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Sample records for microarray technology accessible

  1. DNA Microarray Technology

    Science.gov (United States)

    Skip to main content DNA Microarray Technology Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions Funding ...

  2. DNA Microarray Technology; TOPICAL

    International Nuclear Information System (INIS)

    WERNER-WASHBURNE, MARGARET; DAVIDSON, GEORGE S.

    2002-01-01

    Collaboration between Sandia National Laboratories and the University of New Mexico Biology Department resulted in the capability to train students in microarray techniques and the interpretation of data from microarray experiments. These studies provide for a better understanding of the role of stationary phase and the gene regulation involved in exit from stationary phase, which may eventually have important clinical implications. Importantly, this research trained numerous students and is the basis for three new Ph.D. projects

  3. Current Knowledge on Microarray Technology - An Overview

    African Journals Online (AJOL)

    Erah

    This paper reviews basics and updates of each microarray technology and serves to .... through protein microarrays. Protein microarrays also known as protein chips are nothing but grids that ... conditioned media, patient sera, plasma and urine. Clontech ... based antibody arrays) is similar to membrane-based antibody ...

  4. Tissue Microarray TechnologyA Brief Review

    Directory of Open Access Journals (Sweden)

    Ramya S Vokuda

    2018-01-01

    Full Text Available In this era of modern revolutionisation in the field of medical laboratory technology, everyone is aiming at taking the innovations from laboratory to bed side. One such technique that is most relevant to the pathologic community is Tissue Microarray (TMA technology. This is becoming quite popular amongst all the members of this family, right from laboratory scientists to clinicians and residents to technologists. The reason for this technique to gain popularity is attributed to its cost effectiveness and time saving protocols. Though, every technique is accompanied by disadvantages, the benefits out number them. This technique is very versatile as many downstream molecular assays such as immunohistochemistry, cytogenetic studies, Fluorescent In situ-Hybridisation (FISH etc., can be carried out on a single slide with multiple numbers of samples. It is a very practical approach that aids effectively to identify novel biomarkers in cancer diagnostics and therapeutics. It helps in assessing the molecular markers on a large scale very quickly. Also, the quality assurance protocols in pathological laboratory has exploited TMA to a great extent. However, the application of TMA technology is beyond oncology. This review shall focus on the different aspects of this technology such as construction of TMA, instrumentation, types, advantages and disadvantages and utilisation of the technique in various disease conditions.

  5. Advanced microarray technologies for clinical diagnostics

    NARCIS (Netherlands)

    Pierik, Anke

    2011-01-01

    DNA microarrays become increasingly important in the field of clinical diagnostics. These microarrays, also called DNA chips, are small solid substrates, typically having a maximum surface area of a few cm2, onto which many spots are arrayed in a pre-determined pattern. Each of these spots contains

  6. DNA microarray technology in nutraceutical and food safety.

    Science.gov (United States)

    Liu-Stratton, Yiwen; Roy, Sashwati; Sen, Chandan K

    2004-04-15

    The quality and quantity of diet is a key determinant of health and disease. Molecular diagnostics may play a key role in food safety related to genetically modified foods, food-borne pathogens and novel nutraceuticals. Functional outcomes in biology are determined, for the most part, by net balance between sets of genes related to the specific outcome in question. The DNA microarray technology offers a new dimension of strength in molecular diagnostics by permitting the simultaneous analysis of large sets of genes. Automation of assay and novel bioinformatics tools make DNA microarrays a robust technology for diagnostics. Since its development a few years ago, this technology has been used for the applications of toxicogenomics, pharmacogenomics, cell biology, and clinical investigations addressing the prevention and intervention of diseases. Optimization of this technology to specifically address food safety is a vast resource that remains to be mined. Efforts to develop diagnostic custom arrays and simplified bioinformatics tools for field use are warranted.

  7. Art : accessible, renewable technology

    International Nuclear Information System (INIS)

    Middleton, C.D.

    2004-01-01

    This paper focuses on the role of non-governmental organization (NGO) citizen groups in Ontario in the use and production of electricity. NGOs have the potential to act both directly on their own accord, and indirectly by pressuring government and others. Current demand for electricity is divided between industrial, commercial and residential users. Citizens have an important role to play in reducing energy demand. On the supply side, there is a revival of interest in renewable energy based on wind, photovoltaic and local-hydro technologies as a result of the escalating environmental and economic costs of coal and nuclear generation. However, citizen groups have greater interest and enthusiasm than technical expertise, creating a mismatch between technological solutions and human need or use of them. This paper discusses how this mismatch applies to renewable-energy technologies, many of which are not especially user-friendly, or accessible. While alternative technologies are increasingly welcomed by government, industry is developing a large and growing array of technological devices. In between this is the citizen, who, despite keen interest, can be overwhelmed by the complexity of the situation. This paper links the theoretical perspective to the real world with a discussion of the dynamics between people and renewable energy in citizen groups and makes particular reference to one group, Citizens for Renewable Energy, that has been making renewable energy technology more accessible to its members for over a decade

  8. Reverse phase protein microarray technology in traumatic brain injury.

    Science.gov (United States)

    Gyorgy, Andrea B; Walker, John; Wingo, Dan; Eidelman, Ofer; Pollard, Harvey B; Molnar, Andras; Agoston, Denes V

    2010-09-30

    Antibody based, high throughput proteomics technology represents an exciting new approach in understanding the pathobiologies of complex disorders such as cancer, stroke and traumatic brain injury. Reverse phase protein microarray (RPPA) can complement the classical methods based on mass spectrometry as a high throughput validation and quantification method. RPPA technology can address problematic issues, such as sample complexity, sensitivity, quantification, reproducibility and throughput, which are currently associated with mass spectrometry-based approaches. However, there are technical challenges, predominantly associated with the selection and use of antibodies, preparation and representation of samples and with analyzing and quantifying primary RPPA data. Here we present ways to identify and overcome some of the current issues associated with RPPA. We believe that using stringent quality controls, improved bioinformatics analysis and interpretation of primary RPPA data, this method will significantly contribute in generating new level of understanding about complex disorders at the level of systems biology. Published by Elsevier B.V.

  9. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola

    2012-01-01

    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray...... of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research....

  10. SCK-CEN Genomic Platform: the microarray technology

    International Nuclear Information System (INIS)

    Benotmane, R.

    2006-01-01

    The human body contains approximately 10 14 cells, wherein each one is a nucleus. The nucleus contains 2x23 chromosomes, or two complete sets of the human genome, one set coming from the mother and the other from the father. In principle each set includes 30.000-40.000 genes. If the genome was a book, it would be twenty-three chapters, called chromosomes,each chapter with several thousand stories, called genes. Each story made up of paragraphs, called exons and introns. Each paragraph made up of 3 letter words, called codons. Each word is written with letters called bases (AGCT). But the whole is written in a single very long sentence, which is the DNA molecule or deoxy nucleic acid. The usual state of DNA is two complementary strands intertwined forming a double helix. In the cell, DNA is duplicated during each cell division to ensure the transmission of the genome to the daughter cells. For expression, the DNA is transcribed to messenger RNA. The RNA is edited and finally translated to a protein, each three bases coding for one amino acid. When the whole message is translated, the chain of amino acids folds itself up into a distinctive shape that depends on its sequence. Proteins are the effectors of the genes, and are responsible for all metabolic, hormonal and enzymatic reactions in the cells. The expressed RNA determines the amount of proteins to be produced and subsequently the desired effect (strong or weak) in the cell. The microarray technology aims at quantifying the amount of RNA present in the cell from each expressed gene, and at evaluating the changes of these amounts after exposure of the cell to toxic chemicals, ionising radiation or other stress components. The global picture of expressed genes helps to understand the affected genetic pathways in the cell at the molecular level. The microarray technology is used in the Radiobiology and Microbiology topics to study the effect of ionising radiation on human cells and mouse tissue, as well as the

  11. A random-access microarray for programmable droplet storage, retrieval and manipulation

    International Nuclear Information System (INIS)

    Tseng, Yi-Ming; Wang, Jhih-Jhe; Su, Yu-Chuan

    2012-01-01

    This article presents an integrated microfluidic system that is capable of programmably metering, entrapping, coalescing, addressably storing, retrieving and manipulating emulsion droplets. A multilayer, flexible PDMS chip with specially designed fluidic channels dynamically reconfigured by pneumatically actuated diaphragms is utilized to integrate a variety of droplet manipulation schemes. Once droplets are formed, their motions are coordinated by a 2D multiplexing scheme, which exploits the bidirectional movement of diaphragms to implement a random-access microarray. In the prototype demonstration, a PDMS molding and bonding process is used to fabricate the proposed microfluidic system. Emulsion droplets with desired volumes and compositions are produced, addressably stored, manipulated and retrieved from a 4 × 4 array, which employs just 4 (= 2 × log 2 4) control inputs for the operation. It has been demonstrated that (1) the integration of droplet manipulation and 2D multiplexing schemes can be achieved readily using bidirectional diaphragm valves, (2) multiplexing of an N × N array could be realized utilizing only 2 × log 2 N control inputs and (3) a multifunctional, random-access microarray can be accomplished employing a multilayer PDMS chip. As such, the demonstrated random-access microarray could potentially serve as a platform for continuous tracking and multistep processing of emulsion droplets, which is desired for various biological and chemical applications. (paper)

  12. Polysaccharide microarray technology for the detection of Burkholderia pseudomallei and Burkholderia mallei antibodies.

    Science.gov (United States)

    Parthasarathy, Narayanan; DeShazer, David; England, Marilyn; Waag, David M

    2006-11-01

    A polysaccharide microarray platform was prepared by immobilizing Burkholderia pseudomallei and Burkholderia mallei polysaccharides. This polysaccharide array was tested with success for detecting B. pseudomallei and B. mallei serum (human and animal) antibodies. The advantages of this microarray technology over the current serodiagnosis of the above bacterial infections were discussed.

  13. Novel Protein Microarray Technology to Examine Men with Prostate Cancer

    National Research Council Canada - National Science Library

    Lilja, Hans

    2005-01-01

    The authors developed a novel macro and nanoporous silicon surface for protein microarrays to facilitate high-throughput biomarker discovery, and high-density protein-chip array analyses of complex biological samples...

  14. Accessible Electronic and Information Technology

    Science.gov (United States)

    This Policy establishes EPA's responsibilities and procedures for making its Electronic and Information Technology (EIT) products accessible to all people, including people with disabilities, in accordance with Section 508 of the Rehabilitation Act.

  15. Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

    Science.gov (United States)

    In the 2007 Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation (CNV) was analyzed ...

  16. Application of Microarray technology in research and diagnostics

    DEFF Research Database (Denmark)

    Helweg-Larsen, Rehannah Borup

    The overall purpose of this thesis is to evaluate the use of microarray analysis to investigate the transcriptome of human cancers and human follicular cells and define the correlation between expression of human genes and specific cancer types as well as the developmental competence of the oocyte...

  17. MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies

    Directory of Open Access Journals (Sweden)

    Beaudoing Emmanuel

    2006-09-01

    Full Text Available Abstract Background High throughput gene expression profiling (GEP is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. Results MAF (MicroArray Facility is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking, data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. Conclusion MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for

  18. Microarray technology for major chemical contaminants analysis in food: current status and prospects.

    Science.gov (United States)

    Zhang, Zhaowei; Li, Peiwu; Hu, Xiaofeng; Zhang, Qi; Ding, Xiaoxia; Zhang, Wen

    2012-01-01

    Chemical contaminants in food have caused serious health issues in both humans and animals. Microarray technology is an advanced technique suitable for the analysis of chemical contaminates. In particular, immuno-microarray approach is one of the most promising methods for chemical contaminants analysis. The use of microarrays for the analysis of chemical contaminants is the subject of this review. Fabrication strategies and detection methods for chemical contaminants are discussed in detail. Application to the analysis of mycotoxins, biotoxins, pesticide residues, and pharmaceutical residues is also described. Finally, future challenges and opportunities are discussed.

  19. DNA Microarray Technologies: A Novel Approach to Geonomic Research

    Energy Technology Data Exchange (ETDEWEB)

    Hinman, R.; Thrall, B.; Wong, K,

    2002-01-01

    A cDNA microarray allows biologists to examine the expression of thousands of genes simultaneously. Researchers may analyze the complete transcriptional program of an organism in response to specific physiological or developmental conditions. By design, a cDNA microarray is an experiment with many variables and few controls. One question that inevitably arises when working with a cDNA microarray is data reproducibility. How easy is it to confirm mRNA expression patterns? In this paper, a case study involving the treatment of a murine macrophage RAW 264.7 cell line with tumor necrosis factor alpha (TNF) was used to obtain a rough estimate of data reproducibility. Two trials were examined and a list of genes displaying either a > 2-fold or > 4-fold increase in gene expression was compiled. Variations in signal mean ratios between the two slides were observed. We can assume that erring in reproducibility may be compensated by greater inductive levels of similar genes. Steps taken to obtain results included serum starvation of cells before treatment, tests of mRNA for quality/consistency, and data normalization.

  20. Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei

    OpenAIRE

    Zirlinger, M.; Kreiman, Gabriel; Anderson, D. J.

    2001-01-01

    Microarray technology represents a potentially powerful method for identifying cell type- and regionally restricted genes expressed in the brain. Here we have combined a microarray analysis of differential gene expression among five selected brain regions, including the amygdala, cerebellum, hippocampus, olfactory bulb, and periaqueductal gray, with in situ hybridization. On average, 0.3% of the 34,000 genes interrogated were highly enriched in each of the five regions...

  1. Glycoprofiling of Early Gastric Cancer Using Lectin Microarray Technology.

    Science.gov (United States)

    Li, Taijie; Mo, Cuiju; Qin, Xue; Li, Shan; Liu, Yinkun; Liu, Zhiming

    2018-01-01

    Recently, studies have reported that protein glycosylation plays an important role in the occurrence and development of cancer. Gastric cancer is a common cancer with high morbidity and mortality owing to most gastric cancers are discovered only at an advanced stage. Here, we aim to discover novel specific serum glycanbased biomarkers for gastric cancer. A lectin microarray with 50 kinds of tumor-associated lectin was used to detect the glycan profiles of serum samples between early gastric cancer and healthy controls. Then lectin blot was performed to validate the differences. The result of the lectin microarray showed that the signal intensities of 13 lectins showed significant differences between the healthy controls and early gastric cancer. Compared to the healthy, the normalized fluorescent intensities of the lectins PWA, LEL, and STL were significantly increased, and it implied that their specifically recognized GlcNAc showed an especially elevated expression in early gastric cancer. Moreover, the binding affinity of the lectins EEL, RCA-II, RCA-I, VAL, DSA, PHA-L, UEA, and CAL were higher in the early gastric cancer than in healthy controls. These glycan structures containing GalNAc, terminal Galβ 1-4 GlcNAc, Tri/tetraantennary N-glycan, β-1, 6GlcNAc branching structure, α-linked fucose residues, and Tn antigen were elevated in gastric cancer. While the two lectins CFL GNL reduced their binding ability. In addition, their specifically recognized N-acetyl-D-galactosamine structure and (α-1,3) mannose residues were decreased in early gastric cancer. Furthermore, lectin blot results of LEL, STL, PHA-L, RCA-I were consistent with the results of the lectin microarray. The findings of our study clarify the specific alterations for glycosylation during the pathogenesis of gastric cancer. The specific high expression of GlcNAc structure may act as a potential early diagnostic marker for gastric cancer.

  2. Development and Validation of Protein Microarray Technology for Simultaneous Inflammatory Mediator Detection in Human Sera

    Directory of Open Access Journals (Sweden)

    Senthooran Selvarajah

    2014-01-01

    Full Text Available Biomarkers, including cytokines, can help in the diagnosis, prognosis, and prediction of treatment response across a wide range of disease settings. Consequently, the recent emergence of protein microarray technology, which is able to quantify a range of inflammatory mediators in a large number of samples simultaneously, has become highly desirable. However, the cost of commercial systems remains somewhat prohibitive. Here we show the development, validation, and implementation of an in-house microarray platform which enables the simultaneous quantitative analysis of multiple protein biomarkers. The accuracy and precision of the in-house microarray system were investigated according to the Food and Drug Administration (FDA guidelines for pharmacokinetic assay validation. The assay fell within these limits for all but the very low-abundant cytokines, such as interleukin- (IL- 10. Additionally, there were no significant differences between cytokine detection using our microarray system and the “gold standard” ELISA format. Crucially, future biomarker detection need not be limited to the 16 cytokines shown here but could be expanded as required. In conclusion, we detail a bespoke protein microarray system, utilizing well-validated ELISA reagents, that allows accurate, precise, and reproducible multiplexed biomarker quantification, comparable with commercial ELISA, and allowing customization beyond that of similar commercial microarrays.

  3. Usefulness of the SNP microarray technology to identify rare mutations in the case of perinatal death

    DEFF Research Database (Denmark)

    Hoeffding, L. K.; Kock, K. F.; Johnsen, Iben Birgit Gade

    2015-01-01

    The single nucleotide polymorphism (SNP) microarray technology has emerged as a powerful tool to screen the whole genome for sub-microscopic duplications and deletions that are not detectable by traditional cytogenetic analysis. Case: We report a case of a female twin born at 27th week of gestation...

  4. Validation of tissue microarray technology in squamous cell carcinoma of the esophagus

    NARCIS (Netherlands)

    Boone, Judith; van Hillegersberg, Richard; van Diest, Paul J.; Offerhaus, G. Johan A.; Borel Rinkes, Inne H. M.; ten Kate, Fiebo J. W.

    2008-01-01

    Tissue microarray (TMA) technology has been developed to facilitate high-throughput immunohistochemical and in situ hybridization analysis of tissues by inserting small tissue biopsy cores into a single paraffin block. Several studies have revealed novel prognostic biomarkers in esophageal squamous

  5. Review Article: Current Knowledge on Microarray Technology - An ...

    African Journals Online (AJOL)

    Abstract. The completion of whole genome sequencing projects has led to a rapid increase in the availability of genetic information. ... It has emerged as one of the most important technology in the field of molecular biology and transcriptomics.

  6. Comparing microarrays and next-generation sequencing technologies for microbial ecology research.

    Science.gov (United States)

    Roh, Seong Woon; Abell, Guy C J; Kim, Kyoung-Ho; Nam, Young-Do; Bae, Jin-Woo

    2010-06-01

    Recent advances in molecular biology have resulted in the application of DNA microarrays and next-generation sequencing (NGS) technologies to the field of microbial ecology. This review aims to examine the strengths and weaknesses of each of the methodologies, including depth and ease of analysis, throughput and cost-effectiveness. It also intends to highlight the optimal application of each of the individual technologies toward the study of a particular environment and identify potential synergies between the two main technologies, whereby both sample number and coverage can be maximized. We suggest that the efficient use of microarray and NGS technologies will allow researchers to advance the field of microbial ecology, and importantly, improve our understanding of the role of microorganisms in their various environments.

  7. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses

    Science.gov (United States)

    Stokes, Todd H; Torrance, JT; Li, Henry; Wang, May D

    2008-01-01

    (Semantic Agents) such as Google to further enhance data discovery. Conclusions Microarray data and meta information in ArrayWiki are distributed and visualized using a novel and compact data storage format, BioPNG. Also, they are open to the research community for curation, modification, and contribution. By making a small investment of time to learn the syntax and structure common to all sites running MediaWiki software, domain scientists and practioners can all contribute to make better use of microarray technologies in research and medical practices. ArrayWiki is available at . PMID:18541053

  8. Database Access through Java Technologies

    Directory of Open Access Journals (Sweden)

    Nicolae MERCIOIU

    2010-09-01

    Full Text Available As a high level development environment, the Java technologies offer support to the development of distributed applications, independent of the platform, providing a robust set of methods to access the databases, used to create software components on the server side, as well as on the client side. Analyzing the evolution of Java tools to access data, we notice that these tools evolved from simple methods that permitted the queries, the insertion, the update and the deletion of the data to advanced implementations such as distributed transactions, cursors and batch files. The client-server architectures allows through JDBC (the Java Database Connectivity the execution of SQL (Structured Query Language instructions and the manipulation of the results in an independent and consistent manner. The JDBC API (Application Programming Interface creates the level of abstractization needed to allow the call of SQL queries to any DBMS (Database Management System. In JDBC the native driver and the ODBC (Open Database Connectivity-JDBC bridge and the classes and interfaces of the JDBC API will be described. The four steps needed to build a JDBC driven application are presented briefly, emphasizing on the way each step has to be accomplished and the expected results. In each step there are evaluations on the characteristics of the database systems and the way the JDBC programming interface adapts to each one. The data types provided by SQL2 and SQL3 standards are analyzed by comparison with the Java data types, emphasizing on the discrepancies between those and the SQL types, but also the methods that allow the conversion between different types of data through the methods of the ResultSet object. Next, starting from the metadata role and studying the Java programming interfaces that allow the query of result sets, we will describe the advanced features of the data mining with JDBC. As alternative to result sets, the Rowsets add new functionalities that

  9. Marginalized Student Access to Technology Education

    Science.gov (United States)

    Kurtcu, Wanda M.

    2017-01-01

    The purpose of this paper is to investigate how a teacher can disrupt an established curriculum that continues the cycle of inequity of access to science, technology, engineering, and math (STEM) curriculum by students in alternative education. For this paper, I will focus on the technology components of the STEM curriculum. Technology in the…

  10. Seamless access to OER with mobile technologies

    NARCIS (Netherlands)

    Tabuenca, Bernardo

    2014-01-01

    This presentation provides insight on how ubiquitous technology can support lifelong learners facilitating access across context. The 3LHub tool is presented as suitable tool to scaffold personal learning ecologies.

  11. Technology Adoption: Influence of Availability and Accessibility

    Science.gov (United States)

    McConnell, William Stewart

    2009-01-01

    Farmers are small business leaders using available technology to remain competitive. The availability of technology is dependent on the suppliers' use of the marketing mix 4Ps theory--product, price, placement, and promotion. The purpose of this study was to determine how the relation between availability and accessibility influences the adoption…

  12. Marginalized Student Access to Technology Education

    Science.gov (United States)

    Kurtcu, Wanda M.

    The purpose of this paper is to investigate how a teacher can disrupt an established curriculum that continues the cycle of inequity of access to science, technology, engineering, and math (STEM) curriculum by students in alternative education. For this paper, I will focus on the technology components of the STEM curriculum. Technology in the United States, if not the world economy, is developing at a rapid pace. Many areas of day to day living, from applying for a job to checking one's bank account online, involve a component of science and technology. The 'gap' in technology education is emphasized between the 'haves and have-nots', which is delineated along socio-economic lines. Marginalized students in alternative education programs use this equipment for little else than remedial programs and credit recovery. This level of inequity further widens in alternative education programs and affects the achievement of marginalized students in credit recovery or alternative education classes instead of participation technology classes. For the purposes of this paper I focus on how can I decrease the inequity of student access to 21st century technology education in an alternative education program by addressing the established curriculum of the program and modifying structural barriers of marginalized student access to a technology focused curriculum.

  13. Novel in silico technology in combination with microarrays: a state-of-the-art technology for allergy diagnosis and management?

    Science.gov (United States)

    Melioli, Giovanni; Passalacqua, Giovanni; Canonica, Giorgio W

    2014-12-01

    'Allergen microarrays, in poly-sensitized allergic patients, represent a real value added in the accurate IgE profiling and in the identification of allergen(s) to administer for an effective allergen immunotherapy.' Allergen microarrays (AMA) were developed in the early 2000s to improve the diagnostic pathway of patients with allergic reactions. Nowadays, AMA are constituted by more than 100 different components (either purified or recombinant), representing genuine and cross-reacting molecules from plants and animals. The cost of the procedure had suggested its use as third-level diagnostics (following in vivo- and in vitro-specific IgE tests) in poly-sensitized patients. The complexity of the interpretation had inspired the development of in silico technologies to help clinicians in their work. Both machine learning techniques and expert systems are now available. In particular, an expert system that has been recently developed not only identifies positive and negative components but also lists dangerous components and classifies patients based on their potential responsiveness to allergen immunotherapy, on the basis of published algorithms. For these characteristics, AMA represents the state-of-the-art technology for allergy diagnosis in poly-sensitized patients.

  14. Freeing up access to CERN technology

    CERN Multimedia

    Joannah Caborn Wengler

    2012-01-01

    In line with CERN’s principle of maximising the dissemination of knowledge to society, the Knowledge Transfer (KT) Group has launched a new collaborative initiative to share the products of CERN’s scientific and technological labours: Easy Access IP, where IP stands for intellectual property.   CERN has a whole portfolio of dissemination channels designed and implemented by the KT Group, with Easy Access IP being the latest addition. “Inspired by the UK’s Easy Access Innovation initiative, our scheme involves making some of CERN's technologies available royalty-free and through a more agile licensing process,” explains Giovanni Anelli, head of the Group. “This approach seems to be an appropriate model for CERN, where the ultimate goal of technology transfer is not to generate income but to transfer knowledge to external partners.” The new scheme, as the name suggests, is designed to make it easier for industry and othe...

  15. Fitting new technologies into the safety paradigm: use of microarrays in transfusion.

    Science.gov (United States)

    Fournier-Wirth, C; Coste, J

    2007-01-01

    Until the late 1990s, mandatory blood screening for transmissible infectious agents depended entirely on antigen/antibody-based detection assays. The recent emergence of Nucleic acid Amplification Technologies (NAT) has revolutionised viral diagnosis, not only by increasing the level of sensitivity but also by facilitating the detection of several viruses in parallel by multiplexing specific primers. In more complex biological situations, when a broad spectrum of pathogens must be screened, the limitations of these first generation technologies became apparent. High throughput systems, such as DNA Arrays, permit a conceptually new approach. These miniaturised micro systems allow the detection of hundreds of different targets simultaneously, inducing a dramatic decrease in reagent consumption, a reduction in the number of confirmation tests and a simplification of data interpretation. However, the systems currently available require additional instrumentation and reagents for sample preparation and target amplification prior to detection on the DNA array. A major challenge in the area of DNA detection is the development of methods that do not rely on target amplification systems. Likewise, the advances of protein microarrays have lagged because of poor stability of proteins, complex coupling chemistry and weak detection signals. Emerging technologies like Biosensors and nano-particle based DNA or Protein Bio-Barcode Amplification Assays are promising diagnostic tools for a wide range of clinical applications, including blood donation screening.

  16. Access to the Arts through Assistive Technology.

    Science.gov (United States)

    Frame, Charles

    Personnel in the rehabilitation field have come to recognize the possibilities and implications of computers as assistive technology for disabled persons. This manual provides information on how to adapt the Unicorn Board, Touch Talker/Light Talker overlays, the Adaptive Firmware Card setup disk, and Trace-Transparent Access Module (T-TAM) to…

  17. Information and communication technology resources access and ...

    African Journals Online (AJOL)

    Journal Home > Vol 14, No 1 (2017) > ... The ability to undertake effective legal research is one of the skills required of a lawyer but ... The use of Information and communication technology by Nigerian lawyers deals with ... for Researchers · for Journals · for Authors · for Policy Makers · about Open Access · Journal Quality.

  18. Training Database Technology in DBMS MS Access

    Directory of Open Access Journals (Sweden)

    Nataliya Evgenievna Surkova

    2015-05-01

    Full Text Available The article describes the methodological issues of learning relational database technology and management systems relational databases. DBMS Microsoft Access is the primer for learning of DBMS. This methodology allows to generate some general cultural competence, such as the possession of the main methods, ways and means of production, storage and processing of information, computer skills as a means of managing information. Also must formed professional competence such as the ability to collect, analyze and process the data necessary for solving the professional tasks, the ability to use solutions for analytical and research tasks modern technology and information technology.

  19. Scientific information: technology, will and access

    Directory of Open Access Journals (Sweden)

    Ana M. B. Pavani

    2007-12-01

    Full Text Available This article addresses the access to information from a point of view that relates the evolution of technology to the methods of treating information and to the desire for knowledge. The first part introduces some important events in ancient times, the end of the middle ages/beginning of the modern age and the XIX century. Then, it presents an overview of the current situation of traditional libraries and compares some characteristics with the corresponding ones for digital libraries. It ends by mentioning the international efforts towards open archives and open access to information; it shows examples of positive results.

  20. K-12 Technology Accessibility: The Message from State Governments

    Science.gov (United States)

    Shaheen, Natalie L.; Lazar, Jonathan

    2018-01-01

    This study examined state education technology plans and technology accessibility statutes to attempt to answer the question--is K-12 instructional technology accessibility discussed in state-level technology accessibility statutes and education technology plans across the 50 United States? When a K-12 school district is planning the construction…

  1. Programming and Technology for Accessibility in Geoscience

    Science.gov (United States)

    Sevre, E.; Lee, S.

    2013-12-01

    Many people, students and professors alike, shy away from learning to program because it is often believed to be something scary or unattainable. However, integration of programming into geoscience education can be a valuable tool for increasing the accessibility of content for all who are interested. It is my goal to dispel these myths and convince people that: 1) Students with disabilities can use programming to increase their role in the classroom, 2) Everyone can learn to write programs to simplify daily tasks, 3) With a deep understanding of the task, anyone can write a program to do a complex task, 4) Technology can be combined with programming to create an inclusive environment for all students of geoscience, and 5) More advanced knowledge of programming and technology can lead geoscientists to create software to serve as assistive technology in the classroom. It is my goal to share my experiences using technology to enhance the classroom experience as a way of addressing the aforementioned issues. Through my experience, I have found that programming skills can be included and learned by all to enhance the content of courses without detracting from curriculum. I hope that, through this knowledge, geoscience courses can become more accessible for people with disabilities by including programming and technology to the benefit of all involved.

  2. Annotating breast cancer microarray samples using ontologies

    Science.gov (United States)

    Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

    2008-01-01

    As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108

  3. Training Database Technology in DBMS MS Access

    OpenAIRE

    Nataliya Evgenievna Surkova

    2015-01-01

    The article describes the methodological issues of learning relational database technology and management systems relational databases. DBMS Microsoft Access is the primer for learning of DBMS. This methodology allows to generate some general cultural competence, such as the possession of the main methods, ways and means of production, storage and processing of information, computer skills as a means of managing information. Also must formed professional competence such as the ability to coll...

  4. Microarrays (DNA Chips) for the Classroom Laboratory

    Science.gov (United States)

    Barnard, Betsy; Sussman, Michael; BonDurant, Sandra Splinter; Nienhuis, James; Krysan, Patrick

    2006-01-01

    We have developed and optimized the necessary laboratory materials to make DNA microarray technology accessible to all high school students at a fraction of both cost and data size. The primary component is a DNA chip/array that students "print" by hand and then analyze using research tools that have been adapted for classroom use. The…

  5. Personalized medicine and access to genetic technologies.

    Science.gov (United States)

    den Exter, André

    2010-01-01

    Personalized medicine started after the Human Genome Project and is a relatively new concept that will dramatically change clinical practice. It offers clear clinical advantages by applying genetic diagnostic tests and then treating the patient with targeted medicines based on his or her genetic make-up. Its potential seems promising but there are quite a few legal concerns. One of these questions deals with the right to health care and access to genetic technologies. In this paper, the author explains the meaning of such a right to health care under international human rights law, its relevance for making genetic services eligible for public funding, how to cope with quality concerns of commercial testing, and finally, the patentability controversy and clinical access to genetic information. Apart from more traditional human rights concerns (consent, privacy, confidentiality) and genetics, States should be aware of the meaning of the equal access concept under international law and its consequences when introducing new technologies such genetic testing and services.

  6. Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC study

    Directory of Open Access Journals (Sweden)

    Dial Stacey L

    2008-07-01

    Full Text Available Abstract Background The MicroArray Quality Control (MAQC project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (Nat Biotechnol 24:1115-22, 2006. The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan® Gene Expression PCR Assay, Standardized (Sta RT-PCR™ and QuantiGene®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR® Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT2 Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency. Results The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes. Conclusion These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.

  7. eSensor: an electrochemical detection-based DNA microarray technology enabling sample-to-answer molecular diagnostics

    Science.gov (United States)

    Liu, Robin H.; Longiaru, Mathew

    2009-05-01

    DNA microarrays are becoming a widespread tool used in life science and drug screening due to its many benefits of miniaturization and integration. Microarrays permit a highly multiplexed DNA analysis. Recently, the development of new detection methods and simplified methodologies has rapidly expanded the use of microarray technologies from predominantly gene expression analysis into the arena of diagnostics. Osmetech's eSensor® is an electrochemical detection platform based on a low-to- medium density DNA hybridization array on a cost-effective printed circuit board substrate. eSensor® has been cleared by FDA for Warfarin sensitivity test and Cystic Fibrosis Carrier Detection. Other genetic-based diagnostic and infectious disease detection tests are under development. The eSensor® platform eliminates the need for an expensive laser-based optical system and fluorescent reagents. It allows one to perform hybridization and detection in a single and small instrument without any fluidic processing and handling. Furthermore, the eSensor® platform is readily adaptable to on-chip sample-to-answer genetic analyses using microfluidics technology. The eSensor® platform provides a cost-effective solution to direct sample-to-answer genetic analysis, and thus have a potential impact in the fields of point-of-care genetic analysis, environmental testing, and biological warfare agent detection.

  8. Use of the cDNA microarray technology in thesafety assessment of GM food plants

    DEFF Research Database (Denmark)

    Pedersen, Jan W.; Knudsen, Ib; Eriksen, Folmer Damsted

    This report focuses on new analytical approaches that might give more insight into possible changes in a genetically modified plant. Primarily the focus is on the new DNA microarray technique but also proteomics and metabolomics are discussed.The report describes the new techniques and evaluates ...

  9. Use of the cDNA microarray technology in the safety assessment of GM food plants

    NARCIS (Netherlands)

    Kok, E.J.; Kleter, G.A.; Dijk, van J.P.

    2003-01-01

    This report focuses on new analytical approaches that might give more insight into possible changes in a genetically modified plant. Primarily the focus is on the new DNA microarray technique but also proteomics and metabolomics are discussed.The report describes the new techniques and evaluates the

  10. Development and Use of Integrated Microarray-Based Genomic Technologies for Assessing Microbial Community Composition and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    J. Zhou; S.-K. Rhee; C. Schadt; T. Gentry; Z. He; X. Li; X. Liu; J. Liebich; S.C. Chong; L. Wu

    2004-03-17

    different microbial communities and processes at the NABIR-FRC in Oak Ridge, TN. One project involves the monitoring of the development and dynamics of the microbial community of a fluidized bed reactor (FBR) used for reducing nitrate and the other project monitors microbial community responses to stimulation of uranium reducing populations via ethanol donor additions in situ and in a model system. Additionally, we are developing novel strategies for increasing microarray hybridization sensitivity. Finally, great improvements to our methods of probe design were made by the development of a new computer program, CommOligo. CommOligo designs unique and group-specific oligo probes for whole-genomes, metagenomes, and groups of environmental sequences and uses a new global alignment algorithm to design single or multiple probes for each gene or group. We are now using this program to design a more comprehensive functional gene array for environmental studies. Overall, our results indicate that the 50mer-based microarray technology has potential as a specific and quantitative tool to reveal the composition of microbial communities and their dynamics important to processes within contaminated environments.

  11. Experience With Rapid Microarray-Based Diagnostic Technology and Antimicrobial Stewardship for Patients With Gram-Positive Bacteremia.

    Science.gov (United States)

    Neuner, Elizabeth A; Pallotta, Andrea M; Lam, Simon W; Stowe, David; Gordon, Steven M; Procop, Gary W; Richter, Sandra S

    2016-11-01

    OBJECTIVE To describe the impact of rapid diagnostic microarray technology and antimicrobial stewardship for patients with Gram-positive blood cultures. DESIGN Retrospective pre-intervention/post-intervention study. SETTING A 1,200-bed academic medical center. PATIENTS Inpatients with blood cultures positive for Staphylococcus aureus, Enterococcus faecalis, E. faecium, Streptococcus pneumoniae, S. pyogenes, S. agalactiae, S. anginosus, Streptococcus spp., and Listeria monocytogenes during the 6 months before and after implementation of Verigene Gram-positive blood culture microarray (BC-GP) with an antimicrobial stewardship intervention. METHODS Before the intervention, no rapid diagnostic technology was used or antimicrobial stewardship intervention was undertaken, except for the use of peptide nucleic acid fluorescent in situ hybridization and MRSA agar to identify staphylococcal isolates. After the intervention, all Gram-positive blood cultures underwent BC-GP microarray and the antimicrobial stewardship intervention consisting of real-time notification and pharmacist review. RESULTS In total, 513 patients with bacteremia were included in this study: 280 patients with S. aureus, 150 patients with enterococci, 82 patients with stretococci, and 1 patient with L. monocytogenes. The number of antimicrobial switches was similar in the pre-BC-GP (52%; 155 of 300) and post-BC-GP (50%; 107 of 213) periods. The time to antimicrobial switch was significantly shorter in the post-BC-GP group than in the pre-BC-GP group: 48±41 hours versus 75±46 hours, respectively (P<.001). The most common antimicrobial switch was de-escalation and time to de-escalation, was significantly shorter in the post-BC-GP group than in the pre-BC-GP group: 53±41 hours versus 82±48 hours, respectively (P<.001). There was no difference in mortality or hospital length of stay as a result of the intervention. CONCLUSIONS The combination of a rapid microarray diagnostic test with an antimicrobial

  12. GeneRank: Using search engine technology for the analysis of microarray experiments

    Directory of Open Access Journals (Sweden)

    Breitling Rainer

    2005-09-01

    Full Text Available Abstract Background Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method – based on the PageRank algorithm employed by the popular search engine Google – that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information. Results GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings. Conclusion Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments.

  13. GeneRank: using search engine technology for the analysis of microarray experiments.

    Science.gov (United States)

    Morrison, Julie L; Breitling, Rainer; Higham, Desmond J; Gilbert, David R

    2005-09-21

    Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method--based on the PageRank algorithm employed by the popular search engine Google--that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information. GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings. Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments.

  14. Language and technology literacy barriers to accessing government services

    CSIR Research Space (South Africa)

    Barnard, E

    2003-01-01

    Full Text Available of field experiments are done to gain an improved understanding of the extent to which citizens’ exposure to technology and home language affect their ability to access electronic services. These experiments will influence technology development...

  15. Synthesis and conformational characterization of functional di-block copolymer brushes for microarray technology

    Energy Technology Data Exchange (ETDEWEB)

    Di Carlo, Gabriele; Damin, Francesco [Institute of Chemistry of Molecular Recognition, National Research Council of Italy, Via M. Bianco 9, 20131 Milano (Italy); Armelao, Lidia [ISTM-CNR and INSTM, Department of Chemistry, University of Padova, Via F. Marzolo 1, 35131 Padova (Italy); Maccato, Chiara [Department of Chemistry and INSTM, University of Padova, Via F. Marzolo 1, 35131 Padova (Italy); Unlu, Selim [Department of Electrical and Computer Engineering, Boston University, St. Mary Street 8, Boston, MA 02215 (United States); Department of Biomedical Engineering, Boston University, St. Mary Street 8, Boston, MA 02215 (United States); Spuhler, Philipp S. [Department of Biomedical Engineering, Boston University, St. Mary Street 8, Boston, MA 02215 (United States); Chiari, Marcella, E-mail: marcella.chiari@icrm.cnr.it [Institute of Chemistry of Molecular Recognition, National Research Council of Italy, Via M. Bianco 9, 20131 Milano (Italy)

    2012-02-01

    Surface initiated polymerization (SIP) coupled with reversible addition-fragmentation chain transfer polymerization (RAFT) was used to functionalize microarray glass slides with block polymer brushes. N,N-dimethylacrylamide (DMA) and N-acryloyloxysuccinimide (NAS) (graft-poly[DMA-b-(DMA-co-NAS)]) brushes, with di-block architecture, were prepared from a novel RAFT chain transfer agent bearing a silanating moiety (RAFT silane) directly anchored onto the glass surfaces. Conformational characterization of the coatings was performed by Self Spectral Interference Fluorescence Microscopy (SSFM), an innovative technique that describes the location of a fluorescent DNA molecule relative to a surface with sub-nanometer accuracy. X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy (SEM) were used to characterize the coatings composition and morphology.

  16. Synthesis and conformational characterization of functional di-block copolymer brushes for microarray technology

    International Nuclear Information System (INIS)

    Di Carlo, Gabriele; Damin, Francesco; Armelao, Lidia; Maccato, Chiara; Unlu, Selim; Spuhler, Philipp S.; Chiari, Marcella

    2012-01-01

    Surface initiated polymerization (SIP) coupled with reversible addition-fragmentation chain transfer polymerization (RAFT) was used to functionalize microarray glass slides with block polymer brushes. N,N-dimethylacrylamide (DMA) and N-acryloyloxysuccinimide (NAS) (graft-poly[DMA-b-(DMA-co-NAS)]) brushes, with di-block architecture, were prepared from a novel RAFT chain transfer agent bearing a silanating moiety (RAFT silane) directly anchored onto the glass surfaces. Conformational characterization of the coatings was performed by Self Spectral Interference Fluorescence Microscopy (SSFM), an innovative technique that describes the location of a fluorescent DNA molecule relative to a surface with sub-nanometer accuracy. X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy (SEM) were used to characterize the coatings composition and morphology.

  17. High-throughput immunophenotyping of 43 ferret lymphomas using tissue microarray technology

    DEFF Research Database (Denmark)

    Hammer, Anne Sofie; Williams, B.; Dietz, H.H.

    2007-01-01

    To validate the use of the tissue microarray (TMA) method for immunophenotyping of ferret lymphomas, a TMA was constructed containing duplicate 1-mm cores sampled from 112 paraffin-embedded lymphoma tissue specimens obtained from 43 ferret lymphoma cases. Immunohistochemical (IHC) expression of CD3......, CD79 alpha, and Ki-67 (MIB-1) was determined by TMA and whole mount (WM) staining of each individual case for result comparison. There was a high correlation between CD79 alpha and CD3 results comparing ferret TMA and WM sections (kappa statistic 0.71-0.73 for single-core TMA and 0.......79-0.95 for duplicate-core TMA) and between continuous data from Ki-67 staining of ferret TMA sections and WM sections (concordance correlation coefficients 0.77 for single cores and 0.87 for duplicate cores). Subsequently, a panel of commercially available antibodies was applied to the TMA for the analysis...

  18. Technological Innovation and Cooperation for Foreign Information Access Program

    Science.gov (United States)

    Office of Postsecondary Education, US Department of Education, 2012

    2012-01-01

    The Technological Innovation and Cooperation for Foreign Information Access (TICFIA) Program supports projects focused on developing innovative technologies for accessing, collecting, organizing, preserving, and disseminating information from foreign sources to address the U.S.' teaching and research needs in international education and foreign…

  19. Technology for People, Not Disabilities: Ensuring Access and Inclusion

    Science.gov (United States)

    Foley, Alan; Ferri, Beth A.

    2012-01-01

    The potential of technology to connect people and provide access to education, commerce, employment and entertainment has never been greater or more rapidly changing. Communication technologies and new media promise to "revolutionize our lives" by breaking down barriers and expanding access for disabled people. Yet, it is also true that technology…

  20. Nano-sized titanium dioxide-induced splenic toxicity: A biological pathway explored using microarray technology

    Energy Technology Data Exchange (ETDEWEB)

    Sheng, Lei [Medical College of Soochow University, Suzhou 215123 (China); Wang, Ling [Library of Soochow University, Suzhou 215123 (China); Sang, Xuezi; Zhao, Xiaoyang; Hong, Jie; Cheng, Shen; Yu, Xiaohong; Liu, Dong; Xu, Bingqing; Hu, Renping; Sun, Qingqing; Cheng, Jie; Cheng, Zhe; Gui, Suxin [Medical College of Soochow University, Suzhou 215123 (China); Hong, Fashui, E-mail: Hongfsh_cn@sina.com [Medical College of Soochow University, Suzhou 215123 (China)

    2014-08-15

    Highlights: • Exposure to TiO{sub 2} NPs could be accumulated in the spleen. • Exposure to TiO{sub 2} NPs caused spleen lesions in mice. • Exposure to TiO{sub 2} NPs resulted in immune dysfunction in mice. • Exposure to TiO{sub 2} NPs caused alteration of 1041 genes expression of known function in the spleen. - Abstract: Titanium dioxide nanoparticles (TiO{sub 2} NPs) have been widely used in various areas, and its potential toxicity has gained wide attention. However, the molecular mechanisms of multiple genes working together in the TiO{sub 2} NP-induced splenic injury are not well understood. In the present study, 2.5, 5, or 10 mg/kg body weight TiO{sub 2} NPs were administered to the mice by intragastric administration for 90 consecutive days, their immune capacity in the spleen as well as the gene-expressed characteristics in the mouse damaged spleen were investigated using microarray assay. The findings showed that with increased dose, TiO{sub 2} NP exposure resulted in the increases of spleen indices, immune dysfunction, and severe macrophage infiltration as well as apoptosis in the spleen. Importantly, microarray data showed significant alterations in the expressions of 1041 genes involved in immune/inflammatory responses, apoptosis, oxidative stress, stress responses, metabolic processes, ion transport, signal transduction, cell proliferation/division, cytoskeleton and translation in the 10 mg/kg TiO{sub 2} NP-exposed spleen. Specifically, Cyp2e1, Sod3, Mt1, Mt2, Atf4, Chac1, H2-k1, Cxcl13, Ccl24, Cd14, Lbp, Cd80, Cd86, Cd28, Il7r, Il12a, Cfd, and Fcnb may be potential biomarkers of spleen toxicity following exposure to TiO{sub 2} NPs.

  1. RFID Based Security Access Control System with GSM Technology

    OpenAIRE

    Peter Adole; Joseph M. Môm; Gabriel A. Igwue

    2016-01-01

    The security challenges being encountered in many places today require electronic means of controlling access to secured premises in addition to the available security personnel. Various technologies were used in different forms to solve these challenges. The Radio Frequency Identification (RFID) Based Access Control Security system with GSM technology presented in this work helps to prevent unauthorized access to controlled environments (secured premises). This is achieved mainly...

  2. Instructional Technology for Rural Schools: Access and Acquisition

    Science.gov (United States)

    Sundeen, Todd H.; Sundeen, Darrelanne M.

    2013-01-01

    Integrating instructional technology into all classrooms has the potential to transform modern education and student learning. However, access to technology is not equally available to all districts or schools. Decreased funding and budgetary restraints have had a direct impact on technology acquisition in many rural school districts. One of the…

  3. Factors associated with access of rural women to technology in ...

    African Journals Online (AJOL)

    A descriptive, correlational study was conducted to: describe the channels through which rural women obtain information regarding technology, and factors promoting access of women to technology; determine the contribution of technology to socio-economic development; and describe the relationships among factors ...

  4. Discovery of distinctive gene expression profiles in rheumatoid synovium using cDNA microarray technology: evidence for the existence of multiple pathways of tissue destruction and repair.

    NARCIS (Netherlands)

    Kraan, TC van der Pouw; Gaalen, van FA; Huizinga, T.W.; Pieterman, E; Breedveld, F.C.; Verweij, C.L.

    2003-01-01

    Rheumatoid arthritis (RA) is a heterogeneous disease. We used cDNA microarray technology to subclassify RA patients and disclose disease pathways in rheumatoid synovium. Hierarchical clustering of gene expression data identified two main groups of tissues (RA-I and RA-II). A total of 121 genes were

  5. Identification of human papillomavirus (HPV) subtype in oral cancer patients through microarray technology.

    Science.gov (United States)

    Kim, Soung Min; Kwon, Ik Jae; Myoung, Hoon; Lee, Jong Ho; Lee, Suk Keun

    2018-02-01

    Human papilloma virus (HPV) is the main source of cervical cancer. Many recent studies have revealed the prevalence and prognosis of HPV associated with oropharyngeal squamous cell carcinoma, but fewer reports have evaluated HPV in oral squamous cell carcinoma (OSCC). The purpose of this study was to determine the prevalence and prognosis of HPV associated with OSCC according to HPV and tumor types. We used a DNA chip kit (MY-HPV chip kit ® , Mygene Co., Korea) to detect high-risk HPV subtypes (16, 18, 31, 33, 35, 39, 45, 51, 52, 54, 56, 58) and low-risk subtypes (6, 11, 34, 40, 42, 43, 44) among 187 patients. The prevalence was determined by Chi-square and Fisher's exact tests, and the prognosis was calculated by the Kaplan-Meier method and the log-rank test. The overall prevalence of HPV in OSCC was 7.0% for all HPV positives and 4.3% for high-risk HPV positives. The prevalence of HPV was significantly higher in individuals under 65 years old and in those with tumors in the tongue and gum regions. The prognosis did not differ between the HPV-positive and -negative groups. Although the prevalence of HPV-positive cases in OSCC was low (7.0, 4.3%) and the prognosis did not depend on HPV positivity, HPV-associated OSCC should be considered in the evaluation and treatment of oral cancer patients. In addition, separating high- and low-risk groups based on the HPV status of other body parts might not be appropriate. The DNA microarray method can accurately detect known HPV subtypes simultaneously, but has limitations in detecting new subtypes. Vaccines can also be used to prevent HPV-associated OSCC in patients, so further studies on the prognosis and efficacy of vaccines should be undertaken.

  6. The potential use of mobile technology: enhancing accessibility and ...

    African Journals Online (AJOL)

    The potential use of mobile technology: enhancing accessibility and communication in a blended ... South African Journal of Education ... Recommendations, limitations of the present study, and suggestions for future research were made.

  7. Analysis of a simulated microarray dataset: Comparison of methods for data normalisation and detection of differential expression (Open Access publication

    Directory of Open Access Journals (Sweden)

    Mouzaki Daphné

    2007-11-01

    Full Text Available Abstract Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised data are also abundant, and no clear consensus has yet been reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. With the a priori knowledge of which genes are differentially expressed, it is possible to compare the success of each approach quantitatively. Use of an intensity-dependent normalisation procedure was common, as was correction for multiple testing. Most variety in performance resulted from differing approaches to data quality and the use of different statistical tests. Very few of the methods used any kind of background correction. A number of approaches achieved a success rate of 95% or above, with relatively small numbers of false positives and negatives. Applying stringent spot selection criteria and elimination of data did not improve the false positive rate and greatly increased the false negative rate. However, most approaches performed well, and it is encouraging that widely available techniques can achieve such good results on a very noisy data set.

  8. Plug-and-actuate on demand: multimodal individual addressability of microarray plates using modular hybrid acoustic wave technology.

    Science.gov (United States)

    Rezk, Amgad R; Ramesan, Shwathy; Yeo, Leslie Y

    2018-01-30

    The microarray titre plate remains a fundamental workhorse in genomic, proteomic and cellomic analyses that underpin the drug discovery process. Nevertheless, liquid handling technologies for sample dispensing, processing and transfer have not progressed significantly beyond conventional robotic micropipetting techniques, which are not only at their fundamental sample size limit, but are also prone to mechanical failure and contamination. This is because alternative technologies to date suffer from a number of constraints, mainly their limitation to carry out only a single liquid operation such as dispensing or mixing at a given time, and their inability to address individual wells, particularly at high throughput. Here, we demonstrate the possibility for true sequential or simultaneous single- and multi-well addressability in a 96-well plate using a reconfigurable modular platform from which MHz-order hybrid surface and bulk acoustic waves can be coupled to drive a variety of microfluidic modes including mixing, sample preconcentration and droplet jetting/ejection in individual or multiple wells on demand, thus constituting a highly versatile yet simple setup capable of improving the functionality of existing laboratory protocols and processes.

  9. Access to information technology and willingness to receive text ...

    African Journals Online (AJOL)

    Over the past decade, new technologies and methods of communication have ... To determine access to information technology and willingness to receive short message service (SMS) text message reminders for childhood immunisation .... Table 1 shows the attitude of the mothers towards reminders for immunisations.

