the importance of consulting and integrating knowledge-users throughout research. They also have high expectations for the GET-FACTS integrated process; that this model of doing science will create better scientists (e.g. improve communication skills) and make the scientific output more useful and relevant. Our work highlights both the unique contributions that knowledge-users can offer to knowledge creation as well as the challenges of trying to unify members from such different communities (policy/advocacy and biomedical science). There remains a real need to develop more touch points and opportunities for collaboration if true integration is to be achieved. Despite the obstacles, this model can help change the way knowledge is created in the biomedical world. ᅟ. Despite the burden of food allergic disease many questions remain as to its origins, determinants and best

  15. SVIP-N 1.0: An integrated visualization platform for neutronics analysis

    International Nuclear Information System (INIS)

    Luo Yuetong; Long Pengcheng; Wu Guoyong; Zeng Qin; Hu Liqin; Zou Jun

    2010-01-01

    Post-processing is an important part of neutronics analysis, and SVIP-N 1.0 (scientific visualization integrated platform for neutronics analysis) is designed to ease post-processing of neutronics analysis through visualization technologies. Main capabilities of SVIP-N 1.0 include: (1) ability of manage neutronics analysis result; (2) ability to preprocess neutronics analysis result; (3) ability to visualization neutronics analysis result data in different way. The paper describes the system architecture and main features of SVIP-N, some advanced visualization used in SVIP-N 1.0 and some preliminary applications, such as ITER.

  16. MetaABC--an integrated metagenomics platform for data adjustment, binning and clustering.

    Science.gov (United States)

    Su, Chien-Hao; Hsu, Ming-Tsung; Wang, Tse-Yi; Chiang, Sufeng; Cheng, Jen-Hao; Weng, Francis C; Kao, Cheng-Yan; Wang, Daryi; Tsai, Huai-Kuang

    2011-08-15

    MetaABC is a metagenomic platform that integrates several binning tools coupled with methods for removing artifacts, analyzing unassigned reads and controlling sampling biases. It allows users to arrive at a better interpretation via series of distinct combinations of analysis tools. After execution, MetaABC provides outputs in various visual formats such as tables, pie and bar charts as well as clustering result diagrams. MetaABC source code and documentation are available at http://bits2.iis.sinica.edu.tw/MetaABC/ CONTACT: dywang@gate.sinica.edu.tw; hktsai@iis.sinica.edu.tw Supplementary data are available at Bioinformatics online.

  17. Wafer Scale Integration of CMOS Chips for Biomedical Applications via Self-Aligned Masking.

    Science.gov (United States)

    Uddin, Ashfaque; Milaninia, Kaveh; Chen, Chin-Hsuan; Theogarajan, Luke

    2011-12-01

    This paper presents a novel technique for the integration of small CMOS chips into a large area substrate. A key component of the technique is the CMOS chip based self-aligned masking. This allows for the fabrication of sockets in wafers that are at most 5 µm larger than the chip on each side. The chip and the large area substrate are bonded onto a carrier such that the top surfaces of the two components are flush. The unique features of this technique enable the integration of macroscale components, such as leads and microfluidics. Furthermore, the integration process allows for MEMS micromachining after CMOS die-wafer integration. To demonstrate the capabilities of the proposed technology, a low-power integrated potentiostat chip for biosensing implemented in the AMI 0.5 µm CMOS technology is integrated in a silicon substrate. The horizontal gap and the vertical displacement between the chip and the large area substrate measured after the integration were 4 µm and 0.5 µm, respectively. A number of 104 interconnects are patterned with high-precision alignment. Electrical measurements have shown that the functionality of the chip is not affected by the integration process.

  18. Quality control of next-generation sequencing library through an integrative digital microfluidic platform.

    Science.gov (United States)

    Thaitrong, Numrin; Kim, Hanyoup; Renzi, Ronald F; Bartsch, Michael S; Meagher, Robert J; Patel, Kamlesh D

    2012-12-01

    We have developed an automated quality control (QC) platform for next-generation sequencing (NGS) library characterization by integrating a droplet-based digital microfluidic (DMF) system with a capillary-based reagent delivery unit and a quantitative CE module. Using an in-plane capillary-DMF interface, a prepared sample droplet was actuated into position between the ground electrode and the inlet of the separation capillary to complete the circuit for an electrokinetic injection. Using a DNA ladder as an internal standard, the CE module with a compact LIF detector was capable of detecting dsDNA in the range of 5-100 pg/μL, suitable for the amount of DNA required by the Illumina Genome Analyzer sequencing platform. This DMF-CE platform consumes tenfold less sample volume than the current Agilent BioAnalyzer QC technique, preserving precious sample while providing necessary sensitivity and accuracy for optimal sequencing performance. The ability of this microfluidic system to validate NGS library preparation was demonstrated by examining the effects of limited-cycle PCR amplification on the size distribution and the yield of Illumina-compatible libraries, demonstrating that as few as ten cycles of PCR bias the size distribution of the library toward undesirable larger fragments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Minilaparoscopic hysterectomy made easy: first report on alternative instrumentation and new integrated energy platform.

    Science.gov (United States)

    Ng, Ying Woo; Lim, Li Min; Fong, Yoke Fai

    2014-05-01

    Minilaparoscopy is an attractive approach for hysterectomy due to advantages such as reduced morbidities and enhanced cosmesis. However, it has not been popularized due to the lack of suitable instruments and high technical demand. We aim to highlight the first case of minilaparoscopic hysterectomy reported in Asia and the use of a new integrated energy platform, Thunderbeat. We would like to propose an alternative method of instrumentation, so as to improve the feasibility and safety of minilaparoscopic hysterectomy. The first minilaparoscopic hysterectomy in Singapore was successfully completed using the alternative instrumentation and new energy platform. There was no conversion or complication during the surgery. The patient recovered uneventfully. To our knowledge, this is the first report on the use of such alternative instrumentation. This approach in instrumentation and the new energy platform will improve the feasibility and speed of the surgery and ensure safety in our patients. © 2014 The Authors. Journal of Obstetrics and Gynaecology Research © 2014 Japan Society of Obstetrics and Gynecology.

  20. Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

    Science.gov (United States)

    Roever, Stefan

    2012-01-01

    A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

  1. Integration of reconfigurable potentiometric electrochemical sensors into a digital microfluidic platform.

    Science.gov (United States)

    Farzbod, Ali; Moon, Hyejin

    2018-05-30

    This paper presents the demonstration of on-chip fabrication of a potassium-selective sensor array enabled by electrowetting on dielectric digital microfluidics for the first time. This demonstration proves the concept that electrochemical sensors can be seamlessly integrated with sample preparation units in a digital microfluidic platform. More significantly, the successful on-chip fabrication of a sensor array indicates that sensors become reconfigurable and have longer lifetime in a digital microfluidic platform. The on-chip fabrication of ion-selective electrodes includes electroplating Ag followed by forming AgCl layer by chemical oxidation and depositing a thin layer of desired polymer-based ion selective membrane on one of the sensor electrodes. In this study, potassium ionophores work as potassium ion channels and make the membrane selective to potassium ions. This selectiveness results in the voltage difference across the membrane layer, which is correlated with potassium ion concentration. The calibration curve of the fabricated potassium-selective electrode demonstrates the slope of 58 mV/dec for potassium concentration in KCl sample solutions and shows good agreement with the ideal Nernstian response. The proposed sensor platform is an outstanding candidate for a portable home-use for continuous monitoring of ions thanks to its advantages such as easy automation of sample preparation and detection processes, elongated sensor lifetime, minimal membrane and sample consumption, and user-definable/reconfigurable sensor array. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Miniaturized Integrated Platform for Electrical and Optical Monitoring of Cell Cultures

    Directory of Open Access Journals (Sweden)

    Costin Brasoveanu

    2012-08-01

    Full Text Available The following paper describes the design and functions of a miniaturized integrated platform for optical and electrical monitoring of cell cultures and the necessary steps in the fabrication and testing of a silicon microchip Micro ElectroMechanical Systems (MEMS-based technology for cell data recording, monitoring and stimulation. The silicon microchip consists of a MEMS machined device containing a shank of 240 μm width, 3 mm long and 50 μm thick and an enlarged area of 5 mm × 5 mm hosting the pads for electrical connections. Ten platinum electrodes and five sensors are placed on the shank and are connected with the external electronics through the pads. The sensors aim to monitor the pH, the temperature and the impedance of the cell culture. The electrodes are bidirectional and can be used both for electrical potential recording and stimulation of cells. The fabrication steps are presented, along with the electrical and optical characterization of the system. The target of the research is to develop a new and reconfigurable platform according to the particular applications needs, as a tool for the biologist, chemists and medical doctors working is the field of cell culture monitoring in terms of growth, maintenance conditions, reaction to electrical or chemical stimulation (drugs, toxicants, etc.. HaCaT (Immortalised Human Keratinocyte cell culture has been used for demonstration purposes in order to provide information on the platform electrical and optical functions.

  3. A Single-Chip Solar Energy Harvesting IC Using Integrated Photodiodes for Biomedical Implant Applications.

    Science.gov (United States)

    Chen, Zhiyuan; Law, Man-Kay; Mak, Pui-In; Martins, Rui P

    2017-02-01

    In this paper, an ultra-compact single-chip solar energy harvesting IC using on-chip solar cell for biomedical implant applications is presented. By employing an on-chip charge pump with parallel connected photodiodes, a 3.5 × efficiency improvement can be achieved when compared with the conventional stacked photodiode approach to boost the harvested voltage while preserving a single-chip solution. A photodiode-assisted dual startup circuit (PDSC) is also proposed to improve the area efficiency and increase the startup speed by 77%. By employing an auxiliary charge pump (AQP) using zero threshold voltage (ZVT) devices in parallel with the main charge pump, a low startup voltage of 0.25 V is obtained while minimizing the reversion loss. A 4 V in gate drive voltage is utilized to reduce the conduction loss. Systematic charge pump and solar cell area optimization is also introduced to improve the energy harvesting efficiency. The proposed system is implemented in a standard 0.18- [Formula: see text] CMOS technology and occupies an active area of 1.54 [Formula: see text]. Measurement results show that the on-chip charge pump can achieve a maximum efficiency of 67%. With an incident power of 1.22 [Formula: see text] from a halogen light source, the proposed energy harvesting IC can deliver an output power of 1.65 [Formula: see text] at 64% charge pump efficiency. The chip prototype is also verified using in-vitro experiment.

  4. Using a blog as an integrated eLearning tool and platform.

    Science.gov (United States)

    Goh, Poh Sun

    2016-06-01

    Technology enhanced learning or eLearning allows educators to expand access to educational content, promotes engagement with students and makes it easier for students to access educational material at a time, place and pace which suits them. The challenge for educators beginning their eLearning journey is to decide where to start, which includes the choice of an eLearning tool and platform. This article will share one educator's decision making process, and experience using blogs as a flexible and versatile integrated eLearning tool and platform. Apart from being a cost effective/free tool and platform, blogs offer the possibility of creating a hyperlinked indexed content repository, for both created and curated educational material; as well as a distribution and engagement tool and platform. Incorporating pedagogically sound activities and educational practices into a blog promote a structured templated teaching process, which can be reproduced. Moving from undergraduate to postgraduate training, educational blogs supported by a comprehensive online case-based repository offer the possibility of training beyond competency towards proficiency and expert level performance through a process of deliberate practice. By documenting educational content and the student engagement and learning process, as well as feedback and personal reflection of educational sessions, blogs can also form the basis for a teaching portfolio, and provide evidence and data of scholarly teaching and educational scholarship. Looking into the future, having a collection of readily accessible indexed hyperlinked teaching material offers the potential to do on the spot teaching with illustrative material called up onto smart surfaces, and displayed on holographic interfaces.

  5. CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

    Science.gov (United States)

    Gai, Xiaowu; Perin, Juan C; Murphy, Kevin; O'Hara, Ryan; D'arcy, Monica; Wenocur, Adam; Xie, Hongbo M; Rappaport, Eric F; Shaikh, Tamim H; White, Peter S

    2010-02-04

    Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated

  6. CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics

    Directory of Open Access Journals (Sweden)

    Rappaport Eric F

    2010-02-01

    Full Text Available Abstract Background Recent studies have shown that copy number variations (CNVs are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. Results We developed a suite of software tools and resources (CNV Workshop for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. Conclusions To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and

  7. Design and Development of ChemInfoCloud: An Integrated Cloud Enabled Platform for Virtual Screening.

    Science.gov (United States)

    Karthikeyan, Muthukumarasamy; Pandit, Deepak; Bhavasar, Arvind; Vyas, Renu

    2015-01-01

    The power of cloud computing and distributed computing has been harnessed to handle vast and heterogeneous data required to be processed in any virtual screening protocol. A cloud computing platorm ChemInfoCloud was built and integrated with several chemoinformatics and bioinformatics tools. The robust engine performs the core chemoinformatics tasks of lead generation, lead optimisation and property prediction in a fast and efficient manner. It has also been provided with some of the bioinformatics functionalities including sequence alignment, active site pose prediction and protein ligand docking. Text mining, NMR chemical shift (1H, 13C) prediction and reaction fingerprint generation modules for efficient lead discovery are also implemented in this platform. We have developed an integrated problem solving cloud environment for virtual screening studies that also provides workflow management, better usability and interaction with end users using container based virtualization, OpenVz.

  8. Multilayered photonic integration on SOI platform using waveguide-based bridge structure

    Science.gov (United States)

    Majumder, Saikat; Chakraborty, Rajib

    2018-06-01

    A waveguide based structure on silicon on insulator platform is proposed for vertical integration in photonic integrated circuits. The structure consists of two multimode interference couplers connected by a single mode (SM) section which can act as a bridge over any other underlying device. Two more SM sections acts as input and output of the first and second multimode couplers respectively. Potential application of this structure is in multilayered photonic links. It is shown that the efficiency of the structure can be improved by making some design modifications. The entire simulation is done using effective-index based matrix method. The feature size chosen are comparable to waveguides fabricated previously so as to fabricate the proposed structure easily.

  9. Migration of the Almaraz NPP integrated operation management system to a new computer platform

    International Nuclear Information System (INIS)

    Gonzalez Crego, E.; Martin Lopez-Suevos, C.

    1996-01-01

    In all power plants, it becomes necessary, with the passage of time, to migrate the initial operation management systems to adapt them to current technologies. That is a good time to improve the inclusion of data in the corporative database and standardize the system interfaces and operation, whilst maintaining data system operability. This article contains Almaraz experience in migrating its Integrated Operation Management System to an advanced computer platform based on open systems (UNIX), communications network (ETHERNET) and database (ORACLE). To this effect, clear objectives and strict standards were established to facilitate the work. The most noteworthy results obtained are: Better quality of information and structure in the corporative database Standardised user interface in all applications. Joint migration of applications for Maintenance, Components and Spare parts, Warehouses and Purchases. Integration of new applications into the system. Introduction of the navigator, which allows movement around the database using all available applications. (Author)

  10. BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines.

    Science.gov (United States)

    Jácome, Alberto G; Fdez-Riverola, Florentino; Lourenço, Anália

    2016-07-01

    Text mining and semantic analysis approaches can be applied to the construction of biomedical domain-specific search engines and provide an attractive alternative to create personalized and enhanced search experiences. Therefore, this work introduces the new open-source BIOMedical Search Engine Framework for the fast and lightweight development of domain-specific search engines. The rationale behind this framework is to incorporate core features typically available in search engine frameworks with flexible and extensible technologies to retrieve biomedical documents, annotate meaningful domain concepts, and develop highly customized Web search interfaces. The BIOMedical Search Engine Framework integrates taggers for major biomedical concepts, such as diseases, drugs, genes, proteins, compounds and organisms, and enables the use of domain-specific controlled vocabulary. Technologies from the Typesafe Reactive Platform, the AngularJS JavaScript framework and the Bootstrap HTML/CSS framework support the customization of the domain-oriented search application. Moreover, the RESTful API of the BIOMedical Search Engine Framework allows the integration of the search engine into existing systems or a complete web interface personalization. The construction of the Smart Drug Search is described as proof-of-concept of the BIOMedical Search Engine Framework. This public search engine catalogs scientific literature about antimicrobial resistance, microbial virulence and topics alike. The keyword-based queries of the users are transformed into concepts and search results are presented and ranked accordingly. The semantic graph view portraits all the concepts found in the results, and the researcher may look into the relevance of different concepts, the strength of direct relations, and non-trivial, indirect relations. The number of occurrences of the concept shows its importance to the query, and the frequency of concept co-occurrence is indicative of biological relations

  11. A commercial real-time manufacturing integration platform for the new control system on FTU

    International Nuclear Information System (INIS)

    Panella, M.; Bertocchi, A.; Bozzolan, V.; Buceti, G.; Centioli, C.; Imparato, A.; Mazza, G.; Torelli, C.; Vitale, V.

    1999-01-01

    In 1994 a working group was set up in Frascati to investigate how to build up a new control system for FTU (Frascati tokamak upgrade) considering the evolution in the information technology. Strong emphasis was placed on the use of standard solutions (be they de-facto or de-jure) and commercial platforms where-ever possible. This paper describes our operational experience with the new control system based on the commercial DEC BASEstar family of products. BASEstar is based on client/server computing technologies, providing an environment to collect, process, manage, distribute and integrate real time manufacturing data. UNIX, VMS, PC Win, OS-9 are integrated to handle hosts, PC, VME CPUs. A 4 GL programming language, CIMfast, has been used to handle via automatic procedures the tokamak discharge. X11 standard based mimics are available to display the plants status. A real flexibility of the whole system has been experience and the further use of the this system has been planned for the ITER DTP (divertor test platform). (orig.)

  12. Integration of nanostructured materials with MEMS microhotplate platforms to enhance chemical sensor performance

    International Nuclear Information System (INIS)

    Benkstein, Kurt D.; Martinez, Carlos J.; Li, Guofeng; Meier, Douglas C.; Montgomery, Christopher B.; Semancik, Steve

    2006-01-01

    The development of miniaturized chemical sensors is an increasingly active area of research. Such devices, particularly when they feature low mass and low power budgets, can impact a broad range of applications including industrial process monitoring, building security and extraterrestrial exploration. Nanostructured materials, because of their high surface area, can provide critical enhancements in the performance of chemical microsensors. We have worked to integrate nanomaterial films with MEMS (microelectromechanical systems) microhotplate platforms developed at the National Institute of Standards and Technology in order to gain the benefits of both the materials and the platforms in high-performance chemical sensor arrays. Here, we describe our success in overcoming the challenges of integration and the benefits that we have achieved with regard to the critical sensor performance characteristics of sensor response, speed, stability and selectivity. Nanostructured metal oxide sensing films were locally deposited onto microhotplates via chemical vapor deposition and microcapillary pipetting, and conductive polymer nanoparticle films were deposited via electrophoretic patterning. All films were characterized by scanning electron microscopy and evaluated as conductometric gas sensors

  13. Titanium dioxide nanowire sensor array integration on CMOS platform using deterministic assembly.

    Science.gov (United States)

    Gall, Oren Z; Zhong, Xiahua; Schulman, Daniel S; Kang, Myungkoo; Razavieh, Ali; Mayer, Theresa S

    2017-06-30

    Nanosensor arrays have recently received significant attention due to their utility in a wide range of applications, including gas sensing, fuel cells, internet of things, and portable health monitoring systems. Less attention has been given to the production of sensor platforms in the μW range for ultra-low power applications. Here, we discuss how to scale the nanosensor energy demand by developing a process for integration of nanowire sensing arrays on a monolithic CMOS chip. This work demonstrates an off-chip nanowire fabrication method; subsequently nanowires link to a fused SiO 2 substrate using electric-field assisted directed assembly. The nanowire resistances shown in this work have the highest resistance uniformity reported to date of 18%, which enables a practical roadmap towards the coupling of nanosensors to CMOS circuits and signal processing systems. The article also presents the utility of optimizing annealing conditions of the off-chip metal-oxides prior to CMOS integration to avoid limitations of thermal budget and process incompatibility. In the context of the platform demonstrated here, directed assembly is a powerful tool that can realize highly uniform, cross-reactive arrays of different types of metal-oxide nanosensors suited for gas discrimination and signal processing systems.

  14. Integration of the HTC Vive into the medical platform MeVisLab

    Science.gov (United States)

    Egger, Jan; Gall, Markus; Wallner, Jürgen; de Almeida Germano Boechat, Pedro; Hann, Alexander; Li, Xing; Chen, Xiaojun; Schmalstieg, Dieter

    2017-03-01

    Virtual Reality (VR) is an immersive technology that replicates an environment via computer-simulated reality. VR gets a lot of attention in computer games but has also great potential in other areas, like the medical domain. Examples are planning, simulations and training of medical interventions, like for facial surgeries where an aesthetic outcome is important. However, importing medical data into VR devices is not trivial, especially when a direct connection and visualization from your own application is needed. Furthermore, most researcher don't build their medical applications from scratch, rather they use platforms, like MeVisLab, Slicer or MITK. The platforms have in common that they integrate and build upon on libraries like ITK and VTK, further providing a more convenient graphical interface to them for the user. In this contribution, we demonstrate the usage of a VR device for medical data under MeVisLab. Therefore, we integrated the OpenVR library into MeVisLab as an own module. This enables the direct and uncomplicated usage of head mounted displays, like the HTC Vive under MeVisLab. Summarized, medical data from other MeVisLab modules can directly be connected per drag-and-drop to our VR module and will be rendered inside the HTC Vive for an immersive inspection.

  15. Integrated microfluidic capillary in a waveguide resonator for chemical and biomedical sensing

    International Nuclear Information System (INIS)

    Pavuluri, S K; Lopez-Villarroya, R; McKeever, E; Goussetis, G; Desmulliez, M P Y; Kavanagh, D

    2009-01-01

    A novel microfluidic sensing device based on waveguide cavity filters is proposed for the characterisation, detection of cells in solution and chemical substances in micro-litre volumes. The sensor consists of a micromachined microfluidic channel within a waveguide-based resonator localised increased near-fields and could potentially be designed for different frequency regimes to improve the sensitivity. The present sensor has been proposed for fabrication in different manufacturing platforms and an initial prototype with a 100μm micromachined channel that is embedded within an X-band E-plane waveguide has been fabricated and tested. The design methodology for the microfluidic channel and the E-plane filter is also presented.

  16. An integrated platform for gas-diffusion separation and electrochemical determination of ethanol on fermentation broths

    Energy Technology Data Exchange (ETDEWEB)

    Giordano, Gabriela Furlan [Microfabrication Laboratory, Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970 (Brazil); Department of Analytical Chemistry, Institute of Chemistry – UNICAMP, Campinas, SP 13083-970 (Brazil); National Institute of Science and Technology of Bioanalytics, Institute of Chemistry – UNICAMP, Campinas, SP 13083-970 (Brazil); Vieira, Luis Carlos Silveira; Gobbi, Angelo Luiz [Microfabrication Laboratory, Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970 (Brazil); Lima, Renato Sousa [Microfabrication Laboratory, Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970 (Brazil); Department of Analytical Chemistry, Institute of Chemistry – UNICAMP, Campinas, SP 13083-970 (Brazil); National Institute of Science and Technology of Bioanalytics, Institute of Chemistry – UNICAMP, Campinas, SP 13083-970 (Brazil); Kubota, Lauro Tatsuo, E-mail: kubota@iqm.unicamp.br [Department of Analytical Chemistry, Institute of Chemistry – UNICAMP, Campinas, SP 13083-970 (Brazil); National Institute of Science and Technology of Bioanalytics, Institute of Chemistry – UNICAMP, Campinas, SP 13083-970 (Brazil)

    2015-05-22

    Highlights: • Integrated platform was developed to determine ethanol in fermentation broths. • The designed system integrates gas diffusion separation with voltammetric detection. • Detector relied on Ni(OH){sub 2}-modified electrode stabilized by Co{sup 2+} and Cd{sup 2+} insertion. • Separation was made by PTFE membrane separating sample from electrolyte (receptor). • Despite the sample complexity, accurate tests were achieved by direct interpolation. - Abstract: An integrated platform was developed for point-of-use determination of ethanol in sugar cane fermentation broths. Such analysis is important because ethanol reduces its fuel production efficiency by altering the alcoholic fermentation step when in excess. The custom-designed platform integrates gas diffusion separation with voltammetric detection in a single analysis module. The detector relied on a Ni(OH){sub 2}-modified electrode. It was stabilized by uniformly depositing cobalt and cadmium hydroxides as shown by XPS measurements. Such tests were in accordance with the hypothesis related to stabilization of the Ni(OH){sub 2} structure by insertion of Co{sup 2+} and Cd{sup 2+} ions in this structure. The separation step, in turn, was based on a hydrophobic PTFE membrane, which separates the sample from receptor solution (electrolyte) where the electrodes were placed. Parameters of limit of detection and analytical sensitivity were estimated to be 0.2% v/v and 2.90 μA % (v/v){sup −1}, respectively. Samples of fermentation broth were analyzed by both standard addition method and direct interpolation in saline medium based-analytical curve. In this case, the saline solution exhibited ionic strength similar to those of the samples intended to surpass the tonometry colligative effect of the samples over analyte concentration data by attributing the reduction in quantity of diffused ethanol vapor majorly to the electrolyte. The approach of analytical curve provided rapid, simple and accurate

  17. Developing a problem-based learning (PBL) curriculum for professionalism and scientific integrity training for biomedical graduate students.

    Science.gov (United States)

    Jones, Nancy L; Peiffer, Ann M; Lambros, Ann; Guthold, Martin; Johnson, A Daniel; Tytell, Michael; Ronca, April E; Eldridge, J Charles

    2010-10-01

    A multidisciplinary faculty committee designed a curriculum to shape biomedical graduate students into researchers with a high commitment to professionalism and social responsibility and to provide students with tools to navigate complex, rapidly evolving academic and societal environments with a strong ethical commitment. The curriculum used problem-based learning (PBL), because it is active and learner-centred and focuses on skill and process development. Two courses were developed: Scientific Professionalism: Scientific Integrity addressed discipline-specific and broad professional norms and obligations for the ethical practice of science and responsible conduct of research (RCR). Scientific Professionalism: Bioethics and Social Responsibility focused on current ethical and bioethical issues within the scientific profession, and implications of research for society. Each small-group session examined case scenarios that included: (1) learning objectives for professional norms and obligations; (2) key ethical issues and philosophies within each topic area; (3) one or more of the RCR instructional areas; and (4) at least one type of moral reflection. Cases emphasised professional standards, obligations and underlying philosophies for the ethical practice of science, competing interests of stakeholders and oversight of science (internal and external). To our knowledge, this is the first use of a longitudinal, multi-semester PBL course to teach scientific integrity and professionalism. Both faculty and students endorsed the active learning approach for these topics, in contrast to a compliance-based approach that emphasises learning rules and regulations.

  18. Monolithic photonic integration technology platform and devices at wavelengths beyond 2 μm for gas spectroscopy applications

    NARCIS (Netherlands)

    Latkowski, S.; van Veldhoven, P.J.; Hänsel, A.; D'Agostino, D.; Rabbani-Haghighi, H.; Docter, B.; Bhattacharya, N.; Thijs, P.J.A.; Ambrosius, H.P.M.M.; Smit, M.K.; Williams, K.A.; Bente, E.A.J.M.

    2017-01-01

    In this paper a generic monolithic photonic integration technology platform and tunable laser devices for gas sensing applications at 2 μm will be presented. The basic set of long wavelength optical functions which is fundamental for a generic photonic integration approach is realized using planar,

  19. Time-varying spatial data integration and visualization: 4 Dimensions Environmental Observations Platform (4-DEOS)

    Science.gov (United States)

    Paciello, Rossana; Coviello, Irina; Filizzola, Carolina; Genzano, Nicola; Lisi, Mariano; Mazzeo, Giuseppe; Pergola, Nicola; Sileo, Giancanio; Tramutoli, Valerio

    2014-05-01

    In environmental studies the integration of heterogeneous and time-varying data, is a very common requirement for investigating and possibly visualize correlations among physical parameters underlying the dynamics of complex phenomena. Datasets used in such kind of applications has often different spatial and temporal resolutions. In some case superimposition of asynchronous layers is required. Traditionally the platforms used to perform spatio-temporal visual data analyses allow to overlay spatial data, managing the time using 'snapshot' data model, each stack of layers being labeled with different time. But this kind of architecture does not incorporate the temporal indexing neither the third spatial dimension which is usually given as an independent additional layer. Conversely, the full representation of a generic environmental parameter P(x,y,z,t) in the 4D space-time domain could allow to handle asynchronous datasets as well as less traditional data-products (e.g. vertical sections, punctual time-series, etc.) . In this paper we present the 4 Dimensions Environmental Observation Platform (4-DEOS), a system based on a web services architecture Client-Broker-Server. This platform is a new open source solution for both a timely access and an easy integration and visualization of heterogeneous (maps, vertical profiles or sections, punctual time series, etc.) asynchronous, geospatial products. The innovative aspect of the 4-DEOS system is that users can analyze data/products individually moving through time, having also the possibility to stop the display of some data/products and focus on other parameters for better studying their temporal evolution. This platform gives the opportunity to choose between two distinct display modes for time interval or for single instant. Users can choose to visualize data/products in two ways: i) showing each parameter in a dedicated window or ii) visualize all parameters overlapped in a single window. A sliding time bar, allows

  20. Integrated Semantics Service Platform for the Internet of Things: A Case Study of a Smart Office

    Directory of Open Access Journals (Sweden)

    Minwoo Ryu

    2015-01-01

    Full Text Available The Internet of Things (IoT allows machines and devices in the world to connect with each other and generate a huge amount of data, which has a great potential to provide useful knowledge across service domains. Combining the context of IoT with semantic technologies, we can build integrated semantic systems to support semantic interoperability. In this paper, we propose an integrated semantic service platform (ISSP to support ontological models in various IoT-based service domains of a smart city. In particular, we address three main problems for providing integrated semantic services together with IoT systems: semantic discovery, dynamic semantic representation, and semantic data repository for IoT resources. To show the feasibility of the ISSP, we develop a prototype service for a smart office using the ISSP, which can provide a preset, personalized office environment by interpreting user text input via a smartphone. We also discuss a scenario to show how the ISSP-based method would help build a smart city, where services in each service domain can discover and exploit IoT resources that are wanted across domains. We expect that our method could eventually contribute to providing people in a smart city with more integrated, comprehensive services based on semantic interoperability.

  1. A multi-landing pad DNA integration platform for mammalian cell engineering

    Science.gov (United States)

    Gaidukov, Leonid; Wroblewska, Liliana; Teague, Brian; Nelson, Tom; Zhang, Xin; Liu, Yan; Jagtap, Kalpana; Mamo, Selamawit; Tseng, Wen Allen; Lowe, Alexis; Das, Jishnu; Bandara, Kalpanie; Baijuraj, Swetha; Summers, Nevin M; Zhang, Lin; Weiss, Ron

    2018-01-01

    Abstract Engineering mammalian cell lines that stably express many transgenes requires the precise insertion of large amounts of heterologous DNA into well-characterized genomic loci, but current methods are limited. To facilitate reliable large-scale engineering of CHO cells, we identified 21 novel genomic sites that supported stable long-term expression of transgenes, and then constructed cell lines containing one, two or three ‘landing pad’ recombination sites at selected loci. By using a highly efficient BxB1 recombinase along with different selection markers at each site, we directed recombinase-mediated insertion of heterologous DNA to selected sites, including targeting all three with a single transfection. We used this method to controllably integrate up to nine copies of a monoclonal antibody, representing about 100 kb of heterologous DNA in 21 transcriptional units. Because the integration was targeted to pre-validated loci, recombinant protein expression remained stable for weeks and additional copies of the antibody cassette in the integrated payload resulted in a linear increase in antibody expression. Overall, this multi-copy site-specific integration platform allows for controllable and reproducible insertion of large amounts of DNA into stable genomic sites, which has broad applications for mammalian synthetic biology, recombinant protein production and biomanufacturing. PMID:29617873

  2. Integrated Semantics Service Platform for the Internet of Things: A Case Study of a Smart Office

    Science.gov (United States)

    Ryu, Minwoo; Kim, Jaeho; Yun, Jaeseok

    2015-01-01

    The Internet of Things (IoT) allows machines and devices in the world to connect with each other and generate a huge amount of data, which has a great potential to provide useful knowledge across service domains. Combining the context of IoT with semantic technologies, we can build integrated semantic systems to support semantic interoperability. In this paper, we propose an integrated semantic service platform (ISSP) to support ontological models in various IoT-based service domains of a smart city. In particular, we address three main problems for providing integrated semantic services together with IoT systems: semantic discovery, dynamic semantic representation, and semantic data repository for IoT resources. To show the feasibility of the ISSP, we develop a prototype service for a smart office using the ISSP, which can provide a preset, personalized office environment by interpreting user text input via a smartphone. We also discuss a scenario to show how the ISSP-based method would help build a smart city, where services in each service domain can discover and exploit IoT resources that are wanted across domains. We expect that our method could eventually contribute to providing people in a smart city with more integrated, comprehensive services based on semantic interoperability. PMID:25608216

  3. Integrated semantics service platform for the Internet of Things: a case study of a smart office.

    Science.gov (United States)

    Ryu, Minwoo; Kim, Jaeho; Yun, Jaeseok

    2015-01-19

    The Internet of Things (IoT) allows machines and devices in the world to connect with each other and generate a huge amount of data, which has a great potential to provide useful knowledge across service domains. Combining the context of IoT with semantic technologies, we can build integrated semantic systems to support semantic interoperability. In this paper, we propose an integrated semantic service platform (ISSP) to support ontological models in various IoT-based service domains of a smart city. In particular, we address three main problems for providing integrated semantic services together with IoT systems: semantic discovery, dynamic semantic representation, and semantic data repository for IoT resources. To show the feasibility of the ISSP, we develop a prototype service for a smart office using the ISSP, which can provide a preset, personalized office environment by interpreting user text input via a smartphone. We also discuss a scenario to show how the ISSP-based method would help build a smart city, where services in each service domain can discover and exploit IoT resources that are wanted across domains. We expect that our method could eventually contribute to providing people in a smart city with more integrated, comprehensive services based on semantic interoperability.

  4. Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data

    Directory of Open Access Journals (Sweden)

    Bisakha Ray

    2017-08-01

    Full Text Available The amounts and types of available multimodal tumor data are rapidly increasing, and their integration is critical for fully understanding the underlying cancer biology and personalizing treatment. However, the development of methods for effectively integrating multimodal data in a principled manner is lagging behind our ability to generate the data. In this article, we introduce an extension to a multiview nonnegative matrix factorization algorithm (NNMF for dimensionality reduction and integration of heterogeneous data types and compare the predictive modeling performance of the method on unimodal and multimodal data. We also present a comparative evaluation of our novel multiview approach and current data integration methods. Our work provides an efficient method to extend an existing dimensionality reduction method. We report rigorous evaluation of the method on large-scale quantitative protein and phosphoprotein tumor data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC acquired using state-of-the-art liquid chromatography mass spectrometry. Exome sequencing and RNA-Seq data were also available from The Cancer Genome Atlas for the same tumors. For unimodal data, in case of breast cancer, transcript levels were most predictive of estrogen and progesterone receptor status and copy number variation of human epidermal growth factor receptor 2 status. For ovarian and colon cancers, phosphoprotein and protein levels were most predictive of tumor grade and stage and residual tumor, respectively. When multiview NNMF was applied to multimodal data to predict outcomes, the improvement in performance is not overall statistically significant beyond unimodal data, suggesting that proteomics data may contain more predictive information regarding tumor phenotypes than transcript levels, probably due to the fact that proteins are the functional gene products and therefore a more direct measurement of the functional state of the tumor. Here, we

  5. Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cancer Research Database

    Directory of Open Access Journals (Sweden)

    Vadim Y. Bichutskiy

    2006-01-01

    Full Text Available Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.

  6. An integrated in vitro imaging platform for characterizing filarial parasite behavior within a multicellular microenvironment.

    Directory of Open Access Journals (Sweden)

    Timothy Kassis

    2014-11-01

    Full Text Available Lymphatic Filariasis, a Neglected Tropical Disease, is caused by thread-like parasitic worms, including B. malayi, which migrate to the human lymphatic system following transmission. The parasites reside in collecting lymphatic vessels and lymph nodes for years, often resulting in lymphedema, elephantiasis or hydrocele. The mechanisms driving worm migration and retention within the lymphatics are currently unknown. We have developed an integrated in vitro imaging platform capable of quantifying B. malayi migration and behavior in a multicellular microenvironment relevant to the initial site of worm injection by incorporating the worm in a Polydimethylsiloxane (PDMS microchannel in the presence of human dermal lymphatic endothelial cells (LECs and human dermal fibroblasts (HDFs. The platform utilizes a motorized controllable microscope with CO2 and temperature regulation to allow for worm tracking experiments with high resolution over large length and time scales. Using post-acquisition algorithms, we quantified four parameters: 1 speed, 2 thrashing intensity, 3 percentage of time spent in a given cell region and 4 persistence ratio. We demonstrated the utility of our system by quantifying these parameters for L3 B. malayi in the presence of LECs and HDFs. Speed and thrashing increased in the presence of both cell types and were altered within minutes upon exposure to the anthelmintic drug, tetramisole. The worms displayed no targeted migration towards either cell type for the time course of this study (3 hours. When cells were not present in the chamber, worm thrashing correlated directly with worm speed. However, this correlation was lost in the presence of cells. The described platform provides the ability to further study B. malayi migration and behavior.

  7. InP-based photonic integrated circuit platform on SiC wafer.

    Science.gov (United States)

    Takenaka, Mitsuru; Takagi, Shinichi

    2017-11-27

    We have numerically investigated the properties of an InP-on-SiC wafer as a photonic integrated circuit (PIC) platform. By bonding a thin InP-based semiconductor on a SiC wafer, SiC can be used as waveguide cladding, a heat sink, and a support substrate simultaneously. Since the refractive index of SiC is sufficiently low, PICs can be fabricated using InP-based strip and rib waveguides with a minimum bend radius of approximately 7 μm. High-thermal-conductivity SiC underneath an InP-based waveguide core markedly improves heat dissipation, resulting in superior thermal properties of active devices such as laser diodes. The InP-on-SiC wafer has significantly smaller thermal stress than InP-on-SiO 2 /Si wafer, which prevents the thermal degradation of InP-based devices during high-temperature processes. Thus, InP on SiC provides an ideal platform for high-performance PICs.

