Alchemy: A Web 2.0 Real-time Quality Assurance Platform for Human Immunodeficiency Virus, Hepatitis C Virus, and BK Virus Quantitation Assays.

PubMed

Agosto-Arroyo, Emmanuel; Coshatt, Gina M; Winokur, Thomas S; Harada, Shuko; Park, Seung L

2017-01-01

The molecular diagnostics laboratory faces the challenge of improving test turnaround time (TAT). Low and consistent TATs are of great clinical and regulatory importance, especially for molecular virology tests. Laboratory information systems (LISs) contain all the data elements necessary to do accurate quality assurance (QA) reporting of TAT and other measures, but these reports are in most cases still performed manually: a time-consuming and error-prone task. The aim of this study was to develop a web-based real-time QA platform that would automate QA reporting in the molecular diagnostics laboratory at our institution, and minimize the time expended in preparing these reports. Using a standard Linux, Nginx, MariaDB, PHP stack virtual machine running atop a Dell Precision 5810, we designed and built a web-based QA platform, code-named Alchemy. Data files pulled periodically from the LIS in comma-separated value format were used to autogenerate QA reports for the human immunodeficiency virus (HIV) quantitation, hepatitis C virus (HCV) quantitation, and BK virus (BKV) quantitation. Alchemy allowed the user to select a specific timeframe to be analyzed and calculated key QA statistics in real-time, including the average TAT in days, tests falling outside the expected TAT ranges, and test result ranges. Before implementing Alchemy, reporting QA for the HIV, HCV, and BKV quantitation assays took 45-60 min of personnel time per test every month. With Alchemy, that time has decreased to 15 min total per month. Alchemy allowed the user to select specific periods of time and analyzed the TAT data in-depth without the need of extensive manual calculations. Alchemy has significantly decreased the time and the human error associated with QA report generation in our molecular diagnostics laboratory. Other tests will be added to this web-based platform in future updates. This effort shows the utility of informatician-supervised resident/fellow programming projects as learning

Alchemy: A Web 2.0 Real-time Quality Assurance Platform for Human Immunodeficiency Virus, Hepatitis C Virus, and BK Virus Quantitation Assays

PubMed Central

Agosto-Arroyo, Emmanuel; Coshatt, Gina M.; Winokur, Thomas S.; Harada, Shuko; Park, Seung L.

2017-01-01

Background: The molecular diagnostics laboratory faces the challenge of improving test turnaround time (TAT). Low and consistent TATs are of great clinical and regulatory importance, especially for molecular virology tests. Laboratory information systems (LISs) contain all the data elements necessary to do accurate quality assurance (QA) reporting of TAT and other measures, but these reports are in most cases still performed manually: a time-consuming and error-prone task. The aim of this study was to develop a web-based real-time QA platform that would automate QA reporting in the molecular diagnostics laboratory at our institution, and minimize the time expended in preparing these reports. Methods: Using a standard Linux, Nginx, MariaDB, PHP stack virtual machine running atop a Dell Precision 5810, we designed and built a web-based QA platform, code-named Alchemy. Data files pulled periodically from the LIS in comma-separated value format were used to autogenerate QA reports for the human immunodeficiency virus (HIV) quantitation, hepatitis C virus (HCV) quantitation, and BK virus (BKV) quantitation. Alchemy allowed the user to select a specific timeframe to be analyzed and calculated key QA statistics in real-time, including the average TAT in days, tests falling outside the expected TAT ranges, and test result ranges. Results: Before implementing Alchemy, reporting QA for the HIV, HCV, and BKV quantitation assays took 45–60 min of personnel time per test every month. With Alchemy, that time has decreased to 15 min total per month. Alchemy allowed the user to select specific periods of time and analyzed the TAT data in-depth without the need of extensive manual calculations. Conclusions: Alchemy has significantly decreased the time and the human error associated with QA report generation in our molecular diagnostics laboratory. Other tests will be added to this web-based platform in future updates. This effort shows the utility of informatician

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.

PubMed

Fang, Chao; Zhong, Huanzi; Lin, Yuxiang; Chen, Bing; Han, Mo; Ren, Huahui; Lu, Haorong; Luber, Jacob M; Xia, Min; Li, Wangsheng; Stein, Shayna; Xu, Xun; Zhang, Wenwei; Drmanac, Radoje; Wang, Jian; Yang, Huanming; Hammarström, Lennart; Kostic, Aleksandar D; Kristiansen, Karsten; Li, Junhua

2018-03-01

More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms. Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%-3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms. Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.

A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine

PubMed Central

Stern, Andrew M.; Schurdak, Mark E.; Bahar, Ivet; Berg, Jeremy M.; Taylor, D. Lansing

2016-01-01

Drug candidates exhibiting well-defined pharmacokinetic and pharmacodynamic profiles that are otherwise safe often fail to demonstrate proof-of-concept in phase II and III trials. Innovation in drug discovery and development has been identified as a critical need for improving the efficiency of drug discovery, especially through collaborations between academia, government agencies, and industry. To address the innovation challenge, we describe a comprehensive, unbiased, integrated, and iterative quantitative systems pharmacology (QSP)–driven drug discovery and development strategy and platform that we have implemented at the University of Pittsburgh Drug Discovery Institute. Intrinsic to QSP is its integrated use of multiscale experimental and computational methods to identify mechanisms of disease progression and to test predicted therapeutic strategies likely to achieve clinical validation for appropriate subpopulations of patients. The QSP platform can address biological heterogeneity and anticipate the evolution of resistance mechanisms, which are major challenges for drug development. The implementation of this platform is dedicated to gaining an understanding of mechanism(s) of disease progression to enable the identification of novel therapeutic strategies as well as repurposing drugs. The QSP platform will help promote the paradigm shift from reactive population-based medicine to proactive personalized medicine by focusing on the patient as the starting and the end point. PMID:26962875

Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP).

PubMed

Ma, Hongyan; Delafield, Daniel G; Wang, Zhe; You, Jianlan; Wu, Si

2017-04-01

The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated. To address this challenge, we have developed an Activity-Correlated Quantitative Proteomics Platform (ACPP) that systematically correlates protein-level enzymatic activity patterns and protein elution profiles using a label-free quantitative proteomics approach. The ACPP optimized a high performance anion exchange separation for efficiently fractionating complex protein samples while preserving enzymatic activities. The detected enzymatic activity patterns in sequential fractions using microplate-based assays were cross-correlated with protein elution profiles using a customized pattern-matching algorithm with a correlation R-score. The ACPP has been successfully applied to the identification of two types of "active" biomass-degrading enzymes (i.e., starch hydrolysis enzymes and cellulose hydrolysis enzymes) from Aspergillus niger secretome in a multiplexed fashion. By determining protein elution profiles of 156 proteins in A. niger secretome, we confidently identified the 1,4-α-glucosidase as the major "active" starch hydrolysis enzyme (R = 0.96) and the endoglucanase as the major "active" cellulose hydrolysis enzyme (R = 0.97). The results demonstrated that the ACPP facilitated the discovery of bioactive enzymes from complex protein samples in a high-throughput, multiplexing, and untargeted fashion. Graphical Abstract ᅟ.

Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP)

NASA Astrophysics Data System (ADS)

Ma, Hongyan; Delafield, Daniel G.; Wang, Zhe; You, Jianlan; Wu, Si

2017-04-01

The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated. To address this challenge, we have developed an Activity-Correlated Quantitative Proteomics Platform (ACPP) that systematically correlates protein-level enzymatic activity patterns and protein elution profiles using a label-free quantitative proteomics approach. The ACPP optimized a high performance anion exchange separation for efficiently fractionating complex protein samples while preserving enzymatic activities. The detected enzymatic activity patterns in sequential fractions using microplate-based assays were cross-correlated with protein elution profiles using a customized pattern-matching algorithm with a correlation R-score. The ACPP has been successfully applied to the identification of two types of "active" biomass-degrading enzymes (i.e., starch hydrolysis enzymes and cellulose hydrolysis enzymes) from Aspergillus niger secretome in a multiplexed fashion. By determining protein elution profiles of 156 proteins in A. niger secretome, we confidently identified the 1,4-α-glucosidase as the major "active" starch hydrolysis enzyme (R = 0.96) and the endoglucanase as the major "active" cellulose hydrolysis enzyme (R = 0.97). The results demonstrated that the ACPP facilitated the discovery of bioactive enzymes from complex protein samples in a high-throughput, multiplexing, and untargeted fashion.

Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer.

PubMed

Hoffman, Melissa A; Fang, Bin; Haura, Eric B; Rix, Uwe; Koomen, John M

2018-01-05

Recent developments in instrumentation and bioinformatics have led to new quantitative mass spectrometry platforms including LC-MS/MS with data-independent acquisition (DIA) and targeted analysis using parallel reaction monitoring mass spectrometry (LC-PRM), which provide alternatives to well-established methods, such as LC-MS/MS with data-dependent acquisition (DDA) and targeted analysis using multiple reaction monitoring mass spectrometry (LC-MRM). These tools have been used to identify signaling perturbations in lung cancers and other malignancies, supporting the development of effective kinase inhibitors and, more recently, providing insights into therapeutic resistance mechanisms and drug repurposing opportunities. However, detection of kinases in biological matrices can be challenging; therefore, activity-based protein profiling enrichment of ATP-utilizing proteins was selected as a test case for exploring the limits of detection of low-abundance analytes in complex biological samples. To examine the impact of different MS acquisition platforms, quantification of kinase ATP uptake following kinase inhibitor treatment was analyzed by four different methods: LC-MS/MS with DDA and DIA, LC-MRM, and LC-PRM. For discovery data sets, DIA increased the number of identified kinases by 21% and reduced missingness when compared with DDA. In this context, MRM and PRM were most effective at identifying global kinome responses to inhibitor treatment, highlighting the value of a priori target identification and manual evaluation of quantitative proteomics data sets. We compare results for a selected set of desthiobiotinylated peptides from PRM, MRM, and DIA and identify considerations for selecting a quantification method and postprocessing steps that should be used for each data acquisition strategy.

Polymer-based platform for microfluidic systems

DOEpatents

Benett, William [Livermore, CA; Krulevitch, Peter [Pleasanton, CA; Maghribi, Mariam [Livermore, CA; Hamilton, Julie [Tracy, CA; Rose, Klint [Boston, MA; Wang, Amy W [Oakland, CA

2009-10-13

A method of forming a polymer-based microfluidic system platform using network building blocks selected from a set of interconnectable network building blocks, such as wire, pins, blocks, and interconnects. The selected building blocks are interconnectably assembled and fixedly positioned in precise positions in a mold cavity of a mold frame to construct a three-dimensional model construction of a microfluidic flow path network preferably having meso-scale dimensions. A hardenable liquid, such as poly (dimethylsiloxane) is then introduced into the mold cavity and hardened to form a platform structure as well as to mold the microfluidic flow path network having channels, reservoirs and ports. Pre-fabricated elbows, T's and other joints are used to interconnect various building block elements together. After hardening the liquid the building blocks are removed from the platform structure to make available the channels, cavities and ports within the platform structure. Microdevices may be embedded within the cast polymer-based platform, or bonded to the platform structure subsequent to molding, to create an integrated microfluidic system. In this manner, the new microfluidic platform is versatile and capable of quickly generating prototype systems, and could easily be adapted to a manufacturing setting.

Developing a Multiplexed Quantitative Cross-Linking Mass Spectrometry Platform for Comparative Structural Analysis of Protein Complexes.

PubMed

Yu, Clinton; Huszagh, Alexander; Viner, Rosa; Novitsky, Eric J; Rychnovsky, Scott D; Huang, Lan

2016-10-18

Cross-linking mass spectrometry (XL-MS) represents a recently popularized hybrid methodology for defining protein-protein interactions (PPIs) and analyzing structures of large protein assemblies. In particular, XL-MS strategies have been demonstrated to be effective in elucidating molecular details of PPIs at the peptide resolution, providing a complementary set of structural data that can be utilized to refine existing complex structures or direct de novo modeling of unknown protein structures. To study structural and interaction dynamics of protein complexes, quantitative cross-linking mass spectrometry (QXL-MS) strategies based on isotope-labeled cross-linkers have been developed. Although successful, these approaches are mostly limited to pairwise comparisons. In order to establish a robust workflow enabling comparative analysis of multiple cross-linked samples simultaneously, we have developed a multiplexed QXL-MS strategy, namely, QMIX (Quantitation of Multiplexed, Isobaric-labeled cross (X)-linked peptides) by integrating MS-cleavable cross-linkers with isobaric labeling reagents. This study has established a new analytical platform for quantitative analysis of cross-linked peptides, which can be directly applied for multiplexed comparisons of the conformational dynamics of protein complexes and PPIs at the proteome scale in future studies.

Quantitative structure-activity relationship: promising advances in drug discovery platforms.

PubMed

Wang, Tao; Wu, Mian-Bin; Lin, Jian-Ping; Yang, Li-Rong

2015-12-01

Quantitative structure-activity relationship (QSAR) modeling is one of the most popular computer-aided tools employed in medicinal chemistry for drug discovery and lead optimization. It is especially powerful in the absence of 3D structures of specific drug targets. QSAR methods have been shown to draw public attention since they were first introduced. In this review, the authors provide a brief discussion of the basic principles of QSAR, model development and model validation. They also highlight the current applications of QSAR in different fields, particularly in virtual screening, rational drug design and multi-target QSAR. Finally, in view of recent controversies, the authors detail the challenges faced by QSAR modeling and the relevant solutions. The aim of this review is to show how QSAR modeling can be applied in novel drug discovery, design and lead optimization. QSAR should intentionally be used as a powerful tool for fragment-based drug design platforms in the field of drug discovery and design. Although there have been an increasing number of experimentally determined protein structures in recent years, a great number of protein structures cannot be easily obtained (i.e., membrane transport proteins and G-protein coupled receptors). Fragment-based drug discovery, such as QSAR, could be applied further and have a significant role in dealing with these problems. Moreover, along with the development of computer software and hardware, it is believed that QSAR will be increasingly important.

A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine.

PubMed

Stern, Andrew M; Schurdak, Mark E; Bahar, Ivet; Berg, Jeremy M; Taylor, D Lansing

2016-07-01

Drug candidates exhibiting well-defined pharmacokinetic and pharmacodynamic profiles that are otherwise safe often fail to demonstrate proof-of-concept in phase II and III trials. Innovation in drug discovery and development has been identified as a critical need for improving the efficiency of drug discovery, especially through collaborations between academia, government agencies, and industry. To address the innovation challenge, we describe a comprehensive, unbiased, integrated, and iterative quantitative systems pharmacology (QSP)-driven drug discovery and development strategy and platform that we have implemented at the University of Pittsburgh Drug Discovery Institute. Intrinsic to QSP is its integrated use of multiscale experimental and computational methods to identify mechanisms of disease progression and to test predicted therapeutic strategies likely to achieve clinical validation for appropriate subpopulations of patients. The QSP platform can address biological heterogeneity and anticipate the evolution of resistance mechanisms, which are major challenges for drug development. The implementation of this platform is dedicated to gaining an understanding of mechanism(s) of disease progression to enable the identification of novel therapeutic strategies as well as repurposing drugs. The QSP platform will help promote the paradigm shift from reactive population-based medicine to proactive personalized medicine by focusing on the patient as the starting and the end point. © 2016 Society for Laboratory Automation and Screening.

Protein-Based Nanomedicine Platforms for Drug Delivery

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

Ma Ham, Aihui; Tang, Zhiwen; Wu, Hong

2009-08-03

Drug delivery systems have been developed for many years, however some limitations still hurdle the pace of going to clinical phase, for example, poor biodistribution, drug molecule cytotoxicity, tissue damage, quick clearance from the circulation system, solubility and stability of drug molecules. To overcome the limitations of drug delivery, biomaterials have to be developed and applied to drug delivery to protect the drug molecules and to enhance the drug’s efficacy. Protein-based nanomedicine platforms for drug delivery are platforms comprised of naturally self-assembled protein subunits of the same protein or a combination of proteins making up a complete system. They aremore » ideal for drug delivery platforms due to their biocompatibility and biodegradability coupled with low toxicity. A variety of proteins have been used and characterized for drug delivery systems including the ferritin/apoferritin protein cage, plant derived viral capsids, the small Heat shock protein (sHsp) cage, albumin, soy and whey protein, collagen, and gelatin. There are many different types and shapes that have been prepared to deliver drug molecules using protein-based platforms including the various protein cages, microspheres, nanoparticles, hydrogels, films, minirods and minipellets. There are over 30 therapeutic compounds that have been investigated with protein-based drug delivery platforms for the potential treatment of various cancers, infectious diseases, chronic diseases, autoimmune diseases. In protein-based drug delivery platforms, protein cage is the most newly developed biomaterials for drug delivery and therapeutic applications. Their uniform sizes, multifunctions, and biodegradability push them to the frontier for drug delivery. In this review, the recent strategic development of drug delivery has been discussed with a special emphasis upon the polymer based, especially protein-based nanomedicine platforms for drug delivery. The advantages and disadvantages are

NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

PubMed

Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

2018-01-01

We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

On-chip quantitative detection of pathogen genes by autonomous microfluidic PCR platform.

PubMed

Tachibana, Hiroaki; Saito, Masato; Shibuya, Shogo; Tsuji, Koji; Miyagawa, Nobuyuki; Yamanaka, Keiichiro; Tamiya, Eiichi

2015-12-15

Polymerase chain reaction (PCR)-based genetic testing has become a routine part of clinical diagnoses and food testing. In these fields, rapid, easy-to-use, and cost-efficient PCR chips are expected to be appeared for providing such testing on-site. In this study, a new autonomous disposable plastic microfluidic PCR chip was created, and was utilized for quantitative detection of pathogenic microorganisms. To control the capillary flow of the following solution in the PCR microchannel, a driving microchannel was newly designed behind the PCR microchannel. This allowed the effective PCR by simply dropping the PCR solution onto the inlet without any external pumps. In order to achieve disposability, injection-molded cyclo-olefin polymer (COP) of a cost-competitive plastic was used for the PCR chip. We discovered that coating the microchannel walls with non-ionic surfactant produced a suitable hydrophilic surface for driving the capillary flow through the 1250-mm long microchannel. As a result, quantitative real-time PCR with the lowest initial concentration of human, Escherichia coli (E. coli), and pathogenic E. coli O157 genomic DNA of 4, 0.0019, 0.031 pg/μl, respectively, was successfully achieved in less than 18 min. Our results indicate that the platform presented in this study provided a rapid, easy-to-use, and low-cost real-time PCR system that could be potentially used for on-site gene testing. Copyright © 2015 Elsevier B.V. All rights reserved.

A Neuron-Based Screening Platform for Optimizing Genetically-Encoded Calcium Indicators

PubMed Central

Schreiter, Eric R.; Hasseman, Jeremy P.; Tsegaye, Getahun; Fosque, Benjamin F.; Behnam, Reza; Shields, Brenda C.; Ramirez, Melissa; Kimmel, Bruce E.; Kerr, Rex A.; Jayaraman, Vivek; Looger, Loren L.; Svoboda, Karel; Kim, Douglas S.

2013-01-01

Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude. PMID:24155972

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

PubMed Central

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W.; Gautier, Virginie W.

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip. PMID:26485569

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells.

PubMed

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W; Gautier, Virginie W

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.

3D tissue engineered micro-tumors for optical-based therapeutic screening platform

NASA Astrophysics Data System (ADS)

Spano, Joseph L.; Schmitt, Trevor J.; Bailey, Ryan C.; Hannon, Timothy S.; Elmajdob, Mohamed; Mason, Eric M.; Ye, Guochang; Das, Soumen; Seal, Sudipta; Fenn, Michael B.

2016-03-01

Melanoma is an underserved area of cancer research, with little focus on studying the effects of tumor extracellular matrix (ECM) properties on melanoma tumor progression, metastasis, and treatment efficacy. We've developed a Raman spectral mapping-based in-vitro screening platform that allows for nondestructive in-situ, multi-time point assessment of a novel potential nanotherapeutic adjuvant, nanoceria (cerium oxide nanoparticles), for treating melanoma. We've focused primarily on understanding melanoma tumor ECM composition and how it influences cell morphology and ICC markers. Furthermore, we aim to correlate this with studies on nanotherapeutic efficacy to coincide with the goal of predicting and preventing metastasis based on ECM composition. We've compiled a Raman spectral database for substrates containing varying compositions of fibronectin, elastin, laminin, and collagens type I and IV. Furthermore, we've developed a machine learning-based semi-quantitative analysis platform utilizing dimensionality reduction with subsequent pixel classification and semi-quantitation of ECM composition using Direct Classical Least Squares for classification and estimation of the reorganization of these components by taking 2D maps using Raman spectroscopy. Gaining an understanding of how tissue properties influence ECM organization has laid the foundation for future work utilizing Raman spectroscopy to assess therapeutic efficacy and matrix reorganization imparted by nanoceria. Specifically, this will allow us to better understand the role of HIF1a in matrix reorganization of the tumor microenvironment. By studying the relationship between substrate modulus and nanoceria's ability to inhibit an ECM that is conducive to tumor formation, we endeavor to show that nanoceria may prevent or even revert tumor conducive microenvironments.

Test Platforms for Model-Based Flight Research

NASA Astrophysics Data System (ADS)

Dorobantu, Andrei

Demonstrating the reliability of flight control algorithms is critical to integrating unmanned aircraft systems into the civilian airspace. For many potential applications, design and certification of these algorithms will rely heavily on mathematical models of the aircraft dynamics. Therefore, the aerospace community must develop flight test platforms to support the advancement of model-based techniques. The University of Minnesota has developed a test platform dedicated to model-based flight research for unmanned aircraft systems. This thesis provides an overview of the test platform and its research activities in the areas of system identification, model validation, and closed-loop control for small unmanned aircraft.

A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics

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

Karpievitch, Yuliya; Stanley, Jeffrey R.; Taverner, Thomas

2009-08-15

Motivation: Quantitative mass spectrometry-based proteomics requires protein-level estimates and associated confidence measures. Challenges include the presence of low quality or incorrectly identified peptides and informative missingness. Furthermore, models are required for rolling peptide-level information up to the protein level. Results: We present a statistical model that carefully accounts for informative missingness in peak intensities and allows unbiased, model-based, protein-level estimation and inference. The model is applicable to both label-based and label-free quantitation experiments. We also provide automated, model-based, algorithms for filtering of proteins and peptides as well as imputation of missing values. Two LC/MS datasets are used to illustrate themore » methods. In simulation studies, our methods are shown to achieve substantially more discoveries than standard alternatives. Availability: The software has been made available in the opensource proteomics platform DAnTE (http://omics.pnl.gov/software/). Contact: adabney@stat.tamu.edu Supplementary information: Supplementary data are available at Bioinformatics online.« less

A CMOS enhanced solid-state nanopore based single molecule detection platform.

PubMed

Chen, Chinhsuan; Yemenicioglu, Sukru; Uddin, Ashfaque; Corgliano, Ellie; Theogarajan, Luke

2013-01-01

Solid-state nanopores have emerged as a single molecule label-free electronic detection platform. Existing transimpedance stages used to measure ionic current nanopores suffer from dynamic range limitations resulting from steady-state baseline currents. We propose a digitally-assisted baseline cancellation CMOS platform that circumvents this issue. Since baseline cancellation is a form of auto-zeroing, the 1/f noise of the system is also reduced. Our proposed design can tolerate a steady state baseline current of 10µA and has a usable bandwidth of 750kHz. Quantitative DNA translocation experiments on 5kbp DNA was performed using a 5nm silicon nitride pore using both the CMOS platform and a commercial system. Comparison of event-count histograms show that the CMOS platform clearly outperforms the commercial system, allowing for unambiguous interpretation of the data.

Thiolene and SIFEL-based Microfluidic Platforms for Liquid-Liquid Extraction

PubMed Central

Goyal, Sachit; Desai, Amit V.; Lewis, Robert W.; Ranganathan, David R.; Li, Hairong; Zeng, Dexing; Reichert, David E.; Kenis, Paul J.A.

2014-01-01

Microfluidic platforms provide several advantages for liquid-liquid extraction (LLE) processes over conventional methods, for example with respect to lower consumption of solvents and enhanced extraction efficiencies due to the inherent shorter diffusional distances. Here, we report the development of polymer-based parallel-flow microfluidic platforms for LLE. To date, parallel-flow microfluidic platforms have predominantly been made out of silicon or glass due to their compatibility with most organic solvents used for LLE. Fabrication of silicon and glass-based LLE platforms typically requires extensive use of photolithography, plasma or laser-based etching, high temperature (anodic) bonding, and/or wet etching with KOH or HF solutions. In contrast, polymeric microfluidic platforms can be fabricated using less involved processes, typically photolithography in combination with replica molding, hot embossing, and/or bonding at much lower temperatures. Here we report the fabrication and testing of microfluidic LLE platforms comprised of thiolene or a perfluoropolyether-based material, SIFEL, where the choice of materials was mainly guided by the need for solvent compatibility and fabrication amenability. Suitable designs for polymer-based LLE platforms that maximize extraction efficiencies within the constraints of the fabrication methods and feasible operational conditions were obtained using analytical modeling. To optimize the performance of the polymer-based LLE platforms, we systematically studied the effect of surface functionalization and of microstructures on the stability of the liquid-liquid interface and on the ability to separate the phases. As demonstrative examples, we report (i) a thiolene-based platform to determine the lipophilicity of caffeine, and (ii) a SIFEL-based platform to extract radioactive copper from an acidic aqueous solution. PMID:25246730

Handheld Microneedle-Based Electrolyte Sensing Platform.

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

Miller, Philip R.; Rivas, Rhiana; Johnson, David

2015-11-01

Sandia National Laboratories will provide technical assistance, within time and budget, to Requester on testing and analyzing a microneedle-based electrolyte sensing platform. Hollow microneedles will be fabricated at Sandia and integrated with a fluidic chip using plastic laminate prototyping technology available at Sandia. In connection with commercial ion selective electrodes the sensing platform will be tested for detection of electrolytes (sodium and/or potassium) within physiological relevant concent ration ranges.

Particle-based platforms for malaria vaccines.

PubMed

Wu, Yimin; Narum, David L; Fleury, Sylvain; Jennings, Gary; Yadava, Anjali

2015-12-22

Recombinant subunit vaccines in general are poor immunogens likely due to the small size of peptides and proteins, combined with the lack or reduced presentation of repetitive motifs and missing complementary signal(s) for optimal triggering of the immune response. Therefore, recombinant subunit vaccines require enhancement by vaccine delivery vehicles in order to attain adequate protective immunity. Particle-based delivery platforms, including particulate antigens and particulate adjuvants, are promising delivery vehicles for modifying the way in which immunogens are presented to both the innate and adaptive immune systems. These particle delivery platforms can also co-deliver non-specific immunostimodulators as additional adjuvants. This paper reviews efforts and advances of the Particle-based delivery platforms in development of vaccines against malaria, a disease that claims over 600,000 lives per year, most of them are children under 5 years of age in sub-Sahara Africa. Copyright © 2015 Elsevier Ltd. All rights reserved.

A statistical framework for protein quantitation in bottom-up MS-based proteomics

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

Karpievitch, Yuliya; Stanley, Jeffrey R.; Taverner, Thomas

2009-08-15

ABSTRACT Motivation: Quantitative mass spectrometry-based proteomics requires protein-level estimates and confidence measures. Challenges include the presence of low-quality or incorrectly identified peptides and widespread, informative, missing data. Furthermore, models are required for rolling peptide-level information up to the protein level. Results: We present a statistical model for protein abundance in terms of peptide peak intensities, applicable to both label-based and label-free quantitation experiments. The model allows for both random and censoring missingness mechanisms and provides naturally for protein-level estimates and confidence measures. The model is also used to derive automated filtering and imputation routines. Three LC-MS datasets are used tomore » illustrate the methods. Availability: The software has been made available in the open-source proteomics platform DAnTE (Polpitiya et al. (2008)) (http://omics.pnl.gov/software/). Contact: adabney@stat.tamu.edu« less

Adaptation of a Simple Microfluidic Platform for High-Dimensional Quantitative Morphological Analysis of Human Mesenchymal Stromal Cells on Polystyrene-Based Substrates.

PubMed

Lam, Johnny; Marklein, Ross A; Jimenez-Torres, Jose A; Beebe, David J; Bauer, Steven R; Sung, Kyung E

2017-12-01

Multipotent stromal cells (MSCs, often called mesenchymal stem cells) have garnered significant attention within the field of regenerative medicine because of their purported ability to differentiate down musculoskeletal lineages. Given the inherent heterogeneity of MSC populations, recent studies have suggested that cell morphology may be indicative of MSC differentiation potential. Toward improving current methods and developing simple yet effective approaches for the morphological evaluation of MSCs, we combined passive pumping microfluidic technology with high-dimensional morphological characterization to produce robust tools for standardized high-throughput analysis. Using ultraviolet (UV) light as a modality for reproducible polystyrene substrate modification, we show that MSCs seeded on microfluidic straight channel devices incorporating UV-exposed substrates exhibited morphological changes that responded accordingly to the degree of substrate modification. Substrate modification also effected greater morphological changes in MSCs seeded at a lower rather than higher density within microfluidic channels. Despite largely comparable trends in morphology, MSCs seeded in microscale as opposed to traditional macroscale platforms displayed much higher sensitivity to changes in substrate properties. In summary, we adapted and qualified microfluidic cell culture platforms comprising simple straight channel arrays as a viable and robust tool for high-throughput quantitative morphological analysis to study cell-material interactions.

Low-cost bioanalysis on paper-based and its hybrid microfluidic platforms.

PubMed

Dou, Maowei; Sanjay, Sharma Timilsina; Benhabib, Merwan; Xu, Feng; Li, XiuJun

2015-12-01

Low-cost assays have broad applications ranging from human health diagnostics and food safety inspection to environmental analysis. Hence, low-cost assays are especially attractive for rural areas and developing countries, where financial resources are limited. Recently, paper-based microfluidic devices have emerged as a low-cost platform which greatly accelerates the point of care (POC) analysis in low-resource settings. This paper reviews recent advances of low-cost bioanalysis on paper-based microfluidic platforms, including fully paper-based and paper hybrid microfluidic platforms. In this review paper, we first summarized the fabrication techniques of fully paper-based microfluidic platforms, followed with their applications in human health diagnostics and food safety analysis. Then we highlighted paper hybrid microfluidic platforms and their applications, because hybrid platforms could draw benefits from multiple device substrates. Finally, we discussed the current limitations and perspective trends of paper-based microfluidic platforms for low-cost assays. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform.

PubMed

Pan, Sheng; Rush, John; Peskind, Elaine R; Galasko, Douglas; Chung, Kathryn; Quinn, Joseph; Jankovic, Joseph; Leverenz, James B; Zabetian, Cyrus; Pan, Catherine; Wang, Yan; Oh, Jung Hun; Gao, Jean; Zhang, Jianpeng; Montine, Thomas; Zhang, Jing

2008-02-01

Targeted quantitative proteomics by mass spectrometry aims to selectively detect one or a panel of peptides/proteins in a complex sample and is particularly appealing for novel biomarker verification/validation because it does not require specific antibodies. Here, we demonstrated the application of targeted quantitative proteomics in searching, identifying, and quantifying selected peptides in human cerebrospinal spinal fluid (CSF) using a matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (MALDI TOF/TOF)-based platform. The approach involved two major components: the use of isotopic-labeled synthetic peptides as references for targeted identification and quantification and a highly selective mass spectrometric analysis based on the unique characteristics of the MALDI instrument. The platform provides high confidence for targeted peptide detection in a complex system and can potentially be developed into a high-throughput system. Using the liquid chromatography (LC) MALDI TOF/TOF platform and the complementary identification strategy, we were able to selectively identify and quantify a panel of targeted peptides in the whole proteome of CSF without prior depletion of abundant proteins. The effectiveness and robustness of the approach associated with different sample complexity, sample preparation strategies, as well as mass spectrometric quantification were evaluated. Other issues related to chromatography separation and the feasibility for high-throughput analysis were also discussed. Finally, we applied targeted quantitative proteomics to analyze a subset of previously identified candidate markers in CSF samples of patients with Parkinson's disease (PD) at different stages and Alzheimer's disease (AD) along with normal controls.

Portable, one-step, and rapid GMR biosensor platform with smartphone interface.

PubMed

Choi, Joohong; Gani, Adi Wijaya; Bechstein, Daniel J B; Lee, Jung-Rok; Utz, Paul J; Wang, Shan X

2016-11-15

Quantitative immunoassay tests in clinical laboratories require trained technicians, take hours to complete with multiple steps, and the instruments used are generally immobile-patient samples have to be sent in to the labs for analysis. This prevents quantitative immunoassay tests to be performed outside laboratory settings. A portable, quantitative immunoassay device will be valuable in rural and resource-limited areas, where access to healthcare is scarce or far away. We have invented Eigen Diagnosis Platform (EDP), a portable quantitative immunoassay platform based on Giant Magnetoresistance (GMR) biosensor technology. The platform does not require a trained technician to operate, and only requires one-step user involvement. It displays quantitative results in less than 15min after sample insertion, and each test costs less than US$4. The GMR biosensor employed in EDP is capable of detecting multiple biomarkers in one test, enabling a wide array of immune diagnostics to be performed simultaneously. In this paper, we describe the design of EDP, and demonstrate its capability. Multiplexed assay of human immunoglobulin G and M (IgG and IgM) antibodies with EDP achieves sensitivities down to 0.07 and 0.33 nanomolar, respectively. The platform will allow lab testing to be performed in remote areas, and open up applications of immunoassay testing in other non-clinical settings, such as home, school, and office. Copyright © 2016 Elsevier B.V. All rights reserved.

Recent Progress in Optical Biosensors Based on Smartphone Platforms

PubMed Central

Geng, Zhaoxin; Zhang, Xiong; Fan, Zhiyuan; Lv, Xiaoqing; Su, Yue; Chen, Hongda

2017-01-01

With a rapid improvement of smartphone hardware and software, especially complementary metal oxide semiconductor (CMOS) cameras, many optical biosensors based on smartphone platforms have been presented, which have pushed the development of the point-of-care testing (POCT). Imaging-based and spectrometry-based detection techniques have been widely explored via different approaches. Combined with the smartphone, imaging-based and spectrometry-based methods are currently used to investigate a wide range of molecular properties in chemical and biological science for biosensing and diagnostics. Imaging techniques based on smartphone-based microscopes are utilized to capture microscale analysts, while spectrometry-based techniques are used to probe reactions or changes of molecules. Here, we critically review the most recent progress in imaging-based and spectrometry-based smartphone-integrated platforms that have been developed for chemical experiments and biological diagnosis. We focus on the analytical performance and the complexity for implementation of the platforms. PMID:29068375

Recent Progress in Optical Biosensors Based on Smartphone Platforms.

PubMed

Geng, Zhaoxin; Zhang, Xiong; Fan, Zhiyuan; Lv, Xiaoqing; Su, Yue; Chen, Hongda

2017-10-25

With a rapid improvement of smartphone hardware and software, especially complementary metal oxide semiconductor (CMOS) cameras, many optical biosensors based on smartphone platforms have been presented, which have pushed the development of the point-of-care testing (POCT). Imaging-based and spectrometry-based detection techniques have been widely explored via different approaches. Combined with the smartphone, imaging-based and spectrometry-based methods are currently used to investigate a wide range of molecular properties in chemical and biological science for biosensing and diagnostics. Imaging techniques based on smartphone-based microscopes are utilized to capture microscale analysts, while spectrometry-based techniques are used to probe reactions or changes of molecules. Here, we critically review the most recent progress in imaging-based and spectrometry-based smartphone-integrated platforms that have been developed for chemical experiments and biological diagnosis. We focus on the analytical performance and the complexity for implementation of the platforms.

Adaptive control of a Stewart platform-based manipulator

NASA Technical Reports Server (NTRS)

Nguyen, Charles C.; Antrazi, Sami S.; Zhou, Zhen-Lei; Campbell, Charles E., Jr.

1993-01-01

A joint-space adaptive control scheme for controlling noncompliant motion of a Stewart platform-based manipulator (SPBM) was implemented in the Hardware Real-Time Emulator at Goddard Space Flight Center. The six-degrees of freedom SPBM uses two platforms and six linear actuators driven by dc motors. The adaptive control scheme is based on proportional-derivative controllers whose gains are adjusted by an adaptation law based on model reference adaptive control and Liapunov direct method. It is concluded that the adaptive control scheme provides superior tracking capability as compared to fixed-gain controllers.

Remote sensing image segmentation based on Hadoop cloud platform

NASA Astrophysics Data System (ADS)

Li, Jie; Zhu, Lingling; Cao, Fubin

2018-01-01

To solve the problem that the remote sensing image segmentation speed is slow and the real-time performance is poor, this paper studies the method of remote sensing image segmentation based on Hadoop platform. On the basis of analyzing the structural characteristics of Hadoop cloud platform and its component MapReduce programming, this paper proposes a method of image segmentation based on the combination of OpenCV and Hadoop cloud platform. Firstly, the MapReduce image processing model of Hadoop cloud platform is designed, the input and output of image are customized and the segmentation method of the data file is rewritten. Then the Mean Shift image segmentation algorithm is implemented. Finally, this paper makes a segmentation experiment on remote sensing image, and uses MATLAB to realize the Mean Shift image segmentation algorithm to compare the same image segmentation experiment. The experimental results show that under the premise of ensuring good effect, the segmentation rate of remote sensing image segmentation based on Hadoop cloud Platform has been greatly improved compared with the single MATLAB image segmentation, and there is a great improvement in the effectiveness of image segmentation.

Cloud Based Applications and Platforms (Presentation)

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

Brodt-Giles, D.

2014-05-15

Presentation to the Cloud Computing East 2014 Conference, where we are highlighting our cloud computing strategy, describing the platforms on the cloud (including Smartgrid.gov), and defining our process for implementing cloud based applications.

Market implementation of the MVA platform for pre-pandemic and pandemic influenza vaccines: A quantitative key opinion leader analysis

PubMed Central

Ramezanpour, Bahar; Pronker, Esther S.; Kreijtz, Joost H.C.M.; Osterhaus, Albert D.M.E.; Claassen, E.

2015-01-01

A quantitative method is presented to rank strengths, weaknesses, opportunities, and threats (SWOT) of modified vaccinia virus Ankara (MVA) as a platform for pre-pandemic and pandemic influenza vaccines. Analytic hierarchy process (AHP) was applied to achieve pairwise comparisons among SWOT factors in order to prioritize them. Key opinion leaders (KOLs) in the influenza vaccine field were interviewed to collect a unique dataset to evaluate the market potential of this platform. The purpose of this study, to evaluate commercial potential of the MVA platform for the development of novel generation pandemic influenza vaccines, is accomplished by using a SWOT and AHP combined analytic method. Application of the SWOT–AHP model indicates that its strengths are considered more important by KOLs than its weaknesses, opportunities, and threats. Particularly, the inherent immunogenicity capability of MVA without the requirement of an adjuvant is the most important factor to increase commercial attractiveness of this platform. Concerns regarding vector vaccines and anti-vector immunity are considered its most important weakness, which might lower public health value of this platform. Furthermore, evaluation of the results of this study emphasizes equally important role that threats and opportunities of this platform play. This study further highlights unmet needs in the influenza vaccine market, which could be addressed by the implementation of the MVA platform. Broad use of MVA in clinical trials shows great promise for this vector as vaccine platform for pre-pandemic and pandemic influenza and threats by other respiratory viruses. Moreover, from the results of the clinical trials seem that MVA is particularly attractive for development of vaccines against pathogens for which no, or only insufficiently effective vaccines, are available. PMID:26048779

DNA aptamer-based colorimetric detection platform for Salmonella Enteritidis.

PubMed

Bayraç, Ceren; Eyidoğan, Füsun; Avni Öktem, Hüseyin

2017-12-15

Food safety is a major issue to protect public health and a key challenge is to find detection methods for identification of hazards in food. Food borne infections affects millions of people each year and among pathogens, Salmonella Enteritidis is most widely found bacteria causing food borne diseases. Therefore, simple, rapid, and specific detection methods are needed for food safety. In this study, we demonstrated the selection of DNA aptamers with high affinity and specificity against S. Enteritidis via Cell Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX) and development of sandwich type aptamer-based colorimetric platforms for its detection. Two highly specific aptamers, crn-1 and crn-2, were developed through 12 rounds of selection with K d of 0.971µM and 0.309µM, respectively. Both aptamers were used to construct sandwich type capillary detection platforms. With the detection limit of 10 3 CFU/mL, crn-1 and crn-2 based platforms detected target bacteria specifically based on color change. This platform is also suitable for detection of S. Enteritidis in complex food matrix. Thus, this is the first to demonstrate use of Salmonella aptamers for development of the colorimetric aptamer-based detection platform in its identification and detection with naked eye in point-of-care. Copyright © 2017 Elsevier B.V. All rights reserved.

Two low-cost digital camera-based platforms for quantitative creatinine analysis in urine.

PubMed

Debus, Bruno; Kirsanov, Dmitry; Yaroshenko, Irina; Sidorova, Alla; Piven, Alena; Legin, Andrey

2015-10-01

In clinical analysis creatinine is a routine biomarker for the assessment of renal and muscular dysfunctions. Although several techniques have been proposed for a fast and accurate quantification of creatinine in human serum or urine, most of them require expensive or complex apparatus, advanced sample preparation or skilled operators. To circumvent these issues, we propose two home-made platforms based on a CD Spectroscope (CDS) and Computer Screen Photo-assisted Technique (CSPT) for the rapid assessment of creatinine level in human urine. Both systems display a linear range (r(2) = 0.9967 and 0.9972, respectively) from 160 μmol L(-1) to 1.6 mmol L(-1) for standard creatinine solutions (n = 15) with respective detection limits of 89 μmol L(-1) and 111 μmol L(-1). Good repeatability was observed for intra-day (1.7-2.9%) and inter-day (3.6-6.5%) measurements evaluated on three consecutive days. The performance of CDS and CSPT was also validated in real human urine samples (n = 26) using capillary electrophoresis data as reference. Corresponding Partial Least-Squares (PLS) regression models provided for mean relative errors below 10% in creatinine quantification. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative multiplex detection of biomarkers on a waveguide-based biosensor using quantum dots

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

Xie, Hongzhi; Mukundan, Harshini; Martinez, Jennifer S

2009-01-01

The quantitative, simultaneous detection of multiple biomarkers with high sensitivity and specificity is critical for biomedical diagnostics, drug discovery and biomarker characterization [Wilson 2006, Tok 2006, Straub 2005, Joos 2002, Jani 2000]. Detection systems relying on optical signal transduction are, in general, advantageous because they are fast, portable, inexpensive, sensitive, and have the potential for multiplex detection of analytes of interest. However, conventional immunoassays for the detection of biomarkers, such as the Enzyme Linked Immunosorbant Assays (ELISAs) are semi-quantitative, time consuming and insensitive. ELISA assays are also limited by high non-specific binding, especially when used with complex biological samples suchmore » as serum and urine (REF). Organic fluorophores that are commonly used in such applications lack photostability and possess a narrow Stoke's shift that makes simultaneous detection of multiple fluorophores with a single excitation source difficult, thereby restricting their use in multiplex assays. The above limitations with traditional assay platforms have resulted in the increased use of nanotechnology-based tools and techniques in the fields of medical imaging [ref], targeted drug delivery [Caruthers 2007, Liu 2007], and sensing [ref]. One such area of increasing interest is the use of semiconductor quantum dots (QDs) for biomedical research and diagnostics [Gao and Cui 2004, Voura 2004, Michalet 2005, Chan 2002, Jaiswal 2004, Gao 2005, Medintz 2005, So 2006 2006, Wu 2003]. Compared to organic dyes, QDs provide several advantages for use in immunoassay platforms, including broad absorption bands with high extinction coefficients, narrow and symmetric emission bands with high quantum yields, high photostablility, and a large Stokes shift [Michalet 2005, Gu 2002]. These features prompted the use of QDs as probes in biodetection [Michalet 2005, Medintz 2005]. For example, Jaiswal et al. reported long term

Smartphone based visual and quantitative assays on upconversional paper sensor.

PubMed

Mei, Qingsong; Jing, Huarong; Li, You; Yisibashaer, Wuerzha; Chen, Jian; Nan Li, Bing; Zhang, Yong

2016-01-15

The integration of smartphone with paper sensors recently has been gain increasing attentions because of the achievement of quantitative and rapid analysis. However, smartphone based upconversional paper sensors have been restricted by the lack of effective methods to acquire luminescence signals on test paper. Herein, by the virtue of 3D printing technology, we exploited an auxiliary reusable device, which orderly assembled a 980nm mini-laser, optical filter and mini-cavity together, for digitally imaging the luminescence variations on test paper and quantitative analyzing pesticide thiram by smartphone. In detail, copper ions decorated NaYF4:Yb/Tm upconversion nanoparticles were fixed onto filter paper to form test paper, and the blue luminescence on it would be quenched after additions of thiram through luminescence resonance energy transfer mechanism. These variations could be monitored by the smartphone camera, and then the blue channel intensities of obtained colored images were calculated to quantify amounts of thiram through a self-written Android program installed on the smartphone, offering a reliable and accurate detection limit of 0.1μM for the system. This work provides an initial demonstration of integrating upconversion nanosensors with smartphone digital imaging for point-of-care analysis on a paper-based platform. Copyright © 2015 Elsevier B.V. All rights reserved.

Market implementation of the MVA platform for pre-pandemic and pandemic influenza vaccines: A quantitative key opinion leader analysis.

PubMed

Ramezanpour, Bahar; Pronker, Esther S; Kreijtz, Joost H C M; Osterhaus, Albert D M E; Claassen, E

2015-08-20

A quantitative method is presented to rank strengths, weaknesses, opportunities, and threats (SWOT) of modified vaccinia virus Ankara (MVA) as a platform for pre-pandemic and pandemic influenza vaccines. Analytic hierarchy process (AHP) was applied to achieve pairwise comparisons among SWOT factors in order to prioritize them. Key opinion leaders (KOLs) in the influenza vaccine field were interviewed to collect a unique dataset to evaluate the market potential of this platform. The purpose of this study, to evaluate commercial potential of the MVA platform for the development of novel generation pandemic influenza vaccines, is accomplished by using a SWOT and AHP combined analytic method. Application of the SWOT-AHP model indicates that its strengths are considered more important by KOLs than its weaknesses, opportunities, and threats. Particularly, the inherent immunogenicity capability of MVA without the requirement of an adjuvant is the most important factor to increase commercial attractiveness of this platform. Concerns regarding vector vaccines and anti-vector immunity are considered its most important weakness, which might lower public health value of this platform. Furthermore, evaluation of the results of this study emphasizes equally important role that threats and opportunities of this platform play. This study further highlights unmet needs in the influenza vaccine market, which could be addressed by the implementation of the MVA platform. Broad use of MVA in clinical trials shows great promise for this vector as vaccine platform for pre-pandemic and pandemic influenza and threats by other respiratory viruses. Moreover, from the results of the clinical trials seem that MVA is particularly attractive for development of vaccines against pathogens for which no, or only insufficiently effective vaccines, are available. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Wandering: A Web-Based Platform for the Creation of Location-Based Interactive Learning Objects

ERIC Educational Resources Information Center

Barak, Miri; Ziv, Shani

2013-01-01

Wandering is an innovative web-based platform that was designed to facilitate outdoor, authentic, and interactive learning via the creation of location-based interactive learning objects (LILOs). Wandering was integrated as part of a novel environmental education program among middle school students. This paper describes the Wandering platform's…

GOLIAH: A Gaming Platform for Home-Based Intervention in Autism - Principles and Design.

PubMed

Bono, Valentina; Narzisi, Antonio; Jouen, Anne-Lise; Tilmont, Elodie; Hommel, Stephane; Jamal, Wasifa; Xavier, Jean; Billeci, Lucia; Maharatna, Koushik; Wald, Mike; Chetouani, Mohamed; Cohen, David; Muratori, Filippo

2016-01-01

Children with Autism need intensive intervention and this is challenging in terms of manpower, costs, and time. Advances in Information Communication Technology and computer gaming may help in this respect by creating a nomadically deployable closed-loop intervention system involving the child and active participation of parents and therapists. An automated serious gaming platform enabling intensive intervention in nomadic settings has been developed by mapping two pivotal skills in autism spectrum disorder: Imitation and Joint Attention (JA). Eleven games - seven Imitations and four JA - were derived from the Early Start Denver Model. The games involved application of visual and audio stimuli with multiple difficulty levels and a wide variety of tasks and actions pertaining to the Imitation and JA. The platform runs on mobile devices and allows the therapist to (1) characterize the child's initial difficulties/strengths, ensuring tailored and adapted intervention by choosing appropriate games and (2) investigate and track the temporal evolution of the child's progress through a set of automatically extracted quantitative performance metrics. The platform allows the therapist to change the game or its difficulty levels during the intervention depending on the child's progress. Performance of the platform was assessed in a 3-month open trial with 10 children with autism (Trial ID: NCT02560415, Clinicaltrials.gov). The children and the parents participated in 80% of the sessions both at home (77.5%) and at the hospital (90%). All children went through all the games but, given the diversity of the games and the heterogeneity of children profiles and abilities, for a given game the number of sessions dedicated to the game varied and could be tailored through automatic scoring. Parents (N = 10) highlighted enhancement in the child's concentration, flexibility, and self-esteem in 78, 89, and 44% of the cases, respectively, and 56% observed an enhanced parents

Communicating climate change adaptation information using web-based platforms

NASA Astrophysics Data System (ADS)

Karali, Eleni; Mattern, Kati

2017-07-01

To facilitate progress in climate change adaptation policy and practice, it is important not only to ensure the production of accurate, comprehensive and relevant information, but also the easy, timely and affordable access to it. This can contribute to better-informed decisions and improve the design and implementation of adaptation policies and other relevant initiatives. Web-based platforms can play an important role in communicating and distributing data, information and knowledge that become constantly available, reaching out to a large group of potential users. Indeed in the last decade there has been an extensive increase in the number of platforms developed for this purpose in many fields including climate change adaptation. This short paper concentrates on the web-based adaptation platforms developed in Europe. It provides an overview of the recently emerged landscape, examines the basic characteristics of a set of platforms that operate at national, transnational and European level, and discusses some of the key challenges related to their development, maintenance and overall management. Findings presented in this short paper are discussed in greater detailed in the Technical Report of the European Environment Agency Overview of climate change adaptation platforms in Europe.

Optofluidic platforms based on surface-enhanced Raman scattering.

PubMed

Lim, Chaesung; Hong, Jongin; Chung, Bong Geun; deMello, Andrew J; Choo, Jaebum

2010-05-01

We report recent progress in the development of surface-enhanced Raman scattering (SERS)-based optofluidic platforms for the fast and sensitive detection of chemical and biological analytes. In the current context, a SERS-based optofluidic platform is defined as an integrated analytical device composed of a microfluidic element and a sensitive Raman spectrometer. Optofluidic devices for SERS detection normally involve nanocolloid-based microfluidic systems or metal nanostructure-embedded microfluidic systems. In the current review, recent advances in both approaches are surveyed and assessed. Additionally, integrated real-time sensing systems that combine portable Raman spectrometers with microfluidic devices are also reviewed. Such real-time sensing systems have significant utility in environmental monitoring, forensic science and homeland defense applications.

Platform based design of EAP transducers in Danfoss PolyPower A/S

NASA Astrophysics Data System (ADS)

Sarban, Rahimullah; Gudlaugsson, Tómas V.

2013-04-01

Electroactive Polymer (EAP) has gained increasing focus, in research communities, in last two decades. Research within the field of EAP has, so far, been mainly focused on material improvements, characterization, modeling and developing demonstrators. As the EAP technology matures, the need for a new area of research namely product development emerges. Product development can be based on an isolated design and production for a single product or platform design where a product family is developed. In platform design the families of products exploits commonality of platform modules while satisfying a variety of different market segments. Platform based approach has the primary benefit of being cost efficient and short lead time to market when new products emerges. Products development based on EAP technology is challenging both technologically as well as from production and processing point of view. Both the technological and processing challenges need to be addressed before a successful implementation of EAP technology into products. Based on this need Danfoss PolyPower A/S has, in 2011, launched a EAP platform project in collaboration with three Danish universities and three commercial organizations. The aim of the project is to develop platform based designs and product family for the EAP components to be used in variety of applications. This paper presents the structure of the platform project as a whole and specifically the platform based designs of EAP transducers. The underlying technologies, essential for EAP transducers, are also presented. Conceptual design and solution for the concepts are presented as well.