  10. Radiation technology enabled market access to Indian mango

    International Nuclear Information System (INIS)

    Sharma, Arun

    2009-01-01

    International trade in agricultural produce is subject to quarantine barriers imposed by importing countries to limit the entry of exotic pests and pathogens. Radiation technology provides an effective alternative to fumigants which are being gradually phased out. The technology has enabled market access to Indian mangoes in the US market after a gap of 18 years. The technology provides opportunity for export of other fruits and vegetables as well to countries like US, Australia and New Zealand. (author)

  11. Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes

    Directory of Open Access Journals (Sweden)

    Bihoreau Marie-Thérèse

    2009-02-01

    Full Text Available Abstract Background Microarray technologies are widely used to quantify the abundance of transcripts corresponding to thousands of genes. To maximise the robustness of transcriptome results, we have tested the performance and reproducibility of rat and mouse gene expression data obtained with Affymetrix, Illumina and Operon platforms. Results We present a thorough analysis of the degree of reproducibility provided by analysing the transcriptomic profile of the same animals of several experimental groups under different popular microarray technologies in different tissues. Concordant results from inter- and intra-platform comparisons were maximised by testing many popular computational methods for generating fold changes and significances and by only considering oligonucleotides giving high expression levels. The choice of Affymetrix signal extraction technique was shown to have the greatest effect on the concordance across platforms. In both species, when choosing optimal methods, the agreement between data generated on the Affymetrix and Illumina was excellent; this was verified using qRT-PCR on a selection of genes present on all platforms. Conclusion This study provides an extensive assessment of analytical methods best suited for processing data from different microarray technologies and can assist integration of technologically different gene expression datasets in biological systems.

  12. Differential screening of phage-ab libraries by oligonucleotide microarray technology.

    Directory of Open Access Journals (Sweden)

    Paolo Monaci

    Full Text Available A novel and efficient tagArray technology was developed that allows rapid identification of antibodies which bind to receptors with a specific expression profile, in the absence of biological information. This method is based on the cloning of a specific, short nucleotide sequence (tag in the phagemid coding for each phage-displayed antibody fragment (phage-Ab present in a library. In order to set up and validate the method we identified about 10,000 different phage-Abs binding to receptors expressed in their native form on the cell surface (10 k Membranome collection and tagged each individual phage-Ab. The frequency of each phage-Ab in a given population can at this point be inferred by measuring the frequency of its associated tag sequence through standard DNA hybridization methods. Using tiny amounts of biological samples we identified phage-Abs binding to receptors preferentially expressed on primary tumor cells rather than on cells obtained from matched normal tissues. These antibodies inhibited cell proliferation in vitro and tumor development in vivo, thus representing therapeutic lead candidates.

  13. Survey of Canadian Myotonic Dystrophy Patients' Access to Computer Technology.

    Science.gov (United States)

    Climans, Seth A; Piechowicz, Christine; Koopman, Wilma J; Venance, Shannon L

    2017-09-01

    Myotonic dystrophy type 1 is an autosomal dominant condition affecting distal hand strength, energy, and cognition. Increasingly, patients and families are seeking information online. An online neuromuscular patient portal under development can help patients access resources and interact with each other regardless of location. It is unknown how individuals living with myotonic dystrophy interact with technology and whether barriers to access exist. We aimed to characterize technology use among participants with myotonic dystrophy and to determine whether there is interest in a patient portal. Surveys were mailed to 156 participants with myotonic dystrophy type 1 registered with the Canadian Neuromuscular Disease Registry. Seventy-five participants (60% female) responded; almost half were younger than 46 years. Most (84%) used the internet; almost half of the responders (47%) used social media. The complexity and cost of technology were commonly cited reasons not to use technology. The majority of responders (76%) were interested in a myotonic dystrophy patient portal. Patients in a Canada-wide registry of myotonic dystrophy have access to and use technology such as computers and mobile phones. These patients expressed interest in a portal that would provide them with an opportunity to network with others with myotonic dystrophy and to access information about the disease.

  14. Access to information technology and willingness to receive text ...

    African Journals Online (AJOL)

    Background. Effective communication is imperative for the delivery and receipt of adequate health care services. Aim. To determine access to information technology and willingness to receive short message service (SMS) text message reminders for childhood immunisation services among mothers in Lagos, Nigeria.

  15. Techno-economic evaluation of broadband access technologies

    DEFF Research Database (Denmark)

    Sigurdsson, Halldór Matthias; Skouby, Knud Erik

    2005-01-01

    Broadband for all is an essential element in the EU policy concerning the future of ICT-based society. The overall purpose of this paper is to present a model for evaluation of different broadband access technologies and to present some preliminary results based on the model that has been carried...

  16. 8th Cambridge Workshop on Universal Access and Assistive Technology

    CERN Document Server

    Lazar, Jonathan; Heylighen, Ann; Dong, Hua

    2016-01-01

    This book presents the proceedings of the 8th Cambridge Workshop on Universal Access and Assistive Technology (CWUAAT '14), incorporating the 11th Cambridge Workshop on Rehabilitation Robotics, held in Cambridge, England in March 2016. It presents novel and state-of-the-art research from an international group of leaders in the fields of universal access and assistive technology. It explores various issues including the reconciliation of usability, accessibility and inclusive design, the design of inclusive assistive and rehabilitation systems, measuring product demand and human capabilities, data mining and visualizing inclusion, legislation in inclusive design, and situational inclusive interfaces (automotive and aerospace). This book provides an invaluable resource to researchers, postgraduates, design practitioners, therapists and clinical practitioners, as well as design teachers.

  17. Optical fiber cabling technologies for flexible access network

    Science.gov (United States)

    Tanji, Hisashi

    2008-07-01

    Fiber-to-the-home (FTTH) outside plant infrastructure should be so designed and constructed as to flexibly deal with increasing subscribers and system evolution to be expected in the future, taking minimization of total cost (CAPEX and OPEX) into consideration. With this in mind, fiber access architectures are reviewed and key technologies on optical fiber and cable for supporting flexible access network are presented. Low loss over wide wavelength (low water peak) and bend-insensitive single mode fiber is a future proof solution. Enhanced separable ribbon facilitates mid-span access to individual fibers in a cable installed, improving fiber utilizing efficiency and flexibility of distribution design. It also contributes to an excellent low PMD characteristic which could be required for video RF overlay system or high capacity long reach metro-access convergence network in the future. Bend-insensitive fiber based cabling technique including field installable connector greatly improves fiber/cable handling in installation and maintenance work.

  18. Direct calibration of PICKY-designed microarrays

    Directory of Open Access Journals (Sweden)

    Ronald Pamela C

    2009-10-01

    Full Text Available Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

  19. Access to augmentative and alternative communication: new technologies and clinical decision-making.

    Science.gov (United States)

    Fager, Susan; Bardach, Lisa; Russell, Susanne; Higginbotham, Jeff

    2012-01-01

    Children with severe physical impairments require a variety of access options to augmentative and alternative communication (AAC) and computer technology. Access technologies have continued to develop, allowing children with severe motor control impairments greater independence and access to communication. This article will highlight new advances in access technology, including eye and head tracking, scanning, and access to mainstream technology, as well as discuss future advances. Considerations for clinical decision-making and implementation of these technologies will be presented along with case illustrations.

  20. Using Technology to Improve Access to Mental Health Services.

    Science.gov (United States)

    Cortelyou-Ward, Kendall; Rotarius, Timothy; Honrado, Jed C

    Mental ill-health is a public health threat that is prevalent throughout the United States. Tens of millions of Americans have been diagnosed along the continuum of mental ill-health, and many more millions of family members and friends are indirectly affected by the pervasiveness of mental ill-health. Issues such as access and the societal stigma related to mental health issues serve as deterrents to patients receiving their necessary care. However, technological advances have shown the potential to increase access to mental health services for many patients.

  1. Enabling Dedicated, Affordable Space Access Through Aggressive Technology Maturation

    Science.gov (United States)

    Jones, Jonathan E.; Kibbey, Timothy P.; Cobb, C. Brent; Harris, Lawanna L.

    2014-01-01

    A launch vehicle at the scale and price point which allows developers to take reasonable risks with high payoff propulsion and avionics hardware solutions does not exist today. Establishing this service provides a ride through the proverbial technology "valley of death" that lies between demonstration in laboratory and flight environments. NASA's NanoLaunch effort will provide the framework to mature both earth-to-orbit and on-orbit propulsion and avionics technologies while also providing affordable, dedicated access to low earth orbit for cubesat class payloads.

  2. The challenge of making nuclear technologies acceptable, accessible and affordable

    International Nuclear Information System (INIS)

    Ramamurthy, V.S.

    2009-01-01

    Full text: It is more than five decades since the first successful demonstration of nuclear power for commercial electricity production. The same decades have also seen the successful demonstration of several other applications of nuclear technologies that can contribute directly to human development, as for example, in the Food and Agriculture, Human and animal Health, Environment and Water sectors. In spite of several successful demonstrations and applications in these fields, it is somewhat strange that their full potential is yet to be realized. More importantly, their availability to populations across the world is highly skewed. Three barriers have been identified for the wide spread use of nuclear technologies for development- Acceptability, Accessibility and Affordability. It is an unfortunate twist of fate that the first public demonstration of nuclear technology was its destructive power. The following demonization of anything nuclear was further compounded by the discussions on the unresolved questions on tackling long lived radioactive wastes, our inability to arrive at a global consensus on nuclear disarmament and issues of nuclear proliferation. These have certainly had a negative impact on the public acceptance of nuclear technologies across the board. While the recent concerns on the global climate change following the emission of carbon-di-oxide from excessive hydrocarbon burning for meeting our increasing energy needs have revived the interest in nuclear energy, a lot needs to be done to de-demonize nuclear technologies in public mind leading to increased acceptance of nuclear technologies for development. Lack of resources, infrastructure and trained man power also have a negative impact on the accessibility and affordability of the nuclear technologies for development. It is argued that only education holds the key for this. The role of international partnerships is also highlighted in realizing the full potential of nuclear technologies for

  3. Exploring Accessibility Scenarios for 2020 in Relation with Future ICT Trends on Assistive Technology and Accessibility

    Directory of Open Access Journals (Sweden)

    Adamantios Koumpis

    2012-01-01

    Full Text Available In this paper we are going to present a set of 5 future scenarios that were developed within the eAccessibility2020 study. The study aims to explore and analyse the referred relationships between the emerging ICT landscape, in the societal and economic context and the development and provision of assistive technologies (AT and e-Accessibility, within a perspective of 10 years. The scenarios were developed after an initial trend analysis that the study team conducted based on data gathering. The scenarios were developed based on a methodology which defined a set of guides for scenario development and a set of visions for the future of eAccessibility.

  4. Disruptive technological advances in vascular access for dialysis: an overview.

    Science.gov (United States)

    Yeo, Wee-Song; Ng, Qin Xiang

    2017-11-29

    End-stage kidney disease (ESKD), one of the most prevalent diseases in the world and with increasing incidence, is associated with significant morbidity and mortality. Current available modes of renal replacement therapy (RRT) include dialysis and renal transplantation. Though renal transplantation is the preferred and ideal mode of RRT, this modality may not be available to all patients with ESKD. Moreover, renal transplant recipients are constantly at risk of complications associated with immunosuppression and immunosuppressant use, and posttransplant lymphoproliferative disorder. Dialysis may be the only available modality in certain patients. However, dialysis has its limitations, which include issues associated with lack of vascular access, risks of infections and vascular thrombosis, decreased quality of life, and absence of biosynthetic functions of the kidney. In particular, the creation and maintenance of hemodialysis vascular access in children poses a unique set of challenges to the pediatric nephrologist owing to the smaller vessel diameters and vascular hyperreactivity compared with adult patients. Vascular access issues continue to be one of the major limiting factors prohibiting the delivery of adequate dialysis in ESKD patients and is the Achilles' heel of hemodialysis. This review aims to provide a critical overview of disruptive technological advances and innovations for vascular access. Novel strategies in preventing neointimal hyperplasia, novel bioengineered products, grafts and devices for vascular access will be discussed. The potential impact of these solutions on improving the morbidity encountered by dialysis patients will also be examined.

  5. Validating an infrared thermal switch as a novel access technology

    Directory of Open Access Journals (Sweden)

    Memarian Negar

    2010-08-01

    Full Text Available Abstract Background Recently, a novel single-switch access technology based on infrared thermography was proposed. The technology exploits the temperature differences between the inside and surrounding areas of the mouth as a switch trigger, thereby allowing voluntary switch activation upon mouth opening. However, for this technology to be clinically viable, it must be validated against a gold standard switch, such as a chin switch, that taps into the same voluntary motion. Methods In this study, we report an experiment designed to gauge the concurrent validity of the infrared thermal switch. Ten able-bodied adults participated in a series of 3 test sessions where they simultaneously used both an infrared thermal and conventional chin switch to perform multiple trials of a number identification task with visual, auditory and audiovisual stimuli. Participants also provided qualitative feedback about switch use. User performance with the two switches was quantified using an efficiency measure based on mutual information. Results User performance (p = 0.16 and response time (p = 0.25 with the infrared thermal switch were comparable to those of the gold standard. Users reported preference for the infrared thermal switch given its non-contact nature and robustness to changes in user posture. Conclusions Thermal infrared access technology appears to be a valid single switch alternative for individuals with disabilities who retain voluntary mouth opening and closing.

  6. Accessing NASA Technology with the World Wide Web

    Science.gov (United States)

    Nelson, Michael L.; Bianco, David J.

    1995-01-01

    NASA Langley Research Center (LaRC) began using the World Wide Web (WWW) in the summer of 1993, becoming the first NASA installation to provide a Center-wide home page. This coincided with a reorganization of LaRC to provide a more concentrated focus on technology transfer to both aerospace and non-aerospace industry. Use of WWW and NCSA Mosaic not only provides automated information dissemination, but also allows for the implementation, evolution and integration of many technology transfer and technology awareness applications. This paper describes several of these innovative applications, including the on-line presentation of the entire Technology OPportunities Showcase (TOPS), an industrial partnering showcase that exists on the Web long after the actual 3-day event ended. The NASA Technical Report Server (NTRS) provides uniform access to many logically similar, yet physically distributed NASA report servers. WWW is also the foundation of the Langley Software Server (LSS), an experimental software distribution system which will distribute LaRC-developed software. In addition to the more formal technology distribution projects, WWW has been successful in connecting people with technologies and people with other people.

  7. Open access for ALICE analysis based on virtualization technology

    CERN Document Server

    Buncic, P; Schutz, Y

    2015-01-01

    Open access is one of the important leverages for long-term data preservation for a HEP experiment. To guarantee the usability of data analysis tools beyond the experiment lifetime it is crucial that third party users from the scientific community have access to the data and associated software. The ALICE Collaboration has developed a layer of lightweight components built on top of virtualization technology to hide the complexity and details of the experiment-specific software. Users can perform basic analysis tasks within CernVM, a lightweight generic virtual machine, paired with an ALICE specific contextualization. Once the virtual machine is launched, a graphical user interface is automatically started without any additional configuration. This interface allows downloading the base ALICE analysis software and running a set of ALICE analysis modules. Currently the available tools include fully documented tutorials for ALICE analysis, such as the measurement of strange particle production or the nuclear modi...

  8. Improving patient access to novel medical technologies in Europe.

    LENUS (Irish Health Repository)

    Kearney, Peter

    2012-02-03

    The European Society of Cardiology (ESC) organized a one-day workshop with clinicians, health economic experts, and health technology appraisal experts to discuss the equity of patient access to novel medical technologies in Europe. Two index technologies were considered: implantable cardioverter defibrillators (ICDs) and drug-eluting stents (DES). The use of ICDs range from 35 implants\\/million population in Portugal to 166 implants\\/million population in Germany, whereas for implants of DES (as percentage of total stents) it is lowest in Germany at 14% and high in Portugal at 65%. These differences can in part be explained by a lack of structured implementation of guidelines, the direct cost in relation to the overall healthcare budget, and to differences in procedures and models applied by Health Technology Assessment (HTA) agencies in Europe. The workshop participants concluded that physicians need to be involved in a more structured way in HTA and need to become better acquainted with its methods and terminology. Clinical guidelines should be systematically translated, explained, disseminated, updated, and adopted by cardiologists in Europe. Clinically appropriate, consistent and transparent health economic models need to be developed and high-quality international outcome and cost data should be used. A process for funding of a technology should be developed after a positive recommendation from HTA agencies. Both the ESC and the national cardiac societies should build-up health economic expertise and engage more actively in discussions with stakeholders involved in the provision of healthcare.

  9. The applied technologies to access clean water for remote communities

    Science.gov (United States)

    Rabindra, I. B.

    2018-01-01

    A lot of research is done to overcome the remote communities to access clean water, yet very little is utilized and implemented by the community. Various reasons can probably be made for, which is the application of research results is assessed less practical. The aims of this paper is seeking a practical approach, how to establish criteria for the design can be easier applied, at the proper locations, the simple construction, effectively producing a volume and quality of clean water designation. The methods used in this paper is a technological model assessment of treatment/filtering clean water produced a variety of previous research, to establish a model of appropriate technology for remote communities. Various research results collected from the study of literature, while the identification of opportunities and threats to its application is done using a SWOT analysis. This article discussion is looking for alternative models of clean water filtration technology from the previous research results, to be selected as appropriate technology, easily applied and bring of many benefits to the remote communities. The conclusions resulting from the discussion in this paper, expected to be used as the basic criteria of design model of clean water filtration technologies that can be accepted and applied effectively by the remote communities.

  10. 7th Cambridge Workshops on Universal Access and Assistive Technology

    CERN Document Server

    Lazar, J; Heylighen, A; Dong, H; Inclusive Designing : Joining Usability, Accessibility, and Inclusion

    2014-01-01

    ‘Inclusive Designing’ presents the proceedings of the seventh Cambridge Workshop on Universal Access and Assistive Technology (CWUAAT '14). It represents a unique multi-disciplinary workshop for the Inclusive Design Research community where designers, computer scientists, engineers, architects, ergonomists, policymakers and user communities can exchange ideas. The research presented at CWUAAT '14 develops methods, technologies, tools and guidance that support product designers and architects to design for the widest possible population for a given range of capabilities, within a contemporary social and economic context. In the context of developing demographic changes leading to greater numbers of older people and people with disabilities, the general field of Inclusive Design Research strives to relate the capabilities of the population to the design of products. Inclusive populations of older people contain a greater variation in sensory, cognitive and physical user capabilities. These variations may be...

  11. Open access for ALICE analysis based on virtualization technology

    International Nuclear Information System (INIS)

    Buncic, P; Gheata, M; Schutz, Y

    2015-01-01

    Open access is one of the important leverages for long-term data preservation for a HEP experiment. To guarantee the usability of data analysis tools beyond the experiment lifetime it is crucial that third party users from the scientific community have access to the data and associated software. The ALICE Collaboration has developed a layer of lightweight components built on top of virtualization technology to hide the complexity and details of the experiment-specific software. Users can perform basic analysis tasks within CernVM, a lightweight generic virtual machine, paired with an ALICE specific contextualization. Once the virtual machine is launched, a graphical user interface is automatically started without any additional configuration. This interface allows downloading the base ALICE analysis software and running a set of ALICE analysis modules. Currently the available tools include fully documented tutorials for ALICE analysis, such as the measurement of strange particle production or the nuclear modification factor in Pb-Pb collisions. The interface can be easily extended to include an arbitrary number of additional analysis modules. We present the current status of the tools used by ALICE through the CERN open access portal, and the plans for future extensions of this system. (paper)

  12. Improving antivenom availability and accessibility: science, technology, and beyond.

    Science.gov (United States)

    Gutiérrez, José María

    2012-09-15

    Snakebite envenomings constitute a serious and neglected public health problem. Despite the fact that effective treatment exists, i.e. administration of animal-derived antivenoms, the availability and accessibility of these life-saving immunobiologicals is deficitary in various parts of the world, particularly in sub-Saharan Africa and some regions of Asia. This article discusses some of the problems that need to be circumvented in order to improve the availability and accessibility of antivenoms. The conglomerate of antivenom manufacturers is highly heterogeneous in terms of technological base, qualification of staff, implementation of Good Manufacturing Practices (GMPs), and volume of production. Therefore, improvements in antivenom quality and availability should be based on strategies tailored to the situation of each region or country; in this context, three different scenarios are discussed. Accessibility of antivenoms demands concerted efforts at multiple levels, including raising the awareness of public health authorities on the relevance of the problem, implementing innovative antivenom purchasing schemes, strengthening national distribution channels on the basis of robust epidemiological information, improving the cold chain and the provision of health services in remote rural settings, supporting the correct use of antivenoms, and promoting the involvement of local community organizations in various aspects of prevention and management. These tasks should be envisaged in terms of synergistic, interprogrammatic and intersectorial interventions, with the participation of many players. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. High-Performance Secure Database Access Technologies for HEP Grids

    Energy Technology Data Exchange (ETDEWEB)

    Matthew Vranicar; John Weicher

    2006-04-17

    The Large Hadron Collider (LHC) at the CERN Laboratory will become the largest scientific instrument in the world when it starts operations in 2007. Large Scale Analysis Computer Systems (computational grids) are required to extract rare signals of new physics from petabytes of LHC detector data. In addition to file-based event data, LHC data processing applications require access to large amounts of data in relational databases: detector conditions, calibrations, etc. U.S. high energy physicists demand efficient performance of grid computing applications in LHC physics research where world-wide remote participation is vital to their success. To empower physicists with data-intensive analysis capabilities a whole hyperinfrastructure of distributed databases cross-cuts a multi-tier hierarchy of computational grids. The crosscutting allows separation of concerns across both the global environment of a federation of computational grids and the local environment of a physicist’s computer used for analysis. Very few efforts are on-going in the area of database and grid integration research. Most of these are outside of the U.S. and rely on traditional approaches to secure database access via an extraneous security layer separate from the database system core, preventing efficient data transfers. Our findings are shared by the Database Access and Integration Services Working Group of the Global Grid Forum, who states that "Research and development activities relating to the Grid have generally focused on applications where data is stored in files. However, in many scientific and commercial domains, database management systems have a central role in data storage, access, organization, authorization, etc, for numerous applications.” There is a clear opportunity for a technological breakthrough, requiring innovative steps to provide high-performance secure database access technologies for grid computing. We believe that an innovative database architecture where the

  14. High-Performance Secure Database Access Technologies for HEP Grids

    International Nuclear Information System (INIS)

    Vranicar, Matthew; Weicher, John

    2006-01-01

    The Large Hadron Collider (LHC) at the CERN Laboratory will become the largest scientific instrument in the world when it starts operations in 2007. Large Scale Analysis Computer Systems (computational grids) are required to extract rare signals of new physics from petabytes of LHC detector data. In addition to file-based event data, LHC data processing applications require access to large amounts of data in relational databases: detector conditions, calibrations, etc. U.S. high energy physicists demand efficient performance of grid computing applications in LHC physics research where world-wide remote participation is vital to their success. To empower physicists with data-intensive analysis capabilities a whole hyperinfrastructure of distributed databases cross-cuts a multi-tier hierarchy of computational grids. The crosscutting allows separation of concerns across both the global environment of a federation of computational grids and the local environment of a physicist's computer used for analysis. Very few efforts are on-going in the area of database and grid integration research. Most of these are outside of the U.S. and rely on traditional approaches to secure database access via an extraneous security layer separate from the database system core, preventing efficient data transfers. Our findings are shared by the Database Access and Integration Services Working Group of the Global Grid Forum, who states that 'Research and development activities relating to the Grid have generally focused on applications where data is stored in files. However, in many scientific and commercial domains, database management systems have a central role in data storage, access, organization, authorization, etc, for numerous applications'. There is a clear opportunity for a technological breakthrough, requiring innovative steps to provide high-performance secure database access technologies for grid computing. We believe that an innovative database architecture where the secure

  15. Additional physical access and new technologies for strengthened safeguards

    International Nuclear Information System (INIS)

    Tuley, N.

    1999-01-01

    For States with additional protocols, the Agency may request complementary access for any of the following reasons: (a) to ensure the absence of undeclared nuclear material and activities at sites of facilities or locations outside facilities (LOFs) or at other locations declared under Article 2 as containing nuclear material (Article 4.a.i); (b) to resolve a question relating to the correctness and completeness of the information provided pursuant to Article 2 or to resolve an inconsistency relating to that information (Article 4.a.ii); and (c) to confirm, for safeguards purposes, the State's declaration of the decommissioned status of a facility or of a LOF where nuclear material was used (Article 4.a.iii). Under additional protocols, the activities that the Agency may carry out in a State include visual observation, environmental sampling and non-destructive measurement. Agency guidelines for complementary access are being developed. In the late 1980s and in the 1990s, new technologies became available enabling the IAEA to detect even minute trace indicators of various types of nuclear activities. This technique which is known as environmental sampling, contributes to the confirmation of the absence of undeclared nuclear material or nuclear activities. Collection of environmental samples at or near a nuclear site combined with ultra-sensitive analytical techniques can reveal signatures of post and current activities in locations where nuclear material is being handled. Another important new technology is remote monitoring which makes use of unattended safeguards instrument systems and ships off-site the data gathered from those instruments to IAEA Headquarters. Cost effectiveness is a prime justification for adding this feature to unattended monitoring systems such as optical surveillance and advanced optical seals. (author)

  16. Crucial design issues for special access technology; a Delphi study.

    Science.gov (United States)

    O'Rourke, Pearl; Ekins, Ray; Timmins, Bernard; Timmins, Fiona; Long, Siobhan; Coyle, Eugene

    2014-01-01

    To develop and demonstrate a method to involve professional users of assistive technology (AT) in the development process of customisable products. Employing the ideas of user participation and mass customisation, this research addresses the need for reduced product costs and optimised product flexibility. An adaptable six-question Delphi study was developed to establish consensus among AT professionals on design issues relating to a specified AT domain requiring innovation. The study is demonstrated for the special access technology (SAT) domain. A modified morphological matrix structures the application of the study results to the product design process. Fourteen professionals from the Republic of Ireland and the UK participated. Consensus was reached on prevalent parts of SAT that malfunction, primary reasons for SAT malfunction, characteristics of clients associated with SAT selection, client needs regarding SAT use and training, desirable traits of SAT and clinicians' frustrations with SAT. The study revealed a range of problems related to SAT, highlighting the complexities of successful SAT adoption. The questions led to differentiated insights and enabled design solution conceptualisation from various perspectives. The approach was found to help facilitate efficient generation and application of professional users' knowledge during the design process of customisable AT.

  17. 76 FR 77738 - Telecommunications Act Accessibility Guidelines; Electronic and Information Technology...

    Science.gov (United States)

    2011-12-14

    ... Telecommunications Act Accessibility Guidelines and its Electronic and Information Technology Accessibility Standards... electronic and information technology covered by Section 508 of the Rehabilitation Act Amendments of 1998. 76.... 2011-07] RIN 3014-AA37 Telecommunications Act Accessibility Guidelines; Electronic and Information...

  18. 39 CFR 255.4 - Accessibility to electronic and information technology.

    Science.gov (United States)

    2010-07-01

    ... AND INFORMATION TECHNOLOGY § 255.4 Accessibility to electronic and information technology. (a) In... burden, that the electronic and information technology the agency procures allows— (1) Individuals with... 39 Postal Service 1 2010-07-01 2010-07-01 false Accessibility to electronic and information...

  19. Metabolic enzyme microarray coupled with miniaturized cell-culture array technology for high-throughput toxicity screening.

    Science.gov (United States)

    Lee, Moo-Yeal; Dordick, Jonathan S; Clark, Douglas S

    2010-01-01

    Due to poor drug candidate safety profiles that are often identified late in the drug development process, the clinical progression of new chemical entities to pharmaceuticals remains hindered, thus resulting in the high cost of drug discovery. To accelerate the identification of safer drug candidates and improve the clinical progression of drug candidates to pharmaceuticals, it is important to develop high-throughput tools that can provide early-stage predictive toxicology data. In particular, in vitro cell-based systems that can accurately mimic the human in vivo response and predict the impact of drug candidates on human toxicology are needed to accelerate the assessment of drug candidate toxicity and human metabolism earlier in the drug development process. The in vitro techniques that provide a high degree of human toxicity prediction will be perhaps more important in cosmetic and chemical industries in Europe, as animal toxicity testing is being phased out entirely in the immediate future.We have developed a metabolic enzyme microarray (the Metabolizing Enzyme Toxicology Assay Chip, or MetaChip) and a miniaturized three-dimensional (3D) cell-culture array (the Data Analysis Toxicology Assay Chip, or DataChip) for high-throughput toxicity screening of target compounds and their metabolic enzyme-generated products. The human or rat MetaChip contains an array of encapsulated metabolic enzymes that is designed to emulate the metabolic reactions in the human or rat liver. The human or rat DataChip contains an array of 3D human or rat cells encapsulated in alginate gels for cell-based toxicity screening. By combining the DataChip with the complementary MetaChip, in vitro toxicity results are obtained that correlate well with in vivo rat data.

  20. Bioinformatics and Microarray Data Analysis on the Cloud.

    Science.gov (United States)

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

    High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data.

  1. Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

    DEFF Research Database (Denmark)

    Novak, Jaroslav P; Kim, Seon-Young; Xu, Jun

    2006-01-01

    BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have...

  2. 48 CFR 3004.470 - Security requirements for access to unclassified facilities, Information Technology resources...

    Science.gov (United States)

    2010-10-01

    ... access to unclassified facilities, Information Technology resources, and sensitive information. 3004.470... Technology resources, and sensitive information. ... ACQUISITION REGULATION (HSAR) GENERAL ADMINISTRATIVE MATTERS Safeguarding Classified and Sensitive Information...

  3. ACCESSING FEDERAL DATA BASES FOR CONTAMINATED SITE CLEAN-UP TECHNOLOGIES

    Science.gov (United States)

    The Federal Remediation Technologies Roundtable (Roundtable) eveloped this publication to provide information on accessing Federal data bases that contain data on innovative remediation technologies. The Roundtable includes representatives from the Department of Defense (DoD), En...

  4. User Management with LDAP(Light weight Directory Access Protocolfor access to technology and Information Services in Companies

    Directory of Open Access Journals (Sweden)

    José Teodoro Mejía Viteri

    2016-08-01

    Full Text Available This research aims to conduct an analysis of management services information and users with LDAP (Lightweight / Simplified Directory Access Protocol, their interaction with other technology services company, allowing it to be accessed through a single user and password. This study allowed us to collect information through a literature review on the LDAP service and its ability to interact with your user directory Open source technology services; also with Windows Server and Active Directory service is used by companies for their ease of management and access resources on Windows clients; is intended to provide an alternative for the implementation of each of the services required by public and private companies with tools free use and access to services for management and administration can be done by integrating or synchronizing with the directory LDAP.

  5. Open access web technology for mathematics learning in higher education

    Directory of Open Access Journals (Sweden)

    Mari Carmen González-Videgaray

    2016-05-01

    Full Text Available Problems with mathematics learning, “math anxiety” or “statistics anxiety” among university students can be avoided by using teaching strategies and technological tools. Besides personal suffering, low achievement in mathematics reduces terminal efficiency and decreases enrollment in careers related to science, technology and mathematics. This paper has two main goals: 1 to offer an organized inventory of open access web resources for math learning in higher education, and 2 to explore to what extent these resources are currently known and used by students and teachers. The first goal was accomplished by running a search in Google and then classifying resources. For the second, we conducted a survey among a sample of students (n=487 and teachers (n=60 from mathematics and engineering within the largest public university in Mexico. We categorized 15 high-quality web resources. Most of them are interactive simulations and computer algebra systems. ResumenLos problemas en el aprendizaje de las matemáticas, como “ansiedad matemática” y “ansiedad estadística” pueden evitarse si se usan estrategias de enseñanza y herramientas tecnológicas. Además de un sufrimiento personal, el bajo rendimiento en matemáticas reduce la eficiencia terminal y decrementa la matrícula en carreras relacionadas con ciencia, tecnología y matemáticas. Este artículo tiene dos objetivos: 1 ofrecer un inventario organizado de recursos web de acceso abierto para aprender matemáticas en la universidad, y 2 explorar en qué medida estos recursos se usan actualmente entre alumnos y profesores. El primer objetivo se logró con un perfil de búsqueda en Google y una clasificación. Para el segundo, se condujo una encuesta en una muestra de estudiantes (n=487 y maestros (n=60 de matemáticas e ingeniería de la universidad más grande de México. Categorizamos 15 recursos web de alta calidad. La mayoría son simulaciones interactivas y

  6. An access technology delivery protocol for children with severe and multiple disabilities: a case demonstration.

    Science.gov (United States)

    Mumford, Leslie; Lam, Rachel; Wright, Virginia; Chau, Tom

    2014-08-01

    This study applied response efficiency theory to create the Access Technology Delivery Protocol (ATDP), a child and family-centred collaborative approach to the implementation of access technologies. We conducted a descriptive, mixed methods case study to demonstrate the ATDP method with a 12-year-old boy with no reliable means of access to an external device. Evaluations of response efficiency, satisfaction, goal attainment, technology use and participation were made after 8 and 16 weeks of training with a custom smile-based access technology. At the 16 week mark, the new access technology offered better response quality; teacher satisfaction was high; average technology usage was 3-4 times per week for up to 1 h each time; switch sensitivity and specificity reached 78% and 64%, respectively, and participation scores increased by 38%. This case supports further development and testing of the ATDP with additional children with multiple or severe disabilities.

  7. Research on optical access network remote management technology

    Science.gov (United States)

    Wang, Wayne; Zou, Chen; Luo, Wenyi

    2008-11-01

    This paper goal is to provide a framework for the remote configuration and management of services for PON (Passive Optical Network) access and fiber access. Also it defines how Auto-Configuration Servers (ACS) in the network can remotely configure, troubleshoot and manage a Passive Optical Network (PON) optical network termination (ONT) with layer 3 capabilities using the CPE WAN management protocol, TR-069.

  8. Access and Use of Information and Communication Technologies by ...

    African Journals Online (AJOL)

    Data were analyzed using descriptive statistics, exploratory factor analysis and simple linear regression. Mobile phone (x = 3.42 ) was highly accessible to extension workers. Also, mobile phone was available in ADP office and very often used. Factors that militated against extension workers' access and use of ICTs were: ...

  9. The application of DNA microarrays in gene expression analysis

    NARCIS (Netherlands)

    Hal, van N.L.W.; Vorst, O.; Houwelingen, van A.M.M.L.; Kok, E.J.; Peijnenburg, A.A.C.M.; Aharoni, A.; Tunen, van A.J.; Keijer, J.

    2000-01-01

    DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed.

  10. Sources of inter-firm heterogeneity in accessing knowledge-creation benefits within technology clusters

    NARCIS (Netherlands)

    Arikan, A.; Knoben, J.

    2014-01-01

    We build on recent literature to highlight the distinction between knowledge-diffusion and knowledge-creation benefits of technology clustering and argue that firms located in technology clusters will have differential access to the latter. To explain the antecedents of such differential access, we

  11. 10 CFR 603.875 - Foreign access to technology and U.S. competitiveness provisions.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Foreign access to technology and U.S. competitiveness... Foreign access to technology and U.S. competitiveness provisions. (a) Consistent with the objective of enhancing national security and United States competitiveness by increasing the public's reliance on the...

  12. Impacts of extension access and cooperative membership on technology adoption and household welfare.

    Science.gov (United States)

    Wossen, Tesfamicheal; Abdoulaye, Tahirou; Alene, Arega; Haile, Mekbib G; Feleke, Shiferaw; Olanrewaju, Adetunji; Manyong, Victor

    2017-08-01

    This paper examines the impacts of access to extension services and cooperative membership on technology adoption, asset ownership and poverty using household-level data from rural Nigeria. Using different matching techniques and endogenous switching regression approach, we find that both extension access and cooperative membership have a positive and statistically significant effect on technology adoption and household welfare. Moreover, we find that both extension access and cooperative membership have heterogeneous impacts. In particular, we find evidence of a positive selection as the average treatment effects of extension access and cooperative membership are higher for farmers with the highest propensity to access extension and cooperative services. The impact of extension services on poverty reduction and of cooperatives on technology adoption is significantly stronger for smallholders with access to formal credit than for those without access. This implies that expanding rural financial markets can maximize the potential positive impacts of extension and cooperative services on farmers' productivity and welfare.

  13. MARS: Microarray analysis, retrieval, and storage system

    Directory of Open Access Journals (Sweden)

    Scheideler Marcel

    2005-04-01

    Full Text Available Abstract Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS, a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

  14. Simulation of microarray data with realistic characteristics

    Directory of Open Access Journals (Sweden)

    Lehmussola Antti

    2006-07-01

    Full Text Available Abstract Background Microarray technologies have become common tools in biological research. As a result, a need for effective computational methods for data analysis has emerged. Numerous different algorithms have been proposed for analyzing the data. However, an objective evaluation of the proposed algorithms is not possible due to the lack of biological ground truth information. To overcome this fundamental problem, the use of simulated microarray data for algorithm validation has been proposed. Results We present a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization. After all these steps are taken into account, the simulated data has realistic biological and statistical characteristics. The applicability of the proposed model is demonstrated by several examples. Conclusion The proposed microarray simulation model is modular and can be used in different kinds of applications. It includes several error models that have been proposed earlier and it can be used with different types of input data. The model can be used to simulate both spotted two-channel and oligonucleotide based single-channel microarrays. All this makes the model a valuable tool for example in validation of data analysis algorithms.

  15. [Detection of a fetus with paternally derived 2q37.3 microdeletion and 20p13p12.2 microduplication using whole genome microarray technology].

    Science.gov (United States)

    Zhang, Lin; Ren, Meihong; Song, Guining; Liu, Xuexia; Wang, Jianliu; Zhang, Xiaohong

    2016-12-10

    To perform prenatal diagnosis for a fetus with multiple malformations. The fetus was subjected to routine karyotyping and whole genome microarray analysis. The parents were subjected to high-resolution chromosome analysis. Fetal ultrasound at 28+4 weeks has indicated intrauterine growth restriction, left kidney agenesis, right kidney dysplasia, ventricular septal defect, and polyhydramnios. Chromosomal analysis showed that the fetus has a karyotype of 46,XY,der(2),der(20), t(2;20)(q37.3;p12.2), t(5;15) (q12.2;q25) pat. SNP array analysis confirmed that the fetus has a 5.283 Mb deletion at 2q37.3 and a 11.641 Mb duplication at 20p13p12.2. High-resolution chromosome analysis suggested that the father has a karyotype of 46,XY,t(2;20)(q37.3;p12.2),t(5;15)(q12.2;q25), while the mother has a normal karyotype. The abnormal phenotype of the fetus may be attributed to a 2q37.3 microdeletion and a 20p13p12.2 microduplication. The father has carried a complex translocation involving four chromosomes. To increase the chance for successful pregnancy, genetic diagnosis and/or assisted reproductive technology are warranted.

  16. A high-density Diversity Arrays Technology (DArT microarray for genome-wide genotyping in Eucalyptus

    Directory of Open Access Journals (Sweden)

    Myburg Alexander A

    2010-06-01

    Full Text Available Abstract Background A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. Findings After testing several genome complexity reduction methods we identified the PstI/TaqI method as the most effective for Eucalyptus and developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56% were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. Conclusions This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees

  17. Accessibility and Usage of Technology by North Carolina Agriculture Teachers

    Science.gov (United States)

    Williams, Maegen R.; Warner, Wendy J.; Flowers, James L.; Croom, D. Barry

    2014-01-01

    This study examined the integration of technology into the instructional process in North Carolina agricultural education classrooms. The study used survey research methodology to collect information on the availability of instructional technology and the frequency of instructional technology use by North Carolina agriculture teachers. The study…

  18. THE MAQC PROJECT: ESTABLISHING QC METRICS AND THRESHOLDS FOR MICROARRAY QUALITY CONTROL

    Science.gov (United States)

    Microarrays represent a core technology in pharmacogenomics and toxicogenomics; however, before this technology can successfully and reliably be applied in clinical practice and regulatory decision-making, standards and quality measures need to be developed. The Microarray Qualit...

  19. Evaluation of Cognitively Accessible Software to Increase Independent Access to Cellphone Technology for People with Intellectual Disability

    Science.gov (United States)

    Stock, S. E.; Davies, D. K.; Wehmeyer, M. L.; Palmer, S. B.

    2008-01-01

    Background: There are over two billion telephones in use worldwide. Yet, for millions of Americans with intellectual disabilities (ID), access to the benefits of cellphone technology is limited because of deficits in literacy, numerical comprehension, the proliferation of features and shrinking size of cellphone hardware and user interfaces.…

  20. Radioactive cDNA microarray in neurospsychiatry

    International Nuclear Information System (INIS)

    Choe, Jae Gol; Shin, Kyung Ho; Lee, Min Soo; Kim, Meyoung Kon

    2003-01-01

    Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen leading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with cell lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA in fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high quality rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. In summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most

  1. Radioactive cDNA microarray in neurospsychiatry

    Energy Technology Data Exchange (ETDEWEB)

    Choe, Jae Gol; Shin, Kyung Ho; Lee, Min Soo; Kim, Meyoung Kon [Korea University Medical School, Seoul (Korea, Republic of)

    2003-02-01

    Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen leading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with cell lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA in fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high quality rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. In summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most

  2. Application of an access technology delivery protocol to two children with cerebral palsy.

    Science.gov (United States)

    Mumford, Leslie; Chau, Tom

    2015-07-14

    This study further delineates the merits and limitations of the Access Technology Delivery Protocol (ATDP) through its application to two children with severe disabilities. We conducted mixed methods case studies to demonstrate the ATDP with two children with no reliable means of access to an external device. Evaluations of response efficiency, satisfaction, goal attainment, technology use and participation were made after 8 and 16 weeks of training with custom access technologies. After 16 weeks, one child's switch offered improved response efficiency, high teacher satisfaction and increased participation. The other child's switch resulted in improved satisfaction and switch effectiveness but lower overall efficiency. The latter child was no longer using his switch by the end of the study. These contrasting findings indicate that changes to any contextual factors that may impact the user's switch performance should mandate a reassessment of the access pathway. Secondly, it is important to ensure that individuals who will be responsible for switch training be identified at the outset and engaged throughout the ATDP. Finally, the ATDP should continue to be tested with individuals with severe disabilities to build an evidence base for the delivery of response efficient access solutions. Implications for Rehabilitation A data-driven, comprehensive access technology delivery protocol for children with complex communication needs could help to mitigate technology abandonment. Successful adoption of an access technology requires personalized design, training of the technology user, the teaching staff, the caregivers and other communication partners, and integration with functional activities.

  3. Access, attitudes and training in information technologies and ...

    African Journals Online (AJOL)

    Background: The Medical Education Partnership Initiative, has helped to mitigate the digital divide in Africa. The aim of the study was to assess the level of access, attitude, and training concerning meaningful use of electronic resources and EBM among medical students at an African medical school. Methods: The study ...

  4. Speech technology for information access: a South African case study

    CSIR Research Space (South Africa)

    Barnard, E

    2010-03-01

    Full Text Available Telephone-based information access has the potential to deliver a significant positive impact in the developing world. We discuss some of the most important issues that must be addressed in order to realize this potential, including matters related...

  5. Videophone Technology and Students with Deaf-Blindness: A Method for Increasing Access and Communication

    Science.gov (United States)

    Emerson, Judith; Bishop, John

    2012-01-01

    Introduction: Seeing the Possibilities with Videophone Technology began as research project funded by the National Center for Technology Innovation. The project implemented a face-to-face social networking program for students with deaf-blindness to investigate the potential for increasing access and communication using videophone technology.…

  6. Exploring Teacher Pedagogy, Stages of Concern and Accessibility as Determinants of Technology Adoption

    Science.gov (United States)

    Burke, Paul F.; Schuck, Sandy; Aubusson, Peter; Kearney, Matthew; Frischknecht, Bart

    2018-01-01

    This research examines how the pedagogical orientations of teachers affect technology adoption in the classroom. At the same time, the authors account for the stage of concern that teachers are experiencing regarding the use of the technology, their access to the technology and the level of schooling at which they teach.The authors' investigation…

  7. Access, attitudes and training in information technologies and ...

    African Journals Online (AJOL)

    and EBM among medical students at an African medical school. ... Keywords: Information technologies, evidence-based medicine, medical students, University of Zimbabwe, College .... United States President's Emergency Plan for AIDS Re-.

  8. Study of LANs access technologies in wind power system

    DEFF Research Database (Denmark)

    Wei, Mu; Chen, Zhe

    2010-01-01

    Due to the energy challenges in the world, new types of generation technologies, such as renewable energy based generators, attract great attention and are being quickly developed, which results in the dramatic developments and changes in modern power systems, the communication technologies play...... a increasingly important role in guaranteeing the power system’s stability, reliability, and security. In this paper the necessity of communication technologies employed in wind power system are introduced. According the International Standards Organization (ISO) reference 7-layered model, the communication...... power environment are explained and discussed. Furthermore the simulation of application of Ethernet in an offshore wind farm communication network by a software, OPNET, is elaborated. With the investigation of the communication technologies in this paper, the offshore wind farm SCADA system can...

  9. Accessible transportation technologies research initiative (ATTRI) : online dialogue.

    Science.gov (United States)

    2014-08-01

    In coordination with Easter Seals Project ACTION (ESPA) and with support from Noblis, ATTRI held an online dialogue from May 15-June 6, 2014 to garner input on : mobility and transportation technology for travelers with disabilities. Participants wer...

  10. Restricted access processor - An application of computer security technology

    Science.gov (United States)

    Mcmahon, E. M.

    1985-01-01

    This paper describes a security guard device that is currently being developed by Computer Sciences Corporation (CSC). The methods used to provide assurance that the system meets its security requirements include the system architecture, a system security evaluation, and the application of formal and informal verification techniques. The combination of state-of-the-art technology and the incorporation of new verification procedures results in a demonstration of the feasibility of computer security technology for operational applications.

  11. Developing technology intelligence strategy to access knowledge of innovation clusters.

    OpenAIRE

    Rani Jeanne Dang; Letizia Mortara; Ruth Thomson; Tim Minshall

    2010-01-01

    Current times are characterised by a knowledge-based economy and fast technological change. In this difficult environment, companies compete to maintain a relevant position through innovation. In response to these challenges, many companies are currently adopting an open approach to innovation, pursuing innovation by combining internal and external resources. Technology intelligence (TI) activities support the implementation of open innovation with the systematic capture and delivery of infor...

  12. Metabolomic Profiling of the Effects of Melittin on Cisplatin Resistant and Cisplatin Sensitive Ovarian Cancer Cells Using Mass Spectrometry and Biolog Microarray Technology

    Directory of Open Access Journals (Sweden)

    Sanad Alonezi

    2016-10-01

    Full Text Available In the present study, liquid chromatography-mass spectrometry (LC-MS was employed to characterise the metabolic profiles of two human ovarian cancer cell lines A2780 (cisplatin-sensitive and A2780CR (cisplatin-resistant in response to their exposure to melittin, a cytotoxic peptide from bee venom. In addition, the metabolomics data were supported by application of Biolog microarray technology to examine the utilisation of carbon sources by the two cell lines. Data extraction with MZmine 2.14 and database searching were applied to provide metabolite lists. Principal component analysis (PCA gave clear separation between the cisplatin-sensitive and resistant strains and their respective controls. The cisplatin-resistant cells were slightly more sensitive to melittin than the sensitive cells with IC50 values of 4.5 and 6.8 μg/mL respectively, although the latter cell line exhibited the greatest metabolic perturbation upon treatment. The changes induced by melittin in the cisplatin-sensitive cells led mostly to reduced levels of amino acids in the proline/glutamine/arginine pathway, as well as to decreased levels of carnitines, polyamines, adenosine triphosphate (ATP and nicotinamide adenine dinucleotide (NAD+. The effects on energy metabolism were supported by the data from the Biolog assays. The lipid compositions of the two cell lines were quite different with the A2780 cells having higher levels of several ether lipids than the A2780CR cells. Melittin also had some effect on the lipid composition of the cells. Overall, this study suggests that melittin might have some potential as an adjuvant therapy in cancer treatment.

  13. Fibre optic microarrays.

    Science.gov (United States)

    Walt, David R

    2010-01-01

    This tutorial review describes how fibre optic microarrays can be used to create a variety of sensing and measurement systems. This review covers the basics of optical fibres and arrays, the different microarray architectures, and describes a multitude of applications. Such arrays enable multiplexed sensing for a variety of analytes including nucleic acids, vapours, and biomolecules. Polymer-coated fibre arrays can be used for measuring microscopic chemical phenomena, such as corrosion and localized release of biochemicals from cells. In addition, these microarrays can serve as a substrate for fundamental studies of single molecules and single cells. The review covers topics of interest to chemists, biologists, materials scientists, and engineers.

  14. cDNA microarray screening in food safety

    International Nuclear Information System (INIS)

    Roy, Sashwati; Sen, Chandan K.

    2006-01-01

    The cDNA microarray technology and related bioinformatics tools presents a wide range of novel application opportunities. The technology may be productively applied to address food safety. In this mini-review article, we present an update highlighting the late breaking discoveries that demonstrate the vitality of cDNA microarray technology as a tool to analyze food safety with reference to microbial pathogens and genetically modified foods. In order to bring the microarray technology to mainstream food safety, it is important to develop robust user-friendly tools that may be applied in a field setting. In addition, there needs to be a standardized process for regulatory agencies to interpret and act upon microarray-based data. The cDNA microarray approach is an emergent technology in diagnostics. Its values lie in being able to provide complimentary molecular insight when employed in addition to traditional tests for food safety, as part of a more comprehensive battery of tests

  15. Accessible Transportation Technologies Research Initiative (ATTRI) : User Needs Assessment: Stakeholder Engagement Report.

    Science.gov (United States)

    2016-05-01

    The Accessible Transportation Technologies Research Initiative (ATTRI) is a joint U.S. Department of Transportation (U.S. DOT) initiative that is co-led by the Federal Highway Administration (FHWA) and the Federal Transit Administration (FTA). ATTRI ...

  16. Comparison of Broadband Wireless Access Technology for HAPS Communication

    Directory of Open Access Journals (Sweden)

    Mingxiang GUAN

    2014-03-01

    Full Text Available An information system formed by HAP (High Altitude Platform will be a new generation-system for the wireless communications and HAPS (HAP Station communication system combines the advantages of both terrestrial and satellite communication systems and avoids, to different extents, their disadvantages. Third generation (3G mobile technology which is specified by the third generation partnership project (3 GPP is definitely one of the candidates. With the success of wireless network, the IEEE 802.16 standard, with its wireless metropolitan area network (MAN air interface appears to be a strong competitor. We provide initial practical comparison of these two technologies for HAPS Communication.

  17. Student Access to Information Technology and Perceptions of Future Opportunities in Two Small Labrador Communities

    Directory of Open Access Journals (Sweden)

    Della Healey

    2002-02-01

    Full Text Available The potential of information technology is increasingly being recognized for the access it provides to educational and vocational opportunities. In Canada, many small schools in rural communities have taken advantage of information technologies to help overcome geographic isolation for students. This article is about students in two small and geographically isolated Labrador communities. Twenty senior students were found to have varying degrees of access to information technologies. Differences were found in their perceptions of the benefits of information technology for their educational and vocational futures.

  18. Radiation immune RAM semiconductor technology for the 80's. [Random Access Memory

    Science.gov (United States)

    Hanna, W. A.; Panagos, P.

    1983-01-01

    This paper presents current and short term future characteristics of RAM semiconductor technologies which were obtained by literature survey and discussions with cognizant Government and industry personnel. In particular, total ionizing dose tolerance and high energy particle susceptibility of the technologies are addressed. Technologies judged compatible with spacecraft applications are ranked to determine the best current and future technology for fast access (less than 60 ns), radiation tolerant RAM.

  19. Wearables for all : development of guidelines to stimulate accessible wearable technology design

    NARCIS (Netherlands)

    Wentzel, Jobke; Velleman, Eric; van der Geest, Thea

    2016-01-01

    In this paper, we present the rationale and approach for establishing guidelines for the development of accessible wearables. Wearable technology is increasingly integrated in our everyday lives. Therefore, ensuring accessibility is pivotal to prevent a digital divide between persons who have and

  20. Assessment of Low-Income Adults' Access to Technology: Implications for Nutrition Education

    Science.gov (United States)

    Neuenschwander, Lauren M.; Abbott, Angela; Mobley, Amy R.

