High dimensional biological data retrieval optimization with NoSQL technology

PubMed Central

2014-01-01

Background High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data. Results In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB. Conclusions The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART's implementation to a more scalable solution for Big Data. PMID:25435347

How large a training set is needed to develop a classifier for microarray data?

PubMed

Dobbin, Kevin K; Zhao, Yingdong; Simon, Richard M

2008-01-01

A common goal of gene expression microarray studies is the development of a classifier that can be used to divide patients into groups with different prognoses, or with different expected responses to a therapy. These types of classifiers are developed on a training set, which is the set of samples used to train a classifier. The question of how many samples are needed in the training set to produce a good classifier from high-dimensional microarray data is challenging. We present a model-based approach to determining the sample size required to adequately train a classifier. It is shown that sample size can be determined from three quantities: standardized fold change, class prevalence, and number of genes or features on the arrays. Numerous examples and important experimental design issues are discussed. The method is adapted to address ex post facto determination of whether the size of a training set used to develop a classifier was adequate. An interactive web site for performing the sample size calculations is provided. We showed that sample size calculations for classifier development from high-dimensional microarray data are feasible, discussed numerous important considerations, and presented examples.

Finding Groups in Gene Expression Data

PubMed Central

2005-01-01

The vast potential of the genomic insight offered by microarray technologies has led to their widespread use since they were introduced a decade ago. Application areas include gene function discovery, disease diagnosis, and inferring regulatory networks. Microarray experiments enable large-scale, high-throughput investigations of gene activity and have thus provided the data analyst with a distinctive, high-dimensional field of study. Many questions in this field relate to finding subgroups of data profiles which are very similar. A popular type of exploratory tool for finding subgroups is cluster analysis, and many different flavors of algorithms have been used and indeed tailored for microarray data. Cluster analysis, however, implies a partitioning of the entire data set, and this does not always match the objective. Sometimes pattern discovery or bump hunting tools are more appropriate. This paper reviews these various tools for finding interesting subgroups. PMID:16046827

HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data.

PubMed

Trivedi, Prinal; Edwards, Jode W; Wang, Jelai; Gadbury, Gary L; Srinivasasainagendra, Vinodh; Zakharkin, Stanislav O; Kim, Kyoungmi; Mehta, Tapan; Brand, Jacob P L; Patki, Amit; Page, Grier P; Allison, David B

2005-04-06

Many efforts in microarray data analysis are focused on providing tools and methods for the qualitative analysis of microarray data. HDBStat! (High-Dimensional Biology-Statistics) is a software package designed for analysis of high dimensional biology data such as microarray data. It was initially developed for the analysis of microarray gene expression data, but it can also be used for some applications in proteomics and other aspects of genomics. HDBStat! provides statisticians and biologists a flexible and easy-to-use interface to analyze complex microarray data using a variety of methods for data preprocessing, quality control analysis and hypothesis testing. Results generated from data preprocessing methods, quality control analysis and hypothesis testing methods are output in the form of Excel CSV tables, graphs and an Html report summarizing data analysis. HDBStat! is a platform-independent software that is freely available to academic institutions and non-profit organizations. It can be downloaded from our website http://www.soph.uab.edu/ssg_content.asp?id=1164.

Two-Dimensional VO2 Mesoporous Microarrays for High-Performance Supercapacitor

NASA Astrophysics Data System (ADS)

Fan, Yuqi; Ouyang, Delong; Li, Bao-Wen; Dang, Feng; Ren, Zongming

2018-05-01

Two-dimensional (2D) mesoporous VO2 microarrays have been prepared using an organic-inorganic liquid interface. The units of microarrays consist of needle-like VO2 particles with a mesoporous structure, in which crack-like pores with a pore size of about 2 nm and depth of 20-100 nm are distributed on the particle surface. The liquid interface acts as a template for the formation of the 2D microarrays, as identified from the kinetic observation. Due to the mesoporous structure of the units and high conductivity of the microarray, such 2D VO2 microarrays exhibit a high specific capacitance of 265 F/g at 1 A/g and excellent rate capability (182 F/g at 10 A/g) and cycling stability, suggesting the effect of unique microstructure for improving the electrochemical performance.

Employing image processing techniques for cancer detection using microarray images.

PubMed

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.

Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation.

PubMed

Richard, Arianne C; Lyons, Paul A; Peters, James E; Biasci, Daniele; Flint, Shaun M; Lee, James C; McKinney, Eoin F; Siegel, Richard M; Smith, Kenneth G C

2014-08-04

Although numerous investigations have compared gene expression microarray platforms, preprocessing methods and batch correction algorithms using constructed spike-in or dilution datasets, there remains a paucity of studies examining the properties of microarray data using diverse biological samples. Most microarray experiments seek to identify subtle differences between samples with variable background noise, a scenario poorly represented by constructed datasets. Thus, microarray users lack important information regarding the complexities introduced in real-world experimental settings. The recent development of a multiplexed, digital technology for nucleic acid measurement enables counting of individual RNA molecules without amplification and, for the first time, permits such a study. Using a set of human leukocyte subset RNA samples, we compared previously acquired microarray expression values with RNA molecule counts determined by the nCounter Analysis System (NanoString Technologies) in selected genes. We found that gene measurements across samples correlated well between the two platforms, particularly for high-variance genes, while genes deemed unexpressed by the nCounter generally had both low expression and low variance on the microarray. Confirming previous findings from spike-in and dilution datasets, this "gold-standard" comparison demonstrated signal compression that varied dramatically by expression level and, to a lesser extent, by dataset. Most importantly, examination of three different cell types revealed that noise levels differed across tissues. Microarray measurements generally correlate with relative RNA molecule counts within optimal ranges but suffer from expression-dependent accuracy bias and precision that varies across datasets. We urge microarray users to consider expression-level effects in signal interpretation and to evaluate noise properties in each dataset independently.

Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora.

PubMed

Nowrousian, Minou; Ringelberg, Carol; Dunlap, Jay C; Loros, Jennifer J; Kück, Ulrich

2005-04-01

The filamentous fungus Sordaria macrospora forms complex three-dimensional fruiting bodies that protect the developing ascospores and ensure their proper discharge. Several regulatory genes essential for fruiting body development were previously isolated by complementation of the sterile mutants pro1, pro11 and pro22. To establish the genetic relationships between these genes and to identify downstream targets, we have conducted cross-species microarray hybridizations using cDNA arrays derived from the closely related fungus Neurospora crassa and RNA probes prepared from wild-type S. macrospora and the three developmental mutants. Of the 1,420 genes which gave a signal with the probes from all the strains used, 172 (12%) were regulated differently in at least one of the three mutants compared to the wild type, and 17 (1.2%) were regulated differently in all three mutant strains. Microarray data were verified by Northern analysis or quantitative real time PCR. Among the genes that are up- or down-regulated in the mutant strains are genes encoding the pheromone precursors, enzymes involved in melanin biosynthesis and a lectin-like protein. Analysis of gene expression in double mutants revealed a complex network of interaction between the pro gene products.

An Efficient Covalent Coating on Glass Slides for Preparation of Optical Oligonucleotide Microarrays

PubMed Central

Pourjahed, Atefeh; Rabiee, Mohammad; Tahriri, Mohammadreza

2013-01-01

Objective(s): Microarrays are potential analyzing tools for genomics and proteomics researches, which is in needed of suitable substrate for coating and also hybridization of biomolecules. Materials and Methods: In this research, a thin film of oxidized agarose was prepared on the glass slides which previously coated with poly-L-lysine (PLL). Some of the aldehyde groups of the activated agarose linked covalently to PLL amine groups; also bound to the amino groups of biomolecules. These linkages were fixed by UV irradiation. The prepared substrates were compared to only agarose-coated and PLL-coated slides. Results: Results on atomic force microscope (AFM) demonstrated that agarose provided three-dimensional surface which had higher loading and bindig capacity for biomolecules than PLL-coated surface which had two-dimensional surface. In addition, the signal-to-noise ratio in hybridization reactions performed on the agarose-PLL coated substrates increased two fold and four fold compared to agarose and PLL coated substrates, respectively. Conclusion: The agarose-PLL microarrays had the highest signal (2546) and lowest background signal (205) in hybridization, suggesting that the prepared slides are suitable in analyzing wide concentration range of analytes. PMID:24570832

Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization

PubMed Central

Girard, Laurie D.; Boissinot, Karel; Peytavi, Régis; Boissinot, Maurice; Bergeron, Michel G.

2014-01-01

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 a high complexity 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-nucleotidesequence-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 of lab-on-chip microfluidic devices, while also reducing consumable costs. At term, it will allow the cost-effective automation of highly multiplexed assays for detection and identification of genetic targets. PMID:25489607

Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization.

PubMed

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 of lab-on-chip microfluidic devices, while also reducing consumable costs. At term, it will allow the cost-effective automation of highly multiplexed assays for detection and identification of genetic targets.

Implementation of mutual information and bayes theorem for classification microarray data

NASA Astrophysics Data System (ADS)

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%.

Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.

PubMed

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.

cDNA Microarray Screening in Food Safety

PubMed Central

ROY, SASHWATI; SEN, CHANDAN K

2009-01-01

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. PMID:16466843

Quality Inspection and Analysis of Three-Dimensional Geographic Information Model Based on Oblique Photogrammetry

NASA Astrophysics Data System (ADS)

Dong, S.; Yan, Q.; Xu, Y.; Bai, J.

2018-04-01

In order to promote the construction of digital geo-spatial framework in China and accelerate the construction of informatization mapping system, three-dimensional geographic information model emerged. The three-dimensional geographic information model based on oblique photogrammetry technology has higher accuracy, shorter period and lower cost than traditional methods, and can more directly reflect the elevation, position and appearance of the features. At this stage, the technology of producing three-dimensional geographic information models based on oblique photogrammetry technology is rapidly developing. The market demand and model results have been emerged in a large amount, and the related quality inspection needs are also getting larger and larger. Through the study of relevant literature, it is found that there are a lot of researches on the basic principles and technical characteristics of this technology, and relatively few studies on quality inspection and analysis. On the basis of summarizing the basic principle and technical characteristics of oblique photogrammetry technology, this paper introduces the inspection contents and inspection methods of three-dimensional geographic information model based on oblique photogrammetry technology. Combined with the actual inspection work, this paper summarizes the quality problems of three-dimensional geographic information model based on oblique photogrammetry technology, analyzes the causes of the problems and puts forward the quality control measures. It provides technical guidance for the quality inspection of three-dimensional geographic information model data products based on oblique photogrammetry technology in China and provides technical support for the vigorous development of three-dimensional geographic information model based on oblique photogrammetry technology.

Plant-pathogen interactions: what microarray tells about it?

PubMed

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.

[Application Progress of Three-dimensional Laser Scanning Technology in Medical Surface Mapping].

PubMed

Zhang, Yonghong; Hou, He; Han, Yuchuan; Wang, Ning; Zhang, Ying; Zhu, Xianfeng; Wang, Mingshi

2016-04-01

The booming three-dimensional laser scanning technology can efficiently and effectively get spatial three-dimensional coordinates of the detected object surface and reconstruct the image at high speed,high precision and large capacity of information.Non-radiation,non-contact and the ability of visualization make it increasingly popular in three-dimensional surface medical mapping.This paper reviews the applications and developments of three-dimensional laser scanning technology in medical field,especially in stomatology,plastic surgery and orthopedics.Furthermore,the paper also discusses the application prospects in the future as well as the biomedical engineering problems it would encounter with.

Flow-pattern Guided Fabrication of High-density Barcode Antibody Microarray

PubMed Central

Ramirez, Lisa S.; Wang, Jun

2016-01-01

Antibody microarray as a well-developed technology is currently challenged by a few other established or emerging high-throughput technologies. In this report, we renovate the antibody microarray technology by using a novel approach for manufacturing and by introducing new features. The fabrication of our high-density antibody microarray is accomplished through perpendicularly oriented flow-patterning of single stranded DNAs and subsequent conversion mediated by DNA-antibody conjugates. This protocol outlines the critical steps in flow-patterning DNA, producing and purifying DNA-antibody conjugates, and assessing the quality of the fabricated microarray. The uniformity and sensitivity are comparable with conventional microarrays, while our microarray fabrication does not require the assistance of an array printer and can be performed in most research laboratories. The other major advantage is that the size of our microarray units is 10 times smaller than that of printed arrays, offering the unique capability of analyzing functional proteins from single cells when interfacing with generic microchip designs. This barcode technology can be widely employed in biomarker detection, cell signaling studies, tissue engineering, and a variety of clinical applications. PMID:26780370

A perspective on microarrays: current applications, pitfalls, and potential uses

PubMed Central

Jaluria, Pratik; Konstantopoulos, Konstantinos; Betenbaugh, Michael; Shiloach, Joseph

2007-01-01

With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. Collectively, the information included in this text will highlight the versatility of microarray technology and provide a glimpse of what the future may hold. PMID:17254338

The application of DNA microarrays in gene expression analysis.

PubMed

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.

Downregulation of Connective Tissue Growth Factor by Three-Dimensional Matrix Enhances Ovarian Carcinoma Cell Invasion

PubMed Central

Barbolina, Maria V.; Adley, Brian P.; Kelly, David L.; Shepard, Jaclyn; Fought, Angela J.; Scholtens, Denise; Penzes, Peter; Shea, Lonnie D.; Sharon Stack, M

2010-01-01

Epithelial ovarian carcinoma (EOC) is a leading cause of death from gynecologic malignancy, due mainly to the prevalence of undetected metastatic disease. The process of cell invasion during intra-peritoneal anchoring of metastatic lesions requires concerted regulation of many processes, including modulation of adhesion to the extracellular matrix and localized invasion. Exploratory cDNA microarray analysis of early response genes (altered after 4 hours of 3-dimensional collagen culture) coupled with confirmatory real-time RT-PCR, multiple three-dimensional cell culture matrices, Western blot, immunostaining, adhesion, migration, and invasion assays were used to identify modulators of adhesion pertinent to EOC progression and metastasis. cDNA microarray analysis indicated a dramatic downregulation of connective tissue growth factor (CTGF) in EOC cells placed in invasion-mimicking conditions (3-dimensional type I collagen). Examination of human EOC specimens revealed that CTGF expression was absent in 46% of the tested samples (n=41), but was present in 100% of normal ovarian epithelium samples (n=7). Reduced CTGF expression occurs in many types of cells and may be a general phenomenon displayed by cells encountering a 3D environment. CTGF levels were inversely correlated with invasion such that downregulation of CTGF increased, while its upregulation reduced, collagen invasion. Cells adhered preferentially to a surface comprised of both collagen I and CTGF relative to either component alone using α6β1 and α3β1 integrins. Together these data suggest that downregulation of CTGF in EOC cells may be important for cell invasion through modulation of cell-matrix adhesion. PMID:19382180

A three-dimensional laser vibration measurement technology realized on five laser beam and its calibration

NASA Astrophysics Data System (ADS)

Li, Lu-Ke; Zhang, Shen-Feng

2018-03-01

Put forward a kind of three-dimensional vibration information technology of vibrating object by the mean of five laser beam of He-Ne laser, and with the help of three-way sensor, measure the three-dimensional laser vibration developed by above mentioned technology. The technology based on the Doppler principle of interference and signal demodulation technology, get the vibration information of the object, through the algorithm processing, extract the three-dimensional vibration information of space objects, and can achieve the function of angle calibration of five beam in the space, which avoid the effects of the mechanical installation error, greatly improve the accuracy of measurement. With the help of a & B K4527 contact three axis sensor, measure and calibrate three-dimensional laser vibrometer, which ensure the accuracy of the measurement data. Summarize the advantages and disadvantages of contact and non-contact sensor, and analysis the future development trends of the sensor industry.

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

EPA Science Inventory

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...

Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology

PubMed Central

Sato, Fumiaki; Tsuchiya, Soken; Terasawa, Kazuya; Tsujimoto, Gozoh

2009-01-01

Over the last decade, DNA microarray technology has provided a great contribution to the life sciences. The MicroArray Quality Control (MAQC) project demonstrated the way to analyze the expression microarray. Recently, microarray technology has been utilized to analyze a comprehensive microRNA expression profiling. Currently, several platforms of microRNA microarray chips are commercially available. Thus, we compared repeatability and comparability of five different microRNA microarray platforms (Agilent, Ambion, Exiqon, Invitrogen and Toray) using 309 microRNAs probes, and the Taqman microRNA system using 142 microRNA probes. This study demonstrated that microRNA microarray has high intra-platform repeatability and comparability to quantitative RT-PCR of microRNA. Among the five platforms, Agilent and Toray array showed relatively better performances than the others. However, the current lineup of commercially available microRNA microarray systems fails to show good inter-platform concordance, probably because of lack of an adequate normalization method and severe divergence in stringency of detection call criteria between different platforms. This study provided the basic information about the performance and the problems specific to the current microRNA microarray systems. PMID:19436744

High-Density Droplet Microarray of Individually Addressable Electrochemical Cells.

PubMed

Zhang, Huijie; Oellers, Tobias; Feng, Wenqian; Abdulazim, Tarik; Saw, En Ning; Ludwig, Alfred; Levkin, Pavel A; Plumeré, Nicolas

2017-06-06

Microarray technology has shown great potential for various types of high-throughput screening applications. The main read-out methods of most microarray platforms, however, are based on optical techniques, limiting the scope of potential applications of such powerful screening technology. Electrochemical methods possess numerous complementary advantages over optical detection methods, including its label-free nature, capability of quantitative monitoring of various reporter molecules, and the ability to not only detect but also address compositions of individual compartments. However, application of electrochemical methods for the purpose of high-throughput screening remains very limited. In this work, we develop a high-density individually addressable electrochemical droplet microarray (eDMA). The eDMA allows for the detection of redox-active reporter molecules irrespective of their electrochemical reversibility in individual nanoliter-sized droplets. Orthogonal band microelectrodes are arranged to form at their intersections an array of three-electrode systems for precise control of the applied potential, which enables direct read-out of the current related to analyte detection. The band microelectrode array is covered with a layer of permeable porous polymethacrylate functionalized with a highly hydrophobic-hydrophilic pattern, forming spatially separated nanoliter-sized droplets on top of each electrochemical cell. Electrochemical characterization of single droplets demonstrates that the underlying electrode system is accessible to redox-active molecules through the hydrophilic polymeric pattern and that the nonwettable hydrophobic boundaries can spatially separate neighboring cells effectively. The eDMA technology opens the possibility to combine the high-throughput biochemical or living cell screenings using the droplet microarray platform with the sequential electrochemical read-out of individual droplets.

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

PubMed

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.

Selective recognition of DNA from olive leaves and olive oil by PNA and modified-PNA microarrays

PubMed Central

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

The Evolution of Photography and Three-Dimensional Imaging in Plastic Surgery.

PubMed

Weissler, Jason M; Stern, Carrie S; Schreiber, Jillian E; Amirlak, Bardia; Tepper, Oren M

2017-03-01

Throughout history, the technological advancements of conventional clinical photography in plastic surgery have not only refined the methods available to the plastic surgeon, but have invigorated the profession through technology. The technology of the once traditional two-dimensional photograph has since been revolutionized and refashioned to incorporate novel applications, which have since become the standard in clinical photography. Contrary to traditional standardized two-dimensional photographs, three-dimensional photography provides the surgeon with an invaluable volumetric and morphologic analysis by demonstrating true surface dimensions both preoperatively and postoperatively. Clinical photography has served as one of the fundamental objective means by which plastic surgeons review outcomes; however, the newer three-dimensional technology has been primarily used to enhance the preoperative consultation with surgical simulations. The authors intend to familiarize readers with the notion that three-dimensional photography extends well beyond its marketing application during surgical consultation. For the cosmetic surgeon, as the application of three-dimensional photography continues to mature in facial plastic surgery, it will continue to bypass the dated conventional photographic methods plastic surgeons once relied on. This article reviews a paradigm shift and provides a historical review of the fascinating evolution of photography in plastic surgery by highlighting the clinical utility of three-dimensional photography as an adjunct to plastic and reconstructive surgery practices. As three-dimensional photographic technology continues to evolve, its application in facial plastic surgery will provide an opportunity for a new objective standard in plastic surgery.

Microarray platform for omics analysis

NASA Astrophysics Data System (ADS)

Mecklenburg, Michael; Xie, Bin

2001-09-01

Microarray technology has revolutionized genetic analysis. However, limitations in genome analysis has lead to renewed interest in establishing 'omic' strategies. As we enter the post-genomic era, new microarray technologies are needed to address these new classes of 'omic' targets, such as proteins, as well as lipids and carbohydrates. We have developed a microarray platform that combines self- assembling monolayers with the biotin-streptavidin system to provide a robust, versatile immobilization scheme. A hydrophobic film is patterned on the surface creating an array of tension wells that eliminates evaporation effects thereby reducing the shear stress to which biomolecules are exposed to during immobilization. The streptavidin linker layer makes it possible to adapt and/or develop microarray based assays using virtually any class of biomolecules including: carbohydrates, peptides, antibodies, receptors, as well as them ore traditional DNA based arrays. Our microarray technology is designed to furnish seamless compatibility across the various 'omic' platforms by providing a common blueprint for fabricating and analyzing arrays. The prototype microarray uses a microscope slide footprint patterned with 2 by 96 flat wells. Data on the microarray platform will be presented.

Emergent FDA biodefense issues for microarray technology: process analytical technology.

PubMed

Weinberg, Sandy

2004-11-01

A successful biodefense strategy relies upon any combination of four approaches. A nation can protect its troops and citizenry first by advanced mass vaccination, second, by responsive ring vaccination, and third, by post-exposure therapeutic treatment (including vaccine therapies). Finally, protection can be achieved by rapid detection followed by exposure limitation (suites and air filters) or immediate treatment (e.g., antibiotics, rapid vaccines and iodine pills). All of these strategies rely upon or are enhanced by microarray technologies. Microarrays can be used to screen, engineer and test vaccines. They are also used to construct early detection tools. While effective biodefense utilizes a variety of tactical tools, microarray technology is a valuable arrow in that quiver.

MICROARRAY QUALITY CONTROL PROJECT: A COMPREHENSIVE GENE EXPRESSION TECHNOLOGY SURVEY DEMONSTRATES MEASURABLE CONSISTENCY AND CONCORDANT RESULTS BETWEEN PLATFORMS

EPA Science Inventory

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, h...

Progress in the application of DNA microarrays.

PubMed Central

Lobenhofer, E K; Bushel, P R; Afshari, C A; Hamadeh, H K

2001-01-01

Microarray technology has been applied to a variety of different fields to address fundamental research questions. The use of microarrays, or DNA chips, to study the gene expression profiles of biologic samples began in 1995. Since that time, the fundamental concepts behind the chip, the technology required for making and using these chips, and the multitude of statistical tools for analyzing the data have been extensively reviewed. For this reason, the focus of this review will be not on the technology itself but on the application of microarrays as a research tool and the future challenges of the field. PMID:11673116

Three-dimensional imaging technology offers promise in medicine.

PubMed

Karako, Kenji; Wu, Qiong; Gao, Jianjun

2014-04-01

Medical imaging plays an increasingly important role in the diagnosis and treatment of disease. Currently, medical equipment mainly has two-dimensional (2D) imaging systems. Although this conventional imaging largely satisfies clinical requirements, it cannot depict pathologic changes in 3 dimensions. The development of three-dimensional (3D) imaging technology has encouraged advances in medical imaging. Three-dimensional imaging technology offers doctors much more information on a pathology than 2D imaging, thus significantly improving diagnostic capability and the quality of treatment. Moreover, the combination of 3D imaging with augmented reality significantly improves surgical navigation process. The advantages of 3D imaging technology have made it an important component of technological progress in the field of medical imaging.

Generation of Viable Cell and Biomaterial Patterns by Laser Transfer

NASA Astrophysics Data System (ADS)

Ringeisen, Bradley

2001-03-01

In order to fabricate and interface biological systems for next generation applications such as biosensors, protein recognition microarrays, and engineered tissues, it is imperative to have a method of accurately and rapidly depositing different active biomaterials in patterns or layered structures. Ideally, the biomaterial structures would also be compatible with many different substrates including technologically relevant platforms such as electronic circuits or various detection devices. We have developed a novel laser-based technique, termed matrix assisted pulsed laser evaporation direct write (MAPLE DW), that is able to direct write patterns and three-dimensional structures of numerous biologically active species ranging from proteins and antibodies to living cells. Specifically, we have shown that MAPLE DW is capable of forming mesoscopic patterns of living prokaryotic cells (E. coli bacteria), living mammalian cells (Chinese hamster ovaries), active proteins (biotinylated bovine serum albumin, horse radish peroxidase), and antibodies specific to a variety of classes of cancer related proteins including intracellular and extracellular matrix proteins, signaling proteins, cell cycle proteins, growth factors, and growth factor receptors. In addition, patterns of viable cells and active biomolecules were deposited on different substrates including metals, semiconductors, nutrient agar, and functionalized glass slides. We will present an explanation of the laser-based transfer mechanism as well as results from our recent efforts to fabricate protein recognition microarrays and tissue-based microfluidic networks.

Bioinformatics/biostatistics: microarray analysis.

PubMed

Eichler, Gabriel S

2012-01-01

The quantity and complexity of the molecular-level data generated in both research and clinical settings require the use of sophisticated, powerful computational interpretation techniques. It is for this reason that bioinformatic analysis of complex molecular profiling data has become a fundamental technology in the development of personalized medicine. This chapter provides a high-level overview of the field of bioinformatics and outlines several, classic bioinformatic approaches. The highlighted approaches can be aptly applied to nearly any sort of high-dimensional genomic, proteomic, or metabolomic experiments. Reviewed technologies in this chapter include traditional clustering analysis, the Gene Expression Dynamics Inspector (GEDI), GoMiner (GoMiner), Gene Set Enrichment Analysis (GSEA), and the Learner of Functional Enrichment (LeFE).

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

PubMed Central

Holloway, Andrew J; Oshlack, Alicia; Diyagama, Dileepa S; Bowtell, David DL; Smyth, Gordon K

2006-01-01

Background Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis. Results A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays. The method consists of an easy-to-construct titration series of RNA samples and an associated statistical analysis using non-linear regression. The method evaluates the precision and responsiveness of each microarray platform on a whole-array basis, i.e., using all the probes, without the need to match probes across platforms. An experiment is conducted to assess and compare four widely used microarray platforms. All four platforms are shown to have satisfactory precision but the commercial platforms are superior for resolving differential expression for genes at lower expression levels. The effective precision of the two-color platforms is improved by allowing for probe-specific dye-effects in the statistical model. The methodology is used to compare three data extraction algorithms for the Affymetrix platforms, demonstrating poor performance for the commonly used proprietary algorithm relative to the other algorithms. For probes which can be matched across platforms, the cross-platform variability is decomposed into within-platform and between-platform components, showing that platform disagreement is almost entirely systematic rather than due to measurement variability. Conclusion The results demonstrate good precision and sensitivity for all the platforms, but highlight the need for improved probe annotation. They quantify the extent to which cross-platform measures can be expected to be less accurate than within-platform comparisons for predicting disease progression or outcome. PMID:17118209

2008 Microarray Research Group (MARG Survey): Sensing the State of Microarray Technology

EPA Science Inventory

Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution and transformation, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. Th...

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

PubMed

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.

[Advances in the research of application of collagen in three-dimensional bioprinting].

PubMed

Li, H H; Luo, P F; Sheng, J J; Liu, G C; Zhu, S H

2016-10-20

As a new industrial technology with characteristics of high precision and accuracy, the application of three-dimensional bioprinting technology is increasingly wide in the field of medical research. Collagen is one of the most common ingredients in tissue, and it has good biological material properties. There are many reports of using collagen as main composition of " ink" of three-dimensional bioprinting technology. However, the applied collagen is mainly from heterogeneous sources, which may cause some problems in application. Recombinant human source collagen can be obtained from microorganism fermentation by transgenic technology, but more research should be done to confirm its property. This article reviews the advances in the research of collagen and its biological application in three-dimensional bioprinting.

Prediction of metabolism-induced hepatotoxicity on three-dimensional hepatic cell culture and enzyme microarrays.

PubMed

Yu, Kyeong-Nam; Nadanaciva, Sashi; Rana, Payal; Lee, Dong Woo; Ku, Bosung; Roth, Alexander D; Dordick, Jonathan S; Will, Yvonne; Lee, Moo-Yeal

2018-03-01

Human liver contains various oxidative and conjugative enzymes that can convert nontoxic parent compounds to toxic metabolites or, conversely, toxic parent compounds to nontoxic metabolites. Unlike primary hepatocytes, which contain myriad drug-metabolizing enzymes (DMEs), but are difficult to culture and maintain physiological levels of DMEs, immortalized hepatic cell lines used in predictive toxicity assays are easy to culture, but lack the ability to metabolize compounds. To address this limitation and predict metabolism-induced hepatotoxicity in high-throughput, we developed an advanced miniaturized three-dimensional (3D) cell culture array (DataChip 2.0) and an advanced metabolizing enzyme microarray (MetaChip 2.0). The DataChip is a functionalized micropillar chip that supports the Hep3B human hepatoma cell line in a 3D microarray format. The MetaChip is a microwell chip containing immobilized DMEs found in the human liver. As a proof of concept for generating compound metabolites in situ on the chip and rapidly assessing their toxicity, 22 model compounds were dispensed into the MetaChip and sandwiched with the DataChip. The IC 50 values obtained from the chip platform were correlated with rat LD 50 values, human C max values, and drug-induced liver injury categories to predict adverse drug reactions in vivo. As a result, the platform had 100% sensitivity, 86% specificity, and 93% overall predictivity at optimum cutoffs of IC 50 and C max values. Therefore, the DataChip/MetaChip platform could be used as a high-throughput, early stage, microscale alternative to conventional in vitro multi-well plate platforms and provide a rapid and inexpensive assessment of metabolism-induced toxicity at early phases of drug development.

Korean, Japanese, and Chinese populations featured similar genes encoding drug-metabolizing enzymes and transporters: a DMET Plus microarray assessment.

PubMed

Yi, SoJeong; An, Hyungmi; Lee, Howard; Lee, Sangin; Ieiri, Ichiro; Lee, Youngjo; Cho, Joo-Youn; Hirota, Takeshi; Fukae, Masato; Yoshida, Kenji; Nagatsuka, Shinichiro; Kimura, Miyuki; Irie, Shin; Sugiyama, Yuichi; Shin, Dong Wan; Lim, Kyoung Soo; Chung, Jae-Yong; Yu, Kyung-Sang; Jang, In-Jin

2014-10-01

Interethnic differences in genetic polymorphism in genes encoding drug-metabolizing enzymes and transporters are one of the major factors that cause ethnic differences in drug response. This study aimed to investigate genetic polymorphisms in genes involved in drug metabolism, transport, and excretion among Korean, Japanese, and Chinese populations, the three major East Asian ethnic groups. The frequencies of 1936 variants representing 225 genes encoding drug-metabolizing enzymes and transporters were determined from 786 healthy participants (448 Korean, 208 Japanese, and 130 Chinese) using the Affymetrix Drug-Metabolizing Enzymes and Transporters Plus microarray. To compare allele or genotype frequencies in the high-dimensional data among the three East Asian ethnic groups, multiple testing, principal component analysis (PCA), and regularized multinomial logit model through least absolute shrinkage and selection operator were used. On microarray analysis, 1071 of 1936 variants (>50% of markers) were found to be monomorphic. In a large number of genetic variants, the fixation index and Pearson's correlation coefficient of minor allele frequencies were less than 0.034 and greater than 0.95, respectively, among the three ethnic groups. PCA identified 47 genetic variants with multiple testing, but was unable to discriminate ethnic groups by the first three components. Multinomial least absolute shrinkage and selection operator analysis identified 269 genetic variants that showed different frequencies among the three ethnic groups. However, none of those variants distinguished between the three ethnic groups during subsequent PCA. Korean, Japanese, and Chinese populations are not pharmacogenetically distant from one another, at least with regard to drug disposition, metabolism, and elimination.

Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species.

PubMed

Vallée, Maud; Gravel, Catherine; Palin, Marie-France; Reghenas, Hélène; Stothard, Paul; Wishart, David S; Sirard, Marc-André

2005-07-01

The main objective of the present study was to identify novel oocyte-specific genes in three different species: bovine, mouse, and Xenopus laevis. To achieve this goal, two powerful technologies were combined: a polymerase chain reaction (PCR)-based cDNA subtraction, and cDNA microarrays. Three subtractive libraries consisting of 3456 clones were established and enriched for oocyte-specific transcripts. Sequencing analysis of the positive insert-containing clones resulted in the following classification: 53% of the clones corresponded to known cDNAs, 26% were classified as uncharacterized cDNAs, and a final 9% were classified as novel sequences. All these clones were used for cDNA microarray preparation. Results from these microarray analyses revealed that in addition to already known oocyte-specific genes, such as GDF9, BMP15, and ZP, known genes with unknown function in the oocyte were identified, such as a MLF1-interacting protein (MLF1IP), B-cell translocation gene 4 (BTG4), and phosphotyrosine-binding protein (xPTB). Furthermore, 15 novel oocyte-specific genes were validated by reverse transcription-PCR to confirm their preferential expression in the oocyte compared to somatic tissues. The results obtained in the present study confirmed that microarray analysis is a robust technique to identify true positives from the suppressive subtractive hybridization experiment. Furthermore, obtaining oocyte-specific genes from three species simultaneously allowed us to look at important genes that are conserved across species. Further characterization of these novel oocyte-specific genes will lead to a better understanding of the molecular mechanisms related to the unique functions found in the oocyte.

Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds.

PubMed

Gong, Ping; Nan, Xiaofei; Barker, Natalie D; Boyd, Robert E; Chen, Yixin; Wilkins, Dawn E; Johnson, David R; Suedel, Burton C; Perkins, Edward J

2016-03-08

Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regression modeling for predicting bioavailability (tissue residue) of explosives compounds in exposed earthworms. In the present study, we further compared 18 different regression models and performed variable selection simultaneously with parameter estimation. This refined approach was applied to both previously collected and newly acquired earthworm microarray gene expression datasets for three explosive compounds. Our results demonstrate that a prediction accuracy of R(2) = 0.71-0.82 was achievable at a relatively low model complexity with as few as 3-10 predictor genes per model. These results are much more encouraging than our previous ones. This study has demonstrated that our approach is promising for bioavailability measurement, which warrants further studies of mixed contamination scenarios in field settings.

The future of microarray technology: networking the genome search.

PubMed

D'Ambrosio, C; Gatta, L; Bonini, S

2005-10-01

In recent years microarray technology has been increasingly used in both basic and clinical research, providing substantial information for a better understanding of genome-environment interactions responsible for diseases, as well as for their diagnosis and treatment. However, in genomic research using microarray technology there are several unresolved issues, including scientific, ethical and legal issues. Networks of excellence like GA(2)LEN may represent the best approach for teaching, cost reduction, data repositories, and functional studies implementation.

DNA Microarray Technology

MedlinePlus

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 ...

An integrated approach for identifying wrongly labelled samples when performing classification in microarray data.

PubMed

Leung, Yuk Yee; Chang, Chun Qi; Hung, Yeung Sam

2012-01-01

Using hybrid approach for gene selection and classification is common as results obtained are generally better than performing the two tasks independently. Yet, for some microarray datasets, both classification accuracy and stability of gene sets obtained still have rooms for improvement. This may be due to the presence of samples with wrong class labels (i.e. outliers). Outlier detection algorithms proposed so far are either not suitable for microarray data, or only solve the outlier detection problem on their own. We tackle the outlier detection problem based on a previously proposed Multiple-Filter-Multiple-Wrapper (MFMW) model, which was demonstrated to yield promising results when compared to other hybrid approaches (Leung and Hung, 2010). To incorporate outlier detection and overcome limitations of the existing MFMW model, three new features are introduced in our proposed MFMW-outlier approach: 1) an unbiased external Leave-One-Out Cross-Validation framework is developed to replace internal cross-validation in the previous MFMW model; 2) wrongly labeled samples are identified within the MFMW-outlier model; and 3) a stable set of genes is selected using an L1-norm SVM that removes any redundant genes present. Six binary-class microarray datasets were tested. Comparing with outlier detection studies on the same datasets, MFMW-outlier could detect all the outliers found in the original paper (for which the data was provided for analysis), and the genes selected after outlier removal were proven to have biological relevance. We also compared MFMW-outlier with PRAPIV (Zhang et al., 2006) based on same synthetic datasets. MFMW-outlier gave better average precision and recall values on three different settings. Lastly, artificially flipped microarray datasets were created by removing our detected outliers and flipping some of the remaining samples' labels. Almost all the 'wrong' (artificially flipped) samples were detected, suggesting that MFMW-outlier was sufficiently powerful to detect outliers in high-dimensional microarray datasets.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

PubMed Central

2012-01-01

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings. PMID:16964229

An improved K-means clustering method for cDNA microarray image segmentation.

PubMed

Wang, T N; Li, T J; Shao, G F; Wu, S X

2015-07-14

Microarray technology is a powerful tool for human genetic research and other biomedical applications. Numerous improvements to the standard K-means algorithm have been carried out to complete the image segmentation step. However, most of the previous studies classify the image into two clusters. In this paper, we propose a novel K-means algorithm, which first classifies the image into three clusters, and then one of the three clusters is divided as the background region and the other two clusters, as the foreground region. The proposed method was evaluated on six different data sets. The analyses of accuracy, efficiency, expression values, special gene spots, and noise images demonstrate the effectiveness of our method in improving the segmentation quality.

A multiplex reverse transcription PCR and automated electronic microarray assay for detection and differentiation of seven viruses affecting swine.

PubMed

Erickson, A; Fisher, M; Furukawa-Stoffer, T; Ambagala, A; Hodko, D; Pasick, J; King, D P; Nfon, C; Ortega Polo, R; Lung, O

2018-04-01

Microarray technology can be useful for pathogen detection as it allows simultaneous interrogation of the presence or absence of a large number of genetic signatures. However, most microarray assays are labour-intensive and time-consuming to perform. This study describes the development and initial evaluation of a multiplex reverse transcription (RT)-PCR and novel accompanying automated electronic microarray assay for simultaneous detection and differentiation of seven important viruses that affect swine (foot-and-mouth disease virus [FMDV], swine vesicular disease virus [SVDV], vesicular exanthema of swine virus [VESV], African swine fever virus [ASFV], classical swine fever virus [CSFV], porcine respiratory and reproductive syndrome virus [PRRSV] and porcine circovirus type 2 [PCV2]). The novel electronic microarray assay utilizes a single, user-friendly instrument that integrates and automates capture probe printing, hybridization, washing and reporting on a disposable electronic microarray cartridge with 400 features. This assay accurately detected and identified a total of 68 isolates of the seven targeted virus species including 23 samples of FMDV, representing all seven serotypes, and 10 CSFV strains, representing all three genotypes. The assay successfully detected viruses in clinical samples from the field, experimentally infected animals (as early as 1 day post-infection (dpi) for FMDV and SVDV, 4 dpi for ASFV, 5 dpi for CSFV), as well as in biological material that were spiked with target viruses. The limit of detection was 10 copies/μl for ASFV, PCV2 and PRRSV, 100 copies/μl for SVDV, CSFV, VESV and 1,000 copies/μl for FMDV. The electronic microarray component had reduced analytical sensitivity for several of the target viruses when compared with the multiplex RT-PCR. The integration of capture probe printing allows custom onsite array printing as needed, while electrophoretically driven hybridization generates results faster than conventional microarrays that rely on passive hybridization. With further refinement, this novel, rapid, highly automated microarray technology has potential applications in multipathogen surveillance of livestock diseases. © 2017 Her Majesty the Queen in Right of Canada • Transboundary and Emerging Diseases.

Applications of microarray technology in breast cancer research

PubMed Central

Cooper, Colin S

2001-01-01

Microarrays provide a versatile platform for utilizing information from the Human Genome Project to benefit human health. This article reviews the ways in which microarray technology may be used in breast cancer research. Its diverse applications include monitoring chromosome gains and losses, tumour classification, drug discovery and development, DNA resequencing, mutation detection and investigating the mechanism of tumour development. PMID:11305951

A Platform for Combined DNA and Protein Microarrays Based on Total Internal Reflection Fluorescence

PubMed Central

Asanov, Alexander; Zepeda, Angélica; Vaca, Luis

2012-01-01

We have developed a novel microarray technology based on total internal reflection fluorescence (TIRF) in combination with DNA and protein bioassays immobilized at the TIRF surface. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing and stringency control, and measure only end-point results, our TIRF microarray technology provides several orders of magnitude better signal-to-background ratio, performs analysis rapidly in one step, and measures the entire course of association and dissociation kinetics between target DNA and protein molecules and the bioassays. In many practical cases detection of only DNA or protein markers alone does not provide the necessary accuracy for diagnosing a disease or detecting a pathogen. Here we describe TIRF microarrays that detect DNA and protein markers simultaneously, which reduces the probabilities of false responses. Supersensitive and multiplexed TIRF DNA and protein microarray technology may provide a platform for accurate diagnosis or enhanced research studies. Our TIRF microarray system can be mounted on upright or inverted microscopes or interfaced directly with CCD cameras equipped with a single objective, facilitating the development of portable devices. As proof-of-concept we applied TIRF microarrays for detecting molecular markers from Bacillus anthracis, the pathogen responsible for anthrax. PMID:22438738

THE ABRF MARG MICROARRAY SURVEY 2005: TAKING THE PULSE ON THE MICROARRAY FIELD

EPA Science Inventory

Over the past several years microarray technology has evolved into a critical component of any discovery based program. Since 1999, the Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) has conducted biennial surveys designed to generate a pr...

A Perspective on DNA Microarrays in Pathology Research and Practice

PubMed Central

Pollack, Jonathan R.

2007-01-01

DNA microarray technology matured in the mid-1990s, and the past decade has witnessed a tremendous growth in its application. DNA microarrays have provided powerful tools for pathology researchers seeking to describe, classify, and understand human disease. There has also been great expectation that the technology would advance the practice of pathology. This review highlights some of the key contributions of DNA microarrays to experimental pathology, focusing in the area of cancer research. Also discussed are some of the current challenges in translating utility to clinical practice. PMID:17600117

A New Classification of Three-Dimensional Printing Technologies: Systematic Review of Three-Dimensional Printing for Patient-Specific Craniomaxillofacial Surgery.

PubMed

Jacobs, Carly A; Lin, Alexander Y

2017-05-01

Three-dimensional printing technology has been advancing in surgical applications. This systematic review examines its patient-specific applications in craniomaxillofacial surgery. Terms related to "three-dimensional printing" and "surgery" were searched on PubMed on May 4, 2015; 313 unique articles were returned. Inclusion and exclusion criteria concentrated on patient-specific surgical applications, yielding 141 full-text articles, of which 33 craniomaxillofacial articles were analyzed. Thirty-three articles included 315 patients who underwent three-dimensional printing-assisted operations. The most common modeling software was Mimics, the most common printing software was 3D Systems, the average time to create a printed object was 18.9 hours (range, 1.5 to 96 hours), and the average cost of a printed object was $1353.31 (range, $69.75 to $5500). Surgical procedures were divided among 203 craniofacial patients (205 three-dimensional printing objects) and 112 maxillofacial patients (137 objects). Printing technologies could be classified as contour models, guides, splints, and implants. For craniofacial patients, 173 contour models (84 percent), 13 guides (6 percent), two splints (1 percent), and 17 implants (8 percent) were made. For maxillofacial patients, 41 contour models (30 percent), 48 guides (35 percent), 40 splints (29 percent), and eight implants (6 percent) were made. These distributions were significantly different (p < 0.0001). Four studies compared three-dimensional printing techniques to conventional techniques; two of them found that three-dimensional printing produced improved outcomes. Three-dimensional printing technology in craniomaxillofacial surgery can be classified into contour models (type I), guides (type II), splints (type III), and implants (type IV). These four methods vary in their use between craniofacial and maxillofacial surgery, reflecting their different goals. This understanding may help advance and predict three-dimensional printing applications for other types of plastic surgery and beyond.

Characterisation of the cancer-associated glucocorticoid system: key role of 11β-hydroxysteroid dehydrogenase type 2.

PubMed

Cirillo, Nicola; Morgan, David J; Pedicillo, Maria Carmela; Celentano, Antonio; Lo Muzio, Lorenzo; McCullough, Michael J; Prime, Stephen S

2017-09-26

Recent studies have shown that production of cortisol not only takes place in several non-adrenal peripheral tissues such as epithelial cells but, also, the local inter-conversion between cortisone and cortisol is regulated by the 11β-hydroxysteroid dehydrogenases (11β-HSDs). However, little is known about the activity of this non-adrenal glucocorticoid system in cancers. The presence of a functioning glucocorticoid system was assessed in human skin squamous cell carcinoma (SCC) and melanoma and further, in 16 epithelial cell lines from 8 different tissue types using ELISA, western blotting and immunofluorescence. 11β-HSD2 was inhibited both pharmacologically and by siRNA technology. Naïve CD8 + T cells were used to test the paracrine effects of cancer-derived cortisol on the immune system in vitro. Functional assays included cell-cell adhesion and cohesion in two- and three-dimensional models. Immunohistochemical data of 11β-HSD expression were generated using tissue microarrays of 40 cases of human SCCs as well as a database featuring 315 cancer cases from 15 different tissues. We show that cortisol production is a common feature of malignant cells and has paracrine functions. Cortisol production correlated with the magnitude of glucocorticoid receptor (GR)-dependent inhibition of tumour-specific CD8 + T cells in vitro. 11β-HSDs were detectable in human skin SCCs and melanoma. Analyses of publicly available protein expression data of 11β-HSDs demonstrated that 11β-HSD1 and -HSD2 were dysregulated in the majority (73%) of malignancies. Pharmacological manipulation of 11β-HSD2 activity by 18β-glycyrrhetinic acid (GA) and silencing by specific siRNAs modulated the bioavailability of cortisol. Cortisol also acted in an autocrine manner and promoted cell invasion in vitro and cell-cell adhesion and cohesion in two- and three-dimensional models. Immunohistochemical analyses using tissue microarrays showed that expression of 11β-HSD2 was significantly reduced in human SCCs of the skin. The results demonstrate evidence of a cancer-associated glucocorticoid system and show for the first time, the functional significance of cancer-derived cortisol in tumour progression.

Differential Expression and Functional Analysis of High-Throughput -Omics Data Using Open Source Tools.

PubMed

Kebschull, Moritz; Fittler, Melanie Julia; Demmer, Ryan T; Papapanou, Panos N

2017-01-01

Today, -omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ, or tissue sample, allow for an unbiased, comprehensive genome-level analysis of complex diseases, offering a large advantage over earlier "candidate" gene or pathway analyses. A primary goal in the analysis of these high-throughput assays is the detection of those features among several thousand that differ between different groups of samples. In the context of oral biology, our group has successfully utilized -omics technology to identify key molecules and pathways in different diagnostic entities of periodontal disease.A major issue when inferring biological information from high-throughput -omics studies is the fact that the sheer volume of high-dimensional data generated by contemporary technology is not appropriately analyzed using common statistical methods employed in the biomedical sciences.In this chapter, we outline a robust and well-accepted bioinformatics workflow for the initial analysis of -omics data generated using microarrays or next-generation sequencing technology using open-source tools. Starting with quality control measures and necessary preprocessing steps for data originating from different -omics technologies, we next outline a differential expression analysis pipeline that can be used for data from both microarray and sequencing experiments, and offers the possibility to account for random or fixed effects. Finally, we present an overview of the possibilities for a functional analysis of the obtained data.

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

PubMed

Honoré, Paul; Granjeaud, Samuel; Tagett, Rebecca; Deraco, Stéphane; Beaudoing, Emmanuel; Rougemont, Jacques; Debono, Stéphane; Hingamp, Pascal

2006-09-20

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. 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. 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 shared facilities and industry service providers alike.

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

PubMed Central

Honoré, Paul; Granjeaud, Samuel; Tagett, Rebecca; Deraco, Stéphane; Beaudoing, Emmanuel; Rougemont, Jacques; Debono, Stéphane; Hingamp, Pascal

2006-01-01

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 shared facilities and industry service providers alike. PMID:16987406

Fuzzy support vector machine for microarray imbalanced data classification

NASA Astrophysics Data System (ADS)

Ladayya, Faroh; Purnami, Santi Wulan; Irhamah

2017-11-01

DNA microarrays are data containing gene expression with small sample sizes and high number of features. Furthermore, imbalanced classes is a common problem in microarray data. This occurs when a dataset is dominated by a class which have significantly more instances than the other minority classes. Therefore, it is needed a classification method that solve the problem of high dimensional and imbalanced data. Support Vector Machine (SVM) is one of the classification methods that is capable of handling large or small samples, nonlinear, high dimensional, over learning and local minimum issues. SVM has been widely applied to DNA microarray data classification and it has been shown that SVM provides the best performance among other machine learning methods. However, imbalanced data will be a problem because SVM treats all samples in the same importance thus the results is bias for minority class. To overcome the imbalanced data, Fuzzy SVM (FSVM) is proposed. This method apply a fuzzy membership to each input point and reformulate the SVM such that different input points provide different contributions to the classifier. The minority classes have large fuzzy membership so FSVM can pay more attention to the samples with larger fuzzy membership. Given DNA microarray data is a high dimensional data with a very large number of features, it is necessary to do feature selection first using Fast Correlation based Filter (FCBF). In this study will be analyzed by SVM, FSVM and both methods by applying FCBF and get the classification performance of them. Based on the overall results, FSVM on selected features has the best classification performance compared to SVM.

The Microarray Revolution: Perspectives from Educators

ERIC Educational Resources Information Center

Brewster, Jay L.; Beason, K. Beth; Eckdahl, Todd T.; Evans, Irene M.

2004-01-01

In recent years, microarray analysis has become a key experimental tool, enabling the analysis of genome-wide patterns of gene expression. This review approaches the microarray revolution with a focus upon four topics: 1) the early development of this technology and its application to cancer diagnostics; 2) a primer of microarray research,…

New bandwidth selection criterion for Kernel PCA: approach to dimensionality reduction and classification problems.

PubMed

Thomas, Minta; De Brabanter, Kris; De Moor, Bart

2014-05-10

DNA microarrays are potentially powerful technology for improving diagnostic classification, treatment selection, and prognostic assessment. The use of this technology to predict cancer outcome has a history of almost a decade. Disease class predictors can be designed for known disease cases and provide diagnostic confirmation or clarify abnormal cases. The main input to this class predictors are high dimensional data with many variables and few observations. Dimensionality reduction of these features set significantly speeds up the prediction task. Feature selection and feature transformation methods are well known preprocessing steps in the field of bioinformatics. Several prediction tools are available based on these techniques. Studies show that a well tuned Kernel PCA (KPCA) is an efficient preprocessing step for dimensionality reduction, but the available bandwidth selection method for KPCA was computationally expensive. In this paper, we propose a new data-driven bandwidth selection criterion for KPCA, which is related to least squares cross-validation for kernel density estimation. We propose a new prediction model with a well tuned KPCA and Least Squares Support Vector Machine (LS-SVM). We estimate the accuracy of the newly proposed model based on 9 case studies. Then, we compare its performances (in terms of test set Area Under the ROC Curve (AUC) and computational time) with other well known techniques such as whole data set + LS-SVM, PCA + LS-SVM, t-test + LS-SVM, Prediction Analysis of Microarrays (PAM) and Least Absolute Shrinkage and Selection Operator (Lasso). Finally, we assess the performance of the proposed strategy with an existing KPCA parameter tuning algorithm by means of two additional case studies. We propose, evaluate, and compare several mathematical/statistical techniques, which apply feature transformation/selection for subsequent classification, and consider its application in medical diagnostics. Both feature selection and feature transformation perform well on classification tasks. Due to the dynamic selection property of feature selection, it is hard to define significant features for the classifier, which predicts classes of future samples. Moreover, the proposed strategy enjoys a distinctive advantage with its relatively lesser time complexity.

Research on three-dimensional real scene technology of Sichuan-Tibet highway

NASA Astrophysics Data System (ADS)

Yin, Peng; Bo, Xianglei; Liu, Fen

2018-04-01

This paper studies the three-dimensional real scene technology in the application of highway simulation, and a system to realize three-dimensional real scene of Sichuan-Tibet highway is presented. This system can improve the defect of the traditional Sichuan-Tibet highway geographic information system from performance and feeling. The Tibet forces can use this system to improve motor adaptive training effect and command decision-making ability.

Importance of the efficiency of double-stranded DNA formation in cDNA synthesis for the imprecision of microarray expression analysis.

PubMed

Thormar, Hans G; Gudmundsson, Bjarki; Eiriksdottir, Freyja; Kil, Siyoen; Gunnarsson, Gudmundur H; Magnusson, Magnus Karl; Hsu, Jason C; Jonsson, Jon J

2013-04-01

The causes of imprecision in microarray expression analysis are poorly understood, limiting the use of this technology in molecular diagnostics. Two-dimensional strandness-dependent electrophoresis (2D-SDE) separates nucleic acid molecules on the basis of length and strandness, i.e., double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and RNA·DNA hybrids. We used 2D-SDE to measure the efficiency of cDNA synthesis and its importance for the imprecision of an in vitro transcription-based microarray expression analysis. The relative amount of double-stranded cDNA formed in replicate experiments that used the same RNA sample template was highly variable, ranging between 0% and 72% of the total DNA. Microarray experiments showed an inverse relationship between the difference between sample pairs in probe variance and the relative amount of dsDNA. Approximately 15% of probes showed between-sample variation (P < 0.05) when the dsDNA percentage was between 12% and 35%. In contrast, only 3% of probes showed between-sample variation when the dsDNA percentage was 69% and 72%. Replication experiments of the 35% dsDNA and 72% dsDNA samples were used to separate sample variation from probe replication variation. The estimated SD of the sample-to-sample variation and of the probe replicates was lower in 72% dsDNA samples than in 35% dsDNA samples. Variation in the relative amount of double-stranded cDNA synthesized can be an important component of the imprecision in T7 RNA polymerase-based microarray expression analysis. © 2013 American Association for Clinical Chemistry

Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α).