Cdk1 activity acts as a quantitative platform for coordinating cell cycle progression with periodic transcription

PubMed Central

Banyai, Gabor; Baïdi, Feriel; Coudreuse, Damien; Szilagyi, Zsolt

2016-01-01

Cell proliferation is regulated by cyclin-dependent kinases (Cdks) and requires the periodic expression of particular gene clusters in different cell cycle phases. However, the interplay between the networks that generate these transcriptional oscillations and the core cell cycle machinery remains largely unexplored. In this work, we use a synthetic regulable Cdk1 module to demonstrate that periodic expression is governed by quantitative changes in Cdk1 activity, with different clusters directly responding to specific activity levels. We further establish that cell cycle events neither participate in nor interfere with the Cdk1-driven transcriptional program, provided that cells are exposed to the appropriate Cdk1 activities. These findings contrast with current models that propose self-sustained and Cdk1-independent transcriptional oscillations. Our work therefore supports a model in which Cdk1 activity serves as a quantitative platform for coordinating cell cycle transitions with the expression of critical genes to bring about proper cell cycle progression. PMID:27045731

An overview on development and application of an experimental platform for quantitative cardiac imaging research in rabbit models of myocardial infarction

PubMed Central

Feng, Yuanbo; Bogaert, Jan; Oyen, Raymond

2014-01-01

To exploit the advantages of using rabbits for cardiac imaging research and to tackle the technical obstacles, efforts have been made under the framework of a doctoral research program. In this overview article, by cross-referencing the current literature, we summarize how we have developed a preclinical cardiac research platform based on modified models of reperfused myocardial infarction (MI) in rabbits; how the in vivo manifestations of cardiac imaging could be closely matched with those ex vivo macro- and microscopic findings; how these imaging outcomes could be quantitatively analyzed, validated and demonstrated; and how we could apply this cardiac imaging platform to provide possible solutions to certain lingering diagnostic and therapeutic problems in experimental cardiology. In particular, tissue components in acute cardiac ischemia have been stratified and characterized, post-infarct lipomatous metaplasia (LM) as a common but hardly illuminated clinical pathology has been identified in rabbit models, and a necrosis avid tracer as well as an anti-ischemic drug have been successfully assessed for their potential utilities in clinical cardiology. These outcomes may interest the researchers in the related fields and help strengthen translational research in cardiovascular diseases. PMID:25392822

An overview on development and application of an experimental platform for quantitative cardiac imaging research in rabbit models of myocardial infarction.

PubMed

Feng, Yuanbo; Bogaert, Jan; Oyen, Raymond; Ni, Yicheng

2014-10-01

To exploit the advantages of using rabbits for cardiac imaging research and to tackle the technical obstacles, efforts have been made under the framework of a doctoral research program. In this overview article, by cross-referencing the current literature, we summarize how we have developed a preclinical cardiac research platform based on modified models of reperfused myocardial infarction (MI) in rabbits; how the in vivo manifestations of cardiac imaging could be closely matched with those ex vivo macro- and microscopic findings; how these imaging outcomes could be quantitatively analyzed, validated and demonstrated; and how we could apply this cardiac imaging platform to provide possible solutions to certain lingering diagnostic and therapeutic problems in experimental cardiology. In particular, tissue components in acute cardiac ischemia have been stratified and characterized, post-infarct lipomatous metaplasia (LM) as a common but hardly illuminated clinical pathology has been identified in rabbit models, and a necrosis avid tracer as well as an anti-ischemic drug have been successfully assessed for their potential utilities in clinical cardiology. These outcomes may interest the researchers in the related fields and help strengthen translational research in cardiovascular diseases.

Dial-in Topological Metamaterials Based on Bistable Stewart Platform.

PubMed

Wu, Ying; Chaunsali, Rajesh; Yasuda, Hiromi; Yu, Kaiping; Yang, Jinkyu

2018-01-08

Recently, there have been significant efforts to guide mechanical energy in structures by relying on a novel topological framework popularized by the discovery of topological insulators. Here, we propose a topological metamaterial system based on the design of the Stewart Platform, which can not only guide mechanical waves robustly in a desired path, but also can be tuned in situ to change this wave path at will. Without resorting to any active materials, the current system harnesses bistablilty in its unit cells, such that tuning can be performed simply by a dial-in action. Consequently, a topological transition mechanism inspired by the quantum valley Hall effect can be achieved. We show the possibility of tuning in a variety of topological and traditional waveguides in the same system, and numerically investigate key qualitative and quantitative differences between them. We observe that even though both types of waveguides can lead to significant wave transmission for a certain frequency range, topological waveguides are distinctive as they support robust, back scattering immune, one-way wave propagation.

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.

PubMed

Tyanova, Stefka; Temu, Tikira; Cox, Juergen

2016-12-01

MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms. Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques. This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda. This protocol update describes an adaptation of an existing protocol that substantially modifies the technique. Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs). The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail. Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs. The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores. The software is written in C# and is freely available at http://www.maxquant.org.

Proteomics: from hypothesis to quantitative assay on a single platform. Guidelines for developing MRM assays using ion trap mass spectrometers.

PubMed

Han, Bomie; Higgs, Richard E

2008-09-01

High-throughput HPLC-mass spectrometry (HPLC-MS) is routinely used to profile biological samples for potential protein markers of disease, drug efficacy and toxicity. The discovery technology has advanced to the point where translating hypotheses from proteomic profiling studies into clinical use is the bottleneck to realizing the full potential of these approaches. The first step in this translation is the development and analytical validation of a higher throughput assay with improved sensitivity and selectivity relative to typical profiling assays. Multiple reaction monitoring (MRM) assays are an attractive approach for this stage of biomarker development given their improved sensitivity and specificity, the speed at which the assays can be developed and the quantitative nature of the assay. While the profiling assays are performed with ion trap mass spectrometers, MRM assays are traditionally developed in quadrupole-based mass spectrometers. Development of MRM assays from the same instrument used in the profiling analysis enables a seamless and rapid transition from hypothesis generation to validation. This report provides guidelines for rapidly developing an MRM assay using the same mass spectrometry platform used for profiling experiments (typically ion traps) and reviews methodological and analytical validation considerations. The analytical validation guidelines presented are drawn from existing practices on immunological assays and are applicable to any mass spectrometry platform technology.

Comparative analysis of two femtosecond LASIK platforms using iTRAQ quantitative proteomics.

PubMed

D'Souza, Sharon; Petznick, Andrea; Tong, Louis; Hall, Reece C; Rosman, Mohamad; Chan, Cordelia; Koh, Siew Kwan; Beuerman, Roger W; Zhou, Lei; Mehta, Jodhbir S

2014-05-06

New femtosecond laser platforms may reduce ocular surface interference and LASIK-associated dry eye. This study investigated tear protein profiles in subjects who underwent LASIK using two femtosecond lasers to assess differences in protein expression. This was a randomized interventional clinical trial involving 22 patients who underwent femtosecond laser refractive surgery with a contralateral paired eye design. Corneal flaps of 22 subjects were created by either Visumax or Intralase laser. Tear samples were collected preoperatively, and at 1 week and 3 months postoperatively using Schirmer's strips. Tear protein ratios were calculated relative to preoperative protein levels at baseline. The main outcome measures were the levels of a panel of dry eye protein markers analyzed using isobaric tagging for relative and absolute quantitation (iTRAQ) mass spectrometry. A total of 824 unique proteins were quantifiable. Tear protein ratios were differentially regulated between the eyes treated with different lasers. The secretoglobulins Lipophilin A (1.80-fold) and Lipophilin C (1.77) were significantly upregulated (P < 0.05) at 1 week postoperatively in Visumax but not in Intralase-treated eyes. At 1 week, orosomucoid1 was upregulated (1.78) in Intralase but not Visumax-treated eyes. In the same eyes, lysozyme, cathepsin B, and lipo-oxygenase were downregulated at 0.44-, 0.64-, and 0.64-folds, respectively. Transglutaminase-2 was downregulated in both groups of eyes. Different laser platforms induce distinct biological responses in the cornea and ocular surface, which manifests as different levels of tear proteins. This study has implications for surgical technology and modulation of wound healing responses. (ClinicalTrials.gov number, NCT01252654.). Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

Gesture therapy: an upper limb virtual reality-based motor rehabilitation platform.

PubMed

Sucar, Luis Enrique; Orihuela-Espina, Felipe; Velazquez, Roger Luis; Reinkensmeyer, David J; Leder, Ronald; Hernández-Franco, Jorge

2014-05-01

Virtual reality platforms capable of assisting rehabilitation must provide support for rehabilitation principles: promote repetition, task oriented training, appropriate feedback, and a motivating environment. As such, development of these platforms is a complex process which has not yet reached maturity. This paper presents our efforts to contribute to this field, presenting Gesture Therapy, a virtual reality-based platform for rehabilitation of the upper limb. We describe the system architecture and main features of the platform and provide preliminary evidence of the feasibility of the platform in its current status.

Web surveillance system using platform-based design

NASA Astrophysics Data System (ADS)

Lin, Shin-Yo; Tsai, Tsung-Han

2004-04-01

A revolutionary methodology of SOPC platform-based design environment for multimedia communications will be developed. We embed a softcore processor to perform the image compression in FPGA. Then, we plug-in an Ethernet daughter board in the SOPC development platform system. Afterward, a web surveillance platform system is presented. The web surveillance system consists of three parts: image capture, web server and JPEG compression. In this architecture, user can control the surveillance system by remote. By the IP address configures to Ethernet daughter board, the user can access the surveillance system via browser. When user access the surveillance system, the CMOS sensor presently capture the remote image. After that, it will feed the captured image with the embedded processor. The embedded processor immediately performs the JPEG compression. Afterward, the user receives the compressed data via Ethernet. To sum up of the above mentioned, the all system will be implemented on APEX20K200E484-2X device.

An integrated platform for directly widely-targeted quantitative analysis of feces part I: Platform configuration and method validation.

PubMed

Song, Yuelin; Song, Qingqing; Li, Jun; Zheng, Jiao; Li, Chun; Zhang, Yuan; Zhang, Lingling; Jiang, Yong; Tu, Pengfei

2016-07-08

Direct analysis is of great importance to understand the real chemical profile of a given sample, notably biological materials, because either chemical degradation or diverse errors and uncertainties might be resulted from sophisticated protocols. In comparison with biofluids, it is still challenging for direct analysis of solid biological samples using high performance liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Herein, a new analytical platform was configured by online hyphenating pressurized liquid extraction (PLE), turbulent flow chromatography (TFC), and LC-MS/MS. A facile, but robust PLE module was constructed based on the phenomenon that noticeable back-pressure can be generated during rapid fluid passing through a narrow tube. TFC column that is advantageous at extracting low molecular analytes from rushing fluid was employed to link at the outlet of the PLE module to capture constituents-of-interest. An electronic 6-port/2-position valve was introduced between TFC column and LC-MS/MS to fragment each measurement into extraction and elution phases, whereas LC-MS/MS took the charge of analyte separation and monitoring. As a proof of concept, simultaneous determination of 24 endogenous substances including eighteen steroids, five eicosanoids, and one porphyrin in feces was carried out in this paper. Method validation assays demonstrated the analytical platform to be qualified for directly simultaneous measurement of diverse endogenous analytes in fecal matrices. Application of this integrated platform on homolog-focused profiling of feces is discussed in a companion paper. Copyright © 2016 Elsevier B.V. All rights reserved.

Improving Evidence Dissemination and Accessibility through a Mobile-based Resource Platform.

PubMed

Zhu, Zheng; Xing, Weijie; Hu, Yan; Zhou, Yingfeng; Gu, Ying

2018-05-28

Current mobile information technologies fundamentally influence evidence dissemination from the perspective of both evidence seekers and evidence providers. However, there is no related study which tried using a mobile-based platform to disseminate evidence in China. The main object of this study is to develop a mobile-based evidence resource platform and to evaluate its effects of improving nurses' access to evidence-based practice resources and meeting users' demands. The mobile-based evidence resource platform was developed in 2014. A cross-sectional study was conducted over a period of 2 months between December 2015 and January 2016 to evaluate user experiences of and preferences regarding the platform. Descriptive analysis was adopted to analyze information and its communication effects from December 2014 to March 2017. A total of 472 participants met the inclusion criteria and responded to the survey. High scores were received for the overall rating (4.34 ± 0.67), evidence section (4.30 ± 0.63), learning materials section (4.26 ± 0.65), news section (4.27 ± 0.66), readability (4.38 ± 0.63), design and structure (4.38 ± 0.63), and interactivity (3.58 ± 0.84). As of March 31, 2017, the total number of followers was 28,954. The total number of readings was 584,834. The most current WCI value was 388.72. Our study demonstrated that the mobile-based platform for evidence transfer can promote the accessibility of evidence and meet users' demands. This mobile-based platform is currently available in the WeChat application environment. It will be a wise option for healthcare professionals for the purposes of learning about EBP and disseminating evidence in China.

The development and application of a quantitative peptide microarray platform to SH2 domain specificity space

NASA Astrophysics Data System (ADS)

Engelmann, Brett Warren

The Src homology 2 (SH2) domains evolved alongside protein tyrosine kinases (PTKs) and phosphatases (PTPs) in metazoans to recognize the phosphotyrosine (pY) post-translational modification. The human genome encodes 121 SH2 domains within 111 SH2 domain containing proteins that represent the primary mechanism for cellular signal transduction immediately downstream of PTKs. Despite pY recognition contributing to roughly half of the binding energy, SH2 domains possess substantial binding specificity, or affinity discrimination between phosphopeptide ligands. This specificity is largely imparted by amino acids (AAs) adjacent to the pY, typically from positions +1 to +4 C-terminal to the pY. Much experimental effort has been undertaken to construct preferred binding motifs for many SH2 domains. However, due to limitations in previous experimental methodologies these motifs do not account for the interplay between AAs. It was therefore not known how AAs within the context of individual peptides function to impart SH2 domain specificity. In this work we identified the critical role context plays in defining SH2 domain specificity for physiological ligands. We also constructed a high quality interactome using 50 SH2 domains and 192 physiological ligands. We next developed a quantitative high-throughput (Q-HTP) peptide microarray platform to assess the affinities four SH2 domains have for 124 physiological ligands. We demonstrated the superior characteristics of our platform relative to preceding approaches and validated our results using established biophysical techniques, literature corroboration, and predictive algorithms. The quantitative information provided by the arrays was leveraged to investigate SH2 domain binding distributions and identify points of binding overlap. Our microarray derived affinity estimates were integrated to produce quantitative interaction motifs capable of predicting interactions. Furthermore, our microarrays proved capable of resolving

Kinematics of an in-parallel actuated manipulator based on the Stewart platform mechanism

NASA Technical Reports Server (NTRS)

Williams, Robert L., II

1992-01-01

This paper presents kinematic equations and solutions for an in-parallel actuated robotic mechanism based on Stewart's platform. These equations are required for inverse position and resolved rate (inverse velocity) platform control. NASA LaRC has a Vehicle Emulator System (VES) platform designed by MIT which is based on Stewart's platform. The inverse position solution is straight-forward and computationally inexpensive. Given the desired position and orientation of the moving platform with respect to the base, the lengths of the prismatic leg actuators are calculated. The forward position solution is more complicated and theoretically has 16 solutions. The position and orientation of the moving platform with respect to the base is calculated given the leg actuator lengths. Two methods are pursued in this paper to solve this problem. The resolved rate (inverse velocity) solution is derived. Given the desired Cartesian velocity of the end-effector, the required leg actuator rates are calculated. The Newton-Raphson Jacobian matrix resulting from the second forward position kinematics solution is a modified inverse Jacobian matrix. Examples and simulations are given for the VES.

Prototype development of a web-based participative decision support platform in risk management

NASA Astrophysics Data System (ADS)

Aye, Zar Chi; Olyazadeh, Roya; Jaboyedoff, Michel; Derron, Marc-Henri

2014-05-01

This paper discusses the proposed background architecture and prototype development of an internet-based decision support system (DSS) in the field of natural hazards and risk management using open-source geospatial software and web technologies. It is based on a three-tier, client-server architecture with the support of boundless (opengeo) framework and its client side SDK application environment using customized gxp components and data utility classes. The main purpose of the system is to integrate the workflow of risk management systematically with the diverse involvement of stakeholders from different organizations dealing with natural hazards and risk for evaluation of management measures through the active online participation approach. It aims to develop an adaptive user friendly, web-based environment that allows the users to set up risk management strategies based on actual context and data by integrating web-GIS and DSS functionality associated with process flow and other visualization tools. Web-GIS interface has been integrated within the DSS to deliver maps and provide certain geo-processing capabilities on the web, which can be easily accessible and shared by different organizations located in case study sites of the project. This platform could be envisaged not only as a common web-based platform for the centralized sharing of data such as hazard maps, elements at risk maps and additional information but also to ensure an integrated platform of risk management where the users could upload data, analyze risk and identify possible alternative scenarios for risk reduction especially for floods and landslides, either quantitatively or qualitatively depending on the risk information provided by the stakeholders in case study regions. The level of involvement, access to and interaction with the provided functionality of the system varies depending on the roles and responsibilities of the stakeholders, for example, only the experts (planners, geological

The Study on Collaborative Manufacturing Platform Based on Agent

NASA Astrophysics Data System (ADS)

Zhang, Xiao-yan; Qu, Zheng-geng

To fulfill the trends of knowledge-intensive in collaborative manufacturing development, we have described multi agent architecture supporting knowledge-based platform of collaborative manufacturing development platform. In virtue of wrapper service and communication capacity agents provided, the proposed architecture facilitates organization and collaboration of multi-disciplinary individuals and tools. By effectively supporting the formal representation, capture, retrieval and reuse of manufacturing knowledge, the generalized knowledge repository based on ontology library enable engineers to meaningfully exchange information and pass knowledge across boundaries. Intelligent agent technology increases traditional KBE systems efficiency and interoperability and provides comprehensive design environments for engineers.

Study on the E-commerce platform based on the agent

NASA Astrophysics Data System (ADS)

Fu, Ruixue; Qin, Lishuan; Gao, Yinmin

2011-10-01

To solve problem of dynamic integration in e-commerce, the Multi-Agent architecture of electronic commerce platform system based on Agent and Ontology has been introduced, which includes three major types of agent, Ontology and rule collection. In this architecture, service agent and rule are used to realize the business process reengineering, the reuse of software component, and agility of the electronic commerce platform. To illustrate the architecture, a simulation work has been done and the results imply that the architecture provides a very efficient method to design and implement the flexible, distributed, open and intelligent electronic commerce platform system to solve problem of dynamic integration in ecommerce. The objective of this paper is to illustrate the architecture of electronic commerce platform system, and the approach how Agent and Ontology support the electronic commerce platform system.

Tox21 Enricher: Web-based Chemical/Biological Functional Annotation Analysis Tool Based on Tox21 Toxicity Screening Platform.

PubMed

Hur, Junguk; Danes, Larson; Hsieh, Jui-Hua; McGregor, Brett; Krout, Dakota; Auerbach, Scott

2018-05-01

The US Toxicology Testing in the 21st Century (Tox21) program was established to develop more efficient and human-relevant toxicity assessment methods. The Tox21 program screens >10,000 chemicals using quantitative high-throughput screening (qHTS) of assays that measure effects on toxicity pathways. To date, more than 70 assays have yielded >12 million concentration-response curves. The patterns of activity across assays can be used to define similarity between chemicals. Assuming chemicals with similar activity profiles have similar toxicological properties, we may infer toxicological properties based on its neighbourhood. One approach to inference is chemical/biological annotation enrichment analysis. Here, we present Tox21 Enricher, a web-based chemical annotation enrichment tool for the Tox21 toxicity screening platform. Tox21 Enricher identifies over-represented chemical/biological annotations among lists of chemicals (neighbourhoods), facilitating the identification of the toxicological properties and mechanisms in the chemical set. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

HuMOVE: a low-invasive wearable monitoring platform in sexual medicine.

PubMed

Ciuti, Gastone; Nardi, Matteo; Valdastri, Pietro; Menciassi, Arianna; Basile Fasolo, Ciro; Dario, Paolo

2014-10-01

To investigate an accelerometer-based wearable system, named Human Movement (HuMOVE) platform, designed to enable quantitative and continuous measurement of sexual performance with minimal invasiveness and inconvenience for users. Design, implementation, and development of HuMOVE, a wearable platform equipped with an accelerometer sensor for monitoring inertial parameters for sexual performance assessment and diagnosis, were performed. The system enables quantitative measurement of movement parameters during sexual intercourse, meeting the requirements of wearability, data storage, sampling rate, and interfacing methods, which are fundamental for human sexual intercourse performance analysis. HuMOVE was validated through characterization using a controlled experimental test bench and evaluated in a human model during simulated sexual intercourse conditions. HuMOVE demonstrated to be a robust and quantitative monitoring platform and a reliable candidate for sexual performance evaluation and diagnosis. Characterization analysis on the controlled experimental test bench demonstrated an accurate correlation between the HuMOVE system and data from a reference displacement sensor. Experimental tests in the human model during simulated intercourse conditions confirmed the accuracy of the sexual performance evaluation platform and the effectiveness of the selected and derived parameters. The obtained outcomes also established the project expectations in terms of usability and comfort, evidenced by the questionnaires that highlighted the low invasiveness and acceptance of the device. To the best of our knowledge, HuMOVE platform is the first device for human sexual performance analysis compatible with sexual intercourse; the system has the potential to be a helpful tool for physicians to accurately classify sexual disorders, such as premature or delayed ejaculation. Copyright © 2014 Elsevier Inc. All rights reserved.

Analysis and experimental evaluation of a Stewart platform-based force/torque sensor

NASA Technical Reports Server (NTRS)

Nguyen, Charles C.; Antrazi, Sami S.

1992-01-01

The kinematic analysis and experimentation of a force/torque sensor whose design is based on the mechanism of the Stewart Platform are discussed. Besides being used for measurement of forces/torques, the sensor also serves as a compliant platform which provides passive compliance during a robotic assembly task. It consists of two platforms, the upper compliant platform (UCP) and the lower compliant platform (LCP), coupled together through six spring-loaded pistons whose length variations are measured by six linear voltage differential transformers (LVDT) mounted along the pistons. Solutions to the forward and inverse kinematics of the force sensor are derived. Based on the known spring constant and the piston length changes, forces/torques applied to the LCP gripper are computed using vector algebra. Results of experiments conducted to evaluate the sensing capability of the force sensor are reported and discussed.

Quantitative mass spectrometry: an overview

NASA Astrophysics Data System (ADS)

Urban, Pawel L.

2016-10-01

Mass spectrometry (MS) is a mainstream chemical analysis technique in the twenty-first century. It has contributed to numerous discoveries in chemistry, physics and biochemistry. Hundreds of research laboratories scattered all over the world use MS every day to investigate fundamental phenomena on the molecular level. MS is also widely used by industry-especially in drug discovery, quality control and food safety protocols. In some cases, mass spectrometers are indispensable and irreplaceable by any other metrological tools. The uniqueness of MS is due to the fact that it enables direct identification of molecules based on the mass-to-charge ratios as well as fragmentation patterns. Thus, for several decades now, MS has been used in qualitative chemical analysis. To address the pressing need for quantitative molecular measurements, a number of laboratories focused on technological and methodological improvements that could render MS a fully quantitative metrological platform. In this theme issue, the experts working for some of those laboratories share their knowledge and enthusiasm about quantitative MS. I hope this theme issue will benefit readers, and foster fundamental and applied research based on quantitative MS measurements. This article is part of the themed issue 'Quantitative mass spectrometry'.

A web-based online collaboration platform for formulating engineering design projects

NASA Astrophysics Data System (ADS)

Varikuti, Sainath

Effective communication and collaboration among students, faculty and industrial sponsors play a vital role while formulating and solving engineering design projects. With the advent in the web technology, online platforms and systems have been proposed to facilitate interactions and collaboration among different stakeholders in the context of senior design projects. However, there are noticeable gaps in the literature with respect to understanding the effects of online collaboration platforms for formulating engineering design projects. Most of the existing literature is focused on exploring the utility of online platforms on activities after the problem is defined and teams are formed. Also, there is a lack of mechanisms and tools to guide the project formation phase in senior design projects, which makes it challenging for students and faculty to collaboratively develop and refine project ideas and to establish appropriate teams. In this thesis a web-based online collaboration platform is designed and implemented to share, discuss and obtain feedback on project ideas and to facilitate collaboration among students and faculty prior to the start of the semester. The goal of this thesis is to understand the impact of an online collaboration platform for formulating engineering design projects, and how a web-based online collaboration platform affects the amount of interactions among stakeholders during the early phases of design process. A survey measuring the amount of interactions among students and faculty is administered. Initial findings show a marked improvement in the students' ability to share project ideas and form teams with other students and faculty. Students found the online platform simple to use. The suggestions for improving the tool generally included features that were not necessarily design specific, indicating that the underlying concept of this collaborative platform provides a strong basis and can be extended for future online platforms

Analysis of offshore platforms lifting with fixed pile structure type (fixed platform) based on ASD89

NASA Astrophysics Data System (ADS)

Sugianto, Agus; Indriani, Andi Marini

2017-11-01

Platform construction GTS (Gathering Testing Sattelite) is offshore construction platform with fix pile structure type/fixed platform functioning to support the mining of petroleum exploitation. After construction fabrication process platform was moved to barges, then shipped to the installation site. Moving process is generally done by pull or push based on construction design determined when planning. But at the time of lifting equipment/cranes available in the work area then the moving process can be done by lifting so that moving activity can be implemented more quickly of work. This analysis moving process of GTS platform in a different way that is generally done to GTS platform types by lifting using problem is construction reinforcement required, so the construction can be moved by lifting with analyzing and checking structure working stress that occurs due to construction moving process by lifting AISC code standard and analysis using the SAP2000 structure analysis program. The analysis result showed that existing condition cannot be moved by lifting because stress ratio is above maximum allowable value that is 0.950 (AISC-ASD89). Overstress occurs on the member 295 and 324 with stress ratio value 0.97 and 0.95 so that it is required structural reinforcement. Box plate aplication at both members so that it produces stress ratio values 0.78 at the member 295 and stress ratio of 0.77 at the member 324. These results indicate that the construction have qualified structural reinforcement for being moved by lifting.

Assessing present and future climate changes in Siberia and their regional socioeconomic consequences using a web-based big data geoprocessing platform

NASA Astrophysics Data System (ADS)

Alexeev, V. A.; Gordov, E. P.

2016-12-01

Recently initiated collaborative research project is presented. Its main objective is to develop high spatial and temporal resolution datasets for studying the ongoing and future climate changes in Siberia, caused by global and regional processes in the atmosphere and the ocean. This goal will be achieved by using a set of regional and global climate models for the analysis of the mechanisms of climate change and quantitative assessment of changes in key climate variables, including analysis of extreme weather and climate events and their dynamics, evaluation of the frequency, amplitude and the risks caused by the extreme events in the region. The main practical application of the project is to provide experts, stakeholders and the public with quantitative information about the future climate change in Siberia obtained on the base of a computational web- geoinformation platform. The thematic platform will be developed in order to facilitate processing and analysis of high resolution georeferenced datasets that will be delivered and made available to scientific community, policymakes and other end users as a result of the project. Software packages will be developed to implement calculation of various climatological indicators in order to characterize and diagnose climate change and its dynamics, as well as to archive results in digital form of electronic maps (GIS layers). By achieving these goals the project will provide science based tools necessary for developing mitigation measures for adapting to climate change and reducing negative impact on the population and infrastructure of the region. Financial support of the computational web- geoinformation platform prototype development by the RF Ministry of Education and Science under Agreement 14.613.21.0037 (RFMEFI61315X0037) is acknowledged.

GOLIAH: A Gaming Platform for Home-Based Intervention in Autism – Principles and Design

PubMed Central

Bono, Valentina; Narzisi, Antonio; Jouen, Anne-Lise; Tilmont, Elodie; Hommel, Stephane; Jamal, Wasifa; Xavier, Jean; Billeci, Lucia; Maharatna, Koushik; Wald, Mike; Chetouani, Mohamed; Cohen, David; Muratori, Filippo

2016-01-01

Children with Autism need intensive intervention and this is challenging in terms of manpower, costs, and time. Advances in Information Communication Technology and computer gaming may help in this respect by creating a nomadically deployable closed-loop intervention system involving the child and active participation of parents and therapists. An automated serious gaming platform enabling intensive intervention in nomadic settings has been developed by mapping two pivotal skills in autism spectrum disorder: Imitation and Joint Attention (JA). Eleven games – seven Imitations and four JA – were derived from the Early Start Denver Model. The games involved application of visual and audio stimuli with multiple difficulty levels and a wide variety of tasks and actions pertaining to the Imitation and JA. The platform runs on mobile devices and allows the therapist to (1) characterize the child’s initial difficulties/strengths, ensuring tailored and adapted intervention by choosing appropriate games and (2) investigate and track the temporal evolution of the child’s progress through a set of automatically extracted quantitative performance metrics. The platform allows the therapist to change the game or its difficulty levels during the intervention depending on the child’s progress. Performance of the platform was assessed in a 3-month open trial with 10 children with autism (Trial ID: NCT02560415, Clinicaltrials.gov). The children and the parents participated in 80% of the sessions both at home (77.5%) and at the hospital (90%). All children went through all the games but, given the diversity of the games and the heterogeneity of children profiles and abilities, for a given game the number of sessions dedicated to the game varied and could be tailored through automatic scoring. Parents (N = 10) highlighted enhancement in the child’s concentration, flexibility, and self-esteem in 78, 89, and 44% of the cases, respectively, and 56% observed an enhanced

[Dental education for college students based on WeChat public platform].

PubMed

Chen, Chuan-Jun; Sun, Tan

2016-06-01

The authors proposed a model for dental education based on WeChat public platform. In this model, teachers send various kinds of digital teaching information such as PPT，word and video to the WeChat public platform and students share the information for preview before class and differentiate the key-point knowledge from those information for in-depth learning in class. Teachers also send reference materials for expansive learning after class. Questionaire through the WeChat public platform is used to evaluate teaching effect of teachers and improvement may be taken based on the feedback questionnaire. A discussion and interaction based on WeCchat between students and teacher can be aroused on a specific topic to reach a proper solution. With technique development of mobile terminal, mobile class will come true in near future.

Grid-based platform for training in Earth Observation

NASA Astrophysics Data System (ADS)

Petcu, Dana; Zaharie, Daniela; Panica, Silviu; Frincu, Marc; Neagul, Marian; Gorgan, Dorian; Stefanut, Teodor

2010-05-01

GiSHEO platform [1] providing on-demand services for training and high education in Earth Observation is developed, in the frame of an ESA funded project through its PECS programme, to respond to the needs of powerful education resources in remote sensing field. It intends to be a Grid-based platform of which potential for experimentation and extensibility are the key benefits compared with a desktop software solution. Near-real time applications requiring simultaneous multiple short-time-response data-intensive tasks, as in the case of a short time training event, are the ones that are proved to be ideal for this platform. The platform is based on Globus Toolkit 4 facilities for security and process management, and on the clusters of four academic institutions involved in the project. The authorization uses a VOMS service. The main public services are the followings: the EO processing services (represented through special WSRF-type services); the workflow service exposing a particular workflow engine; the data indexing and discovery service for accessing the data management mechanisms; the processing services, a collection allowing easy access to the processing platform. The WSRF-type services for basic satellite image processing are reusing free image processing tools, OpenCV and GDAL. New algorithms and workflows were develop to tackle with challenging problems like detecting the underground remains of old fortifications, walls or houses. More details can be found in [2]. Composed services can be specified through workflows and are easy to be deployed. The workflow engine, OSyRIS (Orchestration System using a Rule based Inference Solution), is based on DROOLS, and a new rule-based workflow language, SILK (SImple Language for worKflow), has been built. Workflow creation in SILK can be done with or without a visual designing tools. The basics of SILK are the tasks and relations (rules) between them. It is similar with the SCUFL language, but not relying on XML in

General Platform for Systematic Quantitative Evaluation of Small-Molecule Permeability in Bacteria

PubMed Central

2015-01-01

The chemical features that impact small-molecule permeability across bacterial membranes are poorly understood, and the resulting lack of tools to predict permeability presents a major obstacle to the discovery and development of novel antibiotics. Antibacterials are known to have vastly different structural and physicochemical properties compared to nonantiinfective drugs, as illustrated herein by principal component analysis (PCA). To understand how these properties influence bacterial permeability, we have developed a systematic approach to evaluate the penetration of diverse compounds into bacteria with distinct cellular envelopes. Intracellular compound accumulation is quantitated using LC-MS/MS, then PCA and Pearson pairwise correlations are used to identify structural and physicochemical parameters that correlate with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations between chemical structure and permeability that differ among the various bacteria. Effects of cotreatment with efflux pump inhibitors were also investigated. This sets the stage for use of this platform in larger prospective analyses of diverse chemotypes to identify global relationships between chemical structure and bacterial permeability that would enable the development of predictive tools to accelerate antibiotic drug discovery. PMID:25198656

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

Multimodal Microchannel and Nanowell-Based Microfluidic Platforms for Bioimaging

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

Geng, Tao; Smallwood, Chuck R.; Zhu, Ying

2017-03-30

Modern live-cell imaging approaches permit real-time visualization of biological processes. However, limitations for unicellular organism trapping, culturing and long-term imaging can preclude complete understanding of how such microorganisms respond to perturbations in their local environment or linking single-cell variability to whole population dynamics. We have developed microfluidic platforms to overcome prior technical bottlenecks to allow both chemostat and compartmentalized cellular growth conditions using the same device. Additionally, a nanowell-based platform enables a high throughput approach to scale up compartmentalized imaging optimized within the microfluidic device. These channel and nanowell platforms are complementary, and both provide fine control over the localmore » environment as well as the ability to add/replace media components at any experimental time point.« less

Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images.

PubMed

Spagnolo, Daniel M; Al-Kofahi, Yousef; Zhu, Peihong; Lezon, Timothy R; Gough, Albert; Stern, Andrew M; Lee, Adrian V; Ginty, Fiona; Sarachan, Brion; Taylor, D Lansing; Chennubhotla, S Chakra

2017-11-01

We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. The THRIVE platform provides an integrated workflow for analyzing whole-slide immunofluorescence images and tissue microarrays, including algorithms for segmentation, quantification, and heterogeneity analysis. THRIVE promotes flexible deployment, a maintainable code base using open-source libraries, and an extensible framework for customizing algorithms with ease. THRIVE was designed with highly multiplexed immunofluorescence images in mind, and, by providing a platform to efficiently analyze high-dimensional immunofluorescence signals, we hope to advance these data toward mainstream adoption in cancer research. Cancer Res; 77(21); e71-74. ©2017 AACR . ©2017 American Association for Cancer Research.

Mobile work platform for initial lunar base construction

NASA Technical Reports Server (NTRS)

Brazell, James W.; Maclaren, Brice K.; Mcmurray, Gary V.; Williams, Wendell M.

1992-01-01

Described is a system of equipment intended for site preparation and construction of a lunar base. The proximate era of lunar exploration and the initial phase of outpost habitation are addressed. Drilling, leveling, trenching, and cargo handling are within the scope of the system's capabilities. The centerpiece is a three-legged mobile work platform, named SKITTER. Using standard interfaces, the system is modular in nature and analogous to the farmer's tractor and implement set. Conceptually somewhat different from their Earthbound counterparts, the implements are designed to take advantage of the lunar environment as well as the capabilities of the work platform. The proposed system is mechanically simple and weight efficient.

A Web-Based Earth-Systems Knowledge Portal and Collaboration Platform

NASA Astrophysics Data System (ADS)

D'Agnese, F. A.; Turner, A. K.

2010-12-01

In support of complex water-resource sustainability projects in the Great Basin region of the United States, Earth Knowledge, Inc. has developed several web-based data management and analysis platforms that have been used by its scientists, clients, and public to facilitate information exchanges, collaborations, and decision making. These platforms support accurate water-resource decision-making by combining second-generation internet (Web 2.0) technologies with traditional 2D GIS and web-based 2D and 3D mapping systems such as Google Maps, and Google Earth. Most data management and analysis systems use traditional software systems to address the data needs and usage behavior of the scientific community. In contrast, these platforms employ more accessible open-source and “off-the-shelf” consumer-oriented, hosted web-services. They exploit familiar software tools using industry standard protocols, formats, and APIs to discover, process, fuse, and visualize earth, engineering, and social science datasets. Thus, they respond to the information needs and web-interface expectations of both subject-matter experts and the public. Because the platforms continue to gather and store all the contributions of their broad-spectrum of users, each new assessment leverages the data, information, and expertise derived from previous investigations. In the last year, Earth Knowledge completed a conceptual system design and feasibility study for a platform, which has a Knowledge Portal providing access to users wishing to retrieve information or knowledge developed by the science enterprise and a Collaboration Environment Module, a framework that links the user-access functions to a Technical Core supporting technical and scientific analyses including Data Management, Analysis and Modeling, and Decision Management, and to essential system administrative functions within an Administrative Module. The over-riding technical challenge is the design and development of a single

Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies.

PubMed

Lee, Jinho; Geiss, Gary K; Demirkan, Gokhan; Vellano, Christopher P; Filanoski, Brian; Lu, Yiling; Ju, Zhenlin; Yu, Shuangxing; Guo, Huifang; Bogatzki, Lisa Y; Carter, Warren; Meredith, Rhonda K; Krishnamurthy, Savitri; Ding, Zhiyong; Beechem, Joseph M; Mills, Gordon B

2018-06-01

Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed "batch effects" which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Free web-based modelling platform for managed aquifer recharge (MAR) applications

NASA Astrophysics Data System (ADS)

Stefan, Catalin; Junghanns, Ralf; Glaß, Jana; Sallwey, Jana; Fatkhutdinov, Aybulat; Fichtner, Thomas; Barquero, Felix; Moreno, Miguel; Bonilla, José; Kwoyiga, Lydia

2017-04-01

Managed aquifer recharge represents a valuable instrument for sustainable water resources management. The concept implies purposeful infiltration of surface water into underground for later recovery or environmental benefits. Over decades, MAR schemes were successfully installed worldwide for a variety of reasons: to maximize the natural storage capacity of aquifers, physical aquifer management, water quality management, and ecological benefits. The INOWAS-DSS platform provides a collection of free web-based tools for planning, management and optimization of main components of MAR schemes. The tools are grouped into 13 specific applications that cover most relevant challenges encountered at MAR sites, both from quantitative and qualitative perspectives. The applications include among others the optimization of MAR site location, the assessment of saltwater intrusion, the restoration of groundwater levels in overexploited aquifers, the maximization of natural storage capacity of aquifers, the improvement of water quality, the design and operational optimization of MAR schemes, clogging development and risk assessment. The platform contains a collection of about 35 web-based tools of various degrees of complexity, which are either included in application specific workflows or used as standalone modelling instruments. Among them are simple tools derived from data mining and empirical equations, analytical groundwater related equations, as well as complex numerical flow and transport models (MODFLOW, MT3DMS and SEAWAT). Up to now, the simulation core of the INOWAS-DSS, which is based on the finite differences groundwater flow model MODFLOW, is implemented and runs on the web. A scenario analyser helps to easily set up and evaluate new management options as well as future development such as land use and climate change and compare them to previous scenarios. Additionally simple tools such as analytical equations to assess saltwater intrusion are already running online

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

NASA Astrophysics Data System (ADS)

Yang, Weiqiang; Dong, Yiqiang

2018-05-01

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

A Software Platform for Post-Processing Waveform-Based NDE

NASA Technical Reports Server (NTRS)

Roth, Donald J.; Martin, Richard E.; Seebo, Jeff P.; Trinh, Long B.; Walker, James L.; Winfree, William P.

2007-01-01

Ultrasonic, microwave, and terahertz nondestructive evaluation imaging systems generally require the acquisition of waveforms at each scan point to form an image. For such systems, signal and image processing methods are commonly needed to extract information from the waves and improve resolution of, and highlight, defects in the image. Since some similarity exists for all waveform-based NDE methods, it would seem a common software platform containing multiple signal and image processing techniques to process the waveforms and images makes sense where multiple techniques, scientists, engineers, and organizations are involved. This presentation describes NASA Glenn Research Center's approach in developing a common software platform for processing waveform-based NDE signals and images. This platform is currently in use at NASA Glenn and at Lockheed Martin Michoud Assembly Facility for processing of pulsed terahertz and ultrasonic data. Highlights of the software operation will be given. A case study will be shown for use with terahertz data. The authors also request scientists and engineers who are interested in sharing customized signal and image processing algorithms to contribute to this effort by letting the authors code up and include these algorithms in future releases.

Structurally Integrated Photoluminescent Chemical and Biological Sensors: An Organic Light-Emitting Diode-Based Platform

NASA Astrophysics Data System (ADS)

Shinar, J.; Shinar, R.

The chapter describes the development, advantages, challenges, and potential of an emerging, compact photoluminescence-based sensing platform for chemical and biological analytes, including multiple analytes. In this platform, the excitation source is an array of organic light-emitting device (OLED) pixels that is structurally integrated with the sensing component. Steps towards advanced integration with additionally a thin-film-based photodetector are also described. The performance of the OLED-based sensing platform is examined for gas-phase and dissolved oxygen, glucose, lactate, ethanol, hydrazine, and anthrax lethal factor.

Quantitative geomorphologic studies from spaceborne platforms

NASA Technical Reports Server (NTRS)

Williams, R. S., Jr.

1985-01-01

Although LANDSAT images of our planet represent a quantum improvement in the availability of a global image-data set for independent or comparative regional geomorphic studies of landforms, such images have several limitations which restrict their suitability for quantitative geomorphic investigations. The three most serious deficiencies are: (1) photogrammetric inaccuracies, (2) two-dimensional nature of the data, and (3) spatial resolution. These deficiencies are discussed, as well as the use of stereoscopic images and laser altimeter data.

Extreme sensitivity biosensing platform based on hyperbolic metamaterials

NASA Astrophysics Data System (ADS)

Sreekanth, Kandammathe Valiyaveedu; Alapan, Yunus; Elkabbash, Mohamed; Ilker, Efe; Hinczewski, Michael; Gurkan, Umut A.; de Luca, Antonio; Strangi, Giuseppe

2016-06-01

Optical sensor technology offers significant opportunities in the field of medical research and clinical diagnostics, particularly for the detection of small numbers of molecules in highly diluted solutions. Several methods have been developed for this purpose, including label-free plasmonic biosensors based on metamaterials. However, the detection of lower-molecular-weight (<500 Da) biomolecules in highly diluted solutions is still a challenging issue owing to their lower polarizability. In this context, we have developed a miniaturized plasmonic biosensor platform based on a hyperbolic metamaterial that can support highly confined bulk plasmon guided modes over a broad wavelength range from visible to near infrared. By exciting these modes using a grating-coupling technique, we achieved different extreme sensitivity modes with a maximum of 30,000 nm per refractive index unit (RIU) and a record figure of merit (FOM) of 590. We report the ability of the metamaterial platform to detect ultralow-molecular-weight (244 Da) biomolecules at picomolar concentrations using a standard affinity model streptavidin-biotin.

Transaction-based building controls framework, Volume 2: Platform descriptive model and requirements

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

Akyol, Bora A.; Haack, Jereme N.; Carpenter, Brandon J.

Transaction-based Building Controls (TBC) offer a control systems platform that provides an agent execution environment that meets the growing requirements for security, resource utilization, and reliability. This report outlines the requirements for a platform to meet these needs and describes an illustrative/exemplary implementation.

Simultaneous and quantitative monitoring of co-cultured Pseudomonas aeruginosa and Staphylococcus aureus with antibiotics on a diffusometric platform

NASA Astrophysics Data System (ADS)

Chung, Chih-Yao; Wang, Jhih-Cheng; Chuang, Han-Sheng

2017-04-01

Successful treatments against bacterial infections depend on antimicrobial susceptibility testing (AST). However, conventional AST requires more than 24 h to obtain an outcome, thereby contributing to high patient mortality. An antibiotic therapy based on experiences is therefore necessary for saving lives and escalating the emergence of multidrug-resistant pathogens. Accordingly, a fast and effective drug screen is necessary for the appropriate administration of antibiotics. The mixed pathogenic nature of infectious diseases emphasizes the need to develop an assay system for polymicrobial infections. On this basis, we present a novel technique for simultaneous and quantitative monitoring of co-cultured microorganisms by coupling optical diffusometry with bead-based immunoassays. This simple integration simultaneously achieves a rapid AST analysis for two pathogens. Triple color particles were simultaneously recorded and subsequently analyzed by functionalizing different fluorescent color particles with dissimilar pathogen-specific antibodies. Results suggested that the effect of the antibiotic, gentamicin, on co-cultured Pseudomonas aeruginosa and Staphylococcus aureus was effectively distinguished by the proposed technique. This study revealed a multiplexed and time-saving (within 2 h) platform with a small sample volume (~0.5 μL) and a low initial bacterial count (50 CFU per droplet, ~105 CFU/mL) for continuously monitoring the growth of co-cultured microorganisms. This technique provides insights into timely therapies against polymicrobial diseases in the near future.

Simulation platform of LEO satellite communication system based on OPNET

NASA Astrophysics Data System (ADS)

Zhang, Yu; Zhang, Yong; Li, Xiaozhuo; Wang, Chuqiao; Li, Haihao

2018-02-01

For the purpose of verifying communication protocol in the low earth orbit (LEO) satellite communication system, an Optimized Network Engineering Tool (OPNET) based simulation platform is built. Using the three-layer modeling mechanism, the network model, the node model and the process model of the satellite communication system are built respectively from top to bottom, and the protocol will be implemented by finite state machine and Proto-C language. According to satellite orbit parameters, orbit files are generated via Satellite Tool Kit (STK) and imported into OPNET, and the satellite nodes move along their orbits. The simulation platform adopts time-slot-driven mode, divides simulation time into continuous time slots, and allocates slot number for each time slot. A resource allocation strategy is simulated on this platform, and the simulation results such as resource utilization rate, system throughput and packet delay are analyzed, which indicate that this simulation platform has outstanding versatility.

Design challenges in nanoparticle-based platforms: Implications for targeted drug delivery systems

NASA Astrophysics Data System (ADS)

Mullen, Douglas Gurnett

Characterization and control of heterogeneous distributions of nanoparticle-ligand components are major design challenges for nanoparticle-based platforms. This dissertation begins with an examination of poly(amidoamine) (PAMAM) dendrimer-based targeted delivery platform. A folic acid targeted modular platform was developed to target human epithelial cancer cells. Although active targeting was observed in vitro, active targeting was not found in vivo using a mouse tumor model. A major flaw of this platform design was that it did not provide for characterization or control of the component distribution. Motivated by the problems experienced with the modular design, the actual composition of nanoparticle-ligand distributions were examined using a model dendrimer-ligand system. High Pressure Liquid Chromatography (HPLC) resolved the distribution of components in samples with mean ligand/dendrimer ratios ranging from 0.4 to 13. A peak fitting analysis enabled the quantification of the component distribution. Quantified distributions were found to be significantly more heterogeneous than commonly expected and standard analytical parameters, namely the mean ligand/nanoparticle ratio, failed to adequately represent the component heterogeneity. The distribution of components was also found to be sensitive to particle modifications that preceded the ligand conjugation. With the knowledge gained from this detailed distribution analysis, a new platform design was developed to provide a system with dramatically improved control over the number of components and with improved batch reproducibility. Using semi-preparative HPLC, individual dendrimer-ligand components were isolated. The isolated dendrimer with precise numbers of ligands were characterized by NMR and analytical HPLC. In total, nine different dendrimer-ligand components were obtained with degrees of purity ≥80%. This system has the potential to serve as a platform to which a precise number of functional molecules

Comparison of Two Commercial Automated Nucleic Acid Extraction and Integrated Quantitation Real-Time PCR Platforms for the Detection of Cytomegalovirus in Plasma

PubMed Central

Tsai, Huey-Pin; Tsai, You-Yuan; Lin, I-Ting; Kuo, Pin-Hwa; Chen, Tsai-Yun; Chang, Kung-Chao; Wang, Jen-Ren

2016-01-01

Quantitation of cytomegalovirus (CMV) viral load in the transplant patients has become a standard practice for monitoring the response to antiviral therapy. The cut-off values of CMV viral load assays for preemptive therapy are different due to the various assay designs employed. To establish a sensitive and reliable diagnostic assay for preemptive therapy of CMV infection, two commercial automated platforms including m2000sp extraction system integrated the Abbott RealTime (m2000rt) and the Roche COBAS AmpliPrep for extraction integrated COBAS Taqman (CAP/CTM) were evaluated using WHO international CMV standards and 110 plasma specimens from transplant patients. The performance characteristics, correlation, and workflow of the two platforms were investigated. The Abbott RealTime assay correlated well with the Roche CAP/CTM assay (R2 = 0.9379, P<0.01). The Abbott RealTime assay exhibited higher sensitivity for the detection of CMV viral load, and viral load values measured with Abbott RealTime assay were on average 0.76 log10 IU/mL higher than those measured with the Roche CAP/CTM assay (P<0.0001). Workflow analysis on a small batch size at one time, using the Roche CAP/CTM platform had a shorter hands-on time than the Abbott RealTime platform. In conclusion, these two assays can provide reliable data for different purpose in a clinical virology laboratory setting. PMID:27494707

Multifunctional sample preparation kit and on-chip quantitative nucleic acid sequence-based amplification tests for microbial detection.

PubMed

Zhao, Xinyan; Dong, Tao

2012-10-16

This study reports a quantitative nucleic acid sequence-based amplification (Q-NASBA) microfluidic platform composed of a membrane-based sampling module, a sample preparation cassette, and a 24-channel Q-NASBA chip for environmental investigations on aquatic microorganisms. This low-cost and highly efficient sampling module, having seamless connection with the subsequent steps of sample preparation and quantitative detection, is designed for the collection of microbial communities from aquatic environments. Eight kinds of commercial membrane filters are relevantly analyzed using Saccharomyces cerevisiae, Escherichia coli, and Staphylococcus aureus as model microorganisms. After the microorganisms are concentrated on the membrane filters, the retentate can be easily conserved in a transport medium (TM) buffer and sent to a remote laboratory. A Q-NASBA-oriented sample preparation cassette is originally designed to extract DNA/RNA molecules directly from the captured cells on the membranes. Sequentially, the extract is analyzed within Q-NASBA chips that are compatible with common microplate readers in laboratories. Particularly, a novel analytical algorithmic method is developed for simple but robust on-chip Q-NASBA assays. The reported multifunctional microfluidic system could detect a few microorganisms quantitatively and simultaneously. Further research should be conducted to simplify and standardize ecological investigations on aquatic environments.

[Application of the life sciences platform based on oracle to biomedical informations].

PubMed

Zhao, Zhi-Yun; Li, Tai-Huan; Yang, Hong-Qiao

2008-03-01

The life sciences platform based on Oracle database technology is introduced in this paper. By providing a powerful data access, integrating a variety of data types, and managing vast quantities of data, the software presents a flexible, safe and scalable management platform for biomedical data processing.

Observation duration analysis for Earth surface features from a Moon-based platform

NASA Astrophysics Data System (ADS)

Ye, Hanlin; Guo, Huadong; Liu, Guang; Ren, Yuanzhen

2018-07-01

Earth System Science is a discipline that performs holistic and comprehensive research on various components of the Earth. One of a key issue for the Earth monitoring and observation is to enhance the observation duration, the time intervals during which the Earth surface features can be observed by sensors. In this work, we propose to utilise the Moon as an Earth observation platform. Thanks to the long distance between the Earth and the Moon, and the vast space on the lunar surface which is suitable for sensor installation, this Earth observation platform could have large spatial coverage, long temporal duration, and could perform multi-layer detection of the Earth. The line of sight between a proposed Moon-based platform and the Earth will change with different lunar surface positions; therefore, in this work, the position of the lunar surface was divided into four regions, including one full observation region and three incomplete observation regions. As existing methods are not able to perform global-scale observations, a Boolean matrix method was established to calculate the necessary observation durations from a Moon-based platform. Based on Jet Propulsion Laboratory (JPL) ephemerides and Earth Orientation Parameters (EOP), a formula was developed to describe the geometrical relationship between the Moon-based platform and Earth surface features in the unified spatial coordinate system and the unified time system. In addition, we compared the observation geometries at different positions on the lunar surface and two parameters that are vital to observation duration calculations were considered. Finally, an analysis method was developed. We found that the observation duration of a given Earth surface feature shows little difference regardless of sensor position within the full observation region. However, the observation duration for sensors in the incomplete observation regions is reduced by at least half. In summary, our results demonstrate the suitability

Portable GMR Handheld Platform for the Detection of Influenza A Virus.

PubMed

Wu, Kai; Klein, Todd; Krishna, Venkatramana D; Su, Diqing; Perez, Andres M; Wang, Jian-Ping

2017-11-22

Influenza A virus (IAV) is a common respiratory pathogen infecting many hosts including humans, pigs (swine influenza virus or SIV), and birds (avian influenza virus or AIV). Monitoring swine and avian influenza viruses in the wild, farms, and live poultry markets is of great significance for human and veterinary public health. A portable, sensitive, and quantitative immunoassay device will be of high demand especially in the rural and resource-limited areas. We report herein our Z-Lab point-of-care (POC) device for sensitive and specific detection of swine influenza viruses with minimum sample handling and laboratory skill requirements. In the present study, a portable and quantitative immunoassay platform based on giant magnetoresistive (GMR) technology is used for the detection of IAV nucleoprotein (NP) and purified H3N2v. Z-Lab displays quantitative results in less than 10 min with sensitivities down to 15 ng/mL and 125 TCID 50 /mL for IAV nucleoprotein and purified H3N2v, respectively. This platform allows lab-testing to be performed outdoors and opens up the applications of immunoassays in nonclinical settings.

Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline

PubMed Central

Schilling, Birgit; Rardin, Matthew J.; MacLean, Brendan X.; Zawadzka, Anna M.; Frewen, Barbara E.; Cusack, Michael P.; Sorensen, Dylan J.; Bereman, Michael S.; Jing, Enxuan; Wu, Christine C.; Verdin, Eric; Kahn, C. Ronald; MacCoss, Michael J.; Gibson, Bradford W.

2012-01-01

Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need for improved label-free approaches. This need is particularly pressing for workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as isobaric tags for relative and absolute quantitation and tandem mass tags may prove problematic or where stable isotope labeling with amino acids in cell culture labeling cannot be readily applied. Skyline is a freely available, open source software tool for quantitative data processing and proteomic analysis. We expanded the capabilities of Skyline to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments. Moreover, unlike existing programs, Skyline MS1 filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. The new quantitative and graphical tools now available in Skyline specifically support interrogation of multiple acquisitions for MS1 filtering, including visual inspection of peak picking and both automated and manual integration, key features often lacking in existing software. In addition, Skyline MS1 filtering displays retention time indicators from underlying MS/MS data contained within the spectral library to ensure proper peak selection. The modular structure of Skyline also provides well defined, customizable data reports and thus allows users to directly connect to existing statistical programs for post hoc data analysis. To demonstrate the utility of the MS1 filtering approach, we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important post-translational modifications: acetylation and phosphorylation, in peptide-centric affinity workflows of increasing complexity using mouse and human models. PMID:22454539

a Web-Based Interactive Platform for Co-Clustering Spatio-Temporal Data

NASA Astrophysics Data System (ADS)

Wu, X.; Poorthuis, A.; Zurita-Milla, R.; Kraak, M.-J.

2017-09-01

Since current studies on clustering analysis mainly focus on exploring spatial or temporal patterns separately, a co-clustering algorithm is utilized in this study to enable the concurrent analysis of spatio-temporal patterns. To allow users to adopt and adapt the algorithm for their own analysis, it is integrated within the server side of an interactive web-based platform. The client side of the platform, running within any modern browser, is a graphical user interface (GUI) with multiple linked visualizations that facilitates the understanding, exploration and interpretation of the raw dataset and co-clustering results. Users can also upload their own datasets and adjust clustering parameters within the platform. To illustrate the use of this platform, an annual temperature dataset from 28 weather stations over 20 years in the Netherlands is used. After the dataset is loaded, it is visualized in a set of linked visualizations: a geographical map, a timeline and a heatmap. This aids the user in understanding the nature of their dataset and the appropriate selection of co-clustering parameters. Once the dataset is processed by the co-clustering algorithm, the results are visualized in the small multiples, a heatmap and a timeline to provide various views for better understanding and also further interpretation. Since the visualization and analysis are integrated in a seamless platform, the user can explore different sets of co-clustering parameters and instantly view the results in order to do iterative, exploratory data analysis. As such, this interactive web-based platform allows users to analyze spatio-temporal data using the co-clustering method and also helps the understanding of the results using multiple linked visualizations.

Design and control of multifunctional sorting and training platform based on PLC control

NASA Astrophysics Data System (ADS)

Wan, Hongqiang; Ge, Shuai; Han, Peiying; Li, Fancong; Zhang, Simiao

2018-05-01

Electromechanical integration, as a multi-disciplinary subject, has been paid much attention by universities and is widely used in the automation production of enterprises. Aiming at the problem of the lack of control among enterprises and the lack of training among colleges and universities, this paper presents a design of multifunctional sorting training platform based on PLC control. Firstly, the structure of the platform is determined and three-dimensional modeling is done. Then design the platform's aerodynamic control and electrical control. Finally, realize the platform sorting function through PLC programming and configuration software development. The training platform can be used to design the practical training experiment, which has a strong advance and pertinence in the electromechanical integration teaching. At the same time, the platform makes full use of modular thinking to make the sorting modules more flexible. Compared with the traditional training platform, its teaching effect is more significant.

Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments

PubMed Central

Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

2017-01-01

High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments. PMID:28835734

Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments.

PubMed

Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

2017-01-01

High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments.

A new fusion protein platform for quantitatively measuring activity of multiple proteases

PubMed Central

2014-01-01

Background Recombinant proteins fused with specific cleavage sequences are widely used as substrate for quantitatively analyzing the activity of proteases. Here we propose a new fusion platform for multiple proteases, by using diaminopropionate ammonia-lyase (DAL) as the fusion protein. It was based on the finding that a fused His6-tag could significantly decreases the activities of DAL from E. coli (eDAL) and Salmonella typhimurium (sDAL). Previously, we have shown that His6GST-tagged eDAL could be used to determine the activity of tobacco etch virus protease (TEVp) under different temperatures or in the denaturant at different concentrations. In this report, we will assay different tags and cleavage sequences on DAL for expressing yield in E. coli, stability of the fused proteins and performance of substrate of other common proteases. Results We tested seven different protease cleavage sequences (rhinovirus 3C, TEV protease, factor Xa, Ssp DnaB intein, Sce VMA1 intein, thrombin and enterokinase), three different tags (His6, GST, CBD and MBP) and two different DALs (eDAL and sDAL), for their performance as substrate to the seven corresponding proteases. Among them, we found four active DAL-fusion substrates suitable for TEVp, factor Xa, thrombin and DnaB intein. Enterokinase cleaved eDAL at undesired positions and did not process sDAL. Substitution of GST with MBP increase the expression level of the fused eDAL and this fusion protein was suitable as a substrate for analyzing activity of rhinovirus 3C. We demonstrated that SUMO protease Ulp1 with a N-terminal His6-tag or MBP tag displayed different activity using the designed His6SUMO-eDAL as substrate. Finally, owing to the high level of the DAL-fusion protein in E. coli, these protein substrates can also be detected directly from the crude extract. Conclusion The results show that our designed DAL-fusion proteins can be used to quantify the activities of both sequence- and conformational-specific proteases, with

Tumor-on-a-chip platforms for assessing nanoparticle-based cancer therapy.

PubMed

Wang, Yimin; Cuzzucoli, Fabio; Escobar, Andres; Lu, Siming; Liang, Liguo; Wang, ShuQi

2018-08-17

Cancer has become the most prevalent cause of deaths, placing a huge economic and healthcare burden worldwide. Nanoparticles (NPs), as a key component of nanomedicine, provide alternative options for promoting the efficacy of cancer therapy. Current conventional cancer models have limitations in predicting the effects of various cancer treatments. To overcome these limitations, biomimetic and novel 'tumor-on-a-chip' platforms have emerged with other innovative biomedical engineering methods that enable the evaluation of NP-based cancer therapy. In this review, we first describe cancer models for evaluation of NP-based cancer therapy techniques, and then present the latest advances in 'tumor-on-a-chip' platforms that can potentially facilitate clinical translation of NP-based cancer therapies.

OptoBase: A web platform for molecular optogenetics.

PubMed

Kolar, Katja; Knobloch, Christian; Stork, Hendrik; Žnidarič, Matej; Weber, Wilfried

2018-06-18

OptoBase is an online platform for molecular optogenetics. At its core is a hand-annotated and ontology-supported database that aims to cover all existing optogenetic switches and publications, which is further complemented with a collection of convenient optogenetics-related web tools. OptoBase is meant for both expert optogeneticists, to easily keep track of the field, as well as for all researchers who find optogenetics inviting as a powerful tool to address their biological questions of interest. It is available at https://www.optobase.org. This work also presents OptoBase-based analysis of the trends in molecular optogenetics.

A software platform for continuum modeling of ion channels based on unstructured mesh

NASA Astrophysics Data System (ADS)

Tu, B.; Bai, S. Y.; Chen, M. X.; Xie, Y.; Zhang, L. B.; Lu, B. Z.

2014-01-01

Most traditional continuum molecular modeling adopted finite difference or finite volume methods which were based on a structured mesh (grid). Unstructured meshes were only occasionally used, but an increased number of applications emerge in molecular simulations. To facilitate the continuum modeling of biomolecular systems based on unstructured meshes, we are developing a software platform with tools which are particularly beneficial to those approaches. This work describes the software system specifically for the simulation of a typical, complex molecular procedure: ion transport through a three-dimensional channel system that consists of a protein and a membrane. The platform contains three parts: a meshing tool chain for ion channel systems, a parallel finite element solver for the Poisson-Nernst-Planck equations describing the electrodiffusion process of ion transport, and a visualization program for continuum molecular modeling. The meshing tool chain in the platform, which consists of a set of mesh generation tools, is able to generate high-quality surface and volume meshes for ion channel systems. The parallel finite element solver in our platform is based on the parallel adaptive finite element package PHG which wass developed by one of the authors [1]. As a featured component of the platform, a new visualization program, VCMM, has specifically been developed for continuum molecular modeling with an emphasis on providing useful facilities for unstructured mesh-based methods and for their output analysis and visualization. VCMM provides a graphic user interface and consists of three modules: a molecular module, a meshing module and a numerical module. A demonstration of the platform is provided with a study of two real proteins, the connexin 26 and hemolysin ion channels.

Simple and Sensitive Quantification of MicroRNAs via PS@Au Microspheres-Based DNA Probes and DSN-Assisted Signal Amplification Platform.

PubMed

Zhao, Qian; Piao, Jiafang; Peng, Weipan; Wang, Yang; Zhang, Bo; Gong, Xiaoqun; Chang, Jin

2018-01-31

Identifying the microRNA (miRNA) expression level can provide critical information for early diagnosis of cancers or monitoring the cancer therapeutic efficacy. This paper focused on a kind of gold-nanoparticle-coated polystyrene microbeads (PS@Au microspheres)-based DNA probe as miRNA capture and duplex-specific nuclease (DSN) signal amplification platform based on an RGB value readout for detection of miRNAs. In virtue of the outstanding selectivity and simple experimental operation, 5'-fluorochrome-labeled molecular beacons (MBs) were immobilized on PS@Au microspheres via their 3'-thiol, in the wake of the fluorescence quenching by nanoparticle surface energy transfer (NSET). Target miRNAs were captured by the PS@Au microspheres-based DNA probe through DNA/RNA hybridization. DSN enzyme subsequently selectively cleaved the DNA to recycle the target miRNA and release of fluorophores, thereby triggering the signal amplification with more free fluorophores. The RGB value measurement enabled a detection limit of 50 fM, almost 4 orders of magnitude lower than PS@Au microspheres-based DNA probe detection without DSN. Meanwhile, by different encoding of dyes, miRNA-21 and miRNA-10b were simultaneously detected in the same sample. Considering the ability for quantitation, high sensitivity, and convenient merits, the PS@Au microspheres-based DNA probe and DSN signal amplification platform supplied valuable information for early diagnosis of cancers.

Dielectrophoresis-based microfluidic platforms for cancer diagnostics.

PubMed

Chan, Jun Yuan; Ahmad Kayani, Aminuddin Bin; Md Ali, Mohd Anuar; Kok, Chee Kuang; Yeop Majlis, Burhanuddin; Hoe, Susan Ling Ling; Marzuki, Marini; Khoo, Alan Soo-Beng; Ostrikov, Kostya Ken; Ataur Rahman, Md; Sriram, Sharath

2018-01-01

The recent advancement of dielectrophoresis (DEP)-enabled microfluidic platforms is opening new opportunities for potential use in cancer disease diagnostics. DEP is advantageous because of its specificity, low cost, small sample volume requirement, and tuneable property for microfluidic platforms. These intrinsic advantages have made it especially suitable for developing microfluidic cancer diagnostic platforms. This review focuses on a comprehensive analysis of the recent developments of DEP enabled microfluidic platforms sorted according to the target cancer cell. Each study is critically analyzed, and the features of each platform, the performance, added functionality for clinical use, and the types of samples, used are discussed. We address the novelty of the techniques, strategies, and design configuration used in improving on existing technologies or previous studies. A summary of comparing the developmental extent of each study is made, and we conclude with a treatment of future trends and a brief summary.

Paper based colorimetric biosensing platform utilizing cross-linked siloxane as probe.

PubMed

Zhou, Miao; Yang, Minghui; Zhou, Feimeng

2014-05-15

Paper based colorimetric biosensing platform utilizing cross-linked siloxane 3-aminopropyltriethoxysilane (APTMS) as probe was developed for the detection of a broad range of targets including H2O2, glucose and protein biomarker. APTMS was extensively used for the modification of filter papers to develop paper based analytical devices. We discovered when APTMS was cross-linked with glutaraldehyde (GA), the resulting complex (APTMS-GA) displays brick-red color, and a visual color change was observed when the complex reacted with H2O2. By integrating the APTMS-GA complex with filter paper, the modified paper enables quantitative detection of H2O2 through the monitoring of the color intensity change of the paper via software Image J. Then, with the immobilization of glucose oxidase (GOx) onto the modified paper, glucose can be detected through the detection of enzymatically generated H2O2. For protein biomarker prostate specific antigen (PSA) assay, we immobilized capture, not captured anti-PSA antibody (Ab1) onto the paper surface and using GOx modified gold nanorod (GNR) as detection anti-PSA antibody (Ab2) label. The detection of PSA was also achieved via the liberated H2O2 when the GOx label reacted with glucose. The results demonstrated the possibility of this paper based sensor for the detection of different analytes with wide linear range. The low cost and simplicity of this paper based sensor could be developed for "point-of-care" analysis and find wide application in different areas. © 2013 Published by Elsevier B.V.

A cloud computing based platform for sleep behavior and chronic diseases collaborative research.

PubMed

Kuo, Mu-Hsing; Borycki, Elizabeth; Kushniruk, Andre; Huang, Yueh-Min; Hung, Shu-Hui

2014-01-01

The objective of this study is to propose a Cloud Computing based platform for sleep behavior and chronic disease collaborative research. The platform consists of two main components: (1) a sensing bed sheet with textile sensors to automatically record patient's sleep behaviors and vital signs, and (2) a service-oriented cloud computing architecture (SOCCA) that provides a data repository and allows for sharing and analysis of collected data. Also, we describe our systematic approach to implementing the SOCCA. We believe that the new cloud-based platform can provide nurse and other health professional researchers located in differing geographic locations with a cost effective, flexible, secure and privacy-preserved research environment.

Comparison of reverse transcription-quantitative polymerase chain reaction methods and platforms for single cell gene expression analysis.

PubMed

Fox, Bridget C; Devonshire, Alison S; Baradez, Marc-Olivier; Marshall, Damian; Foy, Carole A

2012-08-15

Single cell gene expression analysis can provide insights into development and disease progression by profiling individual cellular responses as opposed to reporting the global average of a population. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the "gold standard" for the quantification of gene expression levels; however, the technical performance of kits and platforms aimed at single cell analysis has not been fully defined in terms of sensitivity and assay comparability. We compared three kits using purification columns (PicoPure) or direct lysis (CellsDirect and Cells-to-CT) combined with a one- or two-step RT-qPCR approach using dilutions of cells and RNA standards to the single cell level. Single cell-level messenger RNA (mRNA) analysis was possible using all three methods, although the precision, linearity, and effect of lysis buffer and cell background differed depending on the approach used. The impact of using a microfluidic qPCR platform versus a standard instrument was investigated for potential variability introduced by preamplification of template or scaling down of the qPCR to nanoliter volumes using laser-dissected single cell samples. The two approaches were found to be comparable. These studies show that accurate gene expression analysis is achievable at the single cell level and highlight the importance of well-validated experimental procedures for low-level mRNA analysis. Copyright © 2012 Elsevier Inc. All rights reserved.

A Parallel Point Matching Algorithm for Landmark Based Image Registration Using Multicore Platform

PubMed Central

Yang, Lin; Gong, Leiguang; Zhang, Hong; Nosher, John L.; Foran, David J.

2013-01-01

Point matching is crucial for many computer vision applications. Establishing the correspondence between a large number of data points is a computationally intensive process. Some point matching related applications, such as medical image registration, require real time or near real time performance if applied to critical clinical applications like image assisted surgery. In this paper, we report a new multicore platform based parallel algorithm for fast point matching in the context of landmark based medical image registration. We introduced a non-regular data partition algorithm which utilizes the K-means clustering algorithm to group the landmarks based on the number of available processing cores, which optimize the memory usage and data transfer. We have tested our method using the IBM Cell Broadband Engine (Cell/B.E.) platform. The results demonstrated a significant speed up over its sequential implementation. The proposed data partition and parallelization algorithm, though tested only on one multicore platform, is generic by its design. Therefore the parallel algorithm can be extended to other computing platforms, as well as other point matching related applications. PMID:24308014

Cloud Based Earth Observation Data Exploitation Platforms

NASA Astrophysics Data System (ADS)

Romeo, A.; Pinto, S.; Loekken, S.; Marin, A.

2017-12-01

In the last few years data produced daily by several private and public Earth Observation (EO) satellites reached the order of tens of Terabytes, representing for scientists and commercial application developers both a big opportunity for their exploitation and a challenge for their management. New IT technologies, such as Big Data and cloud computing, enable the creation of web-accessible data exploitation platforms, which offer to scientists and application developers the means to access and use EO data in a quick and cost effective way. RHEA Group is particularly active in this sector, supporting the European Space Agency (ESA) in the Exploitation Platforms (EP) initiative, developing technology to build multi cloud platforms for the processing and analysis of Earth Observation data, and collaborating with larger European initiatives such as the European Plate Observing System (EPOS) and the European Open Science Cloud (EOSC). An EP is a virtual workspace, providing a user community with access to (i) large volume of data, (ii) algorithm development and integration environment, (iii) processing software and services (e.g. toolboxes, visualization routines), (iv) computing resources, (v) collaboration tools (e.g. forums, wiki, etc.). When an EP is dedicated to a specific Theme, it becomes a Thematic Exploitation Platform (TEP). Currently, ESA has seven TEPs in a pre-operational phase dedicated to geo-hazards monitoring and prevention, costal zones, forestry areas, hydrology, polar regions, urban areas and food security. On the technology development side, solutions like the multi cloud EO data processing platform provides the technology to integrate ICT resources and EO data from different vendors in a single platform. In particular it offers (i) Multi-cloud data discovery, (ii) Multi-cloud data management and access and (iii) Multi-cloud application deployment. This platform has been demonstrated with the EGI Federated Cloud, Innovation Platform Testbed Poland

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

PubMed

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

2012-05-01

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

Framework Design of Unified Cross-Authentication Based on the Fourth Platform Integrated Payment

NASA Astrophysics Data System (ADS)

Yong, Xu; Yujin, He

The essay advances a unified authentication based on the fourth integrated payment platform. The research aims at improving the compatibility of the authentication in electronic business and providing a reference for the establishment of credit system by seeking a way to carry out a standard unified authentication on a integrated payment platform. The essay introduces the concept of the forth integrated payment platform and finally put forward the whole structure and different components. The main issue of the essay is about the design of the credit system of the fourth integrated payment platform and the PKI/CA structure design.

A surface enhanced Raman scattering quantitative analytical platform for detection of trace Cu coupled the catalytic reaction and gold nanoparticle aggregation with label-free Victoria blue B molecular probe.

PubMed

Li, Chongning; Ouyang, Huixiang; Tang, Xueping; Wen, Guiqing; Liang, Aihui; Jiang, Zhiliang

2017-01-15

With development of economy and society, there is an urgent need to develop convenient and sensitive methods for detection of Cu 2+ pollution in water. In this article, a simple and sensitive SERS sensor was proposed to quantitative analysis of trace Cu 2+ in water. The SERS sensor platform was prepared a common gold nanoparticle (AuNP)-SiO 2 sol substrate platform by adsorbing HSA, coupling with the catalytic reaction of Cu 2+ -ascorbic acid (H 2 A)-dissolved oxygen, and using label-free Victoria blue B (VBB) as SERS molecular probes. The SERS sensor platform response to the AuNP aggregations by hydroxyl radicals (•OH) oxidizing from the Cu 2+ catalytic reaction, which caused the SERS signal enhancement. Therefore, by monitoring the increase of SERS signal, Cu 2+ in water can be determined accurately. The results show that the SERS sensor platforms owns a linear response with a range from 0.025 to 25μmol/L Cu 2+ , and with a detection limit of 0.008μmol/L. In addition, the SERS method demonstrated good specificity for Cu 2+ , which can determined accurately trace Cu 2+ in water samples, and good recovery and accuracy are obtained for the water samples. With its high selectivity and good accuracy, the sensitive SERS quantitative analysis method is expected to be a promising candidate for determining copper ions in environmental monitoring and food safety. Copyright © 2016 Elsevier B.V. All rights reserved.

A web-based platform to support an evidence-based mental health intervention: lessons from the CBITS web site.

PubMed

Vona, Pamela; Wilmoth, Pete; Jaycox, Lisa H; McMillen, Janey S; Kataoka, Sheryl H; Wong, Marleen; DeRosier, Melissa E; Langley, Audra K; Kaufman, Joshua; Tang, Lingqi; Stein, Bradley D

2014-11-01

To explore the role of Web-based platforms in behavioral health, the study examined usage of a Web site for supporting training and implementation of an evidence-based intervention. Using data from an online registration survey and Google Analytics, the investigators examined user characteristics and Web site utilization. Site engagement was substantial across user groups. Visit duration differed by registrants' characteristics. Less experienced clinicians spent more time on the Web site. The training section accounted for most page views across user groups. Individuals previously trained in the Cognitive-Behavioral Intervention for Trauma in Schools intervention viewed more implementation assistance and online community pages than did other user groups. Web-based platforms have the potential to support training and implementation of evidence-based interventions for clinicians of varying levels of experience and may facilitate more rapid dissemination. Web-based platforms may be promising for trauma-related interventions, because training and implementation support should be readily available after a traumatic event.

Reducing Response Time Bounds for DAG-Based Task Systems on Heterogeneous Multicore Platforms

DTIC Science & Technology

2016-01-01

synchronous parallel tasks on multicore platforms. In 25th ECRTS, 2013. [10] U. Devi. Soft Real - Time Scheduling on Multiprocessors. PhD thesis...report, Washington University in St Louis, 2014. [18] C. Liu and J. Anderson. Supporting soft real - time DAG-based sys- tems on multiprocessors with...analysis for DAG-based real - time task systems im- plemented on heterogeneous multicore platforms. The spe- cific analysis problem that is considered was

Address-event-based platform for bioinspired spiking systems

NASA Astrophysics Data System (ADS)

Jiménez-Fernández, A.; Luján, C. D.; Linares-Barranco, A.; Gómez-Rodríguez, F.; Rivas, M.; Jiménez, G.; Civit, A.

2007-05-01

Address Event Representation (AER) is an emergent neuromorphic interchip communication protocol that allows a real-time virtual massive connectivity between huge number neurons, located on different chips. By exploiting high speed digital communication circuits (with nano-seconds timings), synaptic neural connections can be time multiplexed, while neural activity signals (with mili-seconds timings) are sampled at low frequencies. Also, neurons generate "events" according to their activity levels. More active neurons generate more events per unit time, and access the interchip communication channel more frequently, while neurons with low activity consume less communication bandwidth. When building multi-chip muti-layered AER systems, it is absolutely necessary to have a computer interface that allows (a) reading AER interchip traffic into the computer and visualizing it on the screen, and (b) converting conventional frame-based video stream in the computer into AER and injecting it at some point of the AER structure. This is necessary for test and debugging of complex AER systems. In the other hand, the use of a commercial personal computer implies to depend on software tools and operating systems that can make the system slower and un-robust. This paper addresses the problem of communicating several AER based chips to compose a powerful processing system. The problem was discussed in the Neuromorphic Engineering Workshop of 2006. The platform is based basically on an embedded computer, a powerful FPGA and serial links, to make the system faster and be stand alone (independent from a PC). A new platform is presented that allow to connect up to eight AER based chips to a Spartan 3 4000 FPGA. The FPGA is responsible of the network communication based in Address-Event and, at the same time, to map and transform the address space of the traffic to implement a pre-processing. A MMU microprocessor (Intel XScale 400MHz Gumstix Connex computer) is also connected to the FPGA

Graphite paper-based bipolar electrode electrochemiluminescence sensing platform.

PubMed

Zhang, Xin; Ding, Shou-Nian

2017-08-15

In this work, aiming at the construction of a disposable, wireless, low-cost and sensitive system for bioassay, we report a closed bipolar electrode electrochemiluminescence (BPE-ECL) sensing platform based on graphite paper as BPE for the first time. Graphite paper is qualified as BPE due to its unique properties such as excellent electrical conductivity, uniform composition and ease of use. This simple BPE-ECL device was applied to the quantitative analysis of oxidant (H 2 O 2 ) and biomarker (CEA) respectively, according to the principle of BPE sensing-charge balance. For the H 2 O 2 analysis, Pt NPs were electrodeposited onto the cathode through a bipolar electrodeposition approach to promote the sensing performance. As a result, this BPE-ECL device exhibited a wide linear range of 0.001-15mM with a low detection limit of 0.5µM (S/N=3) for H 2 O 2 determination. For the determination of CEA, chitosan-multi-walled carbon nanotubes (CS-MWCNTs) were employed to supply a hydrophilic interface for immobilizing primary antibody (Ab 1 ); and Au@Pt nanostructures were conjugated with secondary antibody (Ab 2 ) as catalysts for H 2 O 2 reduction. Under the optimal conditions, the BPE-ECL immunodevice showed a wide linear range of 0.01-60ngmL -1 with a detection limit of 5.0pgmL -1 for CEA. Furthermore, it also displayed satisfactory selectivity, excellent stability and good reproducibility. The developed method opened a new avenue to clinical bioassay. Copyright © 2017 Elsevier B.V. All rights reserved.

Defensive platform size and survivability. [Platform survivability

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

Canavan, Gregory H.

1988-06-01

This report discusses the survivability of space platforms, concentrating on space based kinetic energy interceptors. It evaluates the efficacy of hardening, maneuver, self-defense, and deception in extending the survivability of platforms of varying sizes to expected threats, concluding that they should be adequate in the near and mid terms.

Optical sensor array platform based on polymer electronic devices

NASA Astrophysics Data System (ADS)

Koetse, Marc M.; Rensing, Peter A.; Sharpe, Ruben B. A.; van Heck, Gert T.; Allard, Bart A. M.; Meulendijks, Nicole N. M. M.; Kruijt, Peter G. M.; Tijdink, Marcel W. W. J.; De Zwart, René M.; Houben, René J.; Enting, Erik; van Veen, Sjaak J. J. F.; Schoo, Herman F. M.

2007-10-01

Monitoring of personal wellbeing and optimizing human performance are areas where sensors have only begun to be used. One of the reasons for this is the specific demands that these application areas put on the underlying technology and system properties. In many cases these sensors will be integrated in clothing, be worn on the skin, or may even be placed inside the body. This implies that flexibility and wearability of the systems is essential for their success. Devices based on polymer semiconductors allow for these demands since they can be fabricated with thin film technology. The use of thin film device technology allows for the fabrication of very thin sensors (e.g. integrated in food product packaging), flexible or bendable sensors in wearables, large area/distributed sensors, and intrinsically low-cost applications in disposable products. With thin film device technology a high level of integration can be achieved with parts that analyze signals, process and store data, and interact over a network. Integration of all these functions will inherently lead to better cost/performance ratios, especially if printing and other standard polymer technology such as high precision moulding is applied for the fabrication. In this paper we present an optical transmission sensor array based on polymer semiconductor devices made by thin film technology. The organic devices, light emitting diodes, photodiodes and selective medium chip, are integrated with classic electronic components. Together they form a versatile sensor platform that allows for the quantitative measurement of 100 channels and communicates wireless with a computer. The emphasis is given to the sensor principle, the design, fabrication technology and integration of the thin film devices.

Droplet-based Biosensing for Lab-on-a-Chip, Open Microfluidics Platforms

PubMed Central

Dak, Piyush; Ebrahimi, Aida; Swaminathan, Vikhram; Duarte-Guevara, Carlos; Bashir, Rashid; Alam, Muhammad A.

2016-01-01

Low cost, portable sensors can transform health care by bringing easily available diagnostic devices to low and middle income population, particularly in developing countries. Sample preparation, analyte handling and labeling are primary cost concerns for traditional lab-based diagnostic systems. Lab-on-a-chip (LoC) platforms based on droplet-based microfluidics promise to integrate and automate these complex and expensive laboratory procedures onto a single chip; the cost will be further reduced if label-free biosensors could be integrated onto the LoC platforms. Here, we review some recent developments of label-free, droplet-based biosensors, compatible with “open” digital microfluidic systems. These low-cost droplet-based biosensors overcome some of the fundamental limitations of the classical sensors, enabling timely diagnosis. We identify the key challenges that must be addressed to make these sensors commercially viable and summarize a number of promising research directions. PMID:27089377

Droplet-based Biosensing for Lab-on-a-Chip, Open Microfluidics Platforms.

PubMed

Dak, Piyush; Ebrahimi, Aida; Swaminathan, Vikhram; Duarte-Guevara, Carlos; Bashir, Rashid; Alam, Muhammad A

2016-04-14

Low cost, portable sensors can transform health care by bringing easily available diagnostic devices to low and middle income population, particularly in developing countries. Sample preparation, analyte handling and labeling are primary cost concerns for traditional lab-based diagnostic systems. Lab-on-a-chip (LoC) platforms based on droplet-based microfluidics promise to integrate and automate these complex and expensive laboratory procedures onto a single chip; the cost will be further reduced if label-free biosensors could be integrated onto the LoC platforms. Here, we review some recent developments of label-free, droplet-based biosensors, compatible with "open" digital microfluidic systems. These low-cost droplet-based biosensors overcome some of the fundamental limitations of the classical sensors, enabling timely diagnosis. We identify the key challenges that must be addressed to make these sensors commercially viable and summarize a number of promising research directions.

Development of a cloud-based Bioinformatics Training Platform.

PubMed

Revote, Jerico; Watson-Haigh, Nathan S; Quenette, Steve; Bethwaite, Blair; McGrath, Annette; Shang, Catherine A

2017-05-01

The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. © The Author 2016. Published by Oxford University Press.

Development of a cloud-based Bioinformatics Training Platform

PubMed Central

Revote, Jerico; Watson-Haigh, Nathan S.; Quenette, Steve; Bethwaite, Blair; McGrath, Annette

2017-01-01

Abstract The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. PMID:27084333

Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

PubMed Central

Sun, Zhifu; Cunningham, Julie; Slager, Susan; Kocher, Jean-Pierre

2015-01-01

Bisulfite treatment-based methylation microarray (mainly Illumina 450K Infinium array) and next-generation sequencing (reduced representation bisulfite sequencing, Agilent SureSelect Human Methyl-Seq, NimbleGen SeqCap Epi CpGiant or whole-genome bisulfite sequencing) are commonly used for base resolution DNA methylome research. Although multiple tools and methods have been developed and used for the data preprocessing and analysis, confusions remains for these platforms including how and whether the 450k array should be normalized; which platform should be used to better fit researchers’ needs; and which statistical models would be more appropriate for differential methylation analysis. This review presents the commonly used platforms and compares the pros and cons of each in methylome profiling. We then discuss approaches to study design, data normalization, bias correction and model selection for differentially methylated individual CpGs and regions. PMID:26366945

The Impact of Situation-Based Learning to Students’ Quantitative Literacy

NASA Astrophysics Data System (ADS)

Latifah, T.; Cahya, E.; Suhendra

2017-09-01

Nowadays, the usage of quantities can be seen almost everywhere. There has been an increase of quantitative thinking, such as quantitative reasoning and quantitative literacy, within the context of daily life. However, many people today are still not fully equipped with the knowledge of quantitative thinking. There are still a lot of individuals not having enough quantitative skills to perform well within today’s society. Based on this issue, the research aims to improve students’ quantitative literacy in junior high school. The qualitative analysis of written student work and video observations during the experiment reveal that the impact of situation-based learning affects students’ quantitative literacy.

Design and Promotion Strategy of Marketing Platform of Aquatic Auction based on Internet

NASA Astrophysics Data System (ADS)

Peng, Jianliang

For the online trade and promotion of aquatic products and related materials through the network between supply and demand, the design content and effective promotional strategies of aquatic auctions online marketing platform is proposed in this paper. Design elements involve the location of customer service, the basic function of the platform including the purchase of general orders, online auctions, information dissemination, and recommendation of fine products, human services, and payment preferences. Based on network and mobile e-commerce transaction support, the auction platform makes the transaction of aquatic products well in advance. The results are important practical value for the design and application of online marketing platform of aquatic auction.

A methodology toward manufacturing grid-based virtual enterprise operation platform

NASA Astrophysics Data System (ADS)

Tan, Wenan; Xu, Yicheng; Xu, Wei; Xu, Lida; Zhao, Xianhua; Wang, Li; Fu, Liuliu

2010-08-01

Virtual enterprises (VEs) have become one of main types of organisations in the manufacturing sector through which the consortium companies organise their manufacturing activities. To be competitive, a VE relies on the complementary core competences among members through resource sharing and agile manufacturing capacity. Manufacturing grid (M-Grid) is a platform in which the production resources can be shared. In this article, an M-Grid-based VE operation platform (MGVEOP) is presented as it enables the sharing of production resources among geographically distributed enterprises. The performance management system of the MGVEOP is based on the balanced scorecard and has the capacity of self-learning. The study shows that a MGVEOP can make a semi-automated process possible for a VE, and the proposed MGVEOP is efficient and agile.

A Bluetooth-Based Device Management Platform for Smart Sensor Environment

NASA Astrophysics Data System (ADS)

Lim, Ivan Boon-Kiat; Yow, Kin Choong

In this paper, we propose the use of Bluetooth as the device management platform for the various embedded sensors and actuators in an ambient intelligent environment. We demonstrate the ease of adding Bluetooth capability to common sensor circuits (e.g. motion sensor circuit based on a pyroelectric infrared (PIR) sensor). A central logic application is proposed which controls the operation of controller devices, based on values returned by sensors via Bluetooth. The operation of devices depends on rules that are learnt from user behavior using an Elman recurrent neural network. Overall, Bluetooth has shown its potential in being used as a device management platform in an ambient intelligent environment, which allows sensors and controllers to be deployed even in locations where power sources are not readily available, by using battery power.

A versatile electrophoresis-based self-test platform.

PubMed

Staal, Steven; Ungerer, Mathijn; Floris, Arjan; Ten Brinke, Hans-Willem; Helmhout, Roy; Tellegen, Marian; Janssen, Kjeld; Karstens, Erik; van Arragon, Charlotte; Lenk, Stefan; Staijen, Erik; Bartholomew, Jody; Krabbe, Hans; Movig, Kris; Dubský, Pavel; van den Berg, Albert; Eijkel, Jan

2015-03-01

This paper reports on recent research creating a family of electrophoresis-based point of care devices for the determination of a wide range of ionic analytes in various sample matrices. These devices are based on a first version for the point-of-care measurement of Li(+), reported in 2010 by Floris et al. (Lab Chip 2010, 10, 1799-1806). With respect to this device, significant improvements in accuracy, precision, detection limit, and reliability have been obtained especially by the use of multiple injections of one sample on a single chip and integrated data analysis. Internal and external validation by clinical laboratories for the determination of analytes in real patients by a self-test is reported. For Li(+) in blood better precision than the standard clinical determination for Li(+) was achieved. For Na(+) in human urine the method was found to be within the clinical acceptability limits. In a veterinary application, Ca(2+) and Mg(2+) were determined in bovine blood by means of the same chip, but using a different platform. Finally, promising preliminary results are reported with the Medimate platform for the determination of creatinine in whole blood and quantification of both cations and anions through replicate measurements on the same sample with the same chip. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Remotely Delivered Exercise-Based Cardiac Rehabilitation: Design and Content Development of a Novel mHealth Platform.

PubMed

Rawstorn, Jonathan C; Gant, Nicholas; Meads, Andrew; Warren, Ian; Maddison, Ralph

2016-06-24

Participation in traditional center-based cardiac rehabilitation exercise programs (exCR) is limited by accessibility barriers. Mobile health (mHealth) technologies can overcome these barriers while preserving critical attributes of center-based exCR monitoring and coaching, but these opportunities have not yet been capitalized on. We aimed to design and develop an evidence- and theory-based mHealth platform for remote delivery of exCR to any geographical location. An iterative process was used to design and develop an evidence- and theory-based mHealth platform (REMOTE-CR) that provides real-time remote exercise monitoring and coaching, behavior change education, and social support. The REMOTE-CR platform comprises a commercially available smartphone and wearable sensor, custom smartphone and Web-based applications (apps), and a custom middleware. The platform allows exCR specialists to monitor patients' exercise and provide individualized coaching in real-time, from almost any location, and provide behavior change education and social support. Intervention content incorporates Social Cognitive Theory, Self-determination Theory, and a taxonomy of behavior change techniques. Exercise components are based on guidelines for clinical exercise prescription. The REMOTE-CR platform extends the capabilities of previous telehealth exCR platforms and narrows the gap between existing center- and home-based exCR services. REMOTE-CR can complement center-based exCR by providing an alternative option for patients whose needs are not being met. Remotely monitored exCR may be more cost-effective than establishing additional center-based programs. The effectiveness and acceptability of REMOTE-CR are now being evaluated in a noninferiority randomized controlled trial.

Mounted Smartphones as Measurement and Control Platforms for Motor-Based Laboratory Test-Beds.

PubMed

Frank, Jared A; Brill, Anthony; Kapila, Vikram

2016-08-20

Laboratory education in science and engineering often entails the use of test-beds equipped with costly peripherals for sensing, acquisition, storage, processing, and control of physical behavior. However, costly peripherals are no longer necessary to obtain precise measurements and achieve stable feedback control of test-beds. With smartphones performing diverse sensing and processing tasks, this study examines the feasibility of mounting smartphones directly to test-beds to exploit their embedded hardware and software in the measurement and control of the test-beds. This approach is a first step towards replacing laboratory-grade peripherals with more compact and affordable smartphone-based platforms, whose interactive user interfaces can engender wider participation and engagement from learners. Demonstrative cases are presented in which the sensing, computation, control, and user interaction with three motor-based test-beds are handled by a mounted smartphone. Results of experiments and simulations are used to validate the feasibility of mounted smartphones as measurement and feedback control platforms for motor-based laboratory test-beds, report the measurement precision and closed-loop performance achieved with such platforms, and address challenges in the development of platforms to maintain system stability.

Servo Platform Circuit Design of Pendulous Gyroscope Based on DSP

NASA Astrophysics Data System (ADS)

Tan, Lilong; Wang, Pengcheng; Zhong, Qiyuan; Zhang, Cui; Liu, Yunfei

2018-03-01

In order to solve the problem when a certain type of pendulous gyroscope in the initial installation deviation more than 40 degrees, that the servo platform can not be up to the speed of the gyroscope in the rough north seeking phase. This paper takes the digital signal processor TMS320F28027 as the core, uses incremental digital PID algorithm, carries out the circuit design of the servo platform. Firstly, the hardware circuit is divided into three parts: DSP minimum system, motor driving circuit and signal processing circuit, then the mathematical model of incremental digital PID algorithm is established, based on the model, writes the PID control program in CCS3.3, finally, the servo motor tracking control experiment is carried out, it shows that the design can significantly improve the tracking ability of the servo platform, and the design has good engineering practice.

Wireless Sensor Network-Based Service Provisioning by a Brokering Platform.

PubMed

Guijarro, Luis; Pla, Vicent; Vidal, Jose R; Naldi, Maurizio; Mahmoodi, Toktam

2017-05-12

This paper proposes a business model for providing services based on the Internet of Things through a platform that intermediates between human users and Wireless Sensor Networks (WSNs). The platform seeks to maximize its profit through posting both the price charged to each user and the price paid to each WSN. A complete analysis of the profit maximization problem is performed in this paper. We show that the service provider maximizes its profit by incentivizing all users and all Wireless Sensor Infrastructure Providers (WSIPs) to join the platform. This is true not only when the number of users is high, but also when it is moderate, provided that the costs that the users bear do not trespass a cost ceiling. This cost ceiling depends on the number of WSIPs, on the value of the intrinsic value of the service and on the externality that the WSIP has on the user utility.

Nanovesicle-based bioelectronic nose platform mimicking human olfactory signal transduction.

PubMed

Jin, Hye Jun; Lee, Sang Hun; Kim, Tae Hyun; Park, Juhun; Song, Hyun Seok; Park, Tai Hyun; Hong, Seunghun

2012-05-15

We developed a nanovesicle-based bioelectronic nose (NBN) that could recognize a specific odorant and mimic the receptor-mediated signal transmission of human olfactory systems. To build an NBN, we combined a single-walled carbon nanotube-based field effect transistor with cell-derived nanovesicles containing human olfactory receptors and calcium ion signal pathways. Importantly, the NBN took advantages of cell signal pathways for sensing signal amplification, enabling ≈ 100 times better sensitivity than that of previous bioelectronic noses based on only olfactory receptor protein and carbon nanotube transistors. The NBN sensors exhibited a human-like selectivity with single-carbon-atomic resolution and a high sensitivity of 1 fM detection limit. Moreover, this sensor platform could mimic a receptor-meditated cellular signal transmission in live cells. This sensor platform can be utilized for the study of molecular recognition and biological processes occurring at cell membranes and also for various practical applications such as food screening and medical diagnostics. Copyright © 2012 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Amirebrahimi, S.; Rajabifard, A.

2012-07-01

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

Design of a Physiology-Sensitive VR-Based Social Communication Platform for Children With Autism.

PubMed

Kuriakose, Selvia; Lahiri, Uttama

2017-08-01

Individuals with autism are often characterized by impairments in communication, reciprocal social interaction and explicit expression of their affective states. In conventional techniques, a therapist adjusts the intervention paradigm by monitoring the affective state e.g., anxiety of these individuals for effective floor-time-therapy. Conventional techniques, though powerful, are observation-based and face resource limitations. Technology-assisted systems can provide a quantitative, individualized rehabilitation platform. Presently-available systems are designed primarily to chain learning via aspects of one's performance alone restricting individualization. Specifically, these systems are not sensitive to one's anxiety. Our presented work seeks to bridge this gap by developing a novel VR-based interactive system with Anxiety-Sensitive adaptive technology. Specifically, such a system is capable of objectively identifying and quantifying one's anxiety level from real-time biomarkers, along with performance metrics. In turn it can adaptively respond in an individualized manner to foster improved social communication skills. In our present research, we have used Virtual Reality (VR) to design a proof-of-concept application that exposes participants to social tasks of varying challenges. Results of a preliminary usability study indicate the potential of our VR-based Anxiety-Sensitive system to foster improved task performance, thereby serving as a potent complementary tool in the hands of therapist.

Study on key technologies of vehicle networking system platform for electric automobiles based on micro-service

NASA Astrophysics Data System (ADS)

Ye, Fei

2018-04-01

With the rapid increase of electric automobiles and charging piles, the elastic expansion and online rapid upgrade were required for the vehicle networking system platform (system platform for short). At present, it is difficult to meet the operation needs due to the traditional huge rock architecture used by the system platform. This paper studied the system platform technology architecture based on "cloud platform +micro-service" to obtain a new generation of vehicle networking system platform with the combination of elastic expansion and application, thus significantly improving the service operation ability of system.

Remotely Delivered Exercise-Based Cardiac Rehabilitation: Design and Content Development of a Novel mHealth Platform

PubMed Central

Gant, Nicholas; Meads, Andrew; Warren, Ian; Maddison, Ralph

2016-01-01

Background Participation in traditional center-based cardiac rehabilitation exercise programs (exCR) is limited by accessibility barriers. Mobile health (mHealth) technologies can overcome these barriers while preserving critical attributes of center-based exCR monitoring and coaching, but these opportunities have not yet been capitalized on. Objective We aimed to design and develop an evidence- and theory-based mHealth platform for remote delivery of exCR to any geographical location. Methods An iterative process was used to design and develop an evidence- and theory-based mHealth platform (REMOTE-CR) that provides real-time remote exercise monitoring and coaching, behavior change education, and social support. Results The REMOTE-CR platform comprises a commercially available smartphone and wearable sensor, custom smartphone and Web-based applications (apps), and a custom middleware. The platform allows exCR specialists to monitor patients’ exercise and provide individualized coaching in real-time, from almost any location, and provide behavior change education and social support. Intervention content incorporates Social Cognitive Theory, Self-determination Theory, and a taxonomy of behavior change techniques. Exercise components are based on guidelines for clinical exercise prescription. Conclusions The REMOTE-CR platform extends the capabilities of previous telehealth exCR platforms and narrows the gap between existing center- and home-based exCR services. REMOTE-CR can complement center-based exCR by providing an alternative option for patients whose needs are not being met. Remotely monitored exCR may be more cost-effective than establishing additional center-based programs. The effectiveness and acceptability of REMOTE-CR are now being evaluated in a noninferiority randomized controlled trial. PMID:27342791

Assessing the Effects of Software Platforms on Volumetric Segmentation of Glioblastoma

PubMed Central

Dunn, William D.; Aerts, Hugo J.W.L.; Cooper, Lee A.; Holder, Chad A.; Hwang, Scott N.; Jaffe, Carle C.; Brat, Daniel J.; Jain, Rajan; Flanders, Adam E.; Zinn, Pascal O.; Colen, Rivka R.; Gutman, David A.

2017-01-01

Background Radiological assessments of biologically relevant regions in glioblastoma have been associated with genotypic characteristics, implying a potential role in personalized medicine. Here, we assess the reproducibility and association with survival of two volumetric segmentation platforms and explore how methodology could impact subsequent interpretation and analysis. Methods Post-contrast T1- and T2-weighted FLAIR MR images of 67 TCGA patients were segmented into five distinct compartments (necrosis, contrast-enhancement, FLAIR, post contrast abnormal, and total abnormal tumor volumes) by two quantitative image segmentation platforms - 3D Slicer and a method based on Velocity AI and FSL. We investigated the internal consistency of each platform by correlation statistics, association with survival, and concordance with consensus neuroradiologist ratings using ordinal logistic regression. Results We found high correlations between the two platforms for FLAIR, post contrast abnormal, and total abnormal tumor volumes (spearman’s r(67) = 0.952, 0.959, and 0.969 respectively). Only modest agreement was observed for necrosis and contrast-enhancement volumes (r(67) = 0.693 and 0.773 respectively), likely arising from differences in manual and automated segmentation methods of these regions by 3D Slicer and Velocity AI/FSL, respectively. Survival analysis based on AUC revealed significant predictive power of both platforms for the following volumes: contrast-enhancement, post contrast abnormal, and total abnormal tumor volumes. Finally, ordinal logistic regression demonstrated correspondence to manual ratings for several features. Conclusion Tumor volume measurements from both volumetric platforms produced highly concordant and reproducible estimates across platforms for general features. As automated or semi-automated volumetric measurements replace manual linear or area measurements, it will become increasingly important to keep in mind that measurement

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

PubMed Central

Lee, Joseph C; Stiles, David; Lu, Jun; Cam, Margaret C

2007-01-01

Background Microarrays are a popular tool used in experiments to measure gene expression levels. Improving the reproducibility of microarray results produced by different chips from various manufacturers is important to create comparable and combinable experimental results. Alternative splicing has been cited as a possible cause of differences in expression measurements across platforms, though no study to this point has been conducted to show its influence in cross-platform differences. Results Using probe sequence data, a new microarray probe/transcript annotation was created based on the AceView Aug05 release that allowed for the categorization of genes based on their expression measurements' susceptibility to alternative splicing differences across microarray platforms. Examining gene expression data from multiple platforms in light of the new categorization, genes unsusceptible to alternative splicing differences showed higher signal agreement than those genes most susceptible to alternative splicing differences. The analysis gave rise to a different probe-level visualization method that can highlight probe differences according to transcript specificity. Conclusion The results highlight the need for detailed probe annotation at the transcriptome level. The presence of alternative splicing within a given sample can affect gene expression measurements and is a contributing factor to overall technical differences across platforms. PMID:17708771

Wireless Sensor Network-Based Service Provisioning by a Brokering Platform

PubMed Central

Guijarro, Luis; Pla, Vicent; Vidal, Jose R.; Naldi, Maurizio; Mahmoodi, Toktam

2017-01-01

This paper proposes a business model for providing services based on the Internet of Things through a platform that intermediates between human users and Wireless Sensor Networks (WSNs). The platform seeks to maximize its profit through posting both the price charged to each user and the price paid to each WSN. A complete analysis of the profit maximization problem is performed in this paper. We show that the service provider maximizes its profit by incentivizing all users and all Wireless Sensor Infrastructure Providers (WSIPs) to join the platform. This is true not only when the number of users is high, but also when it is moderate, provided that the costs that the users bear do not trespass a cost ceiling. This cost ceiling depends on the number of WSIPs, on the value of the intrinsic value of the service and on the externality that the WSIP has on the user utility. PMID:28498347

Investigating Teacher Learning Using a Web-Based Writing Platform

ERIC Educational Resources Information Center

Yang, Shih-hsien

2018-01-01

Due to its complex nature and inherent unobservable features, teacher change within a specific context has rarely been investigated despite its importance as an issue in teacher professional development. To meet this challenge, the present study explored how teacher change was nurtured with the support of a web-based writing platform featuring…

Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-09-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Research on website construction based on website group platform of Chengdu sport institution

NASA Astrophysics Data System (ADS)

Hu, Zunyu

2018-04-01

This paper describes the necessity of website construction based on the website group of Chengdu sport institute, and discusses the technical features of the website group, Based on the website group platform architecture, the key technologies such as Web Service, AJAX, RSS and other key technologies are used to realize the construction of the website. Based on the website group platform architecture of the site, it effectively solves the information isolated island between the sites, and realizes the information sharing and resource integration. It is also more convenient that site and other sites have composed of site group integrated operation and maintenance.

Imaging enabled platforms for development of therapeutics

NASA Astrophysics Data System (ADS)

Celli, Jonathan; Rizvi, Imran; Blanden, Adam R.; Evans, Conor L.; Abu-Yousif, Adnan O.; Spring, Bryan Q.; Muzikansky, Alona; Pogue, Brian W.; Finkelstein, Dianne M.; Hasan, Tayyaba

2011-03-01

Advances in imaging and spectroscopic technologies have enabled the optimization of many therapeutic modalities in cancer and noncancer pathologies either by earlier disease detection or by allowing therapy monitoring. Amongst the therapeutic options benefiting from developments in imaging technologies, photodynamic therapy (PDT) is exceptional. PDT is a photochemistry-based therapeutic approach where a light-sensitive molecule (photosensitizer) is activated with light of appropriate energy (wavelength) to produce reactive molecular species such as free radicals and singlet oxygen. These molecular entities then react with biological targets such as DNA, membranes and other cellular components to impair their function and lead to eventual cell and tissue death. Development of PDT-based imaging also provides a platform for rapid screening of new therapeutics in novel in vitro models prior to expensive and labor-intensive animal studies. In this study we demonstrate how an imaging platform can be used for strategizing a novel combination treatment strategy for multifocal ovarian cancer. Using an in vitro 3D model for micrometastatic ovarian cancer in conjunction with quantitative imaging we examine dose and scheduling strategies for PDT in combination with carboplatin, a chemotherapeutic agent presently in clinical use for management of this deadly form of cancer.

Audio-based detection and evaluation of eating behavior using the smartwatch platform.

PubMed

Kalantarian, Haik; Sarrafzadeh, Majid

2015-10-01

In recent years, smartwatches have emerged as a viable platform for a variety of medical and health-related applications. In addition to the benefits of a stable hardware platform, these devices have a significant advantage over other wrist-worn devices, in that user acceptance of watches is higher than other custom hardware solutions. In this paper, we describe signal-processing techniques for identification of chews and swallows using a smartwatch device׳s built-in microphone. Moreover, we conduct a survey to evaluate the potential of the smartwatch as a platform for monitoring nutrition. The focus of this paper is to analyze the overall applicability of a smartwatch-based system for food-intake monitoring. Evaluation results confirm the efficacy of our technique; classification was performed between apple and potato chip bites, water swallows, talking, and ambient noise, with an F-measure of 94.5% based on 250 collected samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

InP-based photonic integrated circuit platform on SiC wafer.

PubMed

Takenaka, Mitsuru; Takagi, Shinichi

2017-11-27

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

Smartphone-based quantitative measurements on holographic sensors.

PubMed

Khalili Moghaddam, Gita; Lowe, Christopher Robin

2017-01-01

The research reported herein integrates a generic holographic sensor platform and a smartphone-based colour quantification algorithm in order to standardise and improve the determination of the concentration of analytes of interest. The utility of this approach has been exemplified by analysing the replay colour of the captured image of a holographic pH sensor in near real-time. Personalised image encryption followed by a wavelet-based image compression method were applied to secure the image transfer across a bandwidth-limited network to the cloud. The decrypted and decompressed image was processed through four principal steps: Recognition of the hologram in the image with a complex background using a template-based approach, conversion of device-dependent RGB values to device-independent CIEXYZ values using a polynomial model of the camera and computation of the CIEL*a*b* values, use of the colour coordinates of the captured image to segment the image, select the appropriate colour descriptors and, ultimately, locate the region of interest (ROI), i.e. the hologram in this case, and finally, application of a machine learning-based algorithm to correlate the colour coordinates of the ROI to the analyte concentration. Integrating holographic sensors and the colour image processing algorithm potentially offers a cost-effective platform for the remote monitoring of analytes in real time in readily accessible body fluids by minimally trained individuals.