    2012-01-01

    Objective: The main objective of this study was to investigate access and use of technologies such as the Internet among Indiana's low-income population. The secondary objective was to determine whether access and use of computers significantly differed by age, race, and/or education level. Methods: Data were collected from low-income adult…

  1. The Evolution of Teachers' Instructional Beliefs and Practices in High-Access-to-Technology Classrooms.

    Science.gov (United States)

    Dwyer, David C.; And Others

    Beginning in 1985, Apple Computer, Inc., and several school districts began a collaboration to examine the impact of computer saturation on instruction and learning in K-12 classrooms. The initial guiding question was simply put: What happens when teachers and students have constant access to technology? To provide "constant access,"…

  2. The potential use of mobile technology: enhancing accessibility and communication in a blended learning course

    OpenAIRE

    Mayisela, Tabisa

    2013-01-01

    Mobile technology is increasingly being used to support blended learning beyond computer centres. It has been considered as a potential solution to the problem of a shortage of computers for accessing online learning materials (courseware) in a blended learning course. The purpose of the study was to establish how the use of mobile technology could enhance accessibility and communication in a blended learning course. Data were solicitedfrom a purposive convenience sample of 36 students engage...

  3. Technology development and market access: from a food sovereignty perspective

    NARCIS (Netherlands)

    Quaye, W.

    2012-01-01

    The concepts of ‘relevant social groups’ and ‘technical code’ are used to investigate the social relations in cowpea variety development (technology studies) and also the relationship of small-scale farmers to the Ghana School Feeding Program

  4. Use of Mobile Phone Technology in Education for Easy Accessibility ...

    African Journals Online (AJOL)

    Information and communication technology has opened up such tremendous vistas for modern societies that any failure to master it would mean a life of permanent subordination. The evolution of Mobile phone makes it possible to work with distance learning, achieve a closer collaboration among teachers and students ...

  5. Access, attitudes and training in information technologies and ...

    African Journals Online (AJOL)

    This impact can be boosted by developing a curriculum with skills necessary in using EBM. Keywords: Information technologies, evidence-based medicine, medical students, University of Zimbabwe, College of Health Sciences. Due to errors in the previous PDF especially in the 'Cite as' authors names, the PDF fulltext has ...

  6. Technology for the Struggling Reader: Free and Easily Accessible Resources

    Science.gov (United States)

    Berkeley, Sheri; Lindstrom, Jennifer H.

    2011-01-01

    A fundamental problem for many struggling readers, their parents, and their teachers is that there are few benchmarks to guide decision making about assistive technological supports when the nature of a disability is cognitive (e.g., specific learning disability, SLD) rather than physical. However, resources such as the National Center on…

  7. Transformational Technologies to Expedite Space Access and Development

    International Nuclear Information System (INIS)

    Rather, John D. G.

    2010-01-01

    Throughout history the emergence of new technologies has enabled unforeseen breakthrough capabilities that rapidly transformed the world. Some global examples from the twentieth century include AC electric power, nuclear energy, and turbojet engines. At the systems level, success of both Apollo and the Space Shuttle programs depended upon taming hydrogen propulsion and developing high-temperature atmospheric reentry materials. Human space development now is stymied because of a great need for breakthrough technologies and strategies. It is believed that new capabilities exist within the present states-of-the-art of superconducting technology that can be implemented to transform the future of human space development. This paper is an overview of three other papers presented within this forum, which summarizes the principles and consequences of StarTram, showing how the resulting breakthrough advantages can lead directly to safe space tourism and massive development of the moon, Mars and the outer solar system. StarTram can implement cost-effective solar power from space, simple utilization of asteroid material to protect humans from ionizing radiation, and effective defense of the Earth from devastating cosmic impacts. Synergistically, StarTram technologies will revolutionize ground transportation on the Earth, leading to enormous reduction in energy consumption and creation of millions of jobs. High energy lasers will also be discussed because of their importance to power beaming applications.

  8. Technology solutions to support supervisory activities and also to provide information access to the society

    Science.gov (United States)

    Paladini, D.; Mello, A. B.

    2016-07-01

    Inmetro's data about the conformity of certificated products, process and services are, usually, displayed at fragmented databases of difficult access for several reasons, for instance, the lack of computational solutions which allow this kind of access to its users. A discussion about some of the technological solutions to support supervisory activities by the appropriate regulatory bodies and also to provide information access to society in general is herein presented, along with a theoretical explanation of the pros and cons of such technologies to the conclusion that a mobile platform seems to be the best tool for the requirements of Inmetro.

  9. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology

    Science.gov (United States)

    Koizumi, Yoshikazu; Kelly, John J.; Nakagawa, Tatsunori; Urakawa, Hidetoshi; El-Fantroussi, Said; Al-Muzaini, Saleh; Fukui, Manabu; Urushigawa, Yoshikuni; Stahl, David A.

    2002-01-01

    A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

  10. Managed access technology to combat contraband cell phones in prison: Findings from a process evaluation.

    Science.gov (United States)

    Grommon, Eric

    2018-02-01

    Cell phones in correctional facilities have emerged as one of the most pervasive forms of modern contraband. This issue has been identified as a top priority for many correctional administrators in the United States. Managed access, a technology that utilizes cellular signals to capture transmissions from contraband phones, has received notable attention as a promising tool to combat this problem. However, this technology has received little evaluative attention. The present study offers a foundational process evaluation and draws upon output measures and stakeholder interviews to identify salient operational challenges and subsequent lessons learned about implementing and maintaining a managed access system. Findings suggest that while managed access captures large volumes of contraband cellular transmissions, the technology requires significant implementation planning, personnel support, and complex partnerships with commercial cellular carriers. Lessons learned provide guidance for practitioners to navigate these challenges and for scholars to improve future evaluations of managed access. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Broadband Optical Access Technologies to Converge towards a Broadband Society in Europe

    Science.gov (United States)

    Coudreuse, Jean-Pierre; Pautonnier, Sophie; Lavillonnière, Eric; Didierjean, Sylvain; Hilt, Benoît; Kida, Toshimichi; Oshima, Kazuyoshi

    This paper provides insights on the status of broadband optical access market and technologies in Europe and on the expected trends for the next generation optical access networks. The final target for most operators, cities or any other player is of course FTTH (Fibre To The Home) deployment although we can expect intermediate steps with copper or wireless technologies. Among the two candidate architectures for FTTH, PON (Passive Optical Network) is by far the most attractive and cost effective solution. We also demonstrate that Ethernet based optical access network is very adequate to all-IP networks without any incidence on the level of quality of service. Finally, we provide feedback from a FTTH pilot network in Colmar (France) based on Gigabit Ethernet PON technology. The interest of this pilot lies on the level of functionality required for broadband optical access networks but also on the development of new home network configurations.

  12. 76 FR 10360 - Access to Confidential Business Information by Guident Technologies Inc. and Its Identified...

    Science.gov (United States)

    2011-02-24

    ... Business Information by Guident Technologies Inc. and Its Identified Subcontractors AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: EPA has authorized its contractor, Guident Technologies... information may be claimed or determined to be Confidential Business Information (CBI). DATES: Access to the...

  13. The Influence of Information Technology Access on Agricultural Research in Nigeria.

    Science.gov (United States)

    Jimba, Samuel Wodi; Atinmo, Morayo Ibironke

    2000-01-01

    Examines the relationship between accessibility to information technology and research publications among users of agricultural libraries in Nigeria. Discusses results of a questionnaire that investigated the use of electronic information resources and considers the effects of information technology and globalization on the economies of developing…

  14. Improving Information Access through Technology: A Plan for Louisiana's Public Libraries.

    Science.gov (United States)

    Jaques, Thomas F.

    Strengthening technology in Louisiana's public libraries will support equitable and convenient access to electronic information resources for all citizens at library sites, in homes, and in business. The plan presented in this document is intended to enhance and expand technology in the state's public libraries. After discussion of the crucial…

  15. Stay in the Box! Embedded Assistive Technology Improves Access for Students with Disabilities

    Directory of Open Access Journals (Sweden)

    Katherine Koch

    2017-11-01

    Full Text Available Assistive technology is not only a required component of a student’s IEP; it can be an effective way to help students with (and without disabilities access their education and to provide them with required instructional accommodations. Teachers, however, are often not adequately prepared in their pre-service course work and ongoing professional development to address the technology needs of their special education students and have not had the opportunities to access technology due to limited availability and cost. While assistive technology can be purchased to augment an existing computer, it is often unnecessary to do that. Both Microsoft and Apple operating systems in “off-the-shelf” computers and handheld devices have embedded assistive technology that is easy to access and easy to use. This embedded technology can help teachers become familiar with technology and assist students with sensory, physical, learning, and attention disabilities, and it might have practical applications with Universal Design for Learning. This paper provides a discussion on how embedded technology can support students with disabilities in the school setting and provides examples for access and use.

  16. Technological advancements and Internet sexuality: does private access to the Internet influence online sexual behavior?

    Science.gov (United States)

    Daneback, Kristian; Månsson, Sven-Axel; Ross, Michael W

    2012-08-01

    The aim of this study was to investigate whether demographic characteristics and sexual behavior online and offline were associated with private, respectively, nonprivate access to the Internet in a Web sample of people who use the Internet for sexual purposes. A total of 1,913 respondents completed an online questionnaire about Internet sexuality, and 1,614 reported using the Internet for sexual purposes. The majority of these respondents reported having access to an Internet-connected computer no one else had access to (62 percent women and 70 percent men). The results showed that it is possible to differentiate between those who have access to an Internet-connected computer no one else has access to and those who have shared access to an Internet-connected computer. Not only did they differ in demographic characteristics, but also in the sexual activities they engaged in on the Internet. Different patterns were found for women and men. For example, men who had private access to Internet-connected computers were more likely than those who had shared access to seek information about sexual issues. Thus, having access to Internet computers no one else has access to may promote sexual knowledge and health for men. The results of this study along with the technological development implies that in future research, attention should be paid to where and how people access the Internet in relation to online behavior in general and online sexual behavior in particular.

  17. Concentration of Access to Information and Communication Technologies in the Municipalities of the Brazilian Legal Amazon.

    Science.gov (United States)

    de Brito, Silvana Rossy; da Silva, Aleksandra do Socorro; Cruz, Adejard Gaia; Monteiro, Maurílio de Abreu; Vijaykumar, Nandamudi Lankalapalli; da Silva, Marcelino Silva; Costa, João Crisóstomo Weyl Albuquerque; Francês, Carlos Renato Lisboa

    2016-01-01

    This study fills demand for data on access and use of information and communication technologies (ICT) in the Brazilian legal Amazon, a region of localities with identical economic, political, and social problems. We use the 2010 Brazilian Demographic Census to compile data on urban and rural households (i) with computers and Internet access, (ii) with mobile phones, and (iii) with fixed phones. To compare the concentration of access to ICT in the municipalities of the Brazilian Amazon with other regions of Brazil, we use a concentration index to quantify the concentration of households in the following classes: with computers and Internet access, with mobile phones, with fixed phones, and no access. These data are analyzed along with municipal indicators on income, education, electricity, and population size. The results show that for urban households, the average concentration in the municipalities of the Amazon for computers and Internet access and for fixed phones is lower than in other regions of the country; meanwhile, that for no access and mobile phones is higher than in any other region. For rural households, the average concentration in the municipalities of the Amazon for computers and Internet access, mobile phones, and fixed phones is lower than in any other region of the country; meanwhile, that for no access is higher than in any other region. In addition, the study shows that education and income are determinants of inequality in accessing ICT in Brazilian municipalities and that the existence of electricity in rural households is directly associated with the ownership of ICT resources.

  18. The potential use of mobile technology: enhancing accessibility and communication in a blended learning course

    Directory of Open Access Journals (Sweden)

    Tabisa Mayisela

    2013-01-01

    Full Text Available Mobile technology is increasingly being used to support blended learning beyond computer centres. It has been considered as a potential solution to the problem of a shortage of computers for accessing online learning materials (courseware in a blended learning course. The purpose of the study was to establish how the use of mobile technology could enhance accessibility and communication in a blended learning course. Data were solicitedfrom a purposive convenience sample of 36 students engaged in the blended learning course. The case study utilized a mixed-methods approach. An unstructured interview was conducted with the course lecturer and these data informed the design of the students' semi-structured questionnaire. It was found that students with access to mobile technology had an increased opportunity to access the courseware of the blended learning course. Mobile technology further enhanced student-to-student and student-to-lecturer communication by means of social networks. The study concludes that mobile technology has the potential to increase accessibility and communication in a blended learning course. Recommendations, limitations of the present study, and suggestionsforfuture research were made.

  19. Extended -Regular Sequence for Automated Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jin Hee-Jeong

    2006-01-01

    Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

  20. The Importance of Normalization on Large and Heterogeneous Microarray Datasets

    Science.gov (United States)

    DNA microarray technology is a powerful functional genomics tool increasingly used for investigating global gene expression in environmental studies. Microarrays can also be used in identifying biological networks, as they give insight on the complex gene-to-gene interactions, ne...

  1. Accessibility

    DEFF Research Database (Denmark)

    Brooks, Anthony Lewis

    2017-01-01

    This contribution is timely as it addresses accessibility in regards system hardware and software aligned with introduction of the Twenty-First Century Communications and Video Accessibility Act (CVAA) and adjoined game industry waiver that comes into force January 2017. This is an act created...... by the USA Federal Communications Commission (FCC) to increase the access of persons with disabilities to modern communications, and for other purposes. The act impacts advanced communications services and products including text messaging; e-mail; instant messaging; video communications; browsers; game...... platforms; and games software. However, the CVAA has no legal status in the EU. This text succinctly introduces and questions implications, impact, and wider adoption. By presenting the full CVAA and game industry waiver the text targets to motivate discussions and further publications on the subject...

  2. [Improving global access to new vaccines: intellectual property, technology transfer, and regulatory pathways].

    Science.gov (United States)

    Crager, Sara Eve

    2015-01-01

    The 2012 World Health Assembly Global Vaccine Action Plan called for global access to new vaccines within 5 years of licensure. Current approaches have proven insufficient to achieve sustainable vaccine pricing within such a timeline. Paralleling the successful strategy of generic competition to bring down drug prices, a clear consensus is emerging that market entry of multiple suppliers is a critical factor in expeditiously bringing down prices of new vaccines. In this context, key target objectives for improving access to new vaccines include overcoming intellectual property obstacles, streamlining regulatory pathways for biosimilar vaccines, and reducing market entry timelines for developing-country vaccine manufacturers by transfer of technology and know-how. I propose an intellectual property, technology, and know-how bank as a new approach to facilitate widespread access to new vaccines in low- and middle-income countries by efficient transfer of patented vaccine technologies to multiple developing-country vaccine manufacturers.

  3. Improving global access to new vaccines: intellectual property, technology transfer, and regulatory pathways.

    Science.gov (United States)

    Crager, Sara Eve

    2014-11-01

    The 2012 World Health Assembly Global Vaccine Action Plan called for global access to new vaccines within 5 years of licensure. Current approaches have proven insufficient to achieve sustainable vaccine pricing within such a timeline. Paralleling the successful strategy of generic competition to bring down drug prices, a clear consensus is emerging that market entry of multiple suppliers is a critical factor in expeditiously bringing down prices of new vaccines. In this context, key target objectives for improving access to new vaccines include overcoming intellectual property obstacles, streamlining regulatory pathways for biosimilar vaccines, and reducing market entry timelines for developing-country vaccine manufacturers by transfer of technology and know-how. I propose an intellectual property, technology, and know-how bank as a new approach to facilitate widespread access to new vaccines in low- and middle-income countries by efficient transfer of patented vaccine technologies to multiple developing-country vaccine manufacturers.

  4. Evolving provider payment models and patient access to innovative medical technology.

    Science.gov (United States)

    Long, Genia; Mortimer, Richard; Sanzenbacher, Geoffrey

    2014-12-01

    Abstract Objective: To investigate the evolving use and expected impact of pay-for-performance (P4P) and risk-based provider reimbursement on patient access to innovative medical technology. Structured interviews with leading private payers representing over 110 million commercially-insured lives exploring current and planned use of P4P provider payment models, evidence requirements for technology assessment and new technology coverage, and the evolving relationship between the two topics. Respondents reported rapid increases in the use of P4P and risk-sharing programs, with roughly half of commercial lives affected 3 years ago, just under two-thirds today, and an expected three-quarters in 3 years. All reported well-established systems for evaluating new technology coverage. Five of nine reported becoming more selective in the past 3 years in approving new technologies; four anticipated that in the next 3 years there will be a higher evidence requirement for new technology access. Similarly, four expected it will become more difficult for clinically appropriate but costly technologies to gain coverage. All reported planning to rely more on these types of provider payment incentives to control costs, but didn't see them as a substitute for payer technology reviews and coverage limitations; they each have a role to play. Interviews limited to nine leading payers with models in place; self-reported data. Likely implications include a more uncertain payment environment for providers, and indirectly for innovative medical technology and future investment, greater reliance on quality and financial metrics, and increased evidence requirements for favorable coverage and utilization decisions. Increasing provider financial risk may challenge the traditional technology adoption paradigm, where payers assumed a 'gatekeeping' role and providers a countervailing patient advocacy role with regard to access to new technology. Increased provider financial risk may result in an

  5. Development of an instrument to measure Faculty's information and communication technology access (FICTA).

    Science.gov (United States)

    Soomro, Kamal Ahmed; Kale, Ugur; Curtis, Reagan; Akcaoglu, Mete; Bernstein, Malayna

    2018-01-01

    The phenomenon of "digital divide" is complex and multidimensional, extending beyond issues of physical access. The purpose of this study was to develop a scale to measure a range of factors related to digital divide among higher education faculty and to evaluate its reliability and validity. Faculty's Information and Communication Technology Access (FICTA) scale was tested and validated with 322 faculty teaching in public and private sector universities. Principal components analysis with varimax rotation confirmed an 8-factor solution corresponding to various dimensions of ICT access. The 57-item FICTA scale demonstrated good psychometric properties and offers researchers a tool to examine faculty's access to ICT at four levels - motivational, physical, skills, and usage access.

  6. The application of DNA microarrays in gene expression analysis.

    Science.gov (United States)

    van Hal, N L; Vorst, O; van Houwelingen, A M; Kok, E J; Peijnenburg, A; Aharoni, A; van Tunen, A J; Keijer, J

    2000-03-31

    DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed. These comprise array manufacturing and design, array hybridisation, scanning, and data handling. Furthermore, it is discussed how DNA microarrays can be applied in the working fields of: safety, functionality and health of food and gene discovery and pathway engineering in plants.

  7. Using mobile technologies to give health students access to learning resources in the UK community setting.

    Science.gov (United States)

    Walton, Graham; Childs, Susan; Blenkinsopp, Elizabeth

    2005-12-01

    This article describes a project which explored the potential for mobile technologies to give health students in the community access to learning resources. The purpose included the need to identify possible barriers students could face in using mobile technologies. Another focus was to assess the students perceptions of the importance of being able to access learning resources in the community. This 1-year project used two main approaches for data collection. A review of the literature on mobile technologies in the health context was conducted. This was used in a systematic way to identify key issues and trends. The literature review was used to inform the design and production of a questionnaire. This was distributed to and completed by a group of community health students at Northumbria University, UK. The questionnaire was piloted and there was a 100% completion rate with 49 returned forms. The literature review indicated that most mobile technology applications were occurring in the US. At the time of the review the most prevalent mobile technologies were PDAs, laptops, WAP phones and portable radios with use being concentrated around doctors in the acute sector. A range of advantages and disadvantages to the technology were discovered. Mobile technologies were mainly being used for clinical rather than learning applications. The students showed a low level of awareness of the technology but placed great importance to accessing learning resources from the community. Significant development and changes are taking place in mobile technologies. Since the data collection for this work was completed in 2004 podcasting and videocasting have become significant in mobile learning for health professionals. Librarians will need to address the relevance and implications of m-learning for their practice. Care and consideration needs to be given on the time and resources librarians allocate for the necessary development work around mobile technologies. Collaboration and

  8. Ethernet access network based on free-space optic deployment technology

    Science.gov (United States)

    Gebhart, Michael; Leitgeb, Erich; Birnbacher, Ulla; Schrotter, Peter

    2004-06-01

    The satisfaction of all communication needs from single households and business companies over a single access infrastructure is probably the most challenging topic in communications technology today. But even though the so-called "Last Mile Access Bottleneck" is well known since more than ten years and many distribution technologies have been tried out, the optimal solution has not yet been found and paying commercial access networks offering all service classes are still rare today. Conventional services like telephone, radio and TV, as well as new and emerging services like email, web browsing, online-gaming, video conferences, business data transfer or external data storage can all be transmitted over the well known and cost effective Ethernet networking protocol standard. Key requirements for the deployment technology driven by the different services are high data rates to the single customer, security, moderate deployment costs and good scalability to number and density of users, quick and flexible deployment without legal impediments and high availability, referring to the properties of optical and wireless communication. We demonstrate all elements of an Ethernet Access Network based on Free Space Optic distribution technology. Main physical parts are Central Office, Distribution Network and Customer Equipment. Transmission of different services, as well as configuration, service upgrades and remote control of the network are handled by networking features over one FSO connection. All parts of the network are proven, the latest commercially available technology. The set up is flexible and can be adapted to any more specific need if required.

  9. Principles of gene microarray data analysis.

    Science.gov (United States)

    Mocellin, Simone; Rossi, Carlo Riccardo

    2007-01-01

    The development of several gene expression profiling methods, such as comparative genomic hybridization (CGH), differential display, serial analysis of gene expression (SAGE), and gene microarray, together with the sequencing of the human genome, has provided an opportunity to monitor and investigate the complex cascade of molecular events leading to tumor development and progression. The availability of such large amounts of information has shifted the attention of scientists towards a nonreductionist approach to biological phenomena. High throughput technologies can be used to follow changing patterns of gene expression over time. Among them, gene microarray has become prominent because it is easier to use, does not require large-scale DNA sequencing, and allows for the parallel quantification of thousands of genes from multiple samples. Gene microarray technology is rapidly spreading worldwide and has the potential to drastically change the therapeutic approach to patients affected with tumor. Therefore, it is of paramount importance for both researchers and clinicians to know the principles underlying the analysis of the huge amount of data generated with microarray technology.

  10. Computational biology of genome expression and regulation--a review of microarray bioinformatics.

    Science.gov (United States)

    Wang, Junbai

    2008-01-01

    Microarray technology is being used widely in various biomedical research areas; the corresponding microarray data analysis is an essential step toward the best utilizing of array technologies. Here we review two components of the microarray data analysis: a low level of microarray data analysis that emphasizes the designing, the quality control, and the preprocessing of microarray experiments, then a high level of microarray data analysis that focuses on the domain-specific microarray applications such as tumor classification, biomarker prediction, analyzing array CGH experiments, and reverse engineering of gene expression networks. Additionally, we will review the recent development of building a predictive model in genome expression and regulation studies. This review may help biologists grasp a basic knowledge of microarray bioinformatics as well as its potential impact on the future evolvement of biomedical research fields.

  11. Student Access to and Skills in Using Technology in an Open and Distance Learning Context

    Directory of Open Access Journals (Sweden)

    Hanlie Liebenberg

    2012-10-01

    Full Text Available Amidst the different challenges facing higher education, and particularly distance education (DE and open distance learning (ODL, access to information and communication technology (ICT and students’ abilities to use ICTs are highly contested issues in the South African higher education landscape. While there are various opinions about the scope and definition of the digital divide, increasing empirical evidence questions the uncritical use of the notion of the digital divide in South African and international higher education discourses.In the context of the University of South Africa (Unisa as a mega ODL institution, students’ access to technology and their functional competence are some of the critical issues to consider as Unisa prepares our graduates for an increasingly digital and networked world.This paper discusses a descriptive study that investigated students’ access to technology and their capabilities in using technology, within the broader discourse of the “digital divide.” Results support literature that challenges a simplistic understanding of the notion of the “digital divide” and reveal that the nature of access is varied.

  12. 32 CFR 37.875 - Should my TIA include a provision concerning foreign access to technology?

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Should my TIA include a provision concerning... Related to Other Administrative Matters Intellectual Property § 37.875 Should my TIA include a provision... provision in the TIA that addresses foreign access to technology developed under the TIA. (b) The provision...

  13. The Potential Use of Mobile Technology: Enhancing Accessibility and Communication in a Blended Learning Course

    Science.gov (United States)

    Mayisela, Tabisa

    2013-01-01

    Mobile technology is increasingly being used to support blended learning beyond computer centres. It has been considered as a potential solution to the problem of a shortage of computers for accessing online learning materials (courseware) in a blended learning course. The purpose of the study was to establish how the use of mobile technology…

  14. Application of Information and Communication Technology (ICT) in Health Information Access and Dissemination in Uganda

    Science.gov (United States)

    Omona, Walter; Ikoja-Odongo, Robert

    2006-01-01

    This paper reports on a study which assessed the application of information and communication technologies (ICT) in health information access and dissemination in Uganda. The project focused not only on information obtainable through libraries for research, teaching, learning and practice, but also on ICT applications concerned with the…

  15. Concentration of Access to Information and Communication Technologies in the Municipalities of the Brazilian Legal Amazon.

    Directory of Open Access Journals (Sweden)

    Silvana Rossy de Brito

    Full Text Available This study fills demand for data on access and use of information and communication technologies (ICT in the Brazilian legal Amazon, a region of localities with identical economic, political, and social problems. We use the 2010 Brazilian Demographic Census to compile data on urban and rural households (i with computers and Internet access, (ii with mobile phones, and (iii with fixed phones. To compare the concentration of access to ICT in the municipalities of the Brazilian Amazon with other regions of Brazil, we use a concentration index to quantify the concentration of households in the following classes: with computers and Internet access, with mobile phones, with fixed phones, and no access. These data are analyzed along with municipal indicators on income, education, electricity, and population size. The results show that for urban households, the average concentration in the municipalities of the Amazon for computers and Internet access and for fixed phones is lower than in other regions of the country; meanwhile, that for no access and mobile phones is higher than in any other region. For rural households, the average concentration in the municipalities of the Amazon for computers and Internet access, mobile phones, and fixed phones is lower than in any other region of the country; meanwhile, that for no access is higher than in any other region. In addition, the study shows that education and income are determinants of inequality in accessing ICT in Brazilian municipalities and that the existence of electricity in rural households is directly associated with the ownership of ICT resources.

  16. Deployment of a Testbed in a Brazilian Research Network using IPv6 and Optical Access Technologies

    Science.gov (United States)

    Martins, Luciano; Ferramola Pozzuto, João; Olimpio Tognolli, João; Chaves, Niudomar Siqueira De A.; Reggiani, Atilio Eduardo; Hortêncio, Claudio Antonio

    2012-04-01

    This article presents the implementation of a testbed and the experimental results obtained with it on the Brazilian Experimental Network of the government-sponsored "GIGA Project." The use of IPv6 integrated to current and emerging optical architectures and technologies, such as dense wavelength division multiplexing and 10-gigabit Ethernet on the core and gigabit capable passive optical network and optical distribution network on access, were tested. These protocols, architectures, and optical technologies are promising and part of a brand new worldwide technological scenario that has being fairly adopted in the networks of enterprises and providers of the world.

  17. Improving collaboration between primary care research networks using Access Grid technology

    Directory of Open Access Journals (Sweden)

    Zsolt Nagykaldi

    2008-05-01

    Full Text Available Access Grid (AG is an Internet2-driven, high performance audio_visual conferencing technology used worldwide by academic and government organisations to enhance communication, human interaction and group collaboration. AG technology is particularly promising for improving academic multi-centre research collaborations. This manuscript describes how the AG technology was utilised by the electronic Primary Care Research Network (ePCRN that is part of the National Institutes of Health (NIH Roadmap initiative to improve primary care research and collaboration among practice- based research networks (PBRNs in the USA. It discusses the design, installation and use of AG implementations, potential future applications, barriers to adoption, and suggested solutions.

  18. High throughput screening of starch structures using carbohydrate microarrays

    DEFF Research Database (Denmark)

    Tanackovic, Vanja; Rydahl, Maja Gro; Pedersen, Henriette Lodberg

    2016-01-01

    In this study we introduce the starch-recognising carbohydrate binding module family 20 (CBM20) from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated...

  19. Variance estimation in the analysis of microarray data

    KAUST Repository

    Wang, Yuedong; Ma, Yanyuan; Carroll, Raymond J.

    2009-01-01

    Microarrays are one of the most widely used high throughput technologies. One of the main problems in the area is that conventional estimates of the variances that are required in the t-statistic and other statistics are unreliable owing

  20. The ethics of attaching research conditions to access to new health technologies.

    Science.gov (United States)

    Holland, Stephen; Hope, Tony

    2012-06-01

    Decisions on which new health technologies to provide are controversial because of the scarcity of healthcare resources, the competing demands of payers, providers and patients and the uncertainty of the evidence base. Given this, additional information about new health technologies is often considered valuable. One response is to make access to a new health technology conditional on further research. Access can be restricted to patients who participate in a research study, such as a randomised controlled trial; alternatively, a new treatment can be made generally available, but only on condition that further evidence is collected (eg, on long-term outcomes and adverse events, in patient registries). The National Institute for Health and Clinical Excellence (NICE), which provides guidance on which new health technologies to make available under the UK's NHS, for example, has made some research conditional recommendations, and the current interest in such options suggests that they are likely to become more prevalent in the future. This paper identifies and discusses the main ethical issues created by this distinctive range of recommendations. We argue that decisions to put research conditions on access to new technologies are compatible with widely accepted values, principles and practices relevant to resource allocation. However, there are important features of these distinctive judgements that must be taken into account by resource allocation decision-making bodies and research ethics committees, and that require new sorts of empirical data.

  1. A Discourse On Broadband Technologies And Curriculum Access In Elective Home Learning

    Directory of Open Access Journals (Sweden)

    Andrew MCAVOY

    2014-12-01

    Full Text Available The extent, to which broadband technologies are being considered, when accessing the curriculum, is increasingly evident in traditional learning environments such as schools and colleges. This article explores the impact that these technologies are having on the home schooling community by offering enhanced access and opportunities. It suggests that they have generated improved choices and greater freedoms for learning communities. They have shone a light on the curriculum and removed it from the shadows. The curriculum is no longer the preserve of the educational establishment. The secret garden has been breached by technologies such as broadband and the democratisation of the curriculum is progressively evident as more diverse learning communities are given increased access and control over the curriculum. The author asks how this is being reflected in policy and translated into practice by the home schooling community whilst acknowledging the contemporary nature of broadband technologies and how they are influencing the decision making process of potential home schoolers. Looking to the future, the author suggests that the political agenda is not providing clear direction and that this is being determined by social reform outside the political sphere and largely driven by the consumer. In this case the learner. The relatively current nature of this debate is in itself justification for further research if we are to develop a clearer understanding of how new technologies such as broadband are influencing policy and practice in the home schooling community.

  2. Guide on Project Web Access of SFR R and D and Technology Monitoring System

    International Nuclear Information System (INIS)

    Lee, Dong Uk; Won, Byung Chool; Lee, Yong Bum; Kim, Young In; Hahn, Do Hee

    2008-09-01

    The SFR R and D and technology monitoring system based on the MS enterprise project management is developed for systematic effective management of 'Development of Basic Key Technologies for Gen IV SFR' project which was performed under the Mid- and Long-term Nuclear R and D Program sponsored by the Ministry of Education, Science and Technology. This system is a tool for project management based on web access. Therefore this manual is a detailed guide for Project Web Access(PWA). Section 1 describes the common guide for using of system functions such as project server 2007 client connection setting, additional outlook function setting etc. The section 2 describes the guide for system administrator. It is described the guide for project management in section 3, 4

  3. Guide on Project Web Access of SFR R and D and Technology Monitoring System

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong Uk; Won, Byung Chool; Lee, Yong Bum; Kim, Young In; Hahn, Do Hee

    2008-09-15

    The SFR R and D and technology monitoring system based on the MS enterprise project management is developed for systematic effective management of 'Development of Basic Key Technologies for Gen IV SFR' project which was performed under the Mid- and Long-term Nuclear R and D Program sponsored by the Ministry of Education, Science and Technology. This system is a tool for project management based on web access. Therefore this manual is a detailed guide for Project Web Access(PWA). Section 1 describes the common guide for using of system functions such as project server 2007 client connection setting, additional outlook function setting etc. The section 2 describes the guide for system administrator. It is described the guide for project management in section 3, 4.

  4. Literacy disparities in patient access and health-related use of Internet and mobile technologies.

    Science.gov (United States)

    Bailey, Stacy C; O'Conor, Rachel; Bojarski, Elizabeth A; Mullen, Rebecca; Patzer, Rachel E; Vicencio, Daniel; Jacobson, Kara L; Parker, Ruth M; Wolf, Michael S

    2015-12-01

    Age and race-related disparities in technology use have been well documented, but less is known about how health literacy influences technology access and use. To assess the association between patients' literacy skills and mobile phone ownership, use of text messaging, Internet access, and use of the Internet for health-related purposes. A secondary analysis utilizing data from 1077 primary care patients enrolled in two, multisite studies from 2011-2013. Patients were administered an in-person, structured interview. Patients with adequate health literacy were more likely to own a mobile phone or smartphone in comparison with patients having marginal or low literacy (mobile phone ownership: 96.8 vs. 95.2 vs. 90.1%, respectively, P Internet from their home (92.1 vs. 74.7 vs. 44.9%, P Internet for email (93.0 vs. 75.7 vs. 38.5%, P technology access and use are widespread, with lower literate patients being less likely to own smartphones or to access and use the Internet, particularly for health reasons. Future interventions should consider these disparities and ensure that health promotion activities do not further exacerbate disparities. © 2014 John Wiley & Sons Ltd.

  5. Information and communication technology platforms deployment: Technology access reaches South African rural areas

    CSIR Research Space (South Africa)

    Foko, TF

    2017-05-01

    Full Text Available though these Platforms were intended to provide unsupervised and unstructured form of learning. Fig. 1: Map showing the sites of deployed ICT Platform 2. Objectives The container Platform project rolled out ICT Platforms for the following purposes...: (i) As information and communication resources; (ii) As learning centres; (iii) As access points to ICTs; (iv) As practical tools for development; and (v) As a tool for bridging the digital Divide. Therefore, the purpose of this paper...

  6. Carbohydrate Microarrays in Plant Science

    DEFF Research Database (Denmark)

    Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.

    2012-01-01

    Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important...... industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high...... for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities....

  7. Testing the Digital Divide: Does Access to High-Quality Use of Technology in Schools Affect Student Achievement?

    Science.gov (United States)

    Talley, Gregory Keith

    2012-01-01

    This study investigates the relationship between access, use of technology and student achievement in public middle schools in Maryland. The objective of this study was to determine whether a digital divide (differences in access and utilization of technology based on student characteristics of race, socioeconomic status, and gender) exists among…

  8. Spin-transfer torque magnetoresistive random-access memory technologies for normally off computing (invited)

    International Nuclear Information System (INIS)

    Ando, K.; Yuasa, S.; Fujita, S.; Ito, J.; Yoda, H.; Suzuki, Y.; Nakatani, Y.; Miyazaki, T.

    2014-01-01

    Most parts of present computer systems are made of volatile devices, and the power to supply them to avoid information loss causes huge energy losses. We can eliminate this meaningless energy loss by utilizing the non-volatile function of advanced spin-transfer torque magnetoresistive random-access memory (STT-MRAM) technology and create a new type of computer, i.e., normally off computers. Critical tasks to achieve normally off computers are implementations of STT-MRAM technologies in the main memory and low-level cache memories. STT-MRAM technology for applications to the main memory has been successfully developed by using perpendicular STT-MRAMs, and faster STT-MRAM technologies for applications to the cache memory are now being developed. The present status of STT-MRAMs and challenges that remain for normally off computers are discussed

  9. Perspectives in understanding open access to research data - infrastructure and technology challenges

    Science.gov (United States)

    Bigagli, Lorenzo; Sondervan, Jeroen

    2014-05-01

    The Policy RECommendations for Open Access to Research Data in Europe (RECODE) project, started in February 2013 with a duration of two years, has the objective to identify a series of targeted and over-arching policy recommendations for Open Access to European research data, based on existing good practice and addressing such hindering factors as stakeholder fragmentation, technical and infrastructural issues, ethical and legal issues, and financial and institutional policies. In this work we focus on the technical and infrastructural aspect, where by "infrastructure" we mean the technological assets (hardware and software), the human resources, and all the policies, processes, procedures and training for managing and supporting its continuous operation and evolution. The context targeted by RECODE includes heterogeneous networks, initiatives, projects and communities that are fragmented by discipline, geography, stakeholder category (publishers, academics, repositories, etc.) as well as other boundaries. Many of these organizations are already addressing key technical and infrastructural barriers to Open Access to research data. Such barriers may include: lack of automatic mechanisms for policy enforcement, lack of metadata and data models supporting open access, obsolescence of infrastructures, scarce awareness about new technological solutions, lack of training and/or expertise on IT and semantics aspects. However, these organizations are often heterogeneous and fragmented by discipline, geography, stakeholder category (publishers, academics, repositories, etc.) as well as other boundaries, and often work in isolation, or with limited contact with one another. RECODE has addressed these challenges, and the possible solutions to mitigate them, engaging all the identified stakeholders in a number of ways, including an online questionnaire, case studies interviews, literature review, a workshop. The conclusions have been validated by the RECODE Advisory Board and

  10. Plant-pathogen interactions: what microarray tells about it?

    Science.gov (United States)

    Lodha, T D; Basak, J

    2012-01-01

    Plant defense responses are mediated by elementary regulatory proteins that affect expression of thousands of genes. Over the last decade, microarray technology has played a key role in deciphering the underlying networks of gene regulation in plants that lead to a wide variety of defence responses. Microarray is an important tool to quantify and profile the expression of thousands of genes simultaneously, with two main aims: (1) gene discovery and (2) global expression profiling. Several microarray technologies are currently in use; most include a glass slide platform with spotted cDNA or oligonucleotides. Till date, microarray technology has been used in the identification of regulatory genes, end-point defence genes, to understand the signal transduction processes underlying disease resistance and its intimate links to other physiological pathways. Microarray technology can be used for in-depth, simultaneous profiling of host/pathogen genes as the disease progresses from infection to resistance/susceptibility at different developmental stages of the host, which can be done in different environments, for clearer understanding of the processes involved. A thorough knowledge of plant disease resistance using successful combination of microarray and other high throughput techniques, as well as biochemical, genetic, and cell biological experiments is needed for practical application to secure and stabilize yield of many crop plants. This review starts with a brief introduction to microarray technology, followed by the basics of plant-pathogen interaction, the use of DNA microarrays over the last decade to unravel the mysteries of plant-pathogen interaction, and ends with the future prospects of this technology.

  11. Language and Text-to-Speech Technologies for Highly Accessible Language & Culture Learning

    Directory of Open Access Journals (Sweden)

    Anouk Gelan

    2011-06-01

    Full Text Available This contribution presents the results of the “Speech technology integrated learning modules for Intercultural Dialogue” project. The project objective was to increase the availability and quality of e-learning opportunities for less widely-used and less taught European languages using a user-friendly and highly accessible learning environment. The integration of new Text-to-Speech developments into web-based authoring software for tutorial CALL had a double goal: on the one hand increase the accessibility of e-learning packages, also for learners having difficulty reading (e.g. dyslexic learners or preferring auditory learning; on the other hand exploiting some didactic possibilities of this technology.

  12. Special Issue Journal of Healthcare Engineering Accessibility, Inclusion and Rehabilitation Using Information Technologies

    DEFF Research Database (Denmark)

    Brooks, Anthony Lewis; González-Cid, Yolanda

    2018-01-01

    limitation to perform tasks that they were formerly unable to accomplish, in inclusion for people with different abilities and preferences, and in rehabilitation. Potential topics include but are not limited to the following: ● Design, evaluation and use of IT to benefit people with disabilities (sensory......, motor and cognitive impairments / multiple disabilities) and elderly people ● Information technologies to accessibility to enable people with functional limitation to perform tasks that they were formerly unable to accomplish ● IT for the inclusion for people with different abilities and preferences......Accessibility, Inclusion and Rehabilitation Using Information Technologies Social exclusion occurs when individuals or even entire communities of people are blocked from rights, opportunities and resources preventing them from full participation in the activities of the society in which they live...

  13. A Comparative Study on Java Technologies for Focus and Cursor Handling in Accessible Dynamic Interactions.

    Science.gov (United States)

    Jitngernmadan, Prajaks; Miesenberger, Klaus

    2015-01-01

    For an interactive application, supporting and guiding the user in fulfilling tasks is most important. The behavior of the application that will guide users through the procedures until they finish the task has to be designed intuitively and well guiding, especially if the users has only restricted or no access to the visual and spatial arrangement on the screen. Therefore, the focus/cursor management plays an important role for orientation and navigating through the interaction. In the frame of ongoing research on a software tool supporting blind people in more efficiently doing mathematical calculations, we researched how Java technologies support implementing an accessible Graphical User Interface (GUI) with an additional focus on usable accessibility in terms of guiding blind users through the process of solving mathematical calculations. We used Java Swing [1] and Eclipse SWT [2] APIs for creating a series of prototypes. We tested a) accessibility and usability of the prototypes for blind people when using screen reader software and refreshable Braille display and b) the implementation support to developers provided by both technologies. It turned out that Eclipse SWT API delivered best results under Windows operating system.

  14. Sustainable Development and Airport Surface Access: The Role of Technological Innovation and Behavioral Change

    Directory of Open Access Journals (Sweden)

    Bilal Qazi

    2013-04-01

    Full Text Available Sustainable development reflects an underlying tension to achieve economic growth whilst addressing environmental challenges, and this is particularly the case for the aviation sector. Although much of the aviation-related focus has fallen on reducing aircraft emissions, airports have also been under increasing pressure to support the vision of a low carbon energy future. One of the main sources of airport-related emissions is passenger journeys to and from airports (the surface access component of air travel, which is the focus of this paper. Two aspects associated with the relationship between sustainable development and airport surface access are considered. Firstly, there is an evaluation of three technological innovation options that will enable sustainable transport solutions for surface access journeys: telepresence systems to reduce drop-off/pick-up trips, techniques to improve public transport and options to encourage the sharing of rides. Secondly, the role of behavioral change for surface access journeys from a theoretical perspective, using empirical data from Manchester airport, is evaluated. Finally, the contribution of technology and behavioral intervention measures to improvements in sustainable development are discussed.

  15. Current status and perceived needs of information technology in Critical Access Hospitals: a survey study

    Directory of Open Access Journals (Sweden)

    George Demiris

    2007-01-01

    Full Text Available The US Congress established the designation of Critical Access Hospitals in 1997, recognising rural hospitals as vital links to health for rural and underserved populations. The intent of the reimbursement system is to improve financial performance, thereby reducing hospital closures. Informatics applications are thought to be tools that can enable the sustainability of such facilities. The aim of this study is to identify the current use of information and communication technology in Critical Access Hospitals, and to assess their readiness and receptiveness for the use of new software and hardware applications and their perceived information technology (IT needs. A survey was mailed to the administrators of all Critical Access Hospitals in one US state (Missouri and a reminder was mailed a few weeks later. Twenty-seven out of 33 surveys were filled out and returned (response rate 82%. While most respondents (66.7% stated that their employees have been somewhat comfortable in using new technology, almost 15% stated that their employees have been somewhat uncomfortable. Similarly, almost 12% of the respondents stated that they themselves felt somewhat uncomfortable introducing new technology. While all facilities have computers, only half of them have a specific IT plan. Findings indicate that Critical Access Hospitals are often struggling with lack of resources and specific applications that address their needs. However, it is widely recognised that IT plays an essential role in the sustainability of their organisations. The study demonstrates that IT applications have to be customised to address the needs and infrastructure of the rural settings in order to be accepted and properly utilised.

  16. An access-technology agnostic delivery model for ICT4D services

    CSIR Research Space (South Africa)

    Herselman, M

    2012-02-01

    Full Text Available systems outlined by Bieber, Mcfall, Rice, and Gurstein (2007). Their deliberations, however, do not address the issue of access-technology agnostic delivery of information. Furthermore, many of the proposed content distribution models involved a single... be implemented. The ?Black Box Testing Technique? (Krichen & Tripakis, 2004) was adopted; this technique hides the complexities of the system components and only focuses on the system functionality as viewed from the end- user perspective in accordance...

  17. Enabling Equal Access to Molecular Diagnostics: What Are the Implications for Policy and Health Technology Assessment?

    Science.gov (United States)

    Plun-Favreau, Juliette; Immonen-Charalambous, Kaisa; Steuten, Lotte; Strootker, Anja; Rouzier, Roman; Horgan, Denis; Lawler, Mark

    2016-01-01

    Molecular diagnostics can offer important benefits to patients and are a key enabler of the integration of personalised medicine into health care systems. However, despite their promise, few molecular diagnostics are embedded into clinical practice (especially in Europe) and access to these technologies remains unequal across countries and sometimes even within individual countries. If research translation and the regulatory environments have proven to be more challenging than expected, reimbursement and value assessment remain the main barriers to providing patients with equal access to molecular diagnostics. Unclear or non-existent reimbursement pathways, together with the lack of clear evidence requirements, have led to significant delays in the assessment of molecular diagnostics technologies in certain countries. Additionally, the lack of dedicated diagnostics budgets and the siloed nature of resource allocation within certain health care systems have significantly delayed diagnostics commissioning. This article will consider the perspectives of different stakeholders (patients, health care payers, health care professionals, and manufacturers) on the provision of a research-enabled, patient-focused molecular diagnostics platform that supports optimal patient care. Through the discussion of specific case studies, and building on the experience from countries that have successfully integrated molecular diagnostics into clinical practice, this article will discuss the necessary evolutions in policy and health technology assessment to ensure that patients can have equal access to appropriate molecular diagnostics. © 2016 S. Karger AG, Basel.

  18. Social Media Use and Access to Digital Technology in US Young Adults in 2016

    Science.gov (United States)

    Johnson, Amanda L; Ilakkuvan, Vinu; Jacobs, Megan A; Graham, Amanda L; Rath, Jessica M

    2017-01-01

    Background In 2015, 90% of US young adults with Internet access used social media. Digital and social media are highly prevalent modalities through which young adults explore identity formation, and by extension, learn and transmit norms about health and risk behaviors during this developmental life stage. Objective The purpose of this study was to provide updated estimates of social media use from 2014 to 2016 and correlates of social media use and access to digital technology in data collected from a national sample of US young adults in 2016. Methods Young adult participants aged 18-24 years in Wave 7 (October 2014, N=1259) and Wave 9 (February 2016, N=989) of the Truth Initiative Young Adult Cohort Study were asked about use frequency for 11 social media sites and access to digital devices, in addition to sociodemographic characteristics. Regular use was defined as using a given social media site at least weekly. Weighted analyses estimated the prevalence of use of each social media site, overlap between regular use of specific sites, and correlates of using a greater number of social media sites regularly. Bivariate analyses identified sociodemographic correlates of access to specific digital devices. Results In 2014, 89.42% (weighted n, 1126/1298) of young adults reported regular use of at least one social media site. This increased to 97.5% (weighted n, 965/989) of young adults in 2016. Among regular users of social media sites in 2016, the top five sites were Tumblr (85.5%), Vine (84.7%), Snapchat (81.7%), Instagram (80.7%), and LinkedIn (78.9%). Respondents reported regularly using an average of 7.6 social media sites, with 85% using 6 or more sites regularly. Overall, 87% of young adults reported access or use of a smartphone with Internet access, 74% a desktop or laptop computer with Internet access, 41% a tablet with Internet access, 29% a smart TV or video game console with Internet access, 11% a cell phone without Internet access, and 3% none of these

  19. Social Media Use and Access to Digital Technology in US Young Adults in 2016.

    Science.gov (United States)

    Villanti, Andrea C; Johnson, Amanda L; Ilakkuvan, Vinu; Jacobs, Megan A; Graham, Amanda L; Rath, Jessica M

    2017-06-07

    In 2015, 90% of US young adults with Internet access used social media. Digital and social media are highly prevalent modalities through which young adults explore identity formation, and by extension, learn and transmit norms about health and risk behaviors during this developmental life stage. The purpose of this study was to provide updated estimates of social media use from 2014 to 2016 and correlates of social media use and access to digital technology in data collected from a national sample of US young adults in 2016. Young adult participants aged 18-24 years in Wave 7 (October 2014, N=1259) and Wave 9 (February 2016, N=989) of the Truth Initiative Young Adult Cohort Study were asked about use frequency for 11 social media sites and access to digital devices, in addition to sociodemographic characteristics. Regular use was defined as using a given social media site at least weekly. Weighted analyses estimated the prevalence of use of each social media site, overlap between regular use of specific sites, and correlates of using a greater number of social media sites regularly. Bivariate analyses identified sociodemographic correlates of access to specific digital devices. In 2014, 89.42% (weighted n, 1126/1298) of young adults reported regular use of at least one social media site. This increased to 97.5% (weighted n, 965/989) of young adults in 2016. Among regular users of social media sites in 2016, the top five sites were Tumblr (85.5%), Vine (84.7%), Snapchat (81.7%), Instagram (80.7%), and LinkedIn (78.9%). Respondents reported regularly using an average of 7.6 social media sites, with 85% using 6 or more sites regularly. Overall, 87% of young adults reported access or use of a smartphone with Internet access, 74% a desktop or laptop computer with Internet access, 41% a tablet with Internet access, 29% a smart TV or video game console with Internet access, 11% a cell phone without Internet access, and 3% none of these. Access to all digital devices with

  20. DNA Microarrays in Comparative Genomics and Transcriptomics

    DEFF Research Database (Denmark)

    Willenbrock, Hanni

    2007-01-01

    at identifying the exact breakpoints where DNA has been gained or lost. In this thesis, three popular methods are compared and a realistic simulation model is presented for generating artificial data with known breakpoints and known DNA copy number. By using simulated data, we obtain a realistic evaluation......During the past few years, innovations in the DNA sequencing technology has led to an explosion in available DNA sequence information. This has revolutionized biological research and promoted the development of high throughput analysis methods that can take advantage of the vast amount of sequence...... data. For this, the DNA microarray technology has gained enormous popularity due to its ability to measure the presence or the activity of thousands of genes simultaneously. Microarrays for high throughput data analyses are not limited to a few organisms but may be applied to everything from bacteria...

  1. Using technology to improve access to specialist care in amyotrophic lateral sclerosis: A systematic review.

    Science.gov (United States)

    Hobson, Esther V; Baird, Wendy O; Cooper, Cindy L; Mawson, Sue; Shaw, Pamela J; Mcdermott, Christopher J

    2016-01-01

    Our objective was to review the evidence for using technology to improve access to specialist care for patients with amyotrophic lateral sclerosis (ALS) and their carers. Medline, Google Scholar and the Cochrane library were searched for articles describing technology that enabled clinical care of patients with ALS or their carers where the patient/carer and clinician were not in the same location. Two applications were identified: telemedicine to facilitate video conferencing as an alternative to outpatient consultations and telehealth monitoring for patients with respiratory failure. One randomized controlled trial using telehealth in patients with respiratory failure including 22 patients with ALS was identified. While rates of hospitalization were reduced, overall mortality was unchanged and there were too few patients with ALS in the study to detect significant benefit. In conclusion, there is limited evidence to support the use of telemedicine or telehealth in the care of patients with ALS. Future research needs to develop an understanding of the key beneficial aspects of the traditional specialist ALS service and how these factors could be delivered using technology. Successful evaluation and implementation of technologies to facilitate access to specialist care will only be possible if all the relevant impacts of an intervention are understood and measured.

  2. Enhancing Ear and Hearing Health Access for Children With Technology and Connectivity.

    Science.gov (United States)

    Swanepoel, De Wet

    2017-10-12

    Technology and connectivity advances are demonstrating increasing potential to improve access of service delivery to persons with hearing loss. This article demonstrates use cases from community-based hearing screening and automated diagnosis of ear disease. This brief report reviews recent evidence for school- and home-based hearing testing in underserved communities using smartphone technologies paired with calibrated headphones. Another area of potential impact facilitated by technology and connectivity is the use of feature extraction algorithms to facilitate automated diagnosis of most common ear conditions from video-otoscopic images. Smartphone hearing screening using calibrated headphones demonstrated equivalent sensitivity and specificity for school-based hearing screening. Automating test sequences with a forced-choice response paradigm allowed persons with minimal training to offer screening in underserved communities. The automated image analysis and diagnosis system for ear disease demonstrated an overall accuracy of 80.6%, which is up to par and exceeds accuracy rates previously reported for general practitioners and pediatricians. The emergence of these tools that capitalize on technology and connectivity advances enables affordable and accessible models of service delivery for community-based ear and hearing care.