PubMed

Giotis, Efstathios S; Robey, Rebecca C; Skinner, Natalie G; Tomlinson, Christopher D; Goodbourn, Stephen; Skinner, Michael A

2016-08-05

Viruses that infect birds pose major threats-to the global supply of chicken, the major, universally-acceptable meat, and as zoonotic agents (e.g. avian influenza viruses H5N1 and H7N9). Controlling these viruses in birds as well as understanding their emergence into, and transmission amongst, humans will require considerable ingenuity and understanding of how different species defend themselves. The type I interferon-coordinated response constitutes the major antiviral innate defence. Although interferon was discovered in chicken cells, details of the response, particularly the identity of hundreds of stimulated genes, are far better described in mammals. Viruses induce interferon-stimulated genes but they also regulate the expression of many hundreds of cellular metabolic and structural genes to facilitate their replication. This study focusses on the potentially anti-viral genes by identifying those induced just by interferon in primary chick embryo fibroblasts. Three transcriptomic technologies were exploited: RNA-seq, a classical 3'-biased chicken microarray and a high density, "sense target", whole transcriptome chicken microarray, with each recognising 120-150 regulated genes (curated for duplication and incorrect assignment of some microarray probesets). Overall, the results are considered robust because 128 of the compiled, curated list of 193 regulated genes were detected by two, or more, of the technologies.

Contact printing of protein microarrays.

PubMed

Austin, John; Holway, Antonia H

2011-01-01

A review is provided of contact-printing technologies for the fabrication of planar protein microarrays. The key printing performance parameters for creating protein arrays are reviewed. Solid pin and quill pin technologies are described and their strengths and weaknesses compared.

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

PubMed

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.

A low density microarray method for the identification of human papillomavirus type 18 variants.

PubMed

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

2013-09-26

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.

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

PubMed Central

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

Carbohydrate Microarray Technology Applied to High-Throughput Mapping of Plant Cell Wall Glycans Using Comprehensive Microarray Polymer Profiling (CoMPP).

PubMed

Kračun, Stjepan Krešimir; Fangel, Jonatan Ulrik; Rydahl, Maja Gro; Pedersen, Henriette Lodberg; Vidal-Melgosa, Silvia; Willats, William George Tycho

2017-01-01

Cell walls are an important feature of plant cells and a major component of the plant glycome. They have both structural and physiological functions and are critical for plant growth and development. The diversity and complexity of these structures demand advanced high-throughput techniques to answer questions about their structure, functions and roles in both fundamental and applied scientific fields. Microarray technology provides both the high-throughput and the feasibility aspects required to meet that demand. In this chapter, some of the most recent microarray-based techniques relating to plant cell walls are described together with an overview of related contemporary techniques applied to carbohydrate microarrays and their general potential in glycoscience. A detailed experimental procedure for high-throughput mapping of plant cell wall glycans using the comprehensive microarray polymer profiling (CoMPP) technique is included in the chapter and provides a good example of both the robust and high-throughput nature of microarrays as well as their applicability to plant glycomics.

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

PubMed

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.

Cambridge Healthtech Institute's Third Annual Conference on Lab-on-a-Chip and Microarrays. 22-24 January 2001, Zurich, Switzerland.

PubMed

Jain, K K

2001-02-01

Cambridge Healthtech Institute's Third Annual Conference on Lab-on-a-Chip and Microarray technology covered the latest advances in this technology and applications in life sciences. Highlights of the meetings are reported briefly with emphasis on applications in genomics, drug discovery and molecular diagnostics. There was an emphasis on microfluidics because of the wide applications in laboratory and drug discovery. The lab-on-a-chip provides the facilities of a complete laboratory in a hand-held miniature device. Several microarray systems have been used for hybridisation and detection techniques. Oligonucleotide scanning arrays provide a versatile tool for the analysis of nucleic acid interactions and provide a platform for improving the array-based methods for investigation of antisense therapeutics. A method for analysing combinatorial DNA arrays using oligonucleotide-modified gold nanoparticle probes and a conventional scanner has considerable potential in molecular diagnostics. Various applications of microarray technology for high-throughput screening in drug discovery and single nucleotide polymorphisms (SNP) analysis were discussed. Protein chips have important applications in proteomics. With the considerable amount of data generated by the different technologies using microarrays, it is obvious that the reading of the information and its interpretation and management through the use of bioinformatics is essential. Various techniques for data analysis were presented. Biochip and microarray technology has an essential role to play in the evolving trends in healthcare, which integrate diagnosis with prevention/treatment and emphasise personalised medicines.

Three-Dimensional Computer Simulation as an Important Competence Based Aspect of a Modern Mining Professional

NASA Astrophysics Data System (ADS)

Aksenova, Olesya; Pachkina, Anna

2017-11-01

The article deals with the problem of necessity of educational process transformation to meet the requirements of modern miming industry; cooperative developing of new educational programs and implementation of educational process taking into account modern manufacturability. The paper proves the idea of introduction into mining professionals learning process studying of three-dimensional models of surface technological complex, ore reserves and underground digging complex as well as creating these models in different graphic editors and working with the information analysis model obtained on the basis of these three-dimensional models. The technological process of manless coal mining at the premises of the mine Polysaevskaya controlled by the information analysis models built on the basis of three-dimensional models of individual objects and technological process as a whole, and at the same time requiring the staff able to use the programs of three-dimensional positioning in the miners and equipment global frame of reference is covered.

Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples.

PubMed

Pine, P S; Boedigheimer, M; Rosenzweig, B A; Turpaz, Y; He, Y D; Delenstarr, G; Ganter, B; Jarnagin, K; Jones, W D; Reid, L H; Thompson, K L

2008-11-01

Effective use of microarray technology in clinical and regulatory settings is contingent on the adoption of standard methods for assessing performance. The MicroArray Quality Control project evaluated the repeatability and comparability of microarray data on the major commercial platforms and laid the groundwork for the application of microarray technology to regulatory assessments. However, methods for assessing performance that are commonly applied to diagnostic assays used in laboratory medicine remain to be developed for microarray assays. A reference system for microarray performance evaluation and process improvement was developed that includes reference samples, metrics and reference datasets. The reference material is composed of two mixes of four different rat tissue RNAs that allow defined target ratios to be assayed using a set of tissue-selective analytes that are distributed along the dynamic range of measurement. The diagnostic accuracy of detected changes in expression ratios, measured as the area under the curve from receiver operating characteristic plots, provides a single commutable value for comparing assay specificity and sensitivity. The utility of this system for assessing overall performance was evaluated for relevant applications like multi-laboratory proficiency testing programs and single-laboratory process drift monitoring. The diagnostic accuracy of detection of a 1.5-fold change in signal level was found to be a sensitive metric for comparing overall performance. This test approaches the technical limit for reliable discrimination of differences between two samples using this technology. We describe a reference system that provides a mechanism for internal and external assessment of laboratory proficiency with microarray technology and is translatable to performance assessments on other whole-genome expression arrays used for basic and clinical research.

Principles of gene microarray data analysis.

PubMed

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.

[Application of three-dimensional digital technology in the diagnosis and treatment planning in orthodontics].

PubMed

Bai, Y X

2016-06-01

Three-dimensional(3D)digital technology has been widely used in the field of orthodontics in clinical examination, diagnosis, treatment and curative effect evaluation. 3D digital technology greatly improves the accuracy of diagnosis and treatment, and provides effective means for personalized orthodontic treatment. This review focuses on the application of 3D digital technology in the field of orthodontics.

Possibilities and limitations of current stereo-endoscopy.

PubMed

Mueller-Richter, U D A; Limberger, A; Weber, P; Ruprecht, K W; Spitzer, W; Schilling, M

2004-06-01

Stereo-endoscopy has become a commonly used technology. In many comparative studies striking advantages of stereo-endoscopy over two-dimensional presentation could not be proven. To show the potential and fields for further improvement of this technology is the aim of this article. The physiological basis of three-dimensional vision limitations of current stereo-endoscopes is discussed and fields for further research are indicated. New developments in spatial picture acquisition and spatial picture presentation are discussed. Current limitations of stereo-endoscopy that prevent a better ranking in comparative studies with two-dimensional presentation are mainly based on insufficient picture acquisition. Devices for three-dimensional picture presentation are at a more advanced developmental stage than devices for three-dimensional picture acquisition. Further research should emphasize the development of new devices for three-dimensional picture acquisition.

IMPROVING THE RELIABILITY OF MICROARRAYS FOR TOXICOLOGY RESEARCH: A COLLABORATIVE APPROACH

EPA Science Inventory

Microarray-based gene expression profiling is a critical tool to identify molecular biomarkers of specific chemical stressors. Although current microarray technologies have progressed from their infancy, biological and technical repeatability and reliability are often still limit...

Three-Dimensional (3D) Printers in Libraries: Perspective and Preliminary Safety Analysis

ERIC Educational Resources Information Center

Bharti, Neelam; Singh, Shailendra

2017-01-01

As an emerging technology, three-dimensional (3D) printing has gained much attention as a rapid prototyping and small-scale manufacturing technology around the world. In the changing scenario of library inclusion, Makerspaces are becoming a part of most public and academic libraries, and 3D printing is one of the technologies included in…

Three-Dimensional Media Technologies: Potentials for Study in Visual Literacy.

ERIC Educational Resources Information Center

Thwaites, Hal

This paper presents an overview of three-dimensional media technologies (3Dmt). Many of the new 3Dmt are the direct result of interactions of computing, communications, and imaging technologies. Computer graphics are particularly well suited to the creation of 3D images due to the high resolution and programmable nature of the current displays.…

Implementation of plaid model biclustering method on microarray of carcinoma and adenoma tumor gene expression data

NASA Astrophysics Data System (ADS)

Ardaneswari, Gianinna; Bustamam, Alhadi; Sarwinda, Devvi

2017-10-01

A Tumor is an abnormal growth of cells that serves no purpose. Carcinoma is a tumor that grows from the top of the cell membrane and the organ adenoma is a benign tumor of the gland-like cells or epithelial tissue. In the field of molecular biology, the development of microarray technology is used in the data store of disease genetic expression. For each of microarray gene, an amount of information is stored for each trait or condition. In gene expression data clustering can be done with a bicluster algorithm, thats clustering method which not only the objects to be clustered, but also the properties or condition of the object. This research proposed Plaid Model Biclustering as one of biclustering method. In this study, we discuss the implementation of Plaid Model Biclustering Method on microarray of Carcinoma and Adenoma tumor gene expression data. From the experimental results, we found three biclusters are formed by Carcinoma gene expression data and four biclusters are formed by Adenoma gene expression data.

SPERM RNA AMPLIFICATION FOR GENE EXPRESSION PROFILING BY DNA MICROARRAY TECHNOLOGY

EPA Science Inventory

Sperm RNA Amplification for Gene Expression Profiling by DNA Microarray Technology
Hongzu Ren, Kary E. Thompson, Judith E. Schmid and David J. Dix, Reproductive Toxicology Division, NHEERL, Office of Research and Development, US Environmental Protection Agency, Research Triang...

Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline

PubMed Central

2013-01-01

Background As high-throughput genomic technologies become accurate and affordable, an increasing number of data sets have been accumulated in the public domain and genomic information integration and meta-analysis have become routine in biomedical research. In this paper, we focus on microarray meta-analysis, where multiple microarray studies with relevant biological hypotheses are combined in order to improve candidate marker detection. Many methods have been developed and applied in the literature, but their performance and properties have only been minimally investigated. There is currently no clear conclusion or guideline as to the proper choice of a meta-analysis method given an application; the decision essentially requires both statistical and biological considerations. Results We performed 12 microarray meta-analysis methods for combining multiple simulated expression profiles, and such methods can be categorized for different hypothesis setting purposes: (1) HS A : DE genes with non-zero effect sizes in all studies, (2) HS B : DE genes with non-zero effect sizes in one or more studies and (3) HS r : DE gene with non-zero effect in "majority" of studies. We then performed a comprehensive comparative analysis through six large-scale real applications using four quantitative statistical evaluation criteria: detection capability, biological association, stability and robustness. We elucidated hypothesis settings behind the methods and further apply multi-dimensional scaling (MDS) and an entropy measure to characterize the meta-analysis methods and data structure, respectively. Conclusions The aggregated results from the simulation study categorized the 12 methods into three hypothesis settings (HS A , HS B , and HS r ). Evaluation in real data and results from MDS and entropy analyses provided an insightful and practical guideline to the choice of the most suitable method in a given application. All source files for simulation and real data are available on the author’s publication website. PMID:24359104

Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline.

PubMed

Chang, Lun-Ching; Lin, Hui-Min; Sibille, Etienne; Tseng, George C

2013-12-21

As high-throughput genomic technologies become accurate and affordable, an increasing number of data sets have been accumulated in the public domain and genomic information integration and meta-analysis have become routine in biomedical research. In this paper, we focus on microarray meta-analysis, where multiple microarray studies with relevant biological hypotheses are combined in order to improve candidate marker detection. Many methods have been developed and applied in the literature, but their performance and properties have only been minimally investigated. There is currently no clear conclusion or guideline as to the proper choice of a meta-analysis method given an application; the decision essentially requires both statistical and biological considerations. We performed 12 microarray meta-analysis methods for combining multiple simulated expression profiles, and such methods can be categorized for different hypothesis setting purposes: (1) HS(A): DE genes with non-zero effect sizes in all studies, (2) HS(B): DE genes with non-zero effect sizes in one or more studies and (3) HS(r): DE gene with non-zero effect in "majority" of studies. We then performed a comprehensive comparative analysis through six large-scale real applications using four quantitative statistical evaluation criteria: detection capability, biological association, stability and robustness. We elucidated hypothesis settings behind the methods and further apply multi-dimensional scaling (MDS) and an entropy measure to characterize the meta-analysis methods and data structure, respectively. The aggregated results from the simulation study categorized the 12 methods into three hypothesis settings (HS(A), HS(B), and HS(r)). Evaluation in real data and results from MDS and entropy analyses provided an insightful and practical guideline to the choice of the most suitable method in a given application. All source files for simulation and real data are available on the author's publication website.

Upregulated epidermal growth factor receptor expression following near-infrared irradiation simulating solar radiation in a three-dimensional reconstructed human corneal epithelial tissue culture model.

PubMed

Tanaka, Yohei; Nakayama, Jun

2016-01-01

Humans are increasingly exposed to near-infrared (NIR) radiation from both natural (eg, solar) and artificial (eg, electrical appliances) sources. Although the biological effects of sun and ultraviolet (UV) exposure have been extensively investigated, the biological effect of NIR radiation is still unclear. We previously reported that NIR as well as UV induces photoaging and standard UV-blocking materials, such as sunglasses, do not sufficiently block NIR. The objective of this study was to investigate changes in gene expression in three-dimensional reconstructed corneal epithelial tissue culture exposed to broad-spectrum NIR irradiation to simulate solar NIR radiation that reaches human tissues. DNA microarray and quantitative real-time polymerase chain reaction analysis were used to assess gene expression levels in a three-dimensional reconstructed corneal epithelial model composed of normal human corneal epithelial cells exposed to water-filtered broad-spectrum NIR irradiation with a contact cooling (20°C). The water-filter allowed 1,000-1,800 nm wavelengths and excluded 1,400-1,500 nm wavelengths. A DNA microarray with >62,000 different probes showed 25 and 150 genes that were up- or downregulated by at least fourfold and twofold, respectively, after NIR irradiation. In particular, epidermal growth factor receptor (EGFR) was upregulated by 19.4-fold relative to control cells. Quantitative real-time polymerase chain reaction analysis revealed that two variants of EGFR in human corneal epithelial tissue were also significantly upregulated after five rounds of 10 J/cm(2) irradiation (P<0.05). We found that NIR irradiation induced the upregulated expression of EGFR in human corneal cells. Since over half of the solar energy reaching the Earth is in the NIR region, which cannot be adequately blocked by eyewear and thus can induce eye damage with intensive or long-term exposure, protection from both UV and NIR radiation may prevent changes in gene expression and in turn eye damage.

Protein Microarray Analysis in Patients With Asthma*

PubMed Central

Kim, Hyo-Bin; Kim, Chang-Keun; Iijima, Koji; Kobayashi, Takao; Kita, Hirohito

2010-01-01

Background Microarray technology offers a new opportunity to gain insight into global gene and protein expression profiles in asthma. To identify novel factors produced in the asthmatic airway, we analyzed sputum samples by using a membrane-based human cytokine microarray technology in patients with bronchial asthma (BA). Methods Induced sputum was obtained from 28 BA subjects, 20 nonasthmatic atopic control (AC) subjects, and 38 nonasthmatic nonatopic normal control (NC) subjects. The microarray samples of subjects were randomly selected from nine BA subjects, three AC subjects, and six NC subjects. Sputum supernatants were analyzed using a custom human cytokine array (RayBio Custom Human Cytokine Array; RayBiotech; Norcross, GA) designed to analyze 79 specific cytokines simultaneously. The levels of growth-regulated oncogene (GRO)-α, eotaxin-2, and pulmonary and activation-regulated chemokine (PARC)/CCL18 were measured by sandwich enzyme-linked immunosorbent assays (ELISAs), and eosinophil-derived neurotoxin (EDN) was measured by radioimmunoassay. Results By microarray, the signal intensities for GRO-α, eotaxin-2, and PARC were significantly higher in BA subjects than in AC and NC subjects (p = 0.036, p = 0.042, and p = 0.033, respectively). By ELISA, the sputum PARC protein levels were significantly higher in BA subjects than in AC and NC subjects (p < 0.0001). Furthermore, PARC levels correlated significantly with sputum eosinophil percentages (r = 0.570, p < 0.0001) and the levels of EDN(r = 0.633, p < 0.0001), the regulated upon activation, normal T cell expressed and secreted cytokine (r = 0.440, p < 0.001), interleukin-4 (r = 0.415, p < 0.01), and interferon-γ (r = 0.491, p < 0.001). Conclusions By a nonbiased screening approach, a chemokine, PARC, is elevated in sputum specimens from patients with asthma. PARC may play important roles in development of airway eosinophilic inflammation in asthma. PMID:19017877

High-resolution liquid patterns via three-dimensional droplet shape control.

PubMed

Raj, Rishi; Adera, Solomon; Enright, Ryan; Wang, Evelyn N

2014-09-25

Understanding liquid dynamics on surfaces can provide insight into nature's design and enable fine manipulation capability in biological, manufacturing, microfluidic and thermal management applications. Of particular interest is the ability to control the shape of the droplet contact area on the surface, which is typically circular on a smooth homogeneous surface. Here, we show the ability to tailor various droplet contact area shapes ranging from squares, rectangles, hexagons, octagons, to dodecagons via the design of the structure or chemical heterogeneity on the surface. We simultaneously obtain the necessary physical insights to develop a universal model for the three-dimensional droplet shape by characterizing the droplet side and top profiles. Furthermore, arrays of droplets with controlled shapes and high spatial resolution can be achieved using this approach. This liquid-based patterning strategy promises low-cost fabrication of integrated circuits, conductive patterns and bio-microarrays for high-density information storage and miniaturized biochips and biosensors, among others.

Non-volatile copolymer compositions for fabricating gel element microarrays

PubMed Central

Golova, Julia B.; Chernov, Boris K.; Perov, Alexander N.; Reynolds, Jennifer; Linger, Yvonne L.; Kukhtin, Alexander; Chandler, Darrell P.

2011-01-01

By modifying polymer compositions and cross-linking reagents, we have developed a simple yet effective manufacturing strategy for copolymerized three-dimensional gel element arrays. A new gel-forming monomer (2-(hydroxyethyl) methacrylamide; HEMAA) was used that possesses low volatility and improves the stability of copolymerized gel element arrays to on-chip thermal cycling procedures relative to previously used monomers. Probe immobilization efficiency within the new polymer was 55%, equivalent to that obtained with acrylamide (AA) and methacrylamide (MA) monomers. Non-specific binding of single stranded targets was equivalent for all monomers. Increasing cross-linker chain length improved hybridization kinetics and end-point signal intensities relative to N,N-methylenebisacrylamide (Bis). The new copolymer formulation was successfully applied to a model orthopox array. Because HEMAA greatly simplifies gel element array manufacture, we expect it (in combination with new cross-linkers described herein) to find widespread application in microarray science. PMID:22033291

Polysaccharide Microarray Technology for the Detection of Burkholderia Pseudomallei and Burkholderia Mallei Antibodies

DTIC Science & Technology

2006-04-27

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... Polysaccharide microarrays; Burkholderia pseudomallei; Burkholderia mallei; Glanders; Melioidosis1. Introduction There has been a great deal of emphasis on the

The Importance of Normalization on Large and Heterogeneous Microarray Datasets

EPA Science Inventory

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...

Microarray expression technology: from start to finish.

PubMed

Elvidge, Gareth

2006-01-01

The recent introduction of new microarray expression technologies and the further development of established platforms ensure that the researcher is presented with a range of options for performing an experiment. Whilst this has opened up the possibilities for future applications, such as exon-specific arrays, increased sample throughput and 'chromatin immunoprecipitation (ChIP) on chip' experiments, the initial decision processes and experiment planning are made more difficult. This review will give an overview of the various technologies that are available to perform a microarray expression experiment, from the initial planning stages through to the final data analysis. Both practical aspects and data analysis options will be considered. The relative advantages and disadvantages will be discussed with insights provided for future directions of the technology.

The use of open source bioinformatics tools to dissect transcriptomic data.

PubMed

Nitsche, Benjamin M; Ram, Arthur F J; Meyer, Vera

2012-01-01

Microarrays are a valuable technology to study fungal physiology on a transcriptomic level. Various microarray platforms are available comprising both single and two channel arrays. Despite different technologies, preprocessing of microarray data generally includes quality control, background correction, normalization, and summarization of probe level data. Subsequently, depending on the experimental design, diverse statistical analysis can be performed, including the identification of differentially expressed genes and the construction of gene coexpression networks.We describe how Bioconductor, a collection of open source and open development packages for the statistical programming language R, can be used for dissecting microarray data. We provide fundamental details that facilitate the process of getting started with R and Bioconductor. Using two publicly available microarray datasets from Aspergillus niger, we give detailed protocols on how to identify differentially expressed genes and how to construct gene coexpression networks.

Transparency-enhancing technology allows three-dimensional assessment of gastrointestinal mucosa: A porcine model.

PubMed

Mizutani, Hiroya; Ono, Satoshi; Ushiku, Tetsuo; Kudo, Yotaro; Ikemura, Masako; Kageyama, Natsuko; Yamamichi, Nobutake; Fujishiro, Mitsuhiro; Someya, Takao; Fukayama, Masashi; Koike, Kazuhiko; Onodera, Hiroshi

2018-02-01

Although high-resolution three-dimensional imaging of endoscopically resected gastrointestinal specimens can help elucidating morphological features of gastrointestinal mucosa or tumor, there are no established methods to achieve this without breaking specimens apart. We evaluated the utility of transparency-enhancing technology for three-dimensional assessment of gastrointestinal mucosa in porcine models. Esophagus, stomach, and colon mucosa samples obtained from a sacrificed swine were formalin-fixed and paraffin-embedded, and subsequently deparaffinized for analysis. The samples were fluorescently stained, optically cleared using transparency-enhancing technology: ilLUmination of Cleared organs to IDentify target molecules method (LUCID), and visualized using laser scanning microscopy. After observation, all specimens were paraffin-embedded again and evaluated by conventional histopathological assessment to measure the impact of transparency-enhancing procedures. As a result, microscopic observation revealed horizontal section views of mucosa at deeper levels and enabled the three-dimensional image reconstruction of glandular and vascular structures. Besides, paraffin-embedded specimens after transparency-enhancing procedures were all assessed appropriately by conventional histopathological staining. These results suggest that transparency-enhancing technology may be feasible for clinical application and enable the three-dimensional structural analysis of endoscopic resected specimen non-destructively. Although there remain many limitations or problems to be solved, this promising technology might represent a novel histopathological method for evaluating gastrointestinal cancers. © 2018 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

A meta-data based method for DNA microarray imputation.

PubMed

Jörnsten, Rebecka; Ouyang, Ming; Wang, Hui-Yu

2007-03-29

DNA microarray experiments are conducted in logical sets, such as time course profiling after a treatment is applied to the samples, or comparisons of the samples under two or more conditions. Due to cost and design constraints of spotted cDNA microarray experiments, each logical set commonly includes only a small number of replicates per condition. Despite the vast improvement of the microarray technology in recent years, missing values are prevalent. Intuitively, imputation of missing values is best done using many replicates within the same logical set. In practice, there are few replicates and thus reliable imputation within logical sets is difficult. However, it is in the case of few replicates that the presence of missing values, and how they are imputed, can have the most profound impact on the outcome of downstream analyses (e.g. significance analysis and clustering). This study explores the feasibility of imputation across logical sets, using the vast amount of publicly available microarray data to improve imputation reliability in the small sample size setting. We download all cDNA microarray data of Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans from the Stanford Microarray Database. Through cross-validation and simulation, we find that, for all three species, our proposed imputation using data from public databases is far superior to imputation within a logical set, sometimes to an astonishing degree. Furthermore, the imputation root mean square error for significant genes is generally a lot less than that of non-significant ones. Since downstream analysis of significant genes, such as clustering and network analysis, can be very sensitive to small perturbations of estimated gene effects, it is highly recommended that researchers apply reliable data imputation prior to further analysis. Our method can also be applied to cDNA microarray experiments from other species, provided good reference data are available.

Integrated Microfluidic Devices for Automated Microarray-Based Gene Expression and Genotyping Analysis

NASA Astrophysics Data System (ADS)

Liu, Robin H.; Lodes, Mike; Fuji, H. Sho; Danley, David; McShea, Andrew

Microarray assays typically involve multistage sample processing and fluidic handling, which are generally labor-intensive and time-consuming. Automation of these processes would improve robustness, reduce run-to-run and operator-to-operator variation, and reduce costs. In this chapter, a fully integrated and self-contained microfluidic biochip device that has been developed to automate the fluidic handling steps for microarray-based gene expression or genotyping analysis is presented. The device consists of a semiconductor-based CustomArray® chip with 12,000 features and a microfluidic cartridge. The CustomArray was manufactured using a semiconductor-based in situ synthesis technology. The micro-fluidic cartridge consists of microfluidic pumps, mixers, valves, fluid channels, and reagent storage chambers. Microarray hybridization and subsequent fluidic handling and reactions (including a number of washing and labeling steps) were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. Electrochemical micropumps were integrated in the cartridge to provide pumping of liquid solutions. A micromixing technique based on gas bubbling generated by electrochemical micropumps was developed. Low-cost check valves were implemented in the cartridge to prevent cross-talk of the stored reagents. Gene expression study of the human leukemia cell line (K562) and genotyping detection and sequencing of influenza A subtypes have been demonstrated using this integrated biochip platform. For gene expression assays, the microfluidic CustomArray device detected sample RNAs with a concentration as low as 0.375 pM. Detection was quantitative over more than three orders of magnitude. Experiment also showed that chip-to-chip variability was low indicating that the integrated microfluidic devices eliminate manual fluidic handling steps that can be a significant source of variability in genomic analysis. The genotyping results showed that the device identified influenza A hemagglutinin and neuraminidase subtypes and sequenced portions of both genes, demonstrating the potential of integrated microfluidic and microarray technology for multiple virus detection. The device provides a cost-effective solution to eliminate labor-intensive and time-consuming fluidic handling steps and allows microarray-based DNA analysis in a rapid and automated fashion.

Applications of 3D printing in the management of severe spinal conditions.

PubMed

Provaggi, Elena; Leong, Julian J H; Kalaskar, Deepak M

2017-06-01

The latest and fastest-growing innovation in the medical field has been the advent of three-dimensional printing technologies, which have recently seen applications in the production of low-cost, patient-specific medical implants. While a wide range of three-dimensional printing systems has been explored in manufacturing anatomical models and devices for the medical setting, their applications are cutting-edge in the field of spinal surgery. This review aims to provide a comprehensive overview and classification of the current applications of three-dimensional printing technologies in spine care. Although three-dimensional printing technology has been widely used for the construction of patient-specific anatomical models of the spine and intraoperative guide templates to provide personalized surgical planning and increase pedicle screw placement accuracy, only few studies have been focused on the manufacturing of spinal implants. Therefore, three-dimensional printed custom-designed intervertebral fusion devices, artificial vertebral bodies and disc substitutes for total disc replacement, along with tissue engineering strategies focused on scaffold constructs for bone and cartilage regeneration, represent a set of promising applications towards the trend of individualized patient care.

Experimental Approaches to Microarray Analysis of Tumor Samples

ERIC Educational Resources Information Center

Furge, Laura Lowe; Winter, Michael B.; Meyers, Jacob I.; Furge, Kyle A.

2008-01-01

Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has…

Challenges of microarray applications for microbial detection and gene expression profiling in food

USDA-ARS?s Scientific Manuscript database

Microarray technology represents one of the latest advances in molecular biology. The diverse types of microarrays have been applied to clinical and environmental microbiology, microbial ecology, and in human, veterinary, and plant diagnostics. Since multiple genes can be analyzed simultaneously, ...

MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering

PubMed Central

Kim, Eun-Youn; Kim, Seon-Young; Ashlock, Daniel; Nam, Dougu

2009-01-01

Background Uncovering subtypes of disease from microarray samples has important clinical implications such as survival time and sensitivity of individual patients to specific therapies. Unsupervised clustering methods have been used to classify this type of data. However, most existing methods focus on clusters with compact shapes and do not reflect the geometric complexity of the high dimensional microarray clusters, which limits their performance. Results We present a cluster-number-based ensemble clustering algorithm, called MULTI-K, for microarray sample classification, which demonstrates remarkable accuracy. The method amalgamates multiple k-means runs by varying the number of clusters and identifies clusters that manifest the most robust co-memberships of elements. In addition to the original algorithm, we newly devised the entropy-plot to control the separation of singletons or small clusters. MULTI-K, unlike the simple k-means or other widely used methods, was able to capture clusters with complex and high-dimensional structures accurately. MULTI-K outperformed other methods including a recently developed ensemble clustering algorithm in tests with five simulated and eight real gene-expression data sets. Conclusion The geometric complexity of clusters should be taken into account for accurate classification of microarray data, and ensemble clustering applied to the number of clusters tackles the problem very well. The C++ code and the data sets tested are available from the authors. PMID:19698124

Three-dimensional imaging and remote sensing imaging; Proceedings of the Meeting, Los Angeles, CA, Jan. 14, 15, 1988

NASA Astrophysics Data System (ADS)

Robbins, Woodrow E.

1988-01-01

The present conference discusses topics in novel technologies and techniques of three-dimensional imaging, human factors-related issues in three-dimensional display system design, three-dimensional imaging applications, and image processing for remote sensing. Attention is given to a 19-inch parallactiscope, a chromostereoscopic CRT-based display, the 'SpaceGraph' true three-dimensional peripheral, advantages of three-dimensional displays, holographic stereograms generated with a liquid crystal spatial light modulator, algorithms and display techniques for four-dimensional Cartesian graphics, an image processing system for automatic retina diagnosis, the automatic frequency control of a pulsed CO2 laser, and a three-dimensional display of magnetic resonance imaging of the spine.

DNA microarrays: a powerful genomic tool for biomedical and clinical research

PubMed Central

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 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, reveal differences in genetic makeup, regulatory mechanisms and subtle variations are approaching the era of personalized medicine. To understand this powerful tool, its versatility and how it is dramatically changing the molecular approach to biomedical and clinical research, this review describes the technology, its applications, a didactic step-by-step review of a typical microarray protocol, and a real experiment. Finally, it calls the attention of the medical community to integrate multidisciplinary teams, to take advantage of this technology and its expanding applications that in a slide reveals our genetic inheritance and destiny. PMID:17660860

Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels.

PubMed

Sevenler, Derin; Daaboul, George G; Ekiz Kanik, Fulya; Ünlü, Neşe Lortlar; Ünlü, M Selim

2018-05-21

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology's Achilles' heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ("digital") regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique's simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.

Enhancing Interdisciplinary Mathematics and Biology Education: A Microarray Data Analysis Course Bridging These Disciplines

ERIC Educational Resources Information Center

Tra, Yolande V.; Evans, Irene M.

2010-01-01

"BIO2010" put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on…

Three-Dimensional Display Technologies for Anatomical Education: A Literature Review

ERIC Educational Resources Information Center

Hackett, Matthew; Proctor, Michael

2016-01-01

Anatomy is a foundational component of biological sciences and medical education and is important for a variety of clinical tasks. To augment current curriculum and improve students' spatial knowledge of anatomy, many educators, anatomists, and researchers use three-dimensional (3D) visualization technologies. This article reviews 3D display…

Recent Advances in Immersive Visualization of Ocean Data: Virtual Reality Through the Web on Your Laptop Computer

NASA Astrophysics Data System (ADS)

Hermann, A. J.; Moore, C.; Soreide, N. N.

2002-12-01

Ocean circulation is irrefutably three dimensional, and powerful new measurement technologies and numerical models promise to expand our three-dimensional knowledge of the dynamics further each year. Yet, most ocean data and model output is still viewed using two-dimensional maps. Immersive visualization techniques allow the investigator to view their data as a three dimensional world of surfaces and vectors which evolves through time. The experience is not unlike holding a part of the ocean basin in one's hand, turning and examining it from different angles. While immersive, three dimensional visualization has been possible for at least a decade, the technology was until recently inaccessible (both physically and financially) for most researchers. It is not yet fully appreciated by practicing oceanographers how new, inexpensive computing hardware and software (e.g. graphics cards and controllers designed for the huge PC gaming market) can be employed for immersive, three dimensional, color visualization of their increasingly huge datasets and model output. In fact, the latest developments allow immersive visualization through web servers, giving scientists the ability to "fly through" three-dimensional data stored half a world away. Here we explore what additional insight is gained through immersive visualization, describe how scientists of very modest means can easily avail themselves of the latest technology, and demonstrate its implementation on a web server for Pacific Ocean model output.

A New Way to Introduce Microarray Technology in a Lecture/Laboratory Setting by Studying the Evolution of This Modern Technology

ERIC Educational Resources Information Center

Rowland-Goldsmith, Melissa

2009-01-01

DNA microarray is an ordered grid containing known sequences of DNA, which represent many of the genes in a particular organism. Each DNA sequence is unique to a specific gene. This technology enables the researcher to screen many genes from cells or tissue grown in different conditions. We developed an undergraduate lecture and laboratory…

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

EPA Science Inventory

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, ...

Human neural stem cell-derived cultures in three-dimensional substrates form spontaneously functional neuronal networks.

PubMed

Smith, Imogen; Silveirinha, Vasco; Stein, Jason L; de la Torre-Ubieta, Luis; Farrimond, Jonathan A; Williamson, Elizabeth M; Whalley, Benjamin J

2017-04-01

Differentiated human neural stem cells were cultured in an inert three-dimensional (3D) scaffold and, unlike two-dimensional (2D) but otherwise comparable monolayer cultures, formed spontaneously active, functional neuronal networks that responded reproducibly and predictably to conventional pharmacological treatments to reveal functional, glutamatergic synapses. Immunocytochemical and electron microscopy analysis revealed a neuronal and glial population, where markers of neuronal maturity were observed in the former. Oligonucleotide microarray analysis revealed substantial differences in gene expression conferred by culturing in a 3D vs a 2D environment. Notable and numerous differences were seen in genes coding for neuronal function, the extracellular matrix and cytoskeleton. In addition to producing functional networks, differentiated human neural stem cells grown in inert scaffolds offer several significant advantages over conventional 2D monolayers. These advantages include cost savings and improved physiological relevance, which make them better suited for use in the pharmacological and toxicological assays required for development of stem cell-based treatments and the reduction of animal use in medical research. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Analytical Protein Microarrays: Advancements Towards Clinical Applications

PubMed Central

Sauer, Ursula

2017-01-01

Protein microarrays represent a powerful technology with the potential to serve as tools for the detection of a broad range of analytes in numerous applications such as diagnostics, drug development, food safety, and environmental monitoring. Key features of analytical protein microarrays include high throughput and relatively low costs due to minimal reagent consumption, multiplexing, fast kinetics and hence measurements, and the possibility of functional integration. So far, especially fundamental studies in molecular and cell biology have been conducted using protein microarrays, while the potential for clinical, notably point-of-care applications is not yet fully utilized. The question arises what features have to be implemented and what improvements have to be made in order to fully exploit the technology. In the past we have identified various obstacles that have to be overcome in order to promote protein microarray technology in the diagnostic field. Issues that need significant improvement to make the technology more attractive for the diagnostic market are for instance: too low sensitivity and deficiency in reproducibility, inadequate analysis time, lack of high-quality antibodies and validated reagents, lack of automation and portable instruments, and cost of instruments necessary for chip production and read-out. The scope of the paper at hand is to review approaches to solve these problems. PMID:28146048

Manufacturing of microarrays.

PubMed

Petersen, David W; Kawasaki, Ernest S

2007-01-01

DNA microarray technology has become a powerful tool in the arsenal of the molecular biologist. Capitalizing on high precision robotics and the wealth of DNA sequences annotated from the genomes of a large number of organisms, the manufacture of microarrays is now possible for the average academic laboratory with the funds and motivation. Microarray production requires attention to both biological and physical resources, including DNA libraries, robotics, and qualified personnel. While the fabrication of microarrays is a very labor-intensive process, production of quality microarrays individually tailored on a project-by-project basis will help researchers shed light on future scientific questions.

Virtual Reality Training With Three-Dimensional Video Games Improves Postural Balance and Lower Extremity Strength in Community-Dwelling Older Adults.

PubMed

Lee, Yongwoo; Choi, Wonjae; Lee, Kyeongjin; Song, Changho; Lee, Seungwon

2017-10-01

Avatar-based three-dimensional technology is a new approach to improve physical function in older adults. The aim of this study was to use three-dimensional video gaming technology in virtual reality training to improve postural balance and lower extremity strength in a population of community-dwelling older adults. The experimental group participated in the virtual reality training program for 60 min, twice a week, for 6 weeks. Both experimental and control groups were given three times for falls prevention education at the first, third, and fifth weeks. The experimental group showed significant improvements not only in static and dynamic postural balance but also lower extremity strength (p < .05). Furthermore, the experimental group was improved to overall parameters compared with the control group (p < .05). Therefore, three-dimensional video gaming technology might be beneficial for improving postural balance and lower extremity strength in community-dwelling older adults.

Integrating Colon Cancer Microarray Data: Associating Locus-Specific Methylation Groups to Gene Expression-Based Classifications.

PubMed

Barat, Ana; Ruskin, Heather J; Byrne, Annette T; Prehn, Jochen H M

2015-11-23

Recently, considerable attention has been paid to gene expression-based classifications of colorectal cancers (CRC) and their association with patient prognosis. In addition to changes in gene expression, abnormal DNA-methylation is known to play an important role in cancer onset and development, and colon cancer is no exception to this rule. Large-scale technologies, such as methylation microarray assays and specific sequencing of methylated DNA, have been used to determine whole genome profiles of CpG island methylation in tissue samples. In this article, publicly available microarray-based gene expression and methylation data sets are used to characterize expression subtypes with respect to locus-specific methylation. A major objective was to determine whether integration of these data types improves previously characterized subtypes, or provides evidence for additional subtypes. We used unsupervised clustering techniques to determine methylation-based subgroups, which are subsequently annotated with three published expression-based classifications, comprising from three to six subtypes. Our results showed that, while methylation profiles provide a further basis for segregation of certain (Inflammatory and Goblet-like) finer-grained expression-based subtypes, they also suggest that other finer-grained subtypes are not distinctive and can be considered as a single subtype.

Integrating Colon Cancer Microarray Data: Associating Locus-Specific Methylation Groups to Gene Expression-Based Classifications

PubMed Central

Barat, Ana; Ruskin, Heather J.; Byrne, Annette T.; Prehn, Jochen H. M.

2015-01-01

Recently, considerable attention has been paid to gene expression-based classifications of colorectal cancers (CRC) and their association with patient prognosis. In addition to changes in gene expression, abnormal DNA-methylation is known to play an important role in cancer onset and development, and colon cancer is no exception to this rule. Large-scale technologies, such as methylation microarray assays and specific sequencing of methylated DNA, have been used to determine whole genome profiles of CpG island methylation in tissue samples. In this article, publicly available microarray-based gene expression and methylation data sets are used to characterize expression subtypes with respect to locus-specific methylation. A major objective was to determine whether integration of these data types improves previously characterized subtypes, or provides evidence for additional subtypes. We used unsupervised clustering techniques to determine methylation-based subgroups, which are subsequently annotated with three published expression-based classifications, comprising from three to six subtypes. Our results showed that, while methylation profiles provide a further basis for segregation of certain (Inflammatory and Goblet-like) finer-grained expression-based subtypes, they also suggest that other finer-grained subtypes are not distinctive and can be considered as a single subtype. PMID:27600244

A Robust Unified Approach to Analyzing Methylation and Gene Expression Data

PubMed Central

Khalili, Abbas; Huang, Tim; Lin, Shili

2009-01-01

Microarray technology has made it possible to investigate expression levels, and more recently methylation signatures, of thousands of genes simultaneously, in a biological sample. Since more and more data from different biological systems or technological platforms are being generated at an incredible rate, there is an increasing need to develop statistical methods that are applicable to multiple data types and platforms. Motivated by such a need, a flexible finite mixture model that is applicable to methylation, gene expression, and potentially data from other biological systems, is proposed. Two major thrusts of this approach are to allow for a variable number of components in the mixture to capture non-biological variation and small biases, and to use a robust procedure for parameter estimation and probe classification. The method was applied to the analysis of methylation signatures of three breast cancer cell lines. It was also tested on three sets of expression microarray data to study its power and type I error rates. Comparison with a number of existing methods in the literature yielded very encouraging results; lower type I error rates and comparable/better power were achieved based on the limited study. Furthermore, the method also leads to more biologically interpretable results for the three breast cancer cell lines. PMID:20161265

High-throughput screening in two dimensions: binding intensity and off-rate on a peptide microarray.

PubMed

Greving, Matthew P; Belcher, Paul E; Cox, Conor D; Daniel, Douglas; Diehnelt, Chris W; Woodbury, Neal W

2010-07-01

We report a high-throughput two-dimensional microarray-based screen, incorporating both target binding intensity and off-rate, which can be used to analyze thousands of compounds in a single binding assay. Relative binding intensities and time-resolved dissociation are measured for labeled tumor necrosis factor alpha (TNF-alpha) bound to a peptide microarray. The time-resolved dissociation is fitted to a one-component exponential decay model, from which relative dissociation rates are determined for all peptides with binding intensities above background. We show that most peptides with the slowest off-rates on the microarray also have the slowest off-rates when measured by surface plasmon resonance (SPR). 2010 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gentry, T.; Schadt, C.; Zhou, J.

Microarray technology has the unparalleled potential tosimultaneously determine the dynamics and/or activities of most, if notall, of the microbial populations in complex environments such as soilsand sediments. Researchers have developed several types of arrays thatcharacterize the microbial populations in these samples based on theirphylogenetic relatedness or functional genomic content. Several recentstudies have used these microarrays to investigate ecological issues;however, most have only analyzed a limited number of samples withrelatively few experiments utilizing the full high-throughput potentialof microarray analysis. This is due in part to the unique analyticalchallenges that these samples present with regard to sensitivity,specificity, quantitation, and data analysis. Thismore » review discussesspecific applications of microarrays to microbial ecology research alongwith some of the latest studies addressing the difficulties encounteredduring analysis of complex microbial communities within environmentalsamples. With continued development, microarray technology may ultimatelyachieve its potential for comprehensive, high-throughput characterizationof microbial populations in near real-time.« less

Towards three-dimensional optical metamaterials

NASA Astrophysics Data System (ADS)

Tanaka, Takuo; Ishikawa, Atsushi

2017-12-01

Metamaterials have opened up the possibility of unprecedented and fascinating concepts and applications in optics and photonics. Examples include negative refraction, perfect lenses, cloaking, perfect absorbers, and so on. Since these metamaterials are man-made materials composed of sub-wavelength structures, their development strongly depends on the advancement of micro- and nano-fabrication technologies. In particular, the realization of three-dimensional metamaterials is one of the big challenges in this research field. In this review, we describe recent progress in the fabrication technologies for three-dimensional metamaterials, as well as proposed applications.

Three-dimensional ultrasound and image-directed surgery: implications for operating room personnel.

PubMed

Macedonia, C

1997-04-01

The proliferation of new imaging technologies is having a profound impact on all surgical specialties. New means of surgical visualization are allowing more surgeries to be performed less invasively. Three-dimensional ultrasound is a technology that has potential as a diagnostic tool, as a presurgical planning simulator, and as an adjunct to image-directed surgery. This article describes how three-dimensional ultrasound is being used by the United States Department of Defense and how it may change the role of the perioperative nurse in the near future.

Use of Microarray to Analyze Gene Expression Profiles of Acute Effects of Prochloraz on Fathead Minnows Pimephales promelas

EPA Science Inventory

Microarray technology is a powerful tool to investigate the gene expression profiles for thousands of genes simultaneously. In recent years, microarrays have been used to characterize environmental pollutants and identify molecular mode(s) of action of chemicals including endocri...

Microarrays Made Simple: "DNA Chips" Paper Activity

ERIC Educational Resources Information Center

Barnard, Betsy

2006-01-01

DNA microarray technology is revolutionizing biological science. DNA microarrays (also called DNA chips) allow simultaneous screening of many genes for changes in expression between different cells. Now researchers can obtain information about genes in days or weeks that used to take months or years. The paper activity described in this article…

Development of a DNA microarray for species identification of quarantine aphids.

PubMed

Lee, Won Sun; Choi, Hwalran; Kang, Jinseok; Kim, Ji-Hoon; Lee, Si Hyeock; Lee, Seunghwan; Hwang, Seung Yong

2013-12-01

Aphid pests are being brought into Korea as a result of increased crop trading. Aphids exist on growth areas of plants, and thus plant growth is seriously affected by aphid pests. However, aphids are very small and have several sexual morphs and life stages, so it is difficult to identify species on the basis of morphological features. This problem was approached using DNA microarray technology. DNA targets of the cytochrome c oxidase subunit I gene were generated with a fluorescent dye-labelled primer and were hybridised onto a DNA microarray consisting of specific probes. After analysing the signal intensity of the specific probes, the unique patterns from the DNA microarray, consisting of 47 species-specific probes, were obtained to identify 23 aphid species. To confirm the accuracy of the developed DNA microarray, ten individual blind samples were used in blind trials, and the identifications were completely consistent with the sequencing data of all individual blind samples. A microarray has been developed to distinguish aphid species. DNA microarray technology provides a rapid, easy, cost-effective and accurate method for identifying aphid species for pest control management. © 2013 Society of Chemical Industry.

Derivation of an artificial gene to improve classification accuracy upon gene selection.

PubMed

Seo, Minseok; Oh, Sejong

2012-02-01

Classification analysis has been developed continuously since 1936. This research field has advanced as a result of development of classifiers such as KNN, ANN, and SVM, as well as through data preprocessing areas. Feature (gene) selection is required for very high dimensional data such as microarray before classification work. The goal of feature selection is to choose a subset of informative features that reduces processing time and provides higher classification accuracy. In this study, we devised a method of artificial gene making (AGM) for microarray data to improve classification accuracy. Our artificial gene was derived from a whole microarray dataset, and combined with a result of gene selection for classification analysis. We experimentally confirmed a clear improvement of classification accuracy after inserting artificial gene. Our artificial gene worked well for popular feature (gene) selection algorithms and classifiers. The proposed approach can be applied to any type of high dimensional dataset. Copyright © 2011 Elsevier Ltd. All rights reserved.

Differences in brain gene expression between sleep and waking as revealed by mRNA differential display and cDNA microarray technology.

PubMed

Cirelli, C; Tononi, G

1999-06-01

The consequences of sleep and sleep deprivation at the molecular level are largely unexplored. Knowledge of such molecular events is essential to understand the restorative processes occurring during sleep as well as the cellular mechanisms of sleep regulation. Here we review the available data about changes in neural gene expression across different behavioural states using candidate gene approaches such as in situ hybridization and immunocytochemistry. We then describe new techniques for systematic screening of gene expression in the brain, such as subtractive hybridization, mRNA differential display, and cDNA microarray technology, outlining advantages and disadvantages of these methods. Finally, we summarize our initial results of a systematic screening of gene expression in the rat brain across behavioural states using mRNA differential display and cDNA microarray technology. The expression pattern of approximately 7000 genes was analysed in the cerebral cortex of rats after 3 h of spontaneous sleep, 3 h of spontaneous waking, or 3 h of sleep deprivation. While the majority of transcripts were expressed at the same level among these three conditions, 14 mRNAs were modulated by sleep and waking. Six transcripts, four more expressed in waking and two more expressed in sleep, corresponded to novel genes. The eight known transcripts were all expressed at higher levels in waking than in sleep and included transcription factors and mitochondrial genes. A possible role for these known transcripts in mediating neural plasticity during waking is discussed.

Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications

PubMed Central

Scheler, Ott; Glynn, Barry; Parkel, Sven; Palta, Priit; Toome, Kadri; Kaplinski, Lauris; Remm, Maido; Maher, Majella; Kurg, Ants

2009-01-01

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. PMID:19445684

Pursuing Mirror Image Reconstruction in Unilateral Microtia: Customizing Auricular Framework by Application of Three-Dimensional Imaging and Three-Dimensional Printing.

PubMed

Chen, Hsin-Yu; Ng, Li-Shia; Chang, Chun-Shin; Lu, Ting-Chen; Chen, Ning-Hung; Chen, Zung-Chung

2017-06-01

Advances in three-dimensional imaging and three-dimensional printing technology have expanded the frontier of presurgical design for microtia reconstruction from two-dimensional curved lines to three-dimensional perspectives. This study presents an algorithm for combining three-dimensional surface imaging, computer-assisted design, and three-dimensional printing to create patient-specific auricular frameworks in unilateral microtia reconstruction. Between January of 2015 and January of 2016, six patients with unilateral microtia were enrolled. The average age of the patients was 7.6 years. A three-dimensional image of the patient's head was captured by 3dMDcranial, and virtual sculpture carried out using Geomagic Freeform software and a Touch X Haptic device for fabrication of the auricular template. Each template was tailored according to the patient's unique auricular morphology. The final construct was mirrored onto the defective side and printed out with biocompatible acrylic material. During the surgery, the prefabricated customized template served as a three-dimensional guide for surgical simulation and sculpture of the MEDPOR framework. Average follow-up was 10.3 months. Symmetric and good aesthetic results with regard to auricular shape, projection, and orientation were obtained. One case with severe implant exposure was salvaged with free temporoparietal fascia transfer and skin grafting. The combination of three-dimensional imaging and manufacturing technology with the malleability of MEDPOR has surpassed existing limitations resulting from the use of autologous materials and the ambiguity of two-dimensional planning. This approach allows surgeons to customize the auricular framework in a highly precise and sophisticated manner, taking a big step closer to the goal of mirror-image reconstruction for unilateral microtia patients. Therapeutic, IV.

Three-Dimensional Printing Surgical Applications.

PubMed

AlAli, Ahmad B; Griffin, Michelle F; Butler, Peter E

2015-01-01

Three-dimensional printing, a technology used for decades in the industrial field, gains a lot of attention in the medical field for its potential benefits. With advancement of desktop printers, this technology is accessible and a lot of research is going on in the medical field. To evaluate its application in surgical field, which may include but not limited to surgical planning, surgical education, implants, and prosthesis, which are the focus of this review. Research was conducted by searching PubMed, Web of science, and other reliable sources. We included original articles and excluded articles based on animals, those more than 10 years old, and those not in English. These articles were evaluated, and relevant studies were included in this review. Three-dimensional printing shows a potential benefit in surgical application. Printed implants were used in patient in a few cases and show successful results; however, longer follow-up and more trials are needed. Surgical and medical education is believed to be more efficient with this technology than the current practice. Printed surgical instrument and surgical planning are also believed to improve with three-dimensional printing. Three-dimensional printing can be a very powerful tool in the near future, which can aid the medical field that is facing a lot of challenges and obstacles. However, despite the reported results, further research on larger samples and analytical measurements should be conducted to ensure this technology's impact on the practice.

A study of metaheuristic algorithms for high dimensional feature selection on microarray data

NASA Astrophysics Data System (ADS)

Dankolo, Muhammad Nasiru; Radzi, Nor Haizan Mohamed; Sallehuddin, Roselina; Mustaffa, Noorfa Haszlinna

2017-11-01

Microarray systems enable experts to examine gene profile at molecular level using machine learning algorithms. It increases the potentials of classification and diagnosis of many diseases at gene expression level. Though, numerous difficulties may affect the efficiency of machine learning algorithms which includes vast number of genes features comprised in the original data. Many of these features may be unrelated to the intended analysis. Therefore, feature selection is necessary to be performed in the data pre-processing. Many feature selection algorithms are developed and applied on microarray which including the metaheuristic optimization algorithms. This paper discusses the application of the metaheuristics algorithms for feature selection in microarray dataset. This study reveals that, the algorithms have yield an interesting result with limited resources thereby saving computational expenses of machine learning algorithms.

APPLICATION OF GENE ARRAY TECHNOLOGY IN THE RESEARCH OF CARDIOPULMONARY TOXICITY INDUCED BY PARTICULATE MATTER (PM) AND ITS CONSTITUENTS.

EPA Science Inventory

Because of its ability to provide a "snap-shot" view of expression of large number of genes simultaneously, the microarray technology may be a useful tool to uncover new mechanisms of toxicity. This proposal will use the state-of-the-art gene microarrays and a new bioinformatic t...