  8. Integrated nanotechnology platform for tumor-targeted multimodal imaging and therapeutic cargo release.

    Science.gov (United States)

    Hosoya, Hitomi; Dobroff, Andrey S; Driessen, Wouter H P; Cristini, Vittorio; Brinker, Lina M; Staquicini, Fernanda I; Cardó-Vila, Marina; D'Angelo, Sara; Ferrara, Fortunato; Proneth, Bettina; Lin, Yu-Shen; Dunphy, Darren R; Dogra, Prashant; Melancon, Marites P; Stafford, R Jason; Miyazono, Kohei; Gelovani, Juri G; Kataoka, Kazunori; Brinker, C Jeffrey; Sidman, Richard L; Arap, Wadih; Pasqualini, Renata

    2016-02-16

    A major challenge of targeted molecular imaging and drug delivery in cancer is establishing a functional combination of ligand-directed cargo with a triggered release system. Here we develop a hydrogel-based nanotechnology platform that integrates tumor targeting, photon-to-heat conversion, and triggered drug delivery within a single nanostructure to enable multimodal imaging and controlled release of therapeutic cargo. In proof-of-concept experiments, we show a broad range of ligand peptide-based applications with phage particles, heat-sensitive liposomes, or mesoporous silica nanoparticles that self-assemble into a hydrogel for tumor-targeted drug delivery. Because nanoparticles pack densely within the nanocarrier, their surface plasmon resonance shifts to near-infrared, thereby enabling a laser-mediated photothermal mechanism of cargo release. We demonstrate both noninvasive imaging and targeted drug delivery in preclinical mouse models of breast and prostate cancer. Finally, we applied mathematical modeling to predict and confirm tumor targeting and drug delivery. These results are meaningful steps toward the design and initial translation of an enabling nanotechnology platform with potential for broad clinical applications.

  9. Optical Beam Deflection Based AFM with Integrated Hardware and Software Platform for an Undergraduate Engineering Laboratory

    Directory of Open Access Journals (Sweden)

    Siu Hong Loh

    2017-02-01

    Full Text Available Atomic force microscopy (AFM has been used extensively in nanoscience research since its invention. Recently, many teaching laboratories in colleges, undergraduate institutions, and even high schools incorporate AFM as an effective teaching tool for nanoscience education. This paper presents an optical beam deflection (OBD based atomic force microscope, designed specifically for the undergraduate engineering laboratory as a teaching instrument. An electronic module for signal conditioning was built with components that are commonly available in an undergraduate electronic laboratory. In addition to off-the-shelf mechanical parts and optics, the design of custom-built mechanical parts waskept as simple as possible. Hence, the overall cost for the setup is greatly reduced. The AFM controller was developed using National Instruments Educational Laboratory Virtual Instrumentation Suite (NI ELVIS, an integrated hardware and software platform which can be programmed in LabVIEW. A simple yet effective control algorithm for scanning and feedback control was developed. Despite the use of an educational platform and low-cost components from the undergraduate laboratory, the developed AFM is capable of performing imaging in constant-force mode with submicron resolution and at reasonable scanning speed (approximately 18 min per image. Therefore, the AFM is suitable to be used as an educational tool for nanoscience. Moreover, the construction of the system can be a valuable educational experience for electronic and mechanical engineering students.

  10. Delivering on Industry Equipment Reliability Goals By Leveraging an Integration Platform and Decision Support Environment

    International Nuclear Information System (INIS)

    Coveney, Maureen K.; Bailey, W. Henry; Parkinson, William

    2004-01-01

    Utilities have invested in many costly enterprise systems - computerized maintenance management systems, document management systems, enterprise grade portals, to name but a few - and often very specialized systems, like data historians, high end diagnostic systems, and other focused and point solutions. From recent industry reports, we now know that the average nuclear power utilizes on average 1900 systems to perform daily work, of which 250 might facilitate the equipment reliability decision-making process. The time has come to leverage the investment in these systems by providing a common platform for integration and decision-making that will further the collective industry aim of enhancing the reliability of our nuclear generation assets to maintain high plant availability and to deliver on plant life extension goals without requiring additional large scale investment in IT infrastructure. (authors)

  11. CoreFlow: A computational platform for integration, analysis and modeling of complex biological data

    DEFF Research Database (Denmark)

    Pasculescu, Adrian; Schoof, Erwin; Creixell, Pau

    2014-01-01

    between data generation, analysis and manuscript writing. CoreFlow is being released to the scientific community as an open-sourced software package complete with proteomics-specific examples, which include corrections for incomplete isotopic labeling of peptides (SILAC) or arginine-to-proline conversion......A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which...... provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Python, or Perl for processing, correcting and modeling this data. CoreFlow organizes these scripts...

  12. Development and Application of integrated monitoring platform for the Doppler Weather SA-BAND Radar

    Science.gov (United States)

    Zhang, Q.; Sun, J.; Zhao, C. C.; Chen, H. Y.

    2017-10-01

    The doppler weather SA-band radar is an important part of modern meteorological observation methods, monitoring the running status of radar and the data transmission is important.This paper introduced the composition of radar system and classification of radar data,analysed the characteristics and laws of the radar when is normal or abnormal. Using Macromedia Dreamweaver and PHP, developed the integrated monitoring platform for the doppler weather SA-band radar which could monitor the real-time radar system running status and important performance indicators such as radar power,status parameters and others on Web page,and when the status is abnormal it will trigger the audio alarm.

  13. The Real-Time Monitoring Service Platform for Land Supervision Based on Cloud Integration

    Science.gov (United States)

    Sun, J.; Mao, M.; Xiang, H.; Wang, G.; Liang, Y.

    2018-04-01

    Remote sensing monitoring has become the important means for land and resources departments to strengthen supervision. Aiming at the problems of low monitoring frequency and poor data currency in current remote sensing monitoring, this paper researched and developed the cloud-integrated real-time monitoring service platform for land supervision which enhanced the monitoring frequency by acquiring the domestic satellite image data overall and accelerated the remote sensing image data processing efficiency by exploiting the intelligent dynamic processing technology of multi-source images. Through the pilot application in Jinan Bureau of State Land Supervision, it has been proved that the real-time monitoring technical method for land supervision is feasible. In addition, the functions of real-time monitoring and early warning are carried out on illegal land use, permanent basic farmland protection and boundary breakthrough in urban development. The application has achieved remarkable results.

  14. Integrated numerical platforms for environmental dose assessments of large tritium inventory facilities

    International Nuclear Information System (INIS)

    Castro, P.; Ardao, J.; Velarde, M.; Sedano, L.; Xiberta, J.

    2013-01-01

    Related with a prospected new scenario of large inventory tritium facilities [KATRIN at TLK, CANDUs, ITER, EAST, other coming] the prescribed dosimetric limits by ICRP-60 for tritium committed-doses are under discussion requiring, in parallel, to surmount the highly conservative assessments by increasing the refinement of dosimetric-assessments in many aspects. Precise Lagrangian-computations of dosimetric cloud-evolution after standardized (normal/incidental/SBO) tritium cloud emissions are today numerically open to the perfect match of real-time meteorological-data, and patterns data at diverse scales for prompt/early and chronic tritium dose assessments. The trends towards integrated-numerical-platforms for environmental-dose assessments of large tritium inventory facilities under development.

  15. Applications integration in a hybrid cloud computing environment: modelling and platform

    Science.gov (United States)

    Li, Qing; Wang, Ze-yuan; Li, Wei-hua; Li, Jun; Wang, Cheng; Du, Rui-yang

    2013-08-01

    With the development of application services providers and cloud computing, more and more small- and medium-sized business enterprises use software services and even infrastructure services provided by professional information service companies to replace all or part of their information systems (ISs). These information service companies provide applications, such as data storage, computing processes, document sharing and even management information system services as public resources to support the business process management of their customers. However, no cloud computing service vendor can satisfy the full functional IS requirements of an enterprise. As a result, enterprises often have to simultaneously use systems distributed in different clouds and their intra enterprise ISs. Thus, this article presents a framework to integrate applications deployed in public clouds and intra ISs. A run-time platform is developed and a cross-computing environment process modelling technique is also developed to improve the feasibility of ISs under hybrid cloud computing environments.

  16. Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis

    Directory of Open Access Journals (Sweden)

    Qu Lijia

    2009-03-01

    Full Text Available Abstract Background Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, researchers usually have to use multiple software packages for their studies because software packages generally focus on specific tasks. It would be beneficial to have a highly integrated platform, in which these tasks can be completed within one package. Moreover, with open source architecture, newly proposed algorithms or methods for spectral processing and data analysis can be implemented much more easily and accessed freely by the public. Results In this paper, we report an open source software tool, Automics, which is specifically designed for NMR-based metabonomics studies. Automics is a highly integrated platform that provides functions covering almost all the stages of NMR-based metabonomics studies. Automics provides high throughput automatic modules with most recently proposed algorithms and powerful manual modules for 1D NMR spectral processing. In addition to spectral processing functions, powerful features for data organization, data pre-processing, and data analysis have been implemented. Nine statistical methods can be applied to analyses including: feature selection (Fisher's criterion, data reduction (PCA, LDA, ULDA, unsupervised clustering (K-Mean and supervised regression and classification (PLS/PLS-DA, KNN, SIMCA, SVM. Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results. The functional ability of Automics is demonstrated with an analysis of a type 2 diabetes metabolic profile. Conclusion Automics facilitates high throughput 1D NMR spectral processing and high dimensional data analysis for NMR-based metabonomics applications. Using Automics, users can complete spectral processing and data analysis within one software package in most cases

  17. Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis.

    Science.gov (United States)

    Wang, Tao; Shao, Kang; Chu, Qinying; Ren, Yanfei; Mu, Yiming; Qu, Lijia; He, Jie; Jin, Changwen; Xia, Bin

    2009-03-16

    Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, researchers usually have to use multiple software packages for their studies because software packages generally focus on specific tasks. It would be beneficial to have a highly integrated platform, in which these tasks can be completed within one package. Moreover, with open source architecture, newly proposed algorithms or methods for spectral processing and data analysis can be implemented much more easily and accessed freely by the public. In this paper, we report an open source software tool, Automics, which is specifically designed for NMR-based metabonomics studies. Automics is a highly integrated platform that provides functions covering almost all the stages of NMR-based metabonomics studies. Automics provides high throughput automatic modules with most recently proposed algorithms and powerful manual modules for 1D NMR spectral processing. In addition to spectral processing functions, powerful features for data organization, data pre-processing, and data analysis have been implemented. Nine statistical methods can be applied to analyses including: feature selection (Fisher's criterion), data reduction (PCA, LDA, ULDA), unsupervised clustering (K-Mean) and supervised regression and classification (PLS/PLS-DA, KNN, SIMCA, SVM). Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results. The functional ability of Automics is demonstrated with an analysis of a type 2 diabetes metabolic profile. Automics facilitates high throughput 1D NMR spectral processing and high dimensional data analysis for NMR-based metabonomics applications. Using Automics, users can complete spectral processing and data analysis within one software package in most cases. Moreover, with its open source architecture, interested

  18. Integrated System Design for a Large Wind Turbine Supported on a Moored Semi-Submersible Platform

    Directory of Open Access Journals (Sweden)

    Jinsong Liu

    2018-01-01

    Full Text Available Over the past few decades, wind energy has emerged as an alternative to conventional power generation that is economical, environmentally friendly and, importantly, renewable. Specifically, offshore wind energy is being considered by a number of countries to harness the stronger and more consistent wind resource compared to that over land. To meet the projected “20% energy from wind by 2030” scenario that was announced in 2006, 54 GW of added wind energy capacity need to come from offshore according to a National Renewable Energy Laboratory (NREL study. In this study, we discuss the development of a semi-submersible floating offshore platform with a catenary mooring system to support a very large 13.2-MW wind turbine with 100-m blades. An iterative design process is applied to baseline models with Froude scaling in order to achieve preliminary static stability. Structural dynamic analyses are performed to investigate the performance of the new model using a finite element method approach for the tower and a boundary integral equation (panel method for the platform. The steady-state response of the system under uniform wind and regular waves is first studied to evaluate the performance of the integrated system. Response amplitude operators (RAOs are computed in the time domain using white-noise wave excitation; this serves to highlight nonlinear, as well as dynamic characteristics of the system. Finally, selected design load cases (DLCs and the stochastic dynamic response of the system are studied to assess the global performance for sea states defined by wind fields with turbulence and long-crested irregular waves.

  19. Sparse canonical methods for biological data integration: application to a cross-platform study

    Directory of Open Access Journals (Sweden)

    Robert-Granié Christèle

    2009-01-01

    Full Text Available Abstract Background In the context of systems biology, few sparse approaches have been proposed so far to integrate several data sets. It is however an important and fundamental issue that will be widely encountered in post genomic studies, when simultaneously analyzing transcriptomics, proteomics and metabolomics data using different platforms, so as to understand the mutual interactions between the different data sets. In this high dimensional setting, variable selection is crucial to give interpretable results. We focus on a sparse Partial Least Squares approach (sPLS to handle two-block data sets, where the relationship between the two types of variables is known to be symmetric. Sparse PLS has been developed either for a regression or a canonical correlation framework and includes a built-in procedure to select variables while integrating data. To illustrate the canonical mode approach, we analyzed the NCI60 data sets, where two different platforms (cDNA and Affymetrix chips were used to study the transcriptome of sixty cancer cell lines. Results We compare the results obtained with two other sparse or related canonical correlation approaches: CCA with Elastic Net penalization (CCA-EN and Co-Inertia Analysis (CIA. The latter does not include a built-in procedure for variable selection and requires a two-step analysis. We stress the lack of statistical criteria to evaluate canonical correlation methods, which makes biological interpretation absolutely necessary to compare the different gene selections. We also propose comprehensive graphical representations of both samples and variables to facilitate the interpretation of the results. Conclusion sPLS and CCA-EN selected highly relevant genes and complementary findings from the two data sets, which enabled a detailed understanding of the molecular characteristics of several groups of cell lines. These two approaches were found to bring similar results, although they highlighted the same

  20. The Enterprise Data Trust at Mayo Clinic: a semantically integrated warehouse of biomedical data.

    Science.gov (United States)

    Chute, Christopher G; Beck, Scott A; Fisk, Thomas B; Mohr, David N

    2010-01-01

    Mayo Clinic's Enterprise Data Trust is a collection of data from patient care, education, research, and administrative transactional systems, organized to support information retrieval, business intelligence, and high-level decision making. Structurally it is a top-down, subject-oriented, integrated, time-variant, and non-volatile collection of data in support of Mayo Clinic's analytic and decision-making processes. It is an interconnected piece of Mayo Clinic's Enterprise Information Management initiative, which also includes Data Governance, Enterprise Data Modeling, the Enterprise Vocabulary System, and Metadata Management. These resources enable unprecedented organization of enterprise information about patient, genomic, and research data. While facile access for cohort definition or aggregate retrieval is supported, a high level of security, retrieval audit, and user authentication ensures privacy, confidentiality, and respect for the trust imparted by our patients for the respectful use of information about their conditions.

  1. Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB.

    Science.gov (United States)

    Chatziioannou, Aristotelis; Moulos, Panagiotis; Kolisis, Fragiskos N

    2009-10-27

    The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods. We describe here Gene ARMADA (Automated Robust MicroArray Data Analysis), a MATLAB implemented platform with a Graphical User Interface. This suite integrates all steps of microarray data analysis including automated data import, noise correction and filtering, normalization, statistical selection of differentially expressed genes, clustering, classification and annotation. In its current version, Gene ARMADA fully supports 2 coloured cDNA and Affymetrix oligonucleotide arrays, plus custom arrays for which experimental details are given in tabular form (Excel spreadsheet, comma separated values, tab-delimited text formats). It also supports the analysis of already processed results through its versatile import editor. Besides being fully automated, Gene ARMADA incorporates numerous functionalities of the Statistics and Bioinformatics Toolboxes of MATLAB. In addition, it provides numerous visualization and exploration tools plus customizable export data formats for seamless integration by other analysis tools or MATLAB, for further processing. Gene ARMADA requires MATLAB 7.4 (R2007a) or higher and is also distributed as a stand-alone application with MATLAB Component Runtime. Gene ARMADA provides a

  2. A Wireless Pressure Sensor Integrated with a Biodegradable Polymer Stent for Biomedical Applications.

    Science.gov (United States)

    Park, Jongsung; Kim, Ji-Kwan; Patil, Swati J; Park, Jun-Kyu; Park, SuA; Lee, Dong-Weon

    2016-06-02

    This paper describes the fabrication and characterization of a wireless pressure sensor for smart stent applications. The micromachined pressure sensor has an area of 3.13 × 3.16 mm² and is fabricated with a photosensitive SU-8 polymer. The wireless pressure sensor comprises a resonant circuit and can be used without the use of an internal power source. The capacitance variations caused by changes in the intravascular pressure shift the resonance frequency of the sensor. This change can be detected using an external antenna, thus enabling the measurement of the pressure changes inside a tube with a simple external circuit. The wireless pressure sensor is capable of measuring pressure from 0 mmHg to 230 mmHg, with a sensitivity of 0.043 MHz/mmHg. The biocompatibility of the pressure sensor was evaluated using cardiac cells isolated from neonatal rat ventricular myocytes. After inserting a metal stent integrated with the pressure sensor into a cardiovascular vessel of an animal, medical systems such as X-ray were employed to consistently monitor the condition of the blood vessel. No abnormality was found in the animal blood vessel for approximately one month. Furthermore, a biodegradable polymer (polycaprolactone) stent was fabricated with a 3D printer. The polymer stent exhibits better sensitivity degradation of the pressure sensor compared to the metal stent.

  3. Ongoing ethical issues concerning authorship in biomedical journals: an integrative review

    Science.gov (United States)

    Kornhaber, Rachel Anne; McLean, Loyola M; Baber, Rodney J

    2015-01-01

    Health professionals publishing within the field of health sciences continue to experience issues concerning appropriate authorship, which have clinical, ethical, and academic implications. This integrative review sought to explore the key issues concerning authorship from a bioethical standpoint, aiming to explore the key features of the authorship debate. Studies were identified through an electronic search, using the PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Scopus databases of peer-reviewed research, published between 2009 and 2014, limited to English language research, with search terms developed to reflect the current issues of authorship. From among the 279 papers identified, 20 research papers met the inclusion criteria. Findings were compiled and then arranged to identify themes and relationships. The review incorporated a wide range of authorship issues encompassing equal-credited authors, honorary (guest/gift) and ghost authorship, perception/experiences of authorship, and guidelines/policies. This review suggests that the International Committee of Medical Journal Editors’ (ICMJE) recommended guidelines for authorship are not reflected in current authorship practices within the domain of health sciences in both low-and high-impact-factor journals. This devaluing of the true importance of authorship has the potential to affect the validity of authorship, diminish the real contributions of the true authors, and negatively affect patient care. PMID:26257520

  4. A Wireless Pressure Sensor Integrated with a Biodegradable Polymer Stent for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Jongsung Park

    2016-06-01

    Full Text Available This paper describes the fabrication and characterization of a wireless pressure sensor for smart stent applications. The micromachined pressure sensor has an area of 3.13 × 3.16 mm2 and is fabricated with a photosensitive SU-8 polymer. The wireless pressure sensor comprises a resonant circuit and can be used without the use of an internal power source. The capacitance variations caused by changes in the intravascular pressure shift the resonance frequency of the sensor. This change can be detected using an external antenna, thus enabling the measurement of the pressure changes inside a tube with a simple external circuit. The wireless pressure sensor is capable of measuring pressure from 0 mmHg to 230 mmHg, with a sensitivity of 0.043 MHz/mmHg. The biocompatibility of the pressure sensor was evaluated using cardiac cells isolated from neonatal rat ventricular myocytes. After inserting a metal stent integrated with the pressure sensor into a cardiovascular vessel of an animal, medical systems such as X-ray were employed to consistently monitor the condition of the blood vessel. No abnormality was found in the animal blood vessel for approximately one month. Furthermore, a biodegradable polymer (polycaprolactone stent was fabricated with a 3D printer. The polymer stent exhibits better sensitivity degradation of the pressure sensor compared to the metal stent.

  5. Ongoing ethical issues concerning authorship in biomedical journals: an integrative review.

    Science.gov (United States)

    Kornhaber, Rachel Anne; McLean, Loyola M; Baber, Rodney J

    2015-01-01

    Health professionals publishing within the field of health sciences continue to experience issues concerning appropriate authorship, which have clinical, ethical, and academic implications. This integrative review sought to explore the key issues concerning authorship from a bioethical standpoint, aiming to explore the key features of the authorship debate. Studies were identified through an electronic search, using the PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Scopus databases of peer-reviewed research, published between 2009 and 2014, limited to English language research, with search terms developed to reflect the current issues of authorship. From among the 279 papers identified, 20 research papers met the inclusion criteria. Findings were compiled and then arranged to identify themes and relationships. The review incorporated a wide range of authorship issues encompassing equal-credited authors, honorary (guest/gift) and ghost authorship, perception/experiences of authorship, and guidelines/policies. This review suggests that the International Committee of Medical Journal Editors' (ICMJE) recommended guidelines for authorship are not reflected in current authorship practices within the domain of health sciences in both low-and high-impact-factor journals. This devaluing of the true importance of authorship has the potential to affect the validity of authorship, diminish the real contributions of the true authors, and negatively affect patient care.

  6. OTEC platform configuration and integration. Appendixes to Volume II. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Price, David

    1978-07-07

    Detailed information and conceptual design drawings for the SPAR and SPHERE platforms for an OTEC commercial plant are presented. A work breakdown structure and a detailed estimate of the SPAR platform weight are included. (WHK)

  7. Health-e-Child: a grid platform for european paediatrics

    International Nuclear Information System (INIS)

    Skaburskas, K; Estrella, F; Shade, J; Manset, D; Revillard, J; Rios, A; Anjum, A; Branson, A; Bloodsworth, P; Hauer, T; McClatchey, R; Rogulin, D

    2008-01-01

    The Health-e-Child (HeC) project [1], [2] is an EC Framework Programme 6 Integrated Project that aims to develop a grid-based integrated healthcare platform for paediatrics. Using this platform biomedical informaticians will integrate heterogeneous data and perform epidemiological studies across Europe. The resulting Grid enabled biomedical information platform will be supported by robust search, optimization and matching techniques for information collected in hospitals across Europe. In particular, paediatricians will be provided with decision support, knowledge discovery and disease modelling applications that will access data in hospitals in the UK, Italy and France, integrated via the Grid. For economy of scale, reusability, extensibility, and maintainability, HeC is being developed on top of an EGEE/gLite [3] based infrastructure that provides all the common data and computation management services required by the applications. This paper discusses some of the major challenges in bio-medical data integration and indicates how these will be resolved in the HeC system. HeC is presented as an example of how computer science (and, in particular Grid infrastructures) originating from high energy physics can be adapted for use by biomedical informaticians to deliver tangible real-world benefits

  8. Silicon based cryogenic platform for the integration of qubit and classical control chips

    Science.gov (United States)

    Leonhardt, T.; Hollmann, A.; Jirovec, D.; Neumann, R.; Klemt, B.; Kindel, S.; Kucharski, M.; Fischer, G.; Bougeard, D.; Bluhm, H.; Schreiber, L. R.

    Electrostatically confined electron-spin-qubits proved viable for quantum information processing. Yet their up-scaling not only demands improvement of physical qubits, but also the development and cryogenic integration of classical control hardware. Therefore, we created a platform to integrate quantum chips and classical electronics. These multilayer interposer chips incorporate passive circuit elements, high bandwidth coplanar wave guides and interconnects for electron spin resonant qubit control as well as low impedance DC microstrips reducing EM-crosstalk from AC to DC lines. We used the interposer for measurements of a Si/SiGe quantum dot at 30 mK. We also characterized a commercial voltage controlled oszillator (VCO) based on hetero-bipolar transistors. Tunable about 30 GHz it is ideal for electron spin resonant qubit control. Cooled from 300 to 4 K it exhibits a slightly increased output power and frequency, while the phase noise level is constant. The device remains functional up to magnetic fields of 6 T.

  9. Resilient and Robust High Performance Computing Platforms for Scientific Computing Integrity

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Yier [Univ. of Central Florida, Orlando, FL (United States)

    2017-07-14

    As technology advances, computer systems are subject to increasingly sophisticated cyber-attacks that compromise both their security and integrity. High performance computing platforms used in commercial and scientific applications involving sensitive, or even classified data, are frequently targeted by powerful adversaries. This situation is made worse by a lack of fundamental security solutions that both perform efficiently and are effective at preventing threats. Current security solutions fail to address the threat landscape and ensure the integrity of sensitive data. As challenges rise, both private and public sectors will require robust technologies to protect its computing infrastructure. The research outcomes from this project try to address all these challenges. For example, we present LAZARUS, a novel technique to harden kernel Address Space Layout Randomization (KASLR) against paging-based side-channel attacks. In particular, our scheme allows for fine-grained protection of the virtual memory mappings that implement the randomization. We demonstrate the effectiveness of our approach by hardening a recent Linux kernel with LAZARUS, mitigating all of the previously presented side-channel attacks on KASLR. Our extensive evaluation shows that LAZARUS incurs only 0.943% overhead for standard benchmarks, and is therefore highly practical. We also introduced HA2lloc, a hardware-assisted allocator that is capable of leveraging an extended memory management unit to detect memory errors in the heap. We also perform testing using HA2lloc in a simulation environment and find that the approach is capable of preventing common memory vulnerabilities.

  10. On-Chip Magnetic Platform for Single-Particle Manipulation with Integrated Electrical Feedback.

    Science.gov (United States)

    Monticelli, Marco; Torti, Andrea; Cantoni, Matteo; Petti, Daniela; Albisetti, Edoardo; Manzin, Alessandra; Guerriero, Erica; Sordan, Roman; Gervasoni, Giacomo; Carminati, Marco; Ferrari, Giorgio; Sampietro, Marco; Bertacco, Riccardo

    2016-02-17

    Methods for the manipulation of single magnetic particles have become very interesting, in particular for in vitro biological studies. Most of these studies require an external microscope to provide the operator with feedback for controlling the particle motion, thus preventing the use of magnetic particles in high-throughput experiments. In this paper, a simple and compact system with integrated electrical feedback is presented, implementing in the very same device both the manipulation and detection of the transit of single particles. The proposed platform is based on zig-zag shaped magnetic nanostructures, where transverse magnetic domain walls are pinned at the corners and attract magnetic particles in suspension. By applying suitable external magnetic fields, the domain walls move to the nearest corner, thus causing the step by step displacement of the particles along the nanostructure. The very same structure is also employed for detecting the bead transit. Indeed, the presence of the magnetic particle in suspension over the domain wall affects the depinning field required for its displacement. This characteristic field can be monitored through anisotropic magnetoresistance measurements, thus implementing an integrated electrical feedback of the bead transit. In particular, the individual manipulation and detection of single 1-μm sized beads is demonstrated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Construction of a test platform for Test Blanket Module (TBM) systems integration and maintenance in ITER Port Cell #16

    Energy Technology Data Exchange (ETDEWEB)

    Vála, Ladislav, E-mail: ladislav.vala@cvrez.cz [Centrum výzkumu Řež, Hlavní 130, 250 68 Husinec-Řež (Czech Republic); Reungoat, Mathieu, E-mail: mathieu.reungoat@cvrez.cz [Centrum výzkumu Řež, Hlavní 130, 250 68 Husinec-Řež (Czech Republic); Vician, Martin [Centrum výzkumu Řež, Hlavní 130, 250 68 Husinec-Řež (Czech Republic); Poitevin, Yves; Ricapito, Italo; Zmitko, Milan; Panayotov, Dobromir [Fusion for Energy, Josep Pla 2, Torres Diagonal Litoral B3, 08019 Barcelona (Spain)

    2015-10-15

    Highlights: • A non-nuclear, full size facility – TBM platform – is under construction in CVR. • It is designed for tests, optimization and validation of TBS maintenance operations. • It will allow testing and validation of specific maintenance tools and RH equipment. • It reproduces ITER Port Cell #16, as well as the TBS interfaces and main equipment. • The TBM platform will be available for full operation in the first half of 2016. - Abstract: This paper describes a project of a non-nuclear, 1:1 scale testing platform dedicated to tests, optimization and validation of integration and maintenance operations for the European TBM systems in the ITER Port Cell #16. This TBM platform is currently under construction in Centrum výzkumu Řež, Czech Republic. The facility is realized within the scope of the SUSEN project and its full operation is foreseen in the first half of 2016.

  12. The development and implementation of MOSAIQ Integration Platform (MIP) based on the radiotherapy workflow

    Science.gov (United States)

    Yang, Xin; He, Zhen-yu; Jiang, Xiao-bo; Lin, Mao-sheng; Zhong, Ning-shan; Hu, Jiang; Qi, Zhen-yu; Bao, Yong; Li, Qiao-qiao; Li, Bao-yue; Hu, Lian-ying; Lin, Cheng-guang; Gao, Yuan-hong; Liu, Hui; Huang, Xiao-yan; Deng, Xiao-wu; Xia, Yun-fei; Liu, Meng-zhong; Sun, Ying

    2017-03-01

    To meet the special demands in China and the particular needs for the radiotherapy department, a MOSAIQ Integration Platform CHN (MIP) based on the workflow of radiation therapy (RT) has been developed, as a supplement system to the Elekta MOSAIQ. The MIP adopts C/S (client-server) structure mode, and its database is based on the Treatment Planning System (TPS) and MOSAIQ SQL Server 2008, running on the hospital local network. Five network servers, as a core hardware, supply data storage and network service based on the cloud services. The core software, using C# programming language, is developed based on Microsoft Visual Studio Platform. The MIP server could offer network service, including entry, query, statistics and print information for about 200 workstations at the same time. The MIP was implemented in the past one and a half years, and some practical patient-oriented functions were developed. And now the MIP is almost covering the whole workflow of radiation therapy. There are 15 function modules, such as: Notice, Appointment, Billing, Document Management (application/execution), System Management, and so on. By June of 2016, recorded data in the MIP are as following: 13546 patients, 13533 plan application, 15475 RT records, 14656 RT summaries, 567048 billing records and 506612 workload records, etc. The MIP based on the RT workflow has been successfully developed and clinically implemented with real-time performance, data security, stable operation. And it is demonstrated to be user-friendly and is proven to significantly improve the efficiency of the department. It is a key to facilitate the information sharing and department management. More functions can be added or modified for further enhancement its potentials in research and clinical practice.

  13. A platform to integrate climate information and rural telemedicine in Malawi

    Science.gov (United States)

    Lowe, R.; Chadza, T.; Chirombo, J.; Fonda, C.; Muyepa, A.; Nkoloma, M.; Pietrosemoli, E.; Radicella, S. M.; Tompkins, A. M.; Zennaro, M.

    2012-04-01

    It is commonly accepted that climate plays a role in the transmission of many infectious diseases, particularly those transmitted by mosquitoes such as malaria, which is one of the most important causes of mortality and morbidity in developing countries. Due to time lags involved in the climate-disease transmission system, lagged observed climate variables could provide some predictive lead for forecasting disease epidemics. This lead time could be extended by using forecasts of the climate in disease prediction models. This project aims to implement a platform for the dissemination of climate-driven disease risk forecasts, using a telemedicine approach. A pilot project has been established in Malawi, where a 162 km wireless link has been installed, spanning from Blantyre City to remote health facilities in the district of Mangochi in the Southern region, bordering Lake Malawi. This long Wi-Fi technology allows rural health facilities to upload real-time disease cases as they occur to an online health information system (DHIS2); a national medical database repository administered by the Ministry of Health. This technology provides a real-time data logging system for disease incidence monitoring and facilitates the flow of information between local and national levels. This platform allows statistical and dynamical disease prediction models to be rapidly updated with real-time climate and epidemiological information. This permits health authorities to target timely interventions ahead of an imminent increase in malaria incidence. By integrating meteorological and health information systems in a statistical-dynamical prediction model, we show that a long-distance Wi-Fi link is a practical and inexpensive means to enable the rapid analysis of real-time information in order to target disease prevention and control measures and mobilise resources at the local level.

  14. [Biomedical informatics].

    Science.gov (United States)

    Capurro, Daniel; Soto, Mauricio; Vivent, Macarena; Lopetegui, Marcelo; Herskovic, Jorge R

    2011-12-01

    Biomedical Informatics is a new discipline that arose from the need to incorporate information technologies to the generation, storage, distribution and analysis of information in the domain of biomedical sciences. This discipline comprises basic biomedical informatics, and public health informatics. The development of the discipline in Chile has been modest and most projects have originated from the interest of individual people or institutions, without a systematic and coordinated national development. Considering the unique features of health care system of our country, research in the area of biomedical informatics is becoming an imperative.

  15. Finding Common Ground: Use of a Geographically-Framed Landscape Template as an Integrating Platform for an International Education Initiative

    Science.gov (United States)

    Brierley, Gary; Li, Xilai; Qiao, Youming; Huang, He Qing; Wang, Zhaoyin

    2018-01-01

    This situated case study outlines how a place-based landscape template provided an integrative platform for the environmental arm of a cross-disciplinary international education initiative, the Three Brothers Project, wherein geographers at the University of Auckland worked alongside engineers at Tsinghua University in Beijing to support…

  16. THE TSUNAMI SERVICE BUS, AN INTEGRATION PLATFORM FOR HETEROGENEOUS SENSOR SYSTEMS

    Science.gov (United States)

    Fleischer, J.; Häner, R.; Herrnkind, S.; Kriegel, U.; Schwarting, H.; Wächter, J.

    2009-12-01

    The Tsunami Service Bus (TSB) is the sensor integration platform of the German Indonesian Tsunami Early Warning System (GITEWS) [1]. The primary goal of GITEWS is to deliver reliable tsunami warnings as fast as possible. This is achieved on basis of various sensor systems like seismometers, ocean instrumentation, and GPS stations, all providing fundamental data to support prediction of tsunami wave propagation by the GITEWS warning center. However, all these sensors come with their own proprietary data formats and specific behavior. Also new sensor types might be added, old sensors will be replaced. To keep GITEWS flexible the TSB was developed in order to access and control sensors in a uniform way. To meet these requirements the TSB follows the architectural blueprint of a Service Oriented Architecture (SOA). The integration platform implements dedicated services communicating via a service infrastructure. The functionality required for early warnings is provided by loosely coupled services replacing the "hard-wired" coupling at data level. Changes in the sensor specification are confined to the data level without affecting the warning center. Great emphasis was laid on following the Sensor Web Enablement (SWE) standard [2], specified by the Open Geospatial Consortium (OGC) [3]. As a result the full functionality needed in GITEWS could be achieved by implementing the four SWE services: The Sensor Observation Service for retrieving sensor measurements, the Sensor Alert Service in order to deliver sensor alerts, the Sensor Planning Service for tasking sensors, and the Web Notification Service for conduction messages to various media channels. Beyond these services the TSB also follows SWE Observation & Measurements specifications (O&M) for data encoding and Sensor Model Language (SensorML) for meta information. Moreover, accessing sensors via the TSB is not restricted to GITEWS. Multiple instances of the TSB can be composed to realize federate warning system

  17. LabKey Server: An open source platform for scientific data integration, analysis and collaboration

    Science.gov (United States)

    2011-01-01

    Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. Results To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350

  18. LabKey Server: An open source platform for scientific data integration, analysis and collaboration

    Directory of Open Access Journals (Sweden)

    Lum Karl

    2011-03-01

    Full Text Available Abstract Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. Results To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i Submitting specimens requests across collaborating organizations (ii Graphically defining new experimental data types, metadata and wizards for data collection (iii Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v Interacting dynamically with external data sources (vi Tracking study participants and cohorts over time (vii Developing custom interfaces using client libraries (viii Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36

  19. LabKey Server: an open source platform for scientific data integration, analysis and collaboration.

    Science.gov (United States)

    Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory; Lum, Karl; Krouse, Kevin; Stearns, David; Connolly, Brian; Skillman, Tom; Igra, Mark

    2011-03-09

    Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks

  20. Integrated culture platform based on a human platelet lysate supplement for the isolation and scalable manufacturing of umbilical cord matrix-derived mesenchymal stem/stromal cells.

    Science.gov (United States)

    de Soure, António M; Fernandes-Platzgummer, Ana; Moreira, Francisco; Lilaia, Carla; Liu, Shi-Hwei; Ku, Chen-Peng; Huang, Yi-Feng; Milligan, William; Cabral, Joaquim M S; da Silva, Cláudia L

    2017-05-01

    Umbilical cord matrix (UCM)-derived mesenchymal stem/stromal cells (MSCs) are promising therapeutic candidates for regenerative medicine settings. UCM MSCs have advantages over adult cells as these can be obtained through a non-invasive harvesting procedure and display a higher proliferative capacity. However, the high cell doses required in the clinical setting make large-scale manufacturing of UCM MSCs mandatory. A commercially available human platelet lysate-based culture supplement (UltraGRO TM , AventaCell BioMedical) (5%(v/v)) was tested to effectively isolate UCM MSCs and to expand these cells under (1) static conditions, using planar culture systems and (2) stirred culture using plastic microcarriers in a spinner flask. The MSC-like cells were isolated from UCM explant cultures after 11 ± 2 days. After five passages in static culture, UCM MSCs retained their immunophenotype and multilineage differentiation potential. The UCM MSCs cultured under static conditions using UltraGRO TM -supplemented medium expanded more rapidly compared with UCM MSCs expanded using a previously established protocol. Importantly, UCM MSCs were successfully expanded under dynamic conditions on plastic microcarriers using UltraGRO TM -supplemented medium in spinner flasks. Upon an initial 54% cell adhesion to the beads, UCM MSCs expanded by >13-fold after 5-6 days, maintaining their immunophenotype and multilineage differentiation ability. The present paper reports the establishment of an easily scalable integrated culture platform based on a human platelet lysate supplement for the effective isolation and expansion of UCM MSCs in a xenogeneic-free microcarrier-based system. This platform represents an important advance in obtaining safer and clinically meaningful MSC numbers for clinical translation. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  1. The VIPER project (Visualization Integration Platform for Exploration Research): a biologically inspired autonomous reconfigurable robotic platform for diverse unstructured environments

    Science.gov (United States)

    Schubert, Oliver J.; Tolle, Charles R.