  3. First improvements in the detection and quantification of label-free nucleic acids by laser-induced breakdown spectroscopy: Application to the deoxyribonucleic acid micro-array technology

    International Nuclear Information System (INIS)

    Le Meur, Julien; Menut, Denis; Wodling, Pascal; Salmon, Laurent; Thro, Pierre-Yves; Chevillard, Sylvie; Ugolin, Nicolas

    2008-01-01

    The accurate quantification of nucleic acids is essential in many fields of modern biology and industry, and in some cases requires the use of fluorescence labeling. Yet, in addition to standardization problems and quantification reproducibility, labeling can modify the physicochemical properties of molecules or affect their stability. To address these limitations, we have developed a novel method to detect and quantify label-free nucleic acids. This method is based on stoichiometric proportioning of phosphorus in the nucleic acid skeleton, using laser-induced breakdown spectroscopy, and a specific statistical analysis, which indicates the error probability for each measurement. The results obtained appear to be quantitative, with a limit of detection of 10 5 nucleotides/μm 2 (i.e. 2 x 10 13 phosphorus atoms/cm 2 ). Initial micro-array analysis has given very encouraging results, which point to new ways of quantifying hybridized nucleic acids. This is essential when comparing molecules of different sequences, which is presently very difficult with fluorescence labeling

  4. First improvements in the detection and quantification of label-free nucleic acids by laser-induced breakdown spectroscopy: Application to the deoxyribonucleic acid micro-array technology

    Energy Technology Data Exchange (ETDEWEB)

    Le Meur, Julien [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France); Menut, Denis [Laboratoire de Reactivite des Surfaces et des Interfaces, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Wodling, Pascal [Laboratoire d' Interaction Laser-Matiere, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Salmon, Laurent [Laboratoire de Reactivite des Surfaces et des Interfaces, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Thro, Pierre-Yves [Laboratoire d' Interaction Laser-Matiere, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Chevillard, Sylvie [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France); Ugolin, Nicolas [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France)], E-mail: nugolin@cea.fr

    2008-04-15

    The accurate quantification of nucleic acids is essential in many fields of modern biology and industry, and in some cases requires the use of fluorescence labeling. Yet, in addition to standardization problems and quantification reproducibility, labeling can modify the physicochemical properties of molecules or affect their stability. To address these limitations, we have developed a novel method to detect and quantify label-free nucleic acids. This method is based on stoichiometric proportioning of phosphorus in the nucleic acid skeleton, using laser-induced breakdown spectroscopy, and a specific statistical analysis, which indicates the error probability for each measurement. The results obtained appear to be quantitative, with a limit of detection of 10{sup 5} nucleotides/{mu}m{sup 2} (i.e. 2 x 10{sup 13} phosphorus atoms/cm{sup 2}). Initial micro-array analysis has given very encouraging results, which point to new ways of quantifying hybridized nucleic acids. This is essential when comparing molecules of different sequences, which is presently very difficult with fluorescence labeling.

  5. RETHINKING STAKEHOLDER ENGAGEMENT AND TECHNOLOGY ACCESS IN HEALTH TECHNOLOGY ASSESSMENT: REACTIONS TO POLICY FORUM DISCUSSIONS.

    Science.gov (United States)

    Sampietro-Colom, Laura; Thomas, Sarah

    2016-01-01

    The need to progress and innovate in health technology assessment (HTA) is a must in a continuously changing environment. The HTAi Policy Forum reflected on two specific areas for development where it was thought there was need for careful consideration and deliberation during the main annual meeting in February 2016. The study by Husereau et al. (1) in this journal presents the discussions resulting from this Forum. To further share the deliberations of the Forum and with a view to opening this debate to the wider HTA community, a panel session during the HTAi Annual Meeting in Tokyo was organized. Presentations at the panel included a summary of the HTAi Policy Forum discussions and perspectives from a patient, a representative of healthcare system provider, and a representative from an HTA organization and industry. This letter presents the issues raised in the panel session.

  6. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    2010-09-01

    Full Text Available International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  7. Microarrays for Universal Detection and Identification of Phytoplasmas

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Nyskjold, Henriette; Bertaccini, Assunta

    2013-01-01

    Detection and identification of phytoplasmas is a laborious process often involving nested PCR followed by restriction enzyme analysis and fine-resolution gel electrophoresis. To improve throughput, other methods are needed. Microarray technology offers a generic assay that can potentially detect...... and differentiate all types of phytoplasmas in one assay. The present protocol describes a microarray-based method for identification of phytoplasmas to 16Sr group level....

  8. Electricity access for geographically disadvantaged rural communities - technology and policy insights

    Energy Technology Data Exchange (ETDEWEB)

    Chaurey, A.; Malini Ranganathan [The Energy and Resources Institute, New Delhi (India). India Habitat Centre; Parimita Mohanty [Jadavpur University, Kolkota (India). School of Energy Studies

    2004-10-01

    The purpose of this paper is to weigh the issues and options for increasing electricity access in remote and geographically challenged villages in interior Rajasthan, the desert state in Western India where power sector reforms are currently underway. By first providing an overview of reforms and various electrification policy initiatives in India, the paper then analyzes the specific problems as studied at the grass-roots level with respect to rural electricity access and the use of off-grid renewables. Finally, it discusses interventions that could facilitate access to electricity by suggesting a sequential distributed generation (DG)-based approach, wherein consecutive DG schemes-incorporating the requisite technological, financial, and institutional arrangements-are designed depending on the developmental requirements of the community. In essence, this approach fits under the broader need to understand how the three ''Rs'' - rural electrification (the process), power sector reforms (the catalyst), and the use of renewable energy technologies (the means)- could potentially converge to meet the needs of India's rural poor. (author)

  9. Electricity access for geographically disadvantaged rural communities--technology and policy insights

    International Nuclear Information System (INIS)

    Chaurey, Akanksha; Ranganathan, Malini; Mohanty, Parimita

    2004-01-01

    The purpose of this paper is to weigh the issues and options for increasing electricity access in remote and geographically challenged villages in interior Rajasthan, the desertstate in Western India where power sector reforms are currently underway. By first providing an overview of reforms and various electrification policy initiatives in India, the paper then analyzes the specific problems as studied at the grass-roots level with respect to rural electricity access and the use of off-grid renewables. Finally, it discusses interventions that could facilitate access to electricity by suggesting a sequential distributed generation (DG)-based approach, wherein consecutive DG schemes--incorporating the requisite technological, financial, and institutional arrangements--are designed depending on the developmental requirements of the community. In essence, this approach fits under the broader need to understand how the three 'Rs'- rural electrification (the process), power sector reforms (the catalyst), and the use of renewable energy technologies (the means) - could potentially converge to meet the needs of India's rural poor

  10. Electricity access for geographically disadvantaged rural communities--technology and policy insights

    Energy Technology Data Exchange (ETDEWEB)

    Chaurey, Akanksha E-mail: akanksha@teri.res.in; Ranganathan, Malini E-mail: malinir@teri.res.in; Mohanty, Parimita

    2004-10-01

    The purpose of this paper is to weigh the issues and options for increasing electricity access in remote and geographically challenged villages in interior Rajasthan, the desertstate in Western India where power sector reforms are currently underway. By first providing an overview of reforms and various electrification policy initiatives in India, the paper then analyzes the specific problems as studied at the grass-roots level with respect to rural electricity access and the use of off-grid renewables. Finally, it discusses interventions that could facilitate access to electricity by suggesting a sequential distributed generation (DG)-based approach, wherein consecutive DG schemes--incorporating the requisite technological, financial, and institutional arrangements--are designed depending on the developmental requirements of the community. In essence, this approach fits under the broader need to understand how the three 'Rs'- rural electrification (the process), power sector reforms (the catalyst), and the use of renewable energy technologies (the means) - could potentially converge to meet the needs of India's rural poor.

  11. An intellectual property sharing initiative in agricultural biotechnology: development of broadly accessible technologies for plant transformation.

    Science.gov (United States)

    Chi-Ham, Cecilia L; Boettiger, Sara; Figueroa-Balderas, Rosa; Bird, Sara; Geoola, Josef N; Zamora, Pablo; Alandete-Saez, Monica; Bennett, Alan B

    2012-06-01

    The Public Intellectual Property Resource for Agriculture (PIPRA) was founded in 2004 by the Rockefeller Foundation in response to concerns that public investments in agricultural biotechnology benefiting developing countries were facing delays, high transaction costs and lack of access to important technologies due to intellectual property right (IPR) issues. From its inception, PIPRA has worked broadly to support a wide range of research in the public sector, in specialty and minor acreage crops as well as crops important to food security in developing countries. In this paper, we review PIPRA's work, discussing the failures, successes, and lessons learned during its years of operation. To address public sector's limited freedom-to-operate, or legal access to third-party rights, in the area of plant transformation, we describe PIPRA's patent 'pool' approach to develop open-access technologies for plant transformation which consolidate patent and tangible property rights in marker-free vector systems. The plant transformation system has been licensed and deployed for both commercial and humanitarian applications in the United States (US) and Africa, respectively. © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

  12. An Alternative Option to Dedicated Braille Notetakers for People with Visual Impairments: Universal Technology for Better Access

    Science.gov (United States)

    Hong, Sunggye

    2012-01-01

    Technology provides equal access to information and helps people with visual impairments to complete tasks more independently. Among various assistive technology options for people with visual impairments, braille notetakers have been considered the most significant because of their technological innovation. Braille notetakers allow users who are…

  13. Expanding Notions of Digital Access: Parents' Negotiation of School-Based Technology Initiatives in New Immigrant Communities

    Science.gov (United States)

    Noguerón-Liu, Silvia

    2017-01-01

    Initiatives to integrate technology in schools are continuously increasing, with efforts to bridge the "homework gap" and provide technology access in low-income households. However, it is critical to include nondominant parents in technology adoption decisions in order to avoid mirroring past patterns of inequality in home-school…

  14. Frontiers in biochip technology

    National Research Council Canada - National Science Library

    Xing, Wan-Li; Cheng, Jing

    2006-01-01

    ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . Haiching Ma, Yuan Wang, Amy S. Pomaybo, and Connie Tsai 2. Improvement of Microarray Technologies for Detecting Single Nucleotide Mismatch...

  15. Research and Design of Dynamic Migration Access Control Technology Based on Heterogeneous Network

    Directory of Open Access Journals (Sweden)

    Wang Feng

    2017-01-01

    Full Text Available With the continuous development of wireless networks, the amount of privacy services in heterogeneous mobile networks is increasing, such as information storage, user access, and so on. Access control security issues for heterogeneous mobile radio network, this paper proposes a dynamic migration access control technology based on heterogeneous network. Through the system architecture of the mutual trust system, we can understand the real-time mobile node failure or abnormal state. To make the service can be terminated for the node. And adopt the 802.1X authentication way to improve the security of the system. Finally, it by combining the actual running test data, the trust update algorithm of the system is optimized to reduce the actual security threats in the environment. Experiments show that the system’s anti-attack, the success rate of access, bit error rate is in line with the expected results. This system can effectively reduce the system authentication information is illegally obtained after the network security protection mechanism failure and reduce the risk of user data leakage.

  16. Developing hybrid near-space technologies for affordable access to suborbital space

    Science.gov (United States)

    Badders, Brian David

    High power rockets and high altitude balloons are two near-space technologies that could be combined in order to provide access to the mesosphere and, eventually, suborbital space. This "rockoon" technology has been used by several large budget space programs before being abandoned in favor of even more expensive, albeit more accurate, ground launch systems. With the increased development of nano-satellites and atmospheric sensors, combined with rising interest in global atmospheric data, there is an increase in desire for affordable access to extreme altitudes that does not necessarily require the precision of ground launches. Development of hybrid near-space technologies for access to over 200k ft. on a small budget brings many challenges within engineering, systems integration, cost analysis, market analysis, and business planning. This research includes the design and simulation testing of all the systems needed for a safe and reusable launch system, the cost analysis for initial production, the development of a business plan, and the development of a marketing plan. This project has both engineering and scientific significance in that it can prove the space readiness of new technologies, raise their technology readiness levels (TRLs), expedite the development process, and also provide new data to the scientific community. It also has the ability to stimulate university involvement in the aerospace industry and help to inspire the next generation of workers in the space sector. Previous development of high altitude balloon/high power rocket hybrid systems have been undertaken by government funded military programs or large aerospace corporations with varying degrees of success. However, there has yet to be a successful flight with this type of system which provides access to the upper mesosphere in a university setting. This project will aim to design and analyze a viable system while testing the engineering process under challenging budgetary constraints. The

  17. Evaluation of Zinc-alpha-2-Glycoprotein and Proteasome Subunit beta-Type 6 Expression in Prostate Cancer Using Tissue Microarray Technology.

    LENUS (Irish Health Repository)

    2010-07-23

    Prostate cancer (CaP) is a significant cause of illness and death in males. Current detection strategies do not reliably detect the disease at an early stage and cannot distinguish aggressive versus nonaggressive CaP leading to potential overtreatment of the disease and associated morbidity. Zinc-alpha-2-glycoprotein (ZAG) and proteasome subunit beta-Type 6 (PSMB-6) were found to be up-regulated in the serum of CaP patients with higher grade tumors after 2-dimensional difference gel electrophoresis analysis. The aim of this study was to investigate if ZAG and PSMB-6 were also overexpressed in prostatic tumor tissue of CaP patients. Immunohistochemical analysis was performed on CaP tissue microarrays with samples from 199 patients. Confirmatory gene expression profiling for ZAG and PSMB-6 were performed on 4 cases using Laser Capture Microdissection and TaqMan real-time polymerase chain reaction. ZAG expression in CaP epithelial cells was inversely associated with Gleason grade (benign prostatic hyperplasia>G3>G4\\/G5). PSMB-6 was not expressed in either tumor or benign epithelium. However, strong PSMB-6 expression was noted in stromal and inflammatory cells. Our results indicate ZAG as a possible predictive marker of Gleason grade. The inverse association between grade and tissue expression with a rising serum protein level is similar to that seen with prostate-specific antigen. In addition, the results for both ZAG and PSMB-6 highlight the challenges in trying to associate the protein levels in serum with tissue expression.

  18. Evaluation of Public E-Services and Information Technology Accessibility in Different Social Groups

    Directory of Open Access Journals (Sweden)

    Ramutė Naujikienė

    2012-12-01

    Full Text Available The purpose of this study is to develop an approach based on the social quality evaluation square model for evaluation of information technology usage in different social groups. Componential view to the accessibility of e-services including IT means providing the possibility to research the influences of different life conditions to usage of the public e-services. The task of this empirical study is directed towards revealing the differences of e-inclusion and e-services accessibility for social groups of citizens of Lithuania, and to compare this accessibility data with other EU countries.Design/methodology/approach—the approach is based on the square model of social quality evaluation of information technology usage in different social groups. The social division square model includes an assessment of quality according to the evaluation of socioeconomic security, social inclusion, social cohesion, and empowerment. Empowerment can be defined as consisting of individual or collective decisions to act on one’s own life.Findings—the results are demonstrated by the accessibility of public e-services data, which are evaluated by the quality of social group development according to IT applications. The hypothesis was confirmed that the e-government activities can be realized by properly selecting and installing technologies, and using technology facilities. E-services influence the capabilities of state officials to apply modern technology and increase the availability of e-services for social groups. Results consist of individual or collective decisions to act on one’s own life, to implementation of effective information technologies in the e-government activities and using of e-services. An important indicator is the implementation of e-services in the activity of citizens. It is submitted as the index of e-participation in dealing with the activities of citizens and the possibilities of authorities directly related with providing services

  19. Evaluation of Public E-Services and Information Technology Accessibility in Different Social Groups

    Directory of Open Access Journals (Sweden)

    Ramutė Naujikienė

    2013-02-01

    Full Text Available The purpose of this study is to develop an approach based on the social quality evaluation square model for evaluation of information technology usage in different social groups. Componential view to the accessibility of e-services including IT means providing the possibility to research the influences of different life conditions to usage of the public e-services. The task of this empirical study is directed towards revealing the differences of e-inclusion and e-services accessibility for social groups of citizens of Lithuania, and to compare this accessibility data with other EU countries. Design/methodology/approach—the approach is based on the square model of social quality evaluation of information technology usage in different social groups. The social division square model includes an assessment of quality according to the evaluation of socioeconomic security, social inclusion, social cohesion, and empowerment. Empowerment can be defined as consisting of individual or collective decisions to act on one’s own life. Findings—the results are demonstrated by the accessibility of public e-services data, which are evaluated by the quality of social group development according to IT applications. The hypothesis was confirmed that the e-government activities can be realized by properly selecting and installing technologies, and using technology facilities. E-services influence the capabilities of state officials to apply modern technology and increase the availability of e-services for social groups. Results consist of individual or collective decisions to act on one’s own life, to implementation of effective information technologies in the e-government activities and using of e-services. An important indicator is the implementation of e-services in the activity of citizens. It is submitted as the index of e-participation in dealing with the activities of citizens and the possibilities of authorities directly related with providing

  20. Accessing and operating agricultural machinery: Advancements in assistive technology for users with impaired mobility.

    Science.gov (United States)

    Ehlers, Shawn G; Field, William E

    2018-02-14

    This research focused on the advancements made in enabling agricultural workers with impaired mobility to access and operate off-road agricultural machinery. Although not a new concept, technological advancements in remote-controlled lifts, electronic actuators, electric over hydraulic controllers, and various modes of hand controls have advanced significantly, allowing operators with limited mobility to resume a high level of productivity in agricultural-related enterprises. In the United States, approximately 1.7% of the population is living with some form of paralysis or significant mobility impairment. When paired with the 2012 USDA Agriculture Census of 3.2 million farmers, it can be extrapolated that these technologies could impact 54,000 agricultural workers who have encountered disabling injuries or disease, which inhibit their ability to access and operate tractors, combines, and other self-propelled agricultural machines. Advancements in agricultural-specific technologies can allow for many of these individuals to regain the ability to effectively operate machinery once more.

  1. Editorial: Models, technologies and approaches toward widening the open access to learning and education

    Directory of Open Access Journals (Sweden)

    Rachid Benlamri

    2016-03-01

    Full Text Available This special issue is devoted to novel models and technologies as well as current methodical approaches and best practices in the field of Open Learning and Open Education as enablers of personal growth, social inclusion, open innovation, and sustainable economic development in the challenging conditions of globalization and world-wide competition in productivity and services. The Open Access to Learning and Education embraces not only various technologies, such as mobile and intelligent technologies, content and data management, user-centered design, but also diverse directions of use, such as e-learning and training, organizational development, Massive Open Online Courses, special needs education, all building an excellent basis for various educational and business arrangements that widen the learning and education opportunities for all people around the globe. Against this background, this special issue demonstrates the immense speed and relentlessness of the Open Access concept growth presenting a wide range of examples toward supporting competency and skills development to ensure highly capable human capital, and solve individual, business, urban, demographic, health as well as social inclusion issues in today’s highly demanding digital economy environment.

  2. Microintaglio Printing for Soft Lithography-Based in Situ Microarrays

    Directory of Open Access Journals (Sweden)

    Manish Biyani

    2015-07-01

    Full Text Available Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called “microintaglio printing technology”, for large-scale bio-microarray fabrication using a microreactor array (µRA-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density, ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era.

  3. Immobilization Techniques for Microarray: Challenges and Applications

    Directory of Open Access Journals (Sweden)

    Satish Balasaheb Nimse

    2014-11-01

    Full Text Available The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

  4. Mining meiosis and gametogenesis with DNA microarrays.

    Science.gov (United States)

    Schlecht, Ulrich; Primig, Michael

    2003-04-01

    Gametogenesis is a key developmental process that involves complex transcriptional regulation of numerous genes including many that are conserved between unicellular eukaryotes and mammals. Recent expression-profiling experiments using microarrays have provided insight into the co-ordinated transcription of several hundred genes during mitotic growth and meiotic development in budding and fission yeast. Furthermore, microarray-based studies have identified numerous loci that are regulated during the cell cycle or expressed in a germ-cell specific manner in eukaryotic model systems like Caenorhabditis elegans, Mus musculus as well as Homo sapiens. The unprecedented amount of information produced by post-genome biology has spawned novel approaches to organizing biological knowledge using currently available information technology. This review outlines experiments that contribute to an emerging comprehensive picture of the molecular machinery governing sexual reproduction in eukaryotes.

  5. DNA microarrays : a molecular cloning manual

    National Research Council Canada - National Science Library

    Sambrook, Joseph; Bowtell, David

    2002-01-01

    .... DNA Microarrays provides authoritative, detailed instruction on the design, construction, and applications of microarrays, as well as comprehensive descriptions of the software tools and strategies...

  6. The Digitally Disadvantaged: Access to Digital Communication Technologies among First Year Students at a Rural South African University

    Science.gov (United States)

    Oyedemi, Toks; Mogano, Saki

    2018-01-01

    Considering the importance of digital skills in university education, this article reports on a study which examined access to technology among first year students at a rural South African university. The study focused on the digital readiness of students prior to their admission to the university, since many universities provide access to…

  7. Wireless Access

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Wireless Access. Wireless connect to the Base station. Easy and Convenient access. Costlier as compared to the wired technology. Reliability challenges. We see it as a complementary technology to the DSL.

  8. Fiber in access technologies and network convergence: an opportunity for optical integration

    Science.gov (United States)

    Ghiggino, Pierpaolo C.

    2008-11-01

    Broadband networks are among the fastest growing segment in telecom. The initial and still very significant push originated with xDSL technologies and indeed a significant amount of research and development is still occurring in this field with impressive results and allowing for a remarkable use of the installed copper infrastructure way beyond its originally planned bandwidth capabilities. However it is clear that ultimately a more suitable fiber based infrastructure will be needed in order to reduce both operational and network technology costs. Such cost reduction in inevitable as the added value to end users is only related to services and these cannot be priced outside a sensible window, whilst the related bandwidth increase is much more dramatic and its huge variability must be met with little or no cost impact by the network and its operation. Fiber in access has indeed the potential to cope with a huge bandwidth demand for many years to come as its inherent bandwidth capabilities are only just tapped by current service requirements. However the whole technology supply chain must follow in line. In particular optical technology must brace itself to cope with the required much larger deployment and greater cost effectiveness, whilst at the same time deliver performance suitable to the bandwidth increase offered in the longer term by the fiber medium. This paper looks at this issues and debates the opportunities for a new class of optical devices making use of the progress in optical integration

  9. Revenue-Maximizing Radio Access Technology Selection with Net Neutrality Compliance in Heterogeneous Wireless Networks

    Directory of Open Access Journals (Sweden)

    Elissar Khloussy

    2018-01-01

    Full Text Available The net neutrality principle states that users should have equal access to all Internet content and that Internet Service Providers (ISPs should not practice differentiated treatment on any of the Internet traffic. While net neutrality aims to restrain any kind of discrimination, it also grants exemption to a certain category of traffic known as specialized services (SS, by allowing the ISP to dedicate part of the resources for the latter. In this work, we consider a heterogeneous LTE/WiFi wireless network and we investigate revenue-maximizing Radio Access Technology (RAT selection strategies that are net neutrality-compliant, with exemption granted to SS traffic. Our objective is to find out how the bandwidth reservation for SS traffic would be made in a way that allows maximizing the revenue while being in compliance with net neutrality and how the choice of the ratio of reserved bandwidth would affect the revenue. The results show that reserving bandwidth for SS traffic in one RAT (LTE can achieve higher revenue. On the other hand, when the capacity is reserved across both LTE and WiFi, higher social benefit in terms of number of admitted users can be realized, as well as lower blocking probability for the Internet access traffic.

  10. Pengujian Kualitas Website Ditinjau dari Perspektif Accessibility, Experience, Marketing dan Technology

    Directory of Open Access Journals (Sweden)

    Diyurman Gea

    2014-06-01

    Full Text Available The purpose of this study was to determine the quality of the websites managed by individuals, companies and governments. The test results would be useful for managers to pay more attention to the quality of the website optimally through several perspectives: accessibility, experience, marketing and technology. The research used samples from 350 websites and the data were divided into seven categories, namely: website managed by SMEs (small and medium, website of universities, website of governments, e-commerce, news websites, website of industrial companies, and website of non-profit organization. We used Nibler as the testing tool to facilitate the assessment process. Data were analyzed using WEKA presented in the form of a decision tree. The results showed that the tested websites had an average value of 4.66 or worse (scale 1-10. The conclusion is that the manager of the website should perform repairs on the data and applications, in particular in the perspective of technology, accessibility and experience.

  11. The use of modern information technology in research on transport accessibility

    Directory of Open Access Journals (Sweden)

    Bartosz BARTOSIEWICZ

    2015-09-01

    Full Text Available Transport accessibility can be analyzed using a number of different methods. The problem with each of them is the difficulty of obtaining data to measure this phenomenon The focus of this article and its main goal are to present methods and tools for gathering data on road traffic; thanks to modern information technology, it is possible to collect real data without the need for large-scale and highly capital-intensive measurements. The application of modern information technology (IT presented in the article, such as computer programs and applications like Google Maps Traffic Overlay and TomTom Live Traffic, enable research to be conducted on a scale that has thus far been unattainable, and allows information to be collected on such criteria as traffic volume, flow, average traffic speed, and actual journey time. Such innovative means of gathering data on automobile traffic open up new perspectives for assessing transport accessibility in terms of automobile traffic by providing high-quality data that meet the requirements for use in primary research.

  12. Leveraging Open Standards and Technologies to Enhance Community Access to Earth Science Lidar Data

    Science.gov (United States)

    Crosby, C. J.; Nandigam, V.; Krishnan, S.; Cowart, C.; Baru, C.; Arrowsmith, R.

    2011-12-01

    Lidar (Light Detection and Ranging) data, collected from space, airborne and terrestrial platforms, have emerged as an invaluable tool for a variety of Earth science applications ranging from ice sheet monitoring to modeling of earth surface processes. However, lidar present a unique suite of challenges from the perspective of building cyberinfrastructure systems that enable the scientific community to access these valuable research datasets. Lidar data are typically characterized by millions to billions of individual measurements of x,y,z position plus attributes; these "raw" data are also often accompanied by derived raster products and are frequently terabytes in size. As a relatively new and rapidly evolving data collection technology, relevant open data standards and software projects are immature compared to those for other remote sensing platforms. The NSF-funded OpenTopography Facility project has developed an online lidar data access and processing system that co-locates data with on-demand processing tools to enable users to access both raw point cloud data as well as custom derived products and visualizations. OpenTopography is built on a Service Oriented Architecture (SOA) in which applications and data resources are deployed as standards compliant (XML and SOAP) Web services with the open source Opal Toolkit. To develop the underlying applications for data access, filtering and conversion, and various processing tasks, OpenTopography has heavily leveraged existing open source software efforts for both lidar and raster data. Operating on the de facto LAS binary point cloud format (maintained by ASPRS), open source libLAS and LASlib libraries provide OpenTopography data ingestion, query and translation capabilities. Similarly, raster data manipulation is performed through a suite of services built on the Geospatial Data Abstraction Library (GDAL). OpenTopography has also developed our own algorithm for high-performance gridding of lidar point cloud data

  13. Geiger mode avalanche photodiodes for microarray systems

    Science.gov (United States)

    Phelan, Don; Jackson, Carl; Redfern, R. Michael; Morrison, Alan P.; Mathewson, Alan

    2002-06-01

    New Geiger Mode Avalanche Photodiodes (GM-APD) have been designed and characterized specifically for use in microarray systems. Critical parameters such as excess reverse bias voltage, hold-off time and optimum operating temperature have been experimentally determined for these photon-counting devices. The photon detection probability, dark count rate and afterpulsing probability have been measured under different operating conditions. An active- quench circuit (AQC) is presented for operating these GM- APDs. This circuit is relatively simple, robust and has such benefits as reducing average power dissipation and afterpulsing. Arrays of these GM-APDs have already been designed and together with AQCs open up the possibility of having a solid-state microarray detector that enables parallel analysis on a single chip. Another advantage of these GM-APDs over current technology is their low voltage CMOS compatibility which could allow for the fabrication of an AQC on the same device. Small are detectors have already been employed in the time-resolved detection of fluorescence from labeled proteins. It is envisaged that operating these new GM-APDs with this active-quench circuit will have numerous applications for the detection of fluorescence in microarray systems.

  14. Assessing the Engagement, Learning, and Overall Experience of Students Operating an Atomic Absorption Spectrophotometer with Remote Access Technology

    Science.gov (United States)

    Erasmus, Daniel J.; Brewer, Sharon E.; Cinel, Bruno

    2015-01-01

    The use of internet-based technologies in the teaching of laboratories has emerged as a promising education tool. This study evaluated the effectiveness of using remote access technology to operate an atomic absorption spectrophotometer in analyzing the iron content in a crude myoglobin extract. Sixty-two students were surveyed on their level of…

  15. Assessing the engagement, learning, and overall experience of students operating an atomic absorption spectrophotometer with remote access technology.

    Science.gov (United States)

    Erasmus, Daniel J; Brewer, Sharon E; Cinel, Bruno

    2015-01-01

    The use of internet-based technologies in the teaching of laboratories has emerged as a promising education tool. This study evaluated the effectiveness of using remote access technology to operate an atomic absorption spectrophotometer in analyzing the iron content in a crude myoglobin extract. Sixty-two students were surveyed on their level of engagement, learning, and overall experience. Feedback from students suggests that the use of remote access technology is effective in teaching students the principles of chemical analysis by atomic absorption spectroscopy. © 2014 The International Union of Biochemistry and Molecular Biology.

  16. Label and Label-Free Detection Techniques for Protein Microarrays

    Directory of Open Access Journals (Sweden)

    Amir Syahir

    2015-04-01

    Full Text Available Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano‑biological events.

  17. A network collaboration implementing technology to improve medication dispensing and administration in critical access hospitals.

    Science.gov (United States)

    Wakefield, Douglas S; Ward, Marcia M; Loes, Jean L; O'Brien, John

    2010-01-01

    We report how seven independent critical access hospitals collaborated with a rural referral hospital to standardize workflow policies and procedures while jointly implementing the same health information technologies (HITs) to enhance medication care processes. The study hospitals implemented the same electronic health record, computerized provider order entry, pharmacy information systems, automated dispensing cabinets (ADC), and barcode medication administration systems. We conducted interviews and examined project documents to explore factors underlying the successful implementation of ADC and barcode medication administration across the network hospitals. These included a shared culture of collaboration; strategic sequencing of HIT component implementation; interface among HIT components; strategic placement of ADCs; disciplined use and sharing of workflow analyses linked with HIT applications; planning for workflow efficiencies; acquisition of adequate supply of HIT-related devices; and establishing metrics to monitor HIT use and outcomes.

  18. Twin-bit via resistive random access memory in 16 nm FinFET logic technologies

    Science.gov (United States)

    Shih, Yi-Hong; Hsu, Meng-Yin; King, Ya-Chin; Lin, Chrong Jung

    2018-04-01

    A via resistive random access memory (RRAM) cell fully compatible with the standard CMOS logic process has been successfully demonstrated for high-density logic nonvolatile memory (NVM) modules in advanced FinFET circuits. In this new cell, the transition metal layers are formed on both sides of a via, given two storage bits per via. In addition to its compact cell area (1T + 14 nm × 32 nm), the twin-bit via RRAM cell features a low operation voltage, a large read window, good data retention, and excellent cycling capability. As fine alignments between mask layers become possible, the twin-bit via RRAM cell is expected to be highly scalable in advanced FinFET technology.

  19. Advanced technologies for scalable ATLAS conditions database access on the grid

    International Nuclear Information System (INIS)

    Basset, R; Canali, L; Girone, M; Hawkings, R; Valassi, A; Viegas, F; Dimitrov, G; Nevski, P; Vaniachine, A; Walker, R; Wong, A

    2010-01-01

    During massive data reprocessing operations an ATLAS Conditions Database application must support concurrent access from numerous ATLAS data processing jobs running on the Grid. By simulating realistic work-flow, ATLAS database scalability tests provided feedback for Conditions Db software optimization and allowed precise determination of required distributed database resources. In distributed data processing one must take into account the chaotic nature of Grid computing characterized by peak loads, which can be much higher than average access rates. To validate database performance at peak loads, we tested database scalability at very high concurrent jobs rates. This has been achieved through coordinated database stress tests performed in series of ATLAS reprocessing exercises at the Tier-1 sites. The goal of database stress tests is to detect scalability limits of the hardware deployed at the Tier-1 sites, so that the server overload conditions can be safely avoided in a production environment. Our analysis of server performance under stress tests indicates that Conditions Db data access is limited by the disk I/O throughput. An unacceptable side-effect of the disk I/O saturation is a degradation of the WLCG 3D Services that update Conditions Db data at all ten ATLAS Tier-1 sites using the technology of Oracle Streams. To avoid such bottlenecks we prototyped and tested a novel approach for database peak load avoidance in Grid computing. Our approach is based upon the proven idea of pilot job submission on the Grid: instead of the actual query, an ATLAS utility library sends to the database server a pilot query first.

  20. IMPACT OF HEALTH TECHNOLOGY ASSESSMENT IN LITIGATION CONCERNING ACCESS TO HIGH-COST DRUGS.

    Science.gov (United States)

    Aleman, Alicia; Perez Galan, Ana

    2017-01-01

    The impact of health technology assessment (HTA) in the judicialization of the right of health has not been deeply studied in Latin American countries. The purpose of this study is to review the process of judicialization of the access to high cost drugs in Uruguay and assess the impact HTAs have had on this process. The methodology used for this study included a comprehensive literature search in electronic databases, local journals, internal documents developed in the Ministry of Health, as well as conducting interviews with key informants. Judicialization of the access of high cost drugs has been increasing since 2010. The strategy of the Ministry of Health of Uruguay to decrease this problem included the organization of roundtables with judges and other stakeholders on the basis of HTA, the training of defense lawyers in the use and interpretation of HTA, and the participation of a professional who develops HTA in the preparation of the defense arguments. A year after the implementation of this strategy, 25 percent of writs of protection were won by the Ministry of Health. Even though the strategy implemented was effective in reducing the loss of litigations, it was not effective in reducing the growing number of writs of protection. It is essential to address this problem in a broad debate and to promote understanding between the parties.

  1. EncyCloudPrado: didactic possibilities of new technologies for accessing information in museums

    Directory of Open Access Journals (Sweden)

    Carolina Fernández Castrillo

    2017-01-01

    Full Text Available The role and the development of museums in the contemporary world is closely related to the possibilities offered by the information and communication technologies (ICT. In line with the educational vocation of museums as cultural institutions, this paper offers a didactic resource to provide an easier access to information and the visualization of the cultural background in the digital age. In the framework of this research it was created the prototype EncyCloudPrado (2016, an interactive installation that allows searches through the online Museo Nacional del Prado's encyclopedia. The results are projected on a 360-degree widescreen as dynamic collages of sounds, documents and images, turning web browsing into a spatial experience. The aim of this study is to determine the degree of acceptance of the use of interactive installations in immersive environments by the generation Z as possible learning tools. It will also be assessed if this type of initiatives may be an incentive to attract more visits to museums and to promote the access to their funds.

  2. Data Collection, Access and Presentation Technologies in the National Ecological Observatory (NEON) Design (Invited)

    Science.gov (United States)

    Aulenbach, S. M.; Berukoff, S. J.

    2010-12-01

    The National Ecological Observatory Network (NEON) will collect data across the United States on the impacts of climate change, land use change and invasive species on ecosystem functions and biodiversity. In-situ sampling and distributed sensor networks, linked by an advanced cyberinfrastructure, will collect site-based data on a variety of organisms, soils, aquatic systems, atmosphere and climate. Targeted airborne remote sensing observations made by NEON as well as geographical data sets and satellite resources produced by Federal agencies will provide data at regional and national scales. The resulting data streams, collected over a 30-year period, will be synthesized into fully traceable information products that are freely and openly accessible to all users. We provide an overview of several collection, access and presentation technologies evaluated for use by observatory systems throughout the data product life cycle. Specifically, we discuss smart phone applications for citizen scientists as well as the use of handheld devices for sample collection and reporting from the field. Protocols for storing, queuing, and retrieving data from observatory sites located throughout the nation are highlighted as are the application of standards throughout the pipelined production of data products. We discuss the automated incorporation of provenance information and digital object identifiers for published data products. The use of widgets and personalized user portals for the discovery and dissemination of NEON data products are also presented.

  3. Emerging use of gene expression microarrays in plant physiology.

    Science.gov (United States)

    Wullschleger, Stan D; Difazio, Stephen P

    2003-01-01

    Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

  4. Emerging Use of Gene Expression Microarrays in Plant Physiology

    Directory of Open Access Journals (Sweden)

    Stephen P. Difazio

    2006-04-01

    Full Text Available Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

  5. Training to use a commercial brain-computer interface as access technology: a case study.

    Science.gov (United States)

    Taherian, Sarvnaz; Selitskiy, Dmitry; Pau, James; Davies, T Claire; Owens, R Glynn

    2016-01-01

    This case study describes how an individual with spastic quadriplegic cerebral palsy was trained over a period of four weeks to use a commercial electroencephalography (EEG)-based brain-computer interface (BCI). The participant spent three sessions exploring the system, and seven sessions playing a game focused on EEG feedback training of left and right arm motor imagery and a customised, training game paradigm was employed. The participant showed improvement in the production of two distinct EEG patterns. The participant's performance was influenced by motivation, fatigue and concentration. Six weeks post-training the participant could still control the BCI and used this to type a sentence using an augmentative and alternative communication application on a wirelessly linked device. The results from this case study highlight the importance of creating a dynamic, relevant and engaging training environment for BCIs. Implications for Rehabilitation Customising a training paradigm to suit the users' interests can influence adherence to assistive technology training. Mood, fatigue, physical illness and motivation influence the usability of a brain-computer interface. Commercial brain-computer interfaces, which require little set up time, may be used as access technology for individuals with severe disabilities.

  6. Access to Digital Communication Technology and Perceptions of Telemedicine for Patient Education among American Indian Patients with Diabetes.

    Science.gov (United States)

    Mathieson, Kathleen; Leafman, Joan S; Horton, Mark B

    2017-01-01

    Health care access for medically underserved patients managing chronic conditions is challenging. While telemedicine can support patient education and engagement, the "digital divide" may be particularly problematic among the medically underserved. This study evaluated physical access to digital devices, use of e-mail and social media tools, and perceptions of telemedicine among American Indian (AI) patients with diabetes mellitus (DM). Survey data were collected from AI patients with DM during teleophthalmology exams. Eighty-eight percent of patients had access to digital device(s), 70% used e-mail, and 56% used social media. Younger age and greater education were positively associated with e-mail and social media use (p < .05). Most (60%) considered telemedicine an excellent medium for health-related patient education. American Indian patients with DM had access enabling patient education via telemedicine. Future work should examine patient technology preferences and effectiveness of technology-based education in improving outcomes among medically underserved populations.

  7. Classification across gene expression microarray studies

    Directory of Open Access Journals (Sweden)

    Kuner Ruprecht

    2009-12-01

    Full Text Available Abstract Background The increasing number of gene expression microarray studies represents an important resource in biomedical research. As a result, gene expression based diagnosis has entered clinical practice for patient stratification in breast cancer. However, the integration and combined analysis of microarray studies remains still a challenge. We assessed the potential benefit of data integration on the classification accuracy and systematically evaluated the generalization performance of selected methods on four breast cancer studies comprising almost 1000 independent samples. To this end, we introduced an evaluation framework which aims to establish good statistical practice and a graphical way to monitor differences. The classification goal was to correctly predict estrogen receptor status (negative/positive and histological grade (low/high of each tumor sample in an independent study which was not used for the training. For the classification we chose support vector machines (SVM, predictive analysis of microarrays (PAM, random forest (RF and k-top scoring pairs (kTSP. Guided by considerations relevant for classification across studies we developed a generalization of kTSP which we evaluated in addition. Our derived version (DV aims to improve the robustness of the intrinsic invariance of kTSP with respect to technologies and preprocessing. Results For each individual study the generalization error was benchmarked via complete cross-validation and was found to be similar for all classification methods. The misclassification rates were substantially higher in classification across studies, when each single study was used as an independent test set while all remaining studies were combined for the training of the classifier. However, with increasing number of independent microarray studies used in the training, the overall classification performance improved. DV performed better than the average and showed slightly less variance. In

  8. A Versatile Microarray Platform for Capturing Rare Cells

    Science.gov (United States)

    Brinkmann, Falko; Hirtz, Michael; Haller, Anna; Gorges, Tobias M.; Vellekoop, Michael J.; Riethdorf, Sabine; Müller, Volkmar; Pantel, Klaus; Fuchs, Harald

    2015-10-01

    Analyses of rare events occurring at extremely low frequencies in body fluids are still challenging. We established a versatile microarray-based platform able to capture single target cells from large background populations. As use case we chose the challenging application of detecting circulating tumor cells (CTCs) - about one cell in a billion normal blood cells. After incubation with an antibody cocktail, targeted cells are extracted on a microarray in a microfluidic chip. The accessibility of our platform allows for subsequent recovery of targets for further analysis. The microarray facilitates exclusion of false positive capture events by co-localization allowing for detection without fluorescent labelling. Analyzing blood samples from cancer patients with our platform reached and partly outreached gold standard performance, demonstrating feasibility for clinical application. Clinical researchers free choice of antibody cocktail without need for altered chip manufacturing or incubation protocol, allows virtual arbitrary targeting of capture species and therefore wide spread applications in biomedical sciences.

  9. Integrated olfactory receptor and microarray gene expression databases

    Directory of Open Access Journals (Sweden)

    Crasto Chiquito J

    2007-06-01

    Full Text Available Abstract Background Gene expression patterns of olfactory receptors (ORs are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB, which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction. Description ORMD is a Web-accessible database that provides a secure data repository for OR microarray experiments. It contains both publicly available and private data; accessing the latter requires authenticated login. The ORMD is designed to allow users to not only deposit gene expression data but also manage their projects/experiments. For example, contributors can choose whether to make their datasets public. For each experiment, users can download the raw data files and view and export the gene expression data. For each OR gene being probed in a microarray experiment, a hyperlink to that gene in ORDB provides access to genomic and proteomic information related to the corresponding olfactory receptor. Individual ORs archived in ORDB are also linked to ORMD, allowing users access to the related microarray gene expression data. Conclusion ORMD serves as a data repository and project management system. It facilitates the study of microarray experiments of gene expression in the olfactory system. In conjunction with ORDB, ORMD integrates gene expression data with the genomic and functional data of ORs, and is thus a useful resource for both olfactory researchers and the public.

  10. Normalization for triple-target microarray experiments

    Directory of Open Access Journals (Sweden)

    Magniette Frederic

    2008-04-01

    Full Text Available Abstract Background Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis allow hybridization up to four samples simultaneously. The two additional dyes are Alexa488 and Alexa494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data. Results We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize p differently labelled targets co-hybridized on a same array, for any value of p greater than 2. Conclusion The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.

  11. Spot detection and image segmentation in DNA microarray data.

    Science.gov (United States)

    Qin, Li; Rueda, Luis; Ali, Adnan; Ngom, Alioune

    2005-01-01

    Following the invention of microarrays in 1994, the development and applications of this technology have grown exponentially. The numerous applications of microarray technology include clinical diagnosis and treatment, drug design and discovery, tumour detection, and environmental health research. One of the key issues in the experimental approaches utilising microarrays is to extract quantitative information from the spots, which represent genes in a given experiment. For this process, the initial stages are important and they influence future steps in the analysis. Identifying the spots and separating the background from the foreground is a fundamental problem in DNA microarray data analysis. In this review, we present an overview of state-of-the-art methods for microarray image segmentation. We discuss the foundations of the circle-shaped approach, adaptive shape segmentation, histogram-based methods and the recently introduced clustering-based techniques. We analytically show that clustering-based techniques are equivalent to the one-dimensional, standard k-means clustering algorithm that utilises the Euclidean distance.

  12. Probe Selection for DNA Microarrays using OligoWiz

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Juncker, Agnieszka; Nielsen, Henrik Bjørn

    2007-01-01

    Nucleotide abundance measurements using DNA microarray technology are possible only if appropriate probes complementary to the target nucleotides can be identified. Here we present a protocol for selecting DNA probes for microarrays using the OligoWiz application. OligoWiz is a client-server appl......Nucleotide abundance measurements using DNA microarray technology are possible only if appropriate probes complementary to the target nucleotides can be identified. Here we present a protocol for selecting DNA probes for microarrays using the OligoWiz application. OligoWiz is a client......-server application that offers a detailed graphical interface and real-time user interaction on the client side, and massive computer power and a large collection of species databases (400, summer 2007) on the server side. Probes are selected according to five weighted scores: cross-hybridization, deltaT(m), folding...... computer skills and can be executed from any Internet-connected computer. The probe selection procedure for a standard microarray design targeting all yeast transcripts can be completed in 1 h....

  13. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

    Directory of Open Access Journals (Sweden)

    Moreau Yves

    2005-05-01

    Full Text Available Abstract Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH. One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

  14. Elucidation of the antibacterial mechanism of the Curvularia haloperoxidase system by DNA microarray profiling

    DEFF Research Database (Denmark)

    Hansen, E.H.; Schembri, Mark; Klemm, Per

    2004-01-01

    was the wild type. Our results demonstrate that DNA microarray technology cannot be used as the only technique to investigate the mechanisms of action of new antimicrobial compounds. However, by combining DNA microarray analysis with the subsequent creation of knockout mutants, we were able to pinpoint one...

  15. Polyadenylation state microarray (PASTA) analysis.

    Science.gov (United States)

    Beilharz, Traude H; Preiss, Thomas

    2011-01-01

    Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly(A) tail length control in a transcriptome, we developed the polyadenylation state microarray (PASTA) method. It involves the purification of mRNA based on poly(A) tail length using thermal elution from poly(U) sepharose, followed by microarray analysis of the resulting fractions. In this chapter we detail our PASTA approach and describe some methods for bulk and mRNA-specific poly(A) tail length measurements of use to monitor the procedure and independently verify the microarray data.

  16. Bacterial identification and subtyping using DNA microarray and DNA sequencing.

    Science.gov (United States)

    Al-Khaldi, Sufian F; Mossoba, Magdi M; Allard, Marc M; Lienau, E Kurt; Brown, Eric D

    2012-01-01

    The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

  17. Access, use and preferences of information and communication technologies by physicians in a general hospital in Peru

    OpenAIRE

    Vásquez-Silva, Luis; Facultad de Medicina. Universidad Peruana Cayetano Heredia. Lima, Perú. Hospital Nacional Cayetano Heredia. Lima, Perú.; Ticse, Ray; Facultad de Medicina. Universidad Peruana Cayetano Heredia. Lima, Perú. Hospital Nacional Cayetano Heredia. Lima, Perú.; Alfaro-Carballido, Luz; Hospital Nacional Cayetano Heredia. Lima, Perú.; Guerra-Castañon, Felix; Facultad de Medicina. Universidad Peruana Cayetano Heredia. Lima, Perú. Hospital Nacional Cayetano Heredia. Lima, Perú.

    2015-01-01

    We assessed the access, use and preferences of information and communication technology (ICT) by physicians who practice at Cayetano Heredia National Hospital. The questionnaire explored the availability and skills of ICT, time, educational activities, search engines and technological applications most used as well as ICT preferences in education.211 physicians were surveyed; laptop use was 93%, tablet and smartphone use was 66% and 88%.68% havemobile Internet. Differences were evident in the...

  18. Cross-platform comparison of microarray data using order restricted inference

    Science.gov (United States)

    Klinglmueller, Florian; Tuechler, Thomas; Posch, Martin

    2013-01-01

    Motivation Titration experiments measuring the gene expression from two different tissues, along with total RNA mixtures of the pure samples, are frequently used for quality evaluation of microarray technologies. Such a design implies that the true mRNA expression of each gene, is either constant or follows a monotonic trend between the mixtures, applying itself to the use of order restricted inference procedures. Exploiting only the postulated monotonicity of titration designs, we propose three statistical analysis methods for the validation of high-throughput genetic data and corresponding preprocessing techniques. Results Our methods allow for inference of accuracy, repeatability and cross-platform agreement, with minimal required assumptions regarding the underlying data generating process. Therefore, they are readily applicable to all sorts of genetic high-throughput data independent of the degree of preprocessing. An application to the EMERALD dataset was used to demonstrate how our methods provide a rich spectrum of easily interpretable quality metrics and allow the comparison of different microarray technologies and normalization methods. The results are on par with previous work, but provide additional new insights that cast doubt on the utility of popular preprocessing techniques, specifically concerning the EMERALD projects dataset. Availability All datasets are available on EBI’s ArrayExpress web site (http://www.ebi.ac.uk/microarray-as/ae/) under accession numbers E-TABM-536, E-TABM-554 and E-TABM-555. Source code implemented in C and R is available at: http://statistics.msi.meduniwien.ac.at/float/cross_platform/. Methods for testing and variance decomposition have been made available in the R-package orQA, which can be downloaded and installed from CRAN http://cran.r-project.org. PMID:21317143

  19. Fertility tourism: circumventive routes that enable access to reproductive technologies and substances.

    Science.gov (United States)

    Bergmann, Sven

    2011-01-01

    “Fertility tourism” is a journalistic eye‐catcher focusing on the phenomenon of patients who search for a reproductive treatment in another country in order to circumvent laws, access restrictions, or waiting lists in their home country. In Europe, the reasons why people seek reproductive treatments outside their national boundaries are quite diverse, in part because regulations differ so much among countries. Beginning with four examples of people who crossed borders for an in vitro fertilization (IVF) treatment with gamete donation, this article provides some insight into these transnational circumvention practices based on material from ethnographic fieldwork and interviews in Spain, Denmark, and the Czech Republic. In all three countries, gamete donation is made strictly anonymous. Clinical practices such as egg donor recruitment and phenotypical matching between donors and recipients serve to naturalize the substitution of gametes and to install social legitimacy through resemblance markers with the prospective child. In comparison to other areas of medical tourism, which are subjects of debate as a consequence of neoliberal health politics and international medical competition, mobility in the area of reproductive technologies is deeply intertwined with new forms of doing kinship. For prospective parents, it holds a promise of generating offspring who could pass as biogenetically conceived children. Therefore, IVF with gamete donation is mostly modeled after conceptions of nature. Through anonymity and concealment it creates forms of nonrelatedness that leave space for future imaginings and traces of transnational genetic creators.

  20. Project WANT - Women's Access to Nuclear Technology, a successful industry/education partnership

    International Nuclear Information System (INIS)

    Widen, W.C.; Roth, G.L.; NIU)

    1987-01-01

    In 1984, the U.S. Congress issued the Carl D. Perkins Act, which charges vocational educators to increase their focus on two broad themes: (a) the elimination of sexual bias and sexual stereotyping in vocational education and (b) the provision of marketable skills to the economically deprived of the nation's work force. In response to this charter, an industry/education partnership was established among the Illinois State Board of Education, Norther Illinois University, and the Westinbghouse Nuclear Training Center. In essence, these partners established Project WANT - Women's Access to Nuclear Technology - with two premier goals: (a) to increase women's awareness regarding nuclear career opportunities and (b) to train and place women in technical professions within the nuclear industry. Feedback from the U.S. Department of Energy (DOE), the Atomic Industrial Forum, and the Bureau of Labor Statistics identifies that <2% of all technical positions within the nuclear power industry are held by women. Hence, one may conclude that there is a definite need to promote sexual equity in the nuclear industry and that Illinois represents a unique environment of opportunity to accomplish this

  1. A Brief Survey of Media Access Control, Data Link Layer, and Protocol Technologies for Lunar Surface Communications

    Science.gov (United States)

    Wallett, Thomas M.

    2009-01-01

    This paper surveys and describes some of the existing media access control and data link layer technologies for possible application in lunar surface communications and the advanced wideband Direct Sequence Code Division Multiple Access (DSCDMA) conceptual systems utilizing phased-array technology that will evolve in the next decade. Time Domain Multiple Access (TDMA) and Code Division Multiple Access (CDMA) are standard Media Access Control (MAC) techniques that can be incorporated into lunar surface communications architectures. Another novel hybrid technique that is recently being developed for use with smart antenna technology combines the advantages of CDMA with those of TDMA. The relatively new and sundry wireless LAN data link layer protocols that are continually under development offer distinct advantages for lunar surface applications over the legacy protocols which are not wireless. Also several communication transport and routing protocols can be chosen with characteristics commensurate with smart antenna systems to provide spacecraft communications for links exhibiting high capacity on the surface of the Moon. The proper choices depend on the specific communication requirements.