Three-dimensional magnetic bubble memory system

NASA Technical Reports Server (NTRS)

Stadler, Henry L. (Inventor); Katti, Romney R. (Inventor); Wu, Jiin-Chuan (Inventor)

1994-01-01

A compact memory uses magnetic bubble technology for providing data storage. A three-dimensional arrangement, in the form of stacks of magnetic bubble layers, is used to achieve high volumetric storage density. Output tracks are used within each layer to allow data to be accessed uniquely and unambiguously. Storage can be achieved using either current access or field access magnetic bubble technology. Optical sensing via the Faraday effect is used to detect data. Optical sensing facilitates the accessing of data from within the three-dimensional package and lends itself to parallel operation for supporting high data rates and vector and parallel processing.

Classification of Microarray Data Using Kernel Fuzzy Inference System

PubMed Central

Kumar Rath, Santanu

2014-01-01

The DNA microarray classification technique has gained more popularity in both research and practice. In real data analysis, such as microarray data, the dataset contains a huge number of insignificant and irrelevant features that tend to lose useful information. Classes with high relevance and feature sets with high significance are generally referred for the selected features, which determine the samples classification into their respective classes. In this paper, kernel fuzzy inference system (K-FIS) algorithm is applied to classify the microarray data (leukemia) using t-test as a feature selection method. Kernel functions are used to map original data points into a higher-dimensional (possibly infinite-dimensional) feature space defined by a (usually nonlinear) function ϕ through a mathematical process called the kernel trick. This paper also presents a comparative study for classification using K-FIS along with support vector machine (SVM) for different set of features (genes). Performance parameters available in the literature such as precision, recall, specificity, F-measure, ROC curve, and accuracy are considered to analyze the efficiency of the classification model. From the proposed approach, it is apparent that K-FIS model obtains similar results when compared with SVM model. This is an indication that the proposed approach relies on kernel function. PMID:27433543

[Application advances of three-dimensional bioprinting in burn and plastic surgery field].

PubMed

Li, R B; Li, M X; Guo, G H; Zhang, H Y

2017-10-20

Three-dimensional bioprinting is one of the latest and fastest growing technologies in the medical field. It has been implemented to print part of the transplantable tissues and organs, such as skin, ear, and bone. This paper introduces the application status, challenges, and application prospect of three-dimensional bioprinting in burn and plastic surgery field.

Visualization of Two Dimensional to Three Dimensional Transformations--Exploration through Technology

ERIC Educational Resources Information Center

Costa, G. B.; Gorak, M.; Melendez, B. S.

2006-01-01

A small class of functions is described that easily lend themselves to two-dimensional and three-dimensional visualizations at the basic calculus level. The intended audience is those educators involved in the instruction of elementary calculus. This note is an educational piece that begins with the question: "What happens if a function defined on…

Method for making a bio-compatible scaffold

DOEpatents

Cesarano, III, Joseph; Stuecker, John N [Albuquerque, NM; Dellinger, Jennifer G [Champaigne, IL; Jamison, Russell D [Urbana, IL

2006-01-31

A method for forming a three-dimensional, biocompatible, porous scaffold structure using a solid freeform fabrication technique (referred to herein as robocasting) that can be used as a medical implant into a living organism, such as a human or other mammal. Imaging technology and analysis is first used to determine the three-dimensional design required for the medical implant, such as a bone implant or graft, fashioned as a three-dimensional, biocompatible scaffold structure. The robocasting technique is used to either directly produce the three-dimensional, porous scaffold structure or to produce an over-sized three-dimensional, porous scaffold lattice which can be machined to produce the designed three-dimensional, porous scaffold structure for implantation.

The emergence and diffusion of DNA microarray technology.

PubMed

Lenoir, Tim; Giannella, Eric

2006-08-22

The network model of innovation widely adopted among researchers in the economics of science and technology posits relatively porous boundaries between firms and academic research programs and a bi-directional flow of inventions, personnel, and tacit knowledge between sites of university and industry innovation. Moreover, the model suggests that these bi-directional flows should be considered as mutual stimulation of research and invention in both industry and academe, operating as a positive feedback loop. One side of this bi-directional flow--namely; the flow of inventions into industry through the licensing of university-based technologies--has been well studied; but the reverse phenomenon of the stimulation of university research through the absorption of new directions emanating from industry has yet to be investigated in much detail. We discuss the role of federal funding of academic research in the microarray field, and the multiple pathways through which federally supported development of commercial microarray technologies have transformed core academic research fields. Our study confirms the picture put forward by several scholars that the open character of networked economies is what makes them truly innovative. In an open system innovations emerge from the network. The emergence and diffusion of microarray technologies we have traced here provides an excellent example of an open system of innovation in action. Whether they originated in a startup company environment that operated like a think-tank, such as Affymax, the research labs of a large firm, such as Agilent, or within a research university, the inventors we have followed drew heavily on knowledge resources from all parts of the network in bringing microarray platforms to light. Federal funding for high-tech startups and new industrial development was important at several phases in the early history of microarrays, and federal funding of academic researchers using microarrays was fundamental to transforming the research agendas of several fields within academe. The typical story told about the role of federal funding emphasizes the spillovers from federally funded academic research to industry. Our study shows that the knowledge spillovers worked both ways, with federal funding of non-university research providing the impetus for reshaping the research agendas of several academic fields.

The emergence and diffusion of DNA microarray technology

PubMed Central

Lenoir, Tim; Giannella, Eric

2006-01-01

The network model of innovation widely adopted among researchers in the economics of science and technology posits relatively porous boundaries between firms and academic research programs and a bi-directional flow of inventions, personnel, and tacit knowledge between sites of university and industry innovation. Moreover, the model suggests that these bi-directional flows should be considered as mutual stimulation of research and invention in both industry and academe, operating as a positive feedback loop. One side of this bi-directional flow – namely; the flow of inventions into industry through the licensing of university-based technologies – has been well studied; but the reverse phenomenon of the stimulation of university research through the absorption of new directions emanating from industry has yet to be investigated in much detail. We discuss the role of federal funding of academic research in the microarray field, and the multiple pathways through which federally supported development of commercial microarray technologies have transformed core academic research fields. Our study confirms the picture put forward by several scholars that the open character of networked economies is what makes them truly innovative. In an open system innovations emerge from the network. The emergence and diffusion of microarray technologies we have traced here provides an excellent example of an open system of innovation in action. Whether they originated in a startup company environment that operated like a think-tank, such as Affymax, the research labs of a large firm, such as Agilent, or within a research university, the inventors we have followed drew heavily on knowledge resources from all parts of the network in bringing microarray platforms to light. Federal funding for high-tech startups and new industrial development was important at several phases in the early history of microarrays, and federal funding of academic researchers using microarrays was fundamental to transforming the research agendas of several fields within academe. The typical story told about the role of federal funding emphasizes the spillovers from federally funded academic research to industry. Our study shows that the knowledge spillovers worked both ways, with federal funding of non-university research providing the impetus for reshaping the research agendas of several academic fields. PMID:16925816

Crossword: A Fully Automated Algorithm for the Segmentation and Quality Control of Protein Microarray Images

PubMed Central

2015-01-01

Biological assays formatted as microarrays have become a critical tool for the generation of the comprehensive data sets required for systems-level understanding of biological processes. Manual annotation of data extracted from images of microarrays, however, remains a significant bottleneck, particularly for protein microarrays due to the sensitivity of this technology to weak artifact signal. In order to automate the extraction and curation of data from protein microarrays, we describe an algorithm called Crossword that logically combines information from multiple approaches to fully automate microarray segmentation. Automated artifact removal is also accomplished by segregating structured pixels from the background noise using iterative clustering and pixel connectivity. Correlation of the location of structured pixels across image channels is used to identify and remove artifact pixels from the image prior to data extraction. This component improves the accuracy of data sets while reducing the requirement for time-consuming visual inspection of the data. Crossword enables a fully automated protocol that is robust to significant spatial and intensity aberrations. Overall, the average amount of user intervention is reduced by an order of magnitude and the data quality is increased through artifact removal and reduced user variability. The increase in throughput should aid the further implementation of microarray technologies in clinical studies. PMID:24417579

Promise and progress in environmental genomics: a status report on the applications of gene expression-based microarray studies in ecologically relevant fish species.

PubMed

Hook, S E

2010-12-01

The advent of any new technology is typically met with great excitement. So it was a few years ago, when the combination of advances in sequencing technology and the development of microarray technology made measurements of global gene expression in ecologically relevant species possible. Many of the review papers published around that time promised that these new technologies would revolutionize environmental biology as they had revolutionized medicine and related fields. A few years have passed since these technological advancements have been made, and the use of microarray studies in non-model fish species has been adopted in many laboratories internationally. Has the relatively widespread adoption of this technology really revolutionized the fields of environmental biology, including ecotoxicology, aquaculture and ecology, as promised? Or have these studies merely become a novelty and a potential distraction for scientists addressing environmentally relevant questions? In this review, the promises made in early review papers, in particular about the advances that the use of microarrays would enable, are summarized; these claims are compared to the results of recent studies to determine whether the forecasted changes have materialized. Some applications, as discussed in the paper, have been realized and have led to advances in their field, others are still under development. © 2010 CSIRO. Journal of Fish Biology © 2010 The Fisheries Society of the British Isles.

A Meta-Analysis of the Educational Effectiveness of Three-Dimensional Visualization Technologies in Teaching Anatomy

ERIC Educational Resources Information Center

Yammine, Kaissar; Violato, Claudio

2015-01-01

Many medical graduates are deficient in anatomy knowledge and perhaps below the standards for safe medical practice. Three-dimensional visualization technology (3DVT) has been advanced as a promising tool to enhance anatomy knowledge. The purpose of this review is to conduct a meta-analysis of the effectiveness of 3DVT in teaching and learning…

Microengineering methods for cell-based microarrays and high-throughput drug-screening applications.

PubMed

Xu, Feng; Wu, JinHui; Wang, ShuQi; Durmus, Naside Gozde; Gurkan, Umut Atakan; Demirci, Utkan

2011-09-01

Screening for effective therapeutic agents from millions of drug candidates is costly, time consuming, and often faces concerns due to the extensive use of animals. To improve cost effectiveness, and to minimize animal testing in pharmaceutical research, in vitro monolayer cell microarrays with multiwell plate assays have been developed. Integration of cell microarrays with microfluidic systems has facilitated automated and controlled component loading, significantly reducing the consumption of the candidate compounds and the target cells. Even though these methods significantly increased the throughput compared to conventional in vitro testing systems and in vivo animal models, the cost associated with these platforms remains prohibitively high. Besides, there is a need for three-dimensional (3D) cell-based drug-screening models which can mimic the in vivo microenvironment and the functionality of the native tissues. Here, we present the state-of-the-art microengineering approaches that can be used to develop 3D cell-based drug-screening assays. We highlight the 3D in vitro cell culture systems with live cell-based arrays, microfluidic cell culture systems, and their application to high-throughput drug screening. We conclude that among the emerging microengineering approaches, bioprinting holds great potential to provide repeatable 3D cell-based constructs with high temporal, spatial control and versatility.

Microengineering Methods for Cell Based Microarrays and High-Throughput Drug Screening Applications

PubMed Central

Xu, Feng; Wu, JinHui; Wang, ShuQi; Durmus, Naside Gozde; Gurkan, Umut Atakan; Demirci, Utkan

2011-01-01

Screening for effective therapeutic agents from millions of drug candidates is costly, time-consuming and often face ethical concerns due to extensive use of animals. To improve cost-effectiveness, and to minimize animal testing in pharmaceutical research, in vitro monolayer cell microarrays with multiwell plate assays have been developed. Integration of cell microarrays with microfluidic systems have facilitated automated and controlled component loading, significantly reducing the consumption of the candidate compounds and the target cells. Even though these methods significantly increased the throughput compared to conventional in vitro testing systems and in vivo animal models, the cost associated with these platforms remains prohibitively high. Besides, there is a need for three-dimensional (3D) cell based drug-screening models, which can mimic the in vivo microenvironment and the functionality of the native tissues. Here, we present the state-of-the-art microengineering approaches that can be used to develop 3D cell based drug screening assays. We highlight the 3D in vitro cell culture systems with live cell-based arrays, microfluidic cell culture systems, and their application to high-throughput drug screening. We conclude that among the emerging microengineering approaches, bioprinting holds a great potential to provide repeatable 3D cell based constructs with high temporal, spatial control and versatility. PMID:21725152

Mass-transport limitations in spot-based microarrays.

PubMed

Zhao, Ming; Wang, Xuefeng; Nolte, David

2010-09-20

Mass transport of analyte to surface-immobilized affinity reagents is the fundamental bottleneck for sensitive detection in solid-support microarrays and biosensors. Analyte depletion in the volume adjacent to the sensor causes deviation from ideal association, significantly slows down reaction kinetics, and causes inhomogeneous binding across the sensor surface. In this paper we use high-resolution molecular interferometric imaging (MI2), a label-free optical interferometry technique for direct detection of molecular films, to study the inhomogeneous distribution of intra-spot binding across 100 micron-diameter protein spots. By measuring intra-spot binding inhomogeneity, reaction kinetics can be determined accurately when combined with a numerical three-dimensional finite element model. To ensure homogeneous binding across a spot, a critical flow rate is identified in terms of the association rate k(a) and the spot diameter. The binding inhomogeneity across a spot can be used to distinguish high-affinity low-concentration specific reactions from low-affinity high-concentration non-specific binding of background proteins.

DNA microarray technology in nutraceutical and food safety.

PubMed

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.

The Glycan Microarray Story from Construction to Applications.

PubMed

Hyun, Ji Young; Pai, Jaeyoung; Shin, Injae

2017-04-18

Not only are glycan-mediated binding processes in cells and organisms essential for a wide range of physiological processes, but they are also implicated in various pathological processes. As a result, elucidation of glycan-associated biomolecular interactions and their consequences is of great importance in basic biological research and biomedical applications. In 2002, we and others were the first to utilize glycan microarrays in efforts aimed at the rapid analysis of glycan-associated recognition events. Because they contain a number of glycans immobilized in a dense and orderly manner on a solid surface, glycan microarrays enable multiple parallel analyses of glycan-protein binding events while utilizing only small amounts of glycan samples. Therefore, this microarray technology has become a leading edge tool in studies aimed at elucidating roles played by glycans and glycan binding proteins in biological systems. In this Account, we summarize our efforts on the construction of glycan microarrays and their applications in studies of glycan-associated interactions. Immobilization strategies of functionalized and unmodified glycans on derivatized glass surfaces are described. Although others have developed immobilization techniques, our efforts have focused on improving the efficiencies and operational simplicity of microarray construction. The microarray-based technology has been most extensively used for rapid analysis of the glycan binding properties of proteins. In addition, glycan microarrays have been employed to determine glycan-protein interactions quantitatively, detect pathogens, and rapidly assess substrate specificities of carbohydrate-processing enzymes. More recently, the microarrays have been employed to identify functional glycans that elicit cell surface lectin-mediated cellular responses. Owing to these efforts, it is now possible to use glycan microarrays to expand the understanding of roles played by glycans and glycan binding proteins in biological systems.

Profiling In Situ Microbial Community Structure with an Amplification Microarray

PubMed Central

Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

2013-01-01

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3−) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

Three-Dimensional Printing Surgical Applications

PubMed Central

Griffin, Michelle F.; Butler, Peter E.

2015-01-01

Introduction: Three-dimensional printing, a technology used for decades in the industrial field, gains a lot of attention in the medical field for its potential benefits. With advancement of desktop printers, this technology is accessible and a lot of research is going on in the medical field. Objective: To evaluate its application in surgical field, which may include but not limited to surgical planning, surgical education, implants, and prosthesis, which are the focus of this review. Methods: Research was conducted by searching PubMed, Web of science, and other reliable sources. We included original articles and excluded articles based on animals, those more than 10 years old, and those not in English. These articles were evaluated, and relevant studies were included in this review. Discussion: Three-dimensional printing shows a potential benefit in surgical application. Printed implants were used in patient in a few cases and show successful results; however, longer follow-up and more trials are needed. Surgical and medical education is believed to be more efficient with this technology than the current practice. Printed surgical instrument and surgical planning are also believed to improve with three-dimensional printing. Conclusion: Three-dimensional printing can be a very powerful tool in the near future, which can aid the medical field that is facing a lot of challenges and obstacles. However, despite the reported results, further research on larger samples and analytical measurements should be conducted to ensure this technology's impact on the practice. PMID:26301002

Real World Audio

NASA Technical Reports Server (NTRS)

1998-01-01

Crystal River Engineering was originally featured in Spinoff 1992 with the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. The Convolvotron was developed for Ames' research on virtual acoustic displays. Crystal River is a now a subsidiary of Aureal Semiconductor, Inc. and they together develop and market the technology, which is a 3-D (three dimensional) audio technology known commercially today as Aureal 3D (A-3D). The technology has been incorporated into video games, surround sound systems, and sound cards.

Bacterial identification and subtyping using DNA microarray and DNA sequencing.

PubMed

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.

Upregulated epidermal growth factor receptor expression following near-infrared irradiation simulating solar radiation in a three-dimensional reconstructed human corneal epithelial tissue culture model

PubMed Central

Tanaka, Yohei; Nakayama, Jun

2016-01-01

Background and objective Humans are increasingly exposed to near-infrared (NIR) radiation from both natural (eg, solar) and artificial (eg, electrical appliances) sources. Although the biological effects of sun and ultraviolet (UV) exposure have been extensively investigated, the biological effect of NIR radiation is still unclear. We previously reported that NIR as well as UV induces photoaging and standard UV-blocking materials, such as sunglasses, do not sufficiently block NIR. The objective of this study was to investigate changes in gene expression in three-dimensional reconstructed corneal epithelial tissue culture exposed to broad-spectrum NIR irradiation to simulate solar NIR radiation that reaches human tissues. Materials and methods DNA microarray and quantitative real-time polymerase chain reaction analysis were used to assess gene expression levels in a three-dimensional reconstructed corneal epithelial model composed of normal human corneal epithelial cells exposed to water-filtered broad-spectrum NIR irradiation with a contact cooling (20°C). The water-filter allowed 1,000–1,800 nm wavelengths and excluded 1,400–1,500 nm wavelengths. Results A DNA microarray with >62,000 different probes showed 25 and 150 genes that were up- or downregulated by at least fourfold and twofold, respectively, after NIR irradiation. In particular, epidermal growth factor receptor (EGFR) was upregulated by 19.4-fold relative to control cells. Quantitative real-time polymerase chain reaction analysis revealed that two variants of EGFR in human corneal epithelial tissue were also significantly upregulated after five rounds of 10 J/cm2 irradiation (P<0.05). Conclusion We found that NIR irradiation induced the upregulated expression of EGFR in human corneal cells. Since over half of the solar energy reaching the Earth is in the NIR region, which cannot be adequately blocked by eyewear and thus can induce eye damage with intensive or long-term exposure, protection from both UV and NIR radiation may prevent changes in gene expression and in turn eye damage. PMID:27536083

The FDA's Experience with Emerging Genomics Technologies-Past, Present, and Future.

PubMed

Xu, Joshua; Thakkar, Shraddha; Gong, Binsheng; Tong, Weida

2016-07-01

The rapid advancement of emerging genomics technologies and their application for assessing safety and efficacy of FDA-regulated products require a high standard of reliability and robustness supporting regulatory decision-making in the FDA. To facilitate the regulatory application, the FDA implemented a novel data submission program, Voluntary Genomics Data Submission (VGDS), and also to engage the stakeholders. As part of the endeavor, for the past 10 years, the FDA has led an international consortium of regulatory agencies, academia, pharmaceutical companies, and genomics platform providers, which was named MicroArray Quality Control Consortium (MAQC), to address issues such as reproducibility, precision, specificity/sensitivity, and data interpretation. Three projects have been completed so far assessing these genomics technologies: gene expression microarrays, whole genome genotyping arrays, and whole transcriptome sequencing (i.e., RNA-seq). The resultant studies provide the basic parameters for fit-for-purpose application of these new data streams in regulatory environments, and the solutions have been made available to the public through peer-reviewed publications. The latest MAQC project is also called the SEquencing Quality Control (SEQC) project focused on next-generation sequencing. Using reference samples with built-in controls, SEQC studies have demonstrated that relative gene expression can be measured accurately and reliably across laboratories and RNA-seq platforms. Besides prediction performance comparable to microarrays in clinical settings and safety assessments, RNA-seq is shown to have better sensitivity for low expression and reveal novel transcriptomic features. Future effort of MAQC will be focused on quality control of whole genome sequencing and targeted sequencing.

Three-dimensional nano-biointerface as a new platform for guiding cell fate.

PubMed

Liu, Xueli; Wang, Shutao

2014-04-21

Three-dimensional nano-biointerface has been emerging as an important topic for chemistry, nanotechnology, and life sciences in recent years. Understanding the exchanges of materials, signals, and energy at biological interfaces has inspired and helped the serial design of three-dimensional nano-biointerfaces. The intimate interactions between cells and nanostructures bring many novel properties, making three-dimensional nano-biointerfaces a powerful platform to guide cell fate in a controllable and accurate way. These advantages and capabilities endow three-dimensional nano-biointerfaces with an indispensable role in developing advanced biological science and technology. This tutorial review is mainly focused on the recent progress of three-dimensional nano-biointerfaces and highlights the new explorations and unique phenomena of three-dimensional nano-biointerfaces for cell-related fundamental studies and biomedical applications. Some basic bio-inspired principles for the design and creation of three-dimensional nano-biointerfaces are also delivered in this review. Current and further challenges of three-dimensional nano-biointerfaces are finally addressed and proposed.

[Rapid prototyping: a very promising method].

PubMed

Haverman, T M; Karagozoglu, K H; Prins, H-J; Schulten, E A J M; Forouzanfar, T

2013-03-01

Rapid prototyping is a method which makes it possible to produce a three-dimensional model based on two-dimensional imaging. Various rapid prototyping methods are available for modelling, such as stereolithography, selective laser sintering, direct laser metal sintering, two-photon polymerization, laminated object manufacturing, three-dimensional printing, three-dimensional plotting, polyjet inkjet technology,fused deposition modelling, vacuum casting and milling. The various methods currently being used in the biomedical sector differ in production, materials and properties of the three-dimensional model which is produced. Rapid prototyping is mainly usedforpreoperative planning, simulation, education, and research into and development of bioengineering possibilities.

Applications of Three-Dimensional Printing in Surgery.

PubMed

Li, Chi; Cheung, Tsz Fung; Fan, Vei Chen; Sin, Kin Man; Wong, Chrisity Wai Yan; Leung, Gilberto Ka Kit

2017-02-01

Three-dimensional (3D) printing is a rapidly advancing technology in the field of surgery. This article reviews its contemporary applications in 3 aspects of surgery, namely, surgical planning, implants and prostheses, and education and training. Three-dimensional printing technology can contribute to surgical planning by depicting precise personalized anatomy and thus a potential improvement in surgical outcome. For implants and prosthesis, the technology might overcome the limitations of conventional methods such as visual discrepancy from the recipient's body and unmatching anatomy. In addition, 3D printing technology could be integrated into medical school curriculum, supplementing the conventional cadaver-based education and training in anatomy and surgery. Future potential applications of 3D printing in surgery, mainly in the areas of skin, nerve, and vascular graft preparation as well as ear reconstruction, are also discussed. Numerous trials and studies are still ongoing. However, scientists and clinicians are still encountering some limitations of the technology including high cost, long processing time, unsatisfactory mechanical properties, and suboptimal accuracy. These limitations might potentially hamper the applications of this technology in daily clinical practice.

High-Density 16S Microarray and Clone Library-Based Microbial Community Composition of the Phoenix Spacecraft Assembly Clean Room

NASA Astrophysics Data System (ADS)

Vaishampayan, Parag; Osman, Shariff; Andersen, Gary; Venkateswaran, Kasthuri

2010-06-01

The bacterial diversity and comparative community structure of a clean room used for assembling the Phoenix spacecraft was characterized throughout the spacecraft assembly process by using 16S rRNA gene cloning/sequencing and DNA microarray (PhyloChip) technologies. Samples were collected from several locations of the clean room at three time points: before Phoenix's arrival (PHX-B), during hardware assembly (PHX-D), and after the spacecraft was removed for launch (PHX-A). Bacterial diversity comprised of all major bacterial phyla of PHX-B was found to be statistically different from PHX-D and PHX-A samples. Due to stringent cleaning and decontamination protocols during assembly, PHX-D bacterial diversity was dramatically reduced when compared to PHX-B and PHX-A samples. Comparative community analysis based on PhyloChip results revealed similar overall trends as were seen in clone libraries, but the high-density phylogenetic microarray detected larger diversity in all sampling events. The decrease in community complexity in PHX-D compared to PHX-B, and the subsequent recurrence of these organisms in PHX-A, speaks to the effectiveness of NASA cleaning protocols. However, the persistence of a subset of bacterial signatures throughout all spacecraft assembly phases underscores the need for continued refinement of sterilization technologies and the implementation of safeguards that monitor and inventory microbial contaminants.

High-density 16S microarray and clone library-based microbial community composition of the Phoenix spacecraft assembly clean room.

PubMed

Vaishampayan, Parag; Osman, Shariff; Andersen, Gary; Venkateswaran, Kasthuri

2010-06-01

The bacterial diversity and comparative community structure of a clean room used for assembling the Phoenix spacecraft was characterized throughout the spacecraft assembly process by using 16S rRNA gene cloning/sequencing and DNA microarray (PhyloChip) technologies. Samples were collected from several locations of the clean room at three time points: before Phoenix's arrival (PHX-B), during hardware assembly (PHX-D), and after the spacecraft was removed for launch (PHX-A). Bacterial diversity comprised of all major bacterial phyla of PHX-B was found to be statistically different from PHX-D and PHX-A samples. Due to stringent cleaning and decontamination protocols during assembly, PHX-D bacterial diversity was dramatically reduced when compared to PHX-B and PHX-A samples. Comparative community analysis based on PhyloChip results revealed similar overall trends as were seen in clone libraries, but the high-density phylogenetic microarray detected larger diversity in all sampling events. The decrease in community complexity in PHX-D compared to PHX-B, and the subsequent recurrence of these organisms in PHX-A, speaks to the effectiveness of NASA cleaning protocols. However, the persistence of a subset of bacterial signatures throughout all spacecraft assembly phases underscores the need for continued refinement of sterilization technologies and the implementation of safeguards that monitor and inventory microbial contaminants.

Methods to study legionella transcriptome in vitro and in vivo.

PubMed

Faucher, Sebastien P; Shuman, Howard A

2013-01-01

The study of transcriptome responses can provide insight into the regulatory pathways and genetic factors that contribute to a specific phenotype. For bacterial pathogens, it can identify putative new virulence systems and shed light on the mechanisms underlying the regulation of virulence factors. Microarrays have been previously used to study gene regulation in Legionella pneumophila. In the past few years a sharp reduction of the costs associated with microarray experiments together with the availability of relatively inexpensive custom-designed commercial microarrays has made microarray technology an accessible tool for the majority of researchers. Here we describe the methodologies to conduct microarray experiments from in vitro and in vivo samples.

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

PubMed

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.

Three-Dimensional Anatomic Evaluation of the Anterior Cruciate Ligament for Planning Reconstruction

PubMed Central

Hoshino, Yuichi; Kim, Donghwi; Fu, Freddie H.

2012-01-01

Anatomic study related to the anterior cruciate ligament (ACL) reconstruction surgery has been developed in accordance with the progress of imaging technology. Advances in imaging techniques, especially the move from two-dimensional (2D) to three-dimensional (3D) image analysis, substantially contribute to anatomic understanding and its application to advanced ACL reconstruction surgery. This paper introduces previous research about image analysis of the ACL anatomy and its application to ACL reconstruction surgery. Crucial bony landmarks for the accurate placement of the ACL graft can be identified by 3D imaging technique. Additionally, 3D-CT analysis of the ACL insertion site anatomy provides better and more consistent evaluation than conventional “clock-face” reference and roentgenologic quadrant method. Since the human anatomy has a complex three-dimensional structure, further anatomic research using three-dimensional imaging analysis and its clinical application by navigation system or other technologies is warranted for the improvement of the ACL reconstruction. PMID:22567310

The benefits of 3D modelling and animation in medical teaching.

PubMed

Vernon, Tim; Peckham, Daniel

2002-12-01

Three-dimensional models created using materials such as wax, bronze and ivory, have been used in the teaching of medicine for many centuries. Today, computer technology allows medical illustrators to create virtual three-dimensional medical models. This paper considers the benefits of using still and animated output from computer-generated models in the teaching of medicine, and examines how three-dimensional models are made.

Why laparoscopists may opt for three-dimensional view: a summary of the full HTA report on 3D versus 2D laparoscopy by S.I.C.E. (Società Italiana di Chirurgia Endoscopica e Nuove Tecnologie).

PubMed

Vettoretto, Nereo; Foglia, Emanuela; Ferrario, Lucrezia; Arezzo, Alberto; Cirocchi, Roberto; Cocorullo, Gianfranco; Currò, Giuseppe; Marchi, Domenico; Portale, Giuseppe; Gerardi, Chiara; Nocco, Umberto; Tringali, Michele; Anania, Gabriele; Piccoli, Micaela; Silecchia, Gianfranco; Morino, Mario; Valeri, Andrea; Lettieri, Emauele

2018-06-01

Three-dimensional view in laparoscopic general, gynaecologic and urologic surgery is an efficient, safe and sustainable innovation. The present paper is an extract taken from a full health technology assessment report on three-dimensional vision technology compared with standard two-dimensional laparoscopic systems. A health technology assessment approach was implemented in order to investigate all the economic, social, ethical and organisational implications related to the adoption of the innovative three-dimensional view. With the support of a multi-disciplinary team, composed of eight experts working in Italian hospitals and Universities, qualitative and quantitative data were collected, by means of literature evidence, validated questionnaire and self-reported interviews, applying a final MCDA quantitative approach, and considering the dimensions resulting from the EUnetHTA Core Model. From systematic search of literature, we retrieved the following studies: 9 on general surgery, 35 on gynaecology and urology, both concerning clinical setting. Considering simulated setting we included: 8 studies regarding pitfalls and drawbacks, 44 on teaching, 12 on surgeons' confidence and comfort and 34 on surgeons' performances. Three-dimensional laparoscopy was shown to have advantages for both the patients and the surgeons, and is confirmed to be a safe, efficacious and sustainable vision technology. The objective of the present paper, under the patronage of Italian Society of Endoscopic Surgery, was achieved in that there has now been produced a scientific report, based on a HTA approach, that may be placed in the hands of surgeons and used to support the decision-making process of the health providers.

DNA microarrays and their use in dermatology.

PubMed

Mlakar, Vid; Glavac, Damjan

2007-03-01

Multiple different DNA microarray technologies are available on the market today. They can be used for studying either DNA or RNA with the purpose of identifying and explaining the role of genes involved in different processes. This paper reviews different DNA microarray platforms available for such studies and their usage in cases of malignant melanomas, psoriasis, and exposure of keratinocytes and melanocytes to UV illumination.

Electrophoretic and field-effect graphene for all-electrical DNA array technology.

PubMed

Xu, Guangyu; Abbott, Jeffrey; Qin, Ling; Yeung, Kitty Y M; Song, Yi; Yoon, Hosang; Kong, Jing; Ham, Donhee

2014-09-05

Field-effect transistor biomolecular sensors based on low-dimensional nanomaterials boast sensitivity, label-free operation and chip-scale construction. Chemical vapour deposition graphene is especially well suited for multiplexed electronic DNA array applications, since its large two-dimensional morphology readily lends itself to top-down fabrication of transistor arrays. Nonetheless, graphene field-effect transistor DNA sensors have been studied mainly at single-device level. Here we create, from chemical vapour deposition graphene, field-effect transistor arrays with two features representing steps towards multiplexed DNA arrays. First, a robust array yield--seven out of eight transistors--is achieved with a 100-fM sensitivity, on par with optical DNA microarrays and at least 10 times higher than prior chemical vapour deposition graphene transistor DNA sensors. Second, each graphene acts as an electrophoretic electrode for site-specific probe DNA immobilization, and performs subsequent site-specific detection of target DNA as a field-effect transistor. The use of graphene as both electrode and transistor suggests a path towards all-electrical multiplexed graphene DNA arrays.

SEURAT: visual analytics for the integrated analysis of microarray data.

PubMed

Gribov, Alexander; Sill, Martin; Lück, Sonja; Rücker, Frank; Döhner, Konstanze; Bullinger, Lars; Benner, Axel; Unwin, Antony

2010-06-03

In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.

A perspective on DNA microarray technology in food and nutritional science.

PubMed

Kato, Hisanori; Saito, Kenji; Kimura, Takeshi

2005-09-01

The functions of nutrients and other foods have been revealed at the level of gene regulation. The advent of DNA microarray technology has enabled us to analyze the body's response to these factors in a much more holistic manner than before. This review is intended to overview the present status of this DNA microarray technology, hoping to provide food and nutrition scientists, especially those who are planning to introduce this technology, with hints and suggestions. The number of papers examining transcriptomics analysis in food and nutrition science has expanded over the last few years. The effects of some dietary conditions and administration of specific nutrients or food factors are studied in various animal models and cultured cells. The target food components range from macronutrients and micronutrients to other functional food factors. Such studies have already yielded fruitful results, which include discovery of novel functions of a food, uncovering hitherto unknown mechanisms of action, and analyses of food safety. The potency of DNA microarray technology in food and nutrition science is broadly recognized. This technique will surely continue to provide researchers and the public with valuable information on the beneficial and adverse effects of food factors. It should also be acknowledged, however, that there remain problems such as standardization of the data and sharing of the results among researchers in this field.

Microarray Technology for the Diagnosis of Fetal Chromosomal Aberrations: Which Platform Should We Use?

PubMed Central

Karampetsou, Evangelia; Morrogh, Deborah; Chitty, Lyn

2014-01-01

The advantage of microarray (array) over conventional karyotype for the diagnosis of fetal pathogenic chromosomal anomalies has prompted the use of microarrays in prenatal diagnostics. In this review we compare the performance of different array platforms (BAC, oligonucleotide CGH, SNP) and designs (targeted, whole genome, whole genome, and targeted, custom) and discuss their advantages and disadvantages in relation to prenatal testing. We also discuss the factors to consider when implementing a microarray testing service for the diagnosis of fetal chromosomal aberrations. PMID:26237396

Short non-coding RNAs as bacteria species identifiers detected by surface plasmon resonance enhanced common path interferometry

NASA Astrophysics Data System (ADS)

Greef, Charles; Petropavlovskikh, Viatcheslav; Nilsen, Oyvind; Khattatov, Boris; Plam, Mikhail; Gardner, Patrick; Hall, John

2008-04-01

Small non-coding RNA sequences have recently been discovered as unique identifiers of certain bacterial species, raising the possibility that they can be used as highly specific Biowarfare Agent detection markers in automated field deployable integrated detection systems. Because they are present in high abundance they could allow genomic based bacterial species identification without the need for pre-assay amplification. Further, a direct detection method would obviate the need for chemical labeling, enabling a rapid, efficient, high sensitivity mechanism for bacterial detection. Surface Plasmon Resonance enhanced Common Path Interferometry (SPR-CPI) is a potentially market disruptive, high sensitivity dual technology that allows real-time direct multiplex measurement of biomolecule interactions, including small molecules, nucleic acids, proteins, and microbes. SPR-CPI measures differences in phase shift of reflected S and P polarized light under Total Internal Reflection (TIR) conditions at a surface, caused by changes in refractive index induced by biomolecular interactions within the evanescent field at the TIR interface. The measurement is performed on a microarray of discrete 2-dimensional areas functionalized with biomolecule capture reagents, allowing simultaneous measurement of up to 100 separate analytes. The optical beam encompasses the entire microarray, allowing a solid state detector system with no scanning requirement. Output consists of simultaneous voltage measurements proportional to the phase differences resulting from the refractive index changes from each microarray feature, and is automatically processed and displayed graphically or delivered to a decision making algorithm, enabling a fully automatic detection system capable of rapid detection and quantification of small nucleic acids at extremely sensitive levels. Proof-of-concept experiments on model systems and cell culture samples have demonstrated utility of the system, and efforts are in progress for full development and deployment of the device. The technology has broad applicability as a universal detection platform for BWA detection, medical diagnostics, and drug discovery research, and represents a new class of instrumentation as a rapid, high sensitivity, label-free methodology.

Enhancing interdisciplinary mathematics and biology education: a microarray data analysis course bridging these disciplines.

PubMed

Tra, Yolande V; Evans, Irene M

2010-01-01

BIO2010 put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on microarray data analysis. We started using Genome Consortium for Active Teaching (GCAT) materials and Microarray Genome and Clustering Tool software and added R statistical software along with Bioconductor packages. In response to student feedback, one microarray data set was fully analyzed in class, starting from preprocessing to gene discovery to pathway analysis using the latter software. A class project was to conduct a similar analysis where students analyzed their own data or data from a published journal paper. This exercise showed the impact that filtering, preprocessing, and different normalization methods had on gene inclusion in the final data set. We conclude that this course achieved its goals to equip students with skills to analyze data from a microarray experiment. We offer our insight about collaborative teaching as well as how other faculty might design and implement a similar interdisciplinary course.

Enhancing Interdisciplinary Mathematics and Biology Education: A Microarray Data Analysis Course Bridging These Disciplines

PubMed Central

Evans, Irene M.

2010-01-01

BIO2010 put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on microarray data analysis. We started using Genome Consortium for Active Teaching (GCAT) materials and Microarray Genome and Clustering Tool software and added R statistical software along with Bioconductor packages. In response to student feedback, one microarray data set was fully analyzed in class, starting from preprocessing to gene discovery to pathway analysis using the latter software. A class project was to conduct a similar analysis where students analyzed their own data or data from a published journal paper. This exercise showed the impact that filtering, preprocessing, and different normalization methods had on gene inclusion in the final data set. We conclude that this course achieved its goals to equip students with skills to analyze data from a microarray experiment. We offer our insight about collaborative teaching as well as how other faculty might design and implement a similar interdisciplinary course. PMID:20810954

DISC-BASED IMMUNOASSAY MICROARRAYS. (R825433)

EPA Science Inventory

Microarray technology as applied to areas that include genomics, diagnostics, environmental, and drug discovery, is an interesting research topic for which different chip-based devices have been developed. As an alternative, we have explored the principle of compact disc-based...

Correlation between Nasoalveolar Molding and Surgical, Aesthetic, Functional and Socioeconomic Outcomes Following Primary Repair Surgery: a Systematic Review.

PubMed

Maillard, Sophie; Retrouvey, Jean-Marc; Ahmed, Mairaj K; Taub, Peter J

2017-01-01

The authors performed a systematic review to evaluate the potential beneficial effects of the nasoalveolar molding appliance on nonsyndromic unilateral clefts of the lip and/or palate prior to primary lip repair. A literature search was performed using three electronic databases (PubMed, Embase, Web of Science) and three journals ("Cleft Palate-Craniofacial Journal", "Plastic and Reconstructive Surgery Journal" and "American Journal of Orthodontics and Dentofacial Orthopaedic") from January 1980 to April 2017. Data extraction was performed with tables treating different subjects: surgical, aesthetical, functional, socio-economical effects of nasoalveolar molding (NAM) appliances and the evolution of NAM appliances, especially three-dimensional technology. Of the 145 articles retrieved in the literature surveys, 28 were qualified for the final analysis and 20 studies were excluded because of their small sample size (less than 10 patients) and/or too long follow-up (exceeded 18 months). Four randomized controlled trials were available. Although literature allowed discussing the short-term benefits of NAM appliance and the three-dimensional technology, scientific evidence is lacking. Based on the results, nasoalveolar molding appliances have positive surgical, aesthetical, functional and socio-economical effects on unilateral clefts of the lip and/or palate treatment before the primary repair surgeries. Three-dimensional technology results in a more efficient and predictable nasoalveolar molding appliance treatment. However, nasoalveolar molding appliance effect in a short term remains unclear with the available literature. Further studies that integrate three-dimensional technology in a large scale are still needed.

Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method.

PubMed

Bengtsson, Henrik; Hössjer, Ola

2006-03-01

Low-level processing and normalization of microarray data are most important steps in microarray analysis, which have profound impact on downstream analysis. Multiple methods have been suggested to date, but it is not clear which is the best. It is therefore important to further study the different normalization methods in detail and the nature of microarray data in general. A methodological study of affine models for gene expression data is carried out. Focus is on two-channel comparative studies, but the findings generalize also to single- and multi-channel data. The discussion applies to spotted as well as in-situ synthesized microarray data. Existing normalization methods such as curve-fit ("lowess") normalization, parallel and perpendicular translation normalization, and quantile normalization, but also dye-swap normalization are revisited in the light of the affine model and their strengths and weaknesses are investigated in this context. As a direct result from this study, we propose a robust non-parametric multi-dimensional affine normalization method, which can be applied to any number of microarrays with any number of channels either individually or all at once. A high-quality cDNA microarray data set with spike-in controls is used to demonstrate the power of the affine model and the proposed normalization method. We find that an affine model can explain non-linear intensity-dependent systematic effects in observed log-ratios. Affine normalization removes such artifacts for non-differentially expressed genes and assures that symmetry between negative and positive log-ratios is obtained, which is fundamental when identifying differentially expressed genes. In addition, affine normalization makes the empirical distributions in different channels more equal, which is the purpose of quantile normalization, and may also explain why dye-swap normalization works or fails. All methods are made available in the aroma package, which is a platform-independent package for R.

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

EPA Science Inventory

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

Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment.

PubMed

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.

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management.

PubMed

Burgarella, Sarah; Cattaneo, Dario; Pinciroli, Francesco; Masseroli, Marco

2005-12-01

Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.

When nano meets stem: the impact of nanotechnology in stem cell biology.

PubMed

Kaur, Savneet; Singhal, Barkha

2012-01-01

Nanotechnology and biomedical treatments using stem cells are among the latest conduits of biotechnological research. Even more recently, scientists have begun finding ways to mate these two specialties of science. The advent of nanotechnology has paved the way for an explicit understanding of stem cell therapy in vivo and by recapitulation of such in vivo environments in the culture, this technology seems to accommodate a great potential in providing new vistas to stem cell research. Nanotechnology carries in its wake, the development of highly stable, efficient and specific gene delivery systems for both in vitro and in vivo genetic engineering of stem cells, use of nanoscale systems (such as microarrays) for investigation of gene expression in stem cells, creation of dynamic three-dimensional nano-environments for in vitro and in vivo maintenance and differentiation of stem cells and development of extremely sensitive in vivo detection systems to gain insights into the mechanisms of stem cell differentiation and apoptosis in different disease models. The present review presents an overview of the current applications and future prospects for the use of nanotechnology in stem cell biology. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Development of monograph titled "augmented chemistry aldehida & keton" with 3 dimensional (3D) illustration as a supplement book on chemistry learning

NASA Astrophysics Data System (ADS)

Damayanti, Latifah Adelina; Ikhsan, Jaslin

2017-05-01

Integration of information technology in education more rapidly performed in a medium of learning. Three-dimensional (3D) molecular modeling was performed in Augmented Reality as a tangible manifestation of increasingly modern technology utilization. Based on augmented reality, three-dimensional virtual object is projected in real time and the exact environment. This paper reviewed the uses of chemical learning supplement book of aldehydes and ketones which are equipped with three-dimensional molecular modeling by which students can inspect molecules from various viewpoints. To plays the 3D illustration printed on the book, smartphones with the open-source software of the technology based integrated Augmented Reality can be used. The aims of this research were to develop the monograph of aldehydes and ketones with 3 dimensional (3D) illustrations, to determine the specification of the monograph, and to determine the quality of the monograph. The quality of the monograph is evaluated by experiencing chemistry teachers on the five aspects of contents/materials, presentations, language and images, graphs, and software engineering, resulted in the result that the book has a very good quality to be used as a chemistry learning supplement book.

[Preliminary construction of three-dimensional visual educational system for clinical dentistry based on world wide web webpage].

PubMed

Hu, Jian; Xu, Xiang-yang; Song, En-min; Tan, Hong-bao; Wang, Yi-ning

2009-09-01

To establish a new visual educational system of virtual reality for clinical dentistry based on world wide web (WWW) webpage in order to provide more three-dimensional multimedia resources to dental students and an online three-dimensional consulting system for patients. Based on computer graphics and three-dimensional webpage technologies, the software of 3Dsmax and Webmax were adopted in the system development. In the Windows environment, the architecture of whole system was established step by step, including three-dimensional model construction, three-dimensional scene setup, transplanting three-dimensional scene into webpage, reediting the virtual scene, realization of interactions within the webpage, initial test, and necessary adjustment. Five cases of three-dimensional interactive webpage for clinical dentistry were completed. The three-dimensional interactive webpage could be accessible through web browser on personal computer, and users could interact with the webpage through rotating, panning and zooming the virtual scene. It is technically feasible to implement the visual educational system of virtual reality for clinical dentistry based on WWW webpage. Information related to clinical dentistry can be transmitted properly, visually and interactively through three-dimensional webpage.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

NASA Technical Reports Server (NTRS)

Royce, Thomas E.; Rozowsky, Joel S.; Bertone, Paul; Samanta, Manoj; Stolc, Viktor; Weissman, Sherman; Snyder, Michael; Gerstein, Mark

2005-01-01

Traditional microarrays use probes complementary to known genes to quantitate the differential gene expression between two or more conditions. Genomic tiling microarray experiments differ in that probes that span a genomic region at regular intervals are used to detect the presence or absence of transcription. This difference means the same sets of biases and the methods for addressing them are unlikely to be relevant to both types of experiment. We introduce the informatics challenges arising in the analysis of tiling microarray experiments as open problems to the scientific community and present initial approaches for the analysis of this nascent technology.

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH

PubMed Central

2009-01-01

Background Comparative genomic hybridization microarrays for the detection of constitutional chromosomal aberrations is the application of microarray technology coming fastest into routine clinical application. Through genotype-phenotype association, it is also an important technique towards the discovery of disease causing genes and genomewide functional annotation in human. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient against a normal reference sample. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation in the "normal" reference instead of a patient aberration. Instead, we apply an experimental loop design that compares three patients in three hybridizations. Results We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of 27 patients seen at our genetics center, we observed that the linear models of the log ratios are advantageous over the mixed models of the absolute intensities. Conclusion The loop design and the performance of the statistical analysis contribute to the quick adoption of array CGH as a routine diagnostic tool. They lower the detection limit of mosaicisms and improve the assignment of copy number variation for genetic association studies. PMID:19925645

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

PubMed

Allemeersch, Joke; Van Vooren, Steven; Hannes, Femke; De Moor, Bart; Vermeesch, Joris Robert; Moreau, Yves

2009-11-19

Comparative genomic hybridization microarrays for the detection of constitutional chromosomal aberrations is the application of microarray technology coming fastest into routine clinical application. Through genotype-phenotype association, it is also an important technique towards the discovery of disease causing genes and genomewide functional annotation in human. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient against a normal reference sample. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation in the "normal" reference instead of a patient aberration. Instead, we apply an experimental loop design that compares three patients in three hybridizations. We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of 27 patients seen at our genetics center, we observed that the linear models of the log ratios are advantageous over the mixed models of the absolute intensities. The loop design and the performance of the statistical analysis contribute to the quick adoption of array CGH as a routine diagnostic tool. They lower the detection limit of mosaicisms and improve the assignment of copy number variation for genetic association studies.

Customizing microarrays for neuroscience drug discovery.

PubMed

Girgenti, Matthew J; Newton, Samuel S

2007-08-01

Microarray-based gene profiling has become the centerpiece of gene expression studies in the biological sciences. The ability to now interrogate the entire genome using a single chip demonstrates the progress in technology and instrumentation that has been made over the last two decades. Although this unbiased approach provides researchers with an immense quantity of data, obtaining meaningful insight is not possible without intensive data analysis and processing. Custom developed arrays have emerged as a viable and attractive alternative that can take advantage of this robust technology and tailor it to suit the needs and requirements of individual investigations. The ability to simplify data analysis, reduce noise and carefully optimize experimental conditions makes it a suitable tool that can be effectively utilized in neuroscience drug discovery efforts. Furthermore, incorporating recent advancements in fine focusing gene profiling to include specific cellular phenotypes can help resolve the complex cellular heterogeneity of the brain. This review surveys the use of microarray technology in neuroscience paying special attention to customized arrays and their potential in drug discovery. Novel applications of microarrays and ancillary techniques, such as laser microdissection, FAC sorting and RNA amplification, have also been discussed. The notion that a hypothesis-driven approach can be integrated into drug development programs is highlighted.

Three-Dimensional Printing Using a Photoinitiated Polymer

ERIC Educational Resources Information Center

Muskin, Joseph; Ragusa, Matthew; Gelsthorpe, Thomas

2010-01-01

Printers capable of producing three-dimensional objects are becoming more common. Most of these printers are impractical for use in the chemistry classroom because of the expense incurred in fabricating a print head that must be controlled in three dimensions. We propose a simpler solution to this problem that allows the emerging technology of…

Biodynamic profiling of three-dimensional tissue growth techniques

NASA Astrophysics Data System (ADS)

Sun, Hao; Merrill, Dan; Turek, John; Nolte, David

2016-03-01

Three-dimensional tissue culture presents a more biologically relevant environment in which to perform drug development than conventional two-dimensional cell culture. However, obtaining high-content information from inside three dimensional tissue has presented an obstacle to rapid adoption of 3D tissue culture for pharmaceutical applications. Biodynamic imaging is a high-content three-dimensional optical imaging technology based on low-coherence interferometry and digital holography that uses intracellular dynamics as high-content image contrast. In this paper, we use biodynamic imaging to compare pharmaceutical responses to Taxol of three-dimensional multicellular spheroids grown by three different growth techniques: rotating bioreactor, hanging-drop and plate-grown spheroids. The three growth techniques have systematic variations among tissue cohesiveness and intracellular activity and consequently display different pharmacodynamics under identical drug dose conditions. The in vitro tissue cultures are also compared to ex vivo living biopsies. These results demonstrate that three-dimensional tissue cultures are not equivalent, and that drug-response studies must take into account the growth method.

IDENTIFYING AND MONITORING ENVIRONMENTAL TOXICITY USING CERIODAPHNIA MICROARRAYS - PHASE I

EPA Science Inventory

The current U.S. Environmental Protection Agency (EPA) SBIR solicitation states that “technology is needed to better identify and monitor sources of pollution and protect water quality.” Microarrays may be particularly well suited to identifying environmental toxic...

Multiplexed fluorescent microarray for human salivary protein analysis using polymer microspheres and fiber-optic bundles.

PubMed

Nie, Shuai; Benito-Peña, Elena; Zhang, Huaibin; Wu, Yue; Walt, David R

2013-10-10

Herein, we describe a protocol for simultaneously measuring six proteins in saliva using a fiber-optic microsphere-based antibody array. The immuno-array technology employed combines the advantages of microsphere-based suspension array fabrication with the use of fluorescence microscopy. As described in the video protocol, commercially available 4.5 μm polymer microspheres were encoded into seven different types, differentiated by the concentration of two fluorescent dyes physically trapped inside the microspheres. The encoded microspheres containing surface carboxyl groups were modified with monoclonal capture antibodies through EDC/NHS coupling chemistry. To assemble the protein microarray, the different types of encoded and functionalized microspheres were mixed and randomly deposited in 4.5 μm microwells, which were chemically etched at the proximal end of a fiber-optic bundle. The fiber-optic bundle was used as both a carrier and for imaging the microspheres. Once assembled, the microarray was used to capture proteins in the saliva supernatant collected from the clinic. The detection was based on a sandwich immunoassay using a mixture of biotinylated detection antibodies for different analytes with a streptavidin-conjugated fluorescent probe, R-phycoerythrin. The microarray was imaged by fluorescence microscopy in three different channels, two for microsphere registration and one for the assay signal. The fluorescence micrographs were then decoded and analyzed using a homemade algorithm in MATLAB.

Recognition of multiple imbalanced cancer types based on DNA microarray data using ensemble classifiers.

PubMed

Yu, Hualong; Hong, Shufang; Yang, Xibei; Ni, Jun; Dan, Yuanyuan; Qin, Bin

2013-01-01

DNA microarray technology can measure the activities of tens of thousands of genes simultaneously, which provides an efficient way to diagnose cancer at the molecular level. Although this strategy has attracted significant research attention, most studies neglect an important problem, namely, that most DNA microarray datasets are skewed, which causes traditional learning algorithms to produce inaccurate results. Some studies have considered this problem, yet they merely focus on binary-class problem. In this paper, we dealt with multiclass imbalanced classification problem, as encountered in cancer DNA microarray, by using ensemble learning. We utilized one-against-all coding strategy to transform multiclass to multiple binary classes, each of them carrying out feature subspace, which is an evolving version of random subspace that generates multiple diverse training subsets. Next, we introduced one of two different correction technologies, namely, decision threshold adjustment or random undersampling, into each training subset to alleviate the damage of class imbalance. Specifically, support vector machine was used as base classifier, and a novel voting rule called counter voting was presented for making a final decision. Experimental results on eight skewed multiclass cancer microarray datasets indicate that unlike many traditional classification approaches, our methods are insensitive to class imbalance.

Genome Consortium for Active Teaching: Meeting the Goals of BIO2010

PubMed Central

Ledbetter, Mary Lee S.; Hoopes, Laura L.M.; Eckdahl, Todd T.; Heyer, Laurie J.; Rosenwald, Anne; Fowlks, Edison; Tonidandel, Scott; Bucholtz, Brooke; Gottfried, Gail

2007-01-01

The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods in undergraduate education. Initially focused on microarray technology, but with an eye toward diversification, GCAT is a community working to improve the education of tomorrow's life science professionals. GCAT participants have access to affordable microarrays, microarray scanners, free software for data analysis, and faculty workshops. Microarrays provided by GCAT have been used by 141 faculty on 134 campuses, including 21 faculty that serve large numbers of underrepresented minority students. An estimated 9480 undergraduates a year will have access to microarrays by 2009 as a direct result of GCAT faculty workshops. Gains for students include significantly improved comprehension of topics in functional genomics and increased interest in research. Faculty reported improved access to new technology and gains in understanding thanks to their involvement with GCAT. GCAT's network of supportive colleagues encourages faculty to explore genomics through student research and to learn a new and complex method with their undergraduates. GCAT is meeting important goals of BIO2010 by making research methods accessible to undergraduates, training faculty in genomics and bioinformatics, integrating mathematics into the biology curriculum, and increasing participation by underrepresented minority students. PMID:17548873

Genome Consortium for Active Teaching: meeting the goals of BIO2010.