Smartphone-based quantitative measurements on holographic sensors

PubMed Central

Khalili Moghaddam, Gita

2017-01-01

The research reported herein integrates a generic holographic sensor platform and a smartphone-based colour quantification algorithm in order to standardise and improve the determination of the concentration of analytes of interest. The utility of this approach has been exemplified by analysing the replay colour of the captured image of a holographic pH sensor in near real-time. Personalised image encryption followed by a wavelet-based image compression method were applied to secure the image transfer across a bandwidth-limited network to the cloud. The decrypted and decompressed image was processed through four principal steps: Recognition of the hologram in the image with a complex background using a template-based approach, conversion of device-dependent RGB values to device-independent CIEXYZ values using a polynomial model of the camera and computation of the CIEL*a*b* values, use of the colour coordinates of the captured image to segment the image, select the appropriate colour descriptors and, ultimately, locate the region of interest (ROI), i.e. the hologram in this case, and finally, application of a machine learning-based algorithm to correlate the colour coordinates of the ROI to the analyte concentration. Integrating holographic sensors and the colour image processing algorithm potentially offers a cost-effective platform for the remote monitoring of analytes in real time in readily accessible body fluids by minimally trained individuals. PMID:29141008

Automated Platform Management System Scheduling

NASA Technical Reports Server (NTRS)

Hull, Larry G.

1990-01-01

The Platform Management System was established to coordinate the operation of platform systems and instruments. The management functions are split between ground and space components. Since platforms are to be out of contact with the ground more than the manned base, the on-board functions are required to be more autonomous than those of the manned base. Under this concept, automated replanning and rescheduling, including on-board real-time schedule maintenance and schedule repair, are required to effectively and efficiently meet Space Station Freedom mission goals. In a FY88 study, we developed several promising alternatives for automated platform planning and scheduling. We recommended both a specific alternative and a phased approach to automated platform resource scheduling. Our recommended alternative was based upon use of exactly the same scheduling engine in both ground and space components of the platform management system. Our phased approach recommendation was based upon evolutionary development of the platform. In the past year, we developed platform scheduler requirements and implemented a rapid prototype of a baseline platform scheduler. Presently we are rehosting this platform scheduler rapid prototype and integrating the scheduler prototype into two Goddard Space Flight Center testbeds, as the ground scheduler in the Scheduling Concepts, Architectures, and Networks Testbed and as the on-board scheduler in the Platform Management System Testbed. Using these testbeds, we will investigate rescheduling issues, evaluate operational performance and enhance the platform scheduler prototype to demonstrate our evolutionary approach to automated platform scheduling. The work described in this paper was performed prior to Space Station Freedom rephasing, transfer of platform responsibility to Code E, and other recently discussed changes. We neither speculate on these changes nor attempt to predict the impact of the final decisions. As a consequence some of our

A Big-Data-based platform of workers' behavior: Observations from the field.

PubMed

Guo, S Y; Ding, L Y; Luo, H B; Jiang, X Y

2016-08-01

Behavior-Based Safety (BBS) has been used in construction to observe, analyze and modify workers' behavior. However, studies have identified that BBS has several limitations, which have hindered its effective implementation. To mitigate the negative impact of BBS, this paper uses a case study approach to develop a Big-Data-based platform to classify, collect and store data about workers' unsafe behavior that is derived from a metro construction project. In developing the platform, three processes were undertaken: (1) a behavioral risk knowledge base was established; (2) images reflecting workers' unsafe behavior were collected from intelligent video surveillance and mobile application; and (3) images with semantic information were stored via a Hadoop Distributed File System (HDFS). The platform was implemented during the construction of the metro-system and it is demonstrated that it can effectively analyze semantic information contained in images, automatically extract workers' unsafe behavior and quickly retrieve on HDFS as well. The research presented in this paper can enable construction organizations with the ability to visualize unsafe acts in real-time and further identify patterns of behavior that can jeopardize safety outcomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Graphene-based platforms for cancer therapeutics.

PubMed

Patel, Sunny C; Lee, Stephen; Lalwani, Gaurav; Suhrland, Cassandra; Chowdhury, Sayan Mullick; Sitharaman, Balaji

2016-01-01

Graphene is a multifunctional carbon nanomaterial and could be utilized to develop platform technologies for cancer therapies. Its surface can be covalently and noncovalently functionalized with anticancer drugs and functional groups that target cancer cells and tissue to improve treatment efficacies. Furthermore, its physicochemical properties can be harnessed to facilitate stimulus responsive therapeutics and drug delivery. This review article summarizes the recent literature specifically focused on development of graphene technologies to treat cancer. We will focus on advances at the interface of graphene based drug/gene delivery, photothermal/photodynamic therapy and combinations of these techniques. We also discuss the current understanding in cytocompatibility and biocompatibility issues related to graphene formulations and their implications pertinent to clinical cancer management.

Wireless implantable electronic platform for chronic fluorescent-based biosensors.

PubMed

Valdastri, Pietro; Susilo, Ekawahyu; Förster, Thilo; Strohhöfer, Christof; Menciassi, Arianna; Dario, Paolo

2011-06-01

The development of a long-term wireless implantable biosensor based on fluorescence intensity measurement poses a number of technical challenges, ranging from biocompatibility to sensor stability over time. One of these challenges is the design of a power efficient and miniaturized electronics, enabling the biosensor to move from bench testing to long term validation, up to its final application in human beings. In this spirit, we present a wireless programmable electronic platform for implantable chronic monitoring of fluorescent-based autonomous biosensors. This system is able to achieve extremely low power operation with bidirectional telemetry, based on the IEEE802.15.4-2003 protocol, thus enabling over three-year battery lifetime and wireless networking of multiple sensors. During the performance of single fluorescent-based sensor measurements, the circuit drives a laser diode, for sensor excitation, and acquires the amplified signals from four different photodetectors. In vitro functionality was preliminarily tested for both glucose and calcium monitoring, simply by changing the analyte-binding protein of the biosensor. Electronics performance was assessed in terms of timing, power consumption, tissue exposure to electromagnetic fields, and in vivo wireless connectivity. The final goal of the presented platform is to be integrated in a complete system for blood glucose level monitoring that may be implanted for at least one year under the skin of diabetic patients. Results reported in this paper may be applied to a wide variety of biosensors based on fluorescence intensity measurement.

Surface Plasmon Resonance Biosensor Based on Smart Phone Platforms

NASA Astrophysics Data System (ADS)

Liu, Yun; Liu, Qiang; Chen, Shimeng; Cheng, Fang; Wang, Hanqi; Peng, Wei

2015-08-01

We demonstrate a fiber optic surface plasmon resonance (SPR) biosensor based on smart phone platforms. The light-weight optical components and sensing element are connected by optical fibers on a phone case. This SPR adaptor can be conveniently installed or removed from smart phones. The measurement, control and reference channels are illuminated by the light entering the lead-in fibers from the phone’s LED flash, while the light from the end faces of the lead-out fibers is detected by the phone’s camera. The SPR-sensing element is fabricated by a light-guiding silica capillary that is stripped off its cladding and coated with 50-nm gold film. Utilizing a smart application to extract the light intensity information from the camera images, the light intensities of each channel are recorded every 0.5 s with refractive index (RI) changes. The performance of the smart phone-based SPR platform for accurate and repeatable measurements was evaluated by detecting different concentrations of antibody binding to a functionalized sensing element, and the experiment results were validated through contrast experiments with a commercial SPR instrument. This cost-effective and portable SPR biosensor based on smart phones has many applications, such as medicine, health and environmental monitoring.

Surface Plasmon Resonance Biosensor Based on Smart Phone Platforms.

PubMed

Liu, Yun; Liu, Qiang; Chen, Shimeng; Cheng, Fang; Wang, Hanqi; Peng, Wei

2015-08-10

We demonstrate a fiber optic surface plasmon resonance (SPR) biosensor based on smart phone platforms. The light-weight optical components and sensing element are connected by optical fibers on a phone case. This SPR adaptor can be conveniently installed or removed from smart phones. The measurement, control and reference channels are illuminated by the light entering the lead-in fibers from the phone's LED flash, while the light from the end faces of the lead-out fibers is detected by the phone's camera. The SPR-sensing element is fabricated by a light-guiding silica capillary that is stripped off its cladding and coated with 50-nm gold film. Utilizing a smart application to extract the light intensity information from the camera images, the light intensities of each channel are recorded every 0.5 s with refractive index (RI) changes. The performance of the smart phone-based SPR platform for accurate and repeatable measurements was evaluated by detecting different concentrations of antibody binding to a functionalized sensing element, and the experiment results were validated through contrast experiments with a commercial SPR instrument. This cost-effective and portable SPR biosensor based on smart phones has many applications, such as medicine, health and environmental monitoring.

Ultrasensitive quantum dots-based DNA detection and hybridization kinetics analysis with evanescent wave biosensing platform.

PubMed

Long, Feng; Wu, Shuxu; He, Miao; Tong, Tiezheng; Shi, Hanchang

2011-01-15

Ultrasensitive DNA detection was achieved using a new biosensing platform based on quantum dots (QDs) and total internal reflection fluorescence, which featured an exceptional detection limit of 3.2 amol of bound target DNA. The reusable sensor surface was produced by covalently immobilizing streptavidin onto a self-assembled alkanethiol monolayer of fiber optic probe through a heterobifunctional reagent. Streptavidin served as a versatile binding element for biotinylated single-strand DNA (ssDNA). The ssDNA-coated fiber probe was evaluated as a nucleic acid biosensor through a DNA-DNA hybridization assay for a 30-mer ssDNA, which were the segments of the uidA gene of Escherichia coli and labeled by QDs using avidin-biotin interaction. Several negative control tests revealed the absence of significant non-specific binding. It also showed that bound target DNA could easily be eluted from the sensor surface using SDS solution (pH 1.9) without any significant loss of performance after more than 30 assay cycles. A quantitative measurement of DNA binding kinetics was achieved with high accuracy, indicating an association rate of 1.38×10(6) M(-1) s(-1) and a dissociation rate of 4.67×10(-3) s(-1). The proposed biosensing platform provides a simple, cheap, fast, and robust solution for many potential applications including clinical diagnosis, pathology, and genetics. Copyright © 2010 Elsevier B.V. All rights reserved.

A web-based platform for virtual screening.

PubMed

Watson, Paul; Verdonk, Marcel; Hartshorn, Michael J

2003-09-01

A fully integrated, web-based, virtual screening platform has been developed to allow rapid virtual screening of large numbers of compounds. ORACLE is used to store information at all stages of the process. The system includes a large database of historical compounds from high throughput screenings (HTS) chemical suppliers, ATLAS, containing over 3.1 million unique compounds with their associated physiochemical properties (ClogP, MW, etc.). The database can be screened using a web-based interface to produce compound subsets for virtual screening or virtual library (VL) enumeration. In order to carry out the latter task within ORACLE a reaction data cartridge has been developed. Virtual libraries can be enumerated rapidly using the web-based interface to the cartridge. The compound subsets can be seamlessly submitted for virtual screening experiments, and the results can be viewed via another web-based interface allowing ad hoc querying of the virtual screening data stored in ORACLE.

Automation Improvements for Synchrotron Based Small Angle Scattering Using an Inexpensive Robotics Platform

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

Quintana, John P.

This paper reports on the progress toward creating semi-autonomous motion control platforms for beamline applications using the iRobot Create registered platform. The goal is to create beamline research instrumentation where the motion paths are based on the local environment rather than position commanded from a control system, have low integration costs and also be scalable and easily maintainable.

Mounted Smartphones as Measurement and Control Platforms for Motor-Based Laboratory Test-Beds †

PubMed Central

Frank, Jared A.; Brill, Anthony; Kapila, Vikram

2016-01-01

Laboratory education in science and engineering often entails the use of test-beds equipped with costly peripherals for sensing, acquisition, storage, processing, and control of physical behavior. However, costly peripherals are no longer necessary to obtain precise measurements and achieve stable feedback control of test-beds. With smartphones performing diverse sensing and processing tasks, this study examines the feasibility of mounting smartphones directly to test-beds to exploit their embedded hardware and software in the measurement and control of the test-beds. This approach is a first step towards replacing laboratory-grade peripherals with more compact and affordable smartphone-based platforms, whose interactive user interfaces can engender wider participation and engagement from learners. Demonstrative cases are presented in which the sensing, computation, control, and user interaction with three motor-based test-beds are handled by a mounted smartphone. Results of experiments and simulations are used to validate the feasibility of mounted smartphones as measurement and feedback control platforms for motor-based laboratory test-beds, report the measurement precision and closed-loop performance achieved with such platforms, and address challenges in the development of platforms to maintain system stability. PMID:27556464

EBprot: Statistical analysis of labeling-based quantitative proteomics data.

PubMed

Koh, Hiromi W L; Swa, Hannah L F; Fermin, Damian; Ler, Siok Ghee; Gunaratne, Jayantha; Choi, Hyungwon

2015-08-01

Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is not incorporated into the differential expression (DE) analysis. Here, we propose a novel probabilistic framework EBprot that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. To illustrate the wide applicability of EBprot in different experimental designs, we applied EBprot to a dataset for lung cancer subtype analysis with biological replicates and another dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells with multiplexed labeling. Through these examples, we show that the peptide-level analysis of EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets. The software suite is freely available on the Sourceforge website http://ebprot.sourceforge.net/. All MS data have been deposited in the ProteomeXchange with identifier PXD001426 (http://proteomecentral.proteomexchange.org/dataset/PXD001426/). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fast neutron counting in a mobile, trailer-based search platform

NASA Astrophysics Data System (ADS)

Hayward, Jason P.; Sparger, John; Fabris, Lorenzo; Newby, Robert J.

2017-12-01

Trailer-based search platforms for detection of radiological and nuclear threats are often based upon coded aperture gamma-ray imaging, because this method can be rendered insensitive to local variations in gamma background while still localizing the source well. Since gamma source emissions are rather easily shielded, in this work we consider the addition of fast neutron counting to a mobile platform for detection of sources containing Pu. A proof-of-concept system capable of combined gamma and neutron coded-aperture imaging was built inside of a trailer and used to detect a 252Cf source while driving along a roadway. Neutron detector types employed included EJ-309 in a detector plane and EJ-299-33 in a front mask plane. While the 252Cf gamma emissions were not readily detectable while driving by at 16.9 m standoff, the neutron emissions can be detected while moving. Mobile detection performance for this system and a scaled-up system design are presented, along with implications for threat sensing.

Implementation and performance test of cloud platform based on Hadoop

NASA Astrophysics Data System (ADS)

Xu, Jingxian; Guo, Jianhong; Ren, Chunlan

2018-01-01

Hadoop, as an open source project for the Apache foundation, is a distributed computing framework that deals with large amounts of data and has been widely used in the Internet industry. Therefore, it is meaningful to study the implementation of Hadoop platform and the performance of test platform. The purpose of this subject is to study the method of building Hadoop platform and to study the performance of test platform. This paper presents a method to implement Hadoop platform and a test platform performance method. Experimental results show that the proposed test performance method is effective and it can detect the performance of Hadoop platform.

Crystallization of bovine insulin on a flow-free droplet-based platform

NASA Astrophysics Data System (ADS)

Chen, Fengjuan; Du, Guanru; Yin, Di; Yin, Ruixue; Zhang, Hongbo; Zhang, Wenjun; Yang, Shih-Mo

2017-03-01

Crystallization is an important process in the pharmaceutical manufacturing industry. In this work, we report a study to create the zinc-free crystals of bovine insulin on a flow-free droplet-based platform we previously developed. The benefit of this platform is its promise to create a single type of crystals under a simpler and more stable environment and with a high throughput. The experimental result shows that the bovine insulin forms a rhombic dodecahedra shape and the coefficient variation (CV) in the size of crystals is less than 5%. These results are very promising for the insulin production.

Microcantilever sensor platform for UGV-based detection

NASA Astrophysics Data System (ADS)

Lawrence, Tyson T.; Halleck, A. E.; Schuler, Peter S.; Mahmud, K. K.; Hicks, David R.

2010-04-01

The increased use of Unmanned Ground Vehicles (UGVs) drives the need for new lightweight, low cost sensors. Microelectromechanical System (MEMS) based microcantilever sensors are a promising technology to meet this need, because they can be manufactured at low cost on a mass scale, and are easily integrated into a UGV platform for detection of explosives and other threat agents. While the technology is extremely sensitive, selectivity is a major challenge and the response modes are not well understood. This work summarizes advances in characterizing ultrasensitive microcantilever responses, sampling considerations, and sensor design and cantilever coating methodologies consistent with UGV point detector needs.

An Innovative, No-cost, Evidence-Based Smartphone Platform for Resident Evaluation.

PubMed

Green, John M

Timely performance evaluation and feedback are critical to resident development. However, formulating and delivering this information disrupts physician workflow, leading to low participation. This study was designed to determine if a locally developed smartphone platform would integrate regular evaluation into daily processes and thus increase faculty participation in timely resident evaluation. Formal, documented resident operative and patient interaction evaluations were compiled over an 8-month study period. The study was divided into two 4-month phases. No changes to the existing evaluation methods were made during Phase 1. Phase 2 began after a washout period of 2 weeks and coincided with the launch of a smartphone-based platform. The platform uses a combination of Likert scale questions and the Dreyfus model of skill acquisition to describe competence levels in technical and nontechnical skills. The instrument inflicts minimal effect on surgeon workflow, with the aim of integrating resident evaluation into daily processes. The number of different faculty members performing evaluations, resident level (postgraduate year), type of interaction or procedure, and competency data were compiled. All evaluations were tracked by the program director as they were automatically uploaded into a database. Faculty members were introduced to the new platform at the beginning of Phase 2, and previous methods of evaluation continued to be encouraged and were considered valid throughout both phases of the study. Data were analyzed using Fisher exact test for specific PGY level, and chi-square test was used for overall program analysis. Statistical significance was set at p < 0.05. Total faculty engagement, that is, number of faculty members completing evaluations, increased from 13% (5/38) in Phase 1 to 53% (20/38) in Phase 2. During Phase 1, all evaluations consisted of online forms through the department's established system or e-mails to the program director. Evaluations

Graphene-based platforms for cancer therapeutics

PubMed Central

Patel, Sunny C; Lee, Stephen; Lalwani, Gaurav; Suhrland, Cassandra; Chowdhury, Sayan Mullick; Sitharaman, Balaji

2016-01-01

Graphene is a multifunctional carbon nanomaterial and could be utilized to develop platform technologies for cancer therapies. Its surface can be covalently and noncovalently functionalized with anticancer drugs and functional groups that target cancer cells and tissue to improve treatment efficacies. Furthermore, its physicochemical properties can be harnessed to facilitate stimulus responsive therapeutics and drug delivery. This review article summarizes the recent literature specifically focused on development of graphene technologies to treat cancer. We will focus on advances at the interface of graphene based drug/gene delivery, photothermal/photodynamic therapy and combinations of these techniques. We also discuss the current understanding in cytocompatibility and biocompatibility issues related to graphene formulations and their implications pertinent to clinical cancer management. PMID:26769305

Microcantilever-based platforms as biosensing tools.

PubMed

Alvarez, Mar; Lechuga, Laura M

2010-05-01

The fast and progressive growth of the biotechnology and pharmaceutical fields forces the development of new and powerful sensing techniques for process optimization and detection of biomolecules at very low concentrations. During the last years, the simplest MEMS structures, i.e. microcantilevers, have become an emerging and promising technology for biosensing applications, due to their small size, fast response, high sensitivity and their compatible integration into "lab-on-a-chip" devices. This article provides an overview of some of the most interesting bio-detections carried out during the last 2-3 years with the microcantilever-based platforms, which highlight the continuous expansion of this kind of sensor in the medical diagnosis field, reaching limits of detection at the single molecule level.

A comparative analysis of high-throughput platforms for validation of a circulating microRNA signature in diabetic retinopathy.

PubMed

Farr, Ryan J; Januszewski, Andrzej S; Joglekar, Mugdha V; Liang, Helena; McAulley, Annie K; Hewitt, Alex W; Thomas, Helen E; Loudovaris, Tom; Kay, Thomas W H; Jenkins, Alicia; Hardikar, Anandwardhan A

2015-06-02

MicroRNAs are now increasingly recognized as biomarkers of disease progression. Several quantitative real-time PCR (qPCR) platforms have been developed to determine the relative levels of microRNAs in biological fluids. We systematically compared the detection of cellular and circulating microRNA using a standard 96-well platform, a high-content microfluidics platform and two ultra-high content platforms. We used extensive analytical tools to compute inter- and intra-run variability and concordance measured using fidelity scoring, coefficient of variation and cluster analysis. We carried out unprejudiced next generation sequencing to identify a microRNA signature for Diabetic Retinopathy (DR) and systematically assessed the validation of this signature on clinical samples using each of the above four qPCR platforms. The results indicate that sensitivity to measure low copy number microRNAs is inversely related to qPCR reaction volume and that the choice of platform for microRNA biomarker validation should be made based on the abundance of miRNAs of interest.

Camera-based ratiometric fluorescence transduction of nucleic acid hybridization with reagentless signal amplification on a paper-based platform using immobilized quantum dots as donors.

PubMed

Noor, M Omair; Krull, Ulrich J

2014-10-21

Paper-based diagnostic assays are gaining increasing popularity for their potential application in resource-limited settings and for point-of-care screening. Achievement of high sensitivity with precision and accuracy can be challenging when using paper substrates. Herein, we implement the red-green-blue color palette of a digital camera for quantitative ratiometric transduction of nucleic acid hybridization on a paper-based platform using immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). A nonenzymatic and reagentless means of signal enhancement for QD-FRET assays on paper substrates is based on the use of dry paper substrates for data acquisition. This approach offered at least a 10-fold higher assay sensitivity and at least a 10-fold lower limit of detection (LOD) as compared to hydrated paper substrates. The surface of paper was modified with imidazole groups to assemble a transduction interface that consisted of immobilized QD-probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as an acceptor. A hybridization event that brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs was responsible for a FRET-sensitized emission from the acceptor dye, which served as an analytical signal. A hand-held UV lamp was used as an excitation source and ratiometric analysis using an iPad camera was possible by a relative intensity analysis of the red (Cy3 photoluminescence (PL)) and green (gQD PL) color channels of the digital camera. For digital imaging using an iPad camera, the LOD of the assay in a sandwich format was 450 fmol with a dynamic range spanning 2 orders of magnitude, while an epifluorescence microscope detection platform offered a LOD of 30 fmol and a dynamic range spanning 3 orders of magnitude. The selectivity of the hybridization assay was demonstrated by detection of a single nucleotide polymorphism at a contrast ratio of 60:1. This work provides an

Electrochemical sensor and biosensor platforms based on advanced nanomaterials for biological and biomedical applications.

PubMed

Maduraiveeran, Govindhan; Sasidharan, Manickam; Ganesan, Vellaichamy

2018-04-30

Introduction of novel functional nanomaterials and analytical technologies signify a foremost possibility for the advance of electrochemical sensor and biosensor platforms/devices for a broad series of applications including biological, biomedical, biotechnological, clinical and medical diagnostics, environmental and health monitoring, and food industries. The design of sensitive and selective electrochemical biological sensor platforms are accomplished conceivably by offering new surface modifications, microfabrication techniques, and diverse nanomaterials with unique properties for in vivo and in vitro medical analysis via relating a sensibly planned electrode/solution interface. The advantageous attributes such as low-cost, miniaturization, energy efficient, easy fabrication, online monitoring, and the simultaneous sensing capability are the driving force towards continued growth of electrochemical biosensing platforms, which have fascinated the interdisciplinary research arenas spanning chemistry, material science, biological science, and medical industries. The electrochemical biosensor platforms have potential applications in the early-stage detection and diagnosis of disease as stout and tunable diagnostic and therapeutic systems. The key aim of this review is to emphasize the newest development in the design of sensing and biosensing platforms based on functional nanomaterials for biological and biomedical applications. High sensitivity and selectivity, fast response, and excellent durability in biological media are all critical aspects which will also be wisely addressed. Potential applications of electrochemical sensor and biosensor platforms based on advanced functional nanomaterials for neuroscience diagnostics, clinical, point-of-care diagnostics and medical industries are also concisely presented. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2015-11-10

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

Using a digital marketing platform for the promotion of an internet based health encyclopedia in saudi arabia.

PubMed

Al Ateeq, Asma; Al Moamary, Eman; Daghestani, Tahani; Al Muallem, Yahya; Al Dogether, Majed; Alsughayr, Abdulrahman; Altuwaijri, Majid; Househ, Mowafa

2015-01-01

The objective of this paper is to investigate the experiences of using a digital marketing platform to promote the use of an internet based health encyclopedia in Saudi Arabia. Key informant interviews, meeting documentation, and Google Analytics were the data collection sources used in the study. Findings show that using a digital marketing platform led to a significant increase in the number of visitors to the health encyclopedia. The results demonstrate that digital marketing platforms are effective tools to be used for promoting internet based health education interventions. Future work will examine long-term educational impacts and costs in using digital marketing platforms to promote online healthcare sites in Saudi Arabia.

Development of an optoelectronic holographic platform for otolaryngology applications

NASA Astrophysics Data System (ADS)

Harrington, Ellery; Dobrev, Ivo; Bapat, Nikhil; Flores, Jorge Mauricio; Furlong, Cosme; Rosowski, John; Cheng, Jeffery Tao; Scarpino, Chris; Ravicz, Michael

2010-08-01

In this paper, we present advances on our development of an optoelectronic holographic computing platform with the ability to quantitatively measure full-field-of-view nanometer-scale movements of the tympanic membrane (TM). These measurements can facilitate otologists' ability to study and diagnose hearing disorders in humans. The holographic platform consists of a laser delivery system and an otoscope. The control software, called LaserView, is written in Visual C++ and handles communication and synchronization between hardware components. It provides a user-friendly interface to allow viewing of holographic images with several tools to automate holography-related tasks and facilitate hardware communication. The software uses a series of concurrent threads to acquire images, control the hardware, and display quantitative holographic data at video rates and in two modes of operation: optoelectronic holography and lensless digital holography. The holographic platform has been used to perform experiments on several live and post-mortem specimens, and is to be deployed in a medical research environment with future developments leading to its eventual clinical use.

Modernizing Immunization Practice Through the Use of Cloud Based Platforms.

PubMed

Bell, Cameron; Atkinson, Katherine M; Wilson, Kumanan

2017-04-01

Collection of timely and accurate immunization information is essential for effective immunization programs. Current immunization information systems have important limitations that impact the ability to collect this data. Based on our experience releasing a national immunization app we describe a cloud-based platform that would allow individuals to store their records digitally and exchange these records with public health information systems thus improving the quality of immunization information held by individuals and public health officials.

A DVE Time Management Simulation and Verification Platform Based on Causality Consistency Middleware

NASA Astrophysics Data System (ADS)

Zhou, Hangjun; Zhang, Wei; Peng, Yuxing; Li, Sikun

During the course of designing a time management algorithm for DVEs, the researchers always become inefficiency for the distraction from the realization of the trivial and fundamental details of simulation and verification. Therefore, a platform having realized theses details is desirable. However, this has not been achieved in any published work to our knowledge. In this paper, we are the first to design and realize a DVE time management simulation and verification platform providing exactly the same interfaces as those defined by the HLA Interface Specification. Moreover, our platform is based on a new designed causality consistency middleware and might offer the comparison of three kinds of time management services: CO, RO and TSO. The experimental results show that the implementation of the platform only costs small overhead, and that the efficient performance of it is highly effective for the researchers to merely focus on the improvement of designing algorithms.

Quantitative learning strategies based on word networks

NASA Astrophysics Data System (ADS)

Zhao, Yue-Tian-Yi; Jia, Zi-Yang; Tang, Yong; Xiong, Jason Jie; Zhang, Yi-Cheng

2018-02-01

Learning English requires a considerable effort, but the way that vocabulary is introduced in textbooks is not optimized for learning efficiency. With the increasing population of English learners, learning process optimization will have significant impact and improvement towards English learning and teaching. The recent developments of big data analysis and complex network science provide additional opportunities to design and further investigate the strategies in English learning. In this paper, quantitative English learning strategies based on word network and word usage information are proposed. The strategies integrate the words frequency with topological structural information. By analyzing the influence of connected learned words, the learning weights for the unlearned words and dynamically updating of the network are studied and analyzed. The results suggest that quantitative strategies significantly improve learning efficiency while maintaining effectiveness. Especially, the optimized-weight-first strategy and segmented strategies outperform other strategies. The results provide opportunities for researchers and practitioners to reconsider the way of English teaching and designing vocabularies quantitatively by balancing the efficiency and learning costs based on the word network.

Gyrocopter-Based Remote Sensing Platform

NASA Astrophysics Data System (ADS)

Weber, I.; Jenal, A.; Kneer, C.; Bongartz, J.

2015-04-01

In this paper the development of a lightweight and highly modularized airborne sensor platform for remote sensing applications utilizing a gyrocopter as a carrier platform is described. The current sensor configuration consists of a high resolution DSLR camera for VIS-RGB recordings. As a second sensor modality, a snapshot hyperspectral camera was integrated in the aircraft. Moreover a custom-developed thermal imaging system composed of a VIS-PAN camera and a LWIR-camera is used for aerial recordings in the thermal infrared range. Furthermore another custom-developed highly flexible imaging system for high resolution multispectral image acquisition with up to six spectral bands in the VIS-NIR range is presented. The performance of the overall system was tested during several flights with all sensor modalities and the precalculated demands with respect to spatial resolution and reliability were validated. The collected data sets were georeferenced, georectified, orthorectified and then stitched to mosaics.

A DICOM Based Collaborative Platform for Real-Time Medical Teleconsultation on Medical Images.

PubMed

Maglogiannis, Ilias; Andrikos, Christos; Rassias, Georgios; Tsanakas, Panayiotis

2017-01-01

The paper deals with the design of a Web-based platform for real-time medical teleconsultation on medical images. The proposed platform combines the principles of heterogeneous Workflow Management Systems (WfMSs), the peer-to-peer networking architecture and the SPA (Single-Page Application) concept, to facilitate medical collaboration among healthcare professionals geographically distributed. The presented work leverages state-of-the-art features of the web to support peer-to-peer communication using the WebRTC (Web Real Time Communication) protocol and client-side data processing for creating an integrated collaboration environment. The paper discusses the technical details of implementation and presents the operation of the platform in practice along with some initial results.

Metrologies for quantitative nanomechanical testing and quality control in semiconductor manufacturing

NASA Astrophysics Data System (ADS)

Pratt, Jon R.; Kramar, John A.; Newell, David B.; Smith, Douglas T.

2005-05-01

If nanomechanical testing is to evolve into a tool for process and quality control in semiconductor fabrication, great advances in throughput, repeatability, and accuracy of the associated instruments and measurements will be required. A recent grant awarded by the NIST Advanced Technology Program seeks to address the throughput issue by developing a high-speed AFM-based platform for quantitative nanomechanical measurements. The following paper speaks to the issue of quantitative accuracy by presenting an overview of various standards and techniques under development at NIST and other national metrology institutes (NMIs) that can provide a metrological basis for nanomechanical testing. The infrastructure we describe places firm emphasis on traceability to the International System of Units, paving the way for truly quantitative, rather than qualitative, physical property testing.

A cross-platform solution for light field based 3D telemedicine.

PubMed

Wang, Gengkun; Xiang, Wei; Pickering, Mark

2016-03-01

Current telehealth services are dominated by conventional 2D video conferencing systems, which are limited in their capabilities in providing a satisfactory communication experience due to the lack of realism. The "immersiveness" provided by 3D technologies has the potential to promote telehealth services to a wider range of applications. However, conventional stereoscopic 3D technologies are deficient in many aspects, including low resolution and the requirement for complicated multi-camera setup and calibration, and special glasses. The advent of light field (LF) photography enables us to record light rays in a single shot and provide glasses-free 3D display with continuous motion parallax in a wide viewing zone, which is ideally suited for 3D telehealth applications. As far as our literature review suggests, there have been no reports of 3D telemedicine systems using LF technology. In this paper, we propose a cross-platform solution for a LF-based 3D telemedicine system. Firstly, a novel system architecture based on LF technology is established, which is able to capture the LF of a patient, and provide an immersive 3D display at the doctor site. For 3D modeling, we further propose an algorithm which is able to convert the captured LF to a 3D model with a high level of detail. For the software implementation on different platforms (i.e., desktop, web-based and mobile phone platforms), a cross-platform solution is proposed. Demo applications have been developed for 2D/3D video conferencing, 3D model display and edit, blood pressure and heart rate monitoring, and patient data viewing functions. The demo software can be extended to multi-discipline telehealth applications, such as tele-dentistry, tele-wound and tele-psychiatry. The proposed 3D telemedicine solution has the potential to revolutionize next-generation telemedicine technologies by providing a high quality immersive tele-consultation experience. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A microcontroller platform for the rapid prototyping of functional electrical stimulation-based gait neuroprostheses.

PubMed

Luzio de Melo, Paulo; da Silva, Miguel Tavares; Martins, Jorge; Newman, Dava

2015-05-01

Functional electrical stimulation (FES) has been used over the last decades as a method to rehabilitate lost motor functions of individuals with spinal cord injury, multiple sclerosis, and post-stroke hemiparesis. Within this field, researchers in need of developing FES-based control solutions for specific disabilities often have to choose between either the acquisition and integration of high-performance industry-level systems, which are rather expensive and hardly portable, or develop custom-made portable solutions, which despite their lower cost, usually require expert-level electronic skills. Here, a flexible low-cost microcontroller-based platform for rapid prototyping of FES neuroprostheses is presented, designed for reduced execution complexity, development time, and production cost. For this reason, the Arduino open-source microcontroller platform was used, together with off-the-shelf components whenever possible. The developed system enables the rapid deployment of portable FES-based gait neuroprostheses, being flexible enough to allow simple open-loop strategies but also more complex closed-loop solutions. The system is based on a modular architecture that allows the development of optimized solutions depending on the desired FES applications, even though the design and testing of the platform were focused toward drop foot correction. The flexibility of the system was demonstrated using two algorithms targeting drop foot condition within different experimental setups. Successful bench testing of the device in healthy subjects demonstrated these neuroprosthesis platform capabilities to correct drop foot. Copyright © 2015 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Models of Quantitative Estimations: Rule-Based and Exemplar-Based Processes Compared

ERIC Educational Resources Information Center

von Helversen, Bettina; Rieskamp, Jorg

2009-01-01

The cognitive processes underlying quantitative estimations vary. Past research has identified task-contingent changes between rule-based and exemplar-based processes (P. Juslin, L. Karlsson, & H. Olsson, 2008). B. von Helversen and J. Rieskamp (2008), however, proposed a simple rule-based model--the mapping model--that outperformed the…

[Research and Implementation of Vital Signs Monitoring System Based on Cloud Platform].

PubMed

Yu, Man; Tan, Anzu; Huang, Jianqi

2018-05-30

Through analyzing the existing problems in the current mode, the vital signs monitoring information system based on cloud platform is designed and developed. The system's aim is to assist nurse carry out vital signs nursing work effectively and accurately. The system collects, uploads and analyzes patient's vital signs data by PDA which connecting medical inspection equipments. Clinical application proved that the system can effectively improve the quality and efficiency of medical care and may reduce medical expenses. It is alse an important practice result to build a medical cloud platform.

Development of an ultra-sensitive Simoa assay to enable GDF11 detection: a comparison across bioanalytical platforms.

PubMed

Myzithras, Maria; Li, Hua; Bigwarfe, Tammy; Waltz, Erica; Gupta, Priyanka; Low, Sarah; Hayes, David B; MacDonnell, Scott; Ahlberg, Jennifer; Franti, Michael; Roberts, Simon

2016-03-01

Four bioanalytical platforms were evaluated to optimize sensitivity and enable detection of recombinant human GDF11 in biological matrices; ELISA, Meso Scale Discovery, Gyrolab xP Workstation and Simoa HD-1. Results & methodology: After completion of custom assay development, the single-molecule ELISA (Simoa) achieved the greatest sensitivity with a lower limit of quantitation of 0.1 ng/ml, an improvement of 100-fold over the next sensitive platform (MSD). This improvement was essential to enable detection of GDF11 in biological samples, and without the technology the sensitivity achieved on the other platforms would not have been sufficient. Other factors such as ease of use, cost, assay time and automation capability can also be considered when developing custom immunoassays, based on the requirements of the bioanalyst.

Classification of cassava genotypes based on qualitative and quantitative data.

PubMed

Oliveira, E J; Oliveira Filho, O S; Santos, V S

2015-02-02

We evaluated the genetic variation of cassava accessions based on qualitative (binomial and multicategorical) and quantitative traits (continuous). We characterized 95 accessions obtained from the Cassava Germplasm Bank of Embrapa Mandioca e Fruticultura; we evaluated these accessions for 13 continuous, 10 binary, and 25 multicategorical traits. First, we analyzed the accessions based only on quantitative traits; next, we conducted joint analysis (qualitative and quantitative traits) based on the Ward-MLM method, which performs clustering in two stages. According to the pseudo-F, pseudo-t2, and maximum likelihood criteria, we identified five and four groups based on quantitative trait and joint analysis, respectively. The smaller number of groups identified based on joint analysis may be related to the nature of the data. On the other hand, quantitative data are more subject to environmental effects in the phenotype expression; this results in the absence of genetic differences, thereby contributing to greater differentiation among accessions. For most of the accessions, the maximum probability of classification was >0.90, independent of the trait analyzed, indicating a good fit of the clustering method. Differences in clustering according to the type of data implied that analysis of quantitative and qualitative traits in cassava germplasm might explore different genomic regions. On the other hand, when joint analysis was used, the means and ranges of genetic distances were high, indicating that the Ward-MLM method is very useful for clustering genotypes when there are several phenotypic traits, such as in the case of genetic resources and breeding programs.

Technology assessment for an integrated PC-based platform for three telemedicine applications

NASA Astrophysics Data System (ADS)

Tohme, Walid G.; Hayes, Wendelin S.; Dai, Hailei L.; Komo, Darmadi; Pahira, John J.; Abernethy, Darrell R.; Rennert, Wolfgang; Kuehl, Karen S.; Hauser, Gabriel J.; Mun, Seong K.

1996-05-01

This paper investigates the design and technical efficacy of an integrated PC based platform for three different medical applications. The technical efficacy of such a telemedicine platform has not been evaluated in the literature and optimal technical requirements have not been developed. The first application, with the Department of Surgery, Division of Urology, tests the utility of a telemedicine platform including radiology images for a surgical stone disease consultation service from an off site location in West Virginia. The second application, with the Department of Internal Medicine, Division of Clinical Pharmacology, investigates the usefulness of telemedicine when used for a clinical pharmacology consultation service from an off-site location. The third application, with the Department of Pediatrics, will test telemedicine for trauma care triage service first within an off-site location in Virginia and then from there to Georgetown University Medical Center.

Portable smartphone based quantitative phase microscope

NASA Astrophysics Data System (ADS)

Meng, Xin; Tian, Xiaolin; Yu, Wei; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Liu, Cheng; Wang, Shouyu

2018-01-01

To realize portable device with high contrast imaging capability, we designed a quantitative phase microscope using transport of intensity equation method based on a smartphone. The whole system employs an objective and an eyepiece as imaging system and a cost-effective LED as illumination source. A 3-D printed cradle is used to align these components. Images of different focal planes are captured by manual focusing, followed by calculation of sample phase via a self-developed Android application. To validate its accuracy, we first tested the device by measuring a random phase plate with known phases, and then red blood cell smear, Pap smear, broad bean epidermis sections and monocot root were also measured to show its performance. Owing to its advantages as accuracy, high-contrast, cost-effective and portability, the portable smartphone based quantitative phase microscope is a promising tool which can be future adopted in remote healthcare and medical diagnosis.

A bioanalytical platform for simultaneous detection and quantification of biological toxins.

PubMed

Weingart, Oliver G; Gao, Hui; Crevoisier, François; Heitger, Friedrich; Avondet, Marc-André; Sigrist, Hans

2012-01-01

Prevalent incidents support the notion that toxins, produced by bacteria, fungi, plants or animals are increasingly responsible for food poisoning or intoxication. Owing to their high toxicity some toxins are also regarded as potential biological warfare agents. Accordingly, control, detection and neutralization of toxic substances are a considerable economic burden to food safety, health care and military biodefense. The present contribution describes a new versatile instrument and related procedures for array-based simultaneous detection of bacterial and plant toxins using a bioanalytical platform which combines the specificity of covalently immobilized capture probes with a dedicated instrumentation and immuno-based microarray analytics. The bioanalytical platform consists of a microstructured polymer slide serving both as support of printed arrays and as incubation chamber. The platform further includes an easy-to-operate instrument for simultaneous slide processing at selectable assay temperature. Cy5 coupled streptavidin is used as unifying fluorescent tracer. Fluorescence image analysis and signal quantitation allow determination of the toxin's identity and concentration. The system's performance has been investigated by immunological detection of Botulinum Neurotoxin type A (BoNT/A), Staphylococcal enterotoxin B (SEB), and the plant toxin ricin. Toxins were detectable at levels as low as 0.5-1 ng · mL(-1) in buffer or in raw milk.

A Bioanalytical Platform for Simultaneous Detection and Quantification of Biological Toxins

PubMed Central

Weingart, Oliver G.; Gao, Hui; Crevoisier, François; Heitger, Friedrich; Avondet, Marc-André; Sigrist, Hans

2012-01-01

Prevalent incidents support the notion that toxins, produced by bacteria, fungi, plants or animals are increasingly responsible for food poisoning or intoxication. Owing to their high toxicity some toxins are also regarded as potential biological warfare agents. Accordingly, control, detection and neutralization of toxic substances are a considerable economic burden to food safety, health care and military biodefense. The present contribution describes a new versatile instrument and related procedures for array-based simultaneous detection of bacterial and plant toxins using a bioanalytical platform which combines the specificity of covalently immobilized capture probes with a dedicated instrumentation and immuno-based microarray analytics. The bioanalytical platform consists of a microstructured polymer slide serving both as support of printed arrays and as incubation chamber. The platform further includes an easy-to-operate instrument for simultaneous slide processing at selectable assay temperature. Cy5 coupled streptavidin is used as unifying fluorescent tracer. Fluorescence image analysis and signal quantitation allow determination of the toxin’s identity and concentration. The system’s performance has been investigated by immunological detection of Botulinum Neurotoxin type A (BoNT/A), Staphylococcal enterotoxin B (SEB), and the plant toxin ricin. Toxins were detectable at levels as low as 0.5–1 ng·mL−1 in buffer or in raw milk. PMID:22438766

Cloud Based Web 3d GIS Taiwan Platform

NASA Astrophysics Data System (ADS)

Tsai, W.-F.; Chang, J.-Y.; Yan, S. Y.; Chen, B.

2011-09-01

This article presents the status of the web 3D GIS platform, which has been developed in the National Applied Research Laboratories. The purpose is to develop a global earth observation 3D GIS platform for applications to disaster monitoring and assessment in Taiwan. For quick response to preliminary and detailed assessment after a natural disaster occurs, the web 3D GIS platform is useful to access, transfer, integrate, display and analyze the multi-scale huge data following the international OGC standard. The framework of cloud service for data warehousing management and efficiency enhancement using VMWare is illustrated in this article.

Design of batch audio/video conversion platform based on JavaEE

NASA Astrophysics Data System (ADS)

Cui, Yansong; Jiang, Lianpin

2018-03-01

With the rapid development of digital publishing industry, the direction of audio / video publishing shows the diversity of coding standards for audio and video files, massive data and other significant features. Faced with massive and diverse data, how to quickly and efficiently convert to a unified code format has brought great difficulties to the digital publishing organization. In view of this demand and present situation in this paper, basing on the development architecture of Sptring+SpringMVC+Mybatis, and combined with the open source FFMPEG format conversion tool, a distributed online audio and video format conversion platform with a B/S structure is proposed. Based on the Java language, the key technologies and strategies designed in the design of platform architecture are analyzed emphatically in this paper, designing and developing a efficient audio and video format conversion system, which is composed of “Front display system”, "core scheduling server " and " conversion server ". The test results show that, compared with the ordinary audio and video conversion scheme, the use of batch audio and video format conversion platform can effectively improve the conversion efficiency of audio and video files, and reduce the complexity of the work. Practice has proved that the key technology discussed in this paper can be applied in the field of large batch file processing, and has certain practical application value.

Platforms.

PubMed

Josko, Deborah

2014-01-01

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

Advances in fragment-based drug discovery platforms.

PubMed

Orita, Masaya; Warizaya, Masaichi; Amano, Yasushi; Ohno, Kazuki; Niimi, Tatsuya

2009-11-01

Fragment-based drug discovery (FBDD) has been established as a powerful alternative and complement to traditional high-throughput screening techniques for identifying drug leads. At present, this technique is widely used among academic groups as well as small biotech and large pharmaceutical companies. In recent years, > 10 new compounds developed with FBDD have entered clinical development, and more and more attention in the drug discovery field is being focused on this technique. Under the FBDD approach, a fragment library of relatively small compounds (molecular mass = 100 - 300 Da) is screened by various methods and the identified fragment hits which normally weakly bind to the target are used as starting points to generate more potent drug leads. Because FBDD is still a relatively new drug discovery technology, further developments and optimizations in screening platforms and fragment exploitation can be expected. This review summarizes recent advances in FBDD platforms and discusses the factors important for the successful application of this technique. Under the FBDD approach, both identifying the starting fragment hit to be developed and generating the drug lead from that starting fragment hit are important. Integration of various techniques, such as computational technology, X-ray crystallography, NMR, surface plasmon resonance, isothermal titration calorimetry, mass spectrometry and high-concentration screening, must be applied in a situation-appropriate manner.

Design of a dynamic test platform for autonomous robot vision systems

NASA Technical Reports Server (NTRS)

Rich, G. C.

1980-01-01

The concept and design of a dynamic test platform for development and evluation of a robot vision system is discussed. The platform is to serve as a diagnostic and developmental tool for future work with the RPI Mars Rover's multi laser/multi detector vision system. The platform allows testing of the vision system while its attitude is varied, statically or periodically. The vision system is mounted on the test platform. It can then be subjected to a wide variety of simulated can thus be examined in a controlled, quantitative fashion. Defining and modeling Rover motions and designing the platform to emulate these motions are also discussed. Individual aspects of the design process are treated separately, as structural, driving linkages, and motors and transmissions.

A platform for population-based weight management: description of a health plan-based integrated systems approach.

PubMed

Pronk, Nicolaas P; Boucher, Jackie L; Gehling, Eve; Boyle, Raymond G; Jeffery, Robert W

2002-10-01

To describe an integrated, operational platform from which mail- and telephone-based health promotion programs are implemented and to specifically relate this approach to weight management programming in a managed care setting. In-depth description of essential systems structures, including people, computer technology, and decision-support protocols. The roles of support staff, counselors, a librarian, and a manager in delivering a weight management program are described. Information availability using computer technology is a critical component in making this system effective and is presented according to its architectural layout and design. Protocols support counselors and administrative support staff in decision making, and a detailed flowchart presents the layout of this part of the system. This platform is described in the context of a weight management program, and we present baseline characteristics of 1801 participants, their behaviors, self-reported medical conditions, and initial pattern of enrollment in the various treatment options. Considering the prevalence and upward trend of overweight and obesity in the United States, a need exists for robust intervention platforms that can systematically support multiple types of programs. Weight management interventions implemented using this platform are scalable to the population level and are sustainable over time despite the limits of defined resources and budgets. The present article describes an innovative approach to reaching a large population with effective programs in an integrated, coordinated, and systematic manner. This comprehensive, robust platform represents an example of how obesity prevention and treatment research may be translated into the applied setting.

[Design of visualized medical images network and web platform based on MeVisLab].

PubMed

Xiang, Jun; Ye, Qing; Yuan, Xun

2017-04-01

With the trend of the development of "Internet +", some further requirements for the mobility of medical images have been required in the medical field. In view of this demand, this paper presents a web-based visual medical imaging platform. First, the feasibility of medical imaging is analyzed and technical points. CT (Computed Tomography) or MRI (Magnetic Resonance Imaging) images are reconstructed three-dimensionally by MeVisLab and packaged as X3D (Extensible 3D Graphics) files shown in the present paper. Then, the B/S (Browser/Server) system specially designed for 3D image is designed by using the HTML 5 and WebGL rendering engine library, and the X3D image file is parsed and rendered by the system. The results of this study showed that the platform was suitable for multiple operating systems to realize the platform-crossing and mobilization of medical image data. The development of medical imaging platform is also pointed out in this paper. It notes that web application technology will not only promote the sharing of medical image data, but also facilitate image-based medical remote consultations and distance learning.

Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma.

PubMed

Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Borchers, Christoph H

2013-07-01

An emerging approach for multiplexed targeted proteomics involves bottom-up LC-MRM-MS, with stable isotope-labeled internal standard peptides, to accurately quantitate panels of putative disease biomarkers in biofluids. In this paper, we used this approach to quantitate 27 candidate cancer-biomarker proteins in human plasma that had not been treated by immunoaffinity depletion or enrichment techniques. These proteins have been reported as biomarkers for a variety of human cancers, from laryngeal to ovarian, with breast cancer having the highest correlation. We implemented measures to minimize the analytical variability, improve the quantitative accuracy, and increase the feasibility and applicability of this MRM-based method. We have demonstrated excellent retention time reproducibility (median interday CV: 0.08%) and signal stability (median interday CV: 4.5% for the analytical platform and 6.1% for the bottom-up workflow) for the 27 biomarker proteins (represented by 57 interference-free peptides). The linear dynamic range for the MRM assays spanned four orders-of-magnitude, with 25 assays covering a 10(3) -10(4) range in protein concentration. The lowest abundance quantifiable protein in our biomarker panel was insulin-like growth factor 1 (calculated concentration: 127 ng/mL). Overall, the analytical performance of this assay demonstrates high robustness and sensitivity, and provides the necessary throughput and multiplexing capabilities required to verify and validate cancer-associated protein biomarker panels in human plasma, prior to clinical use. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Flexible Sensory Platform Based on Oxide-based Neuromorphic Transistors

NASA Astrophysics Data System (ADS)

Liu, Ning; Zhu, Li Qiang; Feng, Ping; Wan, Chang Jin; Liu, Yang Hui; Shi, Yi; Wan, Qing

2015-12-01

Inspired by the dendritic integration and spiking operation of a biological neuron, flexible oxide-based neuromorphic transistors with multiple input gates are fabricated on flexible plastic substrates for pH sensor applications. When such device is operated in a quasi-static dual-gate synergic sensing mode, it shows a high pH sensitivity of ~105 mV/pH. Our results also demonstrate that single-spike dynamic mode can remarkably improve pH sensitivity and reduce response/recover time and power consumption. Moreover, we find that an appropriate negative bias applied on the sensing gate electrode can further enhance the pH sensitivity and reduce the power consumption. Our flexible neuromorphic transistors provide a new-concept sensory platform for biochemical detection with high sensitivity, rapid response and ultralow power consumption.

Flexible Sensory Platform Based on Oxide-based Neuromorphic Transistors

PubMed Central

Liu, Ning; Zhu, Li Qiang; Feng, Ping; Wan, Chang Jin; Liu, Yang Hui; Shi, Yi; Wan, Qing

2015-01-01

Inspired by the dendritic integration and spiking operation of a biological neuron, flexible oxide-based neuromorphic transistors with multiple input gates are fabricated on flexible plastic substrates for pH sensor applications. When such device is operated in a quasi-static dual-gate synergic sensing mode, it shows a high pH sensitivity of ~105 mV/pH. Our results also demonstrate that single-spike dynamic mode can remarkably improve pH sensitivity and reduce response/recover time and power consumption. Moreover, we find that an appropriate negative bias applied on the sensing gate electrode can further enhance the pH sensitivity and reduce the power consumption. Our flexible neuromorphic transistors provide a new-concept sensory platform for biochemical detection with high sensitivity, rapid response and ultralow power consumption. PMID:26656113

Optimized Hypervisor Scheduler for Parallel Discrete Event Simulations on Virtual Machine Platforms

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

Yoginath, Srikanth B; Perumalla, Kalyan S

2013-01-01

With the advent of virtual machine (VM)-based platforms for parallel computing, it is now possible to execute parallel discrete event simulations (PDES) over multiple virtual machines, in contrast to executing in native mode directly over hardware as is traditionally done over the past decades. While mature VM-based parallel systems now offer new, compelling benefits such as serviceability, dynamic reconfigurability and overall cost effectiveness, the runtime performance of parallel applications can be significantly affected. In particular, most VM-based platforms are optimized for general workloads, but PDES execution exhibits unique dynamics significantly different from other workloads. Here we first present results frommore » experiments that highlight the gross deterioration of the runtime performance of VM-based PDES simulations when executed using traditional VM schedulers, quantitatively showing the bad scaling properties of the scheduler as the number of VMs is increased. The mismatch is fundamental in nature in the sense that any fairness-based VM scheduler implementation would exhibit this mismatch with PDES runs. We also present a new scheduler optimized specifically for PDES applications, and describe its design and implementation. Experimental results obtained from running PDES benchmarks (PHOLD and vehicular traffic simulations) over VMs show over an order of magnitude improvement in the run time of the PDES-optimized scheduler relative to the regular VM scheduler, with over 20 reduction in run time of simulations using up to 64 VMs. The observations and results are timely in the context of emerging systems such as cloud platforms and VM-based high performance computing installations, highlighting to the community the need for PDES-specific support, and the feasibility of significantly reducing the runtime overhead for scalable PDES on VM platforms.« less

Magnetoresistive biosensors for quantitative proteomics

NASA Astrophysics Data System (ADS)

Zhou, Xiahan; Huang, Chih-Cheng; Hall, Drew A.