    2004-09-01

    Over the last decade the world has seen numerous autonomous vehicle programs. Wheels and track designs are the basis for many of these vehicles. This is primarily due to four main reasons: a vast preexisting knowledge base for these designs, energy efficiency of power sources, scalability of actuators, and the lack of control systems technologies for handling alternate highly complex distributed systems. Though large efforts seek to improve the mobility of these vehicles, many limitations still exist for these systems within unstructured environments, e.g. limited mobility within industrial and nuclear accident sites where existing plant configurations have been extensively changed. These unstructured operational environments include missions for exploration, reconnaissance, and emergency recovery of objects within reconfigured or collapsed structures, e.g. bombed buildings. More importantly, these environments present a clear and present danger for direct human interactions during the initial phases of recovery operations. Clearly, the current classes of autonomous vehicles are incapable of performing in these environments. Thus the next generation of designs must include highly reconfigurable and flexible autonomous robotic platforms. This new breed of autonomous vehicles will be both highly flexible and environmentally adaptable. Presented in this paper is one of the most successful designs from nature, the snake-eel-worm (SEW). This design implements shape memory alloy (SMA) actuators which allow for scaling of the robotic SEW designs from sub-micron scale to heavy industrial implementations without major conceptual redesigns as required in traditional hydraulic, pneumatic, or motor driven systems. Autonomous vehicles based on the SEW design posses the ability to easily move between air based environments and fluid based environments with limited or no reconfiguration. Under a SEW designed vehicle, one not only achieves vastly improved maneuverability within a

  2. Assessment of cisplatin-induced kidney injury using an integrated rodent platform

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yafei [Global Safety Assessment, AstraZeneca R and D Waltham, MA 02451 (United States); Brott, David [Patient Safety, AstraZeneca R and D Wilmington, DE 19850 (United States); Luo, Wenli [Discovery Statistics, AstraZeneca R and D Waltham, MA 02451 (United States); Gangl, Eric [DMPK, AstraZeneca R and D Waltham, MA 02451 (United States); Kamendi, Harriet; Barthlow, Herbert; Lengel, David; Fikes, James; Kinter, Lewis [Global Safety Assessment, AstraZeneca R and D Waltham, MA 02451 (United States); Valentin, Jean-Pierre [Global Safety Assessment, AstraZeneca R and D Alderley Park, Macclesfield, SK10 4TG (United Kingdom); Bialecki, Russell, E-mail: russell.bialecki@astrazeneca.com [Global Safety Assessment, AstraZeneca R and D Waltham, MA 02451 (United States)

    2013-05-01

    Current diagnosis of drug-induced kidney injury (DIKI) primarily relies on detection of elevated plasma creatinine (Cr) or blood urea nitrogen (BUN) levels; however, both are indices of overall kidney function and changes are delayed with respect to onset of nephron injury. Our aim was to investigate whether early changes in new urinary DIKI biomarkers predict plasma Cr, BUN, renal hemodynamic and kidney morphological changes associated with kidney injury following a single dose of cisplatin (CDDP) using an integrated platform in rodent. Conscious surgically prepared male Han Wistar rats were given a single intraperitoneal dose of CDDP (15 mg/kg). Glomerular filtration rate (GFR), effective renal plasma flow (ERPF), urinalysis, DIKI biomarkers, CDDP pharmacokinetics, blood pressures, heart rate, body temperature and electroencephalogram (EEG) were measured in the same vehicle- or CDDP-treated animals over 72 h. Plasma chemistry (including Cr and BUN) and renal tissues were examined at study termination. Cisplatin caused progressive reductions of GFR, ERPF, heart rate and body temperature from day 1 (0–24 h). DIKI biomarkers including alpha-glutathione S-transferase (α-GST) significantly increased as early as 6 h post-dose, which preceded significant declines of GFR and ERPF (24 h), increased plasma Cr and BUN (72 h), and associated with renal acute tubular necrosis at 72 h post-dose. The present study adds to the current understanding of CDDP action by demonstrating that early increases in urinary excretion of α-GST predict DIKI risk following acute exposure to CDDP in rats, before changes in traditional DIKI markers are evident. - Highlights: ► CDDP causes direct damage to kidneys without affecting EEG or CVS function. ► α-GST and albumin detect DIKI earlier when compared with traditional indices. ► Integrated “cardiovascular-EEG-renal” model to better understand DIKI mechanisms ► Promotes 3R's principles in drug discovery and development.

  3. IMPACT_S: integrated multiprogram platform to analyze and combine tests of selection.

    Directory of Open Access Journals (Sweden)

    Emanuel Maldonado

    Full Text Available Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins. Performing such analyses manually is often a time-consuming process, due to the large number of statistical files generated from multiple approaches, especially when assessing numerous taxa and/or large datasets. We present IMPACT_S, an easy-to-use Graphical User Interface (GUI software, which rapidly and effectively integrates, filters and combines results from three widely used programs for assessing the influence of selection: Codeml (PAML package, Datamonkey and TreeSAAP. It enables the identification and tabulation of sites detected by these programs as evolving under the influence of positive, neutral and/or negative selection in protein-coding genes. IMPACT_S further facilitates the automatic mapping of these sites onto the three-dimensional structures of proteins. Other useful tools incorporated in IMPACT_S include Jmol, Archaeopteryx, Gnuplot, PhyML, a built-in Swiss-Model interface and a PDB downloader. The relevance and functionality of IMPACT_S is shown through a case study on the toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs. IMPACT_S is a platform-independent software released under GPLv3 license, freely available online from http://impact-s.sourceforge.net.

  4. IMPACT_S: integrated multiprogram platform to analyze and combine tests of selection.

    Science.gov (United States)

    Maldonado, Emanuel; Sunagar, Kartik; Almeida, Daniela; Vasconcelos, Vitor; Antunes, Agostinho

    2014-01-01

    Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins. Performing such analyses manually is often a time-consuming process, due to the large number of statistical files generated from multiple approaches, especially when assessing numerous taxa and/or large datasets. We present IMPACT_S, an easy-to-use Graphical User Interface (GUI) software, which rapidly and effectively integrates, filters and combines results from three widely used programs for assessing the influence of selection: Codeml (PAML package), Datamonkey and TreeSAAP. It enables the identification and tabulation of sites detected by these programs as evolving under the influence of positive, neutral and/or negative selection in protein-coding genes. IMPACT_S further facilitates the automatic mapping of these sites onto the three-dimensional structures of proteins. Other useful tools incorporated in IMPACT_S include Jmol, Archaeopteryx, Gnuplot, PhyML, a built-in Swiss-Model interface and a PDB downloader. The relevance and functionality of IMPACT_S is shown through a case study on the toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs). IMPACT_S is a platform-independent software released under GPLv3 license, freely available online from http://impact-s.sourceforge.net.

  5. Assessment of cisplatin-induced kidney injury using an integrated rodent platform

    International Nuclear Information System (INIS)

    Chen, Yafei; Brott, David; Luo, Wenli; Gangl, Eric; Kamendi, Harriet; Barthlow, Herbert; Lengel, David; Fikes, James; Kinter, Lewis; Valentin, Jean-Pierre; Bialecki, Russell

    2013-01-01

    Current diagnosis of drug-induced kidney injury (DIKI) primarily relies on detection of elevated plasma creatinine (Cr) or blood urea nitrogen (BUN) levels; however, both are indices of overall kidney function and changes are delayed with respect to onset of nephron injury. Our aim was to investigate whether early changes in new urinary DIKI biomarkers predict plasma Cr, BUN, renal hemodynamic and kidney morphological changes associated with kidney injury following a single dose of cisplatin (CDDP) using an integrated platform in rodent. Conscious surgically prepared male Han Wistar rats were given a single intraperitoneal dose of CDDP (15 mg/kg). Glomerular filtration rate (GFR), effective renal plasma flow (ERPF), urinalysis, DIKI biomarkers, CDDP pharmacokinetics, blood pressures, heart rate, body temperature and electroencephalogram (EEG) were measured in the same vehicle- or CDDP-treated animals over 72 h. Plasma chemistry (including Cr and BUN) and renal tissues were examined at study termination. Cisplatin caused progressive reductions of GFR, ERPF, heart rate and body temperature from day 1 (0–24 h). DIKI biomarkers including alpha-glutathione S-transferase (α-GST) significantly increased as early as 6 h post-dose, which preceded significant declines of GFR and ERPF (24 h), increased plasma Cr and BUN (72 h), and associated with renal acute tubular necrosis at 72 h post-dose. The present study adds to the current understanding of CDDP action by demonstrating that early increases in urinary excretion of α-GST predict DIKI risk following acute exposure to CDDP in rats, before changes in traditional DIKI markers are evident. - Highlights: ► CDDP causes direct damage to kidneys without affecting EEG or CVS function. ► α-GST and albumin detect DIKI earlier when compared with traditional indices. ► Integrated “cardiovascular-EEG-renal” model to better understand DIKI mechanisms ► Promotes 3R's principles in drug discovery and development

  6. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

    Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  7. MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets.

    Science.gov (United States)

    Lemieux, Sebastien; Sargeant, Tobias; Laperrière, David; Ismail, Houssam; Boucher, Geneviève; Rozendaal, Marieke; Lavallée, Vincent-Philippe; Ashton-Beaucage, Dariel; Wilhelm, Brian; Hébert, Josée; Hilton, Douglas J; Mader, Sylvie; Sauvageau, Guy

    2017-07-27

    Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Spanning Trees Inferred Clustering (MiSTIC), that integrates the direct visualization and comparison of the gene correlation structure between datasets, the analysis of the molecular causes underlying co-variations in gene expression in cancer samples, and the clinical annotation of tumour sets defined by the combined expression of selected biomarkers. We have used MiSTIC to highlight the roles of specific transcription factors in breast cancer subtype specification, to compare the aspects of tumour heterogeneity targeted by different prognostic signatures, and to highlight biomarker interactions in AML. A version of MiSTIC preloaded with datasets described herein can be accessed through a public web server (http://mistic.iric.ca); in addition, the MiSTIC software package can be obtained (github.com/iric-soft/MiSTIC) for local use with personalized datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  9. An integrated telemedicine platform for the assessment of affective physiological states

    Directory of Open Access Journals (Sweden)

    Ganiatsas George

    2006-08-01

    Full Text Available Abstract AUBADE is an integrated platform built for the affective assessment of individuals. The system performs evaluation of the emotional state by classifying vectors of features extracted from: facial Electromyogram, Respiration, Electrodermal Activity and Electrocardiogram. The AUBADE system consists of: (a a multisensorial wearable, (b a data acquisition and wireless communication module, (c a feature extraction module, (d a 3D facial animation module which is used for the projection of the obtained data through a generic 3D face model; whereas the end-user will be able to view the facial expression of the subject in real time, (e an intelligent emotion recognition module, and (f the AUBADE databases where the acquired signals along with the subject's animation videos are saved. The system is designed to be applied to human subjects operating under extreme stress conditions, in particular car racing drivers, and also to patients suffering from neurological and psychological disorders. AUBADE's classification accuracy into five predefined emotional classes (high stress, low stress, disappointment, euphoria and neutral face is 86.0%. The pilot system applications and components are being tested and evaluated on Maserati's car. racing drivers.

  10. Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform.

    Science.gov (United States)

    Dubovenko, Alexey; Nikolsky, Yuri; Rakhmatulin, Eugene; Nikolskaya, Tatiana

    2017-01-01

    Analysis of NGS and other sequencing data, gene variants, gene expression, proteomics, and other high-throughput (OMICs) data is challenging because of its biological complexity and high level of technical and biological noise. One way to deal with both problems is to perform analysis with a high fidelity annotated knowledgebase of protein interactions, pathways, and functional ontologies. This knowledgebase has to be structured in a computer-readable format and must include software tools for managing experimental data, analysis, and reporting. Here, we present MetaCore™ and Key Pathway Advisor (KPA), an integrated platform for functional data analysis. On the content side, MetaCore and KPA encompass a comprehensive database of molecular interactions of different types, pathways, network models, and ten functional ontologies covering human, mouse, and rat genes. The analytical toolkit includes tools for gene/protein list enrichment analysis, statistical "interactome" tool for the identification of over- and under-connected proteins in the dataset, and a biological network analysis module made up of network generation algorithms and filters. The suite also features Advanced Search, an application for combinatorial search of the database content, as well as a Java-based tool called Pathway Map Creator for drawing and editing custom pathway maps. Applications of MetaCore and KPA include molecular mode of action of disease research, identification of potential biomarkers and drug targets, pathway hypothesis generation, analysis of biological effects for novel small molecule compounds and clinical applications (analysis of large cohorts of patients, and translational and personalized medicine).

  11. NEON's Mobile Deployment Platform: A research tool for integrating ecological processes across scales

    Science.gov (United States)

    Sanclements, M.

    2016-12-01

    Here we provide an update on construction of the five NEON Mobile Deployment Platforms (MDPs) as well as a description of the infrastructure and sensors available to researchers in the near future. Additionally, we include information (i.e. timelines and procedures) on requesting MDPs for PI led projects. The MDPs will provide the means to observe stochastic or spatially important events, gradients, or quantities that cannot be reliably observed using fixed location sampling (e.g. fires and floods). Due to the transient temporal and spatial nature of such events, the MDPs are designed to accommodate rapid deployment for time periods up to 1 year. Broadly, the MDPs are comprised of infrastructure and instrumentation capable of functioning individually or in conjunction with one another to support observations of ecological change, as well as education, training and outreach. More specifically, the MDPs include the capability to make tower based measures of ecosystem exchange, radiation, and precipitation in conjunction with baseline soils data such as CO2 flux, and soil temperature and moisture. An aquatics module is also available with the MDP to facilitate research integrating terrestrial and aquatic processes. Ultimately, the NEON MDPs provides a tool for linking PI led research to the continental scale data sets collected by NEON.

  12. A Semantic Big Data Platform for Integrating Heterogeneous Wearable Data in Healthcare.

    Science.gov (United States)

    Mezghani, Emna; Exposito, Ernesto; Drira, Khalil; Da Silveira, Marcos; Pruski, Cédric

    2015-12-01

    Advances supported by emerging wearable technologies in healthcare promise patients a provision of high quality of care. Wearable computing systems represent one of the most thrust areas used to transform traditional healthcare systems into active systems able to continuously monitor and control the patients' health in order to manage their care at an early stage. However, their proliferation creates challenges related to data management and integration. The diversity and variety of wearable data related to healthcare, their huge volume and their distribution make data processing and analytics more difficult. In this paper, we propose a generic semantic big data architecture based on the "Knowledge as a Service" approach to cope with heterogeneity and scalability challenges. Our main contribution focuses on enriching the NIST Big Data model with semantics in order to smartly understand the collected data, and generate more accurate and valuable information by correlating scattered medical data stemming from multiple wearable devices or/and from other distributed data sources. We have implemented and evaluated a Wearable KaaS platform to smartly manage heterogeneous data coming from wearable devices in order to assist the physicians in supervising the patient health evolution and keep the patient up-to-date about his/her status.

  13. The tsunami service bus, an integration platform for heterogeneous sensor systems

    Science.gov (United States)

    Haener, R.; Waechter, J.; Kriegel, U.; Fleischer, J.; Mueller, S.

    2009-04-01

    components remain unchanged, components can be maintained and evolved independently on each other and service functionality as a whole can be reused. In GITEWS the functional integration pattern was adopted by applying the principles of an Enterprise Service Bus (ESB) as a backbone. Four services provided by the so called Tsunami Service Bus (TSB) which are essential for early warning systems are realized compliant to services specified within the Sensor Web Enablement (SWE) initiative of the Open Geospatial Consortium (OGC). 3. ARCHITECTURE The integration platform was developed to access proprietary, heterogeneous sensor data and to provide them in a uniform manner for further use. Its core, the TSB provides both a messaging-backbone and -interfaces on the basis of a Java Messaging Service (JMS). The logical architecture of GITEWS consists of four independent layers: • A resource layer where physical or virtual sensors as well as data or model storages provide relevant measurement-, event- and analysis-data: Utilizable for the TSB are any kind of data. In addition to sensors databases, model data and processing applications are adopted. SWE specifies encoding both to access and to describe these data in a comprehensive way: 1. Sensor Model Language (SensorML): Standardized description of sensors and sensor data 2. Observations and Measurements (O&M): Model and encoding of sensor measurements • A service layer to collect and conduct data from heterogeneous and proprietary resources and provide them via standardized interfaces: The TSB enables interaction with sensors via the following services: 1. Sensor Observation Service (SOS): Standardized access to sensor data 2. Sensor Planning Service (SPS): Controlling of sensors and sensor networks 3. Sensor Alert Service (SAS): Active sending of data if defined events occur 4. Web Notification Service (WNS): Conduction of asynchronous dialogues between services • An orchestration layer where atomic services are composed and

  14. End-to-end integrated security and performance analysis on the DEGAS Choreographer platform

    DEFF Research Database (Denmark)

    Buchholtz, Mikael; Gilmore, Stephen; Haenel, Valentin

    2005-01-01

    We present a software tool platform which facilitates security and performance analysis of systems which starts and ends with UML model descriptions. A UML project is presented to the platform for analysis, formal content is extracted in the form of process calculi descriptions, analysed with the......We present a software tool platform which facilitates security and performance analysis of systems which starts and ends with UML model descriptions. A UML project is presented to the platform for analysis, formal content is extracted in the form of process calculi descriptions, analysed...

  15. Monolithic integration of a silica AWG and Ge photodiodes on Si photonic platform for one-chip WDM receiver.

    Science.gov (United States)

    Nishi, Hidetaka; Tsuchizawa, Tai; Kou, Rai; Shinojima, Hiroyuki; Yamada, Takashi; Kimura, Hideaki; Ishikawa, Yasuhiko; Wada, Kazumi; Yamada, Koji

    2012-04-09

    On the silicon (Si) photonic platform, we monolithically integrated a silica-based arrayed-waveguide grating (AWG) and germanium (Ge) photodiodes (PDs) using low-temperature fabrication technology. We confirmed demultiplexing by the AWG, optical-electrical signal conversion by Ge PDs, and high-speed signal detection at all channels. In addition, we mounted a multichannel transimpedance amplifier/limiting amplifier (TIA/LA) circuit on the fabricated AWG-PD device using flip-chip bonding technology. The results show the promising potential of our Si photonic platform as a photonics-electronics convergence.

  16. A big data geospatial analytics platform - Physical Analytics Integrated Repository and Services (PAIRS)

    Science.gov (United States)

    Hamann, H.; Jimenez Marianno, F.; Klein, L.; Albrecht, C.; Freitag, M.; Hinds, N.; Lu, S.

    2015-12-01

    A big data geospatial analytics platform:Physical Analytics Information Repository and Services (PAIRS)Fernando Marianno, Levente Klein, Siyuan Lu, Conrad Albrecht, Marcus Freitag, Nigel Hinds, Hendrik HamannIBM TJ Watson Research Center, Yorktown Heights, NY 10598A major challenge in leveraging big geospatial data sets is the ability to quickly integrate multiple data sources into physical and statistical models and be run these models in real time. A geospatial data platform called Physical Analytics Information and Services (PAIRS) is developed on top of open source hardware and software stack to manage Terabyte of data. A new data interpolation and re gridding is implemented where any geospatial data layers can be associated with a set of global grid where the grid resolutions is doubling for consecutive layers. Each pixel on the PAIRS grid have an index that is a combination of locations and time stamp. The indexing allow quick access to data sets that are part of a global data layers and allowing to retrieve only the data of interest. PAIRS takes advantages of parallel processing framework (Hadoop) in a cloud environment to digest, curate, and analyze the data sets while being very robust and stable. The data is stored on a distributed no-SQL database (Hbase) across multiple server, data upload and retrieval is parallelized where the original analytics task is broken up is smaller areas/volume, analyzed independently, and then reassembled for the original geographical area. The differentiating aspect of PAIRS is the ability to accelerate model development across large geographical regions and spatial resolution ranging from 0.1 m up to hundreds of kilometer. System performance is benchmarked on real time automated data ingestion and retrieval of Modis and Landsat data layers. The data layers are curated for sensor error, verified for correctness, and analyzed statistically to detect local anomalies. Multi-layer query enable PAIRS to filter different data

  17. Can the Integration of a PLE in an E-Portfolio Platform Improve Generic Competences?

    Science.gov (United States)

    Galván-Fernández, Cristina; Rubio-Hurtado, María José; Martínez-Olmo, Francesc; Rodríguez-Illera, José Luis

    2017-01-01

    The study analyzes the improvement in generic competences through e-portfolio/PLE platform and didactic planning. The new version of the platform, Digital Folder, contains utilities for students and teachers and some PLE components that help the learning process through e-portfolios. Didactic planning is compared for students from the University…

  18. WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results.

    Science.gov (United States)

    Joshi, Vineet K; Freudenberg, Johannes M; Hu, Zhen; Medvedovic, Mario

    2011-01-17

    Cluster analysis methods have been extensively researched, but the adoption of new methods is often hindered by technical barriers in their implementation and use. WebGimm is a free cluster analysis web-service, and an open source general purpose clustering web-server infrastructure designed to facilitate easy deployment of integrated cluster analysis servers based on clustering and functional annotation algorithms implemented in R. Integrated functional analyses and interactive browsing of both, clustering structure and functional annotations provides a complete analytical environment for cluster analysis and interpretation of results. The Java Web Start client-based interface is modeled after the familiar cluster/treeview packages making its use intuitive to a wide array of biomedical researchers. For biomedical researchers, WebGimm provides an avenue to access state of the art clustering procedures. For Bioinformatics methods developers, WebGimm offers a convenient avenue to deploy their newly developed clustering methods. WebGimm server, software and manuals can be freely accessed at http://ClusterAnalysis.org/.

  19. Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research

    NARCIS (Netherlands)

    O. Spjuth (Ola); M. Krestyaninova (Maria); J. Hastings (Janna); H.-Y. Shen (Huei-Yi); J. Heikkinen (Jani); M. Waldenberger (Melanie); A. Langhammer (Arnulf); C. Ladenvall (Claes); T. Esko (Tõnu); M.-A. Persson (Mats-Ake); J. Heggland (Jon); J. Dietrich (Joern); S. Ose (Sandra); C. Gieger (Christian); J.S. Ried (Janina); A. Peters; I. Fortier (Isabel); E.J.C. de Geus (Eco); J. Klovins (Janis); L. Zaharenko (Linda); G. Willemsen (Gonneke); J.J. Hottenga (Jouke Jan); J.-E. Litton (Jan-Eric); J. Karvanen (Juha); D.I. Boomsma (Dorret); L. Groop (Leif); J. Rung (Johan); J. Palmgren (Juni); N.L. Pedersen (Nancy L.); M.I. McCarthy (Mark); C.M. van Duijn (Cornelia); K. Hveem (Kristian); A. Metspalu (Andres); S. Ripatti (Samuli); I. Prokopenko (Inga); J.R. Harris (Jennifer)

    2016-01-01

    textabstractA wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access

  20. How to Support the Integrate Management System through an Enterprise Content Management Platform?

    International Nuclear Information System (INIS)

    Couvreur, D.

    2016-01-01

    Full text: In 2010 the Belgian Nuclear Research Centre SCK-CEN decided to implement an ECM platform in order to manage its information. The main objectives were to centralize in one place all the right and latest versions of information, to improve the usage of internal information and to enhance the efficiency of our activities by standardization and by supporting document management processes. A programme of document migration for the whole institute was set up per group, running over four years. Steps were foreseen such as the comprehension of the activities of the end users in order to increase their efficiency, the analysis of type of documentation, the technical aspects, the migration of documents itself, the training and the most important steps—communication and supporting people to change. In 2013 SCK-CEN decided to implement an Integrated Management System. The objectives were i) to improve the safety performance of the organisation, ii) to foster, strengthen and support a strong safety and organizational culture through the development and reinforcement of good safety attitudes and behaviour in individuals and teams, iii) to structure, but at the same time simplify and make more transparent all processes of SCK-CEN clearly defining responsibilities and authorities, iv) to automate these processes by workflows and support the information and data flow by relevant databases. Intrinsically, both initiatives have the same end objective being the safety of the installations, of the knowledge and transfer of know-how on processes and projects related to radiation protection, reactor technology, waste and disposal, dismantling. In this paper, we will explain through examples. (author

  1. Integration of the virtual model of a Stewart platform with the avatar of a vehicle in a virtual reality

    Science.gov (United States)

    Herbuś, K.; Ociepka, P.

    2016-08-01

    The development of methods of computer aided design and engineering allows conducting virtual tests, among others concerning motion simulation of technical means. The paper presents a method of integrating an object in the form of a virtual model of a Stewart platform with an avatar of a vehicle moving in a virtual environment. The area of the problem includes issues related to the problem of fidelity of mapping the work of the analyzed technical mean. The main object of investigations is a 3D model of a Stewart platform, which is a subsystem of the simulator designated for driving learning for disabled persons. The analyzed model of the platform, prepared for motion simulation, was created in the “Motion Simulation” module of a CAD/CAE class system Siemens PLM NX. Whereas the virtual environment, in which the moves the avatar of the passenger car, was elaborated in a VR class system EON Studio. The element integrating both of the mentioned software environments is a developed application that reads information from the virtual reality (VR) concerning the current position of the car avatar. Then, basing on the accepted algorithm, it sends control signals to respective joints of the model of the Stewart platform (CAD).

  2. An Integrated Web-Based 3d Modeling and Visualization Platform to Support Sustainable Cities

    Science.gov (United States)

    Amirebrahimi, S.; Rajabifard, A.

    2012-07-01

    Sustainable Development is found as the key solution to preserve the sustainability of cities in oppose to ongoing population growth and its negative impacts. This is complex and requires a holistic and multidisciplinary decision making. Variety of stakeholders with different backgrounds also needs to be considered and involved. Numerous web-based modeling and visualization tools have been designed and developed to support this process. There have been some success stories; however, majority failed to bring a comprehensive platform to support different aspects of sustainable development. In this work, in the context of SDI and Land Administration, CSDILA Platform - a 3D visualization and modeling platform -was proposed which can be used to model and visualize different dimensions to facilitate the achievement of sustainability, in particular, in urban context. The methodology involved the design of a generic framework for development of an analytical and visualization tool over the web. CSDILA Platform was then implemented via number of technologies based on the guidelines provided by the framework. The platform has a modular structure and uses Service-Oriented Architecture (SOA). It is capable of managing spatial objects in a 4D data store and can flexibly incorporate a variety of developed models using the platform's API. Development scenarios can be modeled and tested using the analysis and modeling component in the platform and the results are visualized in seamless 3D environment. The platform was further tested using number of scenarios and showed promising results and potentials to serve a wider need. In this paper, the design process of the generic framework, the implementation of CSDILA Platform and technologies used, and also findings and future research directions will be presented and discussed.

  3. VOLTTRON™: An Agent Platform for Integrating Electric Vehicles and Smart Grid

    Energy Technology Data Exchange (ETDEWEB)

    Haack, Jereme N.; Akyol, Bora A.; Tenney, Nathan D.; Carpenter, Brandon J.; Pratt, Richard M.; Carroll, Thomas E.

    2013-12-06

    The VOLTTRON™ platform provides a secure environment for the deployment of intelligent applications in the smart grid. VOLTTRON design is based on the needs of control applications running on small form factor devices, namely security and resource guarantees. Services such as resource discovery, secure agent mobility, and interacting with smart and legacy devices are provided by the platform to ease the development of control applications and accelerate their deployment. VOLTTRON platform has been demonstrated in several different domains that influenced and enhanced its capabilities. This paper will discuss the features of VOLTTRON and highlight its usage to coordinate electric vehicle charging with home energy usage

  4. IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform.

    Science.gov (United States)

    Lee, Tae-Rim; Ahn, Jin Mo; Kim, Gyuhee; Kim, Sangsoo

    2017-12-01

    Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

  5. A central continuous integration platform: Agile Infrastructure use case and future plans

    CERN Multimedia

    CERN. Geneva; ANDERSEN, Terje; GEORGIOU, Stefanos

    2014-01-01

    We shall describe the use of Jenkins as a CI solution by the Configuration Team and present the requirements and plans for a central CI platform, as well as the associated challenges and possible solutions.

  6. Silicon Nitride Photonic Integration Platforms for Visible, Near-Infrared and Mid-Infrared Applications

    Science.gov (United States)

    Micó, Gloria; Pastor, Daniel; Pérez, Daniel; Doménech, José David; Fernández, Juan; Baños, Rocío; Alemany, Rubén; Sánchez, Ana M.; Cirera, Josep M.; Mas, Roser

    2017-01-01

    Silicon nitride photonics is on the rise owing to the broadband nature of the material, allowing applications of biophotonics, tele/datacom, optical signal processing and sensing, from visible, through near to mid-infrared wavelengths. In this paper, a review of the state of the art of silicon nitride strip waveguide platforms is provided, alongside the experimental results on the development of a versatile 300 nm guiding film height silicon nitride platform. PMID:28895906

  7. SAW-Based Phononic Crystal Microfluidic Sensor-Microscale Realization of Velocimetry Approaches for Integrated Analytical Platform Applications.

    Science.gov (United States)

    Oseev, Aleksandr; Lucklum, Ralf; Zubtsov, Mikhail; Schmidt, Marc-Peter; Mukhin, Nikolay V; Hirsch, Soeren

    2017-09-23

    The current work demonstrates a novel surface acoustic wave (SAW) based phononic crystal sensor approach that allows the integration of a velocimetry-based sensor concept into single chip integrated solutions, such as Lab-on-a-Chip devices. The introduced sensor platform merges advantages of ultrasonic velocimetry analytic systems and a microacoustic sensor approach. It is based on the analysis of structural resonances in a periodic composite arrangement of microfluidic channels confined within a liquid analyte. Completed theoretical and experimental investigations show the ability to utilize periodic structure localized modes for the detection of volumetric properties of liquids and prove the efficacy of the proposed sensor concept.

  8. Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform

    Science.gov (United States)

    Moutsatsos, Ioannis K.; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J.; Jenkins, Jeremy L.; Holway, Nicholas; Tallarico, John; Parker, Christian N.

    2016-01-01

    High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an “off-the-shelf,” open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community. PMID:27899692

  9. Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform.

    Science.gov (United States)

    Moutsatsos, Ioannis K; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J; Jenkins, Jeremy L; Holway, Nicholas; Tallarico, John; Parker, Christian N

    2017-03-01

    High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.

  10. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

    Advances in Biomedical Engineering, Volume 6, is a collection of papers that discusses the role of integrated electronics in medical systems and the usage of biological mathematical models in biological systems. Other papers deal with the health care systems, the problems and methods of approach toward rehabilitation, as well as the future of biomedical engineering. One paper discusses the use of system identification as it applies to biological systems to estimate the values of a number of parameters (for example, resistance, diffusion coefficients) by indirect means. More particularly, the i

  11. CoreFlow: a computational platform for integration, analysis and modeling of complex biological data.

    Science.gov (United States)

    Pasculescu, Adrian; Schoof, Erwin M; Creixell, Pau; Zheng, Yong; Olhovsky, Marina; Tian, Ruijun; So, Jonathan; Vanderlaan, Rachel D; Pawson, Tony; Linding, Rune; Colwill, Karen

    2014-04-04

    A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Python, or Perl for processing, correcting and modeling this data. CoreFlow organizes these scripts into project-specific pipelines, tracks interdependencies between related tasks, and enables the generation of summary reports as well as publication-quality images. As a result, the gap between experimental and computational components of a typical large-scale biology project is reduced, decreasing the time between data generation, analysis and manuscript writing. CoreFlow is being released to the scientific community as an open-sourced software package complete with proteomics-specific examples, which include corrections for incomplete isotopic labeling of peptides (SILAC) or arginine-to-proline conversion, and modeling of multiple/selected reaction monitoring (MRM/SRM) results. CoreFlow was purposely designed as an environment for programmers to rapidly perform data analysis. These analyses are assembled into project-specific workflows that are readily shared with biologists to guide the next stages of experimentation. Its simple yet powerful interface provides a structure where scripts can be written and tested virtually simultaneously to shorten the life cycle of code development for a particular task. The scripts are exposed at every step so that a user can quickly see the relationships between the data, the assumptions that have been made, and the manipulations that have been performed. Since the scripts use commonly available programming languages, they can easily be

  12. Development and application of knowledge-based subject group integration platforms:A case study of Shanghai Institute of Ceramics,CAS

    Institute of Scientific and Technical Information of China (English)

    Yu; LIU; Jian; FU; Huijun; ZHENG; Hao; CHEN; Zhiping; YANG

    2014-01-01

    Purpose:According to the different requirements of research group users,we established the knowledge-based subject group integration platforms of Shanghai Institute of Ceramics,the Chinese Academy of Sciences(abbreviated as SIC CAS hereinafter),which were designed and constructed to better meet the needs of CAS research groups for their development,collaboration and communication.Design/methodology/approach:We first identified the requirements of users via preliminary investigation,and then chose CASI1 P,iLibrary and XKE technology,respectively as the building tools compatible with the major demands of users.These steps helped us complete the layout design of SIC CAS integration platforms,as well as its knowledge organization and integration.Findings:According to the need of users,we applied three types of platform construction technologies to five SIC integration platforms,and formulated standard norms for the further construction process,which could provide useful reference for a sustainable development for the extensive construction in CAS institutes.Research limitations:In order to make the SIC integration platforms more intelligent and have more functions,we need to enlarge the scale of the Platforms and upgrade the building tools for the platform construction.Practical implications:The nature of SIC sub-project integration platforms is to construct a content-sensitive environment which can embed knowledge services and knowledge applications seamlessly into scientific activities,so the Platform is expected to be a useful tool to help researchers better understand the recent development of the research field and form collaborations with their peers.Originality/value:SIC integration platforms are the only pilot construction that used 3different platform technologies in the first batch of knowledge-based subject group integration platforms of the Chinese Academy of Sciences.The construction is user-centered throughout the whole process,namely,from the technology

  13. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

    Science.gov (United States)

    Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

    2012-05-01

    MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

  14. Biomedical nanotechnology.

    Science.gov (United States)

    Hurst, Sarah J

    2011-01-01

    This chapter summarizes the roles of nanomaterials in biomedical applications, focusing on those highlighted in this volume. A brief history of nanoscience and technology and a general introduction to the field are presented. Then, the chemical and physical properties of nanostructures that make them ideal for use in biomedical applications are highlighted. Examples of common applications, including sensing, imaging, and therapeutics, are given. Finally, the challenges associated with translating this field from the research laboratory to the clinic setting, in terms of the larger societal implications, are discussed.

  15. Catalyst-Free Vapor-Phase Method for Direct Integration of Gas Sensing Nanostructures with Polymeric Transducing Platforms

    Directory of Open Access Journals (Sweden)

    Stella Vallejos

    2014-01-01

    Full Text Available Tungsten oxide nanoneedles (NNs are grown and integrated directly with polymeric transducing platforms for gas sensors via aerosol-assisted chemical vapor deposition (AACVD method. Material analysis shows the feasibility to grow highly crystalline nanomaterials in the form of NNs with aspect ratios between 80 and 200 and with high concentration of oxygen vacancies at the surface, whereas gas testing demonstrates moderate sensing responses to hydrogen at concentrations between 10 ppm and 50 ppm, which are comparable with results for tungsten oxide NNs grown on silicon transducing platforms. This method is demonstrated to be an attractive route to fabricate next generation of gas sensors devices, provided with flexibility and functionality, with great potential in a cost effective production for large-scale applications.

  16. Creation of an Integrated Environment to Supply e-Learning Platforms with Office Automation Features

    Science.gov (United States)

    Palumbo, Emilio; Verga, Francesca

    2015-01-01

    Over the last years great efforts have been made within the University environment to implement e-learning technologies in the standard educational practice. These learning technologies distribute online educational multimedia contents through technological platforms. Even though specific e-learning tools for technical disciplines were already…

  17. Beyond xMOOCs in healthcare education: study of the feasibility in integrating virtual patient systems and MOOC platforms.

    Science.gov (United States)

    Stathakarou, Natalia; Zary, Nabil; Kononowicz, Andrzej A

    2014-01-01

    Background. Massive Open Online Courses (MOOCs) are an emerging trend in online learning. However, their technology is not yet completely adjusted to the needs of healthcare education. Integration of Virtual Patients within MOOCs to increase interactivity and foster clinical reasoning skills training, has been discussed in the past, but not verified by a practical implementation. Objective. To investigate the technical feasibility of integrating MOOCs with Virtual Patients for the purpose of enabling further research into the potential pedagogical benefits of this approach. Methods. We selected OpenEdx and Open Labyrinth as representative constituents of a MOOC platform and Virtual Patient system integration. Based upon our prior experience we selected the most fundamental technical requirement to address. Grounded in the available literature we identified an e-learning standard to guide the integration. We attempted to demonstrate the feasibility of the integration by designing a "proof-of-concept" prototype. The resulting pilot implementation was subject of verification by two test cases. Results. A Single Sign-On mechanism connecting Open Labyrinth with OpenEdx and based on the IMS LTI standard was successfully implemented and verified. Conclusion. We investigated the technical perspective of integrating Virtual Patients with MOOCs. By addressing this crucial technical requirement we set a base for future research on the educational benefits of using virtual patients in MOOCs. This provides new opportunities for integrating specialized software in healthcare education at massive scale.