PubMed

Campbell, A Malcolm; Ledbetter, Mary Lee S; Hoopes, Laura L M; Eckdahl, Todd T; Heyer, Laurie J; Rosenwald, Anne; Fowlks, Edison; Tonidandel, Scott; Bucholtz, Brooke; Gottfried, Gail

2007-01-01

The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods in undergraduate education. Initially focused on microarray technology, but with an eye toward diversification, GCAT is a community working to improve the education of tomorrow's life science professionals. GCAT participants have access to affordable microarrays, microarray scanners, free software for data analysis, and faculty workshops. Microarrays provided by GCAT have been used by 141 faculty on 134 campuses, including 21 faculty that serve large numbers of underrepresented minority students. An estimated 9480 undergraduates a year will have access to microarrays by 2009 as a direct result of GCAT faculty workshops. Gains for students include significantly improved comprehension of topics in functional genomics and increased interest in research. Faculty reported improved access to new technology and gains in understanding thanks to their involvement with GCAT. GCAT's network of supportive colleagues encourages faculty to explore genomics through student research and to learn a new and complex method with their undergraduates. GCAT is meeting important goals of BIO2010 by making research methods accessible to undergraduates, training faculty in genomics and bioinformatics, integrating mathematics into the biology curriculum, and increasing participation by underrepresented minority students.

Protocols and characterization data for 2D, 3D, and slice-based tumor models from the PREDECT project.

PubMed

de Hoogt, Ronald; Estrada, Marta F; Vidic, Suzana; Davies, Emma J; Osswald, Annika; Barbier, Michael; Santo, Vítor E; Gjerde, Kjersti; van Zoggel, Hanneke J A A; Blom, Sami; Dong, Meng; Närhi, Katja; Boghaert, Erwin; Brito, Catarina; Chong, Yolanda; Sommergruber, Wolfgang; van der Kuip, Heiko; van Weerden, Wytske M; Verschuren, Emmy W; Hickman, John; Graeser, Ralph

2017-11-21

Two-dimensional (2D) culture of cancer cells in vitro does not recapitulate the three-dimensional (3D) architecture, heterogeneity and complexity of human tumors. More representative models are required that better reflect key aspects of tumor biology. These are essential studies of cancer biology and immunology as well as for target validation and drug discovery. The Innovative Medicines Initiative (IMI) consortium PREDECT (www.predect.eu) characterized in vitro models of three solid tumor types with the goal to capture elements of tumor complexity and heterogeneity. 2D culture and 3D mono- and stromal co-cultures of increasing complexity, and precision-cut tumor slice models were established. Robust protocols for the generation of these platforms are described. Tissue microarrays were prepared from all the models, permitting immunohistochemical analysis of individual cells, capturing heterogeneity. 3D cultures were also characterized using image analysis. Detailed step-by-step protocols, exemplary datasets from the 2D, 3D, and slice models, and refined analytical methods were established and are presented.

Protocols and characterization data for 2D, 3D, and slice-based tumor models from the PREDECT project

PubMed Central

de Hoogt, Ronald; Estrada, Marta F.; Vidic, Suzana; Davies, Emma J.; Osswald, Annika; Barbier, Michael; Santo, Vítor E.; Gjerde, Kjersti; van Zoggel, Hanneke J. A. A.; Blom, Sami; Dong, Meng; Närhi, Katja; Boghaert, Erwin; Brito, Catarina; Chong, Yolanda; Sommergruber, Wolfgang; van der Kuip, Heiko; van Weerden, Wytske M.; Verschuren, Emmy W.; Hickman, John; Graeser, Ralph

2017-01-01

Two-dimensional (2D) culture of cancer cells in vitro does not recapitulate the three-dimensional (3D) architecture, heterogeneity and complexity of human tumors. More representative models are required that better reflect key aspects of tumor biology. These are essential studies of cancer biology and immunology as well as for target validation and drug discovery. The Innovative Medicines Initiative (IMI) consortium PREDECT (www.predect.eu) characterized in vitro models of three solid tumor types with the goal to capture elements of tumor complexity and heterogeneity. 2D culture and 3D mono- and stromal co-cultures of increasing complexity, and precision-cut tumor slice models were established. Robust protocols for the generation of these platforms are described. Tissue microarrays were prepared from all the models, permitting immunohistochemical analysis of individual cells, capturing heterogeneity. 3D cultures were also characterized using image analysis. Detailed step-by-step protocols, exemplary datasets from the 2D, 3D, and slice models, and refined analytical methods were established and are presented. PMID:29160867

ASSESSING THE USE OF OLIGONUCLEOTIDE MICROARRAYS FOR FATHEAD MINNOW (PIMEPHALES PROMELAS) TO EXAMINE EXPOSURE VARIABLES

EPA Science Inventory

Microarray technology has proven to be a useful tool for analyzing the transcriptome of various organisms representing conditions such as disease states, developmental stages, and responses to chemical exposure. Although most commercially available arrays are limited to organism...

High brightness x ray source for directed energy and holographic imaging applications, phase 2

NASA Astrophysics Data System (ADS)

McPherson, Armon; Rhodes, Charles K.

1992-03-01

Advances in x-ray imaging technology and x-ray sources are such that a new technology can be brought to commercialization enabling the three-dimensional (3-D) microvisualization of hydrated biological specimens. The Company is engaged in a program whose main goal is the development of a new technology for direct three dimensional (3-D) x-ray holographic imaging. It is believed that this technology will have a wide range of important applications in the defense, medical, and scientific sectors. For example, in the medical area, it is expected that biomedical science will constitute a very active and substantial market, because the application of physical technologies for the direct visualization of biological entities has had a long and extremely fruitful history.

Exploiting fluorescence for multiplex immunoassays on protein microarrays

NASA Astrophysics Data System (ADS)

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

2014-09-01

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.

MALDI-TOF mass spectrometry for quantitative gene expression analysis of acid responses in Staphylococcus aureus.

PubMed

Rode, Tone Mari; Berget, Ingunn; Langsrud, Solveig; Møretrø, Trond; Holck, Askild

2009-07-01

Microorganisms are constantly exposed to new and altered growth conditions, and respond by changing gene expression patterns. Several methods for studying gene expression exist. During the last decade, the analysis of microarrays has been one of the most common approaches applied for large scale gene expression studies. A relatively new method for gene expression analysis is MassARRAY, which combines real competitive-PCR and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. In contrast to microarray methods, MassARRAY technology is suitable for analysing a larger number of samples, though for a smaller set of genes. In this study we compare the results from MassARRAY with microarrays on gene expression responses of Staphylococcus aureus exposed to acid stress at pH 4.5. RNA isolated from the same stress experiments was analysed using both the MassARRAY and the microarray methods. The MassARRAY and microarray methods showed good correlation. Both MassARRAY and microarray estimated somewhat lower fold changes compared with quantitative real-time PCR (qRT-PCR). The results confirmed the up-regulation of the urease genes in acidic environments, and also indicated the importance of metal ion regulation. This study shows that the MassARRAY technology is suitable for gene expression analysis in prokaryotes, and has advantages when a set of genes is being analysed for an organism exposed to many different environmental conditions.

Functional comparison of microarray data across multiple platforms using the method of percentage of overlapping functions.

PubMed

Li, Zhiguang; Kwekel, Joshua C; Chen, Tao

2012-01-01

Functional comparison across microarray platforms is used to assess the comparability or similarity of the biological relevance associated with the gene expression data generated by multiple microarray platforms. Comparisons at the functional level are very important considering that the ultimate purpose of microarray technology is to determine the biological meaning behind the gene expression changes under a specific condition, not just to generate a list of genes. Herein, we present a method named percentage of overlapping functions (POF) and illustrate how it is used to perform the functional comparison of microarray data generated across multiple platforms. This method facilitates the determination of functional differences or similarities in microarray data generated from multiple array platforms across all the functions that are presented on these platforms. This method can also be used to compare the functional differences or similarities between experiments, projects, or laboratories.

ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

PubMed

Dickson, B M; Cornett, E M; Ramjan, Z; Rothbart, S B

2016-01-01

Microarray-based proteomic platforms have emerged as valuable tools for studying various aspects of protein function, particularly in the field of chromatin biochemistry. Microarray technology itself is largely unrestricted in regard to printable material and platform design, and efficient multidimensional optimization of assay parameters requires fluidity in the design and analysis of custom print layouts. This motivates the need for streamlined software infrastructure that facilitates the combined planning and analysis of custom microarray experiments. To this end, we have developed ArrayNinja as a portable, open source, and interactive application that unifies the planning and visualization of microarray experiments and provides maximum flexibility to end users. Array experiments can be planned, stored to a private database, and merged with the imaged results for a level of data interaction and centralization that is not currently attainable with available microarray informatics tools. © 2016 Elsevier Inc. All rights reserved.

[Ten years retrospective review of the application of digital medical technology in general surgery in China].

PubMed

Fang, C H; Lau, Y Y; Zhou, W P; Cai, W

2017-12-01

Digital medical technology is a powerful tool which has forcefully promoted the development of general surgery in China. In this article, we reviews the application status of three-dimensional visualization and three-dimensional printing technology in general surgery, introduces the development situation of surgical navigation guided by optical and electromagnetic technology and preliminary attempt to combined with mixed reality applied to complicated hepatectomy, looks ahead the development direction of digital medicine in the era of artificial intelligence and big data on behalf of surgical robot and radiomics. Surgeons should proactively master these advanced techniques and accelerate the innovative development of general surgery in China.

Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

EPA Science Inventory

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 ...

Three-Dimensional Printing in Orthopedic Surgery.

PubMed

Eltorai, Adam E M; Nguyen, Eric; Daniels, Alan H

2015-11-01

Three-dimensional (3D) printing is emerging as a clinically promising technology for rapid prototyping of surgically implantable products. With this commercially available technology, computed tomography or magnetic resonance images can be used to create graspable objects from 3D reconstructed images. Models can enhance patients' understanding of their pathology and surgeon preoperative planning. Customized implants and casts can be made to match an individual's anatomy. This review outlines 3D printing, its current applications in orthopedics, and promising future directions. Copyright 2015, SLACK Incorporated.

Three-dimensional viscous design methodology for advanced technology aircraft supersonic inlet systems

NASA Technical Reports Server (NTRS)

Anderson, B. H.

1983-01-01

A broad program to develop advanced, reliable, and user oriented three-dimensional viscous design techniques for supersonic inlet systems, and encourage their transfer into the general user community is discussed. Features of the program include: (1) develop effective methods of computing three-dimensional flows within a zonal modeling methodology; (2) ensure reasonable agreement between said analysis and selective sets of benchmark validation data; (3) develop user orientation into said analysis; and (4) explore and develop advanced numerical methodology.

Design and Implementation of 3D Model Data Management System Based on SQL

NASA Astrophysics Data System (ADS)

Li, Shitao; Zhang, Shixin; Zhang, Zhanling; Li, Shiming; Jia, Kun; Hu, Zhongxu; Ping, Liang; Hu, Youming; Li, Yanlei

CAD/CAM technology plays an increasingly important role in the machinery manufacturing industry. As an important means of production, the accumulated three-dimensional models in many years of design work are valuable. Thus the management of these three-dimensional models is of great significance. This paper gives detailed explanation for a method to design three-dimensional model databases based on SQL and to implement the functions such as insertion, modification, inquiry, preview and so on.

Making three-dimensional echocardiography more tangible: a workflow for three-dimensional printing with echocardiographic data.

PubMed

Mashari, Azad; Montealegre-Gallegos, Mario; Knio, Ziyad; Yeh, Lu; Jeganathan, Jelliffe; Matyal, Robina; Khabbaz, Kamal R; Mahmood, Feroze

2016-12-01

Three-dimensional (3D) printing is a rapidly evolving technology with several potential applications in the diagnosis and management of cardiac disease. Recently, 3D printing (i.e. rapid prototyping) derived from 3D transesophageal echocardiography (TEE) has become possible. Due to the multiple steps involved and the specific equipment required for each step, it might be difficult to start implementing echocardiography-derived 3D printing in a clinical setting. In this review, we provide an overview of this process, including its logistics and organization of tools and materials, 3D TEE image acquisition strategies, data export, format conversion, segmentation, and printing. Generation of patient-specific models of cardiac anatomy from echocardiographic data is a feasible, practical application of 3D printing technology. © 2016 The authors.

Multiplexed Simultaneous High Sensitivity Sensors with High-Order Mode Based on the Integration of Photonic Crystal 1 × 3 Beam Splitter and Three Different Single-Slot PCNCs.

PubMed

Zhou, Jian; Huang, Lijun; Fu, Zhongyuan; Sun, Fujun; Tian, Huiping

2016-07-07

We simulated an efficient method for the sensor array of high-sensitivity single-slot photonic crystal nanobeam cavities (PCNCs) on a silicon platform. With the combination of a well-designed photonic crystal waveguide (PhCW) filter and an elaborate single-slot PCNC, a specific high-order resonant mode was filtered for sensing. A 1 × 3 beam splitter carefully established was implemented to split channels and integrate three sensors to realize microarrays. By applying the three-dimensional finite-difference-time-domain (3D-FDTD) method, the sensitivities calculated were S₁ = 492 nm/RIU, S₂ = 244 nm/RIU, and S₃ = 552 nm/RIU, respectively. To the best of our knowledge, this is the first multiplexing design in which each sensor cite features such a high sensitivity simultaneously.

Multiplexed Simultaneous High Sensitivity Sensors with High-Order Mode Based on the Integration of Photonic Crystal 1 × 3 Beam Splitter and Three Different Single-Slot PCNCs

PubMed Central

Zhou, Jian; Huang, Lijun; Fu, Zhongyuan; Sun, Fujun; Tian, Huiping

2016-01-01

We simulated an efficient method for the sensor array of high-sensitivity single-slot photonic crystal nanobeam cavities (PCNCs) on a silicon platform. With the combination of a well-designed photonic crystal waveguide (PhCW) filter and an elaborate single-slot PCNC, a specific high-order resonant mode was filtered for sensing. A 1 × 3 beam splitter carefully established was implemented to split channels and integrate three sensors to realize microarrays. By applying the three-dimensional finite-difference-time-domain (3D-FDTD) method, the sensitivities calculated were S1 = 492 nm/RIU, S2 = 244 nm/RIU, and S3 = 552 nm/RIU, respectively. To the best of our knowledge, this is the first multiplexing design in which each sensor cite features such a high sensitivity simultaneously. PMID:27399712

Exploring Approaches to Teaching in Three-Dimensional Virtual Worlds

ERIC Educational Resources Information Center

Englund, Claire

2017-01-01

Purpose: The purpose of this paper is to explore how teachers' approaches to teaching and conceptions of teaching and learning with educational technology influence the implementation of three-dimensional virtual worlds (3DVWs) in health care education. Design/methodology/approach: Data were collected through thematic interviews with eight…

Clinical use of three-dimensional video measurements of eye movements

NASA Technical Reports Server (NTRS)

Merfeld, D. M.; Black, F. O.; Wade, S.; Paloski, W. H. (Principal Investigator)

1998-01-01

Noninvasive measurements of three-dimensional eye position can be accurately achieved with video methods. A case study showing the potential clinical benefit of these enhanced measurements is presented along with some thoughts about technological advances, essential for clinical application, that are likely to occur in the next several years.

Exploring the User Experience of Three-Dimensional Virtual Learning Environments

ERIC Educational Resources Information Center

Shin, Dong-Hee; Biocca, Frank; Choo, Hyunseung

2013-01-01

This study examines the users' experiences with three-dimensional (3D) virtual environments to investigate the areas of development as a learning application. For the investigation, the modified technology acceptance model (TAM) is used with constructs from expectation-confirmation theory (ECT). Users' responses to questions about cognitive…

Screening Mammalian Cells on a Hydrogel: Functionalized Small Molecule Microarray.

PubMed

Zhu, Biwei; Jiang, Bo; Na, Zhenkun; Yao, Shao Q

2017-01-01

Mammalian cell-based microarray technology has gained wide attention, for its plethora of promising applications. The platform is able to provide simultaneous information on multiple parameters for a given target, or even multiple target proteins, in a complex biological system. Here we describe the preparation of mammalian cell-based microarrays using selectively captured of human prostate cancer cells (PC-3). This platform was then used in controlled drug release and measuring the associated drug effects on these cancer cells.

Low-density microarray technologies for rapid human norovirus genotyping

USDA-ARS?s Scientific Manuscript database

Human noroviruses cause up to 21 million cases of foodborne disease in the United States annually and are the most common cause of acute gastroenteritis in industrialized countries. To reduce the burden of foodborne disease associated with viruses, the use of low density DNA microarrays in conjuncti...

Functionalized carbon micro/nanostructures for biomolecular detection

NASA Astrophysics Data System (ADS)

Penmatsa, Varun

Advancements in the micro-and nano-scale fabrication techniques have opened up new avenues for the development of portable, scalable and easier-to-use biosensors. Over the last few years, electrodes made of carbon have been widely used as sensing units in biosensors due to their attractive physiochemical properties. The aim of this research is to investigate different strategies to develop functionalized high surface carbon micro/nano-structures for electrochemical and biosensing devices. High aspect ratio three-dimensional carbon microarrays were fabricated via carbon microelectromechanical systems (C-MEMS) technique, which is based on pyrolyzing pre-patterned organic photoresist polymers. To further increase the surface area of the carbon microstructures, surface porosity was introduced by two strategies, i.e. (i) using F127 as porogen and (ii) oxygen reactive ion etch (RIE) treatment. Electrochemical characterization showed that porous carbon thin film electrodes prepared by using F127 as porogen had an effective surface area (Aeff 185%) compared to the conventional carbon electrode. To achieve enhanced electrochemical sensitivity for C-MEMS based functional devices, graphene was conformally coated onto high aspect ratio three-dimensional (3D) carbon micropillar arrays using electrostatic spray deposition (ESD) technique. The amperometric response of graphene/carbon micropillar electrode arrays exhibited higher electrochemical activity, improved charge transfer and a linear response towards H2O2 detection between 250μM to 5.5mM. Furthermore, carbon structures with dimensions from 50 nano-to micrometer level have been fabricated by pyrolyzing photo-nanoimprint lithography patterned organic resist polymer. Microstructure, elemental composition and resistivity characterization of the carbon nanostructures produced by this process were very similar to conventional photoresist derived carbon. Surface functionalization of the carbon nanostructures was performed using direct amination technique. Considering the need for requisite functional groups to covalently attach bioreceptors on the carbon surface for biomolecule detection, different oxidation techniques were compared to study the types of carbon-oxygen groups formed on the surface and their percentages with respect to different oxidation pretreatment times. Finally, a label-free detection strategy using signaling aptamer/protein binding complex for platelet-derived growth factor oncoprotein detection on functionalized three-dimensional carbon microarrays platform was demonstrated. The sensor showed near linear relationship between the relative fluorescence difference and protein concentration even in the sub-nanomolar range with an excellent detection limit of 5 pmol.

Application of Mathematical and Three-Dimensional Computer Modeling Tools in the Planning of Processes of Fuel and Energy Complexes

NASA Astrophysics Data System (ADS)

Aksenova, Olesya; Nikolaeva, Evgenia; Cehlár, Michal

2017-11-01

This work aims to investigate the effectiveness of mathematical and three-dimensional computer modeling tools in the planning of processes of fuel and energy complexes at the planning and design phase of a thermal power plant (TPP). A solution for purification of gas emissions at the design development phase of waste treatment systems is proposed employing mathematical and three-dimensional computer modeling - using the E-nets apparatus and the development of a 3D model of the future gas emission purification system. Which allows to visualize the designed result, to select and scientifically prove economically feasible technology, as well as to ensure the high environmental and social effect of the developed waste treatment system. The authors present results of a treatment of planned technological processes and the system for purifying gas emissions in terms of E-nets. using mathematical modeling in the Simulink application. What allowed to create a model of a device from the library of standard blocks and to perform calculations. A three-dimensional model of a system for purifying gas emissions has been constructed. It allows to visualize technological processes and compare them with the theoretical calculations at the design phase of a TPP and. if necessary, make adjustments.

Development and application of a microarray meter tool to optimize microarray experiments

PubMed Central

Rouse, Richard JD; Field, Katrine; Lapira, Jennifer; Lee, Allen; Wick, Ivan; Eckhardt, Colleen; Bhasker, C Ramana; Soverchia, Laura; Hardiman, Gary

2008-01-01

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. PMID:18710498

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

NASA Astrophysics Data System (ADS)

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.

Introducing 3-Dimensional Printing of a Human Anatomic Pathology Specimen: Potential Benefits for Undergraduate and Postgraduate Education and Anatomic Pathology Practice.

PubMed

Mahmoud, Amr; Bennett, Michael

2015-08-01

Three-dimensional (3D) printing, a rapidly advancing technology, is widely applied in fields such as mechanical engineering and architecture. Three-dimensional printing has been introduced recently into medical practice in areas such as reconstructive surgery, as well as in clinical research. Three-dimensionally printed models of anatomic and autopsy pathology specimens can be used for demonstrating pathology entities to undergraduate medical, dental, and biomedical students, as well as for postgraduate training in examination of gross specimens for anatomic pathology residents and pathology assistants, aiding clinicopathological correlation at multidisciplinary team meetings, and guiding reconstructive surgical procedures. To apply 3D printing in anatomic pathology for teaching, training, and clinical correlation purposes. Multicolored 3D printing of human anatomic pathology specimens was achieved using a ZCorp 510 3D printer (3D Systems, Rock Hill, South Carolina) following creation of a 3D model using Autodesk 123D Catch software (Autodesk, Inc, San Francisco, California). Three-dimensionally printed models of anatomic pathology specimens created included pancreatoduodenectomy (Whipple operation) and radical nephrectomy specimens. The models accurately depicted the topographic anatomy of selected specimens and illustrated the anatomic relation of excised lesions to adjacent normal tissues. Three-dimensional printing of human anatomic pathology specimens is achievable. Advances in 3D printing technology may further improve the quality of 3D printable anatomic pathology specimens.

Flow experience among information and communication technology users.

PubMed

Rodríguez-Sánchez, Alma M; Schaufeli, Wilmar B; Salanova, Marisa; Cifre, Eva

2008-02-01

The use of technologies is more common in daily life; working with technologies might be associated with positive experiences such as flow. However, there is little empirical research on flow experiences in technology settings. The main aim of this study was to confirm the three-dimensional construct of flow, i.e., absorption, enjoyment, and intrinsic interest, among 517 Information and Communication Technology users [234 students whose mean age was 23 yr. (SD = 3.8)] from different areas of study, mainly Law, Public Administration, Chemistry, and Psychology, and 283 employees [whose mean age was 33 yr. (SD = 7.8)] of 21 different companies from various sectors of production, namely, public administration, industrial production, and services. Analysis showed, as expected, flow is a three-dimensional psychological construct and invariant among samples of technology users. Practical and theoretical implications as well as further research are discussed.

Diagnostic Pathology and Laboratory Medicine in the Age of “Omics”

PubMed Central

Finn, William G.

2007-01-01

Functional genomics and proteomics involve the simultaneous analysis of hundreds or thousands of expressed genes or proteins and have spawned the modern discipline of computational biology. Novel informatic applications, including sophisticated dimensionality reduction strategies and cancer outlier profile analysis, can distill clinically exploitable biomarkers from enormous experimental datasets. Diagnostic pathologists are now charged with translating the knowledge generated by the “omics” revolution into clinical practice. Food and Drug Administration-approved proprietary testing platforms based on microarray technologies already exist and will expand greatly in the coming years. However, for diagnostic pathology, the greatest promise of the “omics” age resides in the explosion in information technology (IT). IT applications allow for the digitization of histological slides, transforming them into minable data and enabling content-based searching and archiving of histological materials. IT will also allow for the optimization of existing (and often underused) clinical laboratory technologies such as flow cytometry and high-throughput core laboratory functions. The state of pathology practice does not always keep up with the pace of technological advancement. However, to use fully the potential of these emerging technologies for the benefit of patients, pathologists and clinical scientists must embrace the changes and transformational advances that will characterize this new era. PMID:17652635

SEURAT: Visual analytics for the integrated analysis of microarray data

PubMed Central

2010-01-01

Background In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. Results We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. Conclusions The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data. PMID:20525257

Dynamic, electronically switchable surfaces for membrane protein microarrays.

PubMed

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.

Vision in our three-dimensional world

PubMed Central

2016-01-01

Many aspects of our perceptual experience are dominated by the fact that our two eyes point forward. Whilst the location of our eyes leaves the environment behind our head inaccessible to vision, co-ordinated use of our two eyes gives us direct access to the three-dimensional structure of the scene in front of us, through the mechanism of stereoscopic vision. Scientific understanding of the different brain regions involved in stereoscopic vision and three-dimensional spatial cognition is changing rapidly, with consequent influences on fields as diverse as clinical practice in ophthalmology and the technology of virtual reality devices. This article is part of the themed issue ‘Vision in our three-dimensional world’. PMID:27269595

A Novel Approach For Ankle Foot Orthosis Developed By Three Dimensional Technologies

NASA Astrophysics Data System (ADS)

Belokar, R. M.; Banga, H. K.; Kumar, R.

2017-12-01

This study presents a novel approach for testing mechanical properties of medical orthosis developed by three dimensional (3D) technologies. A hand-held type 3D laser scanner is used for generating 3D mesh geometry directly from patient’s limb. Subsequently 3D printable orthotic design is produced from crude input model by means of Computer Aided Design (CAD) software. Fused Deposition Modelling (FDM) method in Additive Manufacturing (AM) technologies is used to fabricate the 3D printable Ankle Foot Orthosis (AFO) prototype in order to test the mechanical properties on printout. According to test results, printed Acrylonitrile Butadiene Styrene (ABS) AFO prototype has sufficient elasticity modulus and durability for patient-specific medical device manufactured by the 3D technologies.

Identifying Fishes through DNA Barcodes and Microarrays.

PubMed

Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N; Weber, Hannes; Blohm, Dietmar

2010-09-07

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.

Advances in cell-free protein array methods.

PubMed

Yu, Xiaobo; Petritis, Brianne; Duan, Hu; Xu, Danke; LaBaer, Joshua

2018-01-01

Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, the pathogen-host relationship, post-translational modifications, and antibody biomarkers of different human diseases. Their role in the first blood-based diagnostic test for early stage breast cancer highlights their value in managing human health. Cell-free protein microarrays will continue to evolve to become widespread tools for research and clinical management. Areas covered: We review the advantages and disadvantages of different cell-free protein arrays, with an emphasis on the methods that have been studied in the last five years. We also discuss the applications of each microarray method. Expert commentary: Given the growing roles and impact of cell-free protein microarrays in research and medicine, we discuss: 1) the current technical and practical limitations of cell-free protein microarrays; 2) the biomarker discovery and verification pipeline using protein microarrays; and 3) how cell-free protein microarrays will advance over the next five years, both in their technology and applications.

Advancing three-dimensional MEMS by complimentary laser micro manufacturing

NASA Astrophysics Data System (ADS)

Palmer, Jeremy A.; Williams, John D.; Lemp, Tom; Lehecka, Tom M.; Medina, Francisco; Wicker, Ryan B.

2006-01-01

This paper describes improvements that enable engineers to create three-dimensional MEMS in a variety of materials. It also provides a means for selectively adding three-dimensional, high aspect ratio features to pre-existing PMMA micro molds for subsequent LIGA processing. This complimentary method involves in situ construction of three-dimensional micro molds in a stand-alone configuration or directly adjacent to features formed by x-ray lithography. Three-dimensional micro molds are created by micro stereolithography (MSL), an additive rapid prototyping technology. Alternatively, three-dimensional features may be added by direct femtosecond laser micro machining. Parameters for optimal femtosecond laser micro machining of PMMA at 800 nanometers are presented. The technical discussion also includes strategies for enhancements in the context of material selection and post-process surface finish. This approach may lead to practical, cost-effective 3-D MEMS with the surface finish and throughput advantages of x-ray lithography. Accurate three-dimensional metal microstructures are demonstrated. Challenges remain in process planning for micro stereolithography and development of buried features following femtosecond laser micro machining.

Overcoming bias and systematic errors in next generation sequencing data.

PubMed

Taub, Margaret A; Corrada Bravo, Hector; Irizarry, Rafael A

2010-12-10

Considerable time and effort has been spent in developing analysis and quality assessment methods to allow the use of microarrays in a clinical setting. As is the case for microarrays and other high-throughput technologies, data from new high-throughput sequencing technologies are subject to technological and biological biases and systematic errors that can impact downstream analyses. Only when these issues can be readily identified and reliably adjusted for will clinical applications of these new technologies be feasible. Although much work remains to be done in this area, we describe consistently observed biases that should be taken into account when analyzing high-throughput sequencing data. In this article, we review current knowledge about these biases, discuss their impact on analysis results, and propose solutions.

Upregulated expression of La ribonucleoprotein domain family member 6 and collagen type I gene following water-filtered broad-spectrum near-infrared irradiation in a 3-dimensional human epidermal tissue culture model as revealed by microarray analysis.

PubMed

Tanaka, Yohei; Nakayama, Jun

2018-05-01

Water-filtered broad-spectrum near-infrared irradiation can induce various biological effects, as our previous clinical, histological, and biochemical investigations have shown. However, few studies that examined the changes thus induced in gene expression. The aim was to investigate the changes in gene expression in a 3-dimensional reconstructed epidermal tissue culture exposed to water-filtered broad-spectrum near-infrared irradiation. DNA microarray and quantitative real-time polymerase chain reaction (PCR) analysis was used to assess gene expression levels in a 3-dimensional reconstructed epidermal model composed of normal human epidermal cells exposed to water-filtered broad-spectrum near-infrared irradiation. The water filter allowed 1000-1800 nm wavelengths and excluded 1400-1500 nm wavelengths, and cells were exposed to 5 or 10 rounds of near-infrared irradiation at 10 J/cm 2 . A DNA microarray with over 50 000 different probes showed 18 genes that were upregulated or downregulated by at least twofold after irradiation. Quantitative real-time PCR revealed that, relative to control cells, the gene encoding La ribonucleoprotein domain family member 6 (LARP6), which regulates collagen expression, was significantly and dose-dependently upregulated (P < 0.05) by water-filtered broad-spectrum near-infrared exposure. Gene encoding transcripts of collagen type I were significantly upregulated compared with controls (P < 0.05). This study demonstrates the ability of water-filtered broad-spectrum near-infrared irradiation to stimulate the production of type I collagen. © 2017 The Australasian College of Dermatologists.

Signal amplification by rolling circle amplification on DNA microarrays

PubMed Central

Nallur, Girish; Luo, Chenghua; Fang, Linhua; Cooley, Stephanie; Dave, Varshal; Lambert, Jeremy; Kukanskis, Kari; Kingsmore, Stephen; Lasken, Roger; Schweitzer, Barry

2001-01-01

While microarrays hold considerable promise in large-scale biology on account of their massively parallel analytical nature, there is a need for compatible signal amplification procedures to increase sensitivity without loss of multiplexing. Rolling circle amplification (RCA) is a molecular amplification method with the unique property of product localization. This report describes the application of RCA signal amplification for multiplexed, direct detection and quantitation of nucleic acid targets on planar glass and gel-coated microarrays. As few as 150 molecules bound to the surface of microarrays can be detected using RCA. Because of the linear kinetics of RCA, nucleic acid target molecules may be measured with a dynamic range of four orders of magnitude. Consequently, RCA is a promising technology for the direct measurement of nucleic acids on microarrays without the need for a potentially biasing preamplification step. PMID:11726701

Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by carB-Based Oligonucleotide Microarray

PubMed Central

Shin, Hwa Hui; Hwang, Byeong Hee; Seo, Jeong Hyun

2014-01-01

It is important to rapidly and selectively detect and analyze pathogenic Salmonella enterica subsp. enterica in contaminated food to reduce the morbidity and mortality of Salmonella infection and to guarantee food safety. In the present work, we developed an oligonucleotide microarray containing duplicate specific capture probes based on the carB gene, which encodes the carbamoyl phosphate synthetase large subunit, as a competent biomarker evaluated by genetic analysis to selectively and efficiently detect and discriminate three S. enterica subsp. enterica serotypes: Choleraesuis, Enteritidis, and Typhimurium. Using the developed microarray system, three serotype targets were successfully analyzed in a range as low as 1.6 to 3.1 nM and were specifically discriminated from each other without nonspecific signals. In addition, the constructed microarray did not have cross-reactivity with other common pathogenic bacteria and even enabled the clear discrimination of the target Salmonella serotype from a bacterial mixture. Therefore, these results demonstrated that our novel carB-based oligonucleotide microarray can be used as an effective and specific detection system for S. enterica subsp. enterica serotypes. PMID:24185846

Specific discrimination of three pathogenic Salmonella enterica subsp. enterica serotypes by carB-based oligonucleotide microarray.

PubMed

Shin, Hwa Hui; Hwang, Byeong Hee; Seo, Jeong Hyun; Cha, Hyung Joon

2014-01-01

It is important to rapidly and selectively detect and analyze pathogenic Salmonella enterica subsp. enterica in contaminated food to reduce the morbidity and mortality of Salmonella infection and to guarantee food safety. In the present work, we developed an oligonucleotide microarray containing duplicate specific capture probes based on the carB gene, which encodes the carbamoyl phosphate synthetase large subunit, as a competent biomarker evaluated by genetic analysis to selectively and efficiently detect and discriminate three S. enterica subsp. enterica serotypes: Choleraesuis, Enteritidis, and Typhimurium. Using the developed microarray system, three serotype targets were successfully analyzed in a range as low as 1.6 to 3.1 nM and were specifically discriminated from each other without nonspecific signals. In addition, the constructed microarray did not have cross-reactivity with other common pathogenic bacteria and even enabled the clear discrimination of the target Salmonella serotype from a bacterial mixture. Therefore, these results demonstrated that our novel carB-based oligonucleotide microarray can be used as an effective and specific detection system for S. enterica subsp. enterica serotypes.

Guiding Exploration through Three-Dimensional Virtual Environments: A Cognitive Load Reduction Approach

ERIC Educational Resources Information Center

Chen, Chwen Jen; Fauzy Wan Ismail, Wan Mohd

2008-01-01

The real-time interactive nature of three-dimensional virtual environments (VEs) makes this technology very appropriate for exploratory learning purposes. However, many studies have shown that the exploration process may cause cognitive overload that affects the learning of domain knowledge. This article reports a quasi-experimental study that…

Investigating Various Application Areas of Three-Dimensional Virtual Worlds for Higher Education

ERIC Educational Resources Information Center

Ghanbarzadeh, Reza; Ghapanchi, Amir Hossein

2018-01-01

Three-dimensional virtual world (3DVW) have been adopted extensively in the education sector worldwide, and there has been remarkable growth in the application of these environments for distance learning. A wide variety of universities and educational organizations across the world have utilized this technology for their regular learning and…

Microarrays (DNA Chips) for the Classroom Laboratory

ERIC Educational Resources Information Center

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…

Clear cell papillary renal cell carcinoma: a chromosomal microarray analysis of two cases using a novel Molecular Inversion Probe (MIP) technology.

PubMed

Alexiev, Borislav A; Zou, Ying S

2014-12-01

Chromosomal microarray analysis using novel Molecular Inversion Probe (MIP) technology demonstrated 2,570 kb copy neutral LOH of 10q11.22 in two clear cell papillary renal cell carcinomas. In addition, one of the tumors had a big 29,784 kb deletion of 13q11-q14.2. There were two variants of unknown significance, a 2,509 kb gain of Xp22.33 and a 257 kb homozygous deletion of 8p11.22. The somatic mutation panel containing 74 mutations in nine genes did not reveal any mutations. Besides identification of submicroscopic duplications or deletions, SNP microarrays can reveal abnormal allelic imbalances including LOH and copy neutral LOH, which cannot be recognized by chromosome, FISH, and non-SNP microarray arrays. To the best of our knowledge, this is the first study demonstrating copy neutral LOH of 10q11.22 in clear cell papillary renal cell carcinomas using the new MIP SNP OncoScan FFPE Assay Kit on formalin-fixed paraffin-embedded tumor samples. Copyright © 2014 Elsevier GmbH. All rights reserved.

The FDA’s Experience with Emerging Genomics Technologies—Past, Present, and Future

PubMed Central

Xu, Joshua; Thakkar, Shraddha; Gong, Binsheng; Tong, Weida

2016-01-01

The rapid advancement of emerging genomics technologies and their application for assessing safety and efficacy of FDA-regulated products require a high standard of reliability and robustness supporting regulatory decision-making in the FDA. To facilitate the regulatory application, the FDA implemented a novel data submission program, Voluntary Genomics Data Submission (VGDS), and also to engage the stakeholders. As part of the endeavor, for the past 10 years, the FDA has led an international consortium of regulatory agencies, academia, pharmaceutical companies, and genomics platform providers, which was named MicroArray Quality Control Consortium (MAQC), to address issues such as reproducibility, precision, specificity/sensitivity, and data interpretation. Three projects have been completed so far assessing these genomics technologies: gene expression microarrays, whole genome genotyping arrays, and whole transcriptome sequencing (i.e., RNA-seq). The resultant studies provide the basic parameters for fit-for-purpose application of these new data streams in regulatory environments, and the solutions have been made available to the public through peer-reviewed publications. The latest MAQC project is also called the SEquencing Quality Control (SEQC) project focused on next-generation sequencing. Using reference samples with built-in controls, SEQC studies have demonstrated that relative gene expression can be measured accurately and reliably across laboratories and RNA-seq platforms. Besides prediction performance comparable to microarrays in clinical settings and safety assessments, RNA-seq is shown to have better sensitivity for low expression and reveal novel transcriptomic features. Future effort of MAQC will be focused on quality control of whole genome sequencing and targeted sequencing. PMID:27116022

Three-dimensional bio-printing.

PubMed

Gu, Qi; Hao, Jie; Lu, YangJie; Wang, Liu; Wallace, Gordon G; Zhou, Qi

2015-05-01

Three-dimensional (3D) printing technology has been widely used in various manufacturing operations including automotive, defence and space industries. 3D printing has the advantages of personalization, flexibility and high resolution, and is therefore becoming increasingly visible in the high-tech fields. Three-dimensional bio-printing technology also holds promise for future use in medical applications. At present 3D bio-printing is mainly used for simulating and reconstructing some hard tissues or for preparing drug-delivery systems in the medical area. The fabrication of 3D structures with living cells and bioactive moieties spatially distributed throughout will be realisable. Fabrication of complex tissues and organs is still at the exploratory stage. This review summarize the development of 3D bio-printing and its potential in medical applications, as well as discussing the current challenges faced by 3D bio-printing.

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina.

PubMed

Bidard, Frédérique; Imbeaud, Sandrine; Reymond, Nancie; Lespinet, Olivier; Silar, Philippe; Clavé, Corinne; Delacroix, Hervé; Berteaux-Lecellier, Véronique; Debuchy, Robert

2010-06-18

The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.

Chipster: user-friendly analysis software for microarray and other high-throughput data.

PubMed

Kallio, M Aleksi; Tuimala, Jarno T; Hupponen, Taavi; Klemelä, Petri; Gentile, Massimiliano; Scheinin, Ilari; Koski, Mikko; Käki, Janne; Korpelainen, Eija I

2011-10-14

The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

Chipster: user-friendly analysis software for microarray and other high-throughput data

PubMed Central

2011-01-01

Background The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Results Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Conclusions Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available. PMID:21999641

16S rRNA based microarray analysis of ten periodontal bacteria in patients with different forms of periodontitis.

PubMed

Topcuoglu, Nursen; Kulekci, Guven

2015-10-01

DNA microarray analysis is a computer based technology, that a reverse capture, which targets 10 periodontal bacteria (ParoCheck) is available for rapid semi-quantitative determination. The aim of this three-year retrospective study was to display the microarray analysis results for the subgingival biofilm samples taken from patient cases diagnosed with different forms of periodontitis. A total of 84 patients with generalized aggressive periodontitis (GAP,n:29), generalized chronic periodontitis (GCP, n:25), peri-implantitis (PI,n:14), localized aggressive periodontitis (LAP,n:8) and refractory chronic periodontitis (RP,n:8) were consecutively selected from the archives of the Oral Microbiological Diagnostic Laboratory. The subgingival biofilm samples were analyzed by the microarray-based identification of 10 selected species. All the tested species were detected in the samples. The red complex bacteria were the most prevalent with very high levels in all groups. Fusobacterium nucleatum was detected in all samples at high levels. The green and blue complex bacteria were less prevalent compared with red and orange complex, except Aggregatibacter actinomycetemcomitas was detected in all LAP group. Positive correlations were found within all the red complex bacteria and between red and orange complex bacteria especially in GCP and GAP groups. Parocheck enables to monitoring of periodontal pathogens in all forms of periodontal disease and can be alternative to other guiding and reliable microbiologic tests. Copyright © 2015 Elsevier Ltd. All rights reserved.

Using Three-Dimensional Printing to Fabricate a Tubing Connector for Dilation and Evacuation.

PubMed

Stitely, Michael L; Paterson, Helen

2016-02-01

This is a proof-of-concept study to show that simple instrumentation problems encountered in surgery can be solved by fabricating devices using a three-dimensional printer. The device used in the study is a simple tubing connector fashioned to connect two segments of suction tubing used in a surgical procedure where no commercially available product for this use is available through our usual suppliers in New Zealand. A cylindrical tubing connector was designed using three-dimensional printing design software. The tubing connector was fabricated using the Makerbot Replicator 2X three-dimensional printer. The connector was used in 15 second-trimester dilation and evacuation procedures. Data forms were completed by the primary operating surgeon. Descriptive statistics were used with the expectation that the device would function as intended in all cases. The three-dimensional printed tubing connector functioned as intended in all 15 instances. Commercially available three-dimensional printing technology can be used to overcome simple instrumentation problems encountered during gynecologic surgical procedures.

Three-dimensional printing and pediatric liver disease.

PubMed

Alkhouri, Naim; Zein, Nizar N

2016-10-01

Enthusiastic physicians and medical researchers are investigating the role of three-dimensional printing in medicine. The purpose of the current review is to provide a concise summary of the role of three-dimensional printing technology as it relates to the field of pediatric hepatology and liver transplantation. Our group and others have recently demonstrated the feasibility of printing three-dimensional livers with identical anatomical and geometrical landmarks to the native liver to facilitate presurgical planning of complex liver surgeries. Medical educators are exploring the use of three-dimensional printed organs in anatomy classes and surgical residencies. Moreover, mini-livers are being developed by regenerative medicine scientist as a way to test new drugs and, eventually, whole livers will be grown in the laboratory to replace organs with end-stage disease solving the organ shortage problem. From presurgical planning to medical education to ultimately the bioprinting of whole organs for transplantation, three-dimensional printing will change medicine as we know in the next few years.

Women's experiences receiving abnormal prenatal chromosomal microarray testing results.

PubMed

Bernhardt, Barbara A; Soucier, Danielle; Hanson, Karen; Savage, Melissa S; Jackson, Laird; Wapner, Ronald J

2013-02-01

Genomic microarrays can detect copy-number variants not detectable by conventional cytogenetics. This technology is diffusing rapidly into prenatal settings even though the clinical implications of many copy-number variants are currently unknown. We conducted a qualitative pilot study to explore the experiences of women receiving abnormal results from prenatal microarray testing performed in a research setting. Participants were a subset of women participating in a multicenter prospective study "Prenatal Cytogenetic Diagnosis by Array-based Copy Number Analysis." Telephone interviews were conducted with 23 women receiving abnormal prenatal microarray results. We found that five key elements dominated the experiences of women who had received abnormal prenatal microarray results: an offer too good to pass up, blindsided by the results, uncertainty and unquantifiable risks, need for support, and toxic knowledge. As prenatal microarray testing is increasingly used, uncertain findings will be common, resulting in greater need for careful pre- and posttest counseling, and more education of and resources for providers so they can adequately support the women who are undergoing testing.

Semiconductor Cubing

NASA Technical Reports Server (NTRS)

1996-01-01

Through Goddard Space Flight Center and Jet Propulsion Laboratory Small Business Innovation Research contracts, Irvine Sensors developed a three-dimensional memory system for a spaceborne data recorder and other applications for NASA. From these contracts, the company created the Memory Short Stack product, a patented technology for stacking integrated circuits that offers higher processing speeds and levels of integration, and lower power requirements. The product is a three-dimensional semiconductor package in which dozens of integrated circuits are stacked upon each other to form a cube. The technology is being used in various computer and telecommunications applications.

Three-dimensional display technologies

PubMed Central

Geng, Jason

2014-01-01

The physical world around us is three-dimensional (3D), yet traditional display devices can show only two-dimensional (2D) flat images that lack depth (i.e., the third dimension) information. This fundamental restriction greatly limits our ability to perceive and to understand the complexity of real-world objects. Nearly 50% of the capability of the human brain is devoted to processing visual information [Human Anatomy & Physiology (Pearson, 2012)]. Flat images and 2D displays do not harness the brain’s power effectively. With rapid advances in the electronics, optics, laser, and photonics fields, true 3D display technologies are making their way into the marketplace. 3D movies, 3D TV, 3D mobile devices, and 3D games have increasingly demanded true 3D display with no eyeglasses (autostereoscopic). Therefore, it would be very beneficial to readers of this journal to have a systematic review of state-of-the-art 3D display technologies. PMID:25530827

Detection of Porphyromonas endodontalis, Porphyromonas gingivalis and Prevotella intermedia in primary endodontic infections in a Chinese population.

PubMed

Cao, H; Qi, Z; Jiang, H; Zhao, J; Liu, Z; Tang, Z

2012-08-01

To assess the prevalence of three black-pigmented bacterial species (Porphyromonas endodontalis, Porphyromonas gingivalis and Prevotella intermedia) using microarray technology in root canals of teeth associated with primary endodontic infections in a Chinese population. Microbial samples were taken from root canals of 80 teeth with pulp necrosis and primary endodontic infections in a Chinese population. DNA extracted from the samples was amplified by PCR with universal bacterial primers based on 16S rRNA gene sequences, and the products hybridized with the microarrays in which the specific oligonucleotide probes were added. The results of hybridization were screened by a confocal laser scanner. Pearson chi-square test and the two-sided Fisher exact test were used to analyse whether a significant association existed between the species and symptoms as well as in co-existence of two target organisms by a statistical software package (SAS 8.02). The 16S rRNA gene microarray detected at least one of the three test species in 76% of the study teeth. P. endodontalis, P. gingivalis and P. intermedia were found in 50%, 33% and 45%, respectively. A significant association was found in the presence of the pair P. endodontalis / P. gingivalis (P < 0.005). Both P. endodontalis (P <0.05) and P. gingivalis (P <0.005) had a statistically significant association with the presence of a sinus tract. The simultaneous presence of P. endodontalis and P. gingivalis was also associated with the presence of a sinus tract (P<0.005) and abscess formation (P<0.05). The three black-pigmented bacteria were prevalent in teeth with pulp necrosis and primary endodontic infections in a Chinese population. P. gingivalis and P. endodontalis were associated with the presence of sinus tract and abscess formation. © 2012 International Endodontic Journal.

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data

PubMed Central

McArt, Darragh G.; Dunne, Philip D.; Blayney, Jaine K.; Salto-Tellez, Manuel; Van Schaeybroeck, Sandra; Hamilton, Peter W.; Zhang, Shu-Dong

2013-01-01

The advent of next generation sequencing technologies (NGS) has expanded the area of genomic research, offering high coverage and increased sensitivity over older microarray platforms. Although the current cost of next generation sequencing is still exceeding that of microarray approaches, the rapid advances in NGS will likely make it the platform of choice for future research in differential gene expression. Connectivity mapping is a procedure for examining the connections among diseases, genes and drugs by differential gene expression initially based on microarray technology, with which a large collection of compound-induced reference gene expression profiles have been accumulated. In this work, we aim to test the feasibility of incorporating NGS RNA-Seq data into the current connectivity mapping framework by utilizing the microarray based reference profiles and the construction of a differentially expressed gene signature from a NGS dataset. This would allow for the establishment of connections between the NGS gene signature and those microarray reference profiles, alleviating the associated incurring cost of re-creating drug profiles with NGS technology. We examined the connectivity mapping approach on a publicly available NGS dataset with androgen stimulation of LNCaP cells in order to extract candidate compounds that could inhibit the proliferative phenotype of LNCaP cells and to elucidate their potential in a laboratory setting. In addition, we also analyzed an independent microarray dataset of similar experimental settings. We found a high level of concordance between the top compounds identified using the gene signatures from the two datasets. The nicotine derivative cotinine was returned as the top candidate among the overlapping compounds with potential to suppress this proliferative phenotype. Subsequent lab experiments validated this connectivity mapping hit, showing that cotinine inhibits cell proliferation in an androgen dependent manner. Thus the results in this study suggest a promising prospect of integrating NGS data with connectivity mapping. PMID:23840550

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

PubMed

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.

Application of 3D Laser Scanning Technology in Inspection and Dynamic Reserves Detection of Open-Pit Mine

NASA Astrophysics Data System (ADS)

Hu, Zhumin; Wei, Shiyu; Jiang, Jun

2017-10-01

The traditional open-pit mine mining rights verification and dynamic reserve detection means rely on the total station and RTK to collect the results of the turning point coordinates of mining surface contours. It resulted in obtaining the results of low precision and large error in the means that is limited by the traditional measurement equipment accuracy and measurement methods. The three-dimensional scanning technology can obtain the three-dimensional coordinate data of the surface of the measured object in a large area at high resolution. This paper expounds the commonly used application of 3D scanning technology in the inspection and dynamic reserve detection of open mine mining rights.

[Manufacture method and clinical application of minimally invasive dental implant guide template based on registration technology].

PubMed

Lin, Zeming; He, Bingwei; Chen, Jiang; D u, Zhibin; Zheng, Jingyi; Li, Yanqin

2012-08-01

To guide doctors in precisely positioning surgical operation, a new production method of minimally invasive implant guide template was presented. The mandible of patient was scanned by CT scanner, and three-dimensional jaw bone model was constructed based on CT images data The professional dental implant software Simplant was used to simulate the plant based on the three-dimensional CT model to determine the location and depth of implants. In the same time, the dental plaster models were scanned by stereo vision system to build the oral mucosa model. Next, curvature registration technology was used to fuse the oral mucosa model and the CT model, then the designed position of implant in the oral mucosa could be determined. The minimally invasive implant guide template was designed in 3-Matic software according to the design position of implant and the oral mucosa model. Finally, the template was produced by rapid prototyping. The three-dimensional registration technology was useful to fuse the CT data and the dental plaster data, and the template was accurate that could provide the doctors a guidance in the actual planting without cut-off mucosa. The guide template which fabricated by comprehensive utilization of three-dimensional registration, Simplant simulation and rapid prototyping positioning are accurate and can achieve the minimally invasive and accuracy implant surgery, this technique is worthy of clinical use.

Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems

PubMed Central

Li, Xiang; Harwood, Valerie J.; Nayak, Bina

2016-01-01

Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment. PMID:26729716

The contribution of the DNA microarray technology to gene expression profiling in Leishmania spp.: a retrospective.

PubMed

Alonso, Ana; Larraga, Vicente; Alcolea, Pedro J

2018-05-07

The first genome project of any living organism excluding viruses, the gammaproteobacteria Haemophilus influenzae, was completed in 1995. Until the last decade, genome sequencing was very tedious because genome survey sequences (GSS) and/or expressed sequence tags (ESTs) belonging to plasmid, cosmid and artificial chromosome genome libraries had to be sequenced and assembled in silico. Nowadays, no genome is completely assembled actually, because gaps and unassembled contigs are always remaining. However, most represent the whole genome of the organism of origin from a practical point of view. The first genome sequencing projects of trypanosomatid parasites were completed in 2005 following those strategies, and belong to Leishmania major, Trypanosoma cruzi and T. brucei. The functional genomics era rapidly developed on the basis of the microarray technology and has been evolving. In the case of the genus Leishmania, substantial biological information about differentiation in the digenetic life cycle of the parasite has been obtained. Later on, next generation sequencing has revolutionized genome sequencing and functional genomics, leading to more sensitive, accurate results by using much less resources. This new technology is more advantageous, but does not invalidate microarray results. In fact, promising vaccine candidates and drug targets have been found on the basis of microarray-based screening and preliminary proof-of-concept tests. Copyright © 2018. Published by Elsevier B.V.

Highly conductive metal interconnects on three-dimensional objects fabricated with omnidirectional ink jet printing technology

NASA Astrophysics Data System (ADS)

Yoshida, Yasunori; Wada, Hikaru; Izumi, Konami; Tokito, Shizuo

2017-05-01

In this work, we demonstrate that highly conductive metal interconnects can be fabricated on the surface of three-dimensional objects using “omnidirectional ink jet” (OIJ) printing technology. OIJ printing technology makes it possible to perform ink jet printing in all directions by combining the motion of a 6-axis vertically articulated robot with precise positioning and a thermal drying process, which allows for the printing of stacked layers. By using OIJ technology, we were the first to successfully fabricate printed interconnect layers having a very low electrical resistance of 12 mΩ over a 10 mm length. Moreover, the results of the high-current test demonstrated that the printed interconnects can withstand high-current-flow of 5 A for 30 min or more.