  2. Intelligent computer aided training systems in the real world: Making the technology accessible to the educational mainstream

    Science.gov (United States)

    Kovarik, Madeline

    1993-01-01

    Intelligent computer aided training systems hold great promise for the application of this technology to mainstream education and training. Yet, this technology, which holds such a vast potential impact for the future of education and training, has had little impact beyond the enclaves of government research labs. This is largely due to the inaccessibility of the technology to those individuals in whose hands it can have the greatest impact, teachers and educators. Simply throwing technology at an educator and expecting them to use it as an effective tool is not the answer. This paper provides a background into the use of technology as a training tool. MindLink, developed by HyperTech Systems, provides trainers with a powerful rule-based tool that can be integrated directly into a Windows application. By embedding expert systems technology it becomes more accessible and easier to master.

  3. Early Patient Access to Medicines: Health Technology Assessment Bodies Need to Catch Up with New Marketing Authorization Methods.

    Science.gov (United States)

    Leyens, Lada; Brand, Angela

    National and international medicines agencies have developed innovative methods to expedite promising new medicines to the market and facilitate early patient access. Some of these approval pathways are the conditional approval and the adaptive pathways by the European Medicines Agency (EMA); the Promising Innovative Medicine (PIM) designation and the Early Access to Medicines Scheme (EAMS) by the Medicines and Healthcare Products Regulatory Agency (MHRA), as well as the Fast Track, Breakthrough or Accelerated Approval methods by the Food and Drug Administration (FDA). However, at least in Europe, these methods cannot achieve the goal of improving timely access for patients to new medicines on their own; the reimbursement process also has to become adaptive and flexible. In the past 2 years, the effective access (national patient access) to newly approved oncology drugs ranged from 1 to 30 months, with an extremely high variability between European countries. The goal of early patient access in Europe can only be achieved if the national health technology assessment bodies, such as NICE (ENG), HAS (FR), G-BA (DE) or AIFA (IT), provide harmonized, transparent, flexible, conditional and adaptive methods that adopt the level of evidence accepted by the medicines agencies. The efforts from medicines agencies are welcome but will be in vain if health technology assessments do not follow with similar initiatives, and the European 'postcode' lottery will continue. © 2016 S. Karger AG, Basel.

  4. Assessment of Computer Technology Availability, Accessibility and Usage by Agricultural Education Student Teachers in Secondary Schools in Botswana

    Science.gov (United States)

    Hulela, K.; Rammolai, M.; Mpatane, W.

    2014-01-01

    This study examines the availability, accessibility and usability of computer as a form of information and communication technologies (ICTs) by student teachers in secondary schools. 44 out of 51 student teachers of Agriculture responded to the questionnaire. Means and percentages were used to analyze the data to establish the availability,…

  5. Examining Stakeholder Perceptions of Accessibility and Utilization of Computer and Internet Technology in the Selinsgrove Area School District

    Science.gov (United States)

    Krause, Lorinda M.

    2014-01-01

    This study utilized a mixed methods approach to examine the issue of how parents, students, and teachers (stakeholders) perceive accessibility and the utilization of computer and Internet technology within the Selinsgrove, Pennsylvania Area School District. Quantitative data was collected through the use of questionnaires distributed to the…

  6. A Survey of Exemplar Teachers' Perceptions, Use, and Access of Computer-Based Games and Technology for Classroom Instruction

    Science.gov (United States)

    Proctor, Michael D.; Marks, Yaela

    2013-01-01

    This research reports and analyzes for archival purposes surveyed perceptions, use, and access by 259 United States based exemplar Primary and Secondary educators of computer-based games and technology for classroom instruction. Participating respondents were considered exemplary as they each won the Milken Educator Award during the 1996-2009…

  7. Children, Technology, and Instruction: A Case Study of Elementary School Children Using an Online Public Access Catalog (OPAC).

    Science.gov (United States)

    Solomon, Paul

    1994-01-01

    Examines elementary school students' use of an online public access catalog to investigate the interaction between children, technology, curriculum, instruction, and learning. Highlights include patterns of successes and breakdowns; search strategies; instructional approaches and childrens' interests; structure of interaction; search terms; and…

  8. Assistive technology access and service delivery in resource-limited environments: introduction to a special issue of Disability and Rehabilitation: Assistive Technology.

    Science.gov (United States)

    Harniss, Mark; Samant Raja, Deepti; Matter, Rebecca

    2015-07-01

    This special issue addresses access to and service delivery of assistive technology (AT) in resource-limited environments (RLEs). Access to AT is complicated not simply by limited funds to purchase AT, but by larger ecosystem weaknesses in RLEs related to legislation and policy, supply, distribution, human resources, consumer demand and accessible design. We present eight diverse articles that address various aspects of the AT ecosystem. These articles represent a wide range of AT, many different countries and different research methods. Our goal is to highlight a topic that has received scant research investigation and limited investment in international development efforts, and offer an insight into how different countries and programs are promoting access to AT. We encourage researchers, funders and non-profit organizations to invest additional effort and resources in this area.

  9. Current Knowledge on Microarray Technology - An Overview

    African Journals Online (AJOL)

    Erah

    Review Article. Current Knowledge ... containing libraries of oligonucleotides robotically ... measurements, and averages over each oligonucleotide. ... quality of chips produced depends critically ..... Bae EK, Lee H, Lee JS, Noh EW. Isolation ...

  10. ADAPTING MICROARRAY TECHNOLOGY FOR USE IN ECOTOXICOGENOMICS

    Science.gov (United States)

    Ecotoxicogenomics includes research to identify differential gene expression in laboratory and field animals exposed to toxicants, and ultimately, to link the earliest indicators of exposure to adverse effects in organisms and populations. The USEPA National Exposure Research La...

  11. A Fisheye Viewer for microarray-based gene expression data.

    Science.gov (United States)

    Wu, Min; Thao, Cheng; Mu, Xiangming; Munson, Ethan V

    2006-10-13

    Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of raw microarray-based gene expression data. This paper presents one such interface--an electronic table (E-table) that uses fisheye distortion technology. The Fisheye Viewer for microarray-based gene expression data has been successfully developed to view MIAME data stored in the MAGE-ML format. The viewer can be downloaded from the project web site http://polaris.imt.uwm.edu:7777/fisheye/. The fisheye viewer was implemented in Java so that it could run on multiple platforms. We implemented the E-table by adapting JTable, a default table implementation in the Java Swing user interface library. Fisheye views use variable magnification to balance magnification for easy viewing and compression for maximizing the amount of data on the screen. This Fisheye Viewer is a lightweight but useful tool for biologists to quickly overview the raw microarray-based gene expression data in an E-table.

  12. A fisheye viewer for microarray-based gene expression data

    Directory of Open Access Journals (Sweden)

    Munson Ethan V

    2006-10-01

    Full Text Available Abstract Background Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of raw microarray-based gene expression data. This paper presents one such interface – an electronic table (E-table that uses fisheye distortion technology. Results The Fisheye Viewer for microarray-based gene expression data has been successfully developed to view MIAME data stored in the MAGE-ML format. The viewer can be downloaded from the project web site http://polaris.imt.uwm.edu:7777/fisheye/. The fisheye viewer was implemented in Java so that it could run on multiple platforms. We implemented the E-table by adapting JTable, a default table implementation in the Java Swing user interface library. Fisheye views use variable magnification to balance magnification for easy viewing and compression for maximizing the amount of data on the screen. Conclusion This Fisheye Viewer is a lightweight but useful tool for biologists to quickly overview the raw microarray-based gene expression data in an E-table.

  13. Advanced Data Mining of Leukemia Cells Micro-Arrays

    Directory of Open Access Journals (Sweden)

    Richard S. Segall

    2009-12-01

    Full Text Available This paper provides continuation and extensions of previous research by Segall and Pierce (2009a that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM. As Segall and Pierce (2009a and Segall and Pierce (2009b the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is provided on the work of others pertaining to the applications of data mining to micro-array databases of Leukemia cells and micro-array databases in general. As noted in predecessor article by Segall and Pierce (2009a, micro-array databases are one of the most popular functional genomics tools in use today. This research in this paper is intended to use advanced data mining technologies for better interpretations and knowledge discovery as generated by the patterns of gene expressions of HL60, Jurkat, NB4 and U937 Leukemia cells. The advanced data mining performed entailed using other data mining tools such as cubic clustering criterion, variable importance rankings, decision trees, and more detailed examinations of data mining statistics and study of other self-organized maps (SOM clustering regions of workspace as generated by SAS Enterprise Miner version 4. Conclusions and future directions of the research are also presented.

  14. Energy access and transition to cleaner cooking fuels and technologies in Sri Lanka: Issues and policy limitations

    International Nuclear Information System (INIS)

    Wickramasinghe, Anoja

    2011-01-01

    Easy energy access is a trigger for human, social, and economic development. A research project was undertaken in Sri Lanka to broaden the understanding of human dimension of energy access and technologies. A questionnaire survey, covering 2269 households, gathered data on socio-economic contexts and issues influencing a transition towards clean cooking facilities. The findings reveal that the transition is impeded by four factors: the lack of motivation and the pressure for switching over to cleaner facilities, the lack of modern energy technology options, the financial risks, and the lack of financing and other support. The paper describes the delicate two-way interrelation between women earning wages and the transitions to cleaner cooking fuels and technologies. The findings suggest the need for a policy framework involving the stakeholders, financing and standardised technologies. To make a change it is proposed to introduce a national, integrated policy incorporating financing and energy governance. - Highlights: ► Households in Sri Lanka lack access to modern energy technology options for cooking. ► Cooking with fuel wood and residues is the norm in Sri Lanka, particularly in rural households. ► A survey of rural households revealed that most cannot afford to switch to cleaner cooking options. ► Most households have little awareness of the health impacts of biomass cooking. ► Women in regular formal employment are more likely to value cleaner cooking options that save time.

  15. Exploiting fluorescence for multiplex immunoassays on protein microarrays

    International Nuclear Information System (INIS)

    Herbáth, Melinda; Balogh, Andrea; Matkó, János; Papp, Krisztián; Prechl, József

    2014-01-01

    Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications. (topical review)

  16. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.

    2005-01-01

    DNA microarrays have changed the field of biomedical sciences over the past 10 years. For several reasons, antibody and other protein microarrays have not developed at the same rate. However, protein and antibody arrays have emerged as a powerful tool to complement DNA microarrays during the post...

  17. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes

    Directory of Open Access Journals (Sweden)

    Eils Roland

    2005-11-01

    Full Text Available Abstract Background The extensive use of DNA microarray technology in the characterization of the cell transcriptome is leading to an ever increasing amount of microarray data from cancer studies. Although similar questions for the same type of cancer are addressed in these different studies, a comparative analysis of their results is hampered by the use of heterogeneous microarray platforms and analysis methods. Results In contrast to a meta-analysis approach where results of different studies are combined on an interpretative level, we investigate here how to directly integrate raw microarray data from different studies for the purpose of supervised classification analysis. We use median rank scores and quantile discretization to derive numerically comparable measures of gene expression from different platforms. These transformed data are then used for training of classifiers based on support vector machines. We apply this approach to six publicly available cancer microarray gene expression data sets, which consist of three pairs of studies, each examining the same type of cancer, i.e. breast cancer, prostate cancer or acute myeloid leukemia. For each pair, one study was performed by means of cDNA microarrays and the other by means of oligonucleotide microarrays. In each pair, high classification accuracies (> 85% were achieved with training and testing on data instances randomly chosen from both data sets in a cross-validation analysis. To exemplify the potential of this cross-platform classification analysis, we use two leukemia microarray data sets to show that important genes with regard to the biology of leukemia are selected in an integrated analysis, which are missed in either single-set analysis. Conclusion Cross-platform classification of multiple cancer microarray data sets yields discriminative gene expression signatures that are found and validated on a large number of microarray samples, generated by different laboratories and

  18. Access to Mobile Communication Technology and Willingness to Participate in Automated Telemedicine Calls Among Chronically Ill Patients in Honduras

    Science.gov (United States)

    Mendoza-Avelares, Milton O.; Milton, Evan C.; Lange, Ilta; Fajardo, Roosevelt

    2010-01-01

    Abstract Objectives: Patients in underdeveloped countries may be left behind by advances in telehealthcare. We surveyed chronically ill patients with low incomes in Honduras to measure their use of mobile technologies and willingness to participate in mobile disease management support. Materials and Methods: 624 chronically ill primary care patients in Honduras were surveyed. We examined variation in telephone access across groups defined by patients' sociodemographic characteristics, diagnoses, and access to care. Logistic regression was used to identify independent correlates of patients' interest in automated telephonic support for disease management. Results: Participants had limited education (mean 4.8 years), and 65% were unemployed. Eighty-four percent had telephone access, and 78% had cell phones. Most respondents had voicemail (61%) and text messaging (58%). Mobile technologies were particularly common among patients who had to forego clinic visits and medications due to cost concerns (each p 80%) reported that they would be willing to receive automated calls focused on appointment reminders, medication adherence, health status monitoring, and self-care education. Patients were more likely to be willing to participate in automated telemedicine services if they had to cancel a clinic appointment due to transportation problems or forego medication due to cost pressures. Conclusions: Even in this poor region of Honduras, most chronically ill patients have access to mobile technology, and most are willing to participate in automated telephone disease management support. Given barriers to in-person care, new models of mobile healthcare should be developed for chronically ill patients in developing countries. PMID:21062234

  19. Fiscal 2000 regional consortium research and development project - regional new technology creation research and development. Development of micro-array for next generation gene analysis (1st fiscal year); 2000 nendo chiiki consortium kenkyu kaihatsu jigyo - chiiki shingijutsu soshutsu kenkyu kaihatsu seika hokokusho. Jisedai idenshi kaiseki micro array no kaihatsu (daiichi nendo)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    Efforts are under way to construct a novel DNA (deoxyribonucleic acid) micro-array for gene diagnosis on the basis of technologies of laser scan type manipulation, nanometric position detection, and micro-machining. Using these technologies, structural changes to accompany reactions induced in the probe DNA deposited on an array are detected for the identification of the DNA. Activities are conducted in the four fields of (1) the study of probe DNA fixation technology, (2) development of an optical detection system, (3) detailed check of DNA micro-array performance evaluation technologies, and (4) a comprehensive survey. In field (1), gold colloid modified DNA molecules are designed and evaluated, and the fixation of DNA to substrates and technologies for integration are studied. In field (2), the gold colloid modified DNA is fixed on a thin gold film, and then a surface plasmon resonance (SPR) is observed in the wake of hybridization. Furthermore, a Brownian motion is observed of the metal particles fixed on a glass substrate via DNA. (NEDO)

  20. 16 CFR 6.152 - Program accessibility: Electronic and information technology.

    Science.gov (United States)

    2010-01-01

    ... information technology. 6.152 Section 6.152 Commercial Practices FEDERAL TRADE COMMISSION ORGANIZATION... information technology. (a) When developing, procuring, maintaining, or using electronic and information... electronic and information technology allows, regardless of the type of medium of the technology: (1...

  1. APPLICATION OF CDNA MICROARRAY TECHNOLOGY TO IN VITRO TOXICOLOGY AND THE SELECTION OF GENES FOR A REAL TIME RT-PCR-BASED SCREEN FOR OXIDATIVE STRESS IN HEP-G2 CELLS

    Science.gov (United States)

    Large-scale analysis of gene expression using cDNA microarrays promises therapid detection of the mode of toxicity for drugs and other chemicals. cDNAmicroarrays were used to examine chemically-induced alterations of geneexpression in HepG2 cells exposed to oxidative ...

  2. Implementation of mutual information and bayes theorem for classification microarray data

    Science.gov (United States)

    Dwifebri Purbolaksono, Mahendra; Widiastuti, Kurnia C.; Syahrul Mubarok, Mohamad; Adiwijaya; Aminy Ma’ruf, Firda

    2018-03-01

    Microarray Technology is one of technology which able to read the structure of gen. The analysis is important for this technology. It is for deciding which attribute is more important than the others. Microarray technology is able to get cancer information to diagnose a person’s gen. Preparation of microarray data is a huge problem and takes a long time. That is because microarray data contains high number of insignificant and irrelevant attributes. So, it needs a method to reduce the dimension of microarray data without eliminating important information in every attribute. This research uses Mutual Information to reduce dimension. System is built with Machine Learning approach specifically Bayes Theorem. This theorem uses a statistical and probability approach. By combining both methods, it will be powerful for Microarray Data Classification. The experiment results show that system is good to classify Microarray data with highest F1-score using Bayesian Network by 91.06%, and Naïve Bayes by 88.85%.

  3. Communication technology access, use, and preferences among primary care patients: from the Residency Research Network of Texas (RRNeT).

    Science.gov (United States)

    Hill, Jason H; Burge, Sandra; Haring, Anna; Young, Richard A

    2012-01-01

    The digital revolution is changing the manner in which patients communicate with their health care providers, yet many patients still lack access to communication technology. We conducted this study to evaluate access to, use of, and preferences for using communication technology among a predominantly low-income patient population. We determined whether access, use, and preferences were associated with type of health insurance, sex, age, and ethnicity. In 2011, medical student researchers administered questionnaires to patients of randomly selected physicians within 9 primary care clinics in the Residency Research Network of Texas. Surveys addressed access to and use of cell phones and home computers and preferences for communicating with health care providers. In this sample of 533 patients (77% response rate), 448 (84%) owned a cell phone and 325 (62%) owned computers. Only 48% reported conducting Internet searches, sending and receiving E-mails, and looking up health information on the Internet. Older individuals, those in government sponsored insurance programs, and individuals from racial/ethnic minority groups had the lowest levels of technology adoption. In addition, more than 60% of patients preferred not to send and receive health information over the Internet, by instant messaging, or by text messaging. Many patients in this sample did not seek health information electronically nor did they want to communicate electronically with their physicians. This finding raises concerns about the vision of the patient-centered medical home to enhance the doctor-patient relationship through communication technology. Our patients represent some of the more vulnerable populations in the United States and, as such, deserve attention from health care policymakers who are promoting widespread use of communication technology.

  4. Hierarchical information representation and efficient classification of gene expression microarray data

    OpenAIRE

    Bosio, Mattia

    2014-01-01

    In the field of computational biology, microarryas are used to measure the activity of thousands of genes at once and create a global picture of cellular function. Microarrays allow scientists to analyze expression of many genes in a single experiment quickly and eficiently. Even if microarrays are a consolidated research technology nowadays and the trends in high-throughput data analysis are shifting towards new technologies like Next Generation Sequencing (NGS), an optimum method for sample...

  5. Employing image processing techniques for cancer detection using microarray images.

    Science.gov (United States)

    Dehghan Khalilabad, Nastaran; Hassanpour, Hamid

    2017-02-01

    Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes. Finally, via the extracted data, cancerous cell is recognized. To evaluate the performance of the proposed system, microarray database is employed which includes Breast cancer, Myeloid Leukemia and Lymphomas from the Stanford Microarray Database. The results indicate that the proposed system is able to identify the type of cancer from the data set with an accuracy of 95.45%, 94.11%, and 100%, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. PIIKA 2: an expanded, web-based platform for analysis of kinome microarray data.

    Directory of Open Access Journals (Sweden)

    Brett Trost

    Full Text Available Kinome microarrays are comprised of peptides that act as phosphorylation targets for protein kinases. This platform is growing in popularity due to its ability to measure phosphorylation-mediated cellular signaling in a high-throughput manner. While software for analyzing data from DNA microarrays has also been used for kinome arrays, differences between the two technologies and associated biologies previously led us to develop Platform for Intelligent, Integrated Kinome Analysis (PIIKA, a software tool customized for the analysis of data from kinome arrays. Here, we report the development of PIIKA 2, a significantly improved version with new features and improvements in the areas of clustering, statistical analysis, and data visualization. Among other additions to the original PIIKA, PIIKA 2 now allows the user to: evaluate statistically how well groups of samples cluster together; identify sets of peptides that have consistent phosphorylation patterns among groups of samples; perform hierarchical clustering analysis with bootstrapping; view false negative probabilities and positive and negative predictive values for t-tests between pairs of samples; easily assess experimental reproducibility; and visualize the data using volcano plots, scatterplots, and interactive three-dimensional principal component analyses. Also new in PIIKA 2 is a web-based interface, which allows users unfamiliar with command-line tools to easily provide input and download the results. Collectively, the additions and improvements described here enhance both the breadth and depth of analyses available, simplify the user interface, and make the software an even more valuable tool for the analysis of kinome microarray data. Both the web-based and stand-alone versions of PIIKA 2 can be accessed via http://saphire.usask.ca.

  7. PIIKA 2: an expanded, web-based platform for analysis of kinome microarray data.

    Science.gov (United States)

    Trost, Brett; Kindrachuk, Jason; Määttänen, Pekka; Napper, Scott; Kusalik, Anthony

    2013-01-01

    Kinome microarrays are comprised of peptides that act as phosphorylation targets for protein kinases. This platform is growing in popularity due to its ability to measure phosphorylation-mediated cellular signaling in a high-throughput manner. While software for analyzing data from DNA microarrays has also been used for kinome arrays, differences between the two technologies and associated biologies previously led us to develop Platform for Intelligent, Integrated Kinome Analysis (PIIKA), a software tool customized for the analysis of data from kinome arrays. Here, we report the development of PIIKA 2, a significantly improved version with new features and improvements in the areas of clustering, statistical analysis, and data visualization. Among other additions to the original PIIKA, PIIKA 2 now allows the user to: evaluate statistically how well groups of samples cluster together; identify sets of peptides that have consistent phosphorylation patterns among groups of samples; perform hierarchical clustering analysis with bootstrapping; view false negative probabilities and positive and negative predictive values for t-tests between pairs of samples; easily assess experimental reproducibility; and visualize the data using volcano plots, scatterplots, and interactive three-dimensional principal component analyses. Also new in PIIKA 2 is a web-based interface, which allows users unfamiliar with command-line tools to easily provide input and download the results. Collectively, the additions and improvements described here enhance both the breadth and depth of analyses available, simplify the user interface, and make the software an even more valuable tool for the analysis of kinome microarray data. Both the web-based and stand-alone versions of PIIKA 2 can be accessed via http://saphire.usask.ca.

  8. Nanomedicine, microarrays and their applications in clinical microbiology

    Directory of Open Access Journals (Sweden)

    Özcan Deveci

    2010-12-01

    Full Text Available Growing interest in the future medical applications of nanotechnology is leading to the emergence of a new scientific field that called as “nanomedicine”. Nanomedicine may be defined as the investigating, treating, reconstructing and controlling human biology and health at the molecular level, using engineered nanodevices and nanostructures. Microarray technology is a revolutionary tool for elucidating roles of genes in infectious diseases, shifting from traditional methods of research to integrated approaches. This technology has great potential to provide medical diagnosis, monitor treatment and help in the development of new tools for infectious disease prevention and/or management. The aim of this paper is to provide an overview of the current application of microarray platforms and nanomedicine in the study of experimental microbiology and the impact of this technology in clinical settings.

  9. Integrating Biological Perspectives:. a Quantum Leap for Microarray Expression Analysis

    Science.gov (United States)

    Wanke, Dierk; Kilian, Joachim; Bloss, Ulrich; Mangelsen, Elke; Supper, Jochen; Harter, Klaus; Berendzen, Kenneth W.

    2009-02-01

    Biologists and bioinformatic scientists cope with the analysis of transcript abundance and the extraction of meaningful information from microarray expression data. By exploiting biological information accessible in public databases, we try to extend our current knowledge over the plant model organism Arabidopsis thaliana. Here, we give two examples of increasing the quality of information gained from large scale expression experiments by the integration of microarray-unrelated biological information: First, we utilize Arabidopsis microarray data to demonstrate that expression profiles are usually conserved between orthologous genes of different organisms. In an initial step of the analysis, orthology has to be inferred unambiguously, which then allows comparison of expression profiles between orthologs. We make use of the publicly available microarray expression data of Arabidopsis and barley, Hordeum vulgare. We found a generally positive correlation in expression trajectories between true orthologs although both organisms are only distantly related in evolutionary time scale. Second, extracting clusters of co-regulated genes implies similarities in transcriptional regulation via similar cis-regulatory elements (CREs). Vice versa approaches, where co-regulated gene clusters are found by investigating on CREs were not successful in general. Nonetheless, in some cases the presence of CREs in a defined position, orientation or CRE-combinations is positively correlated with co-regulated gene clusters. Here, we make use of genes involved in the phenylpropanoid biosynthetic pathway, to give one positive example for this approach.

  10. Understanding access and use of technology among youth with first-episode psychosis to inform the development of technology-enabled therapeutic interventions.

    Science.gov (United States)

    Abdel-Baki, Amal; Lal, Shalini; D-Charron, Olivier; Stip, Emmanuel; Kara, Nadjia

    2017-02-01

    Computers, video games and technological devices are part of young people's everyday lives. However, their use in first-episode psychosis (FEP) treatment is rare. The purpose of this study was to better understand the access and use of technology among individuals with FEP, including gaming activities, to inform future development of technology-enabled therapeutic applications. Self-administered survey on use of technological tools in 71 FEP individuals. PCs/laptops were used by all participants; cellphones/smartphones by 92%, consoles by 83% (mainly male and younger participants). Women texted and used social networks more frequently; men played games (mainly action) more often. The younger individuals reported playing games frequently (32% daily) with less use of the Web and social networks (favourite: Facebook). These data will be useful for developing Web-based psychoeducation tools and cognitive remediation video games for youth with FEP. © 2015 Wiley Publishing Asia Pty Ltd.

  11. A Low Density Microarray Method for the Identification of Human Papillomavirus Type 18 Variants

    Science.gov (United States)

    Meza-Menchaca, Thuluz; Williams, John; Rodríguez-Estrada, Rocío B.; García-Bravo, Aracely; Ramos-Ligonio, Ángel; López-Monteon, Aracely; Zepeda, Rossana C.

    2013-01-01

    We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18's variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings. PMID:24077317

  12. TECHNOLOGY FOR ADMINISTERING OF THE ACCESS TO INFORMATION RESOURCES IN MANAGEMENT SYSTEM ON THE AVIATION ENTERPRISE

    Directory of Open Access Journals (Sweden)

    Andrey V. Degtyarev

    2015-01-01

    Full Text Available The task of administering software-information complex occurs duringthe development of application systems for managing business-processes and is connected with the organization of access forusers to information resources in conditions of multi-user information systems for management. For solution of this problem proposed theapproach, which is based on a hierarchical system of access rightsto information resources on the levels: tool, object and procedural.Keywords: software-information complex, information resources,administering, permissions, separation of powers, access model.

  13. Pervasive Technologies: Access to Knowledge (A2K)in the ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Pervasive networked communication technologies are transforming the way in ... These Third World mass-marketing commercial technology players have been ... The A2K movement advocates a commons approach to cyberspace, media ...

  14. [Access, use and preferences of Information and Communication Technologies by physicians in a general hospital in Peru].

    Science.gov (United States)

    Vásquez-Silva, Luis; Ticse, Ray; Alfaro-Carballido, Luz; Guerra-Castañon, Felix

    2015-01-01

    We assessed the access, use and preferences of information and communication technology (ICT) by physicians who practice at Cayetano Heredia National Hospital. The questionnaire explored the availability and skills of ICT, time, educational activities, search engines and technological applications most used as well as ICT preferences in education.211 physicians were surveyed; laptop use was 93%, tablet and smartphone use was 66% and 88%.68% have mobile Internet. Differences were evident in the frequency of use of ICT in 25-34 year old age group as well as a higher level of skills (pWhatsApp as a means of exchanging images and data related to health, 50% participated in medical blogs, online courses or videoconferences. The use and access of ICT is common among doctors in this hospital and there is positive interest in its use in education.

  15. 12 CFR 352.5 - Accessibility to electronic and information technology.

    Science.gov (United States)

    2010-01-01

    ... and information technology. (a) In accordance with section 508 of the Rehabilitation Act, the FDIC shall ensure, absent an undue burden, that the electronic and information technology the agency develops... or procurement of electronic and information technology that meets the standards published by the...

  16. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

    Science.gov (United States)

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (psunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  17. Recommendations for the use of microarrays in prenatal diagnosis.

    Science.gov (United States)

    Suela, Javier; López-Expósito, Isabel; Querejeta, María Eugenia; Martorell, Rosa; Cuatrecasas, Esther; Armengol, Lluis; Antolín, Eugenia; Domínguez Garrido, Elena; Trujillo-Tiebas, María José; Rosell, Jordi; García Planells, Javier; Cigudosa, Juan Cruz

    2017-04-07

    Microarray technology, recently implemented in international prenatal diagnosis systems, has become one of the main techniques in this field in terms of detection rate and objectivity of the results. This guideline attempts to provide background information on this technology, including technical and diagnostic aspects to be considered. Specifically, this guideline defines: the different prenatal sample types to be used, as well as their characteristics (chorionic villi samples, amniotic fluid, fetal cord blood or miscarriage tissue material); variant reporting policies (including variants of uncertain significance) to be considered in informed consents and prenatal microarray reports; microarray limitations inherent to the technique and which must be taken into account when recommending microarray testing for diagnosis; a detailed clinical algorithm recommending the use of microarray testing and its introduction into routine clinical practice within the context of other genetic tests, including pregnancies in families with a genetic history or specific syndrome suspicion, first trimester increased nuchal translucency or second trimester heart malformation and ultrasound findings not related to a known or specific syndrome. This guideline has been coordinated by the Spanish Association for Prenatal Diagnosis (AEDP, «Asociación Española de Diagnóstico Prenatal»), the Spanish Human Genetics Association (AEGH, «Asociación Española de Genética Humana») and the Spanish Society of Clinical Genetics and Dysmorphology (SEGCyD, «Sociedad Española de Genética Clínica y Dismorfología»). Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

  18. Access-technology agnostic delivery platform for ICT4D services

    CSIR Research Space (South Africa)

    Makitla, I

    2012-10-01

    Full Text Available .kashan.co.za] CONTEXT Capitalising on target resource-constrained rural communities? technological capabilities can be considered a critical consideration when delivering Information and Communication Technology for Development (ICT4D) content and services... to these communities. The core approach of this research project, which is informed by the concept of ?digital difference?[1], is to leverage the existing technological infrastructure and capacity (know-how) in a community to enable delivery of ICT4D content...

  19. Understanding Digital Technology Access and Use Among New York State Residents to Enhance Dissemination of Health Information.

    Science.gov (United States)

    Manganello, Jennifer A; Gerstner, Gena; Pergolino, Kristen; Graham, Yvonne; Strogatz, David

    2016-01-01

    Many state and local health departments, as well as community organizations, have been using new technologies to disseminate health information to targeted populations. Yet little data exist that show access and use patterns, as well as preferences for receiving health information, at the state level. This study was designed to obtain information about media and technology use, and health information seeking patterns, from a sample of New York State (NYS) residents. A cross-sectional telephone survey (with mobile phones and landlines) was developed to assess media and technology access, use patterns, and preferences for receiving health information among a sample of 1350 residents in NYS. The survey used random digit dialing methodology. A weighted analysis was conducted utilizing Stata/SE software. Data suggest that NYS residents have a high level of computer and Internet use; 82% have at least one working computer at home, and 85% use the Internet at least sometimes. Mobile phone use is also high; 90% indicated having a mobile phone, and of those 63% have a smartphone. When asked about preferences for receiving health information from an organization, many people preferred websites (49%); preferences for other sources varied by demographic characteristics. Findings suggest that the Internet and other technologies are viable ways to reach NYS residents, but agencies and organizations should still consider using traditional methods of communication in some cases, and determine appropriate channels based on the population of interest.

  20. Welcome to Processes—A New Open Access Journal on Chemical and Biological Process Technology

    Directory of Open Access Journals (Sweden)

    Michael A. Henson

    2012-11-01

    Full Text Available As the result of remarkable technological progress, this past decade has witnessed considerable advances in our ability to manipulate natural and engineered systems, particularly at the molecular level. These advancements offer the potential to revolutionize our world through the development of novel soft and hard materials and the construction of new cellular platforms for chemical and pharmaceutical synthesis. For these technologies to truly impact society, the development of process technology that will enable effective large-scale production is essential. Improved processes are also needed for more established technologies in chemical and biochemical manufacturing, as these industries face ever increasing competitive pressure that mandates continuous improvement. [...

  1. Enabling technologies for millimeter-wave radio-over-fiber systems in next generation heterogeneous mobile access networks

    Science.gov (United States)

    Zhang, Junwen; Yu, Jianjun; Wang, Jing; Xu, Mu; Cheng, Lin; Lu, Feng; Shen, Shuyi; Yan, Yan; Cho, Hyunwoo; Guidotti, Daniel; Chang, Gee-kung

    2017-01-01

    Fifth-generation (5G) wireless access network promises to support higher access data rate with more than 1,000 times capacity with respect to current long-term evolution (LTE) systems. New radio-access-technologies (RATs) based on higher carrier frequencies to millimeter-wave (MMW) radio-over-fiber, and carrier-aggregation (CA) using multi-band resources are intensively studied to support the high data rate access and effectively use of frequency resources in heterogeneous mobile network (Het-Net). In this paper, we investigate several enabling technologies for MMW RoF systems in 5G Het-Net. Efficient mobile fronthaul (MFH) solutions for 5G centralized radio access network (C-RAN) and beyond are proposed, analyzed and experimentally demonstrated based on the analog scheme. Digital predistortion based on memory polynomial for analog MFH linearization are presented with improved EVM performances and receiver sensitivity. We also propose and experimentally demonstrate a novel inter-/intra- RAT CA scheme for 5G Het- Net. The real-time standard 4G-LTE signal is carrier-aggregated with three broadband 60GHz MMW signals based on proposed optical-domain band-mapping method. RATs based on new waveforms have also been studied here to achieve higher spectral-efficiency (SE) in asynchronous environments. Full-duplex asynchronous quasi-gapless carrier aggregation scheme for MMW ROF inter-/intra-RAT based on the FBMC is also presented with 4G-LTE signals. Compared with OFDM-based signals with large guard-bands, FBMC achieves higher spectral-efficiency with better EVM performance at less received power and smaller guard-bands.

  2. Employing optical code division multiple access technology in the all fiber loop vibration sensor system

    Science.gov (United States)

    Tseng, Shin-Pin; Yen, Chih-Ta; Syu, Rong-Shun; Cheng, Hsu-Chih

    2013-12-01

    This study proposes a spectral amplitude coding-optical code division multiple access (SAC-OCDMA) framework to access the vibration frequency of a test object on the all fiber loop vibration sensor (AFLVS). Each user possesses an individual SAC, and fiber Bragg grating (FBG) encoders/decoders using multiple FBG arrays were adopted, providing excellent orthogonal properties in the frequency domain. The system also mitigates multiple access interference (MAI) among users. When an optical fiber is bent to a point exceeding the critical radius, the fiber loop sensor becomes sensitive to external physical parameters (e.g., temperature, strain, and vibration). The AFLVS involves placing a fiber loop with a specific radius on a designed vibration platform.

  3. Universal access to electricity in Burkina Faso: scaling-up renewable energy technologies

    Science.gov (United States)

    Moner-Girona, M.; Bódis, K.; Huld, T.; Kougias, I.; Szabó, S.

    2016-08-01

    This paper describes the status quo of the power sector in Burkina Faso, its limitations, and develops a new methodology that through spatial analysis processes with the aim to provide a possible pathway for universal electricity access. Following the SE4All initiative approach, it recommends the more extensive use of distributed renewable energy systems to increase access to electricity on an accelerated timeline. Less than 5% of the rural population in Burkina Faso have currently access to electricity and supply is lacking at many social structures such as schools and hospitals. Energy access achievements in Burkina Faso are still very modest. According to the latest SE4All Global Tracking Framework (2015), the access to electricity annual growth rate in Burkina Faso from 2010 to 2012 is 0%. The rural electrification strategy for Burkina Faso is scattered in several electricity sector development policies: there is a need of defining a concrete action plan. Planning and coordination between grid extension and the off-grid electrification programme is essential to reach a long-term sustainable energy model and prevent high avoidable infrastructure investments. This paper goes into details on the methodology and findings of the developed Geographic Information Systems tool. The aim of the dynamic planning tool is to provide support to the national government and development partners to define an alternative electrification plan. Burkina Faso proves to be paradigm case for the methodology as its national policy for electrification is still dominated by grid extension and the government subsidising fossil fuel electricity production. However, the results of our analysis suggest that the current grid extension is becoming inefficient and unsustainable in order to reach the national energy access targets. The results also suggest that Burkina Faso’s rural electrification strategy should be driven local renewable resources to power distributed mini-grids. We find that

  4. A Customized DNA Microarray for Microbial Source Tracking ...

    Science.gov (United States)

    It is estimated that more than 160, 000 miles of rivers and streams in the United States are impaired due to the presence of waterborne pathogens. These pathogens typically originate from human and other animal fecal pollution sources; therefore, a rapid microbial source tracking (MST) method is needed to facilitate water quality assessment and impaired water remediation. We report a novel qualitative DNA microarray technology consisting of 453 probes for the detection of general fecal and host-associated bacteria, viruses, antibiotic resistance, and other environmentally relevant genetic indicators. A novel data normalization and reduction approach is also presented to help alleviate false positives often associated with high-density microarray applications. To evaluate the performance of the approach, DNA and cDNA was isolated from swine, cattle, duck, goose and gull fecal reference samples, as well as soiled poultry liter and raw municipal sewage. Based on nonmetric multidimensional scaling analysis of results, findings suggest that the novel microarray approach may be useful for pathogen detection and identification of fecal contamination in recreational waters. The ability to simultaneously detect a large collection of environmentally important genetic indicators in a single test has the potential to provide water quality managers with a wide range of information in a short period of time. Future research is warranted to measure microarray performance i

  5. Microarrays: Molecular allergology and nanotechnology for personalised medicine (II).

    Science.gov (United States)

    Lucas, J M

    2010-01-01

    Progress in nanotechnology and DNA recombination techniques have produced tools for the diagnosis and investigation of allergy at molecular level. The most advanced examples of such progress are the microarray techniques, which have been expanded not only in research in the field of proteomics but also in application to the clinical setting. Microarrays of allergic components offer results relating to hundreds of allergenic components in a single test, and using a small amount of serum which can be obtained from capillary blood. The availability of new molecules will allow the development of panels including new allergenic components and sources, which will require evaluation for clinical use. Their application opens the door to component-based diagnosis, to the holistic perception of sensitisation as represented by molecular allergy, and to patient-centred medical practice by allowing great diagnostic accuracy and the definition of individualised immunotherapy for each patient. The present article reviews the application of allergenic component microarrays to allergology for diagnosis, management in the form of specific immunotherapy, and epidemiological studies. A review is also made of the use of protein and gene microarray techniques in basic research and in allergological diseases. Lastly, an evaluation is made of the challenges we face in introducing such techniques to clinical practice, and of the future perspectives of this new technology. Copyright 2010 SEICAP. Published by Elsevier Espana. All rights reserved.

  6. See what you eat--broad GMO screening with microarrays.

    Science.gov (United States)

    von Götz, Franz

    2010-03-01

    Despite the controversy of whether genetically modified organisms (GMOs) are beneficial or harmful for humans, animals, and/or ecosystems, the number of cultivated GMOs is increasing every year. Many countries and federations have implemented safety and surveillance systems for GMOs. Potent testing technologies need to be developed and implemented to monitor the increasing number of GMOs. First, these GMO tests need to be comprehensive, i.e., should detect all, or at least the most important, GMOs on the market. This type of GMO screening requires a high degree of parallel tests or multiplexing. To date, DNA microarrays have the highest number of multiplexing capabilities when nucleic acids are analyzed. This trend article focuses on the evolution of DNA microarrays for GMO testing. Over the last 7 years, combinations of multiplex PCR detection and microarray detection have been developed to qualitatively assess the presence of GMOs. One example is the commercially available DualChip GMO (Eppendorf, Germany; http://www.eppendorf-biochip.com), which is the only GMO screening system successfully validated in a multicenter study. With use of innovative amplification techniques, promising steps have recently been taken to make GMO detection with microarrays quantitative.

  7. 76 FR 77816 - Access to Confidential Business Information by Guident Technologies, Inc. and Subcontractor...

    Science.gov (United States)

    2011-12-14

    ... Business Information by Guident Technologies, Inc. and Subcontractor, Impact Innovations Systems, Inc..., Guident Technologies, Inc. of Herndon, VA and subcontractor, Impact Innovations Systems, Inc. of Manassas... Control Act (TSCA). Some of the information may be claimed or determined to be Confidential Business...

  8. Examining Health Information Technology Implementation Success Factors in Critical Access Hospitals

    Science.gov (United States)

    Monkman, Blake D.

    2016-01-01

    As the role of information technology increases throughout the world, healthcare providers in the United States face industry and governmental pressures to implement health information technology (HIT) as a tool to improve healthcare costs, quality, and safety. The problem addressed in this study was the relatively low HIT implementation success…

  9. Urban Adolescent Students and Technology: Access, Use and Interest in Learning Language and Literacy

    Science.gov (United States)

    Li, Jia; Snow, Catherine; White, Claire

    2015-01-01

    Adolescents today have vastly different opportunities to learn and process information via pervasive digital technologies and social media. However, there is scant literature on the impact of these technologies on urban adolescents with lower socioeconomic status. This study of 531 urban students in grades 6-8 used a self-reported survey to…

  10. Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes.

    Science.gov (United States)

    Jahandeh, Nadia; Ranjbar, Reza; Behzadi, Payam; Behzadi, Elham

    2015-01-01

    The pathotypes of uropathogenic Escherichia coli (UPEC) cause different types of urinary tract infections (UTIs). The presence of a wide range of virulence genes in UPEC enables us to design appropriate DNA microarray probes. These probes, which are used in DNA microarray technology, provide us with an accurate and rapid diagnosis and definitive treatment in association with UTIs caused by UPEC pathotypes. The main goal of this article is to introduce the UPEC virulence genes as invaluable approaches for designing DNA microarray probes. Main search engines such as Google Scholar and databases like NCBI were searched to find and study several original pieces of literature, review articles, and DNA gene sequences. In parallel with in silico studies, the experiences of the authors were helpful for selecting appropriate sources and writing this review article. There is a significant variety of virulence genes among UPEC strains. The DNA sequences of virulence genes are fabulous patterns for designing microarray probes. The location of virulence genes and their sequence lengths influence the quality of probes. The use of selected virulence genes for designing microarray probes gives us a wide range of choices from which the best probe candidates can be chosen. DNA microarray technology provides us with an accurate, rapid, cost-effective, sensitive, and specific molecular diagnostic method which is facilitated by designing microarray probes. Via these tools, we are able to have an accurate diagnosis and a definitive treatment regarding UTIs caused by UPEC pathotypes.

  11. Bystander effect: Biological endpoints and microarray analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chaudhry, M. Ahmad [Department of Medical Laboratory and Radiation Sciences, College of Nursing and Health Sciences, University of Vermont, 302 Rowell Building, Burlington, VT 05405 (United States) and DNA Microarray Facility, University of Vermont, Burlington, VT 05405 (United States)]. E-mail: mchaudhr@uvm.edu

    2006-05-11

    In cell populations exposed to ionizing radiation, the biological effects occur in a much larger proportion of cells than are estimated to be traversed by radiation. It has been suggested that irradiated cells are capable of providing signals to the neighboring unirradiated cells resulting in damage to these cells. This phenomenon is termed the bystander effect. The bystander effect induces persistent, long-term, transmissible changes that result in delayed death and neoplastic transformation. Because the bystander effect is relevant to carcinogenesis, it could have significant implications for risk estimation for radiation exposure. The nature of the bystander effect signal and how it impacts the unirradiated cells remains to be elucidated. Examination of the changes in gene expression could provide clues to understanding the bystander effect and could define the signaling pathways involved in sustaining damage to these cells. The microarray technology serves as a tool to gain insight into the molecular pathways leading to bystander effect. Using medium from irradiated normal human diploid lung fibroblasts as a model system we examined gene expression alterations in bystander cells. The microarray data revealed that the radiation-induced gene expression profile in irradiated cells is different from unirradiated bystander cells suggesting that the pathways leading to biological effects in the bystander cells are different from the directly irradiated cells. The genes known to be responsive to ionizing radiation were observed in irradiated cells. Several genes were upregulated in cells receiving media from irradiated cells. Surprisingly no genes were found to be downregulated in these cells. A number of genes belonging to extracellular signaling, growth factors and several receptors were identified in bystander cells. Interestingly 15 genes involved in the cell communication processes were found to be upregulated. The induction of receptors and the cell

  12. Bystander effect: Biological endpoints and microarray analysis

    International Nuclear Information System (INIS)

    Chaudhry, M. Ahmad

    2006-01-01

    In cell populations exposed to ionizing radiation, the biological effects occur in a much larger proportion of cells than are estimated to be traversed by radiation. It has been suggested that irradiated cells are capable of providing signals to the neighboring unirradiated cells resulting in damage to these cells. This phenomenon is termed the bystander effect. The bystander effect induces persistent, long-term, transmissible changes that result in delayed death and neoplastic transformation. Because the bystander effect is relevant to carcinogenesis, it could have significant implications for risk estimation for radiation exposure. The nature of the bystander effect signal and how it impacts the unirradiated cells remains to be elucidated. Examination of the changes in gene expression could provide clues to understanding the bystander effect and could define the signaling pathways involved in sustaining damage to these cells. The microarray technology serves as a tool to gain insight into the molecular pathways leading to bystander effect. Using medium from irradiated normal human diploid lung fibroblasts as a model system we examined gene expression alterations in bystander cells. The microarray data revealed that the radiation-induced gene expression profile in irradiated cells is different from unirradiated bystander cells suggesting that the pathways leading to biological effects in the bystander cells are different from the directly irradiated cells. The genes known to be responsive to ionizing radiation were observed in irradiated cells. Several genes were upregulated in cells receiving media from irradiated cells. Surprisingly no genes were found to be downregulated in these cells. A number of genes belonging to extracellular signaling, growth factors and several receptors were identified in bystander cells. Interestingly 15 genes involved in the cell communication processes were found to be upregulated. The induction of receptors and the cell

  13. Outsourcing a High Speed Internet Access Project: An Information Technology Class Case Study in Three Parts

    Science.gov (United States)

    Platt, Richard G.; Carper, William B.; McCool, Michael

    2010-01-01

    In early 2004, the Hilton Hotels Corporation (HHC) required that all of its hotels (both owned and franchised) install high-speed Internet access (HSIA) in all of their rooms by June 2004. This case focuses on how one of its franchise properties located on the northern gulf coast of Florida (the Hilton Sandestin Beach Golf Resort &…

  14. Access to the Information Superhighway and Emerging Information Technologies by People with Disabilities.

    Science.gov (United States)

    National Council on Disability, Washington, DC.

    This report discusses the growth of the National Information Infrastructure (NII), or the information superhighway, and its implications for people with disabilities. Advantages for people with disabilities include: increasing the ability of individuals with some types of disabilities to access and use information; decreasing personal isolation…

  15. Development of an Instrument to Measure Faculty's Information and Communication Technology Access (FICTA)

    Science.gov (United States)

    Soomro, Kamal Ahmed; Kale, Ugur; Curtis, Reagan; Akcaoglu, Mete; Bernstein, Malayna

    2018-01-01

    The phenomenon of "digital divide" is complex and multidimensional, extending beyond issues of physical access. The purpose of this study was to develop a scale to measure a range of factors related to digital divide among higher education faculty and to evaluate its reliability and validity. Faculty's Information and Communication…

  16. Xylella fastidiosa gene expression analysis by DNA microarrays

    OpenAIRE

    Travensolo,Regiane F.; Carareto-Alves,Lucia M.; Costa,Maria V.C.G.; Lopes,Tiago J.S.; Carrilho,Emanuel; Lemos,Eliana G.M.

    2009-01-01

    Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcrip...

  17. "Harshlighting" small blemishes on microarrays

    Directory of Open Access Journals (Sweden)

    Wittkowski Knut M

    2005-03-01

    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs. Results We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.

  18. Developing technology intelligence strategy to access knowledge of innovation clusters. : The case of KODAK in Cambridge

    OpenAIRE

    Dang , Rani Jeanne; Mortara , Letizia; Thomson , Ruth; Minshall , Tim

    2010-01-01

    International audience; Current times are characterised by a knowledge-based economy and fast technological change. In this difficult environment, companies compete to maintain a relevant position through innovation. In response to these challenges, many companies are currently adopting an open approach to innovation, pursuing innovation by combining internal and external resources. Technology intelligence (TI) activities support the implementation of open innovation with the systematic captu...

  19. Accessing best practice resources using mobile technology in an undergraduate nursing program: a feasibility study.

    Science.gov (United States)

    Mann, Elizabeth G; Medves, Jennifer; Vandenkerkhof, Elizabeth G

    2015-03-01

    Mobile technology presents new opportunities for nursing education and ultimately the provision of nursing care. The aim of this study was to explore the utility of mobile technology in undergraduate nursing education. In this evaluation study, undergraduate nursing students were provided with iPod Touch devices containing best practice guidelines. Computer self-efficacy was assessed, and the Theory of Planned Behavior was used to identify potential predictors of the use of mobile technology. Questionnaires were completed at baseline (n = 33) and postimplementation (n = 23). Feedback on feasibility issues was recorded throughout the study period. Students generally found the devices useful, and few technical problems were identified; however, lack of skill in using the devices and lack of support from staff in the clinical setting were commonly identified issues. Self-efficacy scores were high throughout the study. Attitudes, perceptions of the desirability of use, perceived personal control over use, and intentions of using the device were lower postimplementation than at baseline. Attitude toward the technology predicted intention to use the device after graduation. Mobile technology may promote evidence-informed practice; however, supporting students' acquisition of related skills may optimize use. Successful integration of mobile technology into practice requires attention to factors that affect student attitudes.

  20. Telemental health technology in deaf and general mental-health services: access and use.

    Science.gov (United States)

    Austen, Sally; McGrath, Melissa

    2006-01-01

    Long-distance travel to provide mental health services for deaf people has implications for efficiency, safety, and equality of service. However, uptake of Telemental Health (TMH) has been slow in both deaf and general mental health services. A quantitative study was used to investigate access to TMH and whether staff confidence, experience, or demographics affect TMH use. It was concluded that staff in neither deaf mental health services nor general mental health services had adequate knowledge of or access to TMH. Staff expressed concerns over TMH's appropriateness in their work. Previous use of videoconferencing was assosciated significantly with confidence, but previous use of videophones was not. Neither staff in deaf services nor deaf staff were more experienced with or more confident about videoconferencing, whereas, within deaf services, deaf staff were significantly more confident about videophone use. Training implications are discussed.

  1. Advanced technologies for scalable ATLAS conditions database access on the grid

    CERN Document Server

    Basset, R; Dimitrov, G; Girone, M; Hawkings, R; Nevski, P; Valassi, A; Vaniachine, A; Viegas, F; Walker, R; Wong, A

    2010-01-01

    During massive data reprocessing operations an ATLAS Conditions Database application must support concurrent access from numerous ATLAS data processing jobs running on the Grid. By simulating realistic work-flow, ATLAS database scalability tests provided feedback for Conditions Db software optimization and allowed precise determination of required distributed database resources. In distributed data processing one must take into account the chaotic nature of Grid computing characterized by peak loads, which can be much higher than average access rates. To validate database performance at peak loads, we tested database scalability at very high concurrent jobs rates. This has been achieved through coordinated database stress tests performed in series of ATLAS reprocessing exercises at the Tier-1 sites. The goal of database stress tests is to detect scalability limits of the hardware deployed at the Tier-1 sites, so that the server overload conditions can be safely avoided in a production environment. Our analysi...