2017-08-01

Quantitative proteomics, as a developing method for study of proteins and identification of diseases, reveals more comprehensive and accurate information of an organism than traditional genomics. A variety of platforms, such as mass spectrometry, optical sensors, electrochemical sensors, magnetic sensors, etc., have been developed for detecting proteins quantitatively. The sandwich immunoassay is widely used as a labeled detection method due to its high specificity and flexibility allowing multiple different types of labels. While optical sensors use enzyme and fluorophore labels to detect proteins with high sensitivity, they often suffer from high background signal and challenges in miniaturization. Magnetic biosensors, including nuclear magnetic resonance sensors, oscillator-based sensors, Hall-effect sensors, and magnetoresistive sensors, use the specific binding events between magnetic nanoparticles (MNPs) and target proteins to measure the analyte concentration. Compared with other biosensing techniques, magnetic sensors take advantage of the intrinsic lack of magnetic signatures in biological samples to achieve high sensitivity and high specificity, and are compatible with semiconductor-based fabrication process to have low-cost and small-size for point-of-care (POC) applications. Although still in the development stage, magnetic biosensing is a promising technique for in-home testing and portable disease monitoring.

Integrated Platform for Expedited Synthesis–Purification–Testing of Small Molecule Libraries

PubMed Central

2017-01-01

The productivity of medicinal chemistry programs can be significantly increased through the introduction of automation, leading to shortened discovery cycle times. Herein, we describe a platform that consolidates synthesis, purification, quantitation, dissolution, and testing of small molecule libraries. The system was validated through the synthesis and testing of two libraries of binders of polycomb protein EED, and excellent correlation of obtained data with results generated through conventional approaches was observed. The fully automated and integrated platform enables batch-supported compound synthesis based on a broad array of chemical transformations with testing in a variety of biochemical assay formats. A library turnaround time of between 24 and 36 h was achieved, and notably, each library synthesis produces sufficient amounts of compounds for further evaluation in secondary assays thereby contributing significantly to the shortening of medicinal chemistry discovery cycles. PMID:28435537

The Performance Analysis of a Uav Based Mobile Mapping System Platform

NASA Astrophysics Data System (ADS)

Tsai, M. L.; Chiang, K. W.; Lo, C. F.; Ch, C. H.

2013-08-01

To facilitate applications such as environment detection or disaster monitoring, the development of rapid low cost systems for collecting near real-time spatial information is very critical. Rapid spatial information collection has become an emerging trend for remote sensing and mapping applications. This study develops a Direct Georeferencing (DG) based fixed-wing Unmanned Aerial Vehicle (UAV) photogrammetric platform where an Inertial Navigation System (INS)/Global Positioning System (GPS) integrated Positioning and Orientation System (POS) system is implemented to provide the DG capability of the platform. The performance verification indicates that the proposed platform can capture aerial images successfully. A flight test is performed to verify the positioning accuracy in DG mode without using Ground Control Points (GCP). The preliminary results illustrate that horizontal DG positioning accuracies in the x and y axes are around 5 m with 300 m flight height. The positioning accuracy in the z axis is less than 10 m. Such accuracy is good for near real-time disaster relief. The DG ready function of proposed platform guarantees mapping and positioning capability even in GCP free environments, which is very important for rapid urgent response for disaster relief. Generally speaking, the data processing time for the DG module, including POS solution generalization, interpolation, Exterior Orientation Parameters (EOP) generation, and feature point measurements, is less than one hour.

Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

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

Xie, Fang; Liu, Tao; Qian, Weijun

2011-07-22

Liquid chromatography-mass spectrometry (LC-MS)-based quantitative proteomics has become increasingly applied for a broad range of biological applications due to growing capabilities for broad proteome coverage and good accuracy in quantification. Herein, we review the current LC-MS-based quantification methods with respect to their advantages and limitations, and highlight their potential applications.

Reproducibility and quantitation of amplicon sequencing-based detection

PubMed Central

Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

2011-01-01

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

Versatile electrophoresis-based self-test platform.

PubMed

Guijt, Rosanne M

2015-03-01

Lab on a Chip technology offers the possibility to extract chemical information from a complex sample in a simple, automated way without the need for a laboratory setting. In the health care sector, this chemical information could be used as a diagnostic tool for example to inform dosing. In this issue, the research underpinning a family of electrophoresis-based point-of-care devices for self-testing of ionic analytes in various sample matrices is described [Electrophoresis 2015, 36, 712-721.]. Hardware, software, and methodological chances made to improve the overall analytical performance in terms of accuracy, precision, detection limit, and reliability are discussed. In addition to the main focus of lithium monitoring, new applications including the use of the platform for veterinary purposes, sodium, and for creatinine measurements are included. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Robotic Platform for Quantitative High-Throughput Screening

PubMed Central

Michael, Sam; Auld, Douglas; Klumpp, Carleen; Jadhav, Ajit; Zheng, Wei; Thorne, Natasha; Austin, Christopher P.; Inglese, James

2008-01-01

Abstract High-throughput screening (HTS) is increasingly being adopted in academic institutions, where the decoupling of screening and drug development has led to unique challenges, as well as novel uses of instrumentation, assay formulations, and software tools. Advances in technology have made automated unattended screening in the 1,536-well plate format broadly accessible and have further facilitated the exploration of new technologies and approaches to screening. A case in point is our recently developed quantitative HTS (qHTS) paradigm, which tests each library compound at multiple concentrations to construct concentration-response curves (CRCs) generating a comprehensive data set for each assay. The practical implementation of qHTS for cell-based and biochemical assays across libraries of > 100,000 compounds (e.g., between 700,000 and 2,000,000 sample wells tested) requires maximal efficiency and miniaturization and the ability to easily accommodate many different assay formats and screening protocols. Here, we describe the design and utilization of a fully integrated and automated screening system for qHTS at the National Institutes of Health's Chemical Genomics Center. We report system productivity, reliability, and flexibility, as well as modifications made to increase throughput, add additional capabilities, and address limitations. The combination of this system and qHTS has led to the generation of over 6 million CRCs from > 120 assays in the last 3 years and is a technology that can be widely implemented to increase efficiency of screening and lead generation. PMID:19035846

Quantifying environmental DNA signals for aquatic invasive species across multiple detection platforms.

PubMed

Nathan, Lucas M; Simmons, Megan; Wegleitner, Benjamin J; Jerde, Christopher L; Mahon, Andrew R

2014-11-04

The use of molecular surveillance techniques has become popular among aquatic researchers and managers due to the improved sensitivity and efficiency compared to traditional sampling methods. Rapid expansion in the use of environmental DNA (eDNA), paired with the advancement of molecular technologies, has resulted in new detection platforms and techniques. In this study we present a comparison of three eDNA surveillance platforms: traditional polymerase chain reaction (PCR), quantitative PCR (qPCR), and digital droplet PCR (ddPCR) in which water samples were collected over a 24 h time period from mesocosm experiments containing a population gradient of invasive species densities. All platforms reliably detected the presence of DNA, even at low target organism densities within the first hour. The two quantitative platforms (qPCR and ddPCR) produced similar estimates of DNA concentrations. The analyses completed with ddPCR was faster from sample collection through analyses and cost approximately half the expenditure of qPCR. Although a new platform for eDNA surveillance of aquatic species, ddPCR was consistent with more commonly used qPCR and a cost-effective means of estimating DNA concentrations. Use of ddPCR by researchers and managers should be considered in future eDNA surveillance applications.

Building an Open-source Simulation Platform of Acoustic Radiation Force-based Breast Elastography

PubMed Central

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-01-01

Ultrasound-based elastography including strain elastography (SE), acoustic radiation force Impulse (ARFI) imaging, point shear wave elastography (pSWE) and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. “ground truth”) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity – one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion

Building an open-source simulation platform of acoustic radiation force-based breast elastography

NASA Astrophysics Data System (ADS)

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-03-01

Ultrasound-based elastography including strain elastography, acoustic radiation force impulse (ARFI) imaging, point shear wave elastography and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. ‘ground truth’) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity—one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast

A software platform for phase contrast x-ray breast imaging research.

PubMed

Bliznakova, K; Russo, P; Mettivier, G; Requardt, H; Popov, P; Bravin, A; Buliev, I

2015-06-01

To present and validate a computer-based simulation platform dedicated for phase contrast x-ray breast imaging research. The software platform, developed at the Technical University of Varna on the basis of a previously validated x-ray imaging software simulator, comprises modules for object creation and for x-ray image formation. These modules were updated to take into account the refractive index for phase contrast imaging as well as implementation of the Fresnel-Kirchhoff diffraction theory of the propagating x-ray waves. Projection images are generated in an in-line acquisition geometry. To test and validate the platform, several phantoms differing in their complexity were constructed and imaged at 25 keV and 60 keV at the beamline ID17 of the European Synchrotron Radiation Facility. The software platform was used to design computational phantoms that mimic those used in the experimental study and to generate x-ray images in absorption and phase contrast modes. The visual and quantitative results of the validation process showed an overall good correlation between simulated and experimental images and show the potential of this platform for research in phase contrast x-ray imaging of the breast. The application of the platform is demonstrated in a feasibility study for phase contrast images of complex inhomogeneous and anthropomorphic breast phantoms, compared to x-ray images generated in absorption mode. The improved visibility of mammographic structures suggests further investigation and optimisation of phase contrast x-ray breast imaging, especially when abnormalities are present. The software platform can be exploited also for educational purposes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Developing High-Affinity Protein Capture Agents and Nanotechnology-Based Platforms for In Vitro Diagnostics

NASA Astrophysics Data System (ADS)

Rohde, Rosemary Dyane

In this thesis, I describe projects that were aimed at improving ways to capture proteins for clinical diagnostics. Nanoelectronic sensors, such as silicon nanowires (SiNWs), can provide label-free quantitative measurements of protein biomarkers in real time. One technical challenge for SiNWs is to develop chemistry that can be applied for selectively encoding the nanowire surfaces with capture agents, thus making them sensors that have selectivity for specific proteins. Furthermore, because of the nature of how the sensor works, it is desirable to achieve this spatially selective chemical functionalization without having the silicon undergo oxidation. This method is described here and provides a general platform that can incorporate organic and biological molecules on Si (111) with minimal oxidation of the silicon surface. The development of these devices is, in part, driven by early diagnosis, treatment, monitoring, and personalized medicine---all of which are increasingly requiring quantitative, rapid, and multiparameter measurements. To begin achieving this goal, a large number of protein biomarkers need to be captured and quantitatively measured to create a diagnostic panel. One of the greatest challenges towards making protein-biomarker-based in vitro diagnostics inexpensive involves developing capture agents to detect the proteins. A major thrust of this thesis is to develop multi-valent, high-affinity and high-selectivity protein capture agents using in situ click chemistry. In situ click chemistry is a tool that utilizes the protein itself to catalyze the formation of a biligand from individual azide and alkyne ligands that are co-localized. Large one-bead one-compound (OBOC) libraries of peptides are used to form the body of these ligands, also providing high chemical diversity with minimal synthetic effort. This process can be repeated to identify a triligand, tetraligand, and so forth. Moreover, the resulting multiligand protein capture agents can be

Supporting in- and off-Hospital Patient Management Using a Web-based Integrated Software Platform.

PubMed

Spyropoulos, Basile; Botsivali, Maria; Tzavaras, Aris; Pierros, Vasileios

2015-01-01

In this paper, a Web-based software platform appropriately designed to support the continuity of health care information and management for both in and out of hospital care is presented. The system has some additional features as it is the formation of continuity of care records and the transmission of referral letters with a semantically annotated web service. The platform's Web-orientation provides significant advantages, allowing for easily accomplished remote access.

Design and implementation of a general and automatic test platform base on NI PXI system

NASA Astrophysics Data System (ADS)

Shi, Long

2018-05-01

Aiming at some difficulties of test equipment such as the short product life, poor generality and high development cost, a general and automatic test platform base on NI PXI system is designed in this paper, which is able to meet most test requirements of circuit boards. The test platform is devided into 5 layers, every layer is introduced in detail except for the "Equipment Under Test" layer. An output board of a track-side equipment, which is an important part of high speed train control system, is taken as an example to make the functional circuit test by the test platform. The results show that the test platform is easy to realize add-on functions development, automatic test, wide compatibility and strong generality.

Study on photon transport problem based on the platform of molecular optical simulation environment.

PubMed

Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

2010-01-01

As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SP(n)), and physical measurement to verify the performance of our study method on both accuracy and efficiency.

Simultaneous Quantitative Detection of Helicobacter Pylori Based on a Rapid and Sensitive Testing Platform using Quantum Dots-Labeled Immunochromatiographic Test Strips

NASA Astrophysics Data System (ADS)

Zheng, Yu; Wang, Kan; Zhang, Jingjing; Qin, Weijian; Yan, Xinyu; Shen, Guangxia; Gao, Guo; Pan, Fei; Cui, Daxiang

2016-02-01

Quantum dots-labeled urea-enzyme antibody-based rapid immunochromatographic test strips have been developed as quantitative fluorescence point-of-care tests (POCTs) to detect helicobacter pylori. Presented in this study is a new test strip reader designed to run on tablet personal computers (PCs), which is portable for outdoor detection even without an alternating current (AC) power supply. A Wi-Fi module was integrated into the reader to improve its portability. Patient information was loaded by a barcode scanner, and an application designed to run on tablet PCs was developed to handle the acquired images. A vision algorithm called Kmeans was used for picture processing. Different concentrations of various human blood samples were tested to evaluate the stability and accuracy of the fabricated device. Results demonstrate that the reader can provide an easy, rapid, simultaneous, quantitative detection for helicobacter pylori. The proposed test strip reader has a lighter weight than existing detection readers, and it can run for long durations without an AC power supply, thus verifying that it possesses advantages for outdoor detection. Given its fast detection speed and high accuracy, the proposed reader combined with quantum dots-labeled test strips is suitable for POCTs and owns great potential in applications such as screening patients with infection of helicobacter pylori, etc. in near future.

Model-Based Linkage Analysis of a Quantitative Trait.

PubMed

Song, Yeunjoo E; Song, Sunah; Schnell, Audrey H

2017-01-01

Linkage Analysis is a family-based method of analysis to examine whether any typed genetic markers cosegregate with a given trait, in this case a quantitative trait. If linkage exists, this is taken as evidence in support of a genetic basis for the trait. Historically, linkage analysis was performed using a binary disease trait, but has been extended to include quantitative disease measures. Quantitative traits are desirable as they provide more information than binary traits. Linkage analysis can be performed using single-marker methods (one marker at a time) or multipoint (using multiple markers simultaneously). In model-based linkage analysis the genetic model for the trait of interest is specified. There are many software options for performing linkage analysis. Here, we use the program package Statistical Analysis for Genetic Epidemiology (S.A.G.E.). S.A.G.E. was chosen because it also includes programs to perform data cleaning procedures and to generate and test genetic models for a quantitative trait, in addition to performing linkage analysis. We demonstrate in detail the process of running the program LODLINK to perform single-marker analysis, and MLOD to perform multipoint analysis using output from SEGREG, where SEGREG was used to determine the best fitting statistical model for the trait.

Laser fabrication of porous silicon-based platforms for cell culturing.

PubMed

Peláez, Ramón-J; Afonso, Carmen-N; Vega, Fidel; Recio-Sánchez, Gonzalo; Torres-Costa, Vicente; Manso-Silván, Miguel; García-Ruiz, Josefa-P; Martín-Palma, Raúl-J

2013-11-01

In this study, we explore the selective culturing of human mesenchymal stem cells (hMSCs) on Si-based diffractive platforms. We demonstrate a single-step and flexible method for producing platforms on nanostructured porous silicon (nanoPS) based on the use of single pulses of an excimer laser to expose phase masks. The resulting patterns are typically 1D patterns formed by fringes or 2D patterns formed by circles. They are formed by alternate regions of almost unmodified nanoPS and regions where the nanoPS surface has melted and transformed into Si nanoparticles. The patterns are produced in relatively large areas (a few square millimeters) and can have a wide range of periodicities and aspect ratios. Direct binding, that is, with no previous functionalization of the pattern, alignment, and active polarization of hMSCs are explored. The results show the preferential direct binding of the hMSCs along the transformed regions whenever their width compares with the dimensions of the cells and they escape from patterns for smaller widths suggesting that the selectivity can be tailored through the pattern period. Copyright © 2013 Wiley Periodicals, Inc.

Cultivating engineering innovation ability based on optoelectronic experimental platform

NASA Astrophysics Data System (ADS)

Li, Dangjuan; Wu, Shenjiang

2017-08-01

As the supporting experimental platform of the Xi'an Technological University education reform experimental class, "optical technological innovation experimental platform" integrated the design and comprehensive experiments of the optical multi-class courses. On the basis of summing up the past two years teaching experience, platform pilot projects were improve. It has played a good role by making the use of an open teaching model in the cultivating engineering innovation spirit and scientific thinking of the students.

Design and Evaluation of a Personal Digital Assistant-based Research Platform for Cochlear Implants

PubMed Central

Ali, Hussnain; Lobo, Arthur P.; Loizou, Philipos C.

2014-01-01

This paper discusses the design, development, features, and clinical evaluation of a personal digital assistant (PDA)-based platform for cochlear implant research. This highly versatile and portable research platform allows researchers to design and perform complex experiments with cochlear implants manufactured by Cochlear Corporation with great ease and flexibility. The research platform includes a portable processor for implementing and evaluating novel speech processing algorithms, a stimulator unit which can be used for electrical stimulation and neurophysio-logic studies with animals, and a recording unit for collecting electroencephalogram/evoked potentials from human subjects. The design of the platform for real time and offline stimulation modes is discussed for electric-only and electric plus acoustic stimulation followed by results from an acute study with implant users for speech intelligibility in quiet and noisy conditions. The results are comparable with users’ clinical processor and very promising for undertaking chronic studies. PMID:23674422

OLED-based biosensing platform with ZnO nanoparticles for enzyme immobilization

NASA Astrophysics Data System (ADS)

Cai, Yuankun; Shinar, Ruth; Shinar, Joseph

2009-08-01

Organic light-emitting diode (OLED)-based sensing platforms are attractive for photoluminescence (PL)-based monitoring of a variety of analytes. Among the promising OLED attributes for sensing applications is the thin and flexible size and design of the OLED pixel array that is used for PL excitation. To generate a compact, fielddeployable sensor, other major sensor components, such as the sensing probe and the photodetector, in addition to the thin excitation source, should be compact. To this end, the OLED-based sensing platform was tested with composite thin biosensing films, where oxidase enzymes were immobilized on ZnO nanoparticles, rather than dissolved in solution, to generate a more compact device. The analytes tested, glucose, cholesterol, and lactate, were monitored by following their oxidation reactions in the presence of oxygen and their respective oxidase enzymes. During such reactions, oxygen is consumed and its residual concentration, which is determined by the initial concentration of the above-mentioned analytes, is monitored. The sensors utilized the oxygen-sensitive dye Pt octaethylporphyrin, embedded in polystyrene. The enzymes were sandwiched between two thin ZnO layers, an approach that was found to improve the stability of the sensing probes.

Real-time software-based end-to-end wireless visual communications simulation platform

NASA Astrophysics Data System (ADS)

Chen, Ting-Chung; Chang, Li-Fung; Wong, Andria H.; Sun, Ming-Ting; Hsing, T. Russell

1995-04-01

Wireless channel impairments pose many challenges to real-time visual communications. In this paper, we describe a real-time software based wireless visual communications simulation platform which can be used for performance evaluation in real-time. This simulation platform consists of two personal computers serving as hosts. Major components of each PC host include a real-time programmable video code, a wireless channel simulator, and a network interface for data transport between the two hosts. The three major components are interfaced in real-time to show the interaction of various wireless channels and video coding algorithms. The programmable features in the above components allow users to do performance evaluation of user-controlled wireless channel effects without physically carrying out these experiments which are limited in scope, time-consuming, and costly. Using this simulation platform as a testbed, we have experimented with several wireless channel effects including Rayleigh fading, antenna diversity, channel filtering, symbol timing, modulation, and packet loss.

[Tumor Data Interacted System Design Based on Grid Platform].

PubMed

Liu, Ying; Cao, Jiaji; Zhang, Haowei; Zhang, Ke

2016-06-01

In order to satisfy demands of massive and heterogeneous tumor clinical data processing and the multi-center collaborative diagnosis and treatment for tumor diseases,a Tumor Data Interacted System(TDIS)was established based on grid platform,so that an implementing virtualization platform of tumor diagnosis service was realized,sharing tumor information in real time and carrying on standardized management.The system adopts Globus Toolkit 4.0tools to build the open grid service framework and encapsulats data resources based on Web Services Resource Framework(WSRF).The system uses the middleware technology to provide unified access interface for heterogeneous data interaction,which could optimize interactive process with virtualized service to query and call tumor information resources flexibly.For massive amounts of heterogeneous tumor data,the federated stored and multiple authorized mode is selected as security services mechanism,real-time monitoring and balancing load.The system can cooperatively manage multi-center heterogeneous tumor data to realize the tumor patient data query,sharing and analysis,and compare and match resources in typical clinical database or clinical information database in other service node,thus it can assist doctors in consulting similar case and making up multidisciplinary treatment plan for tumors.Consequently,the system can improve efficiency of diagnosis and treatment for tumor,and promote the development of collaborative tumor diagnosis model.

Development of a comprehensive analytical platform for the detection and quantitation of food fraud using a biomarker approach. The oregano adulteration case study.

PubMed

Wielogorska, Ewa; Chevallier, Olivier; Black, Connor; Galvin-King, Pamela; Delêtre, Marc; Kelleher, Colin T; Haughey, Simon A; Elliott, Christopher T

2018-01-15

Due to increasing number of food fraud incidents, there is an inherent need for the development and implementation of analytical platforms enabling detection and quantitation of adulteration. In this study a set of unique biomarkers of commonly found oregano adulterants became the targets in the development of a LC-MS/MS method which underwent a rigorous in-house validation. The method presented very high selectivity and specificity, excellent linearity (R 2 >0.988) low decision limits and detection capabilities (<2%), acceptable accuracy (intra-assay 92-113%, inter-assay 69-138%) and precision (CV<20%). The method was compared with an established FTIR screening assay and revealed a good correlation of quali- and quantitative results (R 2 >0.81). An assessment of 54 suspected adulterated oregano samples revealed that almost 90% of them contained at least one bulking agent, with a median level of adulteration of 50%. Such innovative methodologies need to be established as routine testing procedures to detect and ultimately deter food fraud. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tele-Medicine Applications of an ISDN-Based Tele-Working Platform

DTIC Science & Technology

2001-10-25

developed over the Hellenic Integrated Services Digital Network (ISDN), is based on user terminals (personal computers), networking apparatus, and a...key infrastructure, ready to offer enhanced message switching and translation in response to market trends [8]. Three (3) years ago, the Hellenic PTT...should outcome to both an integrated Tele- Working platform, a main central database (completed with maintenance facilities), and a ready-to-be

A novel multiplex bead-based platform highlights the diversity of extracellular vesicles

PubMed Central

Koliha, Nina; Wiencek, Yvonne; Heider, Ute; Jüngst, Christian; Kladt, Nikolay; Krauthäuser, Susanne; Johnston, Ian C. D.; Bosio, Andreas; Schauss, Astrid; Wild, Stefan

2016-01-01

The surface protein composition of extracellular vesicles (EVs) is related to the originating cell and may play a role in vesicle function. Knowledge of the protein content of individual EVs is still limited because of the technical challenges to analyse small vesicles. Here, we introduce a novel multiplex bead-based platform to investigate up to 39 different surface markers in one sample. The combination of capture antibody beads with fluorescently labelled detection antibodies allows the analysis of EVs that carry surface markers recognized by both antibodies. This new method enables an easy screening of surface markers on populations of EVs. By combining different capture and detection antibodies, additional information on relative expression levels and potential vesicle subpopulations is gained. We also established a protocol to visualize individual EVs by stimulated emission depletion (STED) microscopy. Thereby, markers on single EVs can be detected by fluorophore-conjugated antibodies. We used the multiplex platform and STED microscopy to show for the first time that NK cell–derived EVs and platelet-derived EVs are devoid of CD9 or CD81, respectively, and that EVs isolated from activated B cells comprise different EV subpopulations. We speculate that, according to our STED data, tetraspanins might not be homogenously distributed but may mostly appear as clusters on EV subpopulations. Finally, we demonstrate that EV mixtures can be separated by magnetic beads and analysed subsequently with the multiplex platform. Both the multiplex bead-based platform and STED microscopy revealed subpopulations of EVs that have been indistinguishable by most analysis tools used so far. We expect that an in-depth view on EV heterogeneity will contribute to our understanding of different EVs and functions. PMID:26901056

RFID-Based Multidisciplinary Educational Platform to Improve the Engineering and Technology Curriculums

ERIC Educational Resources Information Center

Yelamarthi, Kumar

2012-01-01

Multidisciplinary projects involving electrical engineering (EE), mechanical engineering (ME), and computer engineering (CE) students are both exciting and difficult to conceptualize. Answering this challenge, this paper presents a multidisciplinary educational platform on radio frequency identification-based assistive devices. The combination of…

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research.

PubMed

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction.

HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly.

PubMed

Sun, Lidan; Wang, Jing; Zhu, Xuli; Jiang, Libo; Gosik, Kirk; Sang, Mengmeng; Sun, Fengsuo; Cheng, Tangren; Zhang, Qixiang; Wu, Rongling

2017-02-15

Heterophylly, i.e. morphological changes in leaves along the axis of an individual plant, is regarded as a strategy used by plants to cope with environmental change. However, little is known of the extent to which heterophylly is controlled by genes and how each underlying gene exerts its effect on heterophyllous variation. We described a geometric morphometric model that can quantify heterophylly in plants and further constructed an R-based computing platform by integrating this model into a genetic mapping and association setting. The platform, named HpQTL, allows specific quantitative trait loci mediating heterophyllous variation to be mapped throughout the genome. The statistical properties of HpQTL were examined and validated via computer simulation. Its biological relevance was demonstrated by results from a real data analysis of heterophylly in a wood plant, mei (Prunus mume). HpQTL provides a powerful tool to analyze heterophylly and its underlying genetic architecture in a quantitative manner. It also contributes a new approach for genome-wide association studies aimed to dissect the programmed regulation of plant development and evolution. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A novel medical image data-based multi-physics simulation platform for computational life sciences.

PubMed

Neufeld, Esra; Szczerba, Dominik; Chavannes, Nicolas; Kuster, Niels

2013-04-06

Simulating and modelling complex biological systems in computational life sciences requires specialized software tools that can perform medical image data-based modelling, jointly visualize the data and computational results, and handle large, complex, realistic and often noisy anatomical models. The required novel solvers must provide the power to model the physics, biology and physiology of living tissue within the full complexity of the human anatomy (e.g. neuronal activity, perfusion and ultrasound propagation). A multi-physics simulation platform satisfying these requirements has been developed for applications including device development and optimization, safety assessment, basic research, and treatment planning. This simulation platform consists of detailed, parametrized anatomical models, a segmentation and meshing tool, a wide range of solvers and optimizers, a framework for the rapid development of specialized and parallelized finite element method solvers, a visualization toolkit-based visualization engine, a Python scripting interface for customized applications, a coupling framework, and more. Core components are cross-platform compatible and use open formats. Several examples of applications are presented: hyperthermia cancer treatment planning, tumour growth modelling, evaluating the magneto-haemodynamic effect as a biomarker and physics-based morphing of anatomical models.

Research about Memory Detection Based on the Embedded Platform

NASA Astrophysics Data System (ADS)

Sun, Hao; Chu, Jian

As is known to us all, the resources of memory detection of the embedded systems are very limited. Taking the Linux-based embedded arm as platform, this article puts forward two efficient memory detection technologies according to the characteristics of the embedded software. Especially for the programs which need specific libraries, the article puts forwards portable memory detection methods to help program designers to reduce human errors,improve programming quality and therefore make better use of the valuable embedded memory resource.

A Web-Based Visualization and Animation Platform for Digital Logic Design

ERIC Educational Resources Information Center

Shoufan, Abdulhadi; Lu, Zheng; Huss, Sorin A.

2015-01-01

This paper presents a web-based education platform for the visualization and animation of the digital logic design process. This includes the design of combinatorial circuits using logic gates, multiplexers, decoders, and look-up-tables as well as the design of finite state machines. Various configurations of finite state machines can be selected…

Simple and Rapid Determination of Ferulic Acid Levels in Food and Cosmetic Samples Using Paper-Based Platforms

PubMed Central

Tee-ngam, Prinjaporn; Nunant, Namthip; Rattanarat, Poomrat; Siangproh, Weena; Chailapakul, Orawon

2013-01-01

Ferulic acid is an important phenolic antioxidant found in or added to diet supplements, beverages, and cosmetic creams. Two designs of paper-based platforms for the fast, simple and inexpensive evaluation of ferulic acid contents in food and pharmaceutical cosmetics were evaluated. The first, a paper-based electrochemical device, was developed for ferulic acid detection in uncomplicated matrix samples and was created by the photolithographic method. The second, a paper-based colorimetric device was preceded by thin layer chromatography (TLC) for the separation and detection of ferulic acid in complex samples using a silica plate stationary phase and an 85:15:1 (v/v/v) chloroform: methanol: formic acid mobile phase. After separation, ferulic acid containing section of the TLC plate was attached onto the patterned paper containing the colorimetric reagent and eluted with ethanol. The resulting color change was photographed and quantitatively converted to intensity. Under the optimal conditions, the limit of detection of ferulic acid was found to be 1 ppm and 7 ppm (S/N = 3) for first and second designs, respectively, with good agreement with the standard HPLC-UV detection method. Therefore, these methods can be used for the simple, rapid, inexpensive and sensitive quantification of ferulic acid in a variety of samples. PMID:24077320

FaceTOON: a unified platform for feature-based cartoon expression generation

NASA Astrophysics Data System (ADS)

Zaharia, Titus; Marre, Olivier; Prêteux, Françoise; Monjaux, Perrine

2008-02-01

This paper presents the FaceTOON system, a semi-automatic platform dedicated to the creation of verbal and emotional facial expressions, within the applicative framework of 2D cartoon production. The proposed FaceTOON platform makes it possible to rapidly create 3D facial animations with a minimum amount of user interaction. In contrast with existing commercial 3D modeling softwares, which usually require from the users advanced 3D graphics skills and competences, the FaceTOON system is based exclusively on 2D interaction mechanisms, the 3D modeling stage being completely transparent for the user. The system takes as input a neutral 3D face model, free of any facial feature, and a set of 2D drawings, representing the desired facial features. A 2D/3D virtual mapping procedure makes it possible to obtain a ready-for-animation model which can be directly manipulated and deformed for generating expressions. The platform includes a complete set of dedicated tools for 2D/3D interactive deformation, pose management, key-frame interpolation and MPEG-4 compliant animation and rendering. The proposed FaceTOON system is currently considered for industrial evaluation and commercialization by the Quadraxis company.

Reprint of: Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-11-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays

PubMed Central

2011-01-01

Background The processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin structure, which is regulated by DNA methylation and histone modification, is at the center of gene regulation. Immunoprecipitations of chromatin (ChIP) and methylated DNA (MeDIP) represent a major achievement in this area that allow researchers to probe chromatin modifications as well as specific protein-DNA interactions in vivo and to estimate the density of proteins at specific sites genome-wide. Although a critical component of chromatin structure, DNA methylation has often been studied independently of other chromatin events and transcription. Results To allow simultaneous measurements of DNA methylation with other genomic processes, we developed and validated a simple and easy-to-use high throughput microplate-based platform for analysis of DNA methylation. Compared to the traditional beads-based MeDIP the microplate MeDIP was more sensitive and had lower non-specific binding. We integrated the MeDIP method with a microplate ChIP assay which allows measurements of both DNA methylation and histone marks at the same time, Matrix ChIP-MeDIP platform. We illustrated several applications of this platform to relate DNA methylation, with chromatin and transcription events at selected genes in cultured cells, human cancer and in a model of diabetic kidney disease. Conclusion The high throughput capacity of Matrix ChIP-MeDIP to profile tens and potentially hundreds of different genomic events at the same time as DNA methylation represents a powerful platform to explore complex genomic mechanism at selected genes in cultured cells and in whole tissues. In this regard, Matrix ChIP-MeDIP should be useful to complement genome-wide studies where the rich chromatin and transcription database resources provide fruitful foundation to pursue mechanistic

[Development and application of a medical device maintenance information platform based on BS architecture].

PubMed

Liu, Shenglin; Zhang, Xutian; Wang, Guohong; Zhang, Qiang

2012-03-01

Based on specified demands on medical devices maintenance for clinical engineers and Browser/Server architecture technology, a medical device maintenance information platform was developed, which implemented the following modules such as repair, preventive maintenance, accessories management, training, document, system management and regional cooperation. The characteristics of this system were summarized and application in increase of repair efficiency, improvement of preventive maintenance and cost control was introduced. The application of this platform increases medical device maintenance service level.

Quantitation without Calibration: Response Profile as an Indicator of Target Amount.

PubMed

Debnath, Mrittika; Farace, Jessica M; Johnson, Kristopher D; Nesterova, Irina V

2018-06-21

Quantitative assessment of biomarkers is essential in numerous contexts from decision-making in clinical situations to food quality monitoring to interpretation of life-science research findings. However, appropriate quantitation techniques are not as widely addressed as detection methods. One of the major challenges in biomarker's quantitation is the need to have a calibration for correlating a measured signal to a target amount. The step complicates the methodologies and makes them less sustainable. In this work we address the issue via a new strategy: relying on position of response profile rather than on an absolute signal value for assessment of a target's amount. In order to enable the capability we develop a target-probe binding mechanism based on a negative cooperativity effect. A proof-of-concept example demonstrates that the model is suitable for quantitative analysis of nucleic acids over a wide concentration range. The general principles of the platform will be applicable toward a variety of biomarkers such as nucleic acids, proteins, peptides, and others.

Template-based education toolkit for mobile platforms

NASA Astrophysics Data System (ADS)

Golagani, Santosh Chandana; Esfahanian, Moosa; Akopian, David

2012-02-01

Nowadays mobile phones are the most widely used portable devices which evolve very fast adding new features and improving user experiences. The latest generation of hand-held devices called smartphones is equipped with superior memory, cameras and rich multimedia features, empowering people to use their mobile phones not only as a communication tool but also for entertainment purposes. With many young students showing interest in learning mobile application development one should introduce novel learning methods which may adapt to fast technology changes and introduce students to application development. Mobile phones become a common device, and engineering community incorporates phones in various solutions. Overcoming the limitations of conventional undergraduate electrical engineering (EE) education this paper explores the concept of template-based based education in mobile phone programming. The concept is based on developing small exercise templates which students can manipulate and revise for quick hands-on introduction to the application development and integration. Android platform is used as a popular open source environment for application development. The exercises relate to image processing topics typically studied by many students. The goal is to enable conventional course enhancements by incorporating in them short hands-on learning modules.

Microfluidic chip-based technologies: emerging platforms for cancer diagnosis

PubMed Central

2013-01-01

The development of early and personalized diagnostic protocols is considered the most promising avenue to decrease mortality from cancer and improve outcome. The emerging microfluidic-based analyzing platforms hold high promises to fulfill high-throughput and high-precision screening with reduced equipment cost and low analysis time, as compared to traditional bulky counterparts in bench-top laboratories. This article overviewed the potential applications of microfluidic technologies for detection and monitoring of cancer through nucleic acid and protein biomarker analysis. The implications of the technologies in cancer cytology that can provide functional personalized diagnosis were highlighted. Finally, the future niches for using microfluidic-based systems in tumor screening were briefly discussed. PMID:24070124

Mass spectrometry-based monitoring of millisecond protein–ligand binding dynamics using an automated microfluidic platform

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

Cong, Yongzheng; Katipamula, Shanta; Trader, Cameron D.

2016-01-01

Characterizing protein-ligand binding dynamics is crucial for understanding protein function and developing new therapeutic agents. We have developed a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and on-chip electrospray ionization to perform label-free, solution-based monitoring of protein-ligand binding dynamics. This platform offers many advantages including automated processing, rapid mixing, and low sample consumption.

GSP: A web-based platform for designing genome-specific primers in polyploids

USDA-ARS?s Scientific Manuscript database

The sequences among subgenomes in a polyploid species have high similarity. This makes difficult to design genome-specific primers for sequence analysis. We present a web-based platform named GSP for designing genome-specific primers to distinguish subgenome sequences in the polyploid genome backgr...

Fast and automated DNA assays on a compact disc (CD)-based microfluidic platform

NASA Astrophysics Data System (ADS)

Jia, Guangyao

Nucleic acid-based molecular diagnostics offers enormous potential for the rapid and accurate diagnosis of infectious diseases. However, most of the existing commercial tests are time-consuming and technically complicated, and are thus incompatible with the need for rapid identification of infectious agents. We have successfully developed a CD-based microfluidic platform for fast and automated DNA array hybridization and a low cost, disposable plastic microfluidic platform for polymerase chain reaction (PCR). These platforms have proved to be a promising approach to meet the requirements in terms of detection speed and operational convenience in diagnosis of infectious diseases. In the CD-based microfluidic platform for DNA hybridization, convection is introduced to the system to enhance mass transport so as to accelerate the hybridization rate since DNA hybridization is a diffusion limited reaction. Centrifugal force is utilized for sample propulsion and surface force is used for liquid gating. Standard microscope glass slides are used as the substrates for capture probes owing to their compatibility with commercially available instrumentation (e.g. laser scanners) for detection. Microfabricated polydimethylsiloxane (PDMS) structures are used to accomplish the fluidic functions required by the protocols for DNA hybridization. The assembly of the PDMS structure and the glass slide forms a flow-through hybridization unit that can be accommodated onto the CD platform for reagent manipulation. The above scheme has been validated with oligonucleotides as the targets using commercially available enzyme-labeled fluorescence (ELF 97) for detection of the hybridization events, and tested with amplicons of genomic staphylococcus DNA labeled with Cy dye. In both experiments, significantly higher fluorescence intensities were observed in the flow-through hybridization unit compared to the passive assays. The CD fluidic scheme was also adapted to the immobilization of

Whole-body isometric force/torque measurements for functional assessment in neuro-rehabilitation: platform design, development and verification.

PubMed

Mazzoleni, Stefano; Toth, Andras; Munih, Marko; Van Vaerenbergh, Jo; Cavallo, Giuseppe; Micera, Silvestro; Dario, Paolo; Guglielmelli, Eugenio

2009-10-30

One of the main scientific and technological challenges of rehabilitation bioengineering is the development of innovative methodologies, based on the use of appropriate technological devices, for an objective assessment of patients undergoing a rehabilitation treatment. Such tools should be as fast and cheap to use as clinical scales, which are currently the daily instruments most widely used in the routine clinical practice. A human-centered approach was used in the design and development of a mechanical structure equipped with eight force/torque sensors that record quantitative data during the initiation of a predefined set of Activities of Daily Living (ADL) tasks, in isometric conditions. Preliminary results validated the appropriateness, acceptability and functionality of the proposed platform, that has become now a tool used for clinical research in three clinical centres. This paper presented the design and development of an innovative platform for whole-body force and torque measurements on human subjects. The platform has been designed to perform accurate quantitative measurements in isometric conditions with the specific aim to address the needs for functional assessment tests of patients undergoing a rehabilitation treatment as a consequence of a stroke.The versatility of the system also enlightens several other interesting possible areas of application for therapy in neurorehabilitation, for research in basic neuroscience, and more.

Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

PubMed Central

Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

2010-01-01

As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (S P n), and physical measurement to verify the performance of our study method on both accuracy and efficiency. PMID:20445737

Virtual Distances Methodology as Verification Technique for AACMMs with a Capacitive Sensor Based Indexed Metrology Platform.

PubMed

Acero, Raquel; Santolaria, Jorge; Brau, Agustin; Pueo, Marcos

2016-11-18

This paper presents a new verification procedure for articulated arm coordinate measuring machines (AACMMs) together with a capacitive sensor-based indexed metrology platform (IMP) based on the generation of virtual reference distances. The novelty of this procedure lays on the possibility of creating virtual points, virtual gauges and virtual distances through the indexed metrology platform's mathematical model taking as a reference the measurements of a ball bar gauge located in a fixed position of the instrument's working volume. The measurements are carried out with the AACMM assembled on the IMP from the six rotating positions of the platform. In this way, an unlimited number and types of reference distances could be created without the need of using a physical gauge, therefore optimizing the testing time, the number of gauge positions and the space needed in the calibration and verification procedures. Four evaluation methods are presented to assess the volumetric performance of the AACMM. The results obtained proved the suitability of the virtual distances methodology as an alternative procedure for verification of AACMMs using the indexed metrology platform.

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research

PubMed Central

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C.

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction. PMID:24904400

SU-D-BRD-02: A Web-Based Image Processing and Plan Evaluation Platform (WIPPEP) for Future Cloud-Based Radiotherapy

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

Chai, X; Liu, L; Xing, L

Purpose: Visualization and processing of medical images and radiation treatment plan evaluation have traditionally been constrained to local workstations with limited computation power and ability of data sharing and software update. We present a web-based image processing and planning evaluation platform (WIPPEP) for radiotherapy applications with high efficiency, ubiquitous web access, and real-time data sharing. Methods: This software platform consists of three parts: web server, image server and computation server. Each independent server communicates with each other through HTTP requests. The web server is the key component that provides visualizations and user interface through front-end web browsers and relay informationmore » to the backend to process user requests. The image server serves as a PACS system. The computation server performs the actual image processing and dose calculation. The web server backend is developed using Java Servlets and the frontend is developed using HTML5, Javascript, and jQuery. The image server is based on open source DCME4CHEE PACS system. The computation server can be written in any programming language as long as it can send/receive HTTP requests. Our computation server was implemented in Delphi, Python and PHP, which can process data directly or via a C++ program DLL. Results: This software platform is running on a 32-core CPU server virtually hosting the web server, image server, and computation servers separately. Users can visit our internal website with Chrome browser, select a specific patient, visualize image and RT structures belonging to this patient and perform image segmentation running Delphi computation server and Monte Carlo dose calculation on Python or PHP computation server. Conclusion: We have developed a webbased image processing and plan evaluation platform prototype for radiotherapy. This system has clearly demonstrated the feasibility of performing image processing and plan evaluation platform

Does Homework Really Matter for College Students in Quantitatively-Based Courses?

ERIC Educational Resources Information Center

Young, Nichole; Dollman, Amanda; Angel, N. Faye

2016-01-01

This investigation was initiated by two students in an Advanced Computer Applications course. They sought to examine the influence of graded homework on final grades in quantitatively-based business courses. They were provided with data from three quantitatively-based core business courses over a period of five years for a total of 10 semesters of…

Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility.

PubMed

Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Hardie, Darryl B; Borchers, Christoph H

2014-05-01

Accurate and rapid protein quantitation is essential for screening biomarkers for disease stratification and monitoring, and to validate the hundreds of putative markers in human biofluids, including blood plasma. An analytical method that utilizes stable isotope-labeled standard (SIS) peptides and selected/multiple reaction monitoring-mass spectrometry (SRM/MRM-MS) has emerged as a promising technique for determining protein concentrations. This targeted approach has analytical merit, but its true potential (in terms of sensitivity and multiplexing) has yet to be realized. Described herein is a method that extends the multiplexing ability of the MRM method to enable the quantitation 142 high-to-moderate abundance proteins (from 31mg/mL to 44ng/mL) in undepleted and non-enriched human plasma in a single run. The proteins have been reported to be associated to a wide variety of non-communicable diseases (NCDs), from cardiovascular disease (CVD) to diabetes. The concentrations of these proteins in human plasma are inferred from interference-free peptides functioning as molecular surrogates (2 peptides per protein, on average). A revised data analysis strategy, involving the linear regression equation of normal control plasma, has been instituted to enable the facile application to patient samples, as demonstrated in separate nutrigenomics and CVD studies. The exceptional robustness of the LC/MS platform and the quantitative method, as well as its high throughput, makes the assay suitable for application to patient samples for the verification of a condensed or complete protein panel. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge. © 2013.

Material platforms for spin-based photonic quantum technologies

NASA Astrophysics Data System (ADS)

Atatüre, Mete; Englund, Dirk; Vamivakas, Nick; Lee, Sang-Yun; Wrachtrup, Joerg

2018-05-01

A central goal in quantum optics and quantum information science is the development of quantum networks to generate entanglement between distributed quantum memories. Experimental progress relies on the quality and efficiency of the light-matter quantum interface connecting the quantum states of photons to internal states of quantum emitters. Quantum emitters in solids, which have properties resembling those of atoms and ions, offer an opportunity for realizing light-matter quantum interfaces in scalable and compact hardware. These quantum emitters require a material platform that enables stable spin and optical properties, as well as a robust manufacturing of quantum photonic circuits. Because no emitter system is yet perfect and different applications may require different properties, several light-matter quantum interfaces are being developed in various platforms. This Review highlights the progress in three leading material platforms: diamond, silicon carbide and atomically thin semiconductors.

Design, Synthesis, and Biological Functionality of a Dendrimer-based Modular Drug Delivery Platform

PubMed Central

Mullen, Douglas G.; McNerny, Daniel Q.; Desai, Ankur; Cheng, Xue-min; DiMaggio, Stassi C.; Kotlyar, Alina; Zhong, Yueyang; Qin, Suyang; Kelly, Christopher V.; Thomas, Thommey P.; Majoros, Istvan; Orr, Bradford G.; Baker, James R.; Banaszak Holl, Mark M.

2011-01-01

A modular dendrimer-based drug delivery platform was designed to improve upon existing limitations in single dendrimer systems. Using this modular strategy, a biologically active platform containing receptor mediated targeting and fluorescence imaging modules was synthesized by coupling a folic acid (FA) conjugated dendrimer with a fluorescein isothiocyanate (FITC) conjugated dendrimer. The two different dendrimer modules were coupled via the 1,3-dipolar cycloaddition reaction (‘click’ chemistry) between an alkyne moiety on the surface of the first dendrimer and an azide moiety on the second dendrimer. Two simplified model systems were also synthesized to develop appropriate ‘click’ reaction conditions and aid in spectroscopic assignments. Conjugates were characterized by 1H NMR spectroscopy and NOESY. The FA-FITC modular platform was evaluated in vitro with a human epithelial cancer cell line (KB) and found to specifically target the over-expressed folic acid receptor. PMID:21425790

GSP: a web-based platform for designing genome-specific primers in polyploids

USDA-ARS?s Scientific Manuscript database

The primary goal of this research was to develop a web-based platform named GSP for designing genome-specific primers to distinguish subgenome sequences in the polyploid genome background. GSP uses BLAST to extract homeologous sequences of the subgenomes in the existing databases, performed a multip...

In-Space Internet-Based Communications for Space Science Platforms Using Commercial Satellite Networks

NASA Technical Reports Server (NTRS)

Kerczewski, Robert J.; Bhasin, Kul B.; Fabian, Theodore P.; Griner, James H.; Kachmar, Brian A.; Richard, Alan M.

1999-01-01

The continuing technological advances in satellite communications and global networking have resulted in commercial systems that now can potentially provide capabilities for communications with space-based science platforms. This reduces the need for expensive government owned communications infrastructures to support space science missions while simultaneously making available better service to the end users. An interactive, high data rate Internet type connection through commercial space communications networks would enable authorized researchers anywhere to control space-based experiments in near real time and obtain experimental results immediately. A space based communications network architecture consisting of satellite constellations connecting orbiting space science platforms to ground users can be developed to provide this service. The unresolved technical issues presented by this scenario are the subject of research at NASA's Glenn Research Center in Cleveland, Ohio. Assessment of network architectures, identification of required new or improved technologies, and investigation of data communications protocols are being performed through testbed and satellite experiments and laboratory simulations.

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

PubMed Central

Lawless, Craig; Hubbard, Simon J.; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R.

2012-01-01

Abstract New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616

Nanopaper as an Optical Sensing Platform.

PubMed

Morales-Narváez, Eden; Golmohammadi, Hamed; Naghdi, Tina; Yousefi, Hossein; Kostiv, Uliana; Horák, Daniel; Pourreza, Nahid; Merkoçi, Arben

2015-07-28

Bacterial cellulose nanopaper (BC) is a multifunctional material known for numerous desirable properties: sustainability, biocompatibility, biodegradability, optical transparency, thermal properties, flexibility, high mechanical strength, hydrophilicity, high porosity, broad chemical-modification capabilities and high surface area. Herein, we report various nanopaper-based optical sensing platforms and describe how they can be tuned, using nanomaterials, to exhibit plasmonic or photoluminescent properties that can be exploited for sensing applications. We also describe several nanopaper configurations, including cuvettes, plates and spots that we printed or punched on BC. The platforms include a colorimetric-based sensor based on nanopaper containing embedded silver and gold nanoparticles; a photoluminescent-based sensor, comprising CdSe@ZnS quantum dots conjugated to nanopaper; and a potential up-conversion sensing platform constructed from nanopaper functionalized with NaYF4:Yb(3+)@Er(3+)&SiO2 nanoparticles. We have explored modulation of the plasmonic or photoluminescent properties of these platforms using various model biologically relevant analytes. Moreover, we prove that BC is and advantageous preconcentration platform that facilitates the analysis of small volumes of optically active materials (∼4 μL). We are confident that these platforms will pave the way to optical (bio)sensors or theranostic devices that are simple, transparent, flexible, disposable, lightweight, miniaturized and perhaps wearable.

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

PubMed

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

2012-12-01

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

Research based on the SoPC platform of feature-based image registration

NASA Astrophysics Data System (ADS)

Shi, Yue-dong; Wang, Zhi-hui

2015-12-01

This paper focuses on the study of implementing feature-based image registration by System on a Programmable Chip (SoPC) hardware platform. We solidify the image registration algorithm on the FPGA chip, in which embedded soft core processor Nios II can speed up the image processing system. In this way, we can make image registration technology get rid of the PC. And, consequently, this kind of technology will be got an extensive use. The experiment result indicates that our system shows stable performance, particularly in terms of matching processing which noise immunity is good. And feature points of images show a reasonable distribution.

Launching a virtual decision lab: development and field-testing of a web-based patient decision support research platform.

PubMed

Hoffman, Aubri S; Llewellyn-Thomas, Hilary A; Tosteson, Anna N A; O'Connor, Annette M; Volk, Robert J; Tomek, Ivan M; Andrews, Steven B; Bartels, Stephen J

2014-12-12

Over 100 trials show that patient decision aids effectively improve patients' information comprehension and values-based decision making. However, gaps remain in our understanding of several fundamental and applied questions, particularly related to the design of interactive, personalized decision aids. This paper describes an interdisciplinary development process for, and early field testing of, a web-based patient decision support research platform, or virtual decision lab, to address these questions. An interdisciplinary stakeholder panel designed the web-based research platform with three components: a) an introduction to shared decision making, b) a web-based patient decision aid, and c) interactive data collection items. Iterative focus groups provided feedback on paper drafts and online prototypes. A field test assessed a) feasibility for using the research platform, in terms of recruitment, usage, and acceptability; and b) feasibility of using the web-based decision aid component, compared to performance of a videobooklet decision aid in clinical care. This interdisciplinary, theory-based, patient-centered design approach produced a prototype for field-testing in six months. Participants (n = 126) reported that: the decision aid component was easy to use (98%), information was clear (90%), the length was appropriate (100%), it was appropriately detailed (90%), and it held their interest (97%). They spent a mean of 36 minutes using the decision aid and 100% preferred using their home/library computer. Participants scored a mean of 75% correct on the Decision Quality, Knowledge Subscale, and 74 out of 100 on the Preparation for Decision Making Scale. Completing the web-based decision aid reduced mean Decisional Conflict scores from 31.1 to 19.5 (p < 0.01). Combining decision science and health informatics approaches facilitated rapid development of a web-based patient decision support research platform that was feasible for use in research studies in

Single-Cell-Based Platform for Copy Number Variation Profiling through Digital Counting of Amplified Genomic DNA Fragments.