  18. Beyond xMOOCs in healthcare education: study of the feasibility in integrating virtual patient systems and MOOC platforms

    Directory of Open Access Journals (Sweden)

    Natalia Stathakarou

    2014-11-01

    Full Text Available Background. Massive Open Online Courses (MOOCs are an emerging trend in online learning. However, their technology is not yet completely adjusted to the needs of healthcare education. Integration of Virtual Patients within MOOCs to increase interactivity and foster clinical reasoning skills training, has been discussed in the past, but not verified by a practical implementation.Objective. To investigate the technical feasibility of integrating MOOCs with Virtual Patients for the purpose of enabling further research into the potential pedagogical benefits of this approach.Methods. We selected OpenEdx and Open Labyrinth as representative constituents of a MOOC platform and Virtual Patient system integration. Based upon our prior experience we selected the most fundamental technical requirement to address. Grounded in the available literature we identified an e-learning standard to guide the integration. We attempted to demonstrate the feasibility of the integration by designing a “proof-of-concept” prototype. The resulting pilot implementation was subject of verification by two test cases.Results. A Single Sign-On mechanism connecting Open Labyrinth with OpenEdx and based on the IMS LTI standard was successfully implemented and verified.Conclusion. We investigated the technical perspective of integrating Virtual Patients with MOOCs. By addressing this crucial technical requirement we set a base for future research on the educational benefits of using virtual patients in MOOCs. This provides new opportunities for integrating specialized software in healthcare education at massive scale.

  19. IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

    Science.gov (United States)

    Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

    2017-04-07

    Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

  20. Biomedical Engineering

    CERN Document Server

    Suh, Sang C; Tanik, Murat M

    2011-01-01

    Biomedical Engineering: Health Care Systems, Technology and Techniques is an edited volume with contributions from world experts. It provides readers with unique contributions related to current research and future healthcare systems. Practitioners and researchers focused on computer science, bioinformatics, engineering and medicine will find this book a valuable reference.

  1. Integration of the program TNXYZ in the platform SALOME; Integracion del programa TNXYZ en la plataforma SALOME

    Energy Technology Data Exchange (ETDEWEB)

    Chaparro V, F. J.; Silva A, L.; Del Valle G, E. [IPN, Escuela Superior de Fisica y Matematicas, Av. Instituto Politecnico Nacional s/n, U.P. Adolfo Lopez Mateos, Edificio 9, Col. San Pedro Zacatenco, 07738 Mexico D. F. (Mexico); Gomez T, A. M.; Vargas E, S., E-mail: javier.paquito@hotmail.com [ININ, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico)

    2013-10-15

    This work presents the procedure realized to integrate the code TNXYZ like a processing tool to the graphic simulation platform SALOME. The code TNXYZ solves the neutron transport equation in stationary state, for several energy groups, quantizing the angular variable by the discrete ordinates method and the space variable by nodal methods. The platform SALOME is a graphic surrounding designed for the construction, edition and simulation of mechanical models focused to the industry and contrary to other software, it allows to integrate external source codes to the surrounding, to form a complete scheme of execution, supervision, pre and post information processing. The code TNXYZ was programmed in the 90s in a Fortran compiler, but to be used at the present time the code should be actualized to the current compiler characteristics; also, in the original scheme was carried out a modularization process, that is to say, the main program was divided in sections where the code carries out important operations, with the intention of flexibility the data extraction process along its processing sequence and that can be useful in a later development of coupling. Finally, to verify the integration a fuel assembly BWR was modeled, as well as a control cell. The cross sections were obtained with the Monte Carlo Serpent code. Some results obtained with Serpent were used to verify and to begin with the validation of the code, being obtained an acceptable comparison in the infinite multiplication factor. The validation process should extend and one has planned to present in a future work. This work is part of the development of the research group formed between the Escuela Superior de Fisica y Matematicas del Instituto Politecnico Nacional (IPN) and the Instituto Nacional de Investigaciones Nucleares (ININ) in which a simulation Mexican platform of nuclear reactors is developed. (Author)

  2. A Platform of Constructivist Learning in Practice: Computer Literacy Integrated into Elementary School

    Directory of Open Access Journals (Sweden)

    Ivan Garcia

    2010-06-01

    Full Text Available In Mexico, the conventional teaching approach, when applied specifically to elementary school, seems to fall short of attaining the overall quality objective. The main consequence of this problem is when teachers are not sure that their students really understand the dynamic nature of concepts and mechanism since an early age, particularly in elementary school. This paper presents a pedagogical/technological platform, based on constructivism ideas, as a means of making the learning process in elementary school more efficient and interesting. The constructivist platform presented here uses graphical simulators developed for Web 2.0 as a support tool, creating a teaching and learning environment in which practical experiments can be undertaken as each topic is introduced and explained.

  3. Can the integration of a PLE in an e-portfolio platform improve generic competences?

    Directory of Open Access Journals (Sweden)

    Cristina Galván-Fernández

    2017-07-01

    Full Text Available The study analyzes the improvement in generic competences through e-portfolio/PLE platform and didactic planning. The new version of the platform, Digital Folder, contains utilities for students and teachers and some PLE components that help the learning process through e-portfolios. Didactic planning is compared for students from the University of Vic and the University of Barcelona, with a total of 61 participants. A questionnaire has been applied for measuring the use of functions and how much these functions aid in the improvement of the generic competences (reflection, planning and selection of information. The results confirm that the most helpful functions for students are: the Schedule, the Academic tasks, the Teacher’s portfolio and Dialogue with the teacher. However, the implication of these functions in the improvement of the competences depends on didactic planning overall for reflection on learning.

  4. Neutron CSI: Integrated platform for non-destructive composition and stress imaging with neutrons

    International Nuclear Information System (INIS)

    Materna, T.; Pirling, T.

    2011-01-01

    We propose to build an interdisciplinary platform for non-destructive analysis and imaging with neutrons. The project regroups an instrument already available at ILL (Laue-Langevin Institute), SALSA, with a new one for Neutron Tomography coupled to Prompt-Gamma Neutron Activation (PGNA) as well as partial usage of another proposed instrument, FIPPS. The focus of the proposition is the versatility of high spatial resolution and energy-selective neutron tomography to provide a rapid and precise 3D morphological map of an object as well as indirect information on its 3D elemental and structural composition through the scan of Bragg-edges in transmission. Coupled to PGNA imaging and the strain analysis power of SALSA, the aim of the platform is to answer key questions occurring in geological, metallurgical, engineering and medical fields, material research and cultural heritage. (authors)

  5. A Social Environmental Sensor Network Integrated within a Web GIS Platform

    Directory of Open Access Journals (Sweden)

    Yorghos Voutos

    2017-11-01

    Full Text Available We live in an era where typical measures towards the mitigation of environmental degradation follow the identification and recording of natural parameters closely associated with it. In addition, current scientific knowledge on the one hand may be applied to minimize the environmental impact of anthropogenic activities, whereas informatics on the other, playing a key role in this ecosystem, do offer new ways of implementing complex scientific processes regarding the collection, aggregation and analysis of data concerning environmental parameters. Furthermore, another related aspect to consider is the fact that almost all relevant data recordings are influenced by their given spatial characteristics. Taking all aforementioned inputs into account, managing such a great amount of complex and remote data requires specific digital structures; these structures are typically deployed over the Web on an attempt to capitalize existing open software platforms and modern developments of hardware technology. In this paper we present an effort to provide a technical solution based on sensing devices that are based on the well-known Arduino platform and operate continuously for gathering and transmitting of environmental state information. Controls, user interface and extensions of the proposed project rely on the Android mobile device platform (both from the software and hardware side. Finally, a crucial novel aspect of our work is the fact that all herein gathered data carry spatial information, which is rather fundamental for the successful correlation between pollutants and their place of origin. The latter is implemented by an interactive Web GIS platform operating oversight in situ and on a timeline basis.

  6. Thermo-Economic Modelling and Process Integration of CO2-Mitigation Options on Oil and Gas Platforms

    DEFF Research Database (Denmark)

    Nguyen, Tuong-Van; Tock, Laurence; Breuhaus, Peter

    2014-01-01

    recovering CO2 that can be used for enhanced oil recovery. In this paper, a North Sea platform is considered as case study, and the site-scale retrofit integration of these three options is analysed, considering thermodynamic, economic and environmental performance indicators. The results illustrate......The offshore extraction of oil and gas is an energy-intensive process associated with large CO2 and CH4 emissions to the atmosphere and chemicals to the sea. The taxation of these emissions has encouraged the development of more energy-efficient and environmental-friendly solutions, of which three...

  7. Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data

    DEFF Research Database (Denmark)

    Kristensen, Dan Bach; Brønd, Jan Christian; Nielsen, Peter Aagaard

    2004-01-01

    LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which...... is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can...

  8. ICECAP: an integrated, general-purpose, automation-assisted IC50/EC50 assay platform.

    Science.gov (United States)

    Li, Ming; Chou, Judy; King, Kristopher W; Jing, Jing; Wei, Dong; Yang, Liyu

    2015-02-01

    IC50 and EC50 values are commonly used to evaluate drug potency. Mass spectrometry (MS)-centric bioanalytical and biomarker labs are now conducting IC50/EC50 assays, which, if done manually, are tedious and error-prone. Existing bioanalytical sample preparation automation systems cannot meet IC50/EC50 assay throughput demand. A general-purpose, automation-assisted IC50/EC50 assay platform was developed to automate the calculations of spiking solutions and the matrix solutions preparation scheme, the actual spiking and matrix solutions preparations, as well as the flexible sample extraction procedures after incubation. In addition, the platform also automates the data extraction, nonlinear regression curve fitting, computation of IC50/EC50 values, graphing, and reporting. The automation-assisted IC50/EC50 assay platform can process the whole class of assays of varying assay conditions. In each run, the system can handle up to 32 compounds and up to 10 concentration levels per compound, and it greatly improves IC50/EC50 assay experimental productivity and data processing efficiency. © 2014 Society for Laboratory Automation and Screening.

  9. Silicon photonics integrated circuits: a manufacturing platform for high density, low power optical I/O's.

    Science.gov (United States)

    Absil, Philippe P; Verheyen, Peter; De Heyn, Peter; Pantouvaki, Marianna; Lepage, Guy; De Coster, Jeroen; Van Campenhout, Joris

    2015-04-06

    Silicon photonics integrated circuits are considered to enable future computing systems with optical input-outputs co-packaged with CMOS chips to circumvent the limitations of electrical interfaces. In this paper we present the recent progress made to enable dense multiplexing by exploiting the integration advantage of silicon photonics integrated circuits. We also discuss the manufacturability of such circuits, a key factor for a wide adoption of this technology.

  10. The ethics of biomedical big data

    CERN Document Server

    Mittelstadt, Brent Daniel

    2016-01-01

    This book presents cutting edge research on the new ethical challenges posed by biomedical Big Data technologies and practices. ‘Biomedical Big Data’ refers to the analysis of aggregated, very large datasets to improve medical knowledge and clinical care. The book describes the ethical problems posed by aggregation of biomedical datasets and re-use/re-purposing of data, in areas such as privacy, consent, professionalism, power relationships, and ethical governance of Big Data platforms. Approaches and methods are discussed that can be used to address these problems to achieve the appropriate balance between the social goods of biomedical Big Data research and the safety and privacy of individuals. Seventeen original contributions analyse the ethical, social and related policy implications of the analysis and curation of biomedical Big Data, written by leading experts in the areas of biomedical research, medical and technology ethics, privacy, governance and data protection. The book advances our understan...

  11. Research enrichment: evaluation of structured research in the curriculum for dental medicine students as part of the vertical and horizontal integration of biomedical training and discovery

    Directory of Open Access Journals (Sweden)

    Stewart Tanis

    2008-02-01

    Full Text Available Abstract Background Research programs within medical and dental schools are important vehicles for biomedical and clinical discovery, serving as effective teaching and learning tools by providing situations in which predoctoral students develop problem-solving and critical-thinking skills. Although research programs at many medical and dental schools are well-established, they may not be well integrated into the predoctoral curriculum to effectively support the learning objectives for their students. Methods A series of structured seminars, incorporating faculty research, was designed for first-year dental students at the University of Nevada, Las Vegas, School of Dental Medicine to reinforce and support the concepts and skills taught in concurrent courses. A structured research enrichment period was also created to facilitate student engagement in active research using faculty and student curricular release time. Course evaluations and surveys were administered to gauge student perceptions of the curricular integration of research, the impact of these seminars on recruitment to the research program, and overall levels of student satisfaction with research enrichment. Results The analysis of course surveys revealed that students perceived the research-containing seminars effectively illustrated concepts, were logically sequenced, and were well-integrated into their curriculum. In addition, analysis of surveys revealed that the Integration Seminar courses motivated students to engage in research enrichment. Finally, this analysis provided evidence that students were very satisfied with their overall learning experience during research enrichment. Conclusion Curricular integration is one method of improving the teaching and learning of complicated and inter-related concepts, providing an opportunity to incorporate research training and objectives into traditionally separate didactic courses. Despite the benefits of curricular integration, finding

  12. Research enrichment: evaluation of structured research in the curriculum for dental medicine students as part of the vertical and horizontal integration of biomedical training and discovery.

    Science.gov (United States)

    Kingsley, Karl; O'Malley, Susan; Stewart, Tanis; Howard, Katherine M

    2008-02-19

    Research programs within medical and dental schools are important vehicles for biomedical and clinical discovery, serving as effective teaching and learning tools by providing situations in which predoctoral students develop problem-solving and critical-thinking skills. Although research programs at many medical and dental schools are well-established, they may not be well integrated into the predoctoral curriculum to effectively support the learning objectives for their students. A series of structured seminars, incorporating faculty research, was designed for first-year dental students at the University of Nevada, Las Vegas, School of Dental Medicine to reinforce and support the concepts and skills taught in concurrent courses. A structured research enrichment period was also created to facilitate student engagement in active research using faculty and student curricular release time. Course evaluations and surveys were administered to gauge student perceptions of the curricular integration of research, the impact of these seminars on recruitment to the research program, and overall levels of student satisfaction with research enrichment. The analysis of course surveys revealed that students perceived the research-containing seminars effectively illustrated concepts, were logically sequenced, and were well-integrated into their curriculum. In addition, analysis of surveys revealed that the Integration Seminar courses motivated students to engage in research enrichment. Finally, this analysis provided evidence that students were very satisfied with their overall learning experience during research enrichment. Curricular integration is one method of improving the teaching and learning of complicated and inter-related concepts, providing an opportunity to incorporate research training and objectives into traditionally separate didactic courses. Despite the benefits of curricular integration, finding the most appropriate points of integration, obtaining release time

  13. Integrated photonic platform based on semipolar InGaN/GaN multiple section laser diodes

    KAUST Repository

    Shen, Chao

    2017-11-30

    The challenges to realizing III-nitride photonic integrated circuit (PIC) are discussed. Utilizing InGaN-based multi-section laser diode (LD) on semipolar GaN substrate, the seamless on-chip integration of III-nitride waveguide photodetector (WPD) in the visible regime has been demonstrated.

  14. Integrated photonic platform based on semipolar InGaN/GaN multiple section laser diodes

    KAUST Repository

    Shen, Chao; Lee, Changmin; Ng, Tien Khee; Speck, James S.; Nakamura, Shuji; DenBaars, Steven P.; Ooi, Boon S.

    2017-01-01

    The challenges to realizing III-nitride photonic integrated circuit (PIC) are discussed. Utilizing InGaN-based multi-section laser diode (LD) on semipolar GaN substrate, the seamless on-chip integration of III-nitride waveguide photodetector (WPD) in the visible regime has been demonstrated.

  15. Robust integration schemes for junction-based modulators in a 200mm CMOS compatible silicon photonic platform (Conference Presentation)

    Science.gov (United States)

    Szelag, Bertrand; Abraham, Alexis; Brision, Stéphane; Gindre, Paul; Blampey, Benjamin; Myko, André; Olivier, Segolene; Kopp, Christophe

    2017-05-01

    Silicon photonic is becoming a reality for next generation communication system addressing the increasing needs of HPC (High Performance Computing) systems and datacenters. CMOS compatible photonic platforms are developed in many foundries integrating passive and active devices. The use of existing and qualified microelectronics process guarantees cost efficient and mature photonic technologies. Meanwhile, photonic devices have their own fabrication constraints, not similar to those of cmos devices, which can affect their performances. In this paper, we are addressing the integration of PN junction Mach Zehnder modulator in a 200mm CMOS compatible photonic platform. Implantation based device characteristics are impacted by many process variations among which screening layer thickness, dopant diffusion, implantation mask overlay. CMOS devices are generally quite robust with respect to these processes thanks to dedicated design rules. For photonic devices, the situation is different since, most of the time, doped areas must be carefully located within waveguides and CMOS solutions like self-alignment to the gate cannot be applied. In this work, we present different robust integration solutions for junction-based modulators. A simulation setup has been built in order to optimize of the process conditions. It consist in a Mathlab interface coupling process and device electro-optic simulators in order to run many iterations. Illustrations of modulator characteristic variations with process parameters are done using this simulation setup. Parameters under study are, for instance, X and Y direction lithography shifts, screening oxide and slab thicknesses. A robust process and design approach leading to a pn junction Mach Zehnder modulator insensitive to lithography misalignment is then proposed. Simulation results are compared with experimental datas. Indeed, various modulators have been fabricated with different process conditions and integration schemes. Extensive

  16. Arsenic removal from contaminated groundwater by membrane-integrated hybrid plant: optimization and control using Visual Basic platform.

    Science.gov (United States)

    Chakrabortty, S; Sen, M; Pal, P

    2014-03-01

    A simulation software (ARRPA) has been developed in Microsoft Visual Basic platform for optimization and control of a novel membrane-integrated arsenic separation plant in the backdrop of absence of such software. The user-friendly, menu-driven software is based on a dynamic linearized mathematical model, developed for the hybrid treatment scheme. The model captures the chemical kinetics in the pre-treating chemical reactor and the separation and transport phenomena involved in nanofiltration. The software has been validated through extensive experimental investigations. The agreement between the outputs from computer simulation program and the experimental findings are excellent and consistent under varying operating conditions reflecting high degree of accuracy and reliability of the software. High values of the overall correlation coefficient (R (2) = 0.989) and Willmott d-index (0.989) are indicators of the capability of the software in analyzing performance of the plant. The software permits pre-analysis, manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. Performance analysis of the whole system as well as the individual units is possible using the tool. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for removal of arsenic from contaminated groundwater.

  17. GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis

    Directory of Open Access Journals (Sweden)

    Raquel L. Costa

    2017-07-01

    Full Text Available There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were

  18. An integrated movement capture and control platform applied towards autonomous movements of surgical robots.

    Science.gov (United States)

    Daluja, Sachin; Golenberg, Lavie; Cao, Alex; Pandya, Abhilash K; Auner, Gregory W; Klein, Michael D

    2009-01-01

    Robotic surgery has gradually gained acceptance due to its numerous advantages such as tremor filtration, increased dexterity and motion scaling. There remains, however, a significant scope for improvement, especially in the areas of surgeon-robot interface and autonomous procedures. Previous studies have attempted to identify factors affecting a surgeon's performance in a master-slave robotic system by tracking hand movements. These studies relied on conventional optical or magnetic tracking systems, making their use impracticable in the operating room. This study concentrated on building an intrinsic movement capture platform using microcontroller based hardware wired to a surgical robot. Software was developed to enable tracking and analysis of hand movements while surgical tasks were performed. Movement capture was applied towards automated movements of the robotic instruments. By emulating control signals, recorded surgical movements were replayed by the robot's end-effectors. Though this work uses a surgical robot as the platform, the ideas and concepts put forward are applicable to telerobotic systems in general.

  19. Integration of a network aware traffic generation device into a computer network emulation platform

    CSIR Research Space (South Africa)

    Von Solms, S

    2014-07-01

    Full Text Available Flexible, open source network emulation tools can provide network researchers with significant benefits regarding network behaviour and performance. The evaluation of these networks can benefit greatly from the integration of realistic, network...

  20. Integrated management platform of nuclear fuel storage and transportation based on RFID

    International Nuclear Information System (INIS)

    Song Yafeng; Ma Yanqin; Chen Liyu; Jiang Yong; Wu Jianlei; Yang Haibo; Zhang Haiyan

    2012-01-01

    This paper describes integrated system model to improve work efficiency and optimize control measures of nuclear fuel storage and transportation, RFID and information integration technology is introduced, traditional management processes are innovated in data acquisition and monitoring fields as well, system solutions and design model are given by emphasizing on the following key technologies: cascade protection of information system, security protocol of RFID information, algorithm of collision. (authors)

  1. VIRTUAL REALITY-BASED CLOUD BIM PLATFORM FOR INTEGRATED AEC PROJECTS

    OpenAIRE

    Goulding, Jack Steven; Pour Rahimian Leilabadi, Farzad; Wang, Xiangyu

    2014-01-01

    Building Information Modelling (BIM) has demonstrated the need for integrating collaborative design teams’ “project data”, to not only help coordinate the design, engineering, fabrication, construction, and maintenance of various trades, but also facilitate project integration and interchange. Numerous potential benefits have inspired several countries to consider the implications of implementing BIM Level 3 (Cloud) as an innovative way of further enhancing the design, management and delivery...

  2. Multichannel Bipotentiostat Integrated With a Microfluidic Platform for Electrochemical Real-Time Monitoring of Cell Cultures

    DEFF Research Database (Denmark)

    Vergani, Marco; Carminati, Marco; Ferrari, Giorgio

    2012-01-01

    An electrochemical detection system specifically designed for multi-parameter real-time monitoring of stem cell culturing/differentiation in a microfluidic system is presented. It is composed of a very compact 24-channel electronic board, compatible with arrays of microelectrodes and coupled...... to a microfluidic cell culture system. A versatile data acquisition software enables performing amperometry, cyclic voltammetry and impedance spectroscopy in each of the 12 independent chambers over a 100 kHz bandwidth with current resolution down to 5 pA for 100 ms measuring time. The design of the platform, its...... realization and experimental characterization are reported, with emphasis on the analysis of impact of input capacitance (i.e., microelectrode size) and microfluidic pump operation on current noise. Programmable sequences of successive injections of analytes (ferricyanide and dopamine) and rinsing buffer...

  3. Integrated Cu-based TM-pass polarizer using CMOS technology platform

    KAUST Repository

    Ng, Tien Khee

    2010-01-01

    A transverse-magnetic-pass (TM-pass) copper (Cu) polarizer is proposed and analyzed using the previously published two-dimensional Method-of-Lines beam-propagation model. The proposed polarizer exhibits a simulated high-pass filter characteristics, with TM0 and TE0 mode transmissivity of >70% and <5%, respectively, in the wavelength regime of 1.2-1.6 μm. The polarization extinction ratio (PER) given by 10 log10 (PTM0)/(PTE0) is +11.5 dB across the high-pass wavelength regime. To the best of the authors\\' knowledge, we report here the smallest footprint CMOS-platform compatible TM-polarizer.

  4. A Framework to Integrate Public, Dynamic Metrics Into an OER Platform

    Directory of Open Access Journals (Sweden)

    Jaclyn Zetta Cohen

    2014-04-01

    Full Text Available The usage metrics for open educational resources (OER are often either hidden behind an authentication system or shared intermittently in static, aggregated format at the repository level. This paper discusses the first year of University of Michigan’s project to share its OER usage data dynamically, publicly, to synthesize it across different levels within the repository hierarchies, and to aggregate in a method inclusive of content hosted on third-party platforms. The authors analyze their user research with a target audience of faculty authors, multimedia specialists, librarians, and communications specialists. Next, they explore a stratified technical design that allows the dynamic sharing of metrics down to the level of individual resources. The authors conclude that this framework enables sustainable feedback to OER creators, helps to build positive relationships with creators of OER, and allows the institution to move toward sharing OER on a larger scale.

  5. FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

    Directory of Open Access Journals (Sweden)

    Pontarotti Pierre

    2005-08-01

    Full Text Available Abstract Background Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes. Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. Results Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset. The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. Conclusion The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.

  6. Integration Between SCORM Learning Objects and the CIEMAT Virtual Elearning Platform; Integracion de Objetos de Aprendizaje SCORM con la Plataforma de Ensenanza Virtual del CIEMAT

    Energy Technology Data Exchange (ETDEWEB)

    Bailador Ferreras, M A; Troiani, S; Gonzalez Giralda, C; Llorente Herranz, C; Marco Arboli, M L

    2010-08-06

    New information and communications technologies have made a major contribution in the way of understanding the training needs, which have been involved in the change from the traditional teaching to the use of virtual learning platforms. Thus, Ciemat, has installed a virtual platform for education, in particular MOODLE in which have been installed some virtual contents developed with Flash. The next necessary step has been how to integrate the contents with the MOODLE virtual platform, following the aim to know the assessment for learning tracking of the learners. This document provides the technological facts for the integration of the flash virtual contents and the virtual platform in order to achieve the training process is efficiently evaluated. (Author) 5 refs.

  7. Life performance of oil and gas platforms: Site integration and thermodynamic evaluation

    DEFF Research Database (Denmark)

    Nguyen, Tuong-Van; Fülöp, Tamás Gábor; Breuhaus, Peter

    2014-01-01

    requirements are assessed by a process integration study, and the system inefficiencies are pinpointed by performing an exergy accounting. The heating and cooling requirements vary significantly over time, and most inefficiencies take place in processes where chemical exergy is consumed (50-55%), thermal...... exergy is transferred (15-20%), or mechanical exergy is varied (10-15%). These findings are valid for all production periods: this suggests that more attention should be paid on a proper integration of the processing and utility plants, by, for instance, recovering heat from the turbine exhausts and from...

  8. A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs.

    Science.gov (United States)

    Manage, Dammika P; Lauzon, Jana; Atrazhev, Alexey; Morrissey, Yuen C; Edwards, Ann L; Stickel, Alexander J; Crabtree, H John; Pabbaraju, Kanti; Zahariadis, George; Yanow, Stephanie K; Pilarski, Linda M

    2012-05-07

    Herpes simplex virus (HSV) is one of the most prevalent viruses, with acute and recurrent infections in humans. The current gold standard for the diagnosis of HSV is viral culture which takes 2-14 days and has low sensitivity. In contrast, DNA amplification by polymerase chain reaction (PCR) can be performed within 1-2 h. We here describe a multiparameter PCR assay to simultaneously detect HSV-1 and HSV-2 DNA templates, together with integrated positive and negative controls, with product detection by melting curve analysis (MCA), in an array of semi-solid polyacrylamide gel posts. Each gel post is 0.67 μL in volume, and polymerized with all the components required for PCR. Both PCR and MCA can currently be performed in one hour and 20 min. Unprocessed genital swabs collected in universal transport medium were directly added to the reagents before or after polymerization, diffusing from atop the gel posts. The gel post platform detects HSV templates in as little as 2.5 nL of raw sample. In this study, 45 genital swab specimens were tested blindly as a preliminary validation of this platform. The concordance of PCR on gel posts with conventional PCR was 91%. The primer sequestration method introduced here (wherein different primers are placed in different sets of posts) enables the simultaneous detection of multiple pathogens for the same sample, together with positive and negative controls, on a single chip. This platform accepts unprocessed samples and is readily adaptable to detection of multiple different pathogens or biomarkers for point-of-care diagnostics.

  9. Sighten Final Technical Report DEEE0006690 Deploying an integrated and comprehensive solar financing software platform

    Energy Technology Data Exchange (ETDEWEB)

    O' Leary, Conlan [Sighten, Inc., San Francisco, CA (United States)

    2017-10-15

    Over the project, Sighten built a comprehensive software-as-a-service (Saas) platform to automate and streamline the residential solar financing workflow. Before the project period, significant time and money was spent by companies on front-end tools related to system design and proposal creation, but comparatively few resources were available to support the many back-end calculations and data management processes that underpin third party financing. Without a tool like Sighten, the solar financing processes involved passing information from the homeowner prospect into separate tools for system design, financing, and then later to reporting tools including Microsoft Excel, CRM software, in-house software, outside software, and offline, manual processes. Passing data between tools and attempting to connect disparate systems results in inefficiency and inaccuracy for the industry. Sighten was built to consolidate all financial and solar-related calculations in a single software platform. It significantly improves upon the accuracy of these calculations and exposes sophisticated new analysis tools resulting in a rigorous, efficient and cost-effective toolset for scaling residential solar. Widely deploying a platform like Sighten’s significantly and immediately impacts the residential solar space in several important ways: 1) standardizing and improving the quality of all quantitative calculations involved in the residential financing process, most notably project finance, system production and reporting calculations; 2) representing a true step change in terms of reporting and analysis capabilities by maintaining more accurate data and exposing sophisticated tools around simulation, tranching, and financial reporting, among others, to all stakeholders in the space; 3) allowing a broader group of developers/installers/finance companies to access the capital markets by providing an out-of-the-box toolset that handles the execution of running investor capital through a

  10. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

    DEFF Research Database (Denmark)

    King, Zachary A.; Lu, Justin; Dräger, Andreas

    2016-01-01

    Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repo...

  11. Integrative platform based on the mechatronics model for educational technologies focused on competence

    Science.gov (United States)

    Vlaşin, I.; Greta, S.; Dache, L.; Mătieş, V.

    2016-08-01

    Mechatronics is a model of transdisciplinary integration, entirely functional, with remarkable results for mankind. The incredible progress that the global economy has taken in the last decades is based on this new approach, the integrative type, which is present at the foundation of mechatronics. This kind of integrative approach is necessary for building a quality education focused on competence. The requirements from the social and economic environment, the needs of the young people who prepare themselves for an active life and the offers of the education providers are still not too interconnected to offer a satisfying education. This is the reason why the efforts to balance the demand, the needs and the offer are essential to ensure a better integration of students into society. Using a transcultural perspective, we can achieve a constructive approach. The education providers, together with the socio-economic environment, establish a clear structure of competence in multiple domains and of the instruments which can assure it. The scientific demarche, in the spirit of this paper approach the, answers the natural questions from the educational process: „Why, How and What do I learn?”.

  12. Integrating Global Learning into a Psychology Course Using an Online Platform

    Science.gov (United States)

    Forden, Carie L.; Carrillo, Amy M.

    2014-01-01

    There is a demand for the integration of global learning/diversity across the curriculum. A series of cross-cultural assignments was created to facilitate global learning in two social psychology classes, one in Egypt, and one in the USA. In these assignments, students collected data and applied course concepts to real-life problems, then…

  13. Perfusion-based three dimensional (3D) tissue engineering platform with integrated bioimpedance sensing

    DEFF Research Database (Denmark)

    Muhammad, Haseena Bashir; Canali, Chiara; Heiskanen, Arto

    2014-01-01

    We present an 8-channel bioreactor array with integrated bioimpedance sensors, which enables perfusion culture of cells seeded onto porous 3D scaffolds. Results show the capability of the system for monitoring cell proliferation within the scaffolds through a culture period of 19 days....

  14. Integrated freight network model : a GIS-based platform for transportation analyses.

    Science.gov (United States)

    2015-01-01

    The models currently used to examine the behavior transportation systems are usually mode-specific. That is, they focus on a single mode (i.e. railways, highways, or waterways). The lack of : integration limits the usefulness of models to analyze the...

  15. A Sol-gel Integrated Dual-readout Microarray Platform for Quantification and Identification of Prostate-specific Antigen.

    Science.gov (United States)

    Lee, SangWook; Lee, Jong Hyun; Kwon, Hyuck Gi; Laurell, Thomas; Jeong, Ok Chan; Kim, Soyoun

    2018-01-01

    Here, we report a sol-gel integrated affinity microarray for on-chip matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) that enables capture and identification of prostate?specific antigen (PSA) in samples. An anti-PSA antibody (H117) was mixed with a sol?gel, and the mixture was spotted onto a porous silicon (pSi) surface without additional surface modifications. The antibody easily penetrates the sol-gel macropore fluidic network structure, making possible high affinities. To assess the capture affinity of the platform, we performed a direct assay using fluorescein isothiocyanate-labeled PSA. Pure PSA was subjected to on-chip MALDI-TOF-MS analysis, yielding three clear mass peptide peaks (m/z = 1272, 1407, and 1872). The sol-gel microarray platform enables dual readout of PSA both fluorometric and MALDI-TOF MS analysis in biological samples. Here we report a useful method for a means for discovery of biomarkers in complex body fluids.

  16. Electro pneumatic trainer embedded with programmable integrated circuit (PIC) microcontroller and graphical user interface platform for aviation industries training purposes

    Science.gov (United States)

    Burhan, I.; Azman, A. A.; Othman, R.

    2016-10-01

    An electro pneumatic trainer embedded with programmable integrated circuit (PIC) microcontroller and Visual Basic (VB) platform is fabricated as a supporting tool to existing teaching and learning process, and to achieve the objectives and learning outcomes towards enhancing the student's knowledge and hands-on skill, especially in electro pneumatic devices. The existing learning process for electro pneumatic courses conducted in the classroom does not emphasize on simulation and complex practical aspects. VB is used as the platform for graphical user interface (GUI) while PIC as the interface circuit between the GUI and hardware of electro pneumatic apparatus. Fabrication of electro pneumatic trainer interfacing between PIC and VB has been designed and improved by involving multiple types of electro pneumatic apparatus such as linear drive, air motor, semi rotary motor, double acting cylinder and single acting cylinder. Newly fabricated electro pneumatic trainer microcontroller interface can be programmed and re-programmed for numerous combination of tasks. Based on the survey to 175 student participants, 97% of the respondents agreed that the newly fabricated trainer is user friendly, safe and attractive, and 96.8% of the respondents strongly agreed that there is improvement in knowledge development and also hands-on skill in their learning process. Furthermore, the Lab Practical Evaluation record has indicated that the respondents have improved their academic performance (hands-on skills) by an average of 23.5%.

  17. SenSyF Experience on Integration of EO Services in a Generic, Cloud-Based EO Exploitation Platform

    Science.gov (United States)

    Almeida, Nuno; Catarino, Nuno; Gutierrez, Antonio; Grosso, Nuno; Andrade, Joao; Caumont, Herve; Goncalves, Pedro; Villa, Guillermo; Mangin, Antoine; Serra, Romain; Johnsen, Harald; Grydeland, Tom; Emsley, Stephen; Jauch, Eduardo; Moreno, Jose; Ruiz, Antonio

    2016-08-01

    SenSyF is a cloud-based data processing framework for EO- based services. It has been pioneer in addressing Big Data issues from the Earth Observation point of view, and is a precursor of several of the technologies and methodologies that will be deployed in ESA's Thematic Exploitation Platforms and other related systems.The SenSyF system focuses on developing fully automated data management, together with access to a processing and exploitation framework, including Earth Observation specific tools. SenSyF is both a development and validation platform for data intensive applications using Earth Observation data. With SenSyF, scientific, institutional or commercial institutions developing EO- based applications and services can take advantage of distributed computational and storage resources, tailored for applications dependent on big Earth Observation data, and without resorting to deep infrastructure and technological investments.This paper describes the integration process and the experience gathered from different EO Service providers during the project.

  18. Development of a Graphical Tool to integrate the Prometheus AEOlus methodology and Jason Platform

    Directory of Open Access Journals (Sweden)

    Rafhael CUNHA

    2017-07-01

    Full Text Available Software Engineering (SE is an area that intends to build high-quality software in a systematic way. However, traditional software engineering techniques and methods do not support the demand for developing Multiagent Systems (MAS. Therefore a new subarea has been studied, called Agent Oriented Software Engineering (AOSE. The AOSE area proposes solutions to issues related to the development of agent oriented systems. There is still no standardization in this subarea, resulting in several methodologies. Another issue of this subarea is that there are very few tools that are able to automatically generate code. In this work we propose a tool to support the Prometheus AEOlus Methodology because it provides modelling artifacts to all MAS dimensions: agents, environment, interaction, and organization. The tool supports all Prometheus AEOlus artifacts and can automatically generated code to the agent and interaction dimensions in the AgentSpeak Language, which is the language used in the Jason Platform. We have done some validations with the proposed tool and a case study is presented.

  19. Gold Nanocages for Biomedical Applications**

    OpenAIRE

    Skrabalak, Sara E.; Chen, Jingyi; Au, Leslie; Lu, Xianmao; Li, Xingde; Xia, Younan

    2007-01-01

    Nanostructured materials provide a promising platform for early cancer detection and treatment. Here we highlight recent advances in the synthesis and use of Au nanocages for such biomedical applications. Gold nanocages represent a novel class of nanostructures, which can be prepared via a remarkably simple route based on the galvanic replacement reaction between Ag nanocubes and HAuCl4. The Au nanocages have a tunable surface plasmon resonance peak that extends into the near-infrared, where ...

  20. Performance Tuning of Fock Matrix and Two-Electron Integral Calculations for NWChem on Leading HPC Platforms

    Energy Technology Data Exchange (ETDEWEB)

    Shan, Hongzhan; Austin, Brian M.; De Jong, Wibe A.; Oliker, Leonid; Wright, Nicholas J.; Apra, Edoardo

    2014-10-01

    Attaining performance in the evaluation of two-electron repulsion integrals and constructing the Fock matrix is of considerable importance to the computational chemistry community. Due to its numerical complexity improving the performance behavior across a variety of leading supercomputing platforms is an increasing challenge due to the significant diversity in high-performance computing architectures. In this paper, we present our successful tuning methodology for these important numerical methods on the Cray XE6, the Cray XC30, the IBM BG/Q, as well as the Intel Xeon Phi. Our optimization schemes leverage key architectural features including vectorization and simultaneous multithreading, and results in speedups of up to 2.5x compared with the original implementation.

  1. Human health impacts for renewable energy scenarios from the EnerGEO Platform of Integrated Assessment (PIA)

    International Nuclear Information System (INIS)

    Lefevre, Mireille; Gschwind, Benoit; Blanc, Isabelle; Ranchin, Thierry; Cofala, Janusz; Fuss, Sabine

    2013-01-01

    This article reports impact results from running the EnerGEO Platform of Integrated Assessment (PIA) related to human health for different scenarios in Europe. The scenarios were prepared within the EnerGEO project. The idea of this European project is to determine how low carbon scenarios, and in particular scenarios with a high share of renewable energy, affect concentrations of air pollutants and as a consequence affect human health. PM 2.5 concentrations were estimated with the IIASA Greenhouse Gas and Air Pollution Interactions and Synergies (GAINS) model on a time horizon up to the year 2050 for different scenarios. We analyse here the estimation of the Loss of Life Expectancy due to PM 2.5 concentrations for the Baseline scenario taken as a reference and the Maximum renewable power scenario. (orig.)