  2. Sustainable Development and Airport Surface Access: The Role of Technological Innovation and Behavioral Change

    OpenAIRE

    Ryley, Tim; Elmirghani, Jaafar; Budd, Tom; Miyoshi, Chikage; Mason, Keith; Moxon, Richard; Ahmed, Imad; Qazi, Bilal; Zanni, Alberto

    2013-01-01

    Sustainable development reflects an underlying tension to achieve economic growth whilst addressing environmental challenges, and this is particularly the case for the aviation sector. Although much of the aviation-related focus has fallen on reducing aircraft emissions, airports have also been under increasing pressure to support the vision of a low carbon energy future. One of the main sources of airport-related emissions is passenger journeys to and from airports (the surface access compon...

  3. Modern techniques and technologies for unbundled access in the local loop

    Science.gov (United States)

    Bacis Vasile, Irina Bristena; Schiopu, Paul; Marghescu, Cristina

    2015-02-01

    The efficient and unbundled use of the existing telecommunications infrastructure represents a major goal for the development of the services offered by telecommunications providers. A major telecommunications operator can provide services to a subscriber using a copper wire pair or part of the frequency spectrum of a copper wire pair, together with other operators, through a process of unbundling access in the local loop. Since access to the vocal band is an already solved problem, concerns turn to the broadband access with xDSL service delivery on ungrouped subscriber loops; besides the legal and economic aspects involved this has become an engineering problem also. The local loop unbundling methods have a substantial technical impact. This impact should be taken into account right from the design stage and then in the standardization stage of broadband systems intended to operate on copper wire pairs in the local loop. These systems are known under the generic term of xDSL and began to be analyzed in the late 90s. xDSL became the dominant solution for providing Internet at a reasonable price for both residential and business subscribers. In this massive development scenario, certain problems will arise from the early stages of deployment, and another type of problems will occur later on when a large number of systems will be installed in a single beam.

  4. Applications of nanotechnology, next generation sequencing and microarrays in biomedical research.

    Science.gov (United States)

    Elingaramil, Sauli; Li, Xiaolong; He, Nongyue

    2013-07-01

    Next-generation sequencing technologies, microarrays and advances in bio nanotechnology have had an enormous impact on research within a short time frame. This impact appears certain to increase further as many biomedical institutions are now acquiring these prevailing new technologies. Beyond conventional sampling of genome content, wide-ranging applications are rapidly evolving for next-generation sequencing, microarrays and nanotechnology. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted re sequencing and discovery of transcription factor binding sites, noncoding RNA expression profiling and molecular diagnostics. This paper thus discusses current applications of nanotechnology, next-generation sequencing technologies and microarrays in biomedical research and highlights the transforming potential these technologies offer.

  5. Translating microarray data for diagnostic testing in childhood leukaemia

    International Nuclear Information System (INIS)

    Hoffmann, Katrin; Firth, Martin J; Beesley, Alex H; Klerk, Nicholas H de; Kees, Ursula R

    2006-01-01

    Recent findings from microarray studies have raised the prospect of a standardized diagnostic gene expression platform to enhance accurate diagnosis and risk stratification in paediatric acute lymphoblastic leukaemia (ALL). However, the robustness as well as the format for such a diagnostic test remains to be determined. As a step towards clinical application of these findings, we have systematically analyzed a published ALL microarray data set using Robust Multi-array Analysis (RMA) and Random Forest (RF). We examined published microarray data from 104 ALL patients specimens, that represent six different subgroups defined by cytogenetic features and immunophenotypes. Using the decision-tree based supervised learning algorithm Random Forest (RF), we determined a small set of genes for optimal subgroup distinction and subsequently validated their predictive power in an independent patient cohort. We achieved very high overall ALL subgroup prediction accuracies of about 98%, and were able to verify the robustness of these genes in an independent panel of 68 specimens obtained from a different institution and processed in a different laboratory. Our study established that the selection of discriminating genes is strongly dependent on the analysis method. This may have profound implications for clinical use, particularly when the classifier is reduced to a small set of genes. We have demonstrated that as few as 26 genes yield accurate class prediction and importantly, almost 70% of these genes have not been previously identified as essential for class distinction of the six ALL subgroups. Our finding supports the feasibility of qRT-PCR technology for standardized diagnostic testing in paediatric ALL and should, in conjunction with conventional cytogenetics lead to a more accurate classification of the disease. In addition, we have demonstrated that microarray findings from one study can be confirmed in an independent study, using an entirely independent patient cohort

  6. Seeded Bayesian Networks: Constructing genetic networks from microarray data

    Directory of Open Access Journals (Sweden)

    Quackenbush John

    2008-07-01

    Full Text Available Abstract Background DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes that underlie cellular metabolism and physiology. The challenge in analyzing large-scale expression data has been to extract biologically meaningful inferences regarding these processes – often represented as networks – in an environment where the datasets are often imperfect and biological noise can obscure the actual signal. Although many techniques have been developed in an attempt to address these issues, to date their ability to extract meaningful and predictive network relationships has been limited. Here we describe a method that draws on prior information about gene-gene interactions to infer biologically relevant pathways from microarray data. Our approach consists of using preliminary networks derived from the literature and/or protein-protein interaction data as seeds for a Bayesian network analysis of microarray results. Results Through a bootstrap analysis of gene expression data derived from a number of leukemia studies, we demonstrate that seeded Bayesian Networks have the ability to identify high-confidence gene-gene interactions which can then be validated by comparison to other sources of pathway data. Conclusion The use of network seeds greatly improves the ability of Bayesian Network analysis to learn gene interaction networks from gene expression data. We demonstrate that the use of seeds derived from the biomedical literature or high-throughput protein-protein interaction data, or the combination, provides improvement over a standard Bayesian Network analysis, allowing networks involving dynamic processes to be deduced from the static snapshots of biological systems that represent the most common source of microarray data. Software implementing these methods has been included in the widely used TM4 microarray analysis package.

  7. Dye-Doped Silica Nanoparticle Labels/Protein Microarray for Detection of Protein Biomarkers

    OpenAIRE

    Wu, Hong; Huo, Qisheng; Varnum, Susan; Wang, Jun; Liu, Guodong; Nie, Zimin; Liu, Jun; Lin, Yuehe

    2008-01-01

    We report a dye-encapsulated silica nanoparticle as a label, with the advantages of high fluorescence intensity, photostability, and biocompatibility, in conjunction with microarray technology for sensitive immunoassay of a biomarker, Interleukin-6 (IL-6), on a microarray format. The tris (2,2’-bipyridyl)ruthenium (II)chloride hexahydrate (Rubpy) dye was incorporated into silica nanoparticles using a simple one-step microemulsion synthesis. In this synthesis process, Igepal CA520 was used as ...

  8. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

    OpenAIRE

    Rao, Archana N.; Grainger, David W.

    2014-01-01

    Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surface...

  9. DNA Microarrays: a Powerful Genomic Tool for Biomedical and Clinical Research

    OpenAIRE

    Trevino, Victor; Falciani, Francesco; Barrera-Saldaña, Hugo A

    2007-01-01

    Among the many benefits of the Human Genome Project are new and powerful tools such as the genome-wide hybridization devices referred to as microarrays. Initially designed to measure gene transcriptional levels, microarray technologies are now used for comparing other genome features among individuals and their tissues and cells. Results provide valuable information on disease subcategories, disease prognosis, and treatment outcome. Likewise, they reveal differences in genetic makeup, regulat...

  10. Technology Access and Smartphone App Preferences for Medication Adherence in Adolescents and Young Adults With Sickle Cell Disease.

    Science.gov (United States)

    Badawy, Sherif M; Thompson, Alexis A; Liem, Robert I

    2016-05-01

    Hydroxyurea is the only Food and Drug Administration approved medication for sickle cell disease (SCD) with short- and long-term benefits for both morbidity and mortality. However, hydroxyurea underutilization and adherence remain challenges for patients with SCD. The objectives of this study were to determine access to technology among adolescents and young adults (AYA) with SCD and to identify their preferred technology-based strategies for improving medication adherence. A cross-sectional survey was administered in a variety of clinical settings from October 2014 through May 2015 to AYA (12-22 years) with SCD (all genotypes) followed in a Comprehensive Sickle Cell Program. Eighty of 107 eligible participants completed the survey for a 75% response rate. Participants (51% female, 94% Black) had a mean age of 15.3 ± 2.8 years. Most participants (75%) were on a daily medication with about half on hydroxyurea. Forgetfulness (67%) was the most common barrier to medication adherence. The majority of participants (85%) owned smartphones and either owned or had access to electronic tablets (83%), laptops (72%), or desktops (70%). Of the proposed smartphone app features, daily medication reminders were ranked first most frequently, followed by education about SCD, adherence text prompts, education about SCD medications, and medication log. The majority of our AYA with SCD owned smartphones and had access to other electronic devices. Our survey results provided valuable insight into the preferred app features and optimal strategies for developing technology-based interventions, such as a multicomponent app, to increase medication adherence for AYA with SCD or other chronic conditions. © 2016 Wiley Periodicals, Inc.

  11. Learning and mastery behaviours as risk factors to abandonment in a paediatric user of advanced single-switch access technology.

    Science.gov (United States)

    Brian, Leung; Jessica A, Brian; Tom, Chau

    2013-09-01

    The present descriptive case study documents the behaviours of a child single-switch user in the community setting and draws attention to learning and mastery behaviours as risk factors to single-switch abandonment. Our observations were interpreted in the context of a longer term school-based evaluation of an advanced single-switch access technology with a nine year-old user with severe spastic quadriplegic cerebral palsy. The child completed 25 experiment sessions averaging a rate of three sessions every two weeks. During each session he worked on several blocks of single-switch computer activity using his vocal cord vibration switch. Despite high levels of single-switch sensitivity and specificity that suggested a good fit between the participant and the technology, the participant perceived a lower proficiency level of his own abilities, demonstrated impatience and intolerance to interaction errors, and was apprehensive of making mistakes when using his switch in public. The benefit of gaining some degree of independent physical access might not necessarily enhance resilience to interaction errors or bouts of poor task performance. On the other hand, the participant's behaviours were consistent with those of a typically developing child learning or mastering any new skill or task. Implications for Rehabilitation The attitude and behaviour of a paediatric switch user towards skill development can be risk factors to abandonment of an access technology, despite successful clinical trial with the device. Children with severe disabilities can be associated with the same types of skill development behaviour patterns and achievement motivation as their typically developing peers. Empirical observations of the case participant's switch use behaviours suggest that user training could be adaptive in order to account for individual differences in skill development and achievement motivation.

  12. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  13. Efficient, quality-assured data capture in operational research through innovative use of open-access technology.

    Science.gov (United States)

    Kumar, A M V; Naik, B; Guddemane, D K; Bhat, P; Wilson, N; Sreenivas, A N; Lauritsen, J M; Rieder, H L

    2013-03-21

    Ensuring quality of data during electronic data capture has been one of the most neglected components of operational research. Multicentre studies are also challenged with issues about logistics of travel, training, supervision, monitoring and troubleshooting support. Allocating resources to these issues can pose a significant bottleneck for operational research in resource-limited settings. In this article, we describe an innovative and efficient way of coordinating data capture in multicentre operational research using a combination of three open access technologies-EpiData for data capture, Dropbox for sharing files and TeamViewer for providing remote support.

  14. Efficient, quality-assured data capture in operational research through innovative use of open-access technology

    DEFF Research Database (Denmark)

    Kumar, A M V; Naik, B; Guddemane, D K

    2013-01-01

    to these issues can pose a significant bottleneck for operational research in resource-limited settings. In this article, we describe an innovative and efficient way of coordinating data capture in multicentre operational research using a combination of three open access technologies-EpiData for data capture......Ensuring quality of data during electronic data capture has been one of the most neglected components of operational research. Multicentre studies are also challenged with issues about logistics of travel, training, supervision, monitoring and troubleshooting support. Allocating resources...

  15. Dynamic, electronically switchable surfaces for membrane protein microarrays.

    Science.gov (United States)

    Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J

    2006-02-01

    Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.

  16. Transcriptome analysis of zebrafish embryogenesis using microarrays.

    Directory of Open Access Journals (Sweden)

    Sinnakaruppan Mathavan

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  17. A Computational Method based on Radio Frequency Technologies for the Analysis of Accessibility of Disabled People in Sustainable Cities

    Directory of Open Access Journals (Sweden)

    Virgilio Gilart-Iglesias

    2015-11-01

    Full Text Available The sustainability strategy in urban spaces arises from reflecting on how to achieve a more habitable city and is materialized in a series of sustainable transformations aimed at humanizing different environments so that they can be used and enjoyed by everyone without exception and regardless of their ability. Modern communication technologies allow new opportunities to analyze efficiency in the use of urban spaces from several points of view: adequacy of facilities, usability, and social integration capabilities. The research presented in this paper proposes a method to perform an analysis of movement accessibility in sustainable cities based on radio frequency technologies and the ubiquitous computing possibilities of the new Internet of Things paradigm. The proposal can be deployed in both indoor and outdoor environments to check specific locations of a city. Finally, a case study in a controlled context has been simulated to validate the proposal as a pre-deployment step in urban environments.

  18. 'Better justice?' or 'shambolic justice?': Governments' use of information technology for access to law and justice, and the impact on regional and rural legal practitioners

    Directory of Open Access Journals (Sweden)

    Caroline Hart

    2017-04-01

    Full Text Available This paper reports the results of a study on whether government use of information technology potentially compromises access to law and justice by Queensland regional and rural (RR legal practitioners. The paper describes current approaches to the use of information technology by state and federal governments, and provides an insight into the challenges and opportunities identified by individual RR legal practitioners, policy-makers and the judiciary on the use of such technology. The paper makes recommendations to promote increased access to law and justice for RR legal practitioners when using government information technology.

  19. The EADGENE Microarray Data Analysis Workshop

    DEFF Research Database (Denmark)

    de Koning, Dirk-Jan; Jaffrézic, Florence; Lund, Mogens Sandø

    2007-01-01

    Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from...... 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays...... statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful...

  20. Data collection using open access technology in multicentre operational research involving patient interviews.

    Science.gov (United States)

    Shewade, H D; Chadha, S S; Gupta, V; Tripathy, J P; Satyanarayana, S; Sagili, K; Mohanty, S; Bera, O P; Pandey, P; Rajeswaran, P; Jayaraman, G; Santhappan, A; Bajpai, U N; Mamatha, A M; Maiser, R; Naqvi, A J; Pandurangan, S; Nath, S; Ghule, V H; Das, A; Prasad, B M; Biswas, M; Singh, G; Mallick, G; Jeyakumar Jaisingh, A J; Rao, R; Kumar, A M V

    2017-03-21

    Conducting multicentre operational research is challenging due to issues related to the logistics of travel, training, supervision, monitoring and troubleshooting support. This is even more burdensome in resource-constrained settings and if the research includes patient interviews. In this article, we describe an innovative model that uses open access tools such as Dropbox, TeamViewer and CamScanner for efficient, quality-assured data collection in an ongoing multicentre operational research study involving record review and patient interviews. The tools used for data collection have been shared for adaptation and use by other researchers.

  1. The right of all nations to access science, new technologies and sustainable development.

    Science.gov (United States)

    Majidi, Mohammad Reza; Dehshiri, Mohammad Reza

    2009-01-01

    This article explores the need for reflection on the right of developing countries to science and technology in addition to explaining the place of the scientific rights of nations in human rights as a whole. The discussion was conducted in relation to sustainable development. Through the examination of the current situation and the challenges to sustainable development, and taking into account the imbalance in the distribution of the benefits of science and new technologies, the authors advocate a comprehensive approach to promote cooperation and capacity-building in this area. They argue that linkages should be adopted between micro-levels and macro-levels of analysis by elevating rights and related issues from individuals to the national level in the field of the right to science and technology, and from the national to the international level in the field of sustainable development in order to institutionalise and ensure individual and national rights to science, technology and sustainable development. The authors also believe in a multidimensional perspective based on the balanced flourishing of the material and immaterial aspects of humankind in order to realise these rights in the context of dialogue and cultural diversity and to promote the culture of sustainable and dynamic peace based on justice in knowledge societies.

  2. Access to Technology in Transnational Social Fields: Simultaneity and Digital Literacy Socialization of Adult Immigrants

    Science.gov (United States)

    Nogueron-Liu, Silvia

    2013-01-01

    Some studies of technology use by immigrants have explored the role of digital media in their maintenance of affiliations with their nations of origin. However, the potential for transnational social networks to serve as "resources" that facilitate digital literacy socialization for adult immigrant learners remains unexplored. In this…

  3. Utilizing Geo-Referenced Mobile Game Technology for Universally Accessible Virtual Geology Field Trips

    Science.gov (United States)

    Bursztyn, Natalie; Pederson, Joel; Shelton, Brett; Walker, Andrew; Campbell, Todd

    2015-01-01

    Declining interest and low persistence is well documented among undergraduate students in Science, Technology, Engineering, and Math in the United States. For geoscience, field trips are important attractors to students, however with high enrollment courses and increasing costs they are becoming rare. We propose in this concept paper that the…

  4. Programmatic Knowledge Management: Technology, Literacy, and Access in 21st-Century Writing Programs

    Science.gov (United States)

    York, Eric James

    2015-01-01

    Growing out of research in Technical Communication, Composition Studies, and Writing Program Administration, the articles in this dissertation explicitly seek to address changes in the practices and products of writing and writing studies wrought by the so-called "digital revolution" in communication technology, which has been ongoing in…

  5. ICT and accessibility: an action space perspective on the impact of new information and communication technologies

    NARCIS (Netherlands)

    Dijst, M.J.

    2004-01-01

    It is frequently asserted in the literature that new Information and Communication Technologies (ICTs) are on the point of a breakthrough into rapid growth. Although we cannot say whether this breakthrough will indeed take place and ― should it do so ― on what scale, in this paper we nevertheless

  6. The Limitations of Access Alone: Moving Towards Open Processes in Education Technology

    Science.gov (United States)

    Knox, Jeremy

    2013-01-01

    "Openness" has emerged as one of the foremost themes in education, within which an open education movement has enthusiastically embraced digital technologies as the central means of participation and inclusion. Open Educational Resources (OERs) and Massive Open Online Courses (MOOCs) have surfaced at the forefront of this development,…

  7. Improving access to learning in the workplace using technology in an accredited course.

    Science.gov (United States)

    Munro, Kathleen M; Peacock, Susi

    2005-03-01

    This article gives an account of a case study which seeks to explore the potential for using technology to deliver learning in the workplace: a syringe driver course for nurses. We provide a brief overview of workplace learning, continuing professional development and learning technology in the health sciences. The paper then draws upon a three-year project that involved the transition of a traditionally taught, institution-based face-to-face course to work-based learning using technology. Through the evaluation and discussion of the case study we address key issues that have emerged, such as, marketing of the product; in our case it was decided that the most cost-effective way to provide the course and recuperate some costs was to accredit the course by the Institution. Registered practitioners in the workplace assess learning and are linked to the quality assurance mechanisms of the Institution. We also consider some of the major barriers to implementation, highlighting critical areas for consideration for those undertaking a similar project. These include the lack of technical knowledge in the Group, which resulted in a steep learning curve for all members. This and numerous iterations of materials (including video and animations) lengthened the project considerably whilst technological advances meant other more sophisticated technological solutions that became available during the production process were incorporated. A cost benefit analysis would show that the product has been delivered across Scotland and production costs covered and that there have been unquantifiable gains, including improving the external profile of the academic institution and the NHS Trust, developing the technical skills of the Group and providing invaluable experience of working in a cross-disciplinary collaborative working environment.

  8. MAGMA: analysis of two-channel microarrays made easy.

    Science.gov (United States)

    Rehrauer, Hubert; Zoller, Stefan; Schlapbach, Ralph

    2007-07-01

    The web application MAGMA provides a simple and intuitive interface to identify differentially expressed genes from two-channel microarray data. While the underlying algorithms are not superior to those of similar web applications, MAGMA is particularly user friendly and can be used without prior training. The user interface guides the novice user through the most typical microarray analysis workflow consisting of data upload, annotation, normalization and statistical analysis. It automatically generates R-scripts that document MAGMA's entire data processing steps, thereby allowing the user to regenerate all results in his local R installation. The implementation of MAGMA follows the model-view-controller design pattern that strictly separates the R-based statistical data processing, the web-representation and the application logic. This modular design makes the application flexible and easily extendible by experts in one of the fields: statistical microarray analysis, web design or software development. State-of-the-art Java Server Faces technology was used to generate the web interface and to perform user input processing. MAGMA's object-oriented modular framework makes it easily extendible and applicable to other fields and demonstrates that modern Java technology is also suitable for rather small and concise academic projects. MAGMA is freely available at www.magma-fgcz.uzh.ch.

  9. Cost-effective, transfer-free, flexible resistive random access memory using laser-scribed reduced graphene oxide patterning technology.

    Science.gov (United States)

    Tian, He; Chen, Hong-Yu; Ren, Tian-Ling; Li, Cheng; Xue, Qing-Tang; Mohammad, Mohammad Ali; Wu, Can; Yang, Yi; Wong, H-S Philip

    2014-06-11

    Laser scribing is an attractive reduced graphene oxide (rGO) growth and patterning technology because the process is low-cost, time-efficient, transfer-free, and flexible. Various laser-scribed rGO (LSG) components such as capacitors, gas sensors, and strain sensors have been demonstrated. However, obstacles remain toward practical application of the technology where all the components of a system are fabricated using laser scribing. Memory components, if developed, will substantially broaden the application space of low-cost, flexible electronic systems. For the first time, a low-cost approach to fabricate resistive random access memory (ReRAM) using laser-scribed rGO as the bottom electrode is experimentally demonstrated. The one-step laser scribing technology allows transfer-free rGO synthesis directly on flexible substrates or non-flat substrates. Using this time-efficient laser-scribing technology, the patterning of a memory-array area up to 100 cm(2) can be completed in 25 min. Without requiring the photoresist coating for lithography, the surface of patterned rGO remains as clean as its pristine state. Ag/HfOx/LSG ReRAM using laser-scribing technology is fabricated in this work. Comprehensive electrical characteristics are presented including forming-free behavior, stable switching, reasonable reliability performance and potential for 2-bit storage per memory cell. The results suggest that laser-scribing technology can potentially produce more cost-effective and time-effective rGO-based circuits and systems for practical applications.

  10. Post-marketing access to orphan drugs: a critical analysis of health technology assessment and reimbursement decision-making considerations

    Directory of Open Access Journals (Sweden)

    Iskrov G

    2014-01-01

    Full Text Available Georgi Iskrov, Rumen Stefanov Department of Social Medicine and Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria Abstract: This study aims to explore the current rationale of post-marketing access to orphan drugs. As access to orphan medicinal products depends on assessment and appraisal by health authorities, this article is focused on health technology assessment (HTA and reimbursement decision-making considerations for orphan drugs. A critical analysis may identify important factors that could predetermine the combined outcomes of these two processes. Following this objective, an analytical framework was developed, comprising three overlaying issues: to outline what is currently done and what needs to be done in the field of HTA of orphan drugs, to synthesize important variables relevant to the reimbursement decision-making about orphan drugs, and to unveil relationships between theory and practice. Methods for economic evaluation, cost-effectiveness threshold, budget impact, uncertainty of evidence, criteria in reimbursement decision-making, and HTA research agenda are all explored and discussed from an orphan drug perspective. Reimbursement decision-making for orphan drugs is a debate of policy priorities, health system specifics, and societal attitudes. Health authorities need to pursue a multidisciplinary analysis on a range of criteria, ensuring an explicit understanding of the trade-offs for decisions related to eligibility for reimbursement. The only reasonable way to accept a higher valuation of orphan drug benefits is if these are demonstrated empirically. Rarity means that the quality of orphan drug evidence is not the same as for conventional therapies. Closing this gap is another crucial point for the timely access to these products. The generation of evidence goes far beyond pre-market authorization trials and requires transnational cooperation and coordination. Early constructive dialogue among orphan drug

  11. The Research and Development of Access Control Technology%访问控制技术的研究和进展

    Institute of Scientific and Technical Information of China (English)

    訾小超; 张绍莲; 茅兵; 谢立

    2001-01-01

    Access Control(AC)is one of the important technologies of System Security and has been widely studied recently because the traditionary AC technologies can' t meet with the security commands of contemporary imformation system. As a result,the traditionary AC technologies have been developed and some new technologies have been put forward. This paper makes the necessary classification for the more-than-ten-year research results of the AC technology,together with the analysis and predication for the development trend of the AC technology in the future.

  12. Educational policy for the democratization of access to science and technology

    Directory of Open Access Journals (Sweden)

    Alvori Ahlert

    2007-11-01

    Full Text Available State educational services suffered a plague of privatisation during the 1980s and 1990s, inspired by the neoliberal hegemony of the time. This article looks into what contribution education can make to the construction of an informed, and participative democracy. The teaching of science and technology needs to be based on principles of justice and equality, and, to ensure that all have equal opportunity to reach the highest levels, should be public, free and of high quality.

  13. Genotyping microarray (gene chip) for the ABCR (ABCA4) gene.

    Science.gov (United States)

    Jaakson, K; Zernant, J; Külm, M; Hutchinson, A; Tonisson, N; Glavac, D; Ravnik-Glavac, M; Hawlina, M; Meltzer, M R; Caruso, R C; Testa, F; Maugeri, A; Hoyng, C B; Gouras, P; Simonelli, F; Lewis, R A; Lupski, J R; Cremers, F P M; Allikmets, R

    2003-11-01

    Genetic variation in the ABCR (ABCA4) gene has been associated with five distinct retinal phenotypes, including Stargardt disease/fundus flavimaculatus (STGD/FFM), cone-rod dystrophy (CRD), and age-related macular degeneration (AMD). Comparative genetic analyses of ABCR variation and diagnostics have been complicated by substantial allelic heterogeneity and by differences in screening methods. To overcome these limitations, we designed a genotyping microarray (gene chip) for ABCR that includes all approximately 400 disease-associated and other variants currently described, enabling simultaneous detection of all known ABCR variants. The ABCR genotyping microarray (the ABCR400 chip) was constructed by the arrayed primer extension (APEX) technology. Each sequence change in ABCR was included on the chip by synthesis and application of sequence-specific oligonucleotides. We validated the chip by screening 136 confirmed STGD patients and 96 healthy controls, each of whom we had analyzed previously by single strand conformation polymorphism (SSCP) technology and/or heteroduplex analysis. The microarray was >98% effective in determining the existing genetic variation and was comparable to direct sequencing in that it yielded many sequence changes undetected by SSCP. In STGD patient cohorts, the efficiency of the array to detect disease-associated alleles was between 54% and 78%, depending on the ethnic composition and degree of clinical and molecular characterization of a cohort. In addition, chip analysis suggested a high carrier frequency (up to 1:10) of ABCR variants in the general population. The ABCR genotyping microarray is a robust, cost-effective, and comprehensive screening tool for variation in one gene in which mutations are responsible for a substantial fraction of retinal disease. The ABCR chip is a prototype for the next generation of screening and diagnostic tools in ophthalmic genetics, bridging clinical and scientific research. Copyright 2003 Wiley

  14. A microarray analysis of two distinct lymphatic endothelial cell populations

    Directory of Open Access Journals (Sweden)

    Bernhard Schweighofer

    2015-06-01

    Full Text Available We have recently identified lymphatic endothelial cells (LECs to form two morphologically different populations, exhibiting significantly different surface protein expression levels of podoplanin, a major surface marker for this cell type. In vitro shockwave treatment (IVSWT of LECs resulted in enrichment of the podoplaninhigh cell population and was accompanied by markedly increased cell proliferation, as well as 2D and 3D migration. Gene expression profiles of these distinct populations were established using Affymetrix microarray analyses. Here we provide additional details about our dataset (NCBI GEO accession number GSE62510 and describe how we analyzed the data to identify differently expressed genes in these two LEC populations.

  15. Identification of potential biomarkers from microarray experiments using multiple criteria optimization

    International Nuclear Information System (INIS)

    Sánchez-Peña, Matilde L; Isaza, Clara E; Pérez-Morales, Jaileene; Rodríguez-Padilla, Cristina; Castro, José M; Cabrera-Ríos, Mauricio

    2013-01-01

    Microarray experiments are capable of determining the relative expression of tens of thousands of genes simultaneously, thus resulting in very large databases. The analysis of these databases and the extraction of biologically relevant knowledge from them are challenging tasks. The identification of potential cancer biomarker genes is one of the most important aims for microarray analysis and, as such, has been widely targeted in the literature. However, identifying a set of these genes consistently across different experiments, researches, microarray platforms, or cancer types is still an elusive endeavor. Besides the inherent difficulty of the large and nonconstant variability in these experiments and the incommensurability between different microarray technologies, there is the issue of the users having to adjust a series of parameters that significantly affect the outcome of the analyses and that do not have a biological or medical meaning. In this study, the identification of potential cancer biomarkers from microarray data is casted as a multiple criteria optimization (MCO) problem. The efficient solutions to this problem, found here through data envelopment analysis (DEA), are associated to genes that are proposed as potential cancer biomarkers. The method does not require any parameter adjustment by the user, and thus fosters repeatability. The approach also allows the analysis of different microarray experiments, microarray platforms, and cancer types simultaneously. The results include the analysis of three publicly available microarray databases related to cervix cancer. This study points to the feasibility of modeling the selection of potential cancer biomarkers from microarray data as an MCO problem and solve it using DEA. Using MCO entails a new optic to the identification of potential cancer biomarkers as it does not require the definition of a threshold value to establish significance for a particular gene and the selection of a normalization

  16. Microarray analysis of gene expression profiles in ripening pineapple fruits.

    Science.gov (United States)

    Koia, Jonni H; Moyle, Richard L; Botella, Jose R

    2012-12-18

    Pineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening. Microarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested. This is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit

  17. Metric learning for DNA microarray data analysis

    International Nuclear Information System (INIS)

    Takeuchi, Ichiro; Nakagawa, Masao; Seto, Masao

    2009-01-01

    In many microarray studies, gene set selection is an important preliminary step for subsequent main task such as tumor classification, cancer subtype identification, etc. In this paper, we investigate the possibility of using metric learning as an alternative to gene set selection. We develop a simple metric learning algorithm aiming to use it for microarray data analysis. Exploiting a property of the algorithm, we introduce a novel approach for extending the metric learning to be adaptive. We apply the algorithm to previously studied microarray data on malignant lymphoma subtype identification.

  18. Revisiting of Channel Access Mechanisms in Mobile Wireless Networks through Exploiting Physical Layer Technologies

    Directory of Open Access Journals (Sweden)

    Junmei Yao

    2018-01-01

    Full Text Available The wireless local area networks (WLANs have been widely deployed with the rapid development of mobile devices and have further been brought into new applications with infrastructure mobility due to the growth of unmanned aerial vehicles (UAVs. However, the WLANs still face persistent challenge on increasing the network throughput to meet the customer’s requirement and fight against the node mobility. Interference is a well-known issue that would degrade the network performance due to the broadcast characteristics of the wireless signals. Moreover, with infrastructure mobility, the interference becomes the key obstacle in pursuing the channel capacity. Legacy interference management mechanism through the channel access control in the MAC layer design of the 802.11 standard has some well-known drawbacks, such as exposed and hidden terminal problems, inefficient rate adaptation, and retransmission schemes, making the efficient interference management an everlasting research topic over the years. Recently, interference management through exploiting physical layer mechanisms has attracted much research interest and has been proven to be a promising way to improve the network throughput, especially under the infrastructure mobility scenarios which provides more indicators for node dynamics. In this paper, we introduce a series of representative physical layer techniques and analyze how they are exploited for interference management to improve the network performance. We also provide some discussions about the research challenges and give potential future research topics in this area.

  19. A Time-constrained Network Voronoi Construction and Accessibility Analysis in Location-based Service Technology

    Science.gov (United States)

    Yu, W.; Ai, T.

    2014-11-01

    Accessibility analysis usually requires special models of spatial location analysis based on some geometric constructions, such as Voronoi diagram (abbreviated to VD). There are many achievements in classic Voronoi model research, however suffering from the following limitations for location-based services (LBS) applications. (1) It is difficult to objectively reflect the actual service areas of facilities by using traditional planar VDs, because human activities in LBS are usually constrained only to the network portion of the planar space. (2) Although some researchers have adopted network distance to construct VDs, their approaches are used in a static environment, where unrealistic measures of shortest path distance based on assumptions about constant travel speeds through the network were often used. (3) Due to the computational complexity of the shortest-path distance calculating, previous researches tend to be very time consuming, especially for large datasets and if multiple runs are required. To solve the above problems, a novel algorithm is developed in this paper. We apply network-based quadrat system and 1-D sequential expansion to find the corresponding subnetwork for each focus. The idea is inspired by the natural phenomenon that water flow extends along certain linear channels until meets others or arrives at the end of route. In order to accommodate the changes in traffic conditions, the length of network-quadrat is set upon the traffic condition of the corresponding street. The method has the advantage over Dijkstra's algorithm in that the time cost is avoided, and replaced with a linear time operation.

  20. Color coded multiple access scheme for bidirectional multiuser visible light communications in smart home technologies

    Science.gov (United States)

    Tiwari, Samrat Vikramaditya; Sewaiwar, Atul; Chung, Yeon-Ho

    2015-10-01

    In optical wireless communications, multiple channel transmission is an attractive solution to enhancing capacity and system performance. A new modulation scheme called color coded multiple access (CCMA) for bidirectional multiuser visible light communications (VLC) is presented for smart home applications. The proposed scheme uses red, green and blue (RGB) light emitting diodes (LED) for downlink and phosphor based white LED (P-LED) for uplink to establish a bidirectional VLC and also employs orthogonal codes to support multiple users and devices. The downlink transmission for data user devices and smart home devices is provided using red and green colors from the RGB LEDs, respectively, while uplink transmission from both types of devices is performed using the blue color from P-LEDs. Simulations are conducted to verify the performance of the proposed scheme. It is found that the proposed bidirectional multiuser scheme is efficient in terms of data rate and performance. In addition, since the proposed scheme uses RGB signals for downlink data transmission, it provides flicker-free illumination that would lend itself to multiuser VLC system for smart home applications.

  1. Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

    Directory of Open Access Journals (Sweden)

    Tong Weida

    2010-10-01

    Full Text Available Abstract Background The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. In addition, it was not clear whether the two human reference RNA samples established by the MAQC project in 2005 still maintained their transcriptome integrity over a period of four years. Experiments were conducted to answer these questions. Results Microarray data were generated in 2009 in three replicates for each of the two MAQC samples with either expired Affymetrix U133A or unexpired U133Plus2 microarrays. These results were compared with data obtained in 2005 on the U133Plus2 microarray. The percentage of overlap between the lists of differentially expressed genes (DEGs from U133Plus2 microarray data generated in 2009 and in 2005 was 97.44%. While there was some degree of fold change compression in the expired U133A microarrays, the percentage of overlap between the lists of DEGs from the expired and unexpired microarrays was as high as 96.99%. Moreover, the microarray data generated using the expired U133A microarrays in 2009 were highly concordant with microarray and TaqMan® data generated by the MAQC project in 2005. Conclusions Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer’s expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the

  2. Hands-On Open Access Broadband Wireless Technology Lab Mapping Course Outcomes to Lab Experiments

    Directory of Open Access Journals (Sweden)

    Yazan Alqudah

    2012-10-01

    Full Text Available The unprecedented growth in wireless communication is offering opportunities and challenges for educators. Thanks to technology advances and job opportunities, more and more students are interested in wireless communications courses. However, bridging the gap between classroom and real-world experience remains a challenge. Advanced undergraduate communications courses typically focus more on theory. Some courses are given online, and lack hands-on experiments. Driven by feedback from industry and students, we propose practical laboratory experiments that attempt to bridge the gap between classroom and real world. The laboratory exercises take advantage of the infrastructure of deployed wireless networks and allow students to measure, and analyze data, as well as to interact. The proposed labs can be used even in online courses. This paper describes the experiments proposed, the procedures and typical results. The experiments are tied to course objective.

  3. The design of the multipurpose Lusi drone. When technology can access harsh environments.

    Science.gov (United States)

    Romeo, Giovanni; Di Stefano, Giuseppe; Mazzini, Adriano; Iarocci, Alessandro

    2016-04-01

    Extreme and inaccessible environments are a new frontier that unmanned and remotely operated vehicles can today safely access and monitor. The Lusi mud eruption (NE Java Island, Indonesia) represents one of these harsh environments that are totally unreachable with traditional techniques. Here boiling mud is constantly spewed tens of meters in height and tall gas clouds surround the 100 meters wide active crater. The crater is surrounded by a 600 meters circular zone of hot mud that prevents any approach to investigate and sample the eruption site. In the framework of the Lusi Lab project (ERC grant n° 308126) we assembled and designed a multipurpose drone to survey the eruption site. The Lusi drone is equipped with numerous airborne devices suitable for use on board of other multicopters. During the missions three cameras can complete 1) video survey, 2) high resolution photogrammetry of desired and preselected polygons, and 3) thermal photogrammetry surveys with infra-red camera to locate hot fluids seepage areas or faulted zones. Crater sampling and monitoring operations can be pre-planned with a flight software, and the pilot is required only for take-off and landing. An automatic winch allows the deployment of gas, mud and water samplers and contact thermometers to be operated with no risk for the aircraft. During the winch operations (that can be performed automatically) the aircraft hovers at a safety height until the tasks are completed while being controlled by the winch embedded processor. The drone is also equipped with a GPS connected CO2 and CH4 sensors. Gridded surveys using these devices allowed obtaining 2D maps of the concentration and distribution of various gasses over the area covered by the flight path.

  4. Gaining Access.

    Science.gov (United States)

    Wand, Sean; Thermos, Adam C.

    1998-01-01

    Explains the issues to consider before a college decides to purchase a card-access system. The benefits of automation, questions involving implementation, the criteria for technology selection, what typical card technology involves, privacy concerns, and the placement of card readers are discussed. (GR)

  5. Gene Expression and Microarray Investigation of Dendrobium ...

    African Journals Online (AJOL)

    blood glucose > 16.7 mmol/L were used as the model group and treated with Dendrobium mixture. (DEN ... Keywords: Diabetes, Gene expression, Dendrobium mixture, Microarray testing ..... homeostasis in airway smooth muscle. Am J.

  6. SLIMarray: Lightweight software for microarray facility management

    Directory of Open Access Journals (Sweden)

    Marzolf Bruz

    2006-10-01

    Full Text Available Abstract Background Microarray core facilities are commonplace in biological research organizations, and need systems for accurately tracking various logistical aspects of their operation. Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors. Results We present SLIMarray (System for Lab Information Management of Microarrays, an open source, modular database web application capable of managing microarray inventories, sample processing and usage charges. The software allows modular configuration and is well suited for further development, providing users the flexibility to adapt it to their needs. SLIMarray Lite, a version of the software that is especially easy to install and run, is also available. Conclusion SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

  7. Comparison of fingerprint and facial biometric verification technologies for user access and patient identification in a clinical environment

    Science.gov (United States)

    Guo, Bing; Zhang, Yu; Documet, Jorge; Liu, Brent; Lee, Jasper; Shrestha, Rasu; Wang, Kevin; Huang, H. K.

    2007-03-01

    As clinical imaging and informatics systems continue to integrate the healthcare enterprise, the need to prevent patient mis-identification and unauthorized access to clinical data becomes more apparent especially under the Health Insurance Portability and Accountability Act (HIPAA) mandate. Last year, we presented a system to track and verify patients and staff within a clinical environment. This year, we further address the biometric verification component in order to determine which Biometric system is the optimal solution for given applications in the complex clinical environment. We install two biometric identification systems including fingerprint and facial recognition systems at an outpatient imaging facility, Healthcare Consultation Center II (HCCII). We evaluated each solution and documented the advantages and pitfalls of each biometric technology in this clinical environment.

  8. Tongue-operated assistive technology with access to common smartphone applications via Bluetooth link.

    Science.gov (United States)

    Kim, Jeonghee; Park, Hangue; Ghovanloo, Maysam

    2012-01-01

    Tongue Drive System (TDS) is a wireless and wearable assistive technology (AT) that enables people with severe disabilities to control their computers, wheelchairs, and electronic gadgets using their tongue motion. We developed the TDS to control smartphone's (iPhone/iPod Touch) built-in and downloadable apps with a customized Bluetooth mouse module by emulating finger taps on the touchscreen. The TDS-iPhone Bluetooth mouse interface was evaluated by four able-bodied subjects to complete a scenario consisting of seven tasks, which were randomly ordered by using touch on the iPhone screen with index finger, a computer mouse on iPhone, and TDS-iPhone Bluetooth mouse interface with tongue motion. Preliminary results show that the average completion times of a scenario with touch, mouse, and TDS are 165.6 ± 14.50 s, 186.1 ± 15.37 s, and 651.6 ± 113.4 s, respectively, showing that the TDS is 84.37% and 81.16% slower than touch and mouse for speed of typing with negligible errors. Overall, considering the limited number of commands and unfamiliarity of the subjects with the TDS, we achieved acceptable results for hands-free functionality.

  9. A randomized study of internet parent training accessed from community technology centers.

    Science.gov (United States)

    Irvine, A Blair; Gelatt, Vicky A; Hammond, Michael; Seeley, John R

    2015-05-01

    Behavioral parent training (BPT) has been shown to be efficacious to improve parenting skills for problematic interactions with adolescents displaying oppositional and antisocial behaviors. Some research suggests that support group curricula might be transferred to the Internet, and some studies suggest that other curriculum designs might also be effective. In this research, a BPT program for parents of at-risk adolescents was tested on the Internet in a randomized trial (N = 307) from computer labs at six community technology centers in or near large metropolitan areas. The instructional design was based on asynchronous scenario-based e-learning, rather than a traditional parent training model where presentation of course material builds content sequentially over multiple class sessions. Pretest to 30-day follow-up analyses indicated significant treatment effects on parent-reported discipline style (Parenting Scale, Adolescent version), child behavior (Eyberg Child Behavior Inventory), and on social cognitive theory constructs of intentions and self-efficacy. The effect sizes were small to medium. These findings suggest the potential to provide effective parent training programs on the Internet.

  10. PATMA: parser of archival tissue microarray

    Directory of Open Access Journals (Sweden)

    Lukasz Roszkowiak

    2016-12-01

    Full Text Available Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

  11. Accessibility to information and communications technology for the social participation of youths with disabilities: a two-way street.

    Science.gov (United States)

    Schreuer, Naomi; Keter, Ayala; Sachs, Dalia

    2014-01-01

    The current study examined by mixed method the effectiveness of an accessibility to Information and Communications Technology (ICT) program that provided computers, assistive technology, tutors, and internet connection to 65 youths with severe disabilities (aged 13.22 ± 3.4 years) in their homes. The quantitative evaluation included assessment of computer task performance, computer skills, and participation in social ICT leisure activities before and after the program. Findings revealed low baseline and significant progress on most outcome measures 6 months after the program, mostly among those youths who had tutors. Additional in-depth interviews were conducted 1 year later with 10 participants to explore their ICT use and its impact on their social participation. The analysis revealed a significant contribution of the ICT use, while critical thinking about its risks and some disappointment with the social needs that ICT does not address. Our findings raise awareness of 'two-way streets' policies and programs to ensure e-inclusion. Copyright © 2014 John Wiley & Sons, Ltd.

  12. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

    Directory of Open Access Journals (Sweden)

    Toome Kadri

    2011-02-01

    Full Text Available Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  13. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

    LENUS (Irish Health Repository)

    Scheler, Ott

    2011-02-28

    Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal\\/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  14. Gene selection for microarray data classification via subspace learning and manifold regularization.

    Science.gov (United States)

    Tang, Chang; Cao, Lijuan; Zheng, Xiao; Wang, Minhui

    2017-12-19

    With the rapid development of DNA microarray technology, large amount of genomic data has been generated. Classification of these microarray data is a challenge task since gene expression data are often with thousands of genes but a small number of samples. In this paper, an effective gene selection method is proposed to select the best subset of genes for microarray data with the irrelevant and redundant genes removed. Compared with original data, the selected gene subset can benefit the classification task. We formulate the gene selection task as a manifold regularized subspace learning problem. In detail, a projection matrix is used to project the original high dimensional microarray data into a lower dimensional subspace, with the constraint that the original genes can be well represented by the selected genes. Meanwhile, the local manifold structure of original data is preserved by a Laplacian graph regularization term on the low-dimensional data space. The projection matrix can serve as an importance indicator of different genes. An iterative update algorithm is developed for solving the problem. Experimental results on six publicly available microarray datasets and one clinical dataset demonstrate that the proposed method performs better when compared with other state-of-the-art methods in terms of microarray data classification. Graphical Abstract The graphical abstract of this work.

  15. A Reliable and Distributed LIMS for Efficient Management of the Microarray Experiment Environment

    Directory of Open Access Journals (Sweden)

    Jin Hee-Jeong

    2007-03-01

    Full Text Available A microarray is a principal technology in molecular biology. It generates thousands of expressions of genotypes at once. Typically, a microarray experiment contains many kinds of information, such as gene names, sequences, expression profiles, scanned images, and annotation. So, the organization and analysis of vast amounts of data are required. Microarray LIMS (Laboratory Information Management System provides data management, search, and basic analysis. Recently, microarray joint researches, such as the skeletal system disease and anti-cancer medicine have been widely conducted. This research requires data sharing among laboratories within the joint research group. In this paper, we introduce a web based microarray LIMS, SMILE (Small and solid MIcroarray Lims for Experimenters, especially for shared data management. The data sharing function of SMILE is based on Friend-to-Friend (F2F, which is based on anonymous P2P (Peer-to-Peer, in which people connect directly with their “friends”. It only allows its friends to exchange data directly using IP addresses or digital signatures you trust. In SMILE, there are two types of friends: “service provider”, which provides data, and “client”, which is provided with data. So, the service provider provides shared data only to its clients. SMILE provides useful functions for microarray experiments, such as variant data management, image analysis, normalization, system management, project schedule management, and shared data management. Moreover, it connections with two systems: ArrayMall for analyzing microarray images and GENAW for constructing a genetic network. SMILE is available on http://neobio.cs.pusan.ac.kr:8080/smile.

  16. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

    Science.gov (United States)

    Zhang, Wenqian; Yu, Ying; Hertwig, Falk; Thierry-Mieg, Jean; Zhang, Wenwei; Thierry-Mieg, Danielle; Wang, Jian; Furlanello, Cesare; Devanarayan, Viswanath; Cheng, Jie; Deng, Youping; Hero, Barbara; Hong, Huixiao; Jia, Meiwen; Li, Li; Lin, Simon M; Nikolsky, Yuri; Oberthuer, André; Qing, Tao; Su, Zhenqiang; Volland, Ruth; Wang, Charles; Wang, May D; Ai, Junmei; Albanese, Davide; Asgharzadeh, Shahab; Avigad, Smadar; Bao, Wenjun; Bessarabova, Marina; Brilliant, Murray H; Brors, Benedikt; Chierici, Marco; Chu, Tzu-Ming; Zhang, Jibin; Grundy, Richard G; He, Min Max; Hebbring, Scott; Kaufman, Howard L; Lababidi, Samir; Lancashire, Lee J; Li, Yan; Lu, Xin X; Luo, Heng; Ma, Xiwen; Ning, Baitang; Noguera, Rosa; Peifer, Martin; Phan, John H; Roels, Frederik; Rosswog, Carolina; Shao, Susan; Shen, Jie; Theissen, Jessica; Tonini, Gian Paolo; Vandesompele, Jo; Wu, Po-Yen; Xiao, Wenzhong; Xu, Joshua; Xu, Weihong; Xuan, Jiekun; Yang, Yong; Ye, Zhan; Dong, Zirui; Zhang, Ke K; Yin, Ye; Zhao, Chen; Zheng, Yuanting; Wolfinger, Russell D; Shi, Tieliu; Malkas, Linda H; Berthold, Frank; Wang, Jun; Tong, Weida; Shi, Leming; Peng, Zhiyu; Fischer, Matthias

    2015-06-25

    Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.

  17. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L. gene expression oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Paula Fernandez

    Full Text Available Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de. The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons. The resulting Sunflower Unigen Resource (SUR version 1.0 was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01 allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  18. Opportunities for Engaging Low-Income, Vulnerable Populations in Health Care: A Systematic Review of Homeless Persons’ Access to and Use of Information Technologies

    Science.gov (United States)

    Li, Alice E.; Hogan, Timothy P.

    2013-01-01

    We systematically reviewed the health and social science literature on access to and use of information technologies by homeless persons by searching 5 bibliographic databases. Articles were included if they were in English, represented original research, appeared in peer-reviewed publications, and addressed our research questions. Sixteen articles met our inclusion criteria. We found that mobile phone ownership ranged from 44% to 62%; computer ownership, from 24% to 40%; computer access and use, from 47% to 55%; and Internet use, from 19% to 84%. Homeless persons used technologies for a range of purposes, some of which were health related. Many homeless persons had access to information technologies, suggesting possible health benefits to developing programs that link homeless persons to health care through mobile phones and the Internet. PMID:24148036

  19. Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Salomon, Jesper; Søkilde, Rolf

    2009-01-01

    Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two...... technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate...... better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification....

  20. Nanotechnology: moving from microarrays toward nanoarrays.

    Science.gov (United States)

    Chen, Hua; Li, Jun

    2007-01-01

    Microarrays are important tools for high-throughput analysis of biomolecules. The use of microarrays for parallel screening of nucleic acid and protein profiles has become an industry standard. A few limitations of microarrays are the requirement for relatively large sample volumes and elongated incubation time, as well as the limit of detection. In addition, traditional microarrays make use of bulky instrumentation for the detection, and sample amplification and labeling are quite laborious, which increase analysis cost and delays the time for obtaining results. These problems limit microarray techniques from point-of-care and field applications. One strategy for overcoming these problems is to develop nanoarrays, particularly electronics-based nanoarrays. With further miniaturization, higher sensitivity, and simplified sample preparation, nanoarrays could potentially be employed for biomolecular analysis in personal healthcare and monitoring of trace pathogens. In this chapter, it is intended to introduce the concept and advantage of nanotechnology and then describe current methods and protocols for novel nanoarrays in three aspects: (1) label-free nucleic acids analysis using nanoarrays, (2) nanoarrays for protein detection by conventional optical fluorescence microscopy as well as by novel label-free methods such as atomic force microscopy, and (3) nanoarray for enzymatic-based assay. These nanoarrays will have significant applications in drug discovery, medical diagnosis, genetic testing, environmental monitoring, and food safety inspection.

  1. Integrative missing value estimation for microarray data.

    Science.gov (United States)

    Hu, Jianjun; Li, Haifeng; Waterman, Michael S; Zhou, Xianghong Jasmine

    2006-10-12

    Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS) imputation algorithm by up to 15% improvement in our benchmark tests. We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  2. Integrative missing value estimation for microarray data

    Directory of Open Access Journals (Sweden)

    Zhou Xianghong

    2006-10-01

    Full Text Available Abstract Background Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. Results We present the integrative Missing Value Estimation method (iMISS by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS imputation algorithm by up to 15% improvement in our benchmark tests. Conclusion We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  3. Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice

    Directory of Open Access Journals (Sweden)

    Liu Bin

    2008-05-01

    Full Text Available Abstract Background We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features. Results We have produced a genotyping microarray for rice, comprising 880 single feature polymorphism (SFP elements derived from insertions/deletions identified by aligning genomic sequences of the japonica cultivar Nipponbare and the indica cultivar 93-11. The SFPs were experimentally verified by hybridization with labeled genomic DNA prepared from the two cultivars. Using the genotyping microarrays, we found high levels of polymorphism across diverse rice accessions, and were able to classify all five subpopulations of rice with high bootstrap support. The microarrays were used for mapping of a gene conferring resistance to Magnaporthe grisea, the causative organism of rice blast disease, by quantitative genotyping of samples from a recombinant inbred line population pooled by phenotype. Conclusion We anticipate this microarray-based genotyping platform, based on its low cost-per-sample, to be particularly useful in applications requiring whole-genome molecular marker coverage across large numbers of individuals.

  4. Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.