Research of an optimization design method of integral imaging three-dimensional display system

NASA Astrophysics Data System (ADS)

Gao, Hui; Yan, Zhiqiang; Wen, Jun; Jiang, Guanwu

2016-03-01

The information warfare needs a highly transparent environment of battlefield, it follows that true three-dimensional display technology has obvious advantages than traditional display technology in the current field of military science and technology. It also focuses on the research progress of lens array imaging technology and aims at what restrict the development of integral imaging, main including low spatial resolution, narrow depth range and small viewing angle. This paper summarizes the principle, characteristics and development history of the integral imaging. A variety of methods are compared and analyzed that how to improve the resolution, extend depth of field, increase scope and eliminate the artifact aiming at problems currently. And makes a discussion about the experimental results of the research, comparing the display performance of different methods.

[New simulation technologies in neurosurgery].

PubMed

Byvaltsev, V A; Belykh, E G; Konovalov, N A

2016-01-01

The article presents a literature review on the current state of simulation technologies in neurosurgery, a brief description of the basic technology and the classification of simulation models, and examples of simulation models and skills simulators used in neurosurgery. Basic models for the development of physical skills, the spectrum of available computer virtual simulators, and their main characteristics are described. It would be instructive to include microneurosurgical training and a cadaver course of neurosurgical approaches in neurosurgery training programs and to extend the use of three-dimensional imaging. Technologies for producing three-dimensional anatomical models and patient-specific computer simulators as well as improvement of tactile feedback systems and display quality of virtual models are promising areas. Continued professional education necessitates further research for assessing the validity and practical use of simulators and physical models.

Improving Assistive Technology Service by Using 3D Printing: Three Case Studies.

PubMed

Watanabe, Takashi; Hatakeyama, Takuro; Tomiita, Mitsuru

2015-01-01

Assistive technology services are essential for adapting assistive devices to the individual needs of users with disabilities. In this study, we attempted to apply three-dimensional (3D) printing technology to three actual cases, and to study its use, effectiveness, and future applications. We assessed the usefulness of 3D printing technology by categorizing its utilization after reviewing the outcomes of these case studies. In future work, we aim to gather additional case studies and derive information on using 3D printing technology that will enable its effective application in the process of assistive technology services.

Microarray as a First Genetic Test in Global Developmental Delay: A Cost-Effectiveness Analysis

ERIC Educational Resources Information Center

Trakadis, Yannis; Shevell, Michael

2011-01-01

Aim: Microarray technology has a significantly higher clinical yield than karyotyping in individuals with global developmental delay (GDD). Despite this, it has not yet been routinely implemented as a screening test owing to the perception that this approach is more expensive. We aimed to evaluate the effect that replacing karyotype with…

Finding Patterns of Emergence in Science and Technology

DTIC Science & Technology

2012-09-24

formal evaluation scheduled – Case Studies, Eight Examples: Tissue Engineering, Cold Fusion, RF Metamaterials, DNA Microarrays, Genetic Algorithms, RNAi...emerging capabilities Case Studies, Eight Examples: • Tissue Engineering, Cold Fusion, RF Metamaterials, DNA Microarrays, Genetic Algorithms...Evidence Quality (i.e., the rubric ) and deliver comprehensible evidential support for nomination • Demonstrate proof-of-concept nomination for Chinese

An Inexpensive Gel Electrophoresis-Based Polymerase Chain Reaction Method for Quantifying mRNA Levels

ERIC Educational Resources Information Center

Bradford, William D.; Cahoon, Laty; Freel, Sara R.; Hoopes, Laura L. Mays; Eckdahl, Todd T.

2005-01-01

In order to engage their students in a core methodology of the new genomics era, an everincreasing number of faculty at primarily undergraduate institutions are gaining access to microarray technology. Their students are conducting successful microarray experiments designed to address a variety of interesting questions. A next step in these…

A Unique Procedure to Identify Cell Surface Markers Through a Spherical Self-Organizing Map Applied to DNA Microarray Analysis.

PubMed

Sugii, Yuh; Kasai, Tomonari; Ikeda, Masashi; Vaidyanath, Arun; Kumon, Kazuki; Mizutani, Akifumi; Seno, Akimasa; Tokutaka, Heizo; Kudoh, Takayuki; Seno, Masaharu

2016-01-01

To identify cell-specific markers, we designed a DNA microarray platform with oligonucleotide probes for human membrane-anchored proteins. Human glioma cell lines were analyzed using microarray and compared with normal and fetal brain tissues. For the microarray analysis, we employed a spherical self-organizing map, which is a clustering method suitable for the conversion of multidimensional data into two-dimensional data and displays the relationship on a spherical surface. Based on the gene expression profile, the cell surface characteristics were successfully mirrored onto the spherical surface, thereby distinguishing normal brain tissue from the disease model based on the strength of gene expression. The clustered glioma-specific genes were further analyzed by polymerase chain reaction procedure and immunocytochemical staining of glioma cells. Our platform and the following procedure were successfully demonstrated to categorize the genes coding for cell surface proteins that are specific to glioma cells. Our assessment demonstrates that a spherical self-organizing map is a valuable tool for distinguishing cell surface markers and can be employed in marker discovery studies for the treatment of cancer.

AucPR: an AUC-based approach using penalized regression for disease prediction with high-dimensional omics data.

PubMed

Yu, Wenbao; Park, Taesung

2014-01-01

It is common to get an optimal combination of markers for disease classification and prediction when multiple markers are available. Many approaches based on the area under the receiver operating characteristic curve (AUC) have been proposed. Existing works based on AUC in a high-dimensional context depend mainly on a non-parametric, smooth approximation of AUC, with no work using a parametric AUC-based approach, for high-dimensional data. We propose an AUC-based approach using penalized regression (AucPR), which is a parametric method used for obtaining a linear combination for maximizing the AUC. To obtain the AUC maximizer in a high-dimensional context, we transform a classical parametric AUC maximizer, which is used in a low-dimensional context, into a regression framework and thus, apply the penalization regression approach directly. Two kinds of penalization, lasso and elastic net, are considered. The parametric approach can avoid some of the difficulties of a conventional non-parametric AUC-based approach, such as the lack of an appropriate concave objective function and a prudent choice of the smoothing parameter. We apply the proposed AucPR for gene selection and classification using four real microarray and synthetic data. Through numerical studies, AucPR is shown to perform better than the penalized logistic regression and the nonparametric AUC-based method, in the sense of AUC and sensitivity for a given specificity, particularly when there are many correlated genes. We propose a powerful parametric and easily-implementable linear classifier AucPR, for gene selection and disease prediction for high-dimensional data. AucPR is recommended for its good prediction performance. Beside gene expression microarray data, AucPR can be applied to other types of high-dimensional omics data, such as miRNA and protein data.

Plastic Polymers for Efficient DNA Microarray Hybridization: Application to Microbiological Diagnostics▿

PubMed Central

Zhao, Zhengshan; Peytavi, Régis; Diaz-Quijada, Gerardo A.; Picard, Francois J.; Huletsky, Ann; Leblanc, Éric; Frenette, Johanne; Boivin, Guy; Veres, Teodor; Dumoulin, Michel M.; Bergeron, Michel G.

2008-01-01

Fabrication of microarray devices using traditional glass slides is not easily adaptable to integration into microfluidic systems. There is thus a need for the development of polymeric materials showing a high hybridization signal-to-background ratio, enabling sensitive detection of microbial pathogens. We have developed such plastic supports suitable for highly sensitive DNA microarray hybridizations. The proof of concept of this microarray technology was done through the detection of four human respiratory viruses that were amplified and labeled with a fluorescent dye via a sensitive reverse transcriptase PCR (RT-PCR) assay. The performance of the microarray hybridization with plastic supports made of PMMA [poly(methylmethacrylate)]-VSUVT or Zeonor 1060R was compared to that with high-quality glass slide microarrays by using both passive and microfluidic hybridization systems. Specific hybridization signal-to-background ratios comparable to that obtained with high-quality commercial glass slides were achieved with both polymeric substrates. Microarray hybridizations demonstrated an analytical sensitivity equivalent to approximately 100 viral genome copies per RT-PCR, which is at least 100-fold higher than the sensitivities of previously reported DNA hybridizations on plastic supports. Testing of these plastic polymers using a microfluidic microarray hybridization platform also showed results that were comparable to those with glass supports. In conclusion, PMMA-VSUVT and Zeonor 1060R are both suitable for highly sensitive microarray hybridizations. PMID:18784318

Visuospatial Attention in Children with Autism Spectrum Disorder: A Comparison between 2-D and 3-D Environments

ERIC Educational Resources Information Center

Ip, Horace H. S.; Lai, Candy Hoi-Yan; Wong, Simpson W. L.; Tsui, Jenny K. Y.; Li, Richard Chen; Lau, Kate Shuk-Ying; Chan, Dorothy F. Y.

2017-01-01

Previous research has illustrated the unique benefits of three-dimensional (3-D) Virtual Reality (VR) technology in Autism Spectrum Disorder (ASD) children. This study examined the use of 3-D VR technology as an assessment tool in ASD children, and further compared its use to two-dimensional (2-D) tasks. Additionally, we aimed to examine…

The assessment of virtual reality for human anatomy instruction

NASA Technical Reports Server (NTRS)

Benn, Karen P.

1994-01-01

This research project seeks to meet the objective of science training by developing, assessing, and validating virtual reality as a human anatomy training medium. In ideal situations, anatomic models, computer-based instruction, and cadaver dissection are utilized to augment the traditional methods of instruction. At many institutions, lack of financial resources limits anatomy instruction to textbooks and lectures. However, human anatomy is three dimensional, unlike the one dimensional depiction found in textbooks and the two dimensional depiction found on the computer. Virtual reality is a breakthrough technology that allows one to step through the computer screen into a three dimensional world. This technology offers many opportunities to enhance science education. Therefore, a virtual testing environment of the abdominopelvic region of a human cadaver was created to study the placement of body parts within the nine anatomical divisions of the abdominopelvic region and the four abdominal quadrants.

Recommendations for the use of microarrays in prenatal diagnosis.

PubMed

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.

Microintaglio Printing for Soft Lithography-Based in Situ Microarrays

PubMed Central

Biyani, Manish; Ichiki, Takanori

2015-01-01

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. PMID:27600226

Multiclass classification of microarray data samples with a reduced number of genes

PubMed Central

2011-01-01

Background Multiclass classification of microarray data samples with a reduced number of genes is a rich and challenging problem in Bioinformatics research. The problem gets harder as the number of classes is increased. In addition, the performance of most classifiers is tightly linked to the effectiveness of mandatory gene selection methods. Critical to gene selection is the availability of estimates about the maximum number of genes that can be handled by any classification algorithm. Lack of such estimates may lead to either computationally demanding explorations of a search space with thousands of dimensions or classification models based on gene sets of unrestricted size. In the former case, unbiased but possibly overfitted classification models may arise. In the latter case, biased classification models unable to support statistically significant findings may be obtained. Results A novel bound on the maximum number of genes that can be handled by binary classifiers in binary mediated multiclass classification algorithms of microarray data samples is presented. The bound suggests that high-dimensional binary output domains might favor the existence of accurate and sparse binary mediated multiclass classifiers for microarray data samples. Conclusions A comprehensive experimental work shows that the bound is indeed useful to induce accurate and sparse multiclass classifiers for microarray data samples. PMID:21342522

Digital Earth system based river basin data integration

NASA Astrophysics Data System (ADS)

Zhang, Xin; Li, Wanqing; Lin, Chao

2014-12-01

Digital Earth is an integrated approach to build scientific infrastructure. The Digital Earth systems provide a three-dimensional visualization and integration platform for river basin data which include the management data, in situ observation data, remote sensing observation data and model output data. This paper studies the Digital Earth system based river basin data integration technology. Firstly, the construction of the Digital Earth based three-dimensional river basin data integration environment is discussed. Then the river basin management data integration technology is presented which is realized by general database access interface, web service and ActiveX control. Thirdly, the in situ data stored in database tables as records integration is realized with three-dimensional model of the corresponding observation apparatus display in the Digital Earth system by a same ID code. In the next two parts, the remote sensing data and the model output data integration technologies are discussed in detail. The application in the Digital Zhang River basin System of China shows that the method can effectively improve the using efficiency and visualization effect of the data.

Spectral embedding finds meaningful (relevant) structure in image and microarray data

PubMed Central

Higgs, Brandon W; Weller, Jennifer; Solka, Jeffrey L

2006-01-01

Background Accurate methods for extraction of meaningful patterns in high dimensional data have become increasingly important with the recent generation of data types containing measurements across thousands of variables. Principal components analysis (PCA) is a linear dimensionality reduction (DR) method that is unsupervised in that it relies only on the data; projections are calculated in Euclidean or a similar linear space and do not use tuning parameters for optimizing the fit to the data. However, relationships within sets of nonlinear data types, such as biological networks or images, are frequently mis-rendered into a low dimensional space by linear methods. Nonlinear methods, in contrast, attempt to model important aspects of the underlying data structure, often requiring parameter(s) fitting to the data type of interest. In many cases, the optimal parameter values vary when different classification algorithms are applied on the same rendered subspace, making the results of such methods highly dependent upon the type of classifier implemented. Results We present the results of applying the spectral method of Lafon, a nonlinear DR method based on the weighted graph Laplacian, that minimizes the requirements for such parameter optimization for two biological data types. We demonstrate that it is successful in determining implicit ordering of brain slice image data and in classifying separate species in microarray data, as compared to two conventional linear methods and three nonlinear methods (one of which is an alternative spectral method). This spectral implementation is shown to provide more meaningful information, by preserving important relationships, than the methods of DR presented for comparison. Tuning parameter fitting is simple and is a general, rather than data type or experiment specific approach, for the two datasets analyzed here. Tuning parameter optimization is minimized in the DR step to each subsequent classification method, enabling the possibility of valid cross-experiment comparisons. Conclusion Results from the spectral method presented here exhibit the desirable properties of preserving meaningful nonlinear relationships in lower dimensional space and requiring minimal parameter fitting, providing a useful algorithm for purposes of visualization and classification across diverse datasets, a common challenge in systems biology. PMID:16483359

Three dimensional display of underground water-supplying network by combining VTK with SiCAD/open GIS system

NASA Astrophysics Data System (ADS)

Chen, Shaobin; Zhang, Xubo; Wang, Wenyuan; Zhou, Chengping; Ding, Mingyue

2007-11-01

Nowadays many Geographic Information System (GIS) have been widely used in many municipal corporations. Water-supplying corporations in many cities developed GIS application system based on SiCAD/Open GIS platform several years ago for their daily management and engineering construction. With the increasing of commercial business, many corporations now need to add the functionality of three dimensional to display to their GIS System without too much financial cost. Because of the expensiveness of updating SiCAD/Open GIS system to the up-to-date version, the introduction of a third-part 3D display technology is considered. In our solution, Visualization Toolkit (VTK) is used to achieve three dimensional display of underground water-supplying network on the basis of an existing SiCAD/Open GIS system. This paper addresses on the system architecture and key implementation technologies of this solution.

The Scientist, Philosopher, and Rhetorician: The Three Dimensions of Technical Communication and Technology

ERIC Educational Resources Information Center

Garrison, Kevin

2014-01-01

Technical communication's attempt to prioritize theories of scholarship and pedagogy has resulted in several authors contributing a three-dimensional framework to approach technology: the instrumental perspective, the critical humanist perspective, and the user-centered perspective [1-3]. This article traces connections between this framework for…

Statistical issues in signal extraction from microarrays

NASA Astrophysics Data System (ADS)

Bergemann, Tracy; Quiaoit, Filemon; Delrow, Jeffrey J.; Zhao, Lue Ping

2001-06-01

Microarray technologies are increasingly used in biomedical research to study genome-wide expression profiles in the post genomic era. Their popularity is largely due to their high throughput and economical affordability. For example, microarrays have been applied to studies of cell cycle, regulatory circuitry, cancer cell lines, tumor tissues, and drug discoveries. One obstacle facing the continued success of applying microarray technologies, however, is the random variaton present on microarrays: within signal spots, between spots and among chips. In addition, signals extracted by available software packages seem to vary significantly. Despite a variety of software packages, it appears that there are two major approaches to signal extraction. One approach is to focus on the identification of signal regions and hence estimation of signal levels above background levels. The other approach is to use the distribution of intensity values as a way of identifying relevant signals. Building upon both approaches, the objective of our work is to develop a method that is statistically rigorous and also efficient and robust. Statistical issues to be considered here include: (1) how to refine grid alignment so that the overall variation is minimized, (2) how to estimate the signal levels relative to the local background levels as well as the variance of this estimate, and (3) how to integrate red and green channel signals so that the ratio of interest is stable, simultaneously relaxing distributional assumptions.

Multiple biomarkers in molecular oncology. II. Molecular diagnostics applications in breast cancer management.

PubMed

Malinowski, Douglas P

2007-05-01

In recent years, the application of genomic and proteomic technologies to the problem of breast cancer prognosis and the prediction of therapy response have begun to yield encouraging results. Independent studies employing transcriptional profiling of primary breast cancer specimens using DNA microarrays have identified gene expression profiles that correlate with clinical outcome in primary breast biopsy specimens. Recent advances in microarray technology have demonstrated reproducibility, making clinical applications more achievable. In this regard, one such DNA microarray device based upon a 70-gene expression signature was recently cleared by the US FDA for application to breast cancer prognosis. These DNA microarrays often employ at least 70 gene targets for transcriptional profiling and prognostic assessment in breast cancer. The use of PCR-based methods utilizing a small subset of genes has recently demonstrated the ability to predict the clinical outcome in early-stage breast cancer. Furthermore, protein-based immunohistochemistry methods have progressed from using gene clusters and gene expression profiling to smaller subsets of expressed proteins to predict prognosis in early-stage breast cancer. Beyond prognostic applications, DNA microarray-based transcriptional profiling has demonstrated the ability to predict response to chemotherapy in early-stage breast cancer patients. In this review, recent advances in the use of multiple markers for prognosis of disease recurrence in early-stage breast cancer and the prediction of therapy response will be discussed.

[Technology of analysis of epigenetic and structural changes of epithelial tumors genome with NotI-microarrays by the example of human chromosome].

PubMed

Pavlova, T V; Kashuba, V I; Muravenko, O V; Yenamandra, S P; Ivanova, T A; Zabarovskaia, V I; Rakhmanaliev, E R; Petrenko, L A; Pronina, I V; Loginov, V I; Iurkevich, O Iu; Kiselev, L L; Zelenin, A V; Zabarovskiĭ, E R

2009-01-01

New comparative genome hybridization technology on NotI-microarrays is presented (Karolinska Institute International Patent WO02/086163). The method is based on comparative genome hybridization of NotI-probes from tumor and normal genomic DNA with the principle of new DNA NotI-microarrays. Using this method 181 NotI linking loci from human chromosome 3 were analyzed in 200 malignant tumor samples from different organs: kidney, lung, breast, ovary, cervical, prostate. Most frequently (more than in 30%) aberrations--deletions, methylation,--were identified in NotI-sites located in MINT24, BHLHB2, RPL15, RARbeta1, ITGA9, RBSP3, VHL, ZIC4 genes, that suggests they probably are involved in cancer development. Methylation of these genomic loci was confirmed by methylation-specific PCR and bisulfite sequencing. The results demonstrate perspective of using this method to solve some oncogenomic problems.

A photophoretic-trap volumetric display

NASA Astrophysics Data System (ADS)

Smalley, D. E.; Nygaard, E.; Squire, K.; van Wagoner, J.; Rasmussen, J.; Gneiting, S.; Qaderi, K.; Goodsell, J.; Rogers, W.; Lindsey, M.; Costner, K.; Monk, A.; Pearson, M.; Haymore, B.; Peatross, J.

2018-01-01

Free-space volumetric displays, or displays that create luminous image points in space, are the technology that most closely resembles the three-dimensional displays of popular fiction. Such displays are capable of producing images in ‘thin air’ that are visible from almost any direction and are not subject to clipping. Clipping restricts the utility of all three-dimensional displays that modulate light at a two-dimensional surface with an edge boundary; these include holographic displays, nanophotonic arrays, plasmonic displays, lenticular or lenslet displays and all technologies in which the light scattering surface and the image point are physically separate. Here we present a free-space volumetric display based on photophoretic optical trapping that produces full-colour graphics in free space with ten-micrometre image points using persistence of vision. This display works by first isolating a cellulose particle in a photophoretic trap created by spherical and astigmatic aberrations. The trap and particle are then scanned through a display volume while being illuminated with red, green and blue light. The result is a three-dimensional image in free space with a large colour gamut, fine detail and low apparent speckle. This platform, named the Optical Trap Display, is capable of producing image geometries that are currently unobtainable with holographic and light-field technologies, such as long-throw projections, tall sandtables and ‘wrap-around’ displays.

Impact of Profiling Technologies in the Understanding of Recombinant Protein Production

NASA Astrophysics Data System (ADS)

Vijayendran, Chandran; Flaschel, Erwin

Since expression profiling methods have been available in a high throughput fashion, the implication of these technologies in the field of biotechnology has increased dramatically. Microarray technology is one such unique and efficient methodology for simultaneous exploration of expression levels of numerous genes. Likewise, two-dimensional gel electrophoresis or multidimensional liquid chromatography coupled with mass spectrometry are extensively utilised for studying expression levels of numerous proteins. In the field of biotechnology these highly parallel analytical methods have paved the way to study and understand various biological phenomena depending on expression patterns. The next phenomenological level is represented by the metabolome and the (metabolic) fluxome. However, this chapter reviews gene and protein profiling and their impact on understanding recombinant protein production. We focus on the computational methods utilised for the analyses of data obtained from these profiling technologies as well as prominent results focusing on recombinant protein expression with Escherichia coli. Owing to the knowledge accumulated with respect to cellular signals triggered during recombinant protein production, this field is on the way to design strategies for developing improved processes. Both gene and protein profiling have exhibited a handful of functional categories to concentrate on in order to identify target genes and proteins, respectively, involved in the signalling network with major impact on recombinant protein production.

A Newtonian approach to extraordinarily strong negative refraction.

PubMed

Yoon, Hosang; Yeung, Kitty Y M; Umansky, Vladimir; Ham, Donhee

2012-08-02

Metamaterials with negative refractive indices can manipulate electromagnetic waves in unusual ways, and can be used to achieve, for example, sub-diffraction-limit focusing, the bending of light in the 'wrong' direction, and reversed Doppler and Cerenkov effects. These counterintuitive and technologically useful behaviours have spurred considerable efforts to synthesize a broad array of negative-index metamaterials with engineered electric, magnetic or optical properties. Here we demonstrate another route to negative refraction by exploiting the inertia of electrons in semiconductor two-dimensional electron gases, collectively accelerated by electromagnetic waves according to Newton's second law of motion, where this acceleration effect manifests as kinetic inductance. Using kinetic inductance to attain negative refraction was theoretically proposed for three-dimensional metallic nanoparticles and seen experimentally with surface plasmons on the surface of a three-dimensional metal. The two-dimensional electron gas that we use at cryogenic temperatures has a larger kinetic inductance than three-dimensional metals, leading to extraordinarily strong negative refraction at gigahertz frequencies, with an index as large as -700. This pronounced negative refractive index and the corresponding reduction in the effective wavelength opens a path to miniaturization in the science and technology of negative refraction.

A novel surface modification approach for protein and cell microarrays

NASA Astrophysics Data System (ADS)

Kurkuri, Mahaveer D.; Driever, Chantelle; Thissen, Helmut W.; Voelcker, Nicholas H.

2007-01-01

Tissue engineering and stem cell technologies have led to a rapidly increasing interest in the control of the behavior of mammalian cells growing on tissue culture substrates. Multifunctional polymer coatings can assist research in this area in many ways, for example, by providing low non-specific protein adsorption properties and reactive functional groups at the surface. The latter can be used for immobilization of specific biological factors that influence cell behavior. In this study, glass slides were coated with copolymers of glycidyl methacrylate (GMA) and poly(ethylene glycol) methacrylate (PEGMA). The coatings were prepared by three different methods based on dip and spin coating as well as polymer grafting procedures. Coatings were characterized by X-ray photoelectron spectroscopy, surface sensitive infrared spectroscopy, ellipsometry and contact angle measurements. A fluorescently labelled protein was deposited onto reactive coatings using a contact microarrayer. Printing of a model protein (fluorescein labeled bovine serum albumin) was performed at different protein concentrations, pH, temperature, humidity and using different micropins. The arraying of proteins was studied with a microarray scanner. Arrays printed at a protein concentration above 50 μg/mL prepared in pH 5 phosphate buffer at 10°C and 65% relative humidity gave the most favourable results in terms of the homogeneity of the printed spots and the fluorescence intensity.

Genomic analysis of Fusarium verticillioides.

PubMed

Brown, D W; Butchko, R A E; Proctor, R H

2008-09-01

Fusarium verticillioides (teleomorph Gibberella moniliformis) can be either an endophyte of maize, causing no visible disease, or a pathogen-causing disease of ears, stalks, roots and seedlings. At any stage, this fungus can synthesize fumonisins, a family of mycotoxins structurally similar to the sphingolipid sphinganine. Ingestion of fumonisin-contaminated maize has been associated with a number of animal diseases, including cancer in rodents, and exposure has been correlated with human oesophageal cancer in some regions of the world, and some evidence suggests that fumonisins are a risk factor for neural tube defects. A primary goal of the authors' laboratory is to eliminate fumonisin contamination of maize and maize products. Understanding how and why these toxins are made and the F. verticillioides-maize disease process will allow one to develop novel strategies to limit tissue destruction (rot) and fumonisin production. To meet this goal, genomic sequence data, expressed sequence tags (ESTs) and microarrays are being used to identify F. verticillioides genes involved in the biosynthesis of toxins and plant pathogenesis. This paper describes the current status of F. verticillioides genomic resources and three approaches being used to mine microarray data from a wild-type strain cultured in liquid fumonisin production medium for 12, 24, 48, 72, 96 and 120h. Taken together, these approaches demonstrate the power of microarray technology to provide information on different biological processes.

Development of a DNA Microarray-Based Assay for the Detection of Sugar Beet Root Rot Pathogens.

PubMed

Liebe, Sebastian; Christ, Daniela S; Ehricht, Ralf; Varrelmann, Mark

2016-01-01

Sugar beet root rot diseases that occur during the cropping season or in storage are accompanied by high yield losses and a severe reduction of processing quality. The vast diversity of microorganism species involved in rot development requires molecular tools allowing simultaneous identification of many different targets. Therefore, a new microarray technology (ArrayTube) was applied in this study to improve diagnosis of sugar beet root rot diseases. Based on three marker genes (internal transcribed spacer, translation elongation factor 1 alpha, and 16S ribosomal DNA), 42 well-performing probes enabled the identification of prevalent field pathogens (e.g., Aphanomyces cochlioides), storage pathogens (e.g., Botrytis cinerea), and ubiquitous spoilage fungi (e.g., Penicillium expansum). All probes were proven for specificity with pure cultures from 73 microorganism species as well as for in planta detection of their target species using inoculated sugar beet tissue. Microarray-based identification of root rot pathogens in diseased field beets was successfully confirmed by classical detection methods. The high discriminatory potential was proven by Fusarium species differentiation based on a single nucleotide polymorphism. The results demonstrate that the ArrayTube constitute an innovative tool allowing a rapid and reliable detection of plant pathogens particularly when multiple microorganism species are present.

Applications of three-dimensional printing technology in urological practice.

PubMed

Youssef, Ramy F; Spradling, Kyle; Yoon, Renai; Dolan, Benjamin; Chamberlin, Joshua; Okhunov, Zhamshid; Clayman, Ralph; Landman, Jaime

2015-11-01

A rapid expansion in the medical applications of three-dimensional (3D)-printing technology has been seen in recent years. This technology is capable of manufacturing low-cost and customisable surgical devices, 3D models for use in preoperative planning and surgical education, and fabricated biomaterials. While several studies have suggested 3D printers may be a useful and cost-effective tool in urological practice, few studies are available that clearly demonstrate the clinical benefit of 3D-printed materials. Nevertheless, 3D-printing technology continues to advance rapidly and promises to play an increasingly larger role in the field of urology. Herein, we review the current urological applications of 3D printing and discuss the potential impact of 3D-printing technology on the future of urological practice. © 2015 The Authors BJU International © 2015 BJU International Published by John Wiley & Sons Ltd.

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface.

PubMed

Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B; Almon, Richard R; DuBois, Debra C; Jusko, William J; Hoffman, Eric P

2004-01-01

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp).

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface

PubMed Central

Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B.; Almon, Richard R.; DuBois, Debra C.; Jusko, William J.; Hoffman, Eric P.

2004-01-01

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp). PMID:14681485

Teaching veterinary obstetrics using three-dimensional animation technology.

PubMed

Scherzer, Jakob; Buchanan, M Flint; Moore, James N; White, Susan L

2010-01-01

In this three-year study, test scores for students taught veterinary obstetrics in a classroom setting with either traditional media (photographs, text, and two-dimensional graphical presentations) were compared with those for students taught by incorporating three-dimensional (3D) media (linear animations and interactive QuickTime Virtual Reality models) into the classroom lectures. Incorporation of the 3D animations and interactive models significantly increased students' scores on essay questions designed to assess their comprehension of the subject matter. This approach to education may help to better prepare students for dealing with obstetrical cases during their final clinical year and after graduation.

Two- to three-dimensional crossover in a dense electron liquid in silicon

NASA Astrophysics Data System (ADS)

Matmon, Guy; Ginossar, Eran; Villis, Byron J.; Kölker, Alex; Lim, Tingbin; Solanki, Hari; Schofield, Steven R.; Curson, Neil J.; Li, Juerong; Murdin, Ben N.; Fisher, Andrew J.; Aeppli, Gabriel

2018-04-01

Doping of silicon via phosphine exposures alternating with molecular beam epitaxy overgrowth is a path to Si:P substrates for conventional microelectronics and quantum information technologies. The technique also provides a well-controlled material for systematic studies of two-dimensional lattices with a half-filled band. We show here that for a dense (ns=2.8 ×1014 cm-2) disordered two-dimensional array of P atoms, the full field magnitude and angle-dependent magnetotransport is remarkably well described by classic weak localization theory with no corrections due to interaction. The two- to three-dimensional crossover seen upon warming can also be interpreted using scaling concepts developed for anistropic three-dimensional materials, which work remarkably except when the applied fields are nearly parallel to the conducting planes.

Circulating Long Noncoding RNAs as Potential Biomarkers of Sepsis: A Preliminary Study.

PubMed

Dai, Yu; Liang, Zhixin; Li, Yulin; Li, Chunsun; Chen, Liangan

2017-11-01

Long noncoding RNAs (lncRNAs) are becoming promising biomarker candidates in various diseases as assessed via sequencing technologies. Sepsis is a life-threatening disease without ideal biomarkers. The aim of this study was to investigate the expression profile of lncRNAs in the peripheral blood of sepsis patients and to find potential biomarkers of sepsis. A lncRNA expression profile was performed using peripheral blood from three sepsis patients and three healthy volunteers using microarray screening. The differentially expressed lncRNAs were validated by real-time quantitative polymerase chain reaction (qRT-PCR) in a further set of 22 sepsis patients and 22 healthy volunteers. Among 1316 differentially expressed lncRNAs, 771 were downregulated and 545 were upregulated. Results of the qRT-PCR were consistent with the microarray data. lncRNA ENST00000452391.1, uc001vji.1, and uc021zxw.1 were significantly differentially expressed between sepsis patients and healthy volunteers. Moreover, lncRNA ENST00000504301.1 and ENST00000452391.1 were significantly differentially expressed between sepsis survivors and nonsurvivors. The lncRNA expression profile in the peripheral blood of sepsis patients significantly differed from that of healthy volunteers. Circulating lncRNAs may be good candidates for sepsis biomarkers.

Exploring the Educational Potential of Three-Dimensional Multi-User Virtual Worlds for STEM Education: A Mixed-Method Systematic Literature Review

ERIC Educational Resources Information Center

Pellas, Nikolaos; Kazanidis, Ioannis; Konstantinou, Nikolaos; Georgiou, Georgia

2017-01-01

The present literature review builds on the results of 50 research articles published from 2000 until 2016. All these studies have successfully accomplished various learning tasks in the domain of Science, Technology, Engineering, and Mathematics (STEM) education using three-dimensional (3-D) multi-user virtual worlds for Primary, Secondary and…

Dynamic 3D echocardiography in virtual reality

PubMed Central

van den Bosch, Annemien E; Koning, Anton HJ; Meijboom, Folkert J; McGhie, Jackie S; Simoons, Maarten L; van der Spek, Peter J; Bogers, Ad JJC

2005-01-01

Background This pilot study was performed to evaluate whether virtual reality is applicable for three-dimensional echocardiography and if three-dimensional echocardiographic 'holograms' have the potential to become a clinically useful tool. Methods Three-dimensional echocardiographic data sets from 2 normal subjects and from 4 patients with a mitral valve pathological condition were included in the study. The three-dimensional data sets were acquired with the Philips Sonos 7500 echo-system and transferred to the BARCO (Barco N.V., Kortrijk, Belgium) I-space. Ten independent observers assessed the 6 three-dimensional data sets with and without mitral valve pathology. After 10 minutes' instruction in the I-Space, all of the observers could use the virtual pointer that is necessary to create cut planes in the hologram. Results The 10 independent observers correctly assessed the normal and pathological mitral valve in the holograms (analysis time approximately 10 minutes). Conclusion this report shows that dynamic holographic imaging of three-dimensional echocardiographic data is feasible. However, the applicability and use-fullness of this technology in clinical practice is still limited. PMID:16375768

Analysis of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Tiling Microarray (ChIP-on-chip).

PubMed

Gao, Hui; Zhao, Chunyan

2018-01-01

Chromatin immunoprecipitation (ChIP) has become the most effective and widely used tool to study the interactions between specific proteins or modified forms of proteins and a genomic DNA region. Combined with genome-wide profiling technologies, such as microarray hybridization (ChIP-on-chip) or massively parallel sequencing (ChIP-seq), ChIP could provide a genome-wide mapping of in vivo protein-DNA interactions in various organisms. Here, we describe a protocol of ChIP-on-chip that uses tiling microarray to obtain a genome-wide profiling of ChIPed DNA.

Gene expression profiling and pathway analysis in MCF-7 and MDA-MB-231 human breast cancer cell lines treated with dioscin

USDA-ARS?s Scientific Manuscript database

The long-term goal of our study is to understand the genetic and epigenetic mechanisms of breast cancer metastasis in human and to discover new possible genetic markers for use in clinical practice. We have used microarray technology (Human OneArray microarray, phylanxbiotech.com) to compare gene ex...

Development of a Cross-Disciplinary Investigative Model for the Introduction of Microarray Techniques at Non-R1 Undergraduate Institutions

ERIC Educational Resources Information Center

Walker, David E.; Lutz, Gary P.; Alvarez, Consuelo J.

2008-01-01

Integrating advanced biological techniques into instruction at non-R1 institutions can prove to be a challenge. Here, we report the creation of a model for the introduction of gene expression microarray technology into a research laboratory. A student assessment tool was used to evaluate: (1) technical skill development; (2) cross-disciplinary…

ABRF-MARG RESEARCH STUDY: EVALUATION OF SMALL SAMPLE NUCLEIC ACID AMPLIFICATION TECHNOLOGIES FOR GENE EXPRESSION PROFILING

EPA Science Inventory

Microarrays have had a significant impact on many areas of biology. However, there are still many fertile research areas that would benefit from microarray analysis but are limited by the amount of biological material that can be obtained (e.g. samples obtained by small biopsy, f...

MAGMA: analysis of two-channel microarrays made easy.

PubMed

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.

NCBI GEO: archive for functional genomics data sets--10 years on.

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Muertter, Rolf N; Holko, Michelle; Ayanbule, Oluwabukunmi; Yefanov, Andrey; Soboleva, Alexandra

2011-01-01

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Integration of Computed Tomography and Three-Dimensional Echocardiography for Hybrid Three-Dimensional Printing in Congenital Heart Disease.

PubMed

Gosnell, Jordan; Pietila, Todd; Samuel, Bennett P; Kurup, Harikrishnan K N; Haw, Marcus P; Vettukattil, Joseph J

2016-12-01

Three-dimensional (3D) printing is an emerging technology aiding diagnostics, education, and interventional, and surgical planning in congenital heart disease (CHD). Three-dimensional printing has been derived from computed tomography, cardiac magnetic resonance, and 3D echocardiography. However, individually the imaging modalities may not provide adequate visualization of complex CHD. The integration of the strengths of two or more imaging modalities has the potential to enhance visualization of cardiac pathomorphology. We describe the feasibility of hybrid 3D printing from two imaging modalities in a patient with congenitally corrected transposition of the great arteries (L-TGA). Hybrid 3D printing may be useful as an additional tool for cardiologists and cardiothoracic surgeons in planning interventions in children and adults with CHD.

Three-dimensional landing zone joint capability technology demonstration

NASA Astrophysics Data System (ADS)

Savage, James; Goodrich, Shawn; Ott, Carl; Szoboszlay, Zoltan; Perez, Alfonso; Soukup, Joel; Burns, H. N.

2014-06-01

The Three-Dimensional Landing Zone (3D-LZ) Joint Capability Technology Demonstration (JCTD) is a 27-month program to develop an integrated LADAR and FLIR capability upgrade for USAF Combat Search and Rescue HH-60G Pave Hawk helicopters through a retrofit of current Raytheon AN/AAQ-29 turret systems. The 3D-LZ JCTD builds upon a history of technology programs using high-resolution, imaging LADAR to address rotorcraft cruise, approach to landing, landing, and take-off in degraded visual environments with emphasis on brownout, cable warning and obstacle avoidance, and avoidance of controlled flight into terrain. This paper summarizes ladar development, flight test milestones, and plans for a final flight test demonstration and Military Utility Assessment in 2014.

Three-dimensional printing physiology laboratory technology.

PubMed

Sulkin, Matthew S; Widder, Emily; Shao, Connie; Holzem, Katherine M; Gloschat, Christopher; Gutbrod, Sarah R; Efimov, Igor R

2013-12-01

Since its inception in 19th-century Germany, the physiology laboratory has been a complex and expensive research enterprise involving experts in various fields of science and engineering. Physiology research has been critically dependent on cutting-edge technological support of mechanical, electrical, optical, and more recently computer engineers. Evolution of modern experimental equipment is constrained by lack of direct communication between the physiological community and industry producing this equipment. Fortunately, recent advances in open source technologies, including three-dimensional printing, open source hardware and software, present an exciting opportunity to bring the design and development of research instrumentation to the end user, i.e., life scientists. Here we provide an overview on how to develop customized, cost-effective experimental equipment for physiology laboratories.

A DNA microarray-based assay to detect dual infection with two dengue virus serotypes.

PubMed

Díaz-Badillo, Alvaro; Muñoz, María de Lourdes; Perez-Ramirez, Gerardo; Altuzar, Victor; Burgueño, Juan; Mendoza-Alvarez, Julio G; Martínez-Muñoz, Jorge P; Cisneros, Alejandro; Navarrete-Espinosa, Joel; Sanchez-Sinencio, Feliciano

2014-04-25

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.

A DNA Microarray-Based Assay to Detect Dual Infection with Two Dengue Virus Serotypes

PubMed Central

Díaz-Badillo, Alvaro; de Lourdes Muñoz, María; Perez-Ramirez, Gerardo; Altuzar, Victor; Burgueño, Juan; Mendoza-Alvarez, Julio G.; Martínez-Muñoz, Jorge P.; Cisneros, Alejandro; Navarrete-Espinosa, Joel; Sanchez-Sinencio, Feliciano

2014-01-01

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. PMID:24776933

Research on the development of space target detecting system and three-dimensional reconstruction technology

NASA Astrophysics Data System (ADS)

Li, Dong; Wei, Zhen; Song, Dawei; Sun, Wenfeng; Fan, Xiaoyan

2016-11-01

With the development of space technology, the number of spacecrafts and debris are increasing year by year. The demand for detecting and identification of spacecraft is growing strongly, which provides support to the cataloguing, crash warning and protection of aerospace vehicles. The majority of existing approaches for three-dimensional reconstruction is scattering centres correlation, which is based on the radar high resolution range profile (HRRP). This paper proposes a novel method to reconstruct the threedimensional scattering centre structure of target from a sequence of radar ISAR images, which mainly consists of three steps. First is the azimuth scaling of consecutive ISAR images based on fractional Fourier transform (FrFT). The later is the extraction of scattering centres and matching between adjacent ISAR images using grid method. Finally, according to the coordinate matrix of scattering centres, the three-dimensional scattering centre structure is reconstructed using improved factorization method. The three-dimensional structure is featured with stable and intuitive characteristic, which provides a new way to improve the identification probability and reduce the complexity of the model matching library. A satellite model is reconstructed using the proposed method from four consecutive ISAR images. The simulation results prove that the method has gotten a satisfied consistency and accuracy.

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

PubMed Central

2010-01-01

Background The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. Findings We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. Conclusions A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis. PMID:20565839

Identifying novel glioma associated pathways based on systems biology level meta-analysis.

PubMed

Hu, Yangfan; Li, Jinquan; Yan, Wenying; Chen, Jiajia; Li, Yin; Hu, Guang; Shen, Bairong

2013-01-01

With recent advances in microarray technology, including genomics, proteomics, and metabolomics, it brings a great challenge for integrating this "-omics" data to analysis complex disease. Glioma is an extremely aggressive and lethal form of brain tumor, and thus the study of the molecule mechanism underlying glioma remains very important. To date, most studies focus on detecting the differentially expressed genes in glioma. However, the meta-analysis for pathway analysis based on multiple microarray datasets has not been systematically pursued. In this study, we therefore developed a systems biology based approach by integrating three types of omics data to identify common pathways in glioma. Firstly, the meta-analysis has been performed to study the overlapping of signatures at different levels based on the microarray gene expression data of glioma. Among these gene expression datasets, 12 pathways were found in GeneGO database that shared by four stages. Then, microRNA expression profiles and ChIP-seq data were integrated for the further pathway enrichment analysis. As a result, we suggest 5 of these pathways could be served as putative pathways in glioma. Among them, the pathway of TGF-beta-dependent induction of EMT via SMAD is of particular importance. Our results demonstrate that the meta-analysis based on systems biology level provide a more useful approach to study the molecule mechanism of complex disease. The integration of different types of omics data, including gene expression microarrays, microRNA and ChIP-seq data, suggest some common pathways correlated with glioma. These findings will offer useful potential candidates for targeted therapeutic intervention of glioma.

Protein profiles associated with survival in lung adenocarcinoma

PubMed Central

Chen, Guoan; Gharib, Tarek G; Wang, Hong; Huang, Chiang-Ching; Kuick, Rork; Thomas, Dafydd G.; Shedden, Kerby A.; Misek, David E.; Taylor, Jeremy M. G.; Giordano, Thomas J.; Kardia, Sharon L. R.; Iannettoni, Mark D.; Yee, John; Hogg, Philip J.; Orringer, Mark B.; Hanash, Samir M.; Beer, David G.

2003-01-01

Morphologic assessment of lung tumors is informative but insufficient to adequately predict patient outcome. We previously identified transcriptional profiles that predict patient survival, and here we identify proteins associated with patient survival in lung adenocarcinoma. A total of 682 individual protein spots were quantified in 90 lung adenocarcinomas by using quantitative two-dimensional polyacrylamide gel electrophoresis analysis. A leave-one-out cross-validation procedure using the top 20 survival-associated proteins identified by Cox modeling indicated that protein profiles as a whole can predict survival in stage I tumor patients (P = 0.01). Thirty-three of 46 survival-associated proteins were identified by using mass spectrometry. Expression of 12 candidate proteins was confirmed as tumor-derived with immunohistochemical analysis and tissue microarrays. Oligonucleotide microarray results from both the same tumors and from an independent study showed mRNAs associated with survival for 11 of 27 encoded genes. Combined analysis of protein and mRNA data revealed 11 components of the glycolysis pathway as associated with poor survival. Among these candidates, phosphoglycerate kinase 1 was associated with survival in the protein study, in both mRNA studies and in an independent validation set of 117 adenocarcinomas and squamous lung tumors using tissue microarrays. Elevated levels of phosphoglycerate kinase 1 in the serum were also significantly correlated with poor outcome in a validation set of 107 patients with lung adenocarcinomas using ELISA analysis. These studies identify new prognostic biomarkers and indicate that protein expression profiles can predict the outcome of patients with early-stage lung cancer. PMID:14573703

HealthLines

MedlinePlus

... a particular order, and identified shapes on a computer screen. They were divided into three groups. One ... some people. Virtual colonoscopy uses X-ray and computer technology to create three-dimensional images of the ...

Presurgical nasoalveolar molding for cleft lip and palate: the application of digitally designed molds.

PubMed

Shen, Congcong; Yao, Caroline A; Magee, William; Chai, Gang; Zhang, Yan

2015-06-01

The authors present a novel nasoalveolar molding protocol by prefabricating sets of nasoalveolar molding appliances using three-dimensional technology. Prospectively, 17 infants with unilateral complete cleft lip and palate underwent the authors' protocol before primary cheiloplasty. An initial nasoalveolar molding appliance was created based on the patient's first and only in-person maxillary cast, produced from a traditional intraoral dental impression. Thereafter, each patient's molding course was simulated using computer software that aimed to narrow the alveolar gap by 1 mm each week by rotating the greater alveolar segment. A maxillary cast of each predicted molding stage was created using three-dimensional printing. Subsequent appliances were constructed in advance, based on the series of computer-generated casts. Each patient had a total three clinic visits spaced 1 month apart. Anthropometric measurements and bony segment volumes were recorded before and after treatment. Alveolar cleft widths narrowed significantly (p < 0.01), soft-tissue volume of each segment expanded (p < 0.01), and the arc of the alveolus became more contiguous across the cleft (p < 0.01). One patient required a new appliance at the second visit because of bleeding and discomfort. Eleven patients had mucosal irritation and two experienced minor mucosal ulceration. Three-dimensional technology can precisely represent anatomic structures in pediatric clefts. Results from the authors' algorithm are equivalent to those of traditional nasoalveolar molding therapies; however, the number of required clinic visits and appliance adjustments decreased. As three-dimensional technology costs decrease, multidisciplinary teams may design customized nasoalveolar molding treatment with improved efficiency and less burden to medical staff, patients, and families. Therapeutic, IV.

Cruella: developing a scalable tissue microarray data management system.

PubMed

Cowan, James D; Rimm, David L; Tuck, David P

2006-06-01

Compared with DNA microarray technology, relatively little information is available concerning the special requirements, design influences, and implementation strategies of data systems for tissue microarray technology. These issues include the requirement to accommodate new and different data elements for each new project as well as the need to interact with pre-existing models for clinical, biological, and specimen-related data. To design and implement a flexible, scalable tissue microarray data storage and management system that could accommodate information regarding different disease types and different clinical investigators, and different clinical investigation questions, all of which could potentially contribute unforeseen data types that require dynamic integration with existing data. The unpredictability of the data elements combined with the novelty of automated analysis algorithms and controlled vocabulary standards in this area require flexible designs and practical decisions. Our design includes a custom Java-based persistence layer to mediate and facilitate interaction with an object-relational database model and a novel database schema. User interaction is provided through a Java Servlet-based Web interface. Cruella has become an indispensable resource and is used by dozens of researchers every day. The system stores millions of experimental values covering more than 300 biological markers and more than 30 disease types. The experimental data are merged with clinical data that has been aggregated from multiple sources and is available to the researchers for management, analysis, and export. Cruella addresses many of the special considerations for managing tissue microarray experimental data and the associated clinical information. A metadata-driven approach provides a practical solution to many of the unique issues inherent in tissue microarray research, and allows relatively straightforward interoperability with and accommodation of new data models.

A Human Lectin Microarray for Sperm Surface Glycosylation Analysis *

PubMed Central

Sun, Yangyang; Cheng, Li; Gu, Yihua; Xin, Aijie; Wu, Bin; Zhou, Shumin; Guo, Shujuan; Liu, Yin; Diao, Hua; Shi, Huijuan; Wang, Guangyu; Tao, Sheng-ce

2016-01-01

Glycosylation is one of the most abundant and functionally important protein post-translational modifications. As such, technology for efficient glycosylation analysis is in high demand. Lectin microarrays are a powerful tool for such investigations and have been successfully applied for a variety of glycobiological studies. However, most of the current lectin microarrays are primarily constructed from plant lectins, which are not well suited for studies of human glycosylation because of the extreme complexity of human glycans. Herein, we constructed a human lectin microarray with 60 human lectin and lectin-like proteins. All of the lectins and lectin-like proteins were purified from yeast, and most showed binding to human glycans. To demonstrate the applicability of the human lectin microarray, human sperm were probed on the microarray and strong bindings were observed for several lectins, including galectin-1, 7, 8, GalNAc-T6, and ERGIC-53 (LMAN1). These bindings were validated by flow cytometry and fluorescence immunostaining. Further, mass spectrometry analysis showed that galectin-1 binds several membrane-associated proteins including heat shock protein 90. Finally, functional assays showed that binding of galectin-8 could significantly enhance the acrosome reaction within human sperms. To our knowledge, this is the first construction of a human lectin microarray, and we anticipate it will find wide use for a range of human or mammalian studies, alone or in combination with plant lectin microarrays. PMID:27364157

Retinal Optical Coherence Tomography Imaging

NASA Astrophysics Data System (ADS)

Drexler, Wolfgang; Fujimoto, James G.

The eye is essentially transparent, transmitting light with only minimal optical attenuation and scattering providing easy optical access to the anterior segment as well as the retina. For this reason, ophthalmic and especially retinal imaging has been not only the first but also most successful clinical application for optical coherence tomography (OCT). This chapter focuses on the development of OCT technology for retinal imaging. OCT has significantly improved the potential for early diagnosis, understanding of retinal disease pathogenesis, as well as monitoring disease progression and response to therapy. Development of ultrabroad bandwidth light sources and high-speed detection techniques has enabled significant improvements in ophthalmic OCT imaging performance, demonstrating the potential of three-dimensional, ultrahigh-resolution OCT (UHR OCT) to perform noninvasive optical biopsy of the living human retina, i.e., the in vivo visualization of microstructural, intraretinal morphology in situ approaching the resolution of conventional histopathology. Significant improvements in axial resolution and speed not only enable three-dimensional rendering of retinal volumes but also high-definition, two-dimensional tomograms, topographic thickness maps of all major intraretinal layers, as well as volumetric quantification of pathologic intraretinal changes. These advances in OCT technology have also been successfully applied in several animal models of retinal pathologies. The development of light sources emitting at alternative wavelengths, e.g., around #1,060 nm, not only enabled three-dimensional OCT imaging with enhanced choroidal visualization but also improved OCT performance in cataract patients due to reduced scattering losses in this wavelength region. Adaptive optics using deformable mirror technology, with unique high stroke to correct higher-order ocular aberrations, with specially designed optics to compensate chromatic aberration of the human eye, in combination with three-dimensional UHR OCT, recently enabled in vivo cellular resolution retinal imaging.

A novel in vitro three-dimensional retinoblastoma model for evaluating chemotherapeutic drugs

PubMed Central

Mitra, Moutushy; Mohanty, Chandana; Harilal, Anju; Maheswari, Uma K.; Sahoo, Sanjeeb Kumar

2012-01-01

Purpose Novel strategies are being applied for creating better in vitro models that simulate in vivo conditions for testing the efficacy of anticancer drugs. In the present study we developed surface-engineered, large and porous, biodegradable, polymeric microparticles as a scaffold for three dimensional (3-D) growth of a Y79 retinoblastoma (RB) cell line. We evaluated the effect of three anticancer drugs in naïve and nanoparticle-loaded forms on a 3-D versus a two-dimensional (2-D) model. We also studied the influence of microparticles on extracellular matrix (ECM) synthesis and whole genome miRNA-gene expression profiling to identify 3D-responsive genes that are implicated in oncogenesis in RB cells. Methods Poly(D,L)-lactide-co-glycolide (PLGA) microparticles were prepared by the solvent evaporation method. RB cell line Y79 was grown alone or with PLGA–gelatin microparticles. Antiproliferative activity, drug diffusion, and cellular uptake were studied by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, a yellow tetrazole (MTT) assay, fluorescent microscope, and flow cytometry. Extra cellular matrix (ECM) synthesis was observed by collagenase assay and whole genome miRNA-microarray profiling by using an Agilent chip. Results With optimized composition of microparticles and cell culture conditions, an eightfold increase from the seeding density was achieved in 5 days of culture. The antiproliferative effect of the drugs in the 3-D model was significantly lower than in the 2-D suspension, which was evident from the 4.5 to 21.8 fold differences in their IC50 values. Using doxorubicin, the flow cytometry data demonstrated a 4.4 fold lower drug accumulation in the cells grown in the 3-D model at 4 h. The collagen content of the cells grown in the 3-D model was 2.3 fold greater than that of the cells grown in the 2-D model, suggesting greater synthesis of the extracellular matrix in the 3-D model as the extracellular matrix acted as a barrier to drug diffusion. The microarray and miRNA analysis showed changes in several genes and miRNA expression in cells grown in the 3-D model, which could also influence the environment and drug effects. Conclusions Our 3-D retinoblastoma model could be used in developing effective drugs based on a better understanding of the role of chemical, biologic, and physical parameters in the process of drug diffusion through the tumor mass, drug retention, and therapeutic outcome. PMID:22690114

Three-dimensional (3-D) model utilization for fracture reconstruction in oral and maxillofacial surgery: A case report

NASA Astrophysics Data System (ADS)

Damayanti, Ista; Lilies, Latief, Benny S.

2017-02-01

Three-dimensional (3-D) printing has been identified as an innovative manufacturing technology of functional parts. The 3-D model was produced based on CT-Scan using Osyrix software, where automatic segmentation was performed and convert into STL format. This STL format was then ready to be produced physically, layer-by-layer to create 3-D model.

The Virtual University: Creating an Emergent Reality.

ERIC Educational Resources Information Center

Latta, Gail F.