PubMed

Li, Chunmei; Yu, Zhilong; Fu, Yusi; Pang, Yuhong; Huang, Yanyi

2017-04-26

We develop a novel single-cell-based platform through digital counting of amplified genomic DNA fragments, named multifraction amplification (mfA), to detect the copy number variations (CNVs) in a single cell. Amplification is required to acquire genomic information from a single cell, while introducing unavoidable bias. Unlike prevalent methods that directly infer CNV profiles from the pattern of sequencing depth, our mfA platform denatures and separates the DNA molecules from a single cell into multiple fractions of a reaction mix before amplification. By examining the sequencing result of each fraction for a specific fragment and applying a segment-merge maximum likelihood algorithm to the calculation of copy number, we digitize the sequencing-depth-based CNV identification and thus provide a method that is less sensitive to the amplification bias. In this paper, we demonstrate a mfA platform through multiple displacement amplification (MDA) chemistry. When performing the mfA platform, the noise of MDA is reduced; therefore, the resolution of single-cell CNV identification can be improved to 100 kb. We can also determine the genomic region free of allelic drop-out with mfA platform, which is impossible for conventional single-cell amplification methods.

Semi-quantitative visual detection of loop mediated isothermal amplification (LAMP)-generated DNA by distance-based measurement on a paper device.

PubMed

Hongwarittorrn, Irin; Chaichanawongsaroj, Nuntaree; Laiwattanapaisal, Wanida

2017-12-01

A distance-based paper analytical device (dPAD) for loop mediated isothermal amplification (LAMP) detection based on distance measurement was proposed. This approach relied on visual detection by the length of colour developed on the dPAD with reference to semi-quantitative determination of the initial amount of genomic DNA. In this communication, E. coli DNA was chosen as a template DNA for LAMP reaction. In accordance with the principle, the dPAD was immobilized by polyethylenimine (PEI), which is a strong cationic polymer, in the hydrophilic channel of the paper device. Hydroxynaphthol blue (HNB), a colourimetric indicator for monitoring the change of magnesium ion concentration in the LAMP reaction, was used to react with the immobilized PEI. The positive charges of PEI react with the negative charges of free HNB in the LAMP reaction, producing a blue colour deposit on the paper device. Consequently, the apparently visual distance appeared within 5min and length of distance correlated to the amount of DNA in the sample. The distance-based PAD for the visual detection of the LAMP reaction could quantify the initial concentration of genomic DNA as low as 4.14 × 10 3 copiesµL -1 . This distance-based visual semi-quantitative platform is suitable for choice of LAMP detection method, particular in resource-limited settings because of the advantages of low cost, simple fabrication and operation, disposability and portable detection of the dPAD device. Copyright © 2017 Elsevier B.V. All rights reserved.

[Reconstituting evaluation methods based on both qualitative and quantitative paradigms].

PubMed

Miyata, Hiroaki; Okubo, Suguru; Yoshie, Satoru; Kai, Ichiro

2011-01-01

Debate about the relationship between quantitative and qualitative paradigms is often muddled and confusing and the clutter of terms and arguments has resulted in the concepts becoming obscure and unrecognizable. In this study we conducted content analysis regarding evaluation methods of qualitative healthcare research. We extracted descriptions on four types of evaluation paradigm (validity/credibility, reliability/credibility, objectivity/confirmability, and generalizability/transferability), and classified them into subcategories. In quantitative research, there has been many evaluation methods based on qualitative paradigms, and vice versa. Thus, it might not be useful to consider evaluation methods of qualitative paradigm are isolated from those of quantitative methods. Choosing practical evaluation methods based on the situation and prior conditions of each study is an important approach for researchers.

Development of a Web-Based Visualization Platform for Climate Research Using Google Earth

NASA Technical Reports Server (NTRS)

Sun, Xiaojuan; Shen, Suhung; Leptoukh, Gregory G.; Wang, Panxing; Di, Liping; Lu, Mingyue

2011-01-01

Recently, it has become easier to access climate data from satellites, ground measurements, and models from various data centers, However, searching. accessing, and prc(essing heterogeneous data from different sources are very tim -consuming tasks. There is lack of a comprehensive visual platform to acquire distributed and heterogeneous scientific data and to render processed images from a single accessing point for climate studies. This paper. documents the design and implementation of a Web-based visual, interoperable, and scalable platform that is able to access climatological fields from models, satellites, and ground stations from a number of data sources using Google Earth (GE) as a common graphical interface. The development is based on the TCP/IP protocol and various data sharing open sources, such as OPeNDAP, GDS, Web Processing Service (WPS), and Web Mapping Service (WMS). The visualization capability of integrating various measurements into cE extends dramatically the awareness and visibility of scientific results. Using embedded geographic information in the GE, the designed system improves our understanding of the relationships of different elements in a four dimensional domain. The system enables easy and convenient synergistic research on a virtual platform for professionals and the general public, gr$tly advancing global data sharing and scientific research collaboration.

High-throughput detection of ethanol-producing cyanobacteria in a microdroplet platform.

PubMed

Abalde-Cela, Sara; Gould, Anna; Liu, Xin; Kazamia, Elena; Smith, Alison G; Abell, Chris

2015-05-06

Ethanol production by microorganisms is an important renewable energy source. Most processes involve fermentation of sugars from plant feedstock, but there is increasing interest in direct ethanol production by photosynthetic organisms. To facilitate this, a high-throughput screening technique for the detection of ethanol is required. Here, a method for the quantitative detection of ethanol in a microdroplet-based platform is described that can be used for screening cyanobacterial strains to identify those with the highest ethanol productivity levels. The detection of ethanol by enzymatic assay was optimized both in bulk and in microdroplets. In parallel, the encapsulation of engineered ethanol-producing cyanobacteria in microdroplets and their growth dynamics in microdroplet reservoirs were demonstrated. The combination of modular microdroplet operations including droplet generation for cyanobacteria encapsulation, droplet re-injection and pico-injection, and laser-induced fluorescence, were used to create this new platform to screen genetically engineered strains of cyanobacteria with different levels of ethanol production.

High-throughput detection of ethanol-producing cyanobacteria in a microdroplet platform

PubMed Central

Abalde-Cela, Sara; Gould, Anna; Liu, Xin; Kazamia, Elena; Smith, Alison G.; Abell, Chris

2015-01-01

Ethanol production by microorganisms is an important renewable energy source. Most processes involve fermentation of sugars from plant feedstock, but there is increasing interest in direct ethanol production by photosynthetic organisms. To facilitate this, a high-throughput screening technique for the detection of ethanol is required. Here, a method for the quantitative detection of ethanol in a microdroplet-based platform is described that can be used for screening cyanobacterial strains to identify those with the highest ethanol productivity levels. The detection of ethanol by enzymatic assay was optimized both in bulk and in microdroplets. In parallel, the encapsulation of engineered ethanol-producing cyanobacteria in microdroplets and their growth dynamics in microdroplet reservoirs were demonstrated. The combination of modular microdroplet operations including droplet generation for cyanobacteria encapsulation, droplet re-injection and pico-injection, and laser-induced fluorescence, were used to create this new platform to screen genetically engineered strains of cyanobacteria with different levels of ethanol production. PMID:25878135

A tutorial platform suitable for surgical simulator training (SimMentor).

PubMed

Røtnes, Jan Sigurd; Kaasa, Johannes; Westgaard, Geir; Eriksen, Eivind Myrold; Hvidsten, Per Oyvind; Strøm, Kyrre; Sørhus, Vidar; Halbwachs, Yvon; Haug, Einar; Grimnes, Morten; Fontenelle, Hugues; Ekeberg, Tom; Thomassen, Jan B; Elle, Ole Jakob; Fosse, Erik

2002-01-01

The introduction of simulators in surgical training entails the need to develop pedagogic platforms adapted to the potentials and limitations provided by the information technology. As a solution to the technical challenges in treating all possible interaction events and to obtain a suitable pedagogic approach, we have developed a pedagogic platform for surgical training, SimMentor. In SimMentor the procedure to be practiced is divided into a number of natural phases. The trainee will practice on one phase at a time, however he can select the sequence of phases arbitrarily. A phase is taught by letting the trainee alternate freely between 2 modes: 1: A 3-dimensional animated guidance designed for learning the objectives and challenges in a procedure. 2: An interactive training session through the instrument manipulator device designed for training motoric responses based on visual and tactile responses produced by the simulator. The two modes are interfaced with the same virtual reality platform, thus SimMentor allows a seamless transition between the modes. We have developed a prototype simulator for robotic assisted endoscopic CABG (Coronary Artery Bypass Grafting) procedure by first focusing on the anastomosis part of the operation. Tissue, suture and instrument models have been developed and integrated with a simulated model of a beating heart comprises the elements in the simulator engine that is used in construction a training platform for learning different methods for performing a coronary anastomosis procedure. The platform is designed for integrating the following features: 1) practical approach to handle interactivity events with flexible-objects 3D simulators, 2) methods for quantitative evaluations of performance, 3) didactic presentations, 4) effective ways of producing diversity of clinical and pathological training scenarios.

Evolvable Smartphone-Based Platforms for Point-of-Care In-Vitro Diagnostics Applications.

PubMed

Patou, François; AlZahra'a Alatraktchi, Fatima; Kjægaard, Claus; Dimaki, Maria; Madsen, Jan; Svendsen, Winnie E

2016-09-03

The association of smart mobile devices and lab-on-chip technologies offers unprecedented opportunities for the emergence of direct-to-consumer in vitro medical diagnostics applications. Despite their clear transformative potential, obstacles remain to the large-scale disruption and long-lasting success of these systems in the consumer market. For instance, the increasing level of complexity of instrumented lab-on-chip devices, coupled to the sporadic nature of point-of-care testing, threatens the viability of a business model mainly relying on disposable/consumable lab-on-chips. We argued recently that system evolvability, defined as the design characteristic that facilitates more manageable transitions between system generations via the modification of an inherited design, can help remedy these limitations. In this paper, we discuss how platform-based design can constitute a formal entry point to the design and implementation of evolvable smart device/lab-on-chip systems. We present both a hardware/software design framework and the implementation details of a platform prototype enabling at this stage the interfacing of several lab-on-chip variants relying on current- or impedance-based biosensors. Our findings suggest that several change-enabling mechanisms implemented in the higher abstraction software layers of the system can promote evolvability, together with the design of change-absorbing hardware/software interfaces. Our platform architecture is based on a mobile software application programming interface coupled to a modular hardware accessory. It allows the specification of lab-on-chip operation and post-analytic functions at the mobile software layer. We demonstrate its potential by operating a simple lab-on-chip to carry out the detection of dopamine using various electroanalytical methods.

Evolvable Smartphone-Based Platforms for Point-of-Care In-Vitro Diagnostics Applications

PubMed Central

Patou, François; AlZahra’a Alatraktchi, Fatima; Kjægaard, Claus; Dimaki, Maria; Madsen, Jan; Svendsen, Winnie E.

2016-01-01

The association of smart mobile devices and lab-on-chip technologies offers unprecedented opportunities for the emergence of direct-to-consumer in vitro medical diagnostics applications. Despite their clear transformative potential, obstacles remain to the large-scale disruption and long-lasting success of these systems in the consumer market. For instance, the increasing level of complexity of instrumented lab-on-chip devices, coupled to the sporadic nature of point-of-care testing, threatens the viability of a business model mainly relying on disposable/consumable lab-on-chips. We argued recently that system evolvability, defined as the design characteristic that facilitates more manageable transitions between system generations via the modification of an inherited design, can help remedy these limitations. In this paper, we discuss how platform-based design can constitute a formal entry point to the design and implementation of evolvable smart device/lab-on-chip systems. We present both a hardware/software design framework and the implementation details of a platform prototype enabling at this stage the interfacing of several lab-on-chip variants relying on current- or impedance-based biosensors. Our findings suggest that several change-enabling mechanisms implemented in the higher abstraction software layers of the system can promote evolvability, together with the design of change-absorbing hardware/software interfaces. Our platform architecture is based on a mobile software application programming interface coupled to a modular hardware accessory. It allows the specification of lab-on-chip operation and post-analytic functions at the mobile software layer. We demonstrate its potential by operating a simple lab-on-chip to carry out the detection of dopamine using various electroanalytical methods. PMID:27598208

Software-defined Radio Based Measurement Platform for Wireless Networks

PubMed Central

Chao, I-Chun; Lee, Kang B.; Candell, Richard; Proctor, Frederick; Shen, Chien-Chung; Lin, Shinn-Yan

2015-01-01

End-to-end latency is critical to many distributed applications and services that are based on computer networks. There has been a dramatic push to adopt wireless networking technologies and protocols (such as WiFi, ZigBee, WirelessHART, Bluetooth, ISA100.11a, etc.) into time-critical applications. Examples of such applications include industrial automation, telecommunications, power utility, and financial services. While performance measurement of wired networks has been extensively studied, measuring and quantifying the performance of wireless networks face new challenges and demand different approaches and techniques. In this paper, we describe the design of a measurement platform based on the technologies of software-defined radio (SDR) and IEEE 1588 Precision Time Protocol (PTP) for evaluating the performance of wireless networks. PMID:27891210

Phonon-based scalable platform for chip-scale quantum computing

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

Reinke, Charles M.; El-Kady, Ihab

Here, we present a scalable phonon-based quantum computer on a phononic crystal platform. Practical schemes involve selective placement of a single acceptor atom in the peak of the strain field in a high-Q phononic crystal cavity that enables coupling of the phonon modes to the energy levels of the atom. We show theoretical optimization of the cavity design and coupling waveguide, along with estimated performance figures of the coupled system. A qubit can be created by entangling a phonon at the resonance frequency of the cavity with the atom states. Qubits based on this half-sound, half-matter quasi-particle, called a phoniton,more » may outcompete other quantum architectures in terms of combined emission rate, coherence lifetime, and fabrication demands.« less

Phonon-based scalable platform for chip-scale quantum computing

DOE PAGES

Reinke, Charles M.; El-Kady, Ihab

2016-12-19

Here, we present a scalable phonon-based quantum computer on a phononic crystal platform. Practical schemes involve selective placement of a single acceptor atom in the peak of the strain field in a high-Q phononic crystal cavity that enables coupling of the phonon modes to the energy levels of the atom. We show theoretical optimization of the cavity design and coupling waveguide, along with estimated performance figures of the coupled system. A qubit can be created by entangling a phonon at the resonance frequency of the cavity with the atom states. Qubits based on this half-sound, half-matter quasi-particle, called a phoniton,more » may outcompete other quantum architectures in terms of combined emission rate, coherence lifetime, and fabrication demands.« less

Software-defined Radio Based Measurement Platform for Wireless Networks.

PubMed

Chao, I-Chun; Lee, Kang B; Candell, Richard; Proctor, Frederick; Shen, Chien-Chung; Lin, Shinn-Yan

2015-10-01

End-to-end latency is critical to many distributed applications and services that are based on computer networks. There has been a dramatic push to adopt wireless networking technologies and protocols (such as WiFi, ZigBee, WirelessHART, Bluetooth, ISA100.11a, etc. ) into time-critical applications. Examples of such applications include industrial automation, telecommunications, power utility, and financial services. While performance measurement of wired networks has been extensively studied, measuring and quantifying the performance of wireless networks face new challenges and demand different approaches and techniques. In this paper, we describe the design of a measurement platform based on the technologies of software-defined radio (SDR) and IEEE 1588 Precision Time Protocol (PTP) for evaluating the performance of wireless networks.

On the Supply Chain Management Supported by E-Commerce Service Platform for Agreement based Circulation of Fruits and Vegetables

NASA Astrophysics Data System (ADS)

Bao, Liwei; Huang, Yuchi; Ma, Zengjun; Zhang, Jie; Lv, Qingchu

According to analysis of the supply chain process of agricultural products, the IT application requirements of the market entities participating in the agreement based circulation of fruits and vegetables have been discussed. The strategy of supply chain management basing on E-commerce service platform for fruits and vegetables has been proposed in this paper. The architecture and function composing of the service platform have been designed and implemented. The platform is constructed on a set of application service modules User can choose some of the application service modules and define them according to the business process. The application service modules chosen and defined by user are integrated as an application service package and applied as management information system of business process. With the E-commerce service platform, the supply chain management for agreement based circulation of agricultural products of vegetables and fruits can be implemented.

Vulnerability assessment of a space based weapon platform electronic system exposed to a thermonuclear weapon detonation

NASA Astrophysics Data System (ADS)

Perez, C. L.; Johnson, J. O.

Rapidly changing world events, the increased number of nations with inter-continental ballistic missile capability, and the proliferation of nuclear weapon technology will increase the number of nuclear threats facing the world today. Monitoring these nation's activities and providing an early warning and/or intercept system via reconnaissance and surveillance satellites and space based weapon platforms is a viable deterrent against a surprise nuclear attack. However, the deployment of satellite and weapon platform assets in space will subject the sensitive electronic equipment to a variety of natural and man-made radiation environments. These include Van Allen Belt protons and electrons; galactic and solar flare protons; and neutrons, gamma rays, and x-rays from intentionally detonated fission and fusion weapons. In this paper, the MASH vl.0 code system is used to estimate the dose to the critical electronics components of an idealized space based weapon platform from neutron and gamma-ray radiation emitted from a thermonuclear weapon detonation in space. Fluence and dose assessments were performed for the platform fully loaded, and in several stages representing limited engagement scenarios. The results indicate vulnerabilities to the Command, Control, and Communication bay instruments from radiation damage for a nuclear weapon detonation for certain source/platform orientations. The distance at which damage occurs will depend on the weapon yield (n,(gamma)/kiloton) and size (kilotons).

Integrated Spintronic Platforms for Biomolecular Recognition Detection

NASA Astrophysics Data System (ADS)

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

2008-06-01

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

Apparatus, method and system to control accessibility of platform resources based on an integrity level

DOEpatents

Jenkins, Chris; Pierson, Lyndon G.

2016-10-25

Techniques and mechanism to selectively provide resource access to a functional domain of a platform. In an embodiment, the platform includes both a report domain to monitor the functional domain and a policy domain to identify, based on such monitoring, a transition of the functional domain from a first integrity level to a second integrity level. In response to a change in integrity level, the policy domain may configure the enforcement domain to enforce against the functional domain one or more resource accessibility rules corresponding to the second integrity level. In another embodiment, the policy domain automatically initiates operations in aid of transitioning the platform from the second integrity level to a higher integrity level.

A Service-Based Program Evaluation Platform for Enhancing Student Engagement in Assignments

ERIC Educational Resources Information Center

Wu, Ye-Chi; Ma, Lee Wei; Jiau, Hewijin Christine

2013-01-01

Programming assignments are commonly used in computer science education to encourage students to practice target concepts and evaluate their learning status. Ensuring students are engaged in such assignments is critical in attracting and retaining students. To this end, WebHat, a service-based program evaluation platform, is introduced in this…

Interactive Computer-Assisted Instruction in Acid-Base Physiology for Mobile Computer Platforms

ERIC Educational Resources Information Center

Longmuir, Kenneth J.

2014-01-01

In this project, the traditional lecture hall presentation of acid-base physiology in the first-year medical school curriculum was replaced by interactive, computer-assisted instruction designed primarily for the iPad and other mobile computer platforms. Three learning modules were developed, each with ~20 screens of information, on the subjects…

Strategic Industrial Alliances in Paper Industry: XML- vs Ontology-Based Integration Platforms

ERIC Educational Resources Information Center

Naumenko, Anton; Nikitin, Sergiy; Terziyan, Vagan; Zharko, Andriy

2005-01-01

Purpose: To identify cases related to design of ICT platforms for industrial alliances, where the use of Ontology-driven architectures based on Semantic web standards is more advantageous than application of conventional modeling together with XML standards. Design/methodology/approach: A comparative analysis of the two latest and the most obvious…

Exploration Platform in the Earth-Moon Libration System Based on ISS

NASA Technical Reports Server (NTRS)

Raftery, Michael; Derechin, Alexander

2012-01-01

International Space Station (ISS) industry partners have been working for the past two years on concepts using ISS development methods and residual assets to support a broad range of exploration missions. These concepts have matured along with planning details for NASA's Space Launch System (SLS) and Multi-Purpose Crew Vehicle (MPCV) to allow serious consideration for a platform located in the Earth-Moon Libration (EML) system. This platform would provide a flexible basis for future exploration missions and would significantly reduce costs because it will enable re-use of expensive spacecraft and reduce the total number of launches needed to accomplish these missions. ISS provides a robust set of methods which can be used to test systems and capabilities needed for missions to the Moon, Mars, asteroids and other potential destinations. We will show how ISS can be used to reduce risk and improve operational flexibility for missions beyond low earth orbit through the development of a new Exploration Platform based in the EML system. The benefits of using the EML system as a gateway will be presented along with additional details of a lunar exploration mission concept. International cooperation is a critical enabler and ISS has already demonstrated successful management of a large multi-national technical endeavor. We will show how technology developed for ISS can be evolved and adapted to the new exploration challenge. New technology, such as electric propulsion and advanced life support systems can be tested and proven at ISS as part of an incremental development program. Finally, we will describe how the EML Platform could be built and deployed and how International access for crew and cargo could be provided.

ERMHAN: A Context-Aware Service Platform to Support Continuous Care Networks for Home-Based Assistance

PubMed Central

Paganelli, Federica; Spinicci, Emilio; Giuli, Dino

2008-01-01

Continuous care models for chronic diseases pose several technology-oriented challenges for home-based continuous care, where assistance services rely on a close collaboration among different stakeholders such as health operators, patient relatives, and social community members. Here we describe Emilia Romagna Mobile Health Assistance Network (ERMHAN) a multichannel context-aware service platform designed to support care networks in cooperating and sharing information with the goal of improving patient quality of life. In order to meet extensibility and flexibility requirements, this platform has been developed through ontology-based context-aware computing and a service oriented approach. We also provide some preliminary results of performance analysis and user survey activity. PMID:18695739

Smart Web-Based Platform to Support Physical Rehabilitation.

PubMed

Rybarczyk, Yves; Kleine Deters, Jan; Cointe, Clément; Esparza, Danilo

2018-04-26

The enhancement of ubiquitous and pervasive computing brings new perspectives in medical rehabilitation. In that sense, the present study proposes a smart, web-based platform to promote the reeducation of patients after hip replacement surgery. This project focuses on two fundamental aspects in the development of a suitable tele-rehabilitation application, which are: (i) being based on an affordable technology, and (ii) providing the patients with a real-time assessment of the correctness of their movements. A probabilistic approach based on the development and training of ten Hidden Markov Models (HMMs) is used to discriminate in real time the main faults in the execution of the therapeutic exercises. Two experiments are designed to evaluate the precision of the algorithm for classifying movements performed in the laboratory and clinical settings, respectively. A comparative analysis of the data shows that the models are as reliable as the physiotherapists to discriminate and identify the motion errors. The results are discussed in terms of the required setup for a successful application in the field and further implementations to improve the accuracy and usability of the system.

A novel multi-walled carbon nanotube-based antibody conjugate for quantitative and semi-quantitative lateral flow assays.

PubMed

Sun, Wenjuan; Hu, Xiaolong; Liu, Jia; Zhang, Yurong; Lu, Jianzhong; Zeng, Libo

2017-10-01

In this study, the multi-walled carbon nanotubes (MWCNTs) were applied in lateral flow strips (LFS) for semi-quantitative and quantitative assays. Firstly, the solubility of MWCNTs was improved using various surfactants to enhance their biocompatibility for practical application. The dispersed MWCNTs were conjugated with the methamphetamine (MET) antibody in a non-covalent manner and then manufactured into the LFS for the quantitative detection of MET. The MWCNTs-based lateral flow assay (MWCNTs-LFA) exhibited an excellent linear relationship between the values of test line and MET when its concentration ranges from 62.5 to 1500 ng/mL. The sensitivity of the LFS was evaluated by conjugating MWCNTs with HCG antibody and the MWCNTs conjugated method is 10 times more sensitive than the one conjugated with classical colloidal gold nanoparticles. Taken together, our data demonstrate that MWCNTs-LFA is a more sensitive and reliable assay for semi-quantitative and quantitative detection which can be used in forensic analysis.

Planetary Balloon-Based Science Platform Evaluation and Program Implementation

NASA Technical Reports Server (NTRS)

Dankanich, John W.; Kremic, Tibor; Hibbitts, Karl; Young, Eliot F.; Landis, Rob

2016-01-01

This report describes a study evaluating the potential for a balloon-based optical telescope as a planetary science asset to achieve decadal class science. The study considered potential science achievable and science traceability relative to the most recent planetary science decadal survey, potential platform features, and demonstration flights in the evaluation process. Science Potential and Benefits: This study confirms the cost the-benefit value for planetary science purposes. Forty-four (44) important questions of the decadal survey are at least partially addressable through balloon based capabilities. Planetary science through balloon observations can provide significant science through observations in the 300 nm to 5 m range and at longer wavelengths as well. Additionally, balloon missions have demonstrated the ability to progress from concept to observation to publication much faster than a space mission increasing the speed of science return. Planetary science from a balloon-borne platform is a relatively low-cost approach to new science measurements. This is particularly relevant within a cost-constrained planetary science budget. Repeated flights further reduce the cost of the per unit science data. Such flights offer observing time at a very competitive cost. Another advantage for planetary scientists is that a dedicated asset could provide significant new viewing opportunities not possible from the ground and allow unprecedented access to observations that cannot be realized with the time allocation pressures faced by current observing assets. In addition, flight systems that have a relatively short life cycle and where hardware is generally recovered, are excellent opportunities to train early career scientists, engineers, and project managers. The fact that balloon-borne payloads, unlike space missions, are generally recovered offers an excellent tool to test and mature instruments and other space craft systems. Desired Gondola Features: Potential

Applang - A DSL for specification of mobile applications for android platform based on textX

NASA Astrophysics Data System (ADS)

Kosanović, Milan; Dejanović, Igor; Milosavljević, Gordana

2016-06-01

Mobile platforms become a ubiquitous part of our daily lives thus making more pressure to software developers to develop more applications faster and with the support for different mobile operating systems. To foster the faster development of mobile services and applications and to support various mobile operating systems a new software development approaches must be undertaken. Domain-Specific Languages (DSL) are a viable approach that promise to solve a problem of target platform diversity as well as to facilitate rapid application development and shorter time-to-market. This paper presents Applang, a DSL for the specification of mobile applications for the Android platform, based on textX meta-language. The application is described using Applang DSL and the source code for a target platform is automatically generated by the provided code generator. The same application defined using single Applang source can be transformed to various targets with little or no manual modifications.

Towards an open science publishing platform.

PubMed

Tracz, Vitek; Lawrence, Rebecca

2016-01-01

The way science and research is done is rapidly becoming more open and collaborative. The traditional way of publishing new findings in journals is becoming increasingly outdated and no longer serves the needs of much of science. Whilst preprints can bring significant benefits of removing delay and selection, they do not go far enough if simply implemented alongside the existing journal system. We propose that we need a new approach, an Open Science Platform, that takes the benefits of preprints but adds formal, invited, and transparent post-publication peer review. This bypasses the problems of the current journal system and, in doing so, moves the evaluation of research and researchers away from the journal-based Impact Factor and towards a fairer system of article-based qualitative and quantitative indicators. In the long term, it should be irrelevant where a researcher publishes their findings. What is important is that research is shared and made available without delay within a framework that encourages quality standards and requires all players in the research community to work as collaborators.

An MRI-compatible platform for one-dimensional motion management studies in MRI.

PubMed

Nofiele, Joris; Yuan, Qing; Kazem, Mohammad; Tatebe, Ken; Torres, Quinn; Sawant, Amit; Pedrosa, Ivan; Chopra, Rajiv

2016-08-01

Abdominal MRI remains challenging because of respiratory motion. Motion compensation strategies are difficult to compare clinically because of the variability across human subjects. The goal of this study was to evaluate a programmable system for one-dimensional motion management MRI research. A system comprised of a programmable motorized linear stage and computer was assembled and tested in the MRI environment. Tests of the mutual interference between the platform and a whole-body MRI were performed. Organ trajectories generated from a high-temporal resolution scan of a healthy volunteer were used in phantom tests to evaluate the effects of motion on image quality and quantitative MRI measurements. No interference between the motion platform and the MRI was observed, and reliable motion could be produced across a wide range of imaging conditions. Motion-related artifacts commensurate with motion amplitude, frequency, and waveform were observed. T2 measurement of a kidney lesion in an abdominal phantom showed that its value decreased by 67% with physiologic motion, but could be partially recovered with navigator-based motion-compensation. The motion platform can produce reliable linear motion within a whole-body MRI. The system can serve as a foundation for a research platform to investigate and develop motion management approaches for MRI. Magn Reson Med 76:702-712, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Application of A Mobile Platform-based System for the Management of Fundus Diease in Outpatient Settings.

PubMed

Dend, Xun; Li, Hong-Yan; Yin, Hong; Liang, Jian-Hong; Chen, Yi; Li, Xiao-Xin; Zhao, Ming-Wei

2016-08-01

Objective To evaluate the application of a mobile platform-based system in the management of fundus disease in outpatient settings. Methods In the outpatient departments of fundus disease,premature babies requiring eye examination under general anesthesia and adults requiring intraocular surgery were enrolled as the subjects. According to the existing clinical practices,we developed a system that met the requirements of clinical practices and optimized the clinical management. Based on the FileMaker database,the tablet computers were used as the mobile platform and the system could also be run in iPad and PC terminals.Results Since 2013,the system recorded 7500 cases of special examinations. Since July 2015,4100 cases of intravitreal drug injection were also recored in the system. Multiple-point and real-time reservation pattern increased the efficiency and opimize the clinical management. All the clinical data were digitalized. Conclusion The mobile platform-based system can increase the efficacy of examination and other clinical processes and standardize data collection;thus,it is feasible for the clinical practices in outpatient departments of ophthalmology.

Multi-function microfluidic platform for sensor integration.

PubMed

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

2018-03-06

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

A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer

PubMed Central

Gupta, Sudheer; Chaudhary, Kumardeep; Dhanda, Sandeep Kumar; Kumar, Rahul; Kumar, Shailesh; Sehgal, Manika; Nagpal, Gandharva

2016-01-01

Due to advancement in sequencing technology, genomes of thousands of cancer tissues or cell-lines have been sequenced. Identification of cancer-specific epitopes or neoepitopes from cancer genomes is one of the major challenges in the field of immunotherapy or vaccine development. This paper describes a platform Cancertope, developed for designing genome-based immunotherapy or vaccine against a cancer cell. Broadly, the integrated resources on this platform are apportioned into three precise sections. First section explains a cancer-specific database of neoepitopes generated from genome of 905 cancer cell lines. This database harbors wide range of epitopes (e.g., B-cell, CD8+ T-cell, HLA class I, HLA class II) against 60 cancer-specific vaccine antigens. Second section describes a partially personalized module developed for predicting potential neoepitopes against a user-specific cancer genome. Finally, we describe a fully personalized module developed for identification of neoepitopes from genomes of cancerous and healthy cells of a cancer-patient. In order to assist the scientific community, wide range of tools are incorporated in this platform that includes screening of epitopes against human reference proteome (http://www.imtech.res.in/raghava/cancertope/). PMID:27832200

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

PubMed

Tan, Shi Yang; Dutta, Avirup; Jakubovics, Nicholas S; Ang, Mia Yang; Siow, Cheuk Chuen; Mutha, Naresh Vr; Heydari, Hamed; Wee, Wei Yee; Wong, Guat Jah; Choo, Siew Woh

2015-01-16

Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity. To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the

Autonomous self-organizing resource manager for multiple networked platforms

NASA Astrophysics Data System (ADS)

Smith, James F., III

2002-08-01

A fuzzy logic based expert system for resource management has been developed that automatically allocates electronic attack (EA) resources in real-time over many dissimilar autonomous naval platforms defending their group against attackers. The platforms can be very general, e.g., ships, planes, robots, land based facilities, etc. Potential foes the platforms deal with can also be general. This paper provides an overview of the resource manager including the four fuzzy decision trees that make up the resource manager; the fuzzy EA model; genetic algorithm based optimization; co-evolutionary data mining through gaming; and mathematical, computational and hardware based validation. Methods of automatically designing new multi-platform EA techniques are considered. The expert system runs on each defending platform rendering it an autonomous system requiring no human intervention. There is no commanding platform. Instead the platforms work cooperatively as a function of battlespace geometry; sensor data such as range, bearing, ID, uncertainty measures for sensor output; intelligence reports; etc. Computational experiments will show the defending networked platform's ability to self- organize. The platforms' ability to self-organize is illustrated through the output of the scenario generator, a software package that automates the underlying data mining problem and creates a computer movie of the platforms' interaction for evaluation.

Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation.

PubMed

Schilling, Birgit; Rardin, Matthew J; MacLean, Brendan X; Zawadzka, Anna M; Frewen, Barbara E; Cusack, Michael P; Sorensen, Dylan J; Bereman, Michael S; Jing, Enxuan; Wu, Christine C; Verdin, Eric; Kahn, C Ronald; Maccoss, Michael J; Gibson, Bradford W

2012-05-01

Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need for improved label-free approaches. This need is particularly pressing for workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as isobaric tags for relative and absolute quantitation and tandem mass tags may prove problematic or where stable isotope labeling with amino acids in cell culture labeling cannot be readily applied. Skyline is a freely available, open source software tool for quantitative data processing and proteomic analysis. We expanded the capabilities of Skyline to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments. Moreover, unlike existing programs, Skyline MS1 filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. The new quantitative and graphical tools now available in Skyline specifically support interrogation of multiple acquisitions for MS1 filtering, including visual inspection of peak picking and both automated and manual integration, key features often lacking in existing software. In addition, Skyline MS1 filtering displays retention time indicators from underlying MS/MS data contained within the spectral library to ensure proper peak selection. The modular structure of Skyline also provides well defined, customizable data reports and thus allows users to directly connect to existing statistical programs for post hoc data analysis. To demonstrate the utility of the MS1 filtering approach, we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important post-translational modifications: acetylation and phosphorylation, in peptide-centric affinity workflows of increasing complexity using mouse and human models.

Footprints of Fascination: Digital Traces of Public Engagement with Particle Physics on CERN's Social Media Platforms.

PubMed

Kahle, Kate; Sharon, Aviv J; Baram-Tsabari, Ayelet

2016-01-01

Although the scientific community increasingly recognizes that its communication with the public may shape civic engagement with science, few studies have characterized how this communication occurs online. Social media plays a growing role in this engagement, yet it is not known if or how different platforms support different types of engagement. This study sets out to explore how users engage with science communication items on different platforms of social media, and what are the characteristics of the items that tend to attract large numbers of user interactions. Here, user interactions with almost identical items on five of CERN's social media platforms were quantitatively compared over an eight-week period, including likes, comments, shares, click-throughs, and time spent on CERN's site. The most popular items were qualitatively analyzed for content features. Findings indicate that as audience size of a social media platform grows, the total rate of engagement with content tends to grow as well. However, per user, engagement tends to decline with audience size. Across all platforms, similar topics tend to consistently receive high engagement. In particular, awe-inspiring imagery tends to frequently attract high engagement across platforms, independent of newsworthiness. To our knowledge, this study provides the first cross-platform characterization of public engagement with science on social media. Findings, although focused on particle physics, have a multidisciplinary nature; they may serve to benchmark social media analytics for assessing science communication activities in various domains. Evidence-based suggestions for practitioners are also offered.

Footprints of Fascination: Digital Traces of Public Engagement with Particle Physics on CERN's Social Media Platforms

PubMed Central

Baram-Tsabari, Ayelet

2016-01-01

Although the scientific community increasingly recognizes that its communication with the public may shape civic engagement with science, few studies have characterized how this communication occurs online. Social media plays a growing role in this engagement, yet it is not known if or how different platforms support different types of engagement. This study sets out to explore how users engage with science communication items on different platforms of social media, and what are the characteristics of the items that tend to attract large numbers of user interactions. Here, user interactions with almost identical items on five of CERN's social media platforms were quantitatively compared over an eight-week period, including likes, comments, shares, click-throughs, and time spent on CERN's site. The most popular items were qualitatively analyzed for content features. Findings indicate that as audience size of a social media platform grows, the total rate of engagement with content tends to grow as well. However, per user, engagement tends to decline with audience size. Across all platforms, similar topics tend to consistently receive high engagement. In particular, awe-inspiring imagery tends to frequently attract high engagement across platforms, independent of newsworthiness. To our knowledge, this study provides the first cross-platform characterization of public engagement with science on social media. Findings, although focused on particle physics, have a multidisciplinary nature; they may serve to benchmark social media analytics for assessing science communication activities in various domains. Evidence-based suggestions for practitioners are also offered. PMID:27232498

NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds

PubMed Central

Yu, Jun-lan; Chen, Tian-tian; Zhou, Chen; Lian, Fu-lin; Tang, Xu-long; Wen, Yi; Shen, Jing-kang; Xu, Ye-chun; Xiong, Bing; Zhang, Nai-xia

2016-01-01

Aim: Fragment-based lead discovery (FBLD) is a complementary approach in drug research and development. In this study, we established an NMR-based FBLD platform that was used to screen novel scaffolds targeting human bromodomain of BRD4, and investigated the binding interactions between hit compounds and the target protein. Methods: 1D NMR techniques were primarily used to generate the fragment library and to screen compounds. The inhibitory activity of hits on the first bromodomain of BRD4 [BRD4(I)] was examined using fluorescence anisotropy binding assay. 2D NMR and X-ray crystallography were applied to characterize the binding interactions between hit compounds and the target protein. Results: An NMR-based fragment library containing 539 compounds was established, which were clustered into 56 groups (8–10 compounds in each group). Eight hits with new scaffolds were found to inhibit BRD4(I). Four out of the 8 hits (compounds 1, 2, 8 and 9) had IC50 values of 100–260 μmol/L, demonstrating their potential for further BRD4-targeted hit-to-lead optimization. Analysis of the binding interactions revealed that compounds 1 and 2 shared a common quinazolin core structure and bound to BRD4(I) in a non-acetylated lysine mimetic mode. Conclusion: An NMR-based platform for FBLD was established and used in discovery of BRD4-targeted compounds. Four potential hit-to-lead optimization candidates have been found, two of them bound to BRD4(I) in a non-acetylated lysine mimetic mode, being selective BRD4(I) inhibitors. PMID:27238211

A versatile electrowetting-based digital microfluidic platform for quantitative homogeneous and heterogeneous bio-assays

NASA Astrophysics Data System (ADS)

Vergauwe, Nicolas; Witters, Daan; Ceyssens, Frederik; Vermeir, Steven; Verbruggen, Bert; Puers, Robert; Lammertyn, Jeroen

2011-05-01

Electrowetting-on-dielectric (EWOD) lab-on-a-chip systems have already proven their potential within a broad range of bio-assays. Nevertheless, research on the analytical performance of those systems is limited, yet crucial for a further breakthrough in the diagnostic field. Therefore, this paper presents the intrinsic possibilities of an EWOD lab-on-a-chip as a versatile platform for homogeneous and heterogeneous bio-assays with high analytical performance. Both droplet dispensing and splitting cause variations in droplet size, thereby directly influencing the assay's performance. The extent to which they influence the performance is assessed by a theoretical sensitivity analysis, which allows the definition of a basic framework for the reduction of droplet size variability. Taking advantage of the optimized droplet manipulations, both homogeneous and heterogeneous bio-assays are implemented in the EWOD lab-on-a-chip to demonstrate the analytical capabilities and versatility of the device. A fully on-chip enzymatic assay is realized with high analytical performance. It demonstrates the promising capabilities of an EWOD lab-on-a-chip in food-related and medical applications, such as nutritional and blood analyses. Further, a magnetic bio-assay for IgE detection using superparamagnetic nanoparticles is presented whereby the nanoparticles are used as solid carriers during the bio-assay. Crucial elements are the precise manipulation of the superparamagnetic nanoparticles with respect to dispensing and separation. Although the principle of using nano-carriers is demonstrated for protein detection, it can be easily extended to a broader range of bio-related applications like DNA sensing. In heterogeneous bio-assays the chip surface is actively involved during the execution of the bio-assay. Through immobilization of specific biological compounds like DNA, proteins and cells a reactive chip surface is realized, which enhances the bio-assay performance. To demonstrate

A Cloud-Based Internet of Things Platform for Ambient Assisted Living

PubMed Central

Cubo, Javier; Nieto, Adrián; Pimentel, Ernesto

2014-01-01

A common feature of ambient intelligence is that many objects are inter-connected and act in unison, which is also a challenge in the Internet of Things. There has been a shift in research towards integrating both concepts, considering the Internet of Things as representing the future of computing and communications. However, the efficient combination and management of heterogeneous things or devices in the ambient intelligence domain is still a tedious task, and it presents crucial challenges. Therefore, to appropriately manage the inter-connection of diverse devices in these systems requires: (1) specifying and efficiently implementing the devices (e.g., as services); (2) handling and verifying their heterogeneity and composition; and (3) standardizing and managing their data, so as to tackle large numbers of systems together, avoiding standalone applications on local servers. To overcome these challenges, this paper proposes a platform to manage the integration and behavior-aware orchestration of heterogeneous devices as services, stored and accessed via the cloud, with the following contributions: (i) we describe a lightweight model to specify the behavior of devices, to determine the order of the sequence of exchanged messages during the composition of devices; (ii) we define a common architecture using a service-oriented standard environment, to integrate heterogeneous devices by means of their interfaces, via a gateway, and to orchestrate them according to their behavior; (iii) we design a framework based on cloud computing technology, connecting the gateway in charge of acquiring the data from the devices with a cloud platform, to remotely access and monitor the data at run-time and react to emergency situations; and (iv) we implement and generate a novel cloud-based IoT platform of behavior-aware devices as services for ambient intelligence systems, validating the whole approach in real scenarios related to a specific ambient assisted living application

A cloud-based Internet of Things platform for ambient assisted living.

PubMed

Cubo, Javier; Nieto, Adrián; Pimentel, Ernesto

2014-08-04

A common feature of ambient intelligence is that many objects are inter-connected and act in unison, which is also a challenge in the Internet of Things. There has been a shift in research towards integrating both concepts, considering the Internet of Things as representing the future of computing and communications. However, the efficient combination and management of heterogeneous things or devices in the ambient intelligence domain is still a tedious task, and it presents crucial challenges. Therefore, to appropriately manage the inter-connection of diverse devices in these systems requires: (1) specifying and efficiently implementing the devices (e.g., as services); (2) handling and verifying their heterogeneity and composition; and (3) standardizing and managing their data, so as to tackle large numbers of systems together, avoiding standalone applications on local servers. To overcome these challenges, this paper proposes a platform to manage the integration and behavior-aware orchestration of heterogeneous devices as services, stored and accessed via the cloud, with the following contributions: (i) we describe a lightweight model to specify the behavior of devices, to determine the order of the sequence of exchanged messages during the composition of devices; (ii) we define a common architecture using a service-oriented standard environment, to integrate heterogeneous devices by means of their interfaces, via a gateway, and to orchestrate them according to their behavior; (iii) we design a framework based on cloud computing technology, connecting the gateway in charge of acquiring the data from the devices with a cloud platform, to remotely access and monitor the data at run-time and react to emergency situations; and (iv) we implement and generate a novel cloud-based IoT platform of behavior-aware devices as services for ambient intelligence systems, validating the whole approach in real scenarios related to a specific ambient assisted living application.

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

PubMed

Liu, Hong; Crooks, Richard M

2012-03-06

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

A mechanical cell disruption microfluidic platform based on an on-chip micropump.

PubMed

Cheng, Yinuo; Wang, Yue; Wang, Zhiyuan; Huang, Liang; Bi, Mingzhao; Xu, Wenxiao; Wang, Wenhui; Ye, Xiongying

2017-03-01

Cell disruption plays a vital role in detection of intracellular components which contain information about genetic and disease characteristics. In this paper, we demonstrate a novel microfluidic platform based on an on-chip micropump for mechanical cell disruption and sample transport. A 50  μ l cell sample can be effectively lysed through on-chip multi-disruption in 36 s without introducing any chemical agent and suffering from clogging by cellular debris. After 30 cycles of circulating disruption, 80.6% and 90.5% cell disruption rates were achieved for the HEK293 cell sample and human natural killer cell sample, respectively. Profiting from the feature of pump-on-chip, the highly integrated platform enables more convenient and cost-effective cell disruption for the analysis of intracellular components.

A mechanical cell disruption microfluidic platform based on an on-chip micropump

PubMed Central

Cheng, Yinuo; Wang, Yue; Wang, Zhiyuan; Bi, Mingzhao; Xu, Wenxiao; Ye, Xiongying

2017-01-01

Cell disruption plays a vital role in detection of intracellular components which contain information about genetic and disease characteristics. In this paper, we demonstrate a novel microfluidic platform based on an on-chip micropump for mechanical cell disruption and sample transport. A 50 μl cell sample can be effectively lysed through on-chip multi-disruption in 36 s without introducing any chemical agent and suffering from clogging by cellular debris. After 30 cycles of circulating disruption, 80.6% and 90.5% cell disruption rates were achieved for the HEK293 cell sample and human natural killer cell sample, respectively. Profiting from the feature of pump-on-chip, the highly integrated platform enables more convenient and cost-effective cell disruption for the analysis of intracellular components. PMID:28798848

eTRIKS platform: Conception and operation of a highly scalable cloud-based platform for translational research and applications development.

PubMed

Bussery, Justin; Denis, Leslie-Alexandre; Guillon, Benjamin; Liu, Pengfeï; Marchetti, Gino; Rahal, Ghita

2018-04-01

We describe the genesis, design and evolution of a computing platform designed and built to improve the success rate of biomedical translational research. The eTRIKS project platform was developed with the aim of building a platform that can securely host heterogeneous types of data and provide an optimal environment to run tranSMART analytical applications. Many types of data can now be hosted, including multi-OMICS data, preclinical laboratory data and clinical information, including longitudinal data sets. During the last two years, the platform has matured into a robust translational research knowledge management system that is able to host other data mining applications and support the development of new analytical tools. Copyright © 2018 Elsevier Ltd. All rights reserved.

Translational value of liquid chromatography coupled with tandem mass spectrometry-based quantitative proteomics for in vitro-in vivo extrapolation of drug metabolism and transport and considerations in selecting appropriate techniques.

PubMed

Al Feteisi, Hajar; Achour, Brahim; Rostami-Hodjegan, Amin; Barber, Jill

2015-01-01

Drug-metabolizing enzymes and transporters play an important role in drug absorption, distribution, metabolism and excretion and, consequently, they influence drug efficacy and toxicity. Quantification of drug-metabolizing enzymes and transporters in various tissues is therefore essential for comprehensive elucidation of drug absorption, distribution, metabolism and excretion. Recent advances in liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) have improved the quantification of pharmacologically relevant proteins. This report presents an overview of mass spectrometry-based methods currently used for the quantification of drug-metabolizing enzymes and drug transporters, mainly focusing on applications and cost associated with various quantitative strategies based on stable isotope-labeled standards (absolute quantification peptide standards, quantification concatemers, protein standards for absolute quantification) and label-free analysis. In mass spectrometry, there is no simple relationship between signal intensity and analyte concentration. Proteomic strategies are therefore complex and several factors need to be considered when selecting the most appropriate method for an intended application, including the number of proteins and samples. Quantitative strategies require appropriate mass spectrometry platforms, yet choice is often limited by the availability of appropriate instrumentation. Quantitative proteomics research requires specialist practical skills and there is a pressing need to dedicate more effort and investment to training personnel in this area. Large-scale multicenter collaborations are also needed to standardize quantitative strategies in order to improve physiologically based pharmacokinetic models.

A Sustainable Architecture for Lunar Resource Prospecting from an EML-based Exploration Platform

NASA Astrophysics Data System (ADS)

Klaus, K.; Post, K.; Lawrence, S. J.

2012-12-01

Introduction - We present a point of departure architecture for prospecting for Lunar Resources from an Exploration Platform at the Earth - Moon Lagrange points. Included in our study are launch vehicle, cis-lunar transportation architecture, habitat requirements and utilization, lander/rover concepts and sample return. Different transfer design techniques can be explored by mission designers, testing various propulsive systems, maneuvers, rendezvous, and other in-space and surface operations. Understanding the availability of high and low energy trajectory transfer options opens up the possibility of exploring the human and logistics support mission design space and deriving solutions never before contemplated. For sample return missions from the lunar surface, low-energy transfers could be utilized between EML platform and the surface as well as return of samples to EML-based spacecraft. Human Habitation at the Exploration Platform - Telerobotic and telepresence capabilities are considered by the agency to be "grand challenges" for space technology. While human visits to the lunar surface provide optimal opportunities for field geologic exploration, on-orbit telerobotics may provide attractive early opportunities for geologic exploration, resource prospecting, and other precursor activities in advance of human exploration campaigns and ISRU processing. The Exploration Platform provides a perfect port for a small lander which could be refueled and used for multiple missions including sample return. The EVA and robotic capabilities of the EML Exploration Platform allow the lander to be serviced both internally and externally, based on operational requirements. The placement of the platform at an EML point allows the lander to access any site on the lunar surface, thus providing the global lunar surface access that is commonly understood to be required in order to enable a robust lunar exploration program. Designing the sample return lander for low

A silk-based scaffold platform with tunable architecture for engineering critically-sized tissue constructs.

PubMed

Wray, Lindsay S; Rnjak-Kovacina, Jelena; Mandal, Biman B; Schmidt, Daniel F; Gil, Eun Seok; Kaplan, David L

2012-12-01

In the field of tissue engineering and regenerative medicine there is significant unmet need for critically-sized, fully degradable biomaterial scaffold systems with tunable properties for optimizing tissue formation in vitro and tissue regeneration in vivo. To address this need, we have developed a silk-based scaffold platform that has tunable material properties, including localized and bioactive functionalization, degradation rate, and mechanical properties and that provides arrays of linear hollow channels for delivery of oxygen and nutrients throughout the scaffold bulk. The scaffolds can be assembled with dimensions that range from millimeters to centimeters, addressing the need for a critically-sized platform for tissue formation. We demonstrate that the hollow channel arrays support localized and confluent endothelialization. This new platform offers a unique and versatile tool for engineering 'tailored' scaffolds for a range of tissue engineering and regenerative medicine needs. Copyright © 2012 Elsevier Ltd. All rights reserved.

MEMS-based platforms for mechanical manipulation and characterization of cells

NASA Astrophysics Data System (ADS)

Pan, Peng; Wang, Wenhui; Ru, Changhai; Sun, Yu; Liu, Xinyu

2017-12-01

Mechanical manipulation and characterization of single cells are important experimental techniques in biological and medical research. Because of the microscale sizes and highly fragile structures of cells, conventional cell manipulation and characterization techniques are not accurate and/or efficient enough or even cannot meet the more and more demanding needs in different types of cell-based studies. To this end, novel microelectromechanical systems (MEMS)-based technologies have been developed to improve the accuracy, efficiency, and consistency of various cell manipulation and characterization tasks, and enable new types of cell research. This article summarizes existing MEMS-based platforms developed for cell mechanical manipulation and characterization, highlights their specific design considerations making them suitable for their designated tasks, and discuss their advantages and limitations. In closing, an outlook into future trends is also provided.

Quantitative mutant analysis of viral quasispecies by chip-based matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry

PubMed Central

Amexis, Georgios; Oeth, Paul; Abel, Kenneth; Ivshina, Anna; Pelloquin, Francois; Cantor, Charles R.; Braun, Andreas; Chumakov, Konstantin

2001-01-01

RNA viruses exist as quasispecies, heterogeneous and dynamic mixtures of mutants having one or more consensus sequences. An adequate description of the genomic structure of such viral populations must include the consensus sequence(s) plus a quantitative assessment of sequence heterogeneities. For example, in quality control of live attenuated viral vaccines, the presence of even small quantities of mutants or revertants may indicate incomplete or unstable attenuation that may influence vaccine safety. Previously, we demonstrated the monitoring of oral poliovirus vaccine with the use of mutant analysis by PCR and restriction enzyme cleavage (MAPREC). In this report, we investigate genetic variation in live attenuated mumps virus vaccine by using both MAPREC and a platform (DNA MassArray) based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Mumps vaccines prepared from the Jeryl Lynn strain typically contain at least two distinct viral substrains, JL1 and JL2, which have been characterized by full length sequencing. We report the development of assays for characterizing sequence variants in these substrains and demonstrate their use in quantitative analysis of substrains and sequence variations in mixed virus cultures and mumps vaccines. The results obtained from both the MAPREC and MALDI-TOF methods showed excellent correlation. This suggests the potential utility of MALDI-TOF for routine quality control of live viral vaccines and for assessment of genetic stability and quantitative monitoring of genetic changes in other RNA viruses of clinical interest. PMID:11593021

ElectroTaxis-on-a-Chip (ETC): an integrated quantitative high-throughput screening platform for electrical field-directed cell migration.