    Science.gov (United States)

    Chao, Jie; Li, Zhenhua; Li, Jing; Peng, Hongzhen; Su, Shao; Li, Qian; Zhu, Changfeng; Zuo, Xiaolei; Song, Shiping; Wang, Lianhui; Wang, Lihua

    2016-07-15

    Microarrays of biomolecules hold great promise in the fields of genomics, proteomics, and clinical assays on account of their remarkably parallel and high-throughput assay capability. However, the fluorescence detection used in most conventional DNA microarrays is still limited by sensitivity. In this study, we have demonstrated a novel universal and highly sensitive platform for fluorescent detection of sequence specific DNA at the femtomolar level by combining dextran-coated microarrays with hybridization chain reaction (HCR) signal amplification. Three-dimensional dextran matrix was covalently coated on glass surface as the scaffold to immobilize DNA recognition probes to increase the surface binding capacity and accessibility. DNA nanowire tentacles were formed on the matrix surface for efficient signal amplification by capturing multiple fluorescent molecules in a highly ordered way. By quantifying microscopic fluorescent signals, the synergetic effects of dextran and HCR greatly improved sensitivity of DNA microarrays, with a detection limit of 10fM (1×10(5) molecules). This detection assay could recognize one-base mismatch with fluorescence signals dropped down to ~20%. This cost-effective microarray platform also worked well with samples in serum and thus shows great potential for clinical diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

    Science.gov (United States)

    2012-01-01

    Background The combination of chromatin immunoprecipitation with two-channel microarray technology enables genome-wide mapping of binding sites of DNA-interacting proteins (ChIP-on-chip) or sites with methylated CpG di-nucleotides (DNA methylation microarray). These powerful tools are the gateway to understanding gene transcription regulation. Since the goals of such studies, the sample preparation procedures, the microarray content and study design are all different from transcriptomics microarrays, the data pre-processing strategies traditionally applied to transcriptomics microarrays may not be appropriate. Particularly, the main challenge of the normalization of "regulation microarrays" is (i) to make the data of individual microarrays quantitatively comparable and (ii) to keep the signals of the enriched probes, representing DNA sequences from the precipitate, as distinguishable as possible from the signals of the un-enriched probes, representing DNA sequences largely absent from the precipitate. Results We compare several widely used normalization approaches (VSN, LOWESS, quantile, T-quantile, Tukey's biweight scaling, Peng's method) applied to a selection of regulation microarray datasets, ranging from DNA methylation to transcription factor binding and histone modification studies. Through comparison of the data distributions of control probes and gene promoter probes before and after normalization, and assessment of the power to identify known enriched genomic regions after normalization, we demonstrate that there are clear differences in performance between normalization procedures. Conclusion T-quantile normalization applied separately on the channels and Tukey's biweight scaling outperform other methods in terms of the conservation of enriched and un-enriched signal separation, as well as in identification of genomic regions known to be enriched. T-quantile normalization is preferable as it additionally improves comparability between microarrays. In

  6. Discovering biological progression underlying microarray samples.

    Directory of Open Access Journals (Sweden)

    Peng Qiu

    2011-04-01

    Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

  7. Free-space optics technology employed in an UMTS release 4 bearer independent core network access part

    Science.gov (United States)

    Bibac, Ionut

    2005-08-01

    The UMTS Bearer Independent Core Network program introduced the 3rd Generation Partnership Program Release 4 BICN architecture into the legacy UMTS TDM-switched network. BICN is the application of calI server archltecture for voice and circuit switched data, enabling the provisioning of traditional circuit-switched services using a packet-switched transport network. Today"s business climate has made it essential for service providers to develop a comprehensive networking strategy that means introduction of RCBICN networks. The R4-BICN solution to the evolution of the Core Network in UMTS will enable operators to significantly reduce the capital and operational costs of delivering both traditional voice sewices and new multimedia services. To build the optical backbone, which can support the third generation (3G) packetized infrastructure, the operators could choose a fibre connection, or they could retain the benefits of a wireless connectivity by using a FSO - Free Space Optical lmk, the only wireless technology available that is capable of achieving data rates up to 2.4 Gbit/s. FSO offers viable alternatives for both core transmission networks and for replacing microwaves links in NodeB - RNC access networks. The paper and presentation aim to demonstrate the manner in which FSO products and networks are employed into R4-BICN design solutions.

  8. Improving accessibility and mobility in the Masia traditional council area in Vhembe district municipality, Limpopo: Application of low-cost access and mobility technologies

    CSIR Research Space (South Africa)

    Nhemachena, C

    2011-07-01

    Full Text Available Development Goals (MDGs), including those relating to health, maternal and child mortality and education, depends on better access to services, which requires better transport infrastructure and transport services. Starkey et al. (2006) showed... and Makhado. About 66% of the respondents indicated that they are not willing to leave their area permanently, citing the need to develop their area and vested property rights. However, about 27% indicated that they would want to leave their area...

  9. The use of microarrays in microbial ecology

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  10. 3D Biomaterial Microarrays for Regenerative Medicine

    DEFF Research Database (Denmark)

    Gaharwar, Akhilesh K.; Arpanaei, Ayyoob; Andresen, Thomas Lars

    2015-01-01

    Three dimensional (3D) biomaterial microarrays hold enormous promise for regenerative medicine because of their ability to accelerate the design and fabrication of biomimetic materials. Such tissue-like biomaterials can provide an appropriate microenvironment for stimulating and controlling stem...... for tissue engineering and drug screening applications....... cell differentiation into tissue-specifi c lineages. The use of 3D biomaterial microarrays can, if optimized correctly, result in a more than 1000-fold reduction in biomaterials and cells consumption when engineering optimal materials combinations, which makes these miniaturized systems very attractive...

  11. Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks

    Directory of Open Access Journals (Sweden)

    Alina Sîrbu

    2015-05-01

    Full Text Available Microarray technologies have been the basis of numerous important findings regarding gene expression in the few last decades. Studies have generated large amounts of data describing various processes, which, due to the existence of public databases, are widely available for further analysis. Given their lower cost and higher maturity compared to newer sequencing technologies, these data continue to be produced, even though data quality has been the subject of some debate. However, given the large volume of data generated, integration can help overcome some issues related, e.g., to noise or reduced time resolution, while providing additional insight on features not directly addressed by sequencing methods. Here, we present an integration test case based on public Drosophila melanogaster datasets (gene expression, binding site affinities, known interactions. Using an evolutionary computation framework, we show how integration can enhance the ability to recover transcriptional gene regulatory networks from these data, as well as indicating which data types are more important for quantitative and qualitative network inference. Our results show a clear improvement in performance when multiple datasets are integrated, indicating that microarray data will remain a valuable and viable resource for some time to come.

  12. Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks.

    Science.gov (United States)

    Sîrbu, Alina; Crane, Martin; Ruskin, Heather J

    2015-05-14

    Microarray technologies have been the basis of numerous important findings regarding gene expression in the few last decades. Studies have generated large amounts of data describing various processes, which, due to the existence of public databases, are widely available for further analysis. Given their lower cost and higher maturity compared to newer sequencing technologies, these data continue to be produced, even though data quality has been the subject of some debate. However, given the large volume of data generated, integration can help overcome some issues related, e.g., to noise or reduced time resolution, while providing additional insight on features not directly addressed by sequencing methods. Here, we present an integration test case based on public Drosophila melanogaster datasets (gene expression, binding site affinities, known interactions). Using an evolutionary computation framework, we show how integration can enhance the ability to recover transcriptional gene regulatory networks from these data, as well as indicating which data types are more important for quantitative and qualitative network inference. Our results show a clear improvement in performance when multiple datasets are integrated, indicating that microarray data will remain a valuable and viable resource for some time to come.

  13. Development and application of a microarray meter tool to optimize microarray experiments

    Directory of Open Access Journals (Sweden)

    Rouse Richard JD

    2008-07-01

    Full Text Available Abstract Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a a measure of variability in the signal intensities, b a measure of the signal dynamic range and c a measure of variability of the spot morphologies.

  14. Differential access to digital communication technology: association with health and health survey recruitment within an African-American underserviced urban population.

    Science.gov (United States)

    Schneider, John; Makelarski, Jennifer A; Van Haitsma, Martha; Lipton, Rebecca B; Abramsohn, Emily; Lauderdale, Diane S; Lindau, Stacy Tessler

    2011-06-01

    Digital communication technologies (DCT), such as cell phones and the internet, have begun to replace more traditional technologies even in technology-poor communities. We characterized access to DCT in an underserved urban population and whether access is associated with health and study participation. A general probability community sample and a purposive high-turnover housing sample were recruited and re-interviewed after 3 months. Selected characteristics were compared by sample type and retention. Associations between DCT access and self-reported health were examined using multivariable logistic regression. Of 363 eligible individuals, 184 (general community = 119; high-turnover housing = 65) completed the baseline survey. Eighty-four percent of respondents had a cell phone and 62% had ever texted. Ever use of the internet was high (69%) overall, but frequency and years of internet use were higher in the general community sample. Self-reported fair or poor health was more common for residents of cell phone-only households and those with less frequent internet use. Technology use was similar for those retained and not retained. Overall, access to DCT was high in this underserved urban population but varied by sample type. Health varied significantly by DCT use, but study retention did not. These data have implications for incorporating DCT into health-related research in urban populations.

  15. The Electronic Journal of Information Technology in Construction (ITcon): An Open Access Journal Using an Un-Paid, Volunteer-Based Organization

    Science.gov (United States)

    Björk, Bo-Christer; Turk, Žiga

    2006-01-01

    Introduction: This case study is based on the experiences with the Electronic Journal of Information Technology in Construction (ITcon), founded in 1995. Development: This journal is an example of a particular category of open access journals, which use neither author charges nor subscriptions to finance their operations, but rely largely on…

  16. Post-Coma Persons with Extensive Multiple Disabilities Use Microswitch Technology to Access Selected Stimulus Events or Operate a Radio Device

    Science.gov (United States)

    Lancioni, Giulio E.; Singh, Nirbhay N.; O'Reilly, Mark F.; Sigafoos, Jeff; Alberti, Gloria; Oliva, Doretta; Megna, Gianfranco; Iliceto, Carla; Damiani, Sabino; Ricci, Irene; Spica, Antonella

    2011-01-01

    The present two studies extended research evidence on the use of microswitch technology by post-coma persons with multiple disabilities. Specifically, Study I examined whether three adults with a diagnosis of minimally conscious state and multiple disabilities could use microswitches as tools to access brief, selected stimulus events. Study II…

  17. Innovative ICT technologies in urban design for the aged, towards accessible and socio-economically integrated metropolis of the future: a South African example

    CSIR Research Space (South Africa)

    Macagnano, EV

    2008-09-01

    Full Text Available This presentation asks the question "Is the design & structure of our cities conducive to accessibility for all?" The main focus areas of this project are: 1. The People (focus on the aged and people with disabilities), 2. The Technology (focus...

  18. Grand Canyon as a universally accessible virtual field trip for intro Geoscience classes using geo-referenced mobile game technology

    Science.gov (United States)

    Bursztyn, N.; Pederson, J. L.; Shelton, B.

    2012-12-01

    There is a well-documented and nationally reported trend of declining interest, poor preparedness, and lack of diversity within U.S. students pursuing geoscience and other STEM disciplines. We suggest that a primary contributing factor to this problem is that introductory geoscience courses simply fail to inspire (i.e. they are boring). Our experience leads us to believe that the hands-on, contextualized learning of field excursions are often the most impactful component of lower division geoscience classes. However, field trips are becoming increasingly more difficult to run due to logistics and liability, high-enrollments, decreasing financial and administrative support, and exclusivity of the physically disabled. Recent research suggests that virtual field trips can be used to simulate this contextualized physical learning through the use of mobile devices - technology that exists in most students' hands already. Our overarching goal is to enhance interest in introductory geoscience courses by providing the kinetic and physical learning experience of field trips through geo-referenced educational mobile games and test the hypothesis that these experiences can be effectively simulated through virtual field trips. We are doing this by developing "serious" games for mobile devices that deliver introductory geology material in a fun and interactive manner. Our new teaching strategy will enhance undergraduate student learning in the geosciences, be accessible to students of diverse backgrounds and physical abilities, and be easily incorporated into higher education programs and curricula at institutions globally. Our prototype involves students virtually navigating downstream along a scaled down Colorado River through Grand Canyon - physically moving around their campus quad, football field or other real location, using their smart phone or a tablet. As students reach the next designated location, a photo or video in Grand Canyon appears along with a geological

  19. Multisegment one-step RT-PCR fluorescent labeling of influenza A virus genome for use in diagnostic microarray applications

    Energy Technology Data Exchange (ETDEWEB)

    Vasin, A V; Plotnikova, M A; Klotchenko, S A; Elpaeva, E A; Komissarov, A B; Egorov, V V; Kiselev, O I [Research Institute of Influenza of the Ministry of Health and Social Development of the Russian Federation, 15/17 Prof. Popova St., St. Petersburg (Russian Federation); Sandybaev, N T; Chervyakova, O V; Strochkov, V M; Taylakova, E T; Koshemetov, J K; Mamadaliev, S M, E-mail: vasin@influenza.spb.ru [Research Institute for Biological Safety Problems of the RK NBC/SC ME and S RK, Gvardeiskiy (Kazakhstan)

    2011-04-01

    Microarray technology is one of the most challenging methods of influenza A virus subtyping, which is based on the antigenic properties of viral surface glycoproteins - hemagglutinin and neuraminidase. On the example of biochip for detection of influenza A/H5N1 virus we showed the possibility of using multisegment RTPCR method for amplification of fluorescently labeled cDNA of all possible influenza A virus subtypes with a single pair of primers in influenza diagnostic microarrays.

  20. The use of mobile devices as assistive technology in resource-limited environments: access for learners with visual impairments in Kenya.

    Science.gov (United States)

    Foley, Alan R; Masingila, Joanna O

    2015-07-01

    In this paper, the authors explore the use of mobile devices as assistive technology for students with visual impairments in resource-limited environments. This paper provides initial data and analysis from an ongoing project in Kenya using tablet devices to provide access to education and independence for university students with visual impairments in Kenya. The project is a design-based research project in which we have developed and are refining a theoretically grounded intervention--a model for developing communities of practice to support the use of mobile technology as an assistive technology. We are collecting data to assess the efficacy and improve the model as well as inform the literature that has guided the design of the intervention. In examining the impact of the use of mobile devices for the students with visual impairments, we found that the devices provide the students with (a) access to education, (b) the means to participate in everyday life and (c) the opportunity to create a community of practice. Findings from this project suggest that communities of practice are both a viable and a valuable approach for facilitating the diffusion and support of mobile devices as assistive technology for students with visual impairments in resource-limited environments. Implications for Rehabilitation The use of mobile devices as assistive technology in resource-limited environments provides students with visual impairments access to education and enhanced means to participate in everyday life. Communities of practice are both a viable and a valuable approach for facilitating the diffusion and support of mobile devices as assistive technology for students with visual impairments in resource-limited environments. Providing access to assistive technology early and consistently throughout students' schooling builds both their skill and confidence and also demonstrates the capabilities of people with visual impairments to the larger society.

  1. Systematic interpretation of microarray data using experiment annotations

    Directory of Open Access Journals (Sweden)

    Frohme Marcus

    2006-12-01

    Full Text Available Abstract Background Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. Results We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. Conclusion Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.

  2. Validation of the performance of a GMO multiplex screening assay based on microarray detection

    NARCIS (Netherlands)

    Leimanis, S.; Hamels, S.; Naze, F.; Mbongolo, G.; Sneyers, M.; Hochegger, R.; Broll, H.; Roth, L.; Dallmann, K.; Micsinai, A.; Dijk, van J.P.; Kok, E.J.

    2008-01-01

    A new screening method for the detection and identification of GMO, based on the use of multiplex PCR followed by microarray, has been developed and is presented. The technology is based on the identification of quite ubiquitous GMO genetic target elements first amplified by PCR, followed by direct

  3. Transcription analysis of apple fruit development using cDNA microarrays

    NARCIS (Netherlands)

    Soglio, V.; Costa, F.; Molthoff, J.W.; Weemen-Hendriks, M.; Schouten, H.J.; Gianfranceschi, L.

    2009-01-01

    The knowledge of the molecular mechanisms underlying fruit quality traits is fundamental to devise efficient marker-assisted selection strategies and to improve apple breeding. In this study, cDNA microarray technology was used to identify genes whose expression changes during fruit development and

  4. Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

    Science.gov (United States)

    Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

    2012-06-08

    Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

  5. Detection of selected plant viruses by microarrays

    OpenAIRE

    HRABÁKOVÁ, Lenka

    2013-01-01

    The main aim of this master thesis was the simultaneous detection of four selected plant viruses ? Apple mosaic virus, Plum pox virus, Prunus necrotic ringspot virus and Prune harf virus, by microarrays. The intermediate step in the process of the detection was optimizing of multiplex polymerase chain reaction (PCR).

  6. LNA-modified isothermal oligonucleotide microarray for ...

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... the advent of DNA microarray techniques (Lee et al. 2007). ... atoms of ribose to form a bicyclic ribosyl structure. It is the .... 532 nm and emission at 570 nm. The signal ..... sis and validation using real-time PCR. Nucleic Acids ...

  7. Gene Expression Analysis Using Agilent DNA Microarrays

    DEFF Research Database (Denmark)

    Stangegaard, Michael

    2009-01-01

    Hybridization of labeled cDNA to microarrays is an intuitively simple and a vastly underestimated process. If it is not performed, optimized, and standardized with the same attention to detail as e.g., RNA amplification, information may be overlooked or even lost. Careful balancing of the amount ...

  8. Comparing transformation methods for DNA microarray data

    NARCIS (Netherlands)

    Thygesen, Helene H.; Zwinderman, Aeilko H.

    2004-01-01

    Background: When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include

  9. Analyzing Department of Defense's Use of Other Transactions as a Method for Accessing Non-Traditional Technology

    National Research Council Canada - National Science Library

    Gilliland, John

    2001-01-01

    ... technological superiority To attract advanced technology companies that normally do not participate in defense business to the defense market, Congress provided a new contracting authority, Section 845...

  10. Improving Nigerian health policymakers' capacity to access and utilize policy relevant evidence: outcome of information and communication technology training workshop.

    Science.gov (United States)

    Uneke, Chigozie Jesse; Ezeoha, Abel Ebeh; Uro-Chukwu, Henry; Ezeonu, Chinonyelum Thecla; Ogbu, Ogbonnaya; Onwe, Friday; Edoga, Chima

    2015-01-01

    Information and communication technology (ICT) tools are known to facilitate communication and processing of information and sharing of knowledge by electronic means. In Nigeria, the lack of adequate capacity on the use of ICT by health sector policymakers constitutes a major impediment to the uptake of research evidence into the policymaking process. The objective of this study was to improve the knowledge and capacity of policymakers to access and utilize policy relevant evidence. A modified "before and after" intervention study design was used in which outcomes were measured on the target participants both before the intervention is implemented and after. A 4-point likert scale according to the degree of adequacy; 1 = grossly inadequate, 4 = very adequate was employed. This study was conducted in Ebonyi State, south-eastern Nigeria and the participants were career health policy makers. A two-day intensive ICT training workshop was organized for policymakers who had 52 participants in attendance. Topics covered included: (i). intersectoral partnership/collaboration; (ii). Engaging ICT in evidence-informed policy making; use of ICT for evidence synthesis; (iv) capacity development on the use of computer, internet and other ICT. The pre-workshop mean of knowledge and capacity for use of ICT ranged from 2.19-3.05, while the post-workshop mean ranged from 2.67-3.67 on 4-point scale. The percentage increase in mean of knowledge and capacity at the end of the workshop ranged from 8.3%-39.1%. Findings of this study suggest that policymakers' ICT competence relevant to evidence-informed policymaking can be enhanced through training workshop.

  11. A DNA Microarray-Based Assay to Detect Dual Infection with Two Dengue Virus Serotypes

    Directory of Open Access Journals (Sweden)

    Alvaro Díaz-Badillo

    2014-04-01

    Full Text Available Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples.

  12. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  13. An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays

    Directory of Open Access Journals (Sweden)

    Laurenzi Ian J

    2009-12-01

    Full Text Available Abstract Background Although oligonucleotide microarray technology is ubiquitous in genomic research, reproducibility and standardization of expression measurements still concern many researchers. Cross-hybridization between microarray probes and non-target ssDNA has been implicated as a primary factor in sensitivity and selectivity loss. Since hybridization is a chemical process, it may be modeled at a population-level using a combination of material balance equations and thermodynamics. However, the hybridization reaction network may be exceptionally large for commercial arrays, which often possess at least one reporter per transcript. Quantification of the kinetics and equilibrium of exceptionally large chemical systems of this type is numerically infeasible with customary approaches. Results In this paper, we present a robust and computationally efficient algorithm for the simulation of hybridization processes underlying microarray assays. Our method may be utilized to identify the extent to which nucleic acid targets (e.g. cDNA will cross-hybridize with probes, and by extension, characterize probe robustnessusing the information specified by MAGE-TAB. Using this algorithm, we characterize cross-hybridization in a modified commercial microarray assay. Conclusions By integrating stochastic simulation with thermodynamic prediction tools for DNA hybridization, one may robustly and rapidly characterize of the selectivity of a proposed microarray design at the probe and "system" levels. Our code is available at http://www.laurenzi.net.

  14. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.

    Science.gov (United States)

    Rao, Archana N; Grainger, David W

    2014-04-01

    Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

  15. Creation of antifouling microarrays by photopolymerization of zwitterionic compounds for protein assay and cell patterning.

    Science.gov (United States)

    Sun, Xiuhua; Wang, Huaixin; Wang, Yuanyuan; Gui, Taijiang; Wang, Ke; Gao, Changlu

    2018-04-15

    Nonspecific binding or adsorption of biomolecules presents as a major obstacle to higher sensitivity, specificity and reproducibility in microarray technology. We report herein a method to fabricate antifouling microarray via photopolymerization of biomimetic betaine compounds. In brief, carboxybetaine methacrylate was polymerized as arrays for protein sensing, while sulfobetaine methacrylate was polymerized as background. With the abundant carboxyl groups on array surfaces and zwitterionic polymers on the entire surfaces, this microarray allows biomolecular immobilization and recognition with low nonspecific interactions due to its antifouling property. Therefore, low concentration of target molecules can be captured and detected by this microarray. It was proved that a concentration of 10ngmL -1 bovine serum albumin in the sample matrix of bovine serum can be detected by the microarray derivatized with anti-bovine serum albumin. Moreover, with proper hydrophilic-hydrophobic designs, this approach can be applied to fabricate surface-tension droplet arrays, which allows surface-directed cell adhesion and growth. These light controllable approaches constitute a clear improvement in the design of antifouling interfaces, which may lead to greater flexibility in the development of interfacial architectures and wider application in blood contact microdevices. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Support vector machine and principal component analysis for microarray data classification

    Science.gov (United States)

    Astuti, Widi; Adiwijaya

    2018-03-01

    Cancer is a leading cause of death worldwide although a significant proportion of it can be cured if it is detected early. In recent decades, technology called microarray takes an important role in the diagnosis of cancer. By using data mining technique, microarray data classification can be performed to improve the accuracy of cancer diagnosis compared to traditional techniques. The characteristic of microarray data is small sample but it has huge dimension. Since that, there is a challenge for researcher to provide solutions for microarray data classification with high performance in both accuracy and running time. This research proposed the usage of Principal Component Analysis (PCA) as a dimension reduction method along with Support Vector Method (SVM) optimized by kernel functions as a classifier for microarray data classification. The proposed scheme was applied on seven data sets using 5-fold cross validation and then evaluation and analysis conducted on term of both accuracy and running time. The result showed that the scheme can obtained 100% accuracy for Ovarian and Lung Cancer data when Linear and Cubic kernel functions are used. In term of running time, PCA greatly reduced the running time for every data sets.

  17. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

    Science.gov (United States)

    Rao, Archana N.; Grainger, David W.

    2014-01-01

    Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA’s persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools. PMID:24765522

  18. Improved microarray-based decision support with graph encoded interactome data.

    Directory of Open Access Journals (Sweden)

    Anneleen Daemen

    Full Text Available In the past, microarray studies have been criticized due to noise and the limited overlap between gene signatures. Prior biological knowledge should therefore be incorporated as side information in models based on gene expression data to improve the accuracy of diagnosis and prognosis in cancer. As prior knowledge, we investigated interaction and pathway information from the human interactome on different aspects of biological systems. By exploiting the properties of kernel methods, relations between genes with similar functions but active in alternative pathways could be incorporated in a support vector machine classifier based on spectral graph theory. Using 10 microarray data sets, we first reduced the number of data sources relevant for multiple cancer types and outcomes. Three sources on metabolic pathway information (KEGG, protein-protein interactions (OPHID and miRNA-gene targeting (microRNA.org outperformed the other sources with regard to the considered class of models. Both fixed and adaptive approaches were subsequently considered to combine the three corresponding classifiers. Averaging the predictions of these classifiers performed best and was significantly better than the model based on microarray data only. These results were confirmed on 6 validation microarray sets, with a significantly improved performance in 4 of them. Integrating interactome data thus improves classification of cancer outcome for the investigated microarray technologies and cancer types. Moreover, this strategy can be incorporated in any kernel method or non-linear version of a non-kernel method.

  19. Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jianping Hua

    2004-01-01

    Full Text Available This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney test-based algorithm to segment cDNA microarray images, and performs postprocessing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with the background adjustment, are then used for independent compression of the foreground and background. We introduce a new distortion measurement for cDNA microarray image compression and devise a coding scheme by modifying the embedded block coding with optimized truncation (EBCOT algorithm (Taubman, 2000 to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that the bit rate required to ensure sufficiently accurate gene expression measurement varies and depends on the quality of cDNA microarray images. For homogeneously hybridized cDNA microarray images, BASICA is able to provide from a bit rate as low as 5 bpp the gene expression data that are 99% in agreement with those of the original 32 bpp images.

  20. Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications

    Directory of Open Access Journals (Sweden)

    Kaplinski Lauris

    2009-05-01

    Full Text Available Abstract Background Here we present a novel promising microbial diagnostic method that combines the sensitivity of Nucleic Acid Sequence Based Amplification (NASBA with the high information content of microarray technology for the detection of bacterial tmRNA molecules. The NASBA protocol was modified to include aminoallyl-UTP (aaUTP molecules that were incorporated into nascent RNA during the NASBA reaction. Post-amplification labeling with fluorescent dye was carried out subsequently and tmRNA hybridization signal intensities were measured using microarray technology. Significant optimization of the labeled NASBA protocol was required to maintain the required sensitivity of the reactions. Results Two different aaUTP salts were evaluated and optimum final concentrations were identified for both. The final 2 mM concentration of aaUTP Li-salt in NASBA reaction resulted in highest microarray signals overall, being twice as high as the strongest signals with 1 mM aaUTP Na-salt. Conclusion We have successfully demonstrated efficient combination of NASBA amplification technology with microarray based hybridization detection. The method is applicative for many different areas of microbial diagnostics including environmental monitoring, bio threat detection, industrial process monitoring and clinical microbiology.

  1. Exploring the use of internal and externalcontrols for assessing microarray technical performance

    Directory of Open Access Journals (Sweden)

    Game Laurence

    2010-12-01

    Full Text Available Abstract Background The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies. Results A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes" was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification. External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC metrics. Conclusions These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray

  2. Utility of routine postoperative visit after appendectomy and cholecystectomy with evaluation of mobile technology access in an urban safety net population.

    Science.gov (United States)

    Chen, Diane W; Davis, Rachel W; Balentine, Courtney J; Scott, Aaron R; Gao, Yue; Tapia, Nicole M; Berger, David H; Suliburk, James W

    2014-08-01

    The value of routine postoperative visits after general surgery remains unclear. The objective of this study was to evaluate the utility of routine postoperative visits after appendectomy and cholecystectomy and to determine access to mobile technology as an alternative platform for follow-up. Retrospective review of 219 appendectomies and 200 cholecystectomies performed at a safety net hospital. One patient underwent both surgeries. Patient demographics, duration of clinic visit, and need for additional imaging, tests or readmissions were recorded. Access to mobile technology was surveyed by a validated questionnaire. Of 418 patients, 84% percent completed a postoperative visit. At follow-up, 58 patients (14%) required 70 interventions, including staple removal (16, 23%), suture removal (4, 6%), drain removal (8, 11%), additional follow-up (20, 28%), medication action (16, 21%), additional imaging (3, 4%), and readmission (1, 1%). Occupational paperwork (62) and nonsurgical clinic referrals (28) were also performed. Average check-in to check-out time was 100 ± 54 min per patient. One intervention was performed for every 7.8 h of time in the clinic. Additionally, 88% of the surveyed population reported access to cell phone technology, and 69% of patients mobile technology, which is pervasive in our population. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets

    Directory of Open Access Journals (Sweden)

    Cohen Aaron

    2009-02-01

    Full Text Available Abstract Background Summarization of gene information in the literature has the potential to help genomics researchers translate basic research into clinical benefits. Gene expression microarrays have been used to study biomarkers for disease and discover novel types of therapeutics and the task of finding information in journal articles on sets of genes is common for translational researchers working with microarray data. However, manually searching and scanning the literature references returned from PubMed is a time-consuming task for scientists. We built and evaluated an automatic summarizer of information on genes studied in microarray experiments. The Gene Information Clustering and Summarization System (GICSS is a system that integrates two related steps of the microarray data analysis process: functional gene clustering and gene information gathering. The system evaluation was conducted during the process of genomic researchers analyzing their own experimental microarray datasets. Results The clusters generated by GICSS were validated by scientists during their microarray analysis process. In addition, presenting sentences in the abstract provided significantly more important information to the users than just showing the title in the default PubMed format. Conclusion The evaluation results suggest that GICSS can be useful for researchers in genomic area. In addition, the hybrid evaluation method, partway between intrinsic and extrinsic system evaluation, may enable researchers to gauge the true usefulness of the tool for the scientists in their natural analysis workflow and also elicit suggestions for future enhancements. Availability GICSS can be accessed online at: http://ir.ohsu.edu/jianji/index.html

  4. FiGS: a filter-based gene selection workbench for microarray data

    Directory of Open Access Journals (Sweden)

    Yun Taegyun

    2010-01-01

    Full Text Available Abstract Background The selection of genes that discriminate disease classes from microarray data is widely used for the identification of diagnostic biomarkers. Although various gene selection methods are currently available and some of them have shown excellent performance, no single method can retain the best performance for all types of microarray datasets. It is desirable to use a comparative approach to find the best gene selection result after rigorous test of different methodological strategies for a given microarray dataset. Results FiGS is a web-based workbench that automatically compares various gene selection procedures and provides the optimal gene selection result for an input microarray dataset. FiGS builds up diverse gene selection procedures by aligning different feature selection techniques and classifiers. In addition to the highly reputed techniques, FiGS diversifies the gene selection procedures by incorporating gene clustering options in the feature selection step and different data pre-processing options in classifier training step. All candidate gene selection procedures are evaluated by the .632+ bootstrap errors and listed with their classification accuracies and selected gene sets. FiGS runs on parallelized computing nodes that capacitate heavy computations. FiGS is freely accessible at http://gexp.kaist.ac.kr/figs. Conclusion FiGS is an web-based application that automates an extensive search for the optimized gene selection analysis for a microarray dataset in a parallel computing environment. FiGS will provide both an efficient and comprehensive means of acquiring optimal gene sets that discriminate disease states from microarray datasets.

  5. Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Cannataro, Mario

    2013-08-01

    A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power

  6. Integration of microarray analysis into the clinical diagnosis of hematological malignancies: How much can we improve cytogenetic testing?

    Science.gov (United States)

    Peterson, Jess F.; Aggarwal, Nidhi; Smith, Clayton A.; Gollin, Susanne M.; Surti, Urvashi; Rajkovic, Aleksandar; Swerdlow, Steven H.; Yatsenko, Svetlana A.

    2015-01-01

    Purpose To evaluate the clinical utility, diagnostic yield and rationale of integrating microarray analysis in the clinical diagnosis of hematological malignancies in comparison with classical chromosome karyotyping/fluorescence in situ hybridization (FISH). Methods G-banded chromosome analysis, FISH and microarray studies using customized CGH and CGH+SNP designs were performed on 27 samples from patients with hematological malignancies. A comprehensive comparison of the results obtained by three methods was conducted to evaluate benefits and limitations of these techniques for clinical diagnosis. Results Overall, 89.7% of chromosomal abnormalities identified by karyotyping/FISH studies were also detectable by microarray. Among 183 acquired copy number alterations (CNAs) identified by microarray, 94 were additional findings revealed in 14 cases (52%), and at least 30% of CNAs were in genomic regions of diagnostic/prognostic significance. Approximately 30% of novel alterations detected by microarray were >20 Mb in size. Balanced abnormalities were not detected by microarray; however, of the 19 apparently “balanced” rearrangements, 55% (6/11) of recurrent and 13% (1/8) of non-recurrent translocations had alterations at the breakpoints discovered by microarray. Conclusion Microarray technology enables accurate, cost-effective and time-efficient whole-genome analysis at a resolution significantly higher than that of conventional karyotyping and FISH. Array-CGH showed advantage in identification of cryptic imbalances and detection of clonal aberrations in population of non-dividing cancer cells and samples with poor chromosome morphology. The integration of microarray analysis into the cytogenetic diagnosis of hematologic malignancies has the potential to improve patient management by providing clinicians with additional disease specific and potentially clinically actionable genomic alterations. PMID:26299921

  7. RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

    Science.gov (United States)

    Anguita, Alberto; Martin, Luis; Garcia-Remesal, Miguel; Maojo, Victor

    2013-07-01

    This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpress database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  8. Microarrays for the evaluation of cell-biomaterial surface interactions

    Science.gov (United States)

    Thissen, H.; Johnson, G.; McFarland, G.; Verbiest, B. C. H.; Gengenbach, T.; Voelcker, N. H.

    2007-01-01

    The evaluation of cell-material surface interactions is important for the design of novel biomaterials which are used in a variety of biomedical applications. While traditional in vitro test methods have routinely used samples of relatively large size, microarrays representing different biomaterials offer many advantages, including high throughput and reduced sample handling. Here, we describe the simultaneous cell-based testing of matrices of polymeric biomaterials, arrayed on glass slides with a low cell-attachment background coating. Arrays were constructed using a microarray robot at 6 fold redundancy with solid pins having a diameter of 375 μm. Printed solutions contained at least one monomer, an initiator and a bifunctional crosslinker. After subsequent UV polymerisation, the arrays were washed and characterised by X-ray photoelectron spectroscopy. Cell culture experiments were carried out over 24 hours using HeLa cells. After labelling with CellTracker ® Green for the final hour of incubation and subsequent fixation, the arrays were scanned. In addition, individual spots were also viewed by fluorescence microscopy. The evaluation of cell-surface interactions in high-throughput assays as demonstrated here is a key enabling technology for the effective development of future biomaterials.

  9. Microarray Dot Electrodes Utilizing Dielectrophoresis for Cell Characterization

    Directory of Open Access Journals (Sweden)

    Fatimah Ibrahim

    2013-07-01

    Full Text Available During the last three decades; dielectrophoresis (DEP has become a vital tool for cell manipulation and characterization due to its non-invasiveness. It is very useful in the trend towards point-of-care systems. Currently, most efforts are focused on using DEP in biomedical applications, such as the spatial manipulation of cells, the selective separation or enrichment of target cells, high-throughput molecular screening, biosensors and immunoassays. A significant amount of research on DEP has produced a wide range of microelectrode configurations. In this paper; we describe the microarray dot electrode, a promising electrode geometry to characterize and manipulate cells via DEP. The advantages offered by this type of microelectrode are also reviewed. The protocol for fabricating planar microelectrodes using photolithography is documented to demonstrate the fast and cost-effective fabrication process. Additionally; different state-of-the-art Lab-on-a-Chip (LOC devices that have been proposed for DEP applications in the literature are reviewed. We also present our recently designed LOC device, which uses an improved microarray dot electrode configuration to address the challenges facing other devices. This type of LOC system has the capability to boost the implementation of DEP technology in practical settings such as clinical cell sorting, infection diagnosis, and enrichment of particle populations for drug development.

  10. Variance estimation in the analysis of microarray data

    KAUST Repository

    Wang, Yuedong

    2009-04-01

    Microarrays are one of the most widely used high throughput technologies. One of the main problems in the area is that conventional estimates of the variances that are required in the t-statistic and other statistics are unreliable owing to the small number of replications. Various methods have been proposed in the literature to overcome this lack of degrees of freedom problem. In this context, it is commonly observed that the variance increases proportionally with the intensity level, which has led many researchers to assume that the variance is a function of the mean. Here we concentrate on estimation of the variance as a function of an unknown mean in two models: the constant coefficient of variation model and the quadratic variance-mean model. Because the means are unknown and estimated with few degrees of freedom, naive methods that use the sample mean in place of the true mean are generally biased because of the errors-in-variables phenomenon. We propose three methods for overcoming this bias. The first two are variations on the theme of the so-called heteroscedastic simulation-extrapolation estimator, modified to estimate the variance function consistently. The third class of estimators is entirely different, being based on semiparametric information calculations. Simulations show the power of our methods and their lack of bias compared with the naive method that ignores the measurement error. The methodology is illustrated by using microarray data from leukaemia patients.

  11. Application of the micro-array comparative genomic hybridization technology in preimplantation genetic diagnosis%Array-CGH技术在胚胎植入前遗传学诊断中的应用进展

    Institute of Scientific and Technical Information of China (English)

    韩丹; 陈大蔚; 曹云霞; 周平

    2015-01-01

    As a new kind high-throughput genomics technology, micro array-based comparative genomic hybridization (aCGH) has brought the huge change for molecular biology and medical research. Because of the detection range covers the whole genome, high efficiency, easy operation etc, aCGH has been widely used in many areas of human genetic disease diagnosis, tumor genomics, systems biology and prenatal diagnosis. Human preimplantation genetic diagnosis (PGD) is an important part of assisted reproductive technology, with the development of molecular genetics technology, its application range is continuously widening. Based on aCGH technology in PGD for embryonic whole genome screening for aneuploidy and structural abnormalities, human PGD/human preimplantation genetic screening (PGS) implantation rate and clinical pregnancy rate have improved significantly. In this article, we discussed the advantages, disadvantages and prospects of aCGH in prenatal diagnosis.%微阵列比较基因组杂交(aCGH)作为一种新兴的高通量检测技术,给分子生物学及医学研究带来了巨大变化,因其检测范围覆盖全基因组、高效率、操作简便等特点,在人类遗传疾病诊断,肿瘤基因组学,系统生物学研究及产前诊断中已有了广泛应用。植入前遗传学诊断(PGD)是辅助生殖技术的重要组成部分,随着分子遗传学技术的发展,其应用范围也不断拓宽。基于aCGH技术在PGD中对胚胎全染色体组非整倍体及结构异常的筛查,PGD/植入前遗传学筛查(PGS)胚胎植入率和临床妊娠率均有显著提高,本文就aCGH技术在胚胎植入前遗传学诊断中的应用进行综述。

  12. Facilitating RNA structure prediction with microarrays.

    Science.gov (United States)

    Kierzek, Elzbieta; Kierzek, Ryszard; Turner, Douglas H; Catrina, Irina E

    2006-01-17

    Determining RNA secondary structure is important for understanding structure-function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2'-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve the prediction of that secondary structure. When experimental constraints from hybridization results are added to a free-energy minimization algorithm, the prediction of the secondary structure of Escherichia coli 5S rRNA improves from 27 to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2'-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.

  13. Plasmonically amplified fluorescence bioassay with microarray format

    Science.gov (United States)

    Gogalic, S.; Hageneder, S.; Ctortecka, C.; Bauch, M.; Khan, I.; Preininger, Claudia; Sauer, U.; Dostalek, J.

    2015-05-01

    Plasmonic amplification of fluorescence signal in bioassays with microarray detection format is reported. A crossed relief diffraction grating was designed to couple an excitation laser beam to surface plasmons at the wavelength overlapping with the absorption and emission bands of fluorophore Dy647 that was used as a label. The surface of periodically corrugated sensor chip was coated with surface plasmon-supporting gold layer and a thin SU8 polymer film carrying epoxy groups. These groups were employed for the covalent immobilization of capture antibodies at arrays of spots. The plasmonic amplification of fluorescence signal on the developed microarray chip was tested by using interleukin 8 sandwich immunoassay. The readout was performed ex situ after drying the chip by using a commercial scanner with high numerical aperture collecting lens. Obtained results reveal the enhancement of fluorescence signal by a factor of 5 when compared to a regular glass chip.

  14. The Small Payload Access to Space Experiment (SPASE): Using Non-Traditional Aerospace Technology to Enable a New Generation of Low-Cost Missions

    OpenAIRE

    McDermott, Scott; Aamot, L. Eric

    2001-01-01

    Launching on STS-108 Endeavour in late 2001, the Small Payload Access to Space Experiment (SPASE) demonstrates a number of new technologies, efficient ways to conduct a nanospacecraft development program, and how to take such a spacecraft through the Shuttle Hitchhiker safety and integration process. This paper describes the essential “lessons learned” in each of these areas. Commercial solar panels, batteries, imagers, photocells, integrated circuits, and manufacturing techniques are used th...

  15. Effective use of multibeam antenna and space-time multiple access technology in modern mobile communication systems

    OpenAIRE

    Moskalets, N. V.

    2015-01-01

    A possibility for efficient use of radio-frequency spectrum and of corresponding increase in productivity of mobile communication system with space-time multiple access obtained by use of multibeam antenna of base station is considered.

  16. Tissue Microarray Analysis Applied to Bone Diagenesis

    OpenAIRE

    Barrios Mello, Rafael; Regis Silva, Maria Regina; Seixas Alves, Maria Teresa; Evison, Martin; Guimarães, Marco Aurélio; Francisco, Rafaella Arrabaça; Dias Astolphi, Rafael; Miazato Iwamura, Edna Sadayo

    2017-01-01

    Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens....

  17. Emerging new practices in technology to support independent community access for people with intellectual and cognitive disabilities.

    Science.gov (United States)

    Stock, Steven E; Davies, Daniel K; Wehmeyer, Michael L; Lachapelle, Yves

    2011-01-01

    The concept of community access is a multidimensional term, which may involve issues related to physical access, knowledge and information, power and control, relationships and communications, advocacy, participation and quality of life [21]. This paper discusses historical and emerging practices and interventions related to physical access to community and community based information for individuals with cognitive disabilities such as intellectual disability, autism or traumatic brain injury. While much societal attention has been paid to features of independent community access for populations such as individuals with hearing, vision or physical disabilities, less attention has focused on independent community access for people with intellectual and other significant cognitive disabilities. Attitudes and actions by families and professional service communities are often mixed for some individuals in this population. The somewhat limited research base in these areas is explored, including a case study review and results from several promising feasibility studies. The paper concludes with comments concerning future prospects and recommendations for improving independent community access for persons with significant cognitive disabilities.

  18. Restricting Access to ART on the Basis of Criminal Record : An Ethical Analysis of a State-Enforced "Presumption Against Treatment" With Regard to Assisted Reproductive Technologies.

    Science.gov (United States)

    Thompson, Kara; McDougall, Rosalind

    2015-09-01

    As assisted reproductive technologies (ART) become increasingly popular, debate has intensified over the ethical justification for restricting access to ART based on various medical and non-medical factors. In 2010, the Australian state of Victoria enacted world-first legislation that denies access to ART for all patients with certain criminal or child protection histories. Patients and their partners are identified via a compulsory police and child protection check prior to commencing ART and, if found to have a previous relevant conviction or child protection order, are given a "presumption against treatment." This article reviews the legislation and identifies arguments that may be used to justify restricting access to ART for various reasons. The arguments reviewed include limitations of reproductive rights, inheriting undesirable genetic traits, distributive justice, and the welfare of the future child. We show that none of these arguments justifies restricting access to ART in the context of past criminal history. We show that a "presumption against treatment" is an unjustified infringement on reproductive freedom and that it creates various inconsistencies in current social, medical, and legal policy. We argue that a state-enforced policy of restricting access to ART based on the non-medical factor of past criminal history is an example of unjust discrimination and cannot be ethically justified, with one important exception: in cases where ART treatment may be considered futile on the basis that the parents are not expected to raise the resulting child.

  19. A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy

    Directory of Open Access Journals (Sweden)

    Archer Kellie J

    2008-02-01

    Full Text Available Abstract Background With the popularity of DNA microarray technology, multiple groups of researchers have studied the gene expression of similar biological conditions. Different methods have been developed to integrate the results from various microarray studies, though most of them rely on distributional assumptions, such as the t-statistic based, mixed-effects model, or Bayesian model methods. However, often the sample size for each individual microarray experiment is small. Therefore, in this paper we present a non-parametric meta-analysis approach for combining data from independent microarray studies, and illustrate its application on two independent Affymetrix GeneChip studies that compared the gene expression of biopsies from kidney transplant recipients with chronic allograft nephropathy (CAN to those with normal functioning allograft. Results The simulation study comparing the non-parametric meta-analysis approach to a commonly used t-statistic based approach shows that the non-parametric approach has better sensitivity and specificity. For the application on the two CAN studies, we identified 309 distinct genes that expressed differently in CAN. By applying Fisher's exact test to identify enriched KEGG pathways among those genes called differentially expressed, we found 6 KEGG pathways to be over-represented among the identified genes. We used the expression measurements of the identified genes as predictors to predict the class labels for 6 additional biopsy samples, and the predicted results all conformed to their pathologist diagnosed class labels. Conclusion We present a new approach for combining data from multiple independent microarray studies. This approach is non-parametric and does not rely on any distributional assumptions. The rationale behind the approach is logically intuitive and can be easily understood by researchers not having advanced training in statistics. Some of the identified genes and pathways have been

  20. Automating dChip: toward reproducible sharing of microarray data analysis

    Directory of Open Access Journals (Sweden)

    Li Cheng

    2008-05-01

    Full Text Available Abstract Background During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dChip users want to analyze large number of arrays automatically and share data analysis procedures and parameters. Improvement is also needed when the dChip user support team tries to identify the causes of reported analysis errors or bugs from users. Results We report here implementation and application of the dChip automation module. Through this module, dChip automation files can be created to include menu steps, parameters, and data viewpoints to run automatically. A data-packaging function allows convenient transfer from one user to another of the dChip software, microarray data, and analysis procedures, so that the second user can reproduce the entire analysis session of the first user. An analysis report file can also be generated during an automated run, including analysis logs, user comments, and viewpoint screenshots. Conclusion The dChip automation module is a step toward reproducible research, and it can prompt a more convenient and reproducible mechanism for sharing microarray software, data, and analysis procedures and results. Automation data packages can also be used as publication supplements. Similar automation mechanisms could be valuable to the research community if implemented in other genomics and bioinformatics software packages.

  1. Evaluation of artificial time series microarray data for dynamic gene regulatory network inference.

    Science.gov (United States)

    Xenitidis, P; Seimenis, I; Kakolyris, S; Adamopoulos, A

    2017-08-07

    High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process. We examined the effect of various factors on the inference performance such as the network size, the presence of noise in microarray data, and the network sparseness. We used a system theory approach and examined the relationship between the pole placement of the inferred system and the inference performance. We examined the relationship between the inference performance in the time domain and the true system parameter identification. Simulation results indicated that time separation and the percentage of directly triggered genes are crucial factors. Also, network sparseness, the triggering function type and noise in input data affect the inference performance. When two factors were simultaneously varied, it was found that variation of one parameter significantly affects the dynamic response of the other. Crucial factors were also examined using a real GRN and acquired results confirmed simulation findings with artificial data. Different initial conditions were also used as an alternative triggering approach. Relevant results confirmed that the number of datasets constitutes the most significant parameter with regard to the inference performance. Copyright © 2017 Elsevier

  2. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam

    2016-10-09

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  3. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam; Subudhi, Amit; Middha, Sheetal; Acharya, Jyoti; Mugasimangalam, Raja Chinnadurai; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Das, Ashis

    2016-01-01

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  4. AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data

    Directory of Open Access Journals (Sweden)

    Xia Yuannan

    2006-12-01

    Full Text Available Abstract Background DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amount of microarray data and make biological sense of them. Affymetrix GeneChips are widely used microarrays, where a variety of statistical algorithms have been explored and used for detecting significant genes in the experiment. These methods rely solely on the quantitative data, i.e., signal intensity; however, qualitative data are also important parameters in detecting differentially expressed genes. Results AffyMiner is a tool developed for detecting differentially expressed genes in Affymetrix GeneChip microarray data and for associating gene annotation and gene ontology information with the genes detected. AffyMiner consists of the functional modules, GeneFinder for detecting significant genes in a treatment versus control experiment and GOTree for mapping genes of interest onto the Gene Ontology (GO space; and interfaces to run Cluster, a program for clustering analysis, and GenMAPP, a program for pathway analysis. AffyMiner has been used for analyzing the GeneChip data and the results were presented in several publications. Conclusion AffyMiner fills an important gap in finding differentially expressed genes in Affymetrix GeneChip microarray data. AffyMiner effectively deals with multiple replicates in the experiment and takes into account both quantitative and qualitative data in identifying significant genes. AffyMiner reduces the time and effort needed to compare data from multiple arrays and to interpret the possible biological implications associated with significant changes in a gene's expression.

  5. The Smart Home for the Elderly: Perceptions, Technologies and Psychological Accessibilities : The Requirements Analysis for the Elderly in Thailand

    OpenAIRE

    Visutsak , Porawat; DAOUDI , Mohamed

    2017-01-01

    International audience; Various studies of assistive technology, embedded into the house for helping elderly persons have been introduced. There are many terms used to call this assistive technology, such as smart home, intelligent home, and home networking. The current technologies for smart home system can be divided into two basic categories: passive-intervention devices and active-intervention devices. Passive-intervention devices monitor an elderly person's condition and safety without i...

  6. Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray

    Directory of Open Access Journals (Sweden)

    Nobumasa Hitoshi

    2007-04-01

    Full Text Available Abstract Background Mycotoxins are fungal secondary metabolites commonly present in feed and food, and are widely regarded as hazardous contaminants. Citrinin, one of the very well known mycotoxins that was first isolated from Penicillium citrinum, is produced by more than 10 kinds of fungi, and is possibly spread all over the world. However, the information on the action mechanism of the toxin is limited. Thus, we investigated the citrinin-induced genomic response for evaluating its toxicity. Results Citrinin inhibited growth of yeast cells at a concentration higher than 100 ppm. We monitored the citrinin-induced mRNA expression profiles in yeast using the ORF DNA microarray and Oligo DNA microarray, and the expression profiles were compared with those of the other stress-inducing agents. Results obtained from both microarray experiments clustered together, but were different from those of the mycotoxin patulin. The oxidative stress response genes – AADs, FLR1, OYE3, GRE2, and MET17 – were significantly induced. In the functional category, expression of genes involved in "metabolism", "cell rescue, defense and virulence", and "energy" were significantly activated. In the category of "metabolism", genes involved in the glutathione synthesis pathway were activated, and in the category of "cell rescue, defense and virulence", the ABC transporter genes were induced. To alleviate the induced stress, these cells might pump out the citrinin after modification with glutathione. While, the citrinin treatment did not induce the genes involved in the DNA repair. Conclusion Results from both microarray studies suggest that citrinin treatment induced oxidative stress in yeast cells. The genotoxicity was less severe than the patulin, suggesting that citrinin is less toxic than patulin. The reproducibility of the expression profiles was much better with the Oligo DNA microarray. However, the Oligo DNA microarray did not completely overcome cross

  7. Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.

    Science.gov (United States)

    Steger, Doris; Berry, David; Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander

    2011-01-01

    The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.