Higher education has traditionally been defined as a two dimensional affair concerned with content (curriculum) and pedagogy (instructional design). Information technologies are transforming the educational enterprise into a three-dimensional universe through the diversification of instructional delivery systems. The success of higher education in…

[Differentially expressed genes of cell signal transduction associated with benzene poisoning by cDNA microarray].

PubMed

Wang, Hong; Bi, Yongyi; Tao, Ning; Wang, Chunhong

2005-08-01

To detect the differential expression of cell signal transduction genes associated with benzene poisoning, and to explore the pathogenic mechanisms of blood system damage induced by benzene. Peripheral white blood cell gene expression profile of 7 benzene poisoning patients, including one aplastic anemia, was determined by cDNA microarray. Seven chips from normal workers were served as controls. Cluster analysis of gene expression profile was performed. Among the 4265 target genes, 176 genes associated with cell signal transduction were differentially expressed. 35 up-regulated genes including PTPRC, STAT4, IFITM1 etc were found in at least 6 pieces of microarray; 45 down-regulated genes including ARHB, PPP3CB, CDC37 etc were found in at least 5 pieces of microarray. cDNA microarray technology is an effective technique for screening the differentially expressed genes of cell signal transduction. Disorder in cell signal transduction may play certain role in the pathogenic mechanism of benzene poisoning.

Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies.

PubMed

de Souza, Marcela; Matsuzawa, Tetsuhiro; Sakai, Kanae; Muraosa, Yasunori; Lyra, Luzia; Busso-Lopes, Ariane Fidelis; Levin, Anna Sara Shafferman; Schreiber, Angélica Zaninelli; Mikami, Yuzuru; Gonoi, Tohoru; Kamei, Katsuhiko; Moretti, Maria Luiza; Trabasso, Plínio

2017-08-01

The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.

Clustering and Dimensionality Reduction to Discover Interesting Patterns in Binary Data

NASA Astrophysics Data System (ADS)

Palumbo, Francesco; D'Enza, Alfonso Iodice

The attention towards binary data coding increased consistently in the last decade due to several reasons. The analysis of binary data characterizes several fields of application, such as market basket analysis, DNA microarray data, image mining, text mining and web-clickstream mining. The paper illustrates two different approaches exploiting a profitable combination of clustering and dimensionality reduction for the identification of non-trivial association structures in binary data. An application in the Association Rules framework supports the theory with the empirical evidence.

Switching benchmarks in cancer of unknown primary: from autopsy to microarray.

PubMed

Pentheroudakis, George; Golfinopoulos, Vassilios; Pavlidis, Nicholas

2007-09-01

Cancer of unknown primary (CUP) is associated with unknown biology and dismal prognosis. Information on the primary site of origin is scant and has never been analysed. We systematically reviewed all published evidence on the CUP primary site identified by two different approaches, either autopsy or microarray gene expression profiling. Published reports on identification of CUP primary site by autopsy or microarray-based multigene expression platforms were retrieved and analysed for year of publication, primary site, patient age, gender, histology, rate of primary identification, manifestations and metastatic deposits, microarray chip technology, training and validation sets, mathematical modelling, classification accuracy and number of classifying genes. From 1944 to 2000, a total of 884 CUP patients (66% males) underwent autopsy in 12 studies after presenting with metastatic or systemic symptoms and succumbing to their disease. A primary was identified in 644 (73%) of them, mostly in the lung (27%), pancreas (24%), hepatobiliary tree (8%), kidneys (8%), bowel, genital system and stomach, as a small focus of adenocarcinoma or poorly differentiated carcinoma. An unpredictable systemic dissemination was evident with high frequency of lung (46%), nodal (35%), bone (17%), brain (16%) and uncommon (18%) deposits. Between the 1944-1980 and the 1980-2000 series, female representation increased, 'undetermined neoplasm' diagnosis became rarer, pancreatic primaries were found less often while colonic ones were identified more frequently. Four studies using microarray technology profiled more than 500 CUP cases using classifier set of genes (ranging from 10 to 495) and reported strikingly dissimilar frequencies of assigned primary sites (lung 11.5%, pancreas 12.5%, bowel 12%, breast 15%, hepatobiliary tree 8%, kidneys 6%, genital system 9%, bladder 5%) in 75-90% of the cases. Evolution in medical imaging technology, diet and lifestyle habits probably account for changing epidemiology of CUP primaries in autopsies. Discrepant assignment of primary sites by microarrays may be due to the presence of 'sanctuary sites' in autopsies, molecular misclassification and the postulated presence of a pro-metastatic genetic signature. In view of the absence of patient therapeutic or prognostic benefit with primary identification, gene expression profiling should be re-orientated towards unraveling the complex pathophysiology of metastases.

Genomic profiling using array comparative genomic hybridization define distinct subtypes of diffuse large b-cell lymphoma: a review of the literature

PubMed Central

2012-01-01

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin Lymphoma comprising of greater than 30% of adult non-Hodgkin Lymphomas. DLBCL represents a diverse set of lymphomas, defined as diffuse proliferation of large B lymphoid cells. Numerous cytogenetic studies including karyotypes and fluorescent in situ hybridization (FISH), as well as morphological, biological, clinical, microarray and sequencing technologies have attempted to categorize DLBCL into morphological variants, molecular and immunophenotypic subgroups, as well as distinct disease entities. Despite such efforts, most lymphoma remains undistinguishable and falls into DLBCL, not otherwise specified (DLBCL-NOS). The advent of microarray-based studies (chromosome, RNA, gene expression, etc) has provided a plethora of high-resolution data that could potentially facilitate the finer classification of DLBCL. This review covers the microarray data currently published for DLBCL. We will focus on these types of data; 1) array based CGH; 2) classical CGH; and 3) gene expression profiling studies. The aims of this review were three-fold: (1) to catalog chromosome loci that are present in at least 20% or more of distinct DLBCL subtypes; a detailed list of gains and losses for different subtypes was generated in a table form to illustrate specific chromosome loci affected in selected subtypes; (2) to determine common and distinct copy number alterations among the different subtypes and based on this information, characteristic and similar chromosome loci for the different subtypes were depicted in two separate chromosome ideograms; and, (3) to list re-classified subtypes and those that remained indistinguishable after review of the microarray data. To the best of our knowledge, this is the first effort to compile and review available literatures on microarray analysis data and their practical utility in classifying DLBCL subtypes. Although conventional cytogenetic methods such as Karyotypes and FISH have played a major role in classification schemes of lymphomas, better classification models are clearly needed to further understanding the biology, disease outcome and therapeutic management of DLBCL. In summary, microarray data reviewed here can provide better subtype specific classifications models for DLBCL. PMID:22967872

Identification of differentially expressed genes and false discovery rate in microarray studies.

PubMed

Gusnanto, Arief; Calza, Stefano; Pawitan, Yudi

2007-04-01

To highlight the development in microarray data analysis for the identification of differentially expressed genes, particularly via control of false discovery rate. The emergence of high-throughput technology such as microarrays raises two fundamental statistical issues: multiplicity and sensitivity. We focus on the biological problem of identifying differentially expressed genes. First, multiplicity arises due to testing tens of thousands of hypotheses, rendering the standard P value meaningless. Second, known optimal single-test procedures such as the t-test perform poorly in the context of highly multiple tests. The standard approach of dealing with multiplicity is too conservative in the microarray context. The false discovery rate concept is fast becoming the key statistical assessment tool replacing the P value. We review the false discovery rate approach and argue that it is more sensible for microarray data. We also discuss some methods to take into account additional information from the microarrays to improve the false discovery rate. There is growing consensus on how to analyse microarray data using the false discovery rate framework in place of the classical P value. Further research is needed on the preprocessing of the raw data, such as the normalization step and filtering, and on finding the most sensitive test procedure.

Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.

PubMed

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.

Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion

PubMed Central

Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander

2011-01-01

Background 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. Methodology/Principal Findings 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. Conclusions 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. PMID:21858215

Hierarchical Gene Selection and Genetic Fuzzy System for Cancer Microarray Data Classification

PubMed Central

Nguyen, Thanh; Khosravi, Abbas; Creighton, Douglas; Nahavandi, Saeid

2015-01-01

This paper introduces a novel approach to gene selection based on a substantial modification of analytic hierarchy process (AHP). The modified AHP systematically integrates outcomes of individual filter methods to select the most informative genes for microarray classification. Five individual ranking methods including t-test, entropy, receiver operating characteristic (ROC) curve, Wilcoxon and signal to noise ratio are employed to rank genes. These ranked genes are then considered as inputs for the modified AHP. Additionally, a method that uses fuzzy standard additive model (FSAM) for cancer classification based on genes selected by AHP is also proposed in this paper. Traditional FSAM learning is a hybrid process comprising unsupervised structure learning and supervised parameter tuning. Genetic algorithm (GA) is incorporated in-between unsupervised and supervised training to optimize the number of fuzzy rules. The integration of GA enables FSAM to deal with the high-dimensional-low-sample nature of microarray data and thus enhance the efficiency of the classification. Experiments are carried out on numerous microarray datasets. Results demonstrate the performance dominance of the AHP-based gene selection against the single ranking methods. Furthermore, the combination of AHP-FSAM shows a great accuracy in microarray data classification compared to various competing classifiers. The proposed approach therefore is useful for medical practitioners and clinicians as a decision support system that can be implemented in the real medical practice. PMID:25823003

Hierarchical gene selection and genetic fuzzy system for cancer microarray data classification.

PubMed

Nguyen, Thanh; Khosravi, Abbas; Creighton, Douglas; Nahavandi, Saeid

2015-01-01

This paper introduces a novel approach to gene selection based on a substantial modification of analytic hierarchy process (AHP). The modified AHP systematically integrates outcomes of individual filter methods to select the most informative genes for microarray classification. Five individual ranking methods including t-test, entropy, receiver operating characteristic (ROC) curve, Wilcoxon and signal to noise ratio are employed to rank genes. These ranked genes are then considered as inputs for the modified AHP. Additionally, a method that uses fuzzy standard additive model (FSAM) for cancer classification based on genes selected by AHP is also proposed in this paper. Traditional FSAM learning is a hybrid process comprising unsupervised structure learning and supervised parameter tuning. Genetic algorithm (GA) is incorporated in-between unsupervised and supervised training to optimize the number of fuzzy rules. The integration of GA enables FSAM to deal with the high-dimensional-low-sample nature of microarray data and thus enhance the efficiency of the classification. Experiments are carried out on numerous microarray datasets. Results demonstrate the performance dominance of the AHP-based gene selection against the single ranking methods. Furthermore, the combination of AHP-FSAM shows a great accuracy in microarray data classification compared to various competing classifiers. The proposed approach therefore is useful for medical practitioners and clinicians as a decision support system that can be implemented in the real medical practice.

Virtual Education: Guidelines for Using Games Technology

ERIC Educational Resources Information Center

Schofield, Damian

2014-01-01

Advanced three-dimensional virtual environment technology, similar to that used by the film and computer games industry, can allow educational developers to rapidly create realistic online virtual environments. This technology has been used to generate a range of interactive Virtual Reality (VR) learning environments across a spectrum of…

A Molecular Simulation Study of Antibody-Antigen Interactions on Surfaces for the Rational Design of Next-Generation Antibody Microarrays

NASA Astrophysics Data System (ADS)

Bush, Derek B.

Antibody microarrays constitute a next-generation sensing platform that has the potential to revolutionize the way that molecular detection is conducted in many scientific fields. Unfortunately, current technologies have not found mainstream use because of reliability problems that undermine trust in their results. Although several factors are involved, it is believed that undesirable protein interactions with the array surface are a fundamental source of problems where little detail about the molecular-level biophysics are known. A better understanding of antibody stability and antibody-antigen binding on the array surface is needed to improve microarray technology. Despite the availability of many laboratory methods for studying protein stability and binding, these methods either do not work when the protein is attached to a surface or they do not provide the atomistic structural information that is needed to better understand protein behavior on the surface. As a result, molecular simulation has emerged as the primary method for studying proteins on surfaces because it can provide metrics and views of atomistic structures and molecular motion. Using an advanced, coarse-grain, protein-surface model this study investigated how antibodies react to and function on different types of surfaces. Three topics were addressed: (1) the stability of individual antibodies on surfaces, (2) antibody binding to small antigens while on a surface, and (3) antibody binding to large antigens while on a surface. The results indicate that immobilizing antibodies or antibody fragments in an upright orientation on a hydrophilic surface can provide the molecules with thermal stability similar to their native aqueous stability, enhance antigen binding strength, and minimize the entropic cost of binding. Furthermore, the results indicate that it is more difficult for large antigens to approach the surface than small antigens, that multiple binding sites can aid antigen binding, and that antigen flexiblity simultaneously helps and hinders the binding process as it approaches the surface. The results provide hope that next-generation microarrays and other devices decorated with proteins can be improved through rational design.

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine.

PubMed

Xu, Joshua; Gong, Binsheng; Wu, Leihong; Thakkar, Shraddha; Hong, Huixiao; Tong, Weida

2016-03-15

Studies on gene expression in response to therapy have led to the discovery of pharmacogenomics biomarkers and advances in precision medicine. Whole transcriptome sequencing (RNA-seq) is an emerging tool for profiling gene expression and has received wide adoption in the biomedical research community. However, its value in regulatory decision making requires rigorous assessment and consensus between various stakeholders, including the research community, regulatory agencies, and industry. The FDA-led SEquencing Quality Control (SEQC) consortium has made considerable progress in this direction, and is the subject of this review. Specifically, three RNA-seq platforms (Illumina HiSeq, Life Technologies SOLiD, and Roche 454) were extensively evaluated at multiple sites to assess cross-site and cross-platform reproducibility. The results demonstrated that relative gene expression measurements were consistently comparable across labs and platforms, but not so for the measurement of absolute expression levels. As part of the quality evaluation several studies were included to evaluate the utility of RNA-seq in clinical settings and safety assessment. The neuroblastoma study profiled tumor samples from 498 pediatric neuroblastoma patients by both microarray and RNA-seq. RNA-seq offers more utilities than microarray in determining the transcriptomic characteristics of cancer. However, RNA-seq and microarray-based models were comparable in clinical endpoint prediction, even when including additional features unique to RNA-seq beyond gene expression. The toxicogenomics study compared microarray and RNA-seq profiles of the liver samples from rats exposed to 27 different chemicals representing multiple toxicity modes of action. Cross-platform concordance was dependent on chemical treatment and transcript abundance. Though both RNA-seq and microarray are suitable for developing gene expression based predictive models with comparable prediction performance, RNA-seq offers advantages over microarray in profiling genes with low expression. The rat BodyMap study provided a comprehensive rat transcriptomic body map by performing RNA-Seq on 320 samples from 11 organs in either sex of juvenile, adolescent, adult and aged Fischer 344 rats. Lastly, the transferability study demonstrated that signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development using a comprehensive approach with two large clinical data sets. This result suggests continued usefulness of legacy microarray data in the coming RNA-seq era. In conclusion, the SEQC project enhances our understanding of RNA-seq and provides valuable guidelines for RNA-seq based clinical application and safety evaluation to advance precision medicine.

Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars.

PubMed

Ghan, Ryan; Van Sluyter, Steven C; Hochberg, Uri; Degu, Asfaw; Hopper, Daniel W; Tillet, Richard L; Schlauch, Karen A; Haynes, Paul A; Fait, Aaron; Cramer, Grant R

2015-11-16

Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems. Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity (°Brix-to-titratable acidity ratio) from the same experimental vineyard. The cultivars were exposed to a mild, seasonal water-deficit treatment from fruit set until harvest in 2011. Identical sample aliquots were analyzed for transcripts by grapevine whole-genome oligonucleotide microarray and RNAseq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies showed similar results across cultivars in all Omic datasets. Comparison of the processed data of genes mapped in RNAseq and microarray data revealed a strong Pearson's correlation (0.80). The exclusion of probesets associated with genes with potential for cross-hybridization on the microarray improved the correlation to 0.93. The overall concordance of protein with transcript data was low with a Pearson's correlation of 0.27 and 0.24 for the RNAseq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, which distinguished red from white grapes, yet provided detail of individual cultivar differences. The mild water deficit treatment did not significantly alter the abundance of proteins or metabolites measured in the five cultivars, but did have a small effect on gene expression. The five Omic technologies were consistent in distinguishing cultivar variation. There was high concordance between transcriptomic technologies, but generally protein abundance did not correlate well with transcript abundance. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species.

Emerging technology for transonic wind-tunnel-wall interference assessment and corrections

NASA Technical Reports Server (NTRS)

Newman, P. A.; Kemp, W. B., Jr.; Garriz, J. A.

1988-01-01

Several nonlinear transonic codes and a panel method code for wind tunnel/wall interference assessment and correction (WIAC) studies are reviewed. Contrasts between two- and three-dimensional transonic testing factors which affect WIAC procedures are illustrated with airfoil data from the NASA/Langley 0.3-meter transonic cyrogenic tunnel and Pathfinder I data. Also, three-dimensional transonic WIAC results for Mach number and angle-of-attack corrections to data from a relatively large 20 deg swept semispan wing in the solid wall NASA/Ames high Reynolds number Channel I are verified by three-dimensional thin-layer Navier-Stokes free-air solutions.

Research and Practice on New Technology for Architectural Green Environment in Cities

NASA Astrophysics Data System (ADS)

Wu, Zhang; hvung Cho, Jeung

2018-03-01

The importance of urban development has become a topic that has been discussed in all industries for a long time. How to make rational use of existing limited resources for redevelopment has become the primary issue in the future construction of a city. Designers have introduced green three-dimensional environmental design for a city into modern urban design. At present, Japan and South Korea focus on development of green three-dimensional environmental projects for cities, in which application of green three-dimensional building design is particularly prominent. This article learns from successful cases on urban three-dimensional environment design in Japan and Korea and makes profound discussion about how new city-model agriculture develops in China for the purpose of solving the problem of urban construction in China in the aspects of theory and Practice.

Three-Dimensional (3-D) Printing: A Cost-Effective Solution for Improving Global Accessibility to Prostheses.

PubMed

Silva, Kyle; Rand, Stephanie; Cancel, David; Chen, Yuxi; Kathirithamby, Rani; Stern, Michelle

2015-12-01

The lack of access to prostheses is a global problem, partially caused by the high cost associated with the current manufacturing process. Three-dimensional printing is gaining use in the medical field, and one such area is prosthetics. In addition to using cost-effective materials, this technology allows for rapid prototyping, making it an efficient solution for the development of affordable prostheses. If the rehabilitation medicine community embraces this novel technology, we can help alleviate the global disparity of access to prostheses. Copyright © 2015 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

Three-Dimensional Cell Cultures in Drug Discovery and Development

PubMed Central

Fang, Ye; Eglen, Richard M.

2017-01-01

The past decades have witnessed significant efforts toward the development of three-dimensional (3D) cell cultures as systems that better mimic in vivo physiology. Today, 3D cell cultures are emerging, not only as a new tool in early drug discovery but also as potential therapeutics to treat disease. In this review, we assess leading 3D cell culture technologies and their impact on drug discovery, including spheroids, organoids, scaffolds, hydrogels, organs-on-chips, and 3D bioprinting. We also discuss the implementation of these technologies in compound identification, screening, and development, ranging from disease modeling to assessment of efficacy and safety profiles. PMID:28520521

Multiclassifier information fusion methods for microarray pattern recognition

NASA Astrophysics Data System (ADS)

Braun, Jerome J.; Glina, Yan; Judson, Nicholas; Herzig-Marx, Rachel

2004-04-01

This paper addresses automatic recognition of microarray patterns, a capability that could have a major significance for medical diagnostics, enabling development of diagnostic tools for automatic discrimination of specific diseases. The paper presents multiclassifier information fusion methods for microarray pattern recognition. The input space partitioning approach based on fitness measures that constitute an a-priori gauging of classification efficacy for each subspace is investigated. Methods for generation of fitness measures, generation of input subspaces and their use in the multiclassifier fusion architecture are presented. In particular, two-level quantification of fitness that accounts for the quality of each subspace as well as the quality of individual neighborhoods within the subspace is described. Individual-subspace classifiers are Support Vector Machine based. The decision fusion stage fuses the information from mulitple SVMs along with the multi-level fitness information. Final decision fusion stage techniques, including weighted fusion as well as Dempster-Shafer theory based fusion are investigated. It should be noted that while the above methods are discussed in the context of microarray pattern recognition, they are applicable to a broader range of discrimination problems, in particular to problems involving a large number of information sources irreducible to a low-dimensional feature space.

A biomimetic algorithm for the improved detection of microarray features

NASA Astrophysics Data System (ADS)

Nicolau, Dan V., Jr.; Nicolau, Dan V.; Maini, Philip K.

2007-02-01

One the major difficulties of microarray technology relate to the processing of large and - importantly - error-loaded images of the dots on the chip surface. Whatever the source of these errors, those obtained in the first stage of data acquisition - segmentation - are passed down to the subsequent processes, with deleterious results. As it has been demonstrated recently that biological systems have evolved algorithms that are mathematically efficient, this contribution attempts to test an algorithm that mimics a bacterial-"patented" algorithm for the search of available space and nutrients to find, "zero-in" and eventually delimitate the features existent on the microarray surface.

ELISA microarray technology as a high-throughput system for cancer biomarker validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zangar, Richard C.; Daly, Don S.; White, Amanda M.

A large gap currently exists between the ability to discover potential biomarkers and the ability to assess the real value of these proteins for cancer screening. One major challenge in biomarker validation is the inherent variability in biomarker levels. This variability stems from the diversity across the human population and the considerable molecular heterogeneity between individual tumors, even those that originate from a single tissue. Another major challenge with cancer screening is that most cancers are rare in the general population, meaning that the specificity of an assay must be very high if the number of false positive is notmore » going to be much greater than the number of true positives. Because of these challenges with biomarker validation, it is necessary to analysis of thousands of samples before a clear idea of the utility of a screening assay can be determined. Enzyme-linked immunosorbent assay (ELISA) microarray technology can simultaneously quantify levels of multiple proteins and has the potential to accelerate biomarker validation. In this review, we discuss current ELISA microarray technology and the enabling advances needed to achieve the reproducibility and throughput that are required to evaluate cancer biomarkers.« less

3D Laser Scanning in Technology Education.

ERIC Educational Resources Information Center

Flowers, Jim

2000-01-01

A three-dimensional laser scanner can be used as a tool for design and problem solving in technology education. A hands-on experience can enhance learning by captivating students' interest and empowering them with creative tools. (Author/JOW)

Robust gene selection methods using weighting schemes for microarray data analysis.

PubMed

Kang, Suyeon; Song, Jongwoo

2017-09-02

A common task in microarray data analysis is to identify informative genes that are differentially expressed between two different states. Owing to the high-dimensional nature of microarray data, identification of significant genes has been essential in analyzing the data. However, the performances of many gene selection techniques are highly dependent on the experimental conditions, such as the presence of measurement error or a limited number of sample replicates. We have proposed new filter-based gene selection techniques, by applying a simple modification to significance analysis of microarrays (SAM). To prove the effectiveness of the proposed method, we considered a series of synthetic datasets with different noise levels and sample sizes along with two real datasets. The following findings were made. First, our proposed methods outperform conventional methods for all simulation set-ups. In particular, our methods are much better when the given data are noisy and sample size is small. They showed relatively robust performance regardless of noise level and sample size, whereas the performance of SAM became significantly worse as the noise level became high or sample size decreased. When sufficient sample replicates were available, SAM and our methods showed similar performance. Finally, our proposed methods are competitive with traditional methods in classification tasks for microarrays. The results of simulation study and real data analysis have demonstrated that our proposed methods are effective for detecting significant genes and classification tasks, especially when the given data are noisy or have few sample replicates. By employing weighting schemes, we can obtain robust and reliable results for microarray data analysis.

Computational Fluid Dynamics of the Boundary Layer Characteristics of a Pacific Bluefin Tuna

DTIC Science & Technology

2015-09-18

17  LIST OF ABBREVIATIONS AND ACRONYMS 2D Two Dimensional 3D Three Dimensional AUV Autonomous...Finally, this research has the potential to advance technology of various Navy systems, e.g., torpedo and autonomous underwater vehicle ( AUV ) drag

Novel application of three-dimensional technologies in a case of dismemberment.

PubMed

Baier, Waltraud; Norman, Danielle G; Warnett, Jason M; Payne, Mark; Harrison, Nigel P; Hunt, Nicholas C A; Burnett, Brian A; Williams, Mark A

2017-01-01

This case study reports the novel application of three-dimensional technologies such as micro-CT and 3D printing to the forensic investigation of a complex case of dismemberment. Micro-CT was successfully employed to virtually align severed skeletal elements found in different locations, analyse tool marks created during the dismemberment process, and virtually dissect a charred piece of evidence. High resolution 3D prints of the burnt human bone contained within were created for physical visualisation to assist the investigation team. Micro-CT as a forensic radiological method provided vital information and the basis for visualisation both during the investigation and in the subsequent trial making it one of the first examples of such technology in a UK court. Copyright © 2016. Published by Elsevier B.V.

Logistics of Three-dimensional Printing: Primer for Radiologists.

PubMed

Hodgdon, Taryn; Danrad, Raman; Patel, Midhir J; Smith, Stacy E; Richardson, Michael L; Ballard, David H; Ali, Sayed; Trace, Anthony Paul; DeBenedectis, Carolynn M; Zygmont, Matthew E; Lenchik, Leon; Decker, Summer J

2018-01-01

The Association of University Radiologists Radiology Research Alliance Task Force on three-dimensional (3D) printing presents a review of the logistic considerations for establishing a clinical service using this new technology, specifically focused on implications for radiology. Specific topics include printer selection for 3D printing, software selection, creating a 3D model for printing, providing a 3D printing service, research directions, and opportunities for radiologists to be involved in 3D printing. A thorough understanding of the technology and its capabilities is necessary as the field of 3D printing continues to grow. Radiologists are in the unique position to guide this emerging technology and its use in the clinical arena. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsia, Chu Chieh; Chizhikov, Vladimir E.; Yang, Amy X.

Hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus type-1 (HIV-1) are transfusion-transmitted human pathogens that have a major impact on blood safety and public health worldwide. We developed a microarray multiplex assay for the simultaneous detection and discrimination of these three viruses. The microarray consists of 16 oligonucleotide probes, immobilized on a silylated glass slide. Amplicons from multiplex PCR were labeled with Cy-5 and hybridized to the microarray. The assay detected 1 International Unit (IU), 10 IU, 20 IU of HBV, HCV, and HIV-1, respectively, in a single multiplex reaction. The assay also detected and discriminatedmore » the presence of two or three of these viruses in a single sample. Our data represent a proof-of-concept for the possible use of highly sensitive multiplex microarray assay to screen and confirm the presence of these viruses in blood donors and patients.« less

The effect of column purification on cDNA indirect labelling for microarrays

PubMed Central

Molas, M Lia; Kiss, John Z

2007-01-01

Background The success of the microarray reproducibility is dependent upon the performance of standardized procedures. Since the introduction of microarray technology for the analysis of global gene expression, reproducibility of results among different laboratories has been a major problem. Two of the main contributors to this variability are the use of different microarray platforms and different laboratory practices. In this paper, we address the latter question in terms of how variation in one of the steps of a labelling procedure affects the cDNA product prior to microarray hybridization. Results We used a standard procedure to label cDNA for microarray hybridization and employed different types of column chromatography for cDNA purification. After purifying labelled cDNA, we used the Agilent 2100 Bioanalyzer and agarose gel electrophoresis to assess the quality of the labelled cDNA before its hybridization onto a microarray platform. There were major differences in the cDNA profile (i.e. cDNA fragment lengths and abundance) as a result of using four different columns for purification. In addition, different columns have different efficiencies to remove rRNA contamination. This study indicates that the appropriate column to use in this type of protocol has to be experimentally determined. Finally, we present new evidence establishing the importance of testing the method of purification used during an indirect labelling procedure. Our results confirm the importance of assessing the quality of the sample in the labelling procedure prior to hybridization onto a microarray platform. Conclusion Standardization of column purification systems to be used in labelling procedures will improve the reproducibility of microarray results among different laboratories. In addition, implementation of a quality control check point of the labelled samples prior to microarray hybridization will prevent hybridizing a poor quality sample to expensive micorarrays. PMID:17597522

The effect of column purification on cDNA indirect labelling for microarrays.

PubMed

Molas, M Lia; Kiss, John Z

2007-06-27

The success of the microarray reproducibility is dependent upon the performance of standardized procedures. Since the introduction of microarray technology for the analysis of global gene expression, reproducibility of results among different laboratories has been a major problem. Two of the main contributors to this variability are the use of different microarray platforms and different laboratory practices. In this paper, we address the latter question in terms of how variation in one of the steps of a labelling procedure affects the cDNA product prior to microarray hybridization. We used a standard procedure to label cDNA for microarray hybridization and employed different types of column chromatography for cDNA purification. After purifying labelled cDNA, we used the Agilent 2100 Bioanalyzer and agarose gel electrophoresis to assess the quality of the labelled cDNA before its hybridization onto a microarray platform. There were major differences in the cDNA profile (i.e. cDNA fragment lengths and abundance) as a result of using four different columns for purification. In addition, different columns have different efficiencies to remove rRNA contamination. This study indicates that the appropriate column to use in this type of protocol has to be experimentally determined. Finally, we present new evidence establishing the importance of testing the method of purification used during an indirect labelling procedure. Our results confirm the importance of assessing the quality of the sample in the labelling procedure prior to hybridization onto a microarray platform. Standardization of column purification systems to be used in labelling procedures will improve the reproducibility of microarray results among different laboratories. In addition, implementation of a quality control check point of the labelled samples prior to microarray hybridization will prevent hybridizing a poor quality sample to expensive micorarrays.

Engineering Three-Dimensional Collagen-IKVAV Matrix to Mimic Neural Microenvironment

PubMed Central

2013-01-01

Engineering the cellular microenvironment has great potential to create a platform technology toward engineering of tissue and organs. This study aims to engineer a neural microenvironment through fabrication of three-dimensional (3D) engineered collagen matrixes mimicking in-vivo-like conditions. Collagen was chemically modified with a pentapeptide epitope consisting of isoleucine-lysine-valine-alanine-valine (IKVAV) to mimic laminin structure supports of the neural extracellular matrix (ECM). Three-dimensional collagen matrixes with and without IKVAV peptide modification were fabricated by freeze-drying technology and chemical cross-linking with glutaraldehyde. Structural information of 3D collagen matrixes indicated interconnected pores structure with an average pore size of 180 μm. Our results indicated that culture of dorsal root ganglion (DRG) cells in 3D collagen matrix was greatly influenced by 3D culture method and significantly enhanced with engineered collagen matrix conjugated with IKVAV peptide. It may be concluded that an appropriate 3D culture of neurons enables DRG to positively improve the cellular fate toward further acceleration in tissue regeneration. PMID:23705903

Three-Dimensional Bioprinting: Toward the Era of Manufacturing Human Organs as Spare Parts for Healthcare and Medicine^.

PubMed

Mir, Tanveer Ahmad; Nakamura, Makoto

2017-06-01

Three-dimensional (3D) printing technology has been used in industrial worlds for decades. Three-dimensional bioprinting has recently received an increasing attention across the globe among researchers, academicians, students, and even the ordinary people. This emerging technique has a great potential to engineer highly organized functional bioconstructs with complex geometries and tailored components for engineering bioartificial tissues/organs for widespread applications, including transplantation, therapeutic investigation, drug development, bioassay, and disease modeling. Although many specialized 3D printers have been developed and applied to print various types of 3D tissue constructs, bioprinting technologies still have several technical challenges, including high resolution distribution of cells, controlled deposition of bioinks, suitable bioink materials, maturation of cells, and effective vascularization and innervation within engineered complex structures. In this brief review, we discuss about bioprinting approach, current limitations, and possibility of future advancements for producing engineered bioconstructs and bioartificial organs with desired functionalities.

Visualization of spatial-temporal data based on 3D virtual scene

NASA Astrophysics Data System (ADS)

Wang, Xianghong; Liu, Jiping; Wang, Yong; Bi, Junfang

2009-10-01

The main purpose of this paper is to realize the expression of the three-dimensional dynamic visualization of spatialtemporal data based on three-dimensional virtual scene, using three-dimensional visualization technology, and combining with GIS so that the people's abilities of cognizing time and space are enhanced and improved by designing dynamic symbol and interactive expression. Using particle systems, three-dimensional simulation, virtual reality and other visual means, we can simulate the situations produced by changing the spatial location and property information of geographical entities over time, then explore and analyze its movement and transformation rules by changing the interactive manner, and also replay history and forecast of future. In this paper, the main research object is the vehicle track and the typhoon path and spatial-temporal data, through three-dimensional dynamic simulation of its track, and realize its timely monitoring its trends and historical track replaying; according to visualization techniques of spatialtemporal data in Three-dimensional virtual scene, providing us with excellent spatial-temporal information cognitive instrument not only can add clarity to show spatial-temporal information of the changes and developments in the situation, but also be used for future development and changes in the prediction and deduction.

Large three-dimensional photonic crystals based on monocrystalline liquid crystal blue phases.

PubMed

Chen, Chun-Wei; Hou, Chien-Tsung; Li, Cheng-Chang; Jau, Hung-Chang; Wang, Chun-Ta; Hong, Ching-Lang; Guo, Duan-Yi; Wang, Cheng-Yu; Chiang, Sheng-Ping; Bunning, Timothy J; Khoo, Iam-Choon; Lin, Tsung-Hsien

2017-09-28

Although there have been intense efforts to fabricate large three-dimensional photonic crystals in order to realize their full potential, the technologies developed so far are still beset with various material processing and cost issues. Conventional top-down fabrications are costly and time-consuming, whereas natural self-assembly and bottom-up fabrications often result in high defect density and limited dimensions. Here we report the fabrication of extraordinarily large monocrystalline photonic crystals by controlling the self-assembly processes which occur in unique phases of liquid crystals that exhibit three-dimensional photonic-crystalline properties called liquid-crystal blue phases. In particular, we have developed a gradient-temperature technique that enables three-dimensional photonic crystals to grow to lateral dimensions of ~1 cm (~30,000 of unit cells) and thickness of ~100 μm (~ 300 unit cells). These giant single crystals exhibit extraordinarily sharp photonic bandgaps with high reflectivity, long-range periodicity in all dimensions and well-defined lattice orientation.Conventional fabrication approaches for large-size three-dimensional photonic crystals are problematic. By properly controlling the self-assembly processes, the authors report the fabrication of monocrystalline blue phase liquid crystals that exhibit three-dimensional photonic-crystalline properties.

A Three-Dimensional Statistical Average Skull: Application of Biometric Morphing in Generating Missing Anatomy.

PubMed

Teshima, Tara Lynn; Patel, Vaibhav; Mainprize, James G; Edwards, Glenn; Antonyshyn, Oleh M

2015-07-01

The utilization of three-dimensional modeling technology in craniomaxillofacial surgery has grown exponentially during the last decade. Future development, however, is hindered by the lack of a normative three-dimensional anatomic dataset and a statistical mean three-dimensional virtual model. The purpose of this study is to develop and validate a protocol to generate a statistical three-dimensional virtual model based on a normative dataset of adult skulls. Two hundred adult skull CT images were reviewed. The average three-dimensional skull was computed by processing each CT image in the series using thin-plate spline geometric morphometric protocol. Our statistical average three-dimensional skull was validated by reconstructing patient-specific topography in cranial defects. The experiment was repeated 4 times. In each case, computer-generated cranioplasties were compared directly to the original intact skull. The errors describing the difference between the prediction and the original were calculated. A normative database of 33 adult human skulls was collected. Using 21 anthropometric landmark points, a protocol for three-dimensional skull landmarking and data reduction was developed and a statistical average three-dimensional skull was generated. Our results show the root mean square error (RMSE) for restoration of a known defect using the native best match skull, our statistical average skull, and worst match skull was 0.58, 0.74, and 4.4  mm, respectively. The ability to statistically average craniofacial surface topography will be a valuable instrument for deriving missing anatomy in complex craniofacial defects and deficiencies as well as in evaluating morphologic results of surgery.

Visidep (TM): A Three-Dimensional Imaging System For The Unaided Eye

NASA Astrophysics Data System (ADS)

McLaurin, A. Porter; Jones, Edwin R.; Cathey, LeConte

1984-05-01

The VISIDEP process for creating images in three dimensions on flat screens is suitable for photographic, electrographic and computer generated imaging systems. Procedures for generating these images vary from medium to medium due to the specific requirements of each technology. Imaging requirements for photographic and electrographic media are more directly tied to the hardware than are computer based systems. Applications of these technologies are not limited to entertainment, but have implications for training, interactive computer/video systems, medical imaging, and inspection equipment. Through minor modification the system can provide three-dimensional images with accurately measureable relationships for robotics and adds this factor for future developments in artificial intelligence. In almost any area requiring image analysis or critical review, VISIDEP provides the added advantage of three-dimensionality. All of this is readily accomplished without aids to the human eye. The system can be viewed in full color, false-color infra-red, and monochromatic modalities from any angle and is also viewable with a single eye. Thus, the potential of application for this developing system is extensive and covers the broad spectrum of human endeavor from entertainment to scientific study.

Is this the real time for genomics?

PubMed

Guarnaccia, Maria; Gentile, Giulia; Alessi, Enrico; Schneider, Claudio; Petralia, Salvatore; Cavallaro, Sebastiano

2014-01-01

In the last decades, molecular biology has moved from gene-by-gene analysis to more complex studies using a genome-wide scale. Thanks to high-throughput genomic technologies, such as microarrays and next-generation sequencing, a huge amount of information has been generated, expanding our knowledge on the genetic basis of various diseases. Although some of this information could be transferred to clinical diagnostics, the technologies available are not suitable for this purpose. In this review, we will discuss the drawbacks associated with the use of traditional DNA microarrays in diagnostics, pointing out emerging platforms that could overcome these obstacles and offer a more reproducible, qualitative and quantitative multigenic analysis. New miniaturized and automated devices, called Lab-on-Chip, begin to integrate PCR and microarray on the same platform, offering integrated sample-to-result systems. The introduction of this kind of innovative devices may facilitate the transition of genome-based tests into clinical routine. Copyright © 2014. Published by Elsevier Inc.

Ethical issues raised by genetic testing with oligonucleotide microarrays.

PubMed

Grody, Wayne W

2003-02-01

Because genes and alterations within them determine the identity, characteristics, and inheritance of every individual, the application of genetic science to humans has long been surrounded by apprehension, controversy, and real or perceived potential for abuse. Crude eugenics practices of the past now find a theoretical rebirth and transformation through the use of modern molecular genetic technologies for mutation detection, predictive and prenatal diagnosis, and, ultimately, gene replacement. The advent of oligonucleotide microarray analysis, in which hundreds or thousands of genes and mutations can be tested in parallel, offers tremendous promise for more accurate, sensitive, and efficient genetic testing. At the same time, however, this powerful technology dramatically increases the number and scope of ethical concerns accompanying each individual test request. This article considers the evolution and implications of these concerns, from the initial ordering of a microarray test by the physician to such issues as informed consent, privacy, confidentiality, clinical utility, discrimination, stigmatization, ethnic and population impact, and reimbursement.

Face and content validation of a novel three-dimensional printed temporal bone for surgical skills development.

PubMed

Da Cruz, M J; Francis, H W

2015-07-01

To assess the face and content validity of a novel synthetic, three-dimensional printed temporal bone for surgical skills development and training. A synthetic temporal bone was printed using composite materials and three-dimensional printing technology. Surgical trainees were asked to complete three structured temporal bone dissection exercises. Attitudes and impressions were then assessed using a semi-structured questionnaire. Previous cadaver and real operating experiences were used as a reference. Trainees' experiences of the synthetic temporal bone were analysed in terms of four domains: anatomical realism, usefulness as a training tool, task-based usefulness and overall reactions. Responses across all domains indicated a high degree of acceptance, suggesting that the three-dimensional printed temporal bone was a useful tool in skills development. A sophisticated three-dimensional printed temporal bone that demonstrates face and content validity was developed. The efficiency in cost savings coupled with low associated biohazards make it likely that the printed temporal bone will be incorporated into traditional temporal bone skills development programmes in the near future.

A Virtual Education: Guidelines for Using Games Technology

ERIC Educational Resources Information Center

Schofield, Damian

2014-01-01

Advanced three-dimensional virtual environment technology, similar to that used by the film and computer games industry, can allow educational developers to rapidly create realistic online vir-tual environments. This technology has been used to generate a range of interactive Virtual Real-ity (VR) learning environments across a spectrum of…

Determination of Minimum Training Sample Size for Microarray-Based Cancer Outcome Prediction–An Empirical Assessment

PubMed Central

Cheng, Ningtao; Wu, Leihong; Cheng, Yiyu

2013-01-01

The promise of microarray technology in providing prediction classifiers for cancer outcome estimation has been confirmed by a number of demonstrable successes. However, the reliability of prediction results relies heavily on the accuracy of statistical parameters involved in classifiers. It cannot be reliably estimated with only a small number of training samples. Therefore, it is of vital importance to determine the minimum number of training samples and to ensure the clinical value of microarrays in cancer outcome prediction. We evaluated the impact of training sample size on model performance extensively based on 3 large-scale cancer microarray datasets provided by the second phase of MicroArray Quality Control project (MAQC-II). An SSNR-based (scale of signal-to-noise ratio) protocol was proposed in this study for minimum training sample size determination. External validation results based on another 3 cancer datasets confirmed that the SSNR-based approach could not only determine the minimum number of training samples efficiently, but also provide a valuable strategy for estimating the underlying performance of classifiers in advance. Once translated into clinical routine applications, the SSNR-based protocol would provide great convenience in microarray-based cancer outcome prediction in improving classifier reliability. PMID:23861920

Support vector machine and principal component analysis for microarray data classification

NASA Astrophysics Data System (ADS)

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.

Creation of antifouling microarrays by photopolymerization of zwitterionic compounds for protein assay and cell patterning.

PubMed

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.

Emerging Use of Gene Expression Microarrays in Plant Physiology

DOE PAGES

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 weremore » 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.« less

Analysis of traditional versus three-dimensional augmented curriculum on anatomical learning outcome measures.

PubMed

Peterson, Diana Coomes; Mlynarczyk, Gregory S A

2016-11-01

This study examined whether student learning outcome measures are influenced by the addition of three-dimensional and digital teaching tools to a traditional dissection and lecture learning format curricula. The study was performed in a semester long graduate level course that incorporated both gross anatomy and neuroanatomy curricula. Methods compared student examination performance on material taught using lecture and cadaveric dissection teaching tools alone or lecture and cadaveric dissection augmented with computerized three-dimensional teaching tools. Additional analyses were performed to examine potential correlations between question difficulty and format, previous student performance (i.e., undergraduate grade point average), and a student perception survey. The results indicated that students performed better on material in which three-dimensional (3D) technologies are utilized in conjunction with lecture and dissection methodologies. The improvement in performance was observed across the student population primarily on laboratory examinations. Although, student performance was increased, students did not perceive that the use of the additional 3D technology significantly influenced their learning. The results indicate that the addition of 3D learning tools can influence long-term retention of gross anatomy material and should be considered as a beneficial supplement for anatomy courses. Anat Sci Educ 9: 529-536. © 2016 American Association of Anatomists. © 2016 American Association of Anatomists.

Tumor immunology.

PubMed

Mocellin, Simone; Lise, Mario; Nitti, Donato

2007-01-01

Advances in tumor immunology are supporting the clinical implementation of several immunological approaches to cancer in the clinical setting. However, the alternate success of current immunotherapeutic regimens underscores the fact that the molecular mechanisms underlying immune-mediated tumor rejection are still poorly understood. Given the complexity of the immune system network and the multidimensionality of tumor/host interactions, the comprehension of tumor immunology might greatly benefit from high-throughput microarray analysis, which can portrait the molecular kinetics of immune response on a genome-wide scale, thus accelerating the discovery pace and ultimately catalyzing the development of new hypotheses in cell biology. Although in its infancy, the implementation of microarray technology in tumor immunology studies has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to an effective immune response against cancer. Although the general principles of microarray-based gene profiling have rapidly spread in the scientific community, the need for mastering this technique to produce meaningful data and correctly interpret the enormous output of information generated by this technology is critical and represents a tremendous challenge for investigators, as outlined in the first section of this book. In the present Chapter, we report on some of the most significant results obtained with the application of DNA microarray in this oncology field.

NCBI GEO: archive for functional genomics data sets—10 years on

PubMed Central

Barrett, Tanya; Troup, Dennis B.; Wilhite, Stephen E.; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F.; Tomashevsky, Maxim; Marshall, Kimberly A.; Phillippy, Katherine H.; Sherman, Patti M.; Muertter, Rolf N.; Holko, Michelle; Ayanbule, Oluwabukunmi; Yefanov, Andrey; Soboleva, Alexandra

2011-01-01

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/. PMID:21097893

Three-Dimensional Display Technologies for Anatomical Education: A Literature Review

NASA Astrophysics Data System (ADS)

Hackett, Matthew; Proctor, Michael

2016-08-01

Anatomy is a foundational component of biological sciences and medical education and is important for a variety of clinical tasks. To augment current curriculum and improve students' spatial knowledge of anatomy, many educators, anatomists, and researchers use three-dimensional (3D) visualization technologies. This article reviews 3D display technologies and their associated assessments for anatomical education. In the first segment, the review covers the general function of displays employing 3D techniques. The second segment of the review highlights the use and assessment of 3D technology in anatomical education, focusing on factors such as knowledge gains, student perceptions, and cognitive load. The review found 32 articles on the use of 3D displays in anatomical education and another 38 articles on the assessment of 3D displays. The review shows that the majority (74 %) of studies indicate that the use of 3D is beneficial for many tasks in anatomical education, and that student perceptions are positive toward the technology.

Web-Based Learning in the Computer-Aided Design Curriculum.

ERIC Educational Resources Information Center

Sung, Wen-Tsai; Ou, S. C.

2002-01-01

Applies principles of constructivism and virtual reality (VR) to computer-aided design (CAD) curriculum, particularly engineering, by integrating network, VR and CAD technologies into a Web-based learning environment that expands traditional two-dimensional computer graphics into a three-dimensional real-time simulation that enhances user…

TECHNOLOGY EVALUATION REPORT, HYDROTECHNICS IN SITU FLOW SENSOR

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Superfund Innovative Technology Evaluation (SITE) Program evaluated performance of HydroTechnics, Inc. flow sensors in measuring the three-dimensional flow pattern created by operation of the Wasatch Environmental, Inc. (WEI) ground...

Bayes multiple decision functions.

PubMed

Wu, Wensong; Peña, Edsel A

2013-01-01

This paper deals with the problem of simultaneously making many ( M ) binary decisions based on one realization of a random data matrix X . M is typically large and X will usually have M rows associated with each of the M decisions to make, but for each row the data may be low dimensional. Such problems arise in many practical areas such as the biological and medical sciences, where the available dataset is from microarrays or other high-throughput technology and with the goal being to decide which among of many genes are relevant with respect to some phenotype of interest; in the engineering and reliability sciences; in astronomy; in education; and in business. A Bayesian decision-theoretic approach to this problem is implemented with the overall loss function being a cost-weighted linear combination of Type I and Type II loss functions. The class of loss functions considered allows for use of the false discovery rate (FDR), false nondiscovery rate (FNR), and missed discovery rate (MDR) in assessing the quality of decision. Through this Bayesian paradigm, the Bayes multiple decision function (BMDF) is derived and an efficient algorithm to obtain the optimal Bayes action is described. In contrast to many works in the literature where the rows of the matrix X are assumed to be stochastically independent, we allow a dependent data structure with the associations obtained through a class of frailty-induced Archimedean copulas. In particular, non-Gaussian dependent data structure, which is typical with failure-time data, can be entertained. The numerical implementation of the determination of the Bayes optimal action is facilitated through sequential Monte Carlo techniques. The theory developed could also be extended to the problem of multiple hypotheses testing, multiple classification and prediction, and high-dimensional variable selection. The proposed procedure is illustrated for the simple versus simple hypotheses setting and for the composite hypotheses setting through simulation studies. The procedure is also applied to a subset of a microarray data set from a colon cancer study.

Development of a rapid microarray-based DNA subtyping assay for the alleles of Shiga toxins 1 and 2 of Escherichia coli.

PubMed

Geue, Lutz; Stieber, Bettina; Monecke, Stefan; Engelmann, Ines; Gunzer, Florian; Slickers, Peter; Braun, Sascha D; Ehricht, Ralf

2014-08-01

In this study, we developed a new rapid, economic, and automated microarray-based genotyping test for the standardized subtyping of Shiga toxins 1 and 2 of Escherichia coli. The microarrays from Alere Technologies can be used in two different formats, the ArrayTube and the ArrayStrip (which enables high-throughput testing in a 96-well format). One microarray chip harbors all the gene sequences necessary to distinguish between all Stx subtypes, facilitating the identification of single and multiple subtypes within a single isolate in one experiment. Specific software was developed to automatically analyze all data obtained from the microarray. The assay was validated with 21 Shiga toxin-producing E. coli (STEC) reference strains that were previously tested by the complete set of conventional subtyping PCRs. The microarray results showed 100% concordance with the PCR results. Essentially identical results were detected when the standard DNA extraction method was replaced by a time-saving heat lysis protocol. For further validation of the microarray, we identified the Stx subtypes or combinations of the subtypes in 446 STEC field isolates of human and animal origin. In summary, this oligonucleotide array represents an excellent diagnostic tool that provides some advantages over standard PCR-based subtyping. The number of the spotted probes on the microarrays can be increased by additional probes, such as for novel alleles, species markers, or resistance genes, should the need arise. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

A novel approach for discovering condition-specific correlations of gene expressions within biological pathways by using cloud computing technology.

PubMed

Chang, Tzu-Hao; Wu, Shih-Lin; Wang, Wei-Jen; Horng, Jorng-Tzong; Chang, Cheng-Wei

2014-01-01

Microarrays are widely used to assess gene expressions. Most microarray studies focus primarily on identifying differential gene expressions between conditions (e.g., cancer versus normal cells), for discovering the major factors that cause diseases. Because previous studies have not identified the correlations of differential gene expression between conditions, crucial but abnormal regulations that cause diseases might have been disregarded. This paper proposes an approach for discovering the condition-specific correlations of gene expressions within biological pathways. Because analyzing gene expression correlations is time consuming, an Apache Hadoop cloud computing platform was implemented. Three microarray data sets of breast cancer were collected from the Gene Expression Omnibus, and pathway information from the Kyoto Encyclopedia of Genes and Genomes was applied for discovering meaningful biological correlations. The results showed that adopting the Hadoop platform considerably decreased the computation time. Several correlations of differential gene expressions were discovered between the relapse and nonrelapse breast cancer samples, and most of them were involved in cancer regulation and cancer-related pathways. The results showed that breast cancer recurrence might be highly associated with the abnormal regulations of these gene pairs, rather than with their individual expression levels. The proposed method was computationally efficient and reliable, and stable results were obtained when different data sets were used. The proposed method is effective in identifying meaningful biological regulation patterns between conditions.

Adaptation of the Biolog Phenotype MicroArrayTM Technology to Profile the Obligate Anaerobe Geobacter metallireducens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joyner, Dominique; Fortney, Julian; Chakraborty, Romy

2010-05-17

The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organism represents metabolic activity on the array which is detected and measured by the OmniLog(R) system. We have previously adapted the technology for the anaerobic sulfate reducingmore » bacterium Desulfovibrio vulgaris. In this work, we have taken the technology a step further by adapting it for the iron reducing obligate anaerobe Geobacter metallireducens. In an osmotic stress microarray it was determined that the organism has higher sensitivity to impermeable solutes 3-6percent KCl and 2-5percent NaNO3 that result in osmotic stress by osmosis to the cell than to permeable non-ionic solutes represented by 5-20percent ethylene glycol and 2-3percent urea. The osmotic stress microarray also includes an array of osmoprotectants and precursor molecules that were screened to identify substrates that would provide osmotic protection to NaCl stress. None of the substrates tested conferred resistance to elevated concentrations of salt. Verification studies in which G.m. was grown in defined medium amended with 100mM NaCl (MIC) and the common osmoprotectants betaine, glycine and proline supported the PM findings. Further verification was done by analysis of transcriptomic profiles of G.m. grown under 100mM NaCl stress that revealed up-regulation of genes related to degradation rather than accumulation of the above-mentioned osmoprotectants. The phenotypic profile, supported by additional analysis indicates that the accumulation of these osmoprotectants as a response to salt stress does not occur in G.m. and response to stress must occur by other mechanisms. The Phenotype MicroArray technology can be reliably used as a rapid screening tool for characterization in anaerobic microbial ecology.« less

Mobile three-dimensional visualisation technologies for clinician-led fall prevention assessments.

PubMed

Hamm, Julian; Money, Arthur G; Atwal, Anita; Ghinea, Gheorghita

2017-08-01

The assistive equipment provision process is routinely carried out with patients to mitigate fall risk factors via the fitment of assistive equipment within the home. However, currently, over 50% of assistive equipment is abandoned by the patients due to poor fit between the patient and the assistive equipment. This paper explores clinician perceptions of an early stage three-dimensional measurement aid prototype, which provides enhanced assistive equipment provision process guidance to clinicians. Ten occupational therapists trialled the three-dimensional measurement aid prototype application; think-aloud and semi-structured interview data was collected. Usability was measured with the System Usability Scale. Participants scored three-dimensional measurement aid prototype as 'excellent' and agreed strongly with items relating to the usability and learnability of the application. The qualitative analysis identified opportunities for improving existing practice, including, improved interpretation/recording measurements; enhanced collaborative practice within the assistive equipment provision process. Future research is needed to determine the clinical utility of this application compared with two-dimensional counterpart paper-based guidance leaflets.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fournier, Marcia V.; Martin, Katherine J.; Kenny, Paraic A.