  2. INTER-INTEGRATED CIRCUIT (I2C SEBAGAI SISTEM KOMUNIKASI MULTI-MIKROKONTROLER MENGGUNAKAN PLATFORM ARDUINO DAN MATLAB

    Directory of Open Access Journals (Sweden)

    I Nyoman Kusuma Wardana

    2016-06-01

    Full Text Available Pada aplikasi yang menggunakan mikrokontroler sebagai perangkat utama, pengguna sering dihadapkan pada masalah kurangnya jumlah pin yang tersedia pada suatu mikrokontoler. Terdapat dua alternatif yang dapat dilakukan ketika penggunaan pin menjadi masalah yang krusial, yaitu dengan mengganti jenis mikrokontroler atau menggunakan lebih dari satu buah mikrokontroler (multi-mikrokontroler. Kedua alternatif ini memiliki keunggulan dan kelemahannya masing-masing. Pada penelitian ini, penggunaan protokol Inter-integrated Circuit (I2C akan diterapkan untuk sistem multi-mikrokontroler dan multi-sensor menggunakan Platform Arduino yang terkontrol MATLAB. Sebuah Master dan dua buah slave akan diuji pada penelitian ini. Master dan Slave akan sepenuhnya dikontrol menggunakan MATLAB. Kedua slave akan ditanamkan program Arduino, sedangkan Master akan menggunakan program MATLAB. Hasil dari penelitian ini menunjukkan bahwa kedua Slave dapat dikontrol dengan baik, baik membaca sensor yang terpasang maupun mengontrol LED. Sistem komunikasi secara I2C telah terbangun dengan baik.

  3. The Western States Water Mission: A Hyper-Resolution Hydrological Model and Data Integration Platform for the Western United States

    Science.gov (United States)

    Famiglietti, J. S.; David, C. H.; Reager, J. T., II; Oaida, C.; Stampoulis, D.; Levoe, S.; Liu, P. W.; Trangsrud, A.; Basilio, R. R.; Allen, G. H.; Crichton, D. J.; Emery, C. M.; Farr, T.; Granger, S. L.; Hobbs, J.; Malhotra, S.; Osterman, G. B.; Rueckert, M.; Turmon, M.

    2017-12-01

    The Western States Water Mission (WSWM) is a high-resolution (3 km2), hydrological model and data integration platform under development at the Jet Propulsion Laboratory for the last 2 years. Distinctive features of the WSWM are its explicit representations of river networks and deep groundwater, an emphasis on uncertainty quantification, a major visualization and data distribution effort, and its focus on multivariate data assimilation, including GRACE/FO, SMAP, SWOT and MODSCAG fractional snow covered area. Importantly, the WSWM is actively managed as a flight project, i.e. with the rigor of a satellite mission. In this presentation we give an overview of the WSWM, including past accomplishments status, and future plans. In particular, results from recent 30-year simulations with GRACE and MODSCAG assimilation will be presented.

  4. SIM-DSP: A DSP-Enhanced CAD Platform for Signal Integrity Macromodeling and Simulation

    Directory of Open Access Journals (Sweden)

    Chi-Un Lei

    2014-12-01

    Full Text Available Macromodeling-Simulation process for signal integrity verifications has become necessary for the high speed circuit system design. This paper aims to introduce a “VLSI Signal Integrity Macromodeling and Simulation via Digital Signal Processing Techniques” framework (known as SIM-DSP framework, which applies digital signal processing techniques to facilitate the SI verification process in the pre-layout design phase. Core identification modules and peripheral (pre-/post-processing modules have been developed and assembled to form a verification flow. In particular, a single-step discrete cosine transform truncation (DCTT module has been developed for modeling-simulation process. In DCTT, the response modeling problem is classified as a signal compression problem, wherein the system response can be represented by a truncated set of non-pole based DCT bases, and error can be analyzed through Parseval’s theorem. Practical examples are given to show the applicability of our proposed framework.

  5. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

    International Nuclear Information System (INIS)

    Mungall, Christopher J.; McMurry, Julie A.; Köhler, Sebastian; Balhoff, James P.; Borromeo, Charles

    2016-01-01

    The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Nonhuman organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype-phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.

  6. Compliant heterogeneous assemblies of micro-VCSELs as a new materials platform for integrated optoelectronics

    Science.gov (United States)

    Kang, Dongseok; Lee, Sung-Min; Kwong, Anthony; Yoon, Jongseung

    2015-03-01

    Despite many unique advantages, vertical cavity surface emitting lasers (VCSELs) have been available mostly on rigid, planar wafers over restricted areas, thereby limiting their usage for applications that can benefit from large-scale, programmable assemblies, hybrid integration with dissimilar materials and devices, or mechanically flexible constructions. Here, materials design and fabrication strategies that address these limitations of conventional VCSELs are presented. Specialized design of epitaxial materials and etching processes, together with printing-based deterministic assemblies and substrate thermal engineering, enabled defect-free release of microscale VCSELs and their device- and circuit-level implementation on non-native, flexible substrates with performance comparable to devices on the growth substrate.

  7. LEARNING TOOLS INTEROPERABILITY – A NEW STANDARD FOR INTEGRATION OF DISTANCE LEARNING PLATFORMS

    Directory of Open Access Journals (Sweden)

    Oleksandr A. Shcherbyna

    2015-06-01

    Full Text Available For information technology in education there is always an issue of re-usage of electronic educational resources, their transferring possibility from one virtual learning environment to another. Previously, standardized sets of files were used to serve this purpose, for example, SCORM-packages. In this article the new standard Learning Tools Interoperability (LTI is reviewed, which allows users from one environment to access resources from another environment. This makes it possible to integrate them into a single distributed learning environment that is created and shared. The article gives examples of the practical use of standard LTI in Moodle learning management system using External tool and LTI provider plugins.

  8. Analysis of photonic spot profile converter and bridge structure on SOI platform for horizontal and vertical integration

    Science.gov (United States)

    Majumder, Saikat; Jha, Amit Kr.; Biswas, Aishik; Banerjee, Debasmita; Ganguly, Dipankar; Chakraborty, Rajib

    2017-08-01

    Horizontal spot size converter required for horizontal light coupling and vertical bridge structure required for vertical integration are designed on high index contrast SOI platform in order to form more compact integrated photonic circuits. Both the structures are based on the concept of multimode interference. The spot size converter can be realized by successive integration of multimode interference structures with reducing dimension on horizontal plane, whereas the optical bridge structure consists of a number of vertical multimode interference structure connected by single mode sections. The spot size converter can be modified to a spot profile converter when the final single mode waveguide is replaced by a slot waveguide. Analysis have shown that by using three multimode sections in a spot size converter, an Gaussian input having spot diameter of 2.51 μm can be converted to a spot diameter of 0.25 μm. If the output single mode section is replaced by a slot waveguide, this input profile can be converted to a flat top profile of width 50 nm. Similarly, vertical displacement of 8μm is possible by using a combination of two multimode sections and three single mode sections in the vertical bridge structure. The analyses of these two structures are carried out for both TE and TM modes at 1550 nm wavelength using the semi analytical matrix method which is simple and fast in computation time and memory. This work shows that the matrix method is equally applicable for analysis of horizontally as well as vertically integrated photonic circuit.

  9. Experiences from the formal specification of the integration platform and the synthesis of SDT with the software bus

    International Nuclear Information System (INIS)

    Thunem, Harald; Mohn, Peter; Sandmark, Haakon; Stoelen, Ketil

    1999-04-01

    The three year programme 1997-1999 for the OECD Halden Reactor Project (HRP) identifies the need to gain experience from applying formal techniques in real-life system developments. This motivated the initiation of the HRP research activity Integration of Formal Specification in the Development of HAMMLAB 2000 (INT-FS). The principal objective was to experiment with formal techniques in system developments at the HRP; in particular, system developments connected to HAMMLAB 2000 - the computerised laboratory for man-machine-interaction experiments currently under construction. It was hoped that this experimentation with formal techniques should result in a better understanding of how such techniques should be utilised in a more industrial setting. To obtain more knowledge with respect to the practical effects and consequences of an increased level of formalization was another objective. This report summarises experiences, results and conclusions from a pre-study addressing INT-FS related issues connected to the development of the HAMMLAB 2000 Integration Platform (IP). The report starts by giving a brief overview of the IP. Then it describes and summarises experiences from the formalization of a top-level requirements specification for the IP. Finally, it discusses various approaches for the integration of applications generated automatically through the CASE-tool SDT and the Software Bus on which the communication within HAMMLAB 2000 will be based. The report concludes that the selected formalisms and tools are well-suited to describe IP-like systems. The report also concludes that the integration of SDT applications with the Software Bus will not be a major obstacle, and finally that a monitoring component for the IP is well-suited for development within INT-FS (author) (ml)

  10. Development of integrated platform based on chalcogenides for sensing applications in the mid-infrared

    Science.gov (United States)

    Gutierrez-Arroyo, Aldo; Bodiou, Loïc.; Lemaitre, Jonathan; Baudet, Emeline; Baillieul, Marion; Hardy, Isabelle; Caillaud, Celine; Colas, Florent; Boukerma, Kada; Rinnert, Emmanuel; Michel, Karine; Bureau, Bruno; Nazabal, Virginie; Charrier, Joël.

    2018-03-01

    Mid-Infrared (mid-IR) spectral range, spanning from 2 μm to 20 μm, is ideal for chemical sensing using spectroscopy thanks to the presence of vibrational absorption bands of many liquid and gas substances in this wavelength range. Indeed, mid-IR spectroscopy allows simultaneous qualitative and quantitative analysis by, respectively, identifying molecules from their spectral signature and relating the concentrations of different chemical agents to their absorption coefficient according to Beer-Lambert law. In the last years, photonic integrated sensors based on mid-IR spectroscopy have emerged as a cheap, accurate, and compact solution that would enable continuous real-time on-site diagnostics and monitoring of molecular species without the need to collect samples for off-site measurements. Here, we report the design, processing and characterization of a photonic integrated transducer based on selenide ridge waveguides. Evanescent wave detection of chemical substances in liquid phase (isopropyl alcohol, C3H8O, and acetic acid, C2H4O2, both dissolved in cyclohexane) is presented using their absorption at a wavelength of 7.7 μm.

  11. Integrated Affinity Biosensing Platforms on Screen-Printed Electrodes Electrografted with Diazonium Salts

    Directory of Open Access Journals (Sweden)

    Paloma Yáñez-Sedeño

    2018-02-01

    Full Text Available Adequate selection of the electrode surface and the strategies for its modification to enable subsequent immobilization of biomolecules and/or nanomaterials integration play a major role in the performance of electrochemical affinity biosensors. Because of the simplicity, rapidity and versatility, electrografting using diazonium salt reduction is among the most currently used functionalization methods to provide the attachment of an organic layer to a conductive substrate. This particular chemistry has demonstrated to be a powerful tool to covalently immobilize in a stable and reproducible way a wide range of biomolecules or nanomaterials onto different electrode surfaces. Considering the great progress and interesting features arisen in the last years, this paper outlines the potential of diazonium chemistry to prepare single or multianalyte electrochemical affinity biosensors on screen-printed electrodes (SPEs and points out the existing challenges and future directions in this field.

  12. Integrated Affinity Biosensing Platforms on Screen-Printed Electrodes Electrografted with Diazonium Salts.

    Science.gov (United States)

    Yáñez-Sedeño, Paloma; Campuzano, Susana; Pingarrón, José M

    2018-02-24

    Adequate selection of the electrode surface and the strategies for its modification to enable subsequent immobilization of biomolecules and/or nanomaterials integration play a major role in the performance of electrochemical affinity biosensors. Because of the simplicity, rapidity and versatility, electrografting using diazonium salt reduction is among the most currently used functionalization methods to provide the attachment of an organic layer to a conductive substrate. This particular chemistry has demonstrated to be a powerful tool to covalently immobilize in a stable and reproducible way a wide range of biomolecules or nanomaterials onto different electrode surfaces. Considering the great progress and interesting features arisen in the last years, this paper outlines the potential of diazonium chemistry to prepare single or multianalyte electrochemical affinity biosensors on screen-printed electrodes (SPEs) and points out the existing challenges and future directions in this field.

  13. Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells.

    Science.gov (United States)

    Angelici, Bartolomeo; Mailand, Erik; Haefliger, Benjamin; Benenson, Yaakov

    2016-08-30

    One of the goals of synthetic biology is to develop programmable artificial gene networks that can transduce multiple endogenous molecular cues to precisely control cell behavior. Realizing this vision requires interfacing natural molecular inputs with synthetic components that generate functional molecular outputs. Interfacing synthetic circuits with endogenous mammalian transcription factors has been particularly difficult. Here, we describe a systematic approach that enables integration and transduction of multiple mammalian transcription factor inputs by a synthetic network. The approach is facilitated by a proportional amplifier sensor based on synergistic positive autoregulation. The circuits efficiently transduce endogenous transcription factor levels into RNAi, transcriptional transactivation, and site-specific recombination. They also enable AND logic between pairs of arbitrary transcription factors. The results establish a framework for developing synthetic gene networks that interface with cellular processes through transcriptional regulators. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. DNA - An integrated open-source optimization platform for thermo-fluid systems

    DEFF Research Database (Denmark)

    Pierobon, Leonardo; Wronski, Jorrit; Elmegaard, Brian

    2014-01-01

    This paper presents developments and new features added to the simulation tool Dynamic Network Analysis. This open-source software is the result of ongoing development at the Department of Mechanical Engineering, Technical University of Denmark since 1988. Ever since, it has been employed to model...... to extend the capabilities of the software, while at the same time decreasing computational time. Dynamic Network Analysis can now solve non-convex optimization problems by virtue of the fully-embedded genetic algorithm. Moreover, the thermophysical fluid property library has been extended with more than...... 110 fluids by interfacing CoolProp, a high-accuracy open-source property package for pure and pseudo-pure fluids, as well as humid air. Furthermore, the use as time integrator for other tools is demonstrated. The new features are unveiled in two case studies. The first example covers the optimization...

  15. MOVICLOUD: Agent-Based 3D Platform for the Labor Integration of Disabled People

    Directory of Open Access Journals (Sweden)

    Alberto L. Barriuso

    2018-02-01

    Full Text Available Agent-Based Social Simulation (ABSS, used in combination with three-dimensional representation, makes it possible to do near-reality modeling and visualizations of changing and complex environments. In this paper, we describe the design and implementation of a tool that integrates these two techniques. The purpose of this tool is to assist in creating a work environment that is adapted to the needs of people with disabilities. The tool measures the degree of accessibility in the place of work and identifies the architectural barriers of the environment by considering the activities carried out by workers. Thus, thanks to the use of novel mechanisms and simulation techniques more people with disabilities will have the opportunity to work and feel comfortable in the environment. To validate the developed tool, a case study was performed in a real environment.

  16. Discussion on Manufacturing and Services Integration Based on E-Commerce Platform

    Directory of Open Access Journals (Sweden)

    Li Jinfa

    2017-01-01

    Full Text Available The integration of manufacturing and services is the key to adapt to the inevitable requirement of the revolution of the development of a new round of mobile Internet industry. They are also the key and trend of the next period to enhance the quality and efficiency of Chinese’s manufacturing industry to release potential services development fully, and cultivate new economic growth point.Meanwhile it makes it more effective than before.The enterprises can publicize their own values as well as collect and deal with consumer feedback of the product experience more effectively.And then,it can grasp the market trends and adapt to developping world more quickly.

  17. BioPepDB: an integrated data platform for food-derived bioactive peptides.

    Science.gov (United States)

    Li, Qilin; Zhang, Chao; Chen, Hongjun; Xue, Jitong; Guo, Xiaolei; Liang, Ming; Chen, Ming

    2018-03-12

    Food-derived bioactive peptides play critical roles in regulating most biological processes and have considerable biological, medical and industrial importance. However, a large number of active peptides data, including sequence, function, source, commercial product information, references and other information are poorly integrated. BioPepDB is a searchable database of food-derived bioactive peptides and their related articles, including more than four thousand bioactive peptide entries. Moreover, BioPepDB provides modules of prediction and hydrolysis-simulation for discovering novel peptides. It can serve as a reference database to investigate the function of different bioactive peptides. BioPepDB is available at http://bis.zju.edu.cn/biopepdbr/ . The web page utilises Apache, PHP5 and MySQL to provide the user interface for accessing the database and predict novel peptides. The database itself is operated on a specialised server.

  18. Integrated reconfigurable multiple-input–multiple-output antenna system with an ultra-wideband sensing antenna for cognitive radio platforms

    KAUST Repository

    Hussain, Rifaqat

    2015-06-18

    © The Institution of Engineering and Technology 2015. A compact, novel multi-mode, multi-band frequency reconfigurable multiple-input-multiple-output (MIMO) antenna system, integrated with ultra-wideband (UWB) sensing antenna, is presented. The developed model can be used as a complete antenna platform for cognitive radio applications. The antenna system is developed on a single substrate area of dimensions 65 × 120 mm2. The proposed sensing antenna is used to cover a wide range of frequency bands from 710 to 3600 MHz. The frequency reconfigurable dual-element MIMO antenna is integrated with P-type, intrinsic, N-type (PIN) diodes for frequency agility. Different modes of selection are used for the MIMO antenna system reconfigurability to support different wireless system standards. The proposed MIMO antenna configuration is used to cover various frequency bands from 755 to 3450 MHz. The complete system comprising the multi-band reconfigurable MIMO antennas and UWB sensing antenna for cognitive radio applications is proposed with a compact form factor.

  19. Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications.

    Science.gov (United States)

    Hughes, Stephen R; Butt, Tauseef R; Bartolett, Scott; Riedmuller, Steven B; Farrelly, Philip

    2011-08-01

    The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. High-throughput integrated robotic molecular biology platforms that have the capacity to rapidly clone and express heterologous gene open reading frames in bacteria and yeast and to screen large numbers of expressed proteins for optimized function are an important technology for improving microbial strains for biofuel production. The process involves the production of full-length complementary DNA libraries as a source of plasmid-based clones to express the desired proteins in active form for determination of their functions. Proteins that were identified by high-throughput screening as having desired characteristics are overexpressed in microbes to enable them to perform functions that will allow more cost-effective and sustainable production of biofuels. Because the plasmid libraries are composed of several thousand unique genes, automation of the process is essential. This review describes the design and implementation of an automated integrated programmable robotic workcell capable of producing complementary DNA libraries, colony picking, isolating plasmid DNA, transforming yeast and bacteria, expressing protein, and performing appropriate functional assays. These operations will allow tailoring microbial strains to use renewable feedstocks for production of biofuels, bioderived chemicals, fertilizers, and other coproducts for profitable and sustainable biorefineries. Published by Elsevier Inc.

  20. PopHR: a knowledge-based platform to support integration, analysis, and visualization of population health data.

    Science.gov (United States)

    Shaban-Nejad, Arash; Lavigne, Maxime; Okhmatovskaia, Anya; Buckeridge, David L

    2017-01-01

    Population health decision makers must consider complex relationships between multiple concepts measured with differential accuracy from heterogeneous data sources. Population health information systems are currently limited in their ability to integrate data and present a coherent portrait of population health. Consequentially, these systems can provide only basic support for decision makers. The Population Health Record (PopHR) is a semantic web application that automates the integration and extraction of massive amounts of heterogeneous data from multiple distributed sources (e.g., administrative data, clinical records, and survey responses) to support the measurement and monitoring of population health and health system performance for a defined population. The design of the PopHR draws on the theories of the determinants of health and evidence-based public health to harmonize and explicitly link information about a population with evidence about the epidemiology and control of chronic diseases. Organizing information in this manner and linking it explicitly to evidence is expected to improve decision making related to the planning, implementation, and evaluation of population health and health system interventions. In this paper, we describe the PopHR platform and discuss the architecture, design, key modules, and its implementation and use. © 2016 New York Academy of Sciences.

  1. Functional integrity of flexible n-channel metal–oxide–semiconductor field-effect transistors on a reversibly bistable platform

    Energy Technology Data Exchange (ETDEWEB)

    Alfaraj, Nasir; Hussain, Aftab M.; Torres Sevilla, Galo A.; Ghoneim, Mohamed T.; Rojas, Jhonathan P.; Hussain, Muhammad M., E-mail: MuhammadMustafa.Hussain@kaust.edu.sa [Integrated Nanotechnology Laboratory, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia); Aljedaani, Abdulrahman B. [High-Speed Fluids Imaging Laboratory, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia)

    2015-10-26

    Flexibility can bring a new dimension to state-of-the-art electronics, such as rollable displays and integrated circuit systems being transformed into more powerful resources. Flexible electronics are typically hosted on polymeric substrates. Such substrates can be bent and rolled up, but cannot be independently fixed at the rigid perpendicular position necessary to realize rollable display-integrated gadgets and electronics. A reversibly bistable material can assume two stable states in a reversible way: flexibly rolled state and independently unbent state. Such materials are used in cycling and biking safety wristbands and a variety of ankle bracelets for orthopedic healthcare. They are often wrapped around an object with high impulsive force loading. Here, we study the effects of cumulative impulsive force loading on thinned (25 μm) flexible silicon-based n-channel metal–oxide–semiconductor field-effect transistor devices housed on a reversibly bistable flexible platform. We found that the transistors have maintained their high performance level up to an accumulated 180 kN of impact force loading. The gate dielectric layers have maintained their reliability, which is evidenced by the low leakage current densities. Also, we observed low variation in the effective electron mobility values, which manifests that the device channels have maintained their carrier transport properties.

  2. Functional integrity of flexible n-channel metal–oxide–semiconductor field-effect transistors on a reversibly bistable platform

    International Nuclear Information System (INIS)

    Alfaraj, Nasir; Hussain, Aftab M.; Torres Sevilla, Galo A.; Ghoneim, Mohamed T.; Rojas, Jhonathan P.; Hussain, Muhammad M.; Aljedaani, Abdulrahman B.

    2015-01-01

    Flexibility can bring a new dimension to state-of-the-art electronics, such as rollable displays and integrated circuit systems being transformed into more powerful resources. Flexible electronics are typically hosted on polymeric substrates. Such substrates can be bent and rolled up, but cannot be independently fixed at the rigid perpendicular position necessary to realize rollable display-integrated gadgets and electronics. A reversibly bistable material can assume two stable states in a reversible way: flexibly rolled state and independently unbent state. Such materials are used in cycling and biking safety wristbands and a variety of ankle bracelets for orthopedic healthcare. They are often wrapped around an object with high impulsive force loading. Here, we study the effects of cumulative impulsive force loading on thinned (25 μm) flexible silicon-based n-channel metal–oxide–semiconductor field-effect transistor devices housed on a reversibly bistable flexible platform. We found that the transistors have maintained their high performance level up to an accumulated 180 kN of impact force loading. The gate dielectric layers have maintained their reliability, which is evidenced by the low leakage current densities. Also, we observed low variation in the effective electron mobility values, which manifests that the device channels have maintained their carrier transport properties

  3. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

    Science.gov (United States)

    Medina, Ignacio; Carbonell, José; Pulido, Luis; Madeira, Sara C.; Goetz, Stefan; Conesa, Ana; Tárraga, Joaquín; Pascual-Montano, Alberto; Nogales-Cadenas, Ruben; Santoyo, Javier; García, Francisco; Marbà, Martina; Montaner, David; Dopazo, Joaquín

    2010-01-01

    Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls and TDTs, and allows population stratification analysis and correction). All these genomic data analysis facilities are integrated and connected to multiple options for the functional interpretation of the experiments. Different methods of functional enrichment or gene set enrichment can be used to understand the functional basis of the experiment analyzed. Many sources of biological information, which include functional (GO, KEGG, Biocarta, Reactome, etc.), regulatory (Transfac, Jaspar, ORegAnno, miRNAs, etc.), text-mining or protein–protein interaction modules can be used for this purpose. Finally a tool for the de novo functional annotation of sequences has been included in the system. This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org. PMID:20478823

  4. Functional integrity of flexible n-channel metal–oxide–semiconductor field-effect transistors on a reversibly bistable platform

    KAUST Repository

    Alfaraj, Nasir; Hussain, Aftab M.; Torres Sevilla, Galo A.; Ghoneim, Mohamed T.; Rojas, Jhonathan Prieto; Aljedaani, Abdulrahman B.; Hussain, Muhammad Mustafa

    2015-01-01

    Flexibility can bring a new dimension to state-of-the-art electronics, such as rollable displays and integrated circuit systems being transformed into more powerful resources. Flexible electronics are typically hosted on polymeric substrates. Such substrates can be bent and rolled up, but cannot be independently fixed at the rigid perpendicular position necessary to realize rollable display-integrated gadgets and electronics. A reversibly bistable material can assume two stable states in a reversible way: flexibly rolled state and independently unbent state. Such materials are used in cycling and biking safety wristbands and a variety of ankle bracelets for orthopedic healthcare. They are often wrapped around an object with high impulsive force loading. Here, we study the effects of cumulative impulsive force loading on thinned (25 μm) flexible silicon-based n-channel metal–oxide–semiconductor field-effect transistor devices housed on a reversibly bistable flexible platform. We found that the transistors have maintained their high performance level up to an accumulated 180 kN of impact force loading. The gate dielectric layers have maintained their reliability, which is evidenced by the low leakage current densities. Also, we observed low variation in the effective electron mobility values, which manifests that the device channels have maintained their carrier transport properties.

  5. Functional integrity of flexible n-channel metal-oxide-semiconductor field-effect transistors on a reversibly bistable platform

    Science.gov (United States)

    Alfaraj, Nasir; Hussain, Aftab M.; Torres Sevilla, Galo A.; Ghoneim, Mohamed T.; Rojas, Jhonathan P.; Aljedaani, Abdulrahman B.; Hussain, Muhammad M.

    2015-10-01

    Flexibility can bring a new dimension to state-of-the-art electronics, such as rollable displays and integrated circuit systems being transformed into more powerful resources. Flexible electronics are typically hosted on polymeric substrates. Such substrates can be bent and rolled up, but cannot be independently fixed at the rigid perpendicular position necessary to realize rollable display-integrated gadgets and electronics. A reversibly bistable material can assume two stable states in a reversible way: flexibly rolled state and independently unbent state. Such materials are used in cycling and biking safety wristbands and a variety of ankle bracelets for orthopedic healthcare. They are often wrapped around an object with high impulsive force loading. Here, we study the effects of cumulative impulsive force loading on thinned (25 μm) flexible silicon-based n-channel metal-oxide-semiconductor field-effect transistor devices housed on a reversibly bistable flexible platform. We found that the transistors have maintained their high performance level up to an accumulated 180 kN of impact force loading. The gate dielectric layers have maintained their reliability, which is evidenced by the low leakage current densities. Also, we observed low variation in the effective electron mobility values, which manifests that the device channels have maintained their carrier transport properties.

  6. Quantitative photoacoustic integrating sphere (QPAIS platform for absorption coefficient and Grüneisen parameter measurements: Demonstration with human blood

    Directory of Open Access Journals (Sweden)

    Yolanda Villanueva-Palero

    2017-06-01

    Full Text Available Quantitative photoacoustic imaging in biomedicine relies on accurate measurements of relevant material properties of target absorbers. Here, we present a method for simultaneous measurements of the absorption coefficient and Grüneisen parameter of small volume of liquid scattering and absorbing media using a coupled-integrating sphere system which we refer to as quantitative photoacoustic integrating sphere (QPAIS platform. The derived equations do not require absolute magnitudes of optical energy and pressure values, only calibration of the setup using aqueous ink dilutions is necessary. As a demonstration, measurements with blood samples from various human donors are done at room and body temperatures using an incubator. Measured absorption coefficient values are consistent with known oxygen saturation dependence of blood absorption at 750 nm, whereas measured Grüneisen parameter values indicate variability among five different donors. An increasing Grüneisen parameter value with both hematocrit and temperature is observed. These observations are consistent with those reported in literature.

  7. Implementation and management of a biomedical observation dictionary in a large healthcare information system.

    Science.gov (United States)

    Vandenbussche, Pierre-Yves; Cormont, Sylvie; André, Christophe; Daniel, Christel; Delahousse, Jean; Charlet, Jean; Lepage, Eric

    2013-01-01

    This study shows the evolution of a biomedical observation dictionary within the Assistance Publique Hôpitaux Paris (AP-HP), the largest European university hospital group. The different steps are detailed as follows: the dictionary creation, the mapping to logical observation identifier names and codes (LOINC), the integration into a multiterminological management platform and, finally, the implementation in the health information system. AP-HP decided to create a biomedical observation dictionary named AnaBio, to map it to LOINC and to maintain the mapping. A management platform based on methods used for knowledge engineering has been put in place. It aims at integrating AnaBio within the health information system and improving both the quality and stability of the dictionary. This new management platform is now active in AP-HP. The AnaBio dictionary is shared by 120 laboratories and currently includes 50 000 codes. The mapping implementation to LOINC reaches 40% of the AnaBio entries and uses 26% of LOINC records. The results of our work validate the choice made to develop a local dictionary aligned with LOINC. This work constitutes a first step towards a wider use of the platform. The next step will support the entire biomedical production chain, from the clinician prescription, through laboratory tests tracking in the laboratory information system to the communication of results and the use for decision support and biomedical research. In addition, the increase in the mapping implementation to LOINC ensures the interoperability allowing communication with other international health institutions.

  8. Health Information Research Platform (HIReP)--an architecture pattern.

    Science.gov (United States)

    Schreiweis, Björn; Schneider, Gerd; Eichner, Theresia; Bergh, Björn; Heinze, Oliver

    2014-01-01

    Secondary use or single source is still far from routine in healthcare, although lots of data are available either structured or unstructured. As data are stored in multiple systems, using them for biomedical research is difficult. Clinical data warehouses already help overcoming this issue, but currently they are only used for certain parts of biomedical research. A comprehensive research platform based on a generic architecture pattern could increase the benefits of existing data warehouses for both patient care and research by meeting two objectives: serving as a so called single point-of-truth and acting as a mediator between them strengthening interaction and close collaboration. Another effect is to reduce boundaries for the implementation of data warehouses. Taking further settings into account the architecture of a clinical data warehouse supporting patient care and biomedical research needs to be integrated with biomaterial banks and other sources. This work provides a solution conceptualizing a comprehensive architecture pattern of a Health Information Research Platform (HIReP) derived from use cases of the patient care and biomedical research domain. It serves as single IT infrastructure providing solutions for any type of use case.

  9. Prioritizing research for integrated implementation of early childhood development and maternal, newborn, child and adolescent health and nutrition platforms.

    Science.gov (United States)

    Sharma, Renee; Gaffey, Michelle F; Alderman, Harold; Bassani, Diego G; Bogard, Kimber; Darmstadt, Gary L; Das, Jai K; de Graft-Johnson, Joseph E; Hamadani, Jena D; Horton, Susan; Huicho, Luis; Hussein, Julia; Lye, Stephen; Pérez-Escamilla, Rafael; Proulx, Kerrie; Marfo, Kofi; Mathews-Hanna, Vanessa; Mclean, Mireille S; Rahman, Atif; Silver, Karlee L; Singla, Daisy R; Webb, Patrick; Bhutta, Zulfiqar A

    2017-06-01

    Existing health and nutrition services present potential platforms for scaling up delivery of early childhood development (ECD) interventions within sensitive windows across the life course, especially in the first 1000 days from conception to age 2 years. However, there is insufficient knowledge on how to optimize implementation for such strategies in an integrated manner. In light of this knowledge gap, we aimed to systematically identify a set of integrated implementation research priorities for health, nutrition and early child development within the 2015 to 2030 timeframe of the Sustainable Development Goals (SDGs). We applied the Child Health and Nutrition Research Initiative method, and consulted a diverse group of global health experts to develop and score 57 research questions against five criteria: answerability, effectiveness, deliverability, impact, and effect on equity. These questions were ranked using a research priority score, and the average expert agreement score was calculated for each question. The research priority scores ranged from 61.01 to 93.52, with a median of 82.87. The average expert agreement scores ranged from 0.50 to 0.90, with a median of 0.75. The top-ranked research question were: i) "How can interventions and packages to reduce neonatal mortality be expanded to include ECD and stimulation interventions?"; ii) "How does the integration of ECD and MNCAH&N interventions affect human resource requirements and capacity development in resource-poor settings?"; and iii) "How can integrated interventions be tailored to vulnerable refugee and migrant populations to protect against poor ECD and MNCAH&N outcomes?". Most highly-ranked research priorities varied across the life course and highlighted key aspects of scaling up coverage of integrated interventions in resource-limited settings, including: workforce and capacity development, cost-effectiveness and strategies to reduce financial barriers, and quality assessment of programs

  10. LORD: a phenotype-genotype semantically integrated biomedical data tool to support rare disease diagnosis coding in health information systems.

    Science.gov (United States)

    Choquet, Remy; Maaroufi, Meriem; Fonjallaz, Yannick; de Carrara, Albane; Vandenbussche, Pierre-Yves; Dhombres, Ferdinand; Landais, Paul

    Characterizing a rare disease diagnosis for a given patient is often made through expert's networks. It is a complex task that could evolve over time depending on the natural history of the disease and the evolution of the scientific knowledge. Most rare diseases have genetic causes and recent improvements of sequencing techniques contribute to the discovery of many new diseases every year. Diagnosis coding in the rare disease field requires data from multiple knowledge bases to be aggregated in order to offer the clinician a global information space from possible diagnosis to clinical signs (phenotypes) and known genetic mutations (genotype). Nowadays, the major barrier to the coding activity is the lack of consolidation of such information scattered in different thesaurus such as Orphanet, OMIM or HPO. The Linking Open data for Rare Diseases (LORD) web portal we developed stands as the first attempt to fill this gap by offering an integrated view of 8,400 rare diseases linked to more than 14,500 signs and 3,270 genes. The application provides a browsing feature to navigate through the relationships between diseases, signs and genes, and some Application Programming Interfaces to help its integration in health information systems in routine.

  11. Real Time Integration of Field Data Into a GIS Platform for the Management of Hydrological Emergencies

    Science.gov (United States)

    Mangiameli, M.; Mussumeci, G.

    2013-01-01

    A wide series of events requires immediate availability of information and field data to be provided to decision-makers. An example is the necessity of quickly transferring the information acquired from monitoring and alerting sensors or the data of the reconnaissance of damage after a disastrous event to an Emergency Operations Center. To this purpose, we developed an integrated GIS and WebGIS system to dynamically create and populate via Web a database with spatial features. In particular, this work concerns the gathering and transmission of spatial data and related information to the desktop GIS so that they can be displayed and analyzed in real time to characterize the operational scenario and to decide the rescue interventions. As basic software, we used only free and open source: QuantumGIS and Grass as Desktop GIS, Map Server with PMapper application for the Web-Gis functionality and PostGreSQL/PostGIS as Data Base Management System (DBMS). The approach has been designed, developed and successfully tested in the management of GIS-based navigation of an autonomous robot, both to map its trajectories and to assign optimal paths. This paper presents the application of our system to a simulated hydrological event that could interest the province of Catania, in Sicily. In particular, assuming that more teams draw up an inventory of the damage, we highlight the benefits of real-time transmission of the information collected from the field to headquarters.

  12. REAL TIME INTEGRATION OF FIELD DATA INTO A GIS PLATFORM FOR THE MANAGEMENT OF HYDROLOGICAL EMERGENCIES

    Directory of Open Access Journals (Sweden)

    M. Mangiameli

    2014-01-01

    Full Text Available A wide series of events requires immediate availability of information and field data to be provided to decision-makers. An example is the necessity of quickly transferring the information acquired from monitoring and alerting sensors or the data of the reconnaissance of damage after a disastrous event to an Emergency Operations Center. To this purpose, we developed an integrated GIS and WebGIS system to dynamically create and populate via Web a database with spatial features. In particular, this work concerns the gathering and transmission of spatial data and related information to the desktop GIS so that they can be displayed and analyzed in real time to characterize the operational scenario and to decide the rescue interventions. As basic software, we used only free and open source: QuantumGIS and Grass as Desktop GIS, Map Server with PMapper application for the Web-Gis functionality and PostGreSQL/PostGIS as Data Base Management System (DBMS. The approach has been designed, developed and successfully tested in the management of GIS-based navigation of an autonomous robot, both to map its trajectories and to assign optimal paths. This paper presents the application of our system to a simulated hydrological event that could interest the province of Catania, in Sicily. In particular, assuming that more teams draw up an inventory of the damage, we highlight the benefits of real-time transmission of the information collected from the field to headquarters.

  13. Evaluation of inlet sampling integrity on NSF/NCAR airborne platforms

    Science.gov (United States)

    Campos, T. L.; Stith, J. L.; Stephens, B. B.; Romashkin, P.

    2017-12-01

    An inlet test project was conducted during IDEAS-IV-GV (2013), to evaluate the sampling integrity of two inlet designs. Use of a single CO2 sensor provided a high precision detector and a large difference in the mean cabin and external concentrations (500-700 ppmv in the cabin). The original HIAPER Modular InLet (HIMIL) is comprised of a tapered flow straightening flow through `cigar' mounted to a strut. The cigar center sampling line sits 12" from the fuselage skin. An o-ring seals the feedthrough plate coupling sampling lines from the strut into the cigar. However, there is no seal to prevent air inside the strut from seeping out around the cigar body. A pressure-equalizing drain hole in the strut access panel; it was positioned at an approximate distance of 4" from the fuselage to ensure that air from any source that drained out of the strut was confined to a low release point. A second aft-facing inlet design was also evaluated. The sampling center line was moved farther from the fuselage at a height of 16". A similar approach was also applied to sampling locations on the C-130 in 2015. The results of these tests and recommendations for best practices will be presented.

  14. An ultrahigh-accuracy Miniature Dew Point Sensor based on an Integrated Photonics Platform

    Science.gov (United States)

    Tao, Jifang; Luo, Yu; Wang, Li; Cai, Hong; Sun, Tao; Song, Junfeng; Liu, Hui; Gu, Yuandong

    2016-07-01

    The dew point is the temperature at which vapour begins to condense out of the gaseous phase. The deterministic relationship between the dew point and humidity is the basis for the industry-standard “chilled-mirror” dew point hygrometers used for highly accurate humidity measurements, which are essential for a broad range of industrial and metrological applications. However, these instruments have several limitations, such as high cost, large size and slow response. In this report, we demonstrate a compact, integrated photonic dew point sensor (DPS) that features high accuracy, a small footprint, and fast response. The fundamental component of this DPS is a partially exposed photonic micro-ring resonator, which serves two functions simultaneously: 1) sensing the condensed water droplets via evanescent fields and 2) functioning as a highly accurate, in situ temperature sensor based on the thermo-optic effect (TOE). This device virtually eliminates most of the temperature-related errors that affect conventional “chilled-mirror” hygrometers. Moreover, this DPS outperforms conventional “chilled-mirror” hygrometers with respect to size, cost and response time, paving the way for on-chip dew point detection and extension to applications for which the conventional technology is unsuitable because of size, cost, and other constraints.