PubMed

Zhao, Siwei; Zhu, Kan; Zhang, Yan; Zhu, Zijie; Xu, Zhengping; Zhao, Min; Pan, Tingrui

2014-11-21

Both endogenous and externally applied electrical stimulation can affect a wide range of cellular functions, including growth, migration, differentiation and division. Among those effects, the electrical field (EF)-directed cell migration, also known as electrotaxis, has received broad attention because it holds great potential in facilitating clinical wound healing. Electrotaxis experiment is conventionally conducted in centimetre-sized flow chambers built in Petri dishes. Despite the recent efforts to adapt microfluidics for electrotaxis studies, the current electrotaxis experimental setup is still cumbersome due to the needs of an external power supply and EF controlling/monitoring systems. There is also a lack of parallel experimental systems for high-throughput electrotaxis studies. In this paper, we present a first independently operable microfluidic platform for high-throughput electrotaxis studies, integrating all functional components for cell migration under EF stimulation (except microscopy) on a compact footprint (the same as a credit card), referred to as ElectroTaxis-on-a-Chip (ETC). Inspired by the R-2R resistor ladder topology in digital signal processing, we develop a systematic approach to design an infinitely expandable microfluidic generator of EF gradients for high-throughput and quantitative studies of EF-directed cell migration. Furthermore, a vacuum-assisted assembly method is utilized to allow direct and reversible attachment of our device to existing cell culture media on biological surfaces, which separates the cell culture and device preparation/fabrication steps. We have demonstrated that our ETC platform is capable of screening human cornea epithelial cell migration under the stimulation of an EF gradient spanning over three orders of magnitude. The screening results lead to the identification of the EF-sensitive range of that cell type, which can provide valuable guidance to the clinical application of EF-facilitated wound healing.

The Turkish Version of Web-Based Learning Platform Evaluation Scale: Reliability and Validity Study

ERIC Educational Resources Information Center

Dag, Funda

2016-01-01

The purpose of this study is to determine the language equivalence and the validity and reliability of the Turkish version of the "Web-Based Learning Platform Evaluation Scale" ("Web Tabanli Ögrenme Ortami Degerlendirme Ölçegi" [WTÖODÖ]) used in the selection and evaluation of web-based learning environments. Within this scope,…

Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity

PubMed Central

Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A.; Bradford, William D.; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S.; Li, Rong

2015-01-01

Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein−based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. PMID:25823586

A Digital Teaching Platform to Further and Assess Use of Evidence-Based Practices

ERIC Educational Resources Information Center

Bondie, Rhonda

2015-01-01

Advances in online learning have benefited rural special education teacher preparation programs through increased recruitment, access, and collaboration. This paper describes how additional challenges, such as monitoring teacher candidate use of evidence-based practices, can be addressed through a digital teaching platform. Project REACH online is…

3D-Lab: a collaborative web-based platform for molecular modeling.

PubMed

Grebner, Christoph; Norrby, Magnus; Enström, Jonatan; Nilsson, Ingemar; Hogner, Anders; Henriksson, Jonas; Westin, Johan; Faramarzi, Farzad; Werner, Philip; Boström, Jonas

2016-09-01

The use of 3D information has shown impact in numerous applications in drug design. However, it is often under-utilized and traditionally limited to specialists. We want to change that, and present an approach making 3D information and molecular modeling accessible and easy-to-use 'for the people'. A user-friendly and collaborative web-based platform (3D-Lab) for 3D modeling, including a blazingly fast virtual screening capability, was developed. 3D-Lab provides an interface to automatic molecular modeling, like conformer generation, ligand alignments, molecular dockings and simple quantum chemistry protocols. 3D-Lab is designed to be modular, and to facilitate sharing of 3D-information to promote interactions between drug designers. Recent enhancements to our open-source virtual reality tool Molecular Rift are described. The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.

HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors.

PubMed

Qureshi, Abid; Rajput, Akanksha; Kaur, Gazaldeep; Kumar, Manoj

2018-03-09

A number of anti-retroviral drugs are being used for treating Human Immunodeficiency Virus (HIV) infection. Due to emergence of drug resistant strains, there is a constant quest to discover more effective anti-HIV compounds. In this endeavor, computational tools have proven useful in accelerating drug discovery. Although methods were published to design a class of compounds against a specific HIV protein, but an integrated web server for the same is lacking. Therefore, we have developed support vector machine based regression models using experimentally validated data from ChEMBL repository. Quantitative structure activity relationship based features were selected for predicting inhibition activity of a compound against HIV proteins namely protease (PR), reverse transcriptase (RT) and integrase (IN). The models presented a maximum Pearson correlation coefficient of 0.78, 0.76, 0.74 and 0.76, 0.68, 0.72 during tenfold cross-validation on IC 50 and percent inhibition datasets of PR, RT, IN respectively. These models performed equally well on the independent datasets. Chemical space mapping, applicability domain analyses and other statistical tests further support robustness of the predictive models. Currently, we have identified a number of chemical descriptors that are imperative in predicting the compound inhibition potential. HIVprotI platform ( http://bioinfo.imtech.res.in/manojk/hivproti ) would be useful in virtual screening of inhibitors as well as designing of new molecules against the important HIV proteins for therapeutics development.

A Reward-Based Behavioral Platform to Measure Neural Activity during Head-Fixed Behavior.

PubMed

Micallef, Andrew H; Takahashi, Naoya; Larkum, Matthew E; Palmer, Lucy M

2017-01-01

Understanding the neural computations that contribute to behavior requires recording from neurons while an animal is behaving. This is not an easy task as most subcellular recording techniques require absolute head stability. The Go/No-Go sensory task is a powerful decision-driven task that enables an animal to report a binary decision during head-fixation. Here we discuss how to set up an Ardunio and Python based platform system to control a Go/No-Go sensory behavior paradigm. Using an Arduino micro-controller and Python-based custom written program, a reward can be delivered to the animal depending on the decision reported. We discuss the various components required to build the behavioral apparatus that can control and report such a sensory stimulus paradigm. This system enables the end user to control the behavioral testing in real-time and therefore it provides a strong custom-made platform for probing the neural basis of behavior.

A Reward-Based Behavioral Platform to Measure Neural Activity during Head-Fixed Behavior

PubMed Central

Micallef, Andrew H.; Takahashi, Naoya; Larkum, Matthew E.; Palmer, Lucy M.

2017-01-01

Understanding the neural computations that contribute to behavior requires recording from neurons while an animal is behaving. This is not an easy task as most subcellular recording techniques require absolute head stability. The Go/No-Go sensory task is a powerful decision-driven task that enables an animal to report a binary decision during head-fixation. Here we discuss how to set up an Ardunio and Python based platform system to control a Go/No-Go sensory behavior paradigm. Using an Arduino micro-controller and Python-based custom written program, a reward can be delivered to the animal depending on the decision reported. We discuss the various components required to build the behavioral apparatus that can control and report such a sensory stimulus paradigm. This system enables the end user to control the behavioral testing in real-time and therefore it provides a strong custom-made platform for probing the neural basis of behavior. PMID:28620282

Statistical design of quantitative mass spectrometry-based proteomic experiments.

PubMed

Oberg, Ann L; Vitek, Olga

2009-05-01

We review the fundamental principles of statistical experimental design, and their application to quantitative mass spectrometry-based proteomics. We focus on class comparison using Analysis of Variance (ANOVA), and discuss how randomization, replication and blocking help avoid systematic biases due to the experimental procedure, and help optimize our ability to detect true quantitative changes between groups. We also discuss the issues of pooling multiple biological specimens for a single mass analysis, and calculation of the number of replicates in a future study. When applicable, we emphasize the parallels between designing quantitative proteomic experiments and experiments with gene expression microarrays, and give examples from that area of research. We illustrate the discussion using theoretical considerations, and using real-data examples of profiling of disease.

The Osseus platform: a prototype for advanced web-based distributed simulation

NASA Astrophysics Data System (ADS)

Franceschini, Derrick; Riecken, Mark

2016-05-01

Recent technological advances in web-based distributed computing and database technology have made possible a deeper and more transparent integration of some modeling and simulation applications. Despite these advances towards true integration of capabilities, disparate systems, architectures, and protocols will remain in the inventory for some time to come. These disparities present interoperability challenges for distributed modeling and simulation whether the application is training, experimentation, or analysis. Traditional approaches call for building gateways to bridge between disparate protocols and retaining interoperability specialists. Challenges in reconciling data models also persist. These challenges and their traditional mitigation approaches directly contribute to higher costs, schedule delays, and frustration for the end users. Osseus is a prototype software platform originally funded as a research project by the Defense Modeling & Simulation Coordination Office (DMSCO) to examine interoperability alternatives using modern, web-based technology and taking inspiration from the commercial sector. Osseus provides tools and services for nonexpert users to connect simulations, targeting the time and skillset needed to successfully connect disparate systems. The Osseus platform presents a web services interface to allow simulation applications to exchange data using modern techniques efficiently over Local or Wide Area Networks. Further, it provides Service Oriented Architecture capabilities such that finer granularity components such as individual models can contribute to simulation with minimal effort.

Self-Referenced Smartphone-Based Nanoplasmonic Imaging Platform for Colorimetric Biochemical Sensing.

PubMed

Wang, Xinhao; Chang, Te-Wei; Lin, Guohong; Gartia, Manas Ranjan; Liu, Gang Logan

2017-01-03

Colorimetric sensors usually suffer due to errors from variation in light source intensity, the type of light source, the Bayer filter algorithm, and the sensitivity of the camera to incoming light. Here, we demonstrate a self-referenced portable smartphone-based plasmonic sensing platform integrated with an internal reference sample along with an image processing method to perform colorimetric sensing. Two sensing principles based on unique nanoplasmonics enabled phenomena from a nanostructured plasmonic sensor, named as nanoLCA (nano Lycurgus cup array), were demonstrated here for colorimetric biochemical sensing: liquid refractive index sensing and optical absorbance enhancement sensing. Refractive indices of colorless liquids were measured by simple smartphone imaging and color analysis. Optical absorbance enhancement in the colorimetric biochemical assay was achieved by matching the plasmon resonance wavelength with the chromophore's absorbance peak wavelength. Such a sensing mechanism improved the limit of detection (LoD) by 100 times in a microplate reader format. Compared with a traditional colorimetric assay such as urine testing strips, a smartphone plasmon enhanced colorimetric sensing system provided 30 times improvement in the LoD. The platform was applied for simulated urine testing to precisely identify the samples with higher protein concentration, which showed potential point-of-care and early detection of kidney disease with the smartphone plasmonic resonance sensing system.

Quantitative SIMS Imaging of Agar-Based Microbial Communities.

PubMed

Dunham, Sage J B; Ellis, Joseph F; Baig, Nameera F; Morales-Soto, Nydia; Cao, Tianyuan; Shrout, Joshua D; Bohn, Paul W; Sweedler, Jonathan V

2018-05-01

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

[Willingness to accept an Internet-based mobility platform in different age cohorts. Empiric results of the project S-Mobil 100].

PubMed

Beil, J; Cihlar, V; Kruse, A

2015-02-01

The aim of the project S-Mobil 100 is to develop and implement a prototype of an internet-based, generation-appropriate mobility platform in the model region Siegen-Wittgenstein. In the context of an empirical preliminary study, use of technology, experience with technology, general attitudes towards technology, general technology commitment, and the willingness to accept the mobility platform were investigated in different age cohorts. The investigation was carried out using a written survey based on a standardized questionnaire. The sample of 358 persons aged 40-90 years was divided in four age cohorts (40-54, 55-64, 65-74, and 75 + years). Our results show a high willingness to accept the mobility platform in the overall sample. Age, residence, income, and general technology commitment were significant predictors for the judgment of the platform. Although there were group differences in accepting the mobility platform, the older cohorts are also open-minded towards this new technology.

Localizing wushu players on a platform based on a video recording

NASA Astrophysics Data System (ADS)

Peczek, Piotr M.; Zabołotny, Wojciech M.

2017-08-01

This article describes the development of a method to localize an athlete during sports performance on a platform, based on a static video recording. Considered sport for this method is wushu - martial art. However, any other discipline can be applied. There are specified requirements, and 2 algorithms of image processing are described. The next part presents an experiment that was held based on recordings from the Pan American Wushu Championship. Based on those recordings the steps of the algorithm are shown. Results are evaluated manually. The last part of the article concludes if the algorithm is applicable and what improvements have to be implemented to use it during sports competitions as well as for offline analysis.

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data

PubMed Central

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie

2018-01-01

Abstract Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. PMID:29106630

AI based HealthCare Platform for Real Time, Predictive and Prescriptive Analytics using Reactive Programming

NASA Astrophysics Data System (ADS)

Kaur, Jagreet; Singh Mann, Kulwinder, Dr.

2018-01-01

AI in Healthcare needed to bring real, actionable insights and Individualized insights in real time for patients and Doctors to support treatment decisions., We need a Patient Centred Platform for integrating EHR Data, Patient Data, Prescriptions, Monitoring, Clinical research and Data. This paper proposes a generic architecture for enabling AI based healthcare analytics Platform by using open sources Technologies Apache beam, Apache Flink Apache Spark, Apache NiFi, Kafka, Tachyon, Gluster FS, NoSQL- Elasticsearch, Cassandra. This paper will show the importance of applying AI based predictive and prescriptive analytics techniques in Health sector. The system will be able to extract useful knowledge that helps in decision making and medical monitoring in real-time through an intelligent process analysis and big data processing.

Pneumatic Microvalve-Based Hydrodynamic Sample Injection for High-Throughput, Quantitative Zone Electrophoresis in Capillaries

PubMed Central

2015-01-01

A hybrid microchip/capillary electrophoresis (CE) system was developed to allow unbiased and lossless sample loading and high-throughput repeated injections. This new hybrid CE system consists of a poly(dimethylsiloxane) (PDMS) microchip sample injector featuring a pneumatic microvalve that separates a sample introduction channel from a short sample loading channel, and a fused-silica capillary separation column that connects seamlessly to the sample loading channel. The sample introduction channel is pressurized such that when the pneumatic microvalve opens briefly, a variable-volume sample plug is introduced into the loading channel. A high voltage for CE separation is continuously applied across the loading channel and the fused-silica capillary separation column. Analytes are rapidly separated in the fused-silica capillary, and following separation, high-sensitivity MS detection is accomplished via a sheathless CE/ESI-MS interface. The performance evaluation of the complete CE/ESI-MS platform demonstrated that reproducible sample injection with well controlled sample plug volumes could be achieved by using the PDMS microchip injector. The absence of band broadening from microchip to capillary indicated a minimum dead volume at the junction. The capabilities of the new CE/ESI-MS platform in performing high-throughput and quantitative sample analyses were demonstrated by the repeated sample injection without interrupting an ongoing separation and a linear dependence of the total analyte ion abundance on the sample plug volume using a mixture of peptide standards. The separation efficiency of the new platform was also evaluated systematically at different sample injection times, flow rates, and CE separation voltages. PMID:24865952

Pneumatic Microvalve-Based Hydrodynamic Sample Injection for High-Throughput, Quantitative Zone Electrophoresis in Capillaries

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

Kelly, Ryan T.; Wang, Chenchen; Rausch, Sarah J.

2014-07-01

A hybrid microchip/capillary CE system was developed to allow unbiased and lossless sample loading and high throughput repeated injections. This new hybrid CE system consists of a polydimethylsiloxane (PDMS) microchip sample injector featuring a pneumatic microvalve that separates a sample introduction channel from a short sample loading channel and a fused silica capillary separation column that connects seamlessly to the sample loading channel. The sample introduction channel is pressurized such that when the pneumatic microvalve opens briefly, a variable-volume sample plug is introduced into the loading channel. A high voltage for CE separation is continuously applied across the loading channelmore » and the fused silica capillary separation column. Analytes are rapidly separated in the fused silica capillary with high resolution. High sensitivity MS detection after CE separation is accomplished via a sheathless CE/ESI-MS interface. The performance evaluation of the complete CE/ESI-MS platform demonstrated that reproducible sample injection with well controlled sample plug volumes could be achieved by using the PDMS microchip injector. The absence of band broadening from microchip to capillary indicated a minimum dead volume at the junction. The capabilities of the new CE/ESI-MS platform in performing high throughput and quantitative sample analyses were demonstrated by the repeated sample injection without interrupting an ongoing separation and a good linear dependence of the total analyte ion abundance on the sample plug volume using a mixture of peptide standards. The separation efficiency of the new platform was also evaluated systematically at different sample injection times, flow rates and CE separation voltages.« less

Smart home-based health platform for behavioral monitoring and alteration of diabetes patients.

PubMed

Helal, Abdelsalam; Cook, Diane J; Schmalz, Mark

2009-01-01

Researchers and medical practitioners have long sought the ability to continuously and automatically monitor patients beyond the confines of a doctor's office. We describe a smart home monitoring and analysis platform that facilitates the automatic gathering of rich databases of behavioral information in a manner that is transparent to the patient. Collected information will be automatically or manually analyzed and reported to the caregivers and may be interpreted for behavioral modification in the patient. Our health platform consists of five technology layers. The architecture is designed to be flexible, extensible, and transparent, to support plug-and-play operation of new devices and components, and to provide remote monitoring and programming opportunities. The smart home-based health platform technologies have been tested in two physical smart environments. Data that are collected in these implemented physical layers are processed and analyzed by our activity recognition and chewing classification algorithms. All of these components have yielded accurate analyses for subjects in the smart environment test beds. This work represents an important first step in the field of smart environment-based health monitoring and assistance. The architecture can be used to monitor the activity, diet, and exercise compliance of diabetes patients and evaluate the effects of alternative medicine and behavior regimens. We believe these technologies are essential for providing accessible, low-cost health assistance in an individual's own home and for providing the best possible quality of life for individuals with diabetes. © Diabetes Technology Society

The Design of Individual Knowledge Sharing Platform Based on Blog for Online Information Literacy Education

NASA Astrophysics Data System (ADS)

Qun, Zeng; Xiaocheng, Zhong

Knowledge sharing means that an individual, team and organization share the knowledge with other members of the organization in the course of activities through the various ways. This paper analyzes the obstacle factors in knowledge sharing based on the technical point, and chooses the Blog technology to build a platform for improving knowledge sharing between individuals. The construction of the platform is an important foundation for information literacy education, and it also can be used to achieve online information literacy education. Finally, it gives a detailed analysis of its functions, advantages and disadvantages.

Slow erosion of a quantitative apple resistance to Venturia inaequalis based on an isolate-specific Quantitative Trait Locus.

PubMed

Caffier, Valérie; Le Cam, Bruno; Al Rifaï, Mehdi; Bellanger, Marie-Noëlle; Comby, Morgane; Denancé, Caroline; Didelot, Frédérique; Expert, Pascale; Kerdraon, Tifenn; Lemarquand, Arnaud; Ravon, Elisa; Durel, Charles-Eric

2016-10-01

Quantitative plant resistance affects the aggressiveness of pathogens and is usually considered more durable than qualitative resistance. However, the efficiency of a quantitative resistance based on an isolate-specific Quantitative Trait Locus (QTL) is expected to decrease over time due to the selection of isolates with a high level of aggressiveness on resistant plants. To test this hypothesis, we surveyed scab incidence over an eight-year period in an orchard planted with susceptible and quantitatively resistant apple genotypes. We sampled 79 Venturia inaequalis isolates from this orchard at three dates and we tested their level of aggressiveness under controlled conditions. Isolates sampled on resistant genotypes triggered higher lesion density and exhibited a higher sporulation rate on apple carrying the resistance allele of the QTL T1 compared to isolates sampled on susceptible genotypes. Due to this ability to select aggressive isolates, we expected the QTL T1 to be non-durable. However, our results showed that the quantitative resistance based on the QTL T1 remained efficient in orchard over an eight-year period, with only a slow decrease in efficiency and no detectable increase of the aggressiveness of fungal isolates over time. We conclude that knowledge on the specificity of a QTL is not sufficient to evaluate its durability. Deciphering molecular mechanisms associated with resistance QTLs, genetic determinants of aggressiveness and putative trade-offs within pathogen populations is needed to help in understanding the erosion processes. Copyright © 2016 Elsevier B.V. All rights reserved.

The Design and Implementation of Network Teaching Platform Basing on .NET

NASA Astrophysics Data System (ADS)

Yanna, Ren

This paper addresses the problem that students under traditional teaching model have poor operation ability and studies in depth the network teaching platform in domestic colleges and universities, proposing the design concept of network teaching platform of NET + C # + SQL excellent course and designing the overall structure, function module and back-end database of the platform. This paper emphatically expounds the use of MD5 encryption techniques in order to solve data security problems and the assessment of student learning using ADO.NET database access technology as well as the mathematical formula. The example shows that the network teaching platform developed by using WEB application technology has higher safety and availability, and thus improves the students' operation ability.

Quantitative nanoimmunosensor based on dark-field illumination with enhanced sensitivity and on-off switching using scattering signals.

PubMed

Lee, Seungah; Nan, He; Yu, Hyunung; Kang, Seong Ho

2016-05-15

A nanoimmunosensor based on wavelength-dependent dark-field illumination with enhanced sensitivity was used to detect a disease-related protein molecule at zeptomolar (zM) concentrations. The assay platform of 100-nm gold nanospots could be selectively acquired using the wavelength-dependence of enhanced scattering signals from antibody-conjugated plasmonic silver nanoparticles (NPs) with on-off switching using optical filters. Detection of human thyroid-stimulating hormone (hTSH) at a sensitivity of 100 zM, which corresponds to 1-2 molecules per gold spot, was possible within a linear range of 100 zM-100 fM (R=0.9968). A significantly enhanced sensitivity (~4-fold) was achieved with enhanced dark-field illumination compared to using a total internal reflection fluorescence immunosensor. Immunoreactions were confirmed via optical axial-slicing based on the spectral characteristics of two plasmonic NPs. This method of using wavelength-dependent dark-field illumination had an enhanced sensitivity and a wide, linear dynamic range of 100 zM-100 fM, and was an effective tool for quantitatively detecting a single molecule on a nanobiochip for molecular diagnostics. Copyright © 2016 Elsevier B.V. All rights reserved.

A methodology towards virtualisation-based high performance simulation platform supporting multidisciplinary design of complex products

NASA Astrophysics Data System (ADS)

Ren, Lei; Zhang, Lin; Tao, Fei; (Luke) Zhang, Xiaolong; Luo, Yongliang; Zhang, Yabin

2012-08-01

Multidisciplinary design of complex products leads to an increasing demand for high performance simulation (HPS) platforms. One great challenge is how to achieve high efficient utilisation of large-scale simulation resources in distributed and heterogeneous environments. This article reports a virtualisation-based methodology to realise a HPS platform. This research is driven by the issues concerning large-scale simulation resources deployment and complex simulation environment construction, efficient and transparent utilisation of fine-grained simulation resources and high reliable simulation with fault tolerance. A framework of virtualisation-based simulation platform (VSIM) is first proposed. Then the article investigates and discusses key approaches in VSIM, including simulation resources modelling, a method to automatically deploying simulation resources for dynamic construction of system environment, and a live migration mechanism in case of faults in run-time simulation. Furthermore, the proposed methodology is applied to a multidisciplinary design system for aircraft virtual prototyping and some experiments are conducted. The experimental results show that the proposed methodology can (1) significantly improve the utilisation of fine-grained simulation resources, (2) result in a great reduction in deployment time and an increased flexibility for simulation environment construction and (3)achieve fault tolerant simulation.

Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples.

PubMed

Zellner, Maria; Babeluk, Rita; Diestinger, Michael; Pirchegger, Petra; Skeledzic, Senada; Oehler, Rudolf

2008-09-01

Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.

A Cloud Based Real-Time Collaborative Platform for eHealth.

PubMed

Ionescu, Bogdan; Gadea, Cristian; Solomon, Bogdan; Ionescu, Dan; Stoicu-Tivadar, Vasile; Trifan, Mircea

2015-01-01

For more than a decade, the eHealth initiative has been a government concern of many countries. In an Electronic Health Record (EHR) System, there is a need for sharing the data with a group of specialists simultaneously. Collaborative platforms alone are just a part of a solution, while a collaborative platform with parallel editing capabilities and with synchronized data streaming are stringently needed. In this paper, the design and implementation of a collaborative platform used in healthcare is introduced by describing the high level architecture and its implementation. A series of eHealth services are identified and usage examples in a healthcare environment are given.

[Continuum, the continuing education platform based on a competency matrix].

PubMed

Ochoa Sangrador, C; Villaizán Pérez, C; González de Dios, J; Hijano Bandera, F; Málaga Guerrero, S

2016-04-01

Competency-Based Education is a learning method that has changed the traditional teaching-based focus to a learning-based one. Students are the centre of the process, in which they must learn to learn, solve problems, and adapt to changes in their environment. The goal is to provide learning based on knowledge, skills (know-how), attitude and behaviour. These sets of knowledge are called competencies. It is essential to have a reference of the required competencies in order to identify the need for them. Their acquisition is approached through teaching modules, in which one or more skills can be acquired. This teaching strategy has been adopted by Continuum, the distance learning platform of the Spanish Paediatric Association, which has developed a competency matrix based on the Global Paediatric Education Consortium training program. In this article, a review will be presented on the basics of Competency-Based Education and how it is applied in Continuum. Copyright © 2015 Asociación Española de Pediatría. Published by Elsevier España, S.L.U. All rights reserved.

Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity.

PubMed

Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A; Bradford, William D; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S; Li, Rong

2015-03-30

Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein-based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. Copyright © 2015 Zhu et al.

Floor Plans Engine Removal Platform, Hold Down Arm Platform, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Floor Plans - Engine Removal Platform, Hold Down Arm Platform, Hydraulic Equipment Platforms, Isometric Cutaway of Engine Removal Platform, Isometric Cutaway of Hold Down Arm Platform, Isometric Cutaway of Hydraulic Platforms and Engine Support System Access - Marshall Space Flight Center, Saturn V S-IC Static Test Facility, West Test Area, Huntsville, Madison County, AL

From WSN towards WoT: Open API Scheme Based on oneM2M Platforms.

PubMed

Kim, Jaeho; Choi, Sung-Chan; Ahn, Il-Yeup; Sung, Nak-Myoung; Yun, Jaeseok

2016-10-06

Conventional computing systems have been able to be integrated into daily objects and connected to each other due to advances in computing and network technologies, such as wireless sensor networks (WSNs), forming a global network infrastructure, called the Internet of Things (IoT). To support the interconnection and interoperability between heterogeneous IoT systems, the availability of standardized, open application programming interfaces (APIs) is one of the key features of common software platforms for IoT devices, gateways, and servers. In this paper, we present a standardized way of extending previously-existing WSNs towards IoT systems, building the world of the Web of Things (WoT). Based on the oneM2M software platforms developed in the previous project, we introduce a well-designed open API scheme and device-specific thing adaptation software (TAS) enabling WSN elements, such as a wireless sensor node, to be accessed in a standardized way on a global scale. Three pilot services are implemented (i.e., a WiFi-enabled smart flowerpot, voice-based control for ZigBee-connected home appliances, and WiFi-connected AR.Drone control) to demonstrate the practical usability of the open API scheme and TAS modules. Full details on the method of integrating WSN elements into three example systems are described at the programming code level, which is expected to help future researchers in integrating their WSN systems in IoT platforms, such as oneM2M. We hope that the flexibly-deployable, easily-reusable common open API scheme and TAS-based integration method working with the oneM2M platforms will help the conventional WSNs in diverse industries evolve into the emerging WoT solutions.

From WSN towards WoT: Open API Scheme Based on oneM2M Platforms

PubMed Central

Kim, Jaeho; Choi, Sung-Chan; Ahn, Il-Yeup; Sung, Nak-Myoung; Yun, Jaeseok

2016-01-01

Conventional computing systems have been able to be integrated into daily objects and connected to each other due to advances in computing and network technologies, such as wireless sensor networks (WSNs), forming a global network infrastructure, called the Internet of Things (IoT). To support the interconnection and interoperability between heterogeneous IoT systems, the availability of standardized, open application programming interfaces (APIs) is one of the key features of common software platforms for IoT devices, gateways, and servers. In this paper, we present a standardized way of extending previously-existing WSNs towards IoT systems, building the world of the Web of Things (WoT). Based on the oneM2M software platforms developed in the previous project, we introduce a well-designed open API scheme and device-specific thing adaptation software (TAS) enabling WSN elements, such as a wireless sensor node, to be accessed in a standardized way on a global scale. Three pilot services are implemented (i.e., a WiFi-enabled smart flowerpot, voice-based control for ZigBee-connected home appliances, and WiFi-connected AR.Drone control) to demonstrate the practical usability of the open API scheme and TAS modules. Full details on the method of integrating WSN elements into three example systems are described at the programming code level, which is expected to help future researchers in integrating their WSN systems in IoT platforms, such as oneM2M. We hope that the flexibly-deployable, easily-reusable common open API scheme and TAS-based integration method working with the oneM2M platforms will help the conventional WSNs in diverse industries evolve into the emerging WoT solutions. PMID:27782058

The Design and Development of Test Platform for Wheat Precision Seeding Based on Image Processing Techniques

NASA Astrophysics Data System (ADS)

Li, Qing; Lin, Haibo; Xiu, Yu-Feng; Wang, Ruixue; Yi, Chuijie

The test platform of wheat precision seeding based on image processing techniques is designed to develop the wheat precision seed metering device with high efficiency and precision. Using image processing techniques, this platform gathers images of seeds (wheat) on the conveyer belt which are falling from seed metering device. Then these data are processed and analyzed to calculate the qualified rate, reseeding rate and leakage sowing rate, etc. This paper introduces the whole structure, design parameters of the platform and hardware & software of the image acquisition system were introduced, as well as the method of seed identification and seed-space measurement using image's threshold and counting the seed's center. By analyzing the experimental result, the measurement error is less than ± 1mm.

Telescope Array Control System Based on Wireless Touch Screen Platform

NASA Astrophysics Data System (ADS)

Fu, Xia-nan; Huang, Lei; Wei, Jian-yan

2017-10-01

Ground-based Wide Angle Cameras (GMAC) are the ground-based observational facility for the SVOM (Space Variable Object Monitor) astronomical satellite of Sino-French cooperation, and Mini-GWAC is the pathfinder and supplement of GWAC. In the context of the Mini-GWAC telescope array, this paper introduces the design and implementation of a kind of telescope array control system based on the wireless touch screen platform. We describe the development and implementation of the system in detail in terms of control system principle, system hardware structure, software design, experiment, and test etc. The system uses a touch-control PC which is based on the Windows CE system as the upper computer, while the wireless transceiver module and PLC (Programmable Logic Controller) are taken as the system kernel. It has the advantages of low cost, reliable data transmission, and simple operation. And the control system has been applied to the Mini-GWAC successfully.

Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells.

PubMed

Zhu, Ying; Piehowski, Paul D; Zhao, Rui; Chen, Jing; Shen, Yufeng; Moore, Ronald J; Shukla, Anil K; Petyuk, Vladislav A; Campbell-Thompson, Martha; Mathews, Clayton E; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T

2018-02-28

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.

Platform for Post-Processing Waveform-Based NDE

NASA Technical Reports Server (NTRS)

Roth, Don J.

2010-01-01

Signal- and image-processing methods are commonly needed to extract information from the waves, improve resolution of, and highlight defects in an image. Since some similarity exists for all waveform-based nondestructive evaluation (NDE) methods, it would seem that a common software platform containing multiple signal- and image-processing techniques to process the waveforms and images makes sense where multiple techniques, scientists, engineers, and organizations are involved. NDE Wave & Image Processor Version 2.0 software provides a single, integrated signal- and image-processing and analysis environment for total NDE data processing and analysis. It brings some of the most useful algorithms developed for NDE over the past 20 years into a commercial-grade product. The software can import signal/spectroscopic data, image data, and image series data. This software offers the user hundreds of basic and advanced signal- and image-processing capabilities including esoteric 1D and 2D wavelet-based de-noising, de-trending, and filtering. Batch processing is included for signal- and image-processing capability so that an optimized sequence of processing operations can be applied to entire folders of signals, spectra, and images. Additionally, an extensive interactive model-based curve-fitting facility has been included to allow fitting of spectroscopy data such as from Raman spectroscopy. An extensive joint-time frequency module is included for analysis of non-stationary or transient data such as that from acoustic emission, vibration, or earthquake data.

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

NASA Astrophysics Data System (ADS)

Wang, Pu

Surface Enhanced Raman Scattering (SERS) has attracted explosive interest for the wealth of vibrational information it provides with minimal invasive effects to target analyte. Nanotechnology, especially in the form of noble metal nanoparticles exhibit unique electromagnetic and chemical characteristics that are explored to realize ultra-sensitive SERS detection in chemical and biological analysis. Graphene, atom-thick carbon monolayer, exhibits superior chemical stability and bio-compatibility. A combination of SERS-active metal nanostructures and graphene will create various synergies in SERS. The main objective of this research was to exploit the applications of the graphene-Au tip hybrid platform in SERS. The hybrid platform consists of a periodic Au nano-pyramid substrate to provide reproducible plasmonic enhancement, and the superimposed monolayer graphene sheet, serving as "built-in" Raman marker. Extensive theoretical and experimental studies were conducted to determine the potentials of the hybrid platform as SERS substrate. Results from both Finite-Domain Time-Domain (FDTD) numerical simulation and Raman scattering of graphene suggested that the hybrid platform boosted a high density of hotspots yielding 1000 times SERS enhancement of graphene bands. Ultra-high sensitivity of the hybrid platform was demonstrated by bio-molecules including dye, protein and neurotransmitters. Dopamine and serotonin can be detected and distinguished at 10-9 M concentration in the presence of human body fluid. Single molecule detection was obtained using a bi-analyte technique. Graphene supported a vibration mode dependent SERS chemical enhancement of ˜10 to the analyte. Quantitative evaluation of hotspots was presented using spatially resolved Raman mapping of graphene SERS enhancement. Graphene plays a crucial role in quantifying SERS hotspots and paves the path for defining SERS EF that could be universally applied to various SERS systems. A reproducible and statistically

Virtual Distances Methodology as Verification Technique for AACMMs with a Capacitive Sensor Based Indexed Metrology Platform

PubMed Central

Acero, Raquel; Santolaria, Jorge; Brau, Agustin; Pueo, Marcos

2016-01-01

This paper presents a new verification procedure for articulated arm coordinate measuring machines (AACMMs) together with a capacitive sensor-based indexed metrology platform (IMP) based on the generation of virtual reference distances. The novelty of this procedure lays on the possibility of creating virtual points, virtual gauges and virtual distances through the indexed metrology platform’s mathematical model taking as a reference the measurements of a ball bar gauge located in a fixed position of the instrument’s working volume. The measurements are carried out with the AACMM assembled on the IMP from the six rotating positions of the platform. In this way, an unlimited number and types of reference distances could be created without the need of using a physical gauge, therefore optimizing the testing time, the number of gauge positions and the space needed in the calibration and verification procedures. Four evaluation methods are presented to assess the volumetric performance of the AACMM. The results obtained proved the suitability of the virtual distances methodology as an alternative procedure for verification of AACMMs using the indexed metrology platform. PMID:27869722

A microfluidic platform for 3-dimensional cell culture and cell-based assays.

PubMed

Kim, Minseok S; Yeon, Ju Hun; Park, Je-Kyun

2007-02-01

This paper reports a novel microfluidic platform introducing peptide hydrogel to make biocompatible microenvironment as well as realizing in situ cell-based assays. Collagen composite, OPLA and Puramatrix scaffolds are compared to select good environment for human hepatocellular carcinoma cells (HepG2) by albumin measurement. The selected biocompatible self-assembling peptide hydrogel, Puramatrix, is hydrodynamically focused in the middle of main channel of a microfluidic device, and at the same time the cells are 3-dimensionally immobilized and encapsulated without any additional surface treatment. HepG2 cells have been 3-dimensionally cultured in a poly(dimethylsiloxane) (PDMS) microfluidic device for 4 days. The cells cultured in micro peptide scaffold are compared with those cultured by conventional petri dish in morphology and the rate of albumin secretion. By injection of different reagents into either side of the peptide scaffold, the microfluidic device also forms a linear concentration gradient profile across the peptide scaffold due to molecular diffusion. Based on this characteristic, toxicity tests are performed by Triton X-100. As the higher toxicant concentration gradient forms, the wider dead zone of cells in the peptide scaffold represents. This microfluidic platform facilitates in vivo-like 3-dimensional microenvironment, and have a potential for the applications of reliable cell-based screening and assays including cytotoxicity test, real-time cell viability monitoring, and continuous dose-response assay.

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

DOT National Transportation Integrated Search

2009-12-22

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

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

DOT National Transportation Integrated Search

2009-11-23

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

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

Integrated microfluidic platforms for investigating neuronal networks

NASA Astrophysics Data System (ADS)

Kim, Hyung Joon

This dissertation describes the development and application of integrated microfluidics-based assay platforms to study neuronal activities in the nervous system in-vitro. The assay platforms were fabricated using soft lithography and micro/nano fabrication including microfluidics, surface patterning, and nanomaterial synthesis. The use of integrated microfluidics-based assay platform allows culturing and manipulating many types of neuronal tissues in precisely controlled microenvironment. Furthermore, they provide organized multi-cellular in-vitro model, long-term monitoring with live cell imaging, and compatibility with molecular biology techniques and electrophysiology experiment. In this dissertation, the integrated microfluidics-based assay platforms are developed for investigation of neuronal activities such as local protein synthesis, impairment of axonal transport by chemical/physical variants, growth cone path finding under chemical/physical cues, and synaptic transmission in neuronal circuit. Chapter 1 describes the motivation, objectives, and scope for developing in-vitro platform to study various neuronal activities. Chapter 2 introduces microfluidic culture platform for biochemical assay with large-scale neuronal tissues that are utilized as model system in neuroscience research. Chapter 3 focuses on the investigation of impaired axonal transport by beta-Amyloid and oxidative stress. The platform allows to control neuronal processes and to quantify mitochondrial movement in various regions of axons away from applied drugs. Chapter 4 demonstrates the development of microfluidics-based growth cone turning assay to elucidate the mechanism underlying axon guidance under soluble factors and shear flow. Using this platform, the behaviors of growth cone of mammalian neurons are verified under the gradient of inhibitory molecules and also shear flow in well-controlled manner. In Chapter 5, I combine in-vitro multicellular model with microfabricated MEA

Optofluidic time-stretch quantitative phase microscopy.

PubMed

Guo, Baoshan; Lei, Cheng; Wu, Yi; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Lee, Sangwook; Isozaki, Akihiro; Li, Ming; Jiang, Yiyue; Yasumoto, Atsushi; Di Carlo, Dino; Tanaka, Yo; Yatomi, Yutaka; Ozeki, Yasuyuki; Goda, Keisuke

2018-03-01

Innovations in optical microscopy have opened new windows onto scientific research, industrial quality control, and medical practice over the last few decades. One of such innovations is optofluidic time-stretch quantitative phase microscopy - an emerging method for high-throughput quantitative phase imaging that builds on the interference between temporally stretched signal and reference pulses by using dispersive properties of light in both spatial and temporal domains in an interferometric configuration on a microfluidic platform. It achieves the continuous acquisition of both intensity and phase images with a high throughput of more than 10,000 particles or cells per second by overcoming speed limitations that exist in conventional quantitative phase imaging methods. Applications enabled by such capabilities are versatile and include characterization of cancer cells and microalgal cultures. In this paper, we review the principles and applications of optofluidic time-stretch quantitative phase microscopy and discuss its future perspective. Copyright © 2017 Elsevier Inc. All rights reserved.

A Standard-Based Model for Adaptive E-Learning Platform for Mauritian Academic Institutions

ERIC Educational Resources Information Center

Kanaksabee, P.; Odit, M. P.; Ramdoyal, A.

2011-01-01

The key aim of this paper is to introduce a standard-based model for adaptive e-learning platform for Mauritian academic institutions and to investigate the conditions and tools required to implement this model. The main forces of the system are that it allows collaborative learning, communication among user, and reduce considerable paper work.…

[Construction and application of bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer].

PubMed

Fang, Xiang; Li, Ning-qiu; Fu, Xiao-zhe; Li, Kai-bin; Lin, Qiang; Liu, Li-hui; Shi, Cun-bin; Wu, Shu-qin

2015-07-01

As a key component of life science, bioinformatics has been widely applied in genomics, transcriptomics, and proteomics. However, the requirement of high-performance computers rather than common personal computers for constructing a bioinformatics platform significantly limited the application of bioinformatics in aquatic science. In this study, we constructed a bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer. The platform consisted of three functional modules, including genomic and transcriptomic sequencing data analysis, protein structure prediction, and molecular dynamics simulations. To validate the practicability of the platform, we performed bioinformatic analysis on aquatic pathogenic organisms. For example, genes of Flavobacterium johnsoniae M168 were identified and annotated via Blast searches, GO and InterPro annotations. Protein structural models for five small segments of grass carp reovirus HZ-08 were constructed by homology modeling. Molecular dynamics simulations were performed on out membrane protein A of Aeromonas hydrophila, and the changes of system temperature, total energy, root mean square deviation and conformation of the loops during equilibration were also observed. These results showed that the bioinformatic analysis platform for aquatic pathogen has been successfully built on the MilkyWay-2 supercomputer. This study will provide insights into the construction of bioinformatic analysis platform for other subjects.

Quantitation of 47 human tear proteins using high resolution multiple reaction monitoring (HR-MRM) based-mass spectrometry.

PubMed

Tong, Louis; Zhou, Xi Yuan; Jylha, Antti; Aapola, Ulla; Liu, Dan Ning; Koh, Siew Kwan; Tian, Dechao; Quah, Joanne; Uusitalo, Hannu; Beuerman, Roger W; Zhou, Lei

2015-02-06

Tear proteins are intimately related to the pathophysiology of the ocular surface. Many recent studies have demonstrated that the tear is an accessible fluid for studying eye diseases and biomarker discovery. This study describes a high resolution multiple reaction monitoring (HR-MRM) approach for developing assays for quantification of biologically important tear proteins. Human tear samples were collected from 1000 subjects with no eye complaints (411 male, 589 female, average age: 55.5±14.5years) after obtaining informed consent. Tear samples were collected using Schirmer's strips and pooled into a single global control sample. Quantification of proteins was carried out by selecting "signature" peptides derived by trypsin digestion. A 1-h nanoLC-MS/MS run was used to quantify the tear proteins in HR-MRM mode. Good reproducibility of signal intensity (using peak areas) was demonstrated for all 47 HR-MRM assays with an average coefficient of variation (CV%) of 4.82% (range: 1.52-10.30%). All assays showed consistent retention time with a CV of less than 0.80% (average: 0.57%). HR-MRM absolute quantitation of eight tear proteins was demonstrated using stable isotope-labeled peptides. In this study, we demonstrated for the first time the technique to quantify 47 human tear proteins in HR-MRM mode using approximately 1μl of human tear sample. These multiplexed HR-MRM-based assays show great promise of further development for biomarker validation in human tear samples. Both discovery-based and targeted quantitative proteomics can be achieved in a single quadrupole time-of-flight mass spectrometer platform (TripleTOF 5600 system). Copyright © 2015 Elsevier B.V. All rights reserved.

A new task scheduling algorithm based on value and time for cloud platform

NASA Astrophysics Data System (ADS)

Kuang, Ling; Zhang, Lichen

2017-08-01

Tasks scheduling, a key part of increasing resource utilization and enhancing system performance, is a never outdated problem especially in cloud platforms. Based on the value density algorithm of the real-time task scheduling system and the character of the distributed system, the paper present a new task scheduling algorithm by further studying the cloud technology and the real-time system: Least Level Value Density First (LLVDF). The algorithm not only introduces some attributes of time and value for tasks, it also can describe weighting relationships between these properties mathematically. As this feature of the algorithm, it can gain some advantages to distinguish between different tasks more dynamically and more reasonably. When the scheme was used in the priority calculation of the dynamic task scheduling on cloud platform, relying on its advantage, it can schedule and distinguish tasks with large amounts and many kinds more efficiently. The paper designs some experiments, some distributed server simulation models based on M/M/C model of queuing theory and negative arrivals, to compare the algorithm against traditional algorithm to observe and show its characters and advantages.

Microfluidics for cell-based high throughput screening platforms - A review.

PubMed

Du, Guansheng; Fang, Qun; den Toonder, Jaap M J

2016-01-15

In the last decades, the basic techniques of microfluidics for the study of cells such as cell culture, cell separation, and cell lysis, have been well developed. Based on cell handling techniques, microfluidics has been widely applied in the field of PCR (Polymerase Chain Reaction), immunoassays, organ-on-chip, stem cell research, and analysis and identification of circulating tumor cells. As a major step in drug discovery, high-throughput screening allows rapid analysis of thousands of chemical, biochemical, genetic or pharmacological tests in parallel. In this review, we summarize the application of microfluidics in cell-based high throughput screening. The screening methods mentioned in this paper include approaches using the perfusion flow mode, the droplet mode, and the microarray mode. We also discuss the future development of microfluidic based high throughput screening platform for drug discovery. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of an IHE MRRT-compliant open-source web-based reporting platform.

PubMed

Pinto Dos Santos, Daniel; Klos, G; Kloeckner, R; Oberle, R; Dueber, C; Mildenberger, P

2017-01-01

To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. • A platform for structured reporting using IHE MRRT-compliant templates is presented. • Incorporating structured reporting into clinical routine is feasible. • Full source code will be provided upon request under a free license.

Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

PubMed

Sahoo, Satya S; Ramesh, Priya; Welter, Elisabeth; Bukach, Ashley; Valdez, Joshua; Tatsuoka, Curtis; Bamps, Yvan; Stoll, Shelley; Jobst, Barbara C; Sajatovic, Martha

2016-10-01

We present Insight as an integrated database and analysis platform for epilepsy self-management research as part of the national Managing Epilepsy Well Network. Insight is the only available informatics platform for accessing and analyzing integrated data from multiple epilepsy self-management research studies with several new data management features and user-friendly functionalities. The features of Insight include, (1) use of Common Data Elements defined by members of the research community and an epilepsy domain ontology for data integration and querying, (2) visualization tools to support real time exploration of data distribution across research studies, and (3) an interactive visual query interface for provenance-enabled research cohort identification. The Insight platform contains data from five completed epilepsy self-management research studies covering various categories of data, including depression, quality of life, seizure frequency, and socioeconomic information. The data represents over 400 participants with 7552 data points. The Insight data exploration and cohort identification query interface has been developed using Ruby on Rails Web technology and open source Web Ontology Language Application Programming Interface to support ontology-based reasoning. We have developed an efficient ontology management module that automatically updates the ontology mappings each time a new version of the Epilepsy and Seizure Ontology is released. The Insight platform features a Role-based Access Control module to authenticate and effectively manage user access to different research studies. User access to Insight is managed by the Managing Epilepsy Well Network database steering committee consisting of representatives of all current collaborating centers of the Managing Epilepsy Well Network. New research studies are being continuously added to the Insight database and the size as well as the unique coverage of the dataset allows investigators to conduct

The VISPA Internet Platform for Students

NASA Astrophysics Data System (ADS)

Asseldonk, D. v.; Erdmann, M.; Fischer, R.; Glaser, C.; Müller, G.; Quast, T.; Rieger, M.; Urban, M.

2016-04-01

The VISPA internet platform enables users to remotely run Python scripts and view resulting plots or inspect their output data. With a standard web browser as the only user requirement on the client-side, the system becomes suitable for blended learning approaches for university physics students. VISPA was used in two consecutive years each by approx. 100 third year physics students at the RWTH Aachen University for their homework assignments. For example, in one exercise students gained a deeper understanding of Einsteins mass-energy relation by analyzing experimental data of electron-positron pairs revealing J / Ψ and Z particles. Because the students were free to choose their working hours, only few users accessed the platform simultaneously. The positive feedback from students and the stability of the platform lead to further development of the concept. This year, students accessed the platform in parallel while they analyzed the data recorded by demonstrated experiments live in the lecture hall. The platform is based on experience in the development of professional analysis tools. It combines core technologies from previous projects: an object-oriented C++ library, a modular data-driven analysis flow, and visual analysis steering. We present the platform and discuss its benefits in the context of teaching based on surveys that are conducted each semester.

A user-friendly LabVIEW software platform for grating based X-ray phase-contrast imaging.

PubMed

Wang, Shenghao; Han, Huajie; Gao, Kun; Wang, Zhili; Zhang, Can; Yang, Meng; Wu, Zhao; Wu, Ziyu

2015-01-01

X-ray phase-contrast imaging can provide greatly improved contrast over conventional absorption-based imaging for weakly absorbing samples, such as biological soft tissues and fibre composites. In this study, we introduced an easy and fast way to develop a user-friendly software platform dedicated to the new grating-based X-ray phase-contrast imaging setup at the National Synchrotron Radiation Laboratory of the University of Science and Technology of China. The control of 21 motorized stages, of a piezoelectric stage and of an X-ray tube are achieved with this software, it also covers image acquisition with a flat panel detector for automatic phase stepping scan. Moreover, a data post-processing module for signals retrieval and other custom features are in principle available. With a seamless integration of all the necessary functions in one software package, this platform greatly facilitate users' activities during experimental runs with this grating based X-ray phase contrast imaging setup.

Multimodality Imaging with Silica-Based Targeted Nanoparticle Platforms

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

Jason S. Lewis

2012-04-09

Objectives: To synthesize and characterize a C-Dot silica-based nanoparticle containing 'clickable' groups for the subsequent attachment of targeting moieties (e.g., peptides) and multiple contrast agents (e.g., radionuclides with high specific activity) [1,2]. These new constructs will be tested in suitable tumor models in vitro and in vivo to ensure maintenance of target-specificity and high specific activity. Methods: Cy5 dye molecules are cross-linked to a silica precursor which is reacted to form a dye-rich core particle. This core is then encapsulated in a layer of pure silica to create the core-shell C-Dot (Figure 1) [2]. A 'click' chemistry approach has beenmore » used to functionalize the silica shell with radionuclides conferring high contrast and specific activity (e.g. 64Cu and 89Zr) and peptides for tumor targeting (e.g. cRGD and octreotate) [3]. Based on the selective Diels-Alder reaction between tetrazine and norbornene, the reaction is bioorthogonal, highyielding, rapid, and water-compatible. This radiolabeling approach has already been employed successfully with both short peptides (e.g. octreotate) and antibodies (e.g. trastuzumab) as model systems for the ultimate labeling of the nanoparticles [1]. Results: PEGylated C-Dots with a Cy5 core and labeled with tetrazine have been synthesized (d = 55 nm, zeta potential = -3 mV) reliably and reproducibly and have been shown to be stable under physiological conditions for up to 1 month. Characterization of the nanoparticles revealed that the immobilized Cy5 dye within the C-Dots exhibited fluorescence intensities over twice that of the fluorophore alone. The nanoparticles were successfully radiolabeled with Cu-64. Efforts toward the conjugation of targeting peptides (e.g. cRGD) are underway. In vitro stability, specificity, and uptake studies as well as in vivo imaging and biodistribution investigations will be presented. Conclusions: C-Dot silica-based nanoparticles offer a robust, versatile, and

Platform for intraoperative analysis of video streams

NASA Astrophysics Data System (ADS)

Clements, Logan; Galloway, Robert L., Jr.

2004-05-01

Interactive, image-guided surgery (IIGS) has proven to increase the specificity of a variety of surgical procedures. However, current IIGS systems do not compensate for changes that occur intraoperatively and are not reflected in preoperative tomograms. Endoscopes and intraoperative ultrasound, used in minimally invasive surgery, provide real-time (RT) information in a surgical setting. Combining the information from RT imaging modalities with traditional IIGS techniques will further increase surgical specificity by providing enhanced anatomical information. In order to merge these techniques and obtain quantitative data from RT imaging modalities, a platform was developed to allow both the display and processing of video streams in RT. Using a Bandit-II CV frame grabber board (Coreco Imaging, St. Laurent, Quebec) and the associated library API, a dynamic link library was created in Microsoft Visual C++ 6.0 such that the platform could be incorporated into the IIGS system developed at Vanderbilt University. Performance characterization, using two relatively inexpensive host computers, has shown the platform capable of performing simple image processing operations on frames captured from a CCD camera and displaying the processed video data at near RT rates both independent of and while running the IIGS system.

Improving healthcare services using web based platform for management of medical case studies.

PubMed

Ogescu, Cristina; Plaisanu, Claudiu; Udrescu, Florian; Dumitru, Silviu

2008-01-01

The paper presents a web based platform for management of medical cases, support for healthcare specialists in taking the best clinical decision. Research has been oriented mostly on multimedia data management, classification algorithms for querying, retrieving and processing different medical data types (text and images). The medical case studies can be accessed by healthcare specialists and by students as anonymous case studies providing trust and confidentiality in Internet virtual environment. The MIDAS platform develops an intelligent framework to manage sets of medical data (text, static or dynamic images), in order to optimize the diagnosis and the decision process, which will reduce the medical errors and will increase the quality of medical act. MIDAS is an integrated project working on medical information retrieval from heterogeneous, distributed medical multimedia database.

Research and application of mobile teaching platform

NASA Astrophysics Data System (ADS)

Yang, Ping; Xue, Hongjiao

2017-08-01

The application of mobile technology in university digital campus is ripe. This article mainly introduced the necessity of teaching platform based on mobile Internet in the teaching of higher vocational education, and the key to the construction of the feasibility of mobile learning platform, which is a feasible and effective teaching model under the new situation, worthy of promotion. The design and application of teaching platform based on mobile Internet is the change of educational ideas and working methods, and is the new starting point of Higher Vocational education.