To understand how non-malignant human mammary epithelial cells (HMEC) transit from a disorganized proliferating to an organized growth arrested state, and to relate this process to the changes that occur in breast cancer, we studied gene expression changes in non-malignant HMEC grown in three-dimensional cultures, and in a previously published panel of microarray data for 295 breast cancer samples. We hypothesized that the gene expression pattern of organized and growth arrested mammary acini would share similarities with breast tumors with good prognoses. Using Affymetrix HG-U133A microarrays, we analyzed the expression of 22,283 gene transcripts in two HMEC cell lines, 184more » (finite life span) and HMT3522 S1 (immortal non-malignant), on successive days post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. We identified gene expression changes with the same temporal pattern in both lines. We show that genes that are significantly lower in the organized, growth arrested HMEC than in their proliferating counterparts can be used to classify breast cancer patients into poor and good prognosis groups with high accuracy. This study represents a novel unsupervised approach to identifying breast cancer markers that may be of use clinically.« less

Informed Decision-Making in the Context of Prenatal Chromosomal Microarray.

PubMed

Baker, Jessica; Shuman, Cheryl; Chitayat, David; Wasim, Syed; Okun, Nan; Keunen, Johannes; Hofstedter, Renee; Silver, Rachel

2018-03-07

The introduction of chromosomal microarray (CMA) into the prenatal setting has involved considerable deliberation due to the wide range of possible outcomes (e.g., copy number variants of uncertain clinical significance). Such issues are typically discussed in pre-test counseling for pregnant women to support informed decision-making regarding prenatal testing options. This research study aimed to assess the level of informed decision-making with respect to prenatal CMA and the factor(s) influencing decision-making to accept CMA for the selected prenatal testing procedure (i.e., chorionic villus sampling or amniocentesis). We employed a questionnaire that was adapted from a three-dimensional measure previously used to assess informed decision-making with respect to prenatal screening for Down syndrome and neural tube defects. This measure classifies an informed decision as one that is knowledgeable, value-consistent, and deliberated. Our questionnaire also included an optional open-ended question, soliciting factors that may have influenced the participants' decision to accept prenatal CMA; these responses were analyzed qualitatively. Data analysis on 106 participants indicated that 49% made an informed decision (i.e., meeting all three criteria of knowledgeable, deliberated, and value-consistent). Analysis of 59 responses to the open-ended question showed that "the more information the better" emerged as the dominant factor influencing both informed and uninformed participants' decisions to accept prenatal CMA. Despite learning about the key issues in pre-test genetic counseling, our study classified a significant portion of women as making uninformed decisions due to insufficient knowledge, lack of deliberation, value-inconsistency, or a combination of these three measures. Future efforts should focus on developing educational approaches and counseling strategies to effectively increase the rate of informed decision-making among women offered prenatal CMA.

Development and applications of 3-dimensional integration nanotechnologies.

PubMed

Kim, Areum; Choi, Eunmi; Son, Hyungbin; Pyo, Sung Gyu

2014-02-01

Unlike conventional two-dimensional (2D) planar structures, signal or power is supplied through through-silicon via (TSV) in three-dimensional (3D) integration technology to replace wires for binding the chip/wafer. TSVs have becomes an essential technology, as they satisfy Moore's law. This 3D integration technology enables system and sensor functions at a nanoscale via the implementation of a highly integrated nano-semiconductor as well as the fabrication of a single chip with multiple functions. Thus, this technology is considered to be a new area of development for the systemization of the nano-bio area. In this review paper, the basic technology required for such 3D integration is described and methods to measure the bonding strength in order to measure the void occurring during bonding are introduced. Currently, CMOS image sensors and memory chips associated with nanotechnology are being realized on the basis of 3D integration technology. In this paper, we intend to describe the applications of high-performance nano-biosensor technology currently under development and the direction of development of a high performance lab-on-a-chip (LOC).

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

PubMed Central

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 contrast, popular normalization approaches like quantile, LOWESS, Peng's method and VSN normalization alter the data distributions of regulation microarrays to such an extent that using these approaches will impact the reliability of the downstream analysis substantially. PMID:22276688

Development Of A Three-Dimensional Circuit Integration Technology And Computer Architecture

NASA Astrophysics Data System (ADS)

Etchells, R. D.; Grinberg, J.; Nudd, G. R.

1981-12-01

This paper is the first of a series 1,2,3 describing a range of efforts at Hughes Research Laboratories, which are collectively referred to as "Three-Dimensional Microelectronics." The technology being developed is a combination of a unique circuit fabrication/packaging technology and a novel processing architecture. The packaging technology greatly reduces the parasitic impedances associated with signal-routing in complex VLSI structures, while simultaneously allowing circuit densities orders of magnitude higher than the current state-of-the-art. When combined with the 3-D processor architecture, the resulting machine exhibits a one- to two-order of magnitude simultaneous improvement over current state-of-the-art machines in the three areas of processing speed, power consumption, and physical volume. The 3-D architecture is essentially that commonly referred to as a "cellular array", with the ultimate implementation having as many as 512 x 512 processors working in parallel. The three-dimensional nature of the assembled machine arises from the fact that the chips containing the active circuitry of the processor are stacked on top of each other. In this structure, electrical signals are passed vertically through the chips via thermomigrated aluminum feedthroughs. Signals are passed between adjacent chips by micro-interconnects. This discussion presents a broad view of the total effort, as well as a more detailed treatment of the fabrication and packaging technologies themselves. The results of performance simulations of the completed 3-D processor executing a variety of algorithms are also presented. Of particular pertinence to the interests of the focal-plane array community is the simulation of the UNICORNS nonuniformity correction algorithms as executed by the 3-D architecture.

BEST3D user's manual: Boundary Element Solution Technology, 3-Dimensional Version 3.0

NASA Technical Reports Server (NTRS)

1991-01-01

The theoretical basis and programming strategy utilized in the construction of the computer program BEST3D (boundary element solution technology - three dimensional) and detailed input instructions are provided for the use of the program. An extensive set of test cases and sample problems is included in the manual and is also available for distribution with the program. The BEST3D program was developed under the 3-D Inelastic Analysis Methods for Hot Section Components contract (NAS3-23697). The overall objective of this program was the development of new computer programs allowing more accurate and efficient three-dimensional thermal and stress analysis of hot section components, i.e., combustor liners, turbine blades, and turbine vanes. The BEST3D program allows both linear and nonlinear analysis of static and quasi-static elastic problems and transient dynamic analysis for elastic problems. Calculation of elastic natural frequencies and mode shapes is also provided.

Thermoelectric microdevice fabricated by a MEMS-like electrochemical process

NASA Technical Reports Server (NTRS)

Snyder, G. Jeffrey; Lim, James R.; Huang, Chen-Kuo; Fleurial, Jean-Pierre

2003-01-01

Microelectromechanical systems (MEMS) are the basis of many rapidly growing technologies, because they combine miniature sensors and actuators with communications and electronics at low cost. Commercial MEMS fabrication processes are limited to silicon-based materials or two-dimensional structures. Here we show an inexpensive, electrochemical technique to build MEMS-like structures that contain several different metals and semiconductors with three-dimensional bridging structures. We demonstrate this technique by building a working microthermoelectric device. Using repeated exposure and development of multiple photoresist layers, several different metals and thermoelectric materials are fabricated in a three-dimensional structure. A device containing 126 n-type and p-type (Bi, Sb)2Te3 thermoelectric elements, 20 microm tall and 60 microm in diameter with bridging metal interconnects, was fabricated and cooling demonstrated. Such a device should be of technological importance for precise thermal control when operating as a cooler, and for portable power when operating as a micro power generator.

From tissue to silicon to plastic: three-dimensional printing in comparative anatomy and physiology

PubMed Central

Lauridsen, Henrik; Hansen, Kasper; Nørgård, Mathias Ørum; Wang, Tobias; Pedersen, Michael

2016-01-01

Comparative anatomy and physiology are disciplines related to structures and mechanisms in three-dimensional (3D) space. For the past centuries, scientific reports in these fields have relied on written descriptions and two-dimensional (2D) illustrations, but in recent years 3D virtual modelling has entered the scene. However, comprehending complex anatomical structures is hampered by reproduction on flat inherently 2D screens. One way to circumvent this problem is in the production of 3D-printed scale models. We have applied computed tomography and magnetic resonance imaging to produce digital models of animal anatomy well suited to be printed on low-cost 3D printers. In this communication, we report how to apply such technology in comparative anatomy and physiology to aid discovery, description, comprehension and communication, and we seek to inspire fellow researchers in these fields to embrace this emerging technology. PMID:27069653

Application of Tessellation in Architectural Geometry Design

NASA Astrophysics Data System (ADS)

Chang, Wei

2018-06-01

Tessellation plays a significant role in architectural geometry design, which is widely used both through history of architecture and in modern architectural design with the help of computer technology. Tessellation has been found since the birth of civilization. In terms of dimensions, there are two- dimensional tessellations and three-dimensional tessellations; in terms of symmetry, there are periodic tessellations and aperiodic tessellations. Besides, some special types of tessellations such as Voronoi Tessellation and Delaunay Triangles are also included. Both Geometry and Crystallography, the latter of which is the basic theory of three-dimensional tessellations, need to be studied. In history, tessellation was applied into skins or decorations in architecture. The development of Computer technology enables tessellation to be more powerful, as seen in surface control, surface display and structure design, etc. Therefore, research on the application of tessellation in architectural geometry design is of great necessity in architecture studies.

A Three-Dimensional Microdisplacement Sensing System Based on MEMS Bulk-Silicon Technology

PubMed Central

Wu, Junjie; Lei, Lihua; Chen, Xin; Cai, Xiaoyu; Li, Yuan; Han, Tao

2014-01-01

For the dimensional measurement and characterization of microsized and nanosized components, a three-dimensional microdisplacement sensing system was developed using the piezoresistive effect in silicon. The sensor was fabricated using microelectromechanical system bulk-silicon technology, and it was validated using the finite element method. A precise data acquisition circuit with an accuracy of 20 μV was designed to obtain weak voltage signals. By calibration, the sensing system was shown to have a sensitivity of 17.29 mV/μm and 4.59 mV/μm in the axial and lateral directions, respectively; the nonlinearity in these directions was 0.8% and 1.0% full scale, respectively. A full range of 4.6 μm was achieved in the axial direction. Results of a resolution test indicated that the sensing system had a resolution of 5 nm in the axial direction and 10 nm in the lateral direction. PMID:25360581

Three-Dimensional Super-Resolution: Theory, Modeling, and Field Tests Results

NASA Technical Reports Server (NTRS)

Bulyshev, Alexander; Amzajerdian, Farzin; Roback, Vincent E.; Hines, Glenn; Pierrottet, Diego; Reisse, Robert

2014-01-01

Many flash lidar applications continue to demand higher three-dimensional image resolution beyond the current state-of-the-art technology of the detector arrays and their associated readout circuits. Even with the available number of focal plane pixels, the required number of photons for illuminating all the pixels may impose impractical requirements on the laser pulse energy or the receiver aperture size. Therefore, image resolution enhancement by means of a super-resolution algorithm in near real time presents a very attractive solution for a wide range of flash lidar applications. This paper describes a superresolution technique and illustrates its performance and merits for generating three-dimensional image frames at a video rate.

Three clinical experiences with SNP array results consistent with parental incest: a narrative with lessons learned.

PubMed

Helm, Benjamin M; Langley, Katherine; Spangler, Brooke; Vergano, Samantha

2014-08-01

Single nucleotide polymorphism microarrays have the ability to reveal parental consanguinity which may or may not be known to healthcare providers. Consanguinity can have significant implications for the health of patients and for individual and family psychosocial well-being. These results often present ethical and legal dilemmas that can have important ramifications. Unexpected consanguinity can be confounding to healthcare professionals who may be unprepared to handle these results or to communicate them to families or other appropriate representatives. There are few published accounts of experiences with consanguinity and SNP arrays. In this paper we discuss three cases where molecular evidence of parental incest was identified by SNP microarray. We hope to further highlight consanguinity as a potential incidental finding, how the cases were handled by the clinical team, and what resources were found to be most helpful. This paper aims to contribute further to professional discourse on incidental findings with genomic technology and how they were addressed clinically. These experiences may provide some guidance on how others can prepare for these findings and help improve practice. As genetic and genomic testing is utilized more by non-genetics providers, we also hope to inform about the importance of engaging with geneticists and genetic counselors when addressing these findings.

Recent progress in DNA origami technology.

PubMed

Endo, Masayuki; Sugiyama, Hiroshi

2011-06-01

DNA origami is an emerging technology for designing defined two-dimensional DNA nanostructures. In this review, we focus on and describe several types of DNA origami-related studies, as follows: (1) programmed DNA origami assembly, (2) DNA origami-templated molecular assembly, (3) design and construction of various three-dimensional DNA origami structures, (4) programmed functionalization of DNA origami and combination with top-down nanotechnology, (5) single molecular observation on a designed DNA origami, and (6) DNA nanomachines working on a DNA origami. © 2011 by John Wiley & Sons, Inc.

Profiling protein function with small molecule microarrays

PubMed Central

Winssinger, Nicolas; Ficarro, Scott; Schultz, Peter G.; Harris, Jennifer L.

2002-01-01

The regulation of protein function through posttranslational modification, local environment, and protein–protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of a spatially addressable small molecule microarray to an activity-based profile of proteases in crude cell lysates. The potential of this small molecule-based profiling technology is demonstrated by the detection of caspase activation upon induction of apoptosis, characterization of the activated caspase, and inhibition of the caspase-executed apoptotic phenotype using the small molecule inhibitor identified in the microarray-based profile. PMID:12167675

Fabrication of micromechanical and microoptical systems by two-photon polymerization

NASA Astrophysics Data System (ADS)

Reinhardt, Carsten; Ovsianikov, A.; Passinger, Sven; Chichkov, Boris N.

2007-01-01

The recently developed two-photon polymerisation technique is used for the fabrication of two- and three-dimensional structures in photosensitive inorganic-organic hybrid material (ORMOCER), in SU8 , and in positive tone resist with resolutions down to 100nm. In this contribution we present applications of this powerful technology for the realization of micromechanical systems and microoptical components. We will demonstrate results on the fabrication of complex movable three-dimensional micromechanical systems and microfluidic components which cannot be realized by other technologies. This approach of structuring photosensitive materials also provides unique possibilities for the fabrication of different microoptical components such as arbitrary shaped microlenses, microprisms, and 3D-photonic crystals with high optical quality.

Research and development of ultrasonic tomography technology for three-dimensional imaging of internal rail flaws : modeling and simulation.

DOT National Transportation Integrated Search

2013-04-01

This report covers the work performed under the FRA High-Speed BAA 20102011 program to demonstrate the technology of ultrasonic tomography for 3-D imaging of internal rail flaws. There is a need to develop new technologies that are able to quantif...

Echocardiography Comparison Between Two and Three Dimensional Echocardiograms

NASA Technical Reports Server (NTRS)

2003-01-01

Echocardiography uses sound waves to image the heart and other organs. Developing a compact version of the latest technology improved the ease of monitoring crew member health, a critical task during long space flights. NASA researchers plan to adapt the three-dimensional (3-D) echocardiogram for space flight. The two-dimensional (2-D) echocardiogram utilized in orbit on the International Space Station (ISS) was effective, but difficult to use with precision. A heart image from a 2-D echocardiogram (left) is of a better quality than that from a 3-D device (right), but the 3-D imaging procedure is more user-friendly.

Hierarchical classification in high dimensional numerous class cases

NASA Technical Reports Server (NTRS)

Kim, Byungyong; Landgrebe, D. A.

1990-01-01

As progress in new sensor technology continues, increasingly high resolution imaging sensors are being developed. These sensors give more detailed and complex data for each picture element and greatly increase the dimensionality of data over past systems. Three methods for designing a decision tree classifier are discussed: a top down approach, a bottom up approach, and a hybrid approach. Three feature extraction techniques are implemented. Canonical and extended canonical techniques are mainly dependent upon the mean difference between two classes. An autocorrelation technique is dependent upon the correlation differences. The mathematical relationship between sample size, dimensionality, and risk value is derived.

An update on intraoperative three-dimensional transesophageal echocardiography

PubMed Central

2017-01-01

Transesophageal echocardiography (TEE) was first used routinely in the operating rooms in the 1980s to facilitate surgical decision-making. Since then, TEE has evolved from the standard two-dimensional (2D) exam to include focused real-time three-dimensional (RT-3D) imaging both inside and outside the operating rooms. Improved spatial and temporal resolution due to technological advances has expedited surgical interventions in diseased valves. 3D imaging has also emerged as a crucial adjunct in percutaneous interventions for structural heart disease. With continued advancement in software, RT-3D TEE will continue to impact perioperative decisions. PMID:28540070

Rapid and reliable detection and identification of GM events using multiplex PCR coupled with oligonucleotide microarray.

PubMed

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.

Complementary techniques: validation of gene expression data by quantitative real time PCR.

PubMed

Provenzano, Maurizio; Mocellin, Simone

2007-01-01

Microarray technology can be considered the most powerful tool for screening gene expression profiles of biological samples. After data mining, results need to be validated with highly reliable biotechniques allowing for precise quantitation of transcriptional abundance of identified genes. Quantitative real time PCR (qrt-PCR) technology has recently reached a level of sensitivity, accuracy and practical ease that support its use as a routine bioinstrumentation for gene level measurement. Currently, qrt-PCR is considered by most experts the most appropriate method to confirm or confute microarray-generated data. The knowledge of the biochemical principles underlying qrt-PCR as well as some related technical issues must be beard in mind when using this biotechnology.

The cross-validated AUC for MCP-logistic regression with high-dimensional data.

PubMed

Jiang, Dingfeng; Huang, Jian; Zhang, Ying

2013-10-01

We propose a cross-validated area under the receiving operator characteristic (ROC) curve (CV-AUC) criterion for tuning parameter selection for penalized methods in sparse, high-dimensional logistic regression models. We use this criterion in combination with the minimax concave penalty (MCP) method for variable selection. The CV-AUC criterion is specifically designed for optimizing the classification performance for binary outcome data. To implement the proposed approach, we derive an efficient coordinate descent algorithm to compute the MCP-logistic regression solution surface. Simulation studies are conducted to evaluate the finite sample performance of the proposed method and its comparison with the existing methods including the Akaike information criterion (AIC), Bayesian information criterion (BIC) or Extended BIC (EBIC). The model selected based on the CV-AUC criterion tends to have a larger predictive AUC and smaller classification error than those with tuning parameters selected using the AIC, BIC or EBIC. We illustrate the application of the MCP-logistic regression with the CV-AUC criterion on three microarray datasets from the studies that attempt to identify genes related to cancers. Our simulation studies and data examples demonstrate that the CV-AUC is an attractive method for tuning parameter selection for penalized methods in high-dimensional logistic regression models.

Fiber-optic microarray for simultaneous detection of multiple harmful algal bloom species.

PubMed

Ahn, Soohyoun; Kulis, David M; Erdner, Deana L; Anderson, Donald M; Walt, David R

2006-09-01

Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alexandrium fundyense, Alexandrium ostenfeldii, and Pseudo-nitzschia australis. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 mum) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

PubMed

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.

Open-target sparse sensing of biological agents using DNA microarray

PubMed Central

2011-01-01

Background Current biosensors are designed to target and react to specific nucleic acid sequences or structural epitopes. These 'target-specific' platforms require creation of new physical capture reagents when new organisms are targeted. An 'open-target' approach to DNA microarray biosensing is proposed and substantiated using laboratory generated data. The microarray consisted of 12,900 25 bp oligonucleotide capture probes derived from a statistical model trained on randomly selected genomic segments of pathogenic prokaryotic organisms. Open-target detection of organisms was accomplished using a reference library of hybridization patterns for three test organisms whose DNA sequences were not included in the design of the microarray probes. Results A multivariate mathematical model based on the partial least squares regression (PLSR) was developed to detect the presence of three test organisms in mixed samples. When all 12,900 probes were used, the model correctly detected the signature of three test organisms in all mixed samples (mean(R2)) = 0.76, CI = 0.95), with a 6% false positive rate. A sampling algorithm was then developed to sparsely sample the probe space for a minimal number of probes required to capture the hybridization imprints of the test organisms. The PLSR detection model was capable of correctly identifying the presence of the three test organisms in all mixed samples using only 47 probes (mean(R2)) = 0.77, CI = 0.95) with nearly 100% specificity. Conclusions We conceived an 'open-target' approach to biosensing, and hypothesized that a relatively small, non-specifically designed, DNA microarray is capable of identifying the presence of multiple organisms in mixed samples. Coupled with a mathematical model applied to laboratory generated data, and sparse sampling of capture probes, the prototype microarray platform was able to capture the signature of each organism in all mixed samples with high sensitivity and specificity. It was demonstrated that this new approach to biosensing closely follows the principles of sparse sensing. PMID:21801424

MiMiR – an integrated platform for microarray data sharing, mining and analysis

PubMed Central

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-01-01

Background Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. Results A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. Conclusion The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies. PMID:18801157

MiMiR--an integrated platform for microarray data sharing, mining and analysis.

PubMed

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-09-18

Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

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

PubMed Central

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

2008-01-01

Background A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the "curse-of-dimension" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create "intelligent" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. Results To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers (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

Digital Technology in the protection of cultural heritage Bao Fan Temple mural digital mapping survey

NASA Astrophysics Data System (ADS)

Zheng, Y.

2015-08-01

Peng Xi county, Sichuan province, the Bao Fan temple mural digitization survey mapping project: we use three-dimensional laserscanning, multi-baseline definition digital photography, multi-spectral digital image acquisition and other technologies for digital survey mapping. The purpose of this project is to use modern mathematical reconnaissance mapping means to obtain accurate mural shape, color, quality and other data. Combined with field investigation and laboratory analysis results, and based on a comprehensive survey and study, a comprehensive analysis of the historical Bao Fan Temple mural artistic and scientific value was conducted. A study of the mural's many qualities (structural, material, technique, preservation environment, degradation, etc.) reveal all aspects of the information carried by the Bao Fan Temple mural. From multiple angles (archeology, architecture, surveying, conservation science and other disciplines) an assessment for the Bao Fan Temple mural provides basic data and recommendations for conservation of the mural. In order to achieve the conservation of cultural relics in the Bao Fan Temple mural digitization survey mapping process, we try to apply the advantages of three-dimensional laser scanning equipment. For wall murals this means obtaining three-dimensional scale data from the scan of the building and through the analysis of these data to help determine the overall condition of the settlement as well as the deformation of the wall structure. Survey analysis provides an effective set of conclusions and suggestions for appropriate mural conservation. But before data collection, analysis and research need to first to select the appropriate scanning equipment, set the appropriate scanning accuracy and layout position of stations necessary to determine the scope of required data. We use the fine features of the three-dimensional laser scanning measuring arm to scan the mural surface deformation degradation to reflect the actual state of the mural surface patch model. For the degradation of the surface of the pigment layer, we use the patch model to simulate the scan obtained from an analysis. Statistics calculated relatively objective mural surface area from volume data, providing more accurate quantitative data for the mural conservation, especially, providing a viable technology for accurate monitoring of continued degradation. We believe, in order to make use of the three-dimensional laser scanning technology in a digital heritage conservation application, the technology should not only be used to record the object geometry and play a role in record keeping aspects, but, rather, should be used during the investigation to protect against targeted degradation and a more meaningful interpretation function. Like the development of the medical application of X-ray technology not only retains a picture, but more importantly, through this technical interpretation of patient pathology, guides doctors in carrying out the treatment work. Therefore, in the process of digitization of cultural heritage research, the focus should shift to the use of digital technology in the analysis of heritage object degradation and degradation monitoring surveys can promote the application of digital technology in the conservation of cultural heritage.

How Technique Is Changing Science.

ERIC Educational Resources Information Center

Hall, Stephen

1992-01-01

The author describes specific examples of the use of technology in science such as fiberoptic spectroscopy to observe galaxies and conduct three-dimensional maps of the universe. Adduces the following examples of technology influencing scientific investigations: gene cloning, gene sequencing, radioimmunoassays, patch-clamping of neurons, scanning…

Design and Fabrication of a Miniaturized GMI Magnetic Sensor Based on Amorphous Wire by MEMS Technology

PubMed Central

Chen, Jiawen; Li, Jianhua; Li, Yiyuan; Chen, Yulong

2018-01-01

A miniaturized Co-based amorphous wire GMI (Giant magneto-impedance) magnetic sensor was designed and fabricated in this paper. The Co-based amorphous wire was used as the sense element due to its high sensitivity to the magnetic field. A three-dimensional micro coil surrounding the Co-based amorphous wire was fabricated by MEMS (Micro-Electro-Mechanical System) technology, which was used to extract the electrical signal. The three-dimensional micro pick-up coil was designed and simulated with HFSS (High Frequency Structure Simulator) software to determine the key parameters. Surface micro machining MEMS (Micro-Electro-Mechanical System) technology was employed to fabricate the three-dimensional coil. The size of the developed amorphous wire magnetic sensor is 5.6 × 1.5 × 1.1 mm3. Helmholtz coil was used to characterize the performance of the device. The test results of the sensor sample show that the voltage change is 130 mV/Oe and the linearity error is 4.83% in the range of 0~45,000 nT. The results indicate that the developed miniaturized magnetic sensor has high sensitivity. By testing the electrical resistance of the samples, the results also showed high uniformity of each device. PMID:29494477

Three-dimensional bioprinting in tissue engineering and regenerative medicine.

PubMed

Gao, Guifang; Cui, Xiaofeng

2016-02-01

With the advances of stem cell research, development of intelligent biomaterials and three-dimensional biofabrication strategies, highly mimicked tissue or organs can be engineered. Among all the biofabrication approaches, bioprinting based on inkjet printing technology has the promises to deliver and create biomimicked tissue with high throughput, digital control, and the capacity of single cell manipulation. Therefore, this enabling technology has great potential in regenerative medicine and translational applications. The most current advances in organ and tissue bioprinting based on the thermal inkjet printing technology are described in this review, including vasculature, muscle, cartilage, and bone. In addition, the benign side effect of bioprinting to the printed mammalian cells can be utilized for gene or drug delivery, which can be achieved conveniently during precise cell placement for tissue construction. With layer-by-layer assembly, three-dimensional tissues with complex structures can be printed using converted medical images. Therefore, bioprinting based on thermal inkjet is so far the most optimal solution to engineer vascular system to the thick and complex tissues. Collectively, bioprinting has great potential and broad applications in tissue engineering and regenerative medicine. The future advances of bioprinting include the integration of different printing mechanisms to engineer biphasic or triphasic tissues with optimized scaffolds and further understanding of stem cell biology.

Hybrid feature selection algorithm using symmetrical uncertainty and a harmony search algorithm

NASA Astrophysics Data System (ADS)

Salameh Shreem, Salam; Abdullah, Salwani; Nazri, Mohd Zakree Ahmad

2016-04-01

Microarray technology can be used as an efficient diagnostic system to recognise diseases such as tumours or to discriminate between different types of cancers in normal tissues. This technology has received increasing attention from the bioinformatics community because of its potential in designing powerful decision-making tools for cancer diagnosis. However, the presence of thousands or tens of thousands of genes affects the predictive accuracy of this technology from the perspective of classification. Thus, a key issue in microarray data is identifying or selecting the smallest possible set of genes from the input data that can achieve good predictive accuracy for classification. In this work, we propose a two-stage selection algorithm for gene selection problems in microarray data-sets called the symmetrical uncertainty filter and harmony search algorithm wrapper (SU-HSA). Experimental results show that the SU-HSA is better than HSA in isolation for all data-sets in terms of the accuracy and achieves a lower number of genes on 6 out of 10 instances. Furthermore, the comparison with state-of-the-art methods shows that our proposed approach is able to obtain 5 (out of 10) new best results in terms of the number of selected genes and competitive results in terms of the classification accuracy.

Screening for Intellectual Disability Using High-Resolution CMA Technology in a Retrospective Cohort from Central Brazil

PubMed Central

Pereira, Rodrigo Roncato; Pinto, Irene Plaza; Minasi, Lysa Bernardes; de Melo, Aldaires Vieira; da Cruz e Cunha, Damiana Mirian; Cruz, Alex Silva; Ribeiro, Cristiano Luiz; da Silva, Cláudio Carlos; de Melo e Silva, Daniela; da Cruz, Aparecido Divino

2014-01-01

Intellectual disability is a complex, variable, and heterogeneous disorder, representing a disabling condition diagnosed worldwide, and the etiologies are multiple and highly heterogeneous. Microscopic chromosomal abnormalities and well-characterized genetic conditions are the most common causes of intellectual disability. Chromosomal Microarray Analysis analyses have made it possible to identify putatively pathogenic copy number variation that could explain the molecular etiology of intellectual disability. The aim of the current study was to identify possible submicroscopic genomic alterations using a high-density chromosomal microarray in a retrospective cohort of patients with otherwise undiagnosable intellectual disabilities referred by doctors from the public health system in Central Brazil. The CytoScan HD technology was used to detect changes in the genome copy number variation of patients who had intellectual disability and a normal karyotype. The analysis detected 18 CNVs in 60% of patients. Pathogenic CNVs represented about 22%, so it was possible to propose the etiology of intellectual disability for these patients. Likely pathogenic and unknown clinical significance CNVs represented 28% and 50%, respectively. Inherited and de novo CNVs were equally distributed. We report the nature of CNVs in patients from Central Brazil, representing a population not yet screened by microarray technologies. PMID:25061755

Multi-factorial analysis of class prediction error: estimating optimal number of biomarkers for various classification rules.

PubMed

Khondoker, Mizanur R; Bachmann, Till T; Mewissen, Muriel; Dickinson, Paul; Dobrzelecki, Bartosz; Campbell, Colin J; Mount, Andrew R; Walton, Anthony J; Crain, Jason; Schulze, Holger; Giraud, Gerard; Ross, Alan J; Ciani, Ilenia; Ember, Stuart W J; Tlili, Chaker; Terry, Jonathan G; Grant, Eilidh; McDonnell, Nicola; Ghazal, Peter

2010-12-01

Machine learning and statistical model based classifiers have increasingly been used with more complex and high dimensional biological data obtained from high-throughput technologies. Understanding the impact of various factors associated with large and complex microarray datasets on the predictive performance of classifiers is computationally intensive, under investigated, yet vital in determining the optimal number of biomarkers for various classification purposes aimed towards improved detection, diagnosis, and therapeutic monitoring of diseases. We investigate the impact of microarray based data characteristics on the predictive performance for various classification rules using simulation studies. Our investigation using Random Forest, Support Vector Machines, Linear Discriminant Analysis and k-Nearest Neighbour shows that the predictive performance of classifiers is strongly influenced by training set size, biological and technical variability, replication, fold change and correlation between biomarkers. Optimal number of biomarkers for a classification problem should therefore be estimated taking account of the impact of all these factors. A database of average generalization errors is built for various combinations of these factors. The database of generalization errors can be used for estimating the optimal number of biomarkers for given levels of predictive accuracy as a function of these factors. Examples show that curves from actual biological data resemble that of simulated data with corresponding levels of data characteristics. An R package optBiomarker implementing the method is freely available for academic use from the Comprehensive R Archive Network (http://www.cran.r-project.org/web/packages/optBiomarker/).

[Typing and subtyping avian influenza virus using DNA microarrays].

PubMed

Yang, Zhongping; Wang, Xiurong; Tian, Lina; Wang, Yu; Chen, Hualan

2008-07-01

Outbreaks of highly pathogenic avian influenza (HPAI) virus has caused great economic loss to the poultry industry and resulted in human deaths in Thailand and Vietnam since 2004. Rapid typing and subtyping of viruses, especially HPAI from clinical specimens, are desirable for taking prompt control measures to prevent spreading of the disease. We described a simultaneous approach using microarray to detect and subtype avian influenza virus (AIV). We designed primers of probe genes and used reverse transcriptase PCR to prepare cDNAs of AIV M gene, H5, H7, H9 subtypes haemagglutinin genes and N1, N2 subtypes neuraminidase genes. They were cloned, sequenced, reamplified and spotted to form a glass-bound microarrays. We labeled samples using Cy3-dUTP by RT-PCR, hybridized and scanned the microarrays to typing and subtyping AIV. The hybridization pattern agreed perfectly with the known grid location of each probe, no cross hybridization could be detected. Examinating of HA subtypes 1 through 15, 30 infected samples and 21 field samples revealed the DNA microarray assay was more sensitive and specific than RT-PCR test and chicken embryo inoculation. It can simultaneously detect and differentiate the main epidemic AIV. The results show that DNA microarray technology is a useful diagnostic method.

Sequencing ebola and marburg viruses genomes using microarrays.

PubMed

Hardick, Justin; Woelfel, Roman; Gardner, Warren; Ibrahim, Sofi

2016-08-01

Periodic outbreaks of Ebola and Marburg hemorrhagic fevers have occurred in Africa over the past four decades with case fatality rates reaching as high as 90%. The latest Ebola outbreak in West Africa in 2014 raised concerns that these infections can spread across continents and pose serious health risks. Early and accurate identification of the causative agents is necessary to contain outbreaks. In this report, we describe sequencing-by-hybridization (SBH) technique using high density microarrays to identify Ebola and Marburg viruses. The microarrays were designed to interrogate the sequences of entire viral genomes, and were evaluated with three species of Ebolavirus (Reston, Sudan, and Zaire), and three strains of Marburgvirus (Angola, Musoke, and Ravn). The results showed that the consensus sequences generated with four or more hybridizations had 92.1-98.9% accuracy over 95-99% of the genomes. Additionally, with SBH microarrays it was possible to distinguish between different strains of the Lake Victoria Marburgvirus. J. Med. Virol. 88:1303-1308, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Polymer microarray technology for stem cell engineering

PubMed Central

Coyle, Robert; Jia, Jia; Mei, Ying

2015-01-01

Stem cells hold remarkable promise for applications in tissue engineering and disease modeling. During the past decade, significant progress has been made in developing soluble factors (e.g., small molecules and growth factors) to direct stem cells into a desired phenotype. However, the current lack of suitable synthetic materials to regulate stem cell activity has limited the realization of the enormous potential of stem cells. This can be attributed to a large number of materials properties (e.g., chemical structures and physical properties of materials) that can affect stem cell fate. This makes it challenging to design biomaterials to direct stem cell behavior. To address this, polymer microarray technology has been developed to rapidly identify materials for a variety of stem cell applications. In this article, we summarize recent developments in polymer array technology and their applications in stem cell engineering. Statement of significance Stem cells hold remarkable promise for applications in tissue engineering and disease modeling. In the last decade, significant progress has been made in developing chemically defined media to direct stem cells into a desired phenotype. However, the current lack of the suitable synthetic materials to regulate stem cell activities has been limiting the realization of the potential of stem cells. This can be attributed to the number of variables in material properties (e.g., chemical structures and physical properties) that can affect stem cells. Polymer microarray technology has shown to be a powerful tool to rapidly identify materials for a variety of stem cell applications. Here we summarize recent developments in polymer array technology and their applications in stem cell engineering. PMID:26497624

Cardiovascular Imaging and Image Processing: Theory and Practice - 1975

NASA Technical Reports Server (NTRS)

Harrison, Donald C. (Editor); Sandler, Harold (Editor); Miller, Harry A. (Editor); Hood, Manley J. (Editor); Purser, Paul E. (Editor); Schmidt, Gene (Editor)

1975-01-01

Ultrasonography was examined in regard to the developmental highlights and present applicatons of cardiac ultrasound. Doppler ultrasonic techniques and the technology of miniature acoustic element arrays were reported. X-ray angiography was discussed with special considerations on quantitative three dimensional dynamic imaging of structure and function of the cardiopulmonary and circulatory systems in all regions of the body. Nuclear cardiography and scintigraphy, three--dimensional imaging of the myocardium with isotopes, and the commercialization of the echocardioscope were studied.

High throughput gene expression profiling: a molecular approach to integrative physiology

PubMed Central

Liang, Mingyu; Cowley, Allen W; Greene, Andrew S

2004-01-01

Integrative physiology emphasizes the importance of understanding multiple pathways with overlapping, complementary, or opposing effects and their interactions in the context of intact organisms. The DNA microarray technology, the most commonly used method for high-throughput gene expression profiling, has been touted as an integrative tool that provides insights into regulatory pathways. However, the physiology community has been slow in acceptance of these techniques because of early failure in generating useful data and the lack of a cohesive theoretical framework in which experiments can be analysed. With recent advances in both technology and analysis, we propose a concept of multidimensional integration of physiology that incorporates data generated by DNA microarray and other functional, genomic, and proteomic approaches to achieve a truly integrative understanding of physiology. Analysis of several studies performed in simpler organisms or in mammalian model animals supports the feasibility of such multidimensional integration and demonstrates the power of DNA microarray as an indispensable molecular tool for such integration. Evaluation of DNA microarray techniques indicates that these techniques, despite limitations, have advanced to a point where the question-driven profiling research has become a feasible complement to the conventional, hypothesis-driven research. With a keen sense of homeostasis, global regulation, and quantitative analysis, integrative physiologists are uniquely positioned to apply these techniques to enhance the understanding of complex physiological functions. PMID:14678487

Microarray analysis of thyroid stimulating hormone, insulin-like growth factor-1, and insulin-induced gene expression in FRTL-5 thyroid cells.

PubMed

Lee, You Jin; Park, Do Joon; Shin, Chan Soo; Park, Kyong Soo; Kim, Seong Yeon; Lee, Hong Kyu; Park, Young Joo; Cho, Bo Youn

2007-10-01

To determine which genes are regulated by thyroid stimulating hormone (thyrotropin, TSH), insulin and insulin-like growth factor-1 (IGF-1) in the rat thyroid, we used the microarray technology and observed the changes in gene expression. The expressions of genes for bone morphogenetic protein 6, the glucagon receptor, and cyclin D1 were increased by both TSH and IGF-1; for cytochrome P450, 2c37, the expression was decreased by both. Genes for cholecystokinin, glucuronidase, beta, demethyl-Q 7, and cytochrome c oxidase, subunit VIIIa, were up-regulated; the genes for ribosomal protein L37 and ribosomal protein L4 were down-regulated by TSH and insulin. However, there was no gene observed to be regulated by all three: TSH, IGF-1, and insulin molecules studied. These findings suggest that TSH, IGF-1, and insulin stimulate different signal pathways, which can interact with one another to regulate the proliferation of thyrocytes, and thereby provide additional influence on the process of cellular proliferation.

Microarray Analysis of Thyroid Stimulating Hormone, Insulin-Like Growth Factor-1, and Insulin-Induced Gene Expression in FRTL-5 Thyroid Cells

PubMed Central

Lee, You Jin; Park, Do Joon; Shin, Chan Soo; Park, Kyong Soo; Kim, Seong Yeon; Lee, Hong Kyu; Cho, Bo Youn

2007-01-01

To determine which genes are regulated by thyroid stimulating hormone (thyrotropin, TSH), insulin and insulin-like growth factor-1 (IGF-1) in the rat thyroid, we used the microarray technology and observed the changes in gene expression. The expressions of genes for bone morphogenetic protein 6, the glucagon receptor, and cyclin D1 were increased by both TSH and IGF-1; for cytochrome P450, 2c37, the expression was decreased by both. Genes for cholecystokinin, glucuronidase, beta, demethyl-Q 7, and cytochrome c oxidase, subunit VIIIa, were up-regulated; the genes for ribosomal protein L37 and ribosomal protein L4 were down-regulated by TSH and insulin. However, there was no gene observed to be regulated by all three: TSH, IGF-1, and insulin molecules studied. These findings suggest that TSH, IGF-1, and insulin stimulate different signal pathways, which can interact with one another to regulate the proliferation of thyrocytes, and thereby provide additional influence on the process of cellular proliferation. PMID:17982240

Three-dimensional printing in surgery: a review of current surgical applications.

PubMed

Malik, Hammad H; Darwood, Alastair R J; Shaunak, Shalin; Kulatilake, Priyantha; El-Hilly, Abdulrahman A; Mulki, Omar; Baskaradas, Aroon

2015-12-01

Three-dimensional printing (3DP) is gaining increasing recognition as a technique that will transform the landscape of surgical practice. It allows for the rapid conversion of anatomic images into physical objects, which are being used across a variety of surgical specialties. It has been unclear which groups are leading the way in coming up with novel ways of using the technology and what specifically the technology is being used for. The aim of this article was to review the current applications of 3DP in modern surgical practice. An electronic search was carried out in MEDLINE, EMBASE, and PsycINFO for terms related to 3DP. These were then screened for relevance and practical applications of the technology in surgery. Four hundred eighty-eight articles were initially found, and these were eventually narrowed down to 93 full-text articles. It was determined that there were three main areas in which the technology is being used to print: (1) anatomic models, (2) surgical instruments, and (3) implants and prostheses. Different specialties are at different stages in the use of the technology. The costs involved with implementing the technology and time taken for printing are important factors to consider before widespread use. For the foreseeable future, this is an exciting and interesting technology with the capacity to radically change health care and revolutionize modern surgery. Copyright © 2015 Elsevier Inc. All rights reserved.

[RESEARCH PROGRESS OF THREE-DIMENSIONAL PRINTING TECHNIQUE FOR SPINAL IMPLANTS].

PubMed

Lu, Qi; Yu, Binsheng

2016-09-08

To summarize the current research progress of three-dimensional (3D) printing technique for spinal implants manufacture. The recent original literature concerning technology, materials, process, clinical applications, and development direction of 3D printing technique in spinal implants was reviewed and analyzed. At present, 3D printing technologies used to manufacture spinal implants include selective laser sintering, selective laser melting, and electron beam melting. Titanium and its alloys are mainly used. 3D printing spinal implants manufactured by the above materials and technology have been successfully used in clinical. But the problems regarding safety, related complications, cost-benefit analysis, efficacy compared with traditional spinal implants, and the lack of relevant policies and regulations remain to be solved. 3D printing technique is able to provide individual and customized spinal implants for patients, which is helpful for the clinicians to perform operations much more accurately and safely. With the rapid development of 3D printing technology and new materials, more and more 3D printing spinal implants will be developed and used clinically.

Three-Dimensional Modeling May Improve Surgical Education and Clinical Practice.

PubMed

Jones, Daniel B; Sung, Robert; Weinberg, Crispin; Korelitz, Theodore; Andrews, Robert

2016-04-01

Three-dimensional (3D) printing has been used in the manufacturing industry for rapid prototyping and product testing. The aim of our study was to assess the feasibility of creating anatomical 3D models from a digital image using 3D printers. Furthermore, we sought face validity of models and explored potential opportunities for using 3D printing to enhance surgical education and clinical practice. Computed tomography and magnetic resonance images were reviewed, converted to computer models, and printed by stereolithography to create near exact replicas of human organs. Medical students and surgeons provided feedback via survey at the 2014 Surgical Education Week conference. There were 51 respondents, and 95.8% wanted these models for their patients. Cost was a concern, but 82.6% found value in these models at a price less than $500. All respondents thought the models would be useful for integration into the medical school curriculum. Three-dimensional printing is a potentially disruptive technology to improve both surgical education and clinical practice. As the technology matures and cost decreases, we envision 3D models being increasingly used in surgery. © The Author(s) 2015.

Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lambros, Maria Polikandritou, E-mail: mlambros@westernu.edu; Parsa, Cyrus; Mulamalla, HariChandana

2011-02-04

Research highlights: {yields} We irradiated a 3-D human oral cell culture of keratinocytes and fibroblasts with 12 and 2 Gy. {yields} 6 h after irradiation the histopathology and apoptosis of the 3-D culture were evaluated. Microarrays were used to assess the gene expression in the irradiated 3-D tissue. {yields} 12 Gy induced significant histopathologic changes and cellular apoptosis. {yields} 12 Gy significantly affected genes of the NF-kB pathway, inflammatory cytokines and DAMPs. -- Abstract: Mucositis is a debilitating adverse effect of chemotherapy and radiation treatment. It is important to develop a simple and reliable in vitro model, which can routinelymore » be used to screen new drugs for prevention and treatment of mucositis. Furthermore, identifying cell and molecular stresses especially in the initiation phase of mucositis in this model will help towards this end. We evaluated a three-dimensional (3-D) human oral cell culture that consisted of oral keratinocytes and fibroblasts as a model of oral mucositis. The 3-D cell culture model was irradiated with 12 or 2 Gy. Six hours after the irradiation we evaluated microscopic sections of the cell culture for evidence of morphologic changes including apoptosis. We used microarrays to compare the expression of several genes from the irradiated tissue with identical genes from tissue that was not irradiated. We found that irradiation with 12 Gy induced significant histopathologic effects including cellular apoptosis. Irradiation significantly affected the expression of several genes of the NF-kB pathway and several inflammatory cytokines, such as IL-1B, 1L-8, NF-kB1, and FOS compared to tissue that was not irradiated. We identified significant upregulation of several genes that belong to damage-associated molecular patterns (DAMPs) such as HMB1, S100A13, SA10014, and SA10016 in the 3-D tissues that received 12 Gy but not in tissues that received 2 Gy. In conclusion, this model quantifies radiation damage and this is an important first step towards the development 3-D tissue as a screening tool.« less

Conceptual Systems Model as a Tool for Hypothesis Generation and Testing in Ecotoxicological Research

EPA Science Inventory

Microarray, proteomic, and metabonomic technologies are becoming increasingly accessible as tools for ecotoxicology research. Effective use of these technologies will depend, at least in part, on the ability to apply these techniques within a paradigm of hypothesis driven researc...

Novel Three-Dimensional Vertical Interconnect Technology for Microwave and RF Applications

NASA Technical Reports Server (NTRS)

Goverdhanam, Kavita; Simons, Rainee N.; Katehi, Linda P. B.

1999-01-01

In this paper, novel 3D interconnects suitable for applications in microwave and RF integrated circuit technology have been presented. The interconnect fabrication process and design details are presented. In addition, measured and numerically modeled results of the performance of the interconnects have been shown. The results indicate that the proposed technology has tremendous potential applications in integrated circuit technology. C,

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

PubMed Central

Harrison, Andrew; Binder, Hans; Buhot, Arnaud; Burden, Conrad J.; Carlon, Enrico; Gibas, Cynthia; Gamble, Lara J.; Halperin, Avraham; Hooyberghs, Jef; Kreil, David P.; Levicky, Rastislav; Noble, Peter A.; Ott, Albrecht; Pettitt, B. Montgomery; Tautz, Diethard; Pozhitkov, Alexander E.

2013-01-01

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized. PMID:23307556

[Microarray CGH: principle and use for constitutional disorders].

PubMed

Sanlaville, D; Lapierre, J M; Coquin, A; Turleau, C; Vermeesch, J; Colleaux, L; Borck, G; Vekemans, M; Aurias, A; Romana, S P

2005-10-01

Chips technology has allowed to miniaturize process making possible to realize in one step and using the same device a lot of chemical reactions. The application of this technology to molecular cytogenetics resulted in the development of comparative genomic hybridization (CGH) on microarrays technique. Using this technique it is possible to detect very small genetic imbalances anywhere in the genome. Its usefulness has been well documented in cancer and more recently in constitutional disorders. In particular it has been used to detect interstitial and subtelomeric submicroscopic imbalances, to characterize their size at the molecular level or to define the breakpoints of translocation. The challenge today is to transfer this technology in laboratory medicine. Nevertheless this technology remains expensive and the existence of numerous sequence polymorphisms makes its interpretation difficult. Finally its is unlikely that it will make karyotyping obsolete as it does not allow to detect balanced rearrangements which after meiotic segregation might result in genome imbalance in the progeny.

Cellular neural networks, the Navier-Stokes equation, and microarray image reconstruction.

PubMed

Zineddin, Bachar; Wang, Zidong; Liu, Xiaohui

2011-11-01

Although the last decade has witnessed a great deal of improvements achieved for the microarray technology, many major developments in all the main stages of this technology, including image processing, are still needed. Some hardware implementations of microarray image processing have been proposed in the literature and proved to be promising alternatives to the currently available software systems. However, the main drawback of those proposed approaches is the unsuitable addressing of the quantification of the gene spot in a realistic way without any assumption about the image surface. Our aim in this paper is to present a new image-reconstruction algorithm using the cellular neural network that solves the Navier-Stokes equation. This algorithm offers a robust method for estimating the background signal within the gene-spot region. The MATCNN toolbox for Matlab is used to test the proposed method. Quantitative comparisons are carried out, i.e., in terms of objective criteria, between our approach and some other available methods. It is shown that the proposed algorithm gives highly accurate and realistic measurements in a fully automated manner within a remarkably efficient time.

Removing technical variability in RNA-seq data using conditional quantile normalization.

PubMed

Hansen, Kasper D; Irizarry, Rafael A; Wu, Zhijin

2012-04-01

The ability to measure gene expression on a genome-wide scale is one of the most promising accomplishments in molecular biology. Microarrays, the technology that first permitted this, were riddled with problems due to unwanted sources of variability. Many of these problems are now mitigated, after a decade's worth of statistical methodology development. The recently developed RNA sequencing (RNA-seq) technology has generated much excitement in part due to claims of reduced variability in comparison to microarrays. However, we show that RNA-seq data demonstrate unwanted and obscuring variability similar to what was first observed in microarrays. In particular, we find guanine-cytosine content (GC-content) has a strong sample-specific effect on gene expression measurements that, if left uncorrected, leads to false positives in downstream results. We also report on commonly observed data distortions that demonstrate the need for data normalization. Here, we describe a statistical methodology that improves precision by 42% without loss of accuracy. Our resulting conditional quantile normalization algorithm combines robust generalized regression to remove systematic bias introduced by deterministic features such as GC-content and quantile normalization to correct for global distortions.

Epigenomics

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Cloning

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Chromosomes

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Transcriptome

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Multiplexed Analysis of Serum Breast and Ovarian Cancer Markers by Means of Suspension Bead-quantum Dot Microarrays

NASA Astrophysics Data System (ADS)

Brazhnik, Kristina; Sokolova, Zinaida; Baryshnikova, Maria; Bilan, Regina; Nabiev, Igor; Sukhanova, Alyona

Multiplexed analysis of cancer markers is crucial for early tumor diagnosis and screening. We have designed lab-on-a-bead microarray for quantitative detection of three breast cancer markers in human serum. Quantum dots were used as bead-bound fluorescent tags for identifying each marker by means of flow cytometry. Antigen-specific beads reliably detected CA 15-3, CEA, and CA 125 in serum samples, providing clear discrimination between the samples with respect to the antigen levels. The novel microarray is advantageous over the routine single-analyte ones due to the simultaneous detection of various markers. Therefore the developed microarray is a promising tool for serum tumor marker profiling.

Genomic paradigms for food-borne enteric pathogen analysis at the USFDA: case studies highlighting method utility, integration and resolution.

PubMed

Elkins, C A; Kotewicz, M L; Jackson, S A; Lacher, D W; Abu-Ali, G S; Patel, I R

2013-01-01

Modern risk control and food safety practices involving food-borne bacterial pathogens are benefiting from new genomic technologies for rapid, yet highly specific, strain characterisations. Within the United States Food and Drug Administration (USFDA) Center for Food Safety and Applied Nutrition (CFSAN), optical genome mapping and DNA microarray genotyping have been used for several years to quickly assess genomic architecture and gene content, respectively, for outbreak strain subtyping and to enhance retrospective trace-back analyses. The application and relative utility of each method varies with outbreak scenario and the suspect pathogen, with comparative analytical power enhanced by database scale and depth. Integration of these two technologies allows high-resolution scrutiny of the genomic landscapes of enteric food-borne pathogens with notable examples including Shiga toxin-producing Escherichia coli (STEC) and Salmonella enterica serovars from a variety of food commodities. Moreover, the recent application of whole genome sequencing technologies to food-borne pathogen outbreaks and surveillance has enhanced resolution to the single nucleotide scale. This new wealth of sequence data will support more refined next-generation custom microarray designs, targeted re-sequencing and "genomic signature recognition" approaches involving a combination of genes and single nucleotide polymorphism detection to distil strain-specific fingerprinting to a minimised scale. This paper examines the utility of microarrays and optical mapping in analysing outbreaks, reviews best practices and the limits of these technologies for pathogen differentiation, and it considers future integration with whole genome sequencing efforts.

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

PubMed Central

Ryan, Michael C; Zeeberg, Barry R; Caplen, Natasha J; Cleland, James A; Kahn, Ari B; Liu, Hongfang; Weinstein, John N

2008-01-01

Background Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays. For example, RT-PCR validation of gene expression microarray results may be unsuccessful if the two technologies target different splice variants. Effective use of sequence-based technologies requires knowledge of the specific splice variant(s) that are targeted. In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant. Results A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript. Conclusion SpliceCenter provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists. PMID:18638396

Three-Dimensional Images For Robot Vision

NASA Astrophysics Data System (ADS)

McFarland, William D.

1983-12-01

Robots are attracting increased attention in the industrial productivity crisis. As one significant approach for this nation to maintain technological leadership, the need for robot vision has become critical. The "blind" robot, while occupying an economical niche at present is severely limited and job specific, being only one step up from the numerical controlled machines. To successfully satisfy robot vision requirements a three dimensional representation of a real scene must be provided. Several image acquistion techniques are discussed with more emphasis on the laser radar type instruments. The autonomous vehicle is also discussed as a robot form, and the requirements for these applications are considered. The total computer vision system requirement is reviewed with some discussion of the major techniques in the literature for three dimensional scene analysis.

Clinical application of three-dimensional printing technology in craniofacial plastic surgery.

PubMed

Choi, Jong Woo; Kim, Namkug

2015-05-01

Three-dimensional (3D) printing has been particularly widely adopted in medical fields. Application of the 3D printing technique has even been extended to bio-cell printing for 3D tissue/organ development, the creation of scaffolds for tissue engineering, and actual clinical application for various medical parts. Of various medical fields, craniofacial plastic surgery is one of areas that pioneered the use of the 3D printing concept. Rapid prototype technology was introduced in the 1990s to medicine via computer-aided design, computer-aided manufacturing. To investigate the current status of 3D printing technology and its clinical application, a systematic review of the literature was conducted. In addition, the benefits and possibilities of the clinical application of 3D printing in craniofacial surgery are reviewed, based on personal experiences with more than 500 craniofacial cases conducted using 3D printing tactile prototype models.