  15. An integrative multi-platform analysis for discovering biomarkers of osteosarcoma

    International Nuclear Information System (INIS)

    Li, Guodong; Zhang, Wenjuan; Zeng, Huazong; Chen, Lei; Wang, Wenjing; Liu, Jilong; Zhang, Zhiyu; Cai, Zhengdong

    2009-01-01

    SELDI-TOF-MS (Surface Enhanced Laser Desorption/Ionization-Time of Flight-Mass Spectrometry) has become an attractive approach for cancer biomarker discovery due to its ability to resolve low mass proteins and high-throughput capability. However, the analytes from mass spectrometry are described only by their mass-to-charge ratio (m/z) values without further identification and annotation. To discover potential biomarkers for early diagnosis of osteosarcoma, we designed an integrative workflow combining data sets from both SELDI-TOF-MS and gene microarray analysis. After extracting the information for potential biomarkers from SELDI data and microarray analysis, their associations were further inferred by link-test to identify biomarkers that could likely be used for diagnosis. Immuno-blot analysis was then performed to examine whether the expression of the putative biomarkers were indeed altered in serum from patients with osteosarcoma. Six differentially expressed protein peaks with strong statistical significances were detected by SELDI-TOF-MS. Four of the proteins were up-regulated and two of them were down-regulated. Microarray analysis showed that, compared with an osteoblastic cell line, the expression of 653 genes was changed more than 2 folds in three osteosarcoma cell lines. While expression of 310 genes was increased, expression of the other 343 genes was decreased. The two sets of biomarkers candidates were combined by the link-test statistics, indicating that 13 genes were potential biomarkers for early diagnosis of osteosarcoma. Among these genes, cytochrome c1 (CYC-1) was selected for further experimental validation. Link-test on datasets from both SELDI-TOF-MS and microarray high-throughput analysis can accelerate the identification of tumor biomarkers. The result confirmed that CYC-1 may be a promising biomarker for early diagnosis of osteosarcoma

  16. Telemedicine optoelectronic biomedical data processing system

    Science.gov (United States)

    Prosolovska, Vita V.

    2010-08-01

    The telemedicine optoelectronic biomedical data processing system is created to share medical information for the control of health rights and timely and rapid response to crisis. The system includes the main blocks: bioprocessor, analog-digital converter biomedical images, optoelectronic module for image processing, optoelectronic module for parallel recording and storage of biomedical imaging and matrix screen display of biomedical images. Rated temporal characteristics of the blocks defined by a particular triggering optoelectronic couple in analog-digital converters and time imaging for matrix screen. The element base for hardware implementation of the developed matrix screen is integrated optoelectronic couples produced by selective epitaxy.

  17. Development of an Integrated Process, Modeling and Simulation Platform for Performance-Based Design of Low-Energy and High IEQ Buildings

    Science.gov (United States)

    Chen, Yixing

    2013-01-01

    The objective of this study was to develop a "Virtual Design Studio (VDS)": a software platform for integrated, coordinated and optimized design of green building systems with low energy consumption, high indoor environmental quality (IEQ), and high level of sustainability. The VDS is intended to assist collaborating architects,…

  18. Bioinspired methodology for preparing magnetic responsive chitosan beads to be integrated in a tubular bioreactor for biomedical applications.

    Science.gov (United States)

    Song, Wenlong; Oliveira, Mariana B; Sher, Praveen; Gil, Sara; Nóbrega, J Miguel; Mano, João F

    2013-08-01

    Magnetic responsive chitosan beads were prepared using a methodology inspired by the rolling of water droplets over lotus leaves. Liquid precursors containing chitosan and magnetic microparticles were dispensed in the form of spherical droplets and crosslinked with genipin over synthetic superhydrophobic surfaces. Scanning electronic microscopy, histology and micro-computed tomography were employed to characterize the structure of the prepared composite beads and the inner distribution of the magnetic particles. Cellular metabolic activity tests showed that fibroblasts-like (L929 cell line) can adhere and proliferate on the prepared chitosan beads. We hypothesize that such spherical biomaterials could be integrated in a new concept of tubular bioreactor. The magnetic beads can be immobilized by an external magnetic field at specific positions and may be transported along the bioreactor by the drag of the culture medium flow. The system behavior was also studied through numerical modeling, which allowed to identify the relative importance of the main parameters, and to conclude that the distance between carrier beads plays a major role on their interaction with the culture medium and, consequently, on the overall system performance. In an up-scaled version of this bioreactor, the herein presented system may comprise different chambers in serial or parallel configurations. This constitutes a simple way of preparing magnetic responsive beads combined with a new design of bioreactor, which may find application in biomedicine and biotechnology, including in cell expansion for tissue engineering or for the production of therapeutic proteins to be used in cell therapies.

  19. Bioinspired methodology for preparing magnetic responsive chitosan beads to be integrated in a tubular bioreactor for biomedical applications

    International Nuclear Information System (INIS)

    Song, Wenlong; Oliveira, Mariana B; Sher, Praveen; Gil, Sara; Mano, João F; Nóbrega, J Miguel

    2013-01-01

    Magnetic responsive chitosan beads were prepared using a methodology inspired by the rolling of water droplets over lotus leaves. Liquid precursors containing chitosan and magnetic microparticles were dispensed in the form of spherical droplets and crosslinked with genipin over synthetic superhydrophobic surfaces. Scanning electronic microscopy, histology and micro-computed tomography were employed to characterize the structure of the prepared composite beads and the inner distribution of the magnetic particles. Cellular metabolic activity tests showed that fibroblasts-like (L929 cell line) can adhere and proliferate on the prepared chitosan beads. We hypothesize that such spherical biomaterials could be integrated in a new concept of tubular bioreactor. The magnetic beads can be immobilized by an external magnetic field at specific positions and may be transported along the bioreactor by the drag of the culture medium flow. The system behavior was also studied through numerical modeling, which allowed to identify the relative importance of the main parameters, and to conclude that the distance between carrier beads plays a major role on their interaction with the culture medium and, consequently, on the overall system performance. In an up-scaled version of this bioreactor, the herein presented system may comprise different chambers in serial or parallel configurations. This constitutes a simple way of preparing magnetic responsive beads combined with a new design of bioreactor, which may find application in biomedicine and biotechnology, including in cell expansion for tissue engineering or for the production of therapeutic proteins to be used in cell therapies. (paper)

  20. Biomedical engineering and nanotechnology

    International Nuclear Information System (INIS)

    Pawar, S.H.; Khyalappa, R.J.; Yakhmi, J.V.

    2009-01-01

    This book is predominantly a compilation of papers presented in the conference which is focused on the development in biomedical materials, biomedical devises and instrumentation, biomedical effects of electromagnetic radiation, electrotherapy, radiotherapy, biosensors, biotechnology, bioengineering, tissue engineering, clinical engineering and surgical planning, medical imaging, hospital system management, biomedical education, biomedical industry and society, bioinformatics, structured nanomaterial for biomedical application, nano-composites, nano-medicine, synthesis of nanomaterial, nano science and technology development. The papers presented herein contain the scientific substance to suffice the academic directivity of the researchers from the field of biomedicine, biomedical engineering, material science and nanotechnology. Papers relevant to INIS are indexed separately

  1. A Novel Scheme and Evaluations on a Long-Term and Continuous Biosensor Platform Integrated with a Dental Implant Fixture and Its Prosthetic Abutment.

    Science.gov (United States)

    Li, Yu-Jung; Lu, Chih-Cheng

    2015-09-25

    A miniature intra-oral dental implant system including a built-in biosensor device is proposed in this article. The dental implant system, or platform, is replaced over maxilla and allows relatively non-invasive procedures for a novel biosensing scheme for human blood analysis. Due to placement of the implant fixture, periodontal ligaments and the pulp structure, which are regarded as the main origin of pain, are thus removed, and long-term, continuous blood analysis and management through maxillary bone marrow becomes achievable through the dental implant platform. The new pathway of biological sensing is for the first time presented to realize an accurate and painless approach without injections. The dental implant system mainly consists of an implant fixture and a prosthetic abutment, a biosensor module, a bluetooth 4.0 wireless module and a dc button cell battery. The electrochemical biosensor possesses three electrodes, including working, reference and counter ones, which are arranged to pass through the titanium implant fixture below the biosensor module. The electrodes are exposed to the blood pool inside the maxillary bone marrow and perform oxidation/reduction reactions with the coating of biosensing enzyme. To prove the proposed platform, the immobilization process of glucose oxidase (GOD) enzyme and in vitro detections of glucose levels are successfully carried out, and proven sensitivity, linearity and repeatability of the glucose biosensor system are obtained. Moreover, a preliminary canine animal model adopting the new pathway shows significant consistency with the traditional method through dermal pricks for blood sugar detection. Despite the prospective results, further challenges in engineering implementation and clinical practices are addressed and discussed. In brief, the novel biosensing pathway and intra-oral biosensor platform may increasingly reveal their promising value and feasibilities in current bio-medical analysis, diagnosis, drug

  2. A Novel Scheme and Evaluations on a Long-Term and Continuous Biosensor Platform Integrated with a Dental Implant Fixture and Its Prosthetic Abutment

    Directory of Open Access Journals (Sweden)

    Yu-Jung Li

    2015-09-01

    Full Text Available A miniature intra-oral dental implant system including a built-in biosensor device is proposed in this article. The dental implant system, or platform, is replaced over maxilla and allows relatively non-invasive procedures for a novel biosensing scheme for human blood analysis. Due to placement of the implant fixture, periodontal ligaments and the pulp structure, which are regarded as the main origin of pain, are thus removed, and long-term, continuous blood analysis and management through maxillary bone marrow becomes achievable through the dental implant platform. The new pathway of biological sensing is for the first time presented to realize an accurate and painless approach without injections. The dental implant system mainly consists of an implant fixture and a prosthetic abutment, a biosensor module, a bluetooth 4.0 wireless module and a dc button cell battery. The electrochemical biosensor possesses three electrodes, including working, reference and counter ones, which are arranged to pass through the titanium implant fixture below the biosensor module. The electrodes are exposed to the blood pool inside the maxillary bone marrow and perform oxidation/reduction reactions with the coating of biosensing enzyme. To prove the proposed platform, the immobilization process of glucose oxidase (GOD enzyme and in vitro detections of glucose levels are successfully carried out, and proven sensitivity, linearity and repeatability of the glucose biosensor system are obtained. Moreover, a preliminary canine animal model adopting the new pathway shows significant consistency with the traditional method through dermal pricks for blood sugar detection. Despite the prospective results, further challenges in engineering implementation and clinical practices are addressed and discussed. In brief, the novel biosensing pathway and intra-oral biosensor platform may increasingly reveal their promising value and feasibilities in current bio-medical analysis

  3. Integration of the TNXYZ computer program inside the platform Salome; Integracion del programa de computo TNXYZ dentro de la plataforma Salome

    Energy Technology Data Exchange (ETDEWEB)

    Chaparro V, F. J.

    2014-07-01

    The present work shows the procedure carried out to integrate the code TNXYZ as a calculation tool at the graphical simulation platform Salome. The TNXYZ code propose a numerical solution of the neutron transport equation, in several groups of energy, steady-state and three-dimensional geometry. In order to discretized the variables of the transport equation, the code uses the method of discrete ordinates for the angular variable, and a nodal method for the spatial dependence. The Salome platform is a graphical environment designed for building, editing and simulating mechanical models mainly focused on the industry and unlike other software, in order to form a complete scheme of pre and post processing of information, to integrate and control an external source code. Before the integration the in the Salome platform TNXYZ code was upgraded. TNXYZ was programmed in the 90s using Fortran 77 compiler; for this reason the code was adapted to the characteristics of the current Fortran compilers; in addition, with the intention of extracting partial results over the process sequence, the original structure of the program underwent a modularization process, i.e. the main program was divided into sections where the code performs major operations. This procedure is controlled by the information module (YACS) on Salome platform, and it could be useful for a subsequent coupling with thermal-hydraulics codes. Finally, with the help of the Monte Carlo code Serpent several study cases were defined in order to check the process of integration; the verification process consisted in performing a comparison of the results obtained with the code executed as stand-alone and after modernized, integrated and controlled by the Salome platform. (Author)

  4. Development of an electronic claim system based on an integrated electronic health record platform to guarantee interoperability.

    Science.gov (United States)

    Kim, Hwa Sun; Cho, Hune; Lee, In Keun

    2011-06-01

    We design and develop an electronic claim system based on an integrated electronic health record (EHR) platform. This system is designed to be used for ambulatory care by office-based physicians in the United States. This is achieved by integrating various medical standard technologies for interoperability between heterogeneous information systems. The developed system serves as a simple clinical data repository, it automatically fills out the Centers for Medicare and Medicaid Services (CMS)-1500 form based on information regarding the patients and physicians' clinical activities. It supports electronic insurance claims by creating reimbursement charges. It also contains an HL7 interface engine to exchange clinical messages between heterogeneous devices. The system partially prevents physician malpractice by suggesting proper treatments according to patient diagnoses and supports physicians by easily preparing documents for reimbursement and submitting claim documents to insurance organizations electronically, without additional effort by the user. To show the usability of the developed system, we performed an experiment that compares the time spent filling out the CMS-1500 form directly and time required create electronic claim data using the developed system. From the experimental results, we conclude that the system could save considerable time for physicians in making claim documents. The developed system might be particularly useful for those who need a reimbursement-specialized EHR system, even though the proposed system does not completely satisfy all criteria requested by the CMS and Office of the National Coordinator for Health Information Technology (ONC). This is because the criteria are not sufficient but necessary condition for the implementation of EHR systems. The system will be upgraded continuously to implement the criteria and to offer more stable and transparent transmission of electronic claim data.

  5. The Qatar National Historic Environment Record: a Platform for the Development of a Fully-Integrated Cultural Heritage Management Application

    Science.gov (United States)

    Cuttler, R. T. H.; Tonner, T. W. W.; Al-Naimi, F. A.; Dingwall, L. M.; Al-Hemaidi, N.

    2013-07-01

    The development of the Qatar National Historic Environment Record (QNHER) by the Qatar Museums Authority and the University of Birmingham in 2008 was based on a customised, bilingual Access database and ArcGIS. While both platforms are stable and well supported, neither was designed for the documentation and retrieval of cultural heritage data. As a result it was decided to develop a custom application using Open Source code. The core module of this application is now completed and is orientated towards the storage and retrieval of geospatial heritage data for the curation of heritage assets. Based on MIDAS Heritage data standards and regionally relevant thesauri, it is a truly bilingual system. Significant attention has been paid to the user interface, which is userfriendly and intuitive. Based on a suite of web services and accessed through a web browser, the system makes full use of internet resources such as Google Maps and Bing Maps. The application avoids long term vendor ''tie-ins'' and as a fully integrated data management system, is now an important tool for both cultural resource managers and heritage researchers in Qatar.

  6. A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    2009-03-01

    Full Text Available Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning approximately 3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.

  7. Ensembles of indium phosphide nanowires: physical properties and functional devices integrated on non-single crystal platforms

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Nobuhiko P.; Lohn, Andrew; Onishi, Takehiro [University of California, Santa Cruz (United States). Baskin School of Engineering; NASA Ames Research Center, Nanostructured Energy Conversion Technology and Research (NECTAR), Advanced Studies Laboratories, Univ. of California Santa Cruz, Moffett Field, CA (United States); Mathai, Sagi; Li, Xuema; Straznicky, Joseph; Wang, Shih-Yuan; Williams, R.S. [Hewlett-Packard Laboratories, Information and Quantum Systems Laboratory, Palo Alto, CA (United States); Logeeswaran, V.J.; Islam, M.S. [University of California Davis, Electrical and Computer Engineering, Davis, CA (United States)

    2009-06-15

    A new route to grow an ensemble of indium phosphide single-crystal semiconductor nanowires is described. Unlike conventional epitaxial growth of single-crystal semiconductor films, the proposed route for growing semiconductor nanowires does not require a single-crystal semiconductor substrate. In the proposed route, instead of using single-crystal semiconductor substrates that are characterized by their long-range atomic ordering, a template layer that possesses short-range atomic ordering prepared on a non-single-crystal substrate is employed. On the template layer, epitaxial information associated with its short-range atomic ordering is available within an area that is comparable to that of a nanowire root. Thus the template layer locally provides epitaxial information required for the growth of semiconductor nanowires. In the particular demonstration described in this paper, hydrogenated silicon was used as a template layer for epitaxial growth of indium phosphide nanowires. The indium phosphide nanowires grown on the hydrogenerated silicon template layer were found to be single crystal and optically active. Simple photoconductors and pin-diodes were fabricated and tested with the view towards various optoelectronic device applications where group III-V compound semiconductors are functionally integrated onto non-single-crystal platforms. (orig.)

  8. The EnerGEO Platform of Integrated Assessment (PIA). Environmental assessment of scenarios as a web service

    International Nuclear Information System (INIS)

    Blanc, Isabelle; Gschwind, Benoit; Lefevre, Mireille

    2013-01-01

    With the International Energy Agency estimating that global energy demand will increase between 40 and 50 percent by 2030 (compared to 2003), scientists and policymakers are concerned about the sustainability of the current energy system and what environmental pressures might result from the development of future energy systems. EnerGEO is an ongoing FP7 Project (2009-2013) which assesses the current and future impact of energy use on the environment by linking environmental observation systems with the processes involved in exploiting energy resources. The idea of this European project is to determine how low carbon scenarios, and in particular scenarios with a high share of renewable electricity, affect emissions of air pollutants and greenhouse gases (GHG) and contribute to mitigation of negative energy system impacts on human health and ecosystems. A Platform of Integrated Assessment (PIA) has been elaborated to provide impact results for a selection of scenarios via a set of models (large-scale energy models, Life Cycle Assessment models,..). This PIA is currently available through a web service. The concept of the PIA is detailed and to illustrate its interest, a set of results is given with the use of the simulation mode of the European version of GAINS for a selection of scenarios. (orig.)

  9. Ensembles of indium phosphide nanowires: physical properties and functional devices integrated on non-single crystal platforms

    International Nuclear Information System (INIS)

    Kobayashi, Nobuhiko P.; Lohn, Andrew; Onishi, Takehiro; Mathai, Sagi; Li, Xuema; Straznicky, Joseph; Wang, Shih-Yuan; Williams, R.S.; Logeeswaran, V.J.; Islam, M.S.

    2009-01-01

    A new route to grow an ensemble of indium phosphide single-crystal semiconductor nanowires is described. Unlike conventional epitaxial growth of single-crystal semiconductor films, the proposed route for growing semiconductor nanowires does not require a single-crystal semiconductor substrate. In the proposed route, instead of using single-crystal semiconductor substrates that are characterized by their long-range atomic ordering, a template layer that possesses short-range atomic ordering prepared on a non-single-crystal substrate is employed. On the template layer, epitaxial information associated with its short-range atomic ordering is available within an area that is comparable to that of a nanowire root. Thus the template layer locally provides epitaxial information required for the growth of semiconductor nanowires. In the particular demonstration described in this paper, hydrogenated silicon was used as a template layer for epitaxial growth of indium phosphide nanowires. The indium phosphide nanowires grown on the hydrogenerated silicon template layer were found to be single crystal and optically active. Simple photoconductors and pin-diodes were fabricated and tested with the view towards various optoelectronic device applications where group III-V compound semiconductors are functionally integrated onto non-single-crystal platforms. (orig.)

  10. Laser-induced heating integrated with a microfluidic platform for real-time DNA replication and detection

    Science.gov (United States)

    Hung, Min-Sheng; Ho, Chia-Chin; Chen, Chih-Pin

    2016-08-01

    This study developed a microfluidic platform for replicating and detecting DNA in real time by integrating a laser and a microfluidic device composed of polydimethylsiloxane. The design of the microchannels consisted of a laser-heating area and a detection area. An infrared laser was used as the heating source for DNA replication, and the laser power was adjusted to heat the solutions directly. In addition, strong biotin-avidin binding was used to capture and detect the replicated products. The biotin on one end was bound to avidin and anchored to the surface of the microchannels, whereas the biotin on the other end was bound to the quantum dots (Qdots). The results showed that the fluorescent intensity of the Qdots bound to the replicated products in the detection area increased with the number of thermal cycles created by the laser. When the number of thermal cycles was ≥10, the fluorescent intensity of the Qdots was directly detectable on the surface of the microchannels. The proposed method is more sensitive than detection methods entailing gel electrophoresis.

  11. Independent Evaluation of the integrated Community Case Management of Childhood Illness Strategy in Malawi Using a National Evaluation Platform Design.

    Science.gov (United States)

    Amouzou, Agbessi; Kanyuka, Mercy; Hazel, Elizabeth; Heidkamp, Rebecca; Marsh, Andrew; Mleme, Tiope; Munthali, Spy; Park, Lois; Banda, Benjamin; Moulton, Lawrence H; Black, Robert E; Hill, Kenneth; Perin, Jamie; Victora, Cesar G; Bryce, Jennifer

    2016-03-01

    We evaluated the impact of integrated community case management of childhood illness (iCCM) on careseeking for childhood illness and child mortality in Malawi, using a National Evaluation Platform dose-response design with 27 districts as units of analysis. "Dose" variables included density of iCCM providers, drug availability, and supervision, measured through a cross-sectional cellular telephone survey of all iCCM-trained providers. "Response" variables were changes between 2010 and 2014 in careseeking and mortality in children aged 2-59 months, measured through household surveys. iCCM implementation strength was not associated with changes in careseeking or mortality. There were fewer than one iCCM-ready provider per 1,000 under-five children per district. About 70% of sick children were taken outside the home for care in both 2010 and 2014. Careseeking from iCCM providers increased over time from about 2% to 10%; careseeking from other providers fell by a similar amount. Likely contributors to the failure to find impact include low density of iCCM providers, geographic targeting of iCCM to "hard-to-reach" areas although women did not identify distance from a provider as a barrier to health care, and displacement of facility careseeking by iCCM careseeking. This suggests that targeting iCCM solely based on geographic barriers may need to be reconsidered. © The American Society of Tropical Medicine and Hygiene.

  12. Automatic and integrated micro-enzyme assay (AIμEA) platform for highly sensitive thrombin analysis via an engineered fluorescence protein-functionalized monolithic capillary column.

    Science.gov (United States)

    Lin, Lihua; Liu, Shengquan; Nie, Zhou; Chen, Yingzhuang; Lei, Chunyang; Wang, Zhen; Yin, Chao; Hu, Huiping; Huang, Yan; Yao, Shouzhuo

    2015-04-21

    Nowadays, large-scale screening for enzyme discovery, engineering, and drug discovery processes require simple, fast, and sensitive enzyme activity assay platforms with high integration and potential for high-throughput detection. Herein, a novel automatic and integrated micro-enzyme assay (AIμEA) platform was proposed based on a unique microreaction system fabricated by a engineered green fluorescence protein (GFP)-functionalized monolithic capillary column, with thrombin as an example. The recombinant GFP probe was rationally engineered to possess a His-tag and a substrate sequence of thrombin, which enable it to be immobilized on the monolith via metal affinity binding, and to be released after thrombin digestion. Combined with capillary electrophoresis-laser-induced fluorescence (CE-LIF), all the procedures, including thrombin injection, online enzymatic digestion in the microreaction system, and label-free detection of the released GFP, were integrated in a single electrophoretic process. By taking advantage of the ultrahigh loading capacity of the AIμEA platform and the CE automatic programming setup, one microreaction column was sufficient for many times digestion without replacement. The novel microreaction system showed significantly enhanced catalytic efficiency, about 30 fold higher than that of the equivalent bulk reaction. Accordingly, the AIμEA platform was highly sensitive with a limit of detection down to 1 pM of thrombin. Moreover, the AIμEA platform was robust and reliable to detect thrombin in human serum samples and its inhibition by hirudin. Hence, this AIμEA platform exhibits great potential for high-throughput analysis in future biological application, disease diagnostics, and drug screening.

  13. Achieving sustainable ground-water management by using GIS-integrated simulation tools: the EU H2020 FREEWAT platform

    Science.gov (United States)

    Rossetto, Rudy; De Filippis, Giovanna; Borsi, Iacopo; Foglia, Laura; Toegl, Anja; Cannata, Massimiliano; Neumann, Jakob; Vazquez-Sune, Enric; Criollo, Rotman

    2017-04-01

    In order to achieve sustainable and participated ground-water management, innovative software built on the integration of numerical models within GIS software is a perfect candidate to provide a full characterization of quantitative and qualitative aspects of ground- and surface-water resources maintaining the time and spatial dimension. The EU H2020 FREEWAT project (FREE and open source software tools for WATer resource management; Rossetto et al., 2015) aims at simplifying the application of EU water-related Directives through an open-source and public-domain, GIS-integrated simulation platform for planning and management of ground- and surface-water resources. The FREEWAT platform allows to simulate the whole hydrological cycle, coupling the power of GIS geo-processing and post-processing tools in spatial data analysis with that of process-based simulation models. This results in a modeling environment where large spatial datasets can be stored, managed and visualized and where several simulation codes (mainly belonging to the USGS MODFLOW family) are integrated to simulate multiple hydrological, hydrochemical or economic processes. So far, the FREEWAT platform is a large plugin for the QGIS GIS desktop software and it integrates the following capabilities: • the AkvaGIS module allows to produce plots and statistics for the analysis and interpretation of hydrochemical and hydrogeological data; • the Observation Analysis Tool, to facilitate the import, analysis and visualization of time-series data and the use of these data to support model construction and calibration; • groundwater flow simulation in the saturated and unsaturated zones may be simulated using MODFLOW-2005 (Harbaugh, 2005); • multi-species advective-dispersive transport in the saturated zone can be simulated using MT3DMS (Zheng & Wang, 1999); the possibility to simulate viscosity- and density-dependent flows is further accomplished through SEAWAT (Langevin et al., 2007); • sustainable

  14. Proof of concept: concept-based biomedical information retrieval

    NARCIS (Netherlands)

    Trieschnigg, Rudolf Berend

    2010-01-01

    In this thesis we investigate the possibility to integrate domain-specific knowledge into biomedical information retrieval (IR). Recent decades have shown a fast growing interest in biomedical research, reflected by an exponential growth in scientific literature. An important problem for biomedical

  15. A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes.

    Directory of Open Access Journals (Sweden)

    Michael R Lindberg

    Full Text Available Single source and multiple donor (mixed samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes.

  16. A 6.45 μW Self-Powered SoC With Integrated Energy-Harvesting Power Management and ULP Asymmetric Radios for Portable Biomedical Systems.

    Science.gov (United States)

    Roy, Abhishek; Klinefelter, Alicia; Yahya, Farah B; Chen, Xing; Gonzalez-Guerrero, Luisa Patricia; Lukas, Christopher J; Kamakshi, Divya Akella; Boley, James; Craig, Kyle; Faisal, Muhammad; Oh, Seunghyun; Roberts, Nathan E; Shakhsheer, Yousef; Shrivastava, Aatmesh; Vasudevan, Dilip P; Wentzloff, David D; Calhoun, Benton H

    2015-12-01

    This paper presents a batteryless system-on-chip (SoC) that operates off energy harvested from indoor solar cells and/or thermoelectric generators (TEGs) on the body. Fabricated in a commercial 0.13 μW process, this SoC sensing platform consists of an integrated energy harvesting and power management unit (EH-PMU) with maximum power point tracking, multiple sensing modalities, programmable core and a low power microcontroller with several hardware accelerators to enable energy-efficient digital signal processing, ultra-low-power (ULP) asymmetric radios for wireless transmission, and a 100 nW wake-up radio. The EH-PMU achieves a peak end-to-end efficiency of 75% delivering power to a 100 μA load. In an example motion detection application, the SoC reads data from an accelerometer through SPI, processes it, and sends it over the radio. The SPI and digital processing consume only 2.27 μW, while the integrated radio consumes 4.18 μW when transmitting at 187.5 kbps for a total of 6.45 μW.

  17. An integrated development framework for rapid development of platform-independent and reusable satellite on-board software

    Science.gov (United States)

    Ziemke, Claas; Kuwahara, Toshinori; Kossev, Ivan

    2011-09-01

    Even in the field of small satellites, the on-board data handling subsystem has become complex and powerful. With the introduction of powerful CPUs and the availability of considerable amounts of memory on-board a small satellite it has become possible to utilize the flexibility and power of contemporary platform-independent real-time operating systems. Especially the non-commercial sector such like university institutes and community projects such as AMSAT or SSETI are characterized by the inherent lack of financial as well as manpower resources. The opportunity to utilize such real-time operating systems will contribute significantly to achieve a successful mission. Nevertheless the on-board software of a satellite is much more than just an operating system. It has to fulfill a multitude of functional requirements such as: Telecommand interpretation and execution, execution of control loops, generation of telemetry data and frames, failure detection isolation and recovery, the communication with peripherals and so on. Most of the aforementioned tasks are of generic nature and have to be conducted on any satellite with only minor modifications. A general set of functional requirements as well as a protocol for communication is defined in the SA ECSS-E-70-41A standard "Telemetry and telecommand packet utilization". This standard not only defines the communication protocol of the satellite-ground link but also defines a set of so called services which have to be available on-board of every compliant satellite and which are of generic nature. In this paper, a platform-independent and reusable framework is described which is implementing not only the ECSS-E-70-41A standard but also functionalities for interprocess communication, scheduling and a multitude of tasks commonly performed on-board of a satellite. By making use of the capabilities of the high-level programming language C/C++, the powerful open source library BOOST, the real-time operating system RTEMS and

  18. Paradigm change in ocean studies: multi-platform observing and forecasting integrated approach in response to science and society needs

    Science.gov (United States)

    Tintoré, Joaquín

    2017-04-01

    The last 20 years of ocean research have allowed a description of the state of the large-scale ocean circulation. However, it is also well known that there is no such thing as an ocean state and that the ocean varies a wide range of spatial and temporal scales. More recently, in the last 10 years, new monitoring and modelling technologies have emerged allowing quasi real time observation and forecasting of the ocean at regional and local scales. Theses new technologies are key components of recent observing & forecasting systems being progressively implemented in many regional seas and coastal areas of the world oceans. As a result, new capabilities to characterise the ocean state and more important, its variability at small spatial and temporal scales, exists today in many cases in quasi-real time. Examples of relevance for society can be cited, among others our capabilities to detect and understand long-term climatic changes and also our capabilities to better constrain our forecasting capabilities of the coastal ocean circulation at temporal scales from sub-seasonal to inter-annual and spatial from regional to meso and submesoscale. The Mediterranean Sea is a well-known laboratory ocean where meso and submesoscale features can be ideally observed and studied as shown by the key contributions from projects such as Perseus, CMEMS, Jericonext, among others. The challenge for the next 10 years is the integration of theses technologies and multiplatform observing and forecasting systems to (a) monitor the variability at small scales mesoscale/weeks) in order (b) to resolve the sub-basin/seasonal and inter-annual variability and by this (c) establish the decadal variability, understand the associated biases and correct them. In other words, the new observing systems now allow a major change in our focus of ocean observation, now from small to large scales. Recent studies from SOCIB -www.socib.es- have shown the importance of this new small to large-scale multi-platform

  19. An integrated sample pretreatment platform for quantitative N-glycoproteome analysis with combination of on-line glycopeptide enrichment, deglycosylation and dimethyl labeling

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Yejing; Qu, Yanyan; Jiang, Hao; Wu, Qi [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); University of the Chinese Academy of Sciences, Beijing 100039 (China); Zhang, Lihua, E-mail: lihuazhang@dicp.ac.cn [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Yuan, Huiming [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Zhou, Yuan [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); University of the Chinese Academy of Sciences, Beijing 100039 (China); Zhang, Xiaodan; Zhang, Yukui [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China)

    2014-06-23

    Highlights: • An integrated platform for quantitative N-glycoproteome analysis was established. • On-line enrichment, deglycosylation and labeling could be achieved within 160 min. • A N{sub 2}-assisted interface was applied to improve the compatibility of the platform. • The platform exhibited improved quantification accuracy, precision and throughput. - Abstract: Relative quantification of N-glycoproteomes shows great promise for the discovery of candidate biomarkers and therapeutic targets. The traditional protocol for quantitative analysis of glycoproteomes is usually off-line performed, and suffers from long sample preparation time, and the risk of sample loss or contamination due to manual manipulation. In this study, a novel integrated sample preparation platform for quantitative N-glycoproteome analysis was established, with combination of online N-glycopeptide capture by a HILIC column, sample buffer exchange by a N{sub 2}-assisted HILIC–RPLC interface, deglycosylation by a hydrophilic PNGase F immobilized enzymatic reactor (hIMER) and solid dimethyl labeling on a C18 precolumn. To evaluate the performance of such a platform, two equal aliquots of immunoglobulin G (IgG) digests were sequentially pretreated, followed by MALDI-TOF MS analysis. The signal intensity ratio of heavy/light (H/L) labeled deglycosylated peptides with the equal aliquots was 1.00 (RSD = 6.2%, n = 3), much better than those obtained by the offline protocol, with H/L ratio as 0.76 (RSD = 11.6%, n = 3). Additionally, the total on-line sample preparation time was greatly shortened to 160 min, much faster than that of offline approach (24 h). Furthermore, such an integrated pretreatment platform was successfully applied to analyze the two kinds of hepatocarcinoma ascites syngeneic cell lines with high (Hca-F) and low (Hca-P) lymph node metastasis rates. For H/L labeled Hca-P lysates with the equal aliquots, 99.6% of log 2 ratios (H/L) of quantified glycopeptides ranged from −1

  20. Cost-effective improvements of a rotating platform by integration of a high-accuracy inclinometer and encoders for attitude evaluation

    International Nuclear Information System (INIS)

    Wen, Chenyang; He, Shengyang; Hu, Peida; Bu, Changgen

    2017-01-01

    Attitude heading reference systems (AHRSs) based on micro-electromechanical system (MEMS) inertial sensors are widely used because of their low cost, light weight, and low power. However, low-cost AHRSs suffer from large inertial sensor errors. Therefore, experimental performance evaluation of MEMS-based AHRSs after system implementation is necessary. High-accuracy turntables can be used to verify the performance of MEMS-based AHRSs indoors, but they are expensive and unsuitable for outdoor tests. This study developed a low-cost two-axis rotating platform for indoor and outdoor attitude determination. A high-accuracy inclinometer and encoders were integrated into the platform to improve the achievable attitude test accuracy. An attitude error compensation method was proposed to calibrate the initial attitude errors caused by the movements and misalignment angles of the platform. The proposed attitude error determination method was examined through rotating experiments, which showed that the standard deviations of the pitch and roll errors were 0.050° and 0.090°, respectively. The pitch and roll errors both decreased to 0.024° when the proposed attitude error determination method was used. This decrease validates the effectiveness of the compensation method. Experimental results demonstrated that the integration of the inclinometer and encoders improved the performance of the low-cost, two-axis, rotating platform in terms of attitude accuracy. (paper)

  1. Biomedical engineering fundamentals

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering.Biomedical Engineering Fundamentals, the first volume of the handbook, presents material from respected scientists with diverse backgrounds in physiological systems, biomechanics, biomaterials, bioelectric phenomena, and neuroengineering. More than three dozen specific topics are examined, including cardia

  2. A Practical Perspective on the Design and Implementation of Enterprise Integration Solution to improve QoS using SAP NetWeaver Platform

    Directory of Open Access Journals (Sweden)

    K.Krishna Mohan

    2010-06-01

    Full Text Available Most of the enterprise operations require information from several systems within and outside the enterprise(s. The past few years have seen explosive growth in direct program to program interaction for application integration, removing manual steps yielding tremendous improvements in reliability and efficiency. This paper addresses the practical approach for the design and implementation of Enterprise Application Integration in a heterogeneous environment with SAP NetWeaver Platform (i.e. Exchange Infrastructure (XI/Process Integration (PI using a Customizable Tool named TEmplate based Functional Requirements for Integration Design (TEFRID developed by the author(s to improve the Quality of Service (QoS and reduce the development time and cost with the end-to-end scenario development.

  3. Biomedical applications of nanodiamond (Review)

    Science.gov (United States)

    Turcheniuk, K.; Mochalin, Vadym N.

    2017-06-01

    The interest in nanodiamond applications in biology and medicine is on the rise over recent years. This is due to the unique combination of properties that nanodiamond provides. Small size (∼5 nm), low cost, scalable production, negligible toxicity, chemical inertness of diamond core and rich chemistry of nanodiamond surface, as well as bright and robust fluorescence resistant to photobleaching are the distinct parameters that render nanodiamond superior to any other nanomaterial when it comes to biomedical applications. The most exciting recent results have been related to the use of nanodiamonds for drug delivery and diagnostics—two components of a quickly growing area of biomedical research dubbed theranostics. However, nanodiamond offers much more in addition: it can be used to produce biodegradable bone surgery devices, tissue engineering scaffolds, kill drug resistant microbes, help us to fight viruses, and deliver genetic material into cell nucleus. All these exciting opportunities require an in-depth understanding of nanodiamond. This review covers the recent progress as well as general trends in biomedical applications of nanodiamond, and underlines the importance of purification, characterization, and rational modification of this nanomaterial when designing nanodiamond based theranostic platforms.

  4. Superhydrophobic Materials for Biomedical Applications

    Science.gov (United States)

    Colson, Yolonda L.; Grinstaff, Mark W.