Analysis and design of a six-degree-of-freedom Stewart platform-based robotic wrist

NASA Technical Reports Server (NTRS)

Nguyen, Charles C.; Antrazi, Sami; Zhou, Zhen-Lei

1991-01-01

The kinematic analysis and implementation of a six degree of freedom robotic wrist which is mounted to a general open-kinetic chain manipulator to serve as a restbed for studying precision robotic assembly in space is discussed. The wrist design is based on the Stewart Platform mechanism and consists mainly of two platforms and six linear actuators driven by DC motors. Position feedback is achieved by linear displacement transducers mounted along the actuators and force feedback is obtained by a 6 degree of freedom force sensor mounted between the gripper and the payload platform. The robot wrist inverse kinematics which computes the required actuator lengths corresponding to Cartesian variables has a closed-form solution. The forward kinematics is solved iteratively using the Newton-Ralphson method which simultaneously provides a modified Jacobian Matrix which relates length velocities to Cartesian translational velocities and time rates of change of roll-pitch-yaw angles. Results of computer simulation conducted to evaluate the efficiency of the forward kinematics and Modified Jacobian Matrix are discussed.

[The Key Technology Study on Cloud Computing Platform for ECG Monitoring Based on Regional Internet of Things].

PubMed

Yang, Shu; Qiu, Yuyan; Shi, Bo

2016-09-01

This paper explores the methods of building the internet of things of a regional ECG monitoring, focused on the implementation of ECG monitoring center based on cloud computing platform. It analyzes implementation principles of automatic identifi cation in the types of arrhythmia. It also studies the system architecture and key techniques of cloud computing platform, including server load balancing technology, reliable storage of massive smalfi les and the implications of quick search function.

The Personal Motion Platform

NASA Technical Reports Server (NTRS)

Park, Brian Vandellyn

1993-01-01

The Neutral Body Posture experienced in microgravity creates a biomechanical equilibrium by enabling the internal forces within the body to find their own balance. A patented reclining chair based on this posture provides a minimal stress environment for interfacing with computer systems for extended periods. When the chair is mounted on a 3 or 6 axis motion platform, a generic motion simulator for simulated digital environments is created. The Personal Motion Platform provides motional feedback to the occupant in synchronization with their movements inside the digital world which enhances the simulation experience. Existing HMD based simulation systems can be integrated to the turnkey system. Future developments are discussed.

Optical properties of acute kidney injury measured by quantitative phase imaging

PubMed Central

Ban, Sungbea; Min, Eunjung; Baek, Songyee; Kwon, Hyug Moo; Popescu, Gabriel

2018-01-01

The diagnosis of acute kidney disease (AKI) has been examined mainly by histology, immunohistochemistry and western blot. Though these approaches are widely accepted in the field, it has an inherent limitation due to the lack of high-throughput and quantitative information. For a better understanding of prognosis in AKI, we present a new approach using quantitative phase imaging combined with a wide-field scanning platform. Through the phase-delay information from the tissue, we were able to predict a stage of AKI based on various optical properties such as light scattering coefficient and anisotropy. These optical parameters quantify the deterioration process of the AKI model of tissue. Our device would be a very useful tool when it is required to deliver fast feedback of tissue pathology or when diseases are related to mechanical properties such as fibrosis. PMID:29541494

Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics.

PubMed

Jarnuczak, Andrew F; Lee, Dave C H; Lawless, Craig; Holman, Stephen W; Eyers, Claire E; Hubbard, Simon J

2016-09-02

Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from signal intensity alone in the absence of a standard. A deeper understanding of the governing principles of peptide ionization and exploitation of the inherent ionization and detection parameters of individual peptides is thus of great value. Here, using the yeast proteome as a model system, we establish the concept of peptide F-factor as a measure of detectability, closely related to ionization efficiency. F-factor is calculated by normalizing peptide precursor ion intensity by absolute abundance of the parent protein. We investigated F-factor characteristics in different shotgun proteomics experiments, including across multiple ESI-based LC-MS platforms. We show that F-factors mirror previously observed physicochemical predictors as peptide detectability but demonstrate a nonlinear relationship between hydrophobicity and peptide detectability. Similarly, we use F-factors to show how peptide ion coelution adversely affects detectability and ionization. We suggest that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex peptide mixtures, selection of surrogate peptides in targeted MS studies, and for calibration of peptide ion signal in label-free workflows. Data are available via ProteomeXchange with identifier PXD003472.

ArControl: An Arduino-Based Comprehensive Behavioral Platform with Real-Time Performance.

PubMed

Chen, Xinfeng; Li, Haohong

2017-01-01

Studying animal behavior in the lab requires reliable delivering stimulations and monitoring responses. We constructed a comprehensive behavioral platform (ArControl: Arduino Control Platform) that was an affordable, easy-to-use, high-performance solution combined software and hardware components. The hardware component was consisted of an Arduino UNO board and a simple drive circuit. As for software, the ArControl provided a stand-alone and intuitive GUI (graphical user interface) application that did not require users to master scripts. The experiment data were automatically recorded with the built in DAQ (data acquisition) function. The ArControl also allowed the behavioral schedule to be entirely stored in and operated on the Arduino chip. This made the ArControl a genuine, real-time system with high temporal resolution (<1 ms). We tested the ArControl, based on strict performance measurements and two mice behavioral experiments. The results showed that the ArControl was an adaptive and reliable system suitable for behavioral research.

ArControl: An Arduino-Based Comprehensive Behavioral Platform with Real-Time Performance

PubMed Central

Chen, Xinfeng; Li, Haohong

2017-01-01

Studying animal behavior in the lab requires reliable delivering stimulations and monitoring responses. We constructed a comprehensive behavioral platform (ArControl: Arduino Control Platform) that was an affordable, easy-to-use, high-performance solution combined software and hardware components. The hardware component was consisted of an Arduino UNO board and a simple drive circuit. As for software, the ArControl provided a stand-alone and intuitive GUI (graphical user interface) application that did not require users to master scripts. The experiment data were automatically recorded with the built in DAQ (data acquisition) function. The ArControl also allowed the behavioral schedule to be entirely stored in and operated on the Arduino chip. This made the ArControl a genuine, real-time system with high temporal resolution (<1 ms). We tested the ArControl, based on strict performance measurements and two mice behavioral experiments. The results showed that the ArControl was an adaptive and reliable system suitable for behavioral research. PMID:29321735

Open Marketplace for Simulation Software on the Basis of a Web Platform

NASA Astrophysics Data System (ADS)

Kryukov, A. P.; Demichev, A. P.

2016-02-01

The focus in development of a new generation of middleware shifts from the global grid systems to building convenient and efficient web platforms for remote access to individual computing resources. Further line of their development, suggested in this work, is related not only with the quantitative increase in their number and with the expansion of scientific, engineering, and manufacturing areas in which they are used, but also with improved technology for remote deployment of application software on the resources interacting with the web platforms. Currently, the services for providers of application software in the context of scientific-oriented web platforms is not developed enough. The proposed in this work new web platforms of application software market should have all the features of the existing web platforms for submissions of jobs to remote resources plus the provision of specific web services for interaction on market principles between the providers and consumers of application packages. The suggested approach will be approved on the example of simulation applications in the field of nonlinear optics.

Four-hour quantitative real-time polymerase chain reaction-based comprehensive chromosome screening and accumulating evidence of accuracy, safety, predictive value, and clinical efficacy.

PubMed

Treff, Nathan R; Scott, Richard T

2013-03-15

Embryonic comprehensive chromosomal euploidy may represent a powerful biomarker to improve the success of IVF. However, there are a number of aneuploidy screening strategies to consider, including different technologic platforms with which to interrogate the embryonic DNA, and different embryonic developmental stages from which DNA can be analyzed. Although there are advantages and disadvantages associated with each strategy, a series of experiments producing evidence of accuracy, safety, clinical predictive value, and clinical efficacy indicate that trophectoderm biopsy and quantitative real-time polymerase chain reaction (qPCR)-based comprehensive chromosome screening (CCS) may represent a useful strategy to improve the success of IVF. This Biomarkers in Reproductive Medicine special issue review summarizes the accumulated experience with the development and clinical application of a 4-hour blastocyst qPCR-based CCS technology. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Majumder, Saikat; Chakraborty, Rajib

2018-06-01

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

Development of a Cloud Computing-Based Pier Type Port Structure Stability Evaluation Platform Using Fiber Bragg Grating Sensors.

PubMed

Jo, Byung Wan; Jo, Jun Ho; Khan, Rana Muhammad Asad; Kim, Jung Hoon; Lee, Yun Sung

2018-05-23

Structure Health Monitoring is a topic of great interest in port structures due to the ageing of structures and the limitations of evaluating structures. This paper presents a cloud computing-based stability evaluation platform for a pier type port structure using Fiber Bragg Grating (FBG) sensors in a system consisting of a FBG strain sensor, FBG displacement gauge, FBG angle meter, gateway, and cloud computing-based web server. The sensors were installed on core components of the structure and measurements were taken to evaluate the structures. The measurement values were transmitted to the web server via the gateway to analyze and visualize them. All data were analyzed and visualized in the web server to evaluate the structure based on the safety evaluation index (SEI). The stability evaluation platform for pier type port structures involves the efficient monitoring of the structures which can be carried out easily anytime and anywhere by converging new technologies such as cloud computing and FBG sensors. In addition, the platform has been successfully implemented at “Maryang Harbor” situated in Maryang-Meyon of Korea to test its durability.

A highly efficient, high-throughput lipidomics platform for the quantitative detection of eicosanoids in human whole blood.

PubMed

Song, Jiao; Liu, Xuejun; Wu, Jiejun; Meehan, Michael J; Blevitt, Jonathan M; Dorrestein, Pieter C; Milla, Marcos E

2013-02-15

We have developed an ultra-performance liquid chromatography-multiple reaction monitoring/mass spectrometry (UPLC-MRM/MS)-based, high-content, high-throughput platform that enables simultaneous profiling of multiple lipids produced ex vivo in human whole blood (HWB) on treatment with calcium ionophore and its modulation with pharmacological agents. HWB samples were processed in a 96-well plate format compatible with high-throughput sample processing instrumentation. We employed a scheduled MRM (sMRM) method, with a triple-quadrupole mass spectrometer coupled to a UPLC system, to measure absolute amounts of 122 distinct eicosanoids using deuterated internal standards. In a 6.5-min run, we resolved and detected with high sensitivity (lower limit of quantification in the range of 0.4-460 pg) all targeted analytes from a very small HWB sample (2.5 μl). Approximately 90% of the analytes exhibited a dynamic range exceeding 1000. We also developed a tailored software package that dramatically sped up the overall data quantification and analysis process with superior consistency and accuracy. Matrix effects from HWB and precision of the calibration curve were evaluated using this newly developed automation tool. This platform was successfully applied to the global quantification of changes on all 122 eicosanoids in HWB samples from healthy donors in response to calcium ionophore stimulation. Copyright © 2012 Elsevier Inc. All rights reserved.

A Distributed Platform for Global-Scale Agent-Based Models of Disease Transmission

PubMed Central

Parker, Jon; Epstein, Joshua M.

2013-01-01

The Global-Scale Agent Model (GSAM) is presented. The GSAM is a high-performance distributed platform for agent-based epidemic modeling capable of simulating a disease outbreak in a population of several billion agents. It is unprecedented in its scale, its speed, and its use of Java. Solutions to multiple challenges inherent in distributing massive agent-based models are presented. Communication, synchronization, and memory usage are among the topics covered in detail. The memory usage discussion is Java specific. However, the communication and synchronization discussions apply broadly. We provide benchmarks illustrating the GSAM’s speed and scalability. PMID:24465120

Gryphon: A Hybrid Agent-Based Modeling and Simulation Platform for Infectious Diseases

NASA Astrophysics Data System (ADS)

Yu, Bin; Wang, Jijun; McGowan, Michael; Vaidyanathan, Ganesh; Younger, Kristofer

In this paper we present Gryphon, a hybrid agent-based stochastic modeling and simulation platform developed for characterizing the geographic spread of infectious diseases and the effects of interventions. We study both local and non-local transmission dynamics of stochastic simulations based on the published parameters and data for SARS. The results suggest that the expected numbers of infections and the timeline of control strategies predicted by our stochastic model are in reasonably good agreement with previous studies. These preliminary results indicate that Gryphon is able to characterize other future infectious diseases and identify endangered regions in advance.

Modulation of renal oxygenation and perfusion in rat kidney monitored by quantitative diffusion and blood oxygen level dependent magnetic resonance imaging on a clinical 1.5T platform.

PubMed

Jerome, Neil P; Boult, Jessica K R; Orton, Matthew R; d'Arcy, James; Collins, David J; Leach, Martin O; Koh, Dow-Mu; Robinson, Simon P

2016-10-03

To investigate the combined use of intravoxel incoherent motion (IVIM) diffusion-weighted (DW) and blood oxygen level dependent (BOLD) magnetic resonance imaging (MRI) to assess rat renal function using a 1.5T clinical platform. Multiple b-value DW and BOLD MR images were acquired from adult rats using a parallel clinical coil arrangement, enabling quantitation of the apparent diffusion coefficient (ADC), IVIM-derived diffusion coefficient (D), pseudodiffusion coefficient (D*) and perfusion fraction (f), and the transverse relaxation time T 2 *, for whole kidney, renal cortex, and medulla. Following the acquisition of two baseline datasets to assess measurement repeatability, images were acquired following i.v. administration of hydralazine, furosemide, or angiotensin II for up to 40 min. Excellent repeatability (CoV <10 %) was observed for ADC, D, f and T 2 * measured over the whole kidney. Hydralazine induced a marked and significant (p < 0.05) reduction in whole kidney ADC, D, and T 2 *, and a significant (p < 0.05) increase in D* and f. Furosemide significantly (p < 0.05) increased whole kidney ADC, D, and T 2 *. A more variable response to angiotensin II was determined, with a significant (p < 0.05) increase in medulla D* and significant (p < 0.05) reduction in whole kidney T 2 * established. Multiparametric MRI, incorporating quantitation of IVIM DWI and BOLD biomarkers and performed on a clinical platform, can be used to monitor the acute effects of vascular and tubular modulating drugs on rat kidney function in vivo. Clinical adoption of such functional imaging biomarkers can potentially inform on treatment effects in patients with renal dysfunction.

National Community Solar Platform

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

Rupert, Bart

This project was created to provide a National Community Solar Platform (NCSP) portal known as Community Solar Hub, that is available to any entity or individual who wants to develop community solar. This has been done by providing a comprehensive portal to make CEC’s solutions, and other proven community solar solutions, externally available for everyone to access – making the process easy through proven platforms to protect subscribers, developers and utilities. The successful completion of this project provides these tools via a web platform and integration APIs, a wide spectrum of community solar projects included in the platform, multiple groupsmore » of customers (utilities, EPCs, and advocates) using the platform to develop community solar, and open access to anyone interested in community solar. CEC’s Incubator project includes web-based informational resources, integrated systems for project information and billing systems, and engagement with customers and users by community solar experts. The combined effort externalizes much of Clean Energy Collective’s industry-leading expertise, allowing third parties to develop community solar without duplicating expensive start-up efforts. The availability of this platform creates community solar projects that are cheaper to build and cheaper to participate in, furthering the goals of DOE’s SunShot Initiative. Final SF 425 Final SF 428 Final DOE F 2050.11 Final Report Narrative« less

An Open Source Software and Web-GIS Based Platform for Airborne SAR Remote Sensing Data Management, Distribution and Sharing

NASA Astrophysics Data System (ADS)

Changyong, Dou; Huadong, Guo; Chunming, Han; Ming, Liu

2014-03-01

With more and more Earth observation data available to the community, how to manage and sharing these valuable remote sensing datasets is becoming an urgent issue to be solved. The web based Geographical Information Systems (GIS) technology provides a convenient way for the users in different locations to share and make use of the same dataset. In order to efficiently use the airborne Synthetic Aperture Radar (SAR) remote sensing data acquired in the Airborne Remote Sensing Center of the Institute of Remote Sensing and Digital Earth (RADI), Chinese Academy of Sciences (CAS), a Web-GIS based platform for airborne SAR data management, distribution and sharing was designed and developed. The major features of the system include map based navigation search interface, full resolution imagery shown overlaid the map, and all the software adopted in the platform are Open Source Software (OSS). The functions of the platform include browsing the imagery on the map navigation based interface, ordering and downloading data online, image dataset and user management, etc. At present, the system is under testing in RADI and will come to regular operation soon.

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.

PubMed

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie; Zhang, Gong

2018-01-04

Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Wireless Sensor-Based Smart-Clothing Platform for ECG Monitoring

PubMed Central

Lin, Chung-Chih; Yu, Yan-Shuo

2015-01-01

The goal of this study is to use wireless sensor technologies to develop a smart clothes service platform for health monitoring. Our platform consists of smart clothes, a sensor node, a gateway server, and a health cloud. The smart clothes have fabric electrodes to detect electrocardiography (ECG) signals. The sensor node improves the accuracy of QRS complexes detection by morphology analysis and reduces power consumption by the power-saving transmission functionality. The gateway server provides a reconfigurable finite state machine (RFSM) software architecture for abnormal ECG detection to support online updating. Most normal ECG can be filtered out, and the abnormal ECG is further analyzed in the health cloud. Three experiments are conducted to evaluate the platform's performance. The results demonstrate that the signal-to-noise ratio (SNR) of the smart clothes exceeds 37 dB, which is within the “very good signal” interval. The average of the QRS sensitivity and positive prediction is above 99.5%. Power-saving transmission is reduced by nearly 1980 times the power consumption in the best-case analysis. PMID:26640512

Wireless Sensor-Based Smart-Clothing Platform for ECG Monitoring.

PubMed

Wang, Jie; Lin, Chung-Chih; Yu, Yan-Shuo; Yu, Tsang-Chu

2015-01-01

The goal of this study is to use wireless sensor technologies to develop a smart clothes service platform for health monitoring. Our platform consists of smart clothes, a sensor node, a gateway server, and a health cloud. The smart clothes have fabric electrodes to detect electrocardiography (ECG) signals. The sensor node improves the accuracy of QRS complexes detection by morphology analysis and reduces power consumption by the power-saving transmission functionality. The gateway server provides a reconfigurable finite state machine (RFSM) software architecture for abnormal ECG detection to support online updating. Most normal ECG can be filtered out, and the abnormal ECG is further analyzed in the health cloud. Three experiments are conducted to evaluate the platform's performance. The results demonstrate that the signal-to-noise ratio (SNR) of the smart clothes exceeds 37 dB, which is within the "very good signal" interval. The average of the QRS sensitivity and positive prediction is above 99.5%. Power-saving transmission is reduced by nearly 1980 times the power consumption in the best-case analysis.

Helicopter Flight Simulation Motion Platform Requirements

NASA Technical Reports Server (NTRS)

Schroeder, Jeffery Allyn

1999-01-01

To determine motion fidelity requirements, a series of piloted simulations was performed. Several key results were found. First, lateral and vertical translational platform cues had significant effects on fidelity. Their presence improved performance and reduced pilot workload. Second, yaw and roll rotational platform cues were not as important as the translational platform cues. In particular, the yaw rotational motion platform cue did not appear at all useful in improving performance or reducing workload. Third, when the lateral translational platform cue was combined with visual yaw rotational cues, pilots believed the platform was rotating when it was not. Thus, simulator systems can be made more efficient by proper combination of platform and visual cues. Fourth, motion fidelity specifications were revised that now provide simulator users with a better prediction of motion fidelity based upon the frequency responses of their motion control laws. Fifth, vertical platform motion affected pilot estimates of steady-state altitude during altitude repositioning. Finally, the combined results led to a general method for configuring helicopter motion systems and for developing simulator tasks that more likely represent actual flight. The overall results can serve as a guide to future simulator designers and to today's operators.

Cloud Computing-based Platform for Drought Decision-Making using Remote Sensing and Modeling Products: Preliminary Results for Brazil

NASA Astrophysics Data System (ADS)

Vivoni, E.; Mascaro, G.; Shupe, J. W.; Hiatt, C.; Potter, C. S.; Miller, R. L.; Stanley, J.; Abraham, T.; Castilla-Rubio, J.

2012-12-01

Droughts and their hydrological consequences are a major threat to food security throughout the world. In arid and semiarid regions dependent on irrigated agriculture, prolonged droughts lead to significant and recurring economic and social losses. In this contribution, we present preliminary results on integrating a set of multi-resolution drought indices into a cloud computing-based visualization platform. We focused our initial efforts on Brazil due to a severe, on-going drought in a large agricultural area in the northeastern part of the country. The online platform includes drought products developed from: (1) a MODIS-based water stress index (WSI) based on inferences from normalized difference vegetation index and land surface temperature fields, (2) a volumetric water content (VWC) index obtained from application of the NASA CASA model, and (3) a set of AVHRR-based vegetation health indices obtained from NOAA/NESDIS. The drought indices are also presented in terms of anomalies with respect to a baseline period. Since our main objective is to engage stakeholders and decision-makers in Brazil, we incorporated other relevant geospatial data into the platform, including irrigation areas, dams and reservoirs, administrative units and annual climate information. We will also present a set of use cases developed to help stakeholders explore, query and provide feedback that allowed fine-tuning of the drought product delivery, presentation and analysis tools. Finally, we discuss potential next steps in development of the online platform, including applications at finer resolutions in specific basins and at a coarser global scale.

Vapor-phase deposition of polymers as a simple and versatile technique to generate paper-based microfluidic platforms for bioassay applications.

PubMed

Demirel, Gokhan; Babur, Esra

2014-05-21

Given their simplicity and functionality, paper-based microfluidic systems are considered to be ideal and promising bioassay platforms for use in less developed countries or in point-of-care services. Although a series of innovative techniques have recently been demonstrated for the fabrication of such platforms, development of simple, inexpensive and versatile new strategies are still needed in order to reach their full potential. In this communication, we describe a simple yet facile approach to fabricate paper-based sensor platforms with a desired design through a vapor-phase polymer deposition technique. We also show that the fabricated platforms could be readily employed for the detection of various biological target molecules including glucose, protein, ALP, ALT, and uric acid. The limit of detection for each target molecule was calculated to be 25 mg dL(-1) for glucose, 1.04 g L(-1) for protein, 7.81 unit per L for ALP, 1.6 nmol L(-1) for ALT, and 0.13 mmol L(-1) for uric acid.

A GPU OpenCL based cross-platform Monte Carlo dose calculation engine (goMC)

NASA Astrophysics Data System (ADS)

Tian, Zhen; Shi, Feng; Folkerts, Michael; Qin, Nan; Jiang, Steve B.; Jia, Xun

2015-09-01

Monte Carlo (MC) simulation has been recognized as the most accurate dose calculation method for radiotherapy. However, the extremely long computation time impedes its clinical application. Recently, a lot of effort has been made to realize fast MC dose calculation on graphic processing units (GPUs). However, most of the GPU-based MC dose engines have been developed under NVidia’s CUDA environment. This limits the code portability to other platforms, hindering the introduction of GPU-based MC simulations to clinical practice. The objective of this paper is to develop a GPU OpenCL based cross-platform MC dose engine named goMC with coupled photon-electron simulation for external photon and electron radiotherapy in the MeV energy range. Compared to our previously developed GPU-based MC code named gDPM (Jia et al 2012 Phys. Med. Biol. 57 7783-97), goMC has two major differences. First, it was developed under the OpenCL environment for high code portability and hence could be run not only on different GPU cards but also on CPU platforms. Second, we adopted the electron transport model used in EGSnrc MC package and PENELOPE’s random hinge method in our new dose engine, instead of the dose planning method employed in gDPM. Dose distributions were calculated for a 15 MeV electron beam and a 6 MV photon beam in a homogenous water phantom, a water-bone-lung-water slab phantom and a half-slab phantom. Satisfactory agreement between the two MC dose engines goMC and gDPM was observed in all cases. The average dose differences in the regions that received a dose higher than 10% of the maximum dose were 0.48-0.53% for the electron beam cases and 0.15-0.17% for the photon beam cases. In terms of efficiency, goMC was ~4-16% slower than gDPM when running on the same NVidia TITAN card for all the cases we tested, due to both the different electron transport models and the different development environments. The code portability of our new dose engine goMC was validated by

A GPU OpenCL based cross-platform Monte Carlo dose calculation engine (goMC).

PubMed

Tian, Zhen; Shi, Feng; Folkerts, Michael; Qin, Nan; Jiang, Steve B; Jia, Xun

2015-10-07

Monte Carlo (MC) simulation has been recognized as the most accurate dose calculation method for radiotherapy. However, the extremely long computation time impedes its clinical application. Recently, a lot of effort has been made to realize fast MC dose calculation on graphic processing units (GPUs). However, most of the GPU-based MC dose engines have been developed under NVidia's CUDA environment. This limits the code portability to other platforms, hindering the introduction of GPU-based MC simulations to clinical practice. The objective of this paper is to develop a GPU OpenCL based cross-platform MC dose engine named goMC with coupled photon-electron simulation for external photon and electron radiotherapy in the MeV energy range. Compared to our previously developed GPU-based MC code named gDPM (Jia et al 2012 Phys. Med. Biol. 57 7783-97), goMC has two major differences. First, it was developed under the OpenCL environment for high code portability and hence could be run not only on different GPU cards but also on CPU platforms. Second, we adopted the electron transport model used in EGSnrc MC package and PENELOPE's random hinge method in our new dose engine, instead of the dose planning method employed in gDPM. Dose distributions were calculated for a 15 MeV electron beam and a 6 MV photon beam in a homogenous water phantom, a water-bone-lung-water slab phantom and a half-slab phantom. Satisfactory agreement between the two MC dose engines goMC and gDPM was observed in all cases. The average dose differences in the regions that received a dose higher than 10% of the maximum dose were 0.48-0.53% for the electron beam cases and 0.15-0.17% for the photon beam cases. In terms of efficiency, goMC was ~4-16% slower than gDPM when running on the same NVidia TITAN card for all the cases we tested, due to both the different electron transport models and the different development environments. The code portability of our new dose engine goMC was validated by

Crop 3D-a LiDAR based platform for 3D high-throughput crop phenotyping.

PubMed

Guo, Qinghua; Wu, Fangfang; Pang, Shuxin; Zhao, Xiaoqian; Chen, Linhai; Liu, Jin; Xue, Baolin; Xu, Guangcai; Li, Le; Jing, Haichun; Chu, Chengcai

2018-03-01

With the growing population and the reducing arable land, breeding has been considered as an effective way to solve the food crisis. As an important part in breeding, high-throughput phenotyping can accelerate the breeding process effectively. Light detection and ranging (LiDAR) is an active remote sensing technology that is capable of acquiring three-dimensional (3D) data accurately, and has a great potential in crop phenotyping. Given that crop phenotyping based on LiDAR technology is not common in China, we developed a high-throughput crop phenotyping platform, named Crop 3D, which integrated LiDAR sensor, high-resolution camera, thermal camera and hyperspectral imager. Compared with traditional crop phenotyping techniques, Crop 3D can acquire multi-source phenotypic data in the whole crop growing period and extract plant height, plant width, leaf length, leaf width, leaf area, leaf inclination angle and other parameters for plant biology and genomics analysis. In this paper, we described the designs, functions and testing results of the Crop 3D platform, and briefly discussed the potential applications and future development of the platform in phenotyping. We concluded that platforms integrating LiDAR and traditional remote sensing techniques might be the future trend of crop high-throughput phenotyping.

Metocean design parameter estimation for fixed platform based on copula functions

NASA Astrophysics Data System (ADS)

Zhai, Jinjin; Yin, Qilin; Dong, Sheng

2017-08-01

Considering the dependent relationship among wave height, wind speed, and current velocity, we construct novel trivariate joint probability distributions via Archimedean copula functions. Total 30-year data of wave height, wind speed, and current velocity in the Bohai Sea are hindcast and sampled for case study. Four kinds of distributions, namely, Gumbel distribution, lognormal distribution, Weibull distribution, and Pearson Type III distribution, are candidate models for marginal distributions of wave height, wind speed, and current velocity. The Pearson Type III distribution is selected as the optimal model. Bivariate and trivariate probability distributions of these environmental conditions are established based on four bivariate and trivariate Archimedean copulas, namely, Clayton, Frank, Gumbel-Hougaard, and Ali-Mikhail-Haq copulas. These joint probability models can maximize marginal information and the dependence among the three variables. The design return values of these three variables can be obtained by three methods: univariate probability, conditional probability, and joint probability. The joint return periods of different load combinations are estimated by the proposed models. Platform responses (including base shear, overturning moment, and deck displacement) are further calculated. For the same return period, the design values of wave height, wind speed, and current velocity obtained by the conditional and joint probability models are much smaller than those by univariate probability. Considering the dependence among variables, the multivariate probability distributions provide close design parameters to actual sea state for ocean platform design.

VA's Integrated Imaging System on three platforms.

PubMed

Dayhoff, R E; Maloney, D L; Majurski, W J

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability.

VA's Integrated Imaging System on three platforms.

PubMed Central

Dayhoff, R. E.; Maloney, D. L.; Majurski, W. J.

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability. PMID:1482983

MR Imaging-based Semi-quantitative Methods for Knee Osteoarthritis

PubMed Central

JARRAYA, Mohamed; HAYASHI, Daichi; ROEMER, Frank Wolfgang; GUERMAZI, Ali

2016-01-01

Magnetic resonance imaging (MRI)-based semi-quantitative (SQ) methods applied to knee osteoarthritis (OA) have been introduced during the last decade and have fundamentally changed our understanding of knee OA pathology since then. Several epidemiological studies and clinical trials have used MRI-based SQ methods to evaluate different outcome measures. Interest in MRI-based SQ scoring system has led to continuous update and refinement. This article reviews the different SQ approaches for MRI-based whole organ assessment of knee OA and also discuss practical aspects of whole joint assessment. PMID:26632537

MSD-MAP: A Network-Based Systems Biology Platform for Predicting Disease-Metabolite Links.

PubMed

Wathieu, Henri; Issa, Naiem T; Mohandoss, Manisha; Byers, Stephen W; Dakshanamurthy, Sivanesan

2017-01-01

Cancer-associated metabolites result from cell-wide mechanisms of dysregulation. The field of metabolomics has sought to identify these aberrant metabolites as disease biomarkers, clues to understanding disease mechanisms, or even as therapeutic agents. This study was undertaken to reliably predict metabolites associated with colorectal, esophageal, and prostate cancers. Metabolite and disease biological action networks were compared in a computational platform called MSD-MAP (Multi Scale Disease-Metabolite Association Platform). Using differential gene expression analysis with patient-based RNAseq data from The Cancer Genome Atlas, genes up- or down-regulated in cancer compared to normal tissue were identified. Relational databases were used to map biological entities including pathways, functions, and interacting proteins, to those differential disease genes. Similar relational maps were built for metabolites, stemming from known and in silico predicted metabolite-protein associations. The hypergeometric test was used to find statistically significant relationships between disease and metabolite biological signatures at each tier, and metabolites were assessed for multi-scale association with each cancer. Metabolite networks were also directly associated with various other diseases using a disease functional perturbation database. Our platform recapitulated metabolite-disease links that have been empirically verified in the scientific literature, with network-based mapping of jointly-associated biological activity also matching known disease mechanisms. This was true for colorectal, esophageal, and prostate cancers, using metabolite action networks stemming from both predicted and known functional protein associations. By employing systems biology concepts, MSD-MAP reliably predicted known cancermetabolite links, and may serve as a predictive tool to streamline conventional metabolomic profiling methodologies. Copyright© Bentham Science Publishers; For any

A space-based public service platform for terrestrial rescue operations

NASA Technical Reports Server (NTRS)

Fleisig, R.; Bernstein, J.; Cramblit, D. C.

1977-01-01

The space-based Public Service Platform (PSP) is a multibeam, high-gain communications relay satellite that can provide a variety of functions for a large number of people on earth equipped with extremely small, very low cost transceivers. This paper describes the PSP concept, the rationale used to derive the concept, the criteria for selecting specific communication functions to be performed, and the advantages of performing such functions via satellite. The discussion focuses on the benefits of using a PSP for natural disaster warning; control of attendant rescue/assistance operations; and rescue of people in downed aircraft, aboard sinking ships, lost or injured on land.

Comparative immune responses of corals to stressors associated with offshore reef-based tourist platforms

PubMed Central

Lamb, Joleah B; van Oppen, Madeleine J H; Willis, Bette L; Bourne, David G

2015-01-01

Abstract Unravelling the contributions of local anthropogenic and seasonal environmental factors in suppressing the coral immune system is important for prioritizing management actions at reefs exposed to high levels of human activities. Here, we monitor health of the model coral Acropora millepora adjacent to a high-use and an unused reef-based tourist platform, plus a nearby control site without a platform, over 7 months spanning a typical austral summer. Comparisons of temporal patterns in a range of biochemical and genetic immune parameters (Toll-like receptor signalling pathway, lectin–complement system, prophenoloxidase-activating system and green fluorescent protein-like proteins) among healthy, injured and diseased corals revealed that corals exhibit a diverse array of immune responses to environmental and anthropogenic stressors. In healthy corals at the control site, expression of genes involved in the Toll-like receptor signalling pathway (MAPK p38, MEKK1, cFos and ATF4/5) and complement system (C3 and Bf) was modulated by seasonal environmental factors in summer months. Corals at reef platform sites experienced additional stressors over the summer, as evidenced by increased expression of various immune genes, including MAPK p38 and MEKK1. Despite increased expression of immune genes, signs of white syndromes were detected in 31% of study corals near tourist platforms in the warmest summer month. Evidence that colonies developing disease showed reduced expression of genes involved in the complement pathway prior to disease onset suggests that their immune systems may have been compromised. Responses to disease and physical damage primarily involved the melanization cascade and GFP-like proteins, and appeared to be sufficient for recovery when summer heat stress subsided. Overall, seasonal and anthropogenic factors may have interacted synergistically to overwhelm the immune systems of corals near reef platforms, leading to increased disease prevalence

Sample normalization methods in quantitative metabolomics.

PubMed

Wu, Yiman; Li, Liang

2016-01-22

To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

Designing the RiverCare knowledge base and web-collaborative platform to exchange knowledge in river management

NASA Astrophysics Data System (ADS)

Cortes Arevalo, Juliette; den Haan, Robert-Jan; van der Voort, Mascha; Hulscher, Suzanne

2016-04-01

Effective communication strategies are necessary between different scientific disciplines, practitioners and non-experts for a shared understanding and better implementation of river management measures. In that context, the RiverCare program aims to get a better understanding of riverine measures that are being implemented towards self-sustaining multifunctional rivers in the Netherlands. During the RiverCare program, user committees are organized between the researchers and practitioners to discuss the aim and value of RiverCare outputs, related assumptions and uncertainties behind scientific results. Beyond the RiverCare program end, knowledge about river interventions, integrated effects, management and self-sustaining applications will be available to experts and non-experts by means of River Care communication tools: A web-collaborative platform and a serious gaming environment. As part of the communication project of RiverCare, we are designing the RiverCare web-collaborative platform and the knowledge-base behind that platform. We aim at promoting collaborative efforts and knowledge exchange in river management. However, knowledge exchange does not magically happen. Consultation and discussion of RiverCare outputs as well as elicitation of perspectives and preferences from different actors about the effects of riverine measures has to be facilitated. During the RiverCare research activities, the platform will support the user committees or collaborative sessions that are regularly held with the organizations directly benefiting from our research, at project level or in study areas. The design process of the collaborative platform follows an user centred approach to identify user requirements, co-create a conceptual design and iterative develop and evaluate prototypes of the platform. The envisioned web-collaborative platform opens with an explanation and visualisation of the RiverCare outputs that are available in the knowledge base. Collaborative sessions

StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

PubMed

Zheng, Wenning; Tan, Tze King; Paterson, Ian C; Mutha, Naresh V R; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A; Jakubovics, Nicholas S; Choo, Siew Woh

2016-01-01

The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my.

Validation of Greyscale-Based Quantitative Ultrasound in Manual Wheelchair Users

PubMed Central

Collinger, Jennifer L.; Fullerton, Bradley; Impink, Bradley G.; Koontz, Alicia M.; Boninger, Michael L.

2010-01-01

Objective The primary aim of this study is to establish the validity of greyscale-based quantitative ultrasound (QUS) measures of the biceps and supraspinatus tendons. Design Nine QUS measures of the biceps and supraspinatus tendons were computed from ultrasound images collected from sixty-seven manual wheelchair users. Shoulder pathology was measured using questionnaires, physical examination maneuvers, and a clinical ultrasound grading scale. Results Increased age, duration of wheelchair use, and body mass correlated with a darker, more homogenous tendon appearance. Subjects with pain during physical examination tests for biceps tenderness and acromioclavicular joint tenderness exhibited significantly different supraspinatus QUS values. Even when controlling for tendon depth, QUS measures of the biceps tendon differed significantly between subjects with healthy tendons, mild tendinosis, and severe tendinosis. Clinical grading of supraspinatus tendon health was correlated with QUS measures of the supraspinatus tendon. Conclusions Quantitative ultrasound is valid method to quantify tendinopathy and may allow for early detection of tendinosis. Manual wheelchair users are at a high risk for developing shoulder tendon pathology and may benefit from quantitative ultrasound-based research that focuses on identifying interventions designed to reduce this risk. PMID:20407304

Quantitative X-ray Map Analyser (Q-XRMA): A new GIS-based statistical approach to Mineral Image Analysis

NASA Astrophysics Data System (ADS)

Ortolano, Gaetano; Visalli, Roberto; Godard, Gaston; Cirrincione, Rosolino

2018-06-01

We present a new ArcGIS®-based tool developed in the Python programming language for calibrating EDS/WDS X-ray element maps, with the aim of acquiring quantitative information of petrological interest. The calibration procedure is based on a multiple linear regression technique that takes into account interdependence among elements and is constrained by the stoichiometry of minerals. The procedure requires an appropriate number of spot analyses for use as internal standards and provides several test indexes for a rapid check of calibration accuracy. The code is based on an earlier image-processing tool designed primarily for classifying minerals in X-ray element maps; the original Python code has now been enhanced to yield calibrated maps of mineral end-members or the chemical parameters of each classified mineral. The semi-automated procedure can be used to extract a dataset that is automatically stored within queryable tables. As a case study, the software was applied to an amphibolite-facies garnet-bearing micaschist. The calibrated images obtained for both anhydrous (i.e., garnet and plagioclase) and hydrous (i.e., biotite) phases show a good fit with corresponding electron microprobe analyses. This new GIS-based tool package can thus find useful application in petrology and materials science research. Moreover, the huge quantity of data extracted opens new opportunities for the development of a thin-section microchemical database that, using a GIS platform, can be linked with other major global geoscience databases.

Citizen Sensors for SHM: Towards a Crowdsourcing Platform

PubMed Central

Ozer, Ekin; Feng, Maria Q.; Feng, Dongming

2015-01-01

This paper presents an innovative structural health monitoring (SHM) platform in terms of how it integrates smartphone sensors, the web, and crowdsourcing. The ubiquity of smartphones has provided an opportunity to create low-cost sensor networks for SHM. Crowdsourcing has given rise to citizen initiatives becoming a vast source of inexpensive, valuable but heterogeneous data. Previously, the authors have investigated the reliability of smartphone accelerometers for vibration-based SHM. This paper takes a step further to integrate mobile sensing and web-based computing for a prospective crowdsourcing-based SHM platform. An iOS application was developed to enable citizens to measure structural vibration and upload the data to a server with smartphones. A web-based platform was developed to collect and process the data automatically and store the processed data, such as modal properties of the structure, for long-term SHM purposes. Finally, the integrated mobile and web-based platforms were tested to collect the low-amplitude ambient vibration data of a bridge structure. Possible sources of uncertainties related to citizens were investigated, including the phone location, coupling conditions, and sampling duration. The field test results showed that the vibration data acquired by smartphones operated by citizens without expertise are useful for identifying structural modal properties with high accuracy. This platform can be further developed into an automated, smart, sustainable, cost-free system for long-term monitoring of structural integrity of spatially distributed urban infrastructure. Citizen Sensors for SHM will be a novel participatory sensing platform in the way that it offers hybrid solutions to transitional crowdsourcing parameters. PMID:26102490

Droplet Microfluidic and Magnetic Particles Platform for Cancer Typing.

PubMed

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, M; Malaquin, Laurent; Descroix, Stéphanie; de Cremoux, Patricia; Viovy, Jean-Louis

2017-01-01

Analyses of nucleic acids are routinely performed in hospital laboratories to detect gene alterations for cancer diagnosis and treatment decision. Among the different possible investigations, mRNA analysis provides information on abnormal levels of genes expression. Standard laboratory methods are still not adapted to the isolation and quantitation of low mRNA amounts and new techniques needs to be developed in particular for rare subsets analysis. By reducing the volume involved, time process, and the contamination risks, droplet microfluidics provide numerous advantages to perform analysis down to the single cell level.We report on a droplet microfluidic platform based on the manipulation of magnetic particles that allows the clinical analysis of tumor tissues. In particular, it allows the extraction of mRNA from the total-RNA sample, Reverse Transcription, and cDNA amplification, all in droplets.

A New Size-based Platform for Circulating Tumor Cell Detection in Colorectal Cancer Patients.

PubMed

Oh, Bo Young; Kim, Jhingook; Lee, Woo Yong; Kim, Hee Cheol

2017-09-01

Circulating tumor cells (CTCs) might play a significant role in cancer progression and metastasis. However, the ability to detect CTCs is limited, especially in cells undergoing epithelial-mesenchymal transition. In this study, we evaluated a new size-based CTC detection platform and its clinical efficacy in colorectal cancer. Blood samples were obtained from 76 patients with colorectal cancer and 20 healthy control subjects for CTC analysis. CTCs were enriched using a high-density microporous chip filter and were detected using a 4-color staining protocol including 4',6-diamidino-2-phenylindole (DAPI) for nucleated cells, CD45 monoclonal antibody (mAb) as a leukocyte marker, and epithelial cell adhesion molecule (EpCAM) mAb or cytokeratin (CK) mAb as an epithelial cell marker. CTC positivity was defined as DAPI-positive (DAPI + )/CD45 - /EpCAM + or CK + cells and clinical outcomes of patients were analyzed according to CTC counts. CTCs were detected in 50 patients using this size-based filtration platform. CTC + patients were more frequently identified with a high level of carcinoembryonic antigen and advanced stage cancer (P = .038 and P = .017, respectively). CTC counts for patients with stage IV cancer (12.47 ± 24.00) were significantly higher than those for patients with cancers that were stage I to III (2.84 ± 5.29; P = .005) and healthy control subjects (0.25 ± 0.55; P < .001). In addition, progression-free survival tended to be lower in CTC + patients compared with CTC - patients (P = .092). In patients with stage I to III cancer, recurrence occurred only in CTC + patients. CTC positivity was found to correlate with clinical features of colorectal cancer patients. Our results suggest that this new size-based platform has potential for determining prognosis and therapeutic response in colorectal cancer patients. Copyright © 2017 Elsevier Inc. All rights reserved.

Research on sudden environmental pollution public service platform construction based on WebGIS

NASA Astrophysics Data System (ADS)

Bi, T. P.; Gao, D. Y.; Zhong, X. Y.

2016-08-01

In order to actualize the social sharing and service of the emergency-response information for sudden pollution accidents, the public can share the risk source information service, dangerous goods control technology service and so on, The SQL Server and ArcSDE software are used to establish a spatial database to restore all kinds of information including risk sources, hazardous chemicals and handling methods in case of accidents. Combined with Chinese atmospheric environmental assessment standards, the SCREEN3 atmospheric dispersion model and one-dimensional liquid diffusion model are established to realize the query of related information and the display of the diffusion effect under B/S structure. Based on the WebGIS technology, C#.Net language is used to develop the sudden environmental pollution public service platform. As a result, the public service platform can make risk assessments and provide the best emergency processing services.

A Set of Free Cross-Platform Authoring Programs for Flexible Web-Based CALL Exercises

ERIC Educational Resources Information Center

O'Brien, Myles

2012-01-01

The Mango Suite is a set of three freely downloadable cross-platform authoring programs for flexible network-based CALL exercises. They are Adobe Air applications, so they can be used on Windows, Macintosh, or Linux computers, provided the freely-available Adobe Air has been installed on the computer. The exercises which the programs generate are…

An ICT-Based Platform to Monitor Protocols in the Healthcare Environment.

PubMed

Rorís, Víctor M Alonso; Gago, Juan M Santos; Sabucedo, Luis Álvarez; Merino, Mateo Ramos; Valero, Javier Sanz

2016-10-01

Procedures from the healthcare domain involve highly critical actions as they may pose a risk for patients' life. Therefore, a large effort is devoted to the standardization in clinical praxis and to the control of quality for these protocols in order to minimize hazards. In this line, this work is compelled to provide an ICT-based support to carry out these controls in a simple and effective manner. Using a methodology based on HACCP and taking advantage of Semantic tools, a holistic platform of services for traceability and control of processes has been designed and implemented. The applied paradigm is based on the use of Control Points as singular points to generate traces using observations and measures relevant for the processes considered. Based on those, it is possible to offer services for advanced querying and knowledge inference. The local deployment just requires regular mobile phones or tablets making this solution cost-effective and easily replicable.

Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics.

PubMed

Das, Abhiram; Schneider, Hannah; Burridge, James; Ascanio, Ana Karine Martinez; Wojciechowski, Tobias; Topp, Christopher N; Lynch, Jonathan P; Weitz, Joshua S; Bucksch, Alexander

2015-01-01

Plant root systems are key drivers of plant function and yield. They are also under-explored targets to meet global food and energy demands. Many new technologies have been developed to characterize crop root system architecture (CRSA). These technologies have the potential to accelerate the progress in understanding the genetic control and environmental response of CRSA. Putting this potential into practice requires new methods and algorithms to analyze CRSA in digital images. Most prior approaches have solely focused on the estimation of root traits from images, yet no integrated platform exists that allows easy and intuitive access to trait extraction and analysis methods from images combined with storage solutions linked to metadata. Automated high-throughput phenotyping methods are increasingly used in laboratory-based efforts to link plant genotype with phenotype, whereas similar field-based studies remain predominantly manual low-throughput. Here, we present an open-source phenomics platform "DIRT", as a means to integrate scalable supercomputing architectures into field experiments and analysis pipelines. DIRT is an online platform that enables researchers to store images of plant roots, measure dicot and monocot root traits under field conditions, and share data and results within collaborative teams and the broader community. The DIRT platform seamlessly connects end-users with large-scale compute "commons" enabling the estimation and analysis of root phenotypes from field experiments of unprecedented size. DIRT is an automated high-throughput computing and collaboration platform for field based crop root phenomics. The platform is accessible at http://www.dirt.iplantcollaborative.org/ and hosted on the iPlant cyber-infrastructure using high-throughput grid computing resources of the Texas Advanced Computing Center (TACC). DIRT is a high volume central depository and high-throughput RSA trait computation platform for plant scientists working on crop roots

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

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

Zhu, Ying; Piehowski, Paul D.; Zhao, Rui

Nanoscale or single cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (Nanodroplet Processing in One pot for Trace Samples) platform as a major advance in overall sensitivity. NanoPOTS dramatically enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive LC-MS, nanoPOTS allows identification of ~1500 to ~3,000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runsmore » algorithm of MaxQuant, >3000 proteins were consistently identified from as few as 10 cells. Furthermore, we demonstrate robust quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.« less

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

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

Zhu, Ying; Piehowski, Paul D.; Zhao, Rui

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here in this paper, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Betweenmore » Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.« less

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

DOE PAGES

Zhu, Ying; Piehowski, Paul D.; Zhao, Rui; ...

2018-02-28

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here in this paper, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Betweenmore » Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.« less

Microbial Monitoring of Pathogens by Comparing Multiple Real-Time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Birmele, Michele

2012-01-01

The International Space Station (ISS) is a closed environment wih rotations of crew and equipment each introducing their own microbial flora making it necessary to monitor the air, surfaces, and water for microbial contamination. Current microbial monitoring includes labor and time intensive methods to enumerate total bacterial and fungal cells with limited characterization during in-flight testing. Although this culture-based method has been sufficient for monitoring the ISS, future long duration missions will need to perform more comprehensive characterization in-flight, since sample return and ground characterization may not be available. A workshop was held in 2011 at the Johnson Space Center to discuss alternative methodologies and technologies suitable for microbial monitoring for these longterm exploration missions where molecular-based methodologies, such as polymerase chain reaction (PCR), were recommended. In response, a multi-center (Marshall Space Flight Center, Johnson Space Center, Jet Propulsion Laboratory, and Kennedy Space Center) collaborative research effort was initiated to explore novel commercial-off-the-shelf hardware options for spaceflight environmental monitoring. The goal was to evaluate quantitative/semi-quantitative PCR approaches to space applications for low cost in-flight rapid identification of microorganisms affecting crew safety. The initial phase of this project identified commercially available platforms that could be minimally modified to perform nominally in microgravity followed by proof-of-concept testing on the highest qualifying candidates with a universally available test organism, Salmonella enterica. The platforms evaluated during proof-of-concept testing included the iCubate 2.0(TradeMark) (iCubate, Huntsville, AL), RAZOR EX (BioFire Diagnostics; Salt Lake City, Utah) and SmartCycler(TradeMark) (Cepheid; Sunnyvale, CA). The analysis identified two potential technologies (iCubate 2.0 and RAZOR EX) that were able to

Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production.

PubMed

Chen, Xianzhong; Zhou, Li; Tian, Kangming; Kumar, Ashwani; Singh, Suren; Prior, Bernard A; Wang, Zhengxiang

2013-12-01

In order to decrease carbon emissions and negative environmental impacts of various pollutants, more bulk and/or fine chemicals are produced by bioprocesses, replacing the traditional energy and fossil based intensive route. The Gram-negative rod-shaped bacterium, Escherichia coli has been studied extensively on a fundamental and applied level and has become a predominant host microorganism for industrial applications. Furthermore, metabolic engineering of E. coli for the enhanced biochemical production has been significantly promoted by the integrated use of recent developments in systems biology, synthetic biology and evolutionary engineering. In this review, we focus on recent efforts devoted to the use of genetically engineered E. coli as a sustainable platform for the production of industrially important biochemicals such as biofuels, organic acids, amino acids, sugar alcohols and biopolymers. In addition, representative secondary metabolites produced by E. coli will be systematically discussed and the successful strategies for strain improvements will be highlighted. Moreover, this review presents guidelines for future developments in the bio-based chemical production using E. coli as an industrial platform. Copyright © 2013 Elsevier Inc. All rights reserved.

Design of Control Plane Architecture Based on Cloud Platform and Experimental Network Demonstration for Multi-domain SDON

NASA Astrophysics Data System (ADS)

Li, Ming; Yin, Hongxi; Xing, Fangyuan; Wang, Jingchao; Wang, Honghuan

2016-02-01

With the features of network virtualization and resource programming, Software Defined Optical Network (SDON) is considered as the future development trend of optical network, provisioning a more flexible, efficient and open network function, supporting intraconnection and interconnection of data centers. Meanwhile cloud platform can provide powerful computing, storage and management capabilities. In this paper, with the coordination of SDON and cloud platform, a multi-domain SDON architecture based on cloud control plane has been proposed, which is composed of data centers with database (DB), path computation element (PCE), SDON controller and orchestrator. In addition, the structure of the multidomain SDON orchestrator and OpenFlow-enabled optical node are proposed to realize the combination of centralized and distributed effective management and control platform. Finally, the functional verification and demonstration are performed through our optical experiment network.

A detrital sediment budget of a Maldivian reef platform

NASA Astrophysics Data System (ADS)

Morgan, K. M.; Kench, P. S.

2014-10-01

Sediment dynamics are an important control on the morphology and development of reef systems by actively removing and redistributing excess detrital sediment. This study presents quantitative data from direct point measurements of sediment transport on the platform surface and fore-reef slope of Vabbinfaru reef, North Malé Atoll, Maldives. A suite of sediment traps were used to construct actual rates of platform sediment fluxes and off-reef export over different spatial and temporal (seasonal) scales to establish key sediment transport pathways. Findings showed that high sediment fluxes occur on Vabbinfaru platform in the absence of major storm activity (up to 1905 g m- 1 d- 1), with 95% of annual transport occurring during the southwest monsoon as a result of increased wave energy. Climate-driven changes in the platform process regime caused a reversal of net sediment transport pathways between each monsoon season. Off-reef export rates were high, reaching a maximum of 12.58 kg m- 1 y- 1 for gravel and 407 g m- 1 d- 1 for sand-sized sediment. An estimated 127,120 kg is exported from the platform annually equating to a significant loss from the reef sediment budget and contributing to the long-term geomorphic development of the fore-reef slope and atoll basin. Detrital sediment reservoirs on Vabbinfaru are not purely depositional carbonate sinks, but rather temporary stores that are important in the transfer of sediment between reef zones.

A Proposal to Enhance the Use of Learning Platforms in Higher Education

ERIC Educational Resources Information Center

Marques, Bertil P.; Villate, Jaime E.; Vaz de Carvalho, Carlos

2015-01-01

The results of several studies conducted to analyze the quantitative and qualitative use of learning technologies in Higher Education in Portugal showed that, in general, these technologies are not used systematically and effectively and e-learning platforms tend to be relegated to repositories of contents rather than as full-fledged tools…

Analysis of Human Plasma Metabolites across Different Liquid Chromatography - Mass Spectrometry Platforms: Cross-platform Transferable Chemical Signatures