  8. Microarrays in ecological research: A case study of a cDNA microarray for plant-herbivore interactions

    Directory of Open Access Journals (Sweden)

    Gase Klaus

    2004-09-01

    Full Text Available Abstract Background Microarray technology allows researchers to simultaneously monitor changes in the expression ratios (ERs of hundreds of genes and has thereby revolutionized most of biology. Although this technique has the potential of elucidating early stages in an organism's phenotypic response to complex ecological interactions, to date, it has not been fully incorporated into ecological research. This is partially due to a lack of simple procedures of handling and analyzing the expression ratio (ER data produced from microarrays. Results We describe an analysis of the sources of variation in ERs from 73 hybridized cDNA microarrays, each with 234 herbivory-elicited genes from the model ecological expression system, Nicotiana attenuata, using procedures that are commonly used in ecologic research. Each gene is represented by two independently labeled PCR products and each product was arrayed in quadruplicate. We present a robust method of normalizing and analyzing ERs based on arbitrary thresholds and statistical criteria, and characterize a "norm of reaction" of ERs for 6 genes (4 of known function, 2 of unknown with different ERs as determined across all analyzed arrays to provide a biologically-informed alternative to the use of arbitrary expression ratios in determining significance of expression. These gene-specific ERs and their variance (gene CV were used to calculate array-based variances (array CV, which, in turn, were used to study the effects of array age, probe cDNA quantity and quality, and quality of spotted PCR products as estimates of technical variation. Cluster analysis and a Principal Component Analysis (PCA were used to reveal associations among the transcriptional "imprints" of arrays hybridized with cDNA probes derived from mRNA from N. attenuata plants variously elicited and attacked by different herbivore species and from three congeners: N. quadrivalis, N. longiflora and N. clevelandii. Additionally, the PCA

  9. How Music Technology Can Make Sound and Music Worlds Accessible to Student Composers in Further Education Colleges

    Science.gov (United States)

    Kardos, Leah

    2012-01-01

    I am a composer, producer, pianist and part-time music lecturer at a Further Education college where I teach composing on Music Technology courses at levels 3 (equivalent to A-level) and 4 (Undergraduate/Foundation Degree). A "Music Technology" course, distinct from a "Music" course, often attracts applicants from diverse musical backgrounds; it…

  10. Systematic review of communication technologies to promote access and engagement of young people with diabetes into healthcare

    Directory of Open Access Journals (Sweden)

    Griffiths Frances

    2011-01-01

    Full Text Available Abstract Background Research has investigated whether communication technologies (e.g. mobile telephony, forums, email can be used to transfer digital information between healthcare professionals and young people who live with diabetes. The systematic review evaluates the effectiveness and impact of these technologies on communication. Methods Nine electronic databases were searched. Technologies were described and a narrative synthesis of all studies was undertaken. Results Of 20,925 publications identified, 19 met the inclusion criteria, with 18 technologies assessed. Five categories of communication technologies were identified: video-and tele-conferencing (n = 2; mobile telephony (n = 3; telephone support (n = 3; novel electronic communication devices for transferring clinical information (n = 10; and web-based discussion boards (n = 1. Ten studies showed a positive improvement in HbA1c following the intervention with four studies reporting detrimental increases in HbA1c levels. In fifteen studies communication technologies increased the frequency of contact between patient and healthcare professional. Findings were inconsistent of an association between improvements in HbA1c and increased contact. Limited evidence was available concerning behavioural and care coordination outcomes, although improvement in quality of life, patient-caregiver interaction, self-care and metabolic transmission were reported for some communication technologies. Conclusions The breadth of study design and types of technologies reported make the magnitude of benefit and their effects on health difficult to determine. While communication technologies may increase the frequency of contact between patient and health care professional, it remains unclear whether this results in improved outcomes and is often the basis of the intervention itself. Further research is needed to explore the effectiveness and cost effectiveness of increasing the use of communication

  11. Systematic review of communication technologies to promote access and engagement of young people with diabetes into healthcare.

    Science.gov (United States)

    Sutcliffe, Paul; Martin, Steven; Sturt, Jackie; Powell, John; Griffiths, Frances; Adams, Ann; Dale, Jeremy

    2011-01-06

    Research has investigated whether communication technologies (e.g. mobile telephony, forums, email) can be used to transfer digital information between healthcare professionals and young people who live with diabetes. The systematic review evaluates the effectiveness and impact of these technologies on communication. Nine electronic databases were searched. Technologies were described and a narrative synthesis of all studies was undertaken. Of 20,925 publications identified, 19 met the inclusion criteria, with 18 technologies assessed. Five categories of communication technologies were identified: video-and tele-conferencing (n = 2); mobile telephony (n = 3); telephone support (n = 3); novel electronic communication devices for transferring clinical information (n = 10); and web-based discussion boards (n = 1). Ten studies showed a positive improvement in HbA1c following the intervention with four studies reporting detrimental increases in HbA1c levels. In fifteen studies communication technologies increased the frequency of contact between patient and healthcare professional. Findings were inconsistent of an association between improvements in HbA1c and increased contact. Limited evidence was available concerning behavioural and care coordination outcomes, although improvement in quality of life, patient-caregiver interaction, self-care and metabolic transmission were reported for some communication technologies. The breadth of study design and types of technologies reported make the magnitude of benefit and their effects on health difficult to determine. While communication technologies may increase the frequency of contact between patient and health care professional, it remains unclear whether this results in improved outcomes and is often the basis of the intervention itself. Further research is needed to explore the effectiveness and cost effectiveness of increasing the use of communication technologies between young people and healthcare professionals.

  12. Validation of virtual reality simulators: Key to the successful integration of a novel teaching technology into minimal access surgery

    NARCIS (Netherlands)

    Schijven, Marlies P.; Jakimowicz, Jack J.

    2005-01-01

    Minimal access surgery (MAS) requires additional training in the surgical curriculum, as skills needed to perform MAS are quite different from those used in open surgery. Moreover, residents do not seem to experience ample opportunity to gain such skills in the current surgical curriculum. Virtual

  13. 75 FR 24688 - Access to Confidential Business Information by Guident Technologies Inc.’s Identified Subcontractor

    Science.gov (United States)

    2010-05-05

    ... to a particular entity, consult the technical person listed under FOR FURTHER INFORMATION CONTACT. B... Information Systems and for Test Confidential Business Information Tracking Systems (CBITS) and (TCBITS). In... materials on a need-to- know basis only. All access to TSCA CBI under this contract will take place at EPA...

  14. [Access and use of new information and telecommunication technologies among teenagers at high school, health implications. JOITIC Study].

    Science.gov (United States)

    Muñoz-Miralles, Raquel; Ortega-González, Raquel; Batalla-Martínez, Carme; López-Morón, María Rosa; Manresa, Josep Maria; Torán-Monserrat, Pere

    2014-02-01

    To determine ICT accessibility and use among the adolescents attending High School and to analyse related factors. Cross-sectional multicentric study. High Schools participating in the Community Health «Salut i Escola» Programme. 5,538 students from first to fourth degree at 28 centres in the area of Barcelona. Self administered questionnaire including sociodemographic information, ICT use and accessibility. Missing answers were below 1% in all items except in school performance (3,13%); 48,6% were female, mean age 14years (range 11-20); 15,5% foreigners; 23% reported low school performance; 75,2% took extracurricular activities; 88,9% refers a good relationship with their parents. ICT access is homogeneously massive: 98% had a computer at home, 44,8% used it for two or more hours daily. 98,6% could access Internet, 47,2% without parental control. 90% owned a mobile phone (83% in first grade, 95% in fourth); 45,6% owned one before 12years old. Girls use it for social relationships and boys for playing. 68,4% played videogames, 36,5% for three or more hours a week and 66,8% without parental control. Their use decreases with age. The ICT parental control is associated with better school performance. Our high scholars gain access to the ICT at younger ages and they use them in almost every aspect of their lives. There have been detected some gender differences in their use, as well as in the age of the users and between the type of school. Copyright © 2013 Elsevier España, S.L. All rights reserved.

  15. Design of a covalently bonded glycosphingolipid microarray

    DEFF Research Database (Denmark)

    Arigi, Emma; Blixt, Klas Ola; Buschard, Karsten

    2012-01-01

    , the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release...... of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2...

  16. Linking probe thermodynamics to microarray quantification

    International Nuclear Information System (INIS)

    Li, Shuzhao; Pozhitkov, Alexander; Brouwer, Marius

    2010-01-01

    Understanding the difference in probe properties holds the key to absolute quantification of DNA microarrays. So far, Langmuir-like models have failed to link sequence-specific properties to hybridization signals in the presence of a complex hybridization background. Data from washing experiments indicate that the post-hybridization washing has no major effect on the specifically bound targets, which give the final signals. Thus, the amount of specific targets bound to probes is likely determined before washing, by the competition against nonspecific binding. Our competitive hybridization model is a viable alternative to Langmuir-like models. (comment)

  17. A statistical framework for differential network analysis from microarray data

    Directory of Open Access Journals (Sweden)

    Datta Somnath

    2010-02-01

    Full Text Available Abstract Background It has been long well known that genes do not act alone; rather groups of genes act in consort during a biological process. Consequently, the expression levels of genes are dependent on each other. Experimental techniques to detect such interacting pairs of genes have been in place for quite some time. With the advent of microarray technology, newer computational techniques to detect such interaction or association between gene expressions are being proposed which lead to an association network. While most microarray analyses look for genes that are differentially expressed, it is of potentially greater significance to identify how entire association network structures change between two or more biological settings, say normal versus diseased cell types. Results We provide a recipe for conducting a differential analysis of networks constructed from microarray data under two experimental settings. At the core of our approach lies a connectivity score that represents the strength of genetic association or interaction between two genes. We use this score to propose formal statistical tests for each of following queries: (i whether the overall modular structures of the two networks are different, (ii whether the connectivity of a particular set of "interesting genes" has changed between the two networks, and (iii whether the connectivity of a given single gene has changed between the two networks. A number of examples of this score is provided. We carried out our method on two types of simulated data: Gaussian networks and networks based on differential equations. We show that, for appropriate choices of the connectivity scores and tuning parameters, our method works well on simulated data. We also analyze a real data set involving normal versus heavy mice and identify an interesting set of genes that may play key roles in obesity. Conclusions Examining changes in network structure can provide valuable information about the

  18. Rapid and reliable detection and identification of GM events using multiplex PCR coupled with oligonucleotide microarray.

    Science.gov (United States)

    Xu, Xiaodan; Li, Yingcong; Zhao, Heng; Wen, Si-yuan; Wang, Sheng-qi; Huang, Jian; Huang, Kun-lun; Luo, Yun-bo

    2005-05-18

    To devise a rapid and reliable method for the detection and identification of genetically modified (GM) events, we developed a multiplex polymerase chain reaction (PCR) coupled with a DNA microarray system simultaneously aiming at many targets in a single reaction. The system included probes for screening gene, species reference gene, specific gene, construct-specific gene, event-specific gene, and internal and negative control genes. 18S rRNA was combined with species reference genes as internal controls to assess the efficiency of all reactions and to eliminate false negatives. Two sets of the multiplex PCR system were used to amplify four and five targets, respectively. Eight different structure genes could be detected and identified simultaneously for Roundup Ready soybean in a single microarray. The microarray specificity was validated by its ability to discriminate two GM maizes Bt176 and Bt11. The advantages of this method are its high specificity and greatly reduced false-positives and -negatives. The multiplex PCR coupled with microarray technology presented here is a rapid and reliable tool for the simultaneous detection of GM organism ingredients.

  19. Design of an Enterobacteriaceae Pan-genome Microarray Chip

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Ussery, David

    2010-01-01

    -density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability...... to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination...

  20. A Pilot Study to Improve Access to Eye Care Services for Patients in Rural India by Implementing Community Ophthalmology through Innovative Telehealth Technology.

    Science.gov (United States)

    John, Sheila; Premila, M; Javed, Mohd; Vikas, G; Wagholikar, Amol

    2015-01-01

    To inform about a very unique and first of its kind telehealth pilot study in India that has provided virtual telehealth consultation to eye care patients in low resource at remote villages. Provision of Access to eye care services in remote population is always challenging due to pragmatic reasons. Advances in Telehealth technologies have provided an opportunity to improve access to remote population. However, current Telehealth technologies are limited to face-to-face video consultation only. We inform about a pilot study that illustrates real-time imaging access to ophthalmologists. Our innovative software led technology solution allowed screening of patients with varying ocular conditions. Eye camps were conducted in 2 districts in South India over a 12-month period in 2014. Total of 196 eye camps were conducted. Total of 19,634 patients attended the eye camps. Innovative software was used to conduct consultation with the ophthalmologist located in the city hospital. The software enabled virtual visit and allowed instant sharing of fundus camera images for assessment and diagnosis. About 71% of the patients were found to have Refractive Error problems, 15% of them were found to have cataract, 7% of the patients were diagnosed to have Retina problems and 7% of the patients were found to have other ocular diseases. The patients requiring cataract surgery were immediately transferred to city hospital for treatment. Software led assessment of fundus camera images assisted in identifying retinal eye diseases. Our real-time virtual visit software assisted in specialist care provision and illustrated a novel tele health solution for low resource population.

  1. Functional Characterization of Gibberellin-Regulated Genes in Rice Using Microarray System

    OpenAIRE

    Jan, Asad; Komatsu, Setsuko

    2006-01-01

    Gibberellin (GA) is collectively referred to a group of diterpenoid acids, some of which act as plant hormones and are essential for normal plant growth and development. DNA microarray technology has become the standard tool for the parallel quantification of large numbers of messenger RNA transcripts. The power of this approach has been demonstrated in dissecting plant physiology and development, and in unraveling the underlying cellular signaling pathways. To understand the molecular mechan...

  2. New diagnostics for melanoma detection: from artificial intelligence to RNA microarrays.

    Science.gov (United States)

    Ahlgrimm-Siess, Verena; Laimer, Martin; Arzberger, Edith; Hofmann-Wellenhof, Rainer

    2012-07-01

    Early detection of melanoma remains crucial to ensuring a favorable prognosis. Dermoscopy and total body photography are well-established noninvasive aids that increase the diagnostic accuracy of dermatologists in their daily routine, beyond that of a naked-eye examination. New noninvasive diagnostic techniques, such as reflectance confocal microscopy, multispectral digital imaging and RNA microarrays, are currently being investigated to determine their utility for melanoma detection. This review presents emerging technologies for noninvasive melanoma diagnosis, and discusses their advantages and limitations.

  3. Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment.

    Science.gov (United States)

    Severgnini, Marco; Bicciato, Silvio; Mangano, Eleonora; Scarlatti, Francesca; Mezzelani, Alessandra; Mattioli, Michela; Ghidoni, Riccardo; Peano, Clelia; Bonnal, Raoul; Viti, Federica; Milanesi, Luciano; De Bellis, Gianluca; Battaglia, Cristina

    2006-06-01

    Meta-analysis of microarray data is increasingly important, considering both the availability of multiple platforms using disparate technologies and the accumulation in public repositories of data sets from different laboratories. We addressed the issue of comparing gene expression profiles from two microarray platforms by devising a standardized investigative strategy. We tested this procedure by studying MDA-MB-231 cells, which undergo apoptosis on treatment with resveratrol. Gene expression profiles were obtained using high-density, short-oligonucleotide, single-color microarray platforms: GeneChip (Affymetrix) and CodeLink (Amersham). Interplatform analyses were carried out on 8414 common transcripts represented on both platforms, as identified by LocusLink ID, representing 70.8% and 88.6% of annotated GeneChip and CodeLink features, respectively. We identified 105 differentially expressed genes (DEGs) on CodeLink and 42 DEGs on GeneChip. Among them, only 9 DEGs were commonly identified by both platforms. Multiple analyses (BLAST alignment of probes with target sequences, gene ontology, literature mining, and quantitative real-time PCR) permitted us to investigate the factors contributing to the generation of platform-dependent results in single-color microarray experiments. An effective approach to cross-platform comparison involves microarrays of similar technologies, samples prepared by identical methods, and a standardized battery of bioinformatic and statistical analyses.

  4. Comparing transformation methods for DNA microarray data

    Directory of Open Access Journals (Sweden)

    Zwinderman Aeilko H

    2004-06-01

    Full Text Available Abstract Background When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include subtraction of an estimated background signal, subtracting the reference signal, smoothing (to account for nonlinear measurement effects, and more. Different authors use different approaches, and it is generally not clear to users which method they should prefer. Results We used the ratio between biological variance and measurement variance (which is an F-like statistic as a quality measure for transformation methods, and we demonstrate a method for maximizing that variance ratio on real data. We explore a number of transformations issues, including Box-Cox transformation, baseline shift, partial subtraction of the log-reference signal and smoothing. It appears that the optimal choice of parameters for the transformation methods depends on the data. Further, the behavior of the variance ratio, under the null hypothesis of zero biological variance, appears to depend on the choice of parameters. Conclusions The use of replicates in microarray experiments is important. Adjustment for the null-hypothesis behavior of the variance ratio is critical to the selection of transformation method.

  5. Programmable Ultra Lightweight System Adaptable Radio (PULSAR) Low Cost Telemetry - Access from Space Advanced Technologies or Down the Middle

    Science.gov (United States)

    Sims. Herb; Varnavas, Kosta; Eberly, Eric

    2013-01-01

    Software Defined Radio (SDR) technology has been proven in the commercial sector since the early 1990's. Today's rapid advancement in mobile telephone reliability and power management capabilities exemplifies the effectiveness of the SDR technology for the modern communications market. In contrast, presently qualified satellite transponder applications were developed during the early 1960's space program. Programmable Ultra Lightweight System Adaptable Radio (PULSAR, NASA-MSFC SDR) technology revolutionizes satellite transponder technology by increasing data through-put capability by, at least, an order of magnitude. PULSAR leverages existing Marshall Space Flight Center SDR designs and commercially enhanced capabilities to provide a path to a radiation tolerant SDR transponder. These innovations will (1) reduce the cost of NASA Low Earth Orbit (LEO) and Deep Space transponders, (2) decrease power requirements, and (3) a commensurate volume reduction. Also, PULSAR increases flexibility to implement multiple transponder types by utilizing the same hardware with altered logic - no analog hardware change is required - all of which can be accomplished in orbit. This provides high capability, low cost, transponders to programs of all sizes. The final project outcome would be the introduction of a Technology Readiness Level (TRL) 7 low-cost CubeSat to SmallSat telemetry system into the NASA Portfolio.

  6. LTE-advanced a practical systems approach to understanding 3GPP LTE releases 10 and 11 radio access technologies

    CERN Document Server

    Ahmadi, Sassan

    2013-01-01

    This book is an in-depth, systematic and structured technical reference on 3GPP's LTE-Advanced (Releases 10 and 11), covering theory, technology and implementation, written by an author who has been involved in the inception and development of these technologies for over 20 years. The book not only describes the operation of individual components, but also shows how they fit into the overall system and operate from a systems perspective. Uniquely, this book gives in-depth information on upper protocol layers, implementation and deployment issues, and services, making it suitable for engine

  7. Experimental annotation of the human genome using microarray technology.

    Science.gov (United States)

    Shoemaker, D D; Schadt, E E; Armour, C D; He, Y D; Garrett-Engele, P; McDonagh, P D; Loerch, P M; Leonardson, A; Lum, P Y; Cavet, G; Wu, L F; Altschuler, S J; Edwards, S; King, J; Tsang, J S; Schimmack, G; Schelter, J M; Koch, J; Ziman, M; Marton, M J; Li, B; Cundiff, P; Ward, T; Castle, J; Krolewski, M; Meyer, M R; Mao, M; Burchard, J; Kidd, M J; Dai, H; Phillips, J W; Linsley, P S; Stoughton, R; Scherer, S; Boguski, M S

    2001-02-15

    The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

  8. Enabling Access to Medical and Health Education in Rwanda Using Mobile Technology: Needs Assessment for the Development of Mobile Medical Educator Apps.

    Science.gov (United States)

    Rusatira, Jean Christophe; Tomaszewski, Brian; Dusabejambo, Vincent; Ndayiragije, Vincent; Gonsalves, Snedden; Sawant, Aishwarya; Mumararungu, Angeline; Gasana, George; Amendezo, Etienne; Haake, Anne; Mutesa, Leon

    2016-06-01

    Lack of access to health and medical education resources for doctors in the developing world is a serious global health problem. In Rwanda, with a population of 11 million, there is only one medical school, hence a shortage in well-trained medical staff. The growth of interactive health technologies has played a role in the improvement of health care in developed countries and has offered alternative ways to offer continuous medical education while improving patient's care. However, low and middle-income countries (LMIC) like Rwanda have struggled to implement medical education technologies adapted to local settings in medical practice and continuing education. Developing a user-centered mobile computing approach for medical and health education programs has potential to bring continuous medical education to doctors in rural and urban areas of Rwanda and influence patient care outcomes. The aim of this study is to determine user requirements, currently available resources, and perspectives for potential medical education technologies in Rwanda. Information baseline and needs assessments data collection were conducted in all 44 district hospitals (DHs) throughout Rwanda. The research team collected qualitative data through interviews with 16 general practitioners working across Rwanda and 97 self-administered online questionnaires for rural areas. Data were collected and analyzed to address two key questions: (1) what are the currently available tools for the use of mobile-based technology for medical education in Rwanda, and (2) what are user's requirements for the creation of a mobile medical education technology in Rwanda? General practitioners from different hospitals highlighted that none of the available technologies avail local resources such as the Ministry of Health (MOH) clinical treatment guidelines. Considering the number of patients that doctors see in Rwanda, an average of 32 patients per day, there is need for a locally adapted mobile education app

  9. Radioactive cDNA microarray (II): Gene expression profiling of antidepressant treatment by human cDNA microarray

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ji Hye; Kang, Rhee Hun; Ham, Byung Joo; Lee, Min Su; Shin, Kyung Ho; Choe, Jae Gol; Kim, Meyoung Kon [College of Medicine, Univ. of Korea, Seoul (Korea, Republic of)

    2003-07-01

    Major depressive disorder is a prevalent psychiatric disorder in primary care, associated with impaired patient functioning and well-being. Fluoxetine is a selective serotonin-reuptake inhibitors (SSRIs) and is a commonly prescribed antidepressant compound. Its action is primarily attributed to selective inhibition of the reuptake of serotonin (5-hydroxytryptamine) in the central nervous system. Objectives ; the aims of this study were two-fold: (1) to determine the usefulness for investigation of the transcription profiles in depression patients, and (2) to assess the differences in gene expression profiles between positive response group and negative response groups by fluoxetine treatment. This study included 53 patients with major depression (26 in positive response group with antidepressant treatment, 27 in negative response group with antidepressant treatment), and 53 healthy controls. To examine the difference of gene expression profile in depression patients, radioactive complementary DNA microarrays were used to evaluate changes in the expression of 1,152 genes in total. Using 33p-labeled probes, this method provided highly sensitive gene expression profiles including brain receptors, drug metabolism, and cellular signaling. Gene transcription profiles were classified into several categories in accordance with the antidepressant gene-regulation. The gene profiles were significantly up-(22 genes) and down-(16 genes) regulated in the positive response group when compared to the control group. Also, in the negative response group, 35 genes were up-regulated and 8 genes were down-regulated when compared to the control group. Consequently, we demonstrated that radioactive human cDNA microarray is highly likely to be an efficient technology for evaluating the gene regulation of antidepressants, such as selective serotonin-reuptake inhibitors (SSRIs), by using high-throughput biotechnology.

  10. Radioactive cDNA microarray (II): Gene expression profiling of antidepressant treatment by human cDNA microarray

    International Nuclear Information System (INIS)

    Lee, Ji Hye; Kang, Rhee Hun; Ham, Byung Joo; Lee, Min Su; Shin, Kyung Ho; Choe, Jae Gol; Kim, Meyoung Kon

    2003-01-01

    Major depressive disorder is a prevalent psychiatric disorder in primary care, associated with impaired patient functioning and well-being. Fluoxetine is a selective serotonin-reuptake inhibitors (SSRIs) and is a commonly prescribed antidepressant compound. Its action is primarily attributed to selective inhibition of the reuptake of serotonin (5-hydroxytryptamine) in the central nervous system. Objectives ; the aims of this study were two-fold: (1) to determine the usefulness for investigation of the transcription profiles in depression patients, and (2) to assess the differences in gene expression profiles between positive response group and negative response groups by fluoxetine treatment. This study included 53 patients with major depression (26 in positive response group with antidepressant treatment, 27 in negative response group with antidepressant treatment), and 53 healthy controls. To examine the difference of gene expression profile in depression patients, radioactive complementary DNA microarrays were used to evaluate changes in the expression of 1,152 genes in total. Using 33p-labeled probes, this method provided highly sensitive gene expression profiles including brain receptors, drug metabolism, and cellular signaling. Gene transcription profiles were classified into several categories in accordance with the antidepressant gene-regulation. The gene profiles were significantly up-(22 genes) and down-(16 genes) regulated in the positive response group when compared to the control group. Also, in the negative response group, 35 genes were up-regulated and 8 genes were down-regulated when compared to the control group. Consequently, we demonstrated that radioactive human cDNA microarray is highly likely to be an efficient technology for evaluating the gene regulation of antidepressants, such as selective serotonin-reuptake inhibitors (SSRIs), by using high-throughput biotechnology

  11. SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

    Directory of Open Access Journals (Sweden)

    Davies Jonathan J

    2006-12-01

    Full Text Available Abstract Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. Results We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. Conclusion In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA of cancer genomes, can be accessed at http://sigma.bccrc.ca.

  12. Differences in Access to Information and Communication Technologies: Voices of British Muslim Teenage Girls at Islamic Faith Schools

    Science.gov (United States)

    Hardaker, Glenn; Sabki, Aishah; Qazi, Atika; Iqbal, Javed

    2017-01-01

    Purpose: Most research on information and communication technologies (ICT) differences has been related to gender and ethnicity, and to a lesser extent religious affiliation. The purpose of this paper is to contribute to this field of research by situating the discussion in the context of British Muslims and extending current research into ICT…

  13. Evaluation of gene importance in microarray data based upon probability of selection

    Directory of Open Access Journals (Sweden)

    Fu Li M

    2005-03-01

    Full Text Available Abstract Background Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking to metabolic characteristics that contribute to disease development and progression. The microarray approach offers an expedited solution to this problem. However, it has posed a challenging issue to recognize disease-related genes expression patterns embedded in the microarray data. In selecting a small set of biologically significant genes for classifier design, the nature of high data dimensionality inherent in this problem creates substantial amount of uncertainty. Results Here we present a model for probability analysis of selected genes in order to determine their importance. Our contribution is that we show how to derive the P value of each selected gene in multiple gene selection trials based on different combinations of data samples and how to conduct a reliability analysis accordingly. The importance of a gene is indicated by its associated P value in that a smaller value implies higher information content from information theory. On the microarray data concerning the subtype classification of small round blue cell tumors, we demonstrate that the method is capable of finding the smallest set of genes (19 genes with optimal classification performance, compared with results reported in the literature. Conclusion In classifier design based on microarray data, the probability value derived from gene selection based on multiple combinations of data samples enables an effective mechanism for reducing the tendency of fitting local data particularities.

  14. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

    Directory of Open Access Journals (Sweden)

    Reinders Marcel JT

    2009-11-01

    Full Text Available Abstract Background Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear. Results We have performed a comprehensive sensitivity analysis of microarray breast cancer classification under the two types of feature variability mentioned above. We used data from six state of the art preprocessing methods, using a compendium consisting of eight diferent datasets, involving 1131 hybridizations, containing data from both one and two-color array technology. For a wide range of classifiers, we performed a joint study on performance, concordance and stability. In the stability analysis we explicitly tested classifiers for their noise tolerance by using perturbed expression profiles that are based on uncertainty information directly related to the preprocessing methods. Our results indicate that signature composition is strongly influenced by feature variability, even if the array platform and the stratification of patient samples are identical. In addition, we show that there is often a high level of discordance between individual class assignments for signatures constructed on data coming from different preprocessing schemes, even if the actual signature composition is identical

  15. Improving access to health information for older migrants by using grounded theory and social network analysis to understand their information behaviour and digital technology use.

    Science.gov (United States)

    Goodall, K T; Newman, L A; Ward, P R

    2014-11-01

    Migrant well-being can be strongly influenced by the migration experience and subsequent degree of mainstream language acquisition. There is little research on how older Culturally And Linguistically Diverse (CALD) migrants who have 'aged in place' find health information, and the role which digital technology plays in this. Although the research for this paper was not focused on cancer, we draw out implications for providing cancer-related information to this group. We interviewed 54 participants (14 men and 40 women) aged 63-94 years, who were born in Italy or Greece, and who migrated to Australia mostly as young adults after World War II. Constructivist grounded theory and social network analysis were used for data analysis. Participants identified doctors, adult children, local television, spouse, local newspaper and radio as the most important information sources. They did not generally use computers, the Internet or mobile phones to access information. Literacy in their birth language, and the degree of proficiency in understanding and using English, influenced the range of information sources accessed and the means used. The ways in which older CALD migrants seek and access information has important implications for how professionals and policymakers deliver relevant information to them about cancer prevention, screening, support and treatment, particularly as information and resources are moved online as part of e-health. © 2014 John Wiley & Sons Ltd.

  16. A comparison of rural speech-language pathologists' and residents' access to and attitudes towards the use of technology for speech-language pathology service delivery.

    Science.gov (United States)

    Dunkley, Carolyn; Pattie, Lydelle; Wilson, Linda; McAllister, Lindy

    2010-08-01

    This paper reports results and implications of two related studies which investigated (a) access of residents and speech-language pathologists (SLPs) of rural Australia to information and communication technologies (ICT) and (b) their attitudes towards the use of ICT for delivery of speech-language pathology services. Both studies used mail out questionnaires, followed by interviews with a subset of those who completed the questionnaires. Data were obtained from 43 questionnaires from rural residents and 10 interviews with a subset of those residents, and from questionnaires returned by 49 SLPs and 4 interviews with a subset of those SLPs. Results show a mismatch between rural residents' and SLPs' access to and attitudes towards use of ICT for speech-language pathology service delivery. Rural residents had better access and more positive attitudes to the use of ICT for speech-language pathology service delivery than expected by SLPs. The results of this study have important implications for education and professional development of SLPs and for research into the use of ICT for telespeech-language pathology.

  17. The importance of interaction in the implementation of information technology in health care: a symbolic interactionism study on the meaning of accessibility.

    Science.gov (United States)

    Nilsson, Lina; Hofflander, Malin; Eriksén, Sara; Borg, Christel

    2012-12-01

    A challenge when groups from different disciplines work together in implementing health information technology (HIT) in a health-care context is that words often have different meanings depending upon work practices, and definition of situations. Accessibility is a word commonly associated with HIT implementation. This study aimed to investigate different meanings of accessibility when implementing HIT in everyday work practice in a health-care context. It focused on the perspective of nurses to highlight another view of the complex relationship between HIT and information in a health-care context. This is a qualitative study influenced by institutional ethnographic. District nurses and student nurses were interviewed. The results indicate that when implementing HIT accessibility depends on working routines, social structures and patient relationship. The findings of the study suggest that interaction needs to take on a more important role when implementing HIT because people act upon words from the interpreted meaning of them. Symbolic interactionism is proposed as a way to set a mutual stage to facilitate an overall understanding of the importance of the meaning of words. There is a need for making place and space for negotiation of the meaning of words when implementing HIT in everyday work practice.

  18. Shared probe design and existing microarray reanalysis using PICKY

    Directory of Open Access Journals (Sweden)

    Chou Hui-Hsien

    2010-04-01

    Full Text Available Abstract Background Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations. Results PICKY 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. PICKY 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, PICKY does not sacrifice the quality of shared probes when choosing them. The latest PICKY 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making PICKY 2.1 more versatile to microarray users. Conclusions Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations.

  19. A Critical Perspective On Microarray Breast Cancer Gene Expression Profiling

    NARCIS (Netherlands)

    Sontrop, H.M.J.

    2015-01-01

    Microarrays offer biologists an exciting tool that allows the simultaneous assessment of gene expression levels for thousands of genes at once. At the time of their inception, microarrays were hailed as the new dawn in cancer biology and oncology practice with the hope that within a decade diseases

  20. Uses of Dendrimers for DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Jean-Pierre Majoral

    2006-08-01

    Full Text Available Biosensors such as DNA microarrays and microchips are gaining an increasingimportance in medicinal, forensic, and environmental analyses. Such devices are based onthe detection of supramolecular interactions called hybridizations that occur betweencomplementary oligonucleotides, one linked to a solid surface (the probe, and the other oneto be analyzed (the target. This paper focuses on the improvements that hyperbranched andperfectly defined nanomolecules called dendrimers can provide to this methodology. Twomain uses of dendrimers for such purpose have been described up to now; either thedendrimer is used as linker between the solid surface and the probe oligonucleotide, or thedendrimer is used as a multilabeled entity linked to the target oligonucleotide. In the firstcase the dendrimer generally induces a higher loading of probes and an easier hybridization,due to moving away the solid phase. In the second case the high number of localized labels(generally fluorescent induces an increased sensitivity, allowing the detection of smallquantities of biological entities.

  1. Using Palm Technology in Participatory Simulations of Complex Systems: A New Take on Ubiquitous and Accessible Mobile Computing

    Science.gov (United States)

    Klopfer, Eric; Yoon, Susan; Perry, Judy

    2005-09-01

    This paper reports on teachers' perceptions of the educational affordances of a handheld application called Participatory Simulations. It presents evidence from five cases representing each of the populations who work with these computational tools. Evidence across multiple data sources yield similar results to previous research evaluations of handheld activities with respect to enhancing motivation, engagement and self-directed learning. Three additional themes are discussed that provide insight into understanding curricular applicability of Participatory Simulations that suggest a new take on ubiquitous and accessible mobile computing. These themes generally point to the multiple layers of social and cognitive flexibility intrinsic to their design: ease of adaptation to subject-matter content knowledge and curricular integration; facility in attending to teacher-individualized goals; and encouraging the adoption of learner-centered strategies.

  2. Lipid Microarray Biosensor for Biotoxin Detection.

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Anup K.; Throckmorton, Daniel J.; Moran-Mirabal, Jose C.; Edel, Joshua B.; Meyer, Grant D.; Craighead, Harold G.

    2006-05-01

    We present the use of micron-sized lipid domains, patterned onto planar substrates and within microfluidic channels, to assay the binding of bacterial toxins via total internal reflection fluorescence microscopy (TIRFM). The lipid domains were patterned using a polymer lift-off technique and consisted of ganglioside-populated DSPC:cholesterol supported lipid bilayers (SLBs). Lipid patterns were formed on the substrates by vesicle fusion followed by polymer lift-off, which revealed micron-sized SLBs containing either ganglioside GT1b or GM1. The ganglioside-populated SLB arrays were then exposed to either Cholera toxin subunit B (CTB) or Tetanus toxin fragment C (TTC). Binding was assayed on planar substrates by TIRFM down to 1 nM concentration for CTB and 100 nM for TTC. Apparent binding constants extracted from three different models applied to the binding curves suggest that binding of a protein to a lipid-based receptor is strongly affected by the lipid composition of the SLB and by the substrate on which the bilayer is formed. Patterning of SLBs inside microfluidic channels also allowed the preparation of lipid domains with different compositions on a single device. Arrays within microfluidic channels were used to achieve segregation and selective binding from a binary mixture of the toxin fragments in one device. The binding and segregation within the microfluidic channels was assayed with epifluorescence as proof of concept. We propose that the method used for patterning the lipid microarrays on planar substrates and within microfluidic channels can be easily adapted to proteins or nucleic acids and can be used for biosensor applications and cell stimulation assays under different flow conditions. KEYWORDS. Microarray, ganglioside, polymer lift-off, cholera toxin, tetanus toxin, TIRFM, binding constant.4

  3. Versatile High Resolution Oligosaccharide Microarrays for Plant Glycobiology and Cell Wall Research

    DEFF Research Database (Denmark)

    Pedersen, Henriette Lodberg; Fangel, Jonatan Ulrik; McCleary, Barry

    2012-01-01

    Microarrays are powerful tools for high throughput analysis, and hundreds or thousands of molecular interactions can be assessed simultaneously using very small amounts of analytes. Nucleotide microarrays are well established in plant research, but carbohydrate microarrays are much less establish...

  4. A cell spot microarray method for production of high density siRNA transfection microarrays

    Directory of Open Access Journals (Sweden)

    Mpindi John-Patrick

    2011-03-01

    Full Text Available Abstract Background High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible. Results Here, we describe the optimization of a miniaturized cell spot microarray (CSMA method, which facilitates utilization of the transfection microarray technique for disparate RNAi analyses. To promote rapid adaptation of the method, the concept has been tested with a panel of 92 adherent cell types, including primary human cells. We demonstrate the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells. Conclusions The CSMA method facilitates reproducible preparation of highly parallel cell microarrays for large-scale gene knockdown analyses. This will be critical towards expanding the cell based functional genetic screens to include more RNAi constructs, allow combinatorial RNAi analyses, multi-parametric phenotypic readouts or comparative analysis of many different cell types.

  5. Accessing physical activity among young adults attending a university: the role of sex, race/ethnicity, technology use, and sleep.

    Science.gov (United States)

    Towne, Samuel D; Ory, Marcia G; Smith, Matthew Lee; Peres, S Camille; Pickens, Adam W; Mehta, Ranjana K; Benden, Mark

    2017-09-18

    Identifying factors associated with recommended physical activity (PA) levels are critical in efforts to combat the obesity epidemic and related comorbidities. We conducted cross-sectional analyses of college students (n = 490) enrolled in a large southern state university in October of 2014. Our aim was to identify sociodemographic characteristics, technology use, and sleep patterns among college students and their independent relationship to recommended PA. An online survey was sent to all enrolled students. Logistic regression predicted achieving recommended ≥150 min per week of moderate-vigorous PA (MVPA) versus not (≤149 min MVPA). Approximately 69% of study participants were males, 18% were Hispanic, and more than half (60%) were within the normal body mass index (12% were obese). The average age of students was 21 years. On a daily average, individuals used smartphones most often (nearly 4.4 h), followed by laptops at 4.0 h, desktops at 1.2 h, and tablets at 0.6 h. The mean number of hours individuals reported sleeping was 6.7. Sociodemographic factors associated with reporting ≥150 min of MVPA included being male (OR = 4.0, 95% CI 2.2-7.1) versus female, being non-Hispanic White (OR = 1.8, CI 1.1-3.2) versus being a member of minority race group. Behavioral factors associated with reporting ≥150 min of MVPA included technology use (being moderate-heavy (OR = 2.3, CI 1.1-4.8) or heavy (OR = 3.4, CI 1.6-7.5) users of technology), and receiving low-moderate (OR = 1.9, 1.01-3.7) levels of sleep versus the lowest level of sleep. In the current study, minority status and being female were the strongest sociodemographic factors associated with inadequate PA levels, while high technology use (primarily driven by smartphone use) were associated with recommended PA levels. Identifying factors associated with being physically active will allow for targeted interventions to improve the health of young adults.

  6. Migration to Broadband and Ubiquitous Environments by Using Fiber-Optic Technologies in Access/Home Areas

    Science.gov (United States)

    Oguchi, Kimio

    2016-03-01

    The recent dramatic advances in information and communication technologies have yielded new environments. However, adoption still differs area by area. To realize the future broadband environment that everyone can enjoy everywhere, several technical issues have to be resolved before network penetration becomes ubiquitous. One such key is the use of fiber optics for the home and mobile services. This article overviews initial observations drawn from numerical survey data gathered over the last decade in several countries/regions, and gives some example scenarios for network/service evolution. One result implies that implementing new/future services must consider the gross domestic product impact.

  7. Accessing physical activity among young adults attending a university: the role of sex, race/ethnicity, technology use, and sleep

    Directory of Open Access Journals (Sweden)

    Samuel D. Towne

    2017-09-01

    Full Text Available Abstract Background Identifying factors associated with recommended physical activity (PA levels are critical in efforts to combat the obesity epidemic and related comorbidities. Methods We conducted cross-sectional analyses of college students (n = 490 enrolled in a large southern state university in October of 2014. Our aim was to identify sociodemographic characteristics, technology use, and sleep patterns among college students and their independent relationship to recommended PA. An online survey was sent to all enrolled students. Logistic regression predicted achieving recommended ≥150 min per week of moderate-vigorous PA (MVPA versus not (≤149 min MVPA. Results Approximately 69% of study participants were males, 18% were Hispanic, and more than half (60% were within the normal body mass index (12% were obese. The average age of students was 21 years. On a daily average, individuals used smartphones most often (nearly 4.4 h, followed by laptops at 4.0 h, desktops at 1.2 h, and tablets at 0.6 h. The mean number of hours individuals reported sleeping was 6.7. Sociodemographic factors associated with reporting ≥150 min of MVPA included being male (OR = 4.0, 95% CI 2.2–7.1 versus female, being non-Hispanic White (OR = 1.8, CI 1.1–3.2 versus being a member of minority race group. Behavioral factors associated with reporting ≥150 min of MVPA included technology use (being moderate-heavy (OR = 2.3, CI 1.1–4.8 or heavy (OR = 3.4, CI 1.6–7.5 users of technology, and receiving low-moderate (OR = 1.9, 1.01–3.7 levels of sleep versus the lowest level of sleep. Conclusions In the current study, minority status and being female were the strongest sociodemographic factors associated with inadequate PA levels, while high technology use (primarily driven by smartphone use were associated with recommended PA levels. Identifying factors associated with being physically active will allow for targeted interventions to

  8. Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization.

    Science.gov (United States)

    Girard, Laurie D; Boissinot, Karel; Peytavi, Régis; Boissinot, Maurice; Bergeron, Michel G

    2015-02-07

    The combination of molecular diagnostic technologies is increasingly used to overcome limitations on sensitivity, specificity or multiplexing capabilities, and provide efficient lab-on-chip devices. Two such techniques, PCR amplification and microarray hybridization are used serially to take advantage of the high sensitivity and specificity of the former combined with high multiplexing capacities of the latter. These methods are usually performed in different buffers and reaction chambers. However, these elaborate methods have high complexity and cost related to reagent requirements, liquid storage and the number of reaction chambers to integrate into automated devices. Furthermore, microarray hybridizations have a sequence dependent efficiency not always predictable. In this work, we have developed the concept of a structured oligonucleotide probe which is activated by cleavage from polymerase exonuclease activity. This technology is called SCISSOHR for Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction. The SCISSOHR probes enable indexing the target sequence to a tag sequence. The SCISSOHR technology also allows the combination of nucleic acid amplification and microarray hybridization in a single vessel in presence of the PCR buffer only. The SCISSOHR technology uses an amplification probe that is irreversibly modified in presence of the target, releasing a single-stranded DNA tag for microarray hybridization. Each tag is composed of a 3-nucleotide sequence-dependent segment and a unique "target sequence-independent" 14-nucleotide segment allowing for optimal hybridization with minimal cross-hybridization. We evaluated the performance of five (5) PCR buffers to support microarray hybridization, compared to a conventional hybridization buffer. Finally, as a proof of concept, we developed a multiplexed assay for the amplification, detection, and identification of three (3) DNA targets. This new technology will facilitate the design

  9. Selective recognition of DNA from olive leaves and olive oil by PNA and modified-PNA microarrays

    Science.gov (United States)

    Rossi, Stefano; Calabretta, Alessandro; Tedeschi, Tullia; Sforza, Stefano; Arcioni, Sergio; Baldoni, Luciana; Corradini, Roberto; Marchelli, Rosangela

    2012-01-01

    PNA probes for the specific detection of DNA from olive oil samples by microarray technology were developed. The presence of as low as 5% refined hazelnut (Corylus avellana) oil in extra-virgin olive oil (Olea europaea L.) could be detected by using a PNA microarray. A set of two single nucleotide polymorphisms (SNPs) from the Actin gene of Olive was chosen as a model for evaluating the ability of PNA probes for discriminating olive cultivars. Both unmodified and C2-modified PNAs bearing an arginine side-chain were used, the latter showing higher sequence specificity. DNA extracted from leaves of three different cultivars (Ogliarola leccese, Canino and Frantoio) could be easily discriminated using a microarray with unmodified PNA probes, whereas discrimination of DNA from oil samples was more challenging, and could be obtained only by using chiral PNA probes. PMID:22772038

  10. Detecting imbalanced expression of SNP alleles by minisequencing on microarrays

    Directory of Open Access Journals (Sweden)

    Dahlgren Andreas

    2004-10-01

    minisequencing in a microtiter plate format. Conclusions We conclude that microarray based minisequencing is an accurate and accessible tool for multiplexed screening for imbalanced allelic expression in multiple samples and tissues in parallel.

  11. miRNAs modified by dietary lipids in Caco-2 cells. A microarray screening

    Directory of Open Access Journals (Sweden)

    Lidia Daimiel

    2015-09-01

    Full Text Available We performed a screening of miRNAs regulated by dietary lipids in a cellular model of enterocytes, Caco-2 cells. Our aim was to describe new lipid-modified miRNAs with an implication in lipid homeostasis and cardiovascular disease [1,2]. For that purpose, we treated differentiated Caco-2 cells with micelles containing the assayed lipids (cholesterol, conjugated linoleic acid and docosahexaenoic acid and the screening of miRNAs was carried out by microarray using the μParaflo®Microfluidic Biochip Technology of LC Sciences (Huston, TX, USA. Experimental design, microarray description and raw data have been made available in the GEO database with the reference number of GSE59153. Here we described in detail the experimental design and methods used to obtain the relative expression data.

  12. Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays

    Science.gov (United States)

    Jin, Lian-Qun; Li, Jun-Wen; Wang, Sheng-Qi; Chao, Fu-Huan; Wang, Xin-Wei; Yuan, Zheng-Quan

    2005-01-01

    AIM: To detect the common intestinal pathogenic bacteria quickly and accurately. METHODS: A rapid (<3 h) experimental procedure was set up based upon the gene chip technology. Target genes were amplified and hybridized by oligonucleotide microarrays. RESULTS: One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 (96.2%) were identified. CONCLUSION: Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, Proteus sp., Bacillus cereus, Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range, and discrimination power of this assay can be continually improved by adding further oligonucleotides to the arrays without any significant increase of complexity or cost. PMID:16437687

  13. ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development.

    Science.gov (United States)

    Alba, Rob; Fei, Zhangjun; Payton, Paxton; Liu, Yang; Moore, Shanna L; Debbie, Paul; Cohn, Jonathan; D'Ascenzo, Mark; Gordon, Jeffrey S; Rose, Jocelyn K C; Martin, Gregory; Tanksley, Steven D; Bouzayen, Mondher; Jahn, Molly M; Giovannoni, Jim

    2004-09-01

    Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.

  14. Identification of differentially expressed genes in cutaneous squamous cell carcinoma by microarray expression profiling

    Directory of Open Access Journals (Sweden)

    Sterry Wolfram

    2006-08-01

    Full Text Available Abstract Background Carcinogenesis is a multi-step process indicated by several genes up- or down-regulated during tumor progression. This study examined and identified differentially expressed genes in cutaneous squamous cell carcinoma (SCC. Results Three different biopsies of 5 immunosuppressed organ-transplanted recipients each normal skin (all were pooled, actinic keratosis (AK (two were pooled, and invasive SCC and additionally 5 normal skin tissues from immunocompetent patients were analyzed. Thus, total RNA of 15 specimens were used for hybridization with Affymetrix HG-U133A microarray technology containing 22,283 genes. Data analyses were performed by prediction analysis of microarrays using nearest shrunken centroids with the threshold 3.5 and ANOVA analysis was independently performed in order to identify differentially expressed genes (p vs. AK and SCC were observed for 118 genes. Conclusion The majority of identified differentially expressed genes in cutaneous SCC were previously not described.

  15. Integrating Multiple Microarray Data for Cancer Pathway Analysis Using Bootstrapping K-S Test

    Directory of Open Access Journals (Sweden)

    Bing Han

    2009-01-01

    Full Text Available Previous applications of microarray technology for cancer research have mostly focused on identifying genes that are differentially expressed between a particular cancer and normal cells. In a biological system, genes perform different molecular functions and regulate various biological processes via interactions with other genes thus forming a variety of complex networks. Therefore, it is critical to understand the relationship (e.g., interactions between genes across different types of cancer in order to gain insights into the molecular mechanisms of cancer. Here we propose an integrative method based on the bootstrapping Kolmogorov-Smirnov test and a large set of microarray data produced with various types of cancer to discover common molecular changes in cells from normal state to cancerous state. We evaluate our method using three key pathways related to cancer and demonstrate that it is capable of finding meaningful alterations in gene relations.

  16. A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray

    Directory of Open Access Journals (Sweden)

    Fairbanks Benjamin D

    2006-04-01

    Full Text Available Abstract Background DNA microarrays have proven powerful for functional genomics studies. Several technologies exist for the generation of whole-genome arrays. It is well documented that 25mer probes directed against different regions of the same gene produce variable signal intensity values. However, the extent to which this is true for probes of greater length (60mers is not well characterized. Moreover, this information has not previously been reported for whole-genome arrays designed against bacteria, whose genomes may differ substantially in characteristics directly affecting microarray performance. Results We report here an analysis of alternative 60mer probe designs for an in-situ synthesized oligonucleotide array for the GC rich, β-proteobacterium Burkholderia cenocepacia. Probes were designed using the ArrayOligoSel3.5 software package and whole-genome microarrays synthesized by Agilent, Inc. using their in-situ, ink-jet technology platform. We first validated the quality of the microarrays as demonstrated by an average signal to noise ratio of >1000. Next, we determined that the variance of replicate probes (1178 total probes examined of identical sequence was 3.8% whereas the variance of alternative probes (558 total alternative probes examined designs was 9.5%. We determined that depending upon the definition, about 2.4% of replicate and 7.8% of alternative probes produced outlier conclusions. Finally, we determined none of the probe design subscores (GC content, internal repeat, binding energy and self annealment produced by ArrayOligoSel3.5 were predictive or probes that produced outlier signals. Conclusion Our analysis demonstrated that the use of multiple probes per target sequence is not essential for in-situ synthesized 60mer oligonucleotide arrays designed against bacteria. Although probes producing outlier signals were identified, the use of ratios results in less than 10% of such outlier conclusions. We also determined that

  17. Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

    Directory of Open Access Journals (Sweden)

    Thierry-Mieg Danielle

    2009-06-01

    Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

  18. Rapid access to compound libraries through flow technology: fully automated synthesis of a 3-aminoindolizine library via orthogonal diversification.

    Science.gov (United States)

    Lange, Paul P; James, Keith

    2012-10-08

    A novel methodology for the synthesis of druglike heterocycle libraries has been developed through the use of flow reactor technology. The strategy employs orthogonal modification of a heterocyclic core, which is generated in situ, and was used to construct both a 25-membered library of druglike 3-aminoindolizines, and selected examples of a 100-member virtual library. This general protocol allows a broad range of acylation, alkylation and sulfonamidation reactions to be performed in conjunction with a tandem Sonogashira coupling/cycloisomerization sequence. All three synthetic steps were conducted under full automation in the flow reactor, with no handling or isolation of intermediates, to afford the desired products in good yields. This fully automated, multistep flow approach opens the way to highly efficient generation of druglike heterocyclic systems as part of a lead discovery strategy or within a lead optimization program.

  19. Low leakage Ru-strontium titanate-Ru metal-insulator-metal capacitors for sub-20 nm technology node in dynamic random access memory

    Energy Technology Data Exchange (ETDEWEB)

    Popovici, M., E-mail: Mihaela.Ioana.Popovici@imec.be; Swerts, J.; Redolfi, A.; Kaczer, B.; Aoulaiche, M.; Radu, I.; Clima, S.; Everaert, J.-L.; Van Elshocht, S.; Jurczak, M. [Imec, Leuven 3001 (Belgium)

    2014-02-24

    Improved metal-insulator-metal capacitor (MIMCAP) stacks with strontium titanate (STO) as dielectric sandwiched between Ru as top and bottom electrode are shown. The Ru/STO/Ru stack demonstrates clearly its potential to reach sub-20 nm technology nodes for dynamic random access memory. Downscaling of the equivalent oxide thickness, leakage current density (J{sub g}) of the MIMCAPs, and physical thickness of the STO have been realized by control of the Sr/Ti ratio and grain size using a heterogeneous TiO{sub 2}/STO based nanolaminate stack deposition and a two-step crystallization anneal. Replacement of TiN with Ru as both top and bottom electrodes reduces the amount of electrically active defects and is essential to achieve a low leakage current in the MIM capacitor.

  20. Use of computer access technology as an alternative to writing for a pre-school child with athetoid cerebral palsy--a case report.

    Science.gov (United States)

    Dhas, Brightlin Nithis; Samuel, Preethy Sarah; Manigandan, C

    2014-07-01

    The purpose of this study was to demonstrate the use of an outcome-driven model of decision-making in the implementation of computer access technology (CAT) for a pre-school child with athetoid cerebral palsy. The child did not have the fine motor skills required to hold a pencil but had the cognitive abilities to learn to write; therefore, we explored the use of a CAT device to enable written communication. Case study methodology was used to describe the selection process, child-level outcomes, and clinical challenges faced by the therapist in the use of a consortium model that was designed for an outcome-driven model of decision-making. The critical role of an occupational therapist in this process using a family-centered approach is discussed.