    2016-01-01

    Superhydrophobic surfaces are actively studied across a wide range of applications and industries, and are now finding increased use in the biomedical arena as substrates to control protein adsorption, cellular interaction, and bacterial growth, as well as platforms for drug delivery devices and for diagnostic tools. The commonality in the design of these materials is to create a stable or metastable air state at the material surface, which lends itself to a number of unique properties. These activities are catalyzing the development of new materials, applications, and fabrication techniques, as well as collaborations across material science, chemistry, engineering, and medicine given the interdisciplinary nature of this work. The review begins with a discussion of superhydrophobicity, and then explores biomedical applications that are utilizing superhydrophobicity in depth including material selection characteristics, in vitro performance, and in vivo performance. General trends are offered for each application in addition to discussion of conflicting data in the literature, and the review concludes with the authors’ future perspectives on the utility of superhydrophobic surfaces for biomedical applications. PMID:27449946

  5. COEUS: "semantic web in a box" for biomedical applications.

    Science.gov (United States)

    Lopes, Pedro; Oliveira, José Luís

    2012-12-17

    As the "omics" revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter's complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a "semantic web in a box" approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.

  6. Introduction to biomedical engineering

    CERN Document Server

    Enderle, John D; Blanchard, Susan M

    2005-01-01

    Under the direction of John Enderle, Susan Blanchard and Joe Bronzino, leaders in the field have contributed chapters on the most relevant subjects for biomedical engineering students. These chapters coincide with courses offered in all biomedical engineering programs so that it can be used at different levels for a variety of courses of this evolving field. Introduction to Biomedical Engineering, Second Edition provides a historical perspective of the major developments in the biomedical field. Also contained within are the fundamental principles underlying biomedical engineering design, analysis, and modeling procedures. The numerous examples, drill problems and exercises are used to reinforce concepts and develop problem-solving skills making this book an invaluable tool for all biomedical students and engineers. New to this edition: Computational Biology, Medical Imaging, Genomics and Bioinformatics. * 60% update from first edition to reflect the developing field of biomedical engineering * New chapters o...

  7. Biomedical signal and image processing.

    Science.gov (United States)

    Cerutti, Sergio; Baselli, Giuseppe; Bianchi, Anna; Caiani, Enrico; Contini, Davide; Cubeddu, Rinaldo; Dercole, Fabio; Rienzo, Luca; Liberati, Diego; Mainardi, Luca; Ravazzani, Paolo; Rinaldi, Sergio; Signorini, Maria; Torricelli, Alessandro

    2011-01-01

    Generally, physiological modeling and biomedical signal processing constitute two important paradigms of biomedical engineering (BME): their fundamental concepts are taught starting from undergraduate studies and are more completely dealt with in the last years of graduate curricula, as well as in Ph.D. courses. Traditionally, these two cultural aspects were separated, with the first one more oriented to physiological issues and how to model them and the second one more dedicated to the development of processing tools or algorithms to enhance useful information from clinical data. A practical consequence was that those who did models did not do signal processing and vice versa. However, in recent years,the need for closer integration between signal processing and modeling of the relevant biological systems emerged very clearly [1], [2]. This is not only true for training purposes(i.e., to properly prepare the new professional members of BME) but also for the development of newly conceived research projects in which the integration between biomedical signal and image processing (BSIP) and modeling plays a crucial role. Just to give simple examples, topics such as brain–computer machine or interfaces,neuroengineering, nonlinear dynamical analysis of the cardiovascular (CV) system,integration of sensory-motor characteristics aimed at the building of advanced prostheses and rehabilitation tools, and wearable devices for vital sign monitoring and others do require an intelligent fusion of modeling and signal processing competences that are certainly peculiar of our discipline of BME.

  8. A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Ahrenfeldt, Johanne; Bellod Cisneros, Jose Luis

    2016-01-01

    and made publicly available, providing easy-to-use automated analysis of bacterial whole genome sequencing data. The platform may be of immediate relevance as a guide for investigators using whole genome sequencing for clinical diagnostics and surveillance. The platform is freely available at: https://cge.cbs.dtu.dk/services...... and antimicrobial resistance genes. A short printable report for each sample will be provided and an Excel spreadsheet containing all the metadata and a summary of the results for all submitted samples can be downloaded. The pipeline was benchmarked using datasets previously used to test the individual services...

  9. USA Hire Testing Platform

    Data.gov (United States)

    Office of Personnel Management — The USA Hire Testing Platform delivers tests used in hiring for positions in the Federal Government. To safeguard the integrity of the hiring processes and ensure...

  10. Citizen Science for Mining the Biomedical Literature

    Directory of Open Access Journals (Sweden)

    Ginger Tsueng

    2016-12-01

    Full Text Available Biomedical literature represents one of the largest and fastest growing collections of unstructured biomedical knowledge. Finding critical information buried in the literature can be challenging. To extract information from free-flowing text, researchers need to: 1. identify the entities in the text (named entity recognition, 2. apply a standardized vocabulary to these entities (normalization, and 3. identify how entities in the text are related to one another (relationship extraction. Researchers have primarily approached these information extraction tasks through manual expert curation and computational methods. We have previously demonstrated that named entity recognition (NER tasks can be crowdsourced to a group of non-experts via the paid microtask platform, Amazon Mechanical Turk (AMT, and can dramatically reduce the cost and increase the throughput of biocuration efforts. However, given the size of the biomedical literature, even information extraction via paid microtask platforms is not scalable. With our web-based application Mark2Cure (http://mark2cure.org, we demonstrate that NER tasks also can be performed by volunteer citizen scientists with high accuracy. We apply metrics from the Zooniverse Matrices of Citizen Science Success and provide the results here to serve as a basis of comparison for other citizen science projects. Further, we discuss design considerations, issues, and the application of analytics for successfully moving a crowdsourcing workflow from a paid microtask platform to a citizen science platform. To our knowledge, this study is the first application of citizen science to a natural language processing task.

  11. Biomedical photonics handbook therapeutics and advanced biophotonics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

    Shaped by Quantum Theory, Technology, and the Genomics RevolutionThe integration of photonics, electronics, biomaterials, and nanotechnology holds great promise for the future of medicine. This topic has recently experienced an explosive growth due to the noninvasive or minimally invasive nature and the cost-effectiveness of photonic modalities in medical diagnostics and therapy. The second edition of the Biomedical Photonics Handbook presents recent fundamental developments as well as important applications of biomedical photonics of interest to scientists, engineers, manufacturers, teachers,

  12. Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers.

    Science.gov (United States)

    Irigoyen, Antonio; Jimenez-Luna, Cristina; Benavides, Manuel; Caba, Octavio; Gallego, Javier; Ortuño, Francisco Manuel; Guillen-Ponce, Carmen; Rojas, Ignacio; Aranda, Enrique; Torres, Carolina; Prados, Jose

    2018-01-01

    Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases can be a hard task when working with heterogeneous datasets. Expression data are strongly influenced by technology, sample preparation processes, and/or labeling methods. The proliferation of different microarray platforms for measuring gene expression increases the need to develop models able to compare their results, especially when different technologies can lead to signal values that vary greatly. Integrative meta-analysis can significantly improve the reliability and robustness of DEG detection. The objective of this work was to develop an integrative approach for identifying potential cancer biomarkers by integrating gene expression data from two different platforms. Pancreatic ductal adenocarcinoma (PDAC), where there is an urgent need to find new biomarkers due its late diagnosis, is an ideal candidate for testing this technology. Expression data from two different datasets, namely Affymetrix and Illumina (18 and 36 PDAC patients, respectively), as well as from 18 healthy controls, was used for this study. A meta-analysis based on an empirical Bayesian methodology (ComBat) was then proposed to integrate these datasets. DEGs were finally identified from the integrated data by using the statistical programming language R. After our integrative meta-analysis, 5 genes were commonly identified within the individual analyses of the independent datasets. Also, 28 novel genes that were not reported by the individual analyses ('gained' genes) were also discovered. Several of these gained genes have been already related to other gastroenterological tumors. The proposed integrative meta-analysis has revealed novel DEGs that may play an important role in PDAC and could be potential biomarkers for diagnosing the disease.

  13. Integrated reconfigurable multiple-input–multiple-output antenna system with an ultra-wideband sensing antenna for cognitive radio platforms

    KAUST Repository

    Hussain, Rifaqat; Sharawi, Mohammad S.

    2015-01-01

    . The developed model can be used as a complete antenna platform for cognitive radio applications. The antenna system is developed on a single substrate area of dimensions 65 × 120 mm2. The proposed sensing antenna is used to cover a wide range

  14. Temperature and salinity profiles from CTD casts from the VALDIVIA and other PLATFORMS from a World-Wide Distribution in support of the Integrated Global Ocean Services System (IGOSS) from 01 April 1991 to 30 April 1991 (NODC Accession 9100087)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected from the VALDIVIA and other PLATFORMS in support of the Integrated Global Ocean Services System (IGOSS). Data were collected by US...

  15. Temperature and salinity profiles from CTD casts from the VALKIRIYA and other PLATFORMS from a World-Wide Distribution in support of the Integrated Global Ocean Services System (IGOSS) from 01 February 1991 to 28 February 1991 (NODC Accession 9100049)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected from the VALKIRIYA and other PLATFORMS in support of the Integrated Global Ocean Services System (IGOSS). Data were collected by US...

  16. Temperature and salinity profiles from CTD casts from the ARGOS and other PLATFORMS from a World-Wide Distribution in support of the Integrated Global Ocean Services System (IGOSS) from 01 November 1989 to 30 November 1989 (NODC Accession 8900297)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected from the ARGOS and other PLATFORMS in support of the Integrated Global Ocean Services System (IGOSS). Data were collected by US...

  17. Temperature and salinity profiles from CTD casts from the PASSAT and other PLATFORMS from the North Pacific Ocean in support of the Integrated Global Ocean Services System (IGOSS) from 01 March 1991 to 31 March 1991 (NODC Accession 9100071)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected from the PASSAT and other PLATFORMS in support of the Integrated Global Ocean Services System (IGOSS). Data were collected by US...

  18. Temperature and salinity profiles from CTD casts from the PARIZEAU and other PLATFORMS from a World-Wide distribution in support of the Integrated Global Ocean Services System (IGOSS) from 01 October 1988 to 31 October 1988 (NODC Accession 8800296)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected from the PARIZEAU and other PLATFORMS in support of the Integrated Global Ocean Services System (IGOSS). Data were collected by US...

  19. National platform electromobility. Interims report of the working group 1 propulsion technology and vehicle integration; Nationale Plattform Elektromobilitaet. Zwischenbericht der Arbeitsgruppe 1 Antriebstechnologie und Fahrzeugintegration

    Energy Technology Data Exchange (ETDEWEB)

    Meusinger, Josefin [Koordinierungsstelle der Industrie fuer die Nationale Plattform Elektromobilitaet, Berlin (Germany)

    2010-07-01

    The working group ''Propulsion technology and vehicle integration'' investigates electrical and electrified powertrains for the employment in passenger cars and commercial vehicles regarding to the goals of the national platform electrical mobility. Apart from the optimization of the architecture and the gradual physical integration of the components into drive modules the material research for new magnetic materials, for the surface refinement and basic research for the semiconductor technology/physics is a further compelling condition for long-term successes in the area of electric drives. Parallel to the increase of unit productions the degree of automation has to be improved significantly. The costs are to be affected positively by large numbers of unit productions. A bundling, acceleration and promotion of the activities from the research to the development in competence centres and landmark projects for the propulsion technology and vehicle integration are recommended. This is to be used by means of the existing instruments of the industrial community research.

  20. National platform electromobility. Interim report of the working group 3 Load infrastructure and rid integration; Nationale Plattform Elektromobilitaet. Zwischenbericht der Arbeitsgruppe 3 Lade-Infrastruktur und Netzintegration

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Stefan [E.ON AG, Duesseldorf (Germany). Political Affairs and Communications Energy Mix, Environment, Efficiency; Ledwon, Martin [Siemens AG, Berlin (Germany). Government Affairs

    2010-07-01

    The contribution under consideration reports on the first intermediate results of the working group 3 ''Load infrastructure and grid integration'' of the national platform electromobility. Next to the representation of the general objective of this working group, the following aspects are considered: (a) Electromobility in the field of tension between the power supply system and renewable production; (b) Possible network loads due to the integration of electrically powered vehicles; (c) Requirements concerning the load infrastructure; (d) Technology development of the load point; (e) Potentials by the integration of electrical mobiles into the Smart Grid; (f) Research and Development roadmap. This contribution finishes with a presentation of a concrete conversion plan for the demand of infrastructure.

  1. SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance.

    Science.gov (United States)

    Chowbina, Sudhir; Hammamieh, Rasha; Kumar, Raina; Chakraborty, Nabarun; Yang, Ruoting; Mudunuri, Uma; Jett, Marti; Palma, Joseph M; Stephens, Robert

    2013-01-01

    SysBioCube is an integrated data warehouse and analysis platform for experimental data relating to diseases of military relevance developed for the US Army Medical Research and Materiel Command Systems Biology Enterprise (SBE). It brings together, under a single database environment, pathophysio-, psychological, molecular and biochemical data from mouse models of post-traumatic stress disorder and (pre-) clinical data from human PTSD patients.. SysBioCube will organize, centralize and normalize this data and provide an access portal for subsequent analysis to the SBE. It provides new or expanded browsing, querying and visualization to provide better understanding of the systems biology of PTSD, all brought about through the integrated environment. We employ Oracle database technology to store the data using an integrated hierarchical database schema design. The web interface provides researchers with systematic information and option to interrogate the profiles of pan-omics component across different data types, experimental designs and other covariates.

  2. Systematic Integration of Innovation in Process Improvement Projects Using the Enhanced Sigma-TRIZ Algorithm and Its Effective Use by Means of a Knowledge Management Software Platform

    Directory of Open Access Journals (Sweden)

    Mircea FULEA

    2009-01-01

    Full Text Available In an evolving, highly turbulent and uncertain socio-economic environment, organizations must consider strategies of systematic and continuous integration of innovation within their business systems, as a fundamental condition for sustainable development. Adequate methodologies are required in this respect. A mature framework for integrating innovative problem solving approaches within business process improvement methodologies is proposed in this paper. It considers a TRIZ-centred algorithm in the improvement phase of the DMAIC methodology. The new tool is called enhanced sigma-TRIZ. A case study reveals the practical application of the proposed methodology. The integration of enhanced sigma-TRIZ within a knowledge management software platform (KMSP is further described. Specific developments to support processes of knowledge creation, knowledge storage and retrieval, knowledge transfer and knowledge application in a friendly and effective way within the KMSP are also highlighted.

  3. 15th International Conference on Biomedical Engineering

    CERN Document Server

    2014-01-01

    This volume presents the proceedings of the 15th ICMBE held from 4th to 7th December 2013, Singapore. Biomedical engineering is applied in most aspects of our healthcare ecosystem. From electronic health records to diagnostic tools to therapeutic, rehabilitative and regenerative treatments, the work of biomedical engineers is evident. Biomedical engineers work at the intersection of engineering, life sciences and healthcare. The engineers would use principles from applied science including mechanical, electrical, chemical and computer engineering together with physical sciences including physics, chemistry and mathematics to apply them to biology and medicine. Applying such concepts to the human body is very much the same concepts that go into building and programming a machine. The goal is to better understand, replace or fix a target system to ultimately improve the quality of healthcare. With this understanding, the conference proceedings offer a single platform for individuals and organisations working i...

  4. Biomedical applications using low temperature plasma technology

    International Nuclear Information System (INIS)

    Dai Xiujuan; Jiang Nan

    2006-01-01

    Low temperature plasma technology and biomedicine are two different subjects, but the combination of the two may play a critical role in modern science and technology. The 21 st century is believed to be a biotechnology century. Plasma technology is becoming a widely used platform for the fabrication of biomaterials and biomedical devices. In this paper some of the technologies used for material surface modification are briefly introduced. Some biomedical applications using plasma technology are described, followed by suggestions as to how a bridge between plasma technology and biomedicine can be built. A pulsed plasma technique that is used for surface functionalization is discussed in detail as an example of this kind of bridge or combination. Finally, it is pointed out that the combination of biomedical and plasma technology will be an important development for revolutionary 21st century technologies that requires different experts from different fields to work together. (authors)

  5. Biomedical engineering principles

    CERN Document Server

    Ritter, Arthur B; Valdevit, Antonio; Ascione, Alfred N

    2011-01-01

    Introduction: Modeling of Physiological ProcessesCell Physiology and TransportPrinciples and Biomedical Applications of HemodynamicsA Systems Approach to PhysiologyThe Cardiovascular SystemBiomedical Signal ProcessingSignal Acquisition and ProcessingTechniques for Physiological Signal ProcessingExamples of Physiological Signal ProcessingPrinciples of BiomechanicsPractical Applications of BiomechanicsBiomaterialsPrinciples of Biomedical Capstone DesignUnmet Clinical NeedsEntrepreneurship: Reasons why Most Good Designs Never Get to MarketAn Engineering Solution in Search of a Biomedical Problem

  6. Fundamental of biomedical engineering

    CERN Document Server

    Sawhney, GS

    2007-01-01

    About the Book: A well set out textbook explains the fundamentals of biomedical engineering in the areas of biomechanics, biofluid flow, biomaterials, bioinstrumentation and use of computing in biomedical engineering. All these subjects form a basic part of an engineer''s education. The text is admirably suited to meet the needs of the students of mechanical engineering, opting for the elective of Biomedical Engineering. Coverage of bioinstrumentation, biomaterials and computing for biomedical engineers can meet the needs of the students of Electronic & Communication, Electronic & Instrumenta

  7. Contribution to global computation infrastructure: inter-platform delegation, integration of standard services and application to high-energy physics

    International Nuclear Information System (INIS)

    Lodygensky, Oleg

    2006-01-01

    The generalization and implementation of the current information resources, particularly the large storing capacities and the networks allow conceiving new methods of work and ways of entertainment. Centralized stand-alone, monolithic computing stations have been gradually replaced by distributed client-tailored architectures which in turn are challenged by the new distributed systems called 'pair-by pair' systems. This migration is no longer with the specialists' realm but users of more modest skills get used with this new techniques for e-mailing commercial information and exchanging various sorts of files on a 'equal-to-equal' basis. Trade, industry and research as well make profits largely of the new technique called 'grid', this new technique of handling information at a global scale. The present work concerns the grid utilisation for computation. A synergy was created with Paris-Sud University at Orsay, between the Information Research Laboratory (LRI) and the Linear Accelerator Laboratory (LAL) in order to foster the works on grid infrastructure of high research interest for LRI and offering new working methods for LAL. The results of the work developed within this inter-disciplinary-collaboration are based on XtremWeb, the research and production platform for global computation elaborated at LRI. First one presents the current status of the large-scale distributed systems, their basic principles and user-oriented architecture. The XtremWeb is then described focusing the modifications which were effected upon both architecture and implementation in order to fulfill optimally the requirements imposed to such a platform. Then one presents studies with the platform allowing a generalization of the inter-grid resources and development of a user-oriented grid adapted to special services, as well,. Finally one presents the operation modes, the problems to solve and the advantages of this new platform for the high-energy research community, the most demanding

  8. A Self-Sustained Wireless Multi-Sensor Platform Integrated with Printable Organic Sensors for Indoor Environmental Monitoring

    Directory of Open Access Journals (Sweden)

    Chun-Chang Wu

    2017-03-01

    Full Text Available A self-sustained multi-sensor platform for indoor environmental monitoring is proposed in this paper. To reduce the cost and power consumption of the sensing platform, in the developed platform, organic materials of PEDOT:PSS and PEDOT:PSS/EB-PANI are used as the sensing films for humidity and CO2 detection, respectively. Different from traditional gas sensors, these organic sensing films can operate at room temperature without heating processes or infrared transceivers so that the power consumption of the developed humidity and the CO2 sensors can be as low as 10 μW and 5 μW, respectively. To cooperate with these low-power sensors, a Complementary Metal-Oxide-Semiconductor (CMOS system-on-chip (SoC is designed to amplify and to read out multiple sensor signals with low power consumption. The developed SoC includes an analog-front-end interface circuit (AFE, an analog-to-digital convertor (ADC, a digital controller and a power management unit (PMU. Scheduled by the digital controller, the sensing circuits are power gated with a small duty-cycle to reduce the average power consumption to 3.2 μW. The designed PMU converts the power scavenged from a dye sensitized solar cell (DSSC module into required supply voltages for SoC circuits operation under typical indoor illuminance conditions. To our knowledge, this is the first multiple environmental parameters (Temperature/CO2/Humidity sensing platform that demonstrates a true self-powering functionality for long-term operations.

  9. A Self-Sustained Wireless Multi-Sensor Platform Integrated with Printable Organic Sensors for Indoor Environmental Monitoring.

    Science.gov (United States)

    Wu, Chun-Chang; Chuang, Wen-Yu; Wu, Ching-Da; Su, Yu-Cheng; Huang, Yung-Yang; Huang, Yang-Jing; Peng, Sheng-Yu; Yu, Shih-An; Lin, Chih-Ting; Lu, Shey-Shi

    2017-03-29

    A self-sustained multi-sensor platform for indoor environmental monitoring is proposed in this paper. To reduce the cost and power consumption of the sensing platform, in the developed platform, organic materials of PEDOT:PSS and PEDOT:PSS/EB-PANI are used as the sensing films for humidity and CO₂ detection, respectively. Different from traditional gas sensors, these organic sensing films can operate at room temperature without heating processes or infrared transceivers so that the power consumption of the developed humidity and the CO₂ sensors can be as low as 10 μW and 5 μW, respectively. To cooperate with these low-power sensors, a Complementary Metal-Oxide-Semiconductor (CMOS) system-on-chip (SoC) is designed to amplify and to read out multiple sensor signals with low power consumption. The developed SoC includes an analog-front-end interface circuit (AFE), an analog-to-digital convertor (ADC), a digital controller and a power management unit (PMU). Scheduled by the digital controller, the sensing circuits are power gated with a small duty-cycle to reduce the average power consumption to 3.2 μW. The designed PMU converts the power scavenged from a dye sensitized solar cell (DSSC) module into required supply voltages for SoC circuits operation under typical indoor illuminance conditions. To our knowledge, this is the first multiple environmental parameters (Temperature/CO₂/Humidity) sensing platform that demonstrates a true self-powering functionality for long-term operations.

  10. B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data.

    Science.gov (United States)

    Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

    2017-12-12

    Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA's complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform.

  11. Design and simulation of material-integrated distributed sensor processing with a code-based agent platform and mobile multi-agent systems.

    Science.gov (United States)

    Bosse, Stefan

    2015-02-16

    Multi-agent systems (MAS) can be used for decentralized and self-organizing data processing in a distributed system, like a resource-constrained sensor network, enabling distributed information extraction, for example, based on pattern recognition and self-organization, by decomposing complex tasks in simpler cooperative agents. Reliable MAS-based data processing approaches can aid the material-integration of structural-monitoring applications, with agent processing platforms scaled to the microchip level. The agent behavior, based on a dynamic activity-transition graph (ATG) model, is implemented with program code storing the control and the data state of an agent, which is novel. The program code can be modified by the agent itself using code morphing techniques and is capable of migrating in the network between nodes. The program code is a self-contained unit (a container) and embeds the agent data, the initialization instructions and the ATG behavior implementation. The microchip agent processing platform used for the execution of the agent code is a standalone multi-core stack machine with a zero-operand instruction format, leading to a small-sized agent program code, low system complexity and high system performance. The agent processing is token-queue-based, similar to Petri-nets. The agent platform can be implemented in software, too, offering compatibility at the operational and code level, supporting agent processing in strong heterogeneous networks. In this work, the agent platform embedded in a large-scale distributed sensor network is simulated at the architectural level by using agent-based simulation techniques.

  12. Design and Simulation of Material-Integrated Distributed Sensor Processing with a Code-Based Agent Platform and Mobile Multi-Agent Systems

    Directory of Open Access Journals (Sweden)

    Stefan Bosse

    2015-02-01

    Full Text Available Multi-agent systems (MAS can be used for decentralized and self-organizing data processing in a distributed system, like a resource-constrained sensor network, enabling distributed information extraction, for example, based on pattern recognition and self-organization, by decomposing complex tasks in simpler cooperative agents. Reliable MAS-based data processing approaches can aid the material-integration of structural-monitoring applications, with agent processing platforms scaled to the microchip level. The agent behavior, based on a dynamic activity-transition graph (ATG model, is implemented with program code storing the control and the data state of an agent, which is novel. The program code can be modified by the agent itself using code morphing techniques and is capable of migrating in the network between nodes. The program code is a self-contained unit (a container and embeds the agent data, the initialization instructions and the ATG behavior implementation. The microchip agent processing platform used for the execution of the agent code is a standalone multi-core stack machine with a zero-operand instruction format, leading to a small-sized agent program code, low system complexity and high system performance. The agent processing is token-queue-based, similar to Petri-nets. The agent platform can be implemented in software, too, offering compatibility at the operational and code level, supporting agent processing in strong heterogeneous networks. In this work, the agent platform embedded in a large-scale distributed sensor network is simulated at the architectural level by using agent-based simulation techniques.

  13. Biomedical applications engineering tasks

    Science.gov (United States)

    Laenger, C. J., Sr.

    1976-01-01

    The engineering tasks performed in response to needs articulated by clinicians are described. Initial contacts were made with these clinician-technology requestors by the Southwest Research Institute NASA Biomedical Applications Team. The basic purpose of the program was to effectively transfer aerospace technology into functional hardware to solve real biomedical problems.

  14. Design optimization and tolerance analysis of a spot-size converter for the taper-assisted vertical integration platform in InP.

    Science.gov (United States)

    Tolstikhin, Valery; Saeidi, Shayan; Dolgaleva, Ksenia

    2018-05-01

    We report on the design optimization and tolerance analysis of a multistep lateral-taper spot-size converter based on indium phosphide (InP), performed using the Monte Carlo method. Being a natural fit to (and a key building block of) the regrowth-free taper-assisted vertical integration platform, such a spot-size converter enables efficient and displacement-tolerant fiber coupling to InP-based photonic integrated circuits at a wavelength of 1.31 μm. An exemplary four-step lateral-taper design featuring 0.35 dB coupling loss at optimal alignment of a standard single-mode fiber; ≥7  μm 1 dB displacement tolerance in any direction in a facet plane; and great stability against manufacturing variances is demonstrated.

  15. Optimizing biomedical science learning in a veterinary curriculum: a review.

    Science.gov (United States)

    Warren, Amy L; Donnon, Tyrone

    2013-01-01

    As veterinary medical curricula evolve, the time dedicated to biomedical science teaching, as well as the role of biomedical science knowledge in veterinary education, has been scrutinized. Aside from being mandated by accrediting bodies, biomedical science knowledge plays an important role in developing clinical, diagnostic, and therapeutic reasoning skills in the application of clinical skills, in supporting evidence-based veterinary practice and life-long learning, and in advancing biomedical knowledge and comparative medicine. With an increasing volume and fast pace of change in biomedical knowledge, as well as increased demands on curricular time, there has been pressure to make biomedical science education efficient and relevant for veterinary medicine. This has lead to a shift in biomedical education from fact-based, teacher-centered and discipline-based teaching to applicable, student-centered, integrated teaching. This movement is supported by adult learning theories and is thought to enhance students' transference of biomedical science into their clinical practice. The importance of biomedical science in veterinary education and the theories of biomedical science learning will be discussed in this article. In addition, we will explore current advances in biomedical teaching methodologies that are aimed to maximize knowledge retention and application for clinical veterinary training and practice.

  16. X-CHIP: an integrated platform for high-throughput protein crystallization and on-the-chip X-ray diffraction data collection

    International Nuclear Information System (INIS)

    Kisselman, Gera; Qiu, Wei; Romanov, Vladimir; Thompson, Christine M.; Lam, Robert; Battaile, Kevin P.; Pai, Emil F.; Chirgadze, Nickolay Y.

    2011-01-01

    The X-CHIP (X-ray Crystallography High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The X-CHIP (X-ray Crystallization High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The system has been designed for crystallization condition screening, visual crystal inspection, initial X-ray screening and data collection in a high-throughput fashion. X-ray diffraction data acquisition can be performed directly on-the-chip at room temperature using an in situ approach. The capabilities of the chip eliminate the necessity for manual crystal handling and cryoprotection of crystal samples, while allowing data collection from multiple crystals in the same drop. This technology would be especially beneficial for projects with large volumes of data, such as protein-complex studies and fragment-based screening. The platform employs hydrophilic and hydrophobic concentric ring surfaces on a miniature plate transparent to visible light and X-rays to create a well defined and stable microbatch crystallization environment. The results of crystallization and data-collection experiments demonstrate that high-quality well diffracting crystals can be grown and high-resolution diffraction data sets can be collected using this technology. Furthermore, the quality of a single-wavelength anomalous dispersion data set collected with the X-CHIP at room temperature was sufficient to generate interpretable electron-density maps. This technology is highly resource-efficient owing to the use of nanolitre-scale drop volumes. It does not require any modification for most in-house and synchrotron beamline systems and offers

  17. Intrant ELISA: A Novel Approach to Fabrication of Electrospun Fiber Mat-Assisted Biosensor Platforms and Their Integration within Standard Analytical Well Plates

    Directory of Open Access Journals (Sweden)

    Samira Hosseini

    2016-11-01

    Full Text Available A combination of far-field electrospinning (FFES and free-radical polymerization has been used to fabricate coated electrospun polymer fiber mats as a new type of biosensor platform. Poly (3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV electrospun fibers were dip-coated with different compositions of poly methyl methacrylate-co-methacrylic acid (poly(MMA-co-MAA. This synergistic approach utilizes large specific surface area of PHBV fibers and co-polymer coatings that feature an optimum concentration of surface carboxyl (–COOH groups. The platform surface morphology, porosity and tunable hydrophobicity enhance biomolecular interactions via plurality of molecular forces. These customized fiber mats have been integrated into a newly designed 96-well plate called an “intrant enzyme-linked immunosorbent assay” or i-ELISA. I-ELISA allows colorimetric sandwich assay to be carried out without any modifications or additional steps in ELISA methodology. By introducing the fiber mats in fabrication of i-ELISA via extensions on the lid, we address some of the limitations of the previous designs while demonstrating an enhanced signal intensity up to 12 times higher than that of conventional assays. With improved sensitivity, specificity and accuracy in the detection of dengue virus, i-ELISA has proven to be a reliable platform for biomolecular recognition. The proposed fiber mat-assisted well plate in this study holds great potential as a universal approach for integration of different types of fiber mats with pre-designed specific properties in order to enhance the detection sensitivity of the assay.

  18. X-CHIP: an integrated platform for high-throughput protein crystallization and on-the-chip X-ray diffraction data collection

    Energy Technology Data Exchange (ETDEWEB)

    Kisselman, Gera; Qiu, Wei; Romanov, Vladimir; Thompson, Christine M.; Lam, Robert [Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4 (Canada); Battaile, Kevin P. [Argonne National Laboratory, Argonne, Illinois 60439 (United States); Pai, Emil F.; Chirgadze, Nickolay Y., E-mail: nchirgad@uhnresearch.ca [Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4 (Canada); University of Toronto, Toronto, Ontario M5S 1A8 (Canada)

    2011-06-01

    The X-CHIP (X-ray Crystallography High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The X-CHIP (X-ray Crystallization High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The system has been designed for crystallization condition screening, visual crystal inspection, initial X-ray screening and data collection in a high-throughput fashion. X-ray diffraction data acquisition can be performed directly on-the-chip at room temperature using an in situ approach. The capabilities of the chip eliminate the necessity for manual crystal handling and cryoprotection of crystal samples, while allowing data collection from multiple crystals in the same drop. This technology would be especially beneficial for projects with large volumes of data, such as protein-complex studies and fragment-based screening. The platform employs hydrophilic and hydrophobic concentric ring surfaces on a miniature plate transparent to visible light and X-rays to create a well defined and stable microbatch crystallization environment. The results of crystallization and data-collection experiments demonstrate that high-quality well diffracting crystals can be grown and high-resolution diffraction data sets can be collected using this technology. Furthermore, the quality of a single-wavelength anomalous dispersion data set collected with the X-CHIP at room temperature was sufficient to generate interpretable electron-density maps. This technology is highly resource-efficient owing to the use of nanolitre-scale drop volumes. It does not require any modification for most in-house and synchrotron beamline systems and offers

  19. Electrical Design and Evaluation of Asynchronous Serial Bus Communication Network of 48 Sensor Platform LSIs with Single-Ended I/O for Integrated MEMS-LSI Sensors

    Science.gov (United States)

    Shao, Chenzhong; Tanaka, Shuji; Nakayama, Takahiro; Hata, Yoshiyuki

    2018-01-01

    For installing many sensors in a limited space with a limited computing resource, the digitization of the sensor output at the site of sensation has advantages such as a small amount of wiring, low signal interference and high scalability. For this purpose, we have developed a dedicated Complementary Metal-Oxide-Semiconductor (CMOS) Large-Scale Integration (LSI) (referred to as “sensor platform LSI”) for bus-networked Micro-Electro-Mechanical-Systems (MEMS)-LSI integrated sensors. In this LSI, collision avoidance, adaptation and event-driven functions are simply implemented to relieve data collision and congestion in asynchronous serial bus communication. In this study, we developed a network system with 48 sensor platform LSIs based on Printed Circuit Board (PCB) in a backbone bus topology with the bus length being 2.4 m. We evaluated the serial communication performance when 48 LSIs operated simultaneously with the adaptation function. The number of data packets received from each LSI was almost identical, and the average sampling frequency of 384 capacitance channels (eight for each LSI) was 73.66 Hz. PMID:29342923

  20. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery.

    Science.gov (United States)

    Therrien, Eric; Englebienne, Pablo; Arrowsmith, Andrew G; Mendoza-Sanchez, Rodrigo; Corbeil, Christopher R; Weill, Nathanael; Campagna-Slater, Valérie; Moitessier, Nicolas

    2012-01-23

    As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.

  1. Electrical Design and Evaluation of Asynchronous Serial Bus Communication Network of 48 Sensor Platform LSIs with Single-Ended I/O for Integrated MEMS-LSI Sensors

    Directory of Open Access Journals (Sweden)

    Chenzhong Shao

    2018-01-01

    Full Text Available For installing many sensors in a limited space with a limited computing resource, the digitization of the sensor output at the site of sensation has advantages such as a small amount of wiring, low signal interference and high scalability. For this purpose, we have developed a dedicated Complementary Metal-Oxide-Semiconductor (CMOS Large-Scale Integration (LSI (referred to as “sensor platform LSI” for bus-networked Micro-Electro-Mechanical-Systems (MEMS-LSI integrated sensors. In this LSI, collision avoidance, adaptation and event-driven functions are simply implemented to relieve data collision and congestion in asynchronous serial bus communication. In this study, we developed a network system with 48 sensor platform LSIs based on Printed Circuit Board (PCB in a backbone bus topology with the bus length being 2.4 m. We evaluated the serial communication performance when 48 LSIs operated simultaneously with the adaptation function. The number of data packets received from each LSI was almost identical, and the average sampling frequency of 384 capacitance channels (eight for each LSI was 73.66 Hz.

  2. A computational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks

    Directory of Open Access Journals (Sweden)

    Thomas eEissing

    2011-02-01

    Full Text Available Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.

  3. Integrated chemical sensor array platform based on a light emitting diode, xerogel-derived sensor elements, and high-speed pin printing

    International Nuclear Information System (INIS)

    Cho, Eun Jeong; Bright, Frank V.

    2002-01-01

    We report a new, solid-state, integrated optical array sensor platform. By using pin printing technology in concert with sol-gel-processing methods, we form discrete xerogel-based microsensor elements that are on the order of 100 μm in diameter and 1 μm thick directly on the face of a light emitting diode (LED). The LED serves as the light source to excite chemically responsive luminophores sequestered within the doped xerogel microsensors and the analyte-dependent emission from within the doped xerogel is detected with a charge coupled device (CCD). We overcome the problem of background illumination from the LED reaching the CCD and the associated biasing that results by coating the LED first with a thin layer of blue paint. The thin paint layer serves as an optical filter, knocking out the LEDs red-edge spectral tail. The problem of the spatially-dependent fluence across the LED face is solved entirely by performing ratiometric measurements. We illustrate the performance of the new sensor scheme by forming an array of 100 discrete O 2 -responsive sensing elements on the face of a single LED. The combination of pin printing with an integrated sensor and light source platform results in a rapid method of forming (∼1 s per sensor element) reusable sensor arrays. The entire sensor array can be calibrated using just one sensor element. Array-to-array reproducibly is <8%. Arrays can be formed using single or multiple pins with indistinguishable analytical performance

  4. High Level of Integration in Integrated Disease Management Leads to Higher Usage in the e-Vita Study: Self-Management of Chronic Obstructive Pulmonary Disease With Web-Based Platforms in a Parallel Cohort Design.

    Science.gov (United States)

    Talboom-Kamp, Esther Pwa; Verdijk, Noortje A; Kasteleyn, Marise J; Harmans, Lara M; Talboom, Irvin Jsh; Numans, Mattijs E; Chavannes, Niels H

    2017-05-31

    Worldwide, nearly 3 million people die of chronic obstructive pulmonary disease (COPD) every year. Integrated disease management (IDM) improves disease-specific quality of life and exercise capacity for people with COPD, but can also reduce hospital admissions and hospital days. Self-management of COPD through eHealth interventions has shown to be an effective method to improve the quality and efficiency of IDM in several settings, but it remains unknown which factors influence usage of eHealth and change in behavior of patients. Our study, e-Vita COPD, compares different levels of integration of Web-based self-management platforms in IDM in three primary care settings. The main aim of this study is to analyze the factors that successfully promote the use of a self-management platform for COPD patients. The e-Vita COPD study compares three different approaches to incorporating eHealth via Web-based self-management platforms into IDM of COPD using a parallel cohort design. Three groups integrated the platforms to different levels. In groups 1 (high integration) and 2 (medium integration), randomization was performed to two levels of personal assistance for patients (high and low assistance); in group 3 there was no integration into disease management (none integration). Every visit to the e-Vita and Zorgdraad COPD Web platforms was tracked objectively by collecting log data (sessions and services). At the first log-in, patients completed a baseline questionnaire. Baseline characteristics were automatically extracted from the log files including age, gender, education level, scores on the Clinical COPD Questionnaire (CCQ), dyspnea scale (MRC), and quality of life questionnaire (EQ5D). To predict the use of the platforms, multiple linear regression analyses for the different independent variables were performed: integration in IDM (high, medium, none), personal assistance for the participants (high vs low), educational level, and self-efficacy level (General Self

  5. Payment Platform

    DEFF Research Database (Denmark)

    Hjelholt, Morten; Damsgaard, Jan

    2012-01-01

    thoroughly and substitute current payment standards in the decades to come. This paper portrays how digital payment platforms evolve in socio-technical niches and how various technological platforms aim for institutional attention in their attempt to challenge earlier platforms and standards. The paper...... applies a co-evolutionary multilevel perspective to model the interplay and processes between technology and society wherein digital payment platforms potentially will substitute other payment platforms just like the credit card negated the check. On this basis this paper formulate a multilevel conceptual...