A Review of Current Clinical Applications of Three-Dimensional Printing in Spine Surgery

PubMed Central

Job, Alan Varkey; Chen, Jing; Baek, Jung Hwan

2018-01-01

Three-dimensional (3D) printing is a transformative technology with a potentially wide range of applications in the field of orthopaedic spine surgery. This article aims to review the current applications, limitations, and future developments of 3D printing technology in orthopaedic spine surgery. Current preoperative applications of 3D printing include construction of complex 3D anatomic models for improved visual understanding, preoperative surgical planning, and surgical simulations for resident education. Intraoperatively, 3D printers have been successfully used in surgical guidance systems and in the creation of patient specific implantable devices. Furthermore, 3D printing is revolutionizing the field of regenerative medicine and tissue engineering, allowing construction of biocompatible scaffolds suitable for cell growth and vasculature. Advances in printing technology and evidence of positive clinical outcomes are needed before there is an expansion of 3D printing applied to the clinical setting. PMID:29503698

A Review of Current Clinical Applications of Three-Dimensional Printing in Spine Surgery.

PubMed

Cho, Woojin; Job, Alan Varkey; Chen, Jing; Baek, Jung Hwan

2018-02-01

Three-dimensional (3D) printing is a transformative technology with a potentially wide range of applications in the field of orthopaedic spine surgery. This article aims to review the current applications, limitations, and future developments of 3D printing technology in orthopaedic spine surgery. Current preoperative applications of 3D printing include construction of complex 3D anatomic models for improved visual understanding, preoperative surgical planning, and surgical simulations for resident education. Intraoperatively, 3D printers have been successfully used in surgical guidance systems and in the creation of patient specific implantable devices. Furthermore, 3D printing is revolutionizing the field of regenerative medicine and tissue engineering, allowing construction of biocompatible scaffolds suitable for cell growth and vasculature. Advances in printing technology and evidence of positive clinical outcomes are needed before there is an expansion of 3D printing applied to the clinical setting.

Clinical Application of Three-Dimensional Printing Technology in Craniofacial Plastic Surgery

PubMed Central

Kim, Namkug

2015-01-01

Three-dimensional (3D) printing has been particularly widely adopted in medical fields. Application of the 3D printing technique has even been extended to bio-cell printing for 3D tissue/organ development, the creation of scaffolds for tissue engineering, and actual clinical application for various medical parts. Of various medical fields, craniofacial plastic surgery is one of areas that pioneered the use of the 3D printing concept. Rapid prototype technology was introduced in the 1990s to medicine via computer-aided design, computer-aided manufacturing. To investigate the current status of 3D printing technology and its clinical application, a systematic review of the literature was conducted. In addition, the benefits and possibilities of the clinical application of 3D printing in craniofacial surgery are reviewed, based on personal experiences with more than 500 craniofacial cases conducted using 3D printing tactile prototype models. PMID:26015880

On-Chip, Amplification-Free Quantification of Nucleic Acid for Point-of-Care Diagnosis

NASA Astrophysics Data System (ADS)

Yen, Tony Minghung

This dissertation demonstrates three physical device concepts to overcome limitations in point-of-care quantification of nucleic acids. Enabling sensitive, high throughput nucleic acid quantification on a chip, outside of hospital and centralized laboratory setting, is crucial for improving pathogen detection and cancer diagnosis and prognosis. Among existing platforms, microarray have the advantages of being amplification free, low instrument cost, and high throughput, but are generally less sensitive compared to sequencing and PCR assays. To bridge this performance gap, this dissertation presents theoretical and experimental progress to develop a platform nucleic acid quantification technology that is drastically more sensitive than current microarrays while compatible with microarray architecture. The first device concept explores on-chip nucleic acid enrichment by natural evaporation of nucleic acid solution droplet. Using a micro-patterned super-hydrophobic black silicon array device, evaporative enrichment is coupled with nano-liter droplet self-assembly workflow to produce a 50 aM concentration sensitivity, 6 orders of dynamic range, and rapid hybridization time at under 5 minutes. The second device concept focuses on improving target copy number sensitivity, instead of concentration sensitivity. A comprehensive microarray physical model taking into account of molecular transport, electrostatic intermolecular interactions, and reaction kinetics is considered to guide device optimization. Device pattern size and target copy number are optimized based on model prediction to achieve maximal hybridization efficiency. At a 100-mum pattern size, a quantum leap in detection limit of 570 copies is achieved using black silicon array device with self-assembled pico-liter droplet workflow. Despite its merits, evaporative enrichment on black silicon device suffers from coffee-ring effect at 100-mum pattern size, and thus not compatible with clinical patient samples. The third device concept utilizes an integrated optomechanical laser system and a Cytop microarray device to reverse coffee-ring effect during evaporative enrichment at 100-mum pattern size. This method, named "laser-induced differential evaporation" is expected to enable 570 copies detection limit for clinical samples in near future. While the work is ongoing as of the writing of this dissertation, a clear research plan is in place to implement this method on microarray platform toward clinical sample testing for disease applications and future commercialization.

An Interactive Augmented Reality Implementation of Hijaiyah Alphabet for Children Education

NASA Astrophysics Data System (ADS)

Rahmat, R. F.; Akbar, F.; Syahputra, M. F.; Budiman, M. A.; Hizriadi, A.

2018-03-01

Hijaiyah alphabet is letters used in the Qur’an. An attractive and exciting learning process of Hijaiyah alphabet is necessary for the children. One of the alternatives to create attractive and interesting learning process of Hijaiyah alphabet is to develop it into a mobile application using augmented reality technology. Augmented reality is a technology that combines two-dimensional or three-dimensional virtual objects into actual three-dimensional circles and projects them in real time. The purpose of application aims to foster the children interest in learning Hijaiyah alphabet. This application is using Smartphone and marker as the medium. It was built using Unity and augmented reality library, namely Vuforia, then using Blender as the 3D object modeling software. The output generated from this research is the learning application of Hijaiyah letters using augmented reality. How to use it is as follows: first, place marker that has been registered and printed; second, the smartphone camera will track the marker. If the marker is invalid, the user should repeat the tracking process. If the marker is valid and identified, the marker will have projected the objects of Hijaiyah alphabet in three-dimensional form. Lastly, the user can learn and understand the shape and pronunciation of Hijaiyah alphabet by touching the virtual button on the marker

Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments

PubMed Central

2012-01-01

Background Because of the large volume of data and the intrinsic variation of data intensity observed in microarray experiments, different statistical methods have been used to systematically extract biological information and to quantify the associated uncertainty. The simplest method to identify differentially expressed genes is to evaluate the ratio of average intensities in two different conditions and consider all genes that differ by more than an arbitrary cut-off value to be differentially expressed. This filtering approach is not a statistical test and there is no associated value that can indicate the level of confidence in the designation of genes as differentially expressed or not differentially expressed. At the same time the fold change by itself provide valuable information and it is important to find unambiguous ways of using this information in expression data treatment. Results A new method of finding differentially expressed genes, called distributional fold change (DFC) test is introduced. The method is based on an analysis of the intensity distribution of all microarray probe sets mapped to a three dimensional feature space composed of average expression level, average difference of gene expression and total variance. The proposed method allows one to rank each feature based on the signal-to-noise ratio and to ascertain for each feature the confidence level and power for being differentially expressed. The performance of the new method was evaluated using the total and partial area under receiver operating curves and tested on 11 data sets from Gene Omnibus Database with independently verified differentially expressed genes and compared with the t-test and shrinkage t-test. Overall the DFC test performed the best – on average it had higher sensitivity and partial AUC and its elevation was most prominent in the low range of differentially expressed features, typical for formalin-fixed paraffin-embedded sample sets. Conclusions The distributional fold change test is an effective method for finding and ranking differentially expressed probesets on microarrays. The application of this test is advantageous to data sets using formalin-fixed paraffin-embedded samples or other systems where degradation effects diminish the applicability of correlation adjusted methods to the whole feature set. PMID:23122055

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

PubMed

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-Liss, Inc.

Genetic Mapping

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Biological Pathways

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

B-acute lymphoblastic leukemia and cystinuria in a patient with duplication 22q11.21 detected by chromosomal microarray analysis.

PubMed

Chang, Vivian Y; Quintero-Rivera, Fabiola; Baldwin, Erin E; Woo, Kathy; Martinez-Agosto, Julian A; Fu, Cecilia; Gomperts, Brigitte N

2011-03-01

Duplication 22q11.2 syndrome is the result of a microduplication of the same chromosomal region that is deleted in DiGeorge and Velocardiofacial syndromes. We describe a patient with dysmorphic features who was diagnosed with pre-B acute lymphoblastic leukemia, and developed cystinuria and pancreatitis during treatment. Duplication 22q11.2 has not been previously described in association with hematologic abnormalities. Chromosomal microarray technology was used to diagnose duplication 22q11.2 syndrome. In this era of advanced genomics, this technology has become an important method for helping to determine the molecular basis of diseases, best treatments and ultimately patient outcomes. Copyright © 2010 Wiley-Liss, Inc.

Joint mapping of genes and conditions via multidimensional unfolding analysis

PubMed Central

Van Deun, Katrijn; Marchal, Kathleen; Heiser, Willem J; Engelen, Kristof; Van Mechelen, Iven

2007-01-01

Background Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expression over profiles but also to gain information on more subtle relations between genes and conditions. Getting a clear visual overview of all these patterns in a single easy-to-grasp representation is a useful preliminary analysis step: We propose to use for this purpose an advanced exploratory method, called multidimensional unfolding. Results We present a novel algorithm for multidimensional unfolding that overcomes both general problems and problems that are specific for the analysis of gene expression data sets. Applying the algorithm to two publicly available microarray compendia illustrates its power as a tool for exploratory data analysis: The unfolding analysis of a first data set resulted in a two-dimensional representation which clearly reveals temporal regulation patterns for the genes and a meaningful structure for the time points, while the analysis of a second data set showed the algorithm's ability to go beyond a mere identification of those genes that discriminate between different patient or tissue types. Conclusion Multidimensional unfolding offers a useful tool for preliminary explorations of microarray data: By relying on an easy-to-grasp low-dimensional geometric framework, relations among genes, among conditions and between genes and conditions are simultaneously represented in an accessible way which may reveal interesting patterns in the data. An additional advantage of the method is that it can be applied to the raw data without necessitating the choice of suitable genewise transformations of the data. PMID:17550582

Karyotype versus microarray testing for genetic abnormalities after stillbirth.

PubMed

Reddy, Uma M; Page, Grier P; Saade, George R; Silver, Robert M; Thorsten, Vanessa R; Parker, Corette B; Pinar, Halit; Willinger, Marian; Stoll, Barbara J; Heim-Hall, Josefine; Varner, Michael W; Goldenberg, Robert L; Bukowski, Radek; Wapner, Ronald J; Drews-Botsch, Carolyn D; O'Brien, Barbara M; Dudley, Donald J; Levy, Brynn

2012-12-06

Genetic abnormalities have been associated with 6 to 13% of stillbirths, but the true prevalence may be higher. Unlike karyotype analysis, microarray analysis does not require live cells, and it detects small deletions and duplications called copy-number variants. The Stillbirth Collaborative Research Network conducted a population-based study of stillbirth in five geographic catchment areas. Standardized postmortem examinations and karyotype analyses were performed. A single-nucleotide polymorphism array was used to detect copy-number variants of at least 500 kb in placental or fetal tissue. Variants that were not identified in any of three databases of apparently unaffected persons were then classified into three groups: probably benign, clinical significance unknown, or pathogenic. We compared the results of karyotype and microarray analyses of samples obtained after delivery. In our analysis of samples from 532 stillbirths, microarray analysis yielded results more often than did karyotype analysis (87.4% vs. 70.5%, P<0.001) and provided better detection of genetic abnormalities (aneuploidy or pathogenic copy-number variants, 8.3% vs. 5.8%; P=0.007). Microarray analysis also identified more genetic abnormalities among 443 antepartum stillbirths (8.8% vs. 6.5%, P=0.02) and 67 stillbirths with congenital anomalies (29.9% vs. 19.4%, P=0.008). As compared with karyotype analysis, microarray analysis provided a relative increase in the diagnosis of genetic abnormalities of 41.9% in all stillbirths, 34.5% in antepartum stillbirths, and 53.8% in stillbirths with anomalies. Microarray analysis is more likely than karyotype analysis to provide a genetic diagnosis, primarily because of its success with nonviable tissue, and is especially valuable in analyses of stillbirths with congenital anomalies or in cases in which karyotype results cannot be obtained. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development.).

LITERATURE REVIEW OF MOLECULAR METHODS FOR SIMULTANEOUS DETECTION OF PATHOGENS IN WATER

EPA Science Inventory

This literature search is a review of molecular technologies (qPCR, microarray, microfluidics and lab-on-a-chip) for simultaneous detection of multiple waterborne pathogens in order to understand the state of the technology. The search content focuses on: pathogen detection witho...

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salloum, Maher; Robinson, David B.

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

DOE PAGES

Salloum, Maher; Robinson, David B.

2018-01-30

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

Gene features selection for three-class disease classification via multiple orthogonal partial least square discriminant analysis and S-plot using microarray data.

PubMed

Yang, Mingxing; Li, Xiumin; Li, Zhibin; Ou, Zhimin; Liu, Ming; Liu, Suhuan; Li, Xuejun; Yang, Shuyu

2013-01-01

DNA microarray analysis is characterized by obtaining a large number of gene variables from a small number of observations. Cluster analysis is widely used to analyze DNA microarray data to make classification and diagnosis of disease. Because there are so many irrelevant and insignificant genes in a dataset, a feature selection approach must be employed in data analysis. The performance of cluster analysis of this high-throughput data depends on whether the feature selection approach chooses the most relevant genes associated with disease classes. Here we proposed a new method using multiple Orthogonal Partial Least Squares-Discriminant Analysis (mOPLS-DA) models and S-plots to select the most relevant genes to conduct three-class disease classification and prediction. We tested our method using Golub's leukemia microarray data. For three classes with subtypes, we proposed hierarchical orthogonal partial least squares-discriminant analysis (OPLS-DA) models and S-plots to select features for two main classes and their subtypes. For three classes in parallel, we employed three OPLS-DA models and S-plots to choose marker genes for each class. The power of feature selection to classify and predict three-class disease was evaluated using cluster analysis. Further, the general performance of our method was tested using four public datasets and compared with those of four other feature selection methods. The results revealed that our method effectively selected the most relevant features for disease classification and prediction, and its performance was better than that of the other methods.

An Integral Method and Its Application to Some Three-Dimensional Boundary-Layer Flows,

DTIC Science & Technology

1979-07-18

M. Scala Dr. H. Lew Mr. J. W. Faust A . Martellucci W. Daskin J. D. Cresswell J. B. Arnaiz L. A . Marshall J. Cassanto R. Hobbs C. Harris F. George P.O...RESEARCH AND TECHNOLOGY DEPARTMENT 18 JULY 1979 Approved for public release, distribution unlimited DTICEILECTE1 APR 2 5 1930,, A NAVAL SURFACE WEAPONS...TITLE (end Subtlle) S. TYPE OF REPORT A PERIOD COVERED I INVTEGRAL M.ETHOD AND ITS 4PPLICATION TO SSOME THREE-DIMENSIONAL BOUNDARY-LAYER FLOWS 6

Three-dimensional quick response code based on inkjet printing of upconversion fluorescent nanoparticles for drug anti-counterfeiting.

PubMed

You, Minli; Lin, Min; Wang, Shurui; Wang, Xuemin; Zhang, Ge; Hong, Yuan; Dong, Yuqing; Jin, Guorui; Xu, Feng

2016-05-21

Medicine counterfeiting is a serious issue worldwide, involving potentially devastating health repercussions. Advanced anti-counterfeit technology for drugs has therefore aroused intensive interest. However, existing anti-counterfeit technologies are associated with drawbacks such as the high cost, complex fabrication process, sophisticated operation and incapability in authenticating drug ingredients. In this contribution, we developed a smart phone recognition based upconversion fluorescent three-dimensional (3D) quick response (QR) code for tracking and anti-counterfeiting of drugs. We firstly formulated three colored inks incorporating upconversion nanoparticles with RGB (i.e., red, green and blue) emission colors. Using a modified inkjet printer, we printed a series of colors by precisely regulating the overlap of these three inks. Meanwhile, we developed a multilayer printing and splitting technology, which significantly increases the information storage capacity per unit area. As an example, we directly printed the upconversion fluorescent 3D QR code on the surface of drug capsules. The 3D QR code consisted of three different color layers with each layer encoded by information of different aspects of the drug. A smart phone APP was designed to decode the multicolor 3D QR code, providing the authenticity and related information of drugs. The developed technology possesses merits in terms of low cost, ease of operation, high throughput and high information capacity, thus holds great potential for drug anti-counterfeiting.

Translating standards into practice - one Semantic Web API for Gene Expression.

PubMed

Deus, Helena F; Prud'hommeaux, Eric; Miller, Michael; Zhao, Jun; Malone, James; Adamusiak, Tomasz; McCusker, Jim; Das, Sudeshna; Rocca Serra, Philippe; Fox, Ronan; Marshall, M Scott

2012-08-01

Sharing and describing experimental results unambiguously with sufficient detail to enable replication of results is a fundamental tenet of scientific research. In today's cluttered world of "-omics" sciences, data standards and standardized use of terminologies and ontologies for biomedical informatics play an important role in reporting high-throughput experiment results in formats that can be interpreted by both researchers and analytical tools. Increasing adoption of Semantic Web and Linked Data technologies for the integration of heterogeneous and distributed health care and life sciences (HCLSs) datasets has made the reuse of standards even more pressing; dynamic semantic query federation can be used for integrative bioinformatics when ontologies and identifiers are reused across data instances. We present here a methodology to integrate the results and experimental context of three different representations of microarray-based transcriptomic experiments: the Gene Expression Atlas, the W3C BioRDF task force approach to reporting Provenance of Microarray Experiments, and the HSCI blood genomics project. Our approach does not attempt to improve the expressivity of existing standards for genomics but, instead, to enable integration of existing datasets published from microarray-based transcriptomic experiments. SPARQL Construct is used to create a posteriori mappings of concepts and properties and linking rules that match entities based on query constraints. We discuss how our integrative approach can encourage reuse of the Experimental Factor Ontology (EFO) and the Ontology for Biomedical Investigations (OBIs) for the reporting of experimental context and results of gene expression studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

PubMed Central

Carter, Mark G; Sharov, Alexei A; VanBuren, Vincent; Dudekula, Dawood B; Carmack, Condie E; Nelson, Charlie; Ko, Minoru SH

2005-01-01

The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of exogenous RNA controls derived from the yeast genome (made freely available without restriction), which allow quantitative estimation of absolute endogenous transcript abundance. PMID:15998450

New diagnostics for melanoma detection: from artificial intelligence to RNA microarrays.

PubMed

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.

Temperature Gradient Effect on Gas Discrimination Power of a Metal-Oxide Thin-Film Sensor Microarray

PubMed Central

Sysoev, Victor V.; Kiselev, Ilya; Frietsch, Markus; Goschnick, Joachim

2004-01-01

The paper presents results concerning the effect of spatial inhomogeneous operating temperature on the gas discrimination power of a gas-sensor microarray, with the latter based on a thin SnO2 film employed in the KAMINA electronic nose. Three different temperature distributions over the substrate are discussed: a nearly homogeneous one and two temperature gradients, equal to approx. 3.3 °C/mm and 6.7 °C/mm, applied across the sensor elements (segments) of the array. The gas discrimination power of the microarray is judged by using the Mahalanobis distance in the LDA (Linear Discrimination Analysis) coordinate system between the data clusters obtained by the response of the microarray to four target vapors: ethanol, acetone, propanol and ammonia. It is shown that the application of a temperature gradient increases the gas discrimination power of the microarray by up to 35 %.

Mouse fetal whole intestine culture system for ex vivo manipulation of signaling pathways and three-dimensional live imaging of villus development.

PubMed

Walton, Katherine D; Kolterud, Asa

2014-09-04

Most morphogenetic processes in the fetal intestine have been inferred from thin sections of fixed tissues, providing snapshots of changes over developmental stages. Three-dimensional information from thin serial sections can be challenging to interpret because of the difficulty of reconstructing serial sections perfectly and maintaining proper orientation of the tissue over serial sections. Recent findings by Grosse et al., 2011 highlight the importance of three- dimensional information in understanding morphogenesis of the developing villi of the intestine(1). Three-dimensional reconstruction of singly labeled intestinal cells demonstrated that the majority of the intestinal epithelial cells contact both the apical and basal surfaces. Furthermore, three-dimensional reconstruction of the actin cytoskeleton at the apical surface of the epithelium demonstrated that the intestinal lumen is continuous and that secondary lumens are an artifact of sectioning. Those two points, along with the demonstration of interkinetic nuclear migration in the intestinal epithelium, defined the developing intestinal epithelium as a pseudostratified epithelium and not stratified as previously thought(1). The ability to observe the epithelium three-dimensionally was seminal to demonstrating this point and redefining epithelial morphogenesis in the fetal intestine. With the evolution of multi-photon imaging technology and three-dimensional reconstruction software, the ability to visualize intact, developing organs is rapidly improving. Two-photon excitation allows less damaging penetration deeper into tissues with high resolution. Two-photon imaging and 3D reconstruction of the whole fetal mouse intestines in Walton et al., 2012 helped to define the pattern of villus outgrowth(2). Here we describe a whole organ culture system that allows ex vivo development of villi and extensions of that culture system to allow the intestines to be three-dimensionally imaged during their development.

Detection of Alicyclobacillus species in fruit juice using a random genomic DNA microarray chip.

PubMed

Jang, Jun Hyeong; Kim, Sun-Joong; Yoon, Bo Hyun; Ryu, Jee-Hoon; Gu, Man Bock; Chang, Hyo-Ihl

2011-06-01

This study describes a method using a DNA microarray chip to rapidly and simultaneously detect Alicyclobacillus species in orange juice based on the hybridization of genomic DNA with random probes. Three food spoilage bacteria were used in this study: Alicyclobacillus acidocaldarius, Alicyclobacillus acidoterrestris, and Alicyclobacillus cycloheptanicus. The three Alicyclobacillus species were adjusted to 2 × 10(3) CFU/ml and inoculated into pasteurized 100% pure orange juice. Cy5-dCTP labeling was used for reference signals, and Cy3-dCTP was labeled for target genomic DNA. The molar ratio of 1:1 of Cy3-dCTP and Cy5-dCTP was used. DNA microarray chips were fabricated using randomly fragmented DNA of Alicyclobacillus spp. and were hybridized with genomic DNA extracted from Bacillus spp. Genomic DNA extracted from Alicyclobacillus spp. showed a significantly higher hybridization rate compared with DNA of Bacillus spp., thereby distinguishing Alicyclobacillus spp. from Bacillus spp. The results showed that the microarray DNA chip containing randomly fragmented genomic DNA was specific and clearly identified specific food spoilage bacteria. This microarray system is a good tool for rapid and specific detection of thermophilic spoilage bacteria, mainly Alicyclobacillus spp., and is useful and applicable to the fruit juice industry.

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

PubMed Central

Barton, G; Abbott, J; Chiba, N; Huang, DW; Huang, Y; Krznaric, M; Mack-Smith, J; Saleem, A; Sherman, BT; Tiwari, B; Tomlinson, C; Aitman, T; Darlington, J; Game, L; Sternberg, MJE; Butcher, SA

2008-01-01

Background Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. Results EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. Conclusion EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume. PMID:19032776

The study of integration about measurable image and 4D production

NASA Astrophysics Data System (ADS)

Zhang, Chunsen; Hu, Pingbo; Niu, Weiyun

2008-12-01

In this paper, we create the geospatial data of three-dimensional (3D) modeling by the combination of digital photogrammetry and digital close-range photogrammetry. For large-scale geographical background, we make the establishment of DEM and DOM combination of three-dimensional landscape model based on the digital photogrammetry which uses aerial image data to make "4D" (DOM: Digital Orthophoto Map, DEM: Digital Elevation Model, DLG: Digital Line Graphic and DRG: Digital Raster Graphic) production. For the range of building and other artificial features which the users are interested in, we realize that the real features of the three-dimensional reconstruction adopting the method of the digital close-range photogrammetry can come true on the basis of following steps : non-metric cameras for data collection, the camera calibration, feature extraction, image matching, and other steps. At last, we combine three-dimensional background and local measurements real images of these large geographic data and realize the integration of measurable real image and the 4D production.The article discussed the way of the whole flow and technology, achieved the three-dimensional reconstruction and the integration of the large-scale threedimensional landscape and the metric building.

Three-Dimensional Printing and Its Applications in Otorhinolaryngology-Head and Neck Surgery.

PubMed

Crafts, Trevor D; Ellsperman, Susan E; Wannemuehler, Todd J; Bellicchi, Travis D; Shipchandler, Taha Z; Mantravadi, Avinash V

2017-06-01

Objective Three-dimensional (3D)-printing technology is being employed in a variety of medical and surgical specialties to improve patient care and advance resident physician training. As the costs of implementing 3D printing have declined, the use of this technology has expanded, especially within surgical specialties. This article explores the types of 3D printing available, highlights the benefits and drawbacks of each methodology, provides examples of how 3D printing has been applied within the field of otolaryngology-head and neck surgery, discusses future innovations, and explores the financial impact of these advances. Data Sources Articles were identified from PubMed and Ovid MEDLINE. Review Methods PubMed and Ovid Medline were queried for English articles published between 2011 and 2016, including a few articles prior to this time as relevant examples. Search terms included 3-dimensional printing, 3 D printing, otolaryngology, additive manufacturing, craniofacial, reconstruction, temporal bone, airway, sinus, cost, and anatomic models. Conclusions Three-dimensional printing has been used in recent years in otolaryngology for preoperative planning, education, prostheses, grafting, and reconstruction. Emerging technologies include the printing of tissue scaffolds for the auricle and nose, more realistic training models, and personalized implantable medical devices. Implications for Practice After the up-front costs of 3D printing are accounted for, its utilization in surgical models, patient-specific implants, and custom instruments can reduce operating room time and thus decrease costs. Educational and training models provide an opportunity to better visualize anomalies, practice surgical technique, predict problems that might arise, and improve quality by reducing mistakes.

Microreplication of laser-fabricated surface and three-dimensional structures

NASA Astrophysics Data System (ADS)

Koroleva, Anastasia; Schlie, Sabrina; Fadeeva, Elena; Gittard, Shaun D.; Miller, Philip; Ovsianikov, Aleksandr; Koch, Jürgen; Narayan, Roger J.; Chichkov, Boris N.

2010-12-01

The fabrication of defined surface topographies and three-dimensional structures is a challenging process for various applications, e.g. in photonics and biomedicine. Laser-based technologies provide a promising approach for the production of such structures. The advantages of femtosecond laser ablation and two-photon polymerization for microstructuring are well known. However, these methods cannot be applied to all materials and are limited by their high cost and long production time. In this study, biomedical applications of an indirect rapid prototyping, molding microreplication of laser-fabricated two- and three-dimensional structures are examined. We demonstrate that by this method any laser-generated surface topography as well as three-dimensional structures can be replicated in various materials without losing the original geometry. The replication into multiple copies enables fast and perfect reproducibility of original microstructures for investigations of cell-surface interactions. Compared to unstructured materials, we observe that microstructures have strong influence on morphology and localization of fibroblasts, whereas neuroblastoma cells are not negatively affected.

Electrical Capacitance Volume Tomography: Design and Applications

PubMed Central

Wang, Fei; Marashdeh, Qussai; Fan, Liang-Shih; Warsito, Warsito

2010-01-01

This article reports recent advances and progress in the field of electrical capacitance volume tomography (ECVT). ECVT, developed from the two-dimensional electrical capacitance tomography (ECT), is a promising non-intrusive imaging technology that can provide real-time three-dimensional images of the sensing domain. Images are reconstructed from capacitance measurements acquired by electrodes placed on the outside boundary of the testing vessel. In this article, a review of progress on capacitance sensor design and applications to multi-phase flows is presented. The sensor shape, electrode configuration, and the number of electrodes that comprise three key elements of three-dimensional capacitance sensors are illustrated. The article also highlights applications of ECVT sensors on vessels of various sizes from 1 to 60 inches with complex geometries. Case studies are used to show the capability and validity of ECVT. The studies provide qualitative and quantitative real-time three-dimensional information of the measuring domain under study. Advantages of ECVT render it a favorable tool to be utilized for industrial applications and fundamental multi-phase flow research. PMID:22294905

Vibration isolation technology: Sensitivity of selected classes of experiments to residual accelerations

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.

1991-01-01

Work was completed on all aspects of the following tasks: order of magnitude estimates; thermo-capillary convection - two-dimensional (fixed planar surface); thermo-capillary convection - three-dimensional and axisymmetric; liquid bridge/floating zone sensitivity; transport in closed containers; interaction: design and development stages; interaction: testing flight hardware; and reporting. Results are included in the Appendices.

Laser Metalworking Technology Transfer.

DTIC Science & Technology

1986-01-01

TI 59 programmable calculator /printer...the .4 one-dimensional heat flow model and should not be used for low processing speed. The program is written for use on a Texas Instrument TI 59 programmable calculator with...speed range, and a three-dimensional model for the low speed ranges. The program is written for use on a Texas Instrument TI 59 . * programmable calculator

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

PubMed

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.

Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform.

PubMed

Salehi, Reza; Tsoi, Stephen C M; Colazo, Marcos G; Ambrose, Divakar J; Robert, Claude; Dyck, Michael K

2017-01-30

Early embryonic loss is a large contributor to infertility in cattle. Moreover, bovine becomes an interesting model to study human preimplantation embryo development due to their similar developmental process. Although genetic factors are known to affect early embryonic development, the discovery of such factors has been a serious challenge. Microarray technology allows quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. One of the main decisions that have to be made when planning a microarray experiment is whether to use a one- or two-color approach. Two-color design increases technical replication, minimizes variability, improves sensitivity and accuracy as well as allows having loop designs, defining the common reference samples. Although microarray is a powerful biological tool, there are potential pitfalls that can attenuate its power. Hence, in this technical paper we demonstrate an optimized protocol for RNA extraction, amplification, labeling, hybridization of the labeled amplified RNA to the array, array scanning and data analysis using the two-color analysis strategy.

Construction of a robust microarray from a non-model species (largemouth bass) using pyrosequencing technology

PubMed Central

Garcia-Reyero, Natàlia; Griffitt, Robert J.; Liu, Li; Kroll, Kevin J.; Farmerie, William G.; Barber, David S.; Denslow, Nancy D.

2009-01-01

A novel custom microarray for largemouth bass (Micropterus salmoides) was designed with sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. This approach yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17β-œstradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to œstradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology. PMID:19936325

Comparative study of classification algorithms for immunosignaturing data

PubMed Central

2012-01-01

Background High-throughput technologies such as DNA, RNA, protein, antibody and peptide microarrays are often used to examine differences across drug treatments, diseases, transgenic animals, and others. Typically one trains a classification system by gathering large amounts of probe-level data, selecting informative features, and classifies test samples using a small number of features. As new microarrays are invented, classification systems that worked well for other array types may not be ideal. Expression microarrays, arguably one of the most prevalent array types, have been used for years to help develop classification algorithms. Many biological assumptions are built into classifiers that were designed for these types of data. One of the more problematic is the assumption of independence, both at the probe level and again at the biological level. Probes for RNA transcripts are designed to bind single transcripts. At the biological level, many genes have dependencies across transcriptional pathways where co-regulation of transcriptional units may make many genes appear as being completely dependent. Thus, algorithms that perform well for gene expression data may not be suitable when other technologies with different binding characteristics exist. The immunosignaturing microarray is based on complex mixtures of antibodies binding to arrays of random sequence peptides. It relies on many-to-many binding of antibodies to the random sequence peptides. Each peptide can bind multiple antibodies and each antibody can bind multiple peptides. This technology has been shown to be highly reproducible and appears promising for diagnosing a variety of disease states. However, it is not clear what is the optimal classification algorithm for analyzing this new type of data. Results We characterized several classification algorithms to analyze immunosignaturing data. We selected several datasets that range from easy to difficult to classify, from simple monoclonal binding to complex binding patterns in asthma patients. We then classified the biological samples using 17 different classification algorithms. Using a wide variety of assessment criteria, we found ‘Naïve Bayes’ far more useful than other widely used methods due to its simplicity, robustness, speed and accuracy. Conclusions ‘Naïve Bayes’ algorithm appears to accommodate the complex patterns hidden within multilayered immunosignaturing microarray data due to its fundamental mathematical properties. PMID:22720696

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

PubMed

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 stewardship intervention improved time to antimicrobial switch, especially time to de-escalation to optimal therapy, in patients with Gram-positive blood cultures. Infect Control Hosp Epidemiol 2016;1-6.

Computer Graphics Instruction in VizClass

ERIC Educational Resources Information Center

Grimes, Douglas; Warschauer, Mark; Hutchinson, Tara; Kuester, Falko

2005-01-01

"VizClass" is a university classroom environment designed to offer students in computer graphics and engineering courses up-to-date visualization technologies. Three digital whiteboards and a three-dimensional stereoscopic display provide complementary display surfaces. Input devices include touchscreens on the digital whiteboards, remote…

Genes misregulated in C. elegans deficient in Dicer, RDE-4, or RDE-1 are enriched for innate immunity genes.

PubMed

Welker, Noah C; Habig, Jeffrey W; Bass, Brenda L

2007-07-01

We describe the first microarray analysis of a whole animal containing a mutation in the Dicer gene. We used adult Caenorhabditis elegans and, to distinguish among different roles of Dicer, we also performed microarray analyses of animals with mutations in rde-4 and rde-1, which are involved in silencing by siRNA, but not miRNA. Surprisingly, we find that the X chromosome is greatly enriched for genes regulated by Dicer. Comparison of all three microarray data sets indicates the majority of Dicer-regulated genes are not dependent on RDE-4 or RDE-1, including the X-linked genes. However, all three data sets are enriched in genes important for innate immunity and, specifically, show increased expression of innate immunity genes.

Genes misregulated in C. elegans deficient in Dicer, RDE-4, or RDE-1 are enriched for innate immunity genes

PubMed Central

Welker, Noah C.; Habig, Jeffrey W.; Bass, Brenda L.

2007-01-01

We describe the first microarray analysis of a whole animal containing a mutation in the Dicer gene. We used adult Caenorhabditis elegans and, to distinguish among different roles of Dicer, we also performed microarray analyses of animals with mutations in rde-4 and rde-1, which are involved in silencing by siRNA, but not miRNA. Surprisingly, we find that the X chromosome is greatly enriched for genes regulated by Dicer. Comparison of all three microarray data sets indicates the majority of Dicer-regulated genes are not dependent on RDE-4 or RDE-1, including the X-linked genes. However, all three data sets are enriched in genes important for innate immunity and, specifically, show increased expression of innate immunity genes. PMID:17526642

BATS: a Bayesian user-friendly software for analyzing time series microarray experiments.

PubMed

Angelini, Claudia; Cutillo, Luisa; De Canditiis, Daniela; Mutarelli, Margherita; Pensky, Marianna

2008-10-06

Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may depend on time. One of the goals of modern molecular biology is the high-throughput identification of genes associated with a particular treatment or a biological process of interest. From methodological and computational point of view, analyzing high-dimensional time course microarray data requires very specific set of tools which are usually not included in standard software packages. Recently, the authors of this paper developed a fully Bayesian approach which allows one to identify differentially expressed genes in a 'one-sample' time-course microarray experiment, to rank them and to estimate their expression profiles. The method is based on explicit expressions for calculations and, hence, very computationally efficient. The software package BATS (Bayesian Analysis of Time Series) presented here implements the methodology described above. It allows an user to automatically identify and rank differentially expressed genes and to estimate their expression profiles when at least 5-6 time points are available. The package has a user-friendly interface. BATS successfully manages various technical difficulties which arise in time-course microarray experiments, such as a small number of observations, non-uniform sampling intervals and replicated or missing data. BATS is a free user-friendly software for the analysis of both simulated and real microarray time course experiments. The software, the user manual and a brief illustrative example are freely available online at the BATS website: http://www.na.iac.cnr.it/bats.

Design, fabrication, and evaluation of on-chip micro-supercapacitors

NASA Astrophysics Data System (ADS)

Beidaghi, Majid; Chen, Wei; Wang, Chunlei

2011-06-01

Development of miniaturized electronic systems has stimulated the demand for miniaturized power sources that can be integrated into such systems. Among the different micro power sources micro electrochemical energy storage and conversion devices are particularly attractive because of their high efficiency and relatively high energy density. Electrochemical micro-capacitors or micro-supercapacitors offer higher power density compared to micro-batteries and micro-fuel cells. In this paper, development of on-chip micro-supercapacitors based on interdigitated C-MEMS electrode microarrays is introduced. C-MEMS electrodes are employed both as electrode material for electric double layer capacitor (EDLC) or as three dimensional (3D) current collectors of EDLC or pseudo-capacitive materials. Recent advancements in fabrication methods of C-MEMS based micro-supercapacitors are discussed and electrochemical properties of C-MEMS electrodes and it composites are reviewed.

Map-Reading Skill Development with 3D Technologies

ERIC Educational Resources Information Center

Carbonell Carrera, Carlos; Avarvarei, Bogdan Vlad; Chelariu, Elena Liliana; Draghia, Lucia; Avarvarei, Simona Catrinel

2017-01-01

Landforms often are represented on maps using abstract cartographic techniques that the reader must interpret for successful three-dimensional terrain visualization. New technologies in 3D landscape representation, both digital and tangible, offer the opportunity to visualize terrain in new ways. The results of a university student workshop, in…

Information Technology Infusion Case Study: Integrating Google Earth(Trademark) into the A-Train Data Depot

NASA Technical Reports Server (NTRS)

Smith, Peter; Kempler, Steven; Leptoukh, Gregory; Chen, Aijun

2010-01-01

This poster paper represents the NASA funded project that was to employ the latest three dimensional visualization technology to explore and provide direct data access to heterogeneous A-Train datasets. Google Earth (tm) provides foundation for organizing, visualizing, publishing and synergizing Earth science data .

Application of Virtual Reality Technology in Biology Education.

ERIC Educational Resources Information Center

Shim, Kew-Cheol; Park, Jong-Seok; Kim, Hyun-Sup; Kim, Jae-Hyun; Park, Young-Chul; Ryu, Hai-Il

2003-01-01

Reports on the findings of a study designed to develop three-dimensional virtual reality technology (VRT) learning programs for middle school students and evaluate the program's educational value. Focuses on the topic of structure and function of the eye. Concludes that VRT simulations allow comfortable interaction with computers and increase the…

SoFoCles: feature filtering for microarray classification based on gene ontology.

PubMed

Papachristoudis, Georgios; Diplaris, Sotiris; Mitkas, Pericles A

2010-02-01

Marker gene selection has been an important research topic in the classification analysis of gene expression data. Current methods try to reduce the "curse of dimensionality" by using statistical intra-feature set calculations, or classifiers that are based on the given dataset. In this paper, we present SoFoCles, an interactive tool that enables semantic feature filtering in microarray classification problems with the use of external, well-defined knowledge retrieved from the Gene Ontology. The notion of semantic similarity is used to derive genes that are involved in the same biological path during the microarray experiment, by enriching a feature set that has been initially produced with legacy methods. Among its other functionalities, SoFoCles offers a large repository of semantic similarity methods that are used in order to derive feature sets and marker genes. The structure and functionality of the tool are discussed in detail, as well as its ability to improve classification accuracy. Through experimental evaluation, SoFoCles is shown to outperform other classification schemes in terms of classification accuracy in two real datasets using different semantic similarity computation approaches.

The Virtual Pelvic Floor, a tele-immersive educational environment.

PubMed Central

Pearl, R. K.; Evenhouse, R.; Rasmussen, M.; Dech, F.; Silverstein, J. C.; Prokasy, S.; Panko, W. B.

1999-01-01

This paper describes the development of the Virtual Pelvic Floor, a new method of teaching the complex anatomy of the pelvic region utilizing virtual reality and advanced networking technology. Virtual reality technology allows improved visualization of three-dimensional structures over conventional media because it supports stereo vision, viewer-centered perspective, large angles of view, and interactivity. Two or more ImmersaDesk systems, drafting table format virtual reality displays, are networked together providing an environment where teacher and students share a high quality three-dimensional anatomical model, and are able to converse, see each other, and to point in three dimensions to indicate areas of interest. This project was realized by the teamwork of surgeons, medical artists and sculptors, computer scientists, and computer visualization experts. It demonstrates the future of virtual reality for surgical education and applications for the Next Generation Internet. Images Figure 1 Figure 2 Figure 3 PMID:10566378

Fully automated analysis of multi-resolution four-channel micro-array genotyping data

NASA Astrophysics Data System (ADS)

Abbaspour, Mohsen; Abugharbieh, Rafeef; Podder, Mohua; Tebbutt, Scott J.

2006-03-01

We present a fully-automated and robust microarray image analysis system for handling multi-resolution images (down to 3-micron with sizes up to 80 MBs per channel). The system is developed to provide rapid and accurate data extraction for our recently developed microarray analysis and quality control tool (SNP Chart). Currently available commercial microarray image analysis applications are inefficient, due to the considerable user interaction typically required. Four-channel DNA microarray technology is a robust and accurate tool for determining genotypes of multiple genetic markers in individuals. It plays an important role in the state of the art trend where traditional medical treatments are to be replaced by personalized genetic medicine, i.e. individualized therapy based on the patient's genetic heritage. However, fast, robust, and precise image processing tools are required for the prospective practical use of microarray-based genetic testing for predicting disease susceptibilities and drug effects in clinical practice, which require a turn-around timeline compatible with clinical decision-making. In this paper we have developed a fully-automated image analysis platform for the rapid investigation of hundreds of genetic variations across multiple genes. Validation tests indicate very high accuracy levels for genotyping results. Our method achieves a significant reduction in analysis time, from several hours to just a few minutes, and is completely automated requiring no manual interaction or guidance.

A fisheye viewer for microarray-based gene expression data

PubMed Central

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

2006-01-01

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 . 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. PMID:17038193

Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress.

PubMed

Scholten, Johannes C M; Culley, David E; Nie, Lei; Munn, Kyle J; Chow, Lely; Brockman, Fred J; Zhang, Weiwen

2007-06-29

The application of DNA microarray technology to investigate multiple-species microbial communities presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri, and Methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community in response to oxidative stress. In order to minimize the possibility of cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. This study showed that S. fumaroxidans and M. hungatei responded to the oxidative stress with up-regulation of several genes known to be involved in reactive oxygen species (ROS) detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. However, D. vulgaris seemed to be less sensitive to the oxidative stress as a member of a four-species community, since no gene involved in ROS detoxification was up-regulated. Our work demonstrated the successful application of microarrays to a multiple-species microbial community, and our preliminary results indicated that this approach could provide novel insights on the metabolism within microbial communities.

A proposed metric for assessing the measurement quality of individual microarrays

PubMed Central

Kim, Kyoungmi; Page, Grier P; Beasley, T Mark; Barnes, Stephen; Scheirer, Katherine E; Allison, David B

2006-01-01

Background High-density microarray technology is increasingly applied to study gene expression levels on a large scale. Microarray experiments rely on several critical steps that may introduce error and uncertainty in analyses. These steps include mRNA sample extraction, amplification and labeling, hybridization, and scanning. In some cases this may be manifested as systematic spatial variation on the surface of microarray in which expression measurements within an individual array may vary as a function of geographic position on the array surface. Results We hypothesized that an index of the degree of spatiality of gene expression measurements associated with their physical geographic locations on an array could indicate the summary of the physical reliability of the microarray. We introduced a novel way to formulate this index using a statistical analysis tool. Our approach regressed gene expression intensity measurements on a polynomial response surface of the microarray's Cartesian coordinates. We demonstrated this method using a fixed model and presented results from real and simulated datasets. Conclusion We demonstrated the potential of such a quantitative metric for assessing the reliability of individual arrays. Moreover, we showed that this procedure can be incorporated into laboratory practice as a means to set quality control specifications and as a tool to determine whether an array has sufficient quality to be retained in terms of spatial correlation of gene expression measurements. PMID:16430768

Real-time three-dimensional ultrasound-assisted axillary plexus block defines soft tissue planes.

PubMed

Clendenen, Steven R; Riutort, Kevin; Ladlie, Beth L; Robards, Christopher; Franco, Carlo D; Greengrass, Roy A

2009-04-01

Two-dimensional (2D) ultrasound is commonly used for regional block of the axillary brachial plexus. In this technical case report, we described a real-time three-dimensional (3D) ultrasound-guided axillary block. The difference between 2D and 3D ultrasound is similar to the difference between plain radiograph and computer tomography. Unlike 2D ultrasound that captures a planar image, 3D ultrasound technology acquires a 3D volume of information that enables multiple planes of view by manipulating the image without movement of the ultrasound probe. Observation of the brachial plexus in cross-section demonstrated distinct linear hyperechoic tissue structures (loose connective tissue) that initially inhibited the flow of the local anesthesia. After completion of the injection, we were able to visualize the influence of arterial pulsation on the spread of the local anesthesia. Possible advantages of this novel technology over current 2D methods are wider image volume and the capability to manipulate the planes of the image without moving the probe.

Holograms as Teaching Agents

NASA Astrophysics Data System (ADS)

Walker, Robin A.

2013-02-01

Hungarian physicist Dennis Gabor won the Pulitzer Prize for his 1947 introduction of basic holographic principles, but it was not until the invention of the laser in 1960 that research scientists, physicians, technologists and the general public began to seriously consider the interdisciplinary potentiality of holography. Questions around whether and when Three-Dimensional (3-D) images and systems would impact American entertainment and the arts would be answered before educators, instructional designers and students would discover how much Three-Dimensional Hologram Technology (3DHT) would affect teaching practices and learning environments. In the following International Symposium on Display Holograms (ISDH) poster presentation, the author features a traditional board game as well as a reflection hologram to illustrate conventional and evolving Three-Dimensional representations and technology for education. Using elements from the American children's toy Operation® (Hasbro, 2005) as well as a reflection hologram of a human brain (Ko, 1998), this poster design highlights the pedagogical effects of 3-D images, games and systems on learning science. As teaching agents, holograms can be considered substitutes for real objects, (human beings, organs, and animated characters) as well as agents (pedagogical, avatars, reflective) in various learning environments using many systems (direct, emergent, augmented reality) and electronic tools (cellphones, computers, tablets, television). In order to understand the particular importance of utilizing holography in school, clinical and public settings, the author identifies advantages and benefits of using 3-D images and technology as instructional tools.

Medical Research System

NASA Technical Reports Server (NTRS)

1993-01-01

Based on Johnson Space Flight Center's development of a rotating bioreactor cell culture apparatus for Space Shuttle medical research, Johnson Space Flight Center engineers who worked on the original project formed a company called Synthecon, with the intention of commercializing the bioreactor technology. Synthecon grows three dimensional tissues in the bioreactor. These are superior to previous two-dimensional tissue samples in the study of human cell growth. A refined version of the Johnson Space Center technology, Synthecon's Rotary Cell Culture System includes a cell culture chamber that rotates around a horizontal axis. The cells establish an orbit that approximates free fall through the liquid medium in the chamber. The technology has significant applications for cancer research and treatment as well as AIDS research.

SYMBIOmatics: synergies in Medical Informatics and Bioinformatics--exploring current scientific literature for emerging topics.

PubMed

Rebholz-Schuhman, Dietrich; Cameron, Graham; Clark, Dominic; van Mulligen, Erik; Coatrieux, Jean-Louis; Del Hoyo Barbolla, Eva; Martin-Sanchez, Fernando; Milanesi, Luciano; Porro, Ivan; Beltrame, Francesco; Tollis, Ioannis; Van der Lei, Johan

2007-03-08

The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical informatics" domain to improve collaborative progress between both domains (ref. to http://www.symbiomatics.org). As part of the project experts in both research fields will be identified and approached through a survey. To provide input to the survey, the scientific literature was analysed to extract topics relevant to both medical informatics and bioinformatics. This paper presents results of a systematic analysis of the scientific literature from medical informatics research and bioinformatics research. In the analysis pairs of words (bigrams) from the leading bioinformatics and medical informatics journals have been used as indication of existing and emerging technologies and topics over the period 2000-2005 ("recent") and 1990-1990 ("past"). We identified emerging topics that were equally important to bioinformatics and medical informatics in recent years such as microarray experiments, ontologies, open source, text mining and support vector machines. Emerging topics that evolved only in bioinformatics were system biology, protein interaction networks and statistical methods for microarray analyses, whereas emerging topics in medical informatics were grid technology and tissue microarrays. We conclude that although both fields have their own specific domains of interest, they share common technological developments that tend to be initiated by new developments in biotechnology and computer science.

SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics – exploring current scientific literature for emerging topics

PubMed Central

Rebholz-Schuhman, Dietrich; Cameron, Graham; Clark, Dominic; van Mulligen, Erik; Coatrieux, Jean-Louis; Del Hoyo Barbolla, Eva; Martin-Sanchez, Fernando; Milanesi, Luciano; Porro, Ivan; Beltrame, Francesco; Tollis, Ioannis; Van der Lei, Johan

2007-01-01

Background The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical informatics" domain to improve collaborative progress between both domains (ref. to ). As part of the project experts in both research fields will be identified and approached through a survey. To provide input to the survey, the scientific literature was analysed to extract topics relevant to both medical informatics and bioinformatics. Results This paper presents results of a systematic analysis of the scientific literature from medical informatics research and bioinformatics research. In the analysis pairs of words (bigrams) from the leading bioinformatics and medical informatics journals have been used as indication of existing and emerging technologies and topics over the period 2000–2005 ("recent") and 1990–1990 ("past"). We identified emerging topics that were equally important to bioinformatics and medical informatics in recent years such as microarray experiments, ontologies, open source, text mining and support vector machines. Emerging topics that evolved only in bioinformatics were system biology, protein interaction networks and statistical methods for microarray analyses, whereas emerging topics in medical informatics were grid technology and tissue microarrays. Conclusion We conclude that although both fields have their own specific domains of interest, they share common technological developments that tend to be initiated by new developments in biotechnology and computer science. PMID:17430562

Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma

PubMed Central

Seliger, Barbara; Dressler, Sven P.; Wang, Ena; Kellner, Roland; Recktenwald, Christian V.; Lottspeich, Friedrich; Marincola, Francesco M.; Baumgärtner, Maja; Atkins, Derek; Lichtenfels, Rudolf

2012-01-01

Results obtained from expression profilings of renal cell carcinoma using different “ome”-based approaches and comprehensive data analysis demonstrated that proteome-based technologies and cDNA microarray analyses complement each other during the discovery phase for disease-related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to upregulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX-defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%) and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome-based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely 3 candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin alpha-1A chain and ubiquitin carboxyl-terminal hydrolase L1 the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors. PMID:19235166

Parents' Experience with Pediatric Microarray: Transferrable Lessons in the Era of Genomic Counseling.

PubMed

Hayeems, R Z; Babul-Hirji, R; Hoang, N; Weksberg, R; Shuman, C

2016-04-01

Advances in genome-based microarray and sequencing technologies hold tremendous promise for understanding, better-managing and/or preventing disease and disease-related risk. Chromosome microarray technology (array based comparative genomic hybridization [aCGH]) is widely utilized in pediatric care to inform diagnostic etiology and medical management. Less clear is how parents experience and perceive the value of this technology. This study explored parents' experiences with aCGH in the pediatric setting, focusing on how they make meaning of various types of test results. We conducted in-person or telephone-based semi-structured interviews with parents of 21 children who underwent aCGH testing in 2010. Transcripts were coded and analyzed thematically according to the principles of interpretive description. We learned that parents expect genomic tests to be of personal use; their experiences with aCGH results characterize this use as intrinsic in the test's ability to provide a much sought-after answer for their child's condition, and instrumental in its ability to guide care, access to services, and family planning. In addition, parents experience uncertainty regardless of whether aCGH results are of pathogenic, uncertain, or benign significance; this triggers frustration, fear, and hope. Findings reported herein better characterize the notion of personal utility and highlight the pervasive nature of uncertainty in the context of genomic testing. Empiric research that links pre-test counseling content and psychosocial outcomes is warranted to optimize patient care.

Parallax scanning methods for stereoscopic three-dimensional imaging

NASA Astrophysics Data System (ADS)

Mayhew, Christopher A.; Mayhew, Craig M.

2012-03-01

Under certain circumstances, conventional stereoscopic imagery is subject to being misinterpreted. Stereo perception created from two static horizontally separated views can create a "cut out" 2D appearance for objects at various planes of depth. The subject volume looks three-dimensional, but the objects themselves appear flat. This is especially true if the images are captured using small disparities. One potential explanation for this effect is that, although three-dimensional perception comes primarily from binocular vision, a human's gaze (the direction and orientation of a person's eyes with respect to their environment) and head motion also contribute additional sub-process information. The absence of this information may be the reason that certain stereoscopic imagery appears "odd" and unrealistic. Another contributing factor may be the absence of vertical disparity information in a traditional stereoscopy display. Recently, Parallax Scanning technologies have been introduced, which provide (1) a scanning methodology, (2) incorporate vertical disparity, and (3) produce stereo images with substantially smaller disparities than the human interocular distances.1 To test whether these three features would improve the realism and reduce the cardboard cutout effect of stereo images, we have applied Parallax Scanning (PS) technologies to commercial stereoscopic digital cinema productions and have tested the results with a panel of stereo experts. These informal experiments show that the addition of PS information into the left and right image capture improves the overall perception of three-dimensionality for most viewers. Parallax scanning significantly increases the set of tools available for 3D storytelling while at the same time presenting imagery that is easy and pleasant to view.