  6. Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

    Science.gov (United States)

    Amith, Muhammad; He, Zhe; Bian, Jiang; Lossio-Ventura, Juan Antonio; Tao, Cui

    2018-04-01

    With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications. Ontology evaluation is an integral part of ontology development and maintenance. In the biomedicine domain, ontology evaluation is often conducted by third parties as a quality assurance (or auditing) effort that focuses on identifying modeling errors and inconsistencies. In this work, we first organized four categorical schemes of ontology evaluation methods in the existing literature to create an integrated taxonomy. Further, to understand the ontology evaluation practice in the biomedicine domain, we reviewed a sample of 200 ontologies from the National Center for Biomedical Ontology (NCBO) BioPortal-the largest repository for biomedical ontologies-and observed that only 15 of these ontologies have documented evaluation in their corresponding inception papers. We then surveyed the recent quality assurance approaches for biomedical ontologies and their use. We also mapped these quality assurance approaches to the ontology evaluation criteria. It is our anticipation that ontology evaluation and quality assurance approaches will be more widely adopted in the development life cycle of biomedical ontologies. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. SATORI: a system for ontology-guided visual exploration of biomedical data repositories.

    Science.gov (United States)

    Lekschas, Fritz; Gehlenborg, Nils

    2018-04-01

    The ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating datasets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find datasets of interest. We developed SATORI-an integrative search and visual exploration interface for the exploration of biomedical data repositories. The design is informed by a requirements analysis through a series of semi-structured interviews. We evaluated the implementation of SATORI in a field study on a real-world data collection. SATORI enables researchers to seamlessly search, browse and semantically query data repositories via two visualizations that are highly interconnected with a powerful search interface. SATORI is an open-source web application, which is freely available at http://satori.refinery-platform.org and integrated into the Refinery Platform. nils@hms.harvard.edu. Supplementary data are available at Bioinformatics online.

  8. Fuel cell-powered microfluidic platform for lab-on-a-chip applications: Integration into an autonomous amperometric sensing device.

    Science.gov (United States)

    Esquivel, J P; Colomer-Farrarons, J; Castellarnau, M; Salleras, M; del Campo, F J; Samitier, J; Miribel-Català, P; Sabaté, N

    2012-11-07

    The present paper reports for the first time the integration of a microfluidic system, electronics modules, amperometric sensor and display, all powered by a single micro direct methanol fuel cell. In addition to activating the electronic circuitry, the integrated power source also acts as a tuneable micropump. The electronics fulfil several functions. First, they regulate the micro fuel cell output power, which off-gas controls the flow rate of different solutions toward an electrochemical sensor through microfluidic channels. Secondly, as the fuel cell powers a three-electrode electrochemical cell, the electronics compare the working electrode output signal with a set reference value. Thirdly, if the concentration measured by the sensor exceeds this threshold value, the electronics switch on an integrated organic display. This integrated approach pushes forward the development of truly autonomous point-of-care devices relying on electrochemical detection.

  9. NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

    Science.gov (United States)

    Martínez-Romero, Marcos; Jonquet, Clement; O'Connor, Martin J; Graybeal, John; Pazos, Alejandro; Musen, Mark A

    2017-06-07

    Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios. Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability

  10. Integrated platform for home services using new products and services for senior citizens Call CNAV-CARSAT 2015.

    Science.gov (United States)

    Noguès, Michel; Laune, Daniel; Paccard, Delphine; Coupet, Anne-Laure; Millot-Keurinck, Justine; Bototo, Narjis; Bertrand, Marine; Bousquet, Jean

    2017-03-01

    This project is part of: i) the risks of ageing prevention policy of the French retirement and occupational health insurance agency of Languedoc Roussillon (Carsat-LR) and ii) the European innovation partnership on active and healthy ageing (EIP on AHA). It aims to support senior citizens who live independently and have been identified at risk of frailty on a social or health level. The purpose is to increase legibility as well as technical and financial access to innovations for vulnerable seniors who are remote from the digital era, through a multiservice user-friendly platform. Launched at the end of 2015, the project rallies over 10 actors of the silver economy currently developing personalised ICT tools to improve the safety and comfort of seniors and the coordination between health and social care. The objective is threefold: i) developing new adapted technologies, ii) having them evaluated by retirees and professionals and iii) making them accessible to the ICT web platform which will provide tutorials and prices and collect opinions from users and professionals. 500 retirees selected by CARSAT-LR will be testing these new devices and solutions which will be provided without charge. The following will be evaluated: i) feedback from users; ii) benefits gained through accessing comprehensive and appropriate information; iii) coordination of caregivers and professionals; iv) enjoyment from using the products (access to games, social links, customer confidence, sense of safety). This is a unique opportunity to mobilise solutions in a structured manner, bringing together competing businesses under a consortium agreement. Advantages for these businesses include acceleration of development and availability of their adapted solutions as well as the possibility to test their products on a significant panel of people. Professional caregiver's data follow-up will identify seniors at risk of frailty, proposing preventive actions and local services tailored to their

  11. Biomedical applications of polymers

    CERN Document Server

    Gebelein, C G

    1991-01-01

    The biomedical applications of polymers span an extremely wide spectrum of uses, including artificial organs, skin and soft tissue replacements, orthopaedic applications, dental applications, and controlled release of medications. No single, short review can possibly cover all these items in detail, and dozens of books andhundreds of reviews exist on biomedical polymers. Only a few relatively recent examples will be cited here;additional reviews are listed under most of the major topics in this book. We will consider each of the majorclassifications of biomedical polymers to some extent, inclu

  12. Handbook of biomedical optics

    CERN Document Server

    Boas, David A

    2011-01-01

    Biomedical optics holds tremendous promise to deliver effective, safe, non- or minimally invasive diagnostics and targeted, customizable therapeutics. Handbook of Biomedical Optics provides an in-depth treatment of the field, including coverage of applications for biomedical research, diagnosis, and therapy. It introduces the theory and fundamentals of each subject, ensuring accessibility to a wide multidisciplinary readership. It also offers a view of the state of the art and discusses advantages and disadvantages of various techniques.Organized into six sections, this handbook: Contains intr

  13. Biomedical Engineering Desk Reference

    CERN Document Server

    Ratner, Buddy D; Schoen, Frederick J; Lemons, Jack E; Dyro, Joseph; Martinsen, Orjan G; Kyle, Richard; Preim, Bernhard; Bartz, Dirk; Grimnes, Sverre; Vallero, Daniel; Semmlow, John; Murray, W Bosseau; Perez, Reinaldo; Bankman, Isaac; Dunn, Stanley; Ikada, Yoshito; Moghe, Prabhas V; Constantinides, Alkis

    2009-01-01

    A one-stop Desk Reference, for Biomedical Engineers involved in the ever expanding and very fast moving area; this is a book that will not gather dust on the shelf. It brings together the essential professional reference content from leading international contributors in the biomedical engineering field. Material covers a broad range of topics including: Biomechanics and Biomaterials; Tissue Engineering; and Biosignal Processing* A hard-working desk reference providing all the essential material needed by biomedical and clinical engineers on a day-to-day basis * Fundamentals, key techniques,

  14. Powering biomedical devices

    CERN Document Server

    Romero, Edwar

    2013-01-01

    From exoskeletons to neural implants, biomedical devices are no less than life-changing. Compact and constant power sources are necessary to keep these devices running efficiently. Edwar Romero's Powering Biomedical Devices reviews the background, current technologies, and possible future developments of these power sources, examining not only the types of biomedical power sources available (macro, mini, MEMS, and nano), but also what they power (such as prostheses, insulin pumps, and muscular and neural stimulators), and how they work (covering batteries, biofluids, kinetic and ther

  15. All-optical SR flip-flop based on SOA-MZI switches monolithically integrated on a generic InP platform

    Science.gov (United States)

    Pitris, St.; Vagionas, Ch.; Kanellos, G. T.; Kisacik, R.; Tekin, T.; Broeke, R.; Pleros, N.

    2016-03-01

    At the dawning of the exaflop era, High Performance Computers are foreseen to exploit integrated all-optical elements, to overcome the speed limitations imposed by electronic counterparts. Drawing from the well-known Memory Wall limitation, imposing a performance gap between processor and memory speeds, research has focused on developing ultra-fast latching devices and all-optical memory elements capable of delivering buffering and switching functionalities at unprecedented bit-rates. Following the master-slave configuration of electronic Flip-Flops, coupled SOA-MZI based switches have been theoretically investigated to exceed 40 Gb/s operation, provided a short coupling waveguide. However, this flip-flop architecture has been only hybridly integrated with silica-on-silicon integration technology exhibiting a total footprint of 45x12 mm2 and intra-Flip-Flop coupling waveguide of 2.5cm, limited at 5 Gb/s operation. Monolithic integration offers the possibility to fabricate multiple active and passive photonic components on a single chip at a close proximity towards, bearing promises for fast all-optical memories. Here, we present for the first time a monolithically integrated all-optical SR Flip-Flop with coupled master-slave SOA-MZI switches. The photonic chip is integrated on a 6x2 mm2 die as a part of a multi-project wafer run using library based components of a generic InP platform, fiber-pigtailed and fully packaged on a temperature controlled ceramic submount module with electrical contacts. The intra Flip-Flop coupling waveguide is 5 mm long, reducing the total footprint by two orders of magnitude. Successful flip flop functionality is evaluated at 10 Gb/s with clear open eye diagram, achieving error free operation with a power penalty of 4dB.

  16. Platform Constellations

    DEFF Research Database (Denmark)

    Staykova, Kalina Stefanova; Damsgaard, Jan

    2016-01-01

    This research paper presents an initial attempt to introduce and explain the emergence of new phenomenon, which we refer to as platform constellations. Functioning as highly modular systems, the platform constellations are collections of highly connected platforms which co-exist in parallel and a......’ acquisition and users’ engagement rates as well as unlock new sources of value creation and diversify revenue streams....

  17. NDE in biomedical engineering

    International Nuclear Information System (INIS)

    Bhagwat, Aditya; Kumar, Pradeep

    2015-01-01

    Biomedical Engineering (BME) is an interdisciplinary field, marking the conjunction of Medical and Engineering disciplines. It combines the design and problem solving skills of engineering with medical and biological sciences to advance health care treatment, including diagnosis, monitoring, and therapy

  18. Biomedical signal analysis

    CERN Document Server

    Rangayyan, Rangaraj M

    2015-01-01

    The book will help assist a reader in the development of techniques for analysis of biomedical signals and computer aided diagnoses with a pedagogical examination of basic and advanced topics accompanied by over 350 figures and illustrations. Wide range of filtering techniques presented to address various applications. 800 mathematical expressions and equations. Practical questions, problems and laboratory exercises. Includes fractals and chaos theory with biomedical applications.

  19. MathWorks Simulink and C++ integration with the new VLT PLC-based standard development platform for instrument control systems

    Science.gov (United States)

    Kiekebusch, Mario J.; Di Lieto, Nicola; Sandrock, Stefan; Popovic, Dan; Chiozzi, Gianluca

    2014-07-01

    ESO is in the process of implementing a new development platform, based on PLCs, for upcoming VLT control systems (new instruments and refurbishing of existing systems to manage obsolescence issues). In this context, we have evaluated the integration and reuse of existing C++ libraries and Simulink models into the real-time environment of BECKHOFF Embedded PCs using the capabilities of the latest version of TwinCAT software and MathWorks Embedded Coder. While doing so the aim was to minimize the impact of the new platform by adopting fully tested solutions implemented in C++. This allows us to reuse the in house expertise, as well as extending the normal capabilities of the traditional PLC programming environments. We present the progress of this work and its application in two concrete cases: 1) field rotation compensation for instrument tracking devices like derotators, 2) the ESO standard axis controller (ESTAC), a generic model-based controller implemented in Simulink and used for the control of telescope main axes.

  20. Lab-on-capillary: a rapid, simple and quantitative genetic analysis platform integrating nucleic acid extraction, amplification and detection.

    Science.gov (United States)

    Fu, Yu; Zhou, Xiaoming; Xing, Da

    2017-12-05

    In this work, we describe for the first time a genetic diagnosis platform employing a polydiallyldimethylammonium chloride (PDDA)-modified capillary and a liquid-based thermalization system for rapid, simple and quantitative DNA analysis with minimal user interaction. Positively charged PDDA is modified on the inner surface of the silicon dioxide capillary by using an electrostatic self-assembly approach that allows the negatively charged DNA to be separated from the lysate in less than 20 seconds. The capillary loaded with the PCR mix is incorporated in the thermalization system, which can achieve on-site real-time PCR. This system is based on the circulation of pre-heated liquids in the chamber, allowing for high-speed thermalization of the capillary and fast amplification. Multiple targets can be simultaneously analysed with multiplex spatial melting. Starting with live Escherichia coli (E. coli) cells in milk, as a realistic sample, the current method can achieve DNA extraction, amplification, and detection within 40 min.

  1. Integrated Observations From Fixed and AUV Platforms in the Littoral Zone at the SFOMC Coastal Ocean Observatory

    Science.gov (United States)

    Dhanak, M. R.

    2001-12-01

    A 12-hour survey of the coastal waters off the east coast of Florida at the South Florida Ocean Measurement Center (SFOMC) coastal ocean observatory, during summer 1999, is described to illustrate the observatory's capabilities for ocean observation. The facility is located close to the Gulf Stream, the continental shelf break being only 3 miles from shore and is therefore influenced by the Gulf Stream meanders and the instability of the horizontal shear layer at its edge. As a result, both cross-shelf and along-shelf components of currents in the littoral zone can undergo dramatic +/- 0.5 m/s oscillations. Observations of surface currents from an OSCR, and of subsurface structure from an autonomous underwater vehicle (AUV) platform, a bottom-mounted ADCP and CT-chain arrays during the survey will be described and compared. The AUV on-board sensors included upward and downward looking 1200kHz ADCP, a CTD package and a small-scale turbulence package, consisting of two shear probes and a fast-response thermistor. Prevailing atmospheric conditions were recorded at an on-site buoy. The combined observations depict flows over a range of scales. Acknowledgements: The observations from the OSCR are due to Nick Shay and Tom Cook (University of Miami), and from the bottom-mounted ADCP, CT chain arrays and the surface buoy are due to Alex Soloviev (Nova Southeastern University) and Mark Luther and Bob Weisberg (University of South Florida).

  2. A Bioengineered Three-Dimensional Cell Culture Platform Integrated with Microfluidics To Address Antimicrobial Resistance in Tuberculosis

    Directory of Open Access Journals (Sweden)

    Magdalena K. Bielecka

    2017-02-01

    Full Text Available Antimicrobial resistance presents one of the most significant threats to human health, with the emergence of totally drug-resistant organisms. We have combined bioengineering, genetically modified bacteria, longitudinal readouts, and fluidics to develop a transformative platform to address the drug development bottleneck, utilizing Mycobacterium tuberculosis as the model organism. We generated microspheres incorporating virulent reporter bacilli, primary human cells, and an extracellular matrix by using bioelectrospray methodology. Granulomas form within the three-dimensional matrix, and mycobacterial stress genes are upregulated. Pyrazinamide, a vital first-line antibiotic for treating human tuberculosis, kills M. tuberculosis in a three-dimensional culture but not in a standard two-dimensional culture or Middlebrook 7H9 broth, demonstrating that antibiotic sensitivity within microspheres reflects conditions in patients. We then performed pharmacokinetic modeling by combining the microsphere system with a microfluidic plate and demonstrated that we can model the effect of dynamic antibiotic concentrations on mycobacterial killing. The microsphere system is highly tractable, permitting variation of cell content, the extracellular matrix, sphere size, the infectious dose, and the surrounding medium with the potential to address a wide array of human infections and the threat of antimicrobial resistance.

  3. Operating Protocol and Networking Issues of a Telemedicine Platform Integrating from Wireless Home Sensors to the Hospital Information System

    Directory of Open Access Journals (Sweden)

    Massimiliano Donati

    2013-01-01

    Full Text Available Chronic heart failure (CHF is among the major causes of hospitalization for elderly citizens. Its considerable impact on patient quality of life, the resources congestion, and the related costs can be efficiently mitigated using remote wireless biosensors networks placed at patient home, able to communicate in secure way over the public Internet with the cardiology departmental Hospital Information System (HIS. In this way, physicians can monitor the situation of several patients at distance and quickly realize and act alterations in vital parameters. In this scenario, the Health@Home (H@H platform is conceived. The pool of Bluetooth sensors enables patients to daily collect vital signs at home in noninvasive fashion. A home gateway receives and processes all signals before sending them to a server node in charge of interfacing with the usual HIS. The novel concept of operating protocol (OP represents a list of actions, remotely configurable, that the domestic network has to follow (required measurements, transmissions, comparisons with personalized thresholds, etc.. The first medical tests on 30 patients (1 month allowed to verify the model, both from the patient and the medical perspective. The main evaluation metrics were usability, flexibility, and reliability of the communication from sensors to HIS.

  4. InGaAsP Mach-Zehnder interferometer optical modulator monolithically integrated with InGaAs driver MOSFET on a III-V CMOS photonics platform.

    Science.gov (United States)

    Park, Jin-Kown; Takagi, Shinichi; Takenaka, Mitsuru

    2018-02-19

    We demonstrated the monolithic integration of a carrier-injection InGaAsP Mach-Zehnder interferometer (MZI) optical modulator and InGaAs metal-oxide-semiconductor field-effect transistor (MOSFET) on a III-V-on-insulator (III-V-OI) wafer. A low-resistivity lateral PIN junction was formed along an InGaAsP rib waveguide by Zn diffusion and Ni-InGaAsP alloy, enabling direct driving of the InGaAsP optical modulator by the InGaAs MOSFET. A π phase shift of the InGaAsP optical modulator was obtained through the injection of a drain current from the InGaAs MOSFET with a gate voltage of approximately 1 V. This proof-of-concept demonstration of the monolithic integration of the InGaAsP optical modulator and InGaAs driver MOSFET will enable us to develop high-performance and low-power electronic-photonic integrated circuits on a III-V CMOS photonics platform.

  5. An Integrated 4-element Slot-Based MIMO and an UWB Sensing Antenna System for CR Platforms

    KAUST Repository

    Hussain, Rifaqat; Sharawi, Mohammad S.; Shamim, Atif

    2017-01-01

    This paper presents a novel integrated antenna system for cognitive radio (CR) applications. The design consists of a compact 4- element reconfigurable annular slot based multiple-input-multiple-output (MIMO) antenna system integrated within an ultra-wide-band (UWB) sensing antenna. All the antenna elements are planar in structure and designed on a single substrate (RO-4350) with dimensions 60×120×1.5 mm3. The frequency reconfigurable slot based MIMO antenna system is tuned over a wide frequency band from 1.77 GHz to 2.51 GHz while the UWB sensing antenna is covering from 0.75~7.65 GHz The proposed antenna system is suitable for CR enabled wireless devices. The envelope correlation coefficient (ECC) did not exceed 0.248 in the entire operating band of the MIMO antenna part. The maximum measured gain of the MIMO antenna is 3.2 dBi with maximum efficiency of 81%.

  6. Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing

    DEFF Research Database (Denmark)

    Oprea, Tudor; Nielsen, Sonny Kim; Ursu, Oleg

    2011-01-01

    benefit from an integrated, semantic-web compliant computer-aided drug repurposing (CADR) effort, one that would enable deep data mining of associations between approved drugs (D), targets (T), clinical outcomes (CO) and SE. We report preliminary results from text mining and multivariate statistics, based...... on 7684 approved drug labels, ADL (Dailymed) via text mining. From the ADL corresponding to 988 unique drugs, the "adverse reactions" section was mapped onto 174 SE, then clustered via principal component analysis into a 5 x 5 self-organizing map that was integrated into a Cytoscape network of SE......Finding new uses for old drugs is a strategy embraced by the pharmaceutical industry, with increasing participation from the academic sector. Drug repurposing efforts focus on identifying novel modes of action, but not in a systematic manner. With intensive data mining and curation, we aim to apply...

  7. An Integrated 4-element Slot-Based MIMO and an UWB Sensing Antenna System for CR Platforms

    KAUST Repository

    Hussain, Rifaqat

    2017-12-08

    This paper presents a novel integrated antenna system for cognitive radio (CR) applications. The design consists of a compact 4- element reconfigurable annular slot based multiple-input-multiple-output (MIMO) antenna system integrated within an ultra-wide-band (UWB) sensing antenna. All the antenna elements are planar in structure and designed on a single substrate (RO-4350) with dimensions 60×120×1.5 mm3. The frequency reconfigurable slot based MIMO antenna system is tuned over a wide frequency band from 1.77 GHz to 2.51 GHz while the UWB sensing antenna is covering from 0.75~7.65 GHz The proposed antenna system is suitable for CR enabled wireless devices. The envelope correlation coefficient (ECC) did not exceed 0.248 in the entire operating band of the MIMO antenna part. The maximum measured gain of the MIMO antenna is 3.2 dBi with maximum efficiency of 81%.

  8. Advances in integrated and sustainable supply chain planning concepts, methods, tools and solution approaches toward a platform for industrial practice

    CERN Document Server

    Laínez-Aguirre, José Miguel

    2015-01-01

    Decision making at the enterprise level often encompass not only production operations and  product R&D, but other strategic functions such as financial planning and marketing. With the aim of maximizing growth and a firm’s value, companies often focus on co-ordinating these functional components as well as traditional hierarchical decision levels. Understanding this interplay can enhance enterprise capabilities of adaptation and response to uncertainties arising from internal processes as well as the external environment. This book presents concepts, methods, tools and solutions based on mathematical programming, which provides the quantitative support needed for integrated decision-making and ultimately for improving the allocation of overall corporate resources (e.g., materials, cash and personnel). Through a systems perspective, the integrated planning of the supply chain also promotes activities of reuse, reduction and recycling for achieving more sustainable environmental impacts of production/di...

  9. Direct Current as an Integrating Platform for ZNE Buildings with EVs and Storage: DC Direct Systems – A Bridge to a Low Carbon Future?

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Karl [California Inst. for Energy and the Environment, Berkeley, CA (United States); Vossos, Vagelis [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kloss, Margarita [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Robinson, Gerald [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Brown, Rich [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2016-09-01

    Cost effective zero net energy (ZNE) schemes exist for many types of residential and commercial buildings. Yet, today’s alternating current (AC) based ZNE designs may be as much as 10% to 20% less efficient, more costly, and more complicated than a design based on direct current (DC) technologies. An increasing number of research organizations and manufacturers are just starting the process of developing products and conducting research and development (R&D) efforts. These early R&D efforts indicate that the use of DC technologies may deliver many energy and non-energy benefits relative to AC-based typologies. DC ZNE schemes may provide for an ideal integrating platform for natively DC-based onsite generation, storage, electric vehicle (EV) charging and end-use loads. Emerging empirical data suggest that DC end-use appliances are more efficient, simpler, more durable, and lower cost. DC technologies appear to provide ratepayers a lower cost pathway to achieve resilient ZNE buildings, and simultaneously yield a plethora of benefits. This paper draws from the current research effort entitled "Direct Current as an Integrating and Enabling Platform," co-led by the Lawrence Berkeley National Laboratory (LBNL), the California Institute for Energy and the Environment (CIEE), the Electric Power Research Institute (EPRI) and funded under the California Energy Commission’s Energy Program Investment Charge (CEC EPIC). The first phase of this EPIC research is focused on assembling and summarizing known global performance information on DC and DC-AC hybrid end-use appliances and power systems. This paper summarizes the information and insights gained from this research effort.

  10. INTEGRACIÓN DE TECNOLOGÍAS EN UNA PLATAFORMA J2EE DIRIGIDA POR MODELOS TECHNOLOGIES INTEGRATION IN A MODEL DRIVEN J2EE PLATFORM

    Directory of Open Access Journals (Sweden)

    David Colque C

    2006-12-01

    Full Text Available Este documento presenta una propuesta de cómo integrar adecuadamente diversas tecnologías de persistencia, de negocios y web en una plataforma J2EE. Esto involucra una arquitectura de múltiples capas, que considera para cada capa el uso de soluciones prácticas efectivas en el desarrollo de software, también se considera el uso del paradigma de desarrollo dirigido por modelos (MDA para facilitar su integración, implementado en el Framework Open Source AndroMDA, y el proceso de desarrollo propuesto por Larman. De este modo se pretende fortalecer el desarrollo orientado a objetos al incorporar una herramienta MDA que genera código a partir de los modelos de cada plataforma específica e incentivar el uso de modelos en el proceso de desarrollo del software, mejorando así la calidad del software, la portabilidad, la interoperabilidad y la reusabilidad, como también la independencia de las tecnologías usadas en cada capa.This work presents a proposal for integrating properly diverse technologies of persistence of business and Web in a J2EE platform. This involves an architecture of diverse layers, which considers the use of effective practical solutions for each layer in the development of the software. Also are considered the use of the Model Driven Architecture Paradigm, for facilitating integration performed in the Open Source AndroMDA Framework, and the development process proposed by Larman. This process is aimed at strengthening the development oriented to objects, when incorporating a MDA tool, which generates codes from the models of every specific platform; encouraging the use of models in the process of software development, improving the quality, the portability, the interoperability, as well as reusing the software, and also the self sufficiency of the technologies used in every layer.

  11. Monolithic photonic integration for visible and short near-infrared wavelengths: technologies and platforms for bio and life science applications

    Science.gov (United States)

    Porcel, Marco A. G.; Artundo, Iñigo; Domenech, J. David; Geuzebroek, Douwe; Sunarto, Rino; Hoofman, Romano

    2018-04-01

    This tutorial aims to provide a general overview on the state-of-the-art of photonic integrated circuits (PICs) in the visible and short near-infrared (NIR) wavelength ranges, mostly focusing in silicon nitride (SiN) substrates, and a guide to the necessary steps in the design toward the fabrication of such PICs. The focus is put on bio- and life sciences, given the adequacy and, thus, a large number of applications in this field.

  12. Innovations in biomedical nanoengineering: nanowell array biosensor

    Science.gov (United States)

    Seo, YoungTae; Jeong, Sunil; Lee, JuKyung; Choi, Hak Soo; Kim, Jonghan; Lee, HeaYeon

    2018-04-01

    Nanostructured biosensors have pioneered biomedical engineering by providing highly sensitive analyses of biomolecules. The nanowell array (NWA)-based biosensing platform is particularly innovative, where the small size of NWs within the array permits extremely profound sensing of a small quantity of biomolecules. Undoubtedly, the NWA geometry of a gently-sloped vertical wall is critical for selective docking of specific proteins without capillary resistances, and nanoprocessing has contributed to the fabrication of NWA electrodes on gold substrate such as molding process, e-beam lithography, and krypton-fluoride (KrF) stepper semiconductor method. The Lee group at the Mara Nanotech has established this NW-based biosensing technology during the past two decades by engineering highly sensitive electrochemical sensors and providing a broad range of detection methods from large molecules (e.g., cells or proteins) to small molecules (e.g., DNA and RNA). Nanosized gold dots in the NWA enhance the detection of electrochemical biosensing to the range of zeptomoles in precision against the complementary target DNA molecules. In this review, we discuss recent innovations in biomedical nanoengineering with a specific focus on novel NWA-based biosensors. We also describe our continuous efforts in achieving a label-free detection without non-specific binding while maintaining the activity and stability of immobilized biomolecules. This research can lay the foundation of a new platform for biomedical nanoengineering systems.

  13. An exploration of the biomedical optics course construction of undergraduate biomedical engineering program in medical colleges

    Science.gov (United States)

    Guo, Shijun; Lyu, Jie; Zhang, Peiming

    2017-08-01

    In this paper, the teaching goals, teaching contents and teaching methods in biomedical optics course construction are discussed. From the dimension of teaching goals, students should master the principle of optical inspection on the human body, diagnosis and treatment of methodology and instruments, through the study of the theory and practice of this course, and can utilize biomedical optics methods to solve practical problems in the clinical medical engineering practice. From the dimension of teaching contents, based on the characteristics of biomedical engineering in medical colleges, the organic integration of engineering aspects, medical optical instruments, and biomedical aspects dispersed in human anatomy, human physiology, clinical medicine fundamental related to the biomedical optics is build. Noninvasive measurement of the human body composition and noninvasive optical imaging of the human body were taken as actual problems in biomedical optics fields. Typical medical applications such as eye optics and laser medicine were also integrated into the theory and practice teaching. From the dimension of teaching methods, referencing to organ-system based medical teaching mode, optical principle and instrument principle were taught by teachers from school of medical instruments, and the histological characteristics and clinical actual need in areas such as digestive diseases and urinary surgery were taught by teachers from school of basic medicine or clinical medicine of medical colleges. Furthermore, clinical application guidance would be provided by physician and surgeons in hospitals.

  14. Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research.

    Science.gov (United States)

    Purawat, Shweta; Cowart, Charles; Amaro, Rommie E; Altintas, Ilkay

    2016-06-01

    The BBDTC (https://biobigdata.ucsd.edu) is a community-oriented platform to encourage high-quality knowledge dissemination with the aim of growing a well-informed biomedical big data community through collaborative efforts on training and education. The BBDTC collaborative is an e-learning platform that supports the biomedical community to access, develop and deploy open training materials. The BBDTC supports Big Data skill training for biomedical scientists at all levels, and from varied backgrounds. The natural hierarchy of courses allows them to be broken into and handled as modules . Modules can be reused in the context of multiple courses and reshuffled, producing a new and different, dynamic course called a playlist . Users may create playlists to suit their learning requirements and share it with individual users or the wider public. BBDTC leverages the maturity and design of the HUBzero content-management platform for delivering educational content. To facilitate the migration of existing content, the BBDTC supports importing and exporting course material from the edX platform. Migration tools will be extended in the future to support other platforms. Hands-on training software packages, i.e., toolboxes , are supported through Amazon EC2 and Virtualbox virtualization technologies, and they are available as: ( i ) downloadable lightweight Virtualbox Images providing a standardized software tool environment with software packages and test data on their personal machines, and ( ii ) remotely accessible Amazon EC2 Virtual Machines for accessing biomedical big data tools and scalable big data experiments. At the moment, the BBDTC site contains three open Biomedical big data training courses with lecture contents, videos and hands-on training utilizing VM toolboxes, covering diverse topics. The courses have enhanced the hands-on learning environment by providing structured content that users can use at their own pace. A four course biomedical big data series is

  15. On-chip hybrid photonic-plasmonic light concentrator for nanofocusing in an integrated silicon photonics platform.

    Science.gov (United States)

    Luo, Ye; Chamanzar, Maysamreza; Apuzzo, Aniello; Salas-Montiel, Rafael; Nguyen, Kim Ngoc; Blaize, Sylvain; Adibi, Ali

    2015-02-11

    The enhancement and confinement of electromagnetic radiation to nanometer scale have improved the performances and decreased the dimensions of optical sources and detectors for several applications including spectroscopy, medical applications, and quantum information. Realization of on-chip nanofocusing devices compatible with silicon photonics platform adds a key functionality and provides opportunities for sensing, trapping, on-chip signal processing, and communications. Here, we discuss the design, fabrication, and experimental demonstration of light nanofocusing in a hybrid plasmonic-photonic nanotaper structure. We discuss the physical mechanisms behind the operation of this device, the coupling mechanisms, and how to engineer the energy transfer from a propagating guided mode to a trapped plasmonic mode at the apex of the plasmonic nanotaper with minimal radiation loss. Optical near-field measurements and Fourier modal analysis carried out using a near-field scanning optical microscope (NSOM) show a tight nanofocusing of light in this structure to an extremely small spot of 0.00563(λ/(2n(rmax)))(3) confined in 3D and an exquisite power input conversion of 92%. Our experiments also verify the mode selectivity of the device (low transmission of a TM-like input mode and high transmission of a TE-like input mode). A large field concentration factor (FCF) of about 4.9 is estimated from our NSOM measurement with a radius of curvature of about 20 nm at the apex of the nanotaper. The agreement between our theory and experimental results reveals helpful insights about the operation mechanism of the device, the interplay of the modes, and the gradual power transfer to the nanotaper apex.

  16. Towards sustainable and multifunctional agriculture in farmland landscapes: Lessons from the integrative approach of a French LTSER platform.

    Science.gov (United States)

    Bretagnolle, Vincent; Berthet, Elsa; Gross, Nicolas; Gauffre, Bertrand; Plumejeaud, Christine; Houte, Sylvie; Badenhausser, Isabelle; Monceau, Karine; Allier, Fabrice; Monestiez, Pascal; Gaba, Sabrina

    2018-06-15

    Agriculture is currently facing unprecedented challenges: ensuring food, fiber and energy production in the face of global change, maintaining the economic performance of farmers and preserving natural resources such as biodiversity and associated key ecosystem services for sustainable agriculture. Addressing these challenges requires innovative landscape scale farming systems that account for changing economic and environmental targets. These novel agricultural systems need to be recognized, accepted and promoted by all stakeholders, including local residents, and supported by public policies. Agroecosystems should be considered as socio-ecological systems and alternative farming systems should be based on ecological principles while taking societal needs into account. This requires an in-depth knowledge of the multiple interactions between sociological and ecological dynamics. Long Term Socio-Ecological Research platforms (LTSER) are ideal for acquiring this knowledge as they (i) are not constrained by traditional disciplinary boundaries, (ii) operate at a large spatial scale involving all stakeholders, and (iii) use systemic approaches to investigate biodiversity and ecosystem services. This study presents the socio-ecological research strategy from the LTSER "Zone Atelier Plaine & Val de Sèvre" (ZA PVS), a large study area where data has been sampled since 1994. Its global aim is to identify effective solutions for agricultural development and the conservation of biodiversity in farmlands. Three main objectives are targeted by the ZAPVS. The first objective is intensive monitoring of landscape features, the main taxa present and agricultural practices. The second objective is the experimental investigation, in real fields with local farmers, of important ecosystem functions and services, in relation to pesticide use, crop production and farming socio-economic value. The third aim is to involve stakeholders through participatory research, citizen science and

  17. Development and integration of block operations for data invariant automation of digital preprocessing and analysis of biological and biomedical Raman spectra.

    Science.gov (United States)

    Schulze, H Georg; Turner, Robin F B

    2015-06-01

    High-throughput information extraction from large numbers of Raman spectra is becoming an increasingly taxing problem due to the proliferation of new applications enabled using advances in instrumentation. Fortunately, in many of these applications, the entire process can be automated, yielding reproducibly good results with significant time and cost savings. Information extraction consists of two stages, preprocessing and analysis. We focus here on the preprocessing stage, which typically involves several steps, such as calibration, background subtraction, baseline flattening, artifact removal, smoothing, and so on, before the resulting spectra can be further analyzed. Because the results of some of these steps can affect the performance of subsequent ones, attention must be given to the sequencing of steps, the compatibility of these sequences, and the propensity of each step to generate spectral distortions. We outline here important considerations to effect full automation of Raman spectral preprocessing: what is considered full automation; putative general principles to effect full automation; the proper sequencing of processing and analysis steps; conflicts and circularities arising from sequencing; and the need for, and approaches to, preprocessing quality control. These considerations are discussed and illustrated with biological and biomedical examples reflecting both successful and faulty preprocessing.

  18. National Community Solar Platform

    Energy Technology Data Exchange (ETDEWEB)

    Rupert, Bart [Clean Energy Collective, Louisville, CO (United States)

    2016-06-30

    This project was created to provide a National Community Solar Platform (NCSP) portal known as Community Solar Hub, that is available to any entity or individual who wants to develop community solar. This has been done by providing a comprehensive portal to make CEC’s solutions, and other proven community solar solutions, externally available for everyone to access – making the process easy through proven platforms to protect subscribers, developers and utilities. The successful completion of this project provides these tools via a web platform and integration APIs, a wide spectrum of community solar projects included in the platform, multiple groups of customers (utilities, EPCs, and advocates) using the platform to develop community solar, and open access to anyone interested in community solar. CEC’s Incubator project includes web-based informational resources, integrated systems for project information and billing systems, and engagement with customers and users by community solar experts. The combined effort externalizes much of Clean Energy Collective’s industry-leading expertise, allowing third parties to develop community solar without duplicating expensive start-up efforts. The availability of this platform creates community solar projects that are cheaper to build and cheaper to participate in, furthering the goals of DOE’s SunShot Initiative. Final SF 425 Final SF 428 Final DOE F 2050.11 Final Report Narrative

  19. Collective intelligence for translational medicine: Crowdsourcing insights and innovation from an interdisciplinary biomedical research community.

    Science.gov (United States)

    Budge, Eleanor Jane; Tsoti, Sandra Maria; Howgate, Daniel James; Sivakumar, Shivan; Jalali, Morteza

    2015-01-01

    Translational medicine bridges the gap between discoveries in biomedical science and their safe and effective clinical application. Despite the gross opportunity afforded by modern research for unparalleled advances in this field, the process of translation remains protracted. Efforts to expedite science translation have included the facilitation of interdisciplinary collaboration within both academic and clinical environments in order to generate integrated working platforms fuelling the sharing of knowledge, expertise, and tools to align biomedical research with clinical need. However, barriers to scientific translation remain, and further progress is urgently required. Collective intelligence and crowdsourcing applications offer the potential for global online networks, allowing connection and collaboration between a wide variety of fields. This would drive the alignment of biomedical science with biotechnology, clinical need, and patient experience, in order to deliver evidence-based innovation which can revolutionize medical care worldwide. Here we discuss